Diff of the two buildlogs: -- --- b1/build.log 2024-05-07 18:47:57.572204552 +0000 +++ b2/build.log 2024-05-07 18:50:20.822109514 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue May 7 06:43:46 -12 2024 -I: pbuilder-time-stamp: 1715107426 +I: Current time: Tue Jun 10 15:11:00 +14 2025 +I: pbuilder-time-stamp: 1749517860 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/3547587/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3522585/tmp/hooks/D01_modify_environment starting +debug: Running on ionos5-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Jun 10 01:11 /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/3522585/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3522585/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="21" [3]="1" [4]="release" [5]="x86_64-pc-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=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='8f375e2b7e54407598ce3a5ff2fbca05' - 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='3547587' - PS1='# ' - PS2='> ' + INVOCATION_ID=1bd2a606ae524077a2f5970ceeed2bde + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=3522585 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.PrSozQgn/pbuilderrc_o01M --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.PrSozQgn/b1 --logfile b1/build.log libvcflib_1.0.9+dfsg1-3.dsc' - SUDO_GID='110' - SUDO_UID='105' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://46.16.76.132:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.PrSozQgn/pbuilderrc_BvLP --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.PrSozQgn/b2 --logfile b2/build.log libvcflib_1.0.9+dfsg1-3.dsc' + SUDO_GID=110 + SUDO_UID=105 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://213.165.73.152:3128 I: uname -a - Linux ionos1-amd64 6.1.0-21-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.90-1 (2024-05-03) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.6.13+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.6.13-1~bpo12+1 (2024-02-15) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 May 5 11:24 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/3547587/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Jun 7 17:46 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/3522585/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 amd64 python3-distutils all 3.12.3-1 [131 kB] Get: 107 http://deb.debian.org/debian trixie/main amd64 python3-dev amd64 3.11.8-1 [26.1 kB] Get: 108 http://deb.debian.org/debian trixie/main amd64 python3-pybind11 all 2.11.1-2 [201 kB] -Fetched 55.8 MB in 1s (49.0 MB/s) +Fetched 55.8 MB in 1s (105 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19698 files and directories currently installed.) @@ -621,8 +653,8 @@ Setting up tzdata (2024a-3) ... Current default time zone: 'Etc/UTC' -Local time is now: Tue May 7 18:45:00 UTC 2024. -Universal Time is now: Tue May 7 18:45:00 UTC 2024. +Local time is now: Tue Jun 10 01:11:32 UTC 2025. +Universal Time is now: Tue Jun 10 01:11:32 UTC 2025. 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/3522585/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/3522585/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 @@ -801,8 +837,8 @@ -- Found libfastahack, version 0.0 -- WFA using include /usr/include/wfa2lib Pandoc needs to be installed to generate the man pages --- Configuring done (9.1s) --- Generating done (0.9s) +-- Configuring done (2.8s) +-- Generating done (0.3s) CMake Warning: Manually-specified variables were not used by the project: @@ -816,7 +852,7 @@ debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1' dh_auto_build - cd obj-x86_64-linux-gnu && make -j20 "INSTALL=install --strip-program=true" VERBOSE=1 + cd obj-x86_64-linux-gnu && make -j42 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/libvcflib-1.0.9+dfsg1 -B/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu//CMakeFiles/progress.marks @@ -828,35 +864,35 @@ make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' make -f CMakeFiles/vcflib.dir/build.make CMakeFiles/vcflib.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-wfa.cpp.o -[ 1%] Building CXX object CMakeFiles/vcflib.dir/src/legacy.cpp.o -[ 1%] Building CXX object CMakeFiles/vcflib.dir/src/murmur3.cpp.o -[ 1%] Building CXX object CMakeFiles/vcflib.dir/src/Variant.cpp.o -[ 2%] Building CXX object CMakeFiles/vcflib.dir/src/rnglib.cpp.o -[ 3%] Building CXX object CMakeFiles/vcflib.dir/src/vcf-c-api.cpp.o -[ 3%] Building CXX object CMakeFiles/vcflib.dir/src/cdflib.cpp.o -[ 4%] Building CXX object CMakeFiles/vcflib.dir/src/var.cpp.o -[ 4%] Building CXX object CMakeFiles/vcflib.dir/src/split.cpp.o -[ 6%] Building CXX object CMakeFiles/vcflib.dir/src/pdflib.cpp.o -[ 6%] Building CXX object CMakeFiles/vcflib.dir/src/LeftAlign.cpp.o -[ 7%] Building CXX object CMakeFiles/vcflib.dir/src/rkmh.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 -fcf-protection -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/var.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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIC -MD -MT CMakeFiles/vcflib.dir/src/legacy.cpp.o -MF CMakeFiles/vcflib.dir/src/legacy.cpp.o.d -o CMakeFiles/vcflib.dir/src/legacy.cpp.o -c /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/legacy.cpp /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 -fcf-protection -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 +[ 3%] Building CXX object CMakeFiles/vcflib.dir/src/vcf-c-api.cpp.o +[ 3%] Building CXX object CMakeFiles/vcflib.dir/src/rnglib.cpp.o +[ 3%] Building CXX object CMakeFiles/vcflib.dir/src/cdflib.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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIC -MD -MT CMakeFiles/vcflib.dir/src/Variant.cpp.o -MF CMakeFiles/vcflib.dir/src/Variant.cpp.o.d -o CMakeFiles/vcflib.dir/src/Variant.cpp.o -c /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.cpp -/usr/bin/c++ -DNO_ZIG=1 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CMakeFiles/vcflib.dir/src/pdflib.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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIC -MD -MT CMakeFiles/vcflib.dir/src/var.cpp.o -MF CMakeFiles/vcflib.dir/src/var.cpp.o.d -o CMakeFiles/vcflib.dir/src/var.cpp.o -c 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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 -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 -fcf-protection -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 @@ -908,7 +944,7 @@ | | | | long long unsigned int uint64_t {aka long unsigned int} | %lu -In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcf-c-api.cpp:9: +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 { | ^~~~~~~~~~~~~~~ @@ -924,7 +960,7 @@ /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/Variant.cpp:10: +In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcf-wfa.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 { | ^~~~~~~~~~~~~~~ @@ -940,7 +976,7 @@ /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/vcf-wfa.cpp:10: +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 { | ^~~~~~~~~~~~~~~ @@ -956,7 +992,7 @@ /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/legacy.cpp:12: +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 { | ^~~~~~~~~~~~~~~ @@ -982,163 +1018,344 @@ make -f CMakeFiles/dumpContigsFromHeader.dir/build.make CMakeFiles/dumpContigsFromHeader.dir/depend make -f CMakeFiles/bFst.dir/build.make CMakeFiles/bFst.dir/depend make -f CMakeFiles/pVst.dir/build.make CMakeFiles/pVst.dir/depend -make -f CMakeFiles/hapLrt.dir/build.make CMakeFiles/hapLrt.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -make -f CMakeFiles/popStats.dir/build.make CMakeFiles/popStats.dir/depend cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfecho.dir/DependInfo.cmake "--color=" +make -f CMakeFiles/hapLrt.dir/build.make CMakeFiles/hapLrt.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/dumpContigsFromHeader.dir/DependInfo.cmake "--color=" +make -f CMakeFiles/popStats.dir/build.make CMakeFiles/popStats.dir/depend +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/bFst.dir/DependInfo.cmake "--color=" make -f CMakeFiles/wcFst.dir/build.make CMakeFiles/wcFst.dir/depend -make -f CMakeFiles/iHS.dir/build.make CMakeFiles/iHS.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/pVst.dir/DependInfo.cmake "--color=" -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -make -f CMakeFiles/segmentFst.dir/build.make CMakeFiles/segmentFst.dir/depend +make -f CMakeFiles/iHS.dir/build.make CMakeFiles/iHS.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/hapLrt.dir/DependInfo.cmake "--color=" -cd 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'/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/iHS.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu 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directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/smoother.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-linux-gnu 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/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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/plotHaps.dir/DependInfo.cmake "--color=" +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/abba-baba.dir/DependInfo.cmake "--color=" +make -f 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CMakeFiles/vcfannotategenotypes.dir/depend +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfhethomratio.dir/DependInfo.cmake "--color=" +make -f CMakeFiles/vcfcommonsamples.dir/build.make CMakeFiles/vcfcommonsamples.dir/depend +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 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CMakeFiles/vcfkeepsamples.dir/build.make CMakeFiles/vcfkeepsamples.dir/depend +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfgenotypes.dir/DependInfo.cmake "--color=" +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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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-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 -fcf-protection -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 +[ 31%] 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 -fcf-protection -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 +[ 31%] Linking CXX executable permuteGPAT++ +/usr/bin/cmake -E cmake_link_script CMakeFiles/permuteGPAT++.dir/link.txt --verbose=1 +[ 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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +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 { | ^~~~~~~~~~~~~~~ @@ -1154,7 +1371,8 @@ /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/vcfecho.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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +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 { | ^~~~~~~~~~~~~~~ @@ -1170,7 +1388,7 @@ /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/hapLrt.cpp:10: +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 { | ^~~~~~~~~~~~~~~ @@ -1186,9 +1404,9 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 19%] Linking CXX executable segmentFst +[ 32%] 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/popStats.cpp:10: +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 { | ^~~~~~~~~~~~~~~ @@ -1204,8 +1422,7 @@ /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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -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/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 { | ^~~~~~~~~~~~~~~ @@ -1215,13 +1432,30 @@ /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/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 { + | ^~~~~~~~~~~~~~~ /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 { | ^~~~~~~~~~~~~~~ +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 | ^~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/iHS.cpp:10: +/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 + | ^~~~~~~~~~~~~~~ +[ 32%] Linking CXX executable segmentIhs +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 { | ^~~~~~~~~~~~~~~ @@ -1237,7 +1471,8 @@ /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/pVst.cpp:10: +/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/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 { | ^~~~~~~~~~~~~~~ @@ -1253,7 +1488,7 @@ /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/abba-baba.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 { | ^~~~~~~~~~~~~~~ @@ -1269,19 +1504,7 @@ /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) - | ^~~~~~~~~~~~~~ -[ 20%] 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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/pFst.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 { | ^~~~~~~~~~~~~~~ @@ -1297,7 +1520,7 @@ /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/plotHaps.cpp:10: +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] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ @@ -1313,13 +1536,7 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 21%] 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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -[ 21%] 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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/wcFst.cpp:10: +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 { | ^~~~~~~~~~~~~~~ @@ -1335,15 +1552,19 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 22%] 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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -[ 23%] 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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -[ 23%] Linking CXX executable segmentIhs -/usr/bin/cmake -E cmake_link_script CMakeFiles/segmentIhs.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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +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 { + | ^~~~~~~~~~~~~~~ +/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/vcfld.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 { @@ -1360,10 +1581,6 @@ /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: -/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: @@ -1376,43 +1593,7 @@ /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-x86_64-linux-gnu' -[ 23%] Built target segmentFst -make -f CMakeFiles/meltEHH.dir/build.make CMakeFiles/meltEHH.dir/depend -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/meltEHH.dir/DependInfo.cmake "--color=" -[ 23%] Linking CXX executable permuteSmooth -/usr/bin/cmake -E cmake_link_script CMakeFiles/permuteSmooth.dir/link.txt --verbose=1 -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -[ 23%] 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 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segmentIhs -make -f CMakeFiles/vcfhetcount.dir/build.make CMakeFiles/vcfhetcount.dir/depend -[ 24%] Built target vcfecho -make -f CMakeFiles/vcfhethomratio.dir/build.make CMakeFiles/vcfhethomratio.dir/depend -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfhetcount.dir/DependInfo.cmake "--color=" -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix 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directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-linux-gnu' -[ 29%] 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 -fcf-protection 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/usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -[ 30%] Built target permuteSmooth -make -f CMakeFiles/vcfgenotypes.dir/build.make CMakeFiles/vcfgenotypes.dir/depend -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfgenotypes.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -make -f CMakeFiles/vcfgenotypes.dir/build.make CMakeFiles/vcfgenotypes.dir/build -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/meltEHH.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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +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 { | ^~~~~~~~~~~~~~~ @@ -1516,15 +1626,7 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 31%] Building CXX object CMakeFiles/vcfgenotypes.dir/src/vcfgenotypes.cpp.o -[ 32%] Linking CXX executable pFst -/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 -fcf-protection -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 -/usr/bin/cmake -E cmake_link_script CMakeFiles/pFst.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +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 { | ^~~~~~~~~~~~~~~ @@ -1556,7 +1659,7 @@ /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/vcfhethomratio.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 { | ^~~~~~~~~~~~~~~ @@ -1572,7 +1675,7 @@ /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/vcffilter.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 { | ^~~~~~~~~~~~~~~ @@ -1588,7 +1691,7 @@ /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/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 { | ^~~~~~~~~~~~~~~ @@ -1604,9 +1707,7 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 33%] Linking CXX executable sequenceDiversity -/usr/bin/cmake -E cmake_link_script CMakeFiles/sequenceDiversity.dir/link.txt --verbose=1 -In file included from 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"--color=" -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-linux-gnu' -[ 34%] Linking CXX executable vcfhethomratio -[ 35%] Linking CXX executable vcfaltcount -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfhethomratio.dir/link.txt --verbose=1 -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfaltcount.dir/link.txt --verbose=1 -[ 36%] 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 -fcf-protection -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 -/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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -[ 36%] Built target plotHaps -make -f CMakeFiles/vcfcommonsamples.dir/build.make CMakeFiles/vcfcommonsamples.dir/depend -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfcommonsamples.dir/DependInfo.cmake "--color=" 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-Wformat -Werror=format-security -fcf-protection -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 -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -[ 37%] Built target genotypeSummary -make -f CMakeFiles/vcfremovesamples.dir/build.make CMakeFiles/vcfremovesamples.dir/depend -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ @@ -1679,57 +1739,7 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 37%] Built target abba-baba -make -f CMakeFiles/vcfkeepsamples.dir/build.make CMakeFiles/vcfkeepsamples.dir/depend -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu 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/usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -make -f CMakeFiles/vcfsamplenames.dir/build.make CMakeFiles/vcfsamplenames.dir/build -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -[ 40%] Building CXX object CMakeFiles/vcfsamplenames.dir/src/vcfsamplenames.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 -fcf-protection -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 -[ 41%] 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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -[ 42%] Linking CXX executable vcffilter -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcffilter.dir/link.txt --verbose=1 -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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 -fcf-protection -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 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/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfgenotypecompare.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-linux-gnu' -[ 43%] 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 -fcf-protection -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 -[ 44%] Linking CXX executable meltEHH -/usr/bin/cmake -E cmake_link_script CMakeFiles/meltEHH.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -[ 44%] Built target vcfaltcount -make -f CMakeFiles/vcffixup.dir/build.make CMakeFiles/vcffixup.dir/depend -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcffixup.dir/DependInfo.cmake "--color=" -[ 44%] Linking CXX executable vcfgenotypes -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfgenotypes.dir/link.txt --verbose=1 -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -make -f CMakeFiles/vcffixup.dir/build.make CMakeFiles/vcffixup.dir/build -In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfannotategenotypes.cpp:10: +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 { | ^~~~~~~~~~~~~~~ @@ -1745,30 +1755,7 @@ /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-x86_64-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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -[ 44%] Building CXX object CMakeFiles/vcffixup.dir/src/vcffixup.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 -fcf-protection -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 -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -[ 44%] Built target bFst -make -f CMakeFiles/vcfclassify.dir/build.make CMakeFiles/vcfclassify.dir/depend -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfclassify.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -make -f CMakeFiles/vcfclassify.dir/build.make CMakeFiles/vcfclassify.dir/build -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -[ 45%] 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 -fcf-protection -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 -[ 45%] Built target hapLrt -make -f CMakeFiles/vcfsamplediff.dir/build.make CMakeFiles/vcfsamplediff.dir/depend -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfsamplediff.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -make -f CMakeFiles/vcfsamplediff.dir/build.make CMakeFiles/vcfsamplediff.dir/build -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfcommonsamples.cpp:10: +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 { | ^~~~~~~~~~~~~~~ @@ -1784,15 +1771,17 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 46%] 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 -fcf-protection -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 -In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfkeepsamples.cpp:10: +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 | ^~~~~~~~~~~~~~~ @@ -1802,46 +1791,7 @@ /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-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -[ 46%] Built target pVst -make -f CMakeFiles/vcfremoveaberrantgenotypes.dir/build.make CMakeFiles/vcfremoveaberrantgenotypes.dir/depend -[ 46%] Built target vcfnullgenofields -make -f CMakeFiles/vcfrandom.dir/build.make CMakeFiles/vcfrandom.dir/depend -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfremoveaberrantgenotypes.dir/DependInfo.cmake "--color=" -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfrandom.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -make -f CMakeFiles/vcfrandom.dir/build.make CMakeFiles/vcfrandom.dir/build -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -[ 46%] 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 -fcf-protection -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 -[ 46%] 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 -fcf-protection -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 -[ 46%] Built target vcfhethomratio -make -f CMakeFiles/vcfparsealts.dir/build.make CMakeFiles/vcfparsealts.dir/depend -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfparsealts.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -make -f CMakeFiles/vcfparsealts.dir/build.make CMakeFiles/vcfparsealts.dir/build -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -[ 47%] 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 -fcf-protection -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 -[ 47%] Built target iHS -make -f CMakeFiles/vcfstats.dir/build.make CMakeFiles/vcfstats.dir/depend -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfstats.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -make -f CMakeFiles/vcfstats.dir/build.make CMakeFiles/vcfstats.dir/build -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -[ 48%] 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 -fcf-protection -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 /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfremovesamples.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 { | ^~~~~~~~~~~~~~~ @@ -1857,16 +1807,7 @@ /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-x86_64-linux-gnu' -[ 48%] Built target vcfhetcount -make -f CMakeFiles/vcfflatten.dir/build.make CMakeFiles/vcfflatten.dir/depend -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfflatten.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -make -f CMakeFiles/vcfflatten.dir/build.make CMakeFiles/vcfflatten.dir/build -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfsamplenames.cpp:10: +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 { | ^~~~~~~~~~~~~~~ @@ -1882,24 +1823,10 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 49%] 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 -fcf-protection -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 -[ 49%] Built target vcfld -make -f CMakeFiles/vcfprimers.dir/build.make CMakeFiles/vcfprimers.dir/depend -[ 49%] Linking CXX executable vcfkeepsamples -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfprimers.dir/DependInfo.cmake "--color=" -/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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -make -f CMakeFiles/vcfprimers.dir/build.make CMakeFiles/vcfprimers.dir/build -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -[ 50%] Linking CXX executable vcfcommonsamples -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfcommonsamples.dir/link.txt --verbose=1 -[ 51%] 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 -fcf-protection -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 -/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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfgenotypecompare.cpp:10: +[ 32%] Linking CXX executable permuteSmooth +/usr/bin/cmake -E cmake_link_script CMakeFiles/permuteSmooth.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +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 { | ^~~~~~~~~~~~~~~ @@ -1912,15 +1839,13 @@ /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-x86_64-linux-gnu' -[ 51%] Built target sequenceDiversity -In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcffixup.cpp:10: +In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/plotHaps.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/include/c++/13/bits/stl_function.h:131:12: note: declared here + 131 | struct 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: @@ -1933,10 +1858,7 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -make -f CMakeFiles/vcfnumalt.dir/build.make CMakeFiles/vcfnumalt.dir/depend -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfnumalt.dir/DependInfo.cmake "--color=" -In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfclassify.cpp:10: +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 { | ^~~~~~~~~~~~~~~ @@ -1952,29 +1874,7 @@ /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-x86_64-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-x86_64-linux-gnu' -[ 51%] Linking CXX executable vcfannotategenotypes -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfannotategenotypes.dir/link.txt --verbose=1 -[ 52%] 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 -fcf-protection -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 -/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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -[ 52%] Linking CXX executable vcfsamplenames -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfsamplenames.dir/link.txt --verbose=1 -[ 53%] Linking CXX executable vcfremovesamples -/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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfremovesamples.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 -fcf-protection -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 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/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfcleancomplex.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -make -f CMakeFiles/vcfcleancomplex.dir/build.make CMakeFiles/vcfcleancomplex.dir/build -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfremoveaberrantgenotypes.cpp:10: +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 { | ^~~~~~~~~~~~~~~ @@ -1990,7 +1890,10 @@ /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/vcfsamplediff.cpp:10: +[ 33%] 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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfsamplenames.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 { | ^~~~~~~~~~~~~~~ @@ -2006,19 +1909,13 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 54%] Building CXX object CMakeFiles/vcfcleancomplex.dir/src/vcfcleancomplex.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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfcleancomplex.dir/src/vcfcleancomplex.cpp.o -MF CMakeFiles/vcfcleancomplex.dir/src/vcfcleancomplex.cpp.o.d -o CMakeFiles/vcfcleancomplex.dir/src/vcfcleancomplex.cpp.o -c /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfcleancomplex.cpp -In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfrandom.cpp:13: +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 { | ^~~~~~~~~~~~~~~ -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 | ^~~~~~~~~~~~~~~ @@ -2028,8 +1925,7 @@ /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-x86_64-linux-gnu' -In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfparsealts.cpp:10: +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 { | ^~~~~~~~~~~~~~~ @@ -2045,11 +1941,7 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 54%] Built target vcfgenotypes -make -f CMakeFiles/vcfintersect.dir/build.make CMakeFiles/vcfintersect.dir/depend -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfintersect.dir/DependInfo.cmake "--color=" -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/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 { | ^~~~~~~~~~~~~~~ @@ -2065,58 +1957,300 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +[ 34%] Linking CXX executable dumpContigsFromHeader +/usr/bin/cmake -E cmake_link_script CMakeFiles/dumpContigsFromHeader.dir/link.txt --verbose=1 +[ 34%] Linking CXX executable vcfkeepsamples +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfkeepsamples.dir/link.txt --verbose=1 +[ 34%] Linking CXX executable vcfclassify +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfclassify.dir/link.txt --verbose=1 +[ 35%] Linking CXX executable vcfremovesamples +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfremovesamples.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so 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CMakeFiles/vcfcleancomplex.dir/depend +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfcleancomplex.dir/DependInfo.cmake "--color=" +[ 51%] Linking CXX executable popStats +/usr/bin/cmake -E cmake_link_script CMakeFiles/popStats.dir/link.txt --verbose=1 +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' +make -f CMakeFiles/vcfcleancomplex.dir/build.make CMakeFiles/vcfcleancomplex.dir/build +make[4]: Entering directory 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/usr/lib/x86_64-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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfflatten.dir/src/vcfflatten.cpp.o -o vcfflatten -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -[ 54%] Built target vcfkeepsamples -[ 54%] Building CXX object CMakeFiles/vcfintersect.dir/src/vcfintersect.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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +[ 57%] Built target dumpContigsFromHeader make -f CMakeFiles/vcfannotate.dir/build.make CMakeFiles/vcfannotate.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 -fcf-protection -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 make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfannotate.dir/DependInfo.cmake "--color=" -[ 54%] Built target vcfcommonsamples -make -f CMakeFiles/vcfallelicprimitives.dir/build.make CMakeFiles/vcfallelicprimitives.dir/depend -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfallelicprimitives.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfannotate.dir/build.make CMakeFiles/vcfannotate.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' +[ 58%] Building CXX object CMakeFiles/vcfannotate.dir/src/vcfannotate.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 -fcf-protection -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]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -make -f CMakeFiles/vcfallelicprimitives.dir/build.make CMakeFiles/vcfallelicprimitives.dir/build -[ 55%] Building CXX object CMakeFiles/vcfannotate.dir/src/vcfannotate.cpp.o -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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 -fcf-protection -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 -[ 55%] Built target meltEHH make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' +[ 58%] Built target vcfecho +make -f CMakeFiles/vcfallelicprimitives.dir/build.make CMakeFiles/vcfallelicprimitives.dir/depend +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' +[ 58%] Built target vcfsamplenames +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfallelicprimitives.dir/DependInfo.cmake "--color=" make -f CMakeFiles/vcfwave.dir/build.make CMakeFiles/vcfwave.dir/depend -[ 55%] Building CXX object CMakeFiles/vcfallelicprimitives.dir/src/vcfallelicprimitives.cpp.o +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfwave.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 -fcf-protection -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 -[ 55%] Built target vcfsamplenames +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' +[ 58%] Built target vcfhetcount +[ 58%] Built target vcfparsealts make -f CMakeFiles/vcfoverlay.dir/build.make CMakeFiles/vcfoverlay.dir/depend +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' +[ 58%] Built target vcfgenotypes +[ 58%] Built target vcfclassify +make -f CMakeFiles/vcfaddinfo.dir/build.make CMakeFiles/vcfaddinfo.dir/depend +make -f CMakeFiles/vcfkeepinfo.dir/build.make CMakeFiles/vcfkeepinfo.dir/depend +make -f CMakeFiles/vcfkeepgeno.dir/build.make CMakeFiles/vcfkeepgeno.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfoverlay.dir/DependInfo.cmake "--color=" +[ 58%] Built target permuteSmooth +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfkeepinfo.dir/DependInfo.cmake "--color=" +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfaddinfo.dir/DependInfo.cmake "--color=" +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfkeepgeno.dir/DependInfo.cmake "--color=" +make -f CMakeFiles/vcfafpath.dir/build.make CMakeFiles/vcfafpath.dir/depend +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' +make -f CMakeFiles/vcfallelicprimitives.dir/build.make CMakeFiles/vcfallelicprimitives.dir/build +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfafpath.dir/DependInfo.cmake "--color=" +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -[ 55%] Linking CXX executable vcfclassify +[ 58%] Built target vcfkeepsamples make -f CMakeFiles/vcfwave.dir/build.make CMakeFiles/vcfwave.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfclassify.dir/link.txt --verbose=1 -[ 56%] Building CXX object CMakeFiles/vcfwave.dir/src/vcfwave.cpp.o +make -f CMakeFiles/vcfcountalleles.dir/build.make CMakeFiles/vcfcountalleles.dir/depend +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfcountalleles.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' +[ 58%] Built target vcfaltcount +make -f CMakeFiles/vcflength.dir/build.make CMakeFiles/vcflength.dir/depend +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcflength.dir/DependInfo.cmake "--color=" +make -f CMakeFiles/vcfkeepinfo.dir/build.make CMakeFiles/vcfkeepinfo.dir/build +[ 58%] Built target vcfhethomratio make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' +[ 58%] Building CXX object CMakeFiles/vcfallelicprimitives.dir/src/vcfallelicprimitives.cpp.o +make -f CMakeFiles/vcfkeepgeno.dir/build.make CMakeFiles/vcfkeepgeno.dir/build +[ 59%] Building CXX object CMakeFiles/vcfwave.dir/src/vcfwave.cpp.o +make -f CMakeFiles/vcfafpath.dir/build.make CMakeFiles/vcfafpath.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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT 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CMakeFiles/vcfrandomsample.dir/depend +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfrandomsample.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' +[ 59%] 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 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CMakeFiles/vcflength.dir/build +make -f CMakeFiles/vcfdistance.dir/build.make CMakeFiles/vcfdistance.dir/build +[ 60%] Building CXX object CMakeFiles/vcfoverlay.dir/src/vcfoverlay.cpp.o make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -[ 57%] Linking CXX executable vcffixup -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcffixup.dir/link.txt --verbose=1 -[ 58%] 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 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/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 -fcf-protection -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 +[ 60%] 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 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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 -fcf-protection -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 +[ 61%] Building CXX object CMakeFiles/vcfdistance.dir/src/vcfdistance.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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfdistance.dir/src/vcfdistance.cpp.o -MF CMakeFiles/vcfdistance.dir/src/vcfdistance.cpp.o.d -o CMakeFiles/vcfdistance.dir/src/vcfdistance.cpp.o -c /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfdistance.cpp +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' +make -f CMakeFiles/vcfentropy.dir/build.make CMakeFiles/vcfentropy.dir/build +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' +[ 61%] Building CXX object 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 -fcf-protection -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-x86_64-linux-gnu' +[ 61%] 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 -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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfentropy.dir/src/vcfentropy.cpp.o -MF CMakeFiles/vcfentropy.dir/src/vcfentropy.cpp.o.d -o CMakeFiles/vcfentropy.dir/src/vcfentropy.cpp.o -c /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfentropy.cpp +[ 61%] Built target vcfcommonsamples +make -f CMakeFiles/vcfglxgt.dir/build.make CMakeFiles/vcfglxgt.dir/depend +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfglxgt.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-linux-gnu' +[ 62%] 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 -fcf-protection -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-x86_64-linux-gnu' +[ 62%] Built target vcfremoveaberrantgenotypes +make -f CMakeFiles/vcfroc.dir/build.make CMakeFiles/vcfroc.dir/depend +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfroc.dir/DependInfo.cmake "--color=" +In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfnumalt.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 { | ^~~~~~~~~~~~~~~ @@ -2133,7 +2267,27 @@ 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfflatten.cpp:10: +make -f CMakeFiles/vcfroc.dir/build.make CMakeFiles/vcfroc.dir/build +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' +[ 62%] 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 -fcf-protection -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 +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' +[ 62%] Built target vcfnullgenofields +[ 62%] Built target vcffixup +make -f CMakeFiles/vcfcheck.dir/build.make CMakeFiles/vcfcheck.dir/depend +make -f CMakeFiles/vcfstreamsort.dir/build.make CMakeFiles/vcfstreamsort.dir/depend +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfcheck.dir/DependInfo.cmake "--color=" +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfstreamsort.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-linux-gnu' +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 { | ^~~~~~~~~~~~~~~ @@ -2149,39 +2303,21 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 59%] Linking CXX executable vcfremoveaberrantgenotypes -[ 59%] Built target vcffilter -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfremoveaberrantgenotypes.dir/link.txt --verbose=1 -make -f CMakeFiles/vcfaddinfo.dir/build.make CMakeFiles/vcfaddinfo.dir/depend -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfaddinfo.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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto 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'/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -make -f CMakeFiles/vcfaddinfo.dir/build.make CMakeFiles/vcfaddinfo.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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +[ 64%] Built target vcfrandom +make -f CMakeFiles/vcfuniq.dir/build.make CMakeFiles/vcfuniq.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libwfa2.so /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -[ 60%] Linking CXX executable vcfgenotypecompare -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfgenotypecompare.dir/link.txt --verbose=1 -[ 60%] 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 -fcf-protection -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 -/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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -[ 61%] Linking CXX executable vcfprimers -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfprimers.dir/link.txt --verbose=1 -[ 61%] 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfprimers.dir/src/vcfprimers.cpp.o -o vcfprimers -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfuniq.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -[ 61%] Built target vcfremovesamples -make -f CMakeFiles/vcfkeepinfo.dir/build.make CMakeFiles/vcfkeepinfo.dir/depend +make -f CMakeFiles/vcfuniq.dir/build.make CMakeFiles/vcfuniq.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfkeepinfo.dir/DependInfo.cmake "--color=" -In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfnumalt.cpp:10: +[ 65%] 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 -fcf-protection -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/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 { | ^~~~~~~~~~~~~~~ @@ -2198,10 +2334,15 @@ 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -make -f CMakeFiles/vcfkeepinfo.dir/build.make CMakeFiles/vcfkeepinfo.dir/build +[ 65%] Built target vcfsamplediff +make -f CMakeFiles/vcfuniqalleles.dir/build.make CMakeFiles/vcfuniqalleles.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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 -fcf-protection -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 +cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfuniqalleles.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-linux-gnu' +[ 66%] 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 -fcf-protection -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/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 { @@ -2218,16 +2359,12 @@ /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-x86_64-linux-gnu' -[ 61%] Built target vcfclassify -make -f CMakeFiles/vcfkeepgeno.dir/build.make CMakeFiles/vcfkeepgeno.dir/depend -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfkeepgeno.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-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 -fcf-protection -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 +[ 67%] Linking CXX executable vcfprimers +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfprimers.dir/link.txt --verbose=1 +[ 67%] 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfprimers.dir/src/vcfprimers.cpp.o -o vcfprimers -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 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 { @@ -2244,7 +2381,7 @@ /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/vcfcleancomplex.cpp:10: +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 { | ^~~~~~~~~~~~~~~ @@ -2260,7 +2397,7 @@ /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/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 { | ^~~~~~~~~~~~~~~ @@ -2276,7 +2413,13 @@ /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/vcfallelicprimitives.cpp:10: +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' +[ 67%] Built target popStats +make -f CMakeFiles/vcfremap.dir/build.make CMakeFiles/vcfremap.dir/depend +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfremap.dir/DependInfo.cmake "--color=" +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 { | ^~~~~~~~~~~~~~~ @@ -2292,21 +2435,13 @@ /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-x86_64-linux-gnu' -[ 61%] Linking CXX executable vcfstats -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfstats.dir/link.txt --verbose=1 -[ 61%] Built target vcfparsealts -/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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libwfa2.so /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -make -f CMakeFiles/vcfafpath.dir/build.make CMakeFiles/vcfafpath.dir/depend -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfafpath.dir/DependInfo.cmake "--color=" -In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfwave.cpp:19: +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 { | ^~~~~~~~~~~~~~~ -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -In file included from /usr/include/c++/13/string:49, - from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfwave.cpp:11: +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 | ^~~~~~~~~~~~~~~ @@ -2316,20 +2451,16 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -make -f CMakeFiles/vcfafpath.dir/build.make CMakeFiles/vcfafpath.dir/build +[ 67%] Built target abba-baba +make -f CMakeFiles/vcf2fasta.dir/build.make CMakeFiles/vcf2fasta.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -[ 61%] Building CXX object CMakeFiles/vcfafpath.dir/src/vcfafpath.cpp.o -[ 61%] Linking CXX executable vcfnumalt -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfnumalt.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 -fcf-protection -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 -/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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfaddinfo.cpp:10: +cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcf2fasta.dir/DependInfo.cmake "--color=" +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 { | ^~~~~~~~~~~~~~~ -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 /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfwave.cpp:11: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -2339,10 +2470,13 @@ /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/vcfkeepinfo.cpp:10: +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' +make -f CMakeFiles/vcfremap.dir/build.make CMakeFiles/vcfremap.dir/build +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 { | ^~~~~~~~~~~~~~~ +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' 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: @@ -2355,23 +2489,9 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 61%] Linking CXX executable vcfflatten -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfflatten.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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfflatten.dir/src/vcfflatten.cpp.o -o vcfflatten -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -[ 61%] Built target vcfremoveaberrantgenotypes -make -f CMakeFiles/vcfcountalleles.dir/build.make CMakeFiles/vcfcountalleles.dir/depend -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfcountalleles.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -make -f CMakeFiles/vcfcountalleles.dir/build.make CMakeFiles/vcfcountalleles.dir/build -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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 -fcf-protection -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 -[ 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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libwfa2.so /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfkeepgeno.cpp:10: +make -f CMakeFiles/vcf2fasta.dir/build.make CMakeFiles/vcf2fasta.dir/build +In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfcountalleles.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 { | ^~~~~~~~~~~~~~~ @@ -2387,51 +2507,13 @@ /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-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -[ 61%] Built target vcffixup -make -f CMakeFiles/vcflength.dir/build.make CMakeFiles/vcflength.dir/depend -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcflength.dir/DependInfo.cmake "--color=" -[ 61%] Built target vcfprimers -make -f CMakeFiles/vcfdistance.dir/build.make CMakeFiles/vcfdistance.dir/depend -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfdistance.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -make -f CMakeFiles/vcflength.dir/build.make CMakeFiles/vcflength.dir/build -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -[ 62%] Building CXX object CMakeFiles/vcflength.dir/src/vcflength.cpp.o -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -make -f CMakeFiles/vcfdistance.dir/build.make CMakeFiles/vcfdistance.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 -fcf-protection -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]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -[ 63%] Linking CXX executable vcfaddinfo -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfaddinfo.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 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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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -[ 64%] Built target vcfrandom -make -f CMakeFiles/vcfrandomsample.dir/build.make CMakeFiles/vcfrandomsample.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfrandomsample.dir/DependInfo.cmake "--color=" -[ 64%] 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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -make -f CMakeFiles/vcfrandomsample.dir/build.make CMakeFiles/vcfrandomsample.dir/build -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -[ 64%] Building CXX object 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 -fcf-protection -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 -[ 64%] Linking CXX executable vcfoverlay -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfoverlay.dir/link.txt --verbose=1 -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/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 { | ^~~~~~~~~~~~~~~ +[ 67%] Building CXX object CMakeFiles/vcfremap.dir/src/vcfremap.cpp.o 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: @@ -2444,25 +2526,10 @@ /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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -[ 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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libwfa2.so /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -[ 65%] Built target vcfsamplediff -make -f CMakeFiles/vcfentropy.dir/build.make CMakeFiles/vcfentropy.dir/depend -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfentropy.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -make -f CMakeFiles/vcfentropy.dir/build.make CMakeFiles/vcfentropy.dir/build -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -[ 65%] 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 -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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfentropy.dir/src/vcfentropy.cpp.o -MF CMakeFiles/vcfentropy.dir/src/vcfentropy.cpp.o.d -o CMakeFiles/vcfentropy.dir/src/vcfentropy.cpp.o -c /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfentropy.cpp -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfcountalleles.cpp:10: +/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 -fcf-protection -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 +[ 67%] Building CXX object CMakeFiles/vcf2fasta.dir/src/vcf2fasta.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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcf2fasta.dir/src/vcf2fasta.cpp.o -MF CMakeFiles/vcf2fasta.dir/src/vcf2fasta.cpp.o.d -o CMakeFiles/vcf2fasta.dir/src/vcf2fasta.cpp.o -c /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcf2fasta.cpp +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 { | ^~~~~~~~~~~~~~~ @@ -2478,27 +2545,8 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 65%] Built target vcfnumalt -make -f CMakeFiles/vcfglxgt.dir/build.make CMakeFiles/vcfglxgt.dir/depend -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfglxgt.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -[ 66%] 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 -fcf-protection -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 -[ 66%] Built target vcfgenotypecompare -make -f CMakeFiles/vcfroc.dir/build.make CMakeFiles/vcfroc.dir/depend -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfroc.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-linux-gnu' -[ 66%] 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 -fcf-protection -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 -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcflength.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 { | ^~~~~~~~~~~~~~~ @@ -2514,16 +2562,8 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 66%] Built target vcfannotategenotypes -make -f CMakeFiles/vcfcheck.dir/build.make CMakeFiles/vcfcheck.dir/depend -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfcheck.dir/DependInfo.cmake "--color=" -[ 67%] Linking CXX executable vcfallelicprimitives make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -make -f CMakeFiles/vcfcheck.dir/build.make CMakeFiles/vcfcheck.dir/build -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfallelicprimitives.dir/link.txt --verbose=1 -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -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/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 { | ^~~~~~~~~~~~~~~ @@ -2539,52 +2579,7 @@ /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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libwfa2.so /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -[ 68%] Linking CXX executable vcfintersect -[ 69%] Building CXX object CMakeFiles/vcfcheck.dir/src/vcfcheck.cpp.o -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfintersect.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 -fcf-protection -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 -/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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -[ 70%] Linking CXX executable vcfafpath -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfafpath.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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -[ 70%] Built target vcfaddinfo -make -f CMakeFiles/vcfstreamsort.dir/build.make CMakeFiles/vcfstreamsort.dir/depend -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfstreamsort.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-linux-gnu' -[ 71%] 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto 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/usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -[ 72%] Built target vcfcleancomplex -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -make -f CMakeFiles/vcfuniq.dir/build.make CMakeFiles/vcfuniq.dir/depend -[ 72%] Linking CXX executable vcflength -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcflength.dir/link.txt --verbose=1 -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfuniq.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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -make -f CMakeFiles/vcfuniq.dir/build.make CMakeFiles/vcfuniq.dir/build -[ 72%] Built target vcfkeepinfo -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -make -f CMakeFiles/vcfuniqalleles.dir/build.make CMakeFiles/vcfuniqalleles.dir/depend -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfuniqalleles.dir/DependInfo.cmake "--color=" -[ 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 -fcf-protection -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 -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-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 -fcf-protection -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/vcfrandomsample.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 { | ^~~~~~~~~~~~~~~ @@ -2600,30 +2595,7 @@ /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-x86_64-linux-gnu' -[ 74%] Built target vcfkeepgeno -make -f CMakeFiles/vcfremap.dir/build.make CMakeFiles/vcfremap.dir/depend -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfremap.dir/DependInfo.cmake "--color=" -[ 75%] Linking CXX executable vcfdistance -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfdistance.dir/link.txt --verbose=1 -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -make -f CMakeFiles/vcfremap.dir/build.make CMakeFiles/vcfremap.dir/build -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -[ 75%] 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 -fcf-protection -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 -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -[ 75%] Built target vcfflatten -make -f CMakeFiles/vcf2fasta.dir/build.make CMakeFiles/vcf2fasta.dir/depend -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcf2fasta.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -make -f CMakeFiles/vcf2fasta.dir/build.make CMakeFiles/vcf2fasta.dir/build -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -[ 75%] Building CXX object CMakeFiles/vcf2fasta.dir/src/vcf2fasta.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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcf2fasta.dir/src/vcf2fasta.cpp.o -MF CMakeFiles/vcf2fasta.dir/src/vcf2fasta.cpp.o.d -o CMakeFiles/vcf2fasta.dir/src/vcf2fasta.cpp.o -c /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcf2fasta.cpp -In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfroc.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 { | ^~~~~~~~~~~~~~~ @@ -2639,7 +2611,31 @@ /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/vcfglxgt.cpp:10: +[ 67%] Built target vcf2tsv +[ 67%] Built target vcffilter +make -f CMakeFiles/vcfsitesummarize.dir/build.make CMakeFiles/vcfsitesummarize.dir/depend +make -f CMakeFiles/vcfbreakmulti.dir/build.make CMakeFiles/vcfbreakmulti.dir/depend +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfsitesummarize.dir/DependInfo.cmake "--color=" +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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/src/vcfsitesummarize.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 -fcf-protection -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 +[ 69%] Linking CXX executable vcfcleancomplex +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfcleancomplex.dir/link.txt --verbose=1 +[ 70%] Linking CXX executable vcfcountalleles +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfcountalleles.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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libwfa2.so /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfstreamsort.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 { | ^~~~~~~~~~~~~~~ @@ -2656,16 +2652,19 @@ 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -[ 75%] Built target vcfcountalleles -make -f CMakeFiles/vcfsitesummarize.dir/build.make CMakeFiles/vcfsitesummarize.dir/depend +[ 70%] Built target wcFst +make -f CMakeFiles/vcfevenregions.dir/build.make CMakeFiles/vcfevenregions.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfsitesummarize.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfevenregions.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -make -f CMakeFiles/vcfsitesummarize.dir/build.make CMakeFiles/vcfsitesummarize.dir/build +make -f CMakeFiles/vcfevenregions.dir/build.make CMakeFiles/vcfevenregions.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -[ 76%] 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 -fcf-protection -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 -In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfentropy.cpp:10: +[ 70%] 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 -fcf-protection -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-x86_64-linux-gnu' +[ 71%] Linking CXX executable vcfkeepinfo +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfkeepinfo.dir/link.txt --verbose=1 +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 { | ^~~~~~~~~~~~~~~ @@ -2681,28 +2680,26 @@ /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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -[ 76%] Built target vcfoverlay -make -f CMakeFiles/vcfbreakmulti.dir/build.make CMakeFiles/vcfbreakmulti.dir/depend +[ 71%] Built target vcfflatten +[ 71%] Built target bFst +make -f CMakeFiles/vcfcat.dir/build.make CMakeFiles/vcfcat.dir/depend +make -f CMakeFiles/vcfgenosummarize.dir/build.make CMakeFiles/vcfgenosummarize.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfbreakmulti.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -make -f CMakeFiles/vcfbreakmulti.dir/build.make CMakeFiles/vcfbreakmulti.dir/build +cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfcat.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -[ 77%] Building CXX object CMakeFiles/vcfbreakmulti.dir/src/vcfbreakmulti.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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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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfgenosummarize.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -[ 77%] Built target vcfafpath -make -f CMakeFiles/vcfevenregions.dir/build.make CMakeFiles/vcfevenregions.dir/depend -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfevenregions.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -make -f CMakeFiles/vcfevenregions.dir/build.make CMakeFiles/vcfevenregions.dir/build +make -f CMakeFiles/vcfcat.dir/build.make CMakeFiles/vcfcat.dir/build +make -f CMakeFiles/vcfgenosummarize.dir/build.make CMakeFiles/vcfgenosummarize.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -[ 78%] Linking CXX executable vcfrandomsample -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfrandomsample.dir/link.txt --verbose=1 -[ 78%] 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 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Building CXX object CMakeFiles/vcfcat.dir/src/vcfcat.cpp.o +[ 73%] 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 -fcf-protection -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 +/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 -fcf-protection -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/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 { @@ -2719,7 +2716,6 @@ /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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 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 { @@ -2736,28 +2732,75 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +[ 74%] Linking CXX executable vcfaddinfo +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfaddinfo.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 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CMakeFiles/vcfgenosamplenames.dir/build.make CMakeFiles/vcfgenosamplenames.dir/depend +make -f CMakeFiles/vcfgeno2haplo.dir/build.make CMakeFiles/vcfgeno2haplo.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfcat.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfgenosamplenames.dir/DependInfo.cmake "--color=" +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfgeno2haplo.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -make -f CMakeFiles/vcfcat.dir/build.make CMakeFiles/vcfcat.dir/build +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' +make -f CMakeFiles/vcfgenosamplenames.dir/build.make CMakeFiles/vcfgenosamplenames.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -[ 79%] 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 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/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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfgenosummarize.dir/DependInfo.cmake "--color=" -[ 80%] Linking CXX executable vcfentropy -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfentropy.dir/link.txt --verbose=1 +[ 74%] Built target vcfprimers +make -f CMakeFiles/vcfleftalign.dir/build.make CMakeFiles/vcfleftalign.dir/depend +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfleftalign.dir/DependInfo.cmake "--color=" +[ 75%] Building CXX object CMakeFiles/vcfgenosamplenames.dir/src/vcfgenosamplenames.cpp.o +[ 75%] Built target genotypeSummary +make -f CMakeFiles/vcfcombine.dir/build.make CMakeFiles/vcfcombine.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 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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 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -make -f CMakeFiles/vcfgenosummarize.dir/build.make CMakeFiles/vcfgenosummarize.dir/build +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' +make -f CMakeFiles/vcfleftalign.dir/build.make CMakeFiles/vcfleftalign.dir/build +make -f CMakeFiles/vcfcombine.dir/build.make CMakeFiles/vcfcombine.dir/build +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' +[ 77%] 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 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfcombine.dir/src/vcfcombine.cpp.o -MF CMakeFiles/vcfcombine.dir/src/vcfcombine.cpp.o.d -o CMakeFiles/vcfcombine.dir/src/vcfcombine.cpp.o -c /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfcombine.cpp +[ 78%] 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 -fcf-protection -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 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-ltabixpp -lwfa2 +[ 80%] Linking CXX executable vcfdistance +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfdistance.dir/link.txt --verbose=1 +[ 80%] Built target sequenceDiversity +make -f CMakeFiles/vcfgeno2alleles.dir/build.make CMakeFiles/vcfgeno2alleles.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfgeno2alleles.dir/DependInfo.cmake "--color=" +[ 81%] Linking CXX executable vcfafpath +[ 82%] Linking CXX executable vcfentropy +/usr/bin/cmake -E cmake_link_script 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/usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfstreamsort.cpp:10: +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' +make -f CMakeFiles/vcfgeno2alleles.dir/build.make CMakeFiles/vcfgeno2alleles.dir/build +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' +[ 82%] Built target vcfnumalt +make -f CMakeFiles/vcfindex.dir/build.make CMakeFiles/vcfindex.dir/depend +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfindex.dir/DependInfo.cmake "--color=" +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 { | ^~~~~~~~~~~~~~~ @@ -2773,9 +2816,84 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 81%] 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 -fcf-protection -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 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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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcf2dag.dir/DependInfo.cmake "--color=" +[ 83%] Linking CXX executable vcflength +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcflength.dir/link.txt --verbose=1 +[ 83%] 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 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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 -fcf-protection -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 +[ 85%] Building CXX object CMakeFiles/vcfqual2info.dir/src/vcfqual2info.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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -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 -fcf-protection -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 +[ 85%] Built target vcfgenotypecompare +make -f CMakeFiles/vcfinfo2qual.dir/build.make CMakeFiles/vcfinfo2qual.dir/depend +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfinfo2qual.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' +make -f CMakeFiles/vcfinfo2qual.dir/build.make CMakeFiles/vcfinfo2qual.dir/build +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' +[ 85%] 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 -fcf-protection -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 +[ 85%] Built target hapLrt +make -f CMakeFiles/vcfglbound.dir/build.make CMakeFiles/vcfglbound.dir/depend +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfglbound.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' +make -f CMakeFiles/vcfglbound.dir/build.make CMakeFiles/vcfglbound.dir/build +[ 85%] Linking CXX executable vcfoverlay +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfoverlay.dir/link.txt --verbose=1 +[ 85%] Linking CXX executable vcfuniq +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' +/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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +[ 86%] 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 -fcf-protection -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 +[ 86%] 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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +[ 86%] 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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +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 { | ^~~~~~~~~~~~~~~ @@ -2791,10 +2909,6 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 82%] 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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -[ 82%] Linking CXX executable vcfcheck 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 { @@ -2811,25 +2925,25 @@ /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/vcfcheck.dir/link.txt --verbose=1 -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -[ 82%] Built target vcfstats -make -f CMakeFiles/vcfgenosamplenames.dir/build.make CMakeFiles/vcfgenosamplenames.dir/depend +[ 86%] Built target vcfcountalleles +make -f CMakeFiles/vcfinfosummarize.dir/build.make CMakeFiles/vcfinfosummarize.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 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'/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' +make -f CMakeFiles/vcfinfosummarize.dir/build.make CMakeFiles/vcfinfosummarize.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfgeno2haplo.dir/DependInfo.cmake "--color=" +[ 86%] 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 -fcf-protection -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 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -make -f CMakeFiles/vcfgenosamplenames.dir/build.make CMakeFiles/vcfgenosamplenames.dir/build -[ 82%] Linking CXX executable vcfuniq 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 { | ^~~~~~~~~~~~~~~ +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 { + | ^~~~~~~~~~~~~~~ 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: @@ -2842,10 +2956,6 @@ /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/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 { - | ^~~~~~~~~~~~~~~ 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: @@ -2858,17 +2968,38 @@ /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/vcfuniq.dir/link.txt --verbose=1 +[ 86%] Linking CXX executable vcfuniqalleles +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfuniqalleles.dir/link.txt --verbose=1 +[ 86%] Built target meltEHH +make -f CMakeFiles/vcfcreatemulti.dir/build.make CMakeFiles/vcfcreatemulti.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfcreatemulti.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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' +make -f CMakeFiles/vcfcreatemulti.dir/build.make CMakeFiles/vcfcreatemulti.dir/build make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-linux-gnu' -[ 83%] 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 -fcf-protection -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 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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 -fcf-protection -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: +[ 86%] Building CXX object CMakeFiles/vcfcreatemulti.dir/src/vcfcreatemulti.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 -fcf-protection -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 +[ 86%] Built target vcfkeepinfo +make -f CMakeFiles/pyvcflib.dir/build.make CMakeFiles/pyvcflib.dir/depend +make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/pyvcflib.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-linux-gnu' +[ 86%] Linking CXX executable vcfwave +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfwave.dir/link.txt --verbose=1 +[ 87%] 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 -fcf-protection -Wdate-time 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/usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' +[ 87%] Built target vcfcleancomplex +[ 87%] 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-x86_64-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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +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 { | ^~~~~~~~~~~~~~~ @@ -2884,6 +3015,7 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +[ 87%] Built target vcfaddinfo 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 { @@ -2900,22 +3032,15 @@ 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directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -[ 84%] Built target vcfrandomsample -make -f CMakeFiles/vcfleftalign.dir/build.make CMakeFiles/vcfleftalign.dir/depend -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfleftalign.dir/DependInfo.cmake "--color=" +[ 87%] Built target vcfkeepgeno make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -make -f CMakeFiles/vcfleftalign.dir/build.make CMakeFiles/vcfleftalign.dir/build -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -[ 85%] 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 -fcf-protection -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 -[ 85%] Linking CXX executable vcfsitesummarize -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfsitesummarize.dir/link.txt --verbose=1 -In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfcat.cpp:10: +[ 87%] Built target vcfdistance +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' +[ 87%] Built target vcfuniq +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' +[ 87%] Built target vcfannotategenotypes +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 { | ^~~~~~~~~~~~~~~ @@ -2931,37 +3056,7 @@ /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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -[ 85%] Linking CXX executable 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-x86_64-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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -[ 85%] Built target vcfcheck -make -f CMakeFiles/vcfcombine.dir/build.make CMakeFiles/vcfcombine.dir/depend -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfcombine.dir/DependInfo.cmake "--color=" -[ 85%] Built target vcfuniq -make -f CMakeFiles/vcfgeno2alleles.dir/build.make CMakeFiles/vcfgeno2alleles.dir/depend -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfgeno2alleles.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -make -f CMakeFiles/vcfcombine.dir/build.make CMakeFiles/vcfcombine.dir/build -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -make -f CMakeFiles/vcfgeno2alleles.dir/build.make CMakeFiles/vcfgeno2alleles.dir/build -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -[ 86%] 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 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfcombine.dir/src/vcfcombine.cpp.o -MF CMakeFiles/vcfcombine.dir/src/vcfcombine.cpp.o.d -o CMakeFiles/vcfcombine.dir/src/vcfcombine.cpp.o -c /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfcombine.cpp -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -[ 87%] 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 -fcf-protection -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 -[ 87%] Built target vcfglxgt -make -f CMakeFiles/vcfindex.dir/build.make CMakeFiles/vcfindex.dir/depend -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfindex.dir/DependInfo.cmake "--color=" -[ 88%] Linking CXX executable vcf2fasta -In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfgenosummarize.cpp:10: +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 { | ^~~~~~~~~~~~~~~ @@ -2977,13 +3072,9 @@ /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/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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -make -f CMakeFiles/vcfindex.dir/build.make CMakeFiles/vcfindex.dir/build -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -[ 88%] 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 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warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { @@ -3000,14 +3091,8 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 89%] Linking CXX executable vcfevenregions -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfevenregions.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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -[ 90%] 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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -[ 90%] Linking CXX executable vcfbreakmulti -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfbreakmulti.dir/link.txt --verbose=1 +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' 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 { @@ -3024,68 +3109,9 @@ /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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto 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/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcf2dag.dir/DependInfo.cmake "--color=" -[ 91%] Built target vcfuniqalleles -make -f CMakeFiles/vcfsample2info.dir/build.make CMakeFiles/vcfsample2info.dir/depend -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfsample2info.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -make -f CMakeFiles/vcf2dag.dir/build.make CMakeFiles/vcf2dag.dir/build -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-linux-gnu' -[ 91%] Linking CXX executable vcfcat -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfcat.dir/link.txt --verbose=1 -[ 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 -fcf-protection -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 -[ 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 -fcf-protection -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 -/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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -[ 91%] Built target vcfentropy -make -f CMakeFiles/vcfqual2info.dir/build.make CMakeFiles/vcfqual2info.dir/depend -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfqual2info.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -make -f CMakeFiles/vcfqual2info.dir/build.make CMakeFiles/vcfqual2info.dir/build -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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 -fcf-protection -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 -[ 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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -[ 91%] Built target vcfintersect -make -f CMakeFiles/vcfinfo2qual.dir/build.make CMakeFiles/vcfinfo2qual.dir/depend -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfinfo2qual.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -make -f CMakeFiles/vcfinfo2qual.dir/build.make CMakeFiles/vcfinfo2qual.dir/build -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -[ 91%] Built target vcfsitesummarize -[ 91%] Building CXX object CMakeFiles/vcfinfo2qual.dir/src/vcfinfo2qual.cpp.o -make -f CMakeFiles/vcfglbound.dir/build.make CMakeFiles/vcfglbound.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 -fcf-protection -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 -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfglbound.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -make -f CMakeFiles/vcfglbound.dir/build.make CMakeFiles/vcfglbound.dir/build -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -[ 91%] Linking CXX executable vcfgenosamplenames -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfgenosamplenames.dir/link.txt --verbose=1 -[ 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 -fcf-protection -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 +[ 87%] Built target vcfstats +[ 87%] Built target vcflength +[ 87%] Built target vcfafpath 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 { @@ -3102,18 +3128,8 @@ /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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -[ 92%] Built target vcfevenregions -make -f CMakeFiles/vcfinfosummarize.dir/build.make CMakeFiles/vcfinfosummarize.dir/depend -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfinfosummarize.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -make -f CMakeFiles/vcfinfosummarize.dir/build.make CMakeFiles/vcfinfosummarize.dir/build -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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 -fcf-protection -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 -In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfleftalign.cpp:10: +In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcf2dag.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 { | ^~~~~~~~~~~~~~~ @@ -3129,7 +3145,7 @@ /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/vcfindex.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 { | ^~~~~~~~~~~~~~~ @@ -3145,17 +3161,11 @@ /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-x86_64-linux-gnu' -[ 92%] Built target vcfallelicprimitives -make -f CMakeFiles/vcfcreatemulti.dir/build.make CMakeFiles/vcfcreatemulti.dir/depend -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfcreatemulti.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -make -f CMakeFiles/vcfcreatemulti.dir/build.make CMakeFiles/vcfcreatemulti.dir/build -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -[ 92%] Building CXX object CMakeFiles/vcfcreatemulti.dir/src/vcfcreatemulti.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 -fcf-protection -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/vcfcombine.cpp:10: +[ 87%] Built target vcfrandomsample +[ 87%] 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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +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 { | ^~~~~~~~~~~~~~~ @@ -3171,20 +3181,10 @@ /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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -[ 92%] Built target vcfcat -make -f CMakeFiles/pyvcflib.dir/build.make CMakeFiles/pyvcflib.dir/depend -make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/pyvcflib.dir/DependInfo.cmake "--color=" +[ 87%] Linking CXX executable vcfsitesummarize +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfsitesummarize.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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-x86_64-linux-gnu' -[ 93%] 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 -fcf-protection -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 -In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcf2dag.cpp:10: +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 { | ^~~~~~~~~~~~~~~ @@ -3200,7 +3200,13 @@ /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/vcfsample2info.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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +[ 87%] Built target vcfglxgt +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' +[ 87%] Built target vcfuniqalleles +[ 88%] Linking CXX executable vcfevenregions +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfevenregions.dir/link.txt --verbose=1 +In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfinfo2qual.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 { | ^~~~~~~~~~~~~~~ @@ -3216,7 +3222,7 @@ /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/vcfqual2info.cpp:10: +In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfglbound.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 { | ^~~~~~~~~~~~~~~ @@ -3232,15 +3238,15 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 94%] Linking CXX executable vcfindex -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfindex.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfindex.dir/src/vcfindex.cpp.o -o vcfindex -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -[ 94%] 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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +[ 89%] 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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +[ 89%] Linking CXX executable vcfgenosummarize +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfgenosummarize.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -[ 94%] Built target vcfbreakmulti -In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfglbound.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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfqual2info.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 { | ^~~~~~~~~~~~~~~ @@ -3256,13 +3262,13 @@ /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-x86_64-linux-gnu' -[ 94%] Built target vcfgenosamplenames -[ 94%] Linking CXX executable vcfgeno2haplo -/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-x86_64-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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -[ 94%] Built target vcfstreamsort +[ 90%] Linking CXX executable vcfcat +[ 90%] Linking CXX executable vcfallelicprimitives +[ 90%] Built target vcfentropy +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfallelicprimitives.dir/link.txt --verbose=1 +/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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libwfa2.so /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfinfosummarize.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 { @@ -3279,11 +3285,21 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +[ 91%] 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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +[ 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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +[ 91%] 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 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struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ @@ -3299,13 +3315,9 @@ /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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfqual2info.dir/src/vcfqual2info.cpp.o -o vcfqual2info -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 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CMakeFiles/vcfcombine.dir/link.txt --verbose=1 +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' +[ 97%] Built target vcfsitesummarize [ 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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so 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[-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 - | ^~~~~~~~~~~~~~~ +/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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfqual2info.dir/src/vcfqual2info.cpp.o -o vcfqual2info -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +[ 99%] Built target vcfgenosamplenames +[ 99%] Linking CXX executable vcfcombine +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfcombine.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' +[ 99%] Built target vcfcat +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' +[ 99%] Built target vcfbreakmulti +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' +[ 99%] Built target vcfevenregions +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' +[ 99%] Built target vcfstreamsort +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' +[ 99%] Built target vcfgeno2alleles +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' +[ 99%] Built target vcfinfo2qual +[ 99%] Built target vcfgenosummarize make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -[ 99%] Built target vcfqual2info [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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 -make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -[100%] Built target vcfinfo2qual +[100%] 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 -fcf-protection -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/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 +[100%] Built target vcfindex make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -[100%] Built target vcfleftalign [100%] Built target vcfsample2info +[100%] Built target vcfannotate make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -[100%] Built target vcfglbound +[100%] Built target vcf2dag make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -[100%] Built target vcfroc make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -[100%] Built target vcf2dag +[100%] Built target vcfqual2info +[100%] Built target vcfglbound +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' [100%] Built target vcfinfosummarize +[100%] Built target vcf2fasta make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' -[100%] Built target vcfcombine +[100%] Built target vcfremap +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' +[100%] Built target vcfleftalign +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' +[100%] Built target vcfwave make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' [100%] Built target vcfcreatemulti make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' +[100%] Built target vcfcombine +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' +[100%] Built target vcfroc +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' +[100%] Built target vcfintersect +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' +[100%] Built target vcfallelicprimitives +make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' [100%] Built target vcfgeno2haplo [100%] Linking CXX shared module pyvcflib.cpython-311-x86_64-linux-gnu.so /usr/bin/cmake -E cmake_link_script CMakeFiles/pyvcflib.dir/link.txt --verbose=1 @@ -3401,34 +3437,34 @@ cd test && ctest . Test project /build/reproducible-path/libvcflib-1.0.9+dfsg1/test Start 1: realign -1/9 Test #1: realign .......................... Passed 0.17 sec +1/9 Test #1: realign .......................... Passed 0.07 sec Start 2: pyvcflib -2/9 Test #2: pyvcflib ......................... Passed 0.13 sec +2/9 Test #2: pyvcflib ......................... Passed 0.21 sec Start 3: vcflib-api -3/9 Test #3: vcflib-api ....................... Passed 0.12 sec +3/9 Test #3: vcflib-api ....................... Passed 0.07 sec Start 4: vcf2tsv -4/9 Test #4: vcf2tsv .......................... Passed 0.18 sec +4/9 Test #4: vcf2tsv .......................... Passed 0.21 sec Start 5: vcfallelicprimitives -5/9 Test #5: vcfallelicprimitives ............. Passed 1.70 sec +5/9 Test #5: vcfallelicprimitives ............. Passed 1.10 sec Start 6: vcfwave -6/9 Test #6: vcfwave .......................... Passed 0.78 sec +6/9 Test #6: vcfwave .......................... Passed 0.75 sec Start 7: vcffilter -7/9 Test #7: vcffilter ........................ Passed 0.27 sec +7/9 Test #7: vcffilter ........................ Passed 0.17 sec Start 8: vcfnulldotslashdot -8/9 Test #8: vcfnulldotslashdot ............... Passed 0.19 sec +8/9 Test #8: vcfnulldotslashdot ............... Passed 0.25 sec Start 9: doc/vcfintersect -9/9 Test #9: doc/vcfintersect ................. Passed 0.11 sec +9/9 Test #9: doc/vcfintersect ................. Passed 0.07 sec 100% tests passed, 0 tests failed out of 9 -Total Test time (real) = 3.67 sec +Total Test time (real) = 3.00 sec cd .. && rm -f build make[1]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1' create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=cmake dh_prep -O--buildsystem=cmake dh_auto_install -O--buildsystem=cmake - cd obj-x86_64-linux-gnu && make -j20 install DESTDIR=/build/reproducible-path/libvcflib-1.0.9\+dfsg1/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + cd obj-x86_64-linux-gnu && make -j42 install DESTDIR=/build/reproducible-path/libvcflib-1.0.9\+dfsg1/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/libvcflib-1.0.9+dfsg1 -B/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall @@ -3673,95 +3709,95 @@ -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/include/vcf-c-api.h -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/include/vcf-wfa.h -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1 --- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfgeno2haplo.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfkeepgeno.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/sequenceDiversity.1 -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfcountalleles.1 --- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfinfo2qual.1 --- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfentropy.1 --- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfparsealts.1 --- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfannotategenotypes.1 --- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfkeepinfo.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/permuteSmooth.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/hapLrt.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfhethomratio.1 -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/permuteGPAT++.1 --- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfsample2info.1 --- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfleftalign.1 --- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcflength.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/pVst.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfinfosummarize.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfkeepinfo.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfnulldotslashdot.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfcommonsamples.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfparsealts.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfallelicprimitives.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfcat.1 -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfuniq.1 --- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfstreamsort.1 --- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfnumalt.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfrandomsample.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfcombine.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/segmentFst.1 -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfstats.1 --- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfsamplenames.1 --- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfuniqalleles.1 --- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfbreakmulti.1 --- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfgeno2alleles.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfentropy.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfrandom.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/wcFst.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfleftalign.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfhetcount.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/meltEHH.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfgenosummarize.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/plotHaps.1 -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/iHS.1 --- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfld.1 --- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfrandomsample.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfindex.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfbreakmulti.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfinfo2qual.1 -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfcleancomplex.1 --- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfhetcount.1 --- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfflatten.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfgeno2haplo.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfevenregions.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfoverlay.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfwave.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfstreamsort.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcflib-api.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcflength.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfgenosamplenames.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfintersect.1 -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/segmentIhs.1 --- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfqual2info.1 --- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfcombine.1 --- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/smoother.1 --- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfecho.1 -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfannotate.1 --- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/pFst.1 --- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfrandom.1 --- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfremoveaberrantgenotypes.1 --- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/pyvcflib.1 --- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/abba-baba.1 --- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcf2tsv.1 --- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/pVst.1 --- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/permuteSmooth.1 --- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/normalize-iHS.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfsample2info.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfprimers.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfafpath.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/bFst.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfld.1 -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/genotypeSummary.1 --- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfcat.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfremovesamples.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfecho.1 -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/popStats.1 --- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcflib-api.1 --- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfkeepgeno.1 --- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfhethomratio.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcf2fasta.1 -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcffixup.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/normalize-iHS.1 -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfnullgenofields.1 --- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfinfosummarize.1 --- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfgenotypecompare.1 --- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfgenosummarize.1 --- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfaddinfo.1 --- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/meltEHH.1 -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcf2dag.1 --- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfclassify.1 --- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/dumpContigsFromHeader.1 --- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfcreatemulti.1 --- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfdistance.1 --- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfremap.1 --- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/wcFst.1 --- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfsamplediff.1 --- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfaltcount.1 --- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/bFst.1 --- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfglbound.1 --- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfintersect.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfgenotypecompare.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcf2tsv.1 -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfroc.1 --- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfgenosamplenames.1 --- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/sequenceDiversity.1 --- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfkeepsamples.1 -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfsitesummarize.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/pyvcflib.1 -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcffilter.1 --- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfevenregions.1 --- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfoverlay.1 --- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfafpath.1 --- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcf2fasta.1 --- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfremovesamples.1 --- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfcommonsamples.1 --- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfindex.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfannotategenotypes.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfkeepsamples.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfnumalt.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfsamplenames.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfcreatemulti.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfglbound.1 -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcflib.1 --- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfnulldotslashdot.1 --- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/hapLrt.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfremoveaberrantgenotypes.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfglxgt.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfremap.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfaltcount.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/dumpContigsFromHeader.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/abba-baba.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfsamplediff.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfflatten.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfdistance.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfqual2info.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfuniqalleles.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfgeno2alleles.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/smoother.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfaddinfo.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/pFst.1 +-- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfclassify.1 -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfcheck.1 -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfgenotypes.1 --- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfglxgt.1 --- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/plotHaps.1 --- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfprimers.1 --- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfallelicprimitives.1 --- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/segmentFst.1 --- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfwave.1 make[1]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1' @@ -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/3522585/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3522585/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/3547587 and its subdirectories -I: Current time: Tue May 7 06:47:56 -12 2024 -I: pbuilder-time-stamp: 1715107676 +I: removing directory /srv/workspace/pbuilder/3522585 and its subdirectories +I: Current time: Tue Jun 10 15:13:19 +14 2025 +I: pbuilder-time-stamp: 1749517999