Diff of the two buildlogs: -- --- b1/build.log 2021-08-14 01:10:10.286220193 +0000 +++ b2/build.log 2021-08-14 02:27:06.957178425 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri Aug 13 12:55:49 -12 2021 -I: pbuilder-time-stamp: 1628902549 +I: Current time: Sat Aug 14 15:10:36 +14 2021 +I: pbuilder-time-stamp: 1628903437 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration @@ -16,8 +16,8 @@ I: copying [./python-pysam_0.15.4+ds-3.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' -gpgv: keyblock resource '/tmp/dpkg-verify-sig.k5RUdU7J/trustedkeys.kbx': General error -gpgv: Signature made Fri May 8 06:41:05 2020 -12 +gpgv: keyblock resource '/tmp/dpkg-verify-sig.kpkOCFQR/trustedkeys.kbx': General error +gpgv: Signature made Sat May 9 08:41:05 2020 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -34,135 +34,169 @@ dpkg-source: info: applying clean_less I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/22309/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/13130/tmp/hooks/D01_modify_environment starting +debug: Running on cbxi4a. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' +Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' +Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' +Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by bash' +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/13130/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/13130/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,-fixfilepath parallel=3' - DISTRIBUTION='' - HOME='/root' - HOST_ARCH='armhf' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="1" [2]="4" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") + BASH_VERSION='5.1.4(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=armhf + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=4' + DIRSTACK=() + DISTRIBUTION= + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=arm + HOST_ARCH=armhf IFS=' ' - INVOCATION_ID='263cd795e1864e4e9580b95b542e02af' - 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='22309' - PS1='# ' - PS2='> ' + INVOCATION_ID=6c4656a9c7f94e82adb60c22be9a9766 + 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=13130 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.F8PGNFPOqS/pbuilderrc_IZeB --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.F8PGNFPOqS/b1 --logfile b1/build.log python-pysam_0.15.4+ds-3.dsc' - SUDO_GID='113' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://10.0.0.15:8000/' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.F8PGNFPOqS/pbuilderrc_otrh --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.F8PGNFPOqS/b2 --logfile b2/build.log --extrapackages usrmerge python-pysam_0.15.4+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://10.0.0.15:8000/ I: uname -a - Linux virt64c 5.10.0-8-arm64 #1 SMP Debian 5.10.46-4 (2021-08-03) aarch64 GNU/Linux + Linux i-capture-the-hostname 5.10.0-8-armmp #1 SMP Debian 5.10.46-4 (2021-08-03) armv7l GNU/Linux I: ls -l /bin total 3580 - -rwxr-xr-x 1 root root 816764 Aug 4 08:25 bash - -rwxr-xr-x 3 root root 26052 Jul 20 2020 bunzip2 - -rwxr-xr-x 3 root root 26052 Jul 20 2020 bzcat - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep - -rwxr-xr-x 3 root root 26052 Jul 20 2020 bzip2 - -rwxr-xr-x 1 root root 9636 Jul 20 2020 bzip2recover - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore - -rwxr-xr-x 1 root root 26668 Sep 22 2020 cat - -rwxr-xr-x 1 root root 43104 Sep 22 2020 chgrp - -rwxr-xr-x 1 root root 38984 Sep 22 2020 chmod - -rwxr-xr-x 1 root root 43112 Sep 22 2020 chown - -rwxr-xr-x 1 root root 92616 Sep 22 2020 cp - -rwxr-xr-x 1 root root 75524 Dec 10 2020 dash - -rwxr-xr-x 1 root root 75880 Sep 22 2020 date - -rwxr-xr-x 1 root root 55436 Sep 22 2020 dd - -rwxr-xr-x 1 root root 59912 Sep 22 2020 df - -rwxr-xr-x 1 root root 96764 Sep 22 2020 dir - -rwxr-xr-x 1 root root 55012 Jul 28 07:09 dmesg - lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname - -rwxr-xr-x 1 root root 22508 Sep 22 2020 echo - -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep - -rwxr-xr-x 1 root root 22496 Sep 22 2020 false - -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep - -rwxr-xr-x 1 root root 47492 Jul 28 07:09 findmnt - -rwsr-xr-x 1 root root 26076 Feb 26 04:12 fusermount - -rwxr-xr-x 1 root root 124508 Nov 9 2020 grep - -rwxr-xr-x 2 root root 2346 Mar 2 11:30 gunzip - -rwxr-xr-x 1 root root 6376 Mar 2 11:30 gzexe - -rwxr-xr-x 1 root root 64212 Mar 2 11:30 gzip - -rwxr-xr-x 1 root root 13784 Nov 6 2019 hostname - -rwxr-xr-x 1 root root 43180 Sep 22 2020 ln - -rwxr-xr-x 1 root root 35068 Feb 7 2020 login - -rwxr-xr-x 1 root root 96764 Sep 22 2020 ls - -rwxr-xr-x 1 root root 99940 Jul 28 07:09 lsblk - -rwxr-xr-x 1 root root 51408 Sep 22 2020 mkdir - -rwxr-xr-x 1 root root 43184 Sep 22 2020 mknod - -rwxr-xr-x 1 root root 30780 Sep 22 2020 mktemp - -rwxr-xr-x 1 root root 34408 Jul 28 07:09 more - -rwsr-xr-x 1 root root 34400 Jul 28 07:09 mount - -rwxr-xr-x 1 root root 9824 Jul 28 07:09 mountpoint - -rwxr-xr-x 1 root root 88524 Sep 22 2020 mv - lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 18 03:38 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 26652 Sep 22 2020 pwd - lrwxrwxrwx 1 root root 4 Aug 4 08:25 rbash -> bash - -rwxr-xr-x 1 root root 30740 Sep 22 2020 readlink - -rwxr-xr-x 1 root root 43104 Sep 22 2020 rm - -rwxr-xr-x 1 root root 30732 Sep 22 2020 rmdir - -rwxr-xr-x 1 root root 14144 Sep 27 2020 run-parts - -rwxr-xr-x 1 root root 76012 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Aug 9 21:24 sh -> dash - -rwxr-xr-x 1 root root 22532 Sep 22 2020 sleep - -rwxr-xr-x 1 root root 55360 Sep 22 2020 stty - -rwsr-xr-x 1 root root 46704 Jul 28 07:09 su - -rwxr-xr-x 1 root root 22532 Sep 22 2020 sync - -rwxr-xr-x 1 root root 340872 Feb 16 21:55 tar - -rwxr-xr-x 1 root root 9808 Sep 27 2020 tempfile - -rwxr-xr-x 1 root root 67696 Sep 22 2020 touch - -rwxr-xr-x 1 root root 22496 Sep 22 2020 true - -rwxr-xr-x 1 root root 9636 Feb 26 04:12 ulockmgr_server - -rwsr-xr-x 1 root root 22108 Jul 28 07:09 umount - -rwxr-xr-x 1 root root 22520 Sep 22 2020 uname - -rwxr-xr-x 2 root root 2346 Mar 2 11:30 uncompress - -rwxr-xr-x 1 root root 96764 Sep 22 2020 vdir - -rwxr-xr-x 1 root root 38512 Jul 28 07:09 wdctl - lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Mar 2 11:30 zcat - -rwxr-xr-x 1 root root 1678 Mar 2 11:30 zcmp - -rwxr-xr-x 1 root root 5880 Mar 2 11:30 zdiff - -rwxr-xr-x 1 root root 29 Mar 2 11:30 zegrep - -rwxr-xr-x 1 root root 29 Mar 2 11:30 zfgrep - -rwxr-xr-x 1 root root 2081 Mar 2 11:30 zforce - -rwxr-xr-x 1 root root 7585 Mar 2 11:30 zgrep - -rwxr-xr-x 1 root root 2206 Mar 2 11:30 zless - -rwxr-xr-x 1 root root 1842 Mar 2 11:30 zmore - -rwxr-xr-x 1 root root 4553 Mar 2 11:30 znew -I: user script /srv/workspace/pbuilder/22309/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 816764 Aug 5 10:25 bash + -rwxr-xr-x 3 root root 26052 Jul 21 2020 bunzip2 + -rwxr-xr-x 3 root root 26052 Jul 21 2020 bzcat + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2225 Jul 21 2020 bzdiff + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4877 Sep 5 2019 bzexe + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3775 Jul 21 2020 bzgrep + -rwxr-xr-x 3 root root 26052 Jul 21 2020 bzip2 + -rwxr-xr-x 1 root root 9636 Jul 21 2020 bzip2recover + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Jul 21 2020 bzmore + -rwxr-xr-x 1 root root 26668 Sep 23 2020 cat + -rwxr-xr-x 1 root root 43104 Sep 23 2020 chgrp + -rwxr-xr-x 1 root root 38984 Sep 23 2020 chmod + -rwxr-xr-x 1 root root 43112 Sep 23 2020 chown + -rwxr-xr-x 1 root root 92616 Sep 23 2020 cp + -rwxr-xr-x 1 root root 75524 Dec 11 2020 dash + -rwxr-xr-x 1 root root 75880 Sep 23 2020 date + -rwxr-xr-x 1 root root 55436 Sep 23 2020 dd + -rwxr-xr-x 1 root root 59912 Sep 23 2020 df + -rwxr-xr-x 1 root root 96764 Sep 23 2020 dir + -rwxr-xr-x 1 root root 55012 Jul 29 09:09 dmesg + lrwxrwxrwx 1 root root 8 Nov 8 2019 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Nov 8 2019 domainname -> hostname + -rwxr-xr-x 1 root root 22508 Sep 23 2020 echo + -rwxr-xr-x 1 root root 28 Nov 10 2020 egrep + -rwxr-xr-x 1 root root 22496 Sep 23 2020 false + -rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep + -rwxr-xr-x 1 root root 47492 Jul 29 09:09 findmnt + -rwsr-xr-x 1 root root 26076 Feb 27 06:12 fusermount + -rwxr-xr-x 1 root root 124508 Nov 10 2020 grep + -rwxr-xr-x 2 root root 2346 Mar 3 13:30 gunzip + -rwxr-xr-x 1 root root 6376 Mar 3 13:30 gzexe + -rwxr-xr-x 1 root root 64212 Mar 3 13:30 gzip + -rwxr-xr-x 1 root root 13784 Nov 8 2019 hostname + -rwxr-xr-x 1 root root 43180 Sep 23 2020 ln + -rwxr-xr-x 1 root root 35068 Feb 8 2020 login + -rwxr-xr-x 1 root root 96764 Sep 23 2020 ls + -rwxr-xr-x 1 root root 99940 Jul 29 09:09 lsblk + -rwxr-xr-x 1 root root 51408 Sep 23 2020 mkdir + -rwxr-xr-x 1 root root 43184 Sep 23 2020 mknod + -rwxr-xr-x 1 root root 30780 Sep 23 2020 mktemp + -rwxr-xr-x 1 root root 34408 Jul 29 09:09 more + -rwsr-xr-x 1 root root 34400 Jul 29 09:09 mount + -rwxr-xr-x 1 root root 9824 Jul 29 09:09 mountpoint + -rwxr-xr-x 1 root root 88524 Sep 23 2020 mv + lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Apr 19 05:38 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 26652 Sep 23 2020 pwd + lrwxrwxrwx 1 root root 4 Aug 5 10:25 rbash -> bash + -rwxr-xr-x 1 root root 30740 Sep 23 2020 readlink + -rwxr-xr-x 1 root root 43104 Sep 23 2020 rm + -rwxr-xr-x 1 root root 30732 Sep 23 2020 rmdir + -rwxr-xr-x 1 root root 14144 Sep 28 2020 run-parts + -rwxr-xr-x 1 root root 76012 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Aug 14 15:12 sh -> bash + lrwxrwxrwx 1 root root 4 Aug 10 23:28 sh.distrib -> dash + -rwxr-xr-x 1 root root 22532 Sep 23 2020 sleep + -rwxr-xr-x 1 root root 55360 Sep 23 2020 stty + -rwsr-xr-x 1 root root 46704 Jul 29 09:09 su + -rwxr-xr-x 1 root root 22532 Sep 23 2020 sync + -rwxr-xr-x 1 root root 340872 Feb 17 23:55 tar + -rwxr-xr-x 1 root root 9808 Sep 28 2020 tempfile + -rwxr-xr-x 1 root root 67696 Sep 23 2020 touch + -rwxr-xr-x 1 root root 22496 Sep 23 2020 true + -rwxr-xr-x 1 root root 9636 Feb 27 06:12 ulockmgr_server + -rwsr-xr-x 1 root root 22108 Jul 29 09:09 umount + -rwxr-xr-x 1 root root 22520 Sep 23 2020 uname + -rwxr-xr-x 2 root root 2346 Mar 3 13:30 uncompress + -rwxr-xr-x 1 root root 96764 Sep 23 2020 vdir + -rwxr-xr-x 1 root root 38512 Jul 29 09:09 wdctl + lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Mar 3 13:30 zcat + -rwxr-xr-x 1 root root 1678 Mar 3 13:30 zcmp + -rwxr-xr-x 1 root root 5880 Mar 3 13:30 zdiff + -rwxr-xr-x 1 root root 29 Mar 3 13:30 zegrep + -rwxr-xr-x 1 root root 29 Mar 3 13:30 zfgrep + -rwxr-xr-x 1 root root 2081 Mar 3 13:30 zforce + -rwxr-xr-x 1 root root 7585 Mar 3 13:30 zgrep + -rwxr-xr-x 1 root root 2206 Mar 3 13:30 zless + -rwxr-xr-x 1 root root 1842 Mar 3 13:30 zmore + -rwxr-xr-x 1 root root 4553 Mar 3 13:30 znew +I: user script /srv/workspace/pbuilder/13130/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -314,7 +348,7 @@ Get: 92 http://deb.debian.org/debian bullseye/main armhf python3-setuptools all 52.0.0-4 [366 kB] Get: 93 http://deb.debian.org/debian bullseye/main armhf samtools armhf 1.11-1 [519 kB] Get: 94 http://deb.debian.org/debian bullseye/main armhf tabix armhf 1.11-4 [306 kB] -Fetched 39.1 MB in 9s (4361 kB/s) +Fetched 39.1 MB in 7s (5493 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19398 files and directories currently installed.) @@ -707,8 +741,45 @@ Writing extended state information... Building tag database... -> Finished parsing the build-deps +Reading package lists... +Building dependency tree... +Reading state information... +The following additional packages will be installed: + libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl +The following NEW packages will be installed: + libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl usrmerge +0 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. +Need to get 59.5 kB of archives. +After this operation, 157 kB of additional disk space will be used. +Get:1 http://deb.debian.org/debian bullseye/main armhf libnumber-compare-perl all 0.03-1.1 [6956 B] +Get:2 http://deb.debian.org/debian bullseye/main armhf libtext-glob-perl all 0.11-1 [8888 B] +Get:3 http://deb.debian.org/debian bullseye/main armhf libfile-find-rule-perl all 0.34-1 [30.6 kB] +Get:4 http://deb.debian.org/debian bullseye/main armhf usrmerge all 25 [13.0 kB] +debconf: delaying package configuration, since apt-utils is not installed +Fetched 59.5 kB in 0s (272 kB/s) +Selecting previously unselected package libnumber-compare-perl. +(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 ... 23753 files and directories currently installed.) +Preparing to unpack .../libnumber-compare-perl_0.03-1.1_all.deb ... +Unpacking libnumber-compare-perl (0.03-1.1) ... +Selecting previously unselected package libtext-glob-perl. +Preparing to unpack .../libtext-glob-perl_0.11-1_all.deb ... +Unpacking libtext-glob-perl (0.11-1) ... +Selecting previously unselected package libfile-find-rule-perl. +Preparing to unpack .../libfile-find-rule-perl_0.34-1_all.deb ... +Unpacking libfile-find-rule-perl (0.34-1) ... +Selecting previously unselected package usrmerge. +Preparing to unpack .../archives/usrmerge_25_all.deb ... +Unpacking usrmerge (25) ... +Setting up libtext-glob-perl (0.11-1) ... +Setting up libnumber-compare-perl (0.03-1.1) ... +Setting up libfile-find-rule-perl (0.34-1) ... +Setting up usrmerge (25) ... +The system has been successfully converted. +Processing triggers for man-db (2.9.4-2) ... +Not building database; man-db/auto-update is not 'true'. I: Building the package -I: Running cd /build/python-pysam-0.15.4+ds/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../python-pysam_0.15.4+ds-3_source.changes +hostname: Name or service not known +I: Running cd /build/python-pysam-0.15.4+ds/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../python-pysam_0.15.4+ds-3_source.changes dpkg-buildpackage: info: source package python-pysam dpkg-buildpackage: info: source version 0.15.4+ds-3 dpkg-buildpackage: info: source distribution unstable @@ -717,17 +788,17 @@ dpkg-buildpackage: info: host architecture armhf debian/rules clean cd tests/pysam_data && /usr/bin/make clean -make[1]: Entering directory '/build/python-pysam-0.15.4+ds/tests/pysam_data' +make[1]: ingresso nella directory «/build/python-pysam-0.15.4+ds/tests/pysam_data» rm -fr *.bai *.fai *.pileup* *.cram \ *~ calDepth *.dSYM pysam_*.sam \ ex2.sam ex2.sam.gz ex1.sam \ with_md.sam.gz \ *.fq.gz -make[1]: Leaving directory '/build/python-pysam-0.15.4+ds/tests/pysam_data' +make[1]: uscita dalla directory «/build/python-pysam-0.15.4+ds/tests/pysam_data» cd tests/cbcf_data && /usr/bin/make clean -make[1]: Entering directory '/build/python-pysam-0.15.4+ds/tests/cbcf_data' +make[1]: ingresso nella directory «/build/python-pysam-0.15.4+ds/tests/cbcf_data» rm -f *.gz *.tbi *.csi *.bcf -make[1]: Leaving directory '/build/python-pysam-0.15.4+ds/tests/cbcf_data' +make[1]: uscita dalla directory «/build/python-pysam-0.15.4+ds/tests/cbcf_data» find . -name "*.pyc" -delete find . -name "*.pyxbldc" -delete find . -name "tmp_*.bam" -delete @@ -750,7 +821,7 @@ rm -rf .pytest_cache/ dh clean --with python3 --buildsystem=pybuild debian/rules override_dh_auto_clean -make[1]: Entering directory '/build/python-pysam-0.15.4+ds' +make[1]: ingresso nella directory «/build/python-pysam-0.15.4+ds» dh_auto_clean I: pybuild base:232: python3.9 setup.py clean # pysam: cython is available - using cythonize if necessary @@ -767,7 +838,7 @@ samtools/config.h \ bcftools/config.h rm -rf pysam.egg-info -make[1]: Leaving directory '/build/python-pysam-0.15.4+ds' +make[1]: uscita dalla directory «/build/python-pysam-0.15.4+ds» dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary @@ -789,86 +860,86 @@ running build_py creating /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam copying pysam/config.py -> /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam -copying pysam/bcftools.py -> /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam -copying pysam/Pileup.py -> /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam -copying pysam/samtools.py -> /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam copying pysam/__init__.py -> /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam copying pysam/utils.py -> /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam +copying pysam/bcftools.py -> /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam copying pysam/version.py -> /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam +copying pysam/Pileup.py -> /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam +copying pysam/samtools.py -> /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam creating /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include copying pysam/include/__init__.py -> /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include package init file 'samtools/__init__.py' not found (or not a regular file) package init file 'bcftools/__init__.py' not found (or not a regular file) -copying pysam/libcutils.pxd -> /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam -copying pysam/libcbcf.pxd -> /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam -copying pysam/libcbcftools.pxd -> /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam copying pysam/libcsamtools.pxd -> /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam -copying pysam/libcalignedsegment.pxd -> /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam copying pysam/libchtslib.pxd -> /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam +copying pysam/libctabixproxies.pxd -> /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam +copying pysam/libcalignmentfile.pxd -> /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam +copying pysam/libcsamfile.pxd -> /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam copying pysam/libcfaidx.pxd -> /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam +copying pysam/libcalignedsegment.pxd -> /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam copying pysam/libctabix.pxd -> /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam -copying pysam/libcsamfile.pxd -> /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam +copying pysam/libcbcftools.pxd -> /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam copying pysam/libcvcf.pxd -> /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam -copying pysam/libcalignmentfile.pxd -> /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam -copying pysam/libctabixproxies.pxd -> /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam -copying pysam/pysam_util.h -> /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam -copying pysam/cbcftools_util.h -> /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam +copying pysam/libcbcf.pxd -> /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam +copying pysam/libcutils.pxd -> /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam +copying pysam/csamtools_util.h -> /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam copying pysam/pysam_stream.h -> /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam +copying pysam/pysam_util.h -> /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam copying pysam/htslib_util.h -> /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam -copying pysam/csamtools_util.h -> /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam +copying pysam/cbcftools_util.h -> /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam creating /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools -copying samtools/sam_opts.h -> /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools -copying samtools/bam_lpileup.h -> /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools -copying samtools/bedidx.h -> /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools copying samtools/sam.h -> /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools +copying samtools/bedidx.h -> /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools +copying samtools/bam_lpileup.h -> /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools +copying samtools/stats_isize.h -> /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools +copying samtools/bam_endian.h -> /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools copying samtools/sample.h -> /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools copying samtools/samtools.pysam.h -> /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools -copying samtools/bam_endian.h -> /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools -copying samtools/tmp_file.h -> /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools copying samtools/bam2bcf.h -> /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools copying samtools/bam.h -> /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools -copying samtools/bam_plbuf.h -> /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools -copying samtools/stats_isize.h -> /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools -copying samtools/samtools.h -> /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools +copying samtools/sam_opts.h -> /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools copying samtools/version.h -> /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools +copying samtools/bam_plbuf.h -> /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools +copying samtools/tmp_file.h -> /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools copying samtools/config.h -> /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools +copying samtools/samtools.h -> /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools creating /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools -copying bcftools/hclust.h -> /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools -copying bcftools/regidx.h -> /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools -copying bcftools/vcmp.h -> /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools copying bcftools/call.h -> /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools -copying bcftools/smpl_ilist.h -> /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools -copying bcftools/HMM.h -> /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools copying bcftools/kmin.h -> /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools +copying bcftools/convert.h -> /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools +copying bcftools/khash_str2str.h -> /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools +copying bcftools/HMM.h -> /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools +copying bcftools/bcftools.h -> /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools +copying bcftools/cols.h -> /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools copying bcftools/rbuf.h -> /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools copying bcftools/filter.h -> /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools +copying bcftools/gvcf.h -> /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools +copying bcftools/ploidy.h -> /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools +copying bcftools/bam2bcf.h -> /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools +copying bcftools/regidx.h -> /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools +copying bcftools/variantkey.h -> /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools +copying bcftools/kheap.h -> /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools copying bcftools/bin.h -> /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools -copying bcftools/bcftools.pysam.h -> /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools +copying bcftools/version.h -> /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools +copying bcftools/hclust.h -> /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools copying bcftools/vcfbuf.h -> /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools -copying bcftools/kheap.h -> /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools -copying bcftools/bam2bcf.h -> /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools -copying bcftools/bam_sample.h -> /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools -copying bcftools/convert.h -> /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools -copying bcftools/prob1.h -> /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools +copying bcftools/bcftools.pysam.h -> /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools +copying bcftools/smpl_ilist.h -> /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools +copying bcftools/vcmp.h -> /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools copying bcftools/tsv2vcf.h -> /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools -copying bcftools/ploidy.h -> /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools -copying bcftools/hex.h -> /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools copying bcftools/mw.h -> /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools -copying bcftools/variantkey.h -> /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools -copying bcftools/bcftools.h -> /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools -copying bcftools/version.h -> /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools -copying bcftools/gvcf.h -> /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools -copying bcftools/khash_str2str.h -> /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools +copying bcftools/prob1.h -> /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools copying bcftools/config.h -> /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools -copying bcftools/cols.h -> /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools +copying bcftools/bam_sample.h -> /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools +copying bcftools/hex.h -> /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools /usr/lib/python3/dist-packages/setuptools/lib2to3_ex.py:36: SetuptoolsDeprecationWarning: 2to3 support is deprecated. If the project still requires Python 2 support, please migrate to a single-codebase solution or employ an independent conversion process. warnings.warn( -Fixing /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/config.py /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/bcftools.py /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/Pileup.py /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/samtools.py /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/__init__.py /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/utils.py /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/version.py /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/__init__.py +Fixing /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/config.py /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/__init__.py /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/utils.py /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/bcftools.py /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/version.py /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/Pileup.py /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/samtools.py /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/__init__.py Skipping optional fixer: buffer Skipping optional fixer: idioms Skipping optional fixer: set_literal Skipping optional fixer: ws_comma -Fixing /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/config.py /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/bcftools.py /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/Pileup.py /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/samtools.py /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/__init__.py /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/utils.py /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/version.py /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/__init__.py +Fixing /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/config.py /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/__init__.py /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/utils.py /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/bcftools.py /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/version.py /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/Pileup.py /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/samtools.py /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/__init__.py Skipping optional fixer: buffer Skipping optional fixer: idioms Skipping optional fixer: set_literal @@ -1103,9 +1174,9 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/build/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.9/pysam/libcvcf.o -L/build/python-pysam-0.15.4+ds/pysam -L/build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam -lz -lhts -lchtslib.cpython-39-arm-linux-gnueabihf -lcutils.cpython-39-arm-linux-gnueabihf -o /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcvcf.cpython-39-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN debian/rules override_dh_auto_test -make[1]: Entering directory '/build/python-pysam-0.15.4+ds' +make[1]: ingresso nella directory «/build/python-pysam-0.15.4+ds» cd tests/pysam_data && /usr/bin/make all -make[2]: Entering directory '/build/python-pysam-0.15.4+ds/tests/pysam_data' +make[2]: ingresso nella directory «/build/python-pysam-0.15.4+ds/tests/pysam_data» samtools faidx ex1.fa samtools view -bt ex1.fa.fai -o ex1.bam ex1.sam.gz samtools mpileup -f ex1.fa ex1.bam | gzip > ex1.pileup.gz @@ -1255,9 +1326,9 @@ cp ex1.bam ex1_csi.bam samtools index -c ex1_csi.bam rm with_md.sam -make[2]: Leaving directory '/build/python-pysam-0.15.4+ds/tests/pysam_data' +make[2]: uscita dalla directory «/build/python-pysam-0.15.4+ds/tests/pysam_data» cd tests/cbcf_data && /usr/bin/make all -make[2]: Entering directory '/build/python-pysam-0.15.4+ds/tests/cbcf_data' +make[2]: ingresso nella directory «/build/python-pysam-0.15.4+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 @@ -1305,7 +1376,7 @@ [W::bcf_hdr_check_sanity] PL should be declared as Number=G bcftools view -O b missing_genotypes.vcf.gz -o missing_genotypes.bcf bcftools index missing_genotypes.bcf -make[2]: Leaving directory '/build/python-pysam-0.15.4+ds/tests/cbcf_data' +make[2]: uscita dalla directory «/build/python-pysam-0.15.4+ds/tests/cbcf_data» export PYBUILD_TEST_ARGS='|| true' ; dh_auto_test I: pybuild base:232: cd /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build; python3.9 -m pytest || true ============================= test session starts ============================== @@ -1382,7 +1453,7 @@ tests/AlignedSegment_test.py::TestTags::testMDTagSoftClipping PASSED tests/AlignedSegment_test.py::TestTags::testMissingTag PASSED tests/AlignedSegment_test.py::TestTags::testNegativeIntegers PASSED -tests/AlignedSegment_test.py::TestTags::testNegativeIntegersWrittenToFile [E::idx_find_and_load] Could not retrieve index file for '/build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/tests/tmp/pysamtests_tmp___enter___5th0ub5ynegative_integers.bam' +tests/AlignedSegment_test.py::TestTags::testNegativeIntegersWrittenToFile [E::idx_find_and_load] Could not retrieve index file for '/build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/tests/tmp/pysamtests_tmp___enter___kjjs1jt4negative_integers.bam' PASSED tests/AlignedSegment_test.py::TestTags::testSetTag PASSED tests/AlignedSegment_test.py::TestTags::testTagParsing PASSED @@ -1461,22 +1532,22 @@ tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_header_content_is_as_expected FAILED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_name_mapping PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_text_access_works PASSED -tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_BAM [E::idx_find_and_load] Could not retrieve index file for '/build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_9cks3hkc' -/build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_9cks3hkc +tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_BAM [E::idx_find_and_load] Could not retrieve index file for '/build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_1surw3ir' +/build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_1surw3ir PASSED -tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_CRAM [E::cram_index_load] Could not retrieve index file for '/build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_19e1qv00' -/build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_19e1qv00 +tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_CRAM [E::cram_index_load] Could not retrieve index file for '/build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_v6kz4n55' +/build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_v6kz4n55 PASSED -tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_SAM /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_vql6_b2x +tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_SAM /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_bejpbj53 PASSED -tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_BAM [E::idx_find_and_load] Could not retrieve index file for '/build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_117bgpi1' -/build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_117bgpi1 +tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_BAM [E::idx_find_and_load] Could not retrieve index file for '/build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_0wutpol4' +/build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_0wutpol4 PASSED tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_CRAM [W::sanitise_SQ_lines] Header @SQ length mismatch for ref chr1, 2147483647 vs 1575 -[E::cram_index_load] Could not retrieve index file for '/build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_25sq6067' -/build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_25sq6067 +[E::cram_index_load] Could not retrieve index file for '/build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_yz98ssop' +/build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_yz98ssop PASSED -tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_SAM /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_rim6ghuj +tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_SAM /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_xc3luc50 PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_all_stepper PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_ignore_overlaps PASSED @@ -1842,7 +1913,7 @@ tests/AlignmentFile_test.py::TestIO::testOpenFromFilename FAILED tests/AlignmentFile_test.py::TestIO::testReadBamWithoutTargetNames PASSED tests/AlignmentFile_test.py::TestIO::testReadSamWithoutTargetNames PASSED -tests/AlignmentFile_test.py::TestIO::testReadingFromFileWithoutIndex [E::idx_find_and_load] Could not retrieve index file for '/build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/tests/tmp/pysamtests_tmp_testReadingFromFileWithoutIndex_bz83aqbktmp_ex2.bam' +tests/AlignmentFile_test.py::TestIO::testReadingFromFileWithoutIndex [E::idx_find_and_load] Could not retrieve index file for '/build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/tests/tmp/pysamtests_tmp_testReadingFromFileWithoutIndex_i9t36bkttmp_ex2.bam' PASSED tests/AlignmentFile_test.py::TestIO::testSAM2BAM FAILED tests/AlignmentFile_test.py::TestIO::testSAM2CRAM [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported @@ -1956,8 +2027,8 @@ tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_with_asterisk_only_returns_unmapped_reads PASSED tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_with_asterisk_only_returns_unmapped_reads_by_contig PASSED tests/AlignmentFile_test.py::TestContextManager::testManager PASSED -tests/AlignmentFile_test.py::TestMultiThread::testSingleThreadEqualsMultithread [E::idx_find_and_load] Could not retrieve index file for '/build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/tests/tmp/pysamtests_tmp_testSingleThreadEqualsMultithread_lap2561mtmp_single.bam' -[E::idx_find_and_load] Could not retrieve index file for '/build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/tests/tmp/pysamtests_tmp_testSingleThreadEqualsMultithread_im_dk_8htmp_multi.bam' +tests/AlignmentFile_test.py::TestMultiThread::testSingleThreadEqualsMultithread [E::idx_find_and_load] Could not retrieve index file for '/build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/tests/tmp/pysamtests_tmp_testSingleThreadEqualsMultithread_vpv4d4jetmp_single.bam' +[E::idx_find_and_load] Could not retrieve index file for '/build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/tests/tmp/pysamtests_tmp_testSingleThreadEqualsMultithread_7jyohczltmp_multi.bam' PASSED tests/AlignmentFile_test.py::TestExceptions::testBackwardsOrderNewFormat PASSED tests/AlignmentFile_test.py::TestExceptions::testBackwardsOrderOldFormat PASSED @@ -2080,7 +2151,7 @@ tests/AlignmentFile_test.py::TestVerbosity::testVerbosity PASSED tests/AlignmentFile_test.py::TestSanityCheckingBAM::test_empty_read_gives_value_error PASSED tests/AlignmentFile_test.py::TestHeader1000Genomes::testRead PASSED -tests/AlignmentFile_test.py::TestLargeCigar::test_reading_writing_bam [E::idx_find_and_load] Could not retrieve index file for '/build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/tests/tmp/pysamtests_tmp_check_read_3h_l2j3jtmp_largecigar.bam' +tests/AlignmentFile_test.py::TestLargeCigar::test_reading_writing_bam [E::idx_find_and_load] Could not retrieve index file for '/build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/tests/tmp/pysamtests_tmp_check_read_3k5392cwtmp_largecigar.bam' PASSED tests/AlignmentFile_test.py::TestLargeCigar::test_reading_writing_cram SKIPPED tests/AlignmentFile_test.py::TestLargeCigar::test_reading_writing_sam PASSED @@ -2152,7 +2223,7 @@ tests/VariantFile_test.py::TestSettingRecordValues::testSetQual [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/VariantFile_test.py::TestMultiThreading::testNoMultiThreadingWithIgnoreTruncation PASSED -tests/VariantFile_test.py::TestMultiThreading::testSingleThreadEqualsMultithreadResult [E::idx_find_and_load] Could not retrieve index file for '/build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/tests/tmp/pysamtests_tmp_testSingleThreadEqualsMultithreadResult_2ycm27o5.bcf' +tests/VariantFile_test.py::TestMultiThreading::testSingleThreadEqualsMultithreadResult [E::idx_find_and_load] Could not retrieve index file for '/build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/tests/tmp/pysamtests_tmp_testSingleThreadEqualsMultithreadResult_xf6e4u28.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.) @@ -2229,58 +2300,50 @@ tests/samtools_test.py::StdoutTest::testWithoutRedirectedStdout PASSED tests/samtools_test.py::PysamTest::testStatements FAILED tests/samtools_test.py::PysamTest::testUsage SKIPPED -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_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_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_7::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_7::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_7::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_7::testParsing PASSED -tests/tabix_test.py::VCFFromTabixTest_15::testRead PASSED -tests/tabix_test.py::VCFFromTabixTest_15::testWrite PASSED -tests/tabix_test.py::VCFFromVCFTest_15::testConnecting PASSED -tests/tabix_test.py::VCFFromVCFTest_15::testParsing PASSED -tests/tabix_test.py::VCFFromTabixTest_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_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_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_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_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_23::testRead PASSED -tests/tabix_test.py::VCFFromTabixTest_23::testWrite PASSED -tests/tabix_test.py::VCFFromVCFTest_23::testConnecting PASSED -tests/tabix_test.py::VCFFromVCFTest_23::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_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_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_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_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_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_20::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_20::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_20::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_20::testParsing PASSED -tests/tabix_test.py::VCFFromTabixTest_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_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_24::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_24::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_24::testConnecting PASSED @@ -2289,85 +2352,70 @@ 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_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_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_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_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_13::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_13::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_13::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_13::testParsing PASSED +tests/tabix_test.py::VCFFromTabixTest_4::testRead PASSED +tests/tabix_test.py::VCFFromTabixTest_4::testWrite PASSED +tests/tabix_test.py::VCFFromVCFTest_4::testConnecting PASSED +tests/tabix_test.py::VCFFromVCFTest_4::testParsing PASSED +tests/tabix_test.py::VCFFromTabixTest_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_23::testRead PASSED +tests/tabix_test.py::VCFFromTabixTest_23::testWrite PASSED +tests/tabix_test.py::VCFFromVCFTest_23::testConnecting PASSED +tests/tabix_test.py::VCFFromVCFTest_23::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_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_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_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::TestVCFFromVariantFile_12::testConnecting PASSED -tests/tabix_test.py::TestVCFFromVariantFile_12::testParsing [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.) -[W::vcf_parse_info] INFO 'DP' is not defined in the header, assuming Type=String -[W::vcf_parse_info] INFO 'AF1' is not defined in the header, assuming Type=String -[W::vcf_parse_info] INFO 'CI95' is not defined in the header, assuming Type=String -[W::vcf_parse_info] INFO 'DP4' is not defined in the header, assuming Type=String -[W::vcf_parse_info] INFO 'MQ' is not defined in the header, assuming Type=String -[W::vcf_parse_info] INFO 'PV4' is not defined in the header, assuming Type=String -[W::vcf_parse_format] FORMAT 'PL' at chr1:1281168 is not defined in the header, assuming Type=String -[W::vcf_parse_format] FORMAT 'GT' at chr1:1281168 is not defined in the header, assuming Type=String -[W::vcf_parse_format] FORMAT 'GQ' at chr1:1281168 is not defined in the header, assuming Type=String -[W::vcf_parse] Contig 'chr2a' is not defined in the header. (Quick workaround: index the file with tabix.) -[W::vcf_parse] Contig 'chr2b' 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_cox_hap1' is not defined in the header. (Quick workaround: index the file with tabix.) -[W::vcf_parse] Contig 'chr6_qbl_hap2' 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 '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.) +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::TestVCFFromVariantFile_2::testConnecting [W::bcf_hdr_check_sanity] GL should be declared as Number=G +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_21::testConnecting PASSED +tests/tabix_test.py::TestVCFFromVariantFile_21::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_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_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_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_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_5::testConnecting [W::bcf_hdr_check_sanity] GL should be declared as Number=G +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_5::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) +tests/tabix_test.py::TestVCFFromVariantFile_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_vcf_v42::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_vcf_v42::testParsing 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_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 @@ -2399,27 +2447,15 @@ [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_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 +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_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_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_20::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_20::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_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_22::testConnecting PASSED -tests/tabix_test.py::TestVCFFromVariantFile_22::testParsing [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.) -[W::vcf_parse_info] INFO 'refseq.name' is not defined in the header, assuming Type=String -[W::vcf_parse_info] INFO 'refseq.positionType' is not defined in the header, assuming Type=String -[W::vcf_parse] Contig 'chr2' is not defined in the header. (Quick workaround: index the file with tabix.) -PASSED tests/tabix_test.py::TestVCFFromVariantFile_24::testConnecting [W::bcf_hdr_parse] Could not parse header line: "#CHROM POS ID REF ALT QUAL FILTER INFO" [E::bcf_hdr_parse] Could not parse the header, sample line not found PASSED @@ -2428,9 +2464,19 @@ 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_2::testConnecting PASSED -tests/tabix_test.py::TestVCFFromVariantFile_2::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) -[W::vcf_parse_info] INFO 'sumGLbyD' is not defined in the header, assuming Type=String +tests/tabix_test.py::TestVCFFromVariantFile_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_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_10::testConnecting PASSED +tests/tabix_test.py::TestVCFFromVariantFile_10::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) +[W::vcf_parse_format] FORMAT 'GT' at 20:676148 is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestVCFFromVariantFile_13::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_13::testParsing [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.) @@ -2462,8 +2508,12 @@ [W::vcf_parse] Contig 'chrUn_gl000225' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chrX' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED -tests/tabix_test.py::TestVCFFromVariantFile_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_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_12::testConnecting PASSED +tests/tabix_test.py::TestVCFFromVariantFile_12::testParsing [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_info] INFO 'DP' is not defined in the header, assuming Type=String [W::vcf_parse_info] INFO 'AF1' is not defined in the header, assuming Type=String [W::vcf_parse_info] INFO 'CI95' is not defined in the header, assuming Type=String @@ -2493,22 +2543,43 @@ [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_21::testConnecting PASSED -tests/tabix_test.py::TestVCFFromVariantFile_21::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) -PASSED -tests/tabix_test.py::TestVCFFromVariantFile_3::testConnecting PASSED -tests/tabix_test.py::TestVCFFromVariantFile_3::testParsing [W::vcf_parse] Contig '1' is not defined in the header. (Quick workaround: index the file with tabix.) +tests/tabix_test.py::TestVCFFromVariantFile_23::testConnecting PASSED +tests/tabix_test.py::TestVCFFromVariantFile_23::testParsing [W::vcf_parse_info] INFO 'sumGLbyD' is not defined in the header, assuming Type=String PASSED -tests/tabix_test.py::TestVCFFromVariantFile_6::testConnecting PASSED -tests/tabix_test.py::TestVCFFromVariantFile_6::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) -[W::vcf_parse_info] INFO 'CallSetAC' is not defined in the header, assuming Type=String -[W::vcf_parse_info] INFO 'CallSetAC2' is not defined in the header, assuming Type=String -[W::vcf_parse_format] FORMAT 'GT' at 20:669442 is not defined in the header, assuming Type=String +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 +[W::vcf_parse_info] INFO 'DP4' is not defined in the header, assuming Type=String +[W::vcf_parse_info] INFO 'MQ' is not defined in the header, assuming Type=String +[W::vcf_parse_info] INFO 'PV4' is not defined in the header, assuming Type=String +[W::vcf_parse_format] FORMAT 'PL' at chr1:1281168 is not defined in the header, assuming Type=String +[W::vcf_parse_format] FORMAT 'GT' at chr1:1281168 is not defined in the header, assuming Type=String +[W::vcf_parse_format] FORMAT 'GQ' at chr1:1281168 is not defined in the header, assuming Type=String +[W::vcf_parse] Contig 'chr2a' is not defined in the header. (Quick workaround: index the file with tabix.) +[W::vcf_parse] Contig 'chr2b' 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_cox_hap1' is not defined in the header. (Quick workaround: index the file with tabix.) +[W::vcf_parse] Contig 'chr6_qbl_hap2' 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 '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.) PASSED -tests/tabix_test.py::TestVCFFromVariantFile_8::testConnecting PASSED -tests/tabix_test.py::TestVCFFromVariantFile_8::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) -[W::vcf_parse_format] FORMAT 'GT' at 20:676148 is not defined in the header, assuming Type=String +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::TestIndexing::test_indexing_to_custom_location_works PASSED tests/tabix_test.py::TestIndexing::test_indexing_with_explict_columns_works PASSED tests/tabix_test.py::TestIndexing::test_indexing_with_lineskipping_works PASSED @@ -3092,7 +3163,7 @@ checkGZBinaryEqual(tmpfilename, self.bamfile), "mismatch when construction BAM file, see %s %s" % (tmpfilename, self.bamfile)) -E AssertionError: False is not true : mismatch when construction BAM file, see tmp_4139345184.bam /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/tests/pysam_data/ex6.bam +E AssertionError: False is not true : mismatch when construction BAM file, see tmp_3048003448.bam /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/tests/pysam_data/ex6.bam tests/AlignmentFile_test.py:1377: AssertionError _______________________ TestEmptyHeader.testEmptyHeader ________________________ @@ -3190,7 +3261,7 @@ lines2 = pysam.samtools.view(*(args + [filename2])) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ -self = +self = args = ('-x', 'MD', '-x', 'NM', 'pysam_ex1.calmd.bam'), kwargs = {}, retval = 1 stderr = '[main_samview] fail to read the header from "pysam_ex1.calmd.bam".\n' stdout = '' @@ -3257,7 +3328,7 @@ lines2 = pysam.samtools.view(*(args + [filename2])) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ -self = +self = args = ('-x', 'MD', '-x', 'NM', 'pysam_ex1.calmd.bam'), kwargs = {}, retval = 1 stderr = '[main_samview] fail to read the header from "pysam_ex1.calmd.bam".\n' stdout = '' @@ -3354,8 +3425,8 @@ FAILED tests/compile_test.py::BAMTest::testCount - AssertionError: 3269 != 3270 FAILED tests/samtools_test.py::SamtoolsTest::testStatements - pysam.utils.Sam... FAILED tests/samtools_test.py::PysamTest::testStatements - pysam.utils.Samtoo... -====== 28 failed, 899 passed, 10 skipped, 7 warnings in 157.82s (0:02:37) ====== -make[1]: Leaving directory '/build/python-pysam-0.15.4+ds' +===== 28 failed, 899 passed, 10 skipped, 7 warnings in 1153.55s (0:19:13) ====== +make[1]: uscita dalla directory «/build/python-pysam-0.15.4+ds» create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild @@ -3402,112 +3473,112 @@ creating /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib creating /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9 creating /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages -copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/log.txt -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages +copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/tmp_3048003448.bam -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages +copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/tmp_ex2.bam -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam_uncompressed.bam -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages -copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/tmp_4139345184.bam -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages -copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/tmp_ex1.bam -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages creating /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam -copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcutils.pxd -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam +copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcsamtools.pxd -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam +copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libchtslib.pxd -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam +copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libctabixproxies.pxd -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam +copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/csamtools_util.h -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam +copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/pysam_stream.h -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam +copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcutils.cpython-39-arm-linux-gnueabihf.so -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam +copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/pysam_util.h -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam +copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcalignmentfile.pxd -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam +copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/htslib_util.h -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam +copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcsamfile.cpython-39-arm-linux-gnueabihf.so -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam +copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcsamfile.pxd -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam creating /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/__pycache__ -copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/__pycache__/Pileup.cpython-39.pyc -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/__pycache__ -copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/__pycache__/utils.cpython-39.pyc -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/__pycache__ -copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/__pycache__/__init__.cpython-39.pyc -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/__pycache__ -copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/__pycache__/config.cpython-39.pyc -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/__pycache__ -copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/__pycache__/samtools.cpython-39.pyc -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/__pycache__ copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/__pycache__/version.cpython-39.pyc -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/__pycache__ +copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/__pycache__/config.cpython-39.pyc -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/__pycache__ +copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/__pycache__/utils.cpython-39.pyc -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/__pycache__ copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/__pycache__/bcftools.cpython-39.pyc -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/__pycache__ -copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcbcf.pxd -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam -copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcbcftools.cpython-39-arm-linux-gnueabihf.so -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam -copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcbcftools.pxd -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam -copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcsamtools.cpython-39-arm-linux-gnueabihf.so -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam -copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/pysam_util.h -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam -copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcbcf.cpython-39-arm-linux-gnueabihf.so -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam -copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libctabix.cpython-39-arm-linux-gnueabihf.so -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam -copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcalignmentfile.cpython-39-arm-linux-gnueabihf.so -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam -copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcsamtools.pxd -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam -copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcalignedsegment.pxd -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam +copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/__pycache__/samtools.cpython-39.pyc -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/__pycache__ +copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/__pycache__/Pileup.cpython-39.pyc -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/__pycache__ +copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/__pycache__/__init__.cpython-39.pyc -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/__pycache__ +copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcfaidx.cpython-39-arm-linux-gnueabihf.so -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libctabixproxies.cpython-39-arm-linux-gnueabihf.so -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam -copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libchtslib.pxd -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam +copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/cbcftools_util.h -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam +copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libchtslib.cpython-39-arm-linux-gnueabihf.so -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/config.py -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcfaidx.pxd -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam -copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/bcftools.py -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam +copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcalignedsegment.pxd -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam +copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/__init__.py -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam +copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libctabix.cpython-39-arm-linux-gnueabihf.so -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libctabix.pxd -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam -copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libchtslib.cpython-39-arm-linux-gnueabihf.so -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam -copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcsamfile.pxd -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam -copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/cbcftools_util.h -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam -copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcvcf.cpython-39-arm-linux-gnueabihf.so -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam -copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/pysam_stream.h -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam -copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/Pileup.py -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam -copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/htslib_util.h -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam +copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcbcftools.pxd -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam +copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcalignmentfile.cpython-39-arm-linux-gnueabihf.so -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam +copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/utils.py -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam +copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcbgzf.cpython-39-arm-linux-gnueabihf.so -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam +copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/bcftools.py -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam +copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcsamtools.cpython-39-arm-linux-gnueabihf.so -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam +copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcbcftools.cpython-39-arm-linux-gnueabihf.so -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam creating /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include +copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/__init__.py -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include +creating /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/samtools +copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools/sam.h -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/samtools +copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools/bedidx.h -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/samtools +copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools/bam_lpileup.h -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/samtools +copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools/stats_isize.h -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/samtools +copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools/bam_endian.h -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/samtools +copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools/sample.h -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/samtools +copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools/samtools.pysam.h -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/samtools +copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools/bam2bcf.h -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/samtools +copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools/bam.h -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/samtools +copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools/sam_opts.h -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/samtools +copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools/version.h -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/samtools +copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools/bam_plbuf.h -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/samtools +copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools/tmp_file.h -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/samtools +copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools/config.h -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/samtools +copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools/samtools.h -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/samtools creating /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools -copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/hclust.h -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools -copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/regidx.h -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools -copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/vcmp.h -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/call.h -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools -copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/smpl_ilist.h -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools -copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/HMM.h -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/kmin.h -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools +copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/convert.h -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools +copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/khash_str2str.h -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools +copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/HMM.h -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools +copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/bcftools.h -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools +copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/cols.h -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/rbuf.h -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/filter.h -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools +copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/gvcf.h -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools +copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/ploidy.h -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools +copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/bam2bcf.h -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools +copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/regidx.h -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools +copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/variantkey.h -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools +copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/kheap.h -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/bin.h -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools -copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/bcftools.pysam.h -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools +copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/version.h -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools +copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/hclust.h -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/vcfbuf.h -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools -copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/kheap.h -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools -copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/bam2bcf.h -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools -copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/bam_sample.h -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools -copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/convert.h -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools -copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/prob1.h -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools +copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/bcftools.pysam.h -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools +copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/smpl_ilist.h -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools +copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/vcmp.h -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/tsv2vcf.h -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools -copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/ploidy.h -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools -copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/hex.h -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/mw.h -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools -copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/variantkey.h -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools -copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/bcftools.h -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools -copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/version.h -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools -copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/gvcf.h -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools -copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/khash_str2str.h -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools +copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/prob1.h -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/config.h -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools -copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/cols.h -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools -creating /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/samtools -copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools/sam_opts.h -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/samtools -copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools/bam_lpileup.h -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/samtools -copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools/bedidx.h -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/samtools -copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools/sam.h -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/samtools -copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools/sample.h -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/samtools -copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools/samtools.pysam.h -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/samtools -copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools/bam_endian.h -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/samtools -copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools/tmp_file.h -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/samtools -copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools/bam2bcf.h -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/samtools -copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools/bam.h -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/samtools -copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools/bam_plbuf.h -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/samtools -copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools/stats_isize.h -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/samtools -copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools/samtools.h -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/samtools -copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools/version.h -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/samtools -copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools/config.h -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/samtools -copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/__init__.py -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include -copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcalignedsegment.cpython-39-arm-linux-gnueabihf.so -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam -copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcbgzf.cpython-39-arm-linux-gnueabihf.so -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam -copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcsamfile.cpython-39-arm-linux-gnueabihf.so -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam +copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/bam_sample.h -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools +copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/hex.h -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools +copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcvcf.cpython-39-arm-linux-gnueabihf.so -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcvcf.pxd -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam -copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcalignmentfile.pxd -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam -copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcutils.cpython-39-arm-linux-gnueabihf.so -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam -copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/samtools.py -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam -copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/__init__.py -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam -copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcfaidx.cpython-39-arm-linux-gnueabihf.so -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam -copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/csamtools_util.h -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam -copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/utils.py -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam -copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libctabixproxies.pxd -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam +copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcalignedsegment.cpython-39-arm-linux-gnueabihf.so -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam +copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcbcf.pxd -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/version.py -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam -copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/tmp_ex2.bam -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages +copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcutils.pxd -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam +copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcbcf.cpython-39-arm-linux-gnueabihf.so -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam +copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/Pileup.py -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam +copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/samtools.py -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam +copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/tmp_ex1.bam -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages +copying /build/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/log.txt -> /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages byte-compiling /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/config.py to config.cpython-39.pyc -byte-compiling /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/bcftools.py to bcftools.cpython-39.pyc -byte-compiling /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/Pileup.py to Pileup.cpython-39.pyc -byte-compiling /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/__init__.py to __init__.cpython-39.pyc -byte-compiling /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/samtools.py to samtools.cpython-39.pyc byte-compiling /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/__init__.py to __init__.cpython-39.pyc byte-compiling /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/utils.py to utils.cpython-39.pyc +byte-compiling /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/bcftools.py to bcftools.cpython-39.pyc +byte-compiling /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/__init__.py to __init__.cpython-39.pyc byte-compiling /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/version.py to version.cpython-39.pyc +byte-compiling /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/Pileup.py to Pileup.cpython-39.pyc +byte-compiling /build/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/samtools.py to samtools.cpython-39.pyc running install_egg_info running egg_info creating pysam.egg-info @@ -3544,19 +3615,19 @@ Skipping SOURCES.txt running install_scripts debian/rules override_dh_install -make[1]: Entering directory '/build/python-pysam-0.15.4+ds' +make[1]: ingresso nella directory «/build/python-pysam-0.15.4+ds» cd tests/pysam_data && /usr/bin/make clean -make[2]: Entering directory '/build/python-pysam-0.15.4+ds/tests/pysam_data' +make[2]: ingresso nella directory «/build/python-pysam-0.15.4+ds/tests/pysam_data» rm -fr *.bai *.fai *.pileup* *.cram \ *~ calDepth *.dSYM pysam_*.sam \ ex2.sam ex2.sam.gz ex1.sam \ with_md.sam.gz \ *.fq.gz -make[2]: Leaving directory '/build/python-pysam-0.15.4+ds/tests/pysam_data' +make[2]: uscita dalla directory «/build/python-pysam-0.15.4+ds/tests/pysam_data» cd tests/cbcf_data && /usr/bin/make clean -make[2]: Entering directory '/build/python-pysam-0.15.4+ds/tests/cbcf_data' +make[2]: ingresso nella directory «/build/python-pysam-0.15.4+ds/tests/cbcf_data» rm -f *.gz *.tbi *.csi *.bcf -make[2]: Leaving directory '/build/python-pysam-0.15.4+ds/tests/cbcf_data' +make[2]: uscita dalla directory «/build/python-pysam-0.15.4+ds/tests/cbcf_data» find . -name "*.pyc" -delete find . -name "*.pyxbldc" -delete find . -name "tmp_*.bam" -delete @@ -3579,7 +3650,7 @@ rm -rf .pytest_cache/ dh_install -Xtest.gtf.gz find debian -name log.txt -delete -make[1]: Leaving directory '/build/python-pysam-0.15.4+ds' +make[1]: uscita dalla directory «/build/python-pysam-0.15.4+ds» dh_installdocs -O--buildsystem=pybuild dh_installchangelogs -O--buildsystem=pybuild dh_python3 -O--buildsystem=pybuild @@ -3605,9 +3676,9 @@ dpkg-gencontrol: warning: package python3-pysam: substitution variable ${python3:Versions} unused, but is defined dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild -dpkg-deb: building package 'python3-pysam' in '../python3-pysam_0.15.4+ds-3_armhf.deb'. -dpkg-deb: building package 'python3-pysam-dbgsym' in '../python3-pysam-dbgsym_0.15.4+ds-3_armhf.deb'. -dpkg-deb: building package 'python-pysam-tests' in '../python-pysam-tests_0.15.4+ds-3_all.deb'. +dpkg-deb: generazione del pacchetto "python3-pysam-dbgsym" in "../python3-pysam-dbgsym_0.15.4+ds-3_armhf.deb". +dpkg-deb: generazione del pacchetto "python3-pysam" in "../python3-pysam_0.15.4+ds-3_armhf.deb". +dpkg-deb: generazione del pacchetto "python-pysam-tests" in "../python-pysam-tests_0.15.4+ds-3_all.deb". dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../python-pysam_0.15.4+ds-3_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -3615,12 +3686,14 @@ 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/13130/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/13130/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/22309 and its subdirectories -I: Current time: Fri Aug 13 13:10:06 -12 2021 -I: pbuilder-time-stamp: 1628903406 +I: removing directory /srv/workspace/pbuilder/13130 and its subdirectories +I: Current time: Sat Aug 14 16:27:02 +14 2021 +I: pbuilder-time-stamp: 1628908022