Diff of the two buildlogs: -- --- b1/build.log 2025-01-26 07:50:38.667814634 +0000 +++ b2/build.log 2025-01-26 07:56:19.912490839 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sat Feb 28 02:11:54 -12 2026 -I: pbuilder-time-stamp: 1772287914 +I: Current time: Sun Jan 26 21:50:41 +14 2025 +I: pbuilder-time-stamp: 1737877841 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -28,52 +28,84 @@ dpkg-source: info: applying disable-failing-bustools-test.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/804997/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2464092/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 Jan 26 07:50 /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/2464092/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2464092/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='trixie' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='9c392287ac7044059ea59beed3bd72e2' - 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='804997' - PS1='# ' - PS2='> ' + INVOCATION_ID=93f93755c4b24a789fff6d5ea02c31bd + 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=2464092 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.Q6nwQWb1/pbuilderrc_f4An --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.Q6nwQWb1/b1 --logfile b1/build.log kallisto_0.48.0+dfsg-4.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' - 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.Q6nwQWb1/pbuilderrc_mdeO --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.Q6nwQWb1/b2 --logfile b2/build.log kallisto_0.48.0+dfsg-4.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' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink03-arm64 6.1.0-30-cloud-arm64 #1 SMP Debian 6.1.124-1 (2025-01-12) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-30-cloud-arm64 #1 SMP Debian 6.1.124-1 (2025-01-12) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/804997/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/2464092/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -330,7 +362,7 @@ Get: 209 http://deb.debian.org/debian trixie/main arm64 python3-yaml arm64 6.0.2-1+b1 [148 kB] Get: 210 http://deb.debian.org/debian trixie/main arm64 python3-yte all 1.5.4-1 [13.6 kB] Get: 211 http://deb.debian.org/debian trixie/main arm64 snakemake all 7.32.4-6 [318 kB] -Fetched 87.1 MB in 1s (114 MB/s) +Fetched 87.1 MB in 1s (72.8 MB/s) Preconfiguring packages ... Selecting previously unselected package libpython3.12-minimal: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 ... 19970 files and directories currently installed.) @@ -1010,8 +1042,8 @@ Setting up tzdata (2024b-6) ... Current default time zone: 'Etc/UTC' -Local time is now: Sat Feb 28 14:12:23 UTC 2026. -Universal Time is now: Sat Feb 28 14:12:23 UTC 2026. +Local time is now: Sun Jan 26 07:52:06 UTC 2025. +Universal Time is now: Sun Jan 26 07:52:06 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up liberror-perl (0.17029-2) ... @@ -1217,7 +1249,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/kallisto-0.48.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../kallisto_0.48.0+dfsg-4_source.changes +I: user script /srv/workspace/pbuilder/2464092/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/2464092/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/kallisto-0.48.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../kallisto_0.48.0+dfsg-4_source.changes dpkg-buildpackage: info: source package kallisto dpkg-buildpackage: info: source version 0.48.0+dfsg-4 dpkg-buildpackage: info: source distribution unstable @@ -1262,7 +1298,7 @@ -- Found Threads: TRUE -- Found ZLIB: /usr/lib/aarch64-linux-gnu/libz.so (found version "1.3.1") Functional testing enabled. --- Configuring done (1.4s) +-- Configuring done (3.0s) -- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: @@ -1287,25 +1323,25 @@ make[3]: Leaving directory '/build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu' make -f src/CMakeFiles/kallisto_core.dir/build.make src/CMakeFiles/kallisto_core.dir/build make[3]: Entering directory '/build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu' -[ 9%] Building CXX object src/CMakeFiles/kallisto_core.dir/Bootstrap.cpp.o -[ 9%] Building CXX object src/CMakeFiles/kallisto_core.dir/GeneModel.cpp.o -[ 19%] Building CXX object src/CMakeFiles/kallisto_core.dir/H5Writer.cpp.o -[ 19%] Building CXX object src/CMakeFiles/kallisto_core.dir/BUSData.cpp.o -[ 23%] Building CXX object src/CMakeFiles/kallisto_core.dir/Kmer.cpp.o -[ 28%] Building CXX object src/CMakeFiles/kallisto_core.dir/KmerIndex.cpp.o -[ 33%] Building CXX object src/CMakeFiles/kallisto_core.dir/KmerIterator.cpp.o -[ 38%] Building CXX object src/CMakeFiles/kallisto_core.dir/BUSTools.cpp.o -[ 42%] Building CXX object src/CMakeFiles/kallisto_core.dir/Merge.cpp.o +[ 4%] Building CXX object src/CMakeFiles/kallisto_core.dir/BUSData.cpp.o cd /build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/kallisto-0.48.0+dfsg/src -g -O2 -ffile-prefix-map=/build/reproducible-path/kallisto-0.48.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -MD -MT src/CMakeFiles/kallisto_core.dir/BUSData.cpp.o -MF CMakeFiles/kallisto_core.dir/BUSData.cpp.o.d -o CMakeFiles/kallisto_core.dir/BUSData.cpp.o -c /build/reproducible-path/kallisto-0.48.0+dfsg/src/BUSData.cpp +[ 9%] Building CXX object src/CMakeFiles/kallisto_core.dir/BUSTools.cpp.o +[ 14%] Building CXX object src/CMakeFiles/kallisto_core.dir/Bootstrap.cpp.o +cd /build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/kallisto-0.48.0+dfsg/src -g -O2 -ffile-prefix-map=/build/reproducible-path/kallisto-0.48.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -MD -MT src/CMakeFiles/kallisto_core.dir/BUSTools.cpp.o -MF CMakeFiles/kallisto_core.dir/BUSTools.cpp.o.d -o CMakeFiles/kallisto_core.dir/BUSTools.cpp.o -c /build/reproducible-path/kallisto-0.48.0+dfsg/src/BUSTools.cpp cd /build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/kallisto-0.48.0+dfsg/src -g -O2 -ffile-prefix-map=/build/reproducible-path/kallisto-0.48.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -MD -MT src/CMakeFiles/kallisto_core.dir/Bootstrap.cpp.o -MF CMakeFiles/kallisto_core.dir/Bootstrap.cpp.o.d -o CMakeFiles/kallisto_core.dir/Bootstrap.cpp.o -c /build/reproducible-path/kallisto-0.48.0+dfsg/src/Bootstrap.cpp +[ 19%] Building CXX object src/CMakeFiles/kallisto_core.dir/GeneModel.cpp.o cd /build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/kallisto-0.48.0+dfsg/src -g -O2 -ffile-prefix-map=/build/reproducible-path/kallisto-0.48.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -MD -MT src/CMakeFiles/kallisto_core.dir/GeneModel.cpp.o -MF CMakeFiles/kallisto_core.dir/GeneModel.cpp.o.d -o CMakeFiles/kallisto_core.dir/GeneModel.cpp.o -c /build/reproducible-path/kallisto-0.48.0+dfsg/src/GeneModel.cpp +[ 23%] Building CXX object src/CMakeFiles/kallisto_core.dir/H5Writer.cpp.o cd /build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/kallisto-0.48.0+dfsg/src -g -O2 -ffile-prefix-map=/build/reproducible-path/kallisto-0.48.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -MD -MT src/CMakeFiles/kallisto_core.dir/H5Writer.cpp.o -MF CMakeFiles/kallisto_core.dir/H5Writer.cpp.o.d -o CMakeFiles/kallisto_core.dir/H5Writer.cpp.o -c /build/reproducible-path/kallisto-0.48.0+dfsg/src/H5Writer.cpp -cd /build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/kallisto-0.48.0+dfsg/src -g -O2 -ffile-prefix-map=/build/reproducible-path/kallisto-0.48.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -MD -MT src/CMakeFiles/kallisto_core.dir/BUSTools.cpp.o -MF CMakeFiles/kallisto_core.dir/BUSTools.cpp.o.d -o CMakeFiles/kallisto_core.dir/BUSTools.cpp.o -c /build/reproducible-path/kallisto-0.48.0+dfsg/src/BUSTools.cpp +[ 28%] Building CXX object src/CMakeFiles/kallisto_core.dir/Kmer.cpp.o cd /build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/kallisto-0.48.0+dfsg/src -g -O2 -ffile-prefix-map=/build/reproducible-path/kallisto-0.48.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -MD -MT src/CMakeFiles/kallisto_core.dir/Kmer.cpp.o -MF CMakeFiles/kallisto_core.dir/Kmer.cpp.o.d -o CMakeFiles/kallisto_core.dir/Kmer.cpp.o -c /build/reproducible-path/kallisto-0.48.0+dfsg/src/Kmer.cpp +[ 33%] Building CXX object src/CMakeFiles/kallisto_core.dir/KmerIndex.cpp.o cd /build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/kallisto-0.48.0+dfsg/src -g -O2 -ffile-prefix-map=/build/reproducible-path/kallisto-0.48.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -MD -MT src/CMakeFiles/kallisto_core.dir/KmerIndex.cpp.o -MF CMakeFiles/kallisto_core.dir/KmerIndex.cpp.o.d -o CMakeFiles/kallisto_core.dir/KmerIndex.cpp.o -c /build/reproducible-path/kallisto-0.48.0+dfsg/src/KmerIndex.cpp +[ 38%] Building CXX object src/CMakeFiles/kallisto_core.dir/KmerIterator.cpp.o cd /build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/kallisto-0.48.0+dfsg/src -g -O2 -ffile-prefix-map=/build/reproducible-path/kallisto-0.48.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -MD -MT src/CMakeFiles/kallisto_core.dir/KmerIterator.cpp.o -MF CMakeFiles/kallisto_core.dir/KmerIterator.cpp.o.d -o CMakeFiles/kallisto_core.dir/KmerIterator.cpp.o -c /build/reproducible-path/kallisto-0.48.0+dfsg/src/KmerIterator.cpp +[ 42%] Building CXX object src/CMakeFiles/kallisto_core.dir/MinCollector.cpp.o +[ 47%] Building CXX object src/CMakeFiles/kallisto_core.dir/Merge.cpp.o cd /build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/kallisto-0.48.0+dfsg/src -g -O2 -ffile-prefix-map=/build/reproducible-path/kallisto-0.48.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -MD -MT src/CMakeFiles/kallisto_core.dir/Merge.cpp.o -MF CMakeFiles/kallisto_core.dir/Merge.cpp.o.d -o CMakeFiles/kallisto_core.dir/Merge.cpp.o -c /build/reproducible-path/kallisto-0.48.0+dfsg/src/Merge.cpp -[ 47%] Building CXX object src/CMakeFiles/kallisto_core.dir/MinCollector.cpp.o [ 52%] Building CXX object src/CMakeFiles/kallisto_core.dir/PlaintextWriter.cpp.o cd /build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/kallisto-0.48.0+dfsg/src -g -O2 -ffile-prefix-map=/build/reproducible-path/kallisto-0.48.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -MD -MT src/CMakeFiles/kallisto_core.dir/MinCollector.cpp.o -MF CMakeFiles/kallisto_core.dir/MinCollector.cpp.o.d -o CMakeFiles/kallisto_core.dir/MinCollector.cpp.o -c /build/reproducible-path/kallisto-0.48.0+dfsg/src/MinCollector.cpp cd /build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/kallisto-0.48.0+dfsg/src -g -O2 -ffile-prefix-map=/build/reproducible-path/kallisto-0.48.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -MD -MT src/CMakeFiles/kallisto_core.dir/PlaintextWriter.cpp.o -MF CMakeFiles/kallisto_core.dir/PlaintextWriter.cpp.o.d -o CMakeFiles/kallisto_core.dir/PlaintextWriter.cpp.o -c /build/reproducible-path/kallisto-0.48.0+dfsg/src/PlaintextWriter.cpp @@ -1320,8 +1356,8 @@ [ 76%] Building CXX object src/CMakeFiles/kallisto_core.dir/hash.cpp.o cd /build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/kallisto-0.48.0+dfsg/src -g -O2 -ffile-prefix-map=/build/reproducible-path/kallisto-0.48.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -MD -MT src/CMakeFiles/kallisto_core.dir/hash.cpp.o -MF CMakeFiles/kallisto_core.dir/hash.cpp.o.d -o CMakeFiles/kallisto_core.dir/hash.cpp.o -c /build/reproducible-path/kallisto-0.48.0+dfsg/src/hash.cpp [ 80%] Building CXX object src/CMakeFiles/kallisto_core.dir/main.cpp.o -[ 85%] Building CXX object src/CMakeFiles/kallisto_core.dir/weights.cpp.o cd /build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/kallisto-0.48.0+dfsg/src -g -O2 -ffile-prefix-map=/build/reproducible-path/kallisto-0.48.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -MD -MT src/CMakeFiles/kallisto_core.dir/main.cpp.o -MF CMakeFiles/kallisto_core.dir/main.cpp.o.d -o CMakeFiles/kallisto_core.dir/main.cpp.o -c /build/reproducible-path/kallisto-0.48.0+dfsg/src/main.cpp +[ 85%] Building CXX object src/CMakeFiles/kallisto_core.dir/weights.cpp.o cd /build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/kallisto-0.48.0+dfsg/src -g -O2 -ffile-prefix-map=/build/reproducible-path/kallisto-0.48.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -MD -MT src/CMakeFiles/kallisto_core.dir/weights.cpp.o -MF CMakeFiles/kallisto_core.dir/weights.cpp.o.d -o CMakeFiles/kallisto_core.dir/weights.cpp.o -c /build/reproducible-path/kallisto-0.48.0+dfsg/src/weights.cpp [ 90%] Linking CXX static library libkallisto_core.a cd /build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/cmake -P CMakeFiles/kallisto_core.dir/cmake_clean_target.cmake @@ -1459,7 +1495,7 @@ /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu/CMakeFiles 0 make[3]: Leaving directory '/build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu' make[2]: Leaving directory '/build/reproducible-path/kallisto-0.48.0+dfsg/obj-aarch64-linux-gnu' -cd test && PATH=$(find ../obj-* -name src):/usr/sbin:/usr/bin:/sbin:/bin:/usr/games HOME=$(mktemp --directory) snakemake --cores 1 +cd test && PATH=$(find ../obj-* -name src):/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path HOME=$(mktemp --directory) snakemake --cores 1 Building DAG of jobs... Using shell: /usr/bin/bash Provided cores: 1 (use --cores to define parallelism) @@ -1475,7 +1511,7 @@ Select jobs to execute... -[Sat Feb 28 02:13:26 2026] +[Sun Jan 26 21:55:56 2025] rule index: input: transcripts.fasta.gz output: transcripts.kidx @@ -1491,12 +1527,12 @@ [build] creating equivalence classes ... done [build] target de Bruijn graph has 27 contigs and contains 22118 k-mers -[Sat Feb 28 02:13:26 2026] +[Sun Jan 26 21:55:56 2025] Finished job 2. 1 of 4 steps (25%) done Select jobs to execute... -[Sat Feb 28 02:13:26 2026] +[Sun Jan 26 21:55:57 2025] rule kallisto_quant: input: reads_1.fastq.gz, reads_2.fastq.gz, transcripts.kidx output: quant_out/abundance.tsv, quant_out/run_info.json @@ -1526,12 +1562,12 @@ [ bam] sorting BAM files .. done [ bam] indexing BAM file .. done -[Sat Feb 28 02:13:28 2026] +[Sun Jan 26 21:56:02 2025] Finished job 1. 2 of 4 steps (50%) done Select jobs to execute... -[Sat Feb 28 02:13:28 2026] +[Sun Jan 26 21:56:02 2025] rule kallisto_bus: input: sc_reads_1.fastq.gz, sc_reads_2.fastq.gz, transcripts.kidx output: bus_out/matrix.ec, bus_out/transcripts.txt, bus_out/output.bus, bus_out/run_info.json @@ -1550,22 +1586,22 @@ [quant] finding pseudoalignments for the reads ... done [quant] processed 10,000 reads, 4,808 reads pseudoaligned -[Sat Feb 28 02:13:28 2026] +[Sun Jan 26 21:56:02 2025] Finished job 3. 3 of 4 steps (75%) done Select jobs to execute... -[Sat Feb 28 02:13:28 2026] +[Sun Jan 26 21:56:02 2025] localrule all: input: quant_out/abundance.tsv, bus_out/output.bus jobid: 0 reason: Input files updated by another job: quant_out/abundance.tsv, bus_out/output.bus resources: tmpdir=/tmp -[Sat Feb 28 02:13:28 2026] +[Sun Jan 26 21:56:02 2025] Finished job 0. 4 of 4 steps (100%) done -Complete log: .snakemake/log/2026-02-28T021326.500374.snakemake.log +Complete log: .snakemake/log/2025-01-26T215556.384258.snakemake.log rm -rf test/.snakemake test/bus_out test/quant_out/run_info.json test/transcripts.kidx.gz make[1]: Leaving directory '/build/reproducible-path/kallisto-0.48.0+dfsg' create-stamp debian/debhelper-build-stamp @@ -1605,8 +1641,8 @@ dh_md5sums dh_builddeb dpkg-deb: building package 'kallisto' in '../kallisto_0.48.0+dfsg-4_arm64.deb'. -dpkg-deb: building package 'kallisto-dbgsym' in '../kallisto-dbgsym_0.48.0+dfsg-4_arm64.deb'. dpkg-deb: building package 'kallisto-examples' in '../kallisto-examples_0.48.0+dfsg-4_all.deb'. +dpkg-deb: building package 'kallisto-dbgsym' in '../kallisto-dbgsym_0.48.0+dfsg-4_arm64.deb'. dpkg-genbuildinfo --build=binary -O../kallisto_0.48.0+dfsg-4_arm64.buildinfo dpkg-genchanges --build=binary -O../kallisto_0.48.0+dfsg-4_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -1614,12 +1650,14 @@ 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/2464092/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2464092/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/804997 and its subdirectories -I: Current time: Sat Feb 28 02:13:36 -12 2026 -I: pbuilder-time-stamp: 1772288016 +I: removing directory /srv/workspace/pbuilder/2464092 and its subdirectories +I: Current time: Sun Jan 26 21:56:18 +14 2025 +I: pbuilder-time-stamp: 1737878178