Diff of the two buildlogs: -- --- b1/build.log 2024-01-07 13:35:57.707706811 +0000 +++ b2/build.log 2024-01-07 13:40:09.414004117 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun Jan 7 01:33:43 -12 2024 -I: pbuilder-time-stamp: 1704634423 +I: Current time: Sun Feb 9 09:59:06 +14 2025 +I: pbuilder-time-stamp: 1739044746 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration @@ -29,49 +29,81 @@ dpkg-source: info: applying use_blastdb_format_4.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/2362848/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1094895/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 Feb 8 19:59 /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/1094895/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1094895/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]="15" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.15(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='bookworm' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=bookworm + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='b43e2a81134b4cfe95da496be906eaff' - 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='2362848' - PS1='# ' - PS2='> ' + INVOCATION_ID=6e1413e74a4a4a078c360d8ae17f640b + 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=1094895 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.1BddBzs6/pbuilderrc_sL3H --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.1BddBzs6/b1 --logfile b1/build.log metastudent-data_2.0.1-8.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://192.168.101.104:3128' + 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.1BddBzs6/pbuilderrc_GSl3 --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.1BddBzs6/b2 --logfile b2/build.log metastudent-data_2.0.1-8.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://192.168.101.104:3128 I: uname -a - Linux codethink04-arm64 6.1.0-17-cloud-arm64 #1 SMP Debian 6.1.69-1 (2023-12-30) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-17-cloud-arm64 #1 SMP Debian 6.1.69-1 (2023-12-30) aarch64 GNU/Linux I: ls -l /bin total 7104 -rwxr-xr-x 1 root root 1346480 Apr 23 2023 bash @@ -129,15 +161,15 @@ -rwxr-xr-x 1 root root 68456 Sep 20 2022 readlink -rwxr-xr-x 1 root root 68592 Sep 20 2022 rm -rwxr-xr-x 1 root root 68480 Sep 20 2022 rmdir - -rwxr-xr-x 1 root root 68392 Jul 28 23:46 run-parts + -rwxr-xr-x 1 root root 68392 Jul 28 2023 run-parts -rwxr-xr-x 1 root root 134536 Jan 5 2023 sed - lrwxrwxrwx 1 root root 4 Jan 5 2023 sh -> dash + lrwxrwxrwx 1 root root 9 Feb 8 19:59 sh -> /bin/bash -rwxr-xr-x 1 root root 68432 Sep 20 2022 sleep -rwxr-xr-x 1 root root 134088 Sep 20 2022 stty -rwsr-xr-x 1 root root 133312 Mar 23 2023 su -rwxr-xr-x 1 root root 68448 Sep 20 2022 sync -rwxr-xr-x 1 root root 539896 Apr 6 2023 tar - -rwxr-xr-x 1 root root 67904 Jul 28 23:46 tempfile + -rwxr-xr-x 1 root root 67904 Jul 28 2023 tempfile -rwxr-xr-x 1 root root 134160 Sep 20 2022 touch -rwxr-xr-x 1 root root 68384 Sep 20 2022 true -rwxr-xr-x 1 root root 67664 Mar 23 2023 ulockmgr_server @@ -157,7 +189,7 @@ -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew -I: user script /srv/workspace/pbuilder/2362848/tmp/hooks/D02_print_environment finished +I: user script /srv/workspace/pbuilder/1094895/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -249,7 +281,7 @@ Get: 49 http://deb.debian.org/debian bookworm/main arm64 ncbi-data all 6.1.20170106+dfsg1-10 [3557 kB] Get: 50 http://deb.debian.org/debian bookworm/main arm64 ncbi-blast+ arm64 2.12.0+ds-3+b1 [10.9 MB] Get: 51 http://deb.debian.org/debian bookworm/main arm64 ncbi-blast+-legacy all 2.12.0+ds-3 [13.5 kB] -Fetched 39.6 MB in 1s (71.6 MB/s) +Fetched 39.6 MB in 0s (118 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-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 ... 18171 files and directories currently installed.) @@ -472,7 +504,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/metastudent-data-2.0.1/ && 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 > ../metastudent-data_2.0.1-8_source.changes +I: user script /srv/workspace/pbuilder/1094895/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for bookworm +I: user script /srv/workspace/pbuilder/1094895/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/metastudent-data-2.0.1/ && 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 > ../metastudent-data_2.0.1-8_source.changes dpkg-buildpackage: info: source package metastudent-data dpkg-buildpackage: info: source version 2.0.1-8 dpkg-buildpackage: info: source distribution unstable @@ -513,35 +549,35 @@ makeblastdb -dbtype prot -in "dataset_201401/CCO/goasp.fasta" -out "dataset_201401/CCO/goasp.fasta" -blastdb_version 4 -Building a new DB, current time: 01/07/2024 13:34:23 +Building a new DB, current time: 02/08/2025 19:59:52 -Building a new DB, current time: 01/07/2024 13:34:23 -New DB name: /build/reproducible-path/metastudent-data-2.0.1/dataset_201401/MFO/goasp.fasta -New DB name: /build/reproducible-path/metastudent-data-2.0.1/dataset_201401/BPO/goasp.fasta -New DB title: dataset_201401/MFO/goasp.fasta -New DB title: dataset_201401/BPO/goasp.fasta -Sequence type: Protein +Building a new DB, current time: 02/08/2025 19:59:52 +New DB name: /build/reproducible-path/metastudent-data-2.0.1/dataset_201401/CCO/goasp.fasta +New DB title: dataset_201401/CCO/goasp.fasta Sequence type: Protein -Building a new DB, current time: 01/07/2024 13:34:23 -New DB name: /build/reproducible-path/metastudent-data-2.0.1/dataset_201401/CCO/goasp.fasta -New DB title: dataset_201401/CCO/goasp.fasta +Building a new DB, current time: 02/08/2025 19:59:52 +New DB name: /build/reproducible-path/metastudent-data-2.0.1/dataset_201401/MFO/goasp.fasta +New DB title: dataset_201401/MFO/goasp.fasta Sequence type: Protein Keep MBits: T Keep MBits: T Maximum file size: 1000000000B +New DB name: /build/reproducible-path/metastudent-data-2.0.1/dataset_201401/BPO/goasp.fasta +New DB title: dataset_201401/BPO/goasp.fasta +Sequence type: Protein Maximum file size: 1000000000B Keep MBits: T Maximum file size: 1000000000B -Adding sequences from FASTA; added 392822 sequences in 8.87098 seconds. +Adding sequences from FASTA; added 459503 sequences in 21.4561 seconds. -Adding sequences from FASTA; added 459503 sequences in 10.5197 seconds. +Adding sequences from FASTA; added 486000 sequences in 21.764 seconds. -Adding sequences from FASTA; added 486000 sequences in 11.9871 seconds. +Adding sequences from FASTA; added 392822 sequences in 22.9839 seconds. make[1]: Leaving directory '/build/reproducible-path/metastudent-data-2.0.1' @@ -581,12 +617,14 @@ 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/1094895/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1094895/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/2362848 and its subdirectories -I: Current time: Sun Jan 7 01:35:56 -12 2024 -I: pbuilder-time-stamp: 1704634556 +I: removing directory /srv/workspace/pbuilder/1094895 and its subdirectories +I: Current time: Sun Feb 9 10:03:07 +14 2025 +I: pbuilder-time-stamp: 1739044987