Sun Jan 7 10:19:40 UTC 2024 I: starting to build python-pbcore/bookworm/armhf on jenkins on '2024-01-07 10:19' Sun Jan 7 10:19:40 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/armhf_11/601/console.log Sun Jan 7 10:19:40 UTC 2024 I: Downloading source for bookworm/python-pbcore=2.1.2+dfsg-5 --2024-01-07 10:19:40-- http://cdn-fastly.deb.debian.org/debian/pool/main/p/python-pbcore/python-pbcore_2.1.2%2bdfsg-5.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2761 (2.7K) [text/prs.lines.tag] Saving to: ‘python-pbcore_2.1.2+dfsg-5.dsc’ 0K .. 100% 380M=0s 2024-01-07 10:19:40 (380 MB/s) - ‘python-pbcore_2.1.2+dfsg-5.dsc’ saved [2761/2761] Sun Jan 7 10:19:40 UTC 2024 I: python-pbcore_2.1.2+dfsg-5.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: python-pbcore Binary: python3-pbcore, python-pbcore-doc Architecture: all Version: 2.1.2+dfsg-5 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Étienne Mollier Homepage: https://github.com/PacificBiosciences/pbcore Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/python-pbcore Vcs-Git: https://salsa.debian.org/med-team/python-pbcore.git Testsuite: autopkgtest Testsuite-Triggers: python3-pytest, python3-pytest-cov, python3-pytest-runner, python3-pytest-xdist Build-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 Package-List: python-pbcore-doc deb doc optional arch=all python3-pbcore deb python optional arch=all Checksums-Sha1: cb0a0ae779a39cbdbf1a75292ce2655dcbb65a9a 2918008 python-pbcore_2.1.2+dfsg.orig.tar.xz 1f81dd55291e883d1618dcc7a43ac383129c8640 59964 python-pbcore_2.1.2+dfsg-5.debian.tar.xz Checksums-Sha256: a31283a37b20aa7b327de78a533254c5892c5519fb8214fd3c1a978855351326 2918008 python-pbcore_2.1.2+dfsg.orig.tar.xz 8f07b0ff3a6f00577344a803822713786f057ef8953a85d4da1b973faf03253b 59964 python-pbcore_2.1.2+dfsg-5.debian.tar.xz Files: b58bb3c6ad20be9ea36bf8a7548bdd84 2918008 python-pbcore_2.1.2+dfsg.orig.tar.xz 823e2c98333770e27cb1b742efb7c4e9 59964 python-pbcore_2.1.2+dfsg-5.debian.tar.xz Dgit: 250b4aab1e0ecd4db1f36846dbc8a49579faca12 debian archive/debian/2.1.2+dfsg-5 https://git.dgit.debian.org/python-pbcore -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmO5lvsUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdrY6w/8DX3UIsgc870uz6DAqSi+ZjZdWKyy /AjNQPQk74sUKwwB4fybZtEQZSW+1SB3vM5186EovOFr1NRLVAZbude63au/4U4t Sy9SbLWFxrpxjj1g8Njldxf9TbJhx7mEXJeprSX5WgrmpgNimerU3G7vF37WIZ4x +rwyc839doP06o0kZ14wr2SywS1Wt0MBgdiwlb0qSrMMjB3fC+Tnd4v/VlbOJmri G0BCLZm/0H6R0/PPbc3ZsvLgrv/BrLEcWjBcr/xiDkGw9if/cX9VR086s8kmROXD 8z6V3MwAa6y9g1+VLn0otdvufTXrZOKfN5/bv/GV9dyXAauDS56xydfymam8SAQg yRRZ7OcdUA4k88x0gkw5Klbdft/nhS3aKMdD6MnX/5r1k7NMHt0FBdOYnBO1r1bL SenlXgq70u7+RCzpDAN4Lh/bwqfJ1ye335dUi0QFMvCqgcph5826FCgrevWjKMx9 zUNM3iBCLbEpERXsOFHBH7uWKAnH+hJTzQqJKenDVd9vsFx5lb0h3LN8UKA5l62u f/VnqdxncEaanSWSKQ7ZYXJUNqtIGna0eMOC0npuXviopkJqCHJyB13ki/qBK4ew EFc0glpfGXiOyTXZX1DIT8/V8m+KkIL3UIITSO6wnZZrwBEKa16rG83ZaD+OiiqE YIhcHFTxMwZiS/U= =uyug -----END PGP SIGNATURE----- Sun Jan 7 10:19:40 UTC 2024 I: Checking whether the package is not for us Sun Jan 7 10:19:40 UTC 2024 I: Starting 1st build on remote node virt32b-armhf-rb.debian.net. Sun Jan 7 10:19:40 UTC 2024 I: Preparing to do remote build '1' on virt32b-armhf-rb.debian.net. Sun Jan 7 10:27:26 UTC 2024 I: Deleting $TMPDIR on virt32b-armhf-rb.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sat Jan 6 22:19:49 -12 2024 I: pbuilder-time-stamp: 1704622789 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 Sat Jan 7 15:59:55 2023 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/18106/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='armhf' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 ' DISTRIBUTION='bookworm' HOME='/root' HOST_ARCH='armhf' IFS=' ' INVOCATION_ID='57ef256f28df42b684ed992c9524fd72' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='18106' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.XmxcTL8j/pbuilderrc_YYwx --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.XmxcTL8j/b1 --logfile b1/build.log python-pbcore_2.1.2+dfsg-5.dsc' SUDO_GID='112' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://10.0.0.15:3142/' I: uname -a Linux virt32b 6.1.0-17-armmp-lpae #1 SMP Debian 6.1.69-1 (2023-12-30) armv7l GNU/Linux I: ls -l /bin total 4964 -rwxr-xr-x 1 root root 838488 Apr 23 2023 bash -rwxr-xr-x 3 root root 67144 Sep 19 2022 bunzip2 -rwxr-xr-x 3 root root 67144 Sep 19 2022 bzcat lrwxrwxrwx 1 root root 6 Sep 19 2022 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Sep 19 2022 bzdiff lrwxrwxrwx 1 root root 6 Sep 19 2022 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe lrwxrwxrwx 1 root root 6 Sep 19 2022 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Sep 19 2022 bzgrep -rwxr-xr-x 3 root root 67144 Sep 19 2022 bzip2 -rwxr-xr-x 1 root root 67112 Sep 19 2022 bzip2recover lrwxrwxrwx 1 root root 6 Sep 19 2022 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Sep 19 2022 bzmore -rwxr-xr-x 1 root root 67632 Sep 20 2022 cat -rwxr-xr-x 1 root root 67676 Sep 20 2022 chgrp -rwxr-xr-x 1 root root 67644 Sep 20 2022 chmod -rwxr-xr-x 1 root root 67684 Sep 20 2022 chown -rwxr-xr-x 1 root root 133532 Sep 20 2022 cp -rwxr-xr-x 1 root root 132868 Jan 5 2023 dash -rwxr-xr-x 1 root root 133220 Sep 20 2022 date -rwxr-xr-x 1 root root 67732 Sep 20 2022 dd -rwxr-xr-x 1 root root 68104 Sep 20 2022 df -rwxr-xr-x 1 root root 133632 Sep 20 2022 dir -rwxr-xr-x 1 root root 59128 Mar 23 2023 dmesg lrwxrwxrwx 1 root root 8 Dec 19 2022 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 19 2022 domainname -> hostname -rwxr-xr-x 1 root root 67560 Sep 20 2022 echo -rwxr-xr-x 1 root root 41 Jan 24 2023 egrep -rwxr-xr-x 1 root root 67548 Sep 20 2022 false -rwxr-xr-x 1 root root 41 Jan 24 2023 fgrep -rwxr-xr-x 1 root root 55748 Mar 23 2023 findmnt -rwsr-xr-x 1 root root 26208 Mar 23 2023 fusermount -rwxr-xr-x 1 root root 128608 Jan 24 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 64220 Apr 10 2022 gzip -rwxr-xr-x 1 root root 67032 Dec 19 2022 hostname -rwxr-xr-x 1 root root 67720 Sep 20 2022 ln -rwxr-xr-x 1 root root 35132 Mar 23 2023 login -rwxr-xr-x 1 root root 133632 Sep 20 2022 ls -rwxr-xr-x 1 root root 136808 Mar 23 2023 lsblk -rwxr-xr-x 1 root root 67800 Sep 20 2022 mkdir -rwxr-xr-x 1 root root 67764 Sep 20 2022 mknod -rwxr-xr-x 1 root root 67596 Sep 20 2022 mktemp -rwxr-xr-x 1 root root 38504 Mar 23 2023 more -rwsr-xr-x 1 root root 38496 Mar 23 2023 mount -rwxr-xr-x 1 root root 9824 Mar 23 2023 mountpoint -rwxr-xr-x 1 root root 133532 Sep 20 2022 mv lrwxrwxrwx 1 root root 8 Dec 19 2022 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 3 2023 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 67608 Sep 20 2022 pwd lrwxrwxrwx 1 root root 4 Apr 23 2023 rbash -> bash -rwxr-xr-x 1 root root 67600 Sep 20 2022 readlink -rwxr-xr-x 1 root root 67672 Sep 20 2022 rm -rwxr-xr-x 1 root root 67600 Sep 20 2022 rmdir -rwxr-xr-x 1 root root 14152 Jul 28 23:46 run-parts -rwxr-xr-x 1 root root 133372 Jan 5 2023 sed lrwxrwxrwx 1 root root 4 Jan 5 2023 sh -> dash -rwxr-xr-x 1 root root 67584 Sep 20 2022 sleep -rwxr-xr-x 1 root root 67644 Sep 20 2022 stty -rwsr-xr-x 1 root root 50800 Mar 23 2023 su -rwxr-xr-x 1 root root 67584 Sep 20 2022 sync -rwxr-xr-x 1 root root 336764 Apr 6 2023 tar -rwxr-xr-x 1 root root 9800 Jul 28 23:46 tempfile -rwxr-xr-x 1 root root 133224 Sep 20 2022 touch -rwxr-xr-x 1 root root 67548 Sep 20 2022 true -rwxr-xr-x 1 root root 9768 Mar 23 2023 ulockmgr_server -rwsr-xr-x 1 root root 22108 Mar 23 2023 umount -rwxr-xr-x 1 root root 67572 Sep 20 2022 uname -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress -rwxr-xr-x 1 root root 133632 Sep 20 2022 vdir -rwxr-xr-x 1 root root 42608 Mar 23 2023 wdctl lrwxrwxrwx 1 root root 8 Dec 19 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/18106/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: armhf 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 ... 17881 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} tzdata{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, 171 newly installed, 0 to remove and 0 not upgraded. Need to get 70.5 MB of archives. After unpacking 253 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main armhf libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 2 http://deb.debian.org/debian bookworm/main armhf libjs-jquery-hotkeys all 0~20130707+git2d51e3a9+dfsg-2.1 [11.5 kB] Get: 3 http://deb.debian.org/debian bookworm/main armhf libpython3.11-minimal armhf 3.11.2-6 [798 kB] Get: 4 http://deb.debian.org/debian bookworm/main armhf libexpat1 armhf 2.5.0-1 [79.9 kB] Get: 5 http://deb.debian.org/debian bookworm/main armhf python3.11-minimal armhf 3.11.2-6 [1714 kB] Get: 6 http://deb.debian.org/debian bookworm/main armhf python3-minimal armhf 3.11.2-1+b1 [26.3 kB] Get: 7 http://deb.debian.org/debian bookworm/main armhf media-types all 10.0.0 [26.1 kB] Get: 8 http://deb.debian.org/debian bookworm/main armhf mailcap all 3.70+nmu1 [32.0 kB] Get: 9 http://deb.debian.org/debian bookworm/main armhf mime-support all 3.66 [10.9 kB] Get: 10 http://deb.debian.org/debian bookworm/main armhf readline-common all 8.2-1.3 [69.0 kB] Get: 11 http://deb.debian.org/debian bookworm/main armhf libreadline8 armhf 8.2-1.3 [144 kB] Get: 12 http://deb.debian.org/debian bookworm/main armhf libpython3.11-stdlib armhf 3.11.2-6 [1678 kB] Get: 13 http://deb.debian.org/debian bookworm/main armhf python3.11 armhf 3.11.2-6 [572 kB] Get: 14 http://deb.debian.org/debian bookworm/main armhf libpython3-stdlib armhf 3.11.2-1+b1 [9296 B] Get: 15 http://deb.debian.org/debian bookworm/main armhf python3 armhf 3.11.2-1+b1 [26.3 kB] Get: 16 http://deb.debian.org/debian bookworm/main armhf sgml-base all 1.31 [15.4 kB] Get: 17 http://deb.debian.org/debian bookworm/main armhf tzdata all 2023c-5+deb12u1 [296 kB] Get: 18 http://deb.debian.org/debian bookworm/main armhf sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 19 http://deb.debian.org/debian bookworm/main armhf openssl armhf 3.0.11-1~deb12u2 [1386 kB] Get: 20 http://deb.debian.org/debian bookworm/main armhf ca-certificates all 20230311 [153 kB] Get: 21 http://deb.debian.org/debian bookworm/main armhf libmagic-mgc armhf 1:5.44-3 [305 kB] Get: 22 http://deb.debian.org/debian bookworm/main armhf libmagic1 armhf 1:5.44-3 [96.5 kB] Get: 23 http://deb.debian.org/debian bookworm/main armhf file armhf 1:5.44-3 [41.6 kB] Get: 24 http://deb.debian.org/debian bookworm/main armhf gettext-base armhf 0.21-12 [157 kB] Get: 25 http://deb.debian.org/debian bookworm/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB] Get: 26 http://deb.debian.org/debian bookworm/main armhf groff-base armhf 1.22.4-10 [825 kB] Get: 27 http://deb.debian.org/debian bookworm/main armhf bsdextrautils armhf 2.38.1-5+b1 [78.6 kB] Get: 28 http://deb.debian.org/debian bookworm/main armhf libpipeline1 armhf 1.5.7-1 [33.6 kB] Get: 29 http://deb.debian.org/debian bookworm/main armhf man-db armhf 2.11.2-2 [1351 kB] Get: 30 http://deb.debian.org/debian bookworm/main armhf m4 armhf 1.4.19-3 [265 kB] Get: 31 http://deb.debian.org/debian bookworm/main armhf autoconf all 2.71-3 [332 kB] Get: 32 http://deb.debian.org/debian bookworm/main armhf autotools-dev all 20220109.1 [51.6 kB] Get: 33 http://deb.debian.org/debian bookworm/main armhf automake all 1:1.16.5-1.3 [823 kB] Get: 34 http://deb.debian.org/debian bookworm/main armhf autopoint all 0.21-12 [495 kB] Get: 35 http://deb.debian.org/debian bookworm/main armhf libdebhelper-perl all 13.11.4 [81.2 kB] Get: 36 http://deb.debian.org/debian bookworm/main armhf libtool all 2.4.7-5 [517 kB] Get: 37 http://deb.debian.org/debian bookworm/main armhf dh-autoreconf all 20 [17.1 kB] Get: 38 http://deb.debian.org/debian bookworm/main armhf libarchive-zip-perl all 1.68-1 [104 kB] Get: 39 http://deb.debian.org/debian bookworm/main armhf libsub-override-perl all 0.09-4 [9304 B] Get: 40 http://deb.debian.org/debian bookworm/main armhf libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 41 http://deb.debian.org/debian bookworm/main armhf dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 42 http://deb.debian.org/debian bookworm/main armhf libelf1 armhf 0.188-2.1 [170 kB] Get: 43 http://deb.debian.org/debian bookworm/main armhf dwz armhf 0.15-1 [101 kB] Get: 44 http://deb.debian.org/debian bookworm/main armhf libicu72 armhf 72.1-3 [9048 kB] Get: 45 http://deb.debian.org/debian bookworm/main armhf libxml2 armhf 2.9.14+dfsg-1.3~deb12u1 [591 kB] Get: 46 http://deb.debian.org/debian bookworm/main armhf gettext armhf 0.21-12 [1229 kB] Get: 47 http://deb.debian.org/debian bookworm/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 48 http://deb.debian.org/debian bookworm/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 49 http://deb.debian.org/debian bookworm/main armhf debhelper all 13.11.4 [942 kB] Get: 50 http://deb.debian.org/debian bookworm/main armhf python3-lib2to3 all 3.11.2-3 [76.3 kB] Get: 51 http://deb.debian.org/debian bookworm/main armhf python3-distutils all 3.11.2-3 [131 kB] Get: 52 http://deb.debian.org/debian bookworm/main armhf dh-python all 5.20230130+deb12u1 [104 kB] Get: 53 http://deb.debian.org/debian bookworm/main armhf xml-core all 0.18+nmu1 [23.8 kB] Get: 54 http://deb.debian.org/debian bookworm/main armhf docutils-common all 0.19+dfsg-6 [127 kB] Get: 55 http://deb.debian.org/debian bookworm/main armhf libfontenc1 armhf 1:1.1.4-1 [21.9 kB] Get: 56 http://deb.debian.org/debian bookworm/main armhf libbrotli1 armhf 1.0.9-2+b6 [271 kB] Get: 57 http://deb.debian.org/debian bookworm/main armhf libpng16-16 armhf 1.6.39-2 [260 kB] Get: 58 http://deb.debian.org/debian bookworm/main armhf libfreetype6 armhf 2.12.1+dfsg-5 [332 kB] Get: 59 http://deb.debian.org/debian bookworm/main armhf x11-common all 1:7.7+23 [252 kB] Get: 60 http://deb.debian.org/debian bookworm/main armhf xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get: 61 http://deb.debian.org/debian bookworm/main armhf xfonts-utils armhf 1:7.7+6 [84.5 kB] Get: 62 http://deb.debian.org/debian bookworm/main armhf fonts-urw-base35 all 20200910-7 [10.8 MB] Get: 63 http://deb.debian.org/debian bookworm/main armhf libaec0 armhf 1.0.6-1+b1 [19.8 kB] Get: 64 http://deb.debian.org/debian bookworm/main armhf libblas3 armhf 3.11.0-2 [105 kB] Get: 65 http://deb.debian.org/debian bookworm/main armhf libbsd0 armhf 0.11.7-2 [113 kB] Get: 66 http://deb.debian.org/debian bookworm/main armhf libsasl2-modules-db armhf 2.1.28+dfsg-10 [19.0 kB] Get: 67 http://deb.debian.org/debian bookworm/main armhf libsasl2-2 armhf 2.1.28+dfsg-10 [52.3 kB] Get: 68 http://deb.debian.org/debian bookworm/main armhf libldap-2.5-0 armhf 2.5.13+dfsg-5 [158 kB] Get: 69 http://deb.debian.org/debian bookworm/main armhf libnghttp2-14 armhf 1.52.0-1+deb12u1 [62.1 kB] Get: 70 http://deb.debian.org/debian bookworm/main armhf libpsl5 armhf 0.21.2-1 [57.5 kB] Get: 71 http://deb.debian.org/debian bookworm/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [55.2 kB] Get: 72 http://deb.debian.org/debian bookworm/main armhf libssh2-1 armhf 1.10.0-3+b1 [163 kB] Get: 73 http://deb.debian.org/debian bookworm/main armhf libcurl3-gnutls armhf 7.88.1-10+deb12u4 [346 kB] Get: 74 http://deb.debian.org/debian bookworm/main armhf libcurl4 armhf 7.88.1-10+deb12u4 [350 kB] Get: 75 http://deb.debian.org/debian bookworm/main armhf libdeflate0 armhf 1.14-1 [52.2 kB] Get: 76 http://deb.debian.org/debian bookworm/main armhf libfribidi0 armhf 1.0.8-2.1 [63.1 kB] Get: 77 http://deb.debian.org/debian bookworm/main armhf libgfortran5 armhf 12.2.0-14 [246 kB] Get: 78 http://deb.debian.org/debian bookworm/main armhf libglib2.0-0 armhf 2.74.6-2 [1227 kB] Get: 79 http://deb.debian.org/debian bookworm/main armhf libgraphite2-3 armhf 1.3.14-1 [70.5 kB] Get: 80 http://deb.debian.org/debian bookworm/main armhf libharfbuzz0b armhf 6.0.0+dfsg-3 [1893 kB] Get: 81 http://deb.debian.org/debian bookworm/main armhf libsz2 armhf 1.0.6-1+b1 [7864 B] Get: 82 http://deb.debian.org/debian bookworm/main armhf libhdf5-103-1 armhf 1.10.8+repack1-1 [1183 kB] Get: 83 http://deb.debian.org/debian bookworm/main armhf libhdf5-hl-100 armhf 1.10.8+repack1-1 [65.3 kB] Get: 84 http://deb.debian.org/debian bookworm/main armhf libhtscodecs2 armhf 1.3.0-4 [60.4 kB] Get: 85 http://deb.debian.org/debian bookworm/main armhf libhts3 armhf 1.16+ds-3 [375 kB] Get: 86 http://deb.debian.org/debian bookworm/main armhf libimagequant0 armhf 2.17.0-1 [27.9 kB] Get: 87 http://deb.debian.org/debian bookworm/main armhf libjbig0 armhf 2.1-6.1 [27.1 kB] Get: 88 http://deb.debian.org/debian bookworm/main armhf libjpeg62-turbo armhf 1:2.1.5-2 [143 kB] Get: 89 http://deb.debian.org/debian bookworm/main armhf libjs-jquery-isonscreen all 1.2.0-1.1 [3196 B] Get: 90 http://deb.debian.org/debian bookworm/main armhf libjs-jquery-metadata all 12-4 [6532 B] Get: 91 http://deb.debian.org/debian bookworm/main armhf libjs-jquery-tablesorter all 1:2.31.3+dfsg1-3 [184 kB] Get: 92 http://deb.debian.org/debian bookworm/main armhf libjs-jquery-throttle-debounce all 1.1+dfsg.1-2 [12.2 kB] Get: 93 http://deb.debian.org/debian bookworm/main armhf libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 94 http://deb.debian.org/debian bookworm/main armhf libjs-sphinxdoc all 5.3.0-4 [130 kB] Get: 95 http://deb.debian.org/debian bookworm/main armhf libjson-perl all 4.10000-1 [87.5 kB] Get: 96 http://deb.debian.org/debian bookworm/main armhf liblapack3 armhf 3.11.0-2 [1724 kB] Get: 97 http://deb.debian.org/debian bookworm/main armhf liblcms2-2 armhf 2.14-2 [125 kB] Get: 98 http://deb.debian.org/debian bookworm/main armhf liblerc4 armhf 4.0.0+ds-2 [137 kB] Get: 99 http://deb.debian.org/debian bookworm/main armhf liblzf1 armhf 3.6-3 [9248 B] Get: 100 http://deb.debian.org/debian bookworm/main armhf libopenjp2-7 armhf 2.5.0-2 [169 kB] Get: 101 http://deb.debian.org/debian bookworm/main armhf libraqm0 armhf 0.7.0-4.1 [9116 B] Get: 102 http://deb.debian.org/debian bookworm/main armhf libwebp7 armhf 1.2.4-0.2+deb12u1 [242 kB] Get: 103 http://deb.debian.org/debian bookworm/main armhf libtiff6 armhf 4.5.0-6+deb12u1 [295 kB] Get: 104 http://deb.debian.org/debian bookworm/main armhf libwebpdemux2 armhf 1.2.4-0.2+deb12u1 [98.4 kB] Get: 105 http://deb.debian.org/debian bookworm/main armhf libwebpmux3 armhf 1.2.4-0.2+deb12u1 [106 kB] Get: 106 http://deb.debian.org/debian bookworm/main armhf libxau6 armhf 1:1.0.9-1 [19.0 kB] Get: 107 http://deb.debian.org/debian bookworm/main armhf libxdmcp6 armhf 1:1.1.2-3 [24.9 kB] Get: 108 http://deb.debian.org/debian bookworm/main armhf libxcb1 armhf 1.15-1 [140 kB] Get: 109 http://deb.debian.org/debian bookworm/main armhf python3-pkg-resources all 66.1.1-1 [296 kB] Get: 110 http://deb.debian.org/debian bookworm/main armhf python3-setuptools all 66.1.1-1 [521 kB] Get: 111 http://deb.debian.org/debian bookworm/main armhf python3-six all 1.16.0-4 [17.5 kB] Get: 112 http://deb.debian.org/debian bookworm/main armhf python3-typing-extensions all 4.4.0-1 [45.2 kB] Get: 113 http://deb.debian.org/debian bookworm/main armhf python3-lazy-object-proxy armhf 1.9.0-1+b1 [19.8 kB] Get: 114 http://deb.debian.org/debian bookworm/main armhf python3-wrapt armhf 1.14.1-2+b2 [39.6 kB] Get: 115 http://deb.debian.org/debian bookworm/main armhf python3-astroid all 2.14.2-1 [209 kB] Get: 116 http://deb.debian.org/debian bookworm/main armhf python3-toml all 0.10.2-1 [16.2 kB] Get: 117 http://deb.debian.org/debian bookworm/main armhf python3-isort all 5.6.4-1 [63.2 kB] Get: 118 http://deb.debian.org/debian bookworm/main armhf python3-more-itertools all 8.10.0-2 [53.0 kB] Get: 119 http://deb.debian.org/debian bookworm/main armhf python3-zipp all 1.0.0-6 [6696 B] Get: 120 http://deb.debian.org/debian bookworm/main armhf python3-importlib-metadata all 4.12.0-1 [24.9 kB] Get: 121 http://deb.debian.org/debian bookworm/main armhf python3-mypy-extensions all 0.4.3-4 [5788 B] Get: 122 http://deb.debian.org/debian bookworm/main armhf python3-logilab-common all 1.9.8-1 [380 kB] Get: 123 http://deb.debian.org/debian bookworm/main armhf python3-dill all 0.3.6-1 [79.5 kB] Get: 124 http://deb.debian.org/debian bookworm/main armhf python3-mccabe all 0.7.0-1 [10.5 kB] Get: 125 http://deb.debian.org/debian bookworm/main armhf python3-platformdirs all 2.6.0-1 [16.3 kB] Get: 126 http://deb.debian.org/debian bookworm/main armhf python3-tomlkit all 0.11.7-1 [40.5 kB] Get: 127 http://deb.debian.org/debian bookworm/main armhf pylint all 2.16.2-2 [339 kB] Get: 128 http://deb.debian.org/debian bookworm/main armhf python-babel-localedata all 2.10.3-1 [5615 kB] Get: 129 http://deb.debian.org/debian bookworm/main armhf python3-alabaster all 0.7.12-1 [20.8 kB] Get: 130 http://deb.debian.org/debian bookworm/main armhf python3-all armhf 3.11.2-1+b1 [1060 B] Get: 131 http://deb.debian.org/debian bookworm/main armhf python3-attr all 22.2.0-1 [65.4 kB] Get: 132 http://deb.debian.org/debian bookworm/main armhf python3-tz all 2022.7.1-4 [30.1 kB] Get: 133 http://deb.debian.org/debian bookworm/main armhf python3-babel all 2.10.3-1 [103 kB] Get: 134 http://deb.debian.org/debian bookworm/main armhf python3-numpy armhf 1:1.24.2-1 [4165 kB] Get: 135 http://deb.debian.org/debian bookworm/main armhf python3-renderpm armhf 3.6.12-1+b1 [66.2 kB] Get: 136 http://deb.debian.org/debian bookworm/main armhf python3-reportlab-accel armhf 3.6.12-1+b1 [37.3 kB] Get: 137 http://deb.debian.org/debian bookworm/main armhf python3-pil armhf 9.4.0-1.1+b1 [438 kB] Get: 138 http://deb.debian.org/debian bookworm/main armhf python3-reportlab all 3.6.12-1 [564 kB] Get: 139 http://deb.debian.org/debian bookworm/main armhf w3c-sgml-lib all 1.3-3 [273 kB] Get: 140 http://deb.debian.org/debian bookworm/main armhf python3-biopython armhf 1.80+dfsg-4+b1 [1568 kB] Get: 141 http://deb.debian.org/debian bookworm/main armhf python3-certifi all 2022.9.24-1 [153 kB] Get: 142 http://deb.debian.org/debian bookworm/main armhf python3-chardet all 5.1.0+dfsg-2 [110 kB] Get: 143 http://deb.debian.org/debian bookworm/main armhf python3-charset-normalizer all 3.0.1-2 [49.3 kB] Get: 144 http://deb.debian.org/debian bookworm/main armhf python3-coverage armhf 6.5.0+dfsg1-2+b1 [152 kB] Get: 145 http://deb.debian.org/debian bookworm/main armhf python3-roman all 3.3-3 [9880 B] Get: 146 http://deb.debian.org/debian bookworm/main armhf python3-docutils all 0.19+dfsg-6 [382 kB] Get: 147 http://deb.debian.org/debian bookworm/main armhf python3-elementpath all 2.5.3-1 [121 kB] Get: 148 http://deb.debian.org/debian bookworm/main armhf python3-execnet all 1.9.0-1 [41.5 kB] Get: 149 http://deb.debian.org/debian bookworm/main armhf python3-h5py-serial armhf 3.7.0-8 [730 kB] Get: 150 http://deb.debian.org/debian bookworm/main armhf python3-h5py all 3.7.0-8 [10.3 kB] Get: 151 http://deb.debian.org/debian bookworm/main armhf python3-idna all 3.3-1 [39.4 kB] Get: 152 http://deb.debian.org/debian bookworm/main armhf python3-imagesize all 1.4.1-1 [6688 B] Get: 153 http://deb.debian.org/debian bookworm/main armhf python3-iniconfig all 1.1.1-2 [6396 B] Get: 154 http://deb.debian.org/debian bookworm/main armhf python3-markupsafe armhf 2.1.2-1+b1 [12.8 kB] Get: 155 http://deb.debian.org/debian bookworm/main armhf python3-jinja2 all 3.1.2-1 [119 kB] Get: 156 http://deb.debian.org/debian bookworm/main armhf python3-packaging all 23.0-1 [32.5 kB] Get: 157 http://deb.debian.org/debian bookworm/main armhf python3-pluggy all 1.0.0+repack-1 [19.7 kB] Get: 158 http://deb.debian.org/debian bookworm/main armhf python3-py all 1.11.0-1 [89.2 kB] Get: 159 http://deb.debian.org/debian bookworm/main armhf python3-pygments all 2.14.0+dfsg-1 [783 kB] Get: 160 http://deb.debian.org/debian bookworm/main armhf python3-pysam armhf 0.20.0+ds-3+b1 [1484 kB] Get: 161 http://deb.debian.org/debian bookworm/main armhf python3-pytest all 7.2.1-2 [236 kB] Get: 162 http://deb.debian.org/debian bookworm/main armhf python3-pytest-cov all 4.0.0-1 [26.1 kB] Get: 163 http://deb.debian.org/debian bookworm/main armhf python3-pytest-runner all 2.11.1-4 [8432 B] Get: 164 http://deb.debian.org/debian bookworm/main armhf python3-pytest-xdist all 3.1.0-1 [39.6 kB] Get: 165 http://deb.debian.org/debian bookworm/main armhf python3-urllib3 all 1.26.12-1 [117 kB] Get: 166 http://deb.debian.org/debian bookworm/main armhf python3-requests all 2.28.1+dfsg-1 [67.9 kB] Get: 167 http://deb.debian.org/debian bookworm/main armhf python3-snowballstemmer all 2.2.0-2 [57.8 kB] Get: 168 http://deb.debian.org/debian bookworm/main armhf sphinx-common all 5.3.0-4 [653 kB] Get: 169 http://deb.debian.org/debian bookworm/main armhf python3-sphinx all 5.3.0-4 [549 kB] Get: 170 http://deb.debian.org/debian bookworm/main armhf python3-uritools all 4.0.0-1 [25.3 kB] Get: 171 http://deb.debian.org/debian bookworm/main armhf python3-xmlschema all 1.10.0-6 [177 kB] Fetched 70.5 MB in 16s (4373 kB/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 ... 17881 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:armhf. Preparing to unpack .../libpython3.11-minimal_3.11.2-6_armhf.deb ... Unpacking libpython3.11-minimal:armhf (3.11.2-6) ... Selecting previously unselected package libexpat1:armhf. Preparing to unpack .../libexpat1_2.5.0-1_armhf.deb ... Unpacking libexpat1:armhf (2.5.0-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.2-6_armhf.deb ... Unpacking python3.11-minimal (3.11.2-6) ... Setting up libpython3.11-minimal:armhf (3.11.2-6) ... Setting up libexpat1:armhf (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 ... 18223 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.2-1+b1_armhf.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:armhf. Preparing to unpack .../5-libreadline8_8.2-1.3_armhf.deb ... Unpacking libreadline8:armhf (8.2-1.3) ... Selecting previously unselected package libpython3.11-stdlib:armhf. Preparing to unpack .../6-libpython3.11-stdlib_3.11.2-6_armhf.deb ... Unpacking libpython3.11-stdlib:armhf (3.11.2-6) ... Selecting previously unselected package python3.11. Preparing to unpack .../7-python3.11_3.11.2-6_armhf.deb ... Unpacking python3.11 (3.11.2-6) ... Selecting previously unselected package libpython3-stdlib:armhf. Preparing to unpack .../8-libpython3-stdlib_3.11.2-1+b1_armhf.deb ... Unpacking libpython3-stdlib:armhf (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 ... 18681 files and directories currently installed.) Preparing to unpack .../000-python3_3.11.2-1+b1_armhf.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 tzdata. 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Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libfontenc1:armhf (1:1.1.4-1) ... Setting up autotools-dev (20220109.1) ... Setting up libblas3:armhf (3.11.0-2) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode Setting up libjpeg62-turbo:armhf (1:2.1.5-2) ... Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up liblzf1:armhf (3.6-3) ... Setting up xfonts-encodings (1:1.0.4-2.2) ... Setting up libfribidi0:armhf (1.0.8-2.1) ... Setting up libimagequant0:armhf (2.17.0-1) ... Setting up libpng16-16:armhf (1.6.39-2) ... Setting up autopoint (0.21-12) ... Setting up libsasl2-2:armhf (2.1.28+dfsg-10) ... Setting up libgfortran5:armhf (12.2.0-14) ... Setting up autoconf (2.71-3) ... Setting up libwebp7:armhf (1.2.4-0.2+deb12u1) ... Setting up sensible-utils (0.0.17+nmu1) ... Setting up libtiff6:armhf (4.5.0-6+deb12u1) ... 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Setting up dwz (0.15-1) ... Setting up libjs-jquery-tablesorter (1:2.31.3+dfsg1-3) ... Setting up groff-base (1.22.4-10) ... Setting up xml-core (0.18+nmu1) ... Setting up libcurl4:armhf (7.88.1-10+deb12u4) ... Setting up libharfbuzz0b:armhf (6.0.0+dfsg-3) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpython3.11-stdlib:armhf (3.11.2-6) ... Setting up libcurl3-gnutls:armhf (7.88.1-10+deb12u4) ... Setting up xfonts-utils (1:7.7+6) ... Setting up man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libraqm0:armhf (0.7.0-4.1) ... Setting up sphinx-common (5.3.0-4) ... Setting up libhdf5-103-1:armhf (1.10.8+repack1-1) ... Setting up libpython3-stdlib:armhf (3.11.2-1+b1) ... Setting up libhdf5-hl-100:armhf (1.10.8+repack1-1) ... Setting up python3.11 (3.11.2-6) ... Setting up libhts3:armhf (1.16+ds-3) ... Setting up debhelper (13.11.4) ... Setting up python3 (3.11.2-1+b1) ... Setting up fonts-urw-base35 (20200910-7) ... Setting up python3-markupsafe (2.1.2-1+b1) ... Setting up python3-platformdirs (2.6.0-1) ... Setting up python3-tz (2022.7.1-4) ... Setting up python3-six (1.16.0-4) ... Setting up python3-pil:armhf (9.4.0-1.1+b1) ... Setting up python3-roman (3.3-3) ... Setting up python3-jinja2 (3.1.2-1) ... Setting up python3-packaging (23.0-1) ... Setting up python3-certifi (2022.9.24-1) ... Setting up python3-snowballstemmer (2.2.0-2) ... Setting up python3-dill (0.3.6-1) ... Setting up python3-reportlab-accel:armhf (3.6.12-1+b1) ... Setting up python3-idna (3.3-1) ... Setting up python3-wrapt (1.14.1-2+b2) ... Setting up python3-elementpath (2.5.3-1) ... Setting up python3-typing-extensions (4.4.0-1) ... Setting up python3-xmlschema (1.10.0-6) ... Setting up python3-toml (0.10.2-1) ... Setting up python3-isort (5.6.4-1) ... Setting up python3-urllib3 (1.26.12-1) ... Setting up python3-pluggy (1.0.0+repack-1) ... Setting up python3-reportlab (3.6.12-1) ... Setting up python3-mccabe (0.7.0-1) ... Setting up python3-lazy-object-proxy (1.9.0-1+b1) ... Setting up python3-execnet (1.9.0-1) ... Setting up python3-tomlkit (0.11.7-1) ... Setting up python3-lib2to3 (3.11.2-3) ... Setting up python3-imagesize (1.4.1-1) ... Setting up python3-uritools (4.0.0-1) ... Setting up python3-pkg-resources (66.1.1-1) ... Setting up python3-distutils (3.11.2-3) ... Setting up dh-python (5.20230130+deb12u1) ... Setting up python3-more-itertools (8.10.0-2) ... Setting up python3-iniconfig (1.1.1-2) ... Setting up python3-attr (22.2.0-1) ... Setting up python3-pysam (0.20.0+ds-3+b1) ... Setting up python3-renderpm:armhf (3.6.12-1+b1) ... Setting up python3-setuptools (66.1.1-1) ... Setting up python3-py (1.11.0-1) ... Setting up python3-babel (2.10.3-1) ... update-alternatives: using /usr/bin/pybabel-python3 to provide /usr/bin/pybabel (pybabel) in auto mode Setting up python3-charset-normalizer (3.0.1-2) ... Setting up python3-pytest (7.2.1-2) ... Setting up python3-alabaster (0.7.12-1) ... Setting up python3-mypy-extensions (0.4.3-4) ... Setting up python3-all (3.11.2-1+b1) ... Setting up python3-coverage (6.5.0+dfsg1-2+b1) ... Setting up python3-pytest-cov (4.0.0-1) ... Setting up python3-zipp (1.0.0-6) ... Setting up python3-pygments (2.14.0+dfsg-1) ... Setting up python3-chardet (5.1.0+dfsg-2) ... Setting up python3-requests (2.28.1+dfsg-1) ... Setting up python3-numpy (1:1.24.2-1) ... Setting up python3-astroid (2.14.2-1) ... Setting up python3-pytest-runner (2.11.1-4) ... Setting up python3-importlib-metadata (4.12.0-1) ... Setting up python3-pytest-xdist (3.1.0-1) ... Setting up python3-logilab-common (1.9.8-1) ... Setting up python3-h5py-serial (3.7.0-8) ... Setting up python3-h5py (3.7.0-8) ... Setting up pylint (2.16.2-2) ... Processing triggers for libc-bin (2.36-9+deb12u3) ... 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 I: Building the package I: Running cd /build/reproducible-path/python-pbcore-2.1.2+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../python-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 armhf 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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore copying pbcore/sequence.py -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore copying pbcore/__init__.py -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore creating /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data copying pbcore/data/__init__.py -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data creating /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io copying pbcore/io/_utils.py -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io copying pbcore/io/GffIO.py -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io copying pbcore/io/__init__.py -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io copying pbcore/io/VcfIO.py -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io copying pbcore/io/FofnIO.py -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io copying pbcore/io/base.py -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io copying pbcore/io/FastaIO.py -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io copying pbcore/io/FastqIO.py -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io copying pbcore/io/opener.py -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io creating /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/chemistry copying pbcore/chemistry/chemistry.py -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/chemistry copying pbcore/chemistry/__init__.py -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/chemistry creating /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/util copying pbcore/util/__init__.py -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/util copying pbcore/util/ToolRunner.py -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/util copying pbcore/util/decorators.py -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/util copying pbcore/util/statistics.py -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/util creating /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/model copying pbcore/model/baseRegions.py -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/model copying pbcore/model/__init__.py -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/model creating /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/__init__.py -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets creating /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/dataset copying pbcore/io/dataset/DataSetMetaTypes.py -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/dataset copying pbcore/io/dataset/DataSetMembers.py -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/dataset copying pbcore/io/dataset/DataSetValidator.py -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/dataset copying pbcore/io/dataset/utils.py -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/dataset copying pbcore/io/dataset/run_split.py -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/dataset copying pbcore/io/dataset/DataSetReader.py -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/dataset copying pbcore/io/dataset/__init__.py -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/dataset copying pbcore/io/dataset/DataSetErrors.py -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/dataset copying pbcore/io/dataset/DataSetIO.py -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/dataset copying pbcore/io/dataset/DataSetWriter.py -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/dataset copying pbcore/io/dataset/DataSetUtils.py -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/dataset creating /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/align copying pbcore/io/align/BamIO.py -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/align copying pbcore/io/align/BamAlignment.py -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/align copying pbcore/io/align/PacBioBamIndex.py -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/align copying pbcore/io/align/__init__.py -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/align copying pbcore/io/align/_AlignmentMixin.py -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/align copying pbcore/io/align/BlasrIO.py -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/align copying pbcore/io/align/_BamSupport.py -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/align 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/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data copying pbcore/data/Fluidigm_human_amplicons.fasta.fai -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data copying pbcore/data/Fluidigm_human_amplicons_tiny.fasta -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data copying pbcore/data/barcodes-ed65-450.fasta -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data copying pbcore/data/barcodes-ed65-450.fasta.fai -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data copying pbcore/data/blasr-output.m4 -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data copying pbcore/data/blasr-output.m5 -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data copying pbcore/data/chemistry.xml -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data copying pbcore/data/empty.aligned_subreads.bam -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data copying pbcore/data/empty.aligned_subreads.bam.pbi -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data copying pbcore/data/empty.ccs.bam -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data copying pbcore/data/empty.ccs.bam.pbi -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data copying pbcore/data/empty2.bam -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data copying pbcore/data/empty2.bam.pbi -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data copying pbcore/data/lambdaNEB.fa -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data copying pbcore/data/lambdaNEB.fa.fai -> /build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data copying pbcore/data/variants.gff -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data copying pbcore/data/weird.fa -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data copying pbcore/data/weird.fa.fai -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data creating /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/chemistry/resources copying pbcore/chemistry/resources/mapping.xml -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/chemistry/resources copying pbcore/data/datasets/CollectionMetadata.xml -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/alignment.dataset.xml -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/barcode.dataset.xml -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/ccsaligned.dataset.xml -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/ccsread.dataset.xml -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/contig.dataset.xml -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/empty_lambda.aligned.bam -> /build/reproducible-path/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/reproducible-path/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/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/fofn.fofn -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/lambda.alignmentset.xml -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/lambda.referenceset.xml -> /build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/pbalchemysim.alignmentset.xml -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/pbalchemysim0.alignmentset.chunk0contigs.xml -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/pbalchemysim0.alignmentset.chunk1contigs.xml -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/pbalchemysim0.alignmentset.xml -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/pbalchemysim0.pbalign.bam -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/pbalchemysim0.pbalign.bam.bai -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/pbalchemysim0.pbalign.bam.pbi -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/pbalchemysim0.reference.fasta -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/pbalchemysim0.reference.fasta.fai -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/pbalchemysim0.referenceset.xml -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/pbalchemysim0.subreads.bam -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/pbalchemysim0.subreads.bam.bai -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/pbalchemysim0.subreads.bam.pbi -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/pbalchemysim0.subreadset.xml -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/pbalchemysim1.alignmentset.xml -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/pbalchemysim1.pbalign.bam -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/pbalchemysim1.pbalign.bam.bai -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/pbalchemysim1.pbalign.bam.pbi -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/pbalchemysim1.subreads.bam -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/pbalchemysim1.subreads.bam.bai -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/pbalchemysim1.subreads.bam.pbi -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/pbalchemysim1.subreadset.xml -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/reference.dataset.xml -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/subread.dataset.xml -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/subreadSetWithStats.xml -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/data/datasets PYTHONPATH=/build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build /usr/bin/make doc make[2]: Entering directory '/build/reproducible-path/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/reproducible-path/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/reproducible-path/python-pbcore-2.1.2+dfsg/doc/pbcore.rst:7: WARNING: toctree contains reference to nonexisting document 'pbcore.deprecated' /build/reproducible-path/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/reproducible-path/python-pbcore-2.1.2+dfsg/doc/modules.rst: WARNING: document isn't included in any toctree /build/reproducible-path/python-pbcore-2.1.2+dfsg/doc/pbcore.data.datasets.rst: WARNING: document isn't included in any toctree /build/reproducible-path/python-pbcore-2.1.2+dfsg/doc/pbcore.io.align.rst: WARNING: document isn't included in any toctree /build/reproducible-path/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/reproducible-path/python-pbcore-2.1.2+dfsg/doc' make[2]: Leaving directory '/build/reproducible-path/python-pbcore-2.1.2+dfsg' make[1]: Leaving directory '/build/reproducible-path/python-pbcore-2.1.2+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/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/reproducible-path/python-pbcore-2.1.2+dfsg, configfile: pytest.ini plugins: cov-4.0.0, xdist-3.1.0 gw0 I / gw1 I / gw2 I / gw3 I [gw0] linux Python 3.11.2 cwd: /build/reproducible-path/python-pbcore-2.1.2+dfsg [gw1] linux Python 3.11.2 cwd: /build/reproducible-path/python-pbcore-2.1.2+dfsg [gw2] linux Python 3.11.2 cwd: /build/reproducible-path/python-pbcore-2.1.2+dfsg [gw3] linux Python 3.11.2 cwd: /build/reproducible-path/python-pbcore-2.1.2+dfsg [gw0] 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] [gw1] Python 3.11.2 (main, Mar 13 2023, 12:18:29) [GCC 12.2.0] [gw3] Python 3.11.2 (main, Mar 13 2023, 12:18:29) [GCC 12.2.0] gw0 [140] / gw1 [140] / gw2 [140] / gw3 [140] scheduling tests via LoadScopeScheduling tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testBasicOperations tests/test_dataset_run_split.py::test tests/test_pbcore_extract_bam_sequence.py::TestCase::test_reverse_complement tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testBasicOperations [gw0] [ 0%] SKIPPED tests/test_dataset_run_split.py::test tests/test_pbcore_io_AlnFileReaders.py::TestCCSBam::testBasicOperations [gw0] [ 1%] SKIPPED tests/test_pbcore_io_AlnFileReaders.py::TestCCSBam::testBasicOperations [gw2] [ 2%] PASSED tests/test_pbcore_extract_bam_sequence.py::TestCase::test_reverse_complement tests/test_pbcore_io_AlnFileReaders.py::TestCCSBam::testQStartEndUnavailable tests/test_pbcore_io_AlnFileReaders.py::TestTranscriptBam::test_transcript_set_support [gw2] [ 2%] SKIPPED tests/test_pbcore_io_AlnFileReaders.py::TestTranscriptBam::test_transcript_set_support tests/test_pbcore_io_AlnFileReaders.py::TestMissingHeaderM5::test_retrieve_read_group_properties [gw0] [ 3%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestCCSBam::testQStartEndUnavailable tests/test_pbcore_io_AlnFileReaders.py::TestEmptyBam::test_empty_bam_reads_in_range [gw0] [ 4%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestEmptyBam::test_empty_bam_reads_in_range tests/test_pbcore_io_AlnFileReaders.py::TestMultipleReadGroups::test_retrieve_read_group_properties [gw1] [ 5%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testBasicOperations tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testStrandOrientation [gw1] [ 5%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testStrandOrientation [gw3] [ 6%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testBasicOperations tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testStrandOrientation [gw3] [ 7%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testStrandOrientation tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testReadName tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testReadName [gw1] [ 7%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testReadName tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testAlignedRead [gw3] [ 8%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testReadName tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testAlignedRead [gw1] [ 9%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testAlignedRead [gw3] [ 10%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testAlignedRead tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testUnalignedRead [gw1] [ 10%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testUnalignedRead tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testUnalignedRead tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testAlignedReference [gw3] [ 11%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testUnalignedRead [gw1] [ 12%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testAlignedReference tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testUnalignedReference tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testAlignedReference [gw1] [ 12%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testUnalignedReference tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testDeletionQV [gw3] [ 13%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testAlignedReference tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testUnalignedReference [gw3] [ 14%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testUnalignedReference tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testDeletionQV [gw1] [ 15%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testDeletionQV tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testTranscript [gw1] [ 15%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testTranscript tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testClippedAlignments [gw3] [ 16%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testDeletionQV [gw1] [ 17%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testClippedAlignments [gw2] [ 17%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestMissingHeaderM5::test_retrieve_read_group_properties tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testTranscript tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testReadsInRange [gw3] [ 18%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testTranscript [gw0] [ 19%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestMultipleReadGroups::test_retrieve_read_group_properties tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testClippedAlignments tests/test_pbcore_io_AlnFileReaders.py::TestUpdatedChemistryMapping::test_load_updated_mapping tests/test_pbcore_io_AlnFileReaders.py::TestMultipleReadGroups::test_sample_names [gw3] [ 20%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testClippedAlignments tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testReadsInRange [gw2] [ 20%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestUpdatedChemistryMapping::test_load_updated_mapping [gw0] [ 21%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestMultipleReadGroups::test_sample_names tests/test_pbcore_io_AlnFileReaders.py::TestBarcodedBam::test_read_lima_demultiplexed_bam tests/test_pbcore_io_BlasrIO.py::test_m4 [gw0] [ 22%] SKIPPED tests/test_pbcore_io_AlnFileReaders.py::TestBarcodedBam::test_read_lima_demultiplexed_bam tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test__init__ [gw0] [ 22%] PASSED tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test__init__ [gw2] [ 23%] PASSED tests/test_pbcore_io_BlasrIO.py::test_m4 tests/test_pbcore_io_BlasrIO.py::test_m5 tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test__str__ [gw0] [ 24%] PASSED tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test__str__ tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test_fromString [gw0] [ 25%] PASSED tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test_fromString [gw2] [ 25%] PASSED tests/test_pbcore_io_BlasrIO.py::test_m5 tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test_reverse_complement1 [gw0] [ 26%] PASSED tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test_reverse_complement1 tests/test_pbcore_io_FastaIO.py::TestFastaReader::test_readFasta tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test_reverse_complement2 [gw0] [ 27%] PASSED tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test_reverse_complement2 tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test_len [gw0] [ 27%] PASSED tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test_len tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test_eq [gw0] [ 28%] PASSED tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test_eq [gw2] [ 29%] PASSED tests/test_pbcore_io_FastaIO.py::TestFastaReader::test_readFasta tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test_not_equal tests/test_pbcore_io_FastaIO.py::TestFastaReader::test_dosLineEndingsFasta [gw0] [ 30%] PASSED tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test_not_equal tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::testIteration [gw0] [ 30%] PASSED tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::testIteration [gw2] [ 31%] PASSED tests/test_pbcore_io_FastaIO.py::TestFastaReader::test_dosLineEndingsFasta tests/test_pbcore_io_FastaIO.py::TestFastaWriter::test_writeFasta1 tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::testAccessByName [gw2] [ 32%] PASSED tests/test_pbcore_io_FastaIO.py::TestFastaWriter::test_writeFasta1 tests/test_pbcore_io_FastaIO.py::TestFastaWriter::test_writeFasta2 [gw0] [ 32%] PASSED tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::testAccessByName tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::testAccessById [gw0] [ 33%] PASSED tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::testAccessById tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::testAccessByPosition [gw0] [ 34%] PASSED tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::testAccessByPosition [gw2] [ 35%] PASSED tests/test_pbcore_io_FastaIO.py::TestFastaWriter::test_writeFasta2 tests/test_pbcore_io_FastqIO.py::TestQvConversion::testAsciiFromQvs [gw2] [ 35%] PASSED tests/test_pbcore_io_FastqIO.py::TestQvConversion::testAsciiFromQvs tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::testSlice [gw0] [ 36%] PASSED tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::testSlice tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::test_dosLineEndingsFasta tests/test_pbcore_io_FastqIO.py::TestQvConversion::testQvsFromAscii [gw2] [ 37%] PASSED tests/test_pbcore_io_FastqIO.py::TestQvConversion::testQvsFromAscii tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test__init__ [gw2] [ 37%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test__init__ tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test__str__ [gw2] [ 38%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test__str__ tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test_fromString [gw2] [ 39%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test_fromString tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test_reverse_complement1 [gw2] [ 40%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test_reverse_complement1 tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test_reverse_complement2 [gw0] [ 40%] PASSED tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::test_dosLineEndingsFasta tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::test_readWeirdFastaIndex [gw0] [ 41%] PASSED tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::test_readWeirdFastaIndex [gw2] [ 42%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test_reverse_complement2 tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test_len tests/test_pbcore_io_FastqIO.py::TestFastqReader::test_readFastq1 [gw0] [ 42%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqReader::test_readFastq1 [gw2] [ 43%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test_len tests/test_pbcore_io_FastqIO.py::TestFastqReader::test_readFastq2 [gw0] [ 44%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqReader::test_readFastq2 tests/test_pbcore_io_FastqIO.py::TestFastqWriter::test_writeFastq1 tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test_eq [gw2] [ 45%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test_eq [gw0] [ 45%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqWriter::test_writeFastq1 tests/test_pbcore_io_FastqIO.py::TestFastqWriter::test_writeFastq2 [gw0] [ 46%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqWriter::test_writeFastq2 tests/test_pbcore_io_FastqIO.py::TestFastqWriter::test_writeFastq3 tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test_not_equal [gw2] [ 47%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test_not_equal tests/test_pbcore_io_FofnIO.py::test_simple [gw2] [ 47%] PASSED tests/test_pbcore_io_FofnIO.py::test_simple [gw0] [ 48%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqWriter::test_writeFastq3 tests/test_pbcore_io_GffIO.py::TestGff3Record::test_str [gw0] [ 49%] PASSED tests/test_pbcore_io_GffIO.py::TestGff3Record::test_str tests/test_pbcore_io_GffIO.py::TestGff3Record::test_modification [gw0] [ 50%] PASSED tests/test_pbcore_io_GffIO.py::TestGff3Record::test_modification tests/test_pbcore_io_GffIO.py::TestGff3Record::test_fromString [gw0] [ 50%] PASSED tests/test_pbcore_io_GffIO.py::TestGff3Record::test_fromString tests/test_pbcore_io_FofnIO.py::test_empty_lines tests/test_pbcore_io_GffIO.py::TestGff3Record::test_get [gw0] [ 51%] PASSED tests/test_pbcore_io_GffIO.py::TestGff3Record::test_get tests/test_pbcore_io_GffIO.py::TestGffWriter::test_writeHeader [gw0] [ 52%] PASSED tests/test_pbcore_io_GffIO.py::TestGffWriter::test_writeHeader [gw2] [ 52%] PASSED tests/test_pbcore_io_FofnIO.py::test_empty_lines tests/test_pbcore_io_GffIO.py::TestGffWriter::test_writeRecord [gw0] [ 53%] PASSED tests/test_pbcore_io_GffIO.py::TestGffWriter::test_writeRecord tests/test_pbcore_io_GffIO.py::TestGffSorting::test_merge_gffs tests/test_pbcore_io_FofnIO.py::test_absolutifying [gw0] [ 54%] PASSED tests/test_pbcore_io_GffIO.py::TestGffSorting::test_merge_gffs tests/test_pbcore_io_GffIO.py::TestGffSorting::test_merge_gffs_sorted [gw2] [ 55%] PASSED tests/test_pbcore_io_FofnIO.py::test_absolutifying [gw0] [ 55%] PASSED tests/test_pbcore_io_GffIO.py::TestGffSorting::test_merge_gffs_sorted tests/test_pbcore_io_GffIO.py::TestGffSorting::test_sort_gff tests/test_pbcore_io_GffIO.py::TestGffReader::test_headers [gw0] [ 56%] PASSED tests/test_pbcore_io_GffIO.py::TestGffSorting::test_sort_gff tests/test_pbcore_io_GffIO.py::TestGffSorting::test_empty_file [gw2] [ 57%] PASSED tests/test_pbcore_io_GffIO.py::TestGffReader::test_headers tests/test_pbcore_io_GffIO.py::TestGffReader::test__iter__ [gw0] [ 57%] PASSED tests/test_pbcore_io_GffIO.py::TestGffSorting::test_empty_file tests/test_pbcore_io_lossless_bam.py::TestCase::test_1 [gw0] [ 58%] SKIPPED tests/test_pbcore_io_lossless_bam.py::TestCase::test_1 tests/test_pbcore_io_unaligned_bam.py::TestUnalignedBam::testInvalidOperations [gw2] [ 59%] PASSED tests/test_pbcore_io_GffIO.py::TestGffReader::test__iter__ tests/test_pbcore_io_VcfIO.py::TestVcfSorting::test_merge_vcfs_sorted [gw2] [ 60%] PASSED tests/test_pbcore_io_VcfIO.py::TestVcfSorting::test_merge_vcfs_sorted [gw0] [ 60%] PASSED tests/test_pbcore_io_unaligned_bam.py::TestUnalignedBam::testInvalidOperations tests/test_pbcore_io_unaligned_bam.py::TestUnalignedBam::testIpd [gw0] [ 61%] PASSED tests/test_pbcore_io_unaligned_bam.py::TestUnalignedBam::testIpd tests/test_pbcore_util_sequences.py::TestReverseComplement::test_reverse [gw0] [ 62%] PASSED tests/test_pbcore_util_sequences.py::TestReverseComplement::test_reverse tests/test_pbcore_util_sequences.py::TestReverseComplement::test_complement [gw0] [ 62%] PASSED tests/test_pbcore_util_sequences.py::TestReverseComplement::test_complement tests/test_pbcore_util.py::TestStatistics::test_accuracy_as_phred_qv [gw2] [ 63%] PASSED tests/test_pbcore_util.py::TestStatistics::test_accuracy_as_phred_qv tests/test_pbcore_util_sequences.py::TestReverseComplement::test_reverseComplement [gw0] [ 64%] PASSED tests/test_pbcore_util_sequences.py::TestReverseComplement::test_reverseComplement tests/test_pbcore_util_sequences.py::TestReverseComplement::test_iupac [gw0] [ 65%] PASSED tests/test_pbcore_util_sequences.py::TestReverseComplement::test_iupac tests/test_pbcore_util_sequences.py::TestReverseComplement::test_complement_error [gw0] [ 65%] PASSED tests/test_pbcore_util_sequences.py::TestReverseComplement::test_complement_error tests/test_pbcore_util.py::TestStatistics::test_phred_qv_as_accuracy tests/test_pbcore_util_sequences.py::TestReverseComplement::test_reverse_complement_error [gw0] [ 66%] PASSED tests/test_pbcore_util_sequences.py::TestReverseComplement::test_reverse_complement_error [gw2] [ 67%] PASSED tests/test_pbcore_util.py::TestStatistics::test_phred_qv_as_accuracy tests/test_pbdataset_utils.py::TestDataSetUtils::test_get_dataset_uuid tests/test_pbdataset_split.py::TestDataSetSplit::test_split [gw3] [ 67%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testReadsInRange tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testReadGroupTable [gw3] [ 68%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testReadGroupTable tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testSequencingChemistry [gw3] [ 69%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testSequencingChemistry tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testMapQV [gw3] [ 70%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testMapQV tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testHoleNumbers [gw1] [ 70%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testReadsInRange tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testReadGroupTable [gw1] [ 71%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testReadGroupTable tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testSequencingChemistry [gw1] [ 72%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testSequencingChemistry tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testSpecVersion [gw1] [ 72%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testSpecVersion [gw3] [ 73%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testHoleNumbers tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testReadScore tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testErrorCounts [gw1] [ 74%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testReadScore [gw3] [ 75%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testErrorCounts tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::test_sample_name_default [gw1] [ 75%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::test_sample_name_default tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testReadsByName tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::test_library_name_default [gw1] [ 76%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::test_library_name_default tests/test_pbindex.py::TestPbIndex::test_pbindex_bam_consistency [gw3] [ 77%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testReadsByName tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::test_empty_bam [gw3] [ 77%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::test_empty_bam tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::test_alignment_identity [gw0] [ 78%] PASSED tests/test_pbdataset_utils.py::TestDataSetUtils::test_get_dataset_uuid tests/test_pbdataset_utils.py::TestDataSetUtils::test_get_dataset_metatype [gw0] [ 79%] PASSED tests/test_pbdataset_utils.py::TestDataSetUtils::test_get_dataset_metatype tests/test_pbdataset_utils.py::TestDataSetUtils::test_dsIdToSuffix [gw0] [ 80%] PASSED tests/test_pbdataset_utils.py::TestDataSetUtils::test_dsIdToSuffix tests/test_pbdataset_utils.py::TestDataSetUtils::test_divideKeys_keysToRanges [gw1] [ 80%] PASSED tests/test_pbindex.py::TestPbIndex::test_pbindex_bam_consistency tests/test_pbindex.py::TestPbIndex::test_pbindex_streaming [gw0] [ 81%] PASSED tests/test_pbdataset_utils.py::TestDataSetUtils::test_divideKeys_keysToRanges [gw1] [ 82%] PASSED tests/test_pbindex.py::TestPbIndex::test_pbindex_streaming tests/test_pbindex.py::TestPbIndex::test_pbindex_streaming_entire [gw1] [ 82%] PASSED tests/test_pbindex.py::TestPbIndex::test_pbindex_streaming_entire tests/test_pbindex.py::TestPbIndex::test_pbindex_with_zmw_index [gw1] [ 83%] PASSED tests/test_pbindex.py::TestPbIndex::test_pbindex_with_zmw_index [gw3] [ 84%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::test_alignment_identity tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::test_alignment_identity_unindexed [gw3] [ 85%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::test_alignment_identity_unindexed [gw2] [ 85%] FAILED tests/test_pbdataset_split.py::TestDataSetSplit::test_split tests/test_pbdataset_split.py::TestDataSetSplit::test_split_zmws [gw2] [ 86%] PASSED tests/test_pbdataset_split.py::TestDataSetSplit::test_split_zmws tests/test_pbdataset_split.py::TestDataSetSplit::test_split_zmws_targetsize [gw2] [ 87%] PASSED tests/test_pbdataset_split.py::TestDataSetSplit::test_split_zmws_targetsize tests/test_pbdataset_split.py::TestDataSetSplit::test_large_split_zmws [gw2] [ 87%] SKIPPED tests/test_pbdataset_split.py::TestDataSetSplit::test_large_split_zmws tests/test_pbdataset_split.py::TestDataSetSplit::test_multi_movie_split_zmws [gw2] [ 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 [gw2] [ 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 [gw2] [ 90%] SKIPPED tests/test_pbdataset_split.py::TestDataSetSplit::test_multi_movie_split_zmws_existing_filters tests/test_pbdataset_split.py::TestDataSetSplit::test_movie_split [gw2] [ 90%] SKIPPED tests/test_pbdataset_split.py::TestDataSetSplit::test_movie_split tests/test_pbdataset_split.py::TestDataSetSplit::test_split_references [gw2] [ 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 [gw2] [ 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 [gw2] [ 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 [gw2] [ 93%] FAILED 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 [gw2] [ 94%] FAILED tests/test_pbdataset_split.py::TestDataSetSplit::test_split_by_contigs_with_split tests/test_pbdataset_split.py::TestDataSetSplit::test_refWindows [gw2] [ 95%] FAILED tests/test_pbdataset_split.py::TestDataSetSplit::test_refWindows tests/test_pbdataset_split.py::TestDataSetSplit::test_huge_zmw_split [gw2] [ 95%] SKIPPED tests/test_pbdataset_split.py::TestDataSetSplit::test_huge_zmw_split tests/test_pbdataset_split.py::TestDataSetSplit::test_subreadset_split_metadata_element_name [gw2] [ 96%] FAILED tests/test_pbdataset_split.py::TestDataSetSplit::test_subreadset_split_metadata_element_name tests/test_pbdataset_split.py::TestDataSetSplit::test_contigset_split [gw2] [ 97%] PASSED tests/test_pbdataset_split.py::TestDataSetSplit::test_contigset_split tests/test_pbdataset_split.py::TestDataSetSplit::test_isBarcoded [gw2] [ 97%] SKIPPED tests/test_pbdataset_split.py::TestDataSetSplit::test_isBarcoded tests/test_pbdataset_split.py::TestDataSetSplit::test_barcode_split_cornercases [gw2] [ 98%] SKIPPED tests/test_pbdataset_split.py::TestDataSetSplit::test_barcode_split_cornercases tests/test_pbdataset_split.py::TestDataSetSplit::test_barcode_split_maxChunks [gw2] [ 99%] SKIPPED tests/test_pbdataset_split.py::TestDataSetSplit::test_barcode_split_maxChunks tests/test_pbdataset_split.py::TestDataSetSplit::test_split_read_groups [gw2] [100%] SKIPPED tests/test_pbdataset_split.py::TestDataSetSplit::test_split_read_groups =================================== FAILURES =================================== _________________________ TestDataSetSplit.test_split __________________________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 self = def test_split(self): ds1 = openDataSet(data.getXml(11)) assert ds1.numExternalResources > 1 > dss = list(ds1.split()) tests/test_pbdataset_split.py:24: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ pbcore/io/dataset/DataSetIO.py:1009: in split if len(self) == 0: pbcore/io/dataset/DataSetIO.py:778: in __len__ self.updateCounts() pbcore/io/dataset/DataSetIO.py:2640: in updateCounts self.assertIndexed() pbcore/io/dataset/DataSetIO.py:2492: in assertIndexed self._assertIndexed(IndexedBamReader) pbcore/io/dataset/DataSetIO.py:2039: in _assertIndexed self._openFiles() pbcore/io/dataset/DataSetIO.py:2172: in _openFiles resource = IndexedBamReader(location) pbcore/io/align/BamIO.py:397: in __init__ super().__init__(fname, referenceFastaFname) pbcore/io/align/BamIO.py:194: in __init__ self._loadReadGroupInfo() pbcore/io/align/BamIO.py:85: in _loadReadGroupInfo rgID = rgAsInt(rg["ID"]) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ rgIdString = 'c967a5cb' def rgAsInt(rgIdString): > return np.int32(int(rgIdString.split("/")[0], 16)) E OverflowError: Python int too large to convert to C long pbcore/io/align/_BamSupport.py:66: OverflowError _______ TestDataSetSplit.test_split_by_contigs_with_split_and_maxChunks ________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 self = def test_split_by_contigs_with_split_and_maxChunks(self): # test to make sure the refWindows work when chunks == # refs > ds3 = AlignmentSet(data.getBam()) tests/test_pbdataset_split.py:415: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ pbcore/io/dataset/DataSetIO.py:2722: in __init__ super().__init__(*files, **kwargs) pbcore/io/dataset/DataSetIO.py:2085: in __init__ super().__init__(*files, **kwargs) pbcore/io/dataset/DataSetIO.py:551: in __init__ self.updateCounts() pbcore/io/dataset/DataSetIO.py:2640: in updateCounts self.assertIndexed() pbcore/io/dataset/DataSetIO.py:2492: in assertIndexed self._assertIndexed(IndexedBamReader) pbcore/io/dataset/DataSetIO.py:2039: in _assertIndexed self._openFiles() pbcore/io/dataset/DataSetIO.py:2172: in _openFiles resource = IndexedBamReader(location) pbcore/io/align/BamIO.py:397: in __init__ super().__init__(fname, referenceFastaFname) pbcore/io/align/BamIO.py:194: in __init__ self._loadReadGroupInfo() pbcore/io/align/BamIO.py:85: in _loadReadGroupInfo rgID = rgAsInt(rg["ID"]) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ rgIdString = 'c967a5cb' def rgAsInt(rgIdString): > return np.int32(int(rgIdString.split("/")[0], 16)) E OverflowError: Python int too large to convert to C long pbcore/io/align/_BamSupport.py:66: OverflowError ______________ TestDataSetSplit.test_split_by_contigs_with_split _______________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 self = def test_split_by_contigs_with_split(self): # test to make sure the refWindows work when chunks == # refs > ds3 = AlignmentSet(data.getBam()) tests/test_pbdataset_split.py:558: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ pbcore/io/dataset/DataSetIO.py:2722: in __init__ super().__init__(*files, **kwargs) pbcore/io/dataset/DataSetIO.py:2085: in __init__ super().__init__(*files, **kwargs) pbcore/io/dataset/DataSetIO.py:551: in __init__ self.updateCounts() pbcore/io/dataset/DataSetIO.py:2640: in updateCounts self.assertIndexed() pbcore/io/dataset/DataSetIO.py:2492: in assertIndexed self._assertIndexed(IndexedBamReader) pbcore/io/dataset/DataSetIO.py:2039: in _assertIndexed self._openFiles() pbcore/io/dataset/DataSetIO.py:2172: in _openFiles resource = IndexedBamReader(location) pbcore/io/align/BamIO.py:397: in __init__ super().__init__(fname, referenceFastaFname) pbcore/io/align/BamIO.py:194: in __init__ self._loadReadGroupInfo() pbcore/io/align/BamIO.py:85: in _loadReadGroupInfo rgID = rgAsInt(rg["ID"]) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ rgIdString = 'c967a5cb' def rgAsInt(rgIdString): > return np.int32(int(rgIdString.split("/")[0], 16)) E OverflowError: Python int too large to convert to C long pbcore/io/align/_BamSupport.py:66: OverflowError _______________________ TestDataSetSplit.test_refWindows _______________________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 self = def test_refWindows(self): > ds = AlignmentSet(data.getBam()) tests/test_pbdataset_split.py:614: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ pbcore/io/dataset/DataSetIO.py:2722: in __init__ super().__init__(*files, **kwargs) pbcore/io/dataset/DataSetIO.py:2085: in __init__ super().__init__(*files, **kwargs) pbcore/io/dataset/DataSetIO.py:551: in __init__ self.updateCounts() pbcore/io/dataset/DataSetIO.py:2640: in updateCounts self.assertIndexed() pbcore/io/dataset/DataSetIO.py:2492: in assertIndexed self._assertIndexed(IndexedBamReader) pbcore/io/dataset/DataSetIO.py:2039: in _assertIndexed self._openFiles() pbcore/io/dataset/DataSetIO.py:2172: in _openFiles resource = IndexedBamReader(location) pbcore/io/align/BamIO.py:397: in __init__ super().__init__(fname, referenceFastaFname) pbcore/io/align/BamIO.py:194: in __init__ self._loadReadGroupInfo() pbcore/io/align/BamIO.py:85: in _loadReadGroupInfo rgID = rgAsInt(rg["ID"]) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ rgIdString = 'c967a5cb' def rgAsInt(rgIdString): > return np.int32(int(rgIdString.split("/")[0], 16)) E OverflowError: Python int too large to convert to C long pbcore/io/align/_BamSupport.py:66: OverflowError _________ TestDataSetSplit.test_subreadset_split_metadata_element_name _________ [gw2] linux -- Python 3.11.2 /usr/bin/python3.11 self = def test_subreadset_split_metadata_element_name(self): fn = tempfile.NamedTemporaryFile(suffix=".subreadset.xml").name log.debug(fn) > sset = SubreadSet(data.getXml(9), data.getXml(12)) tests/test_pbdataset_split.py:645: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ pbcore/io/dataset/DataSetIO.py:2694: in __init__ super().__init__(*files, **kwargs) pbcore/io/dataset/DataSetIO.py:2085: in __init__ super().__init__(*files, **kwargs) pbcore/io/dataset/DataSetIO.py:553: in __init__ self.updateCounts() pbcore/io/dataset/DataSetIO.py:2640: in updateCounts self.assertIndexed() pbcore/io/dataset/DataSetIO.py:2492: in assertIndexed self._assertIndexed(IndexedBamReader) pbcore/io/dataset/DataSetIO.py:2039: in _assertIndexed self._openFiles() pbcore/io/dataset/DataSetIO.py:2172: in _openFiles resource = IndexedBamReader(location) pbcore/io/align/BamIO.py:397: in __init__ super().__init__(fname, referenceFastaFname) pbcore/io/align/BamIO.py:194: in __init__ self._loadReadGroupInfo() pbcore/io/align/BamIO.py:85: in _loadReadGroupInfo rgID = rgAsInt(rg["ID"]) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ rgIdString = 'c967a5cb' def rgAsInt(rgIdString): > return np.int32(int(rgIdString.split("/")[0], 16)) E OverflowError: Python int too large to convert to C long pbcore/io/align/_BamSupport.py:66: OverflowError =============================== warnings summary =============================== tests/test_pbcore_extract_bam_sequence.py: 1 warning tests/test_pbcore_io_AlnFileReaders.py: 118 warnings /build/reproducible-path/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_AlnFileReaders.py: 28 warnings /build/reproducible-path/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/reproducible-path/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/reproducible-path/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_pbcore_io_FastqIO.py: 11 warnings /build/reproducible-path/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") -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html - generated xml file: /build/reproducible-path/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 ============================= 1.47s call tests/test_pbdataset_split.py::TestDataSetSplit::test_subreadset_split_metadata_element_name 0.99s call tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testReadsInRange 0.84s call tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testReadsInRange 0.72s call tests/test_pbdataset_split.py::TestDataSetSplit::test_split_zmws_targetsize 0.70s call tests/test_pbdataset_split.py::TestDataSetSplit::test_contigset_split 0.46s call tests/test_pbdataset_split.py::TestDataSetSplit::test_split_zmws 0.36s call tests/test_pbdataset_split.py::TestDataSetSplit::test_split 0.30s call tests/test_pbdataset_utils.py::TestDataSetUtils::test_get_dataset_uuid 0.27s call tests/test_pbcore_io_AlnFileReaders.py::TestMissingHeaderM5::test_retrieve_read_group_properties 0.25s call tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::test_alignment_identity_unindexed 0.24s call tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::test_alignment_identity 0.21s setup tests/test_pbcore_io_AlnFileReaders.py::TestMultipleReadGroups::test_retrieve_read_group_properties 0.20s setup tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testBasicOperations 0.18s setup tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testBasicOperations 0.14s call tests/test_pbindex.py::TestPbIndex::test_pbindex_bam_consistency 0.09s call tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::test_dosLineEndingsFasta 0.08s call tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testHoleNumbers 0.05s setup tests/test_pbcore_extract_bam_sequence.py::TestCase::test_reverse_complement 0.04s call tests/test_pbdataset_utils.py::TestDataSetUtils::test_get_dataset_metatype 0.04s call tests/test_pbcore_io_AlnFileReaders.py::TestUpdatedChemistryMapping::test_load_updated_mapping =========================== short test summary info ============================ FAILED tests/test_pbdataset_split.py::TestDataSetSplit::test_split - Overflow... FAILED tests/test_pbdataset_split.py::TestDataSetSplit::test_split_by_contigs_with_split_and_maxChunks FAILED tests/test_pbdataset_split.py::TestDataSetSplit::test_split_by_contigs_with_split FAILED tests/test_pbdataset_split.py::TestDataSetSplit::test_refWindows - Ove... FAILED tests/test_pbdataset_split.py::TestDataSetSplit::test_subreadset_split_metadata_element_name =========== 5 failed, 117 passed, 18 skipped, 192 warnings in 33.64s =========== E: pybuild pybuild:388: test: plugin custom failed with: exit code=1: python3.11 setup.py test dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p 3.11 returned exit code 13 make[1]: *** [debian/rules:39: override_dh_auto_test] Error 25 make[1]: Leaving directory '/build/reproducible-path/python-pbcore-2.1.2+dfsg' make: *** [debian/rules:13: binary] Error 2 dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2 I: copying local configuration E: Failed autobuilding of package 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/18106 and its subdirectories Sun Jan 7 10:27:29 UTC 2024 W: No second build log, what happened?