Diff of the two buildlogs: -- --- b1/build.log 2023-04-08 01:40:38.384259719 +0000 +++ b2/build.log 2023-04-08 03:56:54.692889243 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri Apr 7 09:50:45 -12 2023 -I: pbuilder-time-stamp: 1680904245 +I: Current time: Fri May 10 22:03:42 +14 2024 +I: pbuilder-time-stamp: 1715328222 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration @@ -16,7 +16,7 @@ I: copying [./pyranges_0.0.111+ds.orig.tar.xz] I: copying [./pyranges_0.0.111+ds-4.debian.tar.xz] I: Extracting source -gpgv: Signature made Sat Jan 14 08:33:17 2023 -12 +gpgv: Signature made Sun Jan 15 10:33:17 2023 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -30,11 +30,20 @@ dpkg-source: info: applying numpy_1.24.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/20428/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/14380/tmp/hooks/D01_modify_environment starting +debug: Running on codethink9-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 +lrwxrwxrwx 1 root root 4 Jan 6 2023 /bin/sh -> dash +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/14380/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/14380/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' + 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=8' @@ -44,38 +53,38 @@ IFS=' ' LANG='C' - LANGUAGE='en_US:en' + LANGUAGE='nl_BE:nl' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' + 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' - PPID='20428' + PPID='14380' PS1='# ' PS2='> ' 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.FMkHsc5X/pbuilderrc_eUjB --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.FMkHsc5X/b1 --logfile b1/build.log pyranges_0.0.111+ds-4.dsc' + 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.FMkHsc5X/pbuilderrc_rVUe --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.FMkHsc5X/b2 --logfile b2/build.log --extrapackages usrmerge pyranges_0.0.111+ds-4.dsc' SUDO_GID='117' SUDO_UID='110' SUDO_USER='jenkins' TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' + TZ='/usr/share/zoneinfo/Etc/GMT-14' USER='root' USERNAME='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.16:3128' I: uname -a - Linux codethink16-arm64 4.15.0-208-generic #220-Ubuntu SMP Mon Mar 20 14:28:12 UTC 2023 aarch64 GNU/Linux + Linux i-capture-the-hostname 4.15.0-208-generic #220-Ubuntu SMP Mon Mar 20 14:28:12 UTC 2023 aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Apr 4 22:25 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/20428/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 May 9 06:47 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/14380/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -221,7 +230,7 @@ Get: 86 http://deb.debian.org/debian bookworm/main arm64 python3-setuptools all 66.1.1-1 [521 kB] Get: 87 http://deb.debian.org/debian bookworm/main arm64 python3-sorted-nearest arm64 0.0.38+dfsg-1 [402 kB] Get: 88 http://deb.debian.org/debian bookworm/main arm64 samtools arm64 1.16.1-1 [580 kB] -Fetched 43.9 MB in 2s (28.9 MB/s) +Fetched 43.9 MB in 4s (11.0 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 ... 19616 files and directories currently installed.) @@ -591,8 +600,17 @@ Writing extended state information... Building tag database... -> Finished parsing the build-deps +Reading package lists... +Building dependency tree... +Reading state information... +usrmerge is already the newest version (35). +0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/pyranges-0.0.111+ds/ && 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 > ../pyranges_0.0.111+ds-4_source.changes +I: user script /srv/workspace/pbuilder/14380/tmp/hooks/A99_set_merged_usr starting +Re-configuring usrmerge... +I: user script /srv/workspace/pbuilder/14380/tmp/hooks/A99_set_merged_usr finished +hostname: Temporary failure in name resolution +I: Running cd /build/pyranges-0.0.111+ds/ && 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 > ../pyranges_0.0.111+ds-4_source.changes dpkg-buildpackage: info: source package pyranges dpkg-buildpackage: info: source version 0.0.111+ds-4 dpkg-buildpackage: info: source distribution unstable @@ -684,7 +702,7 @@ /build/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/tests/test_binary.py:544: FutureWarning: In a future version of pandas all arguments of DataFrame.drop except for the argument 'labels' will be keyword-only. bedtools_df = bedtools_df.drop("Chromosome2", 1) -.pybuild/cpython3_3.11_pyranges/build/tests/test_binary.py: 12096 warnings +.pybuild/cpython3_3.11_pyranges/build/tests/test_binary.py: 12041 warnings /build/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/pyranges/pyranges.py:2503: FutureWarning: is_monotonic is deprecated and will be removed in a future version. Use is_monotonic_increasing instead. if not result.__IX__.is_monotonic: @@ -698,16 +716,16 @@ bedtools_df = pd.read_csv( -.pybuild/cpython3_3.11_pyranges/build/tests/test_unary.py: 2000 warnings - /build/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/tests/test_unary.py:193: DeprecationWarning: In a future version, `df.iloc[:, i] = newvals` will attempt to set the values inplace instead of always setting a new array. To retain the old behavior, use either `df[df.columns[i]] = newvals` or, if columns are non-unique, `df.isetitem(i, newvals)` - expected.loc[:, "Cluster"] = expected.Cluster.astype(np.int32) - .pybuild/cpython3_3.11_pyranges/build/tests/test_unary.py: 1000 warnings /build/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/tests/test_unary.py:251: FutureWarning: The squeeze argument has been deprecated and will be removed in a future version. Append .squeeze("columns") to the call to squeeze. bedtools_df = pd.read_csv( +.pybuild/cpython3_3.11_pyranges/build/tests/test_unary.py: 2000 warnings + /build/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/tests/test_unary.py:193: DeprecationWarning: In a future version, `df.iloc[:, i] = newvals` will attempt to set the values inplace instead of always setting a new array. To retain the old behavior, use either `df[df.columns[i]] = newvals` or, if columns are non-unique, `df.isetitem(i, newvals)` + expected.loc[:, "Cluster"] = expected.Cluster.astype(np.int32) + .pybuild/cpython3_3.11_pyranges/build/tests/test_concat.py::test_concat_stranded_unstranded .pybuild/cpython3_3.11_pyranges/build/tests/test_concat.py::test_concat_unstranded_stranded /build/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/pyranges/methods/concat.py:47: DeprecationWarning: In a future version, `df.iloc[:, i] = newvals` will attempt to set the values inplace instead of always setting a new array. To retain the old behavior, use either `df[df.columns[i]] = newvals` or, if columns are non-unique, `df.isetitem(i, newvals)` @@ -723,7 +741,7 @@ df.loc[:, names] = df[names].astype(np.int32) -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html -============== 531 passed, 53224 warnings in 13695.50s (3:48:15) =============== +=============== 531 passed, 53169 warnings in 8081.59s (2:14:41) =============== create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild @@ -761,12 +779,14 @@ 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/14380/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/14380/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/20428 and its subdirectories -I: Current time: Fri Apr 7 13:40:36 -12 2023 -I: pbuilder-time-stamp: 1680918036 +I: removing directory /srv/workspace/pbuilder/14380 and its subdirectories +I: Current time: Sat May 11 00:19:53 +14 2024 +I: pbuilder-time-stamp: 1715336393