Diff of the two buildlogs: -- --- b1/build.log 2022-03-01 09:20:05.462803763 +0000 +++ b2/build.log 2022-03-01 09:26:16.411330131 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Feb 28 21:13:56 -12 2022 -I: pbuilder-time-stamp: 1646126036 +I: Current time: Tue Apr 4 05:43:16 +14 2023 +I: pbuilder-time-stamp: 1680536596 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration @@ -16,8 +16,8 @@ I: copying [./python-pysam_0.15.4+ds-3.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' -gpgv: keyblock resource '/tmp/dpkg-verify-sig.t_BMAg8u/trustedkeys.kbx': General error -gpgv: Signature made Fri May 8 06:41:05 2020 -12 +gpgv: keyblock resource '/tmp/dpkg-verify-sig.hEJOiT2h/trustedkeys.kbx': General error +gpgv: Signature made Sat May 9 08:41:05 2020 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -34,135 +34,169 @@ dpkg-source: info: applying clean_less I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/1688501/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1804384/tmp/hooks/D01_modify_environment starting +debug: Running on ionos5-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 +Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' +Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' +Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' +Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by 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/1804384/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1804384/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='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=15' - DISTRIBUTION='' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="1" [2]="4" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.1.4(1)-release' + BUILDDIR=/build + 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,-fixfilepath parallel=16' + DIRSTACK=() + DISTRIBUTION= + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='d58bfc2269ef442391ca45c91678392c' - 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='1688501' - PS1='# ' - PS2='> ' + INVOCATION_ID=0240e3c2e9994e73bf4143859b546096 + 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=1804384 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/tmp.D8HnGsinku/pbuilderrc_DGmj --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.D8HnGsinku/b1 --logfile b1/build.log python-pysam_0.15.4+ds-3.dsc' - SUDO_GID='110' - SUDO_UID='105' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://78.137.99.97:3128' + 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/tmp.D8HnGsinku/pbuilderrc_vYRY --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.D8HnGsinku/b2 --logfile b2/build.log python-pysam_0.15.4+ds-3.dsc' + SUDO_GID=110 + SUDO_UID=105 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://85.184.249.68:3128 I: uname -a - Linux ionos1-amd64 5.10.0-11-amd64 #1 SMP Debian 5.10.92-1 (2022-01-18) x86_64 GNU/Linux + Linux i-capture-the-hostname 5.15.0-0.bpo.3-amd64 #1 SMP Debian 5.15.15-2~bpo11+1 (2022-02-03) x86_64 GNU/Linux I: ls -l /bin total 5476 - -rwxr-xr-x 1 root root 1234376 Aug 4 2021 bash - -rwxr-xr-x 3 root root 38984 Jul 20 2020 bunzip2 - -rwxr-xr-x 3 root root 38984 Jul 20 2020 bzcat - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep - -rwxr-xr-x 3 root root 38984 Jul 20 2020 bzip2 - -rwxr-xr-x 1 root root 18424 Jul 20 2020 bzip2recover - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore - -rwxr-xr-x 1 root root 43936 Sep 23 2020 cat - -rwxr-xr-x 1 root root 72672 Sep 23 2020 chgrp - -rwxr-xr-x 1 root root 64448 Sep 23 2020 chmod - -rwxr-xr-x 1 root root 72672 Sep 23 2020 chown - -rwxr-xr-x 1 root root 151168 Sep 23 2020 cp - -rwxr-xr-x 1 root root 125560 Dec 10 2020 dash - -rwxr-xr-x 1 root root 113664 Sep 23 2020 date - -rwxr-xr-x 1 root root 80968 Sep 23 2020 dd - -rwxr-xr-x 1 root root 93936 Sep 23 2020 df - -rwxr-xr-x 1 root root 147176 Sep 23 2020 dir - -rwxr-xr-x 1 root root 84440 Jul 28 2021 dmesg - lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname - -rwxr-xr-x 1 root root 39712 Sep 23 2020 echo - -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep - -rwxr-xr-x 1 root root 39680 Sep 23 2020 false - -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep - -rwxr-xr-x 1 root root 69032 Jul 28 2021 findmnt - -rwsr-xr-x 1 root root 34896 Feb 26 2021 fusermount - -rwxr-xr-x 1 root root 203072 Nov 9 2020 grep - -rwxr-xr-x 2 root root 2346 Mar 2 2021 gunzip - -rwxr-xr-x 1 root root 6376 Mar 2 2021 gzexe - -rwxr-xr-x 1 root root 98048 Mar 2 2021 gzip - -rwxr-xr-x 1 root root 22600 Nov 6 2019 hostname - -rwxr-xr-x 1 root root 72840 Sep 23 2020 ln - -rwxr-xr-x 1 root root 56952 Feb 7 2020 login - -rwxr-xr-x 1 root root 147176 Sep 23 2020 ls - -rwxr-xr-x 1 root root 149736 Jul 28 2021 lsblk - -rwxr-xr-x 1 root root 85184 Sep 23 2020 mkdir - -rwxr-xr-x 1 root root 76896 Sep 23 2020 mknod - -rwxr-xr-x 1 root root 48064 Sep 23 2020 mktemp - -rwxr-xr-x 1 root root 59632 Jul 28 2021 more - -rwsr-xr-x 1 root root 55528 Jul 28 2021 mount - -rwxr-xr-x 1 root root 18664 Jul 28 2021 mountpoint - -rwxr-xr-x 1 root root 147080 Sep 23 2020 mv - lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 18 2021 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 43872 Sep 23 2020 pwd - lrwxrwxrwx 1 root root 4 Aug 4 2021 rbash -> bash - -rwxr-xr-x 1 root root 52032 Sep 23 2020 readlink - -rwxr-xr-x 1 root root 72704 Sep 23 2020 rm - -rwxr-xr-x 1 root root 52032 Sep 23 2020 rmdir - -rwxr-xr-x 1 root root 27472 Sep 27 2020 run-parts - -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Feb 20 21:26 sh -> dash - -rwxr-xr-x 1 root root 43808 Sep 23 2020 sleep - -rwxr-xr-x 1 root root 84928 Sep 23 2020 stty - -rwsr-xr-x 1 root root 71912 Jul 28 2021 su - -rwxr-xr-x 1 root root 39744 Sep 23 2020 sync - -rwxr-xr-x 1 root root 531928 Feb 16 2021 tar - -rwxr-xr-x 1 root root 14456 Sep 27 2020 tempfile - -rwxr-xr-x 1 root root 101408 Sep 23 2020 touch - -rwxr-xr-x 1 root root 39680 Sep 23 2020 true - -rwxr-xr-x 1 root root 14328 Feb 26 2021 ulockmgr_server - -rwsr-xr-x 1 root root 35040 Jul 28 2021 umount - -rwxr-xr-x 1 root root 39744 Sep 23 2020 uname - -rwxr-xr-x 2 root root 2346 Mar 2 2021 uncompress - -rwxr-xr-x 1 root root 147176 Sep 23 2020 vdir - -rwxr-xr-x 1 root root 63744 Jul 28 2021 wdctl - lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Mar 2 2021 zcat - -rwxr-xr-x 1 root root 1678 Mar 2 2021 zcmp - -rwxr-xr-x 1 root root 5880 Mar 2 2021 zdiff - -rwxr-xr-x 1 root root 29 Mar 2 2021 zegrep - -rwxr-xr-x 1 root root 29 Mar 2 2021 zfgrep - -rwxr-xr-x 1 root root 2081 Mar 2 2021 zforce - -rwxr-xr-x 1 root root 7585 Mar 2 2021 zgrep - -rwxr-xr-x 1 root root 2206 Mar 2 2021 zless - -rwxr-xr-x 1 root root 1842 Mar 2 2021 zmore - -rwxr-xr-x 1 root root 4553 Mar 2 2021 znew -I: user script /srv/workspace/pbuilder/1688501/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1234376 Aug 5 2021 bash + -rwxr-xr-x 3 root root 38984 Jul 21 2020 bunzip2 + -rwxr-xr-x 3 root root 38984 Jul 21 2020 bzcat + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2225 Jul 21 2020 bzdiff + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4877 Sep 5 2019 bzexe + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3775 Jul 21 2020 bzgrep + -rwxr-xr-x 3 root root 38984 Jul 21 2020 bzip2 + -rwxr-xr-x 1 root root 18424 Jul 21 2020 bzip2recover + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Jul 21 2020 bzmore + -rwxr-xr-x 1 root root 43936 Sep 24 2020 cat + -rwxr-xr-x 1 root root 72672 Sep 24 2020 chgrp + -rwxr-xr-x 1 root root 64448 Sep 24 2020 chmod + -rwxr-xr-x 1 root root 72672 Sep 24 2020 chown + -rwxr-xr-x 1 root root 151168 Sep 24 2020 cp + -rwxr-xr-x 1 root root 125560 Dec 11 2020 dash + -rwxr-xr-x 1 root root 113664 Sep 24 2020 date + -rwxr-xr-x 1 root root 80968 Sep 24 2020 dd + -rwxr-xr-x 1 root root 93936 Sep 24 2020 df + -rwxr-xr-x 1 root root 147176 Sep 24 2020 dir + -rwxr-xr-x 1 root root 84440 Jul 29 2021 dmesg + lrwxrwxrwx 1 root root 8 Nov 8 2019 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Nov 8 2019 domainname -> hostname + -rwxr-xr-x 1 root root 39712 Sep 24 2020 echo + -rwxr-xr-x 1 root root 28 Nov 10 2020 egrep + -rwxr-xr-x 1 root root 39680 Sep 24 2020 false + -rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep + -rwxr-xr-x 1 root root 69032 Jul 29 2021 findmnt + -rwsr-xr-x 1 root root 34896 Feb 27 2021 fusermount + -rwxr-xr-x 1 root root 203072 Nov 10 2020 grep + -rwxr-xr-x 2 root root 2346 Mar 3 2021 gunzip + -rwxr-xr-x 1 root root 6376 Mar 3 2021 gzexe + -rwxr-xr-x 1 root root 98048 Mar 3 2021 gzip + -rwxr-xr-x 1 root root 22600 Nov 8 2019 hostname + -rwxr-xr-x 1 root root 72840 Sep 24 2020 ln + -rwxr-xr-x 1 root root 56952 Feb 8 2020 login + -rwxr-xr-x 1 root root 147176 Sep 24 2020 ls + -rwxr-xr-x 1 root root 149736 Jul 29 2021 lsblk + -rwxr-xr-x 1 root root 85184 Sep 24 2020 mkdir + -rwxr-xr-x 1 root root 76896 Sep 24 2020 mknod + -rwxr-xr-x 1 root root 48064 Sep 24 2020 mktemp + -rwxr-xr-x 1 root root 59632 Jul 29 2021 more + -rwsr-xr-x 1 root root 55528 Jul 29 2021 mount + -rwxr-xr-x 1 root root 18664 Jul 29 2021 mountpoint + -rwxr-xr-x 1 root root 147080 Sep 24 2020 mv + lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Apr 19 2021 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 43872 Sep 24 2020 pwd + lrwxrwxrwx 1 root root 4 Aug 5 2021 rbash -> bash + -rwxr-xr-x 1 root root 52032 Sep 24 2020 readlink + -rwxr-xr-x 1 root root 72704 Sep 24 2020 rm + -rwxr-xr-x 1 root root 52032 Sep 24 2020 rmdir + -rwxr-xr-x 1 root root 27472 Sep 28 2020 run-parts + -rwxr-xr-x 1 root root 122224 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Apr 4 05:43 sh -> bash + lrwxrwxrwx 1 root root 4 Mar 27 05:47 sh.distrib -> dash + -rwxr-xr-x 1 root root 43808 Sep 24 2020 sleep + -rwxr-xr-x 1 root root 84928 Sep 24 2020 stty + -rwsr-xr-x 1 root root 71912 Jul 29 2021 su + -rwxr-xr-x 1 root root 39744 Sep 24 2020 sync + -rwxr-xr-x 1 root root 531928 Feb 17 2021 tar + -rwxr-xr-x 1 root root 14456 Sep 28 2020 tempfile + -rwxr-xr-x 1 root root 101408 Sep 24 2020 touch + -rwxr-xr-x 1 root root 39680 Sep 24 2020 true + -rwxr-xr-x 1 root root 14328 Feb 27 2021 ulockmgr_server + -rwsr-xr-x 1 root root 35040 Jul 29 2021 umount + -rwxr-xr-x 1 root root 39744 Sep 24 2020 uname + -rwxr-xr-x 2 root root 2346 Mar 3 2021 uncompress + -rwxr-xr-x 1 root root 147176 Sep 24 2020 vdir + -rwxr-xr-x 1 root root 63744 Jul 29 2021 wdctl + lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Mar 3 2021 zcat + -rwxr-xr-x 1 root root 1678 Mar 3 2021 zcmp + -rwxr-xr-x 1 root root 5880 Mar 3 2021 zdiff + -rwxr-xr-x 1 root root 29 Mar 3 2021 zegrep + -rwxr-xr-x 1 root root 29 Mar 3 2021 zfgrep + -rwxr-xr-x 1 root root 2081 Mar 3 2021 zforce + -rwxr-xr-x 1 root root 7585 Mar 3 2021 zgrep + -rwxr-xr-x 1 root root 2206 Mar 3 2021 zless + -rwxr-xr-x 1 root root 1842 Mar 3 2021 zmore + -rwxr-xr-x 1 root root 4553 Mar 3 2021 znew +I: user script /srv/workspace/pbuilder/1804384/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -314,7 +348,7 @@ Get: 92 http://deb.debian.org/debian bullseye/main amd64 python3-setuptools all 52.0.0-4 [366 kB] Get: 93 http://deb.debian.org/debian bullseye/main amd64 samtools amd64 1.11-1 [545 kB] Get: 94 http://deb.debian.org/debian bullseye/main amd64 tabix amd64 1.11-4 [339 kB] -Fetched 41.7 MB in 1s (50.0 MB/s) +Fetched 41.7 MB in 0s (87.9 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (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 ... 19655 files and directories currently installed.) @@ -708,7 +742,8 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/python-pysam-0.15.4+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 > ../python-pysam_0.15.4+ds-3_source.changes +hostname: Name or service not known +I: Running cd /build/python-pysam-0.15.4+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 > ../python-pysam_0.15.4+ds-3_source.changes dpkg-buildpackage: info: source package python-pysam dpkg-buildpackage: info: source version 0.15.4+ds-3 dpkg-buildpackage: info: source distribution unstable @@ -1382,7 +1417,7 @@ tests/AlignedSegment_test.py::TestTags::testMDTagSoftClipping PASSED tests/AlignedSegment_test.py::TestTags::testMissingTag PASSED tests/AlignedSegment_test.py::TestTags::testNegativeIntegers PASSED -tests/AlignedSegment_test.py::TestTags::testNegativeIntegersWrittenToFile [E::idx_find_and_load] Could not retrieve index file for '/build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/tests/tmp/pysamtests_tmp___enter___m3b6ksrmnegative_integers.bam' +tests/AlignedSegment_test.py::TestTags::testNegativeIntegersWrittenToFile [E::idx_find_and_load] Could not retrieve index file for '/build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/tests/tmp/pysamtests_tmp___enter___jpoztufinegative_integers.bam' PASSED tests/AlignedSegment_test.py::TestTags::testSetTag PASSED tests/AlignedSegment_test.py::TestTags::testTagParsing PASSED @@ -1461,22 +1496,22 @@ tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_header_content_is_as_expected FAILED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_name_mapping PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_text_access_works PASSED -tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_BAM [E::idx_find_and_load] Could not retrieve index file for '/build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_6tbghkev' -/build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_6tbghkev +tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_BAM [E::idx_find_and_load] Could not retrieve index file for '/build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_2tut8tf_' +/build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_2tut8tf_ PASSED -tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_CRAM [E::cram_index_load] Could not retrieve index file for '/build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_z1joxb4r' -/build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_z1joxb4r +tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_CRAM [E::cram_index_load] Could not retrieve index file for '/build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_989u5ssa' +/build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_989u5ssa PASSED -tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_SAM /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_8r3enbpc +tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_SAM /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_x01jhp0f PASSED -tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_BAM [E::idx_find_and_load] Could not retrieve index file for '/build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_vgqwdbnh' -/build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_vgqwdbnh +tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_BAM [E::idx_find_and_load] Could not retrieve index file for '/build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_1fcbx8aa' +/build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_1fcbx8aa PASSED tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_CRAM [W::sanitise_SQ_lines] Header @SQ length mismatch for ref chr1, 2147483647 vs 1575 -[E::cram_index_load] Could not retrieve index file for '/build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_v66aempo' -/build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_v66aempo +[E::cram_index_load] Could not retrieve index file for '/build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_agmcg0ih' +/build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_agmcg0ih PASSED -tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_SAM /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_h5neagbq +tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_SAM /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_247dir37 PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_all_stepper PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_ignore_overlaps PASSED @@ -1842,7 +1877,7 @@ tests/AlignmentFile_test.py::TestIO::testOpenFromFilename FAILED tests/AlignmentFile_test.py::TestIO::testReadBamWithoutTargetNames PASSED tests/AlignmentFile_test.py::TestIO::testReadSamWithoutTargetNames PASSED -tests/AlignmentFile_test.py::TestIO::testReadingFromFileWithoutIndex [E::idx_find_and_load] Could not retrieve index file for '/build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/tests/tmp/pysamtests_tmp_testReadingFromFileWithoutIndex_114hblt1tmp_ex2.bam' +tests/AlignmentFile_test.py::TestIO::testReadingFromFileWithoutIndex [E::idx_find_and_load] Could not retrieve index file for '/build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/tests/tmp/pysamtests_tmp_testReadingFromFileWithoutIndex_mz4payg_tmp_ex2.bam' PASSED tests/AlignmentFile_test.py::TestIO::testSAM2BAM FAILED tests/AlignmentFile_test.py::TestIO::testSAM2CRAM [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported @@ -1956,8 +1991,8 @@ tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_with_asterisk_only_returns_unmapped_reads PASSED tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_with_asterisk_only_returns_unmapped_reads_by_contig PASSED tests/AlignmentFile_test.py::TestContextManager::testManager PASSED -tests/AlignmentFile_test.py::TestMultiThread::testSingleThreadEqualsMultithread [E::idx_find_and_load] Could not retrieve index file for '/build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/tests/tmp/pysamtests_tmp_testSingleThreadEqualsMultithread_0yo0ut3gtmp_single.bam' -[E::idx_find_and_load] Could not retrieve index file for '/build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/tests/tmp/pysamtests_tmp_testSingleThreadEqualsMultithread_81znw9ymtmp_multi.bam' +tests/AlignmentFile_test.py::TestMultiThread::testSingleThreadEqualsMultithread [E::idx_find_and_load] Could not retrieve index file for '/build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/tests/tmp/pysamtests_tmp_testSingleThreadEqualsMultithread_5uhee522tmp_single.bam' +[E::idx_find_and_load] Could not retrieve index file for '/build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/tests/tmp/pysamtests_tmp_testSingleThreadEqualsMultithread_m1qw7f69tmp_multi.bam' PASSED tests/AlignmentFile_test.py::TestExceptions::testBackwardsOrderNewFormat PASSED tests/AlignmentFile_test.py::TestExceptions::testBackwardsOrderOldFormat PASSED @@ -2073,13 +2108,14 @@ tests/AlignmentFile_test.py::TestSamtoolsProxy::testView [E::hts_open_format] Failed to open file "missing_file" : No such file or directory PASSED tests/AlignmentFile_test.py::TestAlignmentFileIndex::testIndex PASSED -tests/AlignmentFile_test.py::TestExplicitIndex::testExplicitIndexBAM PASSED +tests/AlignmentFile_test.py::TestExplicitIndex::testExplicitIndexBAM [W::hts_idx_load3] The index file is older than the data file: /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/tests/pysam_data/ex1.bam.bai +PASSED tests/AlignmentFile_test.py::TestExplicitIndex::testExplicitIndexCRAM PASSED tests/AlignmentFile_test.py::TestExplicitIndex::testRemoteExplicitIndexBAM PASSED tests/AlignmentFile_test.py::TestVerbosity::testVerbosity PASSED tests/AlignmentFile_test.py::TestSanityCheckingBAM::test_empty_read_gives_value_error PASSED tests/AlignmentFile_test.py::TestHeader1000Genomes::testRead PASSED -tests/AlignmentFile_test.py::TestLargeCigar::test_reading_writing_bam [E::idx_find_and_load] Could not retrieve index file for '/build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/tests/tmp/pysamtests_tmp_check_read_f63ab3cetmp_largecigar.bam' +tests/AlignmentFile_test.py::TestLargeCigar::test_reading_writing_bam [E::idx_find_and_load] Could not retrieve index file for '/build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/tests/tmp/pysamtests_tmp_check_read_n89pmggmtmp_largecigar.bam' PASSED tests/AlignmentFile_test.py::TestLargeCigar::test_reading_writing_cram SKIPPED tests/AlignmentFile_test.py::TestLargeCigar::test_reading_writing_sam PASSED @@ -2151,7 +2187,7 @@ tests/VariantFile_test.py::TestSettingRecordValues::testSetQual [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/VariantFile_test.py::TestMultiThreading::testNoMultiThreadingWithIgnoreTruncation PASSED -tests/VariantFile_test.py::TestMultiThreading::testSingleThreadEqualsMultithreadResult [E::idx_find_and_load] Could not retrieve index file for '/build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/tests/tmp/pysamtests_tmp_testSingleThreadEqualsMultithreadResult_pald60a7.bcf' +tests/VariantFile_test.py::TestMultiThreading::testSingleThreadEqualsMultithreadResult [E::idx_find_and_load] Could not retrieve index file for '/build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/tests/tmp/pysamtests_tmp_testSingleThreadEqualsMultithreadResult_9hrocwnn.bcf' PASSED tests/VariantFile_test.py::TestSubsetting::testSubsetting PASSED tests/VariantFile_test.py::TestVCFVersions::test_all_records_can_be_fetched [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) @@ -3091,7 +3127,7 @@ checkGZBinaryEqual(tmpfilename, self.bamfile), "mismatch when construction BAM file, see %s %s" % (tmpfilename, self.bamfile)) -E AssertionError: False is not true : mismatch when construction BAM file, see tmp_140674156464112.bam /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/tests/pysam_data/ex6.bam +E AssertionError: False is not true : mismatch when construction BAM file, see tmp_140111345533232.bam /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/tests/pysam_data/ex6.bam tests/AlignmentFile_test.py:1377: AssertionError _______________________ TestEmptyHeader.testEmptyHeader ________________________ @@ -3217,7 +3253,7 @@ FAILED tests/AlignmentFile_test.py::TestHeaderWithProgramOptions::testHeader FAILED tests/StreamFiledescriptors_test.py::StreamTest::test_text_processing FAILED tests/compile_test.py::BAMTest::testCount - AssertionError: 3269 != 3270 -====== 26 failed, 901 passed, 10 skipped, 7 warnings in 69.17s (0:01:09) ======= +====== 26 failed, 901 passed, 10 skipped, 7 warnings in 62.54s (0:01:02) ======= make[1]: Leaving directory '/build/python-pysam-0.15.4+ds' create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild @@ -3266,7 +3302,7 @@ creating /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9 creating /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/log.txt -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages -copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/tmp_140674156464112.bam -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages +copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/tmp_140111345533232.bam -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam_uncompressed.bam -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/tmp_ex2.bam -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/tmp_ex1.bam -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages @@ -3478,12 +3514,14 @@ 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/1804384/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1804384/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/1688501 and its subdirectories -I: Current time: Mon Feb 28 21:20:05 -12 2022 -I: pbuilder-time-stamp: 1646126405 +I: removing directory /srv/workspace/pbuilder/1804384 and its subdirectories +I: Current time: Tue Apr 4 05:49:26 +14 2023 +I: pbuilder-time-stamp: 1680536966