Diff of the two buildlogs: -- --- b1/build.log 2023-05-13 21:15:39.979365550 +0000 +++ b2/build.log 2023-05-13 21:42:39.752372931 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sat May 13 07:34:42 -12 2023 -I: pbuilder-time-stamp: 1684006482 +I: Current time: Sun May 14 11:16:53 +14 2023 +I: pbuilder-time-stamp: 1684012613 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration @@ -16,7 +16,7 @@ I: copying [./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 @@ -31,135 +31,167 @@ 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/18391/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/14213/tmp/hooks/D01_modify_environment starting +debug: Running on virt32c. +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 14 11:17 /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/14213/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/14213/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='armhf' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=5' - DISTRIBUTION='bookworm' - HOME='/root' - HOST_ARCH='armhf' + 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]="arm-unknown-linux-gnueabihf") + 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=armhf + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=4' + DIRSTACK=() + DISTRIBUTION=bookworm + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=arm + HOST_ARCH=armhf IFS=' ' - INVOCATION_ID='a8edcfd30c7a4cf6b2ce7fc47c8006a1' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='18391' - PS1='# ' - PS2='> ' + INVOCATION_ID=59d49d2f48a044bd859a5158c845752b + LANG=C + LANGUAGE=it_CH:it + LC_ALL=C + MACHTYPE=arm-unknown-linux-gnueabihf + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnueabihf + 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=14213 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.XJiekStG/pbuilderrc_nv3w --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.XJiekStG/b1 --logfile b1/build.log python-pysam_0.20.0+ds-3.dsc' - SUDO_GID='114' - SUDO_UID='109' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://10.0.0.15:3142/' + 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.XJiekStG/pbuilderrc_Gwom --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.XJiekStG/b2 --logfile b2/build.log --extrapackages usrmerge python-pysam_0.20.0+ds-3.dsc' + SUDO_GID=113 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://10.0.0.15:3142/ I: uname -a - Linux ff64a 5.10.0-22-arm64 #1 SMP Debian 5.10.178-3 (2023-04-22) aarch64 GNU/Linux + Linux i-capture-the-hostname 5.10.0-22-armmp-lpae #1 SMP Debian 5.10.178-3 (2023-04-22) armv7l GNU/Linux I: ls -l /bin total 5072 - -rwxr-xr-x 1 root root 838488 Apr 23 09:24 bash - -rwxr-xr-x 3 root root 67144 Sep 18 2022 bunzip2 - -rwxr-xr-x 3 root root 67144 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 67144 Sep 18 2022 bzip2 - -rwxr-xr-x 1 root root 67112 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 67632 Sep 20 2022 cat - -rwxr-xr-x 1 root root 67676 Sep 20 2022 chgrp - -rwxr-xr-x 1 root root 67644 Sep 20 2022 chmod - -rwxr-xr-x 1 root root 67684 Sep 20 2022 chown - -rwxr-xr-x 1 root root 133532 Sep 20 2022 cp - -rwxr-xr-x 1 root root 132868 Jan 5 01:20 dash - -rwxr-xr-x 1 root root 133220 Sep 20 2022 date - -rwxr-xr-x 1 root root 67732 Sep 20 2022 dd - -rwxr-xr-x 1 root root 68104 Sep 20 2022 df - -rwxr-xr-x 1 root root 133632 Sep 20 2022 dir - -rwxr-xr-x 1 root root 59128 Mar 22 21:02 dmesg - lrwxrwxrwx 1 root root 8 Dec 19 01:33 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Dec 19 01:33 domainname -> hostname - -rwxr-xr-x 1 root root 67560 Sep 20 2022 echo - -rwxr-xr-x 1 root root 41 Jan 24 02:43 egrep - -rwxr-xr-x 1 root root 67548 Sep 20 2022 false - -rwxr-xr-x 1 root root 41 Jan 24 02:43 fgrep - -rwxr-xr-x 1 root root 55748 Mar 22 21:02 findmnt - -rwsr-xr-x 1 root root 26208 Mar 22 20:15 fusermount - -rwxr-xr-x 1 root root 128608 Jan 24 02:43 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 64220 Apr 9 2022 gzip - -rwxr-xr-x 1 root root 67032 Dec 19 01:33 hostname - -rwxr-xr-x 1 root root 67720 Sep 20 2022 ln - -rwxr-xr-x 1 root root 35132 Mar 22 21:51 login - -rwxr-xr-x 1 root root 133632 Sep 20 2022 ls - -rwxr-xr-x 1 root root 136808 Mar 22 21:02 lsblk - -rwxr-xr-x 1 root root 67800 Sep 20 2022 mkdir - -rwxr-xr-x 1 root root 67764 Sep 20 2022 mknod - -rwxr-xr-x 1 root root 67596 Sep 20 2022 mktemp - -rwxr-xr-x 1 root root 38504 Mar 22 21:02 more - -rwsr-xr-x 1 root root 38496 Mar 22 21:02 mount - -rwxr-xr-x 1 root root 9824 Mar 22 21:02 mountpoint - -rwxr-xr-x 1 root root 133532 Sep 20 2022 mv - lrwxrwxrwx 1 root root 8 Dec 19 01:33 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 2 18:25 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 67608 Sep 20 2022 pwd - lrwxrwxrwx 1 root root 4 Apr 23 09:24 rbash -> bash - -rwxr-xr-x 1 root root 67600 Sep 20 2022 readlink - -rwxr-xr-x 1 root root 67672 Sep 20 2022 rm - -rwxr-xr-x 1 root root 67600 Sep 20 2022 rmdir - -rwxr-xr-x 1 root root 67400 Nov 2 2022 run-parts - -rwxr-xr-x 1 root root 133372 Jan 5 07:55 sed - lrwxrwxrwx 1 root root 4 Jan 5 01:20 sh -> dash - -rwxr-xr-x 1 root root 67584 Sep 20 2022 sleep - -rwxr-xr-x 1 root root 67644 Sep 20 2022 stty - -rwsr-xr-x 1 root root 50800 Mar 22 21:02 su - -rwxr-xr-x 1 root root 67584 Sep 20 2022 sync - -rwxr-xr-x 1 root root 336764 Apr 6 02:25 tar - -rwxr-xr-x 1 root root 67144 Nov 2 2022 tempfile - -rwxr-xr-x 1 root root 133224 Sep 20 2022 touch - -rwxr-xr-x 1 root root 67548 Sep 20 2022 true - -rwxr-xr-x 1 root root 9768 Mar 22 20:15 ulockmgr_server - -rwsr-xr-x 1 root root 22108 Mar 22 21:02 umount - -rwxr-xr-x 1 root root 67572 Sep 20 2022 uname - -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress - -rwxr-xr-x 1 root root 133632 Sep 20 2022 vdir - -rwxr-xr-x 1 root root 42608 Mar 22 21:02 wdctl - lrwxrwxrwx 1 root root 8 Dec 19 01:33 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/18391/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 838488 Apr 24 11:24 bash + -rwxr-xr-x 3 root root 67144 Sep 19 2022 bunzip2 + -rwxr-xr-x 3 root root 67144 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 67144 Sep 19 2022 bzip2 + -rwxr-xr-x 1 root root 67112 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 67632 Sep 21 2022 cat + -rwxr-xr-x 1 root root 67676 Sep 21 2022 chgrp + -rwxr-xr-x 1 root root 67644 Sep 21 2022 chmod + -rwxr-xr-x 1 root root 67684 Sep 21 2022 chown + -rwxr-xr-x 1 root root 133532 Sep 21 2022 cp + -rwxr-xr-x 1 root root 132868 Jan 6 03:20 dash + -rwxr-xr-x 1 root root 133220 Sep 21 2022 date + -rwxr-xr-x 1 root root 67732 Sep 21 2022 dd + -rwxr-xr-x 1 root root 68104 Sep 21 2022 df + -rwxr-xr-x 1 root root 133632 Sep 21 2022 dir + -rwxr-xr-x 1 root root 59128 Mar 23 23:02 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 67560 Sep 21 2022 echo + -rwxr-xr-x 1 root root 41 Jan 25 04:43 egrep + -rwxr-xr-x 1 root root 67548 Sep 21 2022 false + -rwxr-xr-x 1 root root 41 Jan 25 04:43 fgrep + -rwxr-xr-x 1 root root 55748 Mar 23 23:02 findmnt + -rwsr-xr-x 1 root root 26208 Mar 23 22:15 fusermount + -rwxr-xr-x 1 root root 128608 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 64220 Apr 10 2022 gzip + -rwxr-xr-x 1 root root 67032 Dec 20 03:33 hostname + -rwxr-xr-x 1 root root 67720 Sep 21 2022 ln + -rwxr-xr-x 1 root root 35132 Mar 23 23:51 login + -rwxr-xr-x 1 root root 133632 Sep 21 2022 ls + -rwxr-xr-x 1 root root 136808 Mar 23 23:02 lsblk + -rwxr-xr-x 1 root root 67800 Sep 21 2022 mkdir + -rwxr-xr-x 1 root root 67764 Sep 21 2022 mknod + -rwxr-xr-x 1 root root 67596 Sep 21 2022 mktemp + -rwxr-xr-x 1 root root 38504 Mar 23 23:02 more + -rwsr-xr-x 1 root root 38496 Mar 23 23:02 mount + -rwxr-xr-x 1 root root 9824 Mar 23 23:02 mountpoint + -rwxr-xr-x 1 root root 133532 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 67608 Sep 21 2022 pwd + lrwxrwxrwx 1 root root 4 Apr 24 11:24 rbash -> bash + -rwxr-xr-x 1 root root 67600 Sep 21 2022 readlink + -rwxr-xr-x 1 root root 67672 Sep 21 2022 rm + -rwxr-xr-x 1 root root 67600 Sep 21 2022 rmdir + -rwxr-xr-x 1 root root 67400 Nov 3 2022 run-parts + -rwxr-xr-x 1 root root 133372 Jan 6 09:55 sed + lrwxrwxrwx 1 root root 9 May 14 11:17 sh -> /bin/bash + -rwxr-xr-x 1 root root 67584 Sep 21 2022 sleep + -rwxr-xr-x 1 root root 67644 Sep 21 2022 stty + -rwsr-xr-x 1 root root 50800 Mar 23 23:02 su + -rwxr-xr-x 1 root root 67584 Sep 21 2022 sync + -rwxr-xr-x 1 root root 336764 Apr 7 04:25 tar + -rwxr-xr-x 1 root root 67144 Nov 3 2022 tempfile + -rwxr-xr-x 1 root root 133224 Sep 21 2022 touch + -rwxr-xr-x 1 root root 67548 Sep 21 2022 true + -rwxr-xr-x 1 root root 9768 Mar 23 22:15 ulockmgr_server + -rwsr-xr-x 1 root root 22108 Mar 23 23:02 umount + -rwxr-xr-x 1 root root 67572 Sep 21 2022 uname + -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress + -rwxr-xr-x 1 root root 133632 Sep 21 2022 vdir + -rwxr-xr-x 1 root root 42608 Mar 23 23:02 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/14213/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -305,7 +337,7 @@ Get: 86 http://deb.debian.org/debian bookworm/main armhf python3-setuptools all 66.1.1-1 [521 kB] Get: 87 http://deb.debian.org/debian bookworm/main armhf samtools armhf 1.16.1-1 [575 kB] Get: 88 http://deb.debian.org/debian bookworm/main armhf tabix armhf 1.16+ds-3 [388 kB] -Fetched 39.2 MB in 4s (10.7 MB/s) +Fetched 39.2 MB in 3s (14.7 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:armhf. (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 ... 19329 files and directories currently installed.) @@ -673,8 +705,19 @@ 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/14213/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/14213/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 @@ -683,17 +726,17 @@ dpkg-buildpackage: info: host architecture armhf 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]: ingresso nella directory «/build/python-pysam-0.20.0+ds/tests/pysam_data» 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]: uscita dalla directory «/build/python-pysam-0.20.0+ds/tests/pysam_data» cd tests/cbcf_data && /usr/bin/make clean -make[1]: Entering directory '/build/python-pysam-0.20.0+ds/tests/cbcf_data' +make[1]: ingresso nella directory «/build/python-pysam-0.20.0+ds/tests/cbcf_data» rm -f all.stamp *.gz *.tbi *.csi *.bcf -make[1]: Leaving directory '/build/python-pysam-0.20.0+ds/tests/cbcf_data' +make[1]: uscita dalla directory «/build/python-pysam-0.20.0+ds/tests/cbcf_data» find . -name "*.pyc" -delete find . -name "*.pyxbldc" -delete find . -name "tmp_*.bam" -delete @@ -716,7 +759,7 @@ 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]: ingresso nella directory «/build/python-pysam-0.20.0+ds» dh_auto_clean I: pybuild base:240: python3.11 setup.py clean # pysam: cython is available - using cythonize if necessary @@ -733,7 +776,7 @@ samtools/config.h \ bcftools/config.h rm -rf pysam.egg-info -make[1]: Leaving directory '/build/python-pysam-0.20.0+ds' +make[1]: uscita dalla directory «/build/python-pysam-0.20.0+ds» dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary @@ -754,97 +797,97 @@ running build running build_py creating /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/utils.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/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/__init__.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/bcftools.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 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/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/libcsamtools.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/libchtslib.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/libcutils.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/libcfaidx.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/libcsamtools.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/libcalignmentfile.pxd -> /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/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/libchtslib.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/libcsamfile.pxd -> /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/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/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/py.typed -> /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/libctabix.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 copying pysam/libcsamtools.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/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/libcbgzf.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/libcsamfile.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/libcbcf.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/libcbcftools.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/version.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/libcutils.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/libctabixproxies.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 creating /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/sample.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/consensus_pileup.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/bam_plbuf.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/config.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/stats_isize.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/config.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_lpileup.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/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/tmp_file.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/sample.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/consensus_pileup.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/bam2bcf.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/kmin.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/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/rbuf.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/bam_sample.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/HMM.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/regidx.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/extsort.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/gvcf.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/hex.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/cols.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/bam2bcf.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/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/regidx.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/bin.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/hclust.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/config.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/HMM.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/utlist.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/dbuf.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/dist.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/ploidy.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/mw.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/abuf.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/khash_str2str.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/dist.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/vcfbuf.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/vcmp.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/extsort.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 @@ -1090,9 +1133,9 @@ | ^~~~~~~~~~~~ arm-linux-gnueabihf-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-armhf-cpython-311/pysam/libcvcf.o -L/build/python-pysam-0.20.0+ds/pysam -L/usr/lib/arm-linux-gnueabihf -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/arm-linux-gnueabihf -lz -lhts -lchtslib.cpython-311-arm-linux-gnueabihf -lcutils.cpython-311-arm-linux-gnueabihf -o /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libcvcf.cpython-311-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN debian/rules override_dh_auto_test -make[1]: Entering directory '/build/python-pysam-0.20.0+ds' +make[1]: ingresso nella directory «/build/python-pysam-0.20.0+ds» cd tests/pysam_data && /usr/bin/make all -make[2]: Entering directory '/build/python-pysam-0.20.0+ds/tests/pysam_data' +make[2]: ingresso nella directory «/build/python-pysam-0.20.0+ds/tests/pysam_data» samtools faidx ex1.fa samtools view --no-PG -bo ex1.bam -t ex1.fa.fai ex1.sam.gz samtools mpileup -f ex1.fa ex1.bam | gzip > ex1.pileup.gz @@ -1246,7 +1289,7 @@ dd if=ex2.bam of=ex2_truncated.bam bs=$((`wc -c < ex2.bam`-512)) count=1 1+0 records in 1+0 records out -122292 bytes (122 kB, 119 KiB) copied, 0.00138892 s, 88.0 MB/s +122292 bytes (122 kB, 119 KiB) copied, 0.000931992 s, 131 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 @@ -1259,9 +1302,9 @@ 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]: uscita dalla directory «/build/python-pysam-0.20.0+ds/tests/pysam_data» cd tests/cbcf_data && /usr/bin/make all -make[2]: Entering directory '/build/python-pysam-0.20.0+ds/tests/cbcf_data' +make[2]: ingresso nella directory «/build/python-pysam-0.20.0+ds/tests/cbcf_data» 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 @@ -1310,7 +1353,7 @@ 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]: uscita dalla directory «/build/python-pysam-0.20.0+ds/tests/cbcf_data» 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 ============================== @@ -1393,7 +1436,7 @@ 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___u9m5yt7rnegative_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___v5blzuh9negative_integers.bam' PASSED tests/AlignedSegment_test.py::TestTags::testSetTag PASSED tests/AlignedSegment_test.py::TestTags::testTagParsing PASSED @@ -1472,22 +1515,22 @@ 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_ccmapw6_' -/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_ccmapw6_ +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_vk7_zm7l' +/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_vk7_zm7l 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_3j3p4456' -/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_3j3p4456 +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_gd1qdqjj' +/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_gd1qdqjj 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_y4hvd9ec +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_3xwtf3at 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_tp9c6gr4' -/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_tp9c6gr4 +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_f8q23rkl' +/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_f8q23rkl 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_i_bs6are' -/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_i_bs6are +[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_09zkfbef' +/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_09zkfbef 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_hl47ayx3 +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_tt2uzlm7 PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_all_stepper PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_ignore_overlaps PASSED @@ -1849,7 +1892,7 @@ 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_7pe64ientmp_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_s218zriotmp_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 @@ -1963,8 +2006,8 @@ 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_0q8_3mtytmp_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_dk9eoy_rtmp_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__0zlj3bstmp_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_jst7fiowtmp_multi.bam' PASSED tests/AlignmentFile_test.py::TestExceptions::testBackwardsOrderNewFormat PASSED tests/AlignmentFile_test.py::TestExceptions::testBackwardsOrderOldFormat PASSED @@ -2081,7 +2124,7 @@ 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_vzlaoklitmp_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_a0_jpl5itmp_largecigar.bam' PASSED tests/AlignmentFile_test.py::TestLargeCigar::test_reading_writing_cram SKIPPED tests/AlignmentFile_test.py::TestLargeCigar::test_reading_writing_sam PASSED @@ -2154,7 +2197,7 @@ 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_95pp33cm.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_ybpv6has.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.) @@ -2298,50 +2341,30 @@ 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_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_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_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_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_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_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_10::testRead PASSED -tests/tabix_test.py::VCFFromTabixTest_10::testWrite PASSED -tests/tabix_test.py::VCFFromVCFTest_10::testConnecting PASSED -tests/tabix_test.py::VCFFromVCFTest_10::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_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_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_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_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_issue85::testRead PASSED -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_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_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_23::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_23::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_23::testConnecting PASSED @@ -2350,38 +2373,58 @@ 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_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_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_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_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_5::testRead PASSED 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_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_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_10::testRead PASSED +tests/tabix_test.py::VCFFromTabixTest_10::testWrite PASSED +tests/tabix_test.py::VCFFromVCFTest_10::testConnecting PASSED +tests/tabix_test.py::VCFFromVCFTest_10::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_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_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_issue85::testRead PASSED +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_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_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_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::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.) @@ -2392,8 +2435,22 @@ 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_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_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_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_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_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 [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 @@ -2423,8 +2480,8 @@ [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_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.) +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 @@ -2454,64 +2511,23 @@ [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_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_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_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_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_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_23::testConnecting [W::bcf_hdr_check_sanity] GL should be declared as Number=G 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_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::TestVCFFromVariantFile_issue85::testConnecting [E::bcf_hdr_parse] Could not parse the header, sample line not found +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_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.) PASSED -tests/tabix_test.py::TestVCFFromVariantFile_issue85::testParsing 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 @@ -2543,50 +2559,77 @@ [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_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_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_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_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_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 +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_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.) +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_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.) -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_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_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_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_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 +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_vcf_v42::testConnecting PASSED +tests/tabix_test.py::TestVCFFromVariantFile_vcf_v42::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" +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::TestIndexArgument::testFetchAll PASSED tests/tabix_test.py::TestIndexArgument::testLoadIndexWithoutTbiExtension PASSED @@ -2672,8 +2715,8 @@ return self.run(*args, **kwds) -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html -=========== 938 passed, 11 skipped, 4 warnings in 584.50s (0:09:44) ============ -make[1]: Leaving directory '/build/python-pysam-0.20.0+ds' +=========== 938 passed, 11 skipped, 4 warnings in 154.62s (0:02:34) ============ +make[1]: uscita dalla directory «/build/python-pysam-0.20.0+ds» create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild @@ -2711,127 +2754,127 @@ 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/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/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/utils.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/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/libcvcf.cpython-311-arm-linux-gnueabihf.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/libcfaidx.cpython-311-arm-linux-gnueabihf.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 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/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/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/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/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/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/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/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/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/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/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/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/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/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/__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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/extsort.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/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/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/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/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/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_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.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/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/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/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/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_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/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/libcbcftools.cpython-311-arm-linux-gnueabihf.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/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.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/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/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/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/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/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/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/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/libcfaidx.cpython-311-arm-linux-gnueabihf.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.cpython-311-arm-linux-gnueabihf.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/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/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/libcutils.cpython-311-arm-linux-gnueabihf.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/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/libchtslib.cpython-311-arm-linux-gnueabihf.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/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/utils.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/libcbgzf.cpython-311-arm-linux-gnueabihf.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/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/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/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/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/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/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/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/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/libcalignedsegment.cpython-311-arm-linux-gnueabihf.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.cpython-311-arm-linux-gnueabihf.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.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/libcutils.cpython-311-arm-linux-gnueabihf.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-arm-linux-gnueabihf.so -> /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__/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__/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/__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__/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__/__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__/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__/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/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.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/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/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/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/libcalignmentfile.cpython-311-arm-linux-gnueabihf.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.cpython-311-arm-linux-gnueabihf.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-arm-linux-gnueabihf.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/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/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/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/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.cpython-311-arm-linux-gnueabihf.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/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/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/__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/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/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/libcsamtools.cpython-311-arm-linux-gnueabihf.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.cpython-311-arm-linux-gnueabihf.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/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/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/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/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/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/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.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/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/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/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/libcbcftools.cpython-311-arm-linux-gnueabihf.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/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/libctabix.cpython-311-arm-linux-gnueabihf.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/libcsamtools.cpython-311-arm-linux-gnueabihf.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.cpython-311-arm-linux-gnueabihf.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/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/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/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/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/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/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/libcalignmentfile.pxd -> /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/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/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/config.py to config.cpython-311.pyc +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/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/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/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/libcsamfile.cpython-311-arm-linux-gnueabihf.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/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/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/__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/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/bcftools.py to bcftools.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 running install_egg_info running egg_info creating pysam.egg-info @@ -2865,19 +2908,19 @@ Skipping SOURCES.txt running install_scripts debian/rules override_dh_install -make[1]: Entering directory '/build/python-pysam-0.20.0+ds' +make[1]: ingresso nella directory «/build/python-pysam-0.20.0+ds» cd tests/pysam_data && /usr/bin/make clean -make[2]: Entering directory '/build/python-pysam-0.20.0+ds/tests/pysam_data' +make[2]: ingresso nella directory «/build/python-pysam-0.20.0+ds/tests/pysam_data» 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]: uscita dalla directory «/build/python-pysam-0.20.0+ds/tests/pysam_data» cd tests/cbcf_data && /usr/bin/make clean -make[2]: Entering directory '/build/python-pysam-0.20.0+ds/tests/cbcf_data' +make[2]: ingresso nella directory «/build/python-pysam-0.20.0+ds/tests/cbcf_data» rm -f all.stamp *.gz *.tbi *.csi *.bcf -make[2]: Leaving directory '/build/python-pysam-0.20.0+ds/tests/cbcf_data' +make[2]: uscita dalla directory «/build/python-pysam-0.20.0+ds/tests/cbcf_data» find . -name "*.pyc" -delete find . -name "*.pyxbldc" -delete find . -name "tmp_*.bam" -delete @@ -2900,7 +2943,7 @@ 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]: uscita dalla directory «/build/python-pysam-0.20.0+ds» dh_installdocs -O--buildsystem=pybuild dh_installchangelogs -O--buildsystem=pybuild dh_python3 -O--buildsystem=pybuild @@ -2921,9 +2964,9 @@ dh_gencontrol -O--buildsystem=pybuild dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild -dpkg-deb: building package 'python3-pysam' in '../python3-pysam_0.20.0+ds-3_armhf.deb'. -dpkg-deb: building package 'python3-pysam-dbgsym' in '../python3-pysam-dbgsym_0.20.0+ds-3_armhf.deb'. -dpkg-deb: building package 'python-pysam-tests' in '../python-pysam-tests_0.20.0+ds-3_all.deb'. +dpkg-deb: generazione del pacchetto "python3-pysam" in "../python3-pysam_0.20.0+ds-3_armhf.deb". +dpkg-deb: generazione del pacchetto "python3-pysam-dbgsym" in "../python3-pysam-dbgsym_0.20.0+ds-3_armhf.deb". +dpkg-deb: generazione del pacchetto "python-pysam-tests" in "../python-pysam-tests_0.20.0+ds-3_all.deb". dpkg-genbuildinfo --build=binary -O../python-pysam_0.20.0+ds-3_armhf.buildinfo dpkg-genchanges --build=binary -O../python-pysam_0.20.0+ds-3_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -2931,12 +2974,14 @@ 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/14213/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/14213/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/18391 and its subdirectories -I: Current time: Sat May 13 09:15:24 -12 2023 -I: pbuilder-time-stamp: 1684012524 +I: removing directory /srv/workspace/pbuilder/14213 and its subdirectories +I: Current time: Sun May 14 11:42:27 +14 2023 +I: pbuilder-time-stamp: 1684014147