Diff of the two buildlogs: -- --- b1/build.log 2024-05-09 12:41:51.560866087 +0000 +++ b2/build.log 2024-05-09 12:44:24.778346545 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu May 9 00:39:38 -12 2024 -I: pbuilder-time-stamp: 1715258378 +I: Current time: Thu Jun 12 09:04:54 +14 2025 +I: pbuilder-time-stamp: 1749668694 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -34,51 +34,83 @@ dpkg-source: info: applying shell_syntax.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/3260620/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3959334/tmp/hooks/D01_modify_environment starting +debug: Running on infom02-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Jun 11 19:05 /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/3959334/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3959334/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' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="21" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.21(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='amd64' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='6157aee98d7045d9a7d7c11e89e5adad' - 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='3260620' - PS1='# ' - PS2='> ' + INVOCATION_ID=f2460f18d2a047c6816e901e82a3869f + 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=3959334 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.ejkdaqFm/pbuilderrc_N2PX --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.ejkdaqFm/b1 --logfile b1/build.log discosnp_2.6.2-3.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' + 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.ejkdaqFm/pbuilderrc_biVa --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.ejkdaqFm/b2 --logfile b2/build.log discosnp_2.6.2-3.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' I: uname -a - Linux infom01-amd64 6.1.0-21-cloud-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.90-1 (2024-05-03) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.6.13+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.6.13-1~bpo12+1 (2024-02-15) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 May 8 11:24 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/3260620/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Jun 10 17:51 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/3959334/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -221,7 +253,7 @@ Get: 91 http://deb.debian.org/debian trixie/main amd64 libjpeg-dev amd64 1:2.1.5-3 [71.9 kB] Get: 92 http://deb.debian.org/debian trixie/main amd64 libssl-dev amd64 3.2.1-3 [2699 kB] Get: 93 http://deb.debian.org/debian trixie/main amd64 libhdf5-dev amd64 1.10.10+repack-3.3 [2639 kB] -Fetched 68.5 MB in 1s (119 MB/s) +Fetched 68.5 MB in 1s (86.5 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19699 files and directories currently installed.) @@ -539,8 +571,8 @@ Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' -Local time is now: Thu May 9 12:41:13 UTC 2024. -Universal Time is now: Thu May 9 12:41:13 UTC 2024. +Local time is now: Wed Jun 11 19:06:26 UTC 2025. +Universal Time is now: Wed Jun 11 19:06:26 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... @@ -621,7 +653,11 @@ 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_2.6.2-3_source.changes +I: user script /srv/workspace/pbuilder/3959334/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/3959334/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_2.6.2-3_source.changes dpkg-buildpackage: info: source package discosnp dpkg-buildpackage: info: source version 1:2.6.2-3 dpkg-buildpackage: info: source distribution unstable @@ -663,7 +699,7 @@ CMake that the project does not need compatibility with older versions. --- Configuring done (0.6s) +-- Configuring done (2.9s) -- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: @@ -684,65 +720,65 @@ 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 -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 -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/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/QHC/CMakeFiles/quick_hierarchical_clustering.dir/build.make tools/QHC/CMakeFiles/quick_hierarchical_clustering.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/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=" 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/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=" +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]: Leaving 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' 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 -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/read_file_names/CMakeFiles/read_file_names.dir/build.make tools/read_file_names/CMakeFiles/read_file_names.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[3]: Entering 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]: 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' +[ 5%] Building CXX object tools/kissnp2/CMakeFiles/kissnp2.dir/src/Bubble.cpp.o 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[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[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' -[ 5%] Building CXX object tools/read_file_names/CMakeFiles/read_file_names.dir/src/get_read_file_names.cpp.o -[ 10%] Building CXX object tools/QHC/CMakeFiles/quick_hierarchical_clustering.dir/src/quick_hierarchical_clustering.cpp.o -[ 15%] Building CXX object tools/create_coverage_h5_file/CMakeFiles/create_coverage_h5_file.dir/src/create_coverage_h5_file.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/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 +[ 10%] Building CXX object tools/kissnp2/CMakeFiles/kissnp2.dir/src/Kissnp2.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/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 +[ 15%] Building CXX object tools/kissnp2/CMakeFiles/kissnp2.dir/src/main.cpp.o +[ 20%] Building CXX object tools/kissnp2/CMakeFiles/kissnp2.dir/src/Filter.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/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/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/create_coverage_h5_file/CMakeFiles/create_coverage_h5_file.dir/src/create_coverage_h5_file.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 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 -[ 20%] Building CXX object tools/kissreads2/CMakeFiles/kissreads2.dir/src/fragment.cpp.o -[ 25%] Building CXX object tools/kissnp2/CMakeFiles/kissnp2.dir/src/Bubble.cpp.o -[ 30%] Building CXX object tools/kissreads2/CMakeFiles/kissreads2.dir/src/fragment_index.cpp.o +[ 35%] Building CXX object tools/read_file_names/CMakeFiles/read_file_names.dir/src/get_read_file_names.cpp.o +[ 40%] 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/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 -[ 35%] Building CXX object tools/kissnp2/CMakeFiles/kissnp2.dir/src/Filter.cpp.o -[ 40%] 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/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/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 -[ 45%] Building CXX object tools/kissreads2/CMakeFiles/kissreads2.dir/src/main.cpp.o -[ 55%] Building CXX object tools/kissreads2/CMakeFiles/kissreads2.dir/src/commons.cpp.o -[ 55%] Building CXX object tools/kissreads2/CMakeFiles/kissreads2.dir/src/Kissreads2.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 -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/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 +[ 45%] 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/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/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 -[ 60%] Building CXX object tools/kissnp2/CMakeFiles/kissnp2.dir/src/Kissnp2.cpp.o +[ 50%] Building CXX object tools/kissreads2/CMakeFiles/kissreads2.dir/src/Kissreads2.cpp.o +[ 60%] 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/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/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 -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 +[ 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/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 [ 65%] 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 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 make[3]: Leaving directory '/build/reproducible-path/discosnp-2.6.2/obj-x86_64-linux-gnu' [ 65%] Built target quick_hierarchical_clustering -[ 70%] Building CXX object tools/kissnp2/CMakeFiles/kissnp2.dir/src/main.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/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 +[ 70%] 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/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 [ 75%] 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/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 [ 80%] Building CXX object tools/kissreads2/CMakeFiles/kissreads2.dir/src/read_mapper.cpp.o @@ -836,8 +872,8 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'discosnp-dbgsym' in '../discosnp-dbgsym_2.6.2-3_amd64.deb'. dpkg-deb: building package 'discosnp' in '../discosnp_2.6.2-3_amd64.deb'. +dpkg-deb: building package 'discosnp-dbgsym' in '../discosnp-dbgsym_2.6.2-3_amd64.deb'. dpkg-genbuildinfo --build=binary -O../discosnp_2.6.2-3_amd64.buildinfo dpkg-genchanges --build=binary -O../discosnp_2.6.2-3_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -845,12 +881,14 @@ 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/3959334/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3959334/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/3260620 and its subdirectories -I: Current time: Thu May 9 00:41:50 -12 2024 -I: pbuilder-time-stamp: 1715258510 +I: removing directory /srv/workspace/pbuilder/3959334 and its subdirectories +I: Current time: Thu Jun 12 09:07:23 +14 2025 +I: pbuilder-time-stamp: 1749668843