Diff of the two buildlogs: -- --- b1/build.log 2025-01-15 00:36:47.477808435 +0000 +++ b2/build.log 2025-01-15 00:47:30.316602734 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Feb 16 18:52:11 -12 2026 -I: pbuilder-time-stamp: 1771311131 +I: Current time: Wed Jan 15 14:36:50 +14 2025 +I: pbuilder-time-stamp: 1736901410 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -25,52 +25,84 @@ dpkg-source: info: applying fix_boost_linkage.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/3685758/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/707514/tmp/hooks/D01_modify_environment starting +debug: Running on ionos11-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 Jan 15 00:37 /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/707514/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/707514/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='unstable' - 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=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='006e95e4951640d3960557efe8967f14' - 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='3685758' - PS1='# ' - PS2='> ' + INVOCATION_ID=0886b3a59955439f9aee04f8581ce15d + 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=707514 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.7beJneh2/pbuilderrc_D16J --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.7beJneh2/b1 --logfile b1/build.log python-freecontact_1.1-9.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.7beJneh2/pbuilderrc_hfVz --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.7beJneh2/b2 --logfile b2/build.log python-freecontact_1.1-9.dsc' + SUDO_GID=111 + SUDO_UID=106 + 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 6.11.10+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.11.10-1~bpo12+1 (2024-12-19) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-30-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.124-1 (2025-01-12) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/3685758/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/707514/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -210,7 +242,7 @@ Get: 92 http://deb.debian.org/debian unstable/main amd64 python3-all amd64 3.13.1-2 [1056 B] Get: 93 http://deb.debian.org/debian unstable/main amd64 python3.12-dev amd64 3.12.8-5 [505 kB] Get: 94 http://deb.debian.org/debian unstable/main amd64 python3-all-dev amd64 3.13.1-2 [1076 B] -Fetched 66.4 MB in 5s (13.7 MB/s) +Fetched 66.4 MB in 5s (14.5 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 ... 19850 files and directories currently installed.) @@ -529,8 +561,8 @@ Setting up tzdata (2024b-6) ... Current default time zone: 'Etc/UTC' -Local time is now: Tue Feb 17 06:53:48 UTC 2026. -Universal Time is now: Tue Feb 17 06:53:48 UTC 2026. +Local time is now: Wed Jan 15 00:39:37 UTC 2025. +Universal Time is now: Wed Jan 15 00:39:37 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... @@ -617,7 +649,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/python-freecontact-1.1/ && 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 > ../python-freecontact_1.1-9_source.changes +I: user script /srv/workspace/pbuilder/707514/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/707514/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/python-freecontact-1.1/ && 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 > ../python-freecontact_1.1-9_source.changes dpkg-buildpackage: info: source package python-freecontact dpkg-buildpackage: info: source version 1.1-9 dpkg-buildpackage: info: source distribution unstable @@ -674,30 +710,30 @@ pybuild --test -i python{version} -p "3.12 3.13" I: pybuild base:311: python3.12 /build/reproducible-path/python-freecontact-1.1/test/test01.py ..will use 1 OMP threads -SSE2 veczweight, wchunk = 64 +SSE2 veczweight, wchunk = 128 total weight (variation) of alignment = 620.777515304633 -seq weight loop for 1000 seqs took 0.006352 secs +seq weight loop for 1000 seqs took 0.009076 secs will use 1 OMP threads calculated column aa frequencies, gap cols = 4 -calculated pair frequency table in 0.101263 secs +calculated pair frequency table in 0.30281 secs collected apc_mean[MI] = 0.174031486973761 aa freq sum (cell) = 0.999997158936352, pairfreq sum (cell) = 0.999994420985606 formed covariance matrix (122/126,4) -LU factorization took 7.77666 secs, inverted matrix (incl LUf) in 36.0005 secs +LU factorization took 17.8465 secs, inverted matrix (incl LUf) in 66.004 secs density of inverse covariance matrix = 1 (cksum 346842.2) went back to gapped (126) wwi matrix collected apc_mean[l1norm] = 117.987054769839 collected apc_mean[fro] = 3.35437751555787 -all done in 36.3992 secs +all done in 66.9169 secs will use 1 OMP threads -SSE2 veczweight, wchunk = 64 +SSE2 veczweight, wchunk = 128 total weight (variation) of alignment = 561.595172234625 -seq weight loop for 1000 seqs took 0.006734 secs +seq weight loop for 1000 seqs took 0.00924 secs will use 1 OMP threads calculated column aa frequencies, gap cols = 4 -calculated pair frequency table in 0.127482 secs +calculated pair frequency table in 0.355789 secs collected apc_mean[MI] = 0.165528914074767 aa freq sum (cell) = 0.999993945475299, pairfreq sum (cell) = 0.999988196197513 formed covariance matrix (126/126,4) @@ -715,53 +751,53 @@ cov matrix Cholesky... not positive definite, dmean dev: 0.0143657 cov matrix Cholesky... not positive definite, dmean dev: 0.0129291 cov matrix Cholesky... -shrank covariance matrix in 9.18519 secs +shrank covariance matrix in 27.2275 secs will try rho 0.00178064, exact solution - iteration = 1 iteration = 2 iteration = 3will use 1 OMP threads -SSE2 veczweight, wchunk = 64 + iteration = 1 iteration = 2will use 1 OMP threads +SSE2 veczweight, wchunk = 128 total weight (variation) of alignment = 620.777515304633 will use 1 OMP threads calculated column aa frequencies, gap cols = 4 -calculated pair frequency table in 0.218748 secs +calculated pair frequency table in 0.132178 secs collected apc_mean[MI] = 0.174031486973761 aa freq sum (cell) = 0.999997158936352, pairfreq sum (cell) = 0.999994420985606 formed covariance matrix (122/126,4) -LU factorization took 7.53488 secs, inverted matrix (incl LUf) in 20.372 secs +LU factorization took 10.3389 secs, inverted matrix (incl LUf) in 49.3448 secs density of inverse covariance matrix = 1 (cksum 346842.2) went back to gapped (126) wwi matrix collected apc_mean[l1norm] = 117.987054769839 collected apc_mean[fro] = 3.35437751555787 . ---------------------------------------------------------------------- -Ran 3 tests in 69.837s +Ran 3 tests in 147.646s OK I: pybuild base:311: python3.13 /build/reproducible-path/python-freecontact-1.1/test/test01.py ..will use 1 OMP threads -SSE2 veczweight, wchunk = 64 +SSE2 veczweight, wchunk = 128 total weight (variation) of alignment = 620.777515304633 -seq weight loop for 1000 seqs took 0.006237 secs +seq weight loop for 1000 seqs took 0.014703 secs will use 1 OMP threads calculated column aa frequencies, gap cols = 4 -calculated pair frequency table in 0.101974 secs +calculated pair frequency table in 0.348417 secs collected apc_mean[MI] = 0.174031486973761 aa freq sum (cell) = 0.999997158936352, pairfreq sum (cell) = 0.999994420985606 formed covariance matrix (122/126,4) -LU factorization took 9.98156 secs, inverted matrix (incl LUf) in 25.155 secs +LU factorization took 11.649 secs, inverted matrix (incl LUf) in 53.4247 secs density of inverse covariance matrix = 1 (cksum 346842.2) went back to gapped (126) wwi matrix collected apc_mean[l1norm] = 117.987054769839 collected apc_mean[fro] = 3.35437751555787 -all done in 25.4533 secs +all done in 54.3167 secs will use 1 OMP threads -SSE2 veczweight, wchunk = 64 +SSE2 veczweight, wchunk = 128 total weight (variation) of alignment = 561.595172234625 -seq weight loop for 1000 seqs took 0.006157 secs +seq weight loop for 1000 seqs took 0.009931 secs will use 1 OMP threads calculated column aa frequencies, gap cols = 4 -calculated pair frequency table in 0.104512 secs +calculated pair frequency table in 0.156074 secs collected apc_mean[MI] = 0.165528914074767 aa freq sum (cell) = 0.999993945475299, pairfreq sum (cell) = 0.999988196197513 formed covariance matrix (126/126,4) @@ -779,28 +815,28 @@ cov matrix Cholesky... not positive definite, dmean dev: 0.0143657 cov matrix Cholesky... not positive definite, dmean dev: 0.0129291 cov matrix Cholesky... -shrank covariance matrix in 10.037 secs +shrank covariance matrix in 30.1288 secs will try rho 0.00178064, exact solution - iteration = 1 iteration = 2 iteration = 3will use 1 OMP threads -SSE2 veczweight, wchunk = 64 + iteration = 1 iteration = 2will use 1 OMP threads +SSE2 veczweight, wchunk = 128 total weight (variation) of alignment = 620.777515304633 will use 1 OMP threads calculated column aa frequencies, gap cols = 4 -calculated pair frequency table in 0.105364 secs +calculated pair frequency table in 0.383698 secs collected apc_mean[MI] = 0.174031486973761 aa freq sum (cell) = 0.999997158936352, pairfreq sum (cell) = 0.999994420985606 formed covariance matrix (122/126,4) -LU factorization took 5.66766 secs, inverted matrix (incl LUf) in 18.891 secs +LU factorization took 10.8668 secs, inverted matrix (incl LUf) in 53.8426 secs density of inverse covariance matrix = 1 (cksum 346842.2) went back to gapped (126) wwi matrix collected apc_mean[l1norm] = 117.987054769839 collected apc_mean[fro] = 3.35437751555787 . ---------------------------------------------------------------------- -Ran 3 tests in 59.606s +Ran 3 tests in 144.393s OK - rm -fr -- /tmp/dh-xdg-rundir-tluC5lmv + rm -fr -- /tmp/dh-xdg-rundir-OMsa6aDx make[1]: Leaving directory '/build/reproducible-path/python-freecontact-1.1' create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild -O--builddirectory=/build/reproducible-path/python-freecontact-1.1/builddir @@ -858,9 +894,9 @@ D: dh_python3 dh_python3:205: processing package python3-freecontact... D: dh_python3 fs:50: moving files from debian/python3-freecontact/usr/lib/python3.12/dist-packages to debian/python3-freecontact/usr/lib/python3/dist-packages/ D: dh_python3 fs:50: moving files from debian/python3-freecontact/usr/lib/python3.13/dist-packages to debian/python3-freecontact/usr/lib/python3/dist-packages/ -D: dh_python3 fs:338: package python3-freecontact details = {'requires.txt': set(), 'egg-info': {'debian/python3-freecontact/usr/lib/python3/dist-packages/python_freecontact-1.1.egg-info/PKG-INFO'}, 'dist-info': set(), 'nsp.txt': set(), 'shebangs': set(), 'public_vers': {Version('3')}, 'private_dirs': {}, 'compile': False, 'ext_vers': {Version('3.13'), Version('3.12')}, 'ext_no_version': set()} +D: dh_python3 fs:338: package python3-freecontact details = {'requires.txt': set(), 'egg-info': {'debian/python3-freecontact/usr/lib/python3/dist-packages/python_freecontact-1.1.egg-info/PKG-INFO'}, 'dist-info': set(), 'nsp.txt': set(), 'shebangs': set(), 'public_vers': {Version('3')}, 'private_dirs': {}, 'compile': False, 'ext_vers': {Version('3.12'), Version('3.13')}, 'ext_no_version': set()} D: dh_python3 depends:103: generating dependencies for package python3-freecontact -D: dh_python3 depends:253: D={'python3 (>= 3.12~)', 'python3 (<< 3.14)'}; R=[]; S=[]; E=[], B=[]; RT=[] +D: dh_python3 depends:253: D={'python3 (<< 3.14)', 'python3 (>= 3.12~)'}; R=[]; S=[]; E=[], B=[]; RT=[] dh_installsystemduser -O--buildsystem=pybuild -O--builddirectory=/build/reproducible-path/python-freecontact-1.1/builddir dh_perl -O--buildsystem=pybuild -O--builddirectory=/build/reproducible-path/python-freecontact-1.1/builddir dh_link -O--buildsystem=pybuild -O--builddirectory=/build/reproducible-path/python-freecontact-1.1/builddir @@ -924,10 +960,10 @@ cd debian/.debhelper/python3-freecontact/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/.debhelper/python3-freecontact/dbgsym-root/DEBIAN/md5sums dh_builddeb -O--buildsystem=pybuild -O--builddirectory=/build/reproducible-path/python-freecontact-1.1/builddir - dpkg-deb --root-owner-group --build debian/.debhelper/python3-freecontact/dbgsym-root .. dpkg-deb --root-owner-group --build debian/python3-freecontact .. -dpkg-deb: building package 'python3-freecontact' in '../python3-freecontact_1.1-9_amd64.deb'. + dpkg-deb --root-owner-group --build debian/.debhelper/python3-freecontact/dbgsym-root .. dpkg-deb: building package 'python3-freecontact-dbgsym' in '../python3-freecontact-dbgsym_1.1-9_amd64.deb'. +dpkg-deb: building package 'python3-freecontact' in '../python3-freecontact_1.1-9_amd64.deb'. dpkg-genbuildinfo --build=binary -O../python-freecontact_1.1-9_amd64.buildinfo dpkg-genchanges --build=binary -O../python-freecontact_1.1-9_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -935,12 +971,14 @@ 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/707514/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/707514/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/3685758 and its subdirectories -I: Current time: Mon Feb 16 18:57:46 -12 2026 -I: pbuilder-time-stamp: 1771311466 +I: removing directory /srv/workspace/pbuilder/707514 and its subdirectories +I: Current time: Wed Jan 15 14:47:29 +14 2025 +I: pbuilder-time-stamp: 1736902049