I: pbuilder: network access will be disabled during build I: Current time: Tue May 9 20:39:36 +14 2023 I: pbuilder-time-stamp: 1683614376 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: using eatmydata during job I: Copying source file I: copying [python-pysam_0.20.0+ds-3.dsc] I: copying [./python-pysam_0.20.0+ds.orig.tar.xz] I: copying [./python-pysam_0.20.0+ds-3.debian.tar.xz] I: Extracting source gpgv: Signature made Sun Jan 1 07:45:09 2023 +14 gpgv: using EDDSA key A095B66EE09024BEE6A2F0722A27904BD7243EDA gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./python-pysam_0.20.0+ds-3.dsc: no acceptable signature found dpkg-source: info: extracting python-pysam in python-pysam-0.20.0+ds dpkg-source: info: unpacking python-pysam_0.20.0+ds.orig.tar.xz dpkg-source: info: unpacking python-pysam_0.20.0+ds-3.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying skip_test_remote.patch dpkg-source: info: applying clean_less dpkg-source: info: applying skip-test-on-32-bit.patch dpkg-source: info: applying disable-tests-python3.11.patch dpkg-source: info: applying python3.11.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/29729/tmp/hooks/D01_modify_environment starting debug: Running on ionos12-i386. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 May 9 20:39 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/29729/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/29729/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="15" [3]="1" [4]="release" [5]="i686-pc-linux-gnu") BASH_VERSION='5.2.15(1)-release' BUILDDIR=/build BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=i386 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=7' DIRSTACK=() DISTRIBUTION=bookworm EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=i686 HOST_ARCH=i386 IFS=' ' INVOCATION_ID=df79142fe119430bb31c7c03604b811c LANG=C LANGUAGE=de_CH:de LC_ALL=C LD_LIBRARY_PATH=/usr/lib/libeatmydata LD_PRELOAD=libeatmydata.so MACHTYPE=i686-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=29729 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.GaAQ7Bhk/pbuilderrc_XhEh --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.GaAQ7Bhk/b2 --logfile b2/build.log --extrapackages usrmerge python-pysam_0.20.0+ds-3.dsc' SUDO_GID=112 SUDO_UID=107 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://78.137.99.97:3128 I: uname -a Linux i-capture-the-hostname 5.10.0-22-686-pae #1 SMP Debian 5.10.178-3 (2023-04-22) i686 GNU/Linux I: ls -l /bin total 6036 -rwxr-xr-x 1 root root 1408088 Apr 24 11:24 bash -rwxr-xr-x 3 root root 38404 Sep 19 2022 bunzip2 -rwxr-xr-x 3 root root 38404 Sep 19 2022 bzcat lrwxrwxrwx 1 root root 6 Sep 19 2022 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Sep 19 2022 bzdiff lrwxrwxrwx 1 root root 6 Sep 19 2022 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4893 Nov 28 2021 bzexe lrwxrwxrwx 1 root root 6 Sep 19 2022 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Sep 19 2022 bzgrep -rwxr-xr-x 3 root root 38404 Sep 19 2022 bzip2 -rwxr-xr-x 1 root root 17892 Sep 19 2022 bzip2recover lrwxrwxrwx 1 root root 6 Sep 19 2022 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Sep 19 2022 bzmore -rwxr-xr-x 1 root root 42920 Sep 21 2022 cat -rwxr-xr-x 1 root root 79816 Sep 21 2022 chgrp -rwxr-xr-x 1 root root 67496 Sep 21 2022 chmod -rwxr-xr-x 1 root root 79816 Sep 21 2022 chown -rwxr-xr-x 1 root root 162024 Sep 21 2022 cp -rwxr-xr-x 1 root root 136916 Jan 6 03:20 dash -rwxr-xr-x 1 root root 137160 Sep 21 2022 date -rwxr-xr-x 1 root root 100364 Sep 21 2022 dd -rwxr-xr-x 1 root root 108940 Sep 21 2022 df -rwxr-xr-x 1 root root 162152 Sep 21 2022 dir -rwxr-xr-x 1 root root 87760 Mar 24 00:20 dmesg lrwxrwxrwx 1 root root 8 Dec 20 03:33 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 20 03:33 domainname -> hostname -rwxr-xr-x 1 root root 38760 Sep 21 2022 echo -rwxr-xr-x 1 root root 41 Jan 25 04:43 egrep -rwxr-xr-x 1 root root 34664 Sep 21 2022 false -rwxr-xr-x 1 root root 41 Jan 25 04:43 fgrep -rwxr-xr-x 1 root root 84272 Mar 24 00:20 findmnt -rwsr-xr-x 1 root root 30240 Mar 23 22:38 fusermount -rwxr-xr-x 1 root root 218680 Jan 25 04:43 grep -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe -rwxr-xr-x 1 root root 100952 Apr 10 2022 gzip -rwxr-xr-x 1 root root 21916 Dec 20 03:33 hostname -rwxr-xr-x 1 root root 75756 Sep 21 2022 ln -rwxr-xr-x 1 root root 55600 Mar 24 01:43 login -rwxr-xr-x 1 root root 162152 Sep 21 2022 ls -rwxr-xr-x 1 root root 214568 Mar 24 00:20 lsblk -rwxr-xr-x 1 root root 96328 Sep 21 2022 mkdir -rwxr-xr-x 1 root root 84008 Sep 21 2022 mknod -rwxr-xr-x 1 root root 38792 Sep 21 2022 mktemp -rwxr-xr-x 1 root root 63016 Mar 24 00:20 more -rwsr-xr-x 1 root root 58912 Mar 24 00:20 mount -rwxr-xr-x 1 root root 13856 Mar 24 00:20 mountpoint -rwxr-xr-x 1 root root 157932 Sep 21 2022 mv lrwxrwxrwx 1 root root 8 Dec 20 03:33 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 3 20:25 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 38792 Sep 21 2022 pwd lrwxrwxrwx 1 root root 4 Apr 24 11:24 rbash -> bash -rwxr-xr-x 1 root root 51080 Sep 21 2022 readlink -rwxr-xr-x 1 root root 75720 Sep 21 2022 rm -rwxr-xr-x 1 root root 51080 Sep 21 2022 rmdir -rwxr-xr-x 1 root root 22308 Nov 3 2022 run-parts -rwxr-xr-x 1 root root 133224 Jan 6 09:55 sed lrwxrwxrwx 1 root root 9 May 9 20:39 sh -> /bin/bash -rwxr-xr-x 1 root root 38760 Sep 21 2022 sleep -rwxr-xr-x 1 root root 87976 Sep 21 2022 stty -rwsr-xr-x 1 root root 83492 Mar 24 00:20 su -rwxr-xr-x 1 root root 38792 Sep 21 2022 sync -rwxr-xr-x 1 root root 598456 Apr 7 04:25 tar -rwxr-xr-x 1 root root 13860 Nov 3 2022 tempfile -rwxr-xr-x 1 root root 120776 Sep 21 2022 touch -rwxr-xr-x 1 root root 34664 Sep 21 2022 true -rwxr-xr-x 1 root root 17892 Mar 23 22:38 ulockmgr_server -rwsr-xr-x 1 root root 30236 Mar 24 00:20 umount -rwxr-xr-x 1 root root 38760 Sep 21 2022 uname -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress -rwxr-xr-x 1 root root 162152 Sep 21 2022 vdir -rwxr-xr-x 1 root root 71216 Mar 24 00:20 wdctl lrwxrwxrwx 1 root root 8 Dec 20 03:33 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp -rwxr-xr-x 1 root root 6460 Apr 10 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce -rwxr-xr-x 1 root root 8103 Apr 10 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew I: user script /srv/workspace/pbuilder/29729/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: i386 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), dh-exec, dh-python, libhts-dev (>= 1.14~), zlib1g-dev, python3-all-dev, python3-setuptools, cython3, tabix, samtools, bcftools, python3-pytest dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19604 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on dh-exec; however: Package dh-exec is not installed. pbuilder-satisfydepends-dummy depends on dh-python; however: Package dh-python is not installed. pbuilder-satisfydepends-dummy depends on libhts-dev (>= 1.14~); however: Package libhts-dev is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-all-dev; however: Package python3-all-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on cython3; however: Package cython3 is not installed. pbuilder-satisfydepends-dummy depends on tabix; however: Package tabix is not installed. pbuilder-satisfydepends-dummy depends on samtools; however: Package samtools is not installed. pbuilder-satisfydepends-dummy depends on bcftools; however: Package bcftools is not installed. pbuilder-satisfydepends-dummy depends on python3-pytest; however: Package python3-pytest is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bcftools{a} bsdextrautils{a} cython3{a} debhelper{a} dh-autoreconf{a} dh-exec{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} isa-support{a} libarchive-zip-perl{a} libbrotli1{a} libcurl3-gnutls{a} libcurl4-gnutls-dev{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libelf1{a} libexpat1{a} libexpat1-dev{a} libfile-stripnondeterminism-perl{a} libhts-dev{a} libhts3{a} libhtscodecs2{a} libicu72{a} libjs-jquery{a} libjs-sphinxdoc{a} libjs-underscore{a} libldap-2.5-0{a} liblzma-dev{a} libmagic-mgc{a} libmagic1{a} libncurses6{a} libnghttp2-14{a} libpipeline1{a} libpsl5{a} libpython3-all-dev{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.11{a} libpython3.11-dev{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libreadline8{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} media-types{a} po-debconf{a} python3{a} python3-all{a} python3-all-dev{a} python3-attr{a} python3-dev{a} python3-distutils{a} python3-iniconfig{a} python3-lib2to3{a} python3-minimal{a} python3-more-itertools{a} python3-packaging{a} python3-pkg-resources{a} python3-pluggy{a} python3-py{a} python3-pytest{a} python3-setuptools{a} python3.11{a} python3.11-dev{a} python3.11-minimal{a} readline-common{a} samtools{a} sensible-utils{a} sse2-support{a} tabix{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl javascript-common libarchive-cpio-perl libgpm2 libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx publicsuffix python3-pygments wget 0 packages upgraded, 90 newly installed, 0 to remove and 0 not upgraded. Need to get 43.3 MB of archives. After unpacking 161 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main i386 libpython3.11-minimal i386 3.11.2-6 [813 kB] Get: 2 http://deb.debian.org/debian bookworm/main i386 libexpat1 i386 2.5.0-1 [103 kB] Get: 3 http://deb.debian.org/debian bookworm/main i386 python3.11-minimal i386 3.11.2-6 [2130 kB] Get: 4 http://deb.debian.org/debian bookworm/main i386 python3-minimal i386 3.11.2-1+b1 [26.3 kB] Get: 5 http://deb.debian.org/debian bookworm/main i386 media-types all 10.0.0 [26.1 kB] Get: 6 http://deb.debian.org/debian bookworm/main i386 readline-common all 8.2-1.3 [69.0 kB] Get: 7 http://deb.debian.org/debian bookworm/main i386 libreadline8 i386 8.2-1.3 [171 kB] Get: 8 http://deb.debian.org/debian bookworm/main i386 libpython3.11-stdlib i386 3.11.2-6 [1799 kB] Get: 9 http://deb.debian.org/debian bookworm/main i386 python3.11 i386 3.11.2-6 [572 kB] Get: 10 http://deb.debian.org/debian bookworm/main i386 libpython3-stdlib i386 3.11.2-1+b1 [9308 B] Get: 11 http://deb.debian.org/debian bookworm/main i386 python3 i386 3.11.2-1+b1 [26.3 kB] Get: 12 http://deb.debian.org/debian bookworm/main i386 isa-support i386 15 [9692 B] Get: 13 http://deb.debian.org/debian bookworm/main i386 sse2-support i386 15 [3320 B] Get: 14 http://deb.debian.org/debian bookworm/main i386 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 15 http://deb.debian.org/debian bookworm/main i386 libmagic-mgc i386 1:5.44-3 [305 kB] Get: 16 http://deb.debian.org/debian bookworm/main i386 libmagic1 i386 1:5.44-3 [114 kB] Get: 17 http://deb.debian.org/debian bookworm/main i386 file i386 1:5.44-3 [42.5 kB] Get: 18 http://deb.debian.org/debian bookworm/main i386 gettext-base i386 0.21-12 [162 kB] Get: 19 http://deb.debian.org/debian bookworm/main i386 libuchardet0 i386 0.0.7-1 [67.9 kB] Get: 20 http://deb.debian.org/debian bookworm/main i386 groff-base i386 1.22.4-10 [932 kB] Get: 21 http://deb.debian.org/debian bookworm/main i386 bsdextrautils i386 2.38.1-5+b1 [90.3 kB] Get: 22 http://deb.debian.org/debian bookworm/main i386 libpipeline1 i386 1.5.7-1 [40.0 kB] Get: 23 http://deb.debian.org/debian bookworm/main i386 man-db i386 2.11.2-2 [1397 kB] Get: 24 http://deb.debian.org/debian bookworm/main i386 m4 i386 1.4.19-3 [294 kB] Get: 25 http://deb.debian.org/debian bookworm/main i386 autoconf all 2.71-3 [332 kB] Get: 26 http://deb.debian.org/debian bookworm/main i386 autotools-dev all 20220109.1 [51.6 kB] Get: 27 http://deb.debian.org/debian bookworm/main i386 automake all 1:1.16.5-1.3 [823 kB] Get: 28 http://deb.debian.org/debian bookworm/main i386 autopoint all 0.21-12 [495 kB] Get: 29 http://deb.debian.org/debian bookworm/main i386 libbrotli1 i386 1.0.9-2+b6 [275 kB] Get: 30 http://deb.debian.org/debian bookworm/main i386 libsasl2-modules-db i386 2.1.28+dfsg-10 [21.4 kB] Get: 31 http://deb.debian.org/debian bookworm/main i386 libsasl2-2 i386 2.1.28+dfsg-10 [62.7 kB] Get: 32 http://deb.debian.org/debian bookworm/main i386 libldap-2.5-0 i386 2.5.13+dfsg-5 [196 kB] Get: 33 http://deb.debian.org/debian bookworm/main i386 libnghttp2-14 i386 1.52.0-1 [79.8 kB] Get: 34 http://deb.debian.org/debian bookworm/main i386 libpsl5 i386 0.21.2-1 [59.3 kB] Get: 35 http://deb.debian.org/debian bookworm/main i386 librtmp1 i386 2.4+20151223.gitfa8646d.1-2+b2 [64.3 kB] Get: 36 http://deb.debian.org/debian bookworm/main i386 libssh2-1 i386 1.10.0-3+b1 [187 kB] Get: 37 http://deb.debian.org/debian bookworm/main i386 libcurl3-gnutls i386 7.88.1-9 [412 kB] Get: 38 http://deb.debian.org/debian bookworm/main i386 libdeflate0 i386 1.14-1 [57.5 kB] Get: 39 http://deb.debian.org/debian bookworm/main i386 libhtscodecs2 i386 1.3.0-4 [67.4 kB] Get: 40 http://deb.debian.org/debian bookworm/main i386 libhts3 i386 1.16+ds-3 [469 kB] Get: 41 http://deb.debian.org/debian bookworm/main i386 bcftools i386 1.16-1 [732 kB] Get: 42 http://deb.debian.org/debian bookworm/main i386 cython3 i386 0.29.32-2+b1 [1297 kB] Get: 43 http://deb.debian.org/debian bookworm/main i386 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 44 http://deb.debian.org/debian bookworm/main i386 libtool all 2.4.7-5 [517 kB] Get: 45 http://deb.debian.org/debian bookworm/main i386 dh-autoreconf all 20 [17.1 kB] Get: 46 http://deb.debian.org/debian bookworm/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 47 http://deb.debian.org/debian bookworm/main i386 libsub-override-perl all 0.09-4 [9304 B] Get: 48 http://deb.debian.org/debian bookworm/main i386 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 49 http://deb.debian.org/debian bookworm/main i386 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 50 http://deb.debian.org/debian bookworm/main i386 libelf1 i386 0.188-2.1 [179 kB] Get: 51 http://deb.debian.org/debian bookworm/main i386 dwz i386 0.15-1 [118 kB] Get: 52 http://deb.debian.org/debian bookworm/main i386 libicu72 i386 72.1-3 [9541 kB] Get: 53 http://deb.debian.org/debian bookworm/main i386 libxml2 i386 2.9.14+dfsg-1.2 [720 kB] Get: 54 http://deb.debian.org/debian bookworm/main i386 gettext i386 0.21-12 [1311 kB] Get: 55 http://deb.debian.org/debian bookworm/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 56 http://deb.debian.org/debian bookworm/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 57 http://deb.debian.org/debian bookworm/main i386 debhelper all 13.11.4 [942 kB] Get: 58 http://deb.debian.org/debian bookworm/main i386 dh-exec i386 0.27 [28.2 kB] Get: 59 http://deb.debian.org/debian bookworm/main i386 python3-lib2to3 all 3.11.2-3 [76.3 kB] Get: 60 http://deb.debian.org/debian bookworm/main i386 python3-distutils all 3.11.2-3 [131 kB] Get: 61 http://deb.debian.org/debian bookworm/main i386 dh-python all 5.20230130 [104 kB] Get: 62 http://deb.debian.org/debian bookworm/main i386 libcurl4-gnutls-dev i386 7.88.1-9 [527 kB] Get: 63 http://deb.debian.org/debian bookworm/main i386 libdeflate-dev i386 1.14-1 [53.5 kB] Get: 64 http://deb.debian.org/debian bookworm/main i386 libexpat1-dev i386 2.5.0-1 [158 kB] Get: 65 http://deb.debian.org/debian bookworm/main i386 liblzma-dev i386 5.4.1-0.2 [272 kB] Get: 66 http://deb.debian.org/debian bookworm/main i386 zlib1g-dev i386 1:1.2.13.dfsg-1 [913 kB] Get: 67 http://deb.debian.org/debian bookworm/main i386 libhts-dev i386 1.16+ds-3 [1585 kB] Get: 68 http://deb.debian.org/debian bookworm/main i386 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 69 http://deb.debian.org/debian bookworm/main i386 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 70 http://deb.debian.org/debian bookworm/main i386 libjs-sphinxdoc all 5.3.0-4 [130 kB] Get: 71 http://deb.debian.org/debian bookworm/main i386 libncurses6 i386 6.4-2 [111 kB] Get: 72 http://deb.debian.org/debian bookworm/main i386 libpython3.11 i386 3.11.2-6 [2013 kB] Get: 73 http://deb.debian.org/debian bookworm/main i386 libpython3.11-dev i386 3.11.2-6 [4906 kB] Get: 74 http://deb.debian.org/debian bookworm/main i386 libpython3-dev i386 3.11.2-1+b1 [9580 B] Get: 75 http://deb.debian.org/debian bookworm/main i386 libpython3-all-dev i386 3.11.2-1+b1 [1068 B] Get: 76 http://deb.debian.org/debian bookworm/main i386 python3-all i386 3.11.2-1+b1 [1056 B] Get: 77 http://deb.debian.org/debian bookworm/main i386 python3.11-dev i386 3.11.2-6 [615 kB] Get: 78 http://deb.debian.org/debian bookworm/main i386 python3-dev i386 3.11.2-1+b1 [26.2 kB] Get: 79 http://deb.debian.org/debian bookworm/main i386 python3-all-dev i386 3.11.2-1+b1 [1072 B] Get: 80 http://deb.debian.org/debian bookworm/main i386 python3-attr all 22.2.0-1 [65.4 kB] Get: 81 http://deb.debian.org/debian bookworm/main i386 python3-iniconfig all 1.1.1-2 [6396 B] Get: 82 http://deb.debian.org/debian bookworm/main i386 python3-more-itertools all 8.10.0-2 [53.0 kB] Get: 83 http://deb.debian.org/debian bookworm/main i386 python3-packaging all 23.0-1 [32.5 kB] Get: 84 http://deb.debian.org/debian bookworm/main i386 python3-pkg-resources all 66.1.1-1 [296 kB] Get: 85 http://deb.debian.org/debian bookworm/main i386 python3-pluggy all 1.0.0+repack-1 [19.7 kB] Get: 86 http://deb.debian.org/debian bookworm/main i386 python3-py all 1.11.0-1 [89.2 kB] Get: 87 http://deb.debian.org/debian bookworm/main i386 python3-pytest all 7.2.1-2 [236 kB] Get: 88 http://deb.debian.org/debian bookworm/main i386 python3-setuptools all 66.1.1-1 [521 kB] Get: 89 http://deb.debian.org/debian bookworm/main i386 samtools i386 1.16.1-1 [637 kB] Get: 90 http://deb.debian.org/debian bookworm/main i386 tabix i386 1.16+ds-3 [501 kB] Fetched 43.3 MB in 1s (53.6 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:i386. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19604 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.2-6_i386.deb ... Unpacking libpython3.11-minimal:i386 (3.11.2-6) ... Selecting previously unselected package libexpat1:i386. Preparing to unpack .../libexpat1_2.5.0-1_i386.deb ... Unpacking libexpat1:i386 (2.5.0-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.2-6_i386.deb ... Unpacking python3.11-minimal (3.11.2-6) ... Setting up libpython3.11-minimal:i386 (3.11.2-6) ... Setting up libexpat1:i386 (2.5.0-1) ... Setting up python3.11-minimal (3.11.2-6) ... Selecting previously unselected package python3-minimal. (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 ... 19920 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.2-1+b1_i386.deb ... Unpacking python3-minimal (3.11.2-1+b1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.0.0_all.deb ... Unpacking media-types (10.0.0) ... Selecting previously unselected package readline-common. Preparing to unpack .../2-readline-common_8.2-1.3_all.deb ... Unpacking readline-common (8.2-1.3) ... Selecting previously unselected package libreadline8:i386. Preparing to unpack .../3-libreadline8_8.2-1.3_i386.deb ... Unpacking libreadline8:i386 (8.2-1.3) ... Selecting previously unselected package libpython3.11-stdlib:i386. Preparing to unpack .../4-libpython3.11-stdlib_3.11.2-6_i386.deb ... Unpacking libpython3.11-stdlib:i386 (3.11.2-6) ... Selecting previously unselected package python3.11. Preparing to unpack .../5-python3.11_3.11.2-6_i386.deb ... Unpacking python3.11 (3.11.2-6) ... Selecting previously unselected package libpython3-stdlib:i386. Preparing to unpack .../6-libpython3-stdlib_3.11.2-1+b1_i386.deb ... Unpacking libpython3-stdlib:i386 (3.11.2-1+b1) ... Setting up python3-minimal (3.11.2-1+b1) ... Selecting previously unselected package python3. (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 ... 20354 files and directories currently installed.) Preparing to unpack .../python3_3.11.2-1+b1_i386.deb ... Unpacking python3 (3.11.2-1+b1) ... Selecting previously unselected package isa-support:i386. Preparing to unpack .../isa-support_15_i386.deb ... Unpacking isa-support:i386 (15) ... Setting up isa-support:i386 (15) ... Selecting previously unselected package sse2-support. (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 ... 20394 files and directories currently installed.) Preparing to unpack .../00-sse2-support_15_i386.deb ... Unpacking sse2-support (15) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.17+nmu1_all.deb ... Unpacking sensible-utils (0.0.17+nmu1) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../02-libmagic-mgc_1%3a5.44-3_i386.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:i386. Preparing to unpack .../03-libmagic1_1%3a5.44-3_i386.deb ... Unpacking libmagic1:i386 (1:5.44-3) ... Selecting previously unselected package file. Preparing to unpack .../04-file_1%3a5.44-3_i386.deb ... Unpacking file (1:5.44-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../05-gettext-base_0.21-12_i386.deb ... Unpacking gettext-base (0.21-12) ... Selecting previously unselected package libuchardet0:i386. Preparing to unpack .../06-libuchardet0_0.0.7-1_i386.deb ... Unpacking libuchardet0:i386 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../07-groff-base_1.22.4-10_i386.deb ... Unpacking groff-base (1.22.4-10) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../08-bsdextrautils_2.38.1-5+b1_i386.deb ... Unpacking bsdextrautils (2.38.1-5+b1) ... Selecting previously unselected package libpipeline1:i386. Preparing to unpack .../09-libpipeline1_1.5.7-1_i386.deb ... Unpacking libpipeline1:i386 (1.5.7-1) ... Selecting previously unselected package man-db. Preparing to unpack .../10-man-db_2.11.2-2_i386.deb ... Unpacking man-db (2.11.2-2) ... Selecting previously unselected package m4. Preparing to unpack .../11-m4_1.4.19-3_i386.deb ... Unpacking m4 (1.4.19-3) ... Selecting previously unselected package autoconf. Preparing to unpack .../12-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../13-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../14-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../15-autopoint_0.21-12_all.deb ... Unpacking autopoint (0.21-12) ... Selecting previously unselected package libbrotli1:i386. Preparing to unpack .../16-libbrotli1_1.0.9-2+b6_i386.deb ... Unpacking libbrotli1:i386 (1.0.9-2+b6) ... Selecting previously unselected package libsasl2-modules-db:i386. Preparing to unpack .../17-libsasl2-modules-db_2.1.28+dfsg-10_i386.deb ... Unpacking libsasl2-modules-db:i386 (2.1.28+dfsg-10) ... Selecting previously unselected package libsasl2-2:i386. Preparing to unpack .../18-libsasl2-2_2.1.28+dfsg-10_i386.deb ... Unpacking libsasl2-2:i386 (2.1.28+dfsg-10) ... Selecting previously unselected package libldap-2.5-0:i386. Preparing to unpack .../19-libldap-2.5-0_2.5.13+dfsg-5_i386.deb ... Unpacking libldap-2.5-0:i386 (2.5.13+dfsg-5) ... Selecting previously unselected package libnghttp2-14:i386. Preparing to unpack .../20-libnghttp2-14_1.52.0-1_i386.deb ... Unpacking libnghttp2-14:i386 (1.52.0-1) ... Selecting previously unselected package libpsl5:i386. Preparing to unpack .../21-libpsl5_0.21.2-1_i386.deb ... Unpacking libpsl5:i386 (0.21.2-1) ... Selecting previously unselected package librtmp1:i386. Preparing to unpack .../22-librtmp1_2.4+20151223.gitfa8646d.1-2+b2_i386.deb ... Unpacking librtmp1:i386 (2.4+20151223.gitfa8646d.1-2+b2) ... Selecting previously unselected package libssh2-1:i386. Preparing to unpack .../23-libssh2-1_1.10.0-3+b1_i386.deb ... Unpacking libssh2-1:i386 (1.10.0-3+b1) ... Selecting previously unselected package libcurl3-gnutls:i386. Preparing to unpack .../24-libcurl3-gnutls_7.88.1-9_i386.deb ... Unpacking libcurl3-gnutls:i386 (7.88.1-9) ... Selecting previously unselected package libdeflate0:i386. Preparing to unpack .../25-libdeflate0_1.14-1_i386.deb ... Unpacking libdeflate0:i386 (1.14-1) ... Selecting previously unselected package libhtscodecs2:i386. Preparing to unpack .../26-libhtscodecs2_1.3.0-4_i386.deb ... Unpacking libhtscodecs2:i386 (1.3.0-4) ... Selecting previously unselected package libhts3:i386. Preparing to unpack .../27-libhts3_1.16+ds-3_i386.deb ... Unpacking libhts3:i386 (1.16+ds-3) ... Selecting previously unselected package bcftools. Preparing to unpack .../28-bcftools_1.16-1_i386.deb ... Unpacking bcftools (1.16-1) ... Selecting previously unselected package cython3. Preparing to unpack .../29-cython3_0.29.32-2+b1_i386.deb ... Unpacking cython3 (0.29.32-2+b1) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../30-libdebhelper-perl_13.11.4_all.deb ... Unpacking libdebhelper-perl (13.11.4) ... Selecting previously unselected package libtool. Preparing to unpack .../31-libtool_2.4.7-5_all.deb ... Unpacking libtool (2.4.7-5) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../32-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../33-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../34-libsub-override-perl_0.09-4_all.deb ... Unpacking libsub-override-perl (0.09-4) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../35-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../36-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libelf1:i386. Preparing to unpack .../37-libelf1_0.188-2.1_i386.deb ... Unpacking libelf1:i386 (0.188-2.1) ... Selecting previously unselected package dwz. Preparing to unpack .../38-dwz_0.15-1_i386.deb ... Unpacking dwz (0.15-1) ... Selecting previously unselected package libicu72:i386. Preparing to unpack .../39-libicu72_72.1-3_i386.deb ... Unpacking libicu72:i386 (72.1-3) ... Selecting previously unselected package libxml2:i386. Preparing to unpack .../40-libxml2_2.9.14+dfsg-1.2_i386.deb ... Unpacking libxml2:i386 (2.9.14+dfsg-1.2) ... Selecting previously unselected package gettext. Preparing to unpack .../41-gettext_0.21-12_i386.deb ... Unpacking gettext (0.21-12) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../42-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../43-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../44-debhelper_13.11.4_all.deb ... Unpacking debhelper (13.11.4) ... Selecting previously unselected package dh-exec. Preparing to unpack .../45-dh-exec_0.27_i386.deb ... Unpacking dh-exec (0.27) ... Selecting previously unselected package python3-lib2to3. Preparing to unpack .../46-python3-lib2to3_3.11.2-3_all.deb ... Unpacking python3-lib2to3 (3.11.2-3) ... Selecting previously unselected package python3-distutils. Preparing to unpack .../47-python3-distutils_3.11.2-3_all.deb ... Unpacking python3-distutils (3.11.2-3) ... Selecting previously unselected package dh-python. Preparing to unpack .../48-dh-python_5.20230130_all.deb ... Unpacking dh-python (5.20230130) ... Selecting previously unselected package libcurl4-gnutls-dev:i386. Preparing to unpack .../49-libcurl4-gnutls-dev_7.88.1-9_i386.deb ... Unpacking libcurl4-gnutls-dev:i386 (7.88.1-9) ... Selecting previously unselected package libdeflate-dev:i386. Preparing to unpack .../50-libdeflate-dev_1.14-1_i386.deb ... Unpacking libdeflate-dev:i386 (1.14-1) ... Selecting previously unselected package libexpat1-dev:i386. Preparing to unpack .../51-libexpat1-dev_2.5.0-1_i386.deb ... Unpacking libexpat1-dev:i386 (2.5.0-1) ... Selecting previously unselected package liblzma-dev:i386. Preparing to unpack .../52-liblzma-dev_5.4.1-0.2_i386.deb ... Unpacking liblzma-dev:i386 (5.4.1-0.2) ... Selecting previously unselected package zlib1g-dev:i386. Preparing to unpack .../53-zlib1g-dev_1%3a1.2.13.dfsg-1_i386.deb ... Unpacking zlib1g-dev:i386 (1:1.2.13.dfsg-1) ... Selecting previously unselected package libhts-dev:i386. Preparing to unpack .../54-libhts-dev_1.16+ds-3_i386.deb ... Unpacking libhts-dev:i386 (1.16+ds-3) ... Selecting previously unselected package libjs-jquery. Preparing to unpack .../55-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Selecting previously unselected package libjs-underscore. Preparing to unpack .../56-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Selecting previously unselected package libjs-sphinxdoc. Preparing to unpack .../57-libjs-sphinxdoc_5.3.0-4_all.deb ... Unpacking libjs-sphinxdoc (5.3.0-4) ... Selecting previously unselected package libncurses6:i386. Preparing to unpack .../58-libncurses6_6.4-2_i386.deb ... Unpacking libncurses6:i386 (6.4-2) ... Selecting previously unselected package libpython3.11:i386. Preparing to unpack .../59-libpython3.11_3.11.2-6_i386.deb ... Unpacking libpython3.11:i386 (3.11.2-6) ... Selecting previously unselected package libpython3.11-dev:i386. Preparing to unpack .../60-libpython3.11-dev_3.11.2-6_i386.deb ... Unpacking libpython3.11-dev:i386 (3.11.2-6) ... Selecting previously unselected package libpython3-dev:i386. Preparing to unpack .../61-libpython3-dev_3.11.2-1+b1_i386.deb ... Unpacking libpython3-dev:i386 (3.11.2-1+b1) ... Selecting previously unselected package libpython3-all-dev:i386. Preparing to unpack .../62-libpython3-all-dev_3.11.2-1+b1_i386.deb ... Unpacking libpython3-all-dev:i386 (3.11.2-1+b1) ... Selecting previously unselected package python3-all. Preparing to unpack .../63-python3-all_3.11.2-1+b1_i386.deb ... Unpacking python3-all (3.11.2-1+b1) ... Selecting previously unselected package python3.11-dev. Preparing to unpack .../64-python3.11-dev_3.11.2-6_i386.deb ... Unpacking python3.11-dev (3.11.2-6) ... Selecting previously unselected package python3-dev. Preparing to unpack .../65-python3-dev_3.11.2-1+b1_i386.deb ... Unpacking python3-dev (3.11.2-1+b1) ... Selecting previously unselected package python3-all-dev. Preparing to unpack .../66-python3-all-dev_3.11.2-1+b1_i386.deb ... Unpacking python3-all-dev (3.11.2-1+b1) ... Selecting previously unselected package python3-attr. Preparing to unpack .../67-python3-attr_22.2.0-1_all.deb ... Unpacking python3-attr (22.2.0-1) ... Selecting previously unselected package python3-iniconfig. Preparing to unpack .../68-python3-iniconfig_1.1.1-2_all.deb ... Unpacking python3-iniconfig (1.1.1-2) ... Selecting previously unselected package python3-more-itertools. Preparing to unpack .../69-python3-more-itertools_8.10.0-2_all.deb ... Unpacking python3-more-itertools (8.10.0-2) ... Selecting previously unselected package python3-packaging. Preparing to unpack .../70-python3-packaging_23.0-1_all.deb ... Unpacking python3-packaging (23.0-1) ... Selecting previously unselected package python3-pkg-resources. Preparing to unpack .../71-python3-pkg-resources_66.1.1-1_all.deb ... Unpacking python3-pkg-resources (66.1.1-1) ... Selecting previously unselected package python3-pluggy. Preparing to unpack .../72-python3-pluggy_1.0.0+repack-1_all.deb ... Unpacking python3-pluggy (1.0.0+repack-1) ... Selecting previously unselected package python3-py. Preparing to unpack .../73-python3-py_1.11.0-1_all.deb ... Unpacking python3-py (1.11.0-1) ... Selecting previously unselected package python3-pytest. Preparing to unpack .../74-python3-pytest_7.2.1-2_all.deb ... Unpacking python3-pytest (7.2.1-2) ... Selecting previously unselected package python3-setuptools. Preparing to unpack .../75-python3-setuptools_66.1.1-1_all.deb ... Unpacking python3-setuptools (66.1.1-1) ... Selecting previously unselected package samtools. Preparing to unpack .../76-samtools_1.16.1-1_i386.deb ... Unpacking samtools (1.16.1-1) ... Selecting previously unselected package tabix. Preparing to unpack .../77-tabix_1.16+ds-3_i386.deb ... Unpacking tabix (1.16+ds-3) ... Setting up libhtscodecs2:i386 (1.3.0-4) ... Setting up media-types (10.0.0) ... Setting up libpipeline1:i386 (1.5.7-1) ... Setting up libpsl5:i386 (0.21.2-1) ... Setting up libicu72:i386 (72.1-3) ... Setting up bsdextrautils (2.38.1-5+b1) ... Setting up libmagic-mgc (1:5.44-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.11.4) ... Setting up libbrotli1:i386 (1.0.9-2+b6) ... Setting up libnghttp2-14:i386 (1.52.0-1) ... Setting up libmagic1:i386 (1:5.44-3) ... Setting up libdeflate0:i386 (1.14-1) ... Setting up gettext-base (0.21-12) ... Setting up m4 (1.4.19-3) ... Setting up file (1:5.44-3) ... Setting up sse2-support (15) ... Setting up libsasl2-modules-db:i386 (2.1.28+dfsg-10) ... Setting up autotools-dev (20220109.1) ... Setting up libexpat1-dev:i386 (2.5.0-1) ... Setting up librtmp1:i386 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libncurses6:i386 (6.4-2) ... Setting up autopoint (0.21-12) ... Setting up libsasl2-2:i386 (2.1.28+dfsg-10) ... Setting up autoconf (2.71-3) ... Setting up liblzma-dev:i386 (5.4.1-0.2) ... Setting up zlib1g-dev:i386 (1:1.2.13.dfsg-1) ... Setting up sensible-utils (0.0.17+nmu1) ... Setting up libuchardet0:i386 (0.0.7-1) ... Setting up libsub-override-perl (0.09-4) ... Setting up libssh2-1:i386 (1.10.0-3+b1) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up libdeflate-dev:i386 (1.14-1) ... Setting up tabix (1.16+ds-3) ... Setting up libelf1:i386 (0.188-2.1) ... Setting up readline-common (8.2-1.3) ... Setting up libxml2:i386 (2.9.14+dfsg-1.2) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up gettext (0.21-12) ... Setting up libtool (2.4.7-5) ... Setting up libreadline8:i386 (8.2-1.3) ... Setting up libldap-2.5-0:i386 (2.5.13+dfsg-5) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libjs-sphinxdoc (5.3.0-4) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... Setting up groff-base (1.22.4-10) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpython3.11-stdlib:i386 (3.11.2-6) ... Setting up libcurl3-gnutls:i386 (7.88.1-9) ... Setting up libcurl4-gnutls-dev:i386 (7.88.1-9) ... Setting up man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libpython3-stdlib:i386 (3.11.2-1+b1) ... Setting up python3.11 (3.11.2-6) ... Setting up libhts3:i386 (1.16+ds-3) ... Setting up libpython3.11:i386 (3.11.2-6) ... Setting up bcftools (1.16-1) ... Setting up libhts-dev:i386 (1.16+ds-3) ... Setting up debhelper (13.11.4) ... Setting up python3 (3.11.2-1+b1) ... Setting up dh-exec (0.27) ... Setting up samtools (1.16.1-1) ... Setting up python3-packaging (23.0-1) ... Setting up libpython3.11-dev:i386 (3.11.2-6) ... Setting up cython3 (0.29.32-2+b1) ... Setting up python3-pluggy (1.0.0+repack-1) ... Setting up python3-lib2to3 (3.11.2-3) ... Setting up python3-pkg-resources (66.1.1-1) ... Setting up python3-distutils (3.11.2-3) ... Setting up dh-python (5.20230130) ... Setting up python3-more-itertools (8.10.0-2) ... Setting up python3-iniconfig (1.1.1-2) ... Setting up python3-attr (22.2.0-1) ... Setting up libpython3-dev:i386 (3.11.2-1+b1) ... Setting up python3-setuptools (66.1.1-1) ... Setting up python3-py (1.11.0-1) ... Setting up python3.11-dev (3.11.2-6) ... Setting up python3-pytest (7.2.1-2) ... Setting up python3-all (3.11.2-1+b1) ... Setting up libpython3-all-dev:i386 (3.11.2-1+b1) ... Setting up python3-dev (3.11.2-1+b1) ... Setting up python3-all-dev (3.11.2-1+b1) ... Processing triggers for libc-bin (2.36-9) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... usrmerge is already the newest version (35). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: user script /srv/workspace/pbuilder/29729/tmp/hooks/A99_set_merged_usr starting Re-configuring usrmerge... removed '/etc/unsupported-skip-usrmerge-conversion' The system has been successfully converted. I: user script /srv/workspace/pbuilder/29729/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/python-pysam-0.20.0+ds/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../python-pysam_0.20.0+ds-3_source.changes dpkg-buildpackage: info: source package python-pysam dpkg-buildpackage: info: source version 0.20.0+ds-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Nilesh Patra dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 debian/rules clean cd tests/pysam_data && /usr/bin/make clean make[1]: Verzeichnis „/build/python-pysam-0.20.0+ds/tests/pysam_data“ wird betreten rm -fr *.bai *.csi *.fai *.gzi *.pileup* [a-z]*.cram *.crai \ all.stamp *~ calDepth *.dSYM pysam_*.sam \ ex2.sam ex2.sam.gz ex1.sam ex1.fa.gz \ with_md.sam.gz \ *.fq.gz make[1]: Verzeichnis „/build/python-pysam-0.20.0+ds/tests/pysam_data“ wird verlassen cd tests/cbcf_data && /usr/bin/make clean make[1]: Verzeichnis „/build/python-pysam-0.20.0+ds/tests/cbcf_data“ wird betreten rm -f all.stamp *.gz *.tbi *.csi *.bcf make[1]: Verzeichnis „/build/python-pysam-0.20.0+ds/tests/cbcf_data“ wird verlassen find . -name "*.pyc" -delete find . -name "*.pyxbldc" -delete find . -name "tmp_*.bam" -delete find . -name "*.bai*" -delete find . -name "*.cram*" -delete find . -name "pysam_uncompressed.bam" -delete rm -rf tests/pysam_test_work \ tests/example_htslib.gtf.gz.tbi \ tests/log.txt \ tests/test.bam \ tests/_compile_test.c \ tests/pysam_ex2.sam \ tests/__pycache__ \ pysam/calignmentfile.c \ pysam/cbcf.c \ tests/GRCh38_full_analysis_set_plus_decoy_hla.fa.fai \ tests/pysam_data/ex1.fa.gz \ tests/pysam_data/ex1.fa.gz.gzi \ tests/pysam_data/ex1_csi.bam.csi rm -rf .pytest_cache/ dh clean --with python3 --buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Verzeichnis „/build/python-pysam-0.20.0+ds“ wird betreten dh_auto_clean I: pybuild base:240: python3.11 setup.py clean # pysam: cython is available - using cythonize if necessary # pysam: htslib mode is external # pysam: HTSLIB_CONFIGURE_OPTIONS=None running clean removing '/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build' (and everything under it) 'build/bdist.linux-i386' does not exist -- can't clean it 'build/scripts-3.11' does not exist -- can't clean it rm -f \ pysam/config.py \ pysam/config.h \ pysam/lib*.c \ samtools/config.h \ bcftools/config.h rm -rf pysam.egg-info make[1]: Verzeichnis „/build/python-pysam-0.20.0+ds“ wird verlassen dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary dh binary --with python3 --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild I: pybuild base:240: python3.11 setup.py config # pysam: cython is available - using cythonize if necessary # pysam: htslib mode is external # pysam: HTSLIB_CONFIGURE_OPTIONS=None running config dh_auto_build -O--buildsystem=pybuild I: pybuild base:240: /usr/bin/python3 setup.py build # pysam: cython is available - using cythonize if necessary # pysam: htslib mode is external # pysam: HTSLIB_CONFIGURE_OPTIONS=None running build running build_py creating /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/samtools.py -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/Pileup.py -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/config.py -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/version.py -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/__init__.py -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/utils.py -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/bcftools.py -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam creating /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include copying pysam/include/__init__.py -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include copying pysam/libcsamfile.pxd -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/libcfaidx.pxd -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/libctabixproxies.pxd -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/libchtslib.pxd -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/libcsamtools.pxd -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/libcalignmentfile.pxd -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/libcbcftools.pxd -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/libcalignedsegment.pxd -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/libcutils.pxd -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/libctabix.pxd -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/libcvcf.pxd -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/libcbcf.pxd -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/pysam_stream.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/htslib_util.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/version.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/cbcftools_util.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/pysam_util.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/csamtools_util.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/py.typed -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/libcbcf.pyi -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/libctabix.pyi -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/libcalignmentfile.pyi -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/libcfaidx.pyi -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/version.pyi -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/libcsamtools.pyi -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/libcalignedsegment.pyi -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/libcsamfile.pyi -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/libchtslib.pyi -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/libcbgzf.pyi -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/libcvcf.pyi -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/libcbcftools.pyi -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/libctabixproxies.pyi -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/libcutils.pyi -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam creating /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/bam_lpileup.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/bam_plbuf.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/stats_isize.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/config.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/tmp_file.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/sam_opts.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/bam_ampliconclip.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/consensus_pileup.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/samtools.pysam.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/bedidx.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/samtools.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/bam.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/splaysort.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/sample.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools creating /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/dbuf.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/HMM.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/variantkey.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/rbuf.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/call.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/gvcf.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/abuf.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/bcftools.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/config.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/khash_str2str.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/ploidy.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/hex.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/bam_sample.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/kheap.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/extsort.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/regidx.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/bam2bcf.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/mw.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/tsv2vcf.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/smpl_ilist.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/vcfbuf.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/kmin.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/dist.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/hclust.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/prob1.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/vcmp.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/convert.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/utlist.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/bin.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/filter.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/str_finder.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/bcftools.pysam.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/cols.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools running build_ext cythoning pysam/libchtslib.pyx to pysam/libchtslib.c /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/python-pysam-0.20.0+ds/pysam/libchtslib.pxd tree = Parsing.p_module(s, pxd, full_module_name) cythoning pysam/libcsamtools.pyx to pysam/libcsamtools.c /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/python-pysam-0.20.0+ds/pysam/libcsamtools.pxd tree = Parsing.p_module(s, pxd, full_module_name) cythoning pysam/libcbcftools.pyx to pysam/libcbcftools.c /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/python-pysam-0.20.0+ds/pysam/libcbcftools.pxd tree = Parsing.p_module(s, pxd, full_module_name) cythoning pysam/libcutils.pyx to pysam/libcutils.c /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/python-pysam-0.20.0+ds/pysam/libcutils.pxd tree = Parsing.p_module(s, pxd, full_module_name) cythoning pysam/libcalignmentfile.pyx to pysam/libcalignmentfile.c /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/python-pysam-0.20.0+ds/pysam/libcalignmentfile.pxd tree = Parsing.p_module(s, pxd, full_module_name) warning: pysam/libcalignmentfile.pyx:2573:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation warning: pysam/libcalignmentfile.pyx:2578:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation warning: pysam/libcalignmentfile.pyx:2583:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation warning: pysam/libcalignmentfile.pyx:2622:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation warning: pysam/libcalignmentfile.pyx:2627:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation warning: pysam/libcalignmentfile.pyx:2632:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation cythoning pysam/libcsamfile.pyx to pysam/libcsamfile.c /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/python-pysam-0.20.0+ds/pysam/libcsamfile.pxd tree = Parsing.p_module(s, pxd, full_module_name) cythoning pysam/libcalignedsegment.pyx to pysam/libcalignedsegment.c /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/python-pysam-0.20.0+ds/pysam/libcalignedsegment.pxd tree = Parsing.p_module(s, pxd, full_module_name) cythoning pysam/libctabix.pyx to pysam/libctabix.c /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/python-pysam-0.20.0+ds/pysam/libctabix.pxd tree = Parsing.p_module(s, pxd, full_module_name) cythoning pysam/libcfaidx.pyx to pysam/libcfaidx.c /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/python-pysam-0.20.0+ds/pysam/libcfaidx.pxd tree = Parsing.p_module(s, pxd, full_module_name) cythoning pysam/libcbcf.pyx to pysam/libcbcf.c /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/python-pysam-0.20.0+ds/pysam/libcbcf.pxd tree = Parsing.p_module(s, pxd, full_module_name) cythoning pysam/libcbgzf.pyx to pysam/libcbgzf.c /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/python-pysam-0.20.0+ds/pysam/libcbgzf.pyx tree = Parsing.p_module(s, pxd, full_module_name) cythoning pysam/libctabixproxies.pyx to pysam/libctabixproxies.c /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/python-pysam-0.20.0+ds/pysam/libctabixproxies.pxd tree = Parsing.p_module(s, pxd, full_module_name) cythoning pysam/libcvcf.pyx to pysam/libcvcf.c /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/python-pysam-0.20.0+ds/pysam/libcvcf.pxd tree = Parsing.p_module(s, pxd, full_module_name) warning: pysam/libcvcf.pyx:1083:27: Unreachable code building 'pysam.libchtslib' extension creating build creating build/temp.linux-i386-cpython-311 creating build/temp.linux-i386-cpython-311/pysam i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c pysam/htslib_util.c -o build/temp.linux-i386-cpython-311/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c pysam/libchtslib.c -o build/temp.linux-i386-cpython-311/pysam/libchtslib.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement i686-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i386-cpython-311/pysam/htslib_util.o build/temp.linux-i386-cpython-311/pysam/libchtslib.o -L/build/python-pysam-0.20.0+ds/pysam -L/usr/lib/i386-linux-gnu -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/usr/lib/i386-linux-gnu -lz -lhts -o /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libchtslib.cpython-311-i386-linux-gnu.so -Wl,-rpath,$ORIGIN creating samtools/samtools_config_vars.h for 'pysam.libcsamtools' extension building 'pysam.libcsamtools' extension creating build/temp.linux-i386-cpython-311/samtools creating build/temp.linux-i386-cpython-311/samtools/lz4 i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c pysam/libcsamtools.c -o build/temp.linux-i386-cpython-311/pysam/libcsamtools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c samtools/amplicon_stats.c.pysam.c -o build/temp.linux-i386-cpython-311/samtools/amplicon_stats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c samtools/bam.c.pysam.c -o build/temp.linux-i386-cpython-311/samtools/bam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c samtools/bam2depth.c.pysam.c -o build/temp.linux-i386-cpython-311/samtools/bam2depth.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c samtools/bam_addrprg.c.pysam.c -o build/temp.linux-i386-cpython-311/samtools/bam_addrprg.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c samtools/bam_ampliconclip.c.pysam.c -o build/temp.linux-i386-cpython-311/samtools/bam_ampliconclip.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c samtools/bam_aux.c.pysam.c -o build/temp.linux-i386-cpython-311/samtools/bam_aux.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c samtools/bam_cat.c.pysam.c -o build/temp.linux-i386-cpython-311/samtools/bam_cat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c samtools/bam_color.c.pysam.c -o build/temp.linux-i386-cpython-311/samtools/bam_color.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c samtools/bam_consensus.c.pysam.c -o build/temp.linux-i386-cpython-311/samtools/bam_consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c samtools/bam_fastq.c.pysam.c -o build/temp.linux-i386-cpython-311/samtools/bam_fastq.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c samtools/bam_flags.c.pysam.c -o build/temp.linux-i386-cpython-311/samtools/bam_flags.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c samtools/bam_import.c.pysam.c -o build/temp.linux-i386-cpython-311/samtools/bam_import.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c samtools/bam_index.c.pysam.c -o build/temp.linux-i386-cpython-311/samtools/bam_index.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c samtools/bam_lpileup.c.pysam.c -o build/temp.linux-i386-cpython-311/samtools/bam_lpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c samtools/bam_markdup.c.pysam.c -o build/temp.linux-i386-cpython-311/samtools/bam_markdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c samtools/bam_mate.c.pysam.c -o build/temp.linux-i386-cpython-311/samtools/bam_mate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c samtools/bam_md.c.pysam.c -o build/temp.linux-i386-cpython-311/samtools/bam_md.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c samtools/bam_plbuf.c.pysam.c -o build/temp.linux-i386-cpython-311/samtools/bam_plbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c samtools/bam_plcmd.c.pysam.c -o build/temp.linux-i386-cpython-311/samtools/bam_plcmd.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c samtools/bam_quickcheck.c.pysam.c -o build/temp.linux-i386-cpython-311/samtools/bam_quickcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c samtools/bam_reheader.c.pysam.c -o build/temp.linux-i386-cpython-311/samtools/bam_reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c samtools/bam_rmdup.c.pysam.c -o build/temp.linux-i386-cpython-311/samtools/bam_rmdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c samtools/bam_rmdupse.c.pysam.c -o build/temp.linux-i386-cpython-311/samtools/bam_rmdupse.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c samtools/bam_samples.c.pysam.c -o build/temp.linux-i386-cpython-311/samtools/bam_samples.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c samtools/bam_sort.c.pysam.c -o build/temp.linux-i386-cpython-311/samtools/bam_sort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c samtools/bam_split.c.pysam.c -o build/temp.linux-i386-cpython-311/samtools/bam_split.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c samtools/bam_stat.c.pysam.c -o build/temp.linux-i386-cpython-311/samtools/bam_stat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c samtools/bamshuf.c.pysam.c -o build/temp.linux-i386-cpython-311/samtools/bamshuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c samtools/bamtk.c.pysam.c -o build/temp.linux-i386-cpython-311/samtools/bamtk.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c samtools/bedcov.c.pysam.c -o build/temp.linux-i386-cpython-311/samtools/bedcov.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c samtools/bedidx.c.pysam.c -o build/temp.linux-i386-cpython-311/samtools/bedidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c samtools/consensus_pileup.c.pysam.c -o build/temp.linux-i386-cpython-311/samtools/consensus_pileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c samtools/coverage.c.pysam.c -o build/temp.linux-i386-cpython-311/samtools/coverage.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c samtools/cut_target.c.pysam.c -o build/temp.linux-i386-cpython-311/samtools/cut_target.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c samtools/dict.c.pysam.c -o build/temp.linux-i386-cpython-311/samtools/dict.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c samtools/faidx.c.pysam.c -o build/temp.linux-i386-cpython-311/samtools/faidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c samtools/lz4/lz4.c -o build/temp.linux-i386-cpython-311/samtools/lz4/lz4.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c samtools/padding.c.pysam.c -o build/temp.linux-i386-cpython-311/samtools/padding.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c samtools/phase.c.pysam.c -o build/temp.linux-i386-cpython-311/samtools/phase.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c samtools/reference.c.pysam.c -o build/temp.linux-i386-cpython-311/samtools/reference.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c samtools/sam_opts.c.pysam.c -o build/temp.linux-i386-cpython-311/samtools/sam_opts.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c samtools/sam_utils.c.pysam.c -o build/temp.linux-i386-cpython-311/samtools/sam_utils.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c samtools/sam_view.c.pysam.c -o build/temp.linux-i386-cpython-311/samtools/sam_view.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c samtools/sample.c.pysam.c -o build/temp.linux-i386-cpython-311/samtools/sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c samtools/samtools.pysam.c -o build/temp.linux-i386-cpython-311/samtools/samtools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c samtools/stats.c.pysam.c -o build/temp.linux-i386-cpython-311/samtools/stats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c samtools/stats_isize.c.pysam.c -o build/temp.linux-i386-cpython-311/samtools/stats_isize.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c samtools/tmp_file.c.pysam.c -o build/temp.linux-i386-cpython-311/samtools/tmp_file.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement i686-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i386-cpython-311/pysam/libcsamtools.o build/temp.linux-i386-cpython-311/samtools/amplicon_stats.c.pysam.o build/temp.linux-i386-cpython-311/samtools/bam.c.pysam.o build/temp.linux-i386-cpython-311/samtools/bam2depth.c.pysam.o build/temp.linux-i386-cpython-311/samtools/bam_addrprg.c.pysam.o build/temp.linux-i386-cpython-311/samtools/bam_ampliconclip.c.pysam.o build/temp.linux-i386-cpython-311/samtools/bam_aux.c.pysam.o build/temp.linux-i386-cpython-311/samtools/bam_cat.c.pysam.o build/temp.linux-i386-cpython-311/samtools/bam_color.c.pysam.o build/temp.linux-i386-cpython-311/samtools/bam_consensus.c.pysam.o build/temp.linux-i386-cpython-311/samtools/bam_fastq.c.pysam.o build/temp.linux-i386-cpython-311/samtools/bam_flags.c.pysam.o build/temp.linux-i386-cpython-311/samtools/bam_import.c.pysam.o build/temp.linux-i386-cpython-311/samtools/bam_index.c.pysam.o build/temp.linux-i386-cpython-311/samtools/bam_lpileup.c.pysam.o build/temp.linux-i386-cpython-311/samtools/bam_markdup.c.pysam.o build/temp.linux-i386-cpython-311/samtools/bam_mate.c.pysam.o build/temp.linux-i386-cpython-311/samtools/bam_md.c.pysam.o build/temp.linux-i386-cpython-311/samtools/bam_plbuf.c.pysam.o build/temp.linux-i386-cpython-311/samtools/bam_plcmd.c.pysam.o build/temp.linux-i386-cpython-311/samtools/bam_quickcheck.c.pysam.o build/temp.linux-i386-cpython-311/samtools/bam_reheader.c.pysam.o build/temp.linux-i386-cpython-311/samtools/bam_rmdup.c.pysam.o build/temp.linux-i386-cpython-311/samtools/bam_rmdupse.c.pysam.o build/temp.linux-i386-cpython-311/samtools/bam_samples.c.pysam.o build/temp.linux-i386-cpython-311/samtools/bam_sort.c.pysam.o build/temp.linux-i386-cpython-311/samtools/bam_split.c.pysam.o build/temp.linux-i386-cpython-311/samtools/bam_stat.c.pysam.o build/temp.linux-i386-cpython-311/samtools/bamshuf.c.pysam.o build/temp.linux-i386-cpython-311/samtools/bamtk.c.pysam.o build/temp.linux-i386-cpython-311/samtools/bedcov.c.pysam.o build/temp.linux-i386-cpython-311/samtools/bedidx.c.pysam.o build/temp.linux-i386-cpython-311/samtools/consensus_pileup.c.pysam.o build/temp.linux-i386-cpython-311/samtools/coverage.c.pysam.o build/temp.linux-i386-cpython-311/samtools/cut_target.c.pysam.o build/temp.linux-i386-cpython-311/samtools/dict.c.pysam.o build/temp.linux-i386-cpython-311/samtools/faidx.c.pysam.o build/temp.linux-i386-cpython-311/samtools/lz4/lz4.o build/temp.linux-i386-cpython-311/samtools/padding.c.pysam.o build/temp.linux-i386-cpython-311/samtools/phase.c.pysam.o build/temp.linux-i386-cpython-311/samtools/reference.c.pysam.o build/temp.linux-i386-cpython-311/samtools/sam_opts.c.pysam.o build/temp.linux-i386-cpython-311/samtools/sam_utils.c.pysam.o build/temp.linux-i386-cpython-311/samtools/sam_view.c.pysam.o build/temp.linux-i386-cpython-311/samtools/sample.c.pysam.o build/temp.linux-i386-cpython-311/samtools/samtools.pysam.o build/temp.linux-i386-cpython-311/samtools/stats.c.pysam.o build/temp.linux-i386-cpython-311/samtools/stats_isize.c.pysam.o build/temp.linux-i386-cpython-311/samtools/tmp_file.c.pysam.o -L/build/python-pysam-0.20.0+ds/pysam -L/usr/lib/i386-linux-gnu -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/usr/lib/i386-linux-gnu -lz -lhts -lchtslib.cpython-311-i386-linux-gnu -o /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libcsamtools.cpython-311-i386-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcbcftools' extension creating build/temp.linux-i386-cpython-311/bcftools i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c bcftools/HMM.c.pysam.c -o build/temp.linux-i386-cpython-311/bcftools/HMM.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c bcftools/abuf.c.pysam.c -o build/temp.linux-i386-cpython-311/bcftools/abuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c bcftools/bam2bcf.c.pysam.c -o build/temp.linux-i386-cpython-311/bcftools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c bcftools/bam2bcf_indel.c.pysam.c -o build/temp.linux-i386-cpython-311/bcftools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c bcftools/bam_sample.c.pysam.c -o build/temp.linux-i386-cpython-311/bcftools/bam_sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c bcftools/bcftools.pysam.c -o build/temp.linux-i386-cpython-311/bcftools/bcftools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c bcftools/bin.c.pysam.c -o build/temp.linux-i386-cpython-311/bcftools/bin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c bcftools/ccall.c.pysam.c -o build/temp.linux-i386-cpython-311/bcftools/ccall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c bcftools/cols.c.pysam.c -o build/temp.linux-i386-cpython-311/bcftools/cols.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c bcftools/consensus.c.pysam.c -o build/temp.linux-i386-cpython-311/bcftools/consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c bcftools/convert.c.pysam.c -o build/temp.linux-i386-cpython-311/bcftools/convert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c bcftools/csq.c.pysam.c -o build/temp.linux-i386-cpython-311/bcftools/csq.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c bcftools/dist.c.pysam.c -o build/temp.linux-i386-cpython-311/bcftools/dist.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c bcftools/em.c.pysam.c -o build/temp.linux-i386-cpython-311/bcftools/em.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c bcftools/extsort.c.pysam.c -o build/temp.linux-i386-cpython-311/bcftools/extsort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c bcftools/filter.c.pysam.c -o build/temp.linux-i386-cpython-311/bcftools/filter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c bcftools/gvcf.c.pysam.c -o build/temp.linux-i386-cpython-311/bcftools/gvcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c bcftools/hclust.c.pysam.c -o build/temp.linux-i386-cpython-311/bcftools/hclust.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c bcftools/kmin.c.pysam.c -o build/temp.linux-i386-cpython-311/bcftools/kmin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c bcftools/main.c.pysam.c -o build/temp.linux-i386-cpython-311/bcftools/main.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c bcftools/mcall.c.pysam.c -o build/temp.linux-i386-cpython-311/bcftools/mcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c bcftools/mpileup.c.pysam.c -o build/temp.linux-i386-cpython-311/bcftools/mpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c bcftools/ploidy.c.pysam.c -o build/temp.linux-i386-cpython-311/bcftools/ploidy.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c bcftools/prob1.c.pysam.c -o build/temp.linux-i386-cpython-311/bcftools/prob1.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c bcftools/regidx.c.pysam.c -o build/temp.linux-i386-cpython-311/bcftools/regidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c bcftools/reheader.c.pysam.c -o build/temp.linux-i386-cpython-311/bcftools/reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c bcftools/smpl_ilist.c.pysam.c -o build/temp.linux-i386-cpython-311/bcftools/smpl_ilist.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c bcftools/str_finder.c.pysam.c -o build/temp.linux-i386-cpython-311/bcftools/str_finder.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c bcftools/tabix.c.pysam.c -o build/temp.linux-i386-cpython-311/bcftools/tabix.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c bcftools/tsv2vcf.c.pysam.c -o build/temp.linux-i386-cpython-311/bcftools/tsv2vcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c bcftools/vcfannotate.c.pysam.c -o build/temp.linux-i386-cpython-311/bcftools/vcfannotate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c bcftools/vcfbuf.c.pysam.c -o build/temp.linux-i386-cpython-311/bcftools/vcfbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c bcftools/vcfcall.c.pysam.c -o build/temp.linux-i386-cpython-311/bcftools/vcfcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c bcftools/vcfcnv.c.pysam.c -o build/temp.linux-i386-cpython-311/bcftools/vcfcnv.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c bcftools/vcfconcat.c.pysam.c -o build/temp.linux-i386-cpython-311/bcftools/vcfconcat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c bcftools/vcfconvert.c.pysam.c -o build/temp.linux-i386-cpython-311/bcftools/vcfconvert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c bcftools/vcffilter.c.pysam.c -o build/temp.linux-i386-cpython-311/bcftools/vcffilter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c bcftools/vcfgtcheck.c.pysam.c -o build/temp.linux-i386-cpython-311/bcftools/vcfgtcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c bcftools/vcfhead.c.pysam.c -o build/temp.linux-i386-cpython-311/bcftools/vcfhead.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c bcftools/vcfindex.c.pysam.c -o build/temp.linux-i386-cpython-311/bcftools/vcfindex.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c bcftools/vcfisec.c.pysam.c -o build/temp.linux-i386-cpython-311/bcftools/vcfisec.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c bcftools/vcfmerge.c.pysam.c -o build/temp.linux-i386-cpython-311/bcftools/vcfmerge.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement bcftools/vcfmerge.c.pysam.c: In function ‘maux_init’: bcftools/vcfmerge.c.pysam.c:751:34: warning: argument 1 range [2147483648, 4294967295] exceeds maximum object size 2147483647 [-Walloc-size-larger-than=] 751 | ma->gvcf = (gvcf_aux_t*) calloc(ma->n,sizeof(gvcf_aux_t)); // -Walloc-size-larger-than gives a harmless warning caused by signed integer ma->n | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/htslib/kstring.h:30, from /usr/include/htslib/hts.h:37, from /usr/include/htslib/vcf.h:39, from bcftools/vcfmerge.c.pysam.c:35: /usr/include/stdlib.h:556:14: note: in a call to allocation function ‘calloc’ declared here 556 | extern void *calloc (size_t __nmemb, size_t __size) | ^~~~~~ i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c bcftools/vcfnorm.c.pysam.c -o build/temp.linux-i386-cpython-311/bcftools/vcfnorm.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c bcftools/vcfplugin.c.pysam.c -o build/temp.linux-i386-cpython-311/bcftools/vcfplugin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c bcftools/vcfquery.c.pysam.c -o build/temp.linux-i386-cpython-311/bcftools/vcfquery.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c bcftools/vcfroh.c.pysam.c -o build/temp.linux-i386-cpython-311/bcftools/vcfroh.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c bcftools/vcfsom.c.pysam.c -o build/temp.linux-i386-cpython-311/bcftools/vcfsom.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c bcftools/vcfsort.c.pysam.c -o build/temp.linux-i386-cpython-311/bcftools/vcfsort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c bcftools/vcfstats.c.pysam.c -o build/temp.linux-i386-cpython-311/bcftools/vcfstats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c bcftools/vcfview.c.pysam.c -o build/temp.linux-i386-cpython-311/bcftools/vcfview.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c bcftools/vcmp.c.pysam.c -o build/temp.linux-i386-cpython-311/bcftools/vcmp.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c bcftools/version.c.pysam.c -o build/temp.linux-i386-cpython-311/bcftools/version.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c pysam/libcbcftools.c -o build/temp.linux-i386-cpython-311/pysam/libcbcftools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement i686-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i386-cpython-311/bcftools/HMM.c.pysam.o build/temp.linux-i386-cpython-311/bcftools/abuf.c.pysam.o build/temp.linux-i386-cpython-311/bcftools/bam2bcf.c.pysam.o build/temp.linux-i386-cpython-311/bcftools/bam2bcf_indel.c.pysam.o build/temp.linux-i386-cpython-311/bcftools/bam_sample.c.pysam.o build/temp.linux-i386-cpython-311/bcftools/bcftools.pysam.o build/temp.linux-i386-cpython-311/bcftools/bin.c.pysam.o build/temp.linux-i386-cpython-311/bcftools/ccall.c.pysam.o build/temp.linux-i386-cpython-311/bcftools/cols.c.pysam.o build/temp.linux-i386-cpython-311/bcftools/consensus.c.pysam.o build/temp.linux-i386-cpython-311/bcftools/convert.c.pysam.o build/temp.linux-i386-cpython-311/bcftools/csq.c.pysam.o build/temp.linux-i386-cpython-311/bcftools/dist.c.pysam.o build/temp.linux-i386-cpython-311/bcftools/em.c.pysam.o build/temp.linux-i386-cpython-311/bcftools/extsort.c.pysam.o build/temp.linux-i386-cpython-311/bcftools/filter.c.pysam.o build/temp.linux-i386-cpython-311/bcftools/gvcf.c.pysam.o build/temp.linux-i386-cpython-311/bcftools/hclust.c.pysam.o build/temp.linux-i386-cpython-311/bcftools/kmin.c.pysam.o build/temp.linux-i386-cpython-311/bcftools/main.c.pysam.o build/temp.linux-i386-cpython-311/bcftools/mcall.c.pysam.o build/temp.linux-i386-cpython-311/bcftools/mpileup.c.pysam.o build/temp.linux-i386-cpython-311/bcftools/ploidy.c.pysam.o build/temp.linux-i386-cpython-311/bcftools/prob1.c.pysam.o build/temp.linux-i386-cpython-311/bcftools/regidx.c.pysam.o build/temp.linux-i386-cpython-311/bcftools/reheader.c.pysam.o build/temp.linux-i386-cpython-311/bcftools/smpl_ilist.c.pysam.o build/temp.linux-i386-cpython-311/bcftools/str_finder.c.pysam.o build/temp.linux-i386-cpython-311/bcftools/tabix.c.pysam.o build/temp.linux-i386-cpython-311/bcftools/tsv2vcf.c.pysam.o build/temp.linux-i386-cpython-311/bcftools/vcfannotate.c.pysam.o build/temp.linux-i386-cpython-311/bcftools/vcfbuf.c.pysam.o build/temp.linux-i386-cpython-311/bcftools/vcfcall.c.pysam.o build/temp.linux-i386-cpython-311/bcftools/vcfcnv.c.pysam.o build/temp.linux-i386-cpython-311/bcftools/vcfconcat.c.pysam.o build/temp.linux-i386-cpython-311/bcftools/vcfconvert.c.pysam.o build/temp.linux-i386-cpython-311/bcftools/vcffilter.c.pysam.o build/temp.linux-i386-cpython-311/bcftools/vcfgtcheck.c.pysam.o build/temp.linux-i386-cpython-311/bcftools/vcfhead.c.pysam.o build/temp.linux-i386-cpython-311/bcftools/vcfindex.c.pysam.o build/temp.linux-i386-cpython-311/bcftools/vcfisec.c.pysam.o build/temp.linux-i386-cpython-311/bcftools/vcfmerge.c.pysam.o build/temp.linux-i386-cpython-311/bcftools/vcfnorm.c.pysam.o build/temp.linux-i386-cpython-311/bcftools/vcfplugin.c.pysam.o build/temp.linux-i386-cpython-311/bcftools/vcfquery.c.pysam.o build/temp.linux-i386-cpython-311/bcftools/vcfroh.c.pysam.o build/temp.linux-i386-cpython-311/bcftools/vcfsom.c.pysam.o build/temp.linux-i386-cpython-311/bcftools/vcfsort.c.pysam.o build/temp.linux-i386-cpython-311/bcftools/vcfstats.c.pysam.o build/temp.linux-i386-cpython-311/bcftools/vcfview.c.pysam.o build/temp.linux-i386-cpython-311/bcftools/vcmp.c.pysam.o build/temp.linux-i386-cpython-311/bcftools/version.c.pysam.o build/temp.linux-i386-cpython-311/pysam/libcbcftools.o -L/build/python-pysam-0.20.0+ds/pysam -L/usr/lib/i386-linux-gnu -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/usr/lib/i386-linux-gnu -lz -lhts -lchtslib.cpython-311-i386-linux-gnu -o /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libcbcftools.cpython-311-i386-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcutils' extension i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c pysam/libcutils.c -o build/temp.linux-i386-cpython-311/pysam/libcutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c pysam/pysam_util.c -o build/temp.linux-i386-cpython-311/pysam/pysam_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement i686-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i386-cpython-311/pysam/libcutils.o build/temp.linux-i386-cpython-311/pysam/pysam_util.o -L/build/python-pysam-0.20.0+ds/pysam -L/usr/lib/i386-linux-gnu -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/usr/lib/i386-linux-gnu -lz -lhts -lchtslib.cpython-311-i386-linux-gnu -lcsamtools.cpython-311-i386-linux-gnu -lcbcftools.cpython-311-i386-linux-gnu -o /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libcutils.cpython-311-i386-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcalignmentfile' extension i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c pysam/libcalignmentfile.c -o build/temp.linux-i386-cpython-311/pysam/libcalignmentfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libcalignmentfile.c: In function ‘__pyx_f_5pysam_17libcalignmentfile_20IteratorRowSelection_cnext’: pysam/libcalignmentfile.c:28511:16: warning: ignoring return value of ‘bgzf_seek’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 28511 | (void)(bgzf_seek(hts_get_bgzfp(__pyx_v_self->__pyx_base.htsfile), __pyx_v_pos, 0)); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/libcalignmentfile.c: In function ‘__pyx_pf_5pysam_17libcalignmentfile_13AlignmentFile_6_open’: pysam/libcalignmentfile.c:14228:20: warning: ignoring return value of ‘sam_hdr_write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14228 | (void)(sam_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_hdr)); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i386-cpython-311/pysam/libcalignmentfile.o -L/build/python-pysam-0.20.0+ds/pysam -L/usr/lib/i386-linux-gnu -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/usr/lib/i386-linux-gnu -lz -lhts -lchtslib.cpython-311-i386-linux-gnu -lcutils.cpython-311-i386-linux-gnu -o /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libcalignmentfile.cpython-311-i386-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcsamfile' extension i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c pysam/libcsamfile.c -o build/temp.linux-i386-cpython-311/pysam/libcsamfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement i686-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i386-cpython-311/pysam/libcsamfile.o -L/build/python-pysam-0.20.0+ds/pysam -L/usr/lib/i386-linux-gnu -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/usr/lib/i386-linux-gnu -lz -lhts -lchtslib.cpython-311-i386-linux-gnu -lcutils.cpython-311-i386-linux-gnu -o /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libcsamfile.cpython-311-i386-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcalignedsegment' extension i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c pysam/libcalignedsegment.c -o build/temp.linux-i386-cpython-311/pysam/libcalignedsegment.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libcalignedsegment.c: In function ‘__pyx_pf_5pysam_18libcalignedsegment_14AlignedSegment_18fromstring’: pysam/libcalignedsegment.c:14652:10: warning: ignoring return value of ‘sam_parse1’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14652 | (void)(sam_parse1((&__pyx_v_line), __pyx_v_dest->header->ptr, __pyx_v_dest->_delegate)); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i386-cpython-311/pysam/libcalignedsegment.o -L/build/python-pysam-0.20.0+ds/pysam -L/usr/lib/i386-linux-gnu -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/usr/lib/i386-linux-gnu -lz -lhts -lchtslib.cpython-311-i386-linux-gnu -lcutils.cpython-311-i386-linux-gnu -o /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libcalignedsegment.cpython-311-i386-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libctabix' extension i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c pysam/libctabix.c -o build/temp.linux-i386-cpython-311/pysam/libctabix.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement i686-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i386-cpython-311/pysam/libctabix.o -L/build/python-pysam-0.20.0+ds/pysam -L/usr/lib/i386-linux-gnu -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/usr/lib/i386-linux-gnu -lz -lhts -lchtslib.cpython-311-i386-linux-gnu -lcutils.cpython-311-i386-linux-gnu -o /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libctabix.cpython-311-i386-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcfaidx' extension i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c pysam/libcfaidx.c -o build/temp.linux-i386-cpython-311/pysam/libcfaidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement i686-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i386-cpython-311/pysam/libcfaidx.o -L/build/python-pysam-0.20.0+ds/pysam -L/usr/lib/i386-linux-gnu -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/usr/lib/i386-linux-gnu -lz -lhts -lchtslib.cpython-311-i386-linux-gnu -lcutils.cpython-311-i386-linux-gnu -o /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libcfaidx.cpython-311-i386-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcbcf' extension i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c pysam/libcbcf.c -o build/temp.linux-i386-cpython-311/pysam/libcbcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libcbcf.c: In function ‘__pyx_pf_5pysam_7libcbcf_11VariantFile_6close’: pysam/libcbcf.c:68189:18: warning: ignoring return value of ‘bcf_hdr_write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 68189 | (void)(bcf_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_self->header->ptr)); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/libcbcf.c: In function ‘__pyx_pf_5pysam_7libcbcf_11VariantFile_4__dealloc__’: pysam/libcbcf.c:67914:18: warning: ignoring return value of ‘bcf_hdr_write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 67914 | (void)(bcf_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_self->header->ptr)); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/libcbcf.c: In function ‘__pyx_f_5pysam_7libcbcf_11VariantFile_write’: pysam/libcbcf.c:73032:18: warning: ignoring return value of ‘bcf_hdr_write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 73032 | (void)(bcf_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_self->header->ptr)); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/libcbcf.c: In function ‘__pyx_pf_5pysam_7libcbcf_13VariantHeader_20add_meta’: pysam/libcbcf.c:35496:11: warning: ignoring return value of ‘bcf_hrec_add_key’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 35496 | bcf_hrec_add_key(__pyx_v_hrec, __pyx_t_17, ((int)__pyx_t_18)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/libcbcf.c:35522:11: warning: ignoring return value of ‘bcf_hrec_set_val’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 35522 | bcf_hrec_set_val(__pyx_v_hrec, (__pyx_v_hrec->nkeys - 1), __pyx_t_19, ((int)__pyx_t_18), __pyx_v_quoted); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i386-cpython-311/pysam/libcbcf.o -L/build/python-pysam-0.20.0+ds/pysam -L/usr/lib/i386-linux-gnu -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/usr/lib/i386-linux-gnu -lz -lhts -lchtslib.cpython-311-i386-linux-gnu -lcutils.cpython-311-i386-linux-gnu -o /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libcbcf.cpython-311-i386-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcbgzf' extension i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c pysam/libcbgzf.c -o build/temp.linux-i386-cpython-311/pysam/libcbgzf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement i686-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i386-cpython-311/pysam/libcbgzf.o -L/build/python-pysam-0.20.0+ds/pysam -L/usr/lib/i386-linux-gnu -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/usr/lib/i386-linux-gnu -lz -lhts -lchtslib.cpython-311-i386-linux-gnu -lcutils.cpython-311-i386-linux-gnu -o /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libcbgzf.cpython-311-i386-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libctabixproxies' extension i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c pysam/libctabixproxies.c -o build/temp.linux-i386-cpython-311/pysam/libctabixproxies.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement i686-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i386-cpython-311/pysam/libctabixproxies.o -L/build/python-pysam-0.20.0+ds/pysam -L/usr/lib/i386-linux-gnu -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/usr/lib/i386-linux-gnu -lz -lhts -lchtslib.cpython-311-i386-linux-gnu -lcutils.cpython-311-i386-linux-gnu -o /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libctabixproxies.cpython-311-i386-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcvcf' extension i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/python-pysam-0.20.0+ds/pysam -I/usr/include -I/build/python-pysam-0.20.0+ds/samtools -I/build/python-pysam-0.20.0+ds/samtools/lz4 -I/build/python-pysam-0.20.0+ds/bcftools -I/build/python-pysam-0.20.0+ds -I/usr/include/python3.11 -c pysam/libcvcf.c -o build/temp.linux-i386-cpython-311/pysam/libcvcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libcvcf.c: In function ‘__pyx_pf_5pysam_7libcvcf_3VCF_32parse_data.constprop’: pysam/libcvcf.c:25229:16: warning: ‘__pyx_v_qual’ may be used uninitialized [-Wmaybe-uninitialized] 25229 | __pyx_t_12 = PyFloat_FromDouble(__pyx_v_qual); if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 873, __pyx_L1_error) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/libcvcf.c:19949:10: note: ‘__pyx_v_qual’ was declared here 19949 | double __pyx_v_qual; | ^~~~~~~~~~~~ i686-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i386-cpython-311/pysam/libcvcf.o -L/build/python-pysam-0.20.0+ds/pysam -L/usr/lib/i386-linux-gnu -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/usr/lib/i386-linux-gnu -lz -lhts -lchtslib.cpython-311-i386-linux-gnu -lcutils.cpython-311-i386-linux-gnu -o /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libcvcf.cpython-311-i386-linux-gnu.so -Wl,-rpath,$ORIGIN debian/rules override_dh_auto_test make[1]: Verzeichnis „/build/python-pysam-0.20.0+ds“ wird betreten cd tests/pysam_data && /usr/bin/make all make[2]: Verzeichnis „/build/python-pysam-0.20.0+ds/tests/pysam_data“ wird betreten samtools faidx ex1.fa samtools view --no-PG -bo ex1.bam -t ex1.fa.fai ex1.sam.gz samtools mpileup -f ex1.fa ex1.bam | gzip > ex1.pileup.gz [mpileup] 1 samples in 1 input files gunzip < ex1.sam.gz > ex1.sam samtools index ex1.bam samtools view --no-PG -h ex1.bam | gzip > ex2.sam.gz gunzip < ex2.sam.gz > ex2.sam samtools view --no-PG -bo ex2.bam ex2.sam samtools index ex2.bam samtools calmd --no-PG --output-fmt BAM ex2.bam ex1.fa > with_md.sam.gz [bam_fillmd1] different NM for read 'EAS139_11:7:46:695:738': 3 -> 8 [bam_fillmd1] different NM for read 'EAS218_4:1:48:9:409': 0 -> 5 [bam_fillmd1] different NM for read 'B7_591:7:200:192:373': 0 -> 5 [bam_fillmd1] different NM for read 'EAS56_65:1:163:846:223': 0 -> 5 [bam_fillmd1] different NM for read 'EAS114_30:7:283:799:560': 0 -> 5 [bam_fillmd1] different NM for read 'B7_595:4:84:802:737': 0 -> 4 [bam_fillmd1] different NM for read 'EAS51_66:5:308:400:602': 0 -> 3 [bam_fillmd1] different NM for read 'EAS54_81:2:285:367:932': 0 -> 3 [bam_fillmd1] different NM for read 'EAS114_39:1:70:147:84': 0 -> 3 [bam_fillmd1] different NM for read 'EAS56_53:1:124:243:35': 2 -> 5 [bam_fillmd1] different NM for read 'EAS1_103:2:226:302:758': 2 -> 3 [bam_fillmd1] different NM for read 'EAS114_28:6:175:705:982': 1 -> 0 [bam_fillmd1] different NM for read 'EAS51_64:4:179:389:585': 7 -> 8 [bam_fillmd1] different NM for read 'B7_589:1:122:337:968': 3 -> 2 [bam_fillmd1] different NM for read 'B7_610:4:15:805:420': 4 -> 5 [bam_fillmd1] different NM for read 'B7_591:2:279:124:41': 2 -> 4 [bam_fillmd1] different NM for read 'EAS112_32:8:89:254:332': 0 -> 1 [bam_fillmd1] different NM for read 'B7_597:7:103:731:697': 0 -> 2 [bam_fillmd1] different NM for read 'EAS139_11:2:71:83:58': 0 -> 2 [bam_fillmd1] different NM for read 'EAS192_3:4:63:5:870': 0 -> 2 [bam_fillmd1] different NM for read 'EAS139_19:2:29:1822:1881': 0 -> 2 [bam_fillmd1] different NM for read 'EAS188_7:3:15:568:42': 2 -> 1 [bam_fillmd1] different NM for read 'EAS1_95:4:176:971:874': 0 -> 1 [bam_fillmd1] different NM for read 'EAS1_99:1:34:649:318': 3 -> 4 [bam_fillmd1] different NM for read 'EAS54_65:4:61:346:384': 3 -> 4 [bam_fillmd1] different NM for read 'B7_597:6:20:592:496': 0 -> 1 [bam_fillmd1] different NM for read 'B7_597:4:38:999:463': 2 -> 1 [bam_fillmd1] different NM for read 'EAS114_28:5:23:944:377': 0 -> 3 [bam_fillmd1] different NM for read 'EAS219_1:3:90:219:528': 0 -> 3 [bam_fillmd1] different NM for read 'EAS1_108:5:89:942:84': 0 -> 4 [bam_fillmd1] different NM for read 'EAS1_108:6:159:493:275': 0 -> 5 [bam_fillmd1] different NM for read 'EAS139_11:1:81:1019:558': 0 -> 5 [bam_fillmd1] different NM for read 'EAS51_62:7:162:195:761': 0 -> 4 [bam_fillmd1] different NM for read 'B7_597:3:115:646:430': 0 -> 4 [bam_fillmd1] different NM for read 'EAS114_30:6:243:209:110': 0 -> 4 [bam_fillmd1] different NM for read 'EAS1_108:2:266:994:429': 0 -> 4 [bam_fillmd1] different NM for read 'EAS114_30:5:32:461:154': 0 -> 4 [bam_fillmd1] different NM for read 'EAS114_39:6:7:492:1088': 0 -> 4 [bam_fillmd1] different NM for read 'EAS1_95:6:174:650:125': 0 -> 4 [bam_fillmd1] different NM for read 'EAS56_59:6:89:457:591': 1 -> 5 [bam_fillmd1] different NM for read 'EAS114_39:2:38:670:564': 0 -> 4 [bam_fillmd1] different NM for read 'EAS188_7:4:92:693:228': 1 -> 6 [bam_fillmd1] different NM for read 'EAS218_1:4:61:1369:440': 0 -> 4 [bam_fillmd1] different NM for read 'EAS114_26:4:123:1001:580': 0 -> 4 [bam_fillmd1] different NM for read 'EAS114_39:4:10:1312:1558': 0 -> 4 [bam_fillmd1] different NM for read 'EAS220_1:8:45:178:1321': 0 -> 4 [bam_fillmd1] different NM for read 'EAS56_59:5:125:137:58': 0 -> 4 [bam_fillmd1] different NM for read 'EAS192_3:3:285:349:797': 1 -> 5 [bam_fillmd1] different NM for read 'EAS114_45:5:56:1757:1319': 0 -> 4 [bam_fillmd1] different NM for read 'B7_591:3:291:404:199': 0 -> 4 [bam_fillmd1] different NM for read 'EAS54_65:7:159:253:353': 0 -> 4 [bam_fillmd1] different NM for read 'EAS56_57:1:122:38:103': 0 -> 4 [bam_fillmd1] different NM for read 'EAS188_4:5:103:870:105': 0 -> 4 [bam_fillmd1] different NM for read 'EAS1_105:8:24:718:322': 3 -> 7 [bam_fillmd1] different NM for read 'EAS51_64:6:118:41:489': 0 -> 4 [bam_fillmd1] different NM for read 'EAS56_61:3:165:665:220': 0 -> 4 [bam_fillmd1] different NM for read 'EAS114_30:6:238:803:383': 0 -> 4 [bam_fillmd1] different NM for read 'EAS1_105:3:232:364:583': 0 -> 3 [bam_fillmd1] different NM for read 'B7_595:2:29:729:70': 3 -> 4 [bam_fillmd1] different NM for read 'EAS114_30:6:220:809:850': 4 -> 6 [bam_fillmd1] different NM for read 'EAS54_65:2:264:157:150': 3 -> 5 [bam_fillmd1] different NM for read 'B7_595:8:26:242:35': 2 -> 1 [bam_fillmd1] different NM for read 'B7_610:7:34:144:868': 4 -> 5 [bam_fillmd1] different NM for read 'B7_597:8:147:360:141': 1 -> 2 [bam_fillmd1] different NM for read 'EAS139_19:2:82:154:1333': 0 -> 4 [bam_fillmd1] different NM for read 'EAS56_63:3:41:468:459': 0 -> 3 [bam_fillmd1] different NM for read 'EAS1_97:4:274:287:423': 0 -> 1 [bam_fillmd1] different NM for read 'EAS114_30:2:303:428:326': 0 -> 1 [bam_fillmd1] different NM for read 'EAS54_71:8:105:854:975': 0 -> 3 gunzip < with_md.sam.gz > with_md.sam samtools view --no-PG -bo with_md.bam with_md.sam [W::bam_hdr_read] EOF marker is absent. The input is probably truncated samtools index with_md.bam samtools view --no-PG -bu -o uncompressed.bam ex2.sam samtools view --no-PG -bo MM-chebi.bam MM-chebi.sam samtools view --no-PG -bo MM-double.bam MM-double.sam samtools view --no-PG -bo MM-multi.bam MM-multi.sam samtools view --no-PG -bo MM-orient.bam MM-orient.sam samtools view --no-PG -bo ex10.bam ex10.sam samtools view --no-PG -bo ex3.bam ex3.sam samtools view --no-PG -bo ex4.bam ex4.sam samtools view --no-PG -bo ex5.bam ex5.sam samtools view --no-PG -bo ex6.bam ex6.sam samtools view --no-PG -bo ex8.bam ex8.sam samtools view --no-PG -bo ex9_fail.bam ex9_fail.sam samtools view --no-PG -bo ex9_nofail.bam ex9_nofail.sam samtools view --no-PG -bo ex_spliced.bam ex_spliced.sam samtools view --no-PG -bo example_aligned_pairs.bam example_aligned_pairs.sam samtools view --no-PG -bo example_btag.bam example_btag.sam samtools view --no-PG -bo example_dash_in_chr.bam example_dash_in_chr.sam samtools view --no-PG -bo example_empty_header.bam example_empty_header.sam samtools view --no-PG -bo example_empty_with_header.bam example_empty_with_header.sam samtools view --no-PG -bo example_reverse_complement.bam example_reverse_complement.sam touch tmp.list samtools view --no-PG -bo example_unmapped_reads_no_sq.bam -t tmp.list example_unmapped_reads_no_sq.sam rm -f tmp.list samtools view --no-PG -bo issue100.bam issue100.sam samtools view --no-PG -bo rg_with_tab.bam rg_with_tab.sam samtools view --no-PG -bo softclip.bam softclip.sam samtools view --no-PG -bo tag_bug.bam tag_bug.sam samtools view --no-PG -bo test_mapped_unmapped.bam test_mapped_unmapped.sam samtools view --no-PG -bo test_query_position.bam test_query_position.sam samtools view --no-PG -bo test_unaligned.bam test_unaligned.sam samtools index MM-chebi.bam samtools index MM-double.bam samtools index MM-multi.bam samtools index MM-orient.bam samtools index ex10.bam samtools index ex3.bam samtools index ex4.bam samtools index ex5.bam samtools index ex6.bam samtools index ex8.bam samtools index ex9_fail.bam samtools index ex9_nofail.bam samtools index ex_spliced.bam samtools index example_aligned_pairs.bam samtools index example_btag.bam samtools index example_dash_in_chr.bam samtools index example_empty_header.bam samtools index example_empty_with_header.bam samtools index example_reverse_complement.bam samtools index example_unmapped_reads_no_sq.bam samtools index issue100.bam samtools index rg_with_tab.bam samtools index softclip.bam samtools index tag_bug.bam samtools index test_mapped_unmapped.bam samtools index test_query_position.bam samtools index test_unaligned.bam samtools view --no-PG -Co ex1.cram -T ex1.fa ex1.sam samtools view --no-PG -Co ex2.cram -T ex1.fa ex2.sam samtools view --no-PG -Co ex3.cram -T ex1.fa ex3.sam samtools index ex1.cram samtools index ex2.cram samtools index ex3.cram cp ex1.bam example_bai.bam samtools index example_bai.bam mv example_bai.bam.bai example_bai.bai dd if=ex2.bam of=ex2_truncated.bam bs=$((`wc -c < ex2.bam`-512)) count=1 1+0 Datensätze ein 1+0 Datensätze aus 122292 Bytes (122 kB, 119 KiB) kopiert, 0.000555256 s, 220 MB/s (bgzip -d < ex2.bam; printf '\37\0\0\0\1\0\0\0') | bgzip > ex2_corrupt.bam grep "^@" ex2.sam | samtools view --no-PG -bo empty.bam - samtools index empty.bam cp ex1.bam explicit_index.bam cp ex1.cram explicit_index.cram gzip < faidx_empty_seq.fq > faidx_empty_seq.fq.gz bgzip < ex1.fa > ex1.fa.gz samtools faidx ex1.fa.gz cp ex1.bam ex1_csi.bam samtools index -c ex1_csi.bam touch all.stamp rm with_md.sam make[2]: Verzeichnis „/build/python-pysam-0.20.0+ds/tests/pysam_data“ wird verlassen cd tests/cbcf_data && /usr/bin/make all make[2]: Verzeichnis „/build/python-pysam-0.20.0+ds/tests/cbcf_data“ wird betreten bgzip < example_vcf40.vcf > example_vcf40.vcf.gz tabix -p vcf example_vcf40.vcf.gz # create tbi index bcftools index example_vcf40.vcf.gz # create csi index bgzip < example_vcf42.vcf > example_vcf42.vcf.gz tabix -p vcf example_vcf42.vcf.gz # create tbi index bcftools index example_vcf42.vcf.gz # create csi index bgzip < example_vcf42_only_header.vcf > example_vcf42_only_header.vcf.gz tabix -p vcf example_vcf42_only_header.vcf.gz # create tbi index bcftools index example_vcf42_only_header.vcf.gz # create csi index bgzip < example_vcf42_withcontigs.vcf > example_vcf42_withcontigs.vcf.gz tabix -p vcf example_vcf42_withcontigs.vcf.gz # create tbi index bcftools index example_vcf42_withcontigs.vcf.gz # create csi index bgzip < example_vcf43.vcf > example_vcf43.vcf.gz tabix -p vcf example_vcf43.vcf.gz # create tbi index bcftools index example_vcf43.vcf.gz # create csi index bgzip < example_vcf43_with_utf8.vcf > example_vcf43_with_utf8.vcf.gz tabix -p vcf example_vcf43_with_utf8.vcf.gz # create tbi index bcftools index example_vcf43_with_utf8.vcf.gz # create csi index bgzip < gnomad.vcf > gnomad.vcf.gz tabix -p vcf gnomad.vcf.gz # create tbi index bcftools index gnomad.vcf.gz # create csi index bgzip < gnomad_fixed.vcf > gnomad_fixed.vcf.gz tabix -p vcf gnomad_fixed.vcf.gz # create tbi index bcftools index gnomad_fixed.vcf.gz # create csi index bgzip < missing_genotypes.vcf > missing_genotypes.vcf.gz tabix -p vcf missing_genotypes.vcf.gz # create tbi index bcftools index missing_genotypes.vcf.gz # create csi index bcftools view -O b example_vcf40.vcf.gz -o example_vcf40.bcf bcftools index example_vcf40.bcf bcftools view -O b example_vcf42.vcf.gz -o example_vcf42.bcf bcftools index example_vcf42.bcf bcftools view -O b example_vcf42_only_header.vcf.gz -o example_vcf42_only_header.bcf bcftools index example_vcf42_only_header.bcf bcftools view -O b example_vcf42_withcontigs.vcf.gz -o example_vcf42_withcontigs.bcf bcftools index example_vcf42_withcontigs.bcf bcftools view -O b example_vcf43.vcf.gz -o example_vcf43.bcf bcftools index example_vcf43.bcf bcftools view -O b example_vcf43_with_utf8.vcf.gz -o example_vcf43_with_utf8.bcf bcftools index example_vcf43_with_utf8.bcf bcftools view -O b gnomad.vcf.gz -o gnomad.bcf bcftools index gnomad.bcf bcftools view -O b gnomad_fixed.vcf.gz -o gnomad_fixed.bcf [W::bcf_hdr_check_sanity] PL should be declared as Number=G bcftools index gnomad_fixed.bcf [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 touch all.stamp make[2]: Verzeichnis „/build/python-pysam-0.20.0+ds/tests/cbcf_data“ wird verlassen dh_auto_test I: pybuild base:240: cd /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build; python3.11 -m pytest tests ============================= test session starts ============================== platform linux -- Python 3.11.2, pytest-7.2.1, pluggy-1.0.0+repack -- /usr/bin/python3.11 cachedir: .pytest_cache rootdir: /build/python-pysam-0.20.0+ds, configfile: setup.cfg collecting ... collected 949 items tests/AlignedSegment_test.py::TestAlignedSegment::testBlocks PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testCompare PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testEmpty PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testFullReferencePositions PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testHashing PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testLargeRead PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testNoSequence PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testPositions PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testSettingTagInEmptyRead PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testStrOfEmptyRead PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testUpdate PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testUpdate2 PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testUpdateQual PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testUpdateTlen PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_bin_values_for_mapped_reads_are_updated PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_bin_values_for_unmapped_reads_ignore_length PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_equivalence_matches_only_and_with_seq PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_hard_clipping PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_lowercase_md PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_match_mismatch PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_padding PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_padding_with_seq PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_skip PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_skip_reference PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_soft_clipping PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_uppercase_md PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_with_malformed_MD_tag PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_header_accessible PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_infer_query_length PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_infer_read_length PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_query_length_is_limited PASSED tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_be_set_to_asterisk PASSED tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_be_set_to_chromosome PASSED tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_be_set_to_none PASSED tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_not_be_set_to_unknown_chromosome PASSED tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_to_chromosome PASSED tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_to_missing PASSED tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_to_missing_without_header PASSED tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_without_header PASSED tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_not_be_set_to_unknown_chromosome PASSED tests/AlignedSegment_test.py::TestTidMapping::test_unmapped_tid_is_asterisk_in_output PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_be_set_to_asterisk PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_be_set_to_chromosome PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_be_set_to_none PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_not_be_set_to_unknown_chromosome PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_chromosome PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_equal PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_missing PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_missing_without_header PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_without_header PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_not_be_set_to_unknown_chromosome PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_unmapped_tid_is_asterisk_in_output PASSED tests/AlignedSegment_test.py::TestCigar::testCigar PASSED tests/AlignedSegment_test.py::TestCigar::testCigarString PASSED tests/AlignedSegment_test.py::TestCigarStats::testStats PASSED tests/AlignedSegment_test.py::TestAlignedPairs::testReferenceBases PASSED tests/AlignedSegment_test.py::TestBaseModifications::testChebi PASSED tests/AlignedSegment_test.py::TestBaseModifications::testDouble PASSED tests/AlignedSegment_test.py::TestBaseModifications::testMulti PASSED tests/AlignedSegment_test.py::TestBaseModifications::testOrient PASSED tests/AlignedSegment_test.py::TestTags::testAddTags PASSED tests/AlignedSegment_test.py::TestTags::testAddTagsType PASSED tests/AlignedSegment_test.py::TestTags::testArrayTags PASSED tests/AlignedSegment_test.py::TestTags::testEmptyTag PASSED tests/AlignedSegment_test.py::TestTags::testLongTags PASSED tests/AlignedSegment_test.py::TestTags::testMDTagComplex PASSED tests/AlignedSegment_test.py::TestTags::testMDTagDeletions PASSED tests/AlignedSegment_test.py::TestTags::testMDTagInsertions PASSED tests/AlignedSegment_test.py::TestTags::testMDTagMatchOnly PASSED tests/AlignedSegment_test.py::TestTags::testMDTagRefSkipping PASSED tests/AlignedSegment_test.py::TestTags::testMDTagSoftClipping PASSED tests/AlignedSegment_test.py::TestTags::testMissingTag PASSED tests/AlignedSegment_test.py::TestTags::testNegativeIntegers PASSED tests/AlignedSegment_test.py::TestTags::testNegativeIntegersWrittenToFile [E::idx_find_and_load] Could not retrieve index file for '/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp___enter___vio1yir6negative_integers.bam' PASSED tests/AlignedSegment_test.py::TestTags::testSetTag PASSED tests/AlignedSegment_test.py::TestTags::testTagParsing PASSED tests/AlignedSegment_test.py::TestTags::testTagsUpdatingFloat PASSED tests/AlignedSegment_test.py::TestCopy::testCopy PASSED tests/AlignedSegment_test.py::TestCopy::testDeepCopy PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_A PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_C PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_H PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_I PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_S PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_a PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_automated_type_detection PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_c PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_d PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_f PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_i PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_s PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_A PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_C PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_H PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_I PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_S PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_a PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_automated_type_detection PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_c PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_d PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_f PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_i PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_s PASSED tests/AlignedSegment_test.py::TestEnums::test_cigar_enums_are_defined PASSED tests/AlignedSegment_test.py::TestEnums::test_sam_flags_are_defined PASSED tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_read_can_be_constructed_without_header PASSED tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_read_can_be_written_to_file PASSED tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_reference_id_can_be_set PASSED tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_reference_name_is_not_available PASSED tests/AlignedSegment_test.py::TestForwardStrandValues::test_qualities_are_complemented PASSED tests/AlignedSegment_test.py::TestForwardStrandValues::test_sequence_is_complemented PASSED tests/AlignedSegment_test.py::TestExportImport::test_dict_export PASSED tests/AlignedSegment_test.py::TestExportImport::test_string_export PASSED tests/AlignedSegment_test.py::TestExportImport::test_string_export_import_with_tags PASSED tests/AlignedSegment_test.py::TestExportImport::test_string_export_import_without_tags PASSED tests/AlignedSegment_test.py::TestExportImport::test_to_string_without_alignment_file PASSED tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_dict PASSED tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_header PASSED tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_references PASSED tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_references_without_text PASSED tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_text PASSED tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_access_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_contains_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_get_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_keys_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_len_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_setting_raises_error PASSED tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_values_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_header_content_is_as_expected PASSED tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_name_mapping PASSED tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_text_access_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_access_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_contains_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_get_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_keys_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_len_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_setting_raises_error PASSED tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_values_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_header_content_is_as_expected PASSED tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_name_mapping PASSED tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_text_access_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_access_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_contains_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_get_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_keys_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_len_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_setting_raises_error PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_values_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_header_content_is_as_expected PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_name_mapping PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_text_access_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_BAM [E::idx_find_and_load] Could not retrieve index file for '/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_41zpl20q' /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_41zpl20q PASSED tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_CRAM [E::cram_index_load] Could not retrieve index file for '/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_1bxu8if3' /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_1bxu8if3 PASSED tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_SAM /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_przlytkx PASSED tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_BAM [E::idx_find_and_load] Could not retrieve index file for '/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_pe_nv0g6' /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_pe_nv0g6 PASSED tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_CRAM [W::sanitise_SQ_lines] Header @SQ length mismatch for ref chr1, 2147483647 vs 1575 [E::cram_index_load] Could not retrieve index file for '/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_pxew1l41' /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_pxew1l41 PASSED tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_SAM /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_w3smoqau PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_all_stepper PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_ignore_overlaps PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_base_quality_threshold PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_ignore_orphans PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_mapping_quality_threshold PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_redo_baq PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_all_stepper PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_ignore_overlaps PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_base_quality_threshold PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_ignore_orphans PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_mapping_quality_threshold PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_redo_baq PASSED tests/AlignmentFilePileup_test.py::TestPileupQueryPosition::testPileup PASSED tests/AlignmentFilePileup_test.py::TestPileupObjects::testIteratorOutOfScope SKIPPED tests/AlignmentFilePileup_test.py::TestPileupObjects::testPileupColumn PASSED tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testInverse PASSED tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIterateAll PASSED tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIteratePerContig PASSED tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIterateRanges PASSED tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIterateTruncate PASSED tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testAccessOnClosedIterator PASSED tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testStart PASSED tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testStr PASSED tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testTruncate PASSED tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_depths_are_equal PASSED tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_mapping_qualities_are_equal PASSED tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_bases_with_reference_are_equal PASSED tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_bases_without_reference_are_equal PASSED tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_qualities_are_equal PASSED tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_qualities_from_pileups_are_equal PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARflag PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARpos PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARqname PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARqual PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARquery PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARrname PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARseq PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testOpt PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testTags PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARflag PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARqname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARquery PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARrname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARseq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testOpt PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testTags PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARQueryLength [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARcigar [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARcigarstring [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARflag [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARmapq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARmpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARmrnm [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARqname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARqqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARquery [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARrname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARseq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testOpt [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testPairedBools [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testPresentOptionalFields [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testTags [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARflag PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARqname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARquery PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARrname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARseq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testOpt PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testTags PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARQueryLength [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARcigar [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARcigarstring [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARflag [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARmapq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARmpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARmrnm [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARqname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARqqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARquery [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARrname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARseq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testOpt [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testPairedBools [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testPresentOptionalFields [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testTags [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARflag PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARpos PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARqname PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARqual PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARquery PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARrname PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARseq PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testOpt PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testTags PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARflag PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARpos PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARqname PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARqual PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARquery PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARrname PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARseq PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testOpt PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testTags PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARflag PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARpos PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARqname PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARqual PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARquery PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARrname PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARseq PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testOpt PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testTags PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARflag PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARqname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARquery PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARrname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARseq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testOpt PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testTags PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARflag PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARqname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARquery PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARrname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARseq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testOpt PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testTags PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARQueryLength [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARcigar [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARcigarstring [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARflag [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARmapq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARmpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARmrnm [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARqname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARqqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARquery [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARrname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARseq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testOpt [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testPairedBools [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testPresentOptionalFields [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testTags [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARQueryLength [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARcigar [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARcigarstring [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARflag [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARmapq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARmpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARmrnm [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARqname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARqqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARquery [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARrname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARseq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testOpt [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testPairedBools [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testPresentOptionalFields [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testTags [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARflag PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARqname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARquery PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARrname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARseq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testOpt PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testRaises PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testTags PASSED tests/AlignmentFile_test.py::TestIO::testBAM2BAM PASSED tests/AlignmentFile_test.py::TestIO::testBAM2SAM PASSED tests/AlignmentFile_test.py::TestIO::testBAMWithCSIIndex PASSED tests/AlignmentFile_test.py::TestIO::testBAMWithShortBAI PASSED tests/AlignmentFile_test.py::TestIO::testBAMWithoutAlignedSegments PASSED tests/AlignmentFile_test.py::TestIO::testCRAM2BAM [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestIO::testCRAM2CRAM [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestIO::testCRAM2SAM [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestIO::testEmptyBAM PASSED tests/AlignmentFile_test.py::TestIO::testEmptyWithHeaderBAM PASSED tests/AlignmentFile_test.py::TestIO::testFetchFromClosedFile PASSED tests/AlignmentFile_test.py::TestIO::testFetchFromClosedFileObject PASSED tests/AlignmentFile_test.py::TestIO::testHead PASSED tests/AlignmentFile_test.py::TestIO::testOpenFromFilename PASSED tests/AlignmentFile_test.py::TestIO::testReadBamWithoutTargetNames PASSED tests/AlignmentFile_test.py::TestIO::testReadSamWithoutTargetNames PASSED tests/AlignmentFile_test.py::TestIO::testReadingFromFileWithoutIndex [E::idx_find_and_load] Could not retrieve index file for '/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_testReadingFromFileWithoutIndex_93j2wa0mtmp_ex2.bam' PASSED tests/AlignmentFile_test.py::TestIO::testSAM2BAM PASSED tests/AlignmentFile_test.py::TestIO::testSAM2CRAM [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestIO::testSAM2SAM PASSED tests/AlignmentFile_test.py::TestIO::testSAM2SAMWithoutHeader PASSED tests/AlignmentFile_test.py::TestIO::testWriteUncompressedBAMFile PASSED tests/AlignmentFile_test.py::TestIO::test_accessing_attributes_in_closed_file_raises_errors PASSED tests/AlignmentFile_test.py::TestIO::test_fail_read_sam_without_header PASSED tests/AlignmentFile_test.py::TestIO::test_fail_when_reading_unformatted_files PASSED tests/AlignmentFile_test.py::TestIO::test_fetch_by_tid PASSED tests/AlignmentFile_test.py::TestIO::test_header_available_after_closing_file PASSED tests/AlignmentFile_test.py::TestIO::test_pass_read_sam_with_header_without_header_check PASSED tests/AlignmentFile_test.py::TestIO::test_pass_read_sam_without_header_with_refs PASSED tests/AlignmentFile_test.py::TestIO::test_reference_name_available_after_closing_file PASSED tests/AlignmentFile_test.py::TestIO::test_write_bam_to_unknown_path_fails [E::hts_open_format] Failed to open file "missing_directory/new_file.bam" : No such file or directory PASSED tests/AlignmentFile_test.py::TestAutoDetect::testBAM PASSED tests/AlignmentFile_test.py::TestAutoDetect::testCRAM [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestAutoDetect::testSAM PASSED tests/AlignmentFile_test.py::TestIteratorRowBAM::testIteratePerContig PASSED tests/AlignmentFile_test.py::TestIteratorRowBAM::testIterateRanges PASSED tests/AlignmentFile_test.py::TestIteratorRowAllBAM::testIterate PASSED tests/AlignmentFile_test.py::TestIteratorRowCRAM::testIteratePerContig [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestIteratorRowCRAM::testIterateRanges [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestIteratorRowCRAMWithReferenceFilename::testIteratePerContig [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestIteratorRowCRAMWithReferenceFilename::testIterateRanges [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestFloatTagBug::testFloatTagBug PASSED tests/AlignmentFile_test.py::TestLargeFieldBug::testLargeFileBug PASSED tests/AlignmentFile_test.py::TestClipping::testClipping PASSED tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_from_bam_with_until_eof_reads_unmapped_reads PASSED tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_from_sam_with_until_eof_reads_unmapped_reads PASSED tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_with_asterisk_only_returns_unmapped_reads PASSED tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_with_asterisk_only_returns_unmapped_reads_by_contig PASSED tests/AlignmentFile_test.py::TestContextManager::testManager PASSED tests/AlignmentFile_test.py::TestMultiThread::testSingleThreadEqualsMultithread [E::idx_find_and_load] Could not retrieve index file for '/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_testSingleThreadEqualsMultithread_89ugox6htmp_single.bam' [E::idx_find_and_load] Could not retrieve index file for '/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_testSingleThreadEqualsMultithread_wytkn6_htmp_multi.bam' PASSED tests/AlignmentFile_test.py::TestExceptions::testBackwardsOrderNewFormat PASSED tests/AlignmentFile_test.py::TestExceptions::testBackwardsOrderOldFormat PASSED tests/AlignmentFile_test.py::TestExceptions::testBadContig PASSED tests/AlignmentFile_test.py::TestExceptions::testMeaninglessCrap PASSED tests/AlignmentFile_test.py::TestExceptions::testMissingFile [E::hts_open_format] Failed to open file "exdoesntexist.bam" : No such file or directory [E::hts_open_format] Failed to open file "exdoesntexist.sam" : No such file or directory [E::hts_open_format] Failed to open file "exdoesntexist.bam" : No such file or directory [E::hts_open_format] Failed to open file "exdoesntexist.sam" : No such file or directory PASSED tests/AlignmentFile_test.py::TestExceptions::testOutOfRangNewFormat PASSED tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeLargeNewFormat PASSED tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeLargeOldFormat PASSED tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeNegativeNewFormat PASSED tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeNegativeOldFormat PASSED tests/AlignmentFile_test.py::TestExceptions::testZeroToZero PASSED tests/AlignmentFile_test.py::TestWrongFormat::testOpenBamAsSam PASSED tests/AlignmentFile_test.py::TestWrongFormat::testOpenFastaAsBam PASSED tests/AlignmentFile_test.py::TestWrongFormat::testOpenFastaAsSam PASSED tests/AlignmentFile_test.py::TestWrongFormat::testOpenSamAsBam PASSED tests/AlignmentFile_test.py::TestRegionParsing::test_dash_in_chr PASSED tests/AlignmentFile_test.py::TestDeNovoConstruction::testBAMWholeFile PASSED tests/AlignmentFile_test.py::TestDeNovoConstruction::test_pass_if_reads_binary_equal PASSED tests/AlignmentFile_test.py::TestEmptyHeader::testEmptyHeader PASSED tests/AlignmentFile_test.py::TestEmptyHeader::test_bam_without_seq_in_header [E::idx_find_and_load] Could not retrieve index file for '/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/tests/pysam_data/0example_no_seq_in_header.bam' PASSED tests/AlignmentFile_test.py::TestEmptyHeader::test_bam_without_seq_with_null_bytes_in_header [E::idx_find_and_load] Could not retrieve index file for '/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/tests/pysam_data/0example_no_seq_in_header_null_bytes.bam' PASSED tests/AlignmentFile_test.py::TestMismatchingHeader::testMismatchingHeader PASSED tests/AlignmentFile_test.py::TestHeaderWithProgramOptions::testHeader PASSED tests/AlignmentFile_test.py::TestTruncatedBAM::testTruncatedBam2 PASSED tests/AlignmentFile_test.py::TestTruncatedBAM::testTruncatedBamIterator [W::bam_hdr_read] EOF marker is absent. The input is probably truncated [E::idx_find_and_load] Could not retrieve index file for '/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/tests/pysam_data/ex2_truncated.bam' [E::bgzf_read_block] Failed to read BGZF block data at offset 105180 expected 17578 bytes; hread returned 17094 [E::bgzf_read] Read block operation failed with error 4 after 0 of 4 bytes PASSED tests/AlignmentFile_test.py::TestCorruptBAM::testCorruptBamIterator [E::idx_find_and_load] Could not retrieve index file for '/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/tests/pysam_data/ex2_corrupt.bam' PASSED tests/AlignmentFile_test.py::TestBTagSam::testReadTags PASSED tests/AlignmentFile_test.py::TestBTagSam::testReadWriteTags PASSED tests/AlignmentFile_test.py::TestBTagBam::testReadTags PASSED tests/AlignmentFile_test.py::TestBTagBam::testReadWriteTags PASSED tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetch PASSED tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchUntilEOF PASSED tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchWithRegionFalseTrue PASSED tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchWithRegionTrueFalse PASSED tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchWithRegionTrueTrue PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetch [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchUntilEOF [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchWithRegionFalseTrue [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchWithRegionTrueFalse [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchWithRegionTrueTrue [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetch [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchUntilEOF [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchWithRegionFalseTrue [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchWithRegionTrueFalse [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchWithRegionTrueTrue [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestRemoteFileHTTP::testFetch PASSED tests/AlignmentFile_test.py::TestRemoteFileHTTP::testFetchAll PASSED tests/AlignmentFile_test.py::TestRemoteFileHTTP::testView PASSED tests/AlignmentFile_test.py::TestLargeOptValues::testBAM PASSED tests/AlignmentFile_test.py::TestLargeOptValues::testSAM PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_counts_as_expected PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_nofilter PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_quality_filter PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_read_all PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_read_callback PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_with_coordinates_works PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_without_coordinates_fails PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_wrong_coordinates_fails PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_counting_the_same_region_works PASSED tests/AlignmentFile_test.py::TestFindIntrons::test_all PASSED tests/AlignmentFile_test.py::TestFindIntrons::test_first PASSED tests/AlignmentFile_test.py::TestFindIntrons::test_total PASSED tests/AlignmentFile_test.py::TestLogging::testFail1 PASSED tests/AlignmentFile_test.py::TestLogging::testNoFail1 PASSED tests/AlignmentFile_test.py::TestLogging::testNoFail2 PASSED tests/AlignmentFile_test.py::TestAlignmentFileUtilityFunctions::testCount PASSED tests/AlignmentFile_test.py::TestAlignmentFileUtilityFunctions::testIndexStats PASSED tests/AlignmentFile_test.py::TestAlignmentFileUtilityFunctions::testMate PASSED tests/AlignmentFile_test.py::TestMappedUnmapped::test_counts_of_mapped_and_unmapped_are_correct PASSED tests/AlignmentFile_test.py::TestMappedUnmapped::test_counts_of_mapped_and_unmapped_are_correct_per_chromosome PASSED tests/AlignmentFile_test.py::TestSamtoolsProxy::testIndex PASSED tests/AlignmentFile_test.py::TestSamtoolsProxy::testSort [E::hts_open_format] Failed to open file "missing_file" : No such file or directory PASSED tests/AlignmentFile_test.py::TestSamtoolsProxy::testView [E::hts_open_format] Failed to open file "missing_file" : No such file or directory PASSED tests/AlignmentFile_test.py::TestAlignmentFileIndex::testIndex PASSED tests/AlignmentFile_test.py::TestExplicitIndex::testExplicitIndexBAM [W::hts_idx_load3] The index file is older than the data file: /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/tests/pysam_data/ex1.bam.bai PASSED tests/AlignmentFile_test.py::TestExplicitIndex::testExplicitIndexCRAM PASSED tests/AlignmentFile_test.py::TestExplicitIndex::testRemoteExplicitIndexBAM PASSED tests/AlignmentFile_test.py::TestVerbosity::testVerbosity PASSED tests/AlignmentFile_test.py::TestSanityCheckingBAM::test_empty_read_gives_value_error PASSED tests/AlignmentFile_test.py::TestLargeCigar::test_reading_writing_bam [E::idx_find_and_load] Could not retrieve index file for '/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_check_read_9njkfbiktmp_largecigar.bam' PASSED tests/AlignmentFile_test.py::TestLargeCigar::test_reading_writing_cram SKIPPED tests/AlignmentFile_test.py::TestLargeCigar::test_reading_writing_sam PASSED tests/StreamFiledescriptors_test.py::StreamTest::test_samtools_processing SKIPPED tests/StreamFiledescriptors_test.py::StreamTest::test_text_processing PASSED tests/VariantFile_test.py::TestMissingGenotypes::testVCF PASSED tests/VariantFile_test.py::TestMissingGenotypes::testVCFGZ PASSED tests/VariantFile_test.py::TestMissingSamples::testVCF PASSED tests/VariantFile_test.py::TestMissingSamples::testVCFGZ PASSED tests/VariantFile_test.py::TestMissingSamplesFixed::testVCF [W::bcf_hdr_check_sanity] PL should be declared as Number=G PASSED tests/VariantFile_test.py::TestMissingSamplesFixed::testVCFGZ PASSED tests/VariantFile_test.py::TestOpening::testDetectBCF PASSED tests/VariantFile_test.py::TestOpening::testDetectVCF [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig '17' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/VariantFile_test.py::TestOpening::testDetectVCFGZ PASSED tests/VariantFile_test.py::TestOpening::testEmptyFileVCF PASSED tests/VariantFile_test.py::TestOpening::testEmptyFileVCFFromPath PASSED tests/VariantFile_test.py::TestOpening::testEmptyFileVCFGZOnlyHeader PASSED tests/VariantFile_test.py::TestOpening::testEmptyFileVCFGZWithIndex PASSED tests/VariantFile_test.py::TestOpening::testEmptyFileVCFGZWithoutIndex PASSED tests/VariantFile_test.py::TestOpening::testEmptyFileVCFOnlyHeader PASSED tests/VariantFile_test.py::TestOpening::testMissingFile [E::hts_open_format] Failed to open file "missing_file.vcf" : No such file or directory PASSED tests/VariantFile_test.py::TestOpening::testMissingFileVCFGZ [E::hts_open_format] Failed to open file "missing_file.vcf.gz" : No such file or directory PASSED tests/VariantFile_test.py::TestIndexFormatsVCF::test_bcf_with_csi_index PASSED tests/VariantFile_test.py::TestIndexFormatsVCF::test_bcf_with_prebuilt_csi PASSED tests/VariantFile_test.py::TestIndexFormatsVCF::test_bcf_with_tbi_index_will_produce_csi PASSED tests/VariantFile_test.py::TestIndexFormatsVCF::test_vcf_with_csi_index PASSED tests/VariantFile_test.py::TestIndexFormatsVCF::test_vcf_with_tbi_index PASSED tests/VariantFile_test.py::TestHeader::testIterator PASSED tests/VariantFile_test.py::TestHeader::testStr PASSED tests/VariantFile_test.py::TestParsing::testAlleles PASSED tests/VariantFile_test.py::TestParsing::testAllelesVariantTypes PASSED tests/VariantFile_test.py::TestParsing::testAlt PASSED tests/VariantFile_test.py::TestParsing::testChrom PASSED tests/VariantFile_test.py::TestParsing::testChromFromPath PASSED tests/VariantFile_test.py::TestParsing::testFilter PASSED tests/VariantFile_test.py::TestParsing::testFormat PASSED tests/VariantFile_test.py::TestParsing::testId PASSED tests/VariantFile_test.py::TestParsing::testInfo PASSED tests/VariantFile_test.py::TestParsing::testPos PASSED tests/VariantFile_test.py::TestParsing::testQual PASSED tests/VariantFile_test.py::TestParsing::testRef PASSED tests/VariantFile_test.py::TestParsing::testSampleAlleleIndices PASSED tests/VariantFile_test.py::TestParsing::testSampleAlleles PASSED tests/VariantFile_test.py::TestParsing::testSampleFormats PASSED tests/VariantFile_test.py::TestParsing::testStart PASSED tests/VariantFile_test.py::TestParsing::testStop PASSED tests/VariantFile_test.py::TestIndexFilename::testOpen PASSED tests/VariantFile_test.py::TestConstructionVCFWithContigs::testBase PASSED tests/VariantFile_test.py::TestConstructionVCFWithContigs::testConstructionFromCopy PASSED tests/VariantFile_test.py::TestConstructionVCFWithContigs::testConstructionWithLines PASSED tests/VariantFile_test.py::TestConstructionVCFWithContigs::testConstructionWithRecords PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testBase PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testConstructionFromCopy PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testConstructionWithLines PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testConstructionWithRecords PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testBase PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testConstructionFromCopy PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testConstructionWithLines PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testConstructionWithRecords PASSED tests/VariantFile_test.py::TestSettingRecordValues::testBase PASSED tests/VariantFile_test.py::TestSettingRecordValues::testGenotype [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) (0, 0) PASSED tests/VariantFile_test.py::TestSettingRecordValues::testSetQual [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/VariantFile_test.py::TestMultiThreading::testNoMultiThreadingWithIgnoreTruncation PASSED tests/VariantFile_test.py::TestMultiThreading::testSingleThreadEqualsMultithreadResult [E::idx_find_and_load] Could not retrieve index file for '/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_testSingleThreadEqualsMultithreadResult_j2layntw.bcf' PASSED tests/VariantFile_test.py::TestSubsetting::testSubsetting PASSED tests/VariantFile_test.py::TestVCFVersions::test_all_records_can_be_fetched [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig '17' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig '17' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/VariantFile_test.py::TestUnicode::test_record_with_unicode PASSED tests/VariantRecord_test.py::test_ascii_annotation_can_be_added PASSED tests/VariantRecord_test.py::test_ascii_annotation_with_variable_length_can_be_added PASSED tests/VariantRecord_test.py::test_unicode_annotation_can_be_added PASSED tests/VariantRecord_test.py::test_set_sample_alleles PASSED tests/compile_test.py::BAMTest::testCount PASSED tests/compile_test.py::GTFTest::testCount PASSED tests/faidx_test.py::TestFastaFile::testFetch PASSED tests/faidx_test.py::TestFastaFile::testFetchErrors PASSED tests/faidx_test.py::TestFastaFile::testLength PASSED tests/faidx_test.py::TestFastaFile::testOutOfRangeAccess PASSED tests/faidx_test.py::TestFastaFile::testSequenceLengths PASSED tests/faidx_test.py::TestFastaFile::test_fetch_with_region_and_contig_raises_exception PASSED tests/faidx_test.py::TestFastaFile::test_fetch_with_region_is_equivalent PASSED tests/faidx_test.py::TestFastaFilePathIndex::test_open_file_with_explicit_abritrarily_named_index_succeeds PASSED tests/faidx_test.py::TestFastaFilePathIndex::test_open_file_with_explicit_index_succeeds PASSED tests/faidx_test.py::TestFastaFilePathIndex::test_open_file_without_index_succeeds PASSED tests/faidx_test.py::TestFastaFilePathIndex::test_raise_exception_if_index_is_missing PASSED tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_open_file_with_explicit_abritrarily_named_index_succeeds PASSED tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_open_file_with_explicit_index_succeeds PASSED tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_open_file_without_index_succeeds PASSED tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_raise_exception_if_index_is_missing PASSED tests/faidx_test.py::TestFastxFileFastq::testCounts PASSED tests/faidx_test.py::TestFastxFileFastq::testManager PASSED tests/faidx_test.py::TestFastxFileFastq::testMissingFile PASSED tests/faidx_test.py::TestFastxFileFastq::testSequence PASSED tests/faidx_test.py::TestFastqFileFastq::testCounts PASSED tests/faidx_test.py::TestFastqFileFastq::testManager PASSED tests/faidx_test.py::TestFastqFileFastq::testMissingFile PASSED tests/faidx_test.py::TestFastqFileFastq::testSequence PASSED tests/faidx_test.py::TestFastxFileFasta::testCounts PASSED tests/faidx_test.py::TestFastxFileFasta::testManager PASSED tests/faidx_test.py::TestFastxFileFasta::testMissingFile PASSED tests/faidx_test.py::TestFastxFileFasta::testSequence PASSED tests/faidx_test.py::TestFastxFileFastqStream::testCounts PASSED tests/faidx_test.py::TestFastxFileFastqStream::testManager PASSED tests/faidx_test.py::TestFastxFileFastqStream::testMissingFile PASSED tests/faidx_test.py::TestFastxFileFastqStream::testSequence PASSED tests/faidx_test.py::TestFastxFileWithEmptySequence::testIteration PASSED tests/faidx_test.py::TestRemoteFileFTP::testFTPView PASSED tests/faidx_test.py::TestRemoteFileFTP::test_sequence_lengths_are_available PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_can_be_created_from_scratch PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_comment_can_be_None PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_comment_can_be_modified PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_fail_if_name_is_None PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_fail_if_quality_is_wrong_length PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_name_can_be_modified PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_quality_can_be_modified PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_sequence_can_be_modified PASSED tests/faidx_test.py::TestFastqProxy::test_fastq_proxy_instantiation_raises_error PASSED tests/linking_test.py::TestLinking::test_package_can_be_installed SKIPPED tests/linking_test.py::TestLinkWithRpath::test_package_can_be_installed SKIPPED tests/linking_test.py::TestLinkWithRpath::test_package_tests_pass SKIPPED tests/linking_test.py::TestLinkWithoutRpath::test_package_can_be_installed SKIPPED tests/linking_test.py::TestLinkWithoutRpath::test_package_tests_fail_on_import SKIPPED tests/linking_test.py::TestLinkWithoutRpath::test_package_tests_pass_if_ld_library_path_set SKIPPED tests/samtools_test.py::SamtoolsTest::testStatements PASSED tests/samtools_test.py::SamtoolsTest::testUsage SKIPPED (skipping us...) tests/samtools_test.py::EmptyIndexTest::testEmptyIndex PASSED tests/samtools_test.py::EmptyIndexTest::testEmptyIndexWithExtraArg PASSED tests/samtools_test.py::EmptyIndexTest::testEmptyIndexWithExtraFlag PASSED tests/samtools_test.py::TestReturnType::testReturnValueData PASSED tests/samtools_test.py::TestReturnType::testReturnValueString PASSED tests/samtools_test.py::StdoutTest::testDoubleCalling PASSED tests/samtools_test.py::StdoutTest::testSaveStdout PASSED tests/samtools_test.py::StdoutTest::testWithRedirectedStdout PASSED tests/samtools_test.py::StdoutTest::testWithoutRedirectedStdout PASSED tests/samtools_test.py::PysamTest::testStatements PASSED tests/samtools_test.py::PysamTest::testUsage SKIPPED (skipping usage...) 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 tests/tabix_test.py::TestIndexing::test_indexing_with_preset_works PASSED tests/tabix_test.py::TestCompression::testCompression PASSED tests/tabix_test.py::TestCompression::testIndexPresetCompressed PASSED tests/tabix_test.py::TestCompression::testIndexPresetUncompressed PASSED tests/tabix_test.py::TestCompressionSam::testCompression PASSED tests/tabix_test.py::TestCompressionSam::testIndexPresetCompressed PASSED tests/tabix_test.py::TestCompressionSam::testIndexPresetUncompressed PASSED tests/tabix_test.py::TestCompressionBed::testCompression PASSED tests/tabix_test.py::TestCompressionBed::testIndexPresetCompressed PASSED tests/tabix_test.py::TestCompressionBed::testIndexPresetUncompressed PASSED tests/tabix_test.py::TestCompressionVCF::testCompression PASSED tests/tabix_test.py::TestCompressionVCF::testIndexPresetCompressed PASSED tests/tabix_test.py::TestCompressionVCF::testIndexPresetUncompressed PASSED tests/tabix_test.py::TestGZFile::testAll PASSED tests/tabix_test.py::TestIterationWithoutComments::testAll PASSED tests/tabix_test.py::TestIterationWithoutComments::testGetContigs PASSED tests/tabix_test.py::TestIterationWithoutComments::testHeader PASSED tests/tabix_test.py::TestIterationWithoutComments::testInvalidIntervals PASSED tests/tabix_test.py::TestIterationWithoutComments::testPerContig PASSED tests/tabix_test.py::TestIterationWithoutComments::testPerContig2 PASSED tests/tabix_test.py::TestIterationWithoutComments::testPerContigFromStart PASSED tests/tabix_test.py::TestIterationWithoutComments::testPerContigToEnd PASSED tests/tabix_test.py::TestIterationWithoutComments::testPerInterval PASSED tests/tabix_test.py::TestIterationWithoutComments::testRegionStrings PASSED tests/tabix_test.py::TestIterationWithoutComments::testReopening PASSED tests/tabix_test.py::TestIterationWithComments::testAll PASSED tests/tabix_test.py::TestIterationWithComments::testGetContigs PASSED tests/tabix_test.py::TestIterationWithComments::testHeader PASSED tests/tabix_test.py::TestIterationWithComments::testInvalidIntervals PASSED tests/tabix_test.py::TestIterationWithComments::testPerContig PASSED tests/tabix_test.py::TestIterationWithComments::testPerContig2 PASSED tests/tabix_test.py::TestIterationWithComments::testPerContigFromStart PASSED tests/tabix_test.py::TestIterationWithComments::testPerContigToEnd PASSED tests/tabix_test.py::TestIterationWithComments::testPerInterval PASSED tests/tabix_test.py::TestIterationWithComments::testRegionStrings PASSED tests/tabix_test.py::TestIterationWithComments::testReopening PASSED tests/tabix_test.py::TestIterators::testClosedFile PASSED tests/tabix_test.py::TestIterators::testClosedFileIteration PASSED tests/tabix_test.py::TestIterators::testIteration PASSED tests/tabix_test.py::TestIteratorsGenericCompressed::testClosedFile PASSED tests/tabix_test.py::TestIteratorsGenericCompressed::testClosedFileIteration PASSED tests/tabix_test.py::TestIteratorsGenericCompressed::testIteration PASSED tests/tabix_test.py::TestIteratorsFileCompressed::testClosedFile PASSED tests/tabix_test.py::TestIteratorsFileCompressed::testClosedFileIteration PASSED tests/tabix_test.py::TestIteratorsFileCompressed::testIteration PASSED tests/tabix_test.py::TestIteratorsFileUncompressed::testClosedFile PASSED tests/tabix_test.py::TestIteratorsFileUncompressed::testClosedFileIteration PASSED tests/tabix_test.py::TestIteratorsFileUncompressed::testIteration PASSED tests/tabix_test.py::TestIterationMalformattedGTFFiles::testGTFTooFewFields PASSED tests/tabix_test.py::TestIterationMalformattedGTFFiles::testGTFTooManyFields PASSED tests/tabix_test.py::TestBed::testRead PASSED tests/tabix_test.py::TestBed::testWrite PASSED tests/tabix_test.py::TestUnicode::testFromTabix PASSED tests/tabix_test.py::TestUnicode::testFromVCF PASSED tests/tabix_test.py::TestVCFFromTabix::testRead PASSED tests/tabix_test.py::TestVCFFromTabix::testWrite PASSED tests/tabix_test.py::TestVCFFromVCF::testConnecting PASSED tests/tabix_test.py::TestVCFFromVCF::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_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_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_24::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_24::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_24::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_24::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_21::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_21::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_21::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_21::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_2::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_2::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_2::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_2::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_18::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_18::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_18::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_18::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_11::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_11::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_11::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_11::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_13::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_13::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_13::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_13::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_4::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_4::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_4::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_4::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_20::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_20::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_20::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_20::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_8::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_8::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_8::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_8::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_vcf_v42::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_vcf_v42::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_vcf_v42::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_vcf_v42::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_7::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_7::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_7::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_7::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_15::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_15::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_15::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_15::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_22::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_22::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_22::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_22::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_23::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_23::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_23::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_23::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_6::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_6::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_6::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_6::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_16::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_16::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_16::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_16::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_12::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_12::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_12::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_12::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_9::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_9::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_9::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_9::testParsing PASSED tests/tabix_test.py::TestVCFFromVariantFile::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile::testParsing [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig '17' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestVCFFromVariantFile_issue85::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_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_5::testConnecting [W::bcf_hdr_check_sanity] GL should be declared as Number=G 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_3::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_3::testParsing [W::vcf_parse] Contig '1' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestVCFFromVariantFile_24::testConnecting [E::bcf_hdr_parse_sample_line] Could not parse the "#CHROM.." line, either the fields are incorrect or spaces are present instead of tabs: #CHROM POS ID REF ALT QUAL FILTER INFO PASSED tests/tabix_test.py::TestVCFFromVariantFile_24::testParsing PASSED tests/tabix_test.py::TestVCFFromVariantFile_21::testConnecting [W::bcf_hdr_register_hrec] The definition of Flag "INFO/NotCalledInValidationSamples" is invalid, forcing Number=0 PASSED tests/tabix_test.py::TestVCFFromVariantFile_21::testParsing [W::bcf_hdr_register_hrec] The definition of Flag "INFO/NotCalledInValidationSamples" is invalid, forcing Number=0 [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestVCFFromVariantFile_2::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_2::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_info] INFO 'sumGLbyD' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestVCFFromVariantFile_18::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_18::testParsing [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_info] INFO 'DP' is not defined in the header, assuming Type=String [W::vcf_parse_info] INFO 'AF1' is not defined in the header, assuming Type=String [W::vcf_parse_info] INFO 'CI95' is not defined in the header, assuming Type=String [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_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_13::testConnecting [W::bcf_hrec_check] Invalid tag name: "1000g" [W::bcf_hrec_check] Invalid tag name: "GT:GL:GQ:NR" PASSED tests/tabix_test.py::TestVCFFromVariantFile_13::testParsing [W::bcf_hrec_check] Invalid tag name: "1000g" [W::bcf_hrec_check] Invalid tag name: "GT:GL:GQ:NR" [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_info] INFO 'MMLQ' is not defined in the header, assuming Type=String [W::vcf_parse] Contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr17_gl000205_random' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr18' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr19' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr2' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr21' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr22' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chrUn_gl000214' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chrUn_gl000220' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chrUn_gl000225' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chrX' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestVCFFromVariantFile_4::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_4::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_format] FORMAT 'GT' at 20:249843 is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestVCFFromVariantFile_20::testConnecting [W::bcf_hdr_register_hrec] The definition of Flag "INFO/NotCalledInValidationSamples" is invalid, forcing Number=0 PASSED tests/tabix_test.py::TestVCFFromVariantFile_20::testParsing [W::bcf_hdr_register_hrec] The definition of Flag "INFO/NotCalledInValidationSamples" is invalid, forcing Number=0 [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestVCFFromVariantFile_8::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_8::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_format] FORMAT 'GT' at 20:676148 is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestVCFFromVariantFile_vcf_v42::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_vcf_v42::testParsing PASSED tests/tabix_test.py::TestVCFFromVariantFile_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_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_23::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_23::testParsing [W::vcf_parse_info] INFO 'sumGLbyD' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestVCFFromVariantFile_6::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_6::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_info] INFO 'CallSetAC' is not defined in the header, assuming Type=String [W::vcf_parse_info] INFO 'CallSetAC2' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'GT' at 20:669442 is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestVCFFromVariantFile_16::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_16::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_info] INFO 'sumGLbyD' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestVCFFromVariantFile_12::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_12::testParsing [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_info] INFO 'DP' is not defined in the header, assuming Type=String [W::vcf_parse_info] INFO 'AF1' is not defined in the header, assuming Type=String [W::vcf_parse_info] INFO 'CI95' is not defined in the header, assuming Type=String [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_9::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_9::testParsing [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_info] INFO 'DP' is not defined in the header, assuming Type=String [W::vcf_parse_info] INFO 'AF1' is not defined in the header, assuming Type=String [W::vcf_parse_info] INFO 'CI95' is not defined in the header, assuming Type=String [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::TestIndexArgument::testFetchAll PASSED tests/tabix_test.py::TestIndexArgument::testLoadIndexWithoutTbiExtension PASSED tests/tabix_test.py::TestBackwardsCompatibility::testBED PASSED tests/tabix_test.py::TestBackwardsCompatibility::testBED0v23 PASSED tests/tabix_test.py::TestBackwardsCompatibility::testBED0v26 PASSED tests/tabix_test.py::TestBackwardsCompatibility::testEmpty PASSED tests/tabix_test.py::TestBackwardsCompatibility::testVCF PASSED tests/tabix_test.py::TestBackwardsCompatibility::testVCF0v23 PASSED tests/tabix_test.py::TestBackwardsCompatibility::testVCF0v26 PASSED tests/tabix_test.py::TestMultipleIterators::testDisjointIterators PASSED tests/tabix_test.py::TestMultipleIterators::testDoubleFetch PASSED tests/tabix_test.py::TestMultipleIterators::testJoinedIterators PASSED tests/tabix_test.py::TestMultipleIterators::testScope PASSED tests/tabix_test.py::TestContextManager::testManager PASSED tests/tabix_test.py::TestMultithreadTabixFile::testMultithreadEqualsSinglethread PASSED tests/tabixproxies_test.py::TestBED::testAssignmentToTargetList PASSED tests/tabixproxies_test.py::TestParser::testAssignmentToTargetList PASSED tests/tabixproxies_test.py::TestParser::testCopy PASSED tests/tabixproxies_test.py::TestParser::testIteratorCompressed PASSED tests/tabixproxies_test.py::TestParser::testIteratorUncompressed PASSED tests/tabixproxies_test.py::TestParser::testRead PASSED tests/tabixproxies_test.py::TestParser::testUnset PASSED tests/tabixproxies_test.py::TestParser::testWrite PASSED tests/tabixproxies_test.py::TestGTF::testAssignmentToTargetList PASSED tests/tabixproxies_test.py::TestGTF::testCopy PASSED tests/tabixproxies_test.py::TestGTF::testIteratorCompressed PASSED tests/tabixproxies_test.py::TestGTF::testIteratorUncompressed PASSED tests/tabixproxies_test.py::TestGTF::testRead PASSED tests/tabixproxies_test.py::TestGTF::testUnset PASSED tests/tabixproxies_test.py::TestGTF::testWrite PASSED tests/tabixproxies_test.py::TestGTF::test_added_attribute_is_output PASSED tests/tabixproxies_test.py::TestGTF::test_asdict_can_be_modified PASSED tests/tabixproxies_test.py::TestGTF::test_asdict_contains_attributes PASSED tests/tabixproxies_test.py::TestGTF::test_setAttribute_makes_changes PASSED tests/tabixproxies_test.py::TestGTF::test_setting_end_is_one_based PASSED tests/tabixproxies_test.py::TestGTF::test_setting_feature_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGTF::test_setting_fields PASSED tests/tabixproxies_test.py::TestGTF::test_setting_frame_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGTF::test_setting_score_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGTF::test_setting_source_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGTF::test_setting_start_is_one_based PASSED tests/tabixproxies_test.py::TestGTF::test_setting_strand_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGFF3::testAssignmentToTargetList PASSED tests/tabixproxies_test.py::TestGFF3::testCopy PASSED tests/tabixproxies_test.py::TestGFF3::testIteratorCompressed PASSED tests/tabixproxies_test.py::TestGFF3::testIteratorUncompressed PASSED tests/tabixproxies_test.py::TestGFF3::testRead PASSED tests/tabixproxies_test.py::TestGFF3::testUnset PASSED tests/tabixproxies_test.py::TestGFF3::testWrite PASSED tests/tabixproxies_test.py::TestGFF3::test_added_attribute_is_output PASSED tests/tabixproxies_test.py::TestGFF3::test_asdict_can_be_modified PASSED tests/tabixproxies_test.py::TestGFF3::test_asdict_contains_attributes PASSED tests/tabixproxies_test.py::TestGFF3::test_setAttribute_makes_changes PASSED tests/tabixproxies_test.py::TestGFF3::test_setting_end_is_one_based PASSED tests/tabixproxies_test.py::TestGFF3::test_setting_feature_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGFF3::test_setting_fields PASSED tests/tabixproxies_test.py::TestGFF3::test_setting_frame_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGFF3::test_setting_score_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGFF3::test_setting_source_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGFF3::test_setting_start_is_one_based PASSED tests/tabixproxies_test.py::TestGFF3::test_setting_strand_to_none_produces_dot PASSED tests/test_samtools_python.py::test_idxstats_parse_split_lines PASSED tests/test_samtools_python.py::test_bedcov_split_lines PASSED tests/test_samtools_python.py::test_idxstats_parse PASSED tests/test_samtools_python.py::test_bedcov PASSED =============================== warnings summary =============================== ../../../../../usr/lib/python3/dist-packages/pyximport/pyximport.py:51 /usr/lib/python3/dist-packages/pyximport/pyximport.py:51: DeprecationWarning: the imp module is deprecated in favour of importlib and slated for removal in Python 3.12; see the module's documentation for alternative uses import imp ../../../../../usr/lib/python3/dist-packages/Cython/Tempita/__init__.py:4 /usr/lib/python3/dist-packages/Cython/Tempita/__init__.py:4: DeprecationWarning: 'cgi' is deprecated and slated for removal in Python 3.13 from ._tempita import * ../../../../../usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369 /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/tests/_compile_test.pyx tree = Parsing.p_module(s, pxd, full_module_name) .pybuild/cpython3_3.11_pysam/build/tests/AlignedSegment_test.py::TestAlignedSegment::testLargeRead /usr/lib/python3.11/unittest/case.py:678: DeprecationWarning: It is deprecated to return a value that is not None from a test case (>) return self.run(*args, **kwds) -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html ============ 938 passed, 11 skipped, 4 warnings in 60.48s (0:01:00) ============ make[1]: Verzeichnis „/build/python-pysam-0.20.0+ds“ wird verlassen create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild dh_auto_install -O--buildsystem=pybuild I: pybuild base:240: /usr/bin/python3 setup.py install --root /build/python-pysam-0.20.0+ds/debian/python3-pysam # pysam: cython is available - using cythonize if necessary # pysam: htslib mode is external # pysam: HTSLIB_CONFIGURE_OPTIONS=None running install /usr/lib/python3/dist-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools. warnings.warn( running build running build_py copying pysam/config.py -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam copying samtools/samtools_config_vars.h -> /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools running build_ext skipping 'pysam/libchtslib.c' Cython extension (up-to-date) skipping 'pysam/libcsamtools.c' Cython extension (up-to-date) skipping 'pysam/libcbcftools.c' Cython extension (up-to-date) skipping 'pysam/libcutils.c' Cython extension (up-to-date) skipping 'pysam/libcalignmentfile.c' Cython extension (up-to-date) skipping 'pysam/libcsamfile.c' Cython extension (up-to-date) skipping 'pysam/libcalignedsegment.c' Cython extension (up-to-date) skipping 'pysam/libctabix.c' Cython extension (up-to-date) skipping 'pysam/libcfaidx.c' Cython extension (up-to-date) skipping 'pysam/libcbcf.c' Cython extension (up-to-date) skipping 'pysam/libcbgzf.c' Cython extension (up-to-date) skipping 'pysam/libctabixproxies.c' Cython extension (up-to-date) skipping 'pysam/libcvcf.c' Cython extension (up-to-date) creating samtools/samtools_config_vars.h for 'pysam.libcsamtools' extension running install_lib creating /build/python-pysam-0.20.0+ds/debian/python3-pysam creating /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr creating /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib creating /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11 creating /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages creating /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libcfaidx.cpython-311-i386-linux-gnu.so -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/samtools.py -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/Pileup.py -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libcbcftools.cpython-311-i386-linux-gnu.so -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libcbcf.pyi -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libcvcf.cpython-311-i386-linux-gnu.so -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libcsamfile.pxd -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/pysam_stream.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libctabix.pyi -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libcfaidx.pxd -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libcalignmentfile.pyi -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/config.py -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libcfaidx.pyi -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/htslib_util.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libctabixproxies.pxd -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/version.pyi -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/version.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libcsamtools.pyi -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libcsamtools.cpython-311-i386-linux-gnu.so -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libcbgzf.cpython-311-i386-linux-gnu.so -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libchtslib.pxd -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/cbcftools_util.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libcalignedsegment.cpython-311-i386-linux-gnu.so -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libcsamtools.pxd -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libcbcf.cpython-311-i386-linux-gnu.so -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libcalignmentfile.pxd -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libcbcftools.pxd -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libcalignedsegment.pyi -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libcalignedsegment.pxd -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/version.py -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libcutils.cpython-311-i386-linux-gnu.so -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/__init__.py -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libctabix.cpython-311-i386-linux-gnu.so -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libcutils.pxd -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libcsamfile.pyi -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libchtslib.pyi -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libctabixproxies.cpython-311-i386-linux-gnu.so -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/utils.py -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam creating /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/__pycache__ copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/__pycache__/Pileup.cpython-311.pyc -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/__pycache__ copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/__pycache__/version.cpython-311.pyc -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/__pycache__ copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/__pycache__/__init__.cpython-311.pyc -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/__pycache__ copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/__pycache__/config.cpython-311.pyc -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/__pycache__ copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/__pycache__/utils.cpython-311.pyc -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/__pycache__ copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/__pycache__/bcftools.cpython-311.pyc -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/__pycache__ copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/__pycache__/samtools.cpython-311.pyc -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/__pycache__ copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libcbgzf.pyi -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/pysam_util.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libchtslib.cpython-311-i386-linux-gnu.so -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libcsamfile.cpython-311-i386-linux-gnu.so -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/csamtools_util.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/py.typed -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libcvcf.pyi -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libcalignmentfile.cpython-311-i386-linux-gnu.so -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libctabix.pxd -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libcvcf.pxd -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libcbcftools.pyi -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libctabixproxies.pyi -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libcbcf.pxd -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libcutils.pyi -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam creating /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include creating /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/bam_lpileup.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/bam_plbuf.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/stats_isize.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/config.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/tmp_file.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/sam_opts.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/bam_ampliconclip.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/samtools_config_vars.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/consensus_pileup.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/samtools.pysam.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/bedidx.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/samtools.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/bam.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/splaysort.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/sample.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/__init__.py -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include creating /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/dbuf.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/HMM.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/variantkey.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/rbuf.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/call.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/gvcf.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/abuf.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/bcftools.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/config.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/khash_str2str.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/ploidy.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/hex.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/bam_sample.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/kheap.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/extsort.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/regidx.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/bam2bcf.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/mw.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/tsv2vcf.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/smpl_ilist.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/vcfbuf.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/kmin.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/dist.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/hclust.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/prob1.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/vcmp.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/convert.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/utlist.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/bin.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/filter.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/str_finder.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/bcftools.pysam.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/cols.h -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/bcftools.py -> /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam byte-compiling /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/samtools.py to samtools.cpython-311.pyc byte-compiling /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/Pileup.py to Pileup.cpython-311.pyc byte-compiling /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/config.py to config.cpython-311.pyc byte-compiling /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/version.py to version.cpython-311.pyc byte-compiling /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/__init__.py to __init__.cpython-311.pyc byte-compiling /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/utils.py to utils.cpython-311.pyc byte-compiling /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/__init__.py to __init__.cpython-311.pyc byte-compiling /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/bcftools.py to bcftools.cpython-311.pyc running install_egg_info running egg_info creating pysam.egg-info writing pysam.egg-info/PKG-INFO writing dependency_links to pysam.egg-info/dependency_links.txt writing top-level names to pysam.egg-info/top_level.txt writing manifest file 'pysam.egg-info/SOURCES.txt' reading manifest file 'pysam.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'KNOWN_BUGS' warning: no files found matching 'THANKS' warning: no files found matching 'win32/*.[ch]' no previously-included directories found matching 'tests/' warning: no files found matching 'htslib/LICENSE' warning: no files found matching 'htslib/README' warning: no files found matching '*.[ch]' under directory 'htslib' warning: no previously-included files found matching 'htslib/*config*.h' warning: no files found matching 'htslib/configure.ac' warning: no files found matching 'htslib/m4/*.m4' warning: no files found matching 'htslib/*.in' warning: no files found matching 'htslib/configure' warning: no files found matching 'htslib/version.sh' warning: no files found matching 'htslib/Makefile' warning: no files found matching 'htslib/*.mk' warning: no previously-included files found matching 'htslib/config.mk' warning: no previously-included files found matching 'htslib/htscodecs.mk' adding license file 'COPYING' adding license file 'AUTHORS' writing manifest file 'pysam.egg-info/SOURCES.txt' Copying pysam.egg-info to /build/python-pysam-0.20.0+ds/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam-0.20.0.egg-info Skipping SOURCES.txt running install_scripts debian/rules override_dh_install make[1]: Verzeichnis „/build/python-pysam-0.20.0+ds“ wird betreten cd tests/pysam_data && /usr/bin/make clean make[2]: Verzeichnis „/build/python-pysam-0.20.0+ds/tests/pysam_data“ wird betreten rm -fr *.bai *.csi *.fai *.gzi *.pileup* [a-z]*.cram *.crai \ all.stamp *~ calDepth *.dSYM pysam_*.sam \ ex2.sam ex2.sam.gz ex1.sam ex1.fa.gz \ with_md.sam.gz \ *.fq.gz make[2]: Verzeichnis „/build/python-pysam-0.20.0+ds/tests/pysam_data“ wird verlassen cd tests/cbcf_data && /usr/bin/make clean make[2]: Verzeichnis „/build/python-pysam-0.20.0+ds/tests/cbcf_data“ wird betreten rm -f all.stamp *.gz *.tbi *.csi *.bcf make[2]: Verzeichnis „/build/python-pysam-0.20.0+ds/tests/cbcf_data“ wird verlassen find . -name "*.pyc" -delete find . -name "*.pyxbldc" -delete find . -name "tmp_*.bam" -delete find . -name "*.bai*" -delete find . -name "*.cram*" -delete find . -name "pysam_uncompressed.bam" -delete rm -rf tests/pysam_test_work \ tests/example_htslib.gtf.gz.tbi \ tests/log.txt \ tests/test.bam \ tests/_compile_test.c \ tests/pysam_ex2.sam \ tests/__pycache__ \ pysam/calignmentfile.c \ pysam/cbcf.c \ tests/GRCh38_full_analysis_set_plus_decoy_hla.fa.fai \ tests/pysam_data/ex1.fa.gz \ tests/pysam_data/ex1.fa.gz.gzi \ tests/pysam_data/ex1_csi.bam.csi rm -rf .pytest_cache/ dh_install -Xtest.gtf.gz find debian -name log.txt -delete make[1]: Verzeichnis „/build/python-pysam-0.20.0+ds“ wird verlassen dh_installdocs -O--buildsystem=pybuild dh_installchangelogs -O--buildsystem=pybuild dh_python3 -O--buildsystem=pybuild dh_installsystemduser -O--buildsystem=pybuild dh_lintian -O--buildsystem=pybuild dh_perl -O--buildsystem=pybuild dh_link -O--buildsystem=pybuild dh_strip_nondeterminism -O--buildsystem=pybuild dh_compress -O--buildsystem=pybuild dh_fixperms -O--buildsystem=pybuild dh_missing -O--buildsystem=pybuild dh_dwz -a -O--buildsystem=pybuild dwz: debian/python3-pysam/usr/lib/python3/dist-packages/pysam/libcbcf.cpython-311-i386-linux-gnu.so: DWARF compression not beneficial - old size 1113507 new size 1124039 dh_strip -a -O--buildsystem=pybuild dh_makeshlibs -a -O--buildsystem=pybuild dh_shlibdeps -a -O--buildsystem=pybuild dh_installdeb -O--buildsystem=pybuild dh_gencontrol -O--buildsystem=pybuild dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild dpkg-deb: Paket »python-pysam-tests« wird in »../python-pysam-tests_0.20.0+ds-3_all.deb« gebaut. dpkg-deb: Paket »python3-pysam« wird in »../python3-pysam_0.20.0+ds-3_i386.deb« gebaut. dpkg-deb: Paket »python3-pysam-dbgsym« wird in »../python3-pysam-dbgsym_0.20.0+ds-3_i386.deb« gebaut. dpkg-genbuildinfo --build=binary -O../python-pysam_0.20.0+ds-3_i386.buildinfo dpkg-genchanges --build=binary -O../python-pysam_0.20.0+ds-3_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/29729/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/29729/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/29729 and its subdirectories I: Current time: Tue May 9 20:47:23 +14 2023 I: pbuilder-time-stamp: 1683614843