Diff of the two buildlogs: -- --- b1/build.log 2023-05-13 01:42:35.348788915 +0000 +++ b2/build.log 2023-05-13 01:47:47.899096682 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu Jun 13 20:00:21 -12 2024 -I: pbuilder-time-stamp: 1718352021 +I: Current time: Sat May 13 15:42:39 +14 2023 +I: pbuilder-time-stamp: 1683942159 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 [./mcaller_1.0.3+git20210624.b415090.orig.tar.xz] I: copying [./mcaller_1.0.3+git20210624.b415090-3.debian.tar.xz] I: Extracting source -gpgv: Signature made Wed Apr 27 10:26:52 2022 -12 +gpgv: Signature made Thu Apr 28 12:26:52 2022 +14 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key @@ -30,52 +30,84 @@ dpkg-source: info: applying prefixes.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/14881/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1995/tmp/hooks/D01_modify_environment starting +debug: Running on codethink10-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 May 13 15:42 /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/1995/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1995/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' - 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 + 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' - DISTRIBUTION='bookworm' - HOME='/var/lib/jenkins' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=bookworm + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/var/lib/jenkins + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - 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='14881' - PS1='# ' - PS2='> ' + 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=1995 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.JIUAU8OA/pbuilderrc_bh1x --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.JIUAU8OA/b1 --logfile b1/build.log mcaller_1.0.3+git20210624.b415090-3.dsc' - SUDO_GID='117' - SUDO_UID='110' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - USERNAME='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.16:3128' + 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.JIUAU8OA/pbuilderrc_jNjn --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.JIUAU8OA/b2 --logfile b2/build.log --extrapackages usrmerge mcaller_1.0.3+git20210624.b415090-3.dsc' + SUDO_GID=117 + SUDO_UID=110 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + USERNAME=root + _='I: set' + http_proxy=http://192.168.101.16:3128 I: uname -a - Linux codethink11-arm64 4.15.0-210-generic #221-Ubuntu SMP Tue Apr 18 08:32:48 UTC 2023 aarch64 GNU/Linux + Linux i-capture-the-hostname 4.15.0-210-generic #221-Ubuntu SMP Tue Apr 18 08:32:48 UTC 2023 aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Jun 11 04:47 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/14881/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 May 12 00:25 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/1995/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -287,7 +319,7 @@ Get: 160 http://deb.debian.org/debian bookworm/main arm64 python3-threadpoolctl all 3.1.0-1 [21.2 kB] Get: 161 http://deb.debian.org/debian bookworm/main arm64 python3-sklearn-lib arm64 1.2.1+dfsg-1 [2227 kB] Get: 162 http://deb.debian.org/debian bookworm/main arm64 python3-sklearn all 1.2.1+dfsg-1 [2103 kB] -Fetched 136 MB in 3s (44.2 MB/s) +Fetched 136 MB in 3s (51.4 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.) @@ -963,8 +995,17 @@ 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/mcaller-1.0.3+git20210624.b415090/ && 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 > ../mcaller_1.0.3+git20210624.b415090-3_source.changes +I: user script /srv/workspace/pbuilder/1995/tmp/hooks/A99_set_merged_usr starting +Re-configuring usrmerge... +I: user script /srv/workspace/pbuilder/1995/tmp/hooks/A99_set_merged_usr finished +hostname: Temporary failure in name resolution +I: Running cd /build/mcaller-1.0.3+git20210624.b415090/ && 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 > ../mcaller_1.0.3+git20210624.b415090-3_source.changes dpkg-buildpackage: info: source package mcaller dpkg-buildpackage: info: source version 1.0.3+git20210624.b415090-3 dpkg-buildpackage: info: source distribution unstable @@ -974,19 +1015,19 @@ debian/rules clean dh clean --with python3 debian/rules override_dh_auto_clean -make[1]: Entering directory '/build/mcaller-1.0.3+git20210624.b415090' +make[1]: Map '/build/mcaller-1.0.3+git20210624.b415090' wordt binnengegaan dh_auto_clean #rm -f model_NN_6_m6A.pkl testdata/masonread1.eventalign.diffs.6 testdata/masonread1.eventalign.diffs.6.train rm -rf __pycache__ rm -f model_NN_6_m6A.pkl -make[1]: Leaving directory '/build/mcaller-1.0.3+git20210624.b415090' +make[1]: Map '/build/mcaller-1.0.3+git20210624.b415090' wordt verlaten dh_clean debian/rules binary dh binary --with python3 dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_test -make[1]: Entering directory '/build/mcaller-1.0.3+git20210624.b415090' +make[1]: Map '/build/mcaller-1.0.3+git20210624.b415090' wordt binnengegaan cp -a testdata testdata_save ./mCaller.py -p testdata/test_positions_A.txt -r testdata/pb_ecoli_polished_assembly.fasta -e testdata/masonread1.eventalign.tsv -d r95_twobase_model_NN_6_m6A.pkl -f testdata/masonread1.fastq testdata/ @@ -1020,6 +1061,12 @@ 0 regions with multiple methylated bases 0 observations with skips included 4 observations with too many skips +thread finished processing...: +28 observations +28 positions +0 regions with multiple methylated bases +0 observations with skips included +6 observations with too many skips Error: could not find sequence for reference contig li thread finished processing...: 16 observations @@ -1033,24 +1080,18 @@ 1 regions with multiple methylated bases 0 observations with skips included 10 observations with too many skips -thread finished processing...: -28 observations -28 positions -0 regions with multiple methylated bases -0 observations with skips included -6 observations with too many skips Finished extracting signals Merging files... Training... ['A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A'] -[[-0.18999999999999992, -1.6799999999999997, -2.3, 0.56, -1.41, 1.48, 7.055265349382997], [-1.1300000000000001, -1.67, -1.1, -0.5774999999999999, 0.42, 1.0225, 7.055265349382997], [0.0050000000000000044, -0.29500000000000004, -0.54, 3.96, 1.47, 0.06499999999999995, 7.055265349382997], [3.255, 3.925, 0.03999999999999998, -0.15599999999999997, -1.01, 1.3533333333333333, 7.055265349382997], [-0.07999999999999996, -1.3666666666666665, 0.84, -0.5449999999999999, -3.22, -1.53, 7.055265349382997], [-1.74, -2.56, -2.0774999999999997, 1.84, -0.09999999999999998, -0.3, 7.055265349382997], [1.92, 2.75, 1.59, 1.6433333333333333, 1.59, 1.27, 7.055265349382997], [-2.15, 1.8849999999999998, 2.58, -0.36, 4.26, -2.4625, 7.055265349382997], [1.485, 4.095000000000001, -1.12, -0.91, -0.62, 1.17, 7.055265349382997], [1.095, 0.78, -2.38, 1.47, -1.7149999999999999, -0.8283333333333335, 7.055265349382997]] -['GGATTMTTTCA', 'CTGGAMAAAGC', 'GGGCCMTTACC', 'GGTGGMTGAAT', 'GGTTAMCGCGT', 'TGTGGMGAAAC', 'AGAACMCTTTC', 'AGGCCMTTCAA', 'AATCAMAAGAA', 'TACTTMCCGCA'] -NN general model scores: 1.0,0.5,0.625,0.5,0.875 -Cross validation accuracy: 0.70 (+/- 0.41) +[[-0.18999999999999992, -1.6799999999999997, -2.3, 0.56, -1.41, 1.48, 7.055265349382997], [-1.1300000000000001, -1.67, -1.1, -0.5774999999999999, 0.42, 1.0225, 7.055265349382997], [0.0050000000000000044, -0.29500000000000004, -0.54, 3.96, 1.47, 0.06499999999999995, 7.055265349382997], [3.255, 3.925, 0.03999999999999998, -0.15599999999999997, -1.01, 1.3533333333333333, 7.055265349382997], [-0.07999999999999996, -1.3666666666666665, 0.84, -0.5449999999999999, -3.22, -1.53, 7.055265349382997], [-1.74, -2.56, -2.0774999999999997, 1.84, -0.09999999999999998, -0.3, 7.055265349382997], [1.92, 2.75, 1.59, 1.6433333333333333, 1.59, 1.27, 7.055265349382997], [-1.44, -5.03, 1.4449999999999998, 0.4000000000000001, -0.588, -0.55, 7.055265349382997], [-1.4433333333333334, -0.020000000000000018, -0.0366666666666667, -0.5499999999999999, 0.64, -2.71, 7.055265349382997], [-1.23, -1.635, -0.24, 1.1033333333333333, -2.215, -2.93, 7.055265349382997]] +['GGATTMTTTCA', 'CTGGAMAAAGC', 'GGGCCMTTACC', 'GGTGGMTGAAT', 'GGTTAMCGCGT', 'TGTGGMGAAAC', 'AGAACMCTTTC', 'AAATGMGATTT', 'AGTAGMTTGAT', 'ACTTAMCCGGT'] +NN general model scores: 0.875,0.5,0.5,1.0,0.5 +Cross validation accuracy: 0.68 (+/- 0.44) Finished training rm -rf testdata mv testdata_save testdata -make[1]: Leaving directory '/build/mcaller-1.0.3+git20210624.b415090' +make[1]: Map '/build/mcaller-1.0.3+git20210624.b415090' wordt verlaten create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/mcaller/ @@ -1071,7 +1112,7 @@ dpkg-gencontrol: warning: Depends field of package mcaller: substitution variable ${python3:Depends} used, but is not defined dh_md5sums dh_builddeb -dpkg-deb: building package 'mcaller' in '../mcaller_1.0.3+git20210624.b415090-3_all.deb'. +dpkg-deb: pakket 'mcaller' wordt gebouwd in '../mcaller_1.0.3+git20210624.b415090-3_all.deb'. dpkg-genbuildinfo --build=binary -O../mcaller_1.0.3+git20210624.b415090-3_arm64.buildinfo dpkg-genchanges --build=binary -O../mcaller_1.0.3+git20210624.b415090-3_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -1079,12 +1120,14 @@ 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/1995/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1995/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/14881 and its subdirectories -I: Current time: Thu Jun 13 20:05:33 -12 2024 -I: pbuilder-time-stamp: 1718352333 +I: removing directory /srv/workspace/pbuilder/1995 and its subdirectories +I: Current time: Sat May 13 15:47:46 +14 2023 +I: pbuilder-time-stamp: 1683942466