Diff of the two buildlogs: -- --- b1/build.log 2023-05-02 16:55:18.914479842 +0000 +++ b2/build.log 2023-05-02 17:05:11.036488676 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Jun 3 11:08:34 -12 2024 -I: pbuilder-time-stamp: 1717456114 +I: Current time: Wed May 3 06:55:25 +14 2023 +I: pbuilder-time-stamp: 1683046525 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration @@ -16,7 +16,7 @@ I: copying [./libvcflib_1.0.3+dfsg.orig.tar.xz] I: copying [./libvcflib_1.0.3+dfsg-2.debian.tar.xz] I: Extracting source -gpgv: Signature made Fri Oct 7 02:31:55 2022 -12 +gpgv: Signature made Sat Oct 8 04:31:55 2022 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -35,52 +35,84 @@ dpkg-source: info: applying tests I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/4613/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1421/tmp/hooks/D01_modify_environment starting +debug: Running on codethink12-arm64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 May 3 06:55 /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/1421/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1421/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='arm64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="15" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.15(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=8' - DISTRIBUTION='bookworm' - HOME='/var/lib/jenkins' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=bookworm + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/var/lib/jenkins + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - 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='4613' - PS1='# ' - PS2='> ' + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=1421 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.LJxa088u/pbuilderrc_vZLM --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.LJxa088u/b1 --logfile b1/build.log libvcflib_1.0.3+dfsg-2.dsc' - SUDO_GID='117' - SUDO_UID='110' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - USERNAME='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.16:3128' + 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.LJxa088u/pbuilderrc_D4Fg --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.LJxa088u/b2 --logfile b2/build.log --extrapackages usrmerge libvcflib_1.0.3+dfsg-2.dsc' + SUDO_GID=117 + SUDO_UID=110 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + USERNAME=root + _='I: set' + http_proxy=http://192.168.101.16:3128 I: uname -a - Linux codethink9-arm64 4.15.0-210-generic #221-Ubuntu SMP Tue Apr 18 08:32:48 UTC 2023 aarch64 GNU/Linux + Linux i-capture-the-hostname 4.15.0-210-generic #221-Ubuntu SMP Tue Apr 18 08:32:48 UTC 2023 aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Apr 26 2023 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/4613/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Apr 28 00:25 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/1421/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -213,7 +245,7 @@ Get: 73 http://deb.debian.org/debian bookworm/main arm64 pkgconf-bin arm64 1.8.1-1 [28.9 kB] Get: 74 http://deb.debian.org/debian bookworm/main arm64 pkgconf arm64 1.8.1-1 [25.9 kB] Get: 75 http://deb.debian.org/debian bookworm/main arm64 pkg-config arm64 1.8.1-1 [13.7 kB] -Fetched 35.1 MB in 1s (23.9 MB/s) +Fetched 35.1 MB in 1s (41.8 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libproc2-0:arm64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19616 files and directories currently installed.) @@ -527,8 +559,17 @@ Writing extended state information... Building tag database... -> Finished parsing the build-deps +Reading package lists... +Building dependency tree... +Reading state information... +usrmerge is already the newest version (35). +0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/libvcflib-1.0.3+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../libvcflib_1.0.3+dfsg-2_source.changes +I: user script /srv/workspace/pbuilder/1421/tmp/hooks/A99_set_merged_usr starting +Re-configuring usrmerge... +I: user script /srv/workspace/pbuilder/1421/tmp/hooks/A99_set_merged_usr finished +hostname: Temporary failure in name resolution +I: Running cd /build/libvcflib-1.0.3+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../libvcflib_1.0.3+dfsg-2_source.changes dpkg-buildpackage: info: source package libvcflib dpkg-buildpackage: info: source version 1.0.3+dfsg-2 dpkg-buildpackage: info: source distribution unstable @@ -632,15 +673,15 @@ [ 1%] Building CXX object CMakeFiles/vcflib.dir/src/rnglib.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -Dvcflib_EXPORTS -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -fPIC -MD -MT CMakeFiles/vcflib.dir/src/rnglib.cpp.o -MF CMakeFiles/vcflib.dir/src/rnglib.cpp.o.d -o CMakeFiles/vcflib.dir/src/rnglib.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/rnglib.cpp [ 2%] Building CXX object CMakeFiles/vcflib.dir/src/var.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -Dvcflib_EXPORTS -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -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 /build/libvcflib-1.0.3+dfsg/src/var.cpp -[ 2%] Building CXX object CMakeFiles/vcflib.dir/src/split.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -Dvcflib_EXPORTS -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -fPIC -MD -MT CMakeFiles/vcflib.dir/src/split.cpp.o -MF CMakeFiles/vcflib.dir/src/split.cpp.o.d -o CMakeFiles/vcflib.dir/src/split.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/split.cpp [ 2%] Building CXX object CMakeFiles/vcflib.dir/src/pdflib.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -Dvcflib_EXPORTS -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -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 /build/libvcflib-1.0.3+dfsg/src/var.cpp /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -Dvcflib_EXPORTS -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -fPIC -MD -MT CMakeFiles/vcflib.dir/src/pdflib.cpp.o -MF CMakeFiles/vcflib.dir/src/pdflib.cpp.o.d -o CMakeFiles/vcflib.dir/src/pdflib.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/pdflib.cpp [ 3%] Building CXX object CMakeFiles/vcflib.dir/src/cdflib.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -Dvcflib_EXPORTS -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -fPIC -MD -MT CMakeFiles/vcflib.dir/src/cdflib.cpp.o -MF CMakeFiles/vcflib.dir/src/cdflib.cpp.o.d -o CMakeFiles/vcflib.dir/src/cdflib.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/cdflib.cpp [ 4%] Building C object CMakeFiles/vcflib.dir/filevercmp/filevercmp.c.o /usr/bin/cc -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -Dvcflib_EXPORTS -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/vcflib.dir/filevercmp/filevercmp.c.o -MF CMakeFiles/vcflib.dir/filevercmp/filevercmp.c.o.d -o CMakeFiles/vcflib.dir/filevercmp/filevercmp.c.o -c /build/libvcflib-1.0.3+dfsg/filevercmp/filevercmp.c +[ 4%] Building CXX object CMakeFiles/vcflib.dir/src/split.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -Dvcflib_EXPORTS -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -fPIC -MD -MT CMakeFiles/vcflib.dir/src/split.cpp.o -MF CMakeFiles/vcflib.dir/src/split.cpp.o.d -o CMakeFiles/vcflib.dir/src/split.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/split.cpp In file included from /build/libvcflib-1.0.3+dfsg/src/Variant.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { @@ -664,9 +705,9 @@ make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' [ 5%] Built target vcflib make -f CMakeFiles/vcfecho.dir/build.make CMakeFiles/vcfecho.dir/depend -make -f CMakeFiles/dumpContigsFromHeader.dir/build.make CMakeFiles/dumpContigsFromHeader.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfecho.dir/DependInfo.cmake --color= +make -f CMakeFiles/dumpContigsFromHeader.dir/build.make CMakeFiles/dumpContigsFromHeader.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu/CMakeFiles/dumpContigsFromHeader.dir/DependInfo.cmake --color= make -f CMakeFiles/bFst.dir/build.make CMakeFiles/bFst.dir/depend @@ -679,55 +720,55 @@ make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu/CMakeFiles/hapLrt.dir/DependInfo.cmake --color= make -f CMakeFiles/popStats.dir/build.make CMakeFiles/popStats.dir/depend +make -f CMakeFiles/wcFst.dir/build.make CMakeFiles/wcFst.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu/CMakeFiles/popStats.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]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu/CMakeFiles/wcFst.dir/DependInfo.cmake --color= -make -f CMakeFiles/bFst.dir/build.make CMakeFiles/bFst.dir/build -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -cd /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu/CMakeFiles/iHS.dir/DependInfo.cmake --color= +make -f CMakeFiles/vcfecho.dir/build.make CMakeFiles/vcfecho.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' +make -f CMakeFiles/iHS.dir/build.make CMakeFiles/iHS.dir/depend make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -make -f CMakeFiles/dumpContigsFromHeader.dir/build.make CMakeFiles/dumpContigsFromHeader.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -make -f CMakeFiles/vcfecho.dir/build.make CMakeFiles/vcfecho.dir/build +cd /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu/CMakeFiles/iHS.dir/DependInfo.cmake --color= +make -f CMakeFiles/bFst.dir/build.make CMakeFiles/bFst.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/pVst.dir/build.make CMakeFiles/pVst.dir/build -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -make -f CMakeFiles/hapLrt.dir/build.make CMakeFiles/hapLrt.dir/build +make -f CMakeFiles/dumpContigsFromHeader.dir/build.make CMakeFiles/dumpContigsFromHeader.dir/build +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' +[ 6%] Building CXX object CMakeFiles/vcfecho.dir/src/vcfecho.cpp.o make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfecho.dir/src/vcfecho.cpp.o -MF CMakeFiles/vcfecho.dir/src/vcfecho.cpp.o.d -o CMakeFiles/vcfecho.dir/src/vcfecho.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfecho.cpp make -f CMakeFiles/popStats.dir/build.make CMakeFiles/popStats.dir/build -[ 5%] Building CXX object CMakeFiles/bFst.dir/src/bFst.cpp.o -[ 5%] Building CXX object CMakeFiles/dumpContigsFromHeader.dir/src/dumpContigsFromHeader.cpp.o make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' +make -f CMakeFiles/hapLrt.dir/build.make CMakeFiles/hapLrt.dir/build +[ 6%] Building CXX object CMakeFiles/bFst.dir/src/bFst.cpp.o +[ 6%] Building CXX object CMakeFiles/pVst.dir/src/pVst.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/pVst.dir/src/pVst.cpp.o -MF CMakeFiles/pVst.dir/src/pVst.cpp.o.d -o CMakeFiles/pVst.dir/src/pVst.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/pVst.cpp /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/bFst.dir/src/bFst.cpp.o -MF CMakeFiles/bFst.dir/src/bFst.cpp.o.d -o CMakeFiles/bFst.dir/src/bFst.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/bFst.cpp -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/dumpContigsFromHeader.dir/src/dumpContigsFromHeader.cpp.o -MF CMakeFiles/dumpContigsFromHeader.dir/src/dumpContigsFromHeader.cpp.o.d -o CMakeFiles/dumpContigsFromHeader.dir/src/dumpContigsFromHeader.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/dumpContigsFromHeader.cpp -[ 5%] Building CXX object CMakeFiles/pVst.dir/src/pVst.cpp.o make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/wcFst.dir/build.make CMakeFiles/wcFst.dir/build -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/pVst.dir/src/pVst.cpp.o -MF CMakeFiles/pVst.dir/src/pVst.cpp.o.d -o CMakeFiles/pVst.dir/src/pVst.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/pVst.cpp -[ 6%] Building CXX object CMakeFiles/vcfecho.dir/src/vcfecho.cpp.o make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfecho.dir/src/vcfecho.cpp.o -MF CMakeFiles/vcfecho.dir/src/vcfecho.cpp.o.d -o CMakeFiles/vcfecho.dir/src/vcfecho.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfecho.cpp -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/iHS.dir/build.make CMakeFiles/iHS.dir/build -[ 7%] Building CXX object CMakeFiles/hapLrt.dir/src/hapLrt.cpp.o +[ 7%] Building CXX object CMakeFiles/popStats.dir/src/popStats.cpp.o make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -[ 8%] Building CXX object CMakeFiles/popStats.dir/src/popStats.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/hapLrt.dir/src/hapLrt.cpp.o -MF CMakeFiles/hapLrt.dir/src/hapLrt.cpp.o.d -o CMakeFiles/hapLrt.dir/src/hapLrt.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/hapLrt.cpp /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/popStats.dir/src/popStats.cpp.o -MF CMakeFiles/popStats.dir/src/popStats.cpp.o.d -o CMakeFiles/popStats.dir/src/popStats.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/popStats.cpp -[ 9%] Building CXX object CMakeFiles/wcFst.dir/src/wcFst.cpp.o +[ 7%] Building CXX object CMakeFiles/dumpContigsFromHeader.dir/src/dumpContigsFromHeader.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/dumpContigsFromHeader.dir/src/dumpContigsFromHeader.cpp.o -MF CMakeFiles/dumpContigsFromHeader.dir/src/dumpContigsFromHeader.cpp.o.d -o CMakeFiles/dumpContigsFromHeader.dir/src/dumpContigsFromHeader.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/dumpContigsFromHeader.cpp +[ 8%] Building CXX object CMakeFiles/wcFst.dir/src/wcFst.cpp.o +[ 9%] Building CXX object CMakeFiles/hapLrt.dir/src/hapLrt.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/wcFst.dir/src/wcFst.cpp.o -MF CMakeFiles/wcFst.dir/src/wcFst.cpp.o.d -o CMakeFiles/wcFst.dir/src/wcFst.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/wcFst.cpp [ 10%] Building CXX object CMakeFiles/iHS.dir/src/iHS.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/hapLrt.dir/src/hapLrt.cpp.o -MF CMakeFiles/hapLrt.dir/src/hapLrt.cpp.o.d -o CMakeFiles/hapLrt.dir/src/hapLrt.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/hapLrt.cpp /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/iHS.dir/src/iHS.cpp.o -MF CMakeFiles/iHS.dir/src/iHS.cpp.o.d -o CMakeFiles/iHS.dir/src/iHS.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/iHS.cpp -In file included from /build/libvcflib-1.0.3+dfsg/src/bFst.cpp:10: +In file included from /build/libvcflib-1.0.3+dfsg/src/iHS.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ @@ -743,7 +784,7 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from /build/libvcflib-1.0.3+dfsg/src/hapLrt.cpp:10: +In file included from /build/libvcflib-1.0.3+dfsg/src/popStats.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ @@ -759,7 +800,7 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from /build/libvcflib-1.0.3+dfsg/src/pVst.cpp:10: +In file included from /build/libvcflib-1.0.3+dfsg/src/vcfecho.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ @@ -775,7 +816,7 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from /build/libvcflib-1.0.3+dfsg/src/vcfecho.cpp:10: +In file included from /build/libvcflib-1.0.3+dfsg/src/hapLrt.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ @@ -791,7 +832,7 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from /build/libvcflib-1.0.3+dfsg/src/iHS.cpp:10: +In file included from /build/libvcflib-1.0.3+dfsg/src/pVst.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ @@ -823,7 +864,7 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from /build/libvcflib-1.0.3+dfsg/src/dumpContigsFromHeader.cpp:10: +In file included from /build/libvcflib-1.0.3+dfsg/src/bFst.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ @@ -839,7 +880,7 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from /build/libvcflib-1.0.3+dfsg/src/popStats.cpp:10: +In file included from /build/libvcflib-1.0.3+dfsg/src/dumpContigsFromHeader.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ @@ -863,14 +904,14 @@ make -f CMakeFiles/segmentFst.dir/build.make CMakeFiles/segmentFst.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu/CMakeFiles/segmentFst.dir/DependInfo.cmake --color= +[ 11%] Linking CXX executable vcfecho +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfecho.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/segmentFst.dir/build.make CMakeFiles/segmentFst.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfecho.dir/src/vcfecho.cpp.o -o vcfecho -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp [ 11%] Building CXX object CMakeFiles/segmentFst.dir/src/segmentFst.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/segmentFst.dir/src/segmentFst.cpp.o -MF CMakeFiles/segmentFst.dir/src/segmentFst.cpp.o.d -o CMakeFiles/segmentFst.dir/src/segmentFst.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/segmentFst.cpp -[ 11%] 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/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfecho.dir/src/vcfecho.cpp.o -o vcfecho -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' [ 11%] Built target vcfecho make -f CMakeFiles/segmentIhs.dir/build.make CMakeFiles/segmentIhs.dir/depend @@ -910,6 +951,9 @@ [ 15%] Linking CXX executable popStats /usr/bin/cmake -E cmake_link_script CMakeFiles/popStats.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/popStats.dir/src/popStats.cpp.o -o popStats -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 16%] Linking CXX executable bFst +/usr/bin/cmake -E cmake_link_script CMakeFiles/bFst.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/bFst.dir/src/bFst.cpp.o -o bFst -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp In file included from /build/libvcflib-1.0.3+dfsg/src/genotypeSummary.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { @@ -927,31 +971,29 @@ 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -[ 15%] Built target popStats +[ 16%] Built target popStats make -f CMakeFiles/pFst.dir/build.make CMakeFiles/pFst.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu/CMakeFiles/pFst.dir/DependInfo.cmake --color= -[ 16%] Linking CXX executable wcFst -/usr/bin/cmake -E cmake_link_script CMakeFiles/wcFst.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/wcFst.dir/src/wcFst.cpp.o -o wcFst -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/pFst.dir/build.make CMakeFiles/pFst.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' [ 16%] Building CXX object CMakeFiles/pFst.dir/src/pFst.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/pFst.dir/src/pFst.cpp.o -MF CMakeFiles/pFst.dir/src/pFst.cpp.o.d -o CMakeFiles/pFst.dir/src/pFst.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/pFst.cpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -[ 16%] Built target wcFst +[ 16%] Built target bFst make -f CMakeFiles/smoother.dir/build.make CMakeFiles/smoother.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu/CMakeFiles/smoother.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/smoother.dir/build.make CMakeFiles/smoother.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' +[ 17%] Building CXX object CMakeFiles/smoother.dir/src/smoother.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/smoother.dir/src/smoother.cpp.o -MF CMakeFiles/smoother.dir/src/smoother.cpp.o.d -o CMakeFiles/smoother.dir/src/smoother.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/smoother.cpp In file included from /build/libvcflib-1.0.3+dfsg/src/sequenceDiversity.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ -[ 17%] Building CXX object CMakeFiles/smoother.dir/src/smoother.cpp.o In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: @@ -964,33 +1006,45 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/smoother.dir/src/smoother.cpp.o -MF CMakeFiles/smoother.dir/src/smoother.cpp.o.d -o CMakeFiles/smoother.dir/src/smoother.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/smoother.cpp -[ 18%] Linking CXX executable bFst -/usr/bin/cmake -E cmake_link_script CMakeFiles/bFst.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/bFst.dir/src/bFst.cpp.o -o bFst -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 18%] Linking CXX executable wcFst +/usr/bin/cmake -E cmake_link_script CMakeFiles/wcFst.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/wcFst.dir/src/wcFst.cpp.o -o wcFst -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 19%] Linking CXX executable pVst +/usr/bin/cmake -E cmake_link_script CMakeFiles/pVst.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/pVst.dir/src/pVst.cpp.o -o pVst -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -[ 18%] Built target bFst +[ 19%] Built target wcFst make -f CMakeFiles/vcfld.dir/build.make CMakeFiles/vcfld.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfld.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/vcfld.dir/build.make CMakeFiles/vcfld.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -[ 19%] Building CXX object CMakeFiles/vcfld.dir/src/vcfld.cpp.o +[ 19%] Linking CXX executable iHS +[ 20%] Building CXX object CMakeFiles/vcfld.dir/src/vcfld.cpp.o +/usr/bin/cmake -E cmake_link_script CMakeFiles/iHS.dir/link.txt --verbose=1 /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfld.dir/src/vcfld.cpp.o -MF CMakeFiles/vcfld.dir/src/vcfld.cpp.o.d -o CMakeFiles/vcfld.dir/src/vcfld.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfld.cpp -[ 20%] Linking CXX executable pVst -/usr/bin/cmake -E cmake_link_script CMakeFiles/pVst.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/pVst.dir/src/pVst.cpp.o -o pVst -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/iHS.dir/src/iHS.cpp.o -o iHS -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' [ 20%] Built target pVst make -f CMakeFiles/plotHaps.dir/build.make CMakeFiles/plotHaps.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu/CMakeFiles/plotHaps.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/plotHaps.dir/build.make CMakeFiles/plotHaps.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' +[ 20%] Built target iHS +make -f CMakeFiles/abba-baba.dir/build.make CMakeFiles/abba-baba.dir/depend +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' +cd /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu/CMakeFiles/abba-baba.dir/DependInfo.cmake --color= [ 21%] Building CXX object CMakeFiles/plotHaps.dir/src/plotHaps.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/plotHaps.dir/src/plotHaps.cpp.o -MF CMakeFiles/plotHaps.dir/src/plotHaps.cpp.o.d -o CMakeFiles/plotHaps.dir/src/plotHaps.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/plotHaps.cpp +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' +make -f CMakeFiles/abba-baba.dir/build.make CMakeFiles/abba-baba.dir/build +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' +[ 21%] Building CXX object CMakeFiles/abba-baba.dir/src/abba-baba.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/abba-baba.dir/src/abba-baba.cpp.o -MF CMakeFiles/abba-baba.dir/src/abba-baba.cpp.o.d -o CMakeFiles/abba-baba.dir/src/abba-baba.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/abba-baba.cpp In file included from /build/libvcflib-1.0.3+dfsg/src/pFst.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { @@ -1007,32 +1061,6 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 21%] Linking CXX executable iHS -/usr/bin/cmake -E cmake_link_script CMakeFiles/iHS.dir/link.txt --verbose=1 -[ 21%] Linking CXX executable hapLrt -/usr/bin/cmake -E cmake_link_script CMakeFiles/hapLrt.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/iHS.dir/src/iHS.cpp.o -o iHS -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hapLrt.dir/src/hapLrt.cpp.o -o hapLrt -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -[ 21%] Built target iHS -make -f CMakeFiles/abba-baba.dir/build.make CMakeFiles/abba-baba.dir/depend -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -cd /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu/CMakeFiles/abba-baba.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -make -f CMakeFiles/abba-baba.dir/build.make CMakeFiles/abba-baba.dir/build -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -[ 21%] Building CXX object CMakeFiles/abba-baba.dir/src/abba-baba.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/abba-baba.dir/src/abba-baba.cpp.o -MF CMakeFiles/abba-baba.dir/src/abba-baba.cpp.o.d -o CMakeFiles/abba-baba.dir/src/abba-baba.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/abba-baba.cpp -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -[ 21%] Built target hapLrt -make -f CMakeFiles/permuteGPAT++.dir/build.make CMakeFiles/permuteGPAT++.dir/depend -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -cd /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu/CMakeFiles/permuteGPAT++.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -make -f CMakeFiles/permuteGPAT++.dir/build.make CMakeFiles/permuteGPAT++.dir/build -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -[ 22%] Building CXX object CMakeFiles/permuteGPAT++.dir/src/permuteGPAT++.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/permuteGPAT++.dir/src/permuteGPAT++.cpp.o -MF CMakeFiles/permuteGPAT++.dir/src/permuteGPAT++.cpp.o.d -o CMakeFiles/permuteGPAT++.dir/src/permuteGPAT++.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/permuteGPAT++.cpp In file included from /build/libvcflib-1.0.3+dfsg/src/vcfld.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { @@ -1049,6 +1077,19 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +[ 21%] Linking CXX executable hapLrt +/usr/bin/cmake -E cmake_link_script CMakeFiles/hapLrt.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hapLrt.dir/src/hapLrt.cpp.o -o hapLrt -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' +[ 21%] Built target hapLrt +make -f CMakeFiles/permuteGPAT++.dir/build.make CMakeFiles/permuteGPAT++.dir/depend +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' +cd /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu/CMakeFiles/permuteGPAT++.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' +make -f CMakeFiles/permuteGPAT++.dir/build.make CMakeFiles/permuteGPAT++.dir/build +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' +[ 22%] Building CXX object CMakeFiles/permuteGPAT++.dir/src/permuteGPAT++.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/permuteGPAT++.dir/src/permuteGPAT++.cpp.o -MF CMakeFiles/permuteGPAT++.dir/src/permuteGPAT++.cpp.o.d -o CMakeFiles/permuteGPAT++.dir/src/permuteGPAT++.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/permuteGPAT++.cpp In file included from /build/libvcflib-1.0.3+dfsg/src/plotHaps.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { @@ -1081,11 +1122,11 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 22%] 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/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/permuteGPAT++.dir/src/permuteGPAT++.cpp.o -o permuteGPAT++ -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 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/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/smoother.dir/src/smoother.cpp.o -o smoother -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -[ 22%] Built target permuteGPAT++ +[ 22%] Built target smoother make -f CMakeFiles/permuteSmooth.dir/build.make CMakeFiles/permuteSmooth.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu/CMakeFiles/permuteSmooth.dir/DependInfo.cmake --color= @@ -1094,11 +1135,11 @@ make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' [ 23%] Building CXX object CMakeFiles/permuteSmooth.dir/src/permuteSmooth.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/permuteSmooth.dir/src/permuteSmooth.cpp.o -MF CMakeFiles/permuteSmooth.dir/src/permuteSmooth.cpp.o.d -o CMakeFiles/permuteSmooth.dir/src/permuteSmooth.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/permuteSmooth.cpp -[ 23%] 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/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/smoother.dir/src/smoother.cpp.o -o smoother -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 23%] 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/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/permuteGPAT++.dir/src/permuteGPAT++.cpp.o -o permuteGPAT++ -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -[ 23%] Built target smoother +[ 23%] Built target permuteGPAT++ make -f CMakeFiles/normalize-iHS.dir/build.make CMakeFiles/normalize-iHS.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu/CMakeFiles/normalize-iHS.dir/DependInfo.cmake --color= @@ -1123,72 +1164,56 @@ [ 25%] 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/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic "CMakeFiles/normalize-iHS.dir/src/normalize-iHS.cpp.o" -o normalize-iHS -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -[ 26%] Linking CXX executable pFst -/usr/bin/cmake -E cmake_link_script CMakeFiles/pFst.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/pFst.dir/src/pFst.cpp.o -o pFst -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -[ 26%] Built target normalize-iHS +[ 25%] Built target normalize-iHS make -f CMakeFiles/vcfaltcount.dir/build.make CMakeFiles/vcfaltcount.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfaltcount.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/vcfaltcount.dir/build.make CMakeFiles/vcfaltcount.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -[ 27%] Building CXX object CMakeFiles/vcfaltcount.dir/src/vcfaltcount.cpp.o +[ 26%] Building CXX object CMakeFiles/vcfaltcount.dir/src/vcfaltcount.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfaltcount.dir/src/vcfaltcount.cpp.o -MF CMakeFiles/vcfaltcount.dir/src/vcfaltcount.cpp.o.d -o CMakeFiles/vcfaltcount.dir/src/vcfaltcount.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfaltcount.cpp +[ 26%] 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/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/permuteSmooth.dir/src/permuteSmooth.cpp.o -o permuteSmooth -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -[ 27%] Built target pFst +[ 26%] Built target permuteSmooth make -f CMakeFiles/vcfhetcount.dir/build.make CMakeFiles/vcfhetcount.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfhetcount.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/vcfhetcount.dir/build.make CMakeFiles/vcfhetcount.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -[ 28%] Building CXX object CMakeFiles/vcfhetcount.dir/src/vcfhetcount.cpp.o +[ 27%] Building CXX object CMakeFiles/vcfhetcount.dir/src/vcfhetcount.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfhetcount.dir/src/vcfhetcount.cpp.o -MF CMakeFiles/vcfhetcount.dir/src/vcfhetcount.cpp.o.d -o CMakeFiles/vcfhetcount.dir/src/vcfhetcount.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfhetcount.cpp -[ 28%] 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/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/permuteSmooth.dir/src/permuteSmooth.cpp.o -o permuteSmooth -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 28%] Linking CXX executable sequenceDiversity +/usr/bin/cmake -E cmake_link_script CMakeFiles/sequenceDiversity.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/sequenceDiversity.dir/src/sequenceDiversity.cpp.o -o sequenceDiversity -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 29%] Linking CXX executable pFst +/usr/bin/cmake -E cmake_link_script CMakeFiles/pFst.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/pFst.dir/src/pFst.cpp.o -o pFst -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -[ 28%] Built target permuteSmooth +[ 29%] Built target sequenceDiversity make -f CMakeFiles/vcfhethomratio.dir/build.make CMakeFiles/vcfhethomratio.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfhethomratio.dir/DependInfo.cmake --color= -[ 29%] Linking CXX executable sequenceDiversity -/usr/bin/cmake -E cmake_link_script CMakeFiles/sequenceDiversity.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/sequenceDiversity.dir/src/sequenceDiversity.cpp.o -o sequenceDiversity -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/vcfhethomratio.dir/build.make CMakeFiles/vcfhethomratio.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' [ 30%] Building CXX object CMakeFiles/vcfhethomratio.dir/src/vcfhethomratio.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfhethomratio.dir/src/vcfhethomratio.cpp.o -MF CMakeFiles/vcfhethomratio.dir/src/vcfhethomratio.cpp.o.d -o CMakeFiles/vcfhethomratio.dir/src/vcfhethomratio.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfhethomratio.cpp -In file included from /build/libvcflib-1.0.3+dfsg/src/meltEHH.cpp:10: -/build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 651 | struct stringcasecmp : binary_function { - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/bits/refwrap.h:39, - from /usr/include/c++/12/vector:66, - from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: -/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -/build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 652 | struct charcasecmp : public std::binary_function { - | ^~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -[ 30%] Built target sequenceDiversity +[ 30%] Built target pFst make -f CMakeFiles/vcffilter.dir/build.make CMakeFiles/vcffilter.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcffilter.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/vcffilter.dir/build.make CMakeFiles/vcffilter.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -[ 31%] Building CXX object CMakeFiles/vcffilter.dir/src/vcffilter.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcffilter.dir/src/vcffilter.cpp.o -MF CMakeFiles/vcffilter.dir/src/vcffilter.cpp.o.d -o CMakeFiles/vcffilter.dir/src/vcffilter.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcffilter.cpp -In file included from /build/libvcflib-1.0.3+dfsg/src/vcfhetcount.cpp:10: +[ 31%] Linking CXX executable abba-baba +/usr/bin/cmake -E cmake_link_script CMakeFiles/abba-baba.dir/link.txt --verbose=1 +In file included from /build/libvcflib-1.0.3+dfsg/src/meltEHH.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ @@ -1204,8 +1229,8 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 32%] Linking CXX executable abba-baba -/usr/bin/cmake -E cmake_link_script CMakeFiles/abba-baba.dir/link.txt --verbose=1 +[ 32%] Building CXX object CMakeFiles/vcffilter.dir/src/vcffilter.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcffilter.dir/src/vcffilter.cpp.o -MF CMakeFiles/vcffilter.dir/src/vcffilter.cpp.o.d -o CMakeFiles/vcffilter.dir/src/vcffilter.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcffilter.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic "CMakeFiles/abba-baba.dir/src/abba-baba.cpp.o" -o abba-baba -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' [ 32%] Built target abba-baba @@ -1215,6 +1240,8 @@ make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/vcf2tsv.dir/build.make CMakeFiles/vcf2tsv.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' +[ 33%] Building CXX object CMakeFiles/vcf2tsv.dir/src/vcf2tsv.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcf2tsv.dir/src/vcf2tsv.cpp.o -MF CMakeFiles/vcf2tsv.dir/src/vcf2tsv.cpp.o.d -o CMakeFiles/vcf2tsv.dir/src/vcf2tsv.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcf2tsv.cpp In file included from /build/libvcflib-1.0.3+dfsg/src/vcfaltcount.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { @@ -1231,9 +1258,7 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 33%] Building CXX object CMakeFiles/vcf2tsv.dir/src/vcf2tsv.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcf2tsv.dir/src/vcf2tsv.cpp.o -MF CMakeFiles/vcf2tsv.dir/src/vcf2tsv.cpp.o.d -o CMakeFiles/vcf2tsv.dir/src/vcf2tsv.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcf2tsv.cpp -In file included from /build/libvcflib-1.0.3+dfsg/src/vcffilter.cpp:10: +In file included from /build/libvcflib-1.0.3+dfsg/src/vcfhetcount.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ @@ -1268,29 +1293,32 @@ [ 33%] Linking CXX executable plotHaps /usr/bin/cmake -E cmake_link_script CMakeFiles/plotHaps.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/plotHaps.dir/src/plotHaps.cpp.o -o plotHaps -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +In file included from /build/libvcflib-1.0.3+dfsg/src/vcffilter.cpp:10: +/build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 651 | struct stringcasecmp : binary_function { + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/bits/refwrap.h:39, + from /usr/include/c++/12/vector:66, + from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: +/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +/build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 652 | struct charcasecmp : public std::binary_function { + | ^~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' [ 33%] Built target plotHaps make -f CMakeFiles/vcfgenotypes.dir/build.make CMakeFiles/vcfgenotypes.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfgenotypes.dir/DependInfo.cmake --color= -[ 34%] Linking CXX executable vcfld -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfld.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/vcfgenotypes.dir/build.make CMakeFiles/vcfgenotypes.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfld.dir/src/vcfld.cpp.o -o vcfld -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -[ 34%] Building CXX object CMakeFiles/vcfgenotypes.dir/src/vcfgenotypes.cpp.o +[ 33%] Building CXX object CMakeFiles/vcfgenotypes.dir/src/vcfgenotypes.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -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/libvcflib-1.0.3+dfsg/src/vcfgenotypes.cpp -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -[ 34%] Built target vcfld -make -f CMakeFiles/vcfannotategenotypes.dir/build.make CMakeFiles/vcfannotategenotypes.dir/depend -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -cd /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfannotategenotypes.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -make -f CMakeFiles/vcfannotategenotypes.dir/build.make CMakeFiles/vcfannotategenotypes.dir/build -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -[ 35%] Building CXX object CMakeFiles/vcfannotategenotypes.dir/src/vcfannotategenotypes.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -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/libvcflib-1.0.3+dfsg/src/vcfannotategenotypes.cpp In file included from /build/libvcflib-1.0.3+dfsg/src/vcf2tsv.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { @@ -1307,6 +1335,19 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +[ 34%] Linking CXX executable vcfld +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfld.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfld.dir/src/vcfld.cpp.o -o vcfld -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' +[ 34%] Built target vcfld +make -f CMakeFiles/vcfannotategenotypes.dir/build.make CMakeFiles/vcfannotategenotypes.dir/depend +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' +cd /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfannotategenotypes.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' +make -f CMakeFiles/vcfannotategenotypes.dir/build.make CMakeFiles/vcfannotategenotypes.dir/build +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' +[ 35%] Building CXX object CMakeFiles/vcfannotategenotypes.dir/src/vcfannotategenotypes.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -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/libvcflib-1.0.3+dfsg/src/vcfannotategenotypes.cpp In file included from /build/libvcflib-1.0.3+dfsg/src/vcfgenotypes.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { @@ -1323,6 +1364,9 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +[ 35%] Linking CXX executable vcfaltcount +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfaltcount.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfaltcount.dir/src/vcfaltcount.cpp.o -o vcfaltcount -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp In file included from /build/libvcflib-1.0.3+dfsg/src/vcfannotategenotypes.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { @@ -1339,12 +1383,6 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 35%] Linking CXX executable vcfaltcount -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfaltcount.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfaltcount.dir/src/vcfaltcount.cpp.o -o vcfaltcount -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -[ 35%] Linking CXX executable vcfhetcount -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfhetcount.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfhetcount.dir/src/vcfhetcount.cpp.o -o vcfhetcount -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' [ 35%] Built target vcfaltcount make -f CMakeFiles/vcfcommonsamples.dir/build.make CMakeFiles/vcfcommonsamples.dir/depend @@ -1355,6 +1393,9 @@ make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' [ 36%] Building CXX object CMakeFiles/vcfcommonsamples.dir/src/vcfcommonsamples.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -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/libvcflib-1.0.3+dfsg/src/vcfcommonsamples.cpp +[ 36%] Linking CXX executable vcfhetcount +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfhetcount.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfhetcount.dir/src/vcfhetcount.cpp.o -o vcfhetcount -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' [ 36%] Built target vcfhetcount make -f CMakeFiles/vcfremovesamples.dir/build.make CMakeFiles/vcfremovesamples.dir/depend @@ -1370,6 +1411,14 @@ /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfhethomratio.dir/src/vcfhethomratio.cpp.o -o vcfhethomratio -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' [ 36%] Built target vcfhethomratio +make -f CMakeFiles/vcfkeepsamples.dir/build.make CMakeFiles/vcfkeepsamples.dir/depend +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' +cd /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfkeepsamples.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' +make -f CMakeFiles/vcfkeepsamples.dir/build.make CMakeFiles/vcfkeepsamples.dir/build +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' +[ 37%] Building CXX object CMakeFiles/vcfkeepsamples.dir/src/vcfkeepsamples.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfkeepsamples.dir/src/vcfkeepsamples.cpp.o -MF CMakeFiles/vcfkeepsamples.dir/src/vcfkeepsamples.cpp.o.d -o CMakeFiles/vcfkeepsamples.dir/src/vcfkeepsamples.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfkeepsamples.cpp In file included from /build/libvcflib-1.0.3+dfsg/src/vcfcommonsamples.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { @@ -1386,14 +1435,8 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -make -f CMakeFiles/vcfkeepsamples.dir/build.make CMakeFiles/vcfkeepsamples.dir/depend -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -cd /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfkeepsamples.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -make -f CMakeFiles/vcfkeepsamples.dir/build.make CMakeFiles/vcfkeepsamples.dir/build -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -[ 37%] Building CXX object CMakeFiles/vcfkeepsamples.dir/src/vcfkeepsamples.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfkeepsamples.dir/src/vcfkeepsamples.cpp.o -MF CMakeFiles/vcfkeepsamples.dir/src/vcfkeepsamples.cpp.o.d -o CMakeFiles/vcfkeepsamples.dir/src/vcfkeepsamples.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfkeepsamples.cpp +[ 38%] Linking CXX executable vcf2tsv +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcf2tsv.dir/link.txt --verbose=1 In file included from /build/libvcflib-1.0.3+dfsg/src/vcfremovesamples.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { @@ -1410,10 +1453,15 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 38%] 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/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcf2tsv.dir/src/vcf2tsv.cpp.o -o vcf2tsv -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' +[ 38%] Built target vcf2tsv +make -f CMakeFiles/vcfsamplenames.dir/build.make CMakeFiles/vcfsamplenames.dir/depend +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' +cd /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfsamplenames.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' +make -f CMakeFiles/vcfsamplenames.dir/build.make CMakeFiles/vcfsamplenames.dir/build +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' In file included from /build/libvcflib-1.0.3+dfsg/src/vcfkeepsamples.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { @@ -1430,13 +1478,6 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 38%] Built target vcf2tsv -make -f CMakeFiles/vcfsamplenames.dir/build.make CMakeFiles/vcfsamplenames.dir/depend -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -cd /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfsamplenames.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -make -f CMakeFiles/vcfsamplenames.dir/build.make CMakeFiles/vcfsamplenames.dir/build -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' [ 39%] Building CXX object CMakeFiles/vcfsamplenames.dir/src/vcfsamplenames.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -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/libvcflib-1.0.3+dfsg/src/vcfsamplenames.cpp [ 40%] Linking CXX executable vcfgenotypes @@ -1447,53 +1488,14 @@ make -f CMakeFiles/vcfgenotypecompare.dir/build.make CMakeFiles/vcfgenotypecompare.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfgenotypecompare.dir/DependInfo.cmake --color= -[ 41%] Linking CXX executable meltEHH -/usr/bin/cmake -E cmake_link_script CMakeFiles/meltEHH.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/vcfgenotypecompare.dir/build.make CMakeFiles/vcfgenotypecompare.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/meltEHH.dir/src/meltEHH.cpp.o -o meltEHH -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -[ 41%] Building CXX object CMakeFiles/vcfgenotypecompare.dir/src/vcfgenotypecompare.cpp.o +[ 40%] Building CXX object CMakeFiles/vcfgenotypecompare.dir/src/vcfgenotypecompare.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -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/libvcflib-1.0.3+dfsg/src/vcfgenotypecompare.cpp -[ 42%] Linking CXX executable vcfcommonsamples -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfcommonsamples.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfcommonsamples.dir/src/vcfcommonsamples.cpp.o -o vcfcommonsamples -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -[ 42%] Built target meltEHH -make -f CMakeFiles/vcffixup.dir/build.make CMakeFiles/vcffixup.dir/depend -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -cd /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcffixup.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -make -f CMakeFiles/vcffixup.dir/build.make CMakeFiles/vcffixup.dir/build -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -[ 42%] Building CXX object CMakeFiles/vcffixup.dir/src/vcffixup.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -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/libvcflib-1.0.3+dfsg/src/vcffixup.cpp -[ 42%] Built target vcfcommonsamples -make -f CMakeFiles/vcfclassify.dir/build.make CMakeFiles/vcfclassify.dir/depend -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -cd /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfclassify.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -make -f CMakeFiles/vcfclassify.dir/build.make CMakeFiles/vcfclassify.dir/build -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -[ 43%] Building CXX object CMakeFiles/vcfclassify.dir/src/vcfclassify.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -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/libvcflib-1.0.3+dfsg/src/vcfclassify.cpp -[ 44%] Linking CXX executable vcffilter -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcffilter.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcffilter.dir/src/vcffilter.cpp.o -o vcffilter -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -[ 44%] Built target vcffilter -make -f CMakeFiles/vcfsamplediff.dir/build.make CMakeFiles/vcfsamplediff.dir/depend -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -cd /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfsamplediff.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -make -f CMakeFiles/vcfsamplediff.dir/build.make CMakeFiles/vcfsamplediff.dir/build -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -[ 45%] Building CXX object CMakeFiles/vcfsamplediff.dir/src/vcfsamplediff.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -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/libvcflib-1.0.3+dfsg/src/vcfsamplediff.cpp -[ 46%] 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/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfremovesamples.dir/src/vcfremovesamples.cpp.o -o vcfremovesamples -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 41%] 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/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/meltEHH.dir/src/meltEHH.cpp.o -o meltEHH -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp In file included from /build/libvcflib-1.0.3+dfsg/src/vcfsamplenames.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { @@ -1510,6 +1512,19 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' +[ 41%] Built target meltEHH +make -f CMakeFiles/vcffixup.dir/build.make CMakeFiles/vcffixup.dir/depend +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' +cd /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcffixup.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' +make -f CMakeFiles/vcffixup.dir/build.make CMakeFiles/vcffixup.dir/build +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' +[ 41%] Building CXX object CMakeFiles/vcffixup.dir/src/vcffixup.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -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/libvcflib-1.0.3+dfsg/src/vcffixup.cpp +[ 42%] Linking CXX executable vcfcommonsamples +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfcommonsamples.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfcommonsamples.dir/src/vcfcommonsamples.cpp.o -o vcfcommonsamples -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp In file included from /build/libvcflib-1.0.3+dfsg/src/vcfgenotypecompare.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { @@ -1527,7 +1542,36 @@ 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -[ 46%] Built target vcfremovesamples +[ 42%] Built target vcfcommonsamples +make -f CMakeFiles/vcfclassify.dir/build.make CMakeFiles/vcfclassify.dir/depend +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' +cd /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfclassify.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' +make -f CMakeFiles/vcfclassify.dir/build.make CMakeFiles/vcfclassify.dir/build +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' +[ 43%] Building CXX object CMakeFiles/vcfclassify.dir/src/vcfclassify.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -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/libvcflib-1.0.3+dfsg/src/vcfclassify.cpp +[ 43%] Linking CXX executable vcfkeepsamples +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfkeepsamples.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfkeepsamples.dir/src/vcfkeepsamples.cpp.o -o vcfkeepsamples -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' +[ 43%] Built target vcfkeepsamples +make -f CMakeFiles/vcfsamplediff.dir/build.make CMakeFiles/vcfsamplediff.dir/depend +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' +cd /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfsamplediff.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' +make -f CMakeFiles/vcfsamplediff.dir/build.make CMakeFiles/vcfsamplediff.dir/build +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' +[ 44%] Linking CXX executable vcffilter +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcffilter.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcffilter.dir/src/vcffilter.cpp.o -o vcffilter -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 45%] Building CXX object CMakeFiles/vcfsamplediff.dir/src/vcfsamplediff.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -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/libvcflib-1.0.3+dfsg/src/vcfsamplediff.cpp +[ 46%] Linking CXX executable vcfsamplenames +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfsamplenames.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfsamplenames.dir/src/vcfsamplenames.cpp.o -o vcfsamplenames -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' +[ 46%] Built target vcffilter make -f CMakeFiles/vcfremoveaberrantgenotypes.dir/build.make CMakeFiles/vcfremoveaberrantgenotypes.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfremoveaberrantgenotypes.dir/DependInfo.cmake --color= @@ -1536,9 +1580,19 @@ make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' [ 46%] Building CXX object CMakeFiles/vcfremoveaberrantgenotypes.dir/src/vcfremoveaberrantgenotypes.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -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/libvcflib-1.0.3+dfsg/src/vcfremoveaberrantgenotypes.cpp -[ 46%] Linking CXX executable vcfkeepsamples -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfkeepsamples.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfkeepsamples.dir/src/vcfkeepsamples.cpp.o -o vcfkeepsamples -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' +[ 46%] Built target vcfsamplenames +make -f CMakeFiles/vcfrandom.dir/build.make CMakeFiles/vcfrandom.dir/depend +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' +cd /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfrandom.dir/DependInfo.cmake --color= +[ 47%] Linking CXX executable vcfremovesamples +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfremovesamples.dir/link.txt --verbose=1 +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' +make -f CMakeFiles/vcfrandom.dir/build.make CMakeFiles/vcfrandom.dir/build +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' +[ 48%] Building CXX object CMakeFiles/vcfrandom.dir/src/vcfrandom.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -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/libvcflib-1.0.3+dfsg/src/vcfrandom.cpp +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfremovesamples.dir/src/vcfremovesamples.cpp.o -o vcfremovesamples -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp In file included from /build/libvcflib-1.0.3+dfsg/src/vcffixup.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { @@ -1555,6 +1609,16 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' +[ 48%] Built target vcfremovesamples +make -f CMakeFiles/vcfparsealts.dir/build.make CMakeFiles/vcfparsealts.dir/depend +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' +cd /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfparsealts.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' +make -f CMakeFiles/vcfparsealts.dir/build.make CMakeFiles/vcfparsealts.dir/build +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' +[ 48%] Building CXX object CMakeFiles/vcfparsealts.dir/src/vcfparsealts.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -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/libvcflib-1.0.3+dfsg/src/vcfparsealts.cpp In file included from /build/libvcflib-1.0.3+dfsg/src/vcfclassify.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { @@ -1571,16 +1635,6 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -[ 46%] Built target vcfkeepsamples -make -f CMakeFiles/vcfrandom.dir/build.make CMakeFiles/vcfrandom.dir/depend -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -cd /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfrandom.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -make -f CMakeFiles/vcfrandom.dir/build.make CMakeFiles/vcfrandom.dir/build -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -[ 47%] Building CXX object CMakeFiles/vcfrandom.dir/src/vcfrandom.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -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/libvcflib-1.0.3+dfsg/src/vcfrandom.cpp In file included from /build/libvcflib-1.0.3+dfsg/src/vcfsamplediff.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { @@ -1597,9 +1651,6 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 48%] Linking CXX executable vcfsamplenames -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfsamplenames.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfsamplenames.dir/src/vcfsamplenames.cpp.o -o vcfsamplenames -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp In file included from /build/libvcflib-1.0.3+dfsg/src/vcfremoveaberrantgenotypes.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { @@ -1616,16 +1667,6 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -[ 48%] Built target vcfsamplenames -make -f CMakeFiles/vcfparsealts.dir/build.make CMakeFiles/vcfparsealts.dir/depend -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -cd /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfparsealts.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -make -f CMakeFiles/vcfparsealts.dir/build.make CMakeFiles/vcfparsealts.dir/build -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -[ 48%] Building CXX object CMakeFiles/vcfparsealts.dir/src/vcfparsealts.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -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/libvcflib-1.0.3+dfsg/src/vcfparsealts.cpp In file included from /build/libvcflib-1.0.3+dfsg/src/vcfrandom.cpp:13: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { @@ -1675,53 +1716,37 @@ make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' [ 48%] Building CXX object CMakeFiles/vcfstats.dir/src/vcfstats.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -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/libvcflib-1.0.3+dfsg/src/vcfstats.cpp -[ 49%] Linking CXX executable vcfremoveaberrantgenotypes -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfremoveaberrantgenotypes.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfremoveaberrantgenotypes.dir/src/vcfremoveaberrantgenotypes.cpp.o -o vcfremoveaberrantgenotypes -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -[ 50%] Linking CXX executable vcffixup -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcffixup.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcffixup.dir/src/vcffixup.cpp.o -o vcffixup -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -[ 51%] Linking CXX executable vcfparsealts +[ 49%] Linking CXX executable vcfparsealts /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfparsealts.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfparsealts.dir/src/vcfparsealts.cpp.o -o vcfparsealts -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -In file included from /build/libvcflib-1.0.3+dfsg/src/vcfstats.cpp:10: -/build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 651 | struct stringcasecmp : binary_function { - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/bits/refwrap.h:39, - from /usr/include/c++/12/vector:66, - from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: -/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -/build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 652 | struct charcasecmp : public std::binary_function { - | ^~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -[ 51%] Built target vcfremoveaberrantgenotypes +[ 49%] Built target vcfparsealts make -f CMakeFiles/vcfflatten.dir/build.make CMakeFiles/vcfflatten.dir/depend -[ 51%] Built target vcffixup make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfflatten.dir/DependInfo.cmake --color= -make -f CMakeFiles/vcfprimers.dir/build.make CMakeFiles/vcfprimers.dir/depend -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -cd /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfprimers.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/vcfflatten.dir/build.make CMakeFiles/vcfflatten.dir/build +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' +[ 49%] Building CXX object CMakeFiles/vcfflatten.dir/src/vcfflatten.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -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/libvcflib-1.0.3+dfsg/src/vcfflatten.cpp +[ 50%] Linking CXX executable vcffixup +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcffixup.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcffixup.dir/src/vcffixup.cpp.o -o vcffixup -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 51%] Linking CXX executable vcfremoveaberrantgenotypes +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfremoveaberrantgenotypes.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfremoveaberrantgenotypes.dir/src/vcfremoveaberrantgenotypes.cpp.o -o vcfremoveaberrantgenotypes -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 51%] Built target vcffixup +make -f CMakeFiles/vcfprimers.dir/build.make CMakeFiles/vcfprimers.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' +cd /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfprimers.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/vcfprimers.dir/build.make CMakeFiles/vcfprimers.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -[ 51%] Building CXX object CMakeFiles/vcfflatten.dir/src/vcfflatten.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -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/libvcflib-1.0.3+dfsg/src/vcfflatten.cpp [ 52%] Building CXX object CMakeFiles/vcfprimers.dir/src/vcfprimers.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -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/libvcflib-1.0.3+dfsg/src/vcfprimers.cpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -[ 52%] Built target vcfparsealts +[ 52%] Built target vcfremoveaberrantgenotypes make -f CMakeFiles/vcfnumalt.dir/build.make CMakeFiles/vcfnumalt.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfnumalt.dir/DependInfo.cmake --color= @@ -1733,27 +1758,30 @@ [ 52%] 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/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfsamplediff.dir/src/vcfsamplediff.cpp.o -o vcfsamplediff -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -[ 52%] Linking CXX executable vcfrandom -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfrandom.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfrandom.dir/src/vcfrandom.cpp.o -o vcfrandom -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' +In file included from /build/libvcflib-1.0.3+dfsg/src/vcfstats.cpp:10: +/build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 651 | struct stringcasecmp : binary_function { + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/bits/refwrap.h:39, + from /usr/include/c++/12/vector:66, + from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: +/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +/build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 652 | struct charcasecmp : public std::binary_function { + | ^~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -[ 52%] Built target vcfrandom +[ 52%] Built target vcfsamplediff make -f CMakeFiles/vcfcleancomplex.dir/build.make CMakeFiles/vcfcleancomplex.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfcleancomplex.dir/DependInfo.cmake --color= -[ 52%] Built target vcfsamplediff -make -f CMakeFiles/vcfintersect.dir/build.make CMakeFiles/vcfintersect.dir/depend -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -cd /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfintersect.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -make -f CMakeFiles/vcfintersect.dir/build.make CMakeFiles/vcfintersect.dir/build -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/vcfcleancomplex.dir/build.make CMakeFiles/vcfcleancomplex.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -[ 52%] Building CXX object CMakeFiles/vcfintersect.dir/src/vcfintersect.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -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/libvcflib-1.0.3+dfsg/src/vcfintersect.cpp [ 53%] Building CXX object CMakeFiles/vcfcleancomplex.dir/src/vcfcleancomplex.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -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/libvcflib-1.0.3+dfsg/src/vcfcleancomplex.cpp In file included from /build/libvcflib-1.0.3+dfsg/src/vcfflatten.cpp:10: @@ -1772,6 +1800,14 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +[ 53%] Linking CXX executable vcfrandom +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfrandom.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfrandom.dir/src/vcfrandom.cpp.o -o vcfrandom -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' +[ 53%] Built target vcfrandom +make -f CMakeFiles/vcfintersect.dir/build.make CMakeFiles/vcfintersect.dir/depend +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' +cd /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfintersect.dir/DependInfo.cmake --color= In file included from /build/libvcflib-1.0.3+dfsg/src/vcfprimers.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { @@ -1788,6 +1824,9 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' +make -f CMakeFiles/vcfintersect.dir/build.make CMakeFiles/vcfintersect.dir/build +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' In file included from /build/libvcflib-1.0.3+dfsg/src/vcfnumalt.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { @@ -1804,6 +1843,8 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +[ 53%] Building CXX object CMakeFiles/vcfintersect.dir/src/vcfintersect.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -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/libvcflib-1.0.3+dfsg/src/vcfintersect.cpp In file included from /build/libvcflib-1.0.3+dfsg/src/vcfcleancomplex.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { @@ -1820,8 +1861,9 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 54%] Linking CXX executable vcfgenotypecompare -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfgenotypecompare.dir/link.txt --verbose=1 +[ 54%] Linking CXX executable vcfannotategenotypes +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfannotategenotypes.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfannotategenotypes.dir/src/vcfannotategenotypes.cpp.o -o vcfannotategenotypes -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp In file included from /build/libvcflib-1.0.3+dfsg/src/vcfintersect.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { @@ -1838,9 +1880,8 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfgenotypecompare.dir/src/vcfgenotypecompare.cpp.o -o vcfgenotypecompare -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -[ 54%] Built target vcfgenotypecompare +[ 54%] Built target vcfannotategenotypes make -f CMakeFiles/vcfannotate.dir/build.make CMakeFiles/vcfannotate.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfannotate.dir/DependInfo.cmake --color= @@ -1849,11 +1890,11 @@ make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' [ 55%] Building CXX object CMakeFiles/vcfannotate.dir/src/vcfannotate.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -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/libvcflib-1.0.3+dfsg/src/vcfannotate.cpp -[ 56%] Linking CXX executable vcfannotategenotypes -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfannotategenotypes.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfannotategenotypes.dir/src/vcfannotategenotypes.cpp.o -o vcfannotategenotypes -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 56%] Linking CXX executable vcfgenotypecompare +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfgenotypecompare.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfgenotypecompare.dir/src/vcfgenotypecompare.cpp.o -o vcfgenotypecompare -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -[ 56%] Built target vcfannotategenotypes +[ 56%] Built target vcfgenotypecompare make -f CMakeFiles/vcfallelicprimitives.dir/build.make CMakeFiles/vcfallelicprimitives.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfallelicprimitives.dir/DependInfo.cmake --color= @@ -1875,9 +1916,6 @@ make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' [ 57%] Building CXX object CMakeFiles/vcfoverlay.dir/src/vcfoverlay.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfoverlay.dir/src/vcfoverlay.cpp.o -MF CMakeFiles/vcfoverlay.dir/src/vcfoverlay.cpp.o.d -o CMakeFiles/vcfoverlay.dir/src/vcfoverlay.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfoverlay.cpp -[ 58%] 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/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfnumalt.dir/src/vcfnumalt.cpp.o -o vcfnumalt -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp In file included from /build/libvcflib-1.0.3+dfsg/src/vcfannotate.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { @@ -1894,6 +1932,12 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +[ 58%] 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/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfnumalt.dir/src/vcfnumalt.cpp.o -o vcfnumalt -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 58%] 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/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfcleancomplex.dir/src/vcfcleancomplex.cpp.o -o vcfcleancomplex -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' [ 58%] Built target vcfnumalt make -f CMakeFiles/vcfaddinfo.dir/build.make CMakeFiles/vcfaddinfo.dir/depend @@ -1904,6 +1948,16 @@ make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' [ 58%] Building CXX object CMakeFiles/vcfaddinfo.dir/src/vcfaddinfo.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -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/libvcflib-1.0.3+dfsg/src/vcfaddinfo.cpp +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' +[ 58%] Built target vcfcleancomplex +make -f CMakeFiles/vcfkeepinfo.dir/build.make CMakeFiles/vcfkeepinfo.dir/depend +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' +cd /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfkeepinfo.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' +make -f CMakeFiles/vcfkeepinfo.dir/build.make CMakeFiles/vcfkeepinfo.dir/build +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' +[ 59%] Building CXX object CMakeFiles/vcfkeepinfo.dir/src/vcfkeepinfo.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -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/libvcflib-1.0.3+dfsg/src/vcfkeepinfo.cpp In file included from /build/libvcflib-1.0.3+dfsg/src/vcfallelicprimitives.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { @@ -1920,9 +1974,6 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 58%] 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/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfcleancomplex.dir/src/vcfcleancomplex.cpp.o -o vcfcleancomplex -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp In file included from /build/libvcflib-1.0.3+dfsg/src/vcfoverlay.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { @@ -1939,16 +1990,9 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -[ 58%] Built target vcfcleancomplex -make -f CMakeFiles/vcfkeepinfo.dir/build.make CMakeFiles/vcfkeepinfo.dir/depend -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -cd /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfkeepinfo.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -make -f CMakeFiles/vcfkeepinfo.dir/build.make CMakeFiles/vcfkeepinfo.dir/build -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -[ 59%] Building CXX object CMakeFiles/vcfkeepinfo.dir/src/vcfkeepinfo.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -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/libvcflib-1.0.3+dfsg/src/vcfkeepinfo.cpp +[ 60%] 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/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfflatten.dir/src/vcfflatten.cpp.o -o vcfflatten -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp In file included from /build/libvcflib-1.0.3+dfsg/src/vcfaddinfo.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { @@ -1965,19 +2009,6 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 60%] 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/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfflatten.dir/src/vcfflatten.cpp.o -o vcfflatten -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -[ 60%] Built target vcfflatten -make -f CMakeFiles/vcfkeepgeno.dir/build.make CMakeFiles/vcfkeepgeno.dir/depend -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -cd /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfkeepgeno.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -make -f CMakeFiles/vcfkeepgeno.dir/build.make CMakeFiles/vcfkeepgeno.dir/build -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -[ 61%] Building CXX object CMakeFiles/vcfkeepgeno.dir/src/vcfkeepgeno.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -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/libvcflib-1.0.3+dfsg/src/vcfkeepgeno.cpp In file included from /build/libvcflib-1.0.3+dfsg/src/vcfkeepinfo.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { @@ -1994,6 +2025,16 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' +[ 60%] Built target vcfflatten +make -f CMakeFiles/vcfkeepgeno.dir/build.make CMakeFiles/vcfkeepgeno.dir/depend +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' +cd /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfkeepgeno.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' +make -f CMakeFiles/vcfkeepgeno.dir/build.make CMakeFiles/vcfkeepgeno.dir/build +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' +[ 61%] Building CXX object CMakeFiles/vcfkeepgeno.dir/src/vcfkeepgeno.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -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/libvcflib-1.0.3+dfsg/src/vcfkeepgeno.cpp In file included from /build/libvcflib-1.0.3+dfsg/src/vcfkeepgeno.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { @@ -2026,29 +2067,24 @@ [ 62%] Linking CXX executable vcfkeepinfo /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfkeepinfo.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfkeepinfo.dir/src/vcfkeepinfo.cpp.o -o vcfkeepinfo -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -[ 63%] Linking CXX executable vcfstats -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfstats.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfstats.dir/src/vcfstats.cpp.o -o vcfstats -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -[ 63%] Built target vcfkeepinfo +[ 62%] Built target vcfkeepinfo make -f CMakeFiles/vcfcountalleles.dir/build.make CMakeFiles/vcfcountalleles.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfcountalleles.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/vcfcountalleles.dir/build.make CMakeFiles/vcfcountalleles.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -[ 63%] Building CXX object CMakeFiles/vcfcountalleles.dir/src/vcfcountalleles.cpp.o +[ 62%] Building CXX object CMakeFiles/vcfcountalleles.dir/src/vcfcountalleles.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -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/libvcflib-1.0.3+dfsg/src/vcfcountalleles.cpp +[ 63%] Linking CXX executable vcfstats +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfstats.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfstats.dir/src/vcfstats.cpp.o -o vcfstats -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' [ 63%] Built target vcfstats make -f CMakeFiles/vcflength.dir/build.make CMakeFiles/vcflength.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcflength.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -make -f CMakeFiles/vcflength.dir/build.make CMakeFiles/vcflength.dir/build -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -[ 63%] Building CXX object CMakeFiles/vcflength.dir/src/vcflength.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -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/libvcflib-1.0.3+dfsg/src/vcflength.cpp In file included from /build/libvcflib-1.0.3+dfsg/src/vcfafpath.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { @@ -2065,19 +2101,11 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 63%] 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/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfkeepgeno.dir/src/vcfkeepgeno.cpp.o -o vcfkeepgeno -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -[ 63%] Built target vcfkeepgeno -make -f CMakeFiles/vcfdistance.dir/build.make CMakeFiles/vcfdistance.dir/depend -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -cd /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfdistance.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -make -f CMakeFiles/vcfdistance.dir/build.make CMakeFiles/vcfdistance.dir/build +make -f CMakeFiles/vcflength.dir/build.make CMakeFiles/vcflength.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -[ 63%] Building CXX object CMakeFiles/vcfdistance.dir/src/vcfdistance.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -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/libvcflib-1.0.3+dfsg/src/vcfdistance.cpp +[ 63%] Building CXX object CMakeFiles/vcflength.dir/src/vcflength.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -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/libvcflib-1.0.3+dfsg/src/vcflength.cpp In file included from /build/libvcflib-1.0.3+dfsg/src/vcfcountalleles.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { @@ -2094,6 +2122,19 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +[ 63%] 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/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfkeepgeno.dir/src/vcfkeepgeno.cpp.o -o vcfkeepgeno -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' +[ 63%] Built target vcfkeepgeno +make -f CMakeFiles/vcfdistance.dir/build.make CMakeFiles/vcfdistance.dir/depend +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' +cd /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfdistance.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' +make -f CMakeFiles/vcfdistance.dir/build.make CMakeFiles/vcfdistance.dir/build +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' +[ 63%] Building CXX object CMakeFiles/vcfdistance.dir/src/vcfdistance.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -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/libvcflib-1.0.3+dfsg/src/vcfdistance.cpp In file included from /build/libvcflib-1.0.3+dfsg/src/vcflength.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { @@ -2110,6 +2151,9 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +[ 64%] 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/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfcountalleles.dir/src/vcfcountalleles.cpp.o -o vcfcountalleles -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp In file included from /build/libvcflib-1.0.3+dfsg/src/vcfdistance.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { @@ -2126,11 +2170,8 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 64%] Linking CXX executable vcfoverlay -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfoverlay.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfoverlay.dir/src/vcfoverlay.cpp.o -o vcfoverlay -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -[ 64%] Built target vcfoverlay +[ 64%] Built target vcfcountalleles make -f CMakeFiles/vcfrandomsample.dir/build.make CMakeFiles/vcfrandomsample.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfrandomsample.dir/DependInfo.cmake --color= @@ -2139,11 +2180,11 @@ make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' [ 65%] Building CXX object CMakeFiles/vcfrandomsample.dir/src/vcfrandomsample.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -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/libvcflib-1.0.3+dfsg/src/vcfrandomsample.cpp -[ 66%] 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/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfcountalleles.dir/src/vcfcountalleles.cpp.o -o vcfcountalleles -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 66%] Linking CXX executable vcfoverlay +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfoverlay.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfoverlay.dir/src/vcfoverlay.cpp.o -o vcfoverlay -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -[ 66%] Built target vcfcountalleles +[ 66%] Built target vcfoverlay make -f CMakeFiles/vcfentropy.dir/build.make CMakeFiles/vcfentropy.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfentropy.dir/DependInfo.cmake --color= @@ -2176,14 +2217,30 @@ make -f CMakeFiles/vcfglxgt.dir/build.make CMakeFiles/vcfglxgt.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfglxgt.dir/DependInfo.cmake --color= -[ 68%] Linking CXX executable vcfannotate -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfannotate.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/vcfglxgt.dir/build.make CMakeFiles/vcfglxgt.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' +[ 68%] 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/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfannotate.dir/src/vcfannotate.cpp.o -o vcfannotate -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp [ 69%] Building CXX object CMakeFiles/vcfglxgt.dir/src/vcfglxgt.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -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/libvcflib-1.0.3+dfsg/src/vcfglxgt.cpp +In file included from /build/libvcflib-1.0.3+dfsg/src/vcfentropy.cpp:10: +/build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 651 | struct stringcasecmp : binary_function { + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/bits/refwrap.h:39, + from /usr/include/c++/12/vector:66, + from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: +/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +/build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 652 | struct charcasecmp : public std::binary_function { + | ^~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' [ 69%] Built target vcfannotate make -f CMakeFiles/vcfroc.dir/build.make CMakeFiles/vcfroc.dir/depend @@ -2192,38 +2249,25 @@ make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/vcfroc.dir/build.make CMakeFiles/vcfroc.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -[ 70%] Linking CXX executable vcfintersect -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfintersect.dir/link.txt --verbose=1 -[ 71%] Building CXX object CMakeFiles/vcfroc.dir/src/vcfroc.cpp.o +[ 70%] Building CXX object CMakeFiles/vcfroc.dir/src/vcfroc.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -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/libvcflib-1.0.3+dfsg/src/vcfroc.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfintersect.dir/src/vcfintersect.cpp.o -o vcfintersect -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -[ 72%] Linking CXX executable vcflength +[ 71%] Linking CXX executable vcflength /usr/bin/cmake -E cmake_link_script CMakeFiles/vcflength.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcflength.dir/src/vcflength.cpp.o -o vcflength -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -[ 72%] Built target vcfintersect +[ 71%] Built target vcflength make -f CMakeFiles/vcfcheck.dir/build.make CMakeFiles/vcfcheck.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfcheck.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/vcfcheck.dir/build.make CMakeFiles/vcfcheck.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -[ 72%] Building CXX object CMakeFiles/vcfcheck.dir/src/vcfcheck.cpp.o +[ 71%] Building CXX object CMakeFiles/vcfcheck.dir/src/vcfcheck.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -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/libvcflib-1.0.3+dfsg/src/vcfcheck.cpp -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -[ 72%] Built target vcflength -make -f CMakeFiles/vcfstreamsort.dir/build.make CMakeFiles/vcfstreamsort.dir/depend -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -cd /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfstreamsort.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -make -f CMakeFiles/vcfstreamsort.dir/build.make CMakeFiles/vcfstreamsort.dir/build -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -[ 72%] Building CXX object CMakeFiles/vcfstreamsort.dir/src/vcfstreamsort.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfstreamsort.dir/src/vcfstreamsort.cpp.o -MF CMakeFiles/vcfstreamsort.dir/src/vcfstreamsort.cpp.o.d -o CMakeFiles/vcfstreamsort.dir/src/vcfstreamsort.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfstreamsort.cpp -[ 73%] Linking CXX executable vcfdistance +[ 72%] Linking CXX executable vcfdistance /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfdistance.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfdistance.dir/src/vcfdistance.cpp.o -o vcfdistance -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -In file included from /build/libvcflib-1.0.3+dfsg/src/vcfentropy.cpp:10: +In file included from /build/libvcflib-1.0.3+dfsg/src/vcfroc.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ @@ -2239,6 +2283,16 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' +[ 72%] Built target vcfdistance +make -f CMakeFiles/vcfstreamsort.dir/build.make CMakeFiles/vcfstreamsort.dir/depend +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' +cd /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfstreamsort.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' +make -f CMakeFiles/vcfstreamsort.dir/build.make CMakeFiles/vcfstreamsort.dir/build +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' +[ 72%] Building CXX object CMakeFiles/vcfstreamsort.dir/src/vcfstreamsort.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfstreamsort.dir/src/vcfstreamsort.cpp.o -MF CMakeFiles/vcfstreamsort.dir/src/vcfstreamsort.cpp.o.d -o CMakeFiles/vcfstreamsort.dir/src/vcfstreamsort.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfstreamsort.cpp In file included from /build/libvcflib-1.0.3+dfsg/src/vcfglxgt.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { @@ -2255,8 +2309,11 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +[ 73%] Linking CXX executable vcfintersect +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfintersect.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfintersect.dir/src/vcfintersect.cpp.o -o vcfintersect -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -[ 73%] Built target vcfdistance +[ 73%] Built target vcfintersect make -f CMakeFiles/vcfuniq.dir/build.make CMakeFiles/vcfuniq.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfuniq.dir/DependInfo.cmake --color= @@ -2265,22 +2322,6 @@ make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' [ 74%] Building CXX object CMakeFiles/vcfuniq.dir/src/vcfuniq.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -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/libvcflib-1.0.3+dfsg/src/vcfuniq.cpp -In file included from /build/libvcflib-1.0.3+dfsg/src/vcfroc.cpp:10: -/build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 651 | struct stringcasecmp : binary_function { - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/bits/refwrap.h:39, - from /usr/include/c++/12/vector:66, - from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: -/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -/build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 652 | struct charcasecmp : public std::binary_function { - | ^~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ In file included from /build/libvcflib-1.0.3+dfsg/src/vcfcheck.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { @@ -2329,11 +2370,11 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 74%] Linking CXX executable vcfentropy -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfentropy.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfentropy.dir/src/vcfentropy.cpp.o -o vcfentropy -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 74%] Linking CXX executable vcfallelicprimitives +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfallelicprimitives.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfallelicprimitives.dir/src/vcfallelicprimitives.cpp.o -o vcfallelicprimitives -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -[ 74%] Built target vcfentropy +[ 74%] Built target vcfallelicprimitives make -f CMakeFiles/vcfuniqalleles.dir/build.make CMakeFiles/vcfuniqalleles.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfuniqalleles.dir/DependInfo.cmake --color= @@ -2342,56 +2383,43 @@ make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' [ 75%] Building CXX object CMakeFiles/vcfuniqalleles.dir/src/vcfuniqalleles.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -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/libvcflib-1.0.3+dfsg/src/vcfuniqalleles.cpp +[ 75%] Linking CXX executable vcfentropy +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfentropy.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfentropy.dir/src/vcfentropy.cpp.o -o vcfentropy -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp [ 76%] Linking CXX executable vcfrandomsample /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfrandomsample.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfrandomsample.dir/src/vcfrandomsample.cpp.o -o vcfrandomsample -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -[ 76%] Built target vcfrandomsample +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' +[ 76%] Built target vcfentropy make -f CMakeFiles/vcfremap.dir/build.make CMakeFiles/vcfremap.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfremap.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -make -f CMakeFiles/vcfremap.dir/build.make CMakeFiles/vcfremap.dir/build -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -[ 76%] Building CXX object CMakeFiles/vcfremap.dir/src/vcfremap.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -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/libvcflib-1.0.3+dfsg/src/vcfremap.cpp -[ 77%] Linking CXX executable vcfcheck -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfcheck.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfcheck.dir/src/vcfcheck.cpp.o -o vcfcheck -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -[ 77%] Linking CXX executable vcfuniq -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfuniq.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfuniq.dir/src/vcfuniq.cpp.o -o vcfuniq -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -[ 77%] 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/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfglxgt.dir/src/vcfglxgt.cpp.o -o vcfglxgt -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -[ 77%] Built target vcfcheck +[ 76%] Built target vcfrandomsample make -f CMakeFiles/vcf2fasta.dir/build.make CMakeFiles/vcf2fasta.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcf2fasta.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' +make -f CMakeFiles/vcfremap.dir/build.make CMakeFiles/vcfremap.dir/build +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/vcf2fasta.dir/build.make CMakeFiles/vcf2fasta.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -[ 78%] Building CXX object CMakeFiles/vcf2fasta.dir/src/vcf2fasta.cpp.o +[ 76%] Building CXX object CMakeFiles/vcfremap.dir/src/vcfremap.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -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/libvcflib-1.0.3+dfsg/src/vcfremap.cpp +[ 77%] Building CXX object CMakeFiles/vcf2fasta.dir/src/vcf2fasta.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -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/libvcflib-1.0.3+dfsg/src/vcf2fasta.cpp +[ 78%] 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/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfcheck.dir/src/vcfcheck.cpp.o -o vcfcheck -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -[ 78%] Built target vcfuniq +[ 78%] Built target vcfcheck make -f CMakeFiles/vcfsitesummarize.dir/build.make CMakeFiles/vcfsitesummarize.dir/depend -[ 78%] Built target vcfglxgt make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfsitesummarize.dir/DependInfo.cmake --color= -make -f CMakeFiles/vcfbreakmulti.dir/build.make CMakeFiles/vcfbreakmulti.dir/depend -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -cd /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfbreakmulti.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -make -f CMakeFiles/vcfbreakmulti.dir/build.make CMakeFiles/vcfbreakmulti.dir/build -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/vcfsitesummarize.dir/build.make CMakeFiles/vcfsitesummarize.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -[ 78%] Building CXX object CMakeFiles/vcfbreakmulti.dir/src/vcfbreakmulti.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -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/libvcflib-1.0.3+dfsg/src/vcfbreakmulti.cpp [ 78%] Building CXX object CMakeFiles/vcfsitesummarize.dir/src/vcfsitesummarize.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -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/libvcflib-1.0.3+dfsg/src/vcfsitesummarize.cpp In file included from /build/libvcflib-1.0.3+dfsg/src/vcfuniqalleles.cpp:10: @@ -2410,10 +2438,7 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 78%] Linking CXX executable vcfallelicprimitives -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfallelicprimitives.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfallelicprimitives.dir/src/vcfallelicprimitives.cpp.o -o vcfallelicprimitives -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -In file included from /build/libvcflib-1.0.3+dfsg/src/vcfremap.cpp:10: +In file included from /build/libvcflib-1.0.3+dfsg/src/vcf2fasta.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ @@ -2429,17 +2454,10 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -[ 78%] Built target vcfallelicprimitives -make -f CMakeFiles/vcfcreatemulti.dir/build.make CMakeFiles/vcfcreatemulti.dir/depend -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -cd /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfcreatemulti.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -make -f CMakeFiles/vcfcreatemulti.dir/build.make CMakeFiles/vcfcreatemulti.dir/build -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -[ 78%] Building CXX object CMakeFiles/vcfcreatemulti.dir/src/vcfcreatemulti.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -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/libvcflib-1.0.3+dfsg/src/vcfcreatemulti.cpp -In file included from /build/libvcflib-1.0.3+dfsg/src/vcfsitesummarize.cpp:10: +[ 78%] Linking CXX executable vcfuniq +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfuniq.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfuniq.dir/src/vcfuniq.cpp.o -o vcfuniq -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +In file included from /build/libvcflib-1.0.3+dfsg/src/vcfremap.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ @@ -2455,7 +2473,30 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from /build/libvcflib-1.0.3+dfsg/src/vcf2fasta.cpp:10: +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' +[ 78%] Built target vcfuniq +make -f CMakeFiles/vcfbreakmulti.dir/build.make CMakeFiles/vcfbreakmulti.dir/depend +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' +cd /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfbreakmulti.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' +make -f CMakeFiles/vcfbreakmulti.dir/build.make CMakeFiles/vcfbreakmulti.dir/build +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' +[ 78%] Building CXX object CMakeFiles/vcfbreakmulti.dir/src/vcfbreakmulti.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -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/libvcflib-1.0.3+dfsg/src/vcfbreakmulti.cpp +[ 78%] Linking CXX executable vcfglxgt +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfglxgt.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfglxgt.dir/src/vcfglxgt.cpp.o -o vcfglxgt -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' +[ 78%] Built target vcfglxgt +make -f CMakeFiles/vcfcreatemulti.dir/build.make CMakeFiles/vcfcreatemulti.dir/depend +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' +cd /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfcreatemulti.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' +make -f CMakeFiles/vcfcreatemulti.dir/build.make CMakeFiles/vcfcreatemulti.dir/build +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' +[ 78%] Building CXX object CMakeFiles/vcfcreatemulti.dir/src/vcfcreatemulti.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -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/libvcflib-1.0.3+dfsg/src/vcfcreatemulti.cpp +In file included from /build/libvcflib-1.0.3+dfsg/src/vcfsitesummarize.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ @@ -2487,6 +2528,9 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +[ 78%] Linking CXX executable vcfuniqalleles +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfuniqalleles.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfuniqalleles.dir/src/vcfuniqalleles.cpp.o -o vcfuniqalleles -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp In file included from /build/libvcflib-1.0.3+dfsg/src/vcfcreatemulti.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { @@ -2503,9 +2547,6 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 78%] Linking CXX executable vcfuniqalleles -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfuniqalleles.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfuniqalleles.dir/src/vcfuniqalleles.cpp.o -o vcfuniqalleles -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' [ 78%] Built target vcfuniqalleles make -f CMakeFiles/vcfevenregions.dir/build.make CMakeFiles/vcfevenregions.dir/depend @@ -2516,6 +2557,9 @@ make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' [ 79%] Building CXX object CMakeFiles/vcfevenregions.dir/src/vcfevenregions.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -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/libvcflib-1.0.3+dfsg/src/vcfevenregions.cpp +[ 80%] Linking CXX executable vcfsitesummarize +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfsitesummarize.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfsitesummarize.dir/src/vcfsitesummarize.cpp.o -o vcfsitesummarize -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp In file included from /build/libvcflib-1.0.3+dfsg/src/vcfevenregions.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { @@ -2532,9 +2576,6 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 80%] Linking CXX executable vcfsitesummarize -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfsitesummarize.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfsitesummarize.dir/src/vcfsitesummarize.cpp.o -o vcfsitesummarize -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' [ 80%] Built target vcfsitesummarize make -f CMakeFiles/vcfcat.dir/build.make CMakeFiles/vcfcat.dir/depend @@ -2561,58 +2602,66 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +[ 80%] 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/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcf2fasta.dir/src/vcf2fasta.cpp.o -o vcf2fasta -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 80%] Linking CXX executable vcfevenregions +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfevenregions.dir/link.txt --verbose=1 +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfevenregions.dir/src/vcfevenregions.cpp.o -o vcfevenregions -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp [ 81%] Linking CXX executable vcfbreakmulti +[ 81%] Built target vcf2fasta /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfbreakmulti.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfbreakmulti.dir/src/vcfbreakmulti.cpp.o -o vcfbreakmulti -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -[ 81%] Built target vcfbreakmulti make -f CMakeFiles/vcfgenosummarize.dir/build.make CMakeFiles/vcfgenosummarize.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfgenosummarize.dir/DependInfo.cmake --color= +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfbreakmulti.dir/src/vcfbreakmulti.cpp.o -o vcfbreakmulti -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/vcfgenosummarize.dir/build.make CMakeFiles/vcfgenosummarize.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' [ 82%] Building CXX object CMakeFiles/vcfgenosummarize.dir/src/vcfgenosummarize.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -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/libvcflib-1.0.3+dfsg/src/vcfgenosummarize.cpp -[ 83%] Linking CXX executable vcfstreamsort -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfstreamsort.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfstreamsort.dir/src/vcfstreamsort.cpp.o -o vcfstreamsort -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -[ 83%] Linking CXX executable vcfevenregions -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfevenregions.dir/link.txt --verbose=1 -[ 83%] Built target vcfstreamsort +[ 82%] Built target vcfbreakmulti make -f CMakeFiles/vcfgenosamplenames.dir/build.make CMakeFiles/vcfgenosamplenames.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfgenosamplenames.dir/DependInfo.cmake --color= -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfevenregions.dir/src/vcfevenregions.cpp.o -o vcfevenregions -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/vcfgenosamplenames.dir/build.make CMakeFiles/vcfgenosamplenames.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -[ 84%] Building CXX object CMakeFiles/vcfgenosamplenames.dir/src/vcfgenosamplenames.cpp.o +[ 83%] Building CXX object CMakeFiles/vcfgenosamplenames.dir/src/vcfgenosamplenames.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -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/libvcflib-1.0.3+dfsg/src/vcfgenosamplenames.cpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -[ 84%] Built target vcfevenregions +[ 83%] Built target vcfevenregions make -f CMakeFiles/vcfgeno2haplo.dir/build.make CMakeFiles/vcfgeno2haplo.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfgeno2haplo.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/vcfgeno2haplo.dir/build.make CMakeFiles/vcfgeno2haplo.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -[ 85%] Building CXX object CMakeFiles/vcfgeno2haplo.dir/src/vcfgeno2haplo.cpp.o +[ 84%] Building CXX object CMakeFiles/vcfgeno2haplo.dir/src/vcfgeno2haplo.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -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/libvcflib-1.0.3+dfsg/src/vcfgeno2haplo.cpp -[ 86%] Linking CXX executable vcfremap +[ 85%] 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/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfremap.dir/src/vcfremap.cpp.o -o vcfremap -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -[ 86%] Built target vcfremap +[ 85%] Built target vcfremap make -f CMakeFiles/vcfleftalign.dir/build.make CMakeFiles/vcfleftalign.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfleftalign.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/vcfleftalign.dir/build.make CMakeFiles/vcfleftalign.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -[ 86%] Building CXX object CMakeFiles/vcfleftalign.dir/src/vcfleftalign.cpp.o +[ 85%] Building CXX object CMakeFiles/vcfleftalign.dir/src/vcfleftalign.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -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/libvcflib-1.0.3+dfsg/src/vcfleftalign.cpp +[ 86%] Linking CXX executable vcfcat +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfcat.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfcat.dir/src/vcfcat.cpp.o -o vcfcat -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 87%] Linking CXX executable vcfstreamsort +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfstreamsort.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfstreamsort.dir/src/vcfstreamsort.cpp.o -o vcfstreamsort -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' +[ 87%] Built target vcfcat In file included from /build/libvcflib-1.0.3+dfsg/src/vcfgenosummarize.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { @@ -2629,46 +2678,6 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from /build/libvcflib-1.0.3+dfsg/src/vcfgenosamplenames.cpp:10: -/build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 651 | struct stringcasecmp : binary_function { - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/bits/refwrap.h:39, - from /usr/include/c++/12/vector:66, - from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: -/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -/build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 652 | struct charcasecmp : public std::binary_function { - | ^~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -In file included from /build/libvcflib-1.0.3+dfsg/src/vcfgeno2haplo.cpp:10: -/build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 651 | struct stringcasecmp : binary_function { - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/bits/refwrap.h:39, - from /usr/include/c++/12/vector:66, - from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: -/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -/build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 652 | struct charcasecmp : public std::binary_function { - | ^~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -[ 87%] Linking CXX executable vcfcat -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfcat.dir/link.txt --verbose=1 -[ 87%] 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/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfcat.dir/src/vcfcat.cpp.o -o vcfcat -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcf2fasta.dir/src/vcf2fasta.cpp.o -o vcf2fasta -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -[ 87%] Built target vcfcat make -f CMakeFiles/vcfcombine.dir/build.make CMakeFiles/vcfcombine.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfcombine.dir/DependInfo.cmake --color= @@ -2677,7 +2686,17 @@ make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' [ 88%] Building CXX object CMakeFiles/vcfcombine.dir/src/vcfcombine.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -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/libvcflib-1.0.3+dfsg/src/vcfcombine.cpp -In file included from /build/libvcflib-1.0.3+dfsg/src/vcfleftalign.cpp:10: +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' +[ 88%] Built target vcfstreamsort +make -f CMakeFiles/vcfgeno2alleles.dir/build.make CMakeFiles/vcfgeno2alleles.dir/depend +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' +cd /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfgeno2alleles.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' +make -f CMakeFiles/vcfgeno2alleles.dir/build.make CMakeFiles/vcfgeno2alleles.dir/build +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' +[ 89%] Building CXX object CMakeFiles/vcfgeno2alleles.dir/src/vcfgeno2alleles.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -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/libvcflib-1.0.3+dfsg/src/vcfgeno2alleles.cpp +In file included from /build/libvcflib-1.0.3+dfsg/src/vcfgenosamplenames.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ @@ -2693,43 +2712,7 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 89%] Linking CXX executable vcfcreatemulti -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfcreatemulti.dir/link.txt --verbose=1 -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfcreatemulti.dir/src/vcfcreatemulti.cpp.o -o vcfcreatemulti -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -[ 89%] Built target vcf2fasta -make -f CMakeFiles/vcfgeno2alleles.dir/build.make CMakeFiles/vcfgeno2alleles.dir/depend -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -cd /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfgeno2alleles.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -make -f CMakeFiles/vcfgeno2alleles.dir/build.make CMakeFiles/vcfgeno2alleles.dir/build -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -[ 90%] Building CXX object CMakeFiles/vcfgeno2alleles.dir/src/vcfgeno2alleles.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -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/libvcflib-1.0.3+dfsg/src/vcfgeno2alleles.cpp -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -[ 90%] Built target vcfcreatemulti -make -f CMakeFiles/vcfindex.dir/build.make CMakeFiles/vcfindex.dir/depend -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -cd /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfindex.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -make -f CMakeFiles/vcfindex.dir/build.make CMakeFiles/vcfindex.dir/build -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -[ 91%] Building CXX object CMakeFiles/vcfindex.dir/src/vcfindex.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfindex.dir/src/vcfindex.cpp.o -MF CMakeFiles/vcfindex.dir/src/vcfindex.cpp.o.d -o CMakeFiles/vcfindex.dir/src/vcfindex.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfindex.cpp -[ 91%] Linking CXX executable vcfroc -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfroc.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfroc.dir/src/vcfroc.cpp.o -o vcfroc -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -[ 91%] Built target vcfroc -make -f CMakeFiles/vcf2dag.dir/build.make CMakeFiles/vcf2dag.dir/depend -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -cd /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu 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CMakeFiles/vcf2dag.dir/src/vcf2dag.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcf2dag.cpp -In file included from /build/libvcflib-1.0.3+dfsg/src/vcfcombine.cpp:10: +In file included from /build/libvcflib-1.0.3+dfsg/src/vcfgeno2haplo.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ @@ -2745,7 +2728,7 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from /build/libvcflib-1.0.3+dfsg/src/vcfgeno2alleles.cpp:10: +In file included from /build/libvcflib-1.0.3+dfsg/src/vcfleftalign.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ @@ -2761,7 +2744,7 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from /build/libvcflib-1.0.3+dfsg/src/vcfindex.cpp:10: +In file included from /build/libvcflib-1.0.3+dfsg/src/vcfgeno2alleles.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ @@ -2777,7 +2760,7 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from /build/libvcflib-1.0.3+dfsg/src/vcf2dag.cpp:10: +In file included from /build/libvcflib-1.0.3+dfsg/src/vcfcombine.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ @@ -2793,10 +2776,39 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +[ 89%] Linking CXX executable vcfroc +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfroc.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfroc.dir/src/vcfroc.cpp.o -o vcfroc -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' +[ 89%] Built target vcfroc +make -f CMakeFiles/vcfindex.dir/build.make CMakeFiles/vcfindex.dir/depend +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' +cd /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfindex.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' +make -f CMakeFiles/vcfindex.dir/build.make CMakeFiles/vcfindex.dir/build +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' +[ 90%] Building CXX object CMakeFiles/vcfindex.dir/src/vcfindex.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfindex.dir/src/vcfindex.cpp.o -MF CMakeFiles/vcfindex.dir/src/vcfindex.cpp.o.d -o CMakeFiles/vcfindex.dir/src/vcfindex.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfindex.cpp +[ 91%] Linking CXX executable vcfcreatemulti +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfcreatemulti.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfcreatemulti.dir/src/vcfcreatemulti.cpp.o -o vcfcreatemulti -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' +[ 91%] Built target vcfcreatemulti +make -f CMakeFiles/vcf2dag.dir/build.make CMakeFiles/vcf2dag.dir/depend +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' +cd /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcf2dag.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' +make -f CMakeFiles/vcf2dag.dir/build.make CMakeFiles/vcf2dag.dir/build +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' +[ 92%] Building CXX object CMakeFiles/vcf2dag.dir/src/vcf2dag.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -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/libvcflib-1.0.3+dfsg/src/vcf2dag.cpp [ 92%] 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/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfgenosamplenames.dir/src/vcfgenosamplenames.cpp.o -o vcfgenosamplenames -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' +[ 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/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfgeno2alleles.dir/src/vcfgeno2alleles.cpp.o -o vcfgeno2alleles -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp [ 92%] Built target vcfgenosamplenames make -f CMakeFiles/vcfsample2info.dir/build.make CMakeFiles/vcfsample2info.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' @@ -2806,10 +2818,7 @@ make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' [ 93%] Building CXX object CMakeFiles/vcfsample2info.dir/src/vcfsample2info.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -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/libvcflib-1.0.3+dfsg/src/vcfsample2info.cpp -[ 94%] 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/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfgenosummarize.dir/src/vcfgenosummarize.cpp.o -o vcfgenosummarize -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -In file included from /build/libvcflib-1.0.3+dfsg/src/vcfsample2info.cpp:10: +In file included from /build/libvcflib-1.0.3+dfsg/src/vcfindex.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ @@ -2826,42 +2835,45 @@ 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -[ 94%] Built target vcfgenosummarize +[ 93%] Built target vcfgeno2alleles make -f CMakeFiles/vcfqual2info.dir/build.make CMakeFiles/vcfqual2info.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfqual2info.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/vcfqual2info.dir/build.make CMakeFiles/vcfqual2info.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -[ 95%] Building CXX object CMakeFiles/vcfqual2info.dir/src/vcfqual2info.cpp.o +[ 94%] Building CXX object CMakeFiles/vcfqual2info.dir/src/vcfqual2info.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -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/libvcflib-1.0.3+dfsg/src/vcfqual2info.cpp -[ 95%] 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/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfgeno2alleles.dir/src/vcfgeno2alleles.cpp.o -o vcfgeno2alleles -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -[ 96%] 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/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfindex.dir/src/vcfindex.cpp.o -o vcfindex -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 95%] 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/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfgenosummarize.dir/src/vcfgenosummarize.cpp.o -o vcfgenosummarize -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -[ 96%] Built target vcfindex +[ 95%] Built target vcfgenosummarize make -f CMakeFiles/vcfinfo2qual.dir/build.make CMakeFiles/vcfinfo2qual.dir/depend +In file included from /build/libvcflib-1.0.3+dfsg/src/vcf2dag.cpp:10: +/build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 651 | struct stringcasecmp : binary_function { + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/bits/refwrap.h:39, + from /usr/include/c++/12/vector:66, + from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: +/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +/build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 652 | struct charcasecmp : public std::binary_function { + | ^~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfinfo2qual.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/vcfinfo2qual.dir/build.make CMakeFiles/vcfinfo2qual.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -[ 96%] Building CXX object CMakeFiles/vcfinfo2qual.dir/src/vcfinfo2qual.cpp.o +[ 95%] Building CXX object CMakeFiles/vcfinfo2qual.dir/src/vcfinfo2qual.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -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/libvcflib-1.0.3+dfsg/src/vcfinfo2qual.cpp -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -[ 96%] Built target vcfgeno2alleles -make -f CMakeFiles/vcfglbound.dir/build.make CMakeFiles/vcfglbound.dir/depend -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -cd /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfglbound.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -make -f CMakeFiles/vcfglbound.dir/build.make CMakeFiles/vcfglbound.dir/build -make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -[ 96%] Building CXX object CMakeFiles/vcfglbound.dir/src/vcfglbound.cpp.o -/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -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/libvcflib-1.0.3+dfsg/src/vcfglbound.cpp -In file included from /build/libvcflib-1.0.3+dfsg/src/vcfqual2info.cpp:10: +In file included from /build/libvcflib-1.0.3+dfsg/src/vcfsample2info.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ @@ -2877,7 +2889,7 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from /build/libvcflib-1.0.3+dfsg/src/vcfinfo2qual.cpp:10: +In file included from /build/libvcflib-1.0.3+dfsg/src/vcfqual2info.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ @@ -2893,7 +2905,7 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from /build/libvcflib-1.0.3+dfsg/src/vcfglbound.cpp:10: +In file included from /build/libvcflib-1.0.3+dfsg/src/vcfinfo2qual.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ @@ -2909,39 +2921,61 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -[ 97%] 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/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfleftalign.dir/src/vcfleftalign.cpp.o -o vcfleftalign -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -[ 97%] Linking CXX executable vcf2dag -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcf2dag.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcf2dag.dir/src/vcf2dag.cpp.o -o vcf2dag -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 96%] 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/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfindex.dir/src/vcfindex.cpp.o -o vcfindex -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' +[ 96%] Built target vcfindex +make -f CMakeFiles/vcfglbound.dir/build.make CMakeFiles/vcfglbound.dir/depend +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' +cd /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfglbound.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' +make -f CMakeFiles/vcfglbound.dir/build.make CMakeFiles/vcfglbound.dir/build +make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' +[ 96%] Building CXX object CMakeFiles/vcfglbound.dir/src/vcfglbound.cpp.o +/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -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/libvcflib-1.0.3+dfsg/src/vcfglbound.cpp +[ 97%] Linking CXX executable vcfinfo2qual +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfinfo2qual.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfinfo2qual.dir/src/vcfinfo2qual.cpp.o -o vcfinfo2qual -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -[ 97%] Built target vcfleftalign +[ 97%] Built target vcfinfo2qual make -f CMakeFiles/vcfinfosummarize.dir/build.make CMakeFiles/vcfinfosummarize.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu/CMakeFiles/vcfinfosummarize.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/vcfinfosummarize.dir/build.make CMakeFiles/vcfinfosummarize.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -[ 97%] Linking CXX executable vcfsample2info -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfsample2info.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfsample2info.dir/src/vcfsample2info.cpp.o -o vcfsample2info -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp [ 97%] Building CXX object CMakeFiles/vcfinfosummarize.dir/src/vcfinfosummarize.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -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/libvcflib-1.0.3+dfsg/src/vcfinfosummarize.cpp -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -[ 97%] Built target vcf2dag -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -[ 97%] Built target vcfsample2info [ 97%] Linking CXX executable vcfqual2info /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfqual2info.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfqual2info.dir/src/vcfqual2info.cpp.o -o vcfqual2info -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -[ 98%] Linking CXX executable vcfinfo2qual -/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfinfo2qual.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfinfo2qual.dir/src/vcfinfo2qual.cpp.o -o vcfinfo2qual -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +In file included from /build/libvcflib-1.0.3+dfsg/src/vcfglbound.cpp:10: +/build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 651 | struct stringcasecmp : binary_function { + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/bits/refwrap.h:39, + from /usr/include/c++/12/vector:66, + from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: +/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +/build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 652 | struct charcasecmp : public std::binary_function { + | ^~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -[ 98%] Built target vcfqual2info +[ 97%] Built target vcfqual2info +[ 97%] Linking CXX executable vcfsample2info +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfsample2info.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfsample2info.dir/src/vcfsample2info.cpp.o -o vcfsample2info -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -[ 98%] Built target vcfinfo2qual +[ 97%] Built target vcfsample2info +[ 98%] 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/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfleftalign.dir/src/vcfleftalign.cpp.o -o vcfleftalign -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp In file included from /build/libvcflib-1.0.3+dfsg/src/vcfinfosummarize.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { @@ -2958,16 +2992,23 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' +[ 98%] Built target vcfleftalign +[ 98%] Linking CXX executable vcf2dag +/usr/bin/cmake -E cmake_link_script CMakeFiles/vcf2dag.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcf2dag.dir/src/vcf2dag.cpp.o -o vcf2dag -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +[ 98%] 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/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfcombine.dir/src/vcfcombine.cpp.o -o vcfcombine -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' +[ 98%] Built target vcf2dag +make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' +[ 98%] Built target vcfcombine [ 99%] 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/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfglbound.dir/src/vcfglbound.cpp.o -o vcfglbound -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp -[ 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/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfcombine.dir/src/vcfcombine.cpp.o -o vcfcombine -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' [ 99%] Built target vcfglbound -make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-aarch64-linux-gnu' -[ 99%] Built target vcfcombine [ 99%] 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/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfgeno2haplo.dir/src/vcfgeno2haplo.cpp.o -o vcfgeno2haplo -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp @@ -3011,8 +3052,8 @@ [----------] Global test environment set-up. [----------] 1 test from Variant [ RUN ] Variant.correctGenotype -[ OK ] Variant.correctGenotype (6139 ms) -[----------] 1 test from Variant (6139 ms total) +[ OK ] Variant.correctGenotype (5826 ms) +[----------] 1 test from Variant (5826 ms total) [----------] 4 tests from VariantCallFile [ RUN ] VariantCallFile.open @@ -3020,13 +3061,13 @@ [ RUN ] VariantCallFile.recordCountUncompressed [ OK ] VariantCallFile.recordCountUncompressed (0 ms) [ RUN ] VariantCallFile.recordCountCompressed -[ OK ] VariantCallFile.recordCountCompressed (7 ms) +[ OK ] VariantCallFile.recordCountCompressed (6 ms) [ RUN ] VariantCallFile.sampleNamesCompressed -[ OK ] VariantCallFile.sampleNamesCompressed (3 ms) -[----------] 4 tests from VariantCallFile (12 ms total) +[ OK ] VariantCallFile.sampleNamesCompressed (2 ms) +[----------] 4 tests from VariantCallFile (10 ms total) [----------] Global test environment tear-down -[==========] 5 tests from 2 test suites ran. (6152 ms total) +[==========] 5 tests from 2 test suites ran. (5837 ms total) [ PASSED ] 5 tests. make[2]: Leaving directory '/build/libvcflib-1.0.3+dfsg/test' make[1]: Leaving directory '/build/libvcflib-1.0.3+dfsg' @@ -3403,9 +3444,9 @@ dpkg-gencontrol: warning: package libvcflib-tools: substitution variable ${perl:Depends} unused, but is defined dh_md5sums -O--buildsystem=cmake dh_builddeb -O--buildsystem=cmake +dpkg-deb: building package 'libvcflib1' in '../libvcflib1_1.0.3+dfsg-2_arm64.deb'. dpkg-deb: building package 'libvcflib-dev' in '../libvcflib-dev_1.0.3+dfsg-2_arm64.deb'. dpkg-deb: building package 'libvcflib-tools-dbgsym' in '../libvcflib-tools-dbgsym_1.0.3+dfsg-2_arm64.deb'. -dpkg-deb: building package 'libvcflib1' in '../libvcflib1_1.0.3+dfsg-2_arm64.deb'. dpkg-deb: building package 'libvcflib1-dbgsym' in '../libvcflib1-dbgsym_1.0.3+dfsg-2_arm64.deb'. dpkg-deb: building package 'libvcflib-tools' in '../libvcflib-tools_1.0.3+dfsg-2_arm64.deb'. dpkg-genbuildinfo --build=binary -O../libvcflib_1.0.3+dfsg-2_arm64.buildinfo @@ -3415,12 +3456,14 @@ 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/1421/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1421/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/4613 and its subdirectories -I: Current time: Mon Jun 3 11:18:17 -12 2024 -I: pbuilder-time-stamp: 1717456697 +I: removing directory /srv/workspace/pbuilder/1421 and its subdirectories +I: Current time: Wed May 3 07:05:09 +14 2023 +I: pbuilder-time-stamp: 1683047109