Diff of the two buildlogs: -- --- b1/build.log 2024-05-14 08:41:00.116402888 +0000 +++ b2/build.log 2024-05-14 08:46:25.574568713 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Jun 16 02:50:31 -12 2025 -I: pbuilder-time-stamp: 1750085431 +I: Current time: Tue May 14 22:41:02 +14 2024 +I: pbuilder-time-stamp: 1715676062 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -32,51 +32,83 @@ 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/624464/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1753683/tmp/hooks/D01_modify_environment starting +debug: Running on infom01-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 May 14 08:41 /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/1753683/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1753683/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='f906201f6aa8467891cee91b302d51a5' - 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='624464' - PS1='# ' - PS2='> ' + INVOCATION_ID=96be52237a684a8aac89d000c073fed6 + 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=1753683 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.ZQNOOJRm/pbuilderrc_Ojwb --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.ZQNOOJRm/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' + 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.ZQNOOJRm/pbuilderrc_NQsq --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.ZQNOOJRm/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' I: uname -a - Linux infom02-amd64 6.6.13+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.6.13-1~bpo12+1 (2024-02-15) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-21-cloud-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.90-1 (2024-05-03) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Jun 16 03:14 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/624464/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 May 11 11:26 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/1753683/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -336,7 +368,7 @@ Get: 212 http://deb.debian.org/debian trixie/main amd64 python3-wrapt amd64 1.15.0-2+b1 [49.3 kB] Get: 213 http://deb.debian.org/debian trixie/main amd64 python3-yte all 1.5.4-1 [13.6 kB] Get: 214 http://deb.debian.org/debian trixie/main amd64 snakemake all 7.32.4-3 [318 kB] -Fetched 103 MB in 4s (27.2 MB/s) +Fetched 103 MB in 1s (92.1 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.) @@ -1023,8 +1055,8 @@ Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' -Local time is now: Mon Jun 16 14:54:02 UTC 2025. -Universal Time is now: Mon Jun 16 14:54:02 UTC 2025. +Local time is now: Tue May 14 08:43:29 UTC 2024. +Universal Time is now: Tue May 14 08:43:29 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up liberror-perl (0.17029-2) ... @@ -1232,7 +1264,11 @@ 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/1753683/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/1753683/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 @@ -1276,7 +1312,7 @@ -- Found Threads: TRUE -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.3") Functional testing enabled. --- Configuring done (4.3s) +-- Configuring done (1.3s) -- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: @@ -1301,32 +1337,32 @@ make[3]: Leaving directory '/build/reproducible-path/kallisto-0.48.0+dfsg/obj-x86_64-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-x86_64-linux-gnu' -[ 4%] Building CXX object src/CMakeFiles/kallisto_core.dir/BUSTools.cpp.o -[ 9%] Building CXX object src/CMakeFiles/kallisto_core.dir/H5Writer.cpp.o -cd /build/reproducible-path/kallisto-0.48.0+dfsg/obj-x86_64-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 -fcf-protection -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 -[ 14%] Building CXX object src/CMakeFiles/kallisto_core.dir/Bootstrap.cpp.o +[ 4%] Building CXX object src/CMakeFiles/kallisto_core.dir/BUSData.cpp.o +[ 19%] Building CXX object src/CMakeFiles/kallisto_core.dir/PlaintextWriter.cpp.o +[ 19%] Building CXX object src/CMakeFiles/kallisto_core.dir/Bootstrap.cpp.o +[ 19%] Building CXX object src/CMakeFiles/kallisto_core.dir/BUSTools.cpp.o +[ 33%] Building CXX object src/CMakeFiles/kallisto_core.dir/KmerIterator.cpp.o +[ 33%] Building CXX object src/CMakeFiles/kallisto_core.dir/GeneModel.cpp.o +[ 33%] Building CXX object src/CMakeFiles/kallisto_core.dir/H5Writer.cpp.o +[ 38%] Building CXX object src/CMakeFiles/kallisto_core.dir/MinCollector.cpp.o +[ 42%] Building CXX object src/CMakeFiles/kallisto_core.dir/KmerIndex.cpp.o +cd /build/reproducible-path/kallisto-0.48.0+dfsg/obj-x86_64-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 -fcf-protection -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 +[ 47%] Building CXX object src/CMakeFiles/kallisto_core.dir/ProcessReads.cpp.o +cd /build/reproducible-path/kallisto-0.48.0+dfsg/obj-x86_64-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 -fcf-protection -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 cd /build/reproducible-path/kallisto-0.48.0+dfsg/obj-x86_64-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 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src/CMakeFiles/kallisto_core.dir/KmerIterator.cpp.o -[ 33%] Building CXX object src/CMakeFiles/kallisto_core.dir/Kmer.cpp.o -cd /build/reproducible-path/kallisto-0.48.0+dfsg/obj-x86_64-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 -fcf-protection -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 -cd /build/reproducible-path/kallisto-0.48.0+dfsg/obj-x86_64-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 -fcf-protection -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 -[ 38%] Building CXX object src/CMakeFiles/kallisto_core.dir/KmerIndex.cpp.o -[ 42%] Building CXX object src/CMakeFiles/kallisto_core.dir/PlaintextWriter.cpp.o -[ 19%] Building CXX object src/CMakeFiles/kallisto_core.dir/GeneModel.cpp.o cd /build/reproducible-path/kallisto-0.48.0+dfsg/obj-x86_64-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 -fcf-protection -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 -[ 47%] Building CXX object src/CMakeFiles/kallisto_core.dir/Merge.cpp.o -cd /build/reproducible-path/kallisto-0.48.0+dfsg/obj-x86_64-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 -fcf-protection -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 +[ 52%] Building CXX object src/CMakeFiles/kallisto_core.dir/Merge.cpp.o +cd /build/reproducible-path/kallisto-0.48.0+dfsg/obj-x86_64-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 -fcf-protection -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-x86_64-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 -fcf-protection -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 -cd /build/reproducible-path/kallisto-0.48.0+dfsg/obj-x86_64-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 -fcf-protection -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 -cd /build/reproducible-path/kallisto-0.48.0+dfsg/obj-x86_64-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 -fcf-protection -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 -[ 52%] Building CXX object src/CMakeFiles/kallisto_core.dir/MinCollector.cpp.o +cd /build/reproducible-path/kallisto-0.48.0+dfsg/obj-x86_64-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 -fcf-protection -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 cd /build/reproducible-path/kallisto-0.48.0+dfsg/obj-x86_64-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 -fcf-protection -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 -[ 57%] Building CXX object src/CMakeFiles/kallisto_core.dir/PseudoBam.cpp.o -cd /build/reproducible-path/kallisto-0.48.0+dfsg/obj-x86_64-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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -MD -MT src/CMakeFiles/kallisto_core.dir/PseudoBam.cpp.o -MF CMakeFiles/kallisto_core.dir/PseudoBam.cpp.o.d -o CMakeFiles/kallisto_core.dir/PseudoBam.cpp.o -c /build/reproducible-path/kallisto-0.48.0+dfsg/src/PseudoBam.cpp -[ 61%] Building CXX object src/CMakeFiles/kallisto_core.dir/ProcessReads.cpp.o cd /build/reproducible-path/kallisto-0.48.0+dfsg/obj-x86_64-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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -MD -MT src/CMakeFiles/kallisto_core.dir/ProcessReads.cpp.o -MF CMakeFiles/kallisto_core.dir/ProcessReads.cpp.o.d -o CMakeFiles/kallisto_core.dir/ProcessReads.cpp.o -c /build/reproducible-path/kallisto-0.48.0+dfsg/src/ProcessReads.cpp +cd /build/reproducible-path/kallisto-0.48.0+dfsg/obj-x86_64-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 -fcf-protection -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 +[ 57%] Building CXX object src/CMakeFiles/kallisto_core.dir/Kmer.cpp.o +cd /build/reproducible-path/kallisto-0.48.0+dfsg/obj-x86_64-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 -fcf-protection -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 +[ 61%] Building CXX object src/CMakeFiles/kallisto_core.dir/PseudoBam.cpp.o +cd /build/reproducible-path/kallisto-0.48.0+dfsg/obj-x86_64-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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -MD -MT src/CMakeFiles/kallisto_core.dir/PseudoBam.cpp.o -MF CMakeFiles/kallisto_core.dir/PseudoBam.cpp.o.d -o CMakeFiles/kallisto_core.dir/PseudoBam.cpp.o -c /build/reproducible-path/kallisto-0.48.0+dfsg/src/PseudoBam.cpp [ 66%] Building CXX object src/CMakeFiles/kallisto_core.dir/common.cpp.o cd /build/reproducible-path/kallisto-0.48.0+dfsg/obj-x86_64-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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -MD -MT src/CMakeFiles/kallisto_core.dir/common.cpp.o -MF CMakeFiles/kallisto_core.dir/common.cpp.o.d -o CMakeFiles/kallisto_core.dir/common.cpp.o -c /build/reproducible-path/kallisto-0.48.0+dfsg/src/common.cpp [ 71%] Building CXX object src/CMakeFiles/kallisto_core.dir/h5utils.cpp.o @@ -1473,7 +1509,7 @@ /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/kallisto-0.48.0+dfsg/obj-x86_64-linux-gnu/CMakeFiles 0 make[3]: Leaving directory '/build/reproducible-path/kallisto-0.48.0+dfsg/obj-x86_64-linux-gnu' make[2]: Leaving directory '/build/reproducible-path/kallisto-0.48.0+dfsg/obj-x86_64-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) @@ -1489,7 +1525,7 @@ Select jobs to execute... -[Mon Jun 16 03:02:56 2025] +[Tue May 14 22:46:09 2024] rule index: input: transcripts.fasta.gz output: transcripts.kidx @@ -1505,12 +1541,12 @@ [build] creating equivalence classes ... done [build] target de Bruijn graph has 27 contigs and contains 22118 k-mers -[Mon Jun 16 03:02:56 2025] +[Tue May 14 22:46:09 2024] Finished job 2. 1 of 4 steps (25%) done Select jobs to execute... -[Mon Jun 16 03:02:56 2025] +[Tue May 14 22:46:09 2024] rule kallisto_quant: input: reads_1.fastq.gz, reads_2.fastq.gz, transcripts.kidx output: quant_out/abundance.tsv, quant_out/run_info.json @@ -1540,12 +1576,12 @@ [ bam] sorting BAM files .. done [ bam] indexing BAM file .. done -[Mon Jun 16 03:03:04 2025] +[Tue May 14 22:46:14 2024] Finished job 1. 2 of 4 steps (50%) done Select jobs to execute... -[Mon Jun 16 03:03:04 2025] +[Tue May 14 22:46:14 2024] 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 @@ -1564,22 +1600,22 @@ [quant] finding pseudoalignments for the reads ... done [quant] processed 10,000 reads, 4,808 reads pseudoaligned -[Mon Jun 16 03:03:04 2025] +[Tue May 14 22:46:14 2024] Finished job 3. 3 of 4 steps (75%) done Select jobs to execute... -[Mon Jun 16 03:03:04 2025] +[Tue May 14 22:46:14 2024] 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 + reason: Input files updated by another job: bus_out/output.bus, quant_out/abundance.tsv resources: tmpdir=/tmp -[Mon Jun 16 03:03:04 2025] +[Tue May 14 22:46:14 2024] Finished job 0. 4 of 4 steps (100%) done -Complete log: .snakemake/log/2025-06-16T030255.420060.snakemake.log +Complete log: .snakemake/log/2024-05-14T224609.080171.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 @@ -1624,12 +1660,14 @@ 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/1753683/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1753683/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/624464 and its subdirectories -I: Current time: Mon Jun 16 03:03:59 -12 2025 -I: pbuilder-time-stamp: 1750086239 +I: removing directory /srv/workspace/pbuilder/1753683 and its subdirectories +I: Current time: Tue May 14 22:46:24 +14 2024 +I: pbuilder-time-stamp: 1715676384