I: pbuilder: network access will be disabled during build I: Current time: Mon Jun 3 10:35:38 +14 2024 I: pbuilder-time-stamp: 1717360538 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: Copying source file I: copying [python-pbcore_2.1.2+dfsg-5.dsc] I: copying [./python-pbcore_2.1.2+dfsg.orig.tar.xz] I: copying [./python-pbcore_2.1.2+dfsg-5.debian.tar.xz] I: Extracting source gpgv: Signature made Sun Jan 8 05:59:55 2023 +14 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./python-pbcore_2.1.2+dfsg-5.dsc: no acceptable signature found dpkg-source: info: extracting python-pbcore in python-pbcore-2.1.2+dfsg dpkg-source: info: unpacking python-pbcore_2.1.2+dfsg.orig.tar.xz dpkg-source: info: unpacking python-pbcore_2.1.2+dfsg-5.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying doc-theme.patch dpkg-source: info: applying exclude_test_missing_data.patch dpkg-source: info: applying b24746790c7105212e45dc2f40115d231bd8baae.patch dpkg-source: info: applying seek-curdir-for-xml.patch dpkg-source: info: applying numpy_1.24.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3498304/tmp/hooks/D01_modify_environment starting debug: Running on ionos15-amd64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Jun 3 10:36 /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/3498304/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/3498304/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]="x86_64-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=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16' DIRSTACK=() DISTRIBUTION=bookworm EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=345d68895f3948b585d69179a0ed2e87 LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=3498304 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.gohQ7iCB/pbuilderrc_OPVv --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.gohQ7iCB/b2 --logfile b2/build.log --extrapackages usrmerge python-pbcore_2.1.2+dfsg-5.dsc' SUDO_GID=111 SUDO_UID=106 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://85.184.249.68:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-0.deb11.6-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.15-1~bpo11+1 (2023-03-16) x86_64 GNU/Linux I: ls -l /bin total 5632 -rwxr-xr-x 1 root root 1265648 Apr 24 2023 bash -rwxr-xr-x 3 root root 39224 Sep 19 2022 bunzip2 -rwxr-xr-x 3 root root 39224 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 39224 Sep 19 2022 bzip2 -rwxr-xr-x 1 root root 14568 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 44016 Sep 21 2022 cat -rwxr-xr-x 1 root root 68656 Sep 21 2022 chgrp -rwxr-xr-x 1 root root 64496 Sep 21 2022 chmod -rwxr-xr-x 1 root root 72752 Sep 21 2022 chown -rwxr-xr-x 1 root root 151152 Sep 21 2022 cp -rwxr-xr-x 1 root root 125640 Jan 6 2023 dash -rwxr-xr-x 1 root root 121904 Sep 21 2022 date -rwxr-xr-x 1 root root 89240 Sep 21 2022 dd -rwxr-xr-x 1 root root 102200 Sep 21 2022 df -rwxr-xr-x 1 root root 151344 Sep 21 2022 dir -rwxr-xr-x 1 root root 88656 Mar 24 2023 dmesg lrwxrwxrwx 1 root root 8 Dec 20 2022 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 20 2022 domainname -> hostname -rwxr-xr-x 1 root root 43856 Sep 21 2022 echo -rwxr-xr-x 1 root root 41 Jan 25 2023 egrep -rwxr-xr-x 1 root root 35664 Sep 21 2022 false -rwxr-xr-x 1 root root 41 Jan 25 2023 fgrep -rwxr-xr-x 1 root root 85600 Mar 24 2023 findmnt -rwsr-xr-x 1 root root 35128 Mar 23 2023 fusermount -rwxr-xr-x 1 root root 203152 Jan 25 2023 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 98136 Apr 10 2022 gzip -rwxr-xr-x 1 root root 22680 Dec 20 2022 hostname -rwxr-xr-x 1 root root 72824 Sep 21 2022 ln -rwxr-xr-x 1 root root 53024 Mar 24 2023 login -rwxr-xr-x 1 root root 151344 Sep 21 2022 ls -rwxr-xr-x 1 root root 207168 Mar 24 2023 lsblk -rwxr-xr-x 1 root root 97552 Sep 21 2022 mkdir -rwxr-xr-x 1 root root 72912 Sep 21 2022 mknod -rwxr-xr-x 1 root root 43952 Sep 21 2022 mktemp -rwxr-xr-x 1 root root 59712 Mar 24 2023 more -rwsr-xr-x 1 root root 59704 Mar 24 2023 mount -rwxr-xr-x 1 root root 18744 Mar 24 2023 mountpoint -rwxr-xr-x 1 root root 142968 Sep 21 2022 mv lrwxrwxrwx 1 root root 8 Dec 20 2022 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 3 2023 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 43952 Sep 21 2022 pwd lrwxrwxrwx 1 root root 4 Apr 24 2023 rbash -> bash -rwxr-xr-x 1 root root 52112 Sep 21 2022 readlink -rwxr-xr-x 1 root root 72752 Sep 21 2022 rm -rwxr-xr-x 1 root root 56240 Sep 21 2022 rmdir -rwxr-xr-x 1 root root 27560 Nov 3 2022 run-parts -rwxr-xr-x 1 root root 126424 Jan 6 2023 sed lrwxrwxrwx 1 root root 9 Jun 3 10:36 sh -> /bin/bash -rwxr-xr-x 1 root root 43888 Sep 21 2022 sleep -rwxr-xr-x 1 root root 85008 Sep 21 2022 stty -rwsr-xr-x 1 root root 72000 Mar 24 2023 su -rwxr-xr-x 1 root root 39824 Sep 21 2022 sync -rwxr-xr-x 1 root root 531984 Apr 7 2023 tar -rwxr-xr-x 1 root root 14520 Nov 3 2022 tempfile -rwxr-xr-x 1 root root 109616 Sep 21 2022 touch -rwxr-xr-x 1 root root 35664 Sep 21 2022 true -rwxr-xr-x 1 root root 14568 Mar 23 2023 ulockmgr_server -rwsr-xr-x 1 root root 35128 Mar 24 2023 umount -rwxr-xr-x 1 root root 43888 Sep 21 2022 uname -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress -rwxr-xr-x 1 root root 151344 Sep 21 2022 vdir -rwxr-xr-x 1 root root 72024 Mar 24 2023 wdctl lrwxrwxrwx 1 root root 8 Dec 20 2022 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/3498304/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: amd64 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-python, python3-sphinx, python3-all, python3-setuptools, python3-h5py, python3-numpy, python3-pysam, python3-pytest, python3-uritools, python3-pytest-runner, python3-pytest-xdist, python3-pytest-cov, python3-biopython (>= 1.74), python3-xmlschema, pylint, python3-coverage dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19596 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-python; however: Package dh-python is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinx; however: Package python3-sphinx is not installed. pbuilder-satisfydepends-dummy depends on python3-all; however: Package python3-all is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on python3-h5py; however: Package python3-h5py is not installed. pbuilder-satisfydepends-dummy depends on python3-numpy; however: Package python3-numpy is not installed. pbuilder-satisfydepends-dummy depends on python3-pysam; however: Package python3-pysam is not installed. pbuilder-satisfydepends-dummy depends on python3-pytest; however: Package python3-pytest is not installed. pbuilder-satisfydepends-dummy depends on python3-uritools; however: Package python3-uritools is not installed. pbuilder-satisfydepends-dummy depends on python3-pytest-runner; however: Package python3-pytest-runner is not installed. pbuilder-satisfydepends-dummy depends on python3-pytest-xdist; however: Package python3-pytest-xdist is not installed. pbuilder-satisfydepends-dummy depends on python3-pytest-cov; however: Package python3-pytest-cov is not installed. pbuilder-satisfydepends-dummy depends on python3-biopython (>= 1.74); however: Package python3-biopython is not installed. pbuilder-satisfydepends-dummy depends on python3-xmlschema; however: Package python3-xmlschema is not installed. pbuilder-satisfydepends-dummy depends on pylint; however: Package pylint is not installed. pbuilder-satisfydepends-dummy depends on python3-coverage; however: Package python3-coverage 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} bsdextrautils{a} ca-certificates{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} docutils-common{a} dwz{a} file{a} fonts-urw-base35{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libaec0{a} libarchive-zip-perl{a} libblas3{a} libbrotli1{a} libbsd0{a} libcurl3-gnutls{a} libcurl4{a} libdebhelper-perl{a} libdeflate0{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libfontenc1{a} libfreetype6{a} libfribidi0{a} libgfortran5{a} libglib2.0-0{a} libgraphite2-3{a} libharfbuzz0b{a} libhdf5-103-1{a} libhdf5-hl-100{a} libhts3{a} libhtscodecs2{a} libicu72{a} libimagequant0{a} libjbig0{a} libjpeg62-turbo{a} libjs-jquery{a} libjs-jquery-hotkeys{a} libjs-jquery-isonscreen{a} libjs-jquery-metadata{a} libjs-jquery-tablesorter{a} libjs-jquery-throttle-debounce{a} libjs-sphinxdoc{a} libjs-underscore{a} libjson-perl{a} liblapack3{a} liblcms2-2{a} libldap-2.5-0{a} liblerc4{a} liblzf1{a} libmagic-mgc{a} libmagic1{a} libnghttp2-14{a} libopenjp2-7{a} libpipeline1{a} libpng16-16{a} libpsl5{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libraqm0{a} libreadline8{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1{a} libsub-override-perl{a} libsz2{a} libtiff6{a} libtool{a} libuchardet0{a} libwebp7{a} libwebpdemux2{a} libwebpmux3{a} libxau6{a} libxcb1{a} libxdmcp6{a} libxml2{a} m4{a} mailcap{a} man-db{a} media-types{a} mime-support{a} openssl{a} po-debconf{a} pylint{a} python-babel-localedata{a} python3{a} python3-alabaster{a} python3-all{a} python3-astroid{a} python3-attr{a} python3-babel{a} python3-biopython{a} python3-certifi{a} python3-chardet{a} python3-charset-normalizer{a} python3-coverage{a} python3-dill{a} python3-distutils{a} python3-docutils{a} python3-elementpath{a} python3-execnet{a} python3-h5py{a} python3-h5py-serial{a} python3-idna{a} python3-imagesize{a} python3-importlib-metadata{a} python3-iniconfig{a} python3-isort{a} python3-jinja2{a} python3-lazy-object-proxy{a} python3-lib2to3{a} python3-logilab-common{a} python3-markupsafe{a} python3-mccabe{a} python3-minimal{a} python3-more-itertools{a} python3-mypy-extensions{a} python3-numpy{a} python3-packaging{a} python3-pil{a} python3-pkg-resources{a} python3-platformdirs{a} python3-pluggy{a} python3-py{a} python3-pygments{a} python3-pysam{a} python3-pytest{a} python3-pytest-cov{a} python3-pytest-runner{a} python3-pytest-xdist{a} python3-renderpm{a} python3-reportlab{a} python3-reportlab-accel{a} python3-requests{a} python3-roman{a} python3-setuptools{a} python3-six{a} python3-snowballstemmer{a} python3-sphinx{a} python3-toml{a} python3-tomlkit{a} python3-typing-extensions{a} python3-tz{a} python3-uritools{a} python3-urllib3{a} python3-wrapt{a} python3-xmlschema{a} python3-zipp{a} python3.11{a} python3.11-minimal{a} readline-common{a} sensible-utils{a} sgml-base{a} sphinx-common{a} w3c-sgml-lib{a} x11-common{a} xfonts-encodings{a} xfonts-utils{a} xml-core{a} The following packages are RECOMMENDED but will NOT be installed: curl javascript-common libarchive-cpio-perl libglib2.0-data libjson-xs-perl libldap-common libltdl-dev libmail-sendmail-perl libpaper-utils libsasl2-modules lynx ncbi-blast+ publicsuffix python-biopython-doc python3-olefile python3-tk shared-mime-info wget xdg-user-dirs 0 packages upgraded, 170 newly installed, 0 to remove and 0 not upgraded. Need to get 74.8 MB of archives. After unpacking 280 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 2 http://deb.debian.org/debian bookworm/main amd64 libjs-jquery-hotkeys all 0~20130707+git2d51e3a9+dfsg-2.1 [11.5 kB] Get: 3 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-minimal amd64 3.11.2-6 [813 kB] Get: 4 http://deb.debian.org/debian bookworm/main amd64 libexpat1 amd64 2.5.0-1 [99.3 kB] Get: 5 http://deb.debian.org/debian bookworm/main amd64 python3.11-minimal amd64 3.11.2-6 [2064 kB] Get: 6 http://deb.debian.org/debian bookworm/main amd64 python3-minimal amd64 3.11.2-1+b1 [26.3 kB] Get: 7 http://deb.debian.org/debian bookworm/main amd64 media-types all 10.0.0 [26.1 kB] Get: 8 http://deb.debian.org/debian bookworm/main amd64 mailcap all 3.70+nmu1 [32.0 kB] Get: 9 http://deb.debian.org/debian bookworm/main amd64 mime-support all 3.66 [10.9 kB] Get: 10 http://deb.debian.org/debian bookworm/main amd64 readline-common all 8.2-1.3 [69.0 kB] Get: 11 http://deb.debian.org/debian bookworm/main amd64 libreadline8 amd64 8.2-1.3 [166 kB] Get: 12 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-stdlib amd64 3.11.2-6 [1796 kB] Get: 13 http://deb.debian.org/debian bookworm/main amd64 python3.11 amd64 3.11.2-6 [572 kB] Get: 14 http://deb.debian.org/debian bookworm/main amd64 libpython3-stdlib amd64 3.11.2-1+b1 [9312 B] Get: 15 http://deb.debian.org/debian bookworm/main amd64 python3 amd64 3.11.2-1+b1 [26.3 kB] Get: 16 http://deb.debian.org/debian bookworm/main amd64 sgml-base all 1.31 [15.4 kB] Get: 17 http://deb.debian.org/debian bookworm/main amd64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 18 http://deb.debian.org/debian bookworm/main amd64 openssl amd64 3.0.8-1 [1407 kB] Get: 19 http://deb.debian.org/debian bookworm/main amd64 ca-certificates all 20230311 [153 kB] Get: 20 http://deb.debian.org/debian bookworm/main amd64 libmagic-mgc amd64 1:5.44-3 [305 kB] Get: 21 http://deb.debian.org/debian bookworm/main amd64 libmagic1 amd64 1:5.44-3 [104 kB] Get: 22 http://deb.debian.org/debian bookworm/main amd64 file amd64 1:5.44-3 [42.5 kB] Get: 23 http://deb.debian.org/debian bookworm/main amd64 gettext-base amd64 0.21-12 [160 kB] Get: 24 http://deb.debian.org/debian bookworm/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 25 http://deb.debian.org/debian bookworm/main amd64 groff-base amd64 1.22.4-10 [916 kB] Get: 26 http://deb.debian.org/debian bookworm/main amd64 bsdextrautils amd64 2.38.1-5+b1 [86.6 kB] Get: 27 http://deb.debian.org/debian bookworm/main amd64 libpipeline1 amd64 1.5.7-1 [38.5 kB] Get: 28 http://deb.debian.org/debian bookworm/main amd64 man-db amd64 2.11.2-2 [1386 kB] Get: 29 http://deb.debian.org/debian bookworm/main amd64 m4 amd64 1.4.19-3 [287 kB] Get: 30 http://deb.debian.org/debian bookworm/main amd64 autoconf all 2.71-3 [332 kB] Get: 31 http://deb.debian.org/debian bookworm/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 32 http://deb.debian.org/debian bookworm/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 33 http://deb.debian.org/debian bookworm/main amd64 autopoint all 0.21-12 [495 kB] Get: 34 http://deb.debian.org/debian bookworm/main amd64 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 35 http://deb.debian.org/debian bookworm/main amd64 libtool all 2.4.7-5 [517 kB] Get: 36 http://deb.debian.org/debian bookworm/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 37 http://deb.debian.org/debian bookworm/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 38 http://deb.debian.org/debian bookworm/main amd64 libsub-override-perl all 0.09-4 [9304 B] Get: 39 http://deb.debian.org/debian bookworm/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 40 http://deb.debian.org/debian bookworm/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 41 http://deb.debian.org/debian bookworm/main amd64 libelf1 amd64 0.188-2.1 [174 kB] Get: 42 http://deb.debian.org/debian bookworm/main amd64 dwz amd64 0.15-1 [109 kB] Get: 43 http://deb.debian.org/debian bookworm/main amd64 libicu72 amd64 72.1-3 [9376 kB] Get: 44 http://deb.debian.org/debian bookworm/main amd64 libxml2 amd64 2.9.14+dfsg-1.2 [687 kB] Get: 45 http://deb.debian.org/debian bookworm/main amd64 gettext amd64 0.21-12 [1300 kB] Get: 46 http://deb.debian.org/debian bookworm/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 47 http://deb.debian.org/debian bookworm/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 48 http://deb.debian.org/debian bookworm/main amd64 debhelper all 13.11.4 [942 kB] Get: 49 http://deb.debian.org/debian bookworm/main amd64 python3-lib2to3 all 3.11.2-2 [76.2 kB] Get: 50 http://deb.debian.org/debian bookworm/main amd64 python3-distutils all 3.11.2-2 [131 kB] Get: 51 http://deb.debian.org/debian bookworm/main amd64 dh-python all 5.20230130 [104 kB] Get: 52 http://deb.debian.org/debian bookworm/main amd64 xml-core all 0.18+nmu1 [23.8 kB] Get: 53 http://deb.debian.org/debian bookworm/main amd64 docutils-common all 0.19+dfsg-6 [127 kB] Get: 54 http://deb.debian.org/debian bookworm/main amd64 libfontenc1 amd64 1:1.1.4-1 [24.3 kB] Get: 55 http://deb.debian.org/debian bookworm/main amd64 libbrotli1 amd64 1.0.9-2+b6 [275 kB] Get: 56 http://deb.debian.org/debian bookworm/main amd64 libpng16-16 amd64 1.6.39-2 [276 kB] Get: 57 http://deb.debian.org/debian bookworm/main amd64 libfreetype6 amd64 2.12.1+dfsg-4 [399 kB] Get: 58 http://deb.debian.org/debian bookworm/main amd64 x11-common all 1:7.7+23 [252 kB] Get: 59 http://deb.debian.org/debian bookworm/main amd64 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get: 60 http://deb.debian.org/debian bookworm/main amd64 xfonts-utils amd64 1:7.7+6 [93.0 kB] Get: 61 http://deb.debian.org/debian bookworm/main amd64 fonts-urw-base35 all 20200910-7 [10.8 MB] Get: 62 http://deb.debian.org/debian bookworm/main amd64 libaec0 amd64 1.0.6-1+b1 [21.1 kB] Get: 63 http://deb.debian.org/debian bookworm/main amd64 libblas3 amd64 3.11.0-2 [149 kB] Get: 64 http://deb.debian.org/debian bookworm/main amd64 libbsd0 amd64 0.11.7-2 [117 kB] Get: 65 http://deb.debian.org/debian bookworm/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg-10 [20.3 kB] Get: 66 http://deb.debian.org/debian bookworm/main amd64 libsasl2-2 amd64 2.1.28+dfsg-10 [59.7 kB] Get: 67 http://deb.debian.org/debian bookworm/main amd64 libldap-2.5-0 amd64 2.5.13+dfsg-5 [183 kB] Get: 68 http://deb.debian.org/debian bookworm/main amd64 libnghttp2-14 amd64 1.52.0-1 [72.3 kB] Get: 69 http://deb.debian.org/debian bookworm/main amd64 libpsl5 amd64 0.21.2-1 [58.7 kB] Get: 70 http://deb.debian.org/debian bookworm/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b2 [60.8 kB] Get: 71 http://deb.debian.org/debian bookworm/main amd64 libssh2-1 amd64 1.10.0-3+b1 [179 kB] Get: 72 http://deb.debian.org/debian bookworm/main amd64 libcurl3-gnutls amd64 7.88.1-9 [381 kB] Get: 73 http://deb.debian.org/debian bookworm/main amd64 libcurl4 amd64 7.88.1-9 [386 kB] Get: 74 http://deb.debian.org/debian bookworm/main amd64 libdeflate0 amd64 1.14-1 [61.4 kB] Get: 75 http://deb.debian.org/debian bookworm/main amd64 libfribidi0 amd64 1.0.8-2.1 [65.0 kB] Get: 76 http://deb.debian.org/debian bookworm/main amd64 libgfortran5 amd64 12.2.0-14 [793 kB] Get: 77 http://deb.debian.org/debian bookworm/main amd64 libglib2.0-0 amd64 2.74.6-2 [1398 kB] Get: 78 http://deb.debian.org/debian bookworm/main amd64 libgraphite2-3 amd64 1.3.14-1 [81.2 kB] Get: 79 http://deb.debian.org/debian bookworm/main amd64 libharfbuzz0b amd64 6.0.0+dfsg-3 [1945 kB] Get: 80 http://deb.debian.org/debian bookworm/main amd64 libsz2 amd64 1.0.6-1+b1 [7804 B] Get: 81 http://deb.debian.org/debian bookworm/main amd64 libhdf5-103-1 amd64 1.10.8+repack1-1 [1237 kB] Get: 82 http://deb.debian.org/debian bookworm/main amd64 libhdf5-hl-100 amd64 1.10.8+repack1-1 [67.8 kB] Get: 83 http://deb.debian.org/debian bookworm/main amd64 libhtscodecs2 amd64 1.3.0-4 [87.5 kB] Get: 84 http://deb.debian.org/debian bookworm/main amd64 libhts3 amd64 1.16+ds-3 [430 kB] Get: 85 http://deb.debian.org/debian bookworm/main amd64 libimagequant0 amd64 2.17.0-1 [32.5 kB] Get: 86 http://deb.debian.org/debian bookworm/main amd64 libjbig0 amd64 2.1-6.1 [31.7 kB] Get: 87 http://deb.debian.org/debian bookworm/main amd64 libjpeg62-turbo amd64 1:2.1.5-2 [166 kB] Get: 88 http://deb.debian.org/debian bookworm/main amd64 libjs-jquery-isonscreen all 1.2.0-1.1 [3196 B] Get: 89 http://deb.debian.org/debian bookworm/main amd64 libjs-jquery-metadata all 12-4 [6532 B] Get: 90 http://deb.debian.org/debian bookworm/main amd64 libjs-jquery-tablesorter all 1:2.31.3+dfsg1-3 [184 kB] Get: 91 http://deb.debian.org/debian bookworm/main amd64 libjs-jquery-throttle-debounce all 1.1+dfsg.1-2 [12.2 kB] Get: 92 http://deb.debian.org/debian bookworm/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 93 http://deb.debian.org/debian bookworm/main amd64 libjs-sphinxdoc all 5.3.0-4 [130 kB] Get: 94 http://deb.debian.org/debian bookworm/main amd64 libjson-perl all 4.10000-1 [87.5 kB] Get: 95 http://deb.debian.org/debian bookworm/main amd64 liblapack3 amd64 3.11.0-2 [2323 kB] Get: 96 http://deb.debian.org/debian bookworm/main amd64 liblcms2-2 amd64 2.14-2 [154 kB] Get: 97 http://deb.debian.org/debian bookworm/main amd64 liblerc4 amd64 4.0.0+ds-2 [170 kB] Get: 98 http://deb.debian.org/debian bookworm/main amd64 liblzf1 amd64 3.6-3 [10.2 kB] Get: 99 http://deb.debian.org/debian bookworm/main amd64 libopenjp2-7 amd64 2.5.0-1+b1 [189 kB] Get: 100 http://deb.debian.org/debian bookworm/main amd64 libraqm0 amd64 0.7.0-4.1 [10.6 kB] Get: 101 http://deb.debian.org/debian bookworm/main amd64 libwebp7 amd64 1.2.4-0.1 [285 kB] Get: 102 http://deb.debian.org/debian bookworm/main amd64 libtiff6 amd64 4.5.0-5 [316 kB] Get: 103 http://deb.debian.org/debian bookworm/main amd64 libwebpdemux2 amd64 1.2.4-0.1 [99.2 kB] Get: 104 http://deb.debian.org/debian bookworm/main amd64 libwebpmux3 amd64 1.2.4-0.1 [109 kB] Get: 105 http://deb.debian.org/debian bookworm/main amd64 libxau6 amd64 1:1.0.9-1 [19.7 kB] Get: 106 http://deb.debian.org/debian bookworm/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get: 107 http://deb.debian.org/debian bookworm/main amd64 libxcb1 amd64 1.15-1 [144 kB] Get: 108 http://deb.debian.org/debian bookworm/main amd64 python3-pkg-resources all 66.1.1-1 [296 kB] Get: 109 http://deb.debian.org/debian bookworm/main amd64 python3-setuptools all 66.1.1-1 [521 kB] Get: 110 http://deb.debian.org/debian bookworm/main amd64 python3-six all 1.16.0-4 [17.5 kB] Get: 111 http://deb.debian.org/debian bookworm/main amd64 python3-typing-extensions all 4.4.0-1 [45.2 kB] Get: 112 http://deb.debian.org/debian bookworm/main amd64 python3-lazy-object-proxy amd64 1.9.0-1+b1 [21.5 kB] Get: 113 http://deb.debian.org/debian bookworm/main amd64 python3-wrapt amd64 1.14.1-2+b2 [42.1 kB] Get: 114 http://deb.debian.org/debian bookworm/main amd64 python3-astroid all 2.14.2-1 [209 kB] Get: 115 http://deb.debian.org/debian bookworm/main amd64 python3-toml all 0.10.2-1 [16.2 kB] Get: 116 http://deb.debian.org/debian bookworm/main amd64 python3-isort all 5.6.4-1 [63.2 kB] Get: 117 http://deb.debian.org/debian bookworm/main amd64 python3-more-itertools all 8.10.0-2 [53.0 kB] Get: 118 http://deb.debian.org/debian bookworm/main amd64 python3-zipp all 1.0.0-6 [6696 B] Get: 119 http://deb.debian.org/debian bookworm/main amd64 python3-importlib-metadata all 4.12.0-1 [24.9 kB] Get: 120 http://deb.debian.org/debian bookworm/main amd64 python3-mypy-extensions all 0.4.3-4 [5788 B] Get: 121 http://deb.debian.org/debian bookworm/main amd64 python3-logilab-common all 1.9.8-1 [380 kB] Get: 122 http://deb.debian.org/debian bookworm/main amd64 python3-dill all 0.3.6-1 [79.5 kB] Get: 123 http://deb.debian.org/debian bookworm/main amd64 python3-mccabe all 0.7.0-1 [10.5 kB] Get: 124 http://deb.debian.org/debian bookworm/main amd64 python3-platformdirs all 2.6.0-1 [16.3 kB] Get: 125 http://deb.debian.org/debian bookworm/main amd64 python3-tomlkit all 0.11.7-1 [40.5 kB] Get: 126 http://deb.debian.org/debian bookworm/main amd64 pylint all 2.16.2-2 [339 kB] Get: 127 http://deb.debian.org/debian bookworm/main amd64 python-babel-localedata all 2.10.3-1 [5615 kB] Get: 128 http://deb.debian.org/debian bookworm/main amd64 python3-alabaster all 0.7.12-1 [20.8 kB] Get: 129 http://deb.debian.org/debian bookworm/main amd64 python3-all amd64 3.11.2-1+b1 [1056 B] Get: 130 http://deb.debian.org/debian bookworm/main amd64 python3-attr all 22.2.0-1 [65.4 kB] Get: 131 http://deb.debian.org/debian bookworm/main amd64 python3-tz all 2022.7.1-3 [30.1 kB] Get: 132 http://deb.debian.org/debian bookworm/main amd64 python3-babel all 2.10.3-1 [103 kB] Get: 133 http://deb.debian.org/debian bookworm/main amd64 python3-numpy amd64 1:1.24.2-1 [5209 kB] Get: 134 http://deb.debian.org/debian bookworm/main amd64 python3-renderpm amd64 3.6.12-1+b1 [79.2 kB] Get: 135 http://deb.debian.org/debian bookworm/main amd64 python3-reportlab-accel amd64 3.6.12-1+b1 [38.6 kB] Get: 136 http://deb.debian.org/debian bookworm/main amd64 python3-pil amd64 9.4.0-1.1+b1 [472 kB] Get: 137 http://deb.debian.org/debian bookworm/main amd64 python3-reportlab all 3.6.12-1 [564 kB] Get: 138 http://deb.debian.org/debian bookworm/main amd64 w3c-sgml-lib all 1.3-3 [273 kB] Get: 139 http://deb.debian.org/debian bookworm/main amd64 python3-biopython amd64 1.80+dfsg-4+b1 [1593 kB] Get: 140 http://deb.debian.org/debian bookworm/main amd64 python3-certifi all 2022.9.24-1 [153 kB] Get: 141 http://deb.debian.org/debian bookworm/main amd64 python3-chardet all 5.1.0+dfsg-2 [110 kB] Get: 142 http://deb.debian.org/debian bookworm/main amd64 python3-charset-normalizer all 3.0.1-2 [49.3 kB] Get: 143 http://deb.debian.org/debian bookworm/main amd64 python3-coverage amd64 6.5.0+dfsg1-2+b1 [153 kB] Get: 144 http://deb.debian.org/debian bookworm/main amd64 python3-roman all 3.3-3 [9880 B] Get: 145 http://deb.debian.org/debian bookworm/main amd64 python3-docutils all 0.19+dfsg-6 [382 kB] Get: 146 http://deb.debian.org/debian bookworm/main amd64 python3-elementpath all 2.5.3-1 [121 kB] Get: 147 http://deb.debian.org/debian bookworm/main amd64 python3-execnet all 1.9.0-1 [41.5 kB] Get: 148 http://deb.debian.org/debian bookworm/main amd64 python3-h5py-serial amd64 3.7.0-8 [804 kB] Get: 149 http://deb.debian.org/debian bookworm/main amd64 python3-h5py all 3.7.0-8 [10.3 kB] Get: 150 http://deb.debian.org/debian bookworm/main amd64 python3-idna all 3.3-1 [39.4 kB] Get: 151 http://deb.debian.org/debian bookworm/main amd64 python3-imagesize all 1.4.1-1 [6688 B] Get: 152 http://deb.debian.org/debian bookworm/main amd64 python3-iniconfig all 1.1.1-2 [6396 B] Get: 153 http://deb.debian.org/debian bookworm/main amd64 python3-markupsafe amd64 2.1.2-1+b1 [13.2 kB] Get: 154 http://deb.debian.org/debian bookworm/main amd64 python3-jinja2 all 3.1.2-1 [119 kB] Get: 155 http://deb.debian.org/debian bookworm/main amd64 python3-packaging all 23.0-1 [32.5 kB] Get: 156 http://deb.debian.org/debian bookworm/main amd64 python3-pluggy all 1.0.0+repack-1 [19.7 kB] Get: 157 http://deb.debian.org/debian bookworm/main amd64 python3-py all 1.11.0-1 [89.2 kB] Get: 158 http://deb.debian.org/debian bookworm/main amd64 python3-pygments all 2.14.0+dfsg-1 [783 kB] Get: 159 http://deb.debian.org/debian bookworm/main amd64 python3-pysam amd64 0.20.0+ds-3+b1 [1681 kB] Get: 160 http://deb.debian.org/debian bookworm/main amd64 python3-pytest all 7.2.1-2 [236 kB] Get: 161 http://deb.debian.org/debian bookworm/main amd64 python3-pytest-cov all 4.0.0-1 [26.1 kB] Get: 162 http://deb.debian.org/debian bookworm/main amd64 python3-pytest-runner all 2.11.1-4 [8432 B] Get: 163 http://deb.debian.org/debian bookworm/main amd64 python3-pytest-xdist all 3.1.0-1 [39.6 kB] Get: 164 http://deb.debian.org/debian bookworm/main amd64 python3-urllib3 all 1.26.12-1 [117 kB] Get: 165 http://deb.debian.org/debian bookworm/main amd64 python3-requests all 2.28.1+dfsg-1 [67.9 kB] Get: 166 http://deb.debian.org/debian bookworm/main amd64 python3-snowballstemmer all 2.2.0-2 [57.8 kB] Get: 167 http://deb.debian.org/debian bookworm/main amd64 sphinx-common all 5.3.0-4 [653 kB] Get: 168 http://deb.debian.org/debian bookworm/main amd64 python3-sphinx all 5.3.0-4 [549 kB] Get: 169 http://deb.debian.org/debian bookworm/main amd64 python3-uritools all 4.0.0-1 [25.3 kB] Get: 170 http://deb.debian.org/debian bookworm/main amd64 python3-xmlschema all 1.10.0-6 [177 kB] Fetched 74.8 MB in 2s (33.2 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libjs-jquery. (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 ... 19596 files and directories currently installed.) Preparing to unpack .../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-jquery-hotkeys. Preparing to unpack .../libjs-jquery-hotkeys_0~20130707+git2d51e3a9+dfsg-2.1_all.deb ... Unpacking libjs-jquery-hotkeys (0~20130707+git2d51e3a9+dfsg-2.1) ... Selecting previously unselected package libpython3.11-minimal:amd64. Preparing to unpack .../libpython3.11-minimal_3.11.2-6_amd64.deb ... Unpacking libpython3.11-minimal:amd64 (3.11.2-6) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.5.0-1_amd64.deb ... Unpacking libexpat1:amd64 (2.5.0-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.2-6_amd64.deb ... Unpacking python3.11-minimal (3.11.2-6) ... Setting up libpython3.11-minimal:amd64 (3.11.2-6) ... Setting up libexpat1:amd64 (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 ... 19938 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.2-1+b1_amd64.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 mailcap. Preparing to unpack .../2-mailcap_3.70+nmu1_all.deb ... Unpacking mailcap (3.70+nmu1) ... Selecting previously unselected package mime-support. Preparing to unpack .../3-mime-support_3.66_all.deb ... Unpacking mime-support (3.66) ... Selecting previously unselected package readline-common. Preparing to unpack .../4-readline-common_8.2-1.3_all.deb ... Unpacking readline-common (8.2-1.3) ... Selecting previously unselected package libreadline8:amd64. Preparing to unpack .../5-libreadline8_8.2-1.3_amd64.deb ... Unpacking libreadline8:amd64 (8.2-1.3) ... Selecting previously unselected package libpython3.11-stdlib:amd64. Preparing to unpack .../6-libpython3.11-stdlib_3.11.2-6_amd64.deb ... Unpacking libpython3.11-stdlib:amd64 (3.11.2-6) ... Selecting previously unselected package python3.11. Preparing to unpack .../7-python3.11_3.11.2-6_amd64.deb ... Unpacking python3.11 (3.11.2-6) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../8-libpython3-stdlib_3.11.2-1+b1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (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 ... 20396 files and directories currently installed.) Preparing to unpack .../000-python3_3.11.2-1+b1_amd64.deb ... Unpacking python3 (3.11.2-1+b1) ... Selecting previously unselected package sgml-base. Preparing to unpack .../001-sgml-base_1.31_all.deb ... Unpacking sgml-base (1.31) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../002-sensible-utils_0.0.17+nmu1_all.deb ... Unpacking sensible-utils (0.0.17+nmu1) ... Selecting previously unselected package openssl. Preparing to unpack .../003-openssl_3.0.8-1_amd64.deb ... Unpacking openssl (3.0.8-1) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../004-ca-certificates_20230311_all.deb ... Unpacking ca-certificates (20230311) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../005-libmagic-mgc_1%3a5.44-3_amd64.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../006-libmagic1_1%3a5.44-3_amd64.deb ... Unpacking libmagic1:amd64 (1:5.44-3) ... Selecting previously unselected package file. Preparing to unpack .../007-file_1%3a5.44-3_amd64.deb ... Unpacking file (1:5.44-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../008-gettext-base_0.21-12_amd64.deb ... Unpacking gettext-base (0.21-12) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../009-libuchardet0_0.0.7-1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../010-groff-base_1.22.4-10_amd64.deb ... Unpacking groff-base (1.22.4-10) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../011-bsdextrautils_2.38.1-5+b1_amd64.deb ... Unpacking bsdextrautils (2.38.1-5+b1) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../012-libpipeline1_1.5.7-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.7-1) ... Selecting previously unselected package man-db. Preparing to unpack .../013-man-db_2.11.2-2_amd64.deb ... Unpacking man-db (2.11.2-2) ... Selecting previously unselected package m4. Preparing to unpack .../014-m4_1.4.19-3_amd64.deb ... Unpacking m4 (1.4.19-3) ... Selecting previously unselected package autoconf. 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Setting up python3-h5py (3.7.0-8) ... Setting up pylint (2.16.2-2) ... Processing triggers for libc-bin (2.36-9) ... Processing triggers for sgml-base (1.31) ... Setting up w3c-sgml-lib (1.3-3) ... Setting up docutils-common (0.19+dfsg-6) ... Setting up python3-biopython (1.80+dfsg-4+b1) ... Processing triggers for sgml-base (1.31) ... Setting up python3-docutils (0.19+dfsg-6) ... Setting up python3-sphinx (5.3.0-4) ... Processing triggers for ca-certificates (20230311) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. 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/3498304/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/3498304/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/python-pbcore-2.1.2+dfsg/ && 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-pbcore_2.1.2+dfsg-5_source.changes dpkg-buildpackage: info: source package python-pbcore dpkg-buildpackage: info: source version 2.1.2+dfsg-5 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean debian/rules:55: warning: overriding recipe for target 'override_dh_auto_clean' debian/rules:28: warning: ignoring old recipe for target 'override_dh_auto_clean' dh clean --with python3 --buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Entering directory '/build/python-pbcore-2.1.2+dfsg' debian/rules:55: warning: overriding recipe for target 'override_dh_auto_clean' debian/rules:28: warning: ignoring old recipe for target 'override_dh_auto_clean' rm -f doc/pbcore.data.datasets.rst doc/pbcore.io.align.rst doc/pbcore.io.dataset.pyxb.rst rm -fr coverage.xml .eggs/README.txt .pytest_cache rm -rf .pybuild rm -rf _tmp doc/_build/ find . -name __pycache__ | xargs -r rm -rf rm -f .coverage nosetests.xml rm -rf pbcore.egg-info make[1]: Leaving directory '/build/python-pbcore-2.1.2+dfsg' dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary debian/rules:55: warning: overriding recipe for target 'override_dh_auto_clean' debian/rules:28: warning: ignoring old recipe for target 'override_dh_auto_clean' 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 /usr/lib/python3/dist-packages/setuptools/dist.py:775: UserWarning: Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead warnings.warn( running config debian/rules override_dh_auto_build make[1]: Entering directory '/build/python-pbcore-2.1.2+dfsg' debian/rules:55: warning: overriding recipe for target 'override_dh_auto_clean' debian/rules:28: warning: ignoring old recipe for target 'override_dh_auto_clean' dh_auto_build I: pybuild base:240: /usr/bin/python3 setup.py build /usr/lib/python3/dist-packages/setuptools/dist.py:775: UserWarning: Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead warnings.warn( running build running build_py creating /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore copying pbcore/sequence.py -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore copying pbcore/__init__.py -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore creating /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/util copying pbcore/util/statistics.py -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/util copying pbcore/util/decorators.py -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/util copying pbcore/util/__init__.py -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/util copying pbcore/util/ToolRunner.py -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/util creating /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/model copying pbcore/model/baseRegions.py -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/model copying pbcore/model/__init__.py -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/model creating /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io copying pbcore/io/opener.py -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io copying pbcore/io/base.py -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io copying pbcore/io/_utils.py -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io copying pbcore/io/__init__.py -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io copying pbcore/io/VcfIO.py -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io copying pbcore/io/GffIO.py -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io copying pbcore/io/FofnIO.py -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io copying pbcore/io/FastqIO.py -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io copying pbcore/io/FastaIO.py -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io creating /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data copying pbcore/data/__init__.py -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data creating /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/chemistry copying pbcore/chemistry/chemistry.py -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/chemistry copying pbcore/chemistry/__init__.py -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/chemistry creating /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/dataset copying pbcore/io/dataset/DataSetMembers.py -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/dataset copying pbcore/io/dataset/DataSetValidator.py -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/dataset copying pbcore/io/dataset/utils.py -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/dataset copying pbcore/io/dataset/run_split.py -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/dataset copying pbcore/io/dataset/__init__.py -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/dataset copying pbcore/io/dataset/DataSetWriter.py -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/dataset copying pbcore/io/dataset/DataSetUtils.py -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/dataset copying pbcore/io/dataset/DataSetReader.py -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/dataset copying pbcore/io/dataset/DataSetMetaTypes.py -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/dataset copying pbcore/io/dataset/DataSetIO.py -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/dataset copying pbcore/io/dataset/DataSetErrors.py -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/dataset creating /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/align copying pbcore/io/align/__init__.py -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/align copying pbcore/io/align/_BamSupport.py -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/align copying pbcore/io/align/_AlignmentMixin.py -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/align copying pbcore/io/align/PacBioBamIndex.py -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/align copying pbcore/io/align/BlasrIO.py -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/align copying pbcore/io/align/BamIO.py -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/align copying pbcore/io/align/BamAlignment.py -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/align creating /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/__init__.py -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets running egg_info creating pbcore.egg-info writing pbcore.egg-info/PKG-INFO writing dependency_links to pbcore.egg-info/dependency_links.txt writing entry points to pbcore.egg-info/entry_points.txt writing requirements to pbcore.egg-info/requires.txt writing top-level names to pbcore.egg-info/top_level.txt writing manifest file 'pbcore.egg-info/SOURCES.txt' reading manifest file 'pbcore.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching '*.txt' warning: no directories found matching 'bin' adding license file 'LICENSE' writing manifest file 'pbcore.egg-info/SOURCES.txt' /usr/lib/python3/dist-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'pbcore.chemistry.resources' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'pbcore.chemistry.resources' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'pbcore.chemistry.resources' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'pbcore.chemistry.resources' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) copying pbcore/data/Fluidigm_human_amplicons.fasta -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data copying pbcore/data/Fluidigm_human_amplicons.fasta.fai -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data copying pbcore/data/Fluidigm_human_amplicons_tiny.fasta -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data copying pbcore/data/barcodes-ed65-450.fasta -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data copying pbcore/data/barcodes-ed65-450.fasta.fai -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data copying pbcore/data/blasr-output.m4 -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data copying pbcore/data/blasr-output.m5 -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data copying pbcore/data/chemistry.xml -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data copying pbcore/data/empty.aligned_subreads.bam -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data copying pbcore/data/empty.aligned_subreads.bam.pbi -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data copying pbcore/data/empty.ccs.bam -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data copying pbcore/data/empty.ccs.bam.pbi -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data copying pbcore/data/empty2.bam -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data copying pbcore/data/empty2.bam.pbi -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data copying pbcore/data/lambdaNEB.fa -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data copying pbcore/data/lambdaNEB.fa.fai -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data copying pbcore/data/m130727_114215_42211_c100569412550000001823090301191423_s1_p0.ccs.bam -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data copying pbcore/data/m130727_114215_42211_c100569412550000001823090301191423_s1_p0.ccs.bam.bai -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data copying pbcore/data/m130727_114215_42211_c100569412550000001823090301191423_s1_p0.ccs.bam.pbi -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data copying pbcore/data/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.aligned_subreads.bam -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data copying pbcore/data/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.aligned_subreads.bam.bai -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data copying pbcore/data/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.aligned_subreads.bam.pbi -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data copying pbcore/data/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.scraps.bam -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data copying pbcore/data/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.scraps.bam.pbi -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data copying pbcore/data/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.subreads.bam -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data copying pbcore/data/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.subreads.bam.pbi -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data copying pbcore/data/variants.gff -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data copying pbcore/data/weird.fa -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data copying pbcore/data/weird.fa.fai -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data creating /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/chemistry/resources copying pbcore/chemistry/resources/mapping.xml -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/chemistry/resources copying pbcore/data/datasets/CollectionMetadata.xml -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/alignment.dataset.xml -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/barcode.dataset.xml -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/ccsaligned.dataset.xml -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/ccsread.dataset.xml -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/contig.dataset.xml -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/empty_lambda.aligned.bam -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/empty_lambda.aligned.bam.bai -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/empty_lambda.aligned.bam.pbi -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/fofn.fofn -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/lambda.alignmentset.xml -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/lambda.referenceset.xml -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.subreads.fake_bc.bam -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.subreads.fake_bc.bam.bai -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.subreads.fake_bc.bam.pbi -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/m150430_142051_Mon_p1_b25.sts.xml -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/m150616_053259_ethan_c100710482550000001823136404221563_s1_p0.sts.xml -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/pbalchemysim.alignmentset.xml -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/pbalchemysim0.alignmentset.chunk0contigs.xml -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/pbalchemysim0.alignmentset.chunk1contigs.xml -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/pbalchemysim0.alignmentset.xml -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/pbalchemysim0.pbalign.bam -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/pbalchemysim0.pbalign.bam.bai -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/pbalchemysim0.pbalign.bam.pbi -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/pbalchemysim0.reference.fasta -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/pbalchemysim0.reference.fasta.fai -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/pbalchemysim0.referenceset.xml -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/pbalchemysim0.subreads.bam -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/pbalchemysim0.subreads.bam.bai -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/pbalchemysim0.subreads.bam.pbi -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/pbalchemysim0.subreadset.xml -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/pbalchemysim1.alignmentset.xml -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/pbalchemysim1.pbalign.bam -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/pbalchemysim1.pbalign.bam.bai -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/pbalchemysim1.pbalign.bam.pbi -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/pbalchemysim1.subreads.bam -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/pbalchemysim1.subreads.bam.bai -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/pbalchemysim1.subreads.bam.pbi -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/pbalchemysim1.subreadset.xml -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/reference.dataset.xml -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/subread.dataset.xml -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/subreadSetWithStats.xml -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets PYTHONPATH=/build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build /usr/bin/make doc make[2]: Entering directory '/build/python-pbcore-2.1.2+dfsg' sphinx-apidoc -o doc/ pbcore/ && cd doc/ && make html File doc/pbcore.rst already exists, skipping. File doc/pbcore.chemistry.rst already exists, skipping. File doc/pbcore.data.rst already exists, skipping. Creating file doc/pbcore.data.datasets.rst. File doc/pbcore.io.rst already exists, skipping. Creating file doc/pbcore.io.align.rst. File doc/pbcore.io.dataset.rst already exists, skipping. File doc/pbcore.model.rst already exists, skipping. File doc/pbcore.util.rst already exists, skipping. File doc/modules.rst already exists, skipping. make[3]: Entering directory '/build/python-pbcore-2.1.2+dfsg/doc' sphinx-apidoc -o . -d 4 ../pbcore/ File ./pbcore.rst already exists, skipping. File ./pbcore.chemistry.rst already exists, skipping. File ./pbcore.data.rst already exists, skipping. File ./pbcore.data.datasets.rst already exists, skipping. File ./pbcore.io.rst already exists, skipping. File ./pbcore.io.align.rst already exists, skipping. File ./pbcore.io.dataset.rst already exists, skipping. File ./pbcore.model.rst already exists, skipping. File ./pbcore.util.rst already exists, skipping. File ./modules.rst already exists, skipping. sphinx-build -b html -d _build/doctrees . _build/html Running Sphinx v5.3.0 making output directory... done loading intersphinx inventory from http://docs.python.org/objects.inv... WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'http://docs.python.org/objects.inv' not fetchable due to : HTTPConnectionPool(host='docs.python.org', port=80): Max retries exceeded with url: /objects.inv (Caused by NewConnectionError(': Failed to establish a new connection: [Errno -3] Temporary failure in name resolution')) building [mo]: targets for 0 po files that are out of date building [html]: targets for 11 source files that are out of date updating environment: [new config] 11 added, 0 changed, 0 removed reading sources... [ 9%] index reading sources... [ 18%] modules reading sources... [ 27%] pbcore reading sources... [ 36%] pbcore.chemistry reading sources... [ 45%] pbcore.data reading sources... [ 54%] pbcore.data.datasets reading sources... [ 63%] pbcore.io reading sources... [ 72%] pbcore.io.align reading sources... [ 81%] pbcore.io.dataset reading sources... [ 90%] pbcore.model reading sources... [100%] pbcore.util /build/python-pbcore-2.1.2+dfsg/doc/pbcore.rst:7: WARNING: toctree contains reference to nonexisting document 'pbcore.deprecated' /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/dataset/DataSetMembers.py:docstring of pbcore.io.dataset.DataSetMembers:47: ERROR: Unexpected indentation. WARNING: autodoc: failed to import module 'Process' from module 'pbcore.util'; the following exception was raised: No module named 'pbcore.util.Process' looking for now-outdated files... none found pickling environment... done checking consistency... /build/python-pbcore-2.1.2+dfsg/doc/modules.rst: WARNING: document isn't included in any toctree /build/python-pbcore-2.1.2+dfsg/doc/pbcore.data.datasets.rst: WARNING: document isn't included in any toctree /build/python-pbcore-2.1.2+dfsg/doc/pbcore.io.align.rst: WARNING: document isn't included in any toctree /build/python-pbcore-2.1.2+dfsg/doc/pbcore.io.dataset.rst: WARNING: document isn't included in any toctree done preparing documents... done writing output... [ 9%] index writing output... [ 18%] modules writing output... [ 27%] pbcore writing output... [ 36%] pbcore.chemistry writing output... [ 45%] pbcore.data writing output... [ 54%] pbcore.data.datasets writing output... [ 63%] pbcore.io writing output... [ 72%] pbcore.io.align writing output... [ 81%] pbcore.io.dataset writing output... [ 90%] pbcore.model writing output... [100%] pbcore.util WARNING: dot command 'dot' cannot be run (needed for graphviz output), check the graphviz_dot setting generating indices... genindex py-modindex done writing additional pages... search done copying static files... done copying extra files... done dumping search index in English (code: en)... done dumping object inventory... done build succeeded, 9 warnings. The HTML pages are in _build/html. Build finished. The HTML pages are in _build/html. make[3]: Leaving directory '/build/python-pbcore-2.1.2+dfsg/doc' make[2]: Leaving directory '/build/python-pbcore-2.1.2+dfsg' make[1]: Leaving directory '/build/python-pbcore-2.1.2+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/python-pbcore-2.1.2+dfsg' debian/rules:55: warning: overriding recipe for target 'override_dh_auto_clean' debian/rules:28: warning: ignoring old recipe for target 'override_dh_auto_clean' # we need to exclude tests requiring pbtestdata which is not packaged mkdir -p /tmp/tests_avoid mv `grep -l pbtestdata tests/*.py` /tmp/tests_avoid # for whatever reason this test is failing as well - just skip it for the moment mv tests/test_pbdataset_filters.py /tmp/tests_avoid PYBUILD_SYSTEM=custom \ PYBUILD_TEST_ARGS="{interpreter} setup.py test" \ dh_auto_test I: pybuild base:240: python3.11 setup.py test /usr/lib/python3/dist-packages/setuptools/dist.py:775: UserWarning: Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead warnings.warn( running pytest /usr/lib/python3/dist-packages/setuptools/dist.py:775: UserWarning: Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead warnings.warn( /usr/lib/python3/dist-packages/setuptools/command/easy_install.py:146: EasyInstallDeprecationWarning: easy_install command is deprecated. Use build and pip and other standards-based tools. warnings.warn( /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( WARNING: Testing via this command is deprecated and will be removed in a future version. Users looking for a generic test entry point independent of test runner are encouraged to use tox. running egg_info writing pbcore.egg-info/PKG-INFO writing dependency_links to pbcore.egg-info/dependency_links.txt writing entry points to pbcore.egg-info/entry_points.txt writing requirements to pbcore.egg-info/requires.txt writing top-level names to pbcore.egg-info/top_level.txt reading manifest file 'pbcore.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching '*.txt' warning: no directories found matching 'bin' adding license file 'LICENSE' writing manifest file 'pbcore.egg-info/SOURCES.txt' running build_ext ============================= 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-pbcore-2.1.2+dfsg, configfile: pytest.ini plugins: xdist-3.1.0, cov-4.0.0 gw0 I / gw1 I / gw2 I / gw3 I / gw4 I / gw5 I / gw6 I / gw7 I / gw8 I / gw9 I / gw10 I / gw11 I / gw12 I / gw13 I / gw14 I / gw15 I [gw0] linux Python 3.11.2 cwd: /build/python-pbcore-2.1.2+dfsg [gw1] linux Python 3.11.2 cwd: /build/python-pbcore-2.1.2+dfsg [gw2] linux Python 3.11.2 cwd: /build/python-pbcore-2.1.2+dfsg [gw3] linux Python 3.11.2 cwd: /build/python-pbcore-2.1.2+dfsg [gw4] linux Python 3.11.2 cwd: /build/python-pbcore-2.1.2+dfsg [gw5] linux Python 3.11.2 cwd: /build/python-pbcore-2.1.2+dfsg [gw6] linux Python 3.11.2 cwd: /build/python-pbcore-2.1.2+dfsg [gw7] linux Python 3.11.2 cwd: /build/python-pbcore-2.1.2+dfsg [gw8] linux Python 3.11.2 cwd: /build/python-pbcore-2.1.2+dfsg [gw9] linux Python 3.11.2 cwd: /build/python-pbcore-2.1.2+dfsg [gw10] linux Python 3.11.2 cwd: /build/python-pbcore-2.1.2+dfsg [gw11] linux Python 3.11.2 cwd: /build/python-pbcore-2.1.2+dfsg [gw12] linux Python 3.11.2 cwd: /build/python-pbcore-2.1.2+dfsg [gw13] linux Python 3.11.2 cwd: /build/python-pbcore-2.1.2+dfsg [gw14] linux Python 3.11.2 cwd: /build/python-pbcore-2.1.2+dfsg [gw15] linux Python 3.11.2 cwd: /build/python-pbcore-2.1.2+dfsg [gw3] Python 3.11.2 (main, Mar 13 2023, 12:18:29) [GCC 12.2.0] [gw4] Python 3.11.2 (main, Mar 13 2023, 12:18:29) [GCC 12.2.0] [gw0] Python 3.11.2 (main, Mar 13 2023, 12:18:29) [GCC 12.2.0] [gw1] Python 3.11.2 (main, Mar 13 2023, 12:18:29) [GCC 12.2.0] [gw2] Python 3.11.2 (main, Mar 13 2023, 12:18:29) [GCC 12.2.0] [gw6] Python 3.11.2 (main, Mar 13 2023, 12:18:29) [GCC 12.2.0] [gw5] Python 3.11.2 (main, Mar 13 2023, 12:18:29) [GCC 12.2.0] [gw9] Python 3.11.2 (main, Mar 13 2023, 12:18:29) [GCC 12.2.0] [gw12] Python 3.11.2 (main, Mar 13 2023, 12:18:29) [GCC 12.2.0] [gw8] Python 3.11.2 (main, Mar 13 2023, 12:18:29) [GCC 12.2.0] [gw7] Python 3.11.2 (main, Mar 13 2023, 12:18:29) [GCC 12.2.0] [gw14] Python 3.11.2 (main, Mar 13 2023, 12:18:29) [GCC 12.2.0] [gw10] Python 3.11.2 (main, Mar 13 2023, 12:18:29) [GCC 12.2.0] [gw15] Python 3.11.2 (main, Mar 13 2023, 12:18:29) [GCC 12.2.0] [gw11] Python 3.11.2 (main, Mar 13 2023, 12:18:29) [GCC 12.2.0] [gw13] Python 3.11.2 (main, Mar 13 2023, 12:18:29) [GCC 12.2.0] gw0 [140] / gw1 [140] / gw2 [140] / gw3 [140] / gw4 [140] / gw5 [140] / gw6 [140] / gw7 [140] / gw8 [140] / gw9 [140] / gw10 [140] / gw11 [140] / gw12 [140] / gw13 [140] / gw14 [140] / gw15 [140] scheduling tests via LoadScopeScheduling tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test__init__ tests/test_pbcore_io_AlnFileReaders.py::TestMultipleReadGroups::test_retrieve_read_group_properties tests/test_pbcore_extract_bam_sequence.py::TestCase::test_reverse_complement tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testBasicOperations tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testBasicOperations tests/test_pbcore_io_BlasrIO.py::test_m4 tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::testIteration tests/test_pbcore_io_AlnFileReaders.py::TestCCSBam::testBasicOperations tests/test_pbcore_io_AlnFileReaders.py::TestMissingHeaderM5::test_retrieve_read_group_properties tests/test_pbcore_io_FastaIO.py::TestFastaWriter::test_writeFasta1 tests/test_pbcore_io_FastaIO.py::TestFastaReader::test_readFasta tests/test_pbcore_io_AlnFileReaders.py::TestTranscriptBam::test_transcript_set_support [gw6] [ 0%] SKIPPED tests/test_pbcore_io_AlnFileReaders.py::TestTranscriptBam::test_transcript_set_support tests/test_pbcore_io_AlnFileReaders.py::TestUpdatedChemistryMapping::test_load_updated_mapping [gw10] [ 1%] PASSED tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test__init__ tests/test_pbcore_io_AlnFileReaders.py::TestEmptyBam::test_empty_bam_reads_in_range [gw15] [ 2%] PASSED tests/test_pbcore_io_FastaIO.py::TestFastaReader::test_readFasta [gw12] [ 2%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestMissingHeaderM5::test_retrieve_read_group_properties tests/test_pbcore_io_GffIO.py::TestGffReader::test_headers [gw11] [ 3%] PASSED tests/test_pbcore_io_FastaIO.py::TestFastaWriter::test_writeFasta1 tests/test_pbcore_io_FastaIO.py::TestFastaWriter::test_writeFasta2 tests/test_pbcore_io_FastaIO.py::TestFastaReader::test_dosLineEndingsFasta [gw2] [ 4%] SKIPPED tests/test_pbcore_io_AlnFileReaders.py::TestCCSBam::testBasicOperations tests/test_pbcore_io_AlnFileReaders.py::TestCCSBam::testQStartEndUnavailable [gw12] [ 5%] PASSED tests/test_pbcore_io_GffIO.py::TestGffReader::test_headers [gw9] [ 5%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestMultipleReadGroups::test_retrieve_read_group_properties tests/test_pbcore_io_AlnFileReaders.py::TestMultipleReadGroups::test_sample_names [gw4] [ 6%] PASSED tests/test_pbcore_extract_bam_sequence.py::TestCase::test_reverse_complement tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test__init__ [gw8] [ 7%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestUpdatedChemistryMapping::test_load_updated_mapping tests/test_pbcore_io_GffIO.py::TestGffWriter::test_writeHeader [gw8] [ 7%] PASSED tests/test_pbcore_io_GffIO.py::TestGffWriter::test_writeHeader [gw14] [ 8%] PASSED tests/test_pbcore_io_BlasrIO.py::test_m4 tests/test_pbcore_io_BlasrIO.py::test_m5 [gw14] [ 9%] PASSED tests/test_pbcore_io_BlasrIO.py::test_m5 [gw11] [ 10%] PASSED tests/test_pbcore_io_FastaIO.py::TestFastaWriter::test_writeFasta2 [gw4] [ 10%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test__init__ tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test__str__ tests/test_pbcore_io_unaligned_bam.py::TestUnalignedBam::testInvalidOperations [gw9] [ 11%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestMultipleReadGroups::test_sample_names tests/test_pbcore_io_GffIO.py::TestGff3Record::test_str [gw5] [ 12%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestEmptyBam::test_empty_bam_reads_in_range tests/test_pbcore_io_FofnIO.py::test_simple [gw5] [ 12%] PASSED tests/test_pbcore_io_FofnIO.py::test_simple tests/test_pbcore_io_FofnIO.py::test_empty_lines tests/test_dataset_run_split.py::test [gw3] [ 13%] SKIPPED tests/test_dataset_run_split.py::test tests/test_pbcore_io_FastqIO.py::TestQvConversion::testAsciiFromQvs [gw3] [ 14%] PASSED tests/test_pbcore_io_FastqIO.py::TestQvConversion::testAsciiFromQvs tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test__str__ [gw10] [ 15%] PASSED tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test__str__ tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test_fromString [gw10] [ 15%] PASSED tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test_fromString tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test_reverse_complement1 [gw5] [ 16%] PASSED tests/test_pbcore_io_FofnIO.py::test_empty_lines [gw9] [ 17%] PASSED tests/test_pbcore_io_GffIO.py::TestGff3Record::test_str [gw15] [ 17%] PASSED tests/test_pbcore_io_FastaIO.py::TestFastaReader::test_dosLineEndingsFasta tests/test_pbcore_io_GffIO.py::TestGff3Record::test_modification [gw11] [ 18%] PASSED tests/test_pbcore_io_unaligned_bam.py::TestUnalignedBam::testInvalidOperations [gw13] [ 19%] PASSED tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::testIteration tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::testAccessByName [gw13] [ 20%] PASSED tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::testAccessByName tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::testAccessById [gw13] [ 20%] PASSED tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::testAccessById tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::testAccessByPosition [gw13] [ 21%] PASSED tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::testAccessByPosition tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::testSlice [gw13] [ 22%] PASSED tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::testSlice [gw1] [ 22%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testBasicOperations tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testStrandOrientation [gw1] [ 23%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testStrandOrientation tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testReadName [gw1] [ 24%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testReadName tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testAlignedRead [gw1] [ 25%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testAlignedRead tests/test_pbcore_io_FastqIO.py::TestFastqWriter::test_writeFastq1 [gw6] [ 25%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqWriter::test_writeFastq1 tests/test_pbcore_io_FastqIO.py::TestFastqWriter::test_writeFastq2 [gw6] [ 26%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqWriter::test_writeFastq2 tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::test_dosLineEndingsFasta tests/test_pbcore_io_GffIO.py::TestGffReader::test__iter__ [gw12] [ 27%] PASSED tests/test_pbcore_io_GffIO.py::TestGffReader::test__iter__ tests/test_pbcore_util.py::TestStatistics::test_accuracy_as_phred_qv tests/test_pbcore_io_GffIO.py::TestGffWriter::test_writeRecord [gw8] [ 27%] PASSED tests/test_pbcore_io_GffIO.py::TestGffWriter::test_writeRecord tests/test_pbdataset_split.py::TestDataSetSplit::test_split [gw4] [ 28%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test__str__ tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test_fromString [gw4] [ 29%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test_fromString tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test_reverse_complement1 [gw4] [ 30%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test_reverse_complement1 tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testUnalignedRead [gw1] [ 30%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testUnalignedRead tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testAlignedReference [gw1] [ 31%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testAlignedReference tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test_reverse_complement2 [gw4] [ 32%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test_reverse_complement2 tests/test_pbcore_io_AlnFileReaders.py::TestBarcodedBam::test_read_lima_demultiplexed_bam [gw2] [ 32%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestCCSBam::testQStartEndUnavailable tests/test_pbcore_io_FastqIO.py::TestFastqReader::test_readFastq1 [gw2] [ 33%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqReader::test_readFastq1 [gw7] [ 34%] SKIPPED tests/test_pbcore_io_AlnFileReaders.py::TestBarcodedBam::test_read_lima_demultiplexed_bam tests/test_pbcore_io_GffIO.py::TestGffSorting::test_merge_gffs [gw7] [ 35%] PASSED tests/test_pbcore_io_GffIO.py::TestGffSorting::test_merge_gffs tests/test_pbcore_io_GffIO.py::TestGffSorting::test_merge_gffs_sorted [gw7] [ 35%] PASSED tests/test_pbcore_io_GffIO.py::TestGffSorting::test_merge_gffs_sorted tests/test_pbcore_io_GffIO.py::TestGffSorting::test_sort_gff [gw7] [ 36%] PASSED tests/test_pbcore_io_GffIO.py::TestGffSorting::test_sort_gff [gw0] [ 37%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testBasicOperations tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test_len [gw4] [ 37%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test_len tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test_eq [gw4] [ 38%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test_eq tests/test_pbcore_io_lossless_bam.py::TestCase::test_1 [gw15] [ 39%] SKIPPED tests/test_pbcore_io_lossless_bam.py::TestCase::test_1 tests/test_pbcore_util_sequences.py::TestReverseComplement::test_reverse [gw15] [ 40%] PASSED tests/test_pbcore_util_sequences.py::TestReverseComplement::test_reverse tests/test_pbcore_util_sequences.py::TestReverseComplement::test_complement [gw9] [ 40%] PASSED tests/test_pbcore_io_GffIO.py::TestGff3Record::test_modification tests/test_pbcore_io_GffIO.py::TestGff3Record::test_fromString [gw9] [ 41%] PASSED tests/test_pbcore_io_GffIO.py::TestGff3Record::test_fromString tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testStrandOrientation [gw13] [ 42%] PASSED tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::test_dosLineEndingsFasta [gw15] [ 42%] PASSED tests/test_pbcore_util_sequences.py::TestReverseComplement::test_complement tests/test_pbcore_util_sequences.py::TestReverseComplement::test_reverseComplement [gw15] [ 43%] PASSED tests/test_pbcore_util_sequences.py::TestReverseComplement::test_reverseComplement tests/test_pbcore_util_sequences.py::TestReverseComplement::test_iupac [gw15] [ 44%] PASSED tests/test_pbcore_util_sequences.py::TestReverseComplement::test_iupac tests/test_pbcore_util_sequences.py::TestReverseComplement::test_complement_error tests/test_pbcore_io_VcfIO.py::TestVcfSorting::test_merge_vcfs_sorted [gw14] [ 45%] PASSED tests/test_pbcore_io_VcfIO.py::TestVcfSorting::test_merge_vcfs_sorted tests/test_pbdataset_utils.py::TestDataSetUtils::test_get_dataset_uuid tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testUnalignedReference [gw1] [ 45%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testUnalignedReference tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testDeletionQV [gw1] [ 46%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testDeletionQV tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testTranscript [gw12] [ 47%] PASSED tests/test_pbcore_util.py::TestStatistics::test_accuracy_as_phred_qv [gw10] [ 47%] PASSED tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test_reverse_complement1 tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test_reverse_complement2 [gw10] [ 48%] PASSED tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test_reverse_complement2 tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test_len [gw10] [ 49%] PASSED tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test_len tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test_eq [gw10] [ 50%] PASSED tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test_eq [gw0] [ 50%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testStrandOrientation tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testReadName [gw0] [ 51%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testReadName tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testAlignedRead [gw0] [ 52%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testAlignedRead tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testUnalignedRead [gw0] [ 52%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testUnalignedRead [gw1] [ 53%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testTranscript tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testClippedAlignments [gw1] [ 54%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testClippedAlignments tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testAlignedReference [gw0] [ 55%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testAlignedReference [gw15] [ 55%] PASSED tests/test_pbcore_util_sequences.py::TestReverseComplement::test_complement_error tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testUnalignedReference [gw0] [ 56%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testUnalignedReference tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testReadsInRange tests/test_pbcore_io_unaligned_bam.py::TestUnalignedBam::testIpd [gw11] [ 57%] PASSED tests/test_pbcore_io_unaligned_bam.py::TestUnalignedBam::testIpd tests/test_pbindex.py::TestPbIndex::test_pbindex_bam_consistency tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test_not_equal [gw4] [ 57%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test_not_equal tests/test_pbcore_io_GffIO.py::TestGff3Record::test_get tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testDeletionQV [gw0] [ 58%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testDeletionQV [gw14] [ 59%] PASSED tests/test_pbdataset_utils.py::TestDataSetUtils::test_get_dataset_uuid [gw9] [ 60%] PASSED tests/test_pbcore_io_GffIO.py::TestGff3Record::test_get tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testTranscript [gw0] [ 60%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testTranscript tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testClippedAlignments [gw0] [ 61%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testClippedAlignments tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testReadsInRange tests/test_pbcore_io_FastqIO.py::TestQvConversion::testQvsFromAscii tests/test_pbcore_io_FofnIO.py::test_absolutifying [gw5] [ 62%] PASSED tests/test_pbcore_io_FofnIO.py::test_absolutifying [gw3] [ 62%] PASSED tests/test_pbcore_io_FastqIO.py::TestQvConversion::testQvsFromAscii tests/test_pbcore_util_sequences.py::TestReverseComplement::test_reverse_complement_error [gw15] [ 63%] PASSED tests/test_pbcore_util_sequences.py::TestReverseComplement::test_reverse_complement_error tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test_not_equal [gw10] [ 64%] PASSED tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test_not_equal tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::test_readWeirdFastaIndex [gw13] [ 65%] PASSED tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::test_readWeirdFastaIndex tests/test_pbcore_util.py::TestStatistics::test_phred_qv_as_accuracy [gw12] [ 65%] PASSED tests/test_pbcore_util.py::TestStatistics::test_phred_qv_as_accuracy tests/test_pbdataset_utils.py::TestDataSetUtils::test_get_dataset_metatype tests/test_pbcore_io_FastqIO.py::TestFastqReader::test_readFastq2 [gw2] [ 66%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqReader::test_readFastq2 tests/test_pbcore_io_FastqIO.py::TestFastqWriter::test_writeFastq3 [gw6] [ 67%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqWriter::test_writeFastq3 tests/test_pbcore_io_GffIO.py::TestGffSorting::test_empty_file [gw7] [ 67%] PASSED tests/test_pbcore_io_GffIO.py::TestGffSorting::test_empty_file [gw14] [ 68%] PASSED tests/test_pbdataset_utils.py::TestDataSetUtils::test_get_dataset_metatype tests/test_pbdataset_utils.py::TestDataSetUtils::test_dsIdToSuffix [gw14] [ 69%] PASSED tests/test_pbdataset_utils.py::TestDataSetUtils::test_dsIdToSuffix tests/test_pbdataset_utils.py::TestDataSetUtils::test_divideKeys_keysToRanges [gw11] [ 70%] PASSED tests/test_pbindex.py::TestPbIndex::test_pbindex_bam_consistency tests/test_pbindex.py::TestPbIndex::test_pbindex_streaming [gw14] [ 70%] PASSED tests/test_pbdataset_utils.py::TestDataSetUtils::test_divideKeys_keysToRanges [gw11] [ 71%] PASSED tests/test_pbindex.py::TestPbIndex::test_pbindex_streaming tests/test_pbindex.py::TestPbIndex::test_pbindex_streaming_entire [gw11] [ 72%] PASSED tests/test_pbindex.py::TestPbIndex::test_pbindex_streaming_entire tests/test_pbindex.py::TestPbIndex::test_pbindex_with_zmw_index [gw11] [ 72%] PASSED tests/test_pbindex.py::TestPbIndex::test_pbindex_with_zmw_index [gw8] [ 73%] PASSED tests/test_pbdataset_split.py::TestDataSetSplit::test_split tests/test_pbdataset_split.py::TestDataSetSplit::test_split_zmws [gw1] [ 74%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testReadsInRange tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testReadGroupTable [gw1] [ 75%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testReadGroupTable tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testSequencingChemistry [gw1] [ 75%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testSequencingChemistry tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testMapQV [gw1] [ 76%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testMapQV tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testHoleNumbers [gw0] [ 77%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testReadsInRange tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testReadGroupTable [gw0] [ 77%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testReadGroupTable tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testSequencingChemistry [gw0] [ 78%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testSequencingChemistry tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testSpecVersion [gw0] [ 79%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testSpecVersion tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testReadScore [gw0] [ 80%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testReadScore tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::test_sample_name_default [gw0] [ 80%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::test_sample_name_default [gw1] [ 81%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testHoleNumbers tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testErrorCounts [gw1] [ 82%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testErrorCounts tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::test_library_name_default [gw0] [ 82%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::test_library_name_default tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testReadsByName [gw1] [ 83%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testReadsByName tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::test_empty_bam [gw1] [ 84%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::test_empty_bam tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::test_alignment_identity [gw1] [ 85%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::test_alignment_identity [gw8] [ 85%] PASSED tests/test_pbdataset_split.py::TestDataSetSplit::test_split_zmws tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::test_alignment_identity_unindexed tests/test_pbdataset_split.py::TestDataSetSplit::test_split_zmws_targetsize [gw1] [ 86%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::test_alignment_identity_unindexed [gw8] [ 87%] PASSED tests/test_pbdataset_split.py::TestDataSetSplit::test_split_zmws_targetsize tests/test_pbdataset_split.py::TestDataSetSplit::test_large_split_zmws [gw8] [ 87%] SKIPPED tests/test_pbdataset_split.py::TestDataSetSplit::test_large_split_zmws tests/test_pbdataset_split.py::TestDataSetSplit::test_multi_movie_split_zmws [gw8] [ 88%] SKIPPED tests/test_pbdataset_split.py::TestDataSetSplit::test_multi_movie_split_zmws tests/test_pbdataset_split.py::TestDataSetSplit::test_multi_movie_split_zmws_existing_simple_filters [gw8] [ 89%] SKIPPED tests/test_pbdataset_split.py::TestDataSetSplit::test_multi_movie_split_zmws_existing_simple_filters tests/test_pbdataset_split.py::TestDataSetSplit::test_multi_movie_split_zmws_existing_filters [gw8] [ 90%] SKIPPED tests/test_pbdataset_split.py::TestDataSetSplit::test_multi_movie_split_zmws_existing_filters tests/test_pbdataset_split.py::TestDataSetSplit::test_movie_split [gw8] [ 90%] SKIPPED tests/test_pbdataset_split.py::TestDataSetSplit::test_movie_split tests/test_pbdataset_split.py::TestDataSetSplit::test_split_references [gw8] [ 91%] SKIPPED tests/test_pbdataset_split.py::TestDataSetSplit::test_split_references tests/test_pbdataset_split.py::TestDataSetSplit::test_multi_movie_split_zmws_with_existing_movie_filter [gw8] [ 92%] SKIPPED tests/test_pbdataset_split.py::TestDataSetSplit::test_multi_movie_split_zmws_with_existing_movie_filter tests/test_pbdataset_split.py::TestDataSetSplit::test_split_by_contigs_presplit [gw8] [ 92%] SKIPPED tests/test_pbdataset_split.py::TestDataSetSplit::test_split_by_contigs_presplit tests/test_pbdataset_split.py::TestDataSetSplit::test_split_by_contigs_with_split_and_maxChunks [gw8] [ 93%] PASSED tests/test_pbdataset_split.py::TestDataSetSplit::test_split_by_contigs_with_split_and_maxChunks tests/test_pbdataset_split.py::TestDataSetSplit::test_split_by_contigs_with_split [gw8] [ 94%] PASSED tests/test_pbdataset_split.py::TestDataSetSplit::test_split_by_contigs_with_split tests/test_pbdataset_split.py::TestDataSetSplit::test_refWindows [gw8] [ 95%] PASSED tests/test_pbdataset_split.py::TestDataSetSplit::test_refWindows tests/test_pbdataset_split.py::TestDataSetSplit::test_huge_zmw_split [gw8] [ 95%] SKIPPED tests/test_pbdataset_split.py::TestDataSetSplit::test_huge_zmw_split tests/test_pbdataset_split.py::TestDataSetSplit::test_subreadset_split_metadata_element_name [gw8] [ 96%] PASSED tests/test_pbdataset_split.py::TestDataSetSplit::test_subreadset_split_metadata_element_name tests/test_pbdataset_split.py::TestDataSetSplit::test_contigset_split [gw8] [ 97%] PASSED tests/test_pbdataset_split.py::TestDataSetSplit::test_contigset_split tests/test_pbdataset_split.py::TestDataSetSplit::test_isBarcoded [gw8] [ 97%] SKIPPED tests/test_pbdataset_split.py::TestDataSetSplit::test_isBarcoded tests/test_pbdataset_split.py::TestDataSetSplit::test_barcode_split_cornercases [gw8] [ 98%] SKIPPED tests/test_pbdataset_split.py::TestDataSetSplit::test_barcode_split_cornercases tests/test_pbdataset_split.py::TestDataSetSplit::test_barcode_split_maxChunks [gw8] [ 99%] SKIPPED tests/test_pbdataset_split.py::TestDataSetSplit::test_barcode_split_maxChunks tests/test_pbdataset_split.py::TestDataSetSplit::test_split_read_groups [gw8] [100%] SKIPPED tests/test_pbdataset_split.py::TestDataSetSplit::test_split_read_groups =============================== warnings summary =============================== tests/test_pbcore_extract_bam_sequence.py: 1 warning tests/test_pbcore_io_AlnFileReaders.py: 118 warnings /build/python-pbcore-2.1.2+dfsg/pbcore/io/align/BamAlignment.py:356: DeprecationWarning: tostring() is deprecated. Use tobytes() instead. return _gusfieldTrans[uc].tostring().decode("ascii") tests/test_pbcore_io_FastqIO.py: 11 warnings /build/python-pbcore-2.1.2+dfsg/pbcore/io/FastqIO.py:239: DeprecationWarning: tostring() is deprecated. Use tobytes() instead. return (np.clip(a, 0, 93).astype(np.uint8) + 33).tostring().decode("ascii") tests/test_pbcore_io_AlnFileReaders.py: 28 warnings /build/python-pbcore-2.1.2+dfsg/pbcore/io/align/BamAlignment.py:583: DeprecationWarning: tostring() is deprecated. Use tobytes() instead. return r.tostring().decode("ascii") tests/test_pbcore_io_AlnFileReaders.py: 20 warnings /build/python-pbcore-2.1.2+dfsg/pbcore/io/align/BamAlignment.py:368: DeprecationWarning: tostring() is deprecated. Use tobytes() instead. return y.tostring().decode("ascii") tests/test_pbcore_io_AlnFileReaders.py: 14 warnings /build/python-pbcore-2.1.2+dfsg/pbcore/io/align/BamAlignment.py:535: DeprecationWarning: NumPy will stop allowing conversion of out-of-bound Python integers to integer arrays. The conversion of -1 to uint8 will fail in the future. For the old behavior, usually: np.array(value).astype(dtype)` will give the desired result (the cast overflows). gapCode = data.dtype.type(-1) tests/test_pbdataset_split.py: 12 warnings /build/python-pbcore-2.1.2+dfsg/pbcore/io/align/_BamSupport.py:66: DeprecationWarning: NumPy will stop allowing conversion of out-of-bound Python integers to integer arrays. The conversion of 3379013067 to int32 will fail in the future. For the old behavior, usually: np.array(value).astype(dtype)` will give the desired result (the cast overflows). return np.int32(int(rgIdString.split("/")[0], 16)) tests/test_pbdataset_split.py::TestDataSetSplit::test_split tests/test_pbdataset_split.py::TestDataSetSplit::test_split tests/test_pbdataset_split.py::TestDataSetSplit::test_split tests/test_pbdataset_split.py::TestDataSetSplit::test_split tests/test_pbdataset_split.py::TestDataSetSplit::test_split tests/test_pbdataset_split.py::TestDataSetSplit::test_split tests/test_pbdataset_split.py::TestDataSetSplit::test_subreadset_split_metadata_element_name tests/test_pbdataset_split.py::TestDataSetSplit::test_subreadset_split_metadata_element_name /build/python-pbcore-2.1.2+dfsg/pbcore/io/align/_BamSupport.py:66: DeprecationWarning: NumPy will stop allowing conversion of out-of-bound Python integers to integer arrays. The conversion of 3844501414 to int32 will fail in the future. For the old behavior, usually: np.array(value).astype(dtype)` will give the desired result (the cast overflows). return np.int32(int(rgIdString.split("/")[0], 16)) -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html ------ generated xml file: /build/python-pbcore-2.1.2+dfsg/nosetests.xml ------- ---------- coverage: platform linux, python 3.11.2-final-0 ----------- Coverage XML written to file coverage.xml ============================= slowest 20 durations ============================= 1.11s call tests/test_pbdataset_split.py::TestDataSetSplit::test_split_by_contigs_with_split 1.05s call tests/test_pbdataset_split.py::TestDataSetSplit::test_split_by_contigs_with_split_and_maxChunks 0.95s call tests/test_pbdataset_split.py::TestDataSetSplit::test_split_zmws_targetsize 0.81s call tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testReadsInRange 0.78s call tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testReadsInRange 0.69s call tests/test_pbdataset_split.py::TestDataSetSplit::test_split 0.56s call tests/test_pbdataset_split.py::TestDataSetSplit::test_split_zmws 0.37s call tests/test_pbdataset_split.py::TestDataSetSplit::test_contigset_split 0.26s call tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::test_alignment_identity_unindexed 0.25s call tests/test_pbindex.py::TestPbIndex::test_pbindex_bam_consistency 0.23s teardown tests/test_pbdataset_utils.py::TestDataSetUtils::test_get_dataset_uuid 0.14s call tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::test_alignment_identity 0.10s call tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::test_dosLineEndingsFasta 0.09s call tests/test_pbdataset_split.py::TestDataSetSplit::test_refWindows 0.09s setup tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testBasicOperations 0.09s call tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testHoleNumbers 0.08s setup tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testBasicOperations 0.08s call tests/test_pbdataset_utils.py::TestDataSetUtils::test_get_dataset_uuid 0.05s call tests/test_pbdataset_split.py::TestDataSetSplit::test_subreadset_split_metadata_element_name 0.05s call tests/test_pbcore_io_FastaIO.py::TestFastaReader::test_dosLineEndingsFasta ================ 122 passed, 18 skipped, 212 warnings in 18.02s ================ # copy working test data into doc dir as user examples mkdir -p _tmp/usr/share/doc/python3-pbcore cp -a tests _tmp/usr/share/doc/python3-pbcore find _tmp -type d -name __pycache__ | xargs rm -rf # move back ignored tests mv /tmp/tests_avoid/* tests rmdir /tmp/tests_avoid make[1]: Leaving directory '/build/python-pbcore-2.1.2+dfsg' 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-pbcore-2.1.2+dfsg/debian/python3-pbcore /usr/lib/python3/dist-packages/setuptools/dist.py:775: UserWarning: Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead warnings.warn( 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 running egg_info writing pbcore.egg-info/PKG-INFO writing dependency_links to pbcore.egg-info/dependency_links.txt writing entry points to pbcore.egg-info/entry_points.txt writing requirements to pbcore.egg-info/requires.txt writing top-level names to pbcore.egg-info/top_level.txt reading manifest file 'pbcore.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching '*.txt' warning: no directories found matching 'bin' adding license file 'LICENSE' writing manifest file 'pbcore.egg-info/SOURCES.txt' /usr/lib/python3/dist-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'pbcore.__pycache__' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'pbcore.__pycache__' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'pbcore.__pycache__' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'pbcore.__pycache__' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'pbcore.chemistry.__pycache__' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'pbcore.chemistry.__pycache__' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'pbcore.chemistry.__pycache__' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'pbcore.chemistry.__pycache__' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'pbcore.chemistry.resources' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'pbcore.chemistry.resources' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'pbcore.chemistry.resources' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'pbcore.chemistry.resources' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'pbcore.data.__pycache__' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'pbcore.data.__pycache__' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'pbcore.data.__pycache__' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'pbcore.data.__pycache__' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'pbcore.data.datasets.__pycache__' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'pbcore.data.datasets.__pycache__' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'pbcore.data.datasets.__pycache__' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'pbcore.data.datasets.__pycache__' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'pbcore.io.__pycache__' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'pbcore.io.__pycache__' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'pbcore.io.__pycache__' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'pbcore.io.__pycache__' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'pbcore.io.align.__pycache__' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'pbcore.io.align.__pycache__' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'pbcore.io.align.__pycache__' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'pbcore.io.align.__pycache__' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'pbcore.io.dataset.__pycache__' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'pbcore.io.dataset.__pycache__' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'pbcore.io.dataset.__pycache__' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'pbcore.io.dataset.__pycache__' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'pbcore.util.__pycache__' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'pbcore.util.__pycache__' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'pbcore.util.__pycache__' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'pbcore.util.__pycache__' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) copying pbcore/__pycache__/__init__.cpython-311.pyc -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/__pycache__ copying pbcore/__pycache__/sequence.cpython-311.pyc -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/__pycache__ copying pbcore/util/__pycache__/__init__.cpython-311.pyc -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/util/__pycache__ copying pbcore/util/__pycache__/decorators.cpython-311.pyc -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/util/__pycache__ copying pbcore/util/__pycache__/statistics.cpython-311.pyc -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/util/__pycache__ copying pbcore/io/__pycache__/FastaIO.cpython-311.pyc -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/__pycache__ copying pbcore/io/__pycache__/FastqIO.cpython-311.pyc -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/__pycache__ copying pbcore/io/__pycache__/FofnIO.cpython-311.pyc -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/__pycache__ copying pbcore/io/__pycache__/GffIO.cpython-311.pyc -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/__pycache__ copying pbcore/io/__pycache__/VcfIO.cpython-311.pyc -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/__pycache__ copying pbcore/io/__pycache__/__init__.cpython-311.pyc -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/__pycache__ copying pbcore/io/__pycache__/_utils.cpython-311.pyc -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/__pycache__ copying pbcore/io/__pycache__/base.cpython-311.pyc -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/__pycache__ copying pbcore/io/__pycache__/opener.cpython-311.pyc -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/__pycache__ copying pbcore/data/__pycache__/__init__.cpython-311.pyc -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/__pycache__ copying pbcore/chemistry/__pycache__/__init__.cpython-311.pyc -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/chemistry/__pycache__ copying pbcore/chemistry/__pycache__/chemistry.cpython-311.pyc -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/chemistry/__pycache__ copying pbcore/io/dataset/__pycache__/DataSetErrors.cpython-311.pyc -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/dataset/__pycache__ copying pbcore/io/dataset/__pycache__/DataSetIO.cpython-311.pyc -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/dataset/__pycache__ copying pbcore/io/dataset/__pycache__/DataSetMembers.cpython-311.pyc -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/dataset/__pycache__ copying pbcore/io/dataset/__pycache__/DataSetMetaTypes.cpython-311.pyc -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/dataset/__pycache__ copying pbcore/io/dataset/__pycache__/DataSetReader.cpython-311.pyc -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/dataset/__pycache__ copying pbcore/io/dataset/__pycache__/DataSetUtils.cpython-311.pyc -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/dataset/__pycache__ copying pbcore/io/dataset/__pycache__/DataSetValidator.cpython-311.pyc -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/dataset/__pycache__ copying pbcore/io/dataset/__pycache__/DataSetWriter.cpython-311.pyc -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/dataset/__pycache__ copying pbcore/io/dataset/__pycache__/__init__.cpython-311.pyc -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/dataset/__pycache__ copying pbcore/io/dataset/__pycache__/run_split.cpython-311.pyc -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/dataset/__pycache__ copying pbcore/io/dataset/__pycache__/utils.cpython-311.pyc -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/dataset/__pycache__ copying pbcore/io/align/__pycache__/BamAlignment.cpython-311.pyc -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/align/__pycache__ copying pbcore/io/align/__pycache__/BamIO.cpython-311.pyc -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/align/__pycache__ copying pbcore/io/align/__pycache__/BlasrIO.cpython-311.pyc -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/align/__pycache__ copying pbcore/io/align/__pycache__/PacBioBamIndex.cpython-311.pyc -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/align/__pycache__ copying pbcore/io/align/__pycache__/_AlignmentMixin.cpython-311.pyc -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/align/__pycache__ copying pbcore/io/align/__pycache__/_BamSupport.cpython-311.pyc -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/align/__pycache__ copying pbcore/io/align/__pycache__/__init__.cpython-311.pyc -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/align/__pycache__ copying pbcore/data/datasets/__pycache__/__init__.cpython-311.pyc -> /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets/__pycache__ running install_lib creating /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore creating /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr creating /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib creating /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11 creating /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages creating /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore creating /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/__pycache__ copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/__pycache__/sequence.cpython-311.pyc -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/__pycache__ copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/__pycache__/__init__.cpython-311.pyc -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/__pycache__ creating /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/chemistry creating /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/chemistry/__pycache__ copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/chemistry/__pycache__/chemistry.cpython-311.pyc -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/chemistry/__pycache__ copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/chemistry/__pycache__/__init__.cpython-311.pyc -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/chemistry/__pycache__ creating /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/chemistry/resources copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/chemistry/resources/mapping.xml -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/chemistry/resources copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/chemistry/__init__.py -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/chemistry copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/chemistry/chemistry.py -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/chemistry creating /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/data creating /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/data/__pycache__ copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/__pycache__/__init__.cpython-311.pyc -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/data/__pycache__ copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/weird.fa.fai -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/data copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/weird.fa -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/data copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/variants.gff -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/data copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.subreads.bam.pbi -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/data copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.subreads.bam -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/data copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.scraps.bam.pbi -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/data copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.scraps.bam -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/data copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.aligned_subreads.bam.pbi -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/data copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.aligned_subreads.bam.bai -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/data copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.aligned_subreads.bam -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/data copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/m130727_114215_42211_c100569412550000001823090301191423_s1_p0.ccs.bam.pbi -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/data copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/m130727_114215_42211_c100569412550000001823090301191423_s1_p0.ccs.bam.bai -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/data copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/m130727_114215_42211_c100569412550000001823090301191423_s1_p0.ccs.bam -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/data copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/lambdaNEB.fa.fai -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/data copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/lambdaNEB.fa -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/data copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/empty2.bam.pbi -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/data copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/empty2.bam -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/data copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/empty.ccs.bam.pbi -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/data copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/empty.ccs.bam -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/data copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/empty.aligned_subreads.bam.pbi -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/data copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/empty.aligned_subreads.bam -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/data copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/chemistry.xml -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/data copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/blasr-output.m5 -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/data copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/blasr-output.m4 -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/data copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/barcodes-ed65-450.fasta.fai -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/data copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/barcodes-ed65-450.fasta -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/data copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/Fluidigm_human_amplicons_tiny.fasta -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/data copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/Fluidigm_human_amplicons.fasta.fai -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/data copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/Fluidigm_human_amplicons.fasta -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/data creating /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/data/datasets creating /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/data/datasets/__pycache__ copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets/__pycache__/__init__.cpython-311.pyc -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/data/datasets/__pycache__ copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets/subreadSetWithStats.xml -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/data/datasets copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets/subread.dataset.xml -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/data/datasets copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets/reference.dataset.xml -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/data/datasets copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets/pbalchemysim1.subreadset.xml -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/data/datasets copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets/pbalchemysim1.subreads.bam.pbi -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/data/datasets copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets/pbalchemysim1.subreads.bam.bai -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/data/datasets copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets/pbalchemysim1.subreads.bam -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/data/datasets copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets/pbalchemysim1.pbalign.bam.pbi -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/data/datasets copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets/pbalchemysim1.pbalign.bam.bai -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/data/datasets copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets/pbalchemysim1.pbalign.bam -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/data/datasets copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets/pbalchemysim1.alignmentset.xml -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/data/datasets copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets/pbalchemysim0.subreadset.xml -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/data/datasets copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets/pbalchemysim0.subreads.bam.pbi -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/data/datasets copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets/pbalchemysim0.subreads.bam.bai -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/data/datasets copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets/pbalchemysim0.subreads.bam -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/data/datasets copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets/pbalchemysim0.referenceset.xml -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/data/datasets copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets/pbalchemysim0.reference.fasta.fai -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/data/datasets copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets/pbalchemysim0.reference.fasta -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/data/datasets copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets/pbalchemysim0.pbalign.bam.pbi -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/data/datasets copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets/pbalchemysim0.pbalign.bam.bai -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/data/datasets copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets/pbalchemysim0.pbalign.bam -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/data/datasets copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets/pbalchemysim0.alignmentset.xml -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/data/datasets copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets/pbalchemysim0.alignmentset.chunk1contigs.xml -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/data/datasets copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets/pbalchemysim0.alignmentset.chunk0contigs.xml -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/data/datasets copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets/pbalchemysim.alignmentset.xml -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/data/datasets copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets/m150616_053259_ethan_c100710482550000001823136404221563_s1_p0.sts.xml -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/data/datasets copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets/m150430_142051_Mon_p1_b25.sts.xml -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/data/datasets copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.subreads.fake_bc.bam.pbi -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/data/datasets copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.subreads.fake_bc.bam.bai -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/data/datasets copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.subreads.fake_bc.bam -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/data/datasets copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets/lambda.referenceset.xml -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/data/datasets copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets/lambda.alignmentset.xml -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/data/datasets copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets/fofn.fofn -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/data/datasets copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets/empty_lambda.aligned.bam.pbi -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/data/datasets copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets/empty_lambda.aligned.bam.bai -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/data/datasets copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets/empty_lambda.aligned.bam -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/data/datasets copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets/contig.dataset.xml -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/data/datasets copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets/ccsread.dataset.xml -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/data/datasets copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets/ccsaligned.dataset.xml -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/data/datasets copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets/barcode.dataset.xml -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/data/datasets copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets/alignment.dataset.xml -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/data/datasets copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets/CollectionMetadata.xml -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/data/datasets copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets/__init__.py -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/data/datasets copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/__init__.py -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/data creating /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/io creating /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/io/__pycache__ copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/__pycache__/opener.cpython-311.pyc -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/io/__pycache__ copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/__pycache__/base.cpython-311.pyc -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/io/__pycache__ copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/__pycache__/_utils.cpython-311.pyc -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/io/__pycache__ copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/__pycache__/__init__.cpython-311.pyc -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/io/__pycache__ copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/__pycache__/VcfIO.cpython-311.pyc -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/io/__pycache__ copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/__pycache__/GffIO.cpython-311.pyc -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/io/__pycache__ copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/__pycache__/FofnIO.cpython-311.pyc -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/io/__pycache__ copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/__pycache__/FastqIO.cpython-311.pyc -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/io/__pycache__ copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/__pycache__/FastaIO.cpython-311.pyc -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/io/__pycache__ creating /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/io/align creating /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/io/align/__pycache__ copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/align/__pycache__/__init__.cpython-311.pyc -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/io/align/__pycache__ copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/align/__pycache__/_BamSupport.cpython-311.pyc -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/io/align/__pycache__ copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/align/__pycache__/_AlignmentMixin.cpython-311.pyc -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/io/align/__pycache__ copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/align/__pycache__/PacBioBamIndex.cpython-311.pyc -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/io/align/__pycache__ copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/align/__pycache__/BlasrIO.cpython-311.pyc -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/io/align/__pycache__ copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/align/__pycache__/BamIO.cpython-311.pyc -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/io/align/__pycache__ copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/align/__pycache__/BamAlignment.cpython-311.pyc -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/io/align/__pycache__ copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/align/BamAlignment.py -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/io/align copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/align/BamIO.py -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/io/align copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/align/BlasrIO.py -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/io/align copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/align/PacBioBamIndex.py -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/io/align copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/align/_AlignmentMixin.py -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/io/align copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/align/_BamSupport.py -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/io/align copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/align/__init__.py -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/io/align creating /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/io/dataset creating /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/io/dataset/__pycache__ copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/dataset/__pycache__/utils.cpython-311.pyc -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/io/dataset/__pycache__ copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/dataset/__pycache__/run_split.cpython-311.pyc -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/io/dataset/__pycache__ copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/dataset/__pycache__/__init__.cpython-311.pyc -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/io/dataset/__pycache__ copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/dataset/__pycache__/DataSetWriter.cpython-311.pyc -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/io/dataset/__pycache__ copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/dataset/__pycache__/DataSetValidator.cpython-311.pyc -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/io/dataset/__pycache__ copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/dataset/__pycache__/DataSetUtils.cpython-311.pyc -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/io/dataset/__pycache__ copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/dataset/__pycache__/DataSetReader.cpython-311.pyc -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/io/dataset/__pycache__ copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/dataset/__pycache__/DataSetMetaTypes.cpython-311.pyc -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/io/dataset/__pycache__ copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/dataset/__pycache__/DataSetMembers.cpython-311.pyc -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/io/dataset/__pycache__ copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/dataset/__pycache__/DataSetIO.cpython-311.pyc -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/io/dataset/__pycache__ copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/dataset/__pycache__/DataSetErrors.cpython-311.pyc -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/io/dataset/__pycache__ copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/dataset/DataSetErrors.py -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/io/dataset copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/dataset/DataSetIO.py -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/io/dataset copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/dataset/DataSetMetaTypes.py -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/io/dataset copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/dataset/DataSetReader.py -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/io/dataset copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/dataset/DataSetUtils.py -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/io/dataset copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/dataset/DataSetWriter.py -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/io/dataset copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/dataset/__init__.py -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/io/dataset copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/dataset/run_split.py -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/io/dataset copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/dataset/utils.py -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/io/dataset copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/dataset/DataSetValidator.py -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/io/dataset copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/dataset/DataSetMembers.py -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/io/dataset copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/FastaIO.py -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/io copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/FastqIO.py -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/io copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/FofnIO.py -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/io copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/GffIO.py -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/io copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/VcfIO.py -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/io copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/__init__.py -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/io copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/_utils.py -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/io copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/base.py -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/io copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/opener.py -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/io creating /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/model copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/model/__init__.py -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/model copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/model/baseRegions.py -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/model creating /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/util creating /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/util/__pycache__ copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/util/__pycache__/statistics.cpython-311.pyc -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/util/__pycache__ copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/util/__pycache__/decorators.cpython-311.pyc -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/util/__pycache__ copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/util/__pycache__/__init__.cpython-311.pyc -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/util/__pycache__ copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/util/__pycache__/ToolRunner.cpython-311.pyc -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/util/__pycache__ copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/util/ToolRunner.py -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/util copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/util/__init__.py -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/util copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/util/decorators.py -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/util copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/util/statistics.py -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/util copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/__init__.py -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore copying /build/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/sequence.py -> /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore byte-compiling /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/chemistry/__init__.py to __init__.cpython-311.pyc byte-compiling /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/chemistry/chemistry.py to chemistry.cpython-311.pyc byte-compiling /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/data/datasets/__init__.py to __init__.cpython-311.pyc byte-compiling /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/data/__init__.py to __init__.cpython-311.pyc byte-compiling /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/io/align/BamAlignment.py to BamAlignment.cpython-311.pyc byte-compiling /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/io/align/BamIO.py to BamIO.cpython-311.pyc byte-compiling /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/io/align/BlasrIO.py to BlasrIO.cpython-311.pyc byte-compiling /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/io/align/PacBioBamIndex.py to PacBioBamIndex.cpython-311.pyc byte-compiling /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/io/align/_AlignmentMixin.py to _AlignmentMixin.cpython-311.pyc byte-compiling /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/io/align/_BamSupport.py to _BamSupport.cpython-311.pyc byte-compiling /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/io/align/__init__.py to __init__.cpython-311.pyc byte-compiling /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/io/dataset/DataSetErrors.py to DataSetErrors.cpython-311.pyc byte-compiling /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/io/dataset/DataSetIO.py to DataSetIO.cpython-311.pyc byte-compiling /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/io/dataset/DataSetMetaTypes.py to DataSetMetaTypes.cpython-311.pyc byte-compiling /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/io/dataset/DataSetReader.py to DataSetReader.cpython-311.pyc byte-compiling /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/io/dataset/DataSetUtils.py to DataSetUtils.cpython-311.pyc byte-compiling /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/io/dataset/DataSetWriter.py to DataSetWriter.cpython-311.pyc byte-compiling /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/io/dataset/__init__.py to __init__.cpython-311.pyc byte-compiling /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/io/dataset/run_split.py to run_split.cpython-311.pyc byte-compiling /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/io/dataset/utils.py to utils.cpython-311.pyc byte-compiling /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/io/dataset/DataSetValidator.py to DataSetValidator.cpython-311.pyc byte-compiling /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/io/dataset/DataSetMembers.py to DataSetMembers.cpython-311.pyc byte-compiling /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/io/FastaIO.py to FastaIO.cpython-311.pyc byte-compiling /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/io/FastqIO.py to FastqIO.cpython-311.pyc byte-compiling /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/io/FofnIO.py to FofnIO.cpython-311.pyc byte-compiling /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/io/GffIO.py to GffIO.cpython-311.pyc byte-compiling /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/io/VcfIO.py to VcfIO.cpython-311.pyc byte-compiling /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/io/__init__.py to __init__.cpython-311.pyc byte-compiling /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/io/_utils.py to _utils.cpython-311.pyc byte-compiling /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/io/base.py to base.cpython-311.pyc byte-compiling /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/io/opener.py to opener.cpython-311.pyc byte-compiling /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/model/__init__.py to __init__.cpython-311.pyc byte-compiling /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/model/baseRegions.py to baseRegions.cpython-311.pyc byte-compiling /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/util/ToolRunner.py to ToolRunner.cpython-311.pyc byte-compiling /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/util/__init__.py to __init__.cpython-311.pyc byte-compiling /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/util/decorators.py to decorators.cpython-311.pyc byte-compiling /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/util/statistics.py to statistics.cpython-311.pyc byte-compiling /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/__init__.py to __init__.cpython-311.pyc byte-compiling /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore/sequence.py to sequence.cpython-311.pyc running install_egg_info Copying pbcore.egg-info to /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/lib/python3.11/dist-packages/pbcore-2.2.0.egg-info Skipping SOURCES.txt running install_scripts Installing .open script to /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/bin I: pybuild pybuild:333: chmod -x /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore//usr/lib/python3.11/dist-packages/pbcore/data/datasets/*.xml debian/rules override_dh_install make[1]: Entering directory '/build/python-pbcore-2.1.2+dfsg' debian/rules:55: warning: overriding recipe for target 'override_dh_auto_clean' debian/rules:28: warning: ignoring old recipe for target 'override_dh_auto_clean' dh_install mv /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/bin/.open /build/python-pbcore-2.1.2+dfsg/debian/python3-pbcore/usr/bin/pbopen rmdir /build/python-pbcore-2.1.2+dfsg/debian/python-pbcore-doc/usr/share/doc/python3-pbcore/html/_images/ make[1]: Leaving directory '/build/python-pbcore-2.1.2+dfsg' debian/rules override_dh_installdocs make[1]: Entering directory '/build/python-pbcore-2.1.2+dfsg' debian/rules:55: warning: overriding recipe for target 'override_dh_auto_clean' debian/rules:28: warning: ignoring old recipe for target 'override_dh_auto_clean' dh_installdocs -X _source make[1]: Leaving directory '/build/python-pbcore-2.1.2+dfsg' debian/rules override_dh_installchangelogs make[1]: Entering directory '/build/python-pbcore-2.1.2+dfsg' debian/rules:55: warning: overriding recipe for target 'override_dh_auto_clean' debian/rules:28: warning: ignoring old recipe for target 'override_dh_auto_clean' dh_installchangelogs CHANGELOG.org make[1]: Leaving directory '/build/python-pbcore-2.1.2+dfsg' dh_installman -O--buildsystem=pybuild dh_python3 -O--buildsystem=pybuild dh_installsystemduser -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_installdeb -O--buildsystem=pybuild dh_gencontrol -O--buildsystem=pybuild dpkg-gencontrol: warning: Depends field of package python-pbcore-doc: substitution variable ${sphinxdoc:Depends} used, but is not defined dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild dpkg-deb: building package 'python-pbcore-doc' in '../python-pbcore-doc_2.1.2+dfsg-5_all.deb'. dpkg-deb: building package 'python3-pbcore' in '../python3-pbcore_2.1.2+dfsg-5_all.deb'. dpkg-genbuildinfo --build=binary -O../python-pbcore_2.1.2+dfsg-5_amd64.buildinfo dpkg-genchanges --build=binary -O../python-pbcore_2.1.2+dfsg-5_amd64.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/3498304/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/3498304/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/3498304 and its subdirectories I: Current time: Mon Jun 3 10:44:59 +14 2024 I: pbuilder-time-stamp: 1717361099