Diff of the two buildlogs: -- --- b1/build.log 2025-03-11 18:08:14.747407141 +0000 +++ b2/build.log 2025-03-11 18:11:08.283564509 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Apr 13 12:25:56 -12 2026 -I: pbuilder-time-stamp: 1776126356 +I: Current time: Wed Mar 12 08:08:16 +14 2025 +I: pbuilder-time-stamp: 1741716496 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/2223227/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1028148/tmp/hooks/D01_modify_environment starting +debug: Running on ionos1-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Mar 11 18:08 /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/1028148/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1028148/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' + 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='28da34f217584f76866226501679f576' - 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='2223227' - PS1='# ' - PS2='> ' + INVOCATION_ID=03dd2b5ad63643ff91ba05da2c100385 + 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=1028148 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.RtMUpntC/pbuilderrc_fNDt --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.RtMUpntC/b1 --logfile b1/build.log kallisto_0.48.0+dfsg-4.dsc' - SUDO_GID='111' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://213.165.73.152:3128' + 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.RtMUpntC/pbuilderrc_sivW --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.RtMUpntC/b2 --logfile b2/build.log kallisto_0.48.0+dfsg-4.dsc' + SUDO_GID=110 + SUDO_UID=105 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://46.16.76.132:3128 I: uname -a - Linux ionos15-amd64 6.12.12+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.12-1~bpo12+1 (2025-02-23) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-31-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.128-1 (2025-02-07) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Mar 4 2025 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/2223227/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Mar 4 11:20 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/1028148/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -327,7 +359,7 @@ Get: 206 http://deb.debian.org/debian trixie/main amd64 python3-yaml amd64 6.0.2-1+b2 [136 kB] Get: 207 http://deb.debian.org/debian trixie/main amd64 python3-yte all 1.5.4-1 [13.6 kB] Get: 208 http://deb.debian.org/debian trixie/main amd64 snakemake all 7.32.4-7 [318 kB] -Fetched 92.6 MB in 9s (10.1 MB/s) +Fetched 92.6 MB in 3s (33.0 MB/s) Preconfiguring packages ... Selecting previously unselected package libpython3.13-minimal:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19800 files and directories currently installed.) @@ -995,8 +1027,8 @@ Setting up tzdata (2025a-2) ... Current default time zone: 'Etc/UTC' -Local time is now: Tue Apr 14 00:28:18 UTC 2026. -Universal Time is now: Tue Apr 14 00:28:18 UTC 2026. +Local time is now: Tue Mar 11 18:09:35 UTC 2025. +Universal Time is now: Tue Mar 11 18:09:35 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up liberror-perl (0.17030-1) ... @@ -1200,7 +1232,11 @@ 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/1028148/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/1028148/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 @@ -1245,7 +1281,7 @@ -- Found Threads: TRUE -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.3.1") Functional testing enabled. --- Configuring done (5.0s) +-- Configuring done (1.0s) -- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: @@ -1258,7 +1294,7 @@ -- Build files have been written to: /build/reproducible-path/kallisto-0.48.0+dfsg/obj-x86_64-linux-gnu make[1]: Leaving directory '/build/reproducible-path/kallisto-0.48.0+dfsg' dh_auto_build - cd obj-x86_64-linux-gnu && make -j42 "INSTALL=install --strip-program=true" VERBOSE=1 + cd obj-x86_64-linux-gnu && make -j20 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/kallisto-0.48.0+dfsg/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/kallisto-0.48.0+dfsg -B/build/reproducible-path/kallisto-0.48.0+dfsg/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/kallisto-0.48.0+dfsg/obj-x86_64-linux-gnu/CMakeFiles /build/reproducible-path/kallisto-0.48.0+dfsg/obj-x86_64-linux-gnu//CMakeFiles/progress.marks @@ -1270,41 +1306,41 @@ 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' -[ 9%] Building CXX object src/CMakeFiles/kallisto_core.dir/H5Writer.cpp.o -[ 9%] Building CXX object src/CMakeFiles/kallisto_core.dir/BUSTools.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/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 -[ 19%] Building CXX object src/CMakeFiles/kallisto_core.dir/BUSData.cpp.o +[ 4%] Building CXX object src/CMakeFiles/kallisto_core.dir/KmerIterator.cpp.o +[ 9%] Building CXX object src/CMakeFiles/kallisto_core.dir/BUSData.cpp.o +[ 19%] Building CXX object src/CMakeFiles/kallisto_core.dir/GeneModel.cpp.o [ 19%] Building CXX object src/CMakeFiles/kallisto_core.dir/Bootstrap.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 -[ 23%] Building CXX object src/CMakeFiles/kallisto_core.dir/GeneModel.cpp.o +[ 23%] Building CXX object src/CMakeFiles/kallisto_core.dir/Merge.cpp.o +[ 28%] 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/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 +[ 61%] Building CXX object src/CMakeFiles/kallisto_core.dir/ProcessReads.cpp.o +[ 61%] Building CXX object src/CMakeFiles/kallisto_core.dir/PseudoBam.cpp.o +[ 61%] Building CXX object src/CMakeFiles/kallisto_core.dir/common.cpp.o +[ 61%] Building CXX object src/CMakeFiles/kallisto_core.dir/Kmer.cpp.o +[ 66%] Building CXX object src/CMakeFiles/kallisto_core.dir/h5utils.cpp.o +[ 66%] Building CXX object src/CMakeFiles/kallisto_core.dir/KmerIndex.cpp.o +[ 61%] Building CXX object src/CMakeFiles/kallisto_core.dir/H5Writer.cpp.o +[ 66%] Building CXX object src/CMakeFiles/kallisto_core.dir/BUSTools.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/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 -[ 28%] Building CXX object src/CMakeFiles/kallisto_core.dir/KmerIterator.cpp.o -[ 33%] Building CXX object src/CMakeFiles/kallisto_core.dir/Merge.cpp.o +[ 71%] Building CXX object src/CMakeFiles/kallisto_core.dir/hash.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 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/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 -[ 38%] 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/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 -[ 42%] 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/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 -[ 76%] Building CXX object src/CMakeFiles/kallisto_core.dir/hash.cpp.o -[ 80%] Building CXX object src/CMakeFiles/kallisto_core.dir/ProcessReads.cpp.o -[ 85%] Building CXX object src/CMakeFiles/kallisto_core.dir/PlaintextWriter.cpp.o -[ 85%] Building CXX object src/CMakeFiles/kallisto_core.dir/Kmer.cpp.o -[ 85%] Building CXX object src/CMakeFiles/kallisto_core.dir/h5utils.cpp.o -[ 85%] Building CXX object src/CMakeFiles/kallisto_core.dir/common.cpp.o -[ 85%] Building CXX object src/CMakeFiles/kallisto_core.dir/PseudoBam.cpp.o -[ 85%] Building CXX object src/CMakeFiles/kallisto_core.dir/weights.cpp.o +[ 76%] Building CXX object src/CMakeFiles/kallisto_core.dir/PlaintextWriter.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/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-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/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 -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 -[ 71%] Building CXX object src/CMakeFiles/kallisto_core.dir/main.cpp.o +[ 80%] Building CXX object src/CMakeFiles/kallisto_core.dir/main.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/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/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/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 +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 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 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/h5utils.cpp.o -MF CMakeFiles/kallisto_core.dir/h5utils.cpp.o.d -o CMakeFiles/kallisto_core.dir/h5utils.cpp.o -c /build/reproducible-path/kallisto-0.48.0+dfsg/src/h5utils.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/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 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/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-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/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-x86_64-linux-gnu/src && /usr/bin/cmake -P CMakeFiles/kallisto_core.dir/cmake_clean_target.cmake @@ -1332,7 +1368,7 @@ debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/kallisto-0.48.0+dfsg' dh_auto_test - cd obj-x86_64-linux-gnu && make -j42 test ARGS\+=--verbose ARGS\+=-j42 + cd obj-x86_64-linux-gnu && make -j20 test ARGS\+=--verbose ARGS\+=-j20 make[2]: Entering directory '/build/reproducible-path/kallisto-0.48.0+dfsg/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/kallisto-0.48.0+dfsg -B/build/reproducible-path/kallisto-0.48.0+dfsg/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 test @@ -1442,7 +1478,7 @@ /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) @@ -1458,7 +1494,7 @@ Select jobs to execute... -[Mon Apr 13 12:30:46 2026] +[Wed Mar 12 08:10:53 2025] rule index: input: transcripts.fasta.gz output: transcripts.kidx @@ -1474,12 +1510,12 @@ [build] creating equivalence classes ... done [build] target de Bruijn graph has 27 contigs and contains 22118 k-mers -[Mon Apr 13 12:30:46 2026] +[Wed Mar 12 08:10:53 2025] Finished job 2. 1 of 4 steps (25%) done Select jobs to execute... -[Mon Apr 13 12:30:46 2026] +[Wed Mar 12 08:10:53 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 @@ -1498,12 +1534,12 @@ [quant] finding pseudoalignments for the reads ... done [quant] processed 10,000 reads, 4,808 reads pseudoaligned -[Mon Apr 13 12:30:47 2026] +[Wed Mar 12 08:10:53 2025] Finished job 3. 2 of 4 steps (50%) done Select jobs to execute... -[Mon Apr 13 12:30:47 2026] +[Wed Mar 12 08:10:53 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 @@ -1533,28 +1569,28 @@ [ bam] sorting BAM files .. done [ bam] indexing BAM file .. done -[Mon Apr 13 12:30:50 2026] +[Wed Mar 12 08:10:56 2025] Finished job 1. 3 of 4 steps (75%) done Select jobs to execute... -[Mon Apr 13 12:30:50 2026] +[Wed Mar 12 08:10:56 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 + reason: Input files updated by another job: bus_out/output.bus, quant_out/abundance.tsv resources: tmpdir=/tmp -[Mon Apr 13 12:30:50 2026] +[Wed Mar 12 08:10:56 2025] Finished job 0. 4 of 4 steps (100%) done -Complete log: .snakemake/log/2026-04-13T123045.935864.snakemake.log +Complete log: .snakemake/log/2025-03-12T081053.372084.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 dh_prep dh_auto_install - cd obj-x86_64-linux-gnu && make -j42 install DESTDIR=/build/reproducible-path/kallisto-0.48.0\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + cd obj-x86_64-linux-gnu && make -j20 install DESTDIR=/build/reproducible-path/kallisto-0.48.0\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/kallisto-0.48.0+dfsg/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/kallisto-0.48.0+dfsg -B/build/reproducible-path/kallisto-0.48.0+dfsg/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall @@ -1584,8 +1620,8 @@ dh_md5sums dh_builddeb dpkg-deb: building package 'kallisto' in '../kallisto_0.48.0+dfsg-4_amd64.deb'. -dpkg-deb: building package 'kallisto-dbgsym' in '../kallisto-dbgsym_0.48.0+dfsg-4_amd64.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_amd64.deb'. dpkg-genbuildinfo --build=binary -O../kallisto_0.48.0+dfsg-4_amd64.buildinfo dpkg-genchanges --build=binary -O../kallisto_0.48.0+dfsg-4_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -1593,12 +1629,14 @@ 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/1028148/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1028148/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/2223227 and its subdirectories -I: Current time: Mon Apr 13 12:31:10 -12 2026 -I: pbuilder-time-stamp: 1776126670 +I: removing directory /srv/workspace/pbuilder/1028148 and its subdirectories +I: Current time: Wed Mar 12 08:11:07 +14 2025 +I: pbuilder-time-stamp: 1741716667