Diff of the two buildlogs: -- --- b1/build.log 2025-01-27 15:31:18.165325699 +0000 +++ b2/build.log 2025-01-27 15:32:42.729506808 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Jan 27 03:25:56 -12 2025 -I: pbuilder-time-stamp: 1737991556 +I: Current time: Mon Mar 2 11:54:20 +14 2026 +I: pbuilder-time-stamp: 1772402060 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -31,52 +31,84 @@ dpkg-source: info: applying python3.12-syntax.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/3974424/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/524355/tmp/hooks/D01_modify_environment starting +debug: Running on ionos15-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Mar 1 21:54 /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/524355/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/524355/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='a8131919cf0d430bab3d7b3bbc0e0d38' - 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='3974424' - PS1='# ' - PS2='> ' + INVOCATION_ID=464b358837d94c369596d8e5165698dc + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=524355 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.Waoq4OfH/pbuilderrc_d2o7 --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.Waoq4OfH/b1 --logfile b1/build.log discosnp_2.6.2-4.dsc' - SUDO_GID='111' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://46.16.76.132:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.Waoq4OfH/pbuilderrc_XjVO --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.Waoq4OfH/b2 --logfile b2/build.log discosnp_2.6.2-4.dsc' + SUDO_GID=111 + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://213.165.73.152:3128 I: uname -a - Linux ionos11-amd64 6.1.0-30-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.124-1 (2025-01-12) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.12.9+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.9-1~bpo12+1 (2025-01-19) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/3974424/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/524355/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -259,7 +291,7 @@ Get: 131 http://deb.debian.org/debian unstable/main amd64 libjpeg62-turbo-dev amd64 1:2.1.5-3+b1 [292 kB] Get: 132 http://deb.debian.org/debian unstable/main amd64 libjpeg-dev amd64 1:2.1.5-3+b1 [72.2 kB] Get: 133 http://deb.debian.org/debian unstable/main amd64 libhdf5-dev amd64 1.14.5+repack-3 [3165 kB] -Fetched 82.9 MB in 11s (7887 kB/s) +Fetched 82.9 MB in 5s (15.5 MB/s) Preconfiguring packages ... Selecting previously unselected package libpython3.13-minimal:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19830 files and directories currently installed.) @@ -698,8 +730,8 @@ Setting up tzdata (2025a-1) ... Current default time zone: 'Etc/UTC' -Local time is now: Mon Jan 27 15:28:49 UTC 2025. -Universal Time is now: Mon Jan 27 15:28:49 UTC 2025. +Local time is now: Sun Mar 1 21:54:54 UTC 2026. +Universal Time is now: Sun Mar 1 21:54:54 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... @@ -819,7 +851,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/discosnp-2.6.2/ && 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 > ../discosnp_2.6.2-4_source.changes +I: user script /srv/workspace/pbuilder/524355/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/524355/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/discosnp-2.6.2/ && 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 > ../discosnp_2.6.2-4_source.changes dpkg-buildpackage: info: source package discosnp dpkg-buildpackage: info: source version 1:2.6.2-4 dpkg-buildpackage: info: source distribution unstable @@ -862,8 +898,8 @@ to work with policies introduced by or earlier. --- Configuring done (5.1s) --- Generating done (0.2s) +-- Configuring done (0.5s) +-- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: @@ -875,72 +911,72 @@ -- Build files have been written to: /build/reproducible-path/discosnp-2.6.2/obj-x86_64-linux-gnu dh_auto_build - cd obj-x86_64-linux-gnu && make -j20 "INSTALL=install --strip-program=true" VERBOSE=1 + cd obj-x86_64-linux-gnu && make -j42 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/discosnp-2.6.2/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/discosnp-2.6.2 -B/build/reproducible-path/discosnp-2.6.2/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/discosnp-2.6.2/obj-x86_64-linux-gnu/CMakeFiles /build/reproducible-path/discosnp-2.6.2/obj-x86_64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/discosnp-2.6.2/obj-x86_64-linux-gnu' make -f tools/kissnp2/CMakeFiles/kissnp2.dir/build.make tools/kissnp2/CMakeFiles/kissnp2.dir/depend -make[3]: Entering directory '/build/reproducible-path/discosnp-2.6.2/obj-x86_64-linux-gnu' -cd /build/reproducible-path/discosnp-2.6.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/discosnp-2.6.2 /build/reproducible-path/discosnp-2.6.2/tools/kissnp2 /build/reproducible-path/discosnp-2.6.2/obj-x86_64-linux-gnu /build/reproducible-path/discosnp-2.6.2/obj-x86_64-linux-gnu/tools/kissnp2 /build/reproducible-path/discosnp-2.6.2/obj-x86_64-linux-gnu/tools/kissnp2/CMakeFiles/kissnp2.dir/DependInfo.cmake "--color=" make -f tools/kissreads2/CMakeFiles/kissreads2.dir/build.make tools/kissreads2/CMakeFiles/kissreads2.dir/depend make -f tools/QHC/CMakeFiles/quick_hierarchical_clustering.dir/build.make tools/QHC/CMakeFiles/quick_hierarchical_clustering.dir/depend +make -f tools/read_file_names/CMakeFiles/read_file_names.dir/build.make tools/read_file_names/CMakeFiles/read_file_names.dir/depend +make[3]: Entering directory '/build/reproducible-path/discosnp-2.6.2/obj-x86_64-linux-gnu' +cd /build/reproducible-path/discosnp-2.6.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/discosnp-2.6.2 /build/reproducible-path/discosnp-2.6.2/tools/kissnp2 /build/reproducible-path/discosnp-2.6.2/obj-x86_64-linux-gnu /build/reproducible-path/discosnp-2.6.2/obj-x86_64-linux-gnu/tools/kissnp2 /build/reproducible-path/discosnp-2.6.2/obj-x86_64-linux-gnu/tools/kissnp2/CMakeFiles/kissnp2.dir/DependInfo.cmake "--color=" +make -f tools/create_coverage_h5_file/CMakeFiles/create_coverage_h5_file.dir/build.make tools/create_coverage_h5_file/CMakeFiles/create_coverage_h5_file.dir/depend make[3]: Entering directory '/build/reproducible-path/discosnp-2.6.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/discosnp-2.6.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/discosnp-2.6.2 /build/reproducible-path/discosnp-2.6.2/tools/kissreads2 /build/reproducible-path/discosnp-2.6.2/obj-x86_64-linux-gnu /build/reproducible-path/discosnp-2.6.2/obj-x86_64-linux-gnu/tools/kissreads2 /build/reproducible-path/discosnp-2.6.2/obj-x86_64-linux-gnu/tools/kissreads2/CMakeFiles/kissreads2.dir/DependInfo.cmake "--color=" -make -f tools/read_file_names/CMakeFiles/read_file_names.dir/build.make tools/read_file_names/CMakeFiles/read_file_names.dir/depend make[3]: Entering directory '/build/reproducible-path/discosnp-2.6.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/discosnp-2.6.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/discosnp-2.6.2 /build/reproducible-path/discosnp-2.6.2/tools/QHC /build/reproducible-path/discosnp-2.6.2/obj-x86_64-linux-gnu /build/reproducible-path/discosnp-2.6.2/obj-x86_64-linux-gnu/tools/QHC /build/reproducible-path/discosnp-2.6.2/obj-x86_64-linux-gnu/tools/QHC/CMakeFiles/quick_hierarchical_clustering.dir/DependInfo.cmake "--color=" -make -f tools/create_coverage_h5_file/CMakeFiles/create_coverage_h5_file.dir/build.make tools/create_coverage_h5_file/CMakeFiles/create_coverage_h5_file.dir/depend make[3]: Entering directory '/build/reproducible-path/discosnp-2.6.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/discosnp-2.6.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/discosnp-2.6.2 /build/reproducible-path/discosnp-2.6.2/tools/read_file_names /build/reproducible-path/discosnp-2.6.2/obj-x86_64-linux-gnu /build/reproducible-path/discosnp-2.6.2/obj-x86_64-linux-gnu/tools/read_file_names /build/reproducible-path/discosnp-2.6.2/obj-x86_64-linux-gnu/tools/read_file_names/CMakeFiles/read_file_names.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/discosnp-2.6.2/obj-x86_64-linux-gnu' cd /build/reproducible-path/discosnp-2.6.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/discosnp-2.6.2 /build/reproducible-path/discosnp-2.6.2/tools/create_coverage_h5_file /build/reproducible-path/discosnp-2.6.2/obj-x86_64-linux-gnu /build/reproducible-path/discosnp-2.6.2/obj-x86_64-linux-gnu/tools/create_coverage_h5_file /build/reproducible-path/discosnp-2.6.2/obj-x86_64-linux-gnu/tools/create_coverage_h5_file/CMakeFiles/create_coverage_h5_file.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/discosnp-2.6.2/obj-x86_64-linux-gnu' -make -f tools/kissnp2/CMakeFiles/kissnp2.dir/build.make tools/kissnp2/CMakeFiles/kissnp2.dir/build -make[3]: Entering directory '/build/reproducible-path/discosnp-2.6.2/obj-x86_64-linux-gnu' +make[3]: Leaving directory '/build/reproducible-path/discosnp-2.6.2/obj-x86_64-linux-gnu' +make -f tools/create_coverage_h5_file/CMakeFiles/create_coverage_h5_file.dir/build.make tools/create_coverage_h5_file/CMakeFiles/create_coverage_h5_file.dir/build +make[3]: Leaving directory '/build/reproducible-path/discosnp-2.6.2/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/discosnp-2.6.2/obj-x86_64-linux-gnu' make -f tools/QHC/CMakeFiles/quick_hierarchical_clustering.dir/build.make tools/QHC/CMakeFiles/quick_hierarchical_clustering.dir/build -make[3]: Entering directory '/build/reproducible-path/discosnp-2.6.2/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/discosnp-2.6.2/obj-x86_64-linux-gnu' +make -f tools/kissnp2/CMakeFiles/kissnp2.dir/build.make tools/kissnp2/CMakeFiles/kissnp2.dir/build +make -f tools/kissreads2/CMakeFiles/kissreads2.dir/build.make tools/kissreads2/CMakeFiles/kissreads2.dir/build make -f tools/read_file_names/CMakeFiles/read_file_names.dir/build.make tools/read_file_names/CMakeFiles/read_file_names.dir/build make[3]: Entering directory '/build/reproducible-path/discosnp-2.6.2/obj-x86_64-linux-gnu' -[ 5%] Building CXX object tools/kissnp2/CMakeFiles/kissnp2.dir/src/Filter.cpp.o -[ 10%] Building CXX object tools/kissnp2/CMakeFiles/kissnp2.dir/src/Kissnp2.cpp.o -[ 15%] Building CXX object tools/kissnp2/CMakeFiles/kissnp2.dir/src/Bubble.cpp.o -[ 20%] Building CXX object tools/kissnp2/CMakeFiles/kissnp2.dir/src/main.cpp.o -[ 25%] Building CXX object tools/QHC/CMakeFiles/quick_hierarchical_clustering.dir/src/quick_hierarchical_clustering.cpp.o -cd /build/reproducible-path/discosnp-2.6.2/obj-x86_64-linux-gnu/tools/kissnp2 && /usr/bin/c++ -I/build/reproducible-path/discosnp-2.6.2/tools/kissnp2/src -g -O2 -ffile-prefix-map=/build/reproducible-path/discosnp-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT tools/kissnp2/CMakeFiles/kissnp2.dir/src/Bubble.cpp.o -MF CMakeFiles/kissnp2.dir/src/Bubble.cpp.o.d -o CMakeFiles/kissnp2.dir/src/Bubble.cpp.o -c /build/reproducible-path/discosnp-2.6.2/tools/kissnp2/src/Bubble.cpp -cd /build/reproducible-path/discosnp-2.6.2/obj-x86_64-linux-gnu/tools/QHC && /usr/bin/c++ -I/build/reproducible-path/discosnp-2.6.2/tools/QHC/src -g -O2 -ffile-prefix-map=/build/reproducible-path/discosnp-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT 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/build/reproducible-path/discosnp-2.6.2/obj-x86_64-linux-gnu/tools/kissnp2 && /usr/bin/c++ -I/build/reproducible-path/discosnp-2.6.2/tools/kissnp2/src -g -O2 -ffile-prefix-map=/build/reproducible-path/discosnp-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT tools/kissnp2/CMakeFiles/kissnp2.dir/src/Kissnp2.cpp.o -MF CMakeFiles/kissnp2.dir/src/Kissnp2.cpp.o.d -o CMakeFiles/kissnp2.dir/src/Kissnp2.cpp.o -c /build/reproducible-path/discosnp-2.6.2/tools/kissnp2/src/Kissnp2.cpp -cd /build/reproducible-path/discosnp-2.6.2/obj-x86_64-linux-gnu/tools/kissnp2 && /usr/bin/c++ -I/build/reproducible-path/discosnp-2.6.2/tools/kissnp2/src -g -O2 -ffile-prefix-map=/build/reproducible-path/discosnp-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT tools/kissnp2/CMakeFiles/kissnp2.dir/src/main.cpp.o -MF CMakeFiles/kissnp2.dir/src/main.cpp.o.d -o CMakeFiles/kissnp2.dir/src/main.cpp.o -c /build/reproducible-path/discosnp-2.6.2/tools/kissnp2/src/main.cpp -[ 30%] Building CXX object tools/read_file_names/CMakeFiles/read_file_names.dir/src/get_read_file_names.cpp.o -cd /build/reproducible-path/discosnp-2.6.2/obj-x86_64-linux-gnu/tools/read_file_names && /usr/bin/c++ -I/build/reproducible-path/discosnp-2.6.2/tools/read_file_names/src -g -O2 -ffile-prefix-map=/build/reproducible-path/discosnp-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT tools/read_file_names/CMakeFiles/read_file_names.dir/src/get_read_file_names.cpp.o -MF CMakeFiles/read_file_names.dir/src/get_read_file_names.cpp.o.d -o CMakeFiles/read_file_names.dir/src/get_read_file_names.cpp.o -c /build/reproducible-path/discosnp-2.6.2/tools/read_file_names/src/get_read_file_names.cpp -make[3]: Leaving directory '/build/reproducible-path/discosnp-2.6.2/obj-x86_64-linux-gnu' -make -f tools/create_coverage_h5_file/CMakeFiles/create_coverage_h5_file.dir/build.make tools/create_coverage_h5_file/CMakeFiles/create_coverage_h5_file.dir/build make[3]: Entering directory '/build/reproducible-path/discosnp-2.6.2/obj-x86_64-linux-gnu' -make[3]: Leaving directory '/build/reproducible-path/discosnp-2.6.2/obj-x86_64-linux-gnu' -make -f tools/kissreads2/CMakeFiles/kissreads2.dir/build.make tools/kissreads2/CMakeFiles/kissreads2.dir/build make[3]: Entering directory '/build/reproducible-path/discosnp-2.6.2/obj-x86_64-linux-gnu' +make[3]: Entering directory '/build/reproducible-path/discosnp-2.6.2/obj-x86_64-linux-gnu' +make[3]: Entering directory '/build/reproducible-path/discosnp-2.6.2/obj-x86_64-linux-gnu' +[ 20%] Building CXX object tools/kissnp2/CMakeFiles/kissnp2.dir/src/Bubble.cpp.o +[ 20%] Building CXX object tools/QHC/CMakeFiles/quick_hierarchical_clustering.dir/src/quick_hierarchical_clustering.cpp.o +[ 20%] Building CXX object tools/create_coverage_h5_file/CMakeFiles/create_coverage_h5_file.dir/src/create_coverage_h5_file.cpp.o +[ 20%] Building CXX object tools/read_file_names/CMakeFiles/read_file_names.dir/src/get_read_file_names.cpp.o +[ 35%] Building CXX object tools/kissreads2/CMakeFiles/kissreads2.dir/src/fragment.cpp.o +[ 35%] Building CXX object tools/kissnp2/CMakeFiles/kissnp2.dir/src/Filter.cpp.o [ 35%] Building CXX object tools/kissreads2/CMakeFiles/kissreads2.dir/src/Kissreads2.cpp.o -[ 40%] Building CXX object tools/create_coverage_h5_file/CMakeFiles/create_coverage_h5_file.dir/src/create_coverage_h5_file.cpp.o +[ 45%] Building CXX object tools/kissnp2/CMakeFiles/kissnp2.dir/src/main.cpp.o +[ 45%] Building CXX object tools/kissnp2/CMakeFiles/kissnp2.dir/src/Kissnp2.cpp.o +[ 50%] Building CXX object tools/kissreads2/CMakeFiles/kissreads2.dir/src/commons.cpp.o +cd /build/reproducible-path/discosnp-2.6.2/obj-x86_64-linux-gnu/tools/read_file_names && /usr/bin/c++ -I/build/reproducible-path/discosnp-2.6.2/tools/read_file_names/src -g -O2 -ffile-prefix-map=/build/reproducible-path/discosnp-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT tools/read_file_names/CMakeFiles/read_file_names.dir/src/get_read_file_names.cpp.o -MF CMakeFiles/read_file_names.dir/src/get_read_file_names.cpp.o.d -o CMakeFiles/read_file_names.dir/src/get_read_file_names.cpp.o -c /build/reproducible-path/discosnp-2.6.2/tools/read_file_names/src/get_read_file_names.cpp cd /build/reproducible-path/discosnp-2.6.2/obj-x86_64-linux-gnu/tools/create_coverage_h5_file && /usr/bin/c++ -I/build/reproducible-path/discosnp-2.6.2/tools/create_coverage_h5_file/src -g -O2 -ffile-prefix-map=/build/reproducible-path/discosnp-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT tools/create_coverage_h5_file/CMakeFiles/create_coverage_h5_file.dir/src/create_coverage_h5_file.cpp.o -MF CMakeFiles/create_coverage_h5_file.dir/src/create_coverage_h5_file.cpp.o.d -o CMakeFiles/create_coverage_h5_file.dir/src/create_coverage_h5_file.cpp.o -c /build/reproducible-path/discosnp-2.6.2/tools/create_coverage_h5_file/src/create_coverage_h5_file.cpp -[ 45%] Building CXX object tools/kissreads2/CMakeFiles/kissreads2.dir/src/commons.cpp.o -[ 50%] Building CXX object tools/kissreads2/CMakeFiles/kissreads2.dir/src/fragment.cpp.o -cd /build/reproducible-path/discosnp-2.6.2/obj-x86_64-linux-gnu/tools/kissreads2 && /usr/bin/c++ -I/build/reproducible-path/discosnp-2.6.2/tools/kissreads2/src -g -O2 -ffile-prefix-map=/build/reproducible-path/discosnp-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT tools/kissreads2/CMakeFiles/kissreads2.dir/src/commons.cpp.o -MF CMakeFiles/kissreads2.dir/src/commons.cpp.o.d -o CMakeFiles/kissreads2.dir/src/commons.cpp.o -c /build/reproducible-path/discosnp-2.6.2/tools/kissreads2/src/commons.cpp -[ 55%] Building CXX object tools/kissreads2/CMakeFiles/kissreads2.dir/src/interface_xhash.cpp.o -[ 60%] Building CXX object tools/kissreads2/CMakeFiles/kissreads2.dir/src/outputs.cpp.o -[ 65%] Building CXX object tools/kissreads2/CMakeFiles/kissreads2.dir/src/main.cpp.o +cd /build/reproducible-path/discosnp-2.6.2/obj-x86_64-linux-gnu/tools/QHC && /usr/bin/c++ -I/build/reproducible-path/discosnp-2.6.2/tools/QHC/src -g -O2 -ffile-prefix-map=/build/reproducible-path/discosnp-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT tools/QHC/CMakeFiles/quick_hierarchical_clustering.dir/src/quick_hierarchical_clustering.cpp.o -MF CMakeFiles/quick_hierarchical_clustering.dir/src/quick_hierarchical_clustering.cpp.o.d -o CMakeFiles/quick_hierarchical_clustering.dir/src/quick_hierarchical_clustering.cpp.o -c /build/reproducible-path/discosnp-2.6.2/tools/QHC/src/quick_hierarchical_clustering.cpp +cd /build/reproducible-path/discosnp-2.6.2/obj-x86_64-linux-gnu/tools/kissnp2 && /usr/bin/c++ -I/build/reproducible-path/discosnp-2.6.2/tools/kissnp2/src -g -O2 -ffile-prefix-map=/build/reproducible-path/discosnp-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT tools/kissnp2/CMakeFiles/kissnp2.dir/src/Bubble.cpp.o -MF CMakeFiles/kissnp2.dir/src/Bubble.cpp.o.d -o CMakeFiles/kissnp2.dir/src/Bubble.cpp.o -c /build/reproducible-path/discosnp-2.6.2/tools/kissnp2/src/Bubble.cpp cd /build/reproducible-path/discosnp-2.6.2/obj-x86_64-linux-gnu/tools/kissreads2 && /usr/bin/c++ -I/build/reproducible-path/discosnp-2.6.2/tools/kissreads2/src -g -O2 -ffile-prefix-map=/build/reproducible-path/discosnp-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT tools/kissreads2/CMakeFiles/kissreads2.dir/src/Kissreads2.cpp.o -MF CMakeFiles/kissreads2.dir/src/Kissreads2.cpp.o.d -o CMakeFiles/kissreads2.dir/src/Kissreads2.cpp.o -c /build/reproducible-path/discosnp-2.6.2/tools/kissreads2/src/Kissreads2.cpp +[ 55%] Building CXX object tools/kissreads2/CMakeFiles/kissreads2.dir/src/fragment_index.cpp.o +cd /build/reproducible-path/discosnp-2.6.2/obj-x86_64-linux-gnu/tools/kissnp2 && /usr/bin/c++ -I/build/reproducible-path/discosnp-2.6.2/tools/kissnp2/src -g -O2 -ffile-prefix-map=/build/reproducible-path/discosnp-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT tools/kissnp2/CMakeFiles/kissnp2.dir/src/Filter.cpp.o -MF CMakeFiles/kissnp2.dir/src/Filter.cpp.o.d -o CMakeFiles/kissnp2.dir/src/Filter.cpp.o -c /build/reproducible-path/discosnp-2.6.2/tools/kissnp2/src/Filter.cpp +[ 60%] Building CXX object tools/kissreads2/CMakeFiles/kissreads2.dir/src/main.cpp.o cd /build/reproducible-path/discosnp-2.6.2/obj-x86_64-linux-gnu/tools/kissreads2 && /usr/bin/c++ -I/build/reproducible-path/discosnp-2.6.2/tools/kissreads2/src -g -O2 -ffile-prefix-map=/build/reproducible-path/discosnp-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT tools/kissreads2/CMakeFiles/kissreads2.dir/src/fragment.cpp.o -MF CMakeFiles/kissreads2.dir/src/fragment.cpp.o.d -o CMakeFiles/kissreads2.dir/src/fragment.cpp.o -c /build/reproducible-path/discosnp-2.6.2/tools/kissreads2/src/fragment.cpp -cd /build/reproducible-path/discosnp-2.6.2/obj-x86_64-linux-gnu/tools/kissreads2 && /usr/bin/c++ -I/build/reproducible-path/discosnp-2.6.2/tools/kissreads2/src -g -O2 -ffile-prefix-map=/build/reproducible-path/discosnp-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT tools/kissreads2/CMakeFiles/kissreads2.dir/src/interface_xhash.cpp.o -MF CMakeFiles/kissreads2.dir/src/interface_xhash.cpp.o.d -o CMakeFiles/kissreads2.dir/src/interface_xhash.cpp.o -c /build/reproducible-path/discosnp-2.6.2/tools/kissreads2/src/interface_xhash.cpp +cd /build/reproducible-path/discosnp-2.6.2/obj-x86_64-linux-gnu/tools/kissnp2 && /usr/bin/c++ -I/build/reproducible-path/discosnp-2.6.2/tools/kissnp2/src -g -O2 -ffile-prefix-map=/build/reproducible-path/discosnp-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT tools/kissnp2/CMakeFiles/kissnp2.dir/src/main.cpp.o -MF CMakeFiles/kissnp2.dir/src/main.cpp.o.d -o CMakeFiles/kissnp2.dir/src/main.cpp.o -c /build/reproducible-path/discosnp-2.6.2/tools/kissnp2/src/main.cpp +cd /build/reproducible-path/discosnp-2.6.2/obj-x86_64-linux-gnu/tools/kissreads2 && /usr/bin/c++ -I/build/reproducible-path/discosnp-2.6.2/tools/kissreads2/src -g -O2 -ffile-prefix-map=/build/reproducible-path/discosnp-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT tools/kissreads2/CMakeFiles/kissreads2.dir/src/commons.cpp.o -MF CMakeFiles/kissreads2.dir/src/commons.cpp.o.d -o CMakeFiles/kissreads2.dir/src/commons.cpp.o -c /build/reproducible-path/discosnp-2.6.2/tools/kissreads2/src/commons.cpp +cd /build/reproducible-path/discosnp-2.6.2/obj-x86_64-linux-gnu/tools/kissnp2 && /usr/bin/c++ -I/build/reproducible-path/discosnp-2.6.2/tools/kissnp2/src -g -O2 -ffile-prefix-map=/build/reproducible-path/discosnp-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT tools/kissnp2/CMakeFiles/kissnp2.dir/src/Kissnp2.cpp.o -MF CMakeFiles/kissnp2.dir/src/Kissnp2.cpp.o.d -o CMakeFiles/kissnp2.dir/src/Kissnp2.cpp.o -c /build/reproducible-path/discosnp-2.6.2/tools/kissnp2/src/Kissnp2.cpp +[ 65%] Building CXX object tools/kissreads2/CMakeFiles/kissreads2.dir/src/read_mapper.cpp.o +[ 70%] Building CXX object tools/kissreads2/CMakeFiles/kissreads2.dir/src/outputs.cpp.o cd /build/reproducible-path/discosnp-2.6.2/obj-x86_64-linux-gnu/tools/kissreads2 && /usr/bin/c++ -I/build/reproducible-path/discosnp-2.6.2/tools/kissreads2/src -g -O2 -ffile-prefix-map=/build/reproducible-path/discosnp-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT tools/kissreads2/CMakeFiles/kissreads2.dir/src/main.cpp.o -MF CMakeFiles/kissreads2.dir/src/main.cpp.o.d -o CMakeFiles/kissreads2.dir/src/main.cpp.o -c /build/reproducible-path/discosnp-2.6.2/tools/kissreads2/src/main.cpp -cd /build/reproducible-path/discosnp-2.6.2/obj-x86_64-linux-gnu/tools/kissreads2 && /usr/bin/c++ -I/build/reproducible-path/discosnp-2.6.2/tools/kissreads2/src -g -O2 -ffile-prefix-map=/build/reproducible-path/discosnp-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT tools/kissreads2/CMakeFiles/kissreads2.dir/src/outputs.cpp.o -MF CMakeFiles/kissreads2.dir/src/outputs.cpp.o.d -o CMakeFiles/kissreads2.dir/src/outputs.cpp.o -c /build/reproducible-path/discosnp-2.6.2/tools/kissreads2/src/outputs.cpp -[ 70%] Building CXX object tools/kissreads2/CMakeFiles/kissreads2.dir/src/read_mapper.cpp.o -[ 75%] Building CXX object tools/kissreads2/CMakeFiles/kissreads2.dir/src/fragment_index.cpp.o cd /build/reproducible-path/discosnp-2.6.2/obj-x86_64-linux-gnu/tools/kissreads2 && /usr/bin/c++ -I/build/reproducible-path/discosnp-2.6.2/tools/kissreads2/src -g -O2 -ffile-prefix-map=/build/reproducible-path/discosnp-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT tools/kissreads2/CMakeFiles/kissreads2.dir/src/fragment_index.cpp.o -MF CMakeFiles/kissreads2.dir/src/fragment_index.cpp.o.d -o CMakeFiles/kissreads2.dir/src/fragment_index.cpp.o -c /build/reproducible-path/discosnp-2.6.2/tools/kissreads2/src/fragment_index.cpp cd /build/reproducible-path/discosnp-2.6.2/obj-x86_64-linux-gnu/tools/kissreads2 && /usr/bin/c++ -I/build/reproducible-path/discosnp-2.6.2/tools/kissreads2/src -g -O2 -ffile-prefix-map=/build/reproducible-path/discosnp-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT tools/kissreads2/CMakeFiles/kissreads2.dir/src/read_mapper.cpp.o -MF CMakeFiles/kissreads2.dir/src/read_mapper.cpp.o.d -o CMakeFiles/kissreads2.dir/src/read_mapper.cpp.o -c /build/reproducible-path/discosnp-2.6.2/tools/kissreads2/src/read_mapper.cpp +[ 75%] Building CXX object tools/kissreads2/CMakeFiles/kissreads2.dir/src/interface_xhash.cpp.o +cd /build/reproducible-path/discosnp-2.6.2/obj-x86_64-linux-gnu/tools/kissreads2 && /usr/bin/c++ -I/build/reproducible-path/discosnp-2.6.2/tools/kissreads2/src -g -O2 -ffile-prefix-map=/build/reproducible-path/discosnp-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT tools/kissreads2/CMakeFiles/kissreads2.dir/src/outputs.cpp.o -MF CMakeFiles/kissreads2.dir/src/outputs.cpp.o.d -o CMakeFiles/kissreads2.dir/src/outputs.cpp.o -c /build/reproducible-path/discosnp-2.6.2/tools/kissreads2/src/outputs.cpp +cd /build/reproducible-path/discosnp-2.6.2/obj-x86_64-linux-gnu/tools/kissreads2 && /usr/bin/c++ -I/build/reproducible-path/discosnp-2.6.2/tools/kissreads2/src -g -O2 -ffile-prefix-map=/build/reproducible-path/discosnp-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT tools/kissreads2/CMakeFiles/kissreads2.dir/src/interface_xhash.cpp.o -MF CMakeFiles/kissreads2.dir/src/interface_xhash.cpp.o.d -o CMakeFiles/kissreads2.dir/src/interface_xhash.cpp.o -c /build/reproducible-path/discosnp-2.6.2/tools/kissreads2/src/interface_xhash.cpp [ 80%] Linking CXX executable ../../bin/quick_hierarchical_clustering cd /build/reproducible-path/discosnp-2.6.2/obj-x86_64-linux-gnu/tools/QHC && /usr/bin/cmake -E cmake_link_script CMakeFiles/quick_hierarchical_clustering.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/discosnp-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic -Wl,--dependency-file=CMakeFiles/quick_hierarchical_clustering.dir/link.d CMakeFiles/quick_hierarchical_clustering.dir/src/quick_hierarchical_clustering.cpp.o -o ../../bin/quick_hierarchical_clustering -L/usr/lib/x86_64-linux-gnu/hdf5/serial -Wl,-rpath,/usr/lib/x86_64-linux-gnu/hdf5/serial: -lgatbcore -lhdf5 -lz @@ -951,21 +987,21 @@ /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/discosnp-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic -Wl,--dependency-file=CMakeFiles/read_file_names.dir/link.d CMakeFiles/read_file_names.dir/src/get_read_file_names.cpp.o -o ../../bin/read_file_names -L/usr/lib/x86_64-linux-gnu/hdf5/serial -Wl,-rpath,/usr/lib/x86_64-linux-gnu/hdf5/serial: -lgatbcore -lhdf5 -lz make[3]: Leaving directory '/build/reproducible-path/discosnp-2.6.2/obj-x86_64-linux-gnu' [ 85%] Built target read_file_names -[ 90%] Linking CXX executable ../../bin/kissnp2 -cd /build/reproducible-path/discosnp-2.6.2/obj-x86_64-linux-gnu/tools/kissnp2 && /usr/bin/cmake -E cmake_link_script CMakeFiles/kissnp2.dir/link.txt --verbose=1 -[ 95%] Linking CXX executable ../../bin/create_coverage_h5_file +[ 90%] Linking CXX executable ../../bin/create_coverage_h5_file cd /build/reproducible-path/discosnp-2.6.2/obj-x86_64-linux-gnu/tools/create_coverage_h5_file && /usr/bin/cmake -E cmake_link_script CMakeFiles/create_coverage_h5_file.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/discosnp-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic -Wl,--dependency-file=CMakeFiles/kissnp2.dir/link.d CMakeFiles/kissnp2.dir/src/Bubble.cpp.o CMakeFiles/kissnp2.dir/src/Filter.cpp.o CMakeFiles/kissnp2.dir/src/Kissnp2.cpp.o CMakeFiles/kissnp2.dir/src/main.cpp.o -o ../../bin/kissnp2 -L/usr/lib/x86_64-linux-gnu/hdf5/serial -Wl,-rpath,/usr/lib/x86_64-linux-gnu/hdf5/serial: -lgatbcore -lhdf5 -lz -make[3]: Leaving directory '/build/reproducible-path/discosnp-2.6.2/obj-x86_64-linux-gnu' -[ 95%] Built target kissnp2 -[100%] Linking CXX executable ../../bin/kissreads2 -cd /build/reproducible-path/discosnp-2.6.2/obj-x86_64-linux-gnu/tools/kissreads2 && /usr/bin/cmake -E cmake_link_script CMakeFiles/kissreads2.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/discosnp-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic -Wl,--dependency-file=CMakeFiles/create_coverage_h5_file.dir/link.d CMakeFiles/create_coverage_h5_file.dir/src/create_coverage_h5_file.cpp.o -o ../../bin/create_coverage_h5_file -L/usr/lib/x86_64-linux-gnu/hdf5/serial -Wl,-rpath,/usr/lib/x86_64-linux-gnu/hdf5/serial: -lgatbcore -lhdf5 -lz make[3]: Leaving directory '/build/reproducible-path/discosnp-2.6.2/obj-x86_64-linux-gnu' -[100%] Built target create_coverage_h5_file +[ 90%] Built target create_coverage_h5_file +[ 95%] Linking CXX executable ../../bin/kissreads2 +cd /build/reproducible-path/discosnp-2.6.2/obj-x86_64-linux-gnu/tools/kissreads2 && /usr/bin/cmake -E cmake_link_script CMakeFiles/kissreads2.dir/link.txt --verbose=1 +[100%] Linking CXX executable ../../bin/kissnp2 +cd /build/reproducible-path/discosnp-2.6.2/obj-x86_64-linux-gnu/tools/kissnp2 && /usr/bin/cmake -E cmake_link_script CMakeFiles/kissnp2.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/discosnp-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic -Wl,--dependency-file=CMakeFiles/kissreads2.dir/link.d CMakeFiles/kissreads2.dir/src/Kissreads2.cpp.o CMakeFiles/kissreads2.dir/src/commons.cpp.o CMakeFiles/kissreads2.dir/src/fragment.cpp.o CMakeFiles/kissreads2.dir/src/fragment_index.cpp.o CMakeFiles/kissreads2.dir/src/interface_xhash.cpp.o CMakeFiles/kissreads2.dir/src/main.cpp.o CMakeFiles/kissreads2.dir/src/outputs.cpp.o CMakeFiles/kissreads2.dir/src/read_mapper.cpp.o -o ../../bin/kissreads2 -L/usr/lib/x86_64-linux-gnu/hdf5/serial -Wl,-rpath,/usr/lib/x86_64-linux-gnu/hdf5/serial: -lgatbcore -lhdf5 -lz make[3]: Leaving directory '/build/reproducible-path/discosnp-2.6.2/obj-x86_64-linux-gnu' [100%] Built target kissreads2 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/discosnp-2.6.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic -Wl,--dependency-file=CMakeFiles/kissnp2.dir/link.d CMakeFiles/kissnp2.dir/src/Bubble.cpp.o CMakeFiles/kissnp2.dir/src/Filter.cpp.o CMakeFiles/kissnp2.dir/src/Kissnp2.cpp.o CMakeFiles/kissnp2.dir/src/main.cpp.o -o ../../bin/kissnp2 -L/usr/lib/x86_64-linux-gnu/hdf5/serial -Wl,-rpath,/usr/lib/x86_64-linux-gnu/hdf5/serial: -lgatbcore -lhdf5 -lz +make[3]: Leaving directory '/build/reproducible-path/discosnp-2.6.2/obj-x86_64-linux-gnu' +[100%] Built target kissnp2 make[2]: Leaving directory '/build/reproducible-path/discosnp-2.6.2/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/discosnp-2.6.2/obj-x86_64-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/build/reproducible-path/discosnp-2.6.2/obj-x86_64-linux-gnu' @@ -973,7 +1009,7 @@ create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/discosnp/ - cd obj-x86_64-linux-gnu && make -j20 install DESTDIR=/build/reproducible-path/discosnp-2.6.2/debian/discosnp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + cd obj-x86_64-linux-gnu && make -j42 install DESTDIR=/build/reproducible-path/discosnp-2.6.2/debian/discosnp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/discosnp-2.6.2/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/discosnp-2.6.2 -B/build/reproducible-path/discosnp-2.6.2/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall @@ -1011,6 +1047,7 @@ cp -a debian/mans/*.sh.1 debian/discosnp/usr/share/man/man1 make[1]: Leaving directory '/build/reproducible-path/discosnp-2.6.2' dh_python3 +I: dh_python3 tools:113: replacing shebang in debian/discosnp/usr/share/discosnp/discoSnpRAD/clustering_scripts/fasta_and_cluster_to_filtered_vcf.py I: dh_python3 tools:113: replacing shebang in debian/discosnp/usr/share/discosnp/scripts/create_filtered_vcf.py I: dh_python3 tools:113: replacing shebang in debian/discosnp/usr/share/discosnp/scripts/vcf_formatting_functions.py I: dh_python3 tools:113: replacing shebang in debian/discosnp/usr/share/discosnp/scripts/k3000/K3000_common.py @@ -1019,7 +1056,6 @@ I: dh_python3 tools:113: replacing shebang in debian/discosnp/usr/share/discosnp/scripts/k3000/K3000_node_ids_to_node_sequences.py I: dh_python3 tools:113: replacing shebang in debian/discosnp/usr/share/discosnp/scripts/k3000/K3000_paths_to_fa.py I: dh_python3 tools:113: replacing shebang in debian/discosnp/usr/share/discosnp/scripts/k3000/K3000_phased_paths_to_fa.py -I: dh_python3 tools:113: replacing shebang in debian/discosnp/usr/share/discosnp/discoSnpRAD/clustering_scripts/fasta_and_cluster_to_filtered_vcf.py dh_lintian dh_perl dh_link @@ -1035,8 +1071,8 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'discosnp-dbgsym' in '../discosnp-dbgsym_2.6.2-4_amd64.deb'. dpkg-deb: building package 'discosnp' in '../discosnp_2.6.2-4_amd64.deb'. +dpkg-deb: building package 'discosnp-dbgsym' in '../discosnp-dbgsym_2.6.2-4_amd64.deb'. dpkg-genbuildinfo --build=binary -O../discosnp_2.6.2-4_amd64.buildinfo dpkg-genchanges --build=binary -O../discosnp_2.6.2-4_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -1044,12 +1080,14 @@ 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/524355/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/524355/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/3974424 and its subdirectories -I: Current time: Mon Jan 27 03:31:17 -12 2025 -I: pbuilder-time-stamp: 1737991877 +I: removing directory /srv/workspace/pbuilder/524355 and its subdirectories +I: Current time: Mon Mar 2 11:55:41 +14 2026 +I: pbuilder-time-stamp: 1772402141