Diff of the two buildlogs: -- --- b1/build.log 2023-05-09 06:39:34.879902574 +0000 +++ b2/build.log 2023-05-09 06:47:24.307364098 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Jun 10 00:57:45 -12 2024 -I: pbuilder-time-stamp: 1718024265 +I: Current time: Tue May 9 20:39:36 +14 2023 +I: pbuilder-time-stamp: 1683614376 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration @@ -17,7 +17,7 @@ I: copying [./python-pysam_0.20.0+ds.orig.tar.xz] I: copying [./python-pysam_0.20.0+ds-3.debian.tar.xz] I: Extracting source -gpgv: Signature made Sat Dec 31 05:45:09 2022 -12 +gpgv: Signature made Sun Jan 1 07:45:09 2023 +14 gpgv: using EDDSA key A095B66EE09024BEE6A2F0722A27904BD7243EDA gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./python-pysam_0.20.0+ds-3.dsc: no acceptable signature found @@ -32,137 +32,169 @@ dpkg-source: info: applying python3.11.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/1222/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/29729/tmp/hooks/D01_modify_environment starting +debug: Running on ionos12-i386. +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 9 20:39 /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/29729/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/29729/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='i386' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16' - DISTRIBUTION='bookworm' - HOME='/root' - HOST_ARCH='i386' + 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]="i686-pc-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=i386 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=7' + DIRSTACK=() + DISTRIBUTION=bookworm + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=i686 + HOST_ARCH=i386 IFS=' ' - INVOCATION_ID='4f8690f9933342ac8f8f6665e4898c42' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - LD_LIBRARY_PATH='/usr/lib/libeatmydata' - LD_PRELOAD='libeatmydata.so' - 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='1222' - PS1='# ' - PS2='> ' + INVOCATION_ID=df79142fe119430bb31c7c03604b811c + LANG=C + LANGUAGE=de_CH:de + LC_ALL=C + LD_LIBRARY_PATH=/usr/lib/libeatmydata + LD_PRELOAD=libeatmydata.so + MACHTYPE=i686-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=29729 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.GaAQ7Bhk/pbuilderrc_5TJL --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.GaAQ7Bhk/b1 --logfile b1/build.log python-pysam_0.20.0+ds-3.dsc' - SUDO_GID='112' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://85.184.249.68:3128' + 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.GaAQ7Bhk/pbuilderrc_XhEh --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.GaAQ7Bhk/b2 --logfile b2/build.log --extrapackages usrmerge python-pysam_0.20.0+ds-3.dsc' + SUDO_GID=112 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://78.137.99.97:3128 I: uname -a - Linux ionos6-i386 5.10.0-22-amd64 #1 SMP Debian 5.10.178-3 (2023-04-22) x86_64 GNU/Linux + Linux i-capture-the-hostname 5.10.0-22-686-pae #1 SMP Debian 5.10.178-3 (2023-04-22) i686 GNU/Linux I: ls -l /bin total 6036 - -rwxr-xr-x 1 root root 1408088 Apr 23 2023 bash - -rwxr-xr-x 3 root root 38404 Sep 18 2022 bunzip2 - -rwxr-xr-x 3 root root 38404 Sep 18 2022 bzcat - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep - -rwxr-xr-x 3 root root 38404 Sep 18 2022 bzip2 - -rwxr-xr-x 1 root root 17892 Sep 18 2022 bzip2recover - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore - -rwxr-xr-x 1 root root 42920 Sep 20 2022 cat - -rwxr-xr-x 1 root root 79816 Sep 20 2022 chgrp - -rwxr-xr-x 1 root root 67496 Sep 20 2022 chmod - -rwxr-xr-x 1 root root 79816 Sep 20 2022 chown - -rwxr-xr-x 1 root root 162024 Sep 20 2022 cp - -rwxr-xr-x 1 root root 136916 Jan 5 2023 dash - -rwxr-xr-x 1 root root 137160 Sep 20 2022 date - -rwxr-xr-x 1 root root 100364 Sep 20 2022 dd - -rwxr-xr-x 1 root root 108940 Sep 20 2022 df - -rwxr-xr-x 1 root root 162152 Sep 20 2022 dir - -rwxr-xr-x 1 root root 87760 Mar 22 2023 dmesg - lrwxrwxrwx 1 root root 8 Dec 19 2022 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Dec 19 2022 domainname -> hostname - -rwxr-xr-x 1 root root 38760 Sep 20 2022 echo - -rwxr-xr-x 1 root root 41 Jan 24 2023 egrep - -rwxr-xr-x 1 root root 34664 Sep 20 2022 false - -rwxr-xr-x 1 root root 41 Jan 24 2023 fgrep - -rwxr-xr-x 1 root root 84272 Mar 22 2023 findmnt - -rwsr-xr-x 1 root root 30240 Mar 22 2023 fusermount - -rwxr-xr-x 1 root root 218680 Jan 24 2023 grep - -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip - -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe - -rwxr-xr-x 1 root root 100952 Apr 9 2022 gzip - -rwxr-xr-x 1 root root 21916 Dec 19 2022 hostname - -rwxr-xr-x 1 root root 75756 Sep 20 2022 ln - -rwxr-xr-x 1 root root 55600 Mar 22 2023 login - -rwxr-xr-x 1 root root 162152 Sep 20 2022 ls - -rwxr-xr-x 1 root root 214568 Mar 22 2023 lsblk - -rwxr-xr-x 1 root root 96328 Sep 20 2022 mkdir - -rwxr-xr-x 1 root root 84008 Sep 20 2022 mknod - -rwxr-xr-x 1 root root 38792 Sep 20 2022 mktemp - -rwxr-xr-x 1 root root 63016 Mar 22 2023 more - -rwsr-xr-x 1 root root 58912 Mar 22 2023 mount - -rwxr-xr-x 1 root root 13856 Mar 22 2023 mountpoint - -rwxr-xr-x 1 root root 157932 Sep 20 2022 mv - lrwxrwxrwx 1 root root 8 Dec 19 2022 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 2 2023 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 38792 Sep 20 2022 pwd - lrwxrwxrwx 1 root root 4 Apr 23 2023 rbash -> bash - -rwxr-xr-x 1 root root 51080 Sep 20 2022 readlink - -rwxr-xr-x 1 root root 75720 Sep 20 2022 rm - -rwxr-xr-x 1 root root 51080 Sep 20 2022 rmdir - -rwxr-xr-x 1 root root 22308 Nov 2 2022 run-parts - -rwxr-xr-x 1 root root 133224 Jan 5 2023 sed - lrwxrwxrwx 1 root root 4 Jan 5 2023 sh -> dash - -rwxr-xr-x 1 root root 38760 Sep 20 2022 sleep - -rwxr-xr-x 1 root root 87976 Sep 20 2022 stty - -rwsr-xr-x 1 root root 83492 Mar 22 2023 su - -rwxr-xr-x 1 root root 38792 Sep 20 2022 sync - -rwxr-xr-x 1 root root 598456 Apr 6 2023 tar - -rwxr-xr-x 1 root root 13860 Nov 2 2022 tempfile - -rwxr-xr-x 1 root root 120776 Sep 20 2022 touch - -rwxr-xr-x 1 root root 34664 Sep 20 2022 true - -rwxr-xr-x 1 root root 17892 Mar 22 2023 ulockmgr_server - -rwsr-xr-x 1 root root 30236 Mar 22 2023 umount - -rwxr-xr-x 1 root root 38760 Sep 20 2022 uname - -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress - -rwxr-xr-x 1 root root 162152 Sep 20 2022 vdir - -rwxr-xr-x 1 root root 71216 Mar 22 2023 wdctl - lrwxrwxrwx 1 root root 8 Dec 19 2022 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat - -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp - -rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff - -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep - -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep - -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce - -rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep - -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless - -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore - -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew -I: user script /srv/workspace/pbuilder/1222/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1408088 Apr 24 11:24 bash + -rwxr-xr-x 3 root root 38404 Sep 19 2022 bunzip2 + -rwxr-xr-x 3 root root 38404 Sep 19 2022 bzcat + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2225 Sep 19 2022 bzdiff + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4893 Nov 28 2021 bzexe + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3775 Sep 19 2022 bzgrep + -rwxr-xr-x 3 root root 38404 Sep 19 2022 bzip2 + -rwxr-xr-x 1 root root 17892 Sep 19 2022 bzip2recover + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Sep 19 2022 bzmore + -rwxr-xr-x 1 root root 42920 Sep 21 2022 cat + -rwxr-xr-x 1 root root 79816 Sep 21 2022 chgrp + -rwxr-xr-x 1 root root 67496 Sep 21 2022 chmod + -rwxr-xr-x 1 root root 79816 Sep 21 2022 chown + -rwxr-xr-x 1 root root 162024 Sep 21 2022 cp + -rwxr-xr-x 1 root root 136916 Jan 6 03:20 dash + -rwxr-xr-x 1 root root 137160 Sep 21 2022 date + -rwxr-xr-x 1 root root 100364 Sep 21 2022 dd + -rwxr-xr-x 1 root root 108940 Sep 21 2022 df + -rwxr-xr-x 1 root root 162152 Sep 21 2022 dir + -rwxr-xr-x 1 root root 87760 Mar 24 00:20 dmesg + lrwxrwxrwx 1 root root 8 Dec 20 03:33 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Dec 20 03:33 domainname -> hostname + -rwxr-xr-x 1 root root 38760 Sep 21 2022 echo + -rwxr-xr-x 1 root root 41 Jan 25 04:43 egrep + -rwxr-xr-x 1 root root 34664 Sep 21 2022 false + -rwxr-xr-x 1 root root 41 Jan 25 04:43 fgrep + -rwxr-xr-x 1 root root 84272 Mar 24 00:20 findmnt + -rwsr-xr-x 1 root root 30240 Mar 23 22:38 fusermount + -rwxr-xr-x 1 root root 218680 Jan 25 04:43 grep + -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip + -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe + -rwxr-xr-x 1 root root 100952 Apr 10 2022 gzip + -rwxr-xr-x 1 root root 21916 Dec 20 03:33 hostname + -rwxr-xr-x 1 root root 75756 Sep 21 2022 ln + -rwxr-xr-x 1 root root 55600 Mar 24 01:43 login + -rwxr-xr-x 1 root root 162152 Sep 21 2022 ls + -rwxr-xr-x 1 root root 214568 Mar 24 00:20 lsblk + -rwxr-xr-x 1 root root 96328 Sep 21 2022 mkdir + -rwxr-xr-x 1 root root 84008 Sep 21 2022 mknod + -rwxr-xr-x 1 root root 38792 Sep 21 2022 mktemp + -rwxr-xr-x 1 root root 63016 Mar 24 00:20 more + -rwsr-xr-x 1 root root 58912 Mar 24 00:20 mount + -rwxr-xr-x 1 root root 13856 Mar 24 00:20 mountpoint + -rwxr-xr-x 1 root root 157932 Sep 21 2022 mv + lrwxrwxrwx 1 root root 8 Dec 20 03:33 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Apr 3 20:25 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 38792 Sep 21 2022 pwd + lrwxrwxrwx 1 root root 4 Apr 24 11:24 rbash -> bash + -rwxr-xr-x 1 root root 51080 Sep 21 2022 readlink + -rwxr-xr-x 1 root root 75720 Sep 21 2022 rm + -rwxr-xr-x 1 root root 51080 Sep 21 2022 rmdir + -rwxr-xr-x 1 root root 22308 Nov 3 2022 run-parts + -rwxr-xr-x 1 root root 133224 Jan 6 09:55 sed + lrwxrwxrwx 1 root root 9 May 9 20:39 sh -> /bin/bash + -rwxr-xr-x 1 root root 38760 Sep 21 2022 sleep + -rwxr-xr-x 1 root root 87976 Sep 21 2022 stty + -rwsr-xr-x 1 root root 83492 Mar 24 00:20 su + -rwxr-xr-x 1 root root 38792 Sep 21 2022 sync + -rwxr-xr-x 1 root root 598456 Apr 7 04:25 tar + -rwxr-xr-x 1 root root 13860 Nov 3 2022 tempfile + -rwxr-xr-x 1 root root 120776 Sep 21 2022 touch + -rwxr-xr-x 1 root root 34664 Sep 21 2022 true + -rwxr-xr-x 1 root root 17892 Mar 23 22:38 ulockmgr_server + -rwsr-xr-x 1 root root 30236 Mar 24 00:20 umount + -rwxr-xr-x 1 root root 38760 Sep 21 2022 uname + -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress + -rwxr-xr-x 1 root root 162152 Sep 21 2022 vdir + -rwxr-xr-x 1 root root 71216 Mar 24 00:20 wdctl + lrwxrwxrwx 1 root root 8 Dec 20 03:33 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat + -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp + -rwxr-xr-x 1 root root 6460 Apr 10 2022 zdiff + -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep + -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep + -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce + -rwxr-xr-x 1 root root 8103 Apr 10 2022 zgrep + -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless + -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore + -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew +I: user script /srv/workspace/pbuilder/29729/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -310,7 +342,7 @@ Get: 88 http://deb.debian.org/debian bookworm/main i386 python3-setuptools all 66.1.1-1 [521 kB] Get: 89 http://deb.debian.org/debian bookworm/main i386 samtools i386 1.16.1-1 [637 kB] Get: 90 http://deb.debian.org/debian bookworm/main i386 tabix i386 1.16+ds-3 [501 kB] -Fetched 43.3 MB in 1s (57.0 MB/s) +Fetched 43.3 MB in 1s (53.6 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:i386. (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 ... 19604 files and directories currently installed.) @@ -687,8 +719,19 @@ 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/python-pysam-0.20.0+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_0.20.0+ds-3_source.changes +I: user script /srv/workspace/pbuilder/29729/tmp/hooks/A99_set_merged_usr starting +Re-configuring usrmerge... +removed '/etc/unsupported-skip-usrmerge-conversion' +The system has been successfully converted. +I: user script /srv/workspace/pbuilder/29729/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/python-pysam-0.20.0+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_0.20.0+ds-3_source.changes dpkg-buildpackage: info: source package python-pysam dpkg-buildpackage: info: source version 0.20.0+ds-3 dpkg-buildpackage: info: source distribution unstable @@ -697,17 +740,17 @@ dpkg-buildpackage: info: host architecture i386 debian/rules clean cd tests/pysam_data && /usr/bin/make clean -make[1]: Entering directory '/build/python-pysam-0.20.0+ds/tests/pysam_data' +make[1]: Verzeichnis „/build/python-pysam-0.20.0+ds/tests/pysam_data“ wird betreten rm -fr *.bai *.csi *.fai *.gzi *.pileup* [a-z]*.cram *.crai \ all.stamp *~ calDepth *.dSYM pysam_*.sam \ ex2.sam ex2.sam.gz ex1.sam ex1.fa.gz \ with_md.sam.gz \ *.fq.gz -make[1]: Leaving directory '/build/python-pysam-0.20.0+ds/tests/pysam_data' +make[1]: Verzeichnis „/build/python-pysam-0.20.0+ds/tests/pysam_data“ wird verlassen cd tests/cbcf_data && /usr/bin/make clean -make[1]: Entering directory '/build/python-pysam-0.20.0+ds/tests/cbcf_data' +make[1]: Verzeichnis „/build/python-pysam-0.20.0+ds/tests/cbcf_data“ wird betreten rm -f all.stamp *.gz *.tbi *.csi *.bcf -make[1]: Leaving directory '/build/python-pysam-0.20.0+ds/tests/cbcf_data' +make[1]: Verzeichnis „/build/python-pysam-0.20.0+ds/tests/cbcf_data“ wird verlassen find . -name "*.pyc" -delete find . -name "*.pyxbldc" -delete find . -name "tmp_*.bam" -delete @@ -730,7 +773,7 @@ rm -rf .pytest_cache/ dh clean --with python3 --buildsystem=pybuild debian/rules override_dh_auto_clean -make[1]: Entering directory '/build/python-pysam-0.20.0+ds' +make[1]: Verzeichnis „/build/python-pysam-0.20.0+ds“ wird betreten dh_auto_clean I: pybuild base:240: python3.11 setup.py clean # pysam: cython is available - using cythonize if necessary @@ -747,7 +790,7 @@ samtools/config.h \ bcftools/config.h rm -rf pysam.egg-info -make[1]: Leaving directory '/build/python-pysam-0.20.0+ds' +make[1]: Verzeichnis „/build/python-pysam-0.20.0+ds“ wird verlassen dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary @@ -768,97 +811,97 @@ running build running build_py creating /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -copying pysam/utils.py -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/samtools.py -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -copying pysam/config.py -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/Pileup.py -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam +copying pysam/config.py -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/version.py -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/__init__.py -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam +copying pysam/utils.py -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/bcftools.py -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam creating /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include copying pysam/include/__init__.py -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include -copying pysam/libcsamtools.pxd -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -copying pysam/libcutils.pxd -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -copying pysam/libcbcftools.pxd -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -copying pysam/libctabix.pxd -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/libcsamfile.pxd -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -copying pysam/libcbcf.pxd -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam +copying pysam/libcfaidx.pxd -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/libctabixproxies.pxd -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/libchtslib.pxd -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -copying pysam/libcfaidx.pxd -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -copying pysam/libcalignedsegment.pxd -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam +copying pysam/libcsamtools.pxd -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/libcalignmentfile.pxd -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam +copying pysam/libcbcftools.pxd -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam +copying pysam/libcalignedsegment.pxd -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam +copying pysam/libcutils.pxd -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam +copying pysam/libctabix.pxd -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/libcvcf.pxd -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam +copying pysam/libcbcf.pxd -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam +copying pysam/pysam_stream.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam +copying pysam/htslib_util.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/version.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -copying pysam/pysam_util.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/cbcftools_util.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -copying pysam/htslib_util.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -copying pysam/pysam_stream.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam +copying pysam/pysam_util.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/csamtools_util.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/py.typed -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -copying pysam/libctabixproxies.pyi -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -copying pysam/libcsamfile.pyi -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -copying pysam/libchtslib.pyi -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -copying pysam/libcsamtools.pyi -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -copying pysam/libcvcf.pyi -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/libcbcf.pyi -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -copying pysam/libcalignmentfile.pyi -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/libctabix.pyi -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -copying pysam/version.pyi -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -copying pysam/libcbgzf.pyi -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam +copying pysam/libcalignmentfile.pyi -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/libcfaidx.pyi -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam +copying pysam/version.pyi -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam +copying pysam/libcsamtools.pyi -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/libcalignedsegment.pyi -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam +copying pysam/libcsamfile.pyi -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam +copying pysam/libchtslib.pyi -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam +copying pysam/libcbgzf.pyi -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam +copying pysam/libcvcf.pyi -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/libcbcftools.pyi -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam +copying pysam/libctabixproxies.pyi -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/libcutils.pyi -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam creating /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools +copying samtools/bam_lpileup.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools +copying samtools/bam_plbuf.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/stats_isize.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools -copying samtools/splaysort.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools +copying samtools/config.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools +copying samtools/tmp_file.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools +copying samtools/sam_opts.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools +copying samtools/bam_ampliconclip.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/consensus_pileup.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools +copying samtools/samtools.pysam.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/bedidx.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools -copying samtools/bam_plbuf.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/samtools.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools -copying samtools/sample.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/bam.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools -copying samtools/bam_ampliconclip.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools -copying samtools/samtools.pysam.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools -copying samtools/sam_opts.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools -copying samtools/config.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools -copying samtools/tmp_file.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools -copying samtools/bam_lpileup.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools +copying samtools/splaysort.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools +copying samtools/sample.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools creating /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools -copying bcftools/mw.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools -copying bcftools/vcfbuf.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools -copying bcftools/kmin.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools -copying bcftools/abuf.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/dbuf.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/HMM.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools +copying bcftools/variantkey.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools +copying bcftools/rbuf.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools +copying bcftools/call.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools +copying bcftools/gvcf.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools +copying bcftools/abuf.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/bcftools.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools -copying bcftools/convert.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools -copying bcftools/bin.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools +copying bcftools/config.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/khash_str2str.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools -copying bcftools/variantkey.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/ploidy.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools -copying bcftools/str_finder.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools -copying bcftools/tsv2vcf.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/hex.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools +copying bcftools/bam_sample.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/kheap.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools -copying bcftools/rbuf.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools -copying bcftools/smpl_ilist.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools -copying bcftools/cols.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools -copying bcftools/config.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools -copying bcftools/prob1.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/extsort.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools +copying bcftools/regidx.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/bam2bcf.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools +copying bcftools/mw.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools +copying bcftools/tsv2vcf.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools +copying bcftools/smpl_ilist.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools +copying bcftools/vcfbuf.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools +copying bcftools/kmin.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools +copying bcftools/dist.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools +copying bcftools/hclust.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools +copying bcftools/prob1.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/vcmp.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools +copying bcftools/convert.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/utlist.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools -copying bcftools/bcftools.pysam.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools -copying bcftools/gvcf.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools -copying bcftools/call.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools +copying bcftools/bin.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/filter.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools -copying bcftools/hclust.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools -copying bcftools/bam_sample.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools -copying bcftools/regidx.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools -copying bcftools/dist.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools +copying bcftools/str_finder.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools +copying bcftools/bcftools.pysam.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools +copying bcftools/cols.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools running build_ext cythoning pysam/libchtslib.pyx to pysam/libchtslib.c /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/python-pysam-0.20.0+ds/pysam/libchtslib.pxd @@ -1104,9 +1147,9 @@ | ^~~~~~~~~~~~ i686-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i386-cpython-311/pysam/libcvcf.o -L/build/python-pysam-0.20.0+ds/pysam -L/usr/lib/i386-linux-gnu -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/usr/lib/i386-linux-gnu -lz -lhts -lchtslib.cpython-311-i386-linux-gnu -lcutils.cpython-311-i386-linux-gnu -o /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libcvcf.cpython-311-i386-linux-gnu.so -Wl,-rpath,$ORIGIN debian/rules override_dh_auto_test -make[1]: Entering directory '/build/python-pysam-0.20.0+ds' +make[1]: Verzeichnis „/build/python-pysam-0.20.0+ds“ wird betreten cd tests/pysam_data && /usr/bin/make all -make[2]: Entering directory '/build/python-pysam-0.20.0+ds/tests/pysam_data' +make[2]: Verzeichnis „/build/python-pysam-0.20.0+ds/tests/pysam_data“ wird betreten samtools faidx ex1.fa samtools view --no-PG -bo ex1.bam -t ex1.fa.fai ex1.sam.gz samtools mpileup -f ex1.fa ex1.bam | gzip > ex1.pileup.gz @@ -1258,9 +1301,9 @@ samtools index example_bai.bam mv example_bai.bam.bai example_bai.bai dd if=ex2.bam of=ex2_truncated.bam bs=$((`wc -c < ex2.bam`-512)) count=1 -1+0 records in -1+0 records out -122292 bytes (122 kB, 119 KiB) copied, 0.000212178 s, 576 MB/s +1+0 Datensätze ein +1+0 Datensätze aus +122292 Bytes (122 kB, 119 KiB) kopiert, 0.000555256 s, 220 MB/s (bgzip -d < ex2.bam; printf '\37\0\0\0\1\0\0\0') | bgzip > ex2_corrupt.bam grep "^@" ex2.sam | samtools view --no-PG -bo empty.bam - samtools index empty.bam @@ -1273,9 +1316,9 @@ samtools index -c ex1_csi.bam touch all.stamp rm with_md.sam -make[2]: Leaving directory '/build/python-pysam-0.20.0+ds/tests/pysam_data' +make[2]: Verzeichnis „/build/python-pysam-0.20.0+ds/tests/pysam_data“ wird verlassen cd tests/cbcf_data && /usr/bin/make all -make[2]: Entering directory '/build/python-pysam-0.20.0+ds/tests/cbcf_data' +make[2]: Verzeichnis „/build/python-pysam-0.20.0+ds/tests/cbcf_data“ wird betreten bgzip < example_vcf40.vcf > example_vcf40.vcf.gz tabix -p vcf example_vcf40.vcf.gz # create tbi index bcftools index example_vcf40.vcf.gz # create csi index @@ -1324,7 +1367,7 @@ bcftools view -O b missing_genotypes.vcf.gz -o missing_genotypes.bcf bcftools index missing_genotypes.bcf touch all.stamp -make[2]: Leaving directory '/build/python-pysam-0.20.0+ds/tests/cbcf_data' +make[2]: Verzeichnis „/build/python-pysam-0.20.0+ds/tests/cbcf_data“ wird verlassen dh_auto_test I: pybuild base:240: cd /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build; python3.11 -m pytest tests ============================= test session starts ============================== @@ -1407,7 +1450,7 @@ 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-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp___enter___b3rhlt6onegative_integers.bam' +tests/AlignedSegment_test.py::TestTags::testNegativeIntegersWrittenToFile [E::idx_find_and_load] Could not retrieve index file for '/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp___enter___vio1yir6negative_integers.bam' PASSED tests/AlignedSegment_test.py::TestTags::testSetTag PASSED tests/AlignedSegment_test.py::TestTags::testTagParsing PASSED @@ -1486,22 +1529,22 @@ tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_header_content_is_as_expected PASSED 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-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_0n0wa500' -/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_0n0wa500 +tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_BAM [E::idx_find_and_load] Could not retrieve index file for '/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_41zpl20q' +/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_41zpl20q PASSED -tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_CRAM [E::cram_index_load] Could not retrieve index file for '/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_1ip7d96l' -/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_1ip7d96l +tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_CRAM [E::cram_index_load] Could not retrieve index file for '/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_1bxu8if3' +/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_1bxu8if3 PASSED -tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_SAM /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_4bxzikez +tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_SAM /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_przlytkx PASSED -tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_BAM [E::idx_find_and_load] Could not retrieve index file for '/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_cyo36zn4' -/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_cyo36zn4 +tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_BAM [E::idx_find_and_load] Could not retrieve index file for '/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_pe_nv0g6' +/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_pe_nv0g6 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-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_sbkp38bq' -/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_sbkp38bq +[E::cram_index_load] Could not retrieve index file for '/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_pxew1l41' +/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_pxew1l41 PASSED -tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_SAM /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_vdhmdrcl +tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_SAM /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_w3smoqau PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_all_stepper PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_ignore_overlaps PASSED @@ -1863,7 +1906,7 @@ tests/AlignmentFile_test.py::TestIO::testOpenFromFilename PASSED 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-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_testReadingFromFileWithoutIndex_3ew5emvgtmp_ex2.bam' +tests/AlignmentFile_test.py::TestIO::testReadingFromFileWithoutIndex [E::idx_find_and_load] Could not retrieve index file for '/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_testReadingFromFileWithoutIndex_93j2wa0mtmp_ex2.bam' PASSED tests/AlignmentFile_test.py::TestIO::testSAM2BAM PASSED tests/AlignmentFile_test.py::TestIO::testSAM2CRAM [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused @@ -1977,8 +2020,8 @@ 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-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_testSingleThreadEqualsMultithread_f05fhloxtmp_single.bam' -[E::idx_find_and_load] Could not retrieve index file for '/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_testSingleThreadEqualsMultithread_moqby3vqtmp_multi.bam' +tests/AlignmentFile_test.py::TestMultiThread::testSingleThreadEqualsMultithread [E::idx_find_and_load] Could not retrieve index file for '/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_testSingleThreadEqualsMultithread_89ugox6htmp_single.bam' +[E::idx_find_and_load] Could not retrieve index file for '/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_testSingleThreadEqualsMultithread_wytkn6_htmp_multi.bam' PASSED tests/AlignmentFile_test.py::TestExceptions::testBackwardsOrderNewFormat PASSED tests/AlignmentFile_test.py::TestExceptions::testBackwardsOrderOldFormat PASSED @@ -2095,7 +2138,7 @@ 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::TestLargeCigar::test_reading_writing_bam [E::idx_find_and_load] Could not retrieve index file for '/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_check_read_pjx66s28tmp_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-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_check_read_9njkfbiktmp_largecigar.bam' PASSED tests/AlignmentFile_test.py::TestLargeCigar::test_reading_writing_cram SKIPPED tests/AlignmentFile_test.py::TestLargeCigar::test_reading_writing_sam PASSED @@ -2168,7 +2211,7 @@ 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-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_testSingleThreadEqualsMultithreadResult_d9rj1z09.bcf' +tests/VariantFile_test.py::TestMultiThreading::testSingleThreadEqualsMultithreadResult [E::idx_find_and_load] Could not retrieve index file for '/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_testSingleThreadEqualsMultithreadResult_j2layntw.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.) @@ -2312,46 +2355,6 @@ tests/tabix_test.py::VCFFromTabixTest_issue85::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_issue85::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_issue85::testParsing PASSED -tests/tabix_test.py::VCFFromTabixTest_13::testRead PASSED -tests/tabix_test.py::VCFFromTabixTest_13::testWrite PASSED -tests/tabix_test.py::VCFFromVCFTest_13::testConnecting PASSED -tests/tabix_test.py::VCFFromVCFTest_13::testParsing PASSED -tests/tabix_test.py::VCFFromTabixTest_12::testRead PASSED -tests/tabix_test.py::VCFFromTabixTest_12::testWrite PASSED -tests/tabix_test.py::VCFFromVCFTest_12::testConnecting PASSED -tests/tabix_test.py::VCFFromVCFTest_12::testParsing PASSED -tests/tabix_test.py::VCFFromTabixTest_3::testRead PASSED -tests/tabix_test.py::VCFFromTabixTest_3::testWrite PASSED -tests/tabix_test.py::VCFFromVCFTest_3::testConnecting PASSED -tests/tabix_test.py::VCFFromVCFTest_3::testParsing PASSED -tests/tabix_test.py::VCFFromTabixTest_7::testRead PASSED -tests/tabix_test.py::VCFFromTabixTest_7::testWrite PASSED -tests/tabix_test.py::VCFFromVCFTest_7::testConnecting PASSED -tests/tabix_test.py::VCFFromVCFTest_7::testParsing PASSED -tests/tabix_test.py::VCFFromTabixTest_22::testRead PASSED -tests/tabix_test.py::VCFFromTabixTest_22::testWrite PASSED -tests/tabix_test.py::VCFFromVCFTest_22::testConnecting PASSED -tests/tabix_test.py::VCFFromVCFTest_22::testParsing PASSED -tests/tabix_test.py::VCFFromTabixTest_11::testRead PASSED -tests/tabix_test.py::VCFFromTabixTest_11::testWrite PASSED -tests/tabix_test.py::VCFFromVCFTest_11::testConnecting PASSED -tests/tabix_test.py::VCFFromVCFTest_11::testParsing PASSED -tests/tabix_test.py::VCFFromTabixTest_2::testRead PASSED -tests/tabix_test.py::VCFFromTabixTest_2::testWrite PASSED -tests/tabix_test.py::VCFFromVCFTest_2::testConnecting PASSED -tests/tabix_test.py::VCFFromVCFTest_2::testParsing PASSED -tests/tabix_test.py::VCFFromTabixTest_4::testRead PASSED -tests/tabix_test.py::VCFFromTabixTest_4::testWrite PASSED -tests/tabix_test.py::VCFFromVCFTest_4::testConnecting PASSED -tests/tabix_test.py::VCFFromVCFTest_4::testParsing PASSED -tests/tabix_test.py::VCFFromTabixTest_21::testRead PASSED -tests/tabix_test.py::VCFFromTabixTest_21::testWrite PASSED -tests/tabix_test.py::VCFFromVCFTest_21::testConnecting PASSED -tests/tabix_test.py::VCFFromVCFTest_21::testParsing PASSED -tests/tabix_test.py::VCFFromTabixTest_8::testRead PASSED -tests/tabix_test.py::VCFFromTabixTest_8::testWrite PASSED -tests/tabix_test.py::VCFFromVCFTest_8::testConnecting PASSED -tests/tabix_test.py::VCFFromVCFTest_8::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_10::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_10::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_10::testConnecting PASSED @@ -2360,42 +2363,82 @@ tests/tabix_test.py::VCFFromTabixTest_5::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_5::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_5::testParsing PASSED +tests/tabix_test.py::VCFFromTabixTest_3::testRead PASSED +tests/tabix_test.py::VCFFromTabixTest_3::testWrite PASSED +tests/tabix_test.py::VCFFromVCFTest_3::testConnecting PASSED +tests/tabix_test.py::VCFFromVCFTest_3::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_24::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_24::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_24::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_24::testParsing PASSED +tests/tabix_test.py::VCFFromTabixTest_21::testRead PASSED +tests/tabix_test.py::VCFFromTabixTest_21::testWrite PASSED +tests/tabix_test.py::VCFFromVCFTest_21::testConnecting PASSED +tests/tabix_test.py::VCFFromVCFTest_21::testParsing PASSED +tests/tabix_test.py::VCFFromTabixTest_2::testRead PASSED +tests/tabix_test.py::VCFFromTabixTest_2::testWrite PASSED +tests/tabix_test.py::VCFFromVCFTest_2::testConnecting PASSED +tests/tabix_test.py::VCFFromVCFTest_2::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_18::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_18::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_18::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_18::testParsing PASSED -tests/tabix_test.py::VCFFromTabixTest_16::testRead PASSED -tests/tabix_test.py::VCFFromTabixTest_16::testWrite PASSED -tests/tabix_test.py::VCFFromVCFTest_16::testConnecting PASSED -tests/tabix_test.py::VCFFromVCFTest_16::testParsing PASSED -tests/tabix_test.py::VCFFromTabixTest_6::testRead PASSED -tests/tabix_test.py::VCFFromTabixTest_6::testWrite PASSED -tests/tabix_test.py::VCFFromVCFTest_6::testConnecting PASSED -tests/tabix_test.py::VCFFromVCFTest_6::testParsing PASSED +tests/tabix_test.py::VCFFromTabixTest_11::testRead PASSED +tests/tabix_test.py::VCFFromTabixTest_11::testWrite PASSED +tests/tabix_test.py::VCFFromVCFTest_11::testConnecting PASSED +tests/tabix_test.py::VCFFromVCFTest_11::testParsing PASSED +tests/tabix_test.py::VCFFromTabixTest_13::testRead PASSED +tests/tabix_test.py::VCFFromTabixTest_13::testWrite PASSED +tests/tabix_test.py::VCFFromVCFTest_13::testConnecting PASSED +tests/tabix_test.py::VCFFromVCFTest_13::testParsing PASSED +tests/tabix_test.py::VCFFromTabixTest_4::testRead PASSED +tests/tabix_test.py::VCFFromTabixTest_4::testWrite PASSED +tests/tabix_test.py::VCFFromVCFTest_4::testConnecting PASSED +tests/tabix_test.py::VCFFromVCFTest_4::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_20::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_20::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_20::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_20::testParsing PASSED -tests/tabix_test.py::VCFFromTabixTest_9::testRead PASSED -tests/tabix_test.py::VCFFromTabixTest_9::testWrite PASSED -tests/tabix_test.py::VCFFromVCFTest_9::testConnecting PASSED -tests/tabix_test.py::VCFFromVCFTest_9::testParsing PASSED +tests/tabix_test.py::VCFFromTabixTest_8::testRead PASSED +tests/tabix_test.py::VCFFromTabixTest_8::testWrite PASSED +tests/tabix_test.py::VCFFromVCFTest_8::testConnecting PASSED +tests/tabix_test.py::VCFFromVCFTest_8::testParsing PASSED +tests/tabix_test.py::VCFFromTabixTest_vcf_v42::testRead PASSED +tests/tabix_test.py::VCFFromTabixTest_vcf_v42::testWrite PASSED +tests/tabix_test.py::VCFFromVCFTest_vcf_v42::testConnecting PASSED +tests/tabix_test.py::VCFFromVCFTest_vcf_v42::testParsing PASSED +tests/tabix_test.py::VCFFromTabixTest_7::testRead PASSED +tests/tabix_test.py::VCFFromTabixTest_7::testWrite PASSED +tests/tabix_test.py::VCFFromVCFTest_7::testConnecting PASSED +tests/tabix_test.py::VCFFromVCFTest_7::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_15::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_15::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_15::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_15::testParsing PASSED +tests/tabix_test.py::VCFFromTabixTest_22::testRead PASSED +tests/tabix_test.py::VCFFromTabixTest_22::testWrite PASSED +tests/tabix_test.py::VCFFromVCFTest_22::testConnecting PASSED +tests/tabix_test.py::VCFFromVCFTest_22::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_23::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_23::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_23::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_23::testParsing PASSED -tests/tabix_test.py::VCFFromTabixTest_vcf_v42::testRead PASSED -tests/tabix_test.py::VCFFromTabixTest_vcf_v42::testWrite PASSED -tests/tabix_test.py::VCFFromVCFTest_vcf_v42::testConnecting PASSED -tests/tabix_test.py::VCFFromVCFTest_vcf_v42::testParsing PASSED +tests/tabix_test.py::VCFFromTabixTest_6::testRead PASSED +tests/tabix_test.py::VCFFromTabixTest_6::testWrite PASSED +tests/tabix_test.py::VCFFromVCFTest_6::testConnecting PASSED +tests/tabix_test.py::VCFFromVCFTest_6::testParsing PASSED +tests/tabix_test.py::VCFFromTabixTest_16::testRead PASSED +tests/tabix_test.py::VCFFromTabixTest_16::testWrite PASSED +tests/tabix_test.py::VCFFromVCFTest_16::testConnecting PASSED +tests/tabix_test.py::VCFFromVCFTest_16::testParsing PASSED +tests/tabix_test.py::VCFFromTabixTest_12::testRead PASSED +tests/tabix_test.py::VCFFromTabixTest_12::testWrite PASSED +tests/tabix_test.py::VCFFromVCFTest_12::testConnecting PASSED +tests/tabix_test.py::VCFFromVCFTest_12::testParsing PASSED +tests/tabix_test.py::VCFFromTabixTest_9::testRead PASSED +tests/tabix_test.py::VCFFromTabixTest_9::testWrite PASSED +tests/tabix_test.py::VCFFromVCFTest_9::testConnecting PASSED +tests/tabix_test.py::VCFFromVCFTest_9::testParsing PASSED tests/tabix_test.py::TestVCFFromVariantFile::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile::testParsing [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig '17' is not defined in the header. (Quick workaround: index the file with tabix.) @@ -2404,43 +2447,33 @@ tests/tabix_test.py::TestVCFFromVariantFile_issue85::testConnecting [E::bcf_hdr_parse] Could not parse the header, sample line not found PASSED tests/tabix_test.py::TestVCFFromVariantFile_issue85::testParsing PASSED -tests/tabix_test.py::TestVCFFromVariantFile_13::testConnecting [W::bcf_hrec_check] Invalid tag name: "1000g" -[W::bcf_hrec_check] Invalid tag name: "GT:GL:GQ:NR" -[W::bcf_hdr_check_sanity] GL should be declared as Number=G +tests/tabix_test.py::TestVCFFromVariantFile_10::testConnecting PASSED +tests/tabix_test.py::TestVCFFromVariantFile_10::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) +[W::vcf_parse_format] FORMAT 'GT' at 20:676148 is not defined in the header, assuming Type=String PASSED -tests/tabix_test.py::TestVCFFromVariantFile_13::testParsing [W::bcf_hrec_check] Invalid tag name: "1000g" -[W::bcf_hrec_check] Invalid tag name: "GT:GL:GQ:NR" -[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.) -[W::vcf_parse_info] INFO 'MMLQ' is not defined in the header, assuming Type=String -[W::vcf_parse] Contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.) -[W::vcf_parse] Contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.) -[W::vcf_parse] Contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.) -[W::vcf_parse] Contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.) -[W::vcf_parse] Contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.) -[W::vcf_parse] Contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.) -[W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.) -[W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.) -[W::vcf_parse] Contig 'chr17_gl000205_random' is not defined in the header. (Quick workaround: index the file with tabix.) -[W::vcf_parse] Contig 'chr18' is not defined in the header. (Quick workaround: index the file with tabix.) -[W::vcf_parse] Contig 'chr19' is not defined in the header. (Quick workaround: index the file with tabix.) -[W::vcf_parse] Contig 'chr2' is not defined in the header. (Quick workaround: index the file with tabix.) -[W::vcf_parse] Contig 'chr20' is not defined in the header. (Quick workaround: index the file with tabix.) -[W::vcf_parse] Contig 'chr21' is not defined in the header. (Quick workaround: index the file with tabix.) -[W::vcf_parse] Contig 'chr22' is not defined in the header. (Quick workaround: index the file with tabix.) -[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.) -[W::vcf_parse] Contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.) -[W::vcf_parse] Contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.) -[W::vcf_parse] Contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.) -[W::vcf_parse] Contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.) -[W::vcf_parse] Contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.) -[W::vcf_parse] Contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.) -[W::vcf_parse] Contig 'chrUn_gl000214' is not defined in the header. (Quick workaround: index the file with tabix.) -[W::vcf_parse] Contig 'chrUn_gl000220' is not defined in the header. (Quick workaround: index the file with tabix.) -[W::vcf_parse] Contig 'chrUn_gl000225' is not defined in the header. (Quick workaround: index the file with tabix.) -[W::vcf_parse] Contig 'chrX' is not defined in the header. (Quick workaround: index the file with tabix.) +tests/tabix_test.py::TestVCFFromVariantFile_5::testConnecting [W::bcf_hdr_check_sanity] GL should be declared as Number=G PASSED -tests/tabix_test.py::TestVCFFromVariantFile_12::testConnecting PASSED -tests/tabix_test.py::TestVCFFromVariantFile_12::testParsing [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.) +tests/tabix_test.py::TestVCFFromVariantFile_5::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) +PASSED +tests/tabix_test.py::TestVCFFromVariantFile_3::testConnecting PASSED +tests/tabix_test.py::TestVCFFromVariantFile_3::testParsing [W::vcf_parse] Contig '1' is not defined in the header. (Quick workaround: index the file with tabix.) +PASSED +tests/tabix_test.py::TestVCFFromVariantFile_24::testConnecting [E::bcf_hdr_parse_sample_line] Could not parse the "#CHROM.." line, either the fields are incorrect or spaces are present instead of tabs: + #CHROM POS ID REF ALT QUAL FILTER INFO + +PASSED +tests/tabix_test.py::TestVCFFromVariantFile_24::testParsing PASSED +tests/tabix_test.py::TestVCFFromVariantFile_21::testConnecting [W::bcf_hdr_register_hrec] The definition of Flag "INFO/NotCalledInValidationSamples" is invalid, forcing Number=0 +PASSED +tests/tabix_test.py::TestVCFFromVariantFile_21::testParsing [W::bcf_hdr_register_hrec] The definition of Flag "INFO/NotCalledInValidationSamples" is invalid, forcing Number=0 +[W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) +PASSED +tests/tabix_test.py::TestVCFFromVariantFile_2::testConnecting PASSED +tests/tabix_test.py::TestVCFFromVariantFile_2::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) +[W::vcf_parse_info] INFO 'sumGLbyD' is not defined in the header, assuming Type=String +PASSED +tests/tabix_test.py::TestVCFFromVariantFile_18::testConnecting PASSED +tests/tabix_test.py::TestVCFFromVariantFile_18::testParsing [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_info] INFO 'DP' is not defined in the header, assuming Type=String [W::vcf_parse_info] INFO 'AF1' is not defined in the header, assuming Type=String [W::vcf_parse_info] INFO 'CI95' is not defined in the header, assuming Type=String @@ -2470,54 +2503,88 @@ [W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED -tests/tabix_test.py::TestVCFFromVariantFile_3::testConnecting PASSED -tests/tabix_test.py::TestVCFFromVariantFile_3::testParsing [W::vcf_parse] Contig '1' is not defined in the header. (Quick workaround: index the file with tabix.) -PASSED -tests/tabix_test.py::TestVCFFromVariantFile_7::testConnecting PASSED -tests/tabix_test.py::TestVCFFromVariantFile_7::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) -[W::vcf_parse_format] FORMAT 'GT' at 20:249843 is not defined in the header, assuming Type=String -PASSED -tests/tabix_test.py::TestVCFFromVariantFile_22::testConnecting PASSED -tests/tabix_test.py::TestVCFFromVariantFile_22::testParsing [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.) -[W::vcf_parse_info] INFO 'refseq.name' is not defined in the header, assuming Type=String -[W::vcf_parse_info] INFO 'refseq.positionType' is not defined in the header, assuming Type=String -[W::vcf_parse] Contig 'chr2' is not defined in the header. (Quick workaround: index the file with tabix.) -PASSED tests/tabix_test.py::TestVCFFromVariantFile_11::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_11::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_format] FORMAT 'GT' at 20:669442 is not defined in the header, assuming Type=String PASSED -tests/tabix_test.py::TestVCFFromVariantFile_2::testConnecting PASSED -tests/tabix_test.py::TestVCFFromVariantFile_2::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) -[W::vcf_parse_info] INFO 'sumGLbyD' is not defined in the header, assuming Type=String +tests/tabix_test.py::TestVCFFromVariantFile_13::testConnecting [W::bcf_hrec_check] Invalid tag name: "1000g" +[W::bcf_hrec_check] Invalid tag name: "GT:GL:GQ:NR" +PASSED +tests/tabix_test.py::TestVCFFromVariantFile_13::testParsing [W::bcf_hrec_check] Invalid tag name: "1000g" +[W::bcf_hrec_check] Invalid tag name: "GT:GL:GQ:NR" +[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.) +[W::vcf_parse_info] INFO 'MMLQ' is not defined in the header, assuming Type=String +[W::vcf_parse] Contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.) +[W::vcf_parse] Contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.) +[W::vcf_parse] Contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.) +[W::vcf_parse] Contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.) +[W::vcf_parse] Contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.) +[W::vcf_parse] Contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.) +[W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.) +[W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.) +[W::vcf_parse] Contig 'chr17_gl000205_random' is not defined in the header. (Quick workaround: index the file with tabix.) +[W::vcf_parse] Contig 'chr18' is not defined in the header. (Quick workaround: index the file with tabix.) +[W::vcf_parse] Contig 'chr19' is not defined in the header. (Quick workaround: index the file with tabix.) +[W::vcf_parse] Contig 'chr2' is not defined in the header. (Quick workaround: index the file with tabix.) +[W::vcf_parse] Contig 'chr20' is not defined in the header. (Quick workaround: index the file with tabix.) +[W::vcf_parse] Contig 'chr21' is not defined in the header. (Quick workaround: index the file with tabix.) +[W::vcf_parse] Contig 'chr22' is not defined in the header. (Quick workaround: index the file with tabix.) +[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.) +[W::vcf_parse] Contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.) +[W::vcf_parse] Contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.) +[W::vcf_parse] Contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.) +[W::vcf_parse] Contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.) +[W::vcf_parse] Contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.) +[W::vcf_parse] Contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.) +[W::vcf_parse] Contig 'chrUn_gl000214' is not defined in the header. (Quick workaround: index the file with tabix.) +[W::vcf_parse] Contig 'chrUn_gl000220' is not defined in the header. (Quick workaround: index the file with tabix.) +[W::vcf_parse] Contig 'chrUn_gl000225' is not defined in the header. (Quick workaround: index the file with tabix.) +[W::vcf_parse] Contig 'chrX' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestVCFFromVariantFile_4::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_4::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_format] FORMAT 'GT' at 20:249843 is not defined in the header, assuming Type=String PASSED -tests/tabix_test.py::TestVCFFromVariantFile_21::testConnecting [W::bcf_hdr_register_hrec] The definition of Flag "INFO/NotCalledInValidationSamples" is invalid, forcing Number=0 +tests/tabix_test.py::TestVCFFromVariantFile_20::testConnecting [W::bcf_hdr_register_hrec] The definition of Flag "INFO/NotCalledInValidationSamples" is invalid, forcing Number=0 PASSED -tests/tabix_test.py::TestVCFFromVariantFile_21::testParsing [W::bcf_hdr_register_hrec] The definition of Flag "INFO/NotCalledInValidationSamples" is invalid, forcing Number=0 +tests/tabix_test.py::TestVCFFromVariantFile_20::testParsing [W::bcf_hdr_register_hrec] The definition of Flag "INFO/NotCalledInValidationSamples" is invalid, forcing Number=0 [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestVCFFromVariantFile_8::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_8::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_format] FORMAT 'GT' at 20:676148 is not defined in the header, assuming Type=String PASSED -tests/tabix_test.py::TestVCFFromVariantFile_10::testConnecting PASSED -tests/tabix_test.py::TestVCFFromVariantFile_10::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) -[W::vcf_parse_format] FORMAT 'GT' at 20:676148 is not defined in the header, assuming Type=String +tests/tabix_test.py::TestVCFFromVariantFile_vcf_v42::testConnecting PASSED +tests/tabix_test.py::TestVCFFromVariantFile_vcf_v42::testParsing PASSED +tests/tabix_test.py::TestVCFFromVariantFile_7::testConnecting PASSED +tests/tabix_test.py::TestVCFFromVariantFile_7::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) +[W::vcf_parse_format] FORMAT 'GT' at 20:249843 is not defined in the header, assuming Type=String PASSED -tests/tabix_test.py::TestVCFFromVariantFile_5::testConnecting PASSED -tests/tabix_test.py::TestVCFFromVariantFile_5::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) +tests/tabix_test.py::TestVCFFromVariantFile_15::testConnecting PASSED +tests/tabix_test.py::TestVCFFromVariantFile_15::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) +[W::vcf_parse_format] FORMAT 'GT' at 20:439104 is not defined in the header, assuming Type=String PASSED -tests/tabix_test.py::TestVCFFromVariantFile_24::testConnecting [E::bcf_hdr_parse_sample_line] Could not parse the "#CHROM.." line, either the fields are incorrect or spaces are present instead of tabs: - #CHROM POS ID REF ALT QUAL FILTER INFO - +tests/tabix_test.py::TestVCFFromVariantFile_22::testConnecting PASSED +tests/tabix_test.py::TestVCFFromVariantFile_22::testParsing [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.) +[W::vcf_parse_info] INFO 'refseq.name' is not defined in the header, assuming Type=String +[W::vcf_parse_info] INFO 'refseq.positionType' is not defined in the header, assuming Type=String +[W::vcf_parse] Contig 'chr2' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED -tests/tabix_test.py::TestVCFFromVariantFile_24::testParsing PASSED -tests/tabix_test.py::TestVCFFromVariantFile_18::testConnecting PASSED -tests/tabix_test.py::TestVCFFromVariantFile_18::testParsing [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.) +tests/tabix_test.py::TestVCFFromVariantFile_23::testConnecting PASSED +tests/tabix_test.py::TestVCFFromVariantFile_23::testParsing [W::vcf_parse_info] INFO 'sumGLbyD' is not defined in the header, assuming Type=String +PASSED +tests/tabix_test.py::TestVCFFromVariantFile_6::testConnecting PASSED +tests/tabix_test.py::TestVCFFromVariantFile_6::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) +[W::vcf_parse_info] INFO 'CallSetAC' is not defined in the header, assuming Type=String +[W::vcf_parse_info] INFO 'CallSetAC2' is not defined in the header, assuming Type=String +[W::vcf_parse_format] FORMAT 'GT' at 20:669442 is not defined in the header, assuming Type=String +PASSED +tests/tabix_test.py::TestVCFFromVariantFile_16::testConnecting PASSED +tests/tabix_test.py::TestVCFFromVariantFile_16::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) +[W::vcf_parse_info] INFO 'sumGLbyD' is not defined in the header, assuming Type=String +PASSED +tests/tabix_test.py::TestVCFFromVariantFile_12::testConnecting PASSED +tests/tabix_test.py::TestVCFFromVariantFile_12::testParsing [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_info] INFO 'DP' is not defined in the header, assuming Type=String [W::vcf_parse_info] INFO 'AF1' is not defined in the header, assuming Type=String [W::vcf_parse_info] INFO 'CI95' is not defined in the header, assuming Type=String @@ -2547,21 +2614,6 @@ [W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED -tests/tabix_test.py::TestVCFFromVariantFile_16::testConnecting PASSED -tests/tabix_test.py::TestVCFFromVariantFile_16::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) -[W::vcf_parse_info] INFO 'sumGLbyD' is not defined in the header, assuming Type=String -PASSED -tests/tabix_test.py::TestVCFFromVariantFile_6::testConnecting PASSED -tests/tabix_test.py::TestVCFFromVariantFile_6::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) -[W::vcf_parse_info] INFO 'CallSetAC' is not defined in the header, assuming Type=String -[W::vcf_parse_info] INFO 'CallSetAC2' is not defined in the header, assuming Type=String -[W::vcf_parse_format] FORMAT 'GT' at 20:669442 is not defined in the header, assuming Type=String -PASSED -tests/tabix_test.py::TestVCFFromVariantFile_20::testConnecting [W::bcf_hdr_register_hrec] The definition of Flag "INFO/NotCalledInValidationSamples" is invalid, forcing Number=0 -PASSED -tests/tabix_test.py::TestVCFFromVariantFile_20::testParsing [W::bcf_hdr_register_hrec] The definition of Flag "INFO/NotCalledInValidationSamples" is invalid, forcing Number=0 -[W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) -PASSED tests/tabix_test.py::TestVCFFromVariantFile_9::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_9::testParsing [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_info] INFO 'DP' is not defined in the header, assuming Type=String @@ -2593,15 +2645,6 @@ [W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED -tests/tabix_test.py::TestVCFFromVariantFile_15::testConnecting PASSED -tests/tabix_test.py::TestVCFFromVariantFile_15::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) -[W::vcf_parse_format] FORMAT 'GT' at 20:439104 is not defined in the header, assuming Type=String -PASSED -tests/tabix_test.py::TestVCFFromVariantFile_23::testConnecting PASSED -tests/tabix_test.py::TestVCFFromVariantFile_23::testParsing [W::vcf_parse_info] INFO 'sumGLbyD' is not defined in the header, assuming Type=String -PASSED -tests/tabix_test.py::TestVCFFromVariantFile_vcf_v42::testConnecting PASSED -tests/tabix_test.py::TestVCFFromVariantFile_vcf_v42::testParsing PASSED tests/tabix_test.py::TestIndexArgument::testFetchAll PASSED tests/tabix_test.py::TestIndexArgument::testLoadIndexWithoutTbiExtension PASSED tests/tabix_test.py::TestBackwardsCompatibility::testBED PASSED @@ -2686,8 +2729,8 @@ return self.run(*args, **kwds) -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html -================= 938 passed, 11 skipped, 4 warnings in 31.35s ================= -make[1]: Leaving directory '/build/python-pysam-0.20.0+ds' +============ 938 passed, 11 skipped, 4 warnings in 60.48s (0:01:00) ============ +make[1]: Verzeichnis „/build/python-pysam-0.20.0+ds“ wird verlassen create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild @@ -2725,126 +2768,126 @@ creating /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11 creating /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages creating /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam -copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libctabix.cpython-311-i386-linux-gnu.so -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam -copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libctabixproxies.pyi -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam +copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libcfaidx.cpython-311-i386-linux-gnu.so -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam +copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/samtools.py -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam +copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/Pileup.py -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam +copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libcbcftools.cpython-311-i386-linux-gnu.so -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam +copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libcbcf.pyi -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam +copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libcvcf.cpython-311-i386-linux-gnu.so -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam +copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libcsamfile.pxd -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam +copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/pysam_stream.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam +copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libctabix.pyi -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam +copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libcfaidx.pxd -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam +copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libcalignmentfile.pyi -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam +copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/config.py -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam +copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libcfaidx.pyi -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam +copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/htslib_util.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam +copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libctabixproxies.pxd -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam +copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/version.pyi -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/version.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam -copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libcsamtools.pxd -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam -copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libcsamfile.pyi -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam -copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libchtslib.pyi -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libcsamtools.pyi -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam -copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libcalignedsegment.cpython-311-i386-linux-gnu.so -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam -copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libcvcf.pyi -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam +copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libcsamtools.cpython-311-i386-linux-gnu.so -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libcbgzf.cpython-311-i386-linux-gnu.so -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam -copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libcutils.pxd -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam +copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libchtslib.pxd -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam +copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/cbcftools_util.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam +copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libcalignedsegment.cpython-311-i386-linux-gnu.so -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam +copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libcsamtools.pxd -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam +copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libcbcf.cpython-311-i386-linux-gnu.so -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam +copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libcalignmentfile.pxd -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libcbcftools.pxd -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam -copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/pysam_util.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam +copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libcalignedsegment.pyi -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam +copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libcalignedsegment.pxd -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam +copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/version.py -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam +copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libcutils.cpython-311-i386-linux-gnu.so -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam +copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/__init__.py -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam +copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libctabix.cpython-311-i386-linux-gnu.so -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam +copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libcutils.pxd -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam +copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libcsamfile.pyi -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam +copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libchtslib.pyi -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam +copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libctabixproxies.cpython-311-i386-linux-gnu.so -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/utils.py -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam creating /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/__pycache__ -copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/__pycache__/__init__.cpython-311.pyc -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/__pycache__ +copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/__pycache__/Pileup.cpython-311.pyc -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/__pycache__ copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/__pycache__/version.cpython-311.pyc -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/__pycache__ -copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/__pycache__/samtools.cpython-311.pyc -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/__pycache__ +copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/__pycache__/__init__.cpython-311.pyc -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/__pycache__ +copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/__pycache__/config.cpython-311.pyc -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/__pycache__ copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/__pycache__/utils.cpython-311.pyc -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/__pycache__ copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/__pycache__/bcftools.cpython-311.pyc -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/__pycache__ -copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/__pycache__/config.cpython-311.pyc -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/__pycache__ -copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/__pycache__/Pileup.cpython-311.pyc -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/__pycache__ +copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/__pycache__/samtools.cpython-311.pyc -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/__pycache__ +copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libcbgzf.pyi -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam +copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/pysam_util.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam +copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libchtslib.cpython-311-i386-linux-gnu.so -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam +copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libcsamfile.cpython-311-i386-linux-gnu.so -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam +copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/csamtools_util.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/py.typed -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam +copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libcvcf.pyi -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam +copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libcalignmentfile.cpython-311-i386-linux-gnu.so -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libctabix.pxd -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam -copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libcsamfile.pxd -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam -copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/samtools.py -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam +copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libcvcf.pxd -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam +copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libcbcftools.pyi -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam +copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libctabixproxies.pyi -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam +copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libcbcf.pxd -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam +copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libcutils.pyi -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam creating /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include +creating /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools +copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/bam_lpileup.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools +copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/bam_plbuf.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools +copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/stats_isize.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools +copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/config.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools +copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/tmp_file.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools +copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/sam_opts.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools +copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/bam_ampliconclip.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools +copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/samtools_config_vars.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools +copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/consensus_pileup.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools +copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/samtools.pysam.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools +copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/bedidx.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools +copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/samtools.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools +copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/bam.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools +copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/splaysort.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools +copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/sample.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools +copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/__init__.py -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include creating /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools -copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/mw.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools -copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/vcfbuf.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools -copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/kmin.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools -copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/abuf.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/dbuf.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/HMM.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools +copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/variantkey.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools +copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/rbuf.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools +copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/call.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools +copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/gvcf.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools +copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/abuf.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/bcftools.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools -copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/convert.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools -copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/bin.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools +copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/config.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/khash_str2str.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools -copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/variantkey.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/ploidy.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools -copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/str_finder.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools -copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/tsv2vcf.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/hex.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools +copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/bam_sample.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/kheap.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools -copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/rbuf.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools -copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/smpl_ilist.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools -copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/cols.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools -copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/config.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools -copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/prob1.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/extsort.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools +copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/regidx.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/bam2bcf.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools +copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/mw.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools +copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/tsv2vcf.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools +copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/smpl_ilist.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools +copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/vcfbuf.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools +copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/kmin.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools +copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/dist.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools +copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/hclust.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools +copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/prob1.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/vcmp.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools +copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/convert.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/utlist.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools -copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/bcftools.pysam.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools -copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/gvcf.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools -copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/call.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools +copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/bin.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/filter.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools -copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/hclust.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools -copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/bam_sample.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools -copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/regidx.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools -copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/dist.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools -creating /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools -copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/stats_isize.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools -copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/splaysort.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools -copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/samtools_config_vars.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools -copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/consensus_pileup.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools -copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/bedidx.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools -copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/bam_plbuf.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools -copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/samtools.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools -copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/sample.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools -copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/bam.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools -copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/bam_ampliconclip.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools -copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/samtools.pysam.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools -copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/sam_opts.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools -copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/config.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools -copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/tmp_file.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools -copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/bam_lpileup.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools -copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/__init__.py -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include -copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libchtslib.cpython-311-i386-linux-gnu.so -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam -copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libcbcf.pxd -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam -copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libcbcf.pyi -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam -copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libcbcf.cpython-311-i386-linux-gnu.so -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam -copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/cbcftools_util.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam -copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libctabixproxies.pxd -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam -copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libcsamfile.cpython-311-i386-linux-gnu.so -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam -copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libchtslib.pxd -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam -copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libcfaidx.pxd -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam -copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libcalignmentfile.pyi -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam -copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/config.py -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam -copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/Pileup.py -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam -copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libctabix.pyi -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam -copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/version.py -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam -copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libcvcf.cpython-311-i386-linux-gnu.so -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam -copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/htslib_util.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam -copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/version.pyi -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam -copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libcsamtools.cpython-311-i386-linux-gnu.so -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam -copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libcbgzf.pyi -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam -copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/pysam_stream.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam -copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libcalignedsegment.pxd -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam -copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libcfaidx.pyi -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam -copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/__init__.py -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam -copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libcalignmentfile.pxd -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam -copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libcfaidx.cpython-311-i386-linux-gnu.so -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam +copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/str_finder.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools +copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/bcftools.pysam.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools +copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/cols.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/bcftools.py -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam -copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libcalignedsegment.pyi -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam -copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/csamtools_util.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam -copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libcutils.cpython-311-i386-linux-gnu.so -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam -copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libcbcftools.pyi -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam -copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libcbcftools.cpython-311-i386-linux-gnu.so -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam -copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libcvcf.pxd -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam -copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libcalignmentfile.cpython-311-i386-linux-gnu.so -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam -copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libcutils.pyi -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam -copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libctabixproxies.cpython-311-i386-linux-gnu.so -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam -byte-compiling /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/utils.py to utils.cpython-311.pyc byte-compiling /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/samtools.py to samtools.cpython-311.pyc -byte-compiling /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/__init__.py to __init__.cpython-311.pyc -byte-compiling /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/config.py to config.cpython-311.pyc byte-compiling /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/Pileup.py to Pileup.cpython-311.pyc +byte-compiling /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/config.py to config.cpython-311.pyc byte-compiling /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/version.py to version.cpython-311.pyc byte-compiling /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/__init__.py to __init__.cpython-311.pyc +byte-compiling /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/utils.py to utils.cpython-311.pyc +byte-compiling /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/__init__.py to __init__.cpython-311.pyc byte-compiling /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/bcftools.py to bcftools.cpython-311.pyc running install_egg_info running egg_info @@ -2879,19 +2922,19 @@ Skipping SOURCES.txt running install_scripts debian/rules override_dh_install -make[1]: Entering directory '/build/python-pysam-0.20.0+ds' +make[1]: Verzeichnis „/build/python-pysam-0.20.0+ds“ wird betreten cd tests/pysam_data && /usr/bin/make clean -make[2]: Entering directory '/build/python-pysam-0.20.0+ds/tests/pysam_data' +make[2]: Verzeichnis „/build/python-pysam-0.20.0+ds/tests/pysam_data“ wird betreten rm -fr *.bai *.csi *.fai *.gzi *.pileup* [a-z]*.cram *.crai \ all.stamp *~ calDepth *.dSYM pysam_*.sam \ ex2.sam ex2.sam.gz ex1.sam ex1.fa.gz \ with_md.sam.gz \ *.fq.gz -make[2]: Leaving directory '/build/python-pysam-0.20.0+ds/tests/pysam_data' +make[2]: Verzeichnis „/build/python-pysam-0.20.0+ds/tests/pysam_data“ wird verlassen cd tests/cbcf_data && /usr/bin/make clean -make[2]: Entering directory '/build/python-pysam-0.20.0+ds/tests/cbcf_data' +make[2]: Verzeichnis „/build/python-pysam-0.20.0+ds/tests/cbcf_data“ wird betreten rm -f all.stamp *.gz *.tbi *.csi *.bcf -make[2]: Leaving directory '/build/python-pysam-0.20.0+ds/tests/cbcf_data' +make[2]: Verzeichnis „/build/python-pysam-0.20.0+ds/tests/cbcf_data“ wird verlassen find . -name "*.pyc" -delete find . -name "*.pyxbldc" -delete find . -name "tmp_*.bam" -delete @@ -2914,7 +2957,7 @@ rm -rf .pytest_cache/ dh_install -Xtest.gtf.gz find debian -name log.txt -delete -make[1]: Leaving directory '/build/python-pysam-0.20.0+ds' +make[1]: Verzeichnis „/build/python-pysam-0.20.0+ds“ wird verlassen dh_installdocs -O--buildsystem=pybuild dh_installchangelogs -O--buildsystem=pybuild dh_python3 -O--buildsystem=pybuild @@ -2935,9 +2978,9 @@ dh_gencontrol -O--buildsystem=pybuild dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild -dpkg-deb: building package 'python-pysam-tests' in '../python-pysam-tests_0.20.0+ds-3_all.deb'. -dpkg-deb: building package 'python3-pysam-dbgsym' in '../python3-pysam-dbgsym_0.20.0+ds-3_i386.deb'. -dpkg-deb: building package 'python3-pysam' in '../python3-pysam_0.20.0+ds-3_i386.deb'. +dpkg-deb: Paket »python-pysam-tests« wird in »../python-pysam-tests_0.20.0+ds-3_all.deb« gebaut. +dpkg-deb: Paket »python3-pysam« wird in »../python3-pysam_0.20.0+ds-3_i386.deb« gebaut. +dpkg-deb: Paket »python3-pysam-dbgsym« wird in »../python3-pysam-dbgsym_0.20.0+ds-3_i386.deb« gebaut. dpkg-genbuildinfo --build=binary -O../python-pysam_0.20.0+ds-3_i386.buildinfo dpkg-genchanges --build=binary -O../python-pysam_0.20.0+ds-3_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -2945,12 +2988,14 @@ 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/29729/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/29729/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/1222 and its subdirectories -I: Current time: Mon Jun 10 01:02:33 -12 2024 -I: pbuilder-time-stamp: 1718024553 +I: removing directory /srv/workspace/pbuilder/29729 and its subdirectories +I: Current time: Tue May 9 20:47:23 +14 2023 +I: pbuilder-time-stamp: 1683614843