Diff of the two buildlogs: -- --- b1/build.log 2024-05-15 13:33:34.017741941 +0000 +++ b2/build.log 2024-05-15 13:36:52.601294464 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Jun 17 07:54:27 -12 2025 -I: pbuilder-time-stamp: 1750190067 +I: Current time: Thu May 16 03:33:38 +14 2024 +I: pbuilder-time-stamp: 1715780018 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -35,52 +35,84 @@ dpkg-source: info: applying wfa2_linking I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/2183970/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/668028/tmp/hooks/D01_modify_environment starting +debug: Running on codethink04-arm64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 May 15 13:33 /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/668028/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/668028/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='arm64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="21" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.21(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='4feed423bb834ccd95bfb21c45ec6a71' - 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='2183970' - PS1='# ' - PS2='> ' + INVOCATION_ID=daf8a27dd98f4227acdafabff3031e4a + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=668028 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.Nw0RJ9TN/pbuilderrc_Qdpx --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.Nw0RJ9TN/b1 --logfile b1/build.log libvcflib_1.0.9+dfsg1-3.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.4:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.Nw0RJ9TN/pbuilderrc_HQeg --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.Nw0RJ9TN/b2 --logfile b2/build.log libvcflib_1.0.9+dfsg1-3.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink03-arm64 6.1.0-21-cloud-arm64 #1 SMP Debian 6.1.90-1 (2024-05-03) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-21-cloud-arm64 #1 SMP Debian 6.1.90-1 (2024-05-03) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Jun 15 17:48 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/2183970/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 May 14 11:23 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/668028/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -252,7 +284,7 @@ Get: 106 http://deb.debian.org/debian trixie/main arm64 python3-distutils all 3.12.3-1 [131 kB] Get: 107 http://deb.debian.org/debian trixie/main arm64 python3-dev arm64 3.11.8-1 [26.1 kB] Get: 108 http://deb.debian.org/debian trixie/main arm64 python3-pybind11 all 2.11.1-2 [201 kB] -Fetched 52.9 MB in 0s (124 MB/s) +Fetched 52.9 MB in 0s (123 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:arm64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19744 files and directories currently installed.) @@ -621,8 +653,8 @@ Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' -Local time is now: Tue Jun 17 19:54:49 UTC 2025. -Universal Time is now: Tue Jun 17 19:54:49 UTC 2025. +Local time is now: Wed May 15 13:34:26 UTC 2024. +Universal Time is now: Wed May 15 13:34:26 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... @@ -711,7 +743,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/ && 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_1.0.9+dfsg1-3_source.changes +I: user script /srv/workspace/pbuilder/668028/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/668028/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/ && 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_1.0.9+dfsg1-3_source.changes dpkg-buildpackage: info: source package libvcflib dpkg-buildpackage: info: source version 1.0.9+dfsg1-3 dpkg-buildpackage: info: source distribution unstable @@ -801,7 +837,7 @@ -- Found libfastahack, version 0.0 -- WFA using include /usr/include/wfa2lib Pandoc needs to be installed to generate the man pages --- Configuring done (5.4s) +-- Configuring done (10.2s) -- Generating done (0.2s) CMake Warning: Manually-specified variables were not used by the project: @@ -828,25 +864,25 @@ make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' make -f CMakeFiles/vcflib.dir/build.make CMakeFiles/vcflib.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -[ 0%] Building CXX object CMakeFiles/vcflib.dir/src/legacy.cpp.o -[ 0%] Building CXX object CMakeFiles/vcflib.dir/src/Variant.cpp.o [ 1%] Building CXX object CMakeFiles/vcflib.dir/src/vcf-c-api.cpp.o -[ 2%] Building CXX object CMakeFiles/vcflib.dir/src/rnglib.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -Dvcflib_EXPORTS -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -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-1.0.9+dfsg1/src/vcf-c-api.cpp +[ 1%] Building CXX object CMakeFiles/vcflib.dir/src/legacy.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -Dvcflib_EXPORTS -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto 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-ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -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-1.0.9+dfsg1/src/vcf-wfa.cpp -[ 4%] Building CXX object CMakeFiles/vcflib.dir/src/var.cpp.o +[ 2%] Building CXX object CMakeFiles/vcflib.dir/src/Variant.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -Dvcflib_EXPORTS -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp 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-D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIC -MD -MT CMakeFiles/vcflib.dir/src/cigar.cpp.o -MF CMakeFiles/vcflib.dir/src/cigar.cpp.o.d -o CMakeFiles/vcflib.dir/src/cigar.cpp.o -c /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/cigar.cpp [ 8%] Building CXX object CMakeFiles/vcflib.dir/src/allele.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -Dvcflib_EXPORTS -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIC -MD -MT CMakeFiles/vcflib.dir/src/allele.cpp.o -MF CMakeFiles/vcflib.dir/src/allele.cpp.o.d -o CMakeFiles/vcflib.dir/src/allele.cpp.o -c /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/allele.cpp -In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.cpp:10: -/build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 650 | struct stringcasecmp : binary_function { - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/bits/refwrap.h:39, - from /usr/include/c++/13/vector:68, - from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:12: -/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -/build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:651:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 651 | struct charcasecmp : public std::binary_function { - | ^~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ [ 8%] Building C object CMakeFiles/vcflib.dir/contrib/filevercmp/filevercmp.c.o /usr/bin/cc -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -Dvcflib_EXPORTS -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -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-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -fPIC -MD -MT CMakeFiles/vcflib.dir/contrib/filevercmp/filevercmp.c.o -MF CMakeFiles/vcflib.dir/contrib/filevercmp/filevercmp.c.o.d -o CMakeFiles/vcflib.dir/contrib/filevercmp/filevercmp.c.o -c /build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp/filevercmp.c -In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcf-c-api.cpp:9: -/build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 650 | struct stringcasecmp : binary_function { - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/bits/refwrap.h:39, - from /usr/include/c++/13/vector:68, - from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:12: -/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -/build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:651:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 651 | struct charcasecmp : public std::binary_function { - | ^~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ [ 9%] Building C object CMakeFiles/vcflib.dir/contrib/c-progress-bar/progress.c.o /usr/bin/cc -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -Dvcflib_EXPORTS -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -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-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -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-1.0.9+dfsg1/contrib/c-progress-bar/progress.c -In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/legacy.cpp:12: -/build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 650 | struct stringcasecmp : binary_function { - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/bits/refwrap.h:39, - from /usr/include/c++/13/vector:68, - from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:12: -/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -/build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:651:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 651 | struct charcasecmp : public std::binary_function { - | ^~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ /build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar/progress.c: In function 'print_timedelta': /build/reproducible-path/libvcflib-1.0.9+dfsg1/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); @@ -972,6 +960,54 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/legacy.cpp:12: +/build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 650 | struct stringcasecmp : binary_function { + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/bits/refwrap.h:39, + from /usr/include/c++/13/vector:68, + from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:12: +/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +/build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:651:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 651 | struct charcasecmp : public std::binary_function { + | ^~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.cpp:10: +/build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 650 | struct stringcasecmp : binary_function { + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/bits/refwrap.h:39, + from /usr/include/c++/13/vector:68, + from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:12: +/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +/build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:651:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 651 | struct charcasecmp : public std::binary_function { + | ^~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcf-c-api.cpp:9: +/build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 650 | struct stringcasecmp : binary_function { + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/bits/refwrap.h:39, + from /usr/include/c++/13/vector:68, + from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:12: +/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +/build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:651:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 651 | struct charcasecmp : public std::binary_function { + | ^~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ [ 9%] Linking CXX shared library libvcflib.so /usr/bin/cmake -E cmake_link_script CMakeFiles/vcflib.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libvcflib.so.2 -o libvcflib.so.2 "CMakeFiles/vcflib.dir/src/vcf-c-api.cpp.o" CMakeFiles/vcflib.dir/src/legacy.cpp.o "CMakeFiles/vcflib.dir/src/vcf-wfa.cpp.o" CMakeFiles/vcflib.dir/src/Variant.cpp.o CMakeFiles/vcflib.dir/src/rnglib.cpp.o CMakeFiles/vcflib.dir/src/var.cpp.o CMakeFiles/vcflib.dir/src/pdflib.cpp.o CMakeFiles/vcflib.dir/src/cdflib.cpp.o CMakeFiles/vcflib.dir/src/split.cpp.o CMakeFiles/vcflib.dir/src/rkmh.cpp.o CMakeFiles/vcflib.dir/src/murmur3.cpp.o CMakeFiles/vcflib.dir/src/LeftAlign.cpp.o CMakeFiles/vcflib.dir/src/cigar.cpp.o CMakeFiles/vcflib.dir/src/allele.cpp.o CMakeFiles/vcflib.dir/contrib/filevercmp/filevercmp.c.o "CMakeFiles/vcflib.dir/contrib/c-progress-bar/progress.c.o" -ltabixpp -lwfa2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so @@ -979,11 +1015,11 @@ make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' [ 9%] Built target vcflib make -f CMakeFiles/vcfecho.dir/build.make CMakeFiles/vcfecho.dir/depend -make -f CMakeFiles/dumpContigsFromHeader.dir/build.make CMakeFiles/dumpContigsFromHeader.dir/depend -make -f CMakeFiles/bFst.dir/build.make CMakeFiles/bFst.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +make -f CMakeFiles/dumpContigsFromHeader.dir/build.make CMakeFiles/dumpContigsFromHeader.dir/depend cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu/CMakeFiles/vcfecho.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +make -f CMakeFiles/bFst.dir/build.make CMakeFiles/bFst.dir/depend cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu/CMakeFiles/dumpContigsFromHeader.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' make -f CMakeFiles/pVst.dir/build.make CMakeFiles/pVst.dir/depend @@ -998,83 +1034,83 @@ make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' make -f CMakeFiles/vcfecho.dir/build.make CMakeFiles/vcfecho.dir/build cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu 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/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu/CMakeFiles/wcFst.dir/DependInfo.cmake "--color=" +make -f CMakeFiles/pVst.dir/build.make CMakeFiles/pVst.dir/build make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' make -f CMakeFiles/dumpContigsFromHeader.dir/build.make CMakeFiles/dumpContigsFromHeader.dir/build -cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu 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-o CMakeFiles/bFst.dir/src/bFst.cpp.o -c /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/bFst.cpp make -f CMakeFiles/iHS.dir/build.make CMakeFiles/iHS.dir/depend -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -make -f CMakeFiles/segmentFst.dir/build.make CMakeFiles/segmentFst.dir/depend +/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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-I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/dumpContigsFromHeader.dir/src/dumpContigsFromHeader.cpp.o -MF CMakeFiles/dumpContigsFromHeader.dir/src/dumpContigsFromHeader.cpp.o.d -o CMakeFiles/dumpContigsFromHeader.dir/src/dumpContigsFromHeader.cpp.o -c 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12%] Building CXX object CMakeFiles/wcFst.dir/src/wcFst.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/wcFst.dir/src/wcFst.cpp.o -MF CMakeFiles/wcFst.dir/src/wcFst.cpp.o.d -o CMakeFiles/wcFst.dir/src/wcFst.cpp.o -c /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/wcFst.cpp -[ 12%] Building CXX object CMakeFiles/hapLrt.dir/src/hapLrt.cpp.o -/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/hapLrt.dir/src/hapLrt.cpp.o -MF CMakeFiles/hapLrt.dir/src/hapLrt.cpp.o.d -o 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'/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu/CMakeFiles/genotypeSummary.dir/DependInfo.cmake "--color=" +make -f CMakeFiles/iHS.dir/build.make CMakeFiles/iHS.dir/build +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +make -f CMakeFiles/segmentFst.dir/build.make CMakeFiles/segmentFst.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' make 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-I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/segmentFst.dir/src/segmentFst.cpp.o -MF CMakeFiles/segmentFst.dir/src/segmentFst.cpp.o.d -o CMakeFiles/segmentFst.dir/src/segmentFst.cpp.o -c /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/segmentFst.cpp +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' [ 14%] Building CXX object CMakeFiles/segmentIhs.dir/src/segmentIhs.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -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 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-ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/genotypeSummary.dir/src/genotypeSummary.cpp.o -MF CMakeFiles/genotypeSummary.dir/src/genotypeSummary.cpp.o.d -o CMakeFiles/genotypeSummary.dir/src/genotypeSummary.cpp.o -c /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/genotypeSummary.cpp /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -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-1.0.9+dfsg1/src/sequenceDiversity.cpp -In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfecho.cpp:10: +In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/pVst.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ @@ -1090,7 +1126,16 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/popStats.cpp:10: +/build/reproducible-path/libvcflib-1.0.9+dfsg1/src/pVst.cpp: In function 'void calc(copyNcounts*)': +/build/reproducible-path/libvcflib-1.0.9+dfsg1/src/pVst.cpp:191:24: warning: 'void std::random_shuffle(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' is deprecated: use 'std::shuffle' instead [-Wdeprecated-declarations] + 191 | std::random_shuffle(d->total.begin(), d->total.end()); + | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/functional:67, + from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:24: +/usr/include/c++/13/bits/stl_algo.h:4581:5: note: declared here + 4581 | random_shuffle(_RandomAccessIterator __first, _RandomAccessIterator __last) + | ^~~~~~~~~~~~~~ +In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/iHS.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ @@ -1106,7 +1151,7 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/bFst.cpp:10: +In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/popStats.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ @@ -1122,8 +1167,7 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 15%] Linking CXX executable segmentIhs -In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/dumpContigsFromHeader.cpp:10: +In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/hapLrt.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ @@ -1139,8 +1183,7 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -/usr/bin/cmake -E cmake_link_script CMakeFiles/segmentIhs.dir/link.txt --verbose=1 -In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/sequenceDiversity.cpp:10: +In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/wcFst.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ @@ -1156,7 +1199,9 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/wcFst.cpp:10: +[ 15%] Linking CXX executable segmentIhs +/usr/bin/cmake -E cmake_link_script CMakeFiles/segmentIhs.dir/link.txt --verbose=1 +In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfecho.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ @@ -1173,7 +1218,7 @@ 131 | struct binary_function | ^~~~~~~~~~~~~~~ /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/segmentIhs.dir/src/segmentIhs.cpp.o -o segmentIhs -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/genotypeSummary.cpp:10: +In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/bFst.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ @@ -1189,9 +1234,7 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 15%] Linking CXX executable segmentFst -/usr/bin/cmake -E cmake_link_script CMakeFiles/segmentFst.dir/link.txt --verbose=1 -In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/iHS.cpp:10: +In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/dumpContigsFromHeader.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ @@ -1207,8 +1250,10 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +[ 15%] Linking CXX executable segmentFst +/usr/bin/cmake -E cmake_link_script CMakeFiles/segmentFst.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/segmentFst.dir/src/segmentFst.cpp.o -o segmentFst -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/hapLrt.cpp:10: +In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/sequenceDiversity.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ @@ -1224,10 +1269,7 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 16%] Linking CXX executable vcfecho -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfecho.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfecho.dir/src/vcfecho.cpp.o -o vcfecho -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/pVst.cpp:10: +In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/genotypeSummary.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ @@ -1243,82 +1285,89 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -/build/reproducible-path/libvcflib-1.0.9+dfsg1/src/pVst.cpp: In function 'void calc(copyNcounts*)': -/build/reproducible-path/libvcflib-1.0.9+dfsg1/src/pVst.cpp:191:24: warning: 'void std::random_shuffle(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' is deprecated: use 'std::shuffle' instead [-Wdeprecated-declarations] - 191 | std::random_shuffle(d->total.begin(), d->total.end()); - | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/functional:67, - from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:24: -/usr/include/c++/13/bits/stl_algo.h:4581:5: note: declared here - 4581 | random_shuffle(_RandomAccessIterator __first, _RandomAccessIterator __last) - | ^~~~~~~~~~~~~~ +[ 16%] Linking CXX executable vcfecho +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfecho.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfecho.dir/src/vcfecho.cpp.o -o vcfecho -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +[ 16%] 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-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/pVst.dir/src/pVst.cpp.o -o pVst -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 [ 17%] Linking CXX executable dumpContigsFromHeader /usr/bin/cmake -E cmake_link_script CMakeFiles/dumpContigsFromHeader.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/dumpContigsFromHeader.dir/src/dumpContigsFromHeader.cpp.o -o dumpContigsFromHeader -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' [ 17%] Built target segmentIhs -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' make -f CMakeFiles/pFst.dir/build.make CMakeFiles/pFst.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu/CMakeFiles/pFst.dir/DependInfo.cmake "--color=" -[ 17%] Built target segmentFst +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +[ 18%] Linking CXX executable wcFst +[ 18%] Linking CXX executable popStats +/usr/bin/cmake -E cmake_link_script CMakeFiles/wcFst.dir/link.txt --verbose=1 +/usr/bin/cmake -E cmake_link_script CMakeFiles/popStats.dir/link.txt --verbose=1 +[ 18%] Built target segmentFst make -f CMakeFiles/smoother.dir/build.make CMakeFiles/smoother.dir/depend -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu/CMakeFiles/smoother.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/wcFst.dir/src/wcFst.cpp.o -o wcFst -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/popStats.dir/src/popStats.cpp.o -o popStats -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' make -f CMakeFiles/pFst.dir/build.make CMakeFiles/pFst.dir/build -[ 17%] Linking CXX executable popStats -/usr/bin/cmake -E cmake_link_script 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-Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/popStats.dir/src/popStats.cpp.o -o popStats -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +[ 18%] Building CXX object CMakeFiles/pFst.dir/src/pFst.cpp.o make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -[ 17%] Building CXX object CMakeFiles/pFst.dir/src/pFst.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -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-1.0.9+dfsg1/src/pFst.cpp -[ 17%] Building CXX object CMakeFiles/smoother.dir/src/smoother.cpp.o +[ 18%] Building CXX object CMakeFiles/smoother.dir/src/smoother.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -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-1.0.9+dfsg1/src/smoother.cpp +[ 19%] 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-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/hapLrt.dir/src/hapLrt.cpp.o -o hapLrt -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +[ 20%] Linking CXX executable iHS +/usr/bin/cmake -E cmake_link_script CMakeFiles/iHS.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/iHS.dir/src/iHS.cpp.o -o iHS -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -[ 18%] Linking CXX executable wcFst -/usr/bin/cmake -E cmake_link_script CMakeFiles/wcFst.dir/link.txt --verbose=1 -[ 18%] Built target vcfecho -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/wcFst.dir/src/wcFst.cpp.o -o wcFst -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +[ 20%] Built target vcfecho make -f CMakeFiles/vcfld.dir/build.make CMakeFiles/vcfld.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu/CMakeFiles/vcfld.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' make -f CMakeFiles/vcfld.dir/build.make CMakeFiles/vcfld.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -[ 19%] Building CXX object CMakeFiles/vcfld.dir/src/vcfld.cpp.o -/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -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-1.0.9+dfsg1/src/vcfld.cpp +[ 21%] Building CXX object CMakeFiles/vcfld.dir/src/vcfld.cpp.o make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -[ 19%] Built target dumpContigsFromHeader +/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -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-1.0.9+dfsg1/src/vcfld.cpp +[ 21%] Built target dumpContigsFromHeader make -f CMakeFiles/plotHaps.dir/build.make CMakeFiles/plotHaps.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu/CMakeFiles/plotHaps.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' make -f CMakeFiles/plotHaps.dir/build.make CMakeFiles/plotHaps.dir/build +[ 22%] Linking CXX executable bFst +/usr/bin/cmake -E cmake_link_script CMakeFiles/bFst.dir/link.txt --verbose=1 make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -[ 20%] Building CXX object CMakeFiles/plotHaps.dir/src/plotHaps.cpp.o +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/bFst.dir/src/bFst.cpp.o -o bFst -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +[ 23%] Building CXX object CMakeFiles/plotHaps.dir/src/plotHaps.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -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-1.0.9+dfsg1/src/plotHaps.cpp -[ 21%] Linking CXX executable sequenceDiversity +[ 24%] Linking CXX executable sequenceDiversity /usr/bin/cmake -E cmake_link_script CMakeFiles/sequenceDiversity.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 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-Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/hapLrt.dir/src/hapLrt.cpp.o -o hapLrt -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -[ 23%] Linking CXX executable genotypeSummary +[ 25%] 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-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp 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/usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -[ 24%] 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-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/pVst.dir/src/pVst.cpp.o -o pVst -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -[ 25%] Linking CXX executable bFst -/usr/bin/cmake -E cmake_link_script CMakeFiles/bFst.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/bFst.dir/src/bFst.cpp.o -o bFst -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +[ 25%] Built target wcFst +make -f CMakeFiles/abba-baba.dir/build.make CMakeFiles/abba-baba.dir/depend +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu/CMakeFiles/abba-baba.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +make -f CMakeFiles/abba-baba.dir/build.make CMakeFiles/abba-baba.dir/build +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +[ 25%] Building CXX object CMakeFiles/abba-baba.dir/src/abba-baba.cpp.o +/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -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-1.0.9+dfsg1/src/abba-baba.cpp +[ 26%] Linking CXX executable smoother +/usr/bin/cmake -E cmake_link_script CMakeFiles/smoother.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/smoother.dir/src/smoother.cpp.o -o smoother -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/pFst.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { @@ -1352,26 +1401,15 @@ 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -[ 25%] Built target popStats -make -f CMakeFiles/abba-baba.dir/build.make CMakeFiles/abba-baba.dir/depend -[ 26%] Linking CXX executable smoother -/usr/bin/cmake -E cmake_link_script CMakeFiles/smoother.dir/link.txt --verbose=1 -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends 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[-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { @@ -1388,11 +1426,18 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 27%] Building CXX object CMakeFiles/permuteGPAT++.dir/src/permuteGPAT++.cpp.o -/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time 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'/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +make -f CMakeFiles/permuteSmooth.dir/build.make CMakeFiles/permuteSmooth.dir/build +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +[ 28%] Building CXX object CMakeFiles/permuteSmooth.dir/src/permuteSmooth.cpp.o +/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -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-1.0.9+dfsg1/src/permuteSmooth.cpp +[ 28%] Linking CXX executable vcfld +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfld.dir/link.txt --verbose=1 In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/abba-baba.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { @@ -1409,109 +1454,104 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 28%] Linking CXX executable vcfld -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfld.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfld.dir/src/vcfld.cpp.o -o vcfld -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -[ 28%] Linking CXX executable permuteGPAT++ -/usr/bin/cmake -E cmake_link_script CMakeFiles/permuteGPAT++.dir/link.txt --verbose=1 -[ 28%] Built target bFst -make -f CMakeFiles/permuteSmooth.dir/build.make CMakeFiles/permuteSmooth.dir/depend -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/permuteGPAT++.dir/src/permuteGPAT++.cpp.o -o permuteGPAT++ -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -cd 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-Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -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-1.0.9+dfsg1/src/permuteSmooth.cpp make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' make -f CMakeFiles/normalize-iHS.dir/build.make CMakeFiles/normalize-iHS.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +[ 29%] Building CXX object CMakeFiles/normalize-iHS.dir/src/normalize-iHS.cpp.o +/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -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-1.0.9+dfsg1/src/normalize-iHS.cpp +[ 30%] Linking CXX executable abba-baba +/usr/bin/cmake -E cmake_link_script CMakeFiles/abba-baba.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now "CMakeFiles/abba-baba.dir/src/abba-baba.cpp.o" -o abba-baba -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +[ 30%] Built target bFst +make -f CMakeFiles/meltEHH.dir/build.make CMakeFiles/meltEHH.dir/depend +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu/CMakeFiles/meltEHH.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' make -f CMakeFiles/meltEHH.dir/build.make CMakeFiles/meltEHH.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -[ 29%] Building CXX object CMakeFiles/meltEHH.dir/src/meltEHH.cpp.o +[ 30%] Building CXX object CMakeFiles/meltEHH.dir/src/meltEHH.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -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-1.0.9+dfsg1/src/meltEHH.cpp -[ 29%] Linking CXX executable plotHaps +[ 30%] Linking CXX executable permuteGPAT++ +/usr/bin/cmake -E cmake_link_script CMakeFiles/permuteGPAT++.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/permuteGPAT++.dir/src/permuteGPAT++.cpp.o -o permuteGPAT++ -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -/usr/bin/cmake -E cmake_link_script CMakeFiles/plotHaps.dir/link.txt --verbose=1 -[ 29%] Building CXX object CMakeFiles/normalize-iHS.dir/src/normalize-iHS.cpp.o -/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -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-1.0.9+dfsg1/src/normalize-iHS.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/plotHaps.dir/src/plotHaps.cpp.o -o plotHaps -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -[ 29%] Built target iHS -[ 29%] Built target genotypeSummary +[ 30%] Built target hapLrt make -f CMakeFiles/vcfnullgenofields.dir/build.make 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/build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu/CMakeFiles/vcfaltcount.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' make -f CMakeFiles/vcfnullgenofields.dir/build.make CMakeFiles/vcfnullgenofields.dir/build +[ 30%] Built target iHS +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +make -f CMakeFiles/vcfaltcount.dir/build.make CMakeFiles/vcfaltcount.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu/CMakeFiles/vcfaltcount.dir/DependInfo.cmake "--color=" +[ 31%] Building CXX object CMakeFiles/vcfnullgenofields.dir/src/vcfnullgenofields.cpp.o +/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 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'/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +[ 31%] Built target genotypeSummary make -f CMakeFiles/vcfhetcount.dir/build.make CMakeFiles/vcfhetcount.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu/CMakeFiles/vcfhetcount.dir/DependInfo.cmake "--color=" +[ 31%] Built target permuteGPAT++ +make -f CMakeFiles/vcfhethomratio.dir/build.make CMakeFiles/vcfhethomratio.dir/depend +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu/CMakeFiles/vcfhethomratio.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' make -f CMakeFiles/vcfhetcount.dir/build.make CMakeFiles/vcfhetcount.dir/build make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +make -f CMakeFiles/vcfhethomratio.dir/build.make CMakeFiles/vcfhethomratio.dir/build +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' make[4]: Entering directory 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-fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -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-1.0.9+dfsg1/src/vcfhetcount.cpp -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu/CMakeFiles/vcfhethomratio.dir/DependInfo.cmake "--color=" +[ 31%] Building CXX object CMakeFiles/vcfhethomratio.dir/src/vcfhethomratio.cpp.o +/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -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-1.0.9+dfsg1/src/vcfhethomratio.cpp +[ 32%] Linking CXX executable normalize-iHS +/usr/bin/cmake -E cmake_link_script CMakeFiles/normalize-iHS.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now "CMakeFiles/normalize-iHS.dir/src/normalize-iHS.cpp.o" -o normalize-iHS -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp 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-ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -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-1.0.9+dfsg1/src/vcfhethomratio.cpp -[ 31%] Building CXX object CMakeFiles/vcffilter.dir/src/vcffilter.cpp.o +[ 32%] Building CXX object CMakeFiles/vcffilter.dir/src/vcffilter.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -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-1.0.9+dfsg1/src/vcffilter.cpp make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -[ 31%] Built target pFst +[ 32%] Built target abba-baba make -f CMakeFiles/vcf2tsv.dir/build.make CMakeFiles/vcf2tsv.dir/depend -[ 31%] Linking CXX executable permuteSmooth -/usr/bin/cmake -E cmake_link_script CMakeFiles/permuteSmooth.dir/link.txt --verbose=1 make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu/CMakeFiles/vcf2tsv.dir/DependInfo.cmake "--color=" -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/permuteSmooth.dir/src/permuteSmooth.cpp.o -o permuteSmooth -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' make -f CMakeFiles/vcf2tsv.dir/build.make CMakeFiles/vcf2tsv.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +[ 32%] Building CXX object CMakeFiles/vcf2tsv.dir/src/vcf2tsv.cpp.o In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/meltEHH.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { @@ -1528,7 +1568,6 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 31%] Building CXX object CMakeFiles/vcf2tsv.dir/src/vcf2tsv.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -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-1.0.9+dfsg1/src/vcf2tsv.cpp In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfaltcount.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] @@ -1546,7 +1585,7 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfhetcount.cpp:10: +In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfnullgenofields.cpp:12: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ @@ -1562,10 +1601,40 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 32%] Linking CXX executable normalize-iHS -/usr/bin/cmake -E cmake_link_script CMakeFiles/normalize-iHS.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now "CMakeFiles/normalize-iHS.dir/src/normalize-iHS.cpp.o" -o normalize-iHS -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfnullgenofields.cpp:12: +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +[ 32%] Built target pFst +make -f CMakeFiles/vcfgenotypes.dir/build.make CMakeFiles/vcfgenotypes.dir/depend +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu/CMakeFiles/vcfgenotypes.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +make -f CMakeFiles/vcfgenotypes.dir/build.make CMakeFiles/vcfgenotypes.dir/build +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +[ 33%] Building CXX object CMakeFiles/vcfgenotypes.dir/src/vcfgenotypes.cpp.o +/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -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-1.0.9+dfsg1/src/vcfgenotypes.cpp +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +[ 33%] Built target permuteSmooth +make -f CMakeFiles/vcfannotategenotypes.dir/build.make CMakeFiles/vcfannotategenotypes.dir/depend +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu/CMakeFiles/vcfannotategenotypes.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +make -f CMakeFiles/vcfannotategenotypes.dir/build.make CMakeFiles/vcfannotategenotypes.dir/build +[ 33%] Built target normalize-iHS +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +make -f CMakeFiles/vcfcommonsamples.dir/build.make CMakeFiles/vcfcommonsamples.dir/depend +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu/CMakeFiles/vcfcommonsamples.dir/DependInfo.cmake "--color=" +[ 34%] Building CXX object CMakeFiles/vcfannotategenotypes.dir/src/vcfannotategenotypes.cpp.o +/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfannotategenotypes.dir/src/vcfannotategenotypes.cpp.o -MF CMakeFiles/vcfannotategenotypes.dir/src/vcfannotategenotypes.cpp.o.d -o CMakeFiles/vcfannotategenotypes.dir/src/vcfannotategenotypes.cpp.o -c /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfannotategenotypes.cpp +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +make -f CMakeFiles/vcfcommonsamples.dir/build.make CMakeFiles/vcfcommonsamples.dir/build +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +[ 35%] Building CXX object CMakeFiles/vcfcommonsamples.dir/src/vcfcommonsamples.cpp.o +/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -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-1.0.9+dfsg1/src/vcfcommonsamples.cpp +[ 36%] Linking CXX executable vcfaltcount +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfaltcount.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfaltcount.dir/src/vcfaltcount.cpp.o -o vcfaltcount -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcffilter.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ @@ -1581,8 +1650,7 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcffilter.cpp:10: +In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfhetcount.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ @@ -1598,30 +1666,9 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 32%] Built target abba-baba -make -f CMakeFiles/vcfgenotypes.dir/build.make CMakeFiles/vcfgenotypes.dir/depend -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu/CMakeFiles/vcfgenotypes.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -make -f CMakeFiles/vcfgenotypes.dir/build.make CMakeFiles/vcfgenotypes.dir/build -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -[ 33%] Building CXX object CMakeFiles/vcfgenotypes.dir/src/vcfgenotypes.cpp.o -/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -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-1.0.9+dfsg1/src/vcfgenotypes.cpp -[ 33%] Built target plotHaps -make -f CMakeFiles/vcfannotategenotypes.dir/build.make CMakeFiles/vcfannotategenotypes.dir/depend -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu/CMakeFiles/vcfannotategenotypes.dir/DependInfo.cmake "--color=" -[ 34%] Linking CXX executable vcfaltcount -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfaltcount.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfaltcount.dir/src/vcfaltcount.cpp.o -o vcfaltcount -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -make -f CMakeFiles/vcfannotategenotypes.dir/build.make CMakeFiles/vcfannotategenotypes.dir/build -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -[ 35%] Building CXX object CMakeFiles/vcfannotategenotypes.dir/src/vcfannotategenotypes.cpp.o -/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfannotategenotypes.dir/src/vcfannotategenotypes.cpp.o -MF CMakeFiles/vcfannotategenotypes.dir/src/vcfannotategenotypes.cpp.o.d -o CMakeFiles/vcfannotategenotypes.dir/src/vcfannotategenotypes.cpp.o -c /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfannotategenotypes.cpp -[ 36%] Linking CXX executable vcfhetcount -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfhetcount.dir/link.txt --verbose=1 +[ 36%] 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-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfnullgenofields.dir/src/vcfnullgenofields.cpp.o -o vcfnullgenofields -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfhethomratio.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { @@ -1638,14 +1685,17 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +[ 37%] Linking CXX executable vcfhetcount +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfhetcount.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfhetcount.dir/src/vcfhetcount.cpp.o -o vcfhetcount -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -[ 36%] Built target vcfld make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -make -f CMakeFiles/vcfcommonsamples.dir/build.make CMakeFiles/vcfcommonsamples.dir/depend +[ 37%] Built target plotHaps +make -f CMakeFiles/vcfremovesamples.dir/build.make CMakeFiles/vcfremovesamples.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu/CMakeFiles/vcfcommonsamples.dir/DependInfo.cmake "--color=" -[ 36%] Built target permuteSmooth +cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu/CMakeFiles/vcfremovesamples.dir/DependInfo.cmake "--color=" +[ 37%] Built target vcfld +make -f CMakeFiles/vcfkeepsamples.dir/build.make CMakeFiles/vcfkeepsamples.dir/depend In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcf2tsv.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { @@ -1662,52 +1712,30 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -make -f CMakeFiles/vcfremovesamples.dir/build.make CMakeFiles/vcfremovesamples.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu/CMakeFiles/vcfremovesamples.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 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object CMakeFiles/vcfcommonsamples.dir/src/vcfcommonsamples.cpp.o -/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -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 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-fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfkeepsamples.dir/src/vcfkeepsamples.cpp.o -MF CMakeFiles/vcfkeepsamples.dir/src/vcfkeepsamples.cpp.o.d -o CMakeFiles/vcfkeepsamples.dir/src/vcfkeepsamples.cpp.o -c /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfkeepsamples.cpp +[ 39%] Linking CXX executable meltEHH /usr/bin/cmake -E cmake_link_script CMakeFiles/meltEHH.dir/link.txt --verbose=1 -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/meltEHH.dir/src/meltEHH.cpp.o -o meltEHH -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -[ 38%] Built target normalize-iHS -make -f CMakeFiles/vcfkeepsamples.dir/build.make CMakeFiles/vcfkeepsamples.dir/depend -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu 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-ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfkeepsamples.dir/src/vcfkeepsamples.cpp.o -MF CMakeFiles/vcfkeepsamples.dir/src/vcfkeepsamples.cpp.o.d -o CMakeFiles/vcfkeepsamples.dir/src/vcfkeepsamples.cpp.o -c /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfkeepsamples.cpp make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' [ 39%] Built target vcfaltcount make -f CMakeFiles/vcfsamplenames.dir/build.make CMakeFiles/vcfsamplenames.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu/CMakeFiles/vcfsamplenames.dir/DependInfo.cmake "--color=" -[ 40%] 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-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcffilter.dir/src/vcffilter.cpp.o -o vcffilter -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' make -f CMakeFiles/vcfsamplenames.dir/build.make CMakeFiles/vcfsamplenames.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -[ 41%] Building CXX object CMakeFiles/vcfsamplenames.dir/src/vcfsamplenames.cpp.o -[ 42%] Linking CXX executable vcfhethomratio -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfhethomratio.dir/link.txt --verbose=1 -/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -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-1.0.9+dfsg1/src/vcfsamplenames.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfhethomratio.dir/src/vcfhethomratio.cpp.o -o vcfhethomratio -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfgenotypes.cpp:10: +In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfcommonsamples.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ @@ -1723,10 +1751,11 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 43%] Linking CXX executable vcf2tsv -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcf2tsv.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcf2tsv.dir/src/vcf2tsv.cpp.o -o vcf2tsv -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp 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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-1.0.9+dfsg1/src/vcfsamplenames.cpp +[ 41%] Linking CXX executable vcfhethomratio +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfhethomratio.dir/link.txt --verbose=1 +In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfgenotypes.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ @@ -1742,7 +1771,12 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfremovesamples.cpp:10: +/usr/bin/c++ -g -O2 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-Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcf2tsv.dir/src/vcf2tsv.cpp.o -o vcf2tsv -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +[ 43%] Linking CXX executable vcffilter +In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfannotategenotypes.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ @@ -1758,13 +1792,22 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +/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-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcffilter.dir/src/vcffilter.cpp.o -o vcffilter -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -[ 43%] Built target vcfhetcount +[ 43%] Built target vcfnullgenofields make -f CMakeFiles/vcfgenotypecompare.dir/build.make CMakeFiles/vcfgenotypecompare.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu/CMakeFiles/vcfgenotypecompare.dir/DependInfo.cmake "--color=" -[ 43%] Linking CXX executable vcfgenotypes -In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfcommonsamples.cpp:10: +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +make -f CMakeFiles/vcfgenotypecompare.dir/build.make CMakeFiles/vcfgenotypecompare.dir/build +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +[ 44%] Linking CXX executable vcfcommonsamples +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfcommonsamples.dir/link.txt --verbose=1 +[ 45%] Building CXX object CMakeFiles/vcfgenotypecompare.dir/src/vcfgenotypecompare.cpp.o +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfcommonsamples.dir/src/vcfcommonsamples.cpp.o -o vcfcommonsamples -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -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-1.0.9+dfsg1/src/vcfgenotypecompare.cpp +In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfkeepsamples.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ @@ -1781,16 +1824,19 @@ 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfgenotypes.dir/link.txt --verbose=1 -make -f CMakeFiles/vcfgenotypecompare.dir/build.make CMakeFiles/vcfgenotypecompare.dir/build +[ 45%] Built target vcfhetcount +make -f CMakeFiles/vcffixup.dir/build.make CMakeFiles/vcffixup.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfgenotypes.dir/src/vcfgenotypes.cpp.o -o vcfgenotypes -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -[ 44%] Building CXX object CMakeFiles/vcfgenotypecompare.dir/src/vcfgenotypecompare.cpp.o -/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -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-1.0.9+dfsg1/src/vcfgenotypecompare.cpp -In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfkeepsamples.cpp:10: +cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu/CMakeFiles/vcffixup.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +make -f CMakeFiles/vcffixup.dir/build.make CMakeFiles/vcffixup.dir/build +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +[ 45%] Building CXX object CMakeFiles/vcffixup.dir/src/vcffixup.cpp.o +In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfremovesamples.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ +/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -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-1.0.9+dfsg1/src/vcffixup.cpp In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:12: @@ -1803,11 +1849,13 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +[ 45%] 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-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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/usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -[ 47%] Linking CXX executable vcfkeepsamples -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfkeepsamples.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfkeepsamples.dir/src/vcfkeepsamples.cpp.o -o vcfkeepsamples -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -[ 47%] Built target vcffilter make -f CMakeFiles/vcfsamplediff.dir/build.make CMakeFiles/vcfsamplediff.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu/CMakeFiles/vcfsamplediff.dir/DependInfo.cmake "--color=" +[ 46%] Building CXX object CMakeFiles/vcfclassify.dir/src/vcfclassify.cpp.o +/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -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-1.0.9+dfsg1/src/vcfclassify.cpp make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' make -f CMakeFiles/vcfsamplediff.dir/build.make CMakeFiles/vcfsamplediff.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +[ 47%] Linking CXX executable vcfremovesamples +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfremovesamples.dir/link.txt --verbose=1 [ 48%] Building CXX object CMakeFiles/vcfsamplediff.dir/src/vcfsamplediff.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -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-1.0.9+dfsg1/src/vcfsamplediff.cpp -[ 48%] Built target vcf2tsv -make -f CMakeFiles/vcfremoveaberrantgenotypes.dir/build.make CMakeFiles/vcfremoveaberrantgenotypes.dir/depend -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu/CMakeFiles/vcfremoveaberrantgenotypes.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -[ 48%] Built target vcfsamplenames -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -make -f CMakeFiles/vcfrandom.dir/build.make CMakeFiles/vcfrandom.dir/depend -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu/CMakeFiles/vcfrandom.dir/DependInfo.cmake "--color=" -make -f CMakeFiles/vcfremoveaberrantgenotypes.dir/build.make CMakeFiles/vcfremoveaberrantgenotypes.dir/build -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfremovesamples.dir/src/vcfremovesamples.cpp.o -o vcfremovesamples -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfgenotypecompare.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { @@ -1896,6 +1910,42 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +[ 48%] Built target vcfkeepsamples +make -f CMakeFiles/vcfremoveaberrantgenotypes.dir/build.make CMakeFiles/vcfremoveaberrantgenotypes.dir/depend +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu/CMakeFiles/vcfremoveaberrantgenotypes.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +make -f CMakeFiles/vcfremoveaberrantgenotypes.dir/build.make CMakeFiles/vcfremoveaberrantgenotypes.dir/build +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +[ 48%] Building CXX object CMakeFiles/vcfremoveaberrantgenotypes.dir/src/vcfremoveaberrantgenotypes.cpp.o +/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -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-1.0.9+dfsg1/src/vcfremoveaberrantgenotypes.cpp +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +[ 48%] Built target vcf2tsv +make -f CMakeFiles/vcfrandom.dir/build.make CMakeFiles/vcfrandom.dir/depend +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu/CMakeFiles/vcfrandom.dir/DependInfo.cmake "--color=" +[ 48%] Linking CXX executable vcfsamplenames +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfsamplenames.dir/link.txt --verbose=1 +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +make -f CMakeFiles/vcfrandom.dir/build.make CMakeFiles/vcfrandom.dir/build +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfsamplenames.dir/src/vcfsamplenames.cpp.o -o vcfsamplenames -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +[ 48%] Linking CXX executable vcfannotategenotypes +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfannotategenotypes.dir/link.txt --verbose=1 +[ 48%] Building CXX object CMakeFiles/vcfrandom.dir/src/vcfrandom.cpp.o +/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfrandom.dir/src/vcfrandom.cpp.o -MF CMakeFiles/vcfrandom.dir/src/vcfrandom.cpp.o.d -o CMakeFiles/vcfrandom.dir/src/vcfrandom.cpp.o -c /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfrandom.cpp +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfannotategenotypes.dir/src/vcfannotategenotypes.cpp.o -o vcfannotategenotypes -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +[ 48%] Built target vcfgenotypes +make -f CMakeFiles/vcfparsealts.dir/build.make CMakeFiles/vcfparsealts.dir/depend +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu/CMakeFiles/vcfparsealts.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +make -f CMakeFiles/vcfparsealts.dir/build.make CMakeFiles/vcfparsealts.dir/build +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +[ 49%] Building CXX object CMakeFiles/vcfparsealts.dir/src/vcfparsealts.cpp.o +/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -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-1.0.9+dfsg1/src/vcfparsealts.cpp In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcffixup.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { @@ -1912,35 +1962,34 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 48%] Building CXX object CMakeFiles/vcfremoveaberrantgenotypes.dir/src/vcfremoveaberrantgenotypes.cpp.o -make -f CMakeFiles/vcfrandom.dir/build.make CMakeFiles/vcfrandom.dir/build -[ 48%] Built target vcfremovesamples -/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -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-1.0.9+dfsg1/src/vcfremoveaberrantgenotypes.cpp -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -make -f CMakeFiles/vcfparsealts.dir/build.make CMakeFiles/vcfparsealts.dir/depend -[ 48%] Built target vcfgenotypes -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu/CMakeFiles/vcfparsealts.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +[ 49%] Built target vcfsamplenames make -f CMakeFiles/vcfstats.dir/build.make CMakeFiles/vcfstats.dir/depend -[ 48%] Building CXX object CMakeFiles/vcfrandom.dir/src/vcfrandom.cpp.o make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu/CMakeFiles/vcfstats.dir/DependInfo.cmake "--color=" -/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfrandom.dir/src/vcfrandom.cpp.o -MF CMakeFiles/vcfrandom.dir/src/vcfrandom.cpp.o.d -o CMakeFiles/vcfrandom.dir/src/vcfrandom.cpp.o -c /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfrandom.cpp -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +[ 49%] Linking CXX executable vcfgenotypecompare +[ 49%] Built target vcffilter +make -f CMakeFiles/vcfflatten.dir/build.make CMakeFiles/vcfflatten.dir/depend +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfgenotypecompare.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -make -f CMakeFiles/vcfparsealts.dir/build.make CMakeFiles/vcfparsealts.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' make -f CMakeFiles/vcfstats.dir/build.make CMakeFiles/vcfstats.dir/build +cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu/CMakeFiles/vcfflatten.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -[ 48%] Built target vcfcommonsamples -make -f CMakeFiles/vcfflatten.dir/build.make CMakeFiles/vcfflatten.dir/depend +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfgenotypecompare.dir/src/vcfgenotypecompare.cpp.o -o vcfgenotypecompare -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +[ 50%] Building CXX object CMakeFiles/vcfstats.dir/src/vcfstats.cpp.o +/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose 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+[ 51%] Building CXX object CMakeFiles/vcfflatten.dir/src/vcfflatten.cpp.o +/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -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-1.0.9+dfsg1/src/vcfflatten.cpp +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfclassify.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ -[ 49%] Building CXX object CMakeFiles/vcfstats.dir/src/vcfstats.cpp.o -/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfstats.dir/src/vcfstats.cpp.o -MF CMakeFiles/vcfstats.dir/src/vcfstats.cpp.o.d -o CMakeFiles/vcfstats.dir/src/vcfstats.cpp.o -c /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfstats.cpp In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:12: @@ -1953,45 +2002,14 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu/CMakeFiles/vcfflatten.dir/DependInfo.cmake "--color=" -[ 50%] Building CXX object CMakeFiles/vcfparsealts.dir/src/vcfparsealts.cpp.o -/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp 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/usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -[ 54%] Linking CXX executable vcfclassify -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfclassify.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfclassify.dir/src/vcfclassify.cpp.o -o vcfclassify -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -[ 54%] Linking CXX executable vcfgenotypecompare -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfgenotypecompare.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfgenotypecompare.dir/src/vcfgenotypecompare.cpp.o -o vcfgenotypecompare -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfstats.cpp:10: +In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfsamplediff.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ @@ -2007,7 +2025,14 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfsamplediff.cpp:10: +[ 52%] Building CXX object CMakeFiles/vcfprimers.dir/src/vcfprimers.cpp.o +/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -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-1.0.9+dfsg1/src/vcfprimers.cpp +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +[ 52%] Built target meltEHH +make -f CMakeFiles/vcfnumalt.dir/build.make CMakeFiles/vcfnumalt.dir/depend +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu/CMakeFiles/vcfnumalt.dir/DependInfo.cmake "--color=" +In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfremoveaberrantgenotypes.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ @@ -2023,13 +2048,22 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfremoveaberrantgenotypes.cpp:10: +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +make -f CMakeFiles/vcfnumalt.dir/build.make CMakeFiles/vcfnumalt.dir/build +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +[ 53%] Building CXX object CMakeFiles/vcfnumalt.dir/src/vcfnumalt.cpp.o +/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfnumalt.dir/src/vcfnumalt.cpp.o -MF CMakeFiles/vcfnumalt.dir/src/vcfnumalt.cpp.o.d -o CMakeFiles/vcfnumalt.dir/src/vcfnumalt.cpp.o -c /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfnumalt.cpp +In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfrandom.cpp:13: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/bits/refwrap.h:39, - from /usr/include/c++/13/vector:68, - from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:12: +In file included from /usr/include/c++/13/string:49, + from /usr/include/c++/13/bits/locale_classes.h:40, + from /usr/include/c++/13/bits/ios_base.h:41, + from /usr/include/c++/13/ios:44, + from /usr/include/c++/13/istream:40, + from /usr/include/c++/13/sstream:40, + from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfrandom.cpp:10: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -2039,7 +2073,16 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfflatten.cpp:10: +[ 54%] Linking CXX executable vcffixup +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcffixup.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcffixup.dir/src/vcffixup.cpp.o -o vcffixup -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +[ 54%] Linking CXX executable vcfsamplediff +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfsamplediff.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfsamplediff.dir/src/vcfsamplediff.cpp.o -o vcfsamplediff -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +[ 54%] Linking CXX executable vcfclassify +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfclassify.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfclassify.dir/src/vcfclassify.cpp.o -o vcfclassify -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfparsealts.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ @@ -2055,17 +2098,19 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfrandom.cpp:13: +[ 55%] Linking CXX executable vcfremoveaberrantgenotypes +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfremoveaberrantgenotypes.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfremoveaberrantgenotypes.dir/src/vcfremoveaberrantgenotypes.cpp.o -o vcfremoveaberrantgenotypes -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +[ 56%] Linking CXX executable vcfrandom +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfrandom.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfrandom.dir/src/vcfrandom.cpp.o -o vcfrandom -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfflatten.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/string:49, - from /usr/include/c++/13/bits/locale_classes.h:40, - from /usr/include/c++/13/bits/ios_base.h:41, - from /usr/include/c++/13/ios:44, - from /usr/include/c++/13/istream:40, - from /usr/include/c++/13/sstream:40, - from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfrandom.cpp:10: +In file included from /usr/include/c++/13/bits/refwrap.h:39, + from /usr/include/c++/13/vector:68, + from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:12: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -2075,6 +2120,8 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +[ 56%] Linking CXX executable vcfparsealts +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfparsealts.dir/link.txt --verbose=1 In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfprimers.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { @@ -2091,6 +2138,7 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfparsealts.dir/src/vcfparsealts.cpp.o -o vcfparsealts -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so 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/usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -[ 57%] Built target vcfclassify +[ 56%] Built target vcfclassify make -f CMakeFiles/vcfcleancomplex.dir/build.make CMakeFiles/vcfcleancomplex.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu/CMakeFiles/vcfcleancomplex.dir/DependInfo.cmake "--color=" make[4]: 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -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-1.0.9+dfsg1/src/vcfintersect.cpp +[ 57%] Linking CXX executable vcfnumalt +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfnumalt.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfnumalt.dir/src/vcfnumalt.cpp.o -o vcfnumalt -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so 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/usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -[ 58%] Built target vcffixup +[ 58%] Built target vcfparsealts make -f CMakeFiles/vcfannotate.dir/build.make CMakeFiles/vcfannotate.dir/depend -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 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/build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu/CMakeFiles/vcfallelicprimitives.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -make -f CMakeFiles/vcfwave.dir/build.make CMakeFiles/vcfwave.dir/depend -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu/CMakeFiles/vcfwave.dir/DependInfo.cmake "--color=" make -f CMakeFiles/vcfannotate.dir/build.make CMakeFiles/vcfannotate.dir/build -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -make -f CMakeFiles/vcfoverlay.dir/build.make CMakeFiles/vcfoverlay.dir/depend -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu 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'/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' [ 59%] Building CXX object CMakeFiles/vcfannotate.dir/src/vcfannotate.cpp.o -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -make -f CMakeFiles/vcfwave.dir/build.make CMakeFiles/vcfwave.dir/build /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfannotate.dir/src/vcfannotate.cpp.o -MF CMakeFiles/vcfannotate.dir/src/vcfannotate.cpp.o.d -o CMakeFiles/vcfannotate.dir/src/vcfannotate.cpp.o -c /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfannotate.cpp -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -make -f CMakeFiles/vcfoverlay.dir/build.make CMakeFiles/vcfoverlay.dir/build -[ 59%] Building CXX object CMakeFiles/vcfallelicprimitives.dir/src/vcfallelicprimitives.cpp.o -/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -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-1.0.9+dfsg1/src/vcfallelicprimitives.cpp -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -[ 60%] Building CXX object CMakeFiles/vcfwave.dir/src/vcfwave.cpp.o -/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -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-1.0.9+dfsg1/src/vcfwave.cpp -[ 61%] Building CXX object CMakeFiles/vcfoverlay.dir/src/vcfoverlay.cpp.o -/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfoverlay.dir/src/vcfoverlay.cpp.o -MF CMakeFiles/vcfoverlay.dir/src/vcfoverlay.cpp.o.d -o CMakeFiles/vcfoverlay.dir/src/vcfoverlay.cpp.o -c /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfoverlay.cpp -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -[ 61%] Built target vcfsamplediff -make -f CMakeFiles/vcfaddinfo.dir/build.make CMakeFiles/vcfaddinfo.dir/depend -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu/CMakeFiles/vcfaddinfo.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -make -f CMakeFiles/vcfaddinfo.dir/build.make CMakeFiles/vcfaddinfo.dir/build -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -[ 61%] Building CXX object CMakeFiles/vcfaddinfo.dir/src/vcfaddinfo.cpp.o -/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfaddinfo.dir/src/vcfaddinfo.cpp.o -MF CMakeFiles/vcfaddinfo.dir/src/vcfaddinfo.cpp.o.d -o CMakeFiles/vcfaddinfo.dir/src/vcfaddinfo.cpp.o -c /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfaddinfo.cpp -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -[ 61%] Built target vcfrandom -make -f CMakeFiles/vcfkeepinfo.dir/build.make CMakeFiles/vcfkeepinfo.dir/depend -[ 61%] Built target vcfnumalt -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu/CMakeFiles/vcfkeepinfo.dir/DependInfo.cmake "--color=" -make -f CMakeFiles/vcfkeepgeno.dir/build.make CMakeFiles/vcfkeepgeno.dir/depend +[ 59%] Built target vcfremoveaberrantgenotypes +make -f CMakeFiles/vcfallelicprimitives.dir/build.make CMakeFiles/vcfallelicprimitives.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu/CMakeFiles/vcfkeepgeno.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu/CMakeFiles/vcfallelicprimitives.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -make -f CMakeFiles/vcfkeepinfo.dir/build.make CMakeFiles/vcfkeepinfo.dir/build -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -make -f CMakeFiles/vcfkeepgeno.dir/build.make CMakeFiles/vcfkeepgeno.dir/build +make -f CMakeFiles/vcfallelicprimitives.dir/build.make CMakeFiles/vcfallelicprimitives.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -[ 61%] Building CXX object CMakeFiles/vcfkeepinfo.dir/src/vcfkeepinfo.cpp.o -/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -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-1.0.9+dfsg1/src/vcfkeepinfo.cpp -[ 61%] Building CXX object CMakeFiles/vcfkeepgeno.dir/src/vcfkeepgeno.cpp.o -/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -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 CMakeFiles/vcfkeepgeno.dir/src/vcfkeepgeno.cpp.o -c /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfkeepgeno.cpp +[ 59%] Built target vcfannotategenotypes +make -f CMakeFiles/vcfwave.dir/build.make CMakeFiles/vcfwave.dir/depend In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfcleancomplex.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { @@ -2253,6 +2237,25 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu/CMakeFiles/vcfwave.dir/DependInfo.cmake "--color=" +[ 59%] Building CXX object CMakeFiles/vcfallelicprimitives.dir/src/vcfallelicprimitives.cpp.o +/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -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-1.0.9+dfsg1/src/vcfallelicprimitives.cpp +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +make -f CMakeFiles/vcfwave.dir/build.make CMakeFiles/vcfwave.dir/build +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +[ 59%] Built target vcffixup +make -f CMakeFiles/vcfoverlay.dir/build.make CMakeFiles/vcfoverlay.dir/depend +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu/CMakeFiles/vcfoverlay.dir/DependInfo.cmake "--color=" +[ 60%] Building CXX object CMakeFiles/vcfwave.dir/src/vcfwave.cpp.o +/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -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-1.0.9+dfsg1/src/vcfwave.cpp +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +make -f CMakeFiles/vcfoverlay.dir/build.make CMakeFiles/vcfoverlay.dir/build +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +[ 61%] Building CXX object CMakeFiles/vcfoverlay.dir/src/vcfoverlay.cpp.o +/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfoverlay.dir/src/vcfoverlay.cpp.o -MF CMakeFiles/vcfoverlay.dir/src/vcfoverlay.cpp.o.d -o CMakeFiles/vcfoverlay.dir/src/vcfoverlay.cpp.o -c /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfoverlay.cpp In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfintersect.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { @@ -2270,18 +2273,47 @@ 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -[ 61%] Built target vcfflatten -make -f CMakeFiles/vcfafpath.dir/build.make CMakeFiles/vcfafpath.dir/depend +[ 61%] Built target vcfrandom +make -f CMakeFiles/vcfaddinfo.dir/build.make CMakeFiles/vcfaddinfo.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu/CMakeFiles/vcfafpath.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu/CMakeFiles/vcfaddinfo.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +[ 61%] Built target vcfnumalt +make -f CMakeFiles/vcfkeepinfo.dir/build.make CMakeFiles/vcfkeepinfo.dir/depend make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -make -f CMakeFiles/vcfafpath.dir/build.make CMakeFiles/vcfafpath.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -[ 61%] Building CXX object CMakeFiles/vcfafpath.dir/src/vcfafpath.cpp.o -/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -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-1.0.9+dfsg1/src/vcfafpath.cpp +make -f CMakeFiles/vcfaddinfo.dir/build.make CMakeFiles/vcfaddinfo.dir/build +cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu/CMakeFiles/vcfkeepinfo.dir/DependInfo.cmake "--color=" +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +[ 61%] Building CXX object CMakeFiles/vcfaddinfo.dir/src/vcfaddinfo.cpp.o +/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfaddinfo.dir/src/vcfaddinfo.cpp.o -MF CMakeFiles/vcfaddinfo.dir/src/vcfaddinfo.cpp.o.d -o CMakeFiles/vcfaddinfo.dir/src/vcfaddinfo.cpp.o -c /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfaddinfo.cpp +make -f CMakeFiles/vcfkeepinfo.dir/build.make CMakeFiles/vcfkeepinfo.dir/build +[ 61%] Built target vcfprimers +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +make -f CMakeFiles/vcfkeepgeno.dir/build.make CMakeFiles/vcfkeepgeno.dir/depend +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu/CMakeFiles/vcfkeepgeno.dir/DependInfo.cmake "--color=" +[ 61%] Building CXX object CMakeFiles/vcfkeepinfo.dir/src/vcfkeepinfo.cpp.o +/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -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-1.0.9+dfsg1/src/vcfkeepinfo.cpp +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +make -f CMakeFiles/vcfkeepgeno.dir/build.make CMakeFiles/vcfkeepgeno.dir/build +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +[ 61%] Building CXX object CMakeFiles/vcfkeepgeno.dir/src/vcfkeepgeno.cpp.o +/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -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 CMakeFiles/vcfkeepgeno.dir/src/vcfkeepgeno.cpp.o -c /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfkeepgeno.cpp +[ 61%] Linking CXX executable vcfcleancomplex +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfcleancomplex.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfcleancomplex.dir/src/vcfcleancomplex.cpp.o -o vcfcleancomplex -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libwfa2.so /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +[ 61%] Linking CXX executable vcfstats +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfstats.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfstats.dir/src/vcfstats.cpp.o -o vcfstats -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libwfa2.so /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' [ 61%] Built target vcfgenotypecompare -In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfallelicprimitives.cpp:10: +make -f CMakeFiles/vcfafpath.dir/build.make CMakeFiles/vcfafpath.dir/depend +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu/CMakeFiles/vcfafpath.dir/DependInfo.cmake "--color=" +In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfannotate.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ @@ -2297,9 +2329,19 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +make -f CMakeFiles/vcfafpath.dir/build.make CMakeFiles/vcfafpath.dir/build +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +[ 61%] Building CXX object CMakeFiles/vcfafpath.dir/src/vcfafpath.cpp.o +/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -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-1.0.9+dfsg1/src/vcfafpath.cpp +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +[ 61%] Built target vcfflatten make -f CMakeFiles/vcfcountalleles.dir/build.make CMakeFiles/vcfcountalleles.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu/CMakeFiles/vcfcountalleles.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +make -f CMakeFiles/vcfcountalleles.dir/build.make CMakeFiles/vcfcountalleles.dir/build +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfwave.cpp:19: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { @@ -2315,15 +2357,9 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 61%] Linking CXX executable vcfcleancomplex -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfcleancomplex.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfcleancomplex.dir/src/vcfcleancomplex.cpp.o -o vcfcleancomplex -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libwfa2.so /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -make -f CMakeFiles/vcfcountalleles.dir/build.make CMakeFiles/vcfcountalleles.dir/build -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' [ 61%] Building CXX object CMakeFiles/vcfcountalleles.dir/src/vcfcountalleles.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -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-1.0.9+dfsg1/src/vcfcountalleles.cpp -In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfaddinfo.cpp:10: +In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfoverlay.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ @@ -2339,7 +2375,7 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfoverlay.cpp:10: +In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfallelicprimitives.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ @@ -2355,7 +2391,7 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfkeepgeno.cpp:10: +In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfaddinfo.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ @@ -2371,7 +2407,7 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfannotate.cpp:10: +In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfkeepinfo.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ @@ -2387,13 +2423,20 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 62%] 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-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfaddinfo.dir/src/vcfaddinfo.cpp.o -o vcfaddinfo -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfkeepinfo.cpp:10: +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +[ 61%] Built target vcfcleancomplex +make -f CMakeFiles/vcflength.dir/build.make CMakeFiles/vcflength.dir/depend +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu/CMakeFiles/vcflength.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +make -f CMakeFiles/vcflength.dir/build.make CMakeFiles/vcflength.dir/build +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfkeepgeno.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ +[ 62%] Building CXX object CMakeFiles/vcflength.dir/src/vcflength.cpp.o +/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -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-1.0.9+dfsg1/src/vcflength.cpp In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:12: @@ -2406,9 +2449,43 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 63%] Linking CXX executable vcfkeepgeno +[ 63%] 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-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfaddinfo.dir/src/vcfaddinfo.cpp.o -o vcfaddinfo -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +[ 63%] Linking CXX executable vcfannotate +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfannotate.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfannotate.dir/src/vcfannotate.cpp.o -o vcfannotate -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +[ 64%] Linking CXX executable vcfkeepinfo +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfkeepinfo.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfkeepinfo.dir/src/vcfkeepinfo.cpp.o -o vcfkeepinfo -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +[ 65%] 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-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfkeepgeno.dir/src/vcfkeepgeno.cpp.o -o vcfkeepgeno -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfafpath.cpp:10: +/build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 650 | struct stringcasecmp : binary_function { + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/bits/refwrap.h:39, + from /usr/include/c++/13/vector:68, + from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:12: +/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +[ 65%] Linking CXX executable vcfwave +[ 66%] Linking CXX executable vcfintersect +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfintersect.dir/link.txt --verbose=1 +/build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:651:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 651 | struct charcasecmp : public std::binary_function { + | ^~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfwave.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfintersect.dir/src/vcfintersect.cpp.o -o vcfintersect -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfwave.dir/src/vcfwave.cpp.o -o vcfwave -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libwfa2.so /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp 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/build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { @@ -2425,7 +2502,7 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfafpath.cpp:10: +In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcflength.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ @@ -2442,57 +2519,32 @@ 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -[ 63%] Built target vcfstats -make -f CMakeFiles/vcflength.dir/build.make CMakeFiles/vcflength.dir/depend -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu/CMakeFiles/vcflength.dir/DependInfo.cmake "--color=" -[ 63%] Linking CXX executable vcfoverlay -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfoverlay.dir/link.txt --verbose=1 -[ 64%] Linking CXX executable vcfkeepinfo -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfkeepinfo.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfoverlay.dir/src/vcfoverlay.cpp.o -o vcfoverlay -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -make -f CMakeFiles/vcflength.dir/build.make CMakeFiles/vcflength.dir/build -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard 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-I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -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-1.0.9+dfsg1/src/vcflength.cpp -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -[ 65%] Linking CXX executable vcfwave -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfwave.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 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CMakeFiles/vcfannotate.dir/link.txt --verbose=1 make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu/CMakeFiles/vcfdistance.dir/DependInfo.cmake "--color=" -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfannotate.dir/src/vcfannotate.cpp.o -o vcfannotate 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cmake_link_script CMakeFiles/vcfcountalleles.dir/link.txt --verbose=1 +[ 68%] Linking CXX executable vcfafpath /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfcountalleles.dir/src/vcfcountalleles.cpp.o -o vcfcountalleles -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfafpath.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 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CMakeFiles/vcfrandomsample.dir/src/vcfrandomsample.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -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-1.0.9+dfsg1/src/vcfrandomsample.cpp make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -[ 67%] Linking CXX executable vcfallelicprimitives -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfallelicprimitives.dir/link.txt --verbose=1 -[ 68%] Linking CXX executable vcfintersect -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfintersect.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfallelicprimitives.dir/src/vcfallelicprimitives.cpp.o -o vcfallelicprimitives -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libwfa2.so /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfintersect.dir/src/vcfintersect.cpp.o -o vcfintersect -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 [ 68%] Built target vcfkeepgeno make -f CMakeFiles/vcfentropy.dir/build.make CMakeFiles/vcfentropy.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' @@ -2500,32 +2552,35 @@ make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' make -f CMakeFiles/vcfentropy.dir/build.make CMakeFiles/vcfentropy.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -[ 69%] Linking CXX executable vcfafpath -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfafpath.dir/link.txt --verbose=1 -[ 69%] Building CXX object CMakeFiles/vcfentropy.dir/src/vcfentropy.cpp.o +[ 68%] Building CXX object CMakeFiles/vcfentropy.dir/src/vcfentropy.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include 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-fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfafpath.dir/src/vcfafpath.cpp.o -o vcfafpath -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +[ 69%] 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-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfallelicprimitives.dir/src/vcfallelicprimitives.cpp.o -o vcfallelicprimitives -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libwfa2.so /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +[ 69%] Linking CXX executable vcflength +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcflength.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcflength.dir/src/vcflength.cpp.o -o vcflength -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' [ 69%] Built target vcfcountalleles make -f CMakeFiles/vcfglxgt.dir/build.make CMakeFiles/vcfglxgt.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu/CMakeFiles/vcfglxgt.dir/DependInfo.cmake "--color=" -[ 69%] Built target vcfkeepinfo -make -f CMakeFiles/vcfroc.dir/build.make CMakeFiles/vcfroc.dir/depend -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu/CMakeFiles/vcfroc.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' make -f CMakeFiles/vcfglxgt.dir/build.make CMakeFiles/vcfglxgt.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +[ 70%] Building CXX object CMakeFiles/vcfglxgt.dir/src/vcfglxgt.cpp.o +/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -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-1.0.9+dfsg1/src/vcfglxgt.cpp +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +[ 70%] Built target vcfoverlay +make -f CMakeFiles/vcfroc.dir/build.make CMakeFiles/vcfroc.dir/depend +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu/CMakeFiles/vcfroc.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' make -f CMakeFiles/vcfroc.dir/build.make CMakeFiles/vcfroc.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -[ 70%] Building CXX object CMakeFiles/vcfglxgt.dir/src/vcfglxgt.cpp.o -/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -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-1.0.9+dfsg1/src/vcfglxgt.cpp [ 70%] Building CXX object CMakeFiles/vcfroc.dir/src/vcfroc.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -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-1.0.9+dfsg1/src/vcfroc.cpp -In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfdistance.cpp:10: +In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfentropy.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ @@ -2541,7 +2596,18 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcflength.cpp:10: +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +[ 70%] Built target vcfafpath +make -f CMakeFiles/vcfcheck.dir/build.make CMakeFiles/vcfcheck.dir/depend +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu/CMakeFiles/vcfcheck.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +make -f CMakeFiles/vcfcheck.dir/build.make CMakeFiles/vcfcheck.dir/build +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +[ 71%] Building CXX object CMakeFiles/vcfcheck.dir/src/vcfcheck.cpp.o +/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfcheck.dir/src/vcfcheck.cpp.o -MF CMakeFiles/vcfcheck.dir/src/vcfcheck.cpp.o.d -o CMakeFiles/vcfcheck.dir/src/vcfcheck.cpp.o -c /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfcheck.cpp +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfdistance.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ @@ -2557,6 +2623,25 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +[ 71%] Built target vcfstats +make -f CMakeFiles/vcfstreamsort.dir/build.make CMakeFiles/vcfstreamsort.dir/depend +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu/CMakeFiles/vcfstreamsort.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +make -f CMakeFiles/vcfstreamsort.dir/build.make CMakeFiles/vcfstreamsort.dir/build +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +[ 72%] Building CXX object CMakeFiles/vcfstreamsort.dir/src/vcfstreamsort.cpp.o +/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfstreamsort.dir/src/vcfstreamsort.cpp.o -MF CMakeFiles/vcfstreamsort.dir/src/vcfstreamsort.cpp.o.d -o CMakeFiles/vcfstreamsort.dir/src/vcfstreamsort.cpp.o -c /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfstreamsort.cpp +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +[ 72%] Built target vcfannotate +make -f CMakeFiles/vcfuniq.dir/build.make CMakeFiles/vcfuniq.dir/depend +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu/CMakeFiles/vcfuniq.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +make -f CMakeFiles/vcfuniq.dir/build.make CMakeFiles/vcfuniq.dir/build +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +[ 73%] Building CXX object CMakeFiles/vcfuniq.dir/src/vcfuniq.cpp.o +/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfuniq.dir/src/vcfuniq.cpp.o -MF CMakeFiles/vcfuniq.dir/src/vcfuniq.cpp.o.d -o CMakeFiles/vcfuniq.dir/src/vcfuniq.cpp.o -c /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfuniq.cpp In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfrandomsample.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { @@ -2573,15 +2658,20 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 71%] 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-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfdistance.dir/src/vcfdistance.cpp.o -o vcfdistance -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -[ 71%] Built target vcfoverlay -make -f CMakeFiles/vcfcheck.dir/build.make CMakeFiles/vcfcheck.dir/depend +[ 73%] Built target vcflength +make -f CMakeFiles/vcfuniqalleles.dir/build.make CMakeFiles/vcfuniqalleles.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu/CMakeFiles/vcfcheck.dir/DependInfo.cmake "--color=" -In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfentropy.cpp:10: +cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu/CMakeFiles/vcfuniqalleles.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +make -f CMakeFiles/vcfuniqalleles.dir/build.make CMakeFiles/vcfuniqalleles.dir/build +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +[ 74%] Building CXX object CMakeFiles/vcfuniqalleles.dir/src/vcfuniqalleles.cpp.o +/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -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-1.0.9+dfsg1/src/vcfuniqalleles.cpp +[ 75%] Linking CXX executable vcfentropy +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfentropy.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfentropy.dir/src/vcfentropy.cpp.o -o vcfentropy -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfglxgt.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ @@ -2597,9 +2687,10 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -make -f CMakeFiles/vcfcheck.dir/build.make CMakeFiles/vcfcheck.dir/build -In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfglxgt.cpp:10: +[ 76%] 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-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfdistance.dir/src/vcfdistance.cpp.o -o vcfdistance -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfcheck.cpp:11: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ @@ -2615,13 +2706,7 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -[ 72%] Building CXX object CMakeFiles/vcfcheck.dir/src/vcfcheck.cpp.o -/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree 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std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ @@ -2637,46 +2722,7 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -[ 73%] Linking CXX executable vcfrandomsample -[ 73%] Built target vcfannotate -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfrandomsample.dir/link.txt --verbose=1 -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -make -f CMakeFiles/vcfstreamsort.dir/build.make CMakeFiles/vcfstreamsort.dir/depend -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfrandomsample.dir/src/vcfrandomsample.cpp.o -o vcfrandomsample -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu/CMakeFiles/vcfstreamsort.dir/DependInfo.cmake "--color=" -[ 73%] Built target vcfafpath -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -make -f CMakeFiles/vcfstreamsort.dir/build.make CMakeFiles/vcfstreamsort.dir/build -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -make -f CMakeFiles/vcfuniq.dir/build.make CMakeFiles/vcfuniq.dir/depend -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu 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CMakeFiles/vcfstreamsort.dir/src/vcfstreamsort.cpp.o -MF CMakeFiles/vcfstreamsort.dir/src/vcfstreamsort.cpp.o.d -o CMakeFiles/vcfstreamsort.dir/src/vcfstreamsort.cpp.o -c /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfstreamsort.cpp -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -make -f CMakeFiles/vcfuniq.dir/build.make CMakeFiles/vcfuniq.dir/build -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -[ 75%] Building CXX object CMakeFiles/vcfuniq.dir/src/vcfuniq.cpp.o -/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfuniq.dir/src/vcfuniq.cpp.o -MF CMakeFiles/vcfuniq.dir/src/vcfuniq.cpp.o.d -o CMakeFiles/vcfuniq.dir/src/vcfuniq.cpp.o -c /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfuniq.cpp -[ 76%] Linking CXX executable vcfentropy -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfentropy.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfentropy.dir/src/vcfentropy.cpp.o -o vcfentropy -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -[ 76%] Built target vcfdistance -make -f CMakeFiles/vcfuniqalleles.dir/build.make CMakeFiles/vcfuniqalleles.dir/depend -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu/CMakeFiles/vcfuniqalleles.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -make -f CMakeFiles/vcfuniqalleles.dir/build.make CMakeFiles/vcfuniqalleles.dir/build -[ 77%] Linking CXX executable vcfglxgt -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfglxgt.dir/link.txt --verbose=1 -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfglxgt.dir/src/vcfglxgt.cpp.o -o vcfglxgt -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -[ 78%] Building CXX object CMakeFiles/vcfuniqalleles.dir/src/vcfuniqalleles.cpp.o -/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -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-1.0.9+dfsg1/src/vcfuniqalleles.cpp -In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfcheck.cpp:11: +In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfroc.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ @@ -2692,7 +2738,10 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfstreamsort.cpp:10: +[ 77%] Linking CXX executable vcfrandomsample +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfrandomsample.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfrandomsample.dir/src/vcfrandomsample.cpp.o -o vcfrandomsample -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfuniq.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ @@ -2708,10 +2757,10 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 78%] Linking CXX executable vcfcheck +[ 77%] 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-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfcheck.dir/src/vcfcheck.cpp.o -o vcfcheck -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfuniq.cpp:10: +In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfuniqalleles.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ @@ -2727,8 +2776,11 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +[ 78%] 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-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfglxgt.dir/src/vcfglxgt.cpp.o -o vcfglxgt -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -[ 78%] Built target vcflength +[ 78%] Built target vcfdistance make -f CMakeFiles/vcfremap.dir/build.make CMakeFiles/vcfremap.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu/CMakeFiles/vcfremap.dir/DependInfo.cmake "--color=" @@ -2737,85 +2789,79 @@ make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' [ 78%] Building CXX object CMakeFiles/vcfremap.dir/src/vcfremap.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -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-1.0.9+dfsg1/src/vcfremap.cpp -In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfuniqalleles.cpp:10: -/build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 650 | struct stringcasecmp : binary_function { - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/bits/refwrap.h:39, - from /usr/include/c++/13/vector:68, - from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:12: -/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -/build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:651:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 651 | struct charcasecmp : public std::binary_function { - | ^~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -[ 78%] Built target vcfwave +[ 78%] 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-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfstreamsort.dir/src/vcfstreamsort.cpp.o -o vcfstreamsort -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +[ 78%] Built target vcfentropy make -f CMakeFiles/vcf2fasta.dir/build.make CMakeFiles/vcf2fasta.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu/CMakeFiles/vcf2fasta.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' make -f CMakeFiles/vcf2fasta.dir/build.make CMakeFiles/vcf2fasta.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -[ 78%] Built target vcfrandomsample -make -f CMakeFiles/vcfsitesummarize.dir/build.make CMakeFiles/vcfsitesummarize.dir/depend +[ 78%] Linking CXX executable vcfuniq [ 78%] Building CXX object CMakeFiles/vcf2fasta.dir/src/vcf2fasta.cpp.o +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfuniq.dir/link.txt --verbose=1 +/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp 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78%] Linking CXX executable vcfuniqalleles +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfuniqalleles.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfuniqalleles.dir/src/vcfuniqalleles.cpp.o -o vcfuniqalleles -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +[ 78%] Built target vcfcheck +make -f CMakeFiles/vcfsitesummarize.dir/build.make CMakeFiles/vcfsitesummarize.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu/CMakeFiles/vcfsitesummarize.dir/DependInfo.cmake "--color=" -/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose 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'/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' [ 79%] Building CXX object CMakeFiles/vcfsitesummarize.dir/src/vcfsitesummarize.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -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-1.0.9+dfsg1/src/vcfsitesummarize.cpp -[ 79%] Linking CXX executable vcfuniq -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfuniq.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfuniq.dir/src/vcfuniq.cpp.o -o vcfuniq -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -[ 79%] Built target vcfentropy +[ 79%] Built target vcfrandomsample make -f CMakeFiles/vcfbreakmulti.dir/build.make CMakeFiles/vcfbreakmulti.dir/depend -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu/CMakeFiles/vcfbreakmulti.dir/DependInfo.cmake "--color=" -[ 79%] Linking CXX executable vcfstreamsort -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfstreamsort.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' make -f CMakeFiles/vcfbreakmulti.dir/build.make CMakeFiles/vcfbreakmulti.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfstreamsort.dir/src/vcfstreamsort.cpp.o -o vcfstreamsort -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -[ 80%] Built target vcfglxgt [ 80%] Building CXX object CMakeFiles/vcfbreakmulti.dir/src/vcfbreakmulti.cpp.o -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -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-1.0.9+dfsg1/src/vcfbreakmulti.cpp +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +[ 80%] Built target vcfwave make -f CMakeFiles/vcfevenregions.dir/build.make CMakeFiles/vcfevenregions.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu/CMakeFiles/vcfevenregions.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' make -f CMakeFiles/vcfevenregions.dir/build.make CMakeFiles/vcfevenregions.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -[ 80%] Built target vcfcheck [ 80%] Building CXX object CMakeFiles/vcfevenregions.dir/src/vcfevenregions.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -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-1.0.9+dfsg1/src/vcfevenregions.cpp +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +[ 80%] Built target vcfuniqalleles make -f CMakeFiles/vcfcat.dir/build.make CMakeFiles/vcfcat.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu/CMakeFiles/vcfcat.dir/DependInfo.cmake "--color=" +[ 81%] Linking CXX executable vcfroc +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfroc.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' make -f CMakeFiles/vcfcat.dir/build.make CMakeFiles/vcfcat.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -[ 81%] Building CXX object CMakeFiles/vcfcat.dir/src/vcfcat.cpp.o -/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -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-1.0.9+dfsg1/src/vcfcat.cpp -[ 82%] 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-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfroc.dir/src/vcfroc.cpp.o -o vcfroc -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libwfa2.so /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -[ 82%] Linking CXX executable vcfuniqalleles -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfuniqalleles.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfuniqalleles.dir/src/vcfuniqalleles.cpp.o -o vcfuniqalleles -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfremap.cpp:10: +[ 82%] Building CXX object CMakeFiles/vcfcat.dir/src/vcfcat.cpp.o +/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -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-1.0.9+dfsg1/src/vcfcat.cpp +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +[ 82%] Built target vcfuniq +make -f CMakeFiles/vcfgenosummarize.dir/build.make CMakeFiles/vcfgenosummarize.dir/depend +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu/CMakeFiles/vcfgenosummarize.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +make -f CMakeFiles/vcfgenosummarize.dir/build.make CMakeFiles/vcfgenosummarize.dir/build +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +[ 83%] Building CXX object CMakeFiles/vcfgenosummarize.dir/src/vcfgenosummarize.cpp.o +/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -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-1.0.9+dfsg1/src/vcfgenosummarize.cpp +In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfsitesummarize.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ @@ -2831,12 +2877,7 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -[ 82%] Built target vcfuniq -make -f CMakeFiles/vcfgenosummarize.dir/build.make CMakeFiles/vcfgenosummarize.dir/depend -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu/CMakeFiles/vcfgenosummarize.dir/DependInfo.cmake "--color=" -In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfsitesummarize.cpp:10: +In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfbreakmulti.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ @@ -2852,10 +2893,7 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -make -f CMakeFiles/vcfgenosummarize.dir/build.make CMakeFiles/vcfgenosummarize.dir/build -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcf2fasta.cpp:10: +In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfremap.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ @@ -2871,19 +2909,13 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 83%] Building CXX object CMakeFiles/vcfgenosummarize.dir/src/vcfgenosummarize.cpp.o -/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -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-1.0.9+dfsg1/src/vcfgenosummarize.cpp make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' [ 83%] Built target vcfintersect make -f CMakeFiles/vcfgenosamplenames.dir/build.make CMakeFiles/vcfgenosamplenames.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu/CMakeFiles/vcfgenosamplenames.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -make -f CMakeFiles/vcfgenosamplenames.dir/build.make CMakeFiles/vcfgenosamplenames.dir/build -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -[ 84%] Building CXX object CMakeFiles/vcfgenosamplenames.dir/src/vcfgenosamplenames.cpp.o -/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -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-1.0.9+dfsg1/src/vcfgenosamplenames.cpp -In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfevenregions.cpp:10: +In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcf2fasta.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ @@ -2900,9 +2932,36 @@ 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -[ 84%] Built target vcfuniqalleles +make -f CMakeFiles/vcfgenosamplenames.dir/build.make CMakeFiles/vcfgenosamplenames.dir/build +[ 83%] Built target vcfglxgt +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' make -f CMakeFiles/vcfgeno2haplo.dir/build.make CMakeFiles/vcfgeno2haplo.dir/depend -In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfcat.cpp:10: +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu/CMakeFiles/vcfgeno2haplo.dir/DependInfo.cmake "--color=" +[ 84%] Building CXX object CMakeFiles/vcfgenosamplenames.dir/src/vcfgenosamplenames.cpp.o +/usr/bin/c++ -DNO_ZIG=1 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/build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfgenosamplenames.cpp +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +make -f CMakeFiles/vcfgeno2haplo.dir/build.make CMakeFiles/vcfgeno2haplo.dir/build +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +[ 85%] Building CXX object CMakeFiles/vcfgeno2haplo.dir/src/vcfgeno2haplo.cpp.o +/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -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-1.0.9+dfsg1/src/vcfgeno2haplo.cpp +[ 85%] 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-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfbreakmulti.dir/src/vcfbreakmulti.cpp.o -o vcfbreakmulti -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +[ 85%] Built target vcfstreamsort +make -f CMakeFiles/vcfleftalign.dir/build.make CMakeFiles/vcfleftalign.dir/depend +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu/CMakeFiles/vcfleftalign.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +make -f CMakeFiles/vcfleftalign.dir/build.make CMakeFiles/vcfleftalign.dir/build +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +[ 86%] Building CXX object CMakeFiles/vcfleftalign.dir/src/vcfleftalign.cpp.o +/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -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-1.0.9+dfsg1/src/vcfleftalign.cpp +[ 86%] Linking CXX executable vcfsitesummarize +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfsitesummarize.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfsitesummarize.dir/src/vcfsitesummarize.cpp.o -o vcfsitesummarize -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfevenregions.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ @@ -2918,14 +2977,10 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu/CMakeFiles/vcfgeno2haplo.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -make -f CMakeFiles/vcfgeno2haplo.dir/build.make CMakeFiles/vcfgeno2haplo.dir/build -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -[ 85%] Building CXX object CMakeFiles/vcfgeno2haplo.dir/src/vcfgeno2haplo.cpp.o -/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -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-1.0.9+dfsg1/src/vcfgeno2haplo.cpp -In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfbreakmulti.cpp:10: +[ 87%] 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-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfremap.dir/src/vcfremap.cpp.o -o vcfremap -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfcat.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ @@ -2941,39 +2996,6 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 85%] Linking CXX executable vcfsitesummarize -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfsitesummarize.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfsitesummarize.dir/src/vcfsitesummarize.cpp.o -o vcfsitesummarize -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -[ 85%] Built target vcfallelicprimitives -make -f CMakeFiles/vcfleftalign.dir/build.make CMakeFiles/vcfleftalign.dir/depend -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu/CMakeFiles/vcfleftalign.dir/DependInfo.cmake "--color=" -[ 86%] Linking CXX executable vcfremap -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfremap.dir/link.txt --verbose=1 -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -make -f CMakeFiles/vcfleftalign.dir/build.make CMakeFiles/vcfleftalign.dir/build -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfremap.dir/src/vcfremap.cpp.o -o vcfremap -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -[ 87%] Building CXX object CMakeFiles/vcfleftalign.dir/src/vcfleftalign.cpp.o -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -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-1.0.9+dfsg1/src/vcfleftalign.cpp -[ 87%] Built target vcfstreamsort -make -f CMakeFiles/vcfcombine.dir/build.make CMakeFiles/vcfcombine.dir/depend -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu/CMakeFiles/vcfcombine.dir/DependInfo.cmake "--color=" -[ 87%] 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-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfcat.dir/src/vcfcat.cpp.o -o vcfcat -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -make -f CMakeFiles/vcfcombine.dir/build.make CMakeFiles/vcfcombine.dir/build -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -[ 88%] Building CXX object CMakeFiles/vcfcombine.dir/src/vcfcombine.cpp.o -/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 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-lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -[ 89%] Linking CXX executable vcfbreakmulti In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfgenosummarize.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { @@ -2990,12 +3012,7 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfbreakmulti.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 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binary_function { | ^~~~~~~~~~~~~~~ @@ -3011,7 +3028,13 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfgeno2haplo.cpp:10: +[ 88%] Linking CXX executable vcf2fasta +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcf2fasta.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcf2fasta.dir/src/vcf2fasta.cpp.o -o vcf2fasta -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +[ 88%] Built target vcfallelicprimitives +make -f CMakeFiles/vcfcombine.dir/build.make CMakeFiles/vcfcombine.dir/depend +In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfgenosamplenames.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ @@ -3027,6 +3050,19 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu/CMakeFiles/vcfcombine.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +make -f CMakeFiles/vcfcombine.dir/build.make CMakeFiles/vcfcombine.dir/build +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +[ 89%] Building CXX object CMakeFiles/vcfcombine.dir/src/vcfcombine.cpp.o +/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include 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--verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfevenregions.dir/src/vcfevenregions.cpp.o -o vcfevenregions -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +[ 90%] 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-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfcat.dir/src/vcfcat.cpp.o -o vcfcat -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' [ 90%] Built target vcfsitesummarize make -f CMakeFiles/vcfgeno2alleles.dir/build.make CMakeFiles/vcfgeno2alleles.dir/depend @@ -3037,23 +3073,7 @@ make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' [ 91%] Building CXX object CMakeFiles/vcfgeno2alleles.dir/src/vcfgeno2alleles.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -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-1.0.9+dfsg1/src/vcfgeno2alleles.cpp -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -[ 91%] Linking CXX executable vcfgenosummarize -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfgenosummarize.dir/link.txt --verbose=1 -[ 91%] Built target vcfcat -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfgenosummarize.dir/src/vcfgenosummarize.cpp.o -o vcfgenosummarize -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -make -f CMakeFiles/vcfindex.dir/build.make CMakeFiles/vcfindex.dir/depend -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu/CMakeFiles/vcfindex.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -make -f CMakeFiles/vcfindex.dir/build.make CMakeFiles/vcfindex.dir/build -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -[ 91%] Building CXX object CMakeFiles/vcfindex.dir/src/vcfindex.cpp.o -/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -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-1.0.9+dfsg1/src/vcfindex.cpp -[ 91%] 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-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfgenosamplenames.dir/src/vcfgenosamplenames.cpp.o -o vcfgenosamplenames -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfcombine.cpp:10: +In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfleftalign.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ @@ -3069,7 +3089,33 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfleftalign.cpp:10: +[ 91%] Linking CXX executable vcfgenosamplenames +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfgenosamplenames.dir/link.txt --verbose=1 +[ 91%] 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-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfgenosamplenames.dir/src/vcfgenosamplenames.cpp.o -o vcfgenosamplenames -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfgenosummarize.dir/src/vcfgenosummarize.cpp.o -o vcfgenosummarize -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +[ 91%] Built target vcfbreakmulti +make -f CMakeFiles/vcfindex.dir/build.make CMakeFiles/vcfindex.dir/depend +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu/CMakeFiles/vcfindex.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +make -f CMakeFiles/vcfindex.dir/build.make CMakeFiles/vcfindex.dir/build +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +[ 91%] Building CXX object CMakeFiles/vcfindex.dir/src/vcfindex.cpp.o +/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -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-1.0.9+dfsg1/src/vcfindex.cpp +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +[ 91%] Built target vcfcat +make -f CMakeFiles/vcf2dag.dir/build.make CMakeFiles/vcf2dag.dir/depend +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu/CMakeFiles/vcf2dag.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +make -f CMakeFiles/vcf2dag.dir/build.make CMakeFiles/vcf2dag.dir/build +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +[ 91%] Building CXX object CMakeFiles/vcf2dag.dir/src/vcf2dag.cpp.o +/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -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-1.0.9+dfsg1/src/vcf2dag.cpp +In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfcombine.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ @@ -3087,27 +3133,20 @@ | ^~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' [ 91%] Built target vcfevenregions -make -f CMakeFiles/vcf2dag.dir/build.make CMakeFiles/vcf2dag.dir/depend -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu 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-ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -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-1.0.9+dfsg1/src/vcf2dag.cpp -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -[ 91%] Built target vcfbreakmulti make -f CMakeFiles/vcfsample2info.dir/build.make CMakeFiles/vcfsample2info.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu/CMakeFiles/vcfsample2info.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' make -f CMakeFiles/vcfsample2info.dir/build.make CMakeFiles/vcfsample2info.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -[ 91%] Built target vcfroc -make -f CMakeFiles/vcfqual2info.dir/build.make CMakeFiles/vcfqual2info.dir/depend [ 91%] Building CXX object CMakeFiles/vcfsample2info.dir/src/vcfsample2info.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -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-1.0.9+dfsg1/src/vcfsample2info.cpp +[ 91%] 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-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfleftalign.dir/src/vcfleftalign.cpp.o -o vcfleftalign -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +[ 91%] Built target vcfroc +make -f CMakeFiles/vcfqual2info.dir/build.make CMakeFiles/vcfqual2info.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu/CMakeFiles/vcfqual2info.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' @@ -3115,12 +3154,10 @@ make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' [ 91%] Building CXX object CMakeFiles/vcfqual2info.dir/src/vcfqual2info.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -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-1.0.9+dfsg1/src/vcfqual2info.cpp -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfgeno2alleles.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ -[ 91%] Linking CXX executable vcfleftalign In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:12: @@ -3133,9 +3170,8 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -/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-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat 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/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu/CMakeFiles/vcfinfo2qual.dir/DependInfo.cmake "--color=" @@ -3144,6 +3180,9 @@ make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' [ 91%] Building CXX object CMakeFiles/vcfinfo2qual.dir/src/vcfinfo2qual.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -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-1.0.9+dfsg1/src/vcfinfo2qual.cpp +[ 91%] Linking CXX executable vcfgeno2haplo +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfgeno2haplo.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfgeno2haplo.dir/src/vcfgeno2haplo.cpp.o -o vcfgeno2haplo -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfindex.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { @@ -3161,42 +3200,29 @@ 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -[ 91%] Built target vcfgenosamplenames +[ 91%] Built target vcfremap +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' make -f CMakeFiles/vcfglbound.dir/build.make CMakeFiles/vcfglbound.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +[ 91%] Built target vcfgenosummarize cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu/CMakeFiles/vcfglbound.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -make -f CMakeFiles/vcfglbound.dir/build.make CMakeFiles/vcfglbound.dir/build -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -[ 92%] Building CXX object CMakeFiles/vcfglbound.dir/src/vcfglbound.cpp.o -/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu/CMakeFiles/vcfinfosummarize.dir/DependInfo.cmake "--color=" -[ 92%] Linking CXX executable vcfcombine -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfcombine.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' make -f CMakeFiles/vcfinfosummarize.dir/build.make CMakeFiles/vcfinfosummarize.dir/build -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfcombine.dir/src/vcfcombine.cpp.o -o vcfcombine -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -[ 92%] Building CXX object CMakeFiles/vcfinfosummarize.dir/src/vcfinfosummarize.cpp.o -/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -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-1.0.9+dfsg1/src/vcfinfosummarize.cpp -[ 92%] Built target vcfgenosummarize -make -f CMakeFiles/vcfcreatemulti.dir/build.make CMakeFiles/vcfcreatemulti.dir/depend -[ 92%] Linking CXX executable vcfgeno2haplo +[ 91%] Linking CXX executable vcfgeno2alleles +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfgeno2alleles.dir/link.txt --verbose=1 make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu/CMakeFiles/vcfcreatemulti.dir/DependInfo.cmake "--color=" -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfgeno2haplo.dir/link.txt --verbose=1 -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -make -f CMakeFiles/vcfcreatemulti.dir/build.make CMakeFiles/vcfcreatemulti.dir/build -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp 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-I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -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-1.0.9+dfsg1/src/vcfcreatemulti.cpp -In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcf2dag.cpp:10: +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfgeno2alleles.dir/src/vcfgeno2alleles.cpp.o -o vcfgeno2alleles -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +[ 91%] Building CXX object CMakeFiles/vcfinfosummarize.dir/src/vcfinfosummarize.cpp.o +/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -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-1.0.9+dfsg1/src/vcfinfosummarize.cpp +[ 92%] Building CXX object CMakeFiles/vcfglbound.dir/src/vcfglbound.cpp.o +/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -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-1.0.9+dfsg1/src/vcfglbound.cpp +In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfsample2info.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ @@ -3212,13 +3238,9 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 92%] Linking CXX executable vcfgeno2alleles -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfgeno2alleles.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now 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binary_function { @@ -3250,6 +3286,20 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +[ 93%] Built target vcfgeno2alleles +make -f CMakeFiles/pyvcflib.dir/build.make CMakeFiles/pyvcflib.dir/depend +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu/CMakeFiles/pyvcflib.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +make -f CMakeFiles/pyvcflib.dir/build.make CMakeFiles/pyvcflib.dir/build +[ 93%] Built target vcfleftalign +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +[ 94%] Building CXX object CMakeFiles/pyvcflib.dir/src/pythonffi.cpp.o +/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -Dpyvcflib_EXPORTS -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/python3.11 -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack 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'/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +[ 95%] Built target vcfindex +[ 96%] Linking CXX executable vcf2dag +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcf2dag.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcf2dag.dir/src/vcf2dag.cpp.o -o vcf2dag -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +[ 97%] Linking CXX executable vcfqual2info 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/usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfinfo2qual.dir/src/vcfinfo2qual.cpp.o -o vcfinfo2qual -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -[ 97%] Linking CXX executable vcfglbound -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfglbound.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfglbound.dir/src/vcfglbound.cpp.o -o vcfglbound -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -[ 97%] Built target vcfindex -[ 97%] Built target vcfgeno2alleles -make -f CMakeFiles/pyvcflib.dir/build.make CMakeFiles/pyvcflib.dir/depend -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu/CMakeFiles/pyvcflib.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -make -f CMakeFiles/pyvcflib.dir/build.make CMakeFiles/pyvcflib.dir/build -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -[ 98%] Building CXX object CMakeFiles/pyvcflib.dir/src/pythonffi.cpp.o -/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -Dpyvcflib_EXPORTS -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/python3.11 -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIC -fvisibility=hidden -MD -MT CMakeFiles/pyvcflib.dir/src/pythonffi.cpp.o -MF CMakeFiles/pyvcflib.dir/src/pythonffi.cpp.o.d -o CMakeFiles/pyvcflib.dir/src/pythonffi.cpp.o -c /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/pythonffi.cpp -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -[ 98%] Built target vcfleftalign -[ 99%] 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-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfinfosummarize.dir/src/vcfinfosummarize.cpp.o -o vcfinfosummarize -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -[100%] Linking CXX executable vcfcreatemulti -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfcreatemulti.dir/link.txt --verbose=1 -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfcreatemulti.dir/src/vcfcreatemulti.cpp.o -o vcfcreatemulti -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -[100%] Built target vcfqual2info -[100%] Built target vcfinfo2qual -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -[100%] Built target vcfcombine -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -[100%] Built target vcfglbound -[100%] Built target vcfsample2info In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/pythonffi.cpp:5: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { @@ -3375,14 +3392,33 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +[ 98%] Linking CXX executable vcfglbound +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfglbound.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfglbound.dir/src/vcfglbound.cpp.o -o vcfglbound -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -[100%] Built target vcf2dag +[ 98%] Built target vcfqual2info make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -[100%] Built target vcfinfosummarize +[ 98%] Built target vcf2dag +[ 99%] 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-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfinfosummarize.dir/src/vcfinfosummarize.cpp.o -o vcfinfosummarize -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' -[100%] Built target vcfcreatemulti +[ 99%] Built target vcfsample2info +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +[ 99%] Built target vcfinfo2qual +[100%] 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-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfcreatemulti.dir/src/vcfcreatemulti.cpp.o -o vcfcreatemulti -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +[100%] Built target vcfcombine +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +[100%] Built target vcfglbound +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +[100%] Built target vcfinfosummarize make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' [100%] Built target vcfgeno2haplo +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-aarch64-linux-gnu' +[100%] Built target vcfcreatemulti [100%] Linking CXX shared module pyvcflib.cpython-311-aarch64-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-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -shared -o pyvcflib.cpython-311-aarch64-linux-gnu.so CMakeFiles/pyvcflib.dir/src/pythonffi.cpp.o -Wl,-rpath,"\$ORIGIN:" libvcflib.so.2 -lhts /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libhts.so /usr/lib/aarch64-linux-gnu/libwfa2.so /usr/lib/aarch64-linux-gnu/libsmithwaterman.so /usr/lib/aarch64-linux-gnu/libdisorder.so /usr/lib/aarch64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 @@ -3401,27 +3437,27 @@ cd test && ctest . Test project /build/reproducible-path/libvcflib-1.0.9+dfsg1/test Start 1: realign -1/9 Test #1: realign .......................... Passed 0.14 sec +1/9 Test #1: realign .......................... Passed 0.10 sec Start 2: pyvcflib -2/9 Test #2: pyvcflib ......................... Passed 0.09 sec +2/9 Test #2: pyvcflib ......................... Passed 0.08 sec Start 3: vcflib-api -3/9 Test #3: vcflib-api ....................... Passed 0.08 sec +3/9 Test #3: vcflib-api ....................... Passed 0.09 sec Start 4: vcf2tsv -4/9 Test #4: vcf2tsv .......................... Passed 0.21 sec +4/9 Test #4: vcf2tsv .......................... Passed 0.13 sec Start 5: vcfallelicprimitives -5/9 Test #5: vcfallelicprimitives ............. Passed 1.00 sec +5/9 Test #5: vcfallelicprimitives ............. Passed 0.87 sec Start 6: vcfwave -6/9 Test #6: vcfwave .......................... Passed 0.49 sec +6/9 Test #6: vcfwave .......................... Passed 0.38 sec Start 7: vcffilter -7/9 Test #7: vcffilter ........................ Passed 0.21 sec +7/9 Test #7: vcffilter ........................ Passed 0.15 sec Start 8: vcfnulldotslashdot 8/9 Test #8: vcfnulldotslashdot ............... Passed 0.11 sec Start 9: doc/vcfintersect -9/9 Test #9: doc/vcfintersect ................. Passed 0.10 sec +9/9 Test #9: doc/vcfintersect ................. Passed 0.08 sec 100% tests passed, 0 tests failed out of 9 -Total Test time (real) = 2.43 sec +Total Test time (real) = 2.02 sec cd .. && rm -f build make[1]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1' create-stamp debian/debhelper-build-stamp @@ -3814,10 +3850,10 @@ dpkg-gencontrol: warning: package libvcflib-tools: substitution variable ${perl:Depends} unused, but is defined dh_md5sums -O--buildsystem=cmake dh_builddeb -O--buildsystem=cmake -dpkg-deb: building package 'libvcflib-tools-dbgsym' in '../libvcflib-tools-dbgsym_1.0.9+dfsg1-3_arm64.deb'. -dpkg-deb: building package 'libvcflib2-dbgsym' in '../libvcflib2-dbgsym_1.0.9+dfsg1-3_arm64.deb'. dpkg-deb: building package 'libvcflib-dev' in '../libvcflib-dev_1.0.9+dfsg1-3_arm64.deb'. +dpkg-deb: building package 'libvcflib2-dbgsym' in '../libvcflib2-dbgsym_1.0.9+dfsg1-3_arm64.deb'. dpkg-deb: building package 'libvcflib-tools' in '../libvcflib-tools_1.0.9+dfsg1-3_arm64.deb'. +dpkg-deb: building package 'libvcflib-tools-dbgsym' in '../libvcflib-tools-dbgsym_1.0.9+dfsg1-3_arm64.deb'. dpkg-deb: building package 'libvcflib2' in '../libvcflib2_1.0.9+dfsg1-3_arm64.deb'. dpkg-genbuildinfo --build=binary -O../libvcflib_1.0.9+dfsg1-3_arm64.buildinfo dpkg-genchanges --build=binary -O../libvcflib_1.0.9+dfsg1-3_arm64.changes @@ -3826,12 +3862,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/668028/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/668028/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/2183970 and its subdirectories -I: Current time: Tue Jun 17 07:56:32 -12 2025 -I: pbuilder-time-stamp: 1750190192 +I: removing directory /srv/workspace/pbuilder/668028 and its subdirectories +I: Current time: Thu May 16 03:36:51 +14 2024 +I: pbuilder-time-stamp: 1715780211