Diff of the two buildlogs: -- --- b1/build.log 2025-08-19 08:19:18.949495914 +0000 +++ b2/build.log 2025-08-19 08:20:24.005564641 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Sep 21 02:41:21 -12 2026 -I: pbuilder-time-stamp: 1790001681 +I: Current time: Tue Aug 19 22:19:21 +14 2025 +I: pbuilder-time-stamp: 1755591561 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-reproducible-base.tgz] I: copying local configuration @@ -31,53 +31,85 @@ 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/2445974/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1907524/tmp/hooks/D01_modify_environment starting +debug: Running on codethink04-arm64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Aug 19 08:19 /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/1907524/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1907524/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='arm64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="aarch64-unknown-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=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='forky' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=forky + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='87677a5e64554bb3a802ebf549ad9066' - 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='2445974' - PS1='# ' - PS2='> ' + INVOCATION_ID=6860fe13126c47699ffb4d2fbcee2766 + 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=1907524 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.rCuAlAOr/pbuilderrc_bj5w --distribution forky --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.rCuAlAOr/b1 --logfile b1/build.log discosnp_2.6.2-4.dsc' - SUDO_GID='109' - SUDO_HOME='/var/lib/jenkins' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.4:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.rCuAlAOr/pbuilderrc_YzCi --distribution forky --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.rCuAlAOr/b2 --logfile b2/build.log discosnp_2.6.2-4.dsc' + SUDO_GID=109 + SUDO_HOME=/var/lib/jenkins + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink03-arm64 6.12.41+deb13-cloud-arm64 #1 SMP Debian 6.12.41-1 (2025-08-12) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.12.41+deb13-cloud-arm64 #1 SMP Debian 6.12.41-1 (2025-08-12) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/2445974/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/1907524/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -90,7 +122,7 @@ Depends: debhelper-compat (= 13), dh-sequence-python3, python3, cmake, libgatbcore-dev, libboost-dev, libhdf5-dev, zlib1g-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. -(Reading database ... 20009 files and directories currently installed.) +(Reading database ... 20004 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: @@ -250,10 +282,10 @@ Get: 121 http://deb.debian.org/debian forky/main arm64 libjpeg62-turbo-dev arm64 1:2.1.5-4 [293 kB] Get: 122 http://deb.debian.org/debian forky/main arm64 libjpeg-dev arm64 1:2.1.5-4 [72.2 kB] Get: 123 http://deb.debian.org/debian forky/main arm64 libhdf5-dev arm64 1.14.5+repack-3 [3225 kB] -Fetched 69.6 MB in 1s (109 MB/s) +Fetched 69.6 MB in 0s (251 MB/s) Preconfiguring packages ... Selecting previously unselected package libexpat1: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 ... 20009 files and directories currently installed.) +(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 ... 20004 files and directories currently installed.) Preparing to unpack .../libexpat1_2.7.1-2_arm64.deb ... Unpacking libexpat1:arm64 (2.7.1-2) ... Selecting previously unselected package libpython3.13-minimal:arm64. @@ -266,7 +298,7 @@ Setting up libexpat1:arm64 (2.7.1-2) ... Setting up python3.13-minimal (3.13.6-1) ... Selecting previously unselected package python3-minimal. -(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 ... 20343 files and directories currently installed.) +(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 ... 20338 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.13.5-1_arm64.deb ... Unpacking python3-minimal (3.13.5-1) ... Selecting previously unselected package media-types. @@ -302,7 +334,7 @@ Unpacking libpython3-stdlib:arm64 (3.13.5-1) ... Setting up python3-minimal (3.13.5-1) ... Selecting previously unselected package python3. -(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 ... 21358 files and directories currently installed.) +(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 ... 21353 files and directories currently installed.) Preparing to unpack .../000-python3_3.13.5-1_arm64.deb ... Unpacking python3 (3.13.5-1) ... Selecting previously unselected package libproc2-0:arm64. @@ -659,8 +691,8 @@ Setting up tzdata (2025b-5) ... Current default time zone: 'Etc/UTC' -Local time is now: Mon Sep 21 14:41:45 UTC 2026. -Universal Time is now: Mon Sep 21 14:41:45 UTC 2026. +Local time is now: Tue Aug 19 08:19:45 UTC 2025. +Universal Time is now: Tue Aug 19 08:19:45 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20240727.1) ... @@ -770,7 +802,11 @@ 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/1907524/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for forky +I: user script /srv/workspace/pbuilder/1907524/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 @@ -813,7 +849,7 @@ to work with policies introduced by or earlier. --- Configuring done (1.1s) +-- Configuring done (1.0s) -- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: @@ -848,44 +884,44 @@ make[3]: Entering directory '/build/reproducible-path/discosnp-2.6.2/obj-aarch64-linux-gnu' cd /build/reproducible-path/discosnp-2.6.2/obj-aarch64-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-aarch64-linux-gnu /build/reproducible-path/discosnp-2.6.2/obj-aarch64-linux-gnu/tools/create_coverage_h5_file /build/reproducible-path/discosnp-2.6.2/obj-aarch64-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-aarch64-linux-gnu' -make[3]: Leaving directory '/build/reproducible-path/discosnp-2.6.2/obj-aarch64-linux-gnu' -make -f tools/kissnp2/CMakeFiles/kissnp2.dir/build.make tools/kissnp2/CMakeFiles/kissnp2.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 -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-aarch64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/discosnp-2.6.2/obj-aarch64-linux-gnu' make -f tools/kissreads2/CMakeFiles/kissreads2.dir/build.make tools/kissreads2/CMakeFiles/kissreads2.dir/build make[3]: Leaving directory '/build/reproducible-path/discosnp-2.6.2/obj-aarch64-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-aarch64-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 +[ 5%] Building CXX object tools/create_coverage_h5_file/CMakeFiles/create_coverage_h5_file.dir/src/create_coverage_h5_file.cpp.o +make[3]: Leaving directory '/build/reproducible-path/discosnp-2.6.2/obj-aarch64-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-aarch64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/discosnp-2.6.2/obj-aarch64-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-aarch64-linux-gnu' +cd /build/reproducible-path/discosnp-2.6.2/obj-aarch64-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 -mbranch-protection=standard -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 make[3]: Entering directory '/build/reproducible-path/discosnp-2.6.2/obj-aarch64-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-aarch64-linux-gnu' -[ 5%] Building CXX object tools/read_file_names/CMakeFiles/read_file_names.dir/src/get_read_file_names.cpp.o -[ 15%] Building CXX object tools/kissreads2/CMakeFiles/kissreads2.dir/src/commons.cpp.o -[ 15%] Building CXX object tools/QHC/CMakeFiles/quick_hierarchical_clustering.dir/src/quick_hierarchical_clustering.cpp.o -[ 20%] Building CXX object tools/kissnp2/CMakeFiles/kissnp2.dir/src/Kissnp2.cpp.o -[ 25%] Building CXX object tools/kissnp2/CMakeFiles/kissnp2.dir/src/Bubble.cpp.o -cd /build/reproducible-path/discosnp-2.6.2/obj-aarch64-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 -mbranch-protection=standard -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-aarch64-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 -mbranch-protection=standard -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 +[ 10%] Building CXX object tools/QHC/CMakeFiles/quick_hierarchical_clustering.dir/src/quick_hierarchical_clustering.cpp.o +[ 15%] Building CXX object tools/kissreads2/CMakeFiles/kissreads2.dir/src/Kissreads2.cpp.o +cd /build/reproducible-path/discosnp-2.6.2/obj-aarch64-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 -mbranch-protection=standard -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 +[ 20%] 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-aarch64-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 -mbranch-protection=standard -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-aarch64-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 -mbranch-protection=standard -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-aarch64-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 -mbranch-protection=standard -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 -[ 30%] Building CXX object tools/kissreads2/CMakeFiles/kissreads2.dir/src/interface_xhash.cpp.o +cd /build/reproducible-path/discosnp-2.6.2/obj-aarch64-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 -mbranch-protection=standard -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 +[ 25%] Building CXX object tools/kissreads2/CMakeFiles/kissreads2.dir/src/fragment.cpp.o +[ 30%] Building CXX object tools/kissnp2/CMakeFiles/kissnp2.dir/src/Filter.cpp.o +cd /build/reproducible-path/discosnp-2.6.2/obj-aarch64-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 -mbranch-protection=standard -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-aarch64-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 -mbranch-protection=standard -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 [ 35%] Building CXX object tools/kissreads2/CMakeFiles/kissreads2.dir/src/fragment_index.cpp.o -[ 40%] Building CXX object tools/kissreads2/CMakeFiles/kissreads2.dir/src/Kissreads2.cpp.o -cd /build/reproducible-path/discosnp-2.6.2/obj-aarch64-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 -mbranch-protection=standard -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 -[ 45%] Building CXX object tools/kissreads2/CMakeFiles/kissreads2.dir/src/fragment.cpp.o cd /build/reproducible-path/discosnp-2.6.2/obj-aarch64-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 -mbranch-protection=standard -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-aarch64-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 -mbranch-protection=standard -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 -[ 50%] Building CXX object tools/kissnp2/CMakeFiles/kissnp2.dir/src/main.cpp.o -cd /build/reproducible-path/discosnp-2.6.2/obj-aarch64-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 -mbranch-protection=standard -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 +[ 40%] Building CXX object tools/kissreads2/CMakeFiles/kissreads2.dir/src/commons.cpp.o +[ 45%] Building CXX object tools/kissnp2/CMakeFiles/kissnp2.dir/src/Kissnp2.cpp.o +cd /build/reproducible-path/discosnp-2.6.2/obj-aarch64-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 -mbranch-protection=standard -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 +[ 50%] Building CXX object tools/kissnp2/CMakeFiles/kissnp2.dir/src/Bubble.cpp.o +cd /build/reproducible-path/discosnp-2.6.2/obj-aarch64-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 -mbranch-protection=standard -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/kissnp2/CMakeFiles/kissnp2.dir/src/main.cpp.o +cd /build/reproducible-path/discosnp-2.6.2/obj-aarch64-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 -mbranch-protection=standard -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-aarch64-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 -mbranch-protection=standard -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-aarch64-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 -mbranch-protection=standard -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 -[ 60%] Building CXX object tools/create_coverage_h5_file/CMakeFiles/create_coverage_h5_file.dir/src/create_coverage_h5_file.cpp.o -[ 55%] Building CXX object tools/kissnp2/CMakeFiles/kissnp2.dir/src/Filter.cpp.o -cd /build/reproducible-path/discosnp-2.6.2/obj-aarch64-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 -mbranch-protection=standard -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-aarch64-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 -mbranch-protection=standard -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 [ 65%] Linking CXX executable ../../bin/quick_hierarchical_clustering cd /build/reproducible-path/discosnp-2.6.2/obj-aarch64-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 -mbranch-protection=standard -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/aarch64-linux-gnu/hdf5/serial -Wl,-rpath,/usr/lib/aarch64-linux-gnu/hdf5/serial: -lgatbcore -lhdf5 -lz @@ -1010,12 +1046,14 @@ 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/1907524/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1907524/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/2445974 and its subdirectories -I: Current time: Mon Sep 21 02:42:17 -12 2026 -I: pbuilder-time-stamp: 1790001737 +I: removing directory /srv/workspace/pbuilder/1907524 and its subdirectories +I: Current time: Tue Aug 19 22:20:23 +14 2025 +I: pbuilder-time-stamp: 1755591623