Diff of the two buildlogs: -- --- b1/build.log 2024-04-29 15:23:15.324380128 +0000 +++ b2/build.log 2024-04-29 15:34:07.192610222 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun Jun 1 09:41:22 -12 2025 -I: pbuilder-time-stamp: 1748814082 +I: Current time: Mon Jun 2 11:46:37 +14 2025 +I: pbuilder-time-stamp: 1748814397 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -29,52 +29,84 @@ dpkg-source: info: applying fix_problematic_comparison.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/1872073/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2221546/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 Jun 1 21:46 /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/2221546/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2221546/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]="21" [3]="1" [4]="release" [5]="aarch64-unknown-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=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='2a10c178bbc74b0992c4f6a143e212fa' - 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='1872073' - PS1='# ' - PS2='> ' + INVOCATION_ID=c1f5f76a45d645e79b4e15fd2667e9e6 + 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=2221546 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.09133qLP/pbuilderrc_iAce --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.09133qLP/b1 --logfile b1/build.log tnseq-transit_3.3.4-1.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.09133qLP/pbuilderrc_sLKJ --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.09133qLP/b2 --logfile b2/build.log tnseq-transit_3.3.4-1.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 codethink01-arm64 6.1.0-20-cloud-arm64 #1 SMP Debian 6.1.85-1 (2024-04-11) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-20-cloud-arm64 #1 SMP Debian 6.1.85-1 (2024-04-11) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 May 26 17:47 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/1872073/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 May 24 13:38 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/2221546/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -436,7 +468,7 @@ Get: 150 http://deb.debian.org/debian trixie/main arm64 python3-sklearn all 1.4.1.post1+dfsg-1 [2246 kB] Get: 151 http://deb.debian.org/debian trixie/main arm64 python3-statsmodels-lib arm64 0.14.1+dfsg-2 [2104 kB] Get: 152 http://deb.debian.org/debian trixie/main arm64 python3-statsmodels all 0.14.1+dfsg-2 [4826 kB] -Fetched 135 MB in 2s (87.6 MB/s) +Fetched 135 MB in 1s (145 MB/s) debconf: delaying package configuration, since apt-utils is not installed dpkg: libdb5.3:arm64: dependency problems, but removing anyway as you requested: libperl5.38:arm64 depends on libdb5.3. @@ -954,8 +986,8 @@ Setting up tzdata (2024a-3) ... Current default time zone: 'Etc/UTC' -Local time is now: Sun Jun 1 21:41:55 UTC 2025. -Universal Time is now: Sun Jun 1 21:41:55 UTC 2025. +Local time is now: Sun Jun 1 21:47:41 UTC 2025. +Universal Time is now: Sun Jun 1 21:47:41 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up unicode-data (15.1.0-1) ... @@ -1092,7 +1124,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/tnseq-transit-3.3.4/ && 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_3.3.4-1_source.changes +I: user script /srv/workspace/pbuilder/2221546/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/2221546/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/tnseq-transit-3.3.4/ && 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_3.3.4-1_source.changes dpkg-buildpackage: info: source package tnseq-transit dpkg-buildpackage: info: source version 3.3.4-1 dpkg-buildpackage: info: source distribution unstable @@ -1631,7 +1667,7 @@ 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: 10.71s +[resampling] Time: 14.74s [resampling] Finished resampling Method Removing output file... @@ -1653,7 +1689,7 @@ [resampling] [resampling] Performing Benjamini-Hochberg Correction [resampling] Number of significant conditionally essential genes (Padj<0.05): 35 -[resampling] Time: 6.72s +[resampling] Time: 10.89s [resampling] Finished resampling Method Removing output file... @@ -1672,7 +1708,7 @@ 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: 5.85s +[resampling] Time: 8.70s [resampling] Finished resampling Method 37 35 @@ -1693,7 +1729,7 @@ 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): 35 -[resampling] Time: 14.71s +[resampling] Time: 24.96s [resampling] Finished resampling Method Removing histogram files Removing output file... @@ -1715,7 +1751,7 @@ 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: 25.31s +[resampling] Time: 57.13s [resampling] Finished resampling Method Removing histogram files Removing output file... @@ -1764,7 +1800,7 @@ 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: 1.33s +[resampling] Time: 4.22s [resampling] Finished resampling Method Removing output file... @@ -1786,7 +1822,7 @@ 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: 1.79s +[resampling] Time: 5.98s [resampling] Finished resampling Method Removing output file... @@ -1805,7 +1841,7 @@ 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: 1.43s +[resampling] Time: 5.18s [resampling] Finished resampling Method Removing output file... @@ -1824,7 +1860,7 @@ 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: 1.33s +[resampling] Time: 3.86s [resampling] Finished resampling Method Removing output file... @@ -1843,7 +1879,7 @@ 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: 3.79s +[resampling] Time: 8.66s [resampling] Finished resampling Method Removing output file... @@ -1899,21 +1935,21 @@ [tn_preprocess] /usr/bin/bwa index /build/reproducible-path/tnseq-transit-3.3.4/tests/data/test-multicontig.fna b'[bwa_index] Pack FASTA... 0.03 sec' b'[bwa_index] Construct BWT for the packed sequence...' -b'[bwa_index] 1.93 seconds elapse.' +b'[bwa_index] 1.90 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... 1.18 sec' +b'[bwa_index] Construct SA from BWT and Occ... 1.17 sec' b'[main] Version: 0.7.17-r1188' b'[main] CMD: /usr/bin/bwa index /build/reproducible-path/tnseq-transit-3.3.4/tests/data/test-multicontig.fna' -b'[main] Real time: 4.419 sec; CPU: 3.187 sec' +b'[main] Real time: 9.989 sec; CPU: 3.149 sec' b'' [tn_preprocess] /usr/bin/bwa mem /build/reproducible-path/tnseq-transit-3.3.4/tests/data/test-multicontig.fna /build/reproducible-path/tnseq-transit-3.3.4/tests/test_tpp_temp.trimmed1 > /build/reproducible-path/tnseq-transit-3.3.4/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 0.193 CPU sec, 0.354 real sec' +b'[M::mem_process_seqs] Processed 2500 reads in 0.193 CPU sec, 0.531 real sec' b'[main] Version: 0.7.17-r1188' b'[main] CMD: /usr/bin/bwa mem /build/reproducible-path/tnseq-transit-3.3.4/tests/data/test-multicontig.fna /build/reproducible-path/tnseq-transit-3.3.4/tests/test_tpp_temp.trimmed1' -b'[main] Real time: 0.375 sec; CPU: 0.201 sec' +b'[main] Real time: 0.568 sec; CPU: 0.202 sec' b'' [tn_preprocess] tabulating template counts and statistics for reference genome /build/reproducible-path/tnseq-transit-3.3.4/tests/data/test-multicontig.fna /build/reproducible-path/tnseq-transit-3.3.4/tests/../src/pytpp/tpp_tools.py:387: ResourceWarning: unclosed file <_io.TextIOWrapper name='/build/reproducible-path/tnseq-transit-3.3.4/tests/data/test-multicontig.fna' mode='r' encoding='UTF-8'> @@ -1951,10 +1987,10 @@ [tn_preprocess] /usr/bin/bwa mem /build/reproducible-path/tnseq-transit-3.3.4/tests/data/test-multicontig.fna /build/reproducible-path/tnseq-transit-3.3.4/tests/test_tpp_temp.trimmed1 > /build/reproducible-path/tnseq-transit-3.3.4/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 0.195 CPU sec, 0.195 real sec' +b'[M::mem_process_seqs] Processed 2500 reads in 0.202 CPU sec, 0.527 real sec' b'[main] Version: 0.7.17-r1188' b'[main] CMD: /usr/bin/bwa mem /build/reproducible-path/tnseq-transit-3.3.4/tests/data/test-multicontig.fna /build/reproducible-path/tnseq-transit-3.3.4/tests/test_tpp_temp.trimmed1' -b'[main] Real time: 0.209 sec; CPU: 0.209 sec' +b'[main] Real time: 0.564 sec; CPU: 0.211 sec' b'' [tn_preprocess] tabulating template counts and statistics for reference genome /build/reproducible-path/tnseq-transit-3.3.4/tests/data/test-multicontig.fna [tn_preprocess] writing /build/reproducible-path/tnseq-transit-3.3.4/tests/test_tpp_temp_a.wig @@ -1967,13 +2003,13 @@ test_tpp_protocol_mme1 (tests.test_tpp.TestTPP.test_tpp_protocol_mme1) ... skipped 'requires local data file' ---------------------------------------------------------------------- -Ran 39 tests in 118.526s +Ran 39 tests in 267.768s OK (skipped=6) [resampling] [resampling] Performing Benjamini-Hochberg Correction [resampling] Number of significant conditionally essential genes (Padj<0.05): 0 -[resampling] Time: 1.34s +[resampling] Time: 1.44s [resampling] Finished resampling Method Removing output file... @@ -2039,7 +2075,7 @@ /build/reproducible-path/tnseq-transit-3.3.4/tests/data/test-multicontig-1.fastq # title: Tn-Seq Pre-Processor -# date: 06/01/2025 09:45:15 +# date: 06/02/2025 11:54:46 # command: python python3.11 -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 @@ -2123,7 +2159,7 @@ /build/reproducible-path/tnseq-transit-3.3.4/tests/data/test-multicontig-1.fastq # title: Tn-Seq Pre-Processor -# date: 06/01/2025 09:45:17 +# date: 06/02/2025 11:54:50 # command: python python3.11 -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 @@ -2552,12 +2588,14 @@ 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/2221546/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2221546/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/1872073 and its subdirectories -I: Current time: Sun Jun 1 09:46:14 -12 2025 -I: pbuilder-time-stamp: 1748814374 +I: removing directory /srv/workspace/pbuilder/2221546 and its subdirectories +I: Current time: Mon Jun 2 11:57:05 +14 2025 +I: pbuilder-time-stamp: 1748815025