Diff of the two buildlogs: -- --- b1/build.log 2025-02-06 10:32:41.650411466 +0000 +++ b2/build.log 2025-02-06 10:40:59.179900047 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed Feb 5 22:29:10 -12 2025 -I: pbuilder-time-stamp: 1738837750 +I: Current time: Thu Mar 12 06:56:07 +14 2026 +I: pbuilder-time-stamp: 1773248167 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -27,52 +27,84 @@ dpkg-source: info: applying repair.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/1206982/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3917396/tmp/hooks/D01_modify_environment starting +debug: Running on codethink03-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 Mar 11 16:56 /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/3917396/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3917396/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='352bd7fe9e11437681a2d97e539bcc52' - 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='1206982' - PS1='# ' - PS2='> ' + INVOCATION_ID=e9dac69c93494e7b87fa0b5a45526ce5 + 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=3917396 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.zKecEb8X/pbuilderrc_CaSE --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.zKecEb8X/b1 --logfile b1/build.log tnseq-transit_3.3.12-1.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.zKecEb8X/pbuilderrc_JC01 --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.zKecEb8X/b2 --logfile b2/build.log tnseq-transit_3.3.12-1.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 codethink04-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 14:40 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/1206982/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/3917396/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -286,7 +318,7 @@ Get: 154 http://deb.debian.org/debian trixie/main arm64 python3-sklearn all 1.4.2+dfsg-7 [2248 kB] Get: 155 http://deb.debian.org/debian trixie/main arm64 python3-statsmodels-lib arm64 0.14.4+dfsg-1+b2 [2077 kB] Get: 156 http://deb.debian.org/debian trixie/main arm64 python3-statsmodels all 0.14.4+dfsg-1 [4825 kB] -Fetched 125 MB in 0s (252 MB/s) +Fetched 125 MB in 1s (119 MB/s) Preconfiguring packages ... Selecting previously unselected package libpython3.13-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 ... 19957 files and directories currently installed.) @@ -800,8 +832,8 @@ Setting up tzdata (2024b-6) ... Current default time zone: 'Etc/UTC' -Local time is now: Thu Feb 6 10:29:38 UTC 2025. -Universal Time is now: Thu Feb 6 10:29:38 UTC 2025. +Local time is now: Wed Mar 11 16:57:09 UTC 2026. +Universal Time is now: Wed Mar 11 16:57:09 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up unicode-data (15.1.0-1) ... @@ -942,7 +974,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/tnseq-transit-3.3.12/ && 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 > ../tnseq-transit_3.3.12-1_source.changes +I: user script /srv/workspace/pbuilder/3917396/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/3917396/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/tnseq-transit-3.3.12/ && 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 > ../tnseq-transit_3.3.12-1_source.changes dpkg-buildpackage: info: source package tnseq-transit dpkg-buildpackage: info: source version 3.3.12-1 dpkg-buildpackage: info: source distribution unstable @@ -1457,7 +1493,7 @@ ResourceWarning: Enable tracemalloc to get the object allocation traceback [anova] Adding File: /build/reproducible-path/tnseq-transit-3.3.12/tests/testoutput.txt [anova] Finished Anova analysis -[anova] Time: 0.3s +[anova] Time: 1.2s Removing output file... @@ -1481,7 +1517,7 @@ test_resampling_adaptive (tests.test_analysis_methods.TestMethods.test_resampling_adaptive) ... [resampling] [resampling] Performing Benjamini-Hochberg Correction [resampling] Number of significant conditionally essential genes (Padj<0.05): 35 -[resampling] Time: 8.48s +[resampling] Time: 21.30s [resampling] Finished resampling Method Removing output file... @@ -1503,7 +1539,7 @@ [resampling] [resampling] Performing Benjamini-Hochberg Correction [resampling] Number of significant conditionally essential genes (Padj<0.05): 35 -[resampling] Time: 5.49s +[resampling] Time: 12.97s [resampling] Finished resampling Method Removing output file... @@ -1522,9 +1558,9 @@ test_resampling_histogram (tests.test_analysis_methods.TestMethods.test_resampling_histogram) ... [resampling] [resampling] Performing Benjamini-Hochberg Correction [resampling] Number of significant conditionally essential genes (Padj<0.05): 35 -[resampling] Time: 4.27s +[resampling] Time: 13.92s [resampling] Finished resampling Method -37 +38 35 Removing output file... @@ -1542,8 +1578,8 @@ [resampling] Running Resampling Method... 2.0% [resampling] Running Resampling Method... 3.9% [resampling] Running Resampling Method... 5.9% [resampling] Running Resampling Method... 7.8% [resampling] Running Resampling Method... 9.8% [resampling] Running Resampling Method... 11.8% [resampling] Running Resampling Method... 13.7% [resampling] Running Resampling Method... 15.7% [resampling] Running Resampling Method... 17.6% [resampling] Running Resampling Method... 19.6% [resampling] Running Resampling Method... 21.6% [resampling] Running Resampling Method... 23.5% [resampling] Running Resampling Method... 25.5% [resampling] Running Resampling Method... 27.5% [resampling] Running Resampling Method... 29.4% [resampling] Running Resampling Method... 31.4% [resampling] Running Resampling Method... 33.3% [resampling] Running Resampling Method... 35.3% [resampling] Running Resampling Method... 37.3% [resampling] Running Resampling Method... 39.2% [resampling] Running Resampling Method... 41.2% [resampling] Running Resampling Method... 43.1% [resampling] Running Resampling Method... 45.1% [resampling] Running Resampling Method... 47.1% [resampling] Running Resampling Method... 49.0% [resampling] Running Resampling Method... 51.0% [resampling] Running Resampling Method... 52.9% [resampling] Running Resampling Method... 54.9% [resampling] Running Resampling Method... 56.9% [resampling] Running Resampling Method... 58.8% [resampling] Running Resampling Method... 60.8% [resampling] Running Resampling Method... 62.7% [resampling] Running Resampling Method... 64.7% [resampling] Running Resampling Method... 66.7% [resampling] Running Resampling Method... 68.6% [resampling] Running Resampling Method... 70.6% [resampling] Running Resampling Method... 72.5% [resampling] Running Resampling Method... 74.5% [resampling] Running Resampling Method... 76.5% [resampling] Running Resampling Method... 78.4% [resampling] Running Resampling Method... 80.4% [resampling] Running Resampling Method... 82.4% [resampling] Running Resampling Method... 84.3% [resampling] Running Resampling Method... 86.3% [resampling] Running Resampling Method... 88.2% [resampling] Running Resampling Method... 90.2% [resampling] Running Resampling Method... 92.2% [resampling] Running Resampling Method... 94.1% [resampling] Running Resampling Method... 96.1% [resampling] Running Resampling Method... 98.0% [resampling] Running Resampling Method... 100.0% ok test_resampling_multistrain (tests.test_analysis_methods.TestMethods.test_resampling_multistrain) ... [resampling] [resampling] Performing Benjamini-Hochberg Correction -[resampling] Number of significant conditionally essential genes (Padj<0.05): 34 -[resampling] Time: 10.53s +[resampling] Number of significant conditionally essential genes (Padj<0.05): 35 +[resampling] Time: 22.14s [resampling] Finished resampling Method Removing histogram files Removing output file... @@ -1565,7 +1601,7 @@ test_utest (tests.test_analysis_methods.TestMethods.test_utest) ... [resampling] [resampling] Performing Benjamini-Hochberg Correction [resampling] Number of significant conditionally essential genes (Padj<0.05): 35 -[resampling] Time: 18.45s +[resampling] Time: 41.13s [resampling] Finished resampling Method Removing histogram files Removing output file... @@ -1614,7 +1650,7 @@ test_resampling_Quantile (tests.test_norm_methods.TestNormMethods.test_resampling_Quantile) ... [resampling] [resampling] Performing Benjamini-Hochberg Correction [resampling] Number of significant conditionally essential genes (Padj<0.05): 0 -[resampling] Time: 1.14s +[resampling] Time: 3.51s [resampling] Finished resampling Method Removing output file... @@ -1636,7 +1672,7 @@ test_resampling_TTR (tests.test_norm_methods.TestNormMethods.test_resampling_TTR) ... [resampling] [resampling] Performing Benjamini-Hochberg Correction [resampling] Number of significant conditionally essential genes (Padj<0.05): 0 -[resampling] Time: 1.29s +[resampling] Time: 3.10s [resampling] Finished resampling Method Removing output file... @@ -1655,7 +1691,7 @@ test_resampling_TotReads (tests.test_norm_methods.TestNormMethods.test_resampling_TotReads) ... [resampling] [resampling] Performing Benjamini-Hochberg Correction [resampling] Number of significant conditionally essential genes (Padj<0.05): 0 -[resampling] Time: 1.08s +[resampling] Time: 2.38s [resampling] Finished resampling Method Removing output file... @@ -1674,7 +1710,7 @@ test_resampling_ZINFNB (tests.test_norm_methods.TestNormMethods.test_resampling_ZINFNB) ... [resampling] [resampling] Performing Benjamini-Hochberg Correction [resampling] Number of significant conditionally essential genes (Padj<0.05): 0 -[resampling] Time: 0.99s +[resampling] Time: 2.06s [resampling] Finished resampling Method Removing output file... @@ -1693,7 +1729,7 @@ test_resampling_nonorm (tests.test_norm_methods.TestNormMethods.test_resampling_nonorm) ... [resampling] [resampling] Performing Benjamini-Hochberg Correction [resampling] Number of significant conditionally essential genes (Padj<0.05): 0 -[resampling] Time: 3.28s +[resampling] Time: 6.80s [resampling] Finished resampling Method Removing output file... @@ -1747,23 +1783,23 @@ ResourceWarning: Enable tracemalloc to get the object allocation traceback [tn_preprocess] mapping reads using BWA...(this takes a couple of minutes) [tn_preprocess] /usr/bin/bwa index /build/reproducible-path/tnseq-transit-3.3.12/tests/data/test-multicontig.fna -b'[bwa_index] Pack FASTA... 0.08 sec' +b'[bwa_index] Pack FASTA... 0.03 sec' b'[bwa_index] Construct BWT for the packed sequence...' -b'[bwa_index] 1.80 seconds elapse.' +b'[bwa_index] 1.74 seconds elapse.' b'[bwa_index] Update BWT... 0.02 sec' b'[bwa_index] Pack forward-only FASTA... 0.02 sec' -b'[bwa_index] Construct SA from BWT and Occ... 1.11 sec' +b'[bwa_index] Construct SA from BWT and Occ... 1.17 sec' b'[main] Version: 0.7.18-r1243-dirty' b'[main] CMD: /usr/bin/bwa index /build/reproducible-path/tnseq-transit-3.3.12/tests/data/test-multicontig.fna' -b'[main] Real time: 3.034 sec; CPU: 3.035 sec' +b'[main] Real time: 6.826 sec; CPU: 2.982 sec' b'' [tn_preprocess] /usr/bin/bwa mem /build/reproducible-path/tnseq-transit-3.3.12/tests/data/test-multicontig.fna /build/reproducible-path/tnseq-transit-3.3.12/tests/test_tpp_temp.trimmed1 > /build/reproducible-path/tnseq-transit-3.3.12/tests/test_tpp_temp.sam b'[M::bwa_idx_load_from_disk] read 0 ALT contigs' b'[M::process] read 2500 sequences (304052 bp)...' -b'[M::mem_process_seqs] Processed 2500 reads in 0.241 CPU sec, 0.241 real sec' +b'[M::mem_process_seqs] Processed 2500 reads in 0.188 CPU sec, 0.440 real sec' b'[main] Version: 0.7.18-r1243-dirty' b'[main] CMD: /usr/bin/bwa mem /build/reproducible-path/tnseq-transit-3.3.12/tests/data/test-multicontig.fna /build/reproducible-path/tnseq-transit-3.3.12/tests/test_tpp_temp.trimmed1' -b'[main] Real time: 0.252 sec; CPU: 0.253 sec' +b'[main] Real time: 0.464 sec; CPU: 0.196 sec' b'' [tn_preprocess] tabulating template counts and statistics for reference genome /build/reproducible-path/tnseq-transit-3.3.12/tests/data/test-multicontig.fna /build/reproducible-path/tnseq-transit-3.3.12/tests/../src/pytpp/tpp_tools.py:385: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/reproducible-path/tnseq-transit-3.3.12/tests/data/test-multicontig.fna' mode='r' encoding='UTF-8'> @@ -1801,10 +1837,10 @@ [tn_preprocess] /usr/bin/bwa mem /build/reproducible-path/tnseq-transit-3.3.12/tests/data/test-multicontig.fna /build/reproducible-path/tnseq-transit-3.3.12/tests/test_tpp_temp.trimmed1 > /build/reproducible-path/tnseq-transit-3.3.12/tests/test_tpp_temp.sam b'[M::bwa_idx_load_from_disk] read 0 ALT contigs' b'[M::process] read 2500 sequences (304052 bp)...' -b'[M::mem_process_seqs] Processed 2500 reads in 0.232 CPU sec, 0.231 real sec' +b'[M::mem_process_seqs] Processed 2500 reads in 0.192 CPU sec, 0.457 real sec' b'[main] Version: 0.7.18-r1243-dirty' b'[main] CMD: /usr/bin/bwa mem /build/reproducible-path/tnseq-transit-3.3.12/tests/data/test-multicontig.fna /build/reproducible-path/tnseq-transit-3.3.12/tests/test_tpp_temp.trimmed1' -b'[main] Real time: 0.244 sec; CPU: 0.245 sec' +b'[main] Real time: 0.483 sec; CPU: 0.201 sec' b'' [tn_preprocess] tabulating template counts and statistics for reference genome /build/reproducible-path/tnseq-transit-3.3.12/tests/data/test-multicontig.fna [tn_preprocess] writing /build/reproducible-path/tnseq-transit-3.3.12/tests/test_tpp_temp_a.wig @@ -1817,13 +1853,13 @@ test_tpp_protocol_mme1 (tests.test_tpp.TestTPP.test_tpp_protocol_mme1) ... skipped 'requires local data file' ---------------------------------------------------------------------- -Ran 39 tests in 89.891s +Ran 39 tests in 229.301s OK (skipped=6) [resampling] [resampling] Performing Benjamini-Hochberg Correction [resampling] Number of significant conditionally essential genes (Padj<0.05): 0 -[resampling] Time: 0.99s +[resampling] Time: 2.65s [resampling] Finished resampling Method Removing output file... @@ -1889,7 +1925,7 @@ /build/reproducible-path/tnseq-transit-3.3.12/tests/data/test-multicontig-1.fastq # title: Tn-Seq Pre-Processor -# date: 02/05/2025 22:31:58 +# date: 03/12/2026 07:02:39 # command: python python3.13 -m unittest -v tests/test_analysis_methods.py tests/test_norm_methods.py tests/test_pytransit_tools.py tests/test_tpp.py tests/transit_test.py # transposon type: Himar1 # protocol type: Sassetti @@ -1973,7 +2009,7 @@ /build/reproducible-path/tnseq-transit-3.3.12/tests/data/test-multicontig-1.fastq # title: Tn-Seq Pre-Processor -# date: 02/05/2025 22:32:00 +# date: 03/12/2026 07:02:42 # command: python python3.13 -m unittest -v tests/test_analysis_methods.py tests/test_norm_methods.py tests/test_pytransit_tools.py tests/test_tpp.py tests/transit_test.py # transposon type: Himar1 # protocol type: Sassetti @@ -2401,12 +2437,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/3917396/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3917396/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/1206982 and its subdirectories -I: Current time: Wed Feb 5 22:32:40 -12 2025 -I: pbuilder-time-stamp: 1738837960 +I: removing directory /srv/workspace/pbuilder/3917396 and its subdirectories +I: Current time: Thu Mar 12 07:03:57 +14 2026 +I: pbuilder-time-stamp: 1773248637