Diff of the two buildlogs: -- --- b1/build.log 2024-10-27 14:59:11.252636844 +0000 +++ b2/build.log 2024-10-27 15:03:03.032386089 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun Oct 27 02:51:13 -12 2024 -I: pbuilder-time-stamp: 1730040673 +I: Current time: Mon Oct 28 04:59:20 +14 2024 +I: pbuilder-time-stamp: 1730041160 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -31,52 +31,84 @@ dpkg-source: info: applying rm-pkg_resources.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/28411/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/11063/tmp/hooks/D01_modify_environment starting +debug: Running on virt64a. +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 Oct 27 14:59 /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/11063/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/11063/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='armhf' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='armhf' + 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]="32" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") + BASH_VERSION='5.2.32(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=armhf + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=4 ' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=arm + HOST_ARCH=armhf IFS=' ' - INVOCATION_ID='391d80cd99294af1946fb1a2695e2aef' - 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='28411' - PS1='# ' - PS2='> ' + INVOCATION_ID=77fb3c0820074b108901a2b4235f7543 + LANG=C + LANGUAGE=it_CH:it + LC_ALL=C + MACHTYPE=arm-unknown-linux-gnueabihf + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnueabihf + 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=11063 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.2qH0bqEI/pbuilderrc_iqpv --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.2qH0bqEI/b1 --logfile b1/build.log scoary_1.6.16-9.dsc' - SUDO_GID='113' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://10.0.0.15:3142/' + 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.2qH0bqEI/pbuilderrc_rp8q --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.2qH0bqEI/b2 --logfile b2/build.log scoary_1.6.16-9.dsc' + SUDO_GID=114 + SUDO_UID=108 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://10.0.0.15:3142/ I: uname -a - Linux wbq0 6.1.0-26-armmp #1 SMP Debian 6.1.112-1 (2024-09-30) armv7l GNU/Linux + Linux i-capture-the-hostname 6.1.0-26-arm64 #1 SMP Debian 6.1.112-1 (2024-09-30) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/28411/tmp/hooks/D02_print_environment finished +I: user script /srv/workspace/pbuilder/11063/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -195,7 +227,7 @@ Get: 71 http://deb.debian.org/debian unstable/main armhf python3-numpy armhf 1:1.26.4+ds-11 [3340 kB] Get: 72 http://deb.debian.org/debian unstable/main armhf python3-ete3 all 3.1.3+dfsg-3 [375 kB] Get: 73 http://deb.debian.org/debian unstable/main armhf python3-scipy armhf 1.13.1-5 [15.2 MB] -Fetched 48.0 MB in 5s (9689 kB/s) +Fetched 48.0 MB in 1s (48.0 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.12-minimal:armhf. (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 ... 19667 files and directories currently installed.) @@ -448,8 +480,8 @@ Setting up tzdata (2024b-3) ... Current default time zone: 'Etc/UTC' -Local time is now: Sun Oct 27 14:53:02 UTC 2024. -Universal Time is now: Sun Oct 27 14:53:02 UTC 2024. +Local time is now: Sun Oct 27 15:00:06 UTC 2024. +Universal Time is now: Sun Oct 27 15:00:06 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... @@ -518,7 +550,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/scoary-1.6.16/ && 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 > ../scoary_1.6.16-9_source.changes +I: user script /srv/workspace/pbuilder/11063/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/11063/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/scoary-1.6.16/ && 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 > ../scoary_1.6.16-9_source.changes dpkg-buildpackage: info: source package scoary dpkg-buildpackage: info: source version 1.6.16-9 dpkg-buildpackage: info: source distribution unstable @@ -604,13 +640,13 @@ running build running build_py creating /build/reproducible-path/scoary-1.6.16/.pybuild/cpython3_3.12/build/scoary +copying scoary/classes.py -> /build/reproducible-path/scoary-1.6.16/.pybuild/cpython3_3.12/build/scoary +copying scoary/citation.py -> /build/reproducible-path/scoary-1.6.16/.pybuild/cpython3_3.12/build/scoary copying scoary/vcf2scoary.py -> /build/reproducible-path/scoary-1.6.16/.pybuild/cpython3_3.12/build/scoary -copying scoary/nwkhandler.py -> /build/reproducible-path/scoary-1.6.16/.pybuild/cpython3_3.12/build/scoary -copying scoary/GUI.py -> /build/reproducible-path/scoary-1.6.16/.pybuild/cpython3_3.12/build/scoary copying scoary/__init__.py -> /build/reproducible-path/scoary-1.6.16/.pybuild/cpython3_3.12/build/scoary -copying scoary/citation.py -> /build/reproducible-path/scoary-1.6.16/.pybuild/cpython3_3.12/build/scoary -copying scoary/classes.py -> /build/reproducible-path/scoary-1.6.16/.pybuild/cpython3_3.12/build/scoary +copying scoary/GUI.py -> /build/reproducible-path/scoary-1.6.16/.pybuild/cpython3_3.12/build/scoary copying scoary/methods.py -> /build/reproducible-path/scoary-1.6.16/.pybuild/cpython3_3.12/build/scoary +copying scoary/nwkhandler.py -> /build/reproducible-path/scoary-1.6.16/.pybuild/cpython3_3.12/build/scoary running egg_info creating scoary.egg-info writing scoary.egg-info/PKG-INFO @@ -740,7 +776,7 @@ ==== Finished ==== -Checked a total of 9001 genes for associations to 2 trait(s). Total time used: 66 seconds. +Checked a total of 9001 genes for associations to 2 trait(s). Total time used: 29 seconds. Scoary finished successfully, but with WARNINGS. Please check your log file. Warning. Since 1.5.0 scoary.py is deprecated. Install Scoary using 'pip install scoary instead, and run using scoary ==== Scoary started ==== @@ -777,7 +813,7 @@ ==== Finished ==== -Checked a total of 9001 genes for associations to 2 trait(s). Total time used: 41 seconds. +Checked a total of 9001 genes for associations to 2 trait(s). Total time used: 17 seconds. Scoary finished successfully, but with WARNINGS. Please check your log file. Warning. Since 1.5.0 scoary.py is deprecated. Install Scoary using 'pip install scoary instead, and run using scoary ==== Scoary started ==== @@ -818,7 +854,7 @@ ==== Finished ==== -Checked a total of 9001 genes for associations to 2 trait(s). Total time used: 30 seconds. +Checked a total of 9001 genes for associations to 2 trait(s). Total time used: 12 seconds. Scoary finished successfully, but with WARNINGS. Please check your log file. Warning. Since 1.5.0 scoary.py is deprecated. Install Scoary using 'pip install scoary instead, and run using scoary ==== Scoary started ==== @@ -858,7 +894,7 @@ ==== Finished ==== -Checked a total of 9001 genes for associations to 2 trait(s). Total time used: 46 seconds. +Checked a total of 9001 genes for associations to 2 trait(s). Total time used: 18 seconds. Scoary finished successfully, but with WARNINGS. Please check your log file. /build/reproducible-path/scoary-1.6.16/scoary/vcf2scoary.py:94: SyntaxWarning: "is not" with 'str' literal. Did you mean "!="? if args.types is not "ALL": @@ -961,29 +997,29 @@ running install_lib creating /build/reproducible-path/scoary-1.6.16/debian/scoary/usr/lib/python3.12/dist-packages creating /build/reproducible-path/scoary-1.6.16/debian/scoary/usr/lib/python3.12/dist-packages/scoary -copying /build/reproducible-path/scoary-1.6.16/.pybuild/cpython3_3.12/build/scoary/vcf2scoary.py -> /build/reproducible-path/scoary-1.6.16/debian/scoary/usr/lib/python3.12/dist-packages/scoary -copying /build/reproducible-path/scoary-1.6.16/.pybuild/cpython3_3.12/build/scoary/nwkhandler.py -> /build/reproducible-path/scoary-1.6.16/debian/scoary/usr/lib/python3.12/dist-packages/scoary -copying /build/reproducible-path/scoary-1.6.16/.pybuild/cpython3_3.12/build/scoary/GUI.py -> /build/reproducible-path/scoary-1.6.16/debian/scoary/usr/lib/python3.12/dist-packages/scoary -copying /build/reproducible-path/scoary-1.6.16/.pybuild/cpython3_3.12/build/scoary/__init__.py -> /build/reproducible-path/scoary-1.6.16/debian/scoary/usr/lib/python3.12/dist-packages/scoary creating /build/reproducible-path/scoary-1.6.16/debian/scoary/usr/lib/python3.12/dist-packages/scoary/exampledata -copying /build/reproducible-path/scoary-1.6.16/.pybuild/cpython3_3.12/build/scoary/exampledata/Gene_presence_absence.csv -> /build/reproducible-path/scoary-1.6.16/debian/scoary/usr/lib/python3.12/dist-packages/scoary/exampledata -copying /build/reproducible-path/scoary-1.6.16/.pybuild/cpython3_3.12/build/scoary/exampledata/ExampleTree.nwk -> /build/reproducible-path/scoary-1.6.16/debian/scoary/usr/lib/python3.12/dist-packages/scoary/exampledata -copying /build/reproducible-path/scoary-1.6.16/.pybuild/cpython3_3.12/build/scoary/exampledata/Tetracycline_resistance.csv -> /build/reproducible-path/scoary-1.6.16/debian/scoary/usr/lib/python3.12/dist-packages/scoary/exampledata -copying /build/reproducible-path/scoary-1.6.16/.pybuild/cpython3_3.12/build/scoary/exampledata/ExampleVCFTrait.csv -> /build/reproducible-path/scoary-1.6.16/debian/scoary/usr/lib/python3.12/dist-packages/scoary/exampledata copying /build/reproducible-path/scoary-1.6.16/.pybuild/cpython3_3.12/build/scoary/exampledata/Example.vcf -> /build/reproducible-path/scoary-1.6.16/debian/scoary/usr/lib/python3.12/dist-packages/scoary/exampledata +copying /build/reproducible-path/scoary-1.6.16/.pybuild/cpython3_3.12/build/scoary/exampledata/Tetracycline_resistance.csv -> /build/reproducible-path/scoary-1.6.16/debian/scoary/usr/lib/python3.12/dist-packages/scoary/exampledata +copying /build/reproducible-path/scoary-1.6.16/.pybuild/cpython3_3.12/build/scoary/exampledata/ExampleTree.nwk -> /build/reproducible-path/scoary-1.6.16/debian/scoary/usr/lib/python3.12/dist-packages/scoary/exampledata +copying /build/reproducible-path/scoary-1.6.16/.pybuild/cpython3_3.12/build/scoary/exampledata/Gene_presence_absence.csv -> /build/reproducible-path/scoary-1.6.16/debian/scoary/usr/lib/python3.12/dist-packages/scoary/exampledata copying /build/reproducible-path/scoary-1.6.16/.pybuild/cpython3_3.12/build/scoary/exampledata/Restrict_to.csv -> /build/reproducible-path/scoary-1.6.16/debian/scoary/usr/lib/python3.12/dist-packages/scoary/exampledata -copying /build/reproducible-path/scoary-1.6.16/.pybuild/cpython3_3.12/build/scoary/citation.py -> /build/reproducible-path/scoary-1.6.16/debian/scoary/usr/lib/python3.12/dist-packages/scoary +copying /build/reproducible-path/scoary-1.6.16/.pybuild/cpython3_3.12/build/scoary/exampledata/ExampleVCFTrait.csv -> /build/reproducible-path/scoary-1.6.16/debian/scoary/usr/lib/python3.12/dist-packages/scoary/exampledata copying /build/reproducible-path/scoary-1.6.16/.pybuild/cpython3_3.12/build/scoary/classes.py -> /build/reproducible-path/scoary-1.6.16/debian/scoary/usr/lib/python3.12/dist-packages/scoary +copying /build/reproducible-path/scoary-1.6.16/.pybuild/cpython3_3.12/build/scoary/citation.py -> /build/reproducible-path/scoary-1.6.16/debian/scoary/usr/lib/python3.12/dist-packages/scoary +copying /build/reproducible-path/scoary-1.6.16/.pybuild/cpython3_3.12/build/scoary/vcf2scoary.py -> /build/reproducible-path/scoary-1.6.16/debian/scoary/usr/lib/python3.12/dist-packages/scoary +copying /build/reproducible-path/scoary-1.6.16/.pybuild/cpython3_3.12/build/scoary/__init__.py -> /build/reproducible-path/scoary-1.6.16/debian/scoary/usr/lib/python3.12/dist-packages/scoary +copying /build/reproducible-path/scoary-1.6.16/.pybuild/cpython3_3.12/build/scoary/GUI.py -> /build/reproducible-path/scoary-1.6.16/debian/scoary/usr/lib/python3.12/dist-packages/scoary copying /build/reproducible-path/scoary-1.6.16/.pybuild/cpython3_3.12/build/scoary/methods.py -> /build/reproducible-path/scoary-1.6.16/debian/scoary/usr/lib/python3.12/dist-packages/scoary +copying /build/reproducible-path/scoary-1.6.16/.pybuild/cpython3_3.12/build/scoary/nwkhandler.py -> /build/reproducible-path/scoary-1.6.16/debian/scoary/usr/lib/python3.12/dist-packages/scoary +byte-compiling /build/reproducible-path/scoary-1.6.16/debian/scoary/usr/lib/python3.12/dist-packages/scoary/classes.py to classes.cpython-312.pyc +byte-compiling /build/reproducible-path/scoary-1.6.16/debian/scoary/usr/lib/python3.12/dist-packages/scoary/citation.py to citation.cpython-312.pyc byte-compiling /build/reproducible-path/scoary-1.6.16/debian/scoary/usr/lib/python3.12/dist-packages/scoary/vcf2scoary.py to vcf2scoary.cpython-312.pyc /usr/lib/python3.12/dist-packages/scoary/vcf2scoary.py:94: SyntaxWarning: "is not" with 'str' literal. Did you mean "!="? /usr/lib/python3.12/dist-packages/scoary/vcf2scoary.py:172: SyntaxWarning: "is not" with 'str' literal. Did you mean "!="? -byte-compiling /build/reproducible-path/scoary-1.6.16/debian/scoary/usr/lib/python3.12/dist-packages/scoary/nwkhandler.py to nwkhandler.cpython-312.pyc -byte-compiling /build/reproducible-path/scoary-1.6.16/debian/scoary/usr/lib/python3.12/dist-packages/scoary/GUI.py to GUI.cpython-312.pyc byte-compiling /build/reproducible-path/scoary-1.6.16/debian/scoary/usr/lib/python3.12/dist-packages/scoary/__init__.py to __init__.cpython-312.pyc -byte-compiling /build/reproducible-path/scoary-1.6.16/debian/scoary/usr/lib/python3.12/dist-packages/scoary/citation.py to citation.cpython-312.pyc -byte-compiling /build/reproducible-path/scoary-1.6.16/debian/scoary/usr/lib/python3.12/dist-packages/scoary/classes.py to classes.cpython-312.pyc +byte-compiling /build/reproducible-path/scoary-1.6.16/debian/scoary/usr/lib/python3.12/dist-packages/scoary/GUI.py to GUI.cpython-312.pyc byte-compiling /build/reproducible-path/scoary-1.6.16/debian/scoary/usr/lib/python3.12/dist-packages/scoary/methods.py to methods.cpython-312.pyc +byte-compiling /build/reproducible-path/scoary-1.6.16/debian/scoary/usr/lib/python3.12/dist-packages/scoary/nwkhandler.py to nwkhandler.cpython-312.pyc running install_egg_info Copying scoary.egg-info to /build/reproducible-path/scoary-1.6.16/debian/scoary/usr/lib/python3.12/dist-packages/scoary-1.6.16.egg-info Skipping SOURCES.txt @@ -1015,12 +1051,14 @@ 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/11063/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/11063/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/28411 and its subdirectories -I: Current time: Sun Oct 27 02:59:05 -12 2024 -I: pbuilder-time-stamp: 1730041145 +I: removing directory /srv/workspace/pbuilder/11063 and its subdirectories +I: Current time: Mon Oct 28 05:02:55 +14 2024 +I: pbuilder-time-stamp: 1730041375