Tue Apr 2 14:15:06 UTC 2024 I: starting to build python-pbcore/trixie/i386 on jenkins on '2024-04-02 14:14' Tue Apr 2 14:15:06 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_5/13764/console.log Tue Apr 2 14:15:06 UTC 2024 I: Downloading source for trixie/python-pbcore=2.1.2+dfsg-7 --2024-04-02 14:15:07-- http://deb.debian.org/debian/pool/main/p/python-pbcore/python-pbcore_2.1.2%2bdfsg-7.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2651 (2.6K) [text/prs.lines.tag] Saving to: ‘python-pbcore_2.1.2+dfsg-7.dsc’ 0K .. 100% 386M=0s 2024-04-02 14:15:07 (386 MB/s) - ‘python-pbcore_2.1.2+dfsg-7.dsc’ saved [2651/2651] Tue Apr 2 14:15:07 UTC 2024 I: python-pbcore_2.1.2+dfsg-7.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-7 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, dh-sequence-python3, dh-sequence-sphinxdoc , 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 , 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 298a126a0274f34407be2811ea1f66a7e0b761b2 60160 python-pbcore_2.1.2+dfsg-7.debian.tar.xz Checksums-Sha256: a31283a37b20aa7b327de78a533254c5892c5519fb8214fd3c1a978855351326 2918008 python-pbcore_2.1.2+dfsg.orig.tar.xz d3173c0a14ab52427e554d0065d0109e1fb7799728ce4ae0659a965f9349d91c 60160 python-pbcore_2.1.2+dfsg-7.debian.tar.xz Files: b58bb3c6ad20be9ea36bf8a7548bdd84 2918008 python-pbcore_2.1.2+dfsg.orig.tar.xz db6112a9b7976639a79d39fa61fd9ba7 60160 python-pbcore_2.1.2+dfsg-7.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEck1gkzcRPHEFUNdHPCZ2P2xn5uIFAmX9un8ACgkQPCZ2P2xn 5uJCdxAAxAVm6soJ/gOEeE1/ZrE9lbZK21mLfD1SrVWiIUyaj7WdHZ1FSFia6IBM Npd6Sf0e/Q65zwaRZJtzaUZUzIuI5OMWbm4lT/vQcA4w8TAAKR6DP7lFlu65/pJl oDTUIFef/pUH1KMYhRJwL113Pis20uXf9dgQ9XaDFhxk7ZfFOoiRdV+bEh5eMQvu w2AK0cw7E88Nm8qozpR3p59kZMq4JWvzNf5MznKJMXvbG5R+L2tmALyJ41H90wxJ e53oRgxnxQ2xfm2PDnRRgvTN5KJHYyu2pYngilwBwsOxA9oT9PcyMCosIgCP1jmh azMhIiVKovpdEqV0acIeCIe2NRaRjUTZ+VuwrBhMY3CDx2N8SzhzEA3dtEDRzxCw g9DEK7FA/ooNsVeJuAwcbjnu/ba+ifXop0QPiIkFMi6jUOQ+YpsNkV+MG2cRfOFG /yG/DjSAMBmm+qbxz608HS1UXnxymHb5j2lFMIVwu0sMNSLenIGEF7kPybb/8I7d qhTF2p/djpGtt745FRB1iPPnupEIIGoT4Fb6BaSoEE1OF04PEX6pJSjAgCnJ5hQ0 6bkuzb5X1vy8YuKDy4pcdbdpCnfCrUS1TXsZQSK5PytLX6AeRPKW06mDP1pqoNkX WEuUZe8/XsksdYsXZpoWMO/nw1dNDtjfiEV0pe5KsvqPsWA8nlo= =18Ks -----END PGP SIGNATURE----- Tue Apr 2 14:15:07 UTC 2024 I: Checking whether the package is not for us Tue Apr 2 14:15:07 UTC 2024 I: Starting 1st build on remote node ionos12-i386.debian.net. Tue Apr 2 14:15:07 UTC 2024 I: Preparing to do remote build '1' on ionos12-i386.debian.net. Tue Apr 2 14:18:43 UTC 2024 I: Deleting $TMPDIR on ionos12-i386.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Tue Apr 2 02:15:09 -12 2024 I: pbuilder-time-stamp: 1712067309 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: using eatmydata during job I: Copying source file I: copying [python-pbcore_2.1.2+dfsg-7.dsc] I: copying [./python-pbcore_2.1.2+dfsg.orig.tar.xz] I: copying [./python-pbcore_2.1.2+dfsg-7.debian.tar.xz] I: Extracting source gpgv: Signature made Fri Mar 22 17:06:07 2024 gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./python-pbcore_2.1.2+dfsg-7.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-7.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/50995/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='i386' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=11 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='i386' IFS=' ' INVOCATION_ID='8e6704db4d7943b094984e86a31d1821' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' LD_LIBRARY_PATH='/usr/lib/libeatmydata' LD_PRELOAD='libeatmydata.so' 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='50995' 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.iafCL2mI/pbuilderrc_CVDc --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.iafCL2mI/b1 --logfile b1/build.log python-pbcore_2.1.2+dfsg-7.dsc' SUDO_GID='112' SUDO_UID='107' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://78.137.99.97:3128' I: uname -a Linux ionos12-i386 6.1.0-18-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.76-1 (2024-02-01) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Apr 1 11:25 /bin -> usr/bin I: user script /srv/workspace/pbuilder/50995/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: i386 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), dh-python, dh-sequence-python3, dh-sequence-sphinxdoc, 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, 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 ... 19876 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 dh-sequence-python3; however: Package dh-sequence-python3 is not installed. pbuilder-satisfydepends-dummy depends on dh-sequence-sphinxdoc; however: Package dh-sequence-sphinxdoc 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; 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} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-extra{a} fonts-dejavu-mono{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} libcairo2{a} libcurl3-gnutls{a} libcurl4{a} libdebhelper-perl{a} libdeflate0{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libfontconfig1{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} libpixman-1-0{a} libpng16-16{a} libpsl5{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libraqm0{a} libreadline8{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsharpyuv0{a} libssh2-1{a} libsub-override-perl{a} libsz2{a} libtiff6{a} libtool{a} libuchardet0{a} libwebp7{a} libwebpdemux2{a} libwebpmux3{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb-render0{a} libxcb-shm0{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxml2{a} libxrender1{a} m4{a} man-db{a} media-types{a} netbase{a} openssl{a} po-debconf{a} pylint{a} python-babel-localedata{a} python3{a} python3-alabaster{a} python3-all{a} python3-astroid{a} python3-babel{a} python3-biopython{a} python3-cairo{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-freetype{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-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-pygments{a} python3-pysam{a} python3-pytest{a} python3-pytest-cov{a} python3-pytest-runner{a} python3-pytest-xdist{a} python3-reportlab{a} python3-requests{a} python3-rlpycairo{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-xmlschema{a} python3-zipp{a} python3.11{a} python3.11-minimal{a} python3.12{a} python3.12-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, 185 newly installed, 0 to remove and 0 not upgraded. Need to get 91.2 MB of archives. After unpacking 365 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main i386 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 2 http://deb.debian.org/debian trixie/main i386 libjs-jquery-hotkeys all 0~20130707+git2d51e3a9+dfsg-2.1 [11.5 kB] Get: 3 http://deb.debian.org/debian trixie/main i386 libpython3.11-minimal i386 3.11.8-1 [817 kB] Get: 4 http://deb.debian.org/debian trixie/main i386 libexpat1 i386 2.5.0-2+b2 [104 kB] Get: 5 http://deb.debian.org/debian trixie/main i386 python3.11-minimal i386 3.11.8-1 [2087 kB] Get: 6 http://deb.debian.org/debian trixie/main i386 python3-minimal i386 3.11.6-1 [26.2 kB] Get: 7 http://deb.debian.org/debian trixie/main i386 media-types all 10.1.0 [26.9 kB] Get: 8 http://deb.debian.org/debian trixie/main i386 netbase all 6.4 [12.8 kB] Get: 9 http://deb.debian.org/debian trixie/main i386 tzdata all 2024a-1 [255 kB] Get: 10 http://deb.debian.org/debian trixie/main i386 readline-common all 8.2-3 [69.1 kB] Get: 11 http://deb.debian.org/debian trixie/main i386 libreadline8 i386 8.2-3+b1 [171 kB] Get: 12 http://deb.debian.org/debian trixie/main i386 libpython3.11-stdlib i386 3.11.8-1 [1821 kB] Get: 13 http://deb.debian.org/debian trixie/main i386 python3.11 i386 3.11.8-1 [597 kB] Get: 14 http://deb.debian.org/debian trixie/main i386 libpython3-stdlib i386 3.11.6-1 [9224 B] Get: 15 http://deb.debian.org/debian trixie/main i386 python3 i386 3.11.6-1 [26.2 kB] Get: 16 http://deb.debian.org/debian trixie/main i386 libpython3.12-minimal i386 3.12.2-1 [807 kB] Get: 17 http://deb.debian.org/debian trixie/main i386 python3.12-minimal i386 3.12.2-1 [2244 kB] Get: 18 http://deb.debian.org/debian trixie/main i386 sgml-base all 1.31 [15.4 kB] Get: 19 http://deb.debian.org/debian trixie/main i386 sensible-utils all 0.0.22 [22.4 kB] Get: 20 http://deb.debian.org/debian trixie/main i386 openssl i386 3.1.5-1 [1246 kB] Get: 21 http://deb.debian.org/debian trixie/main i386 ca-certificates all 20240203 [158 kB] Get: 22 http://deb.debian.org/debian trixie/main i386 libmagic-mgc i386 1:5.45-2+b1 [314 kB] Get: 23 http://deb.debian.org/debian trixie/main i386 libmagic1 i386 1:5.45-2+b1 [114 kB] Get: 24 http://deb.debian.org/debian trixie/main i386 file i386 1:5.45-2+b1 [43.0 kB] Get: 25 http://deb.debian.org/debian trixie/main i386 gettext-base i386 0.21-14+b1 [162 kB] Get: 26 http://deb.debian.org/debian trixie/main i386 libuchardet0 i386 0.0.8-1+b1 [69.1 kB] Get: 27 http://deb.debian.org/debian trixie/main i386 groff-base i386 1.23.0-3 [1195 kB] Get: 28 http://deb.debian.org/debian trixie/main i386 bsdextrautils i386 2.39.3-6 [93.3 kB] Get: 29 http://deb.debian.org/debian trixie/main i386 libpipeline1 i386 1.5.7-1+b2 [39.6 kB] Get: 30 http://deb.debian.org/debian trixie/main i386 man-db i386 2.12.0-3 [1413 kB] Get: 31 http://deb.debian.org/debian trixie/main i386 m4 i386 1.4.19-4 [293 kB] Get: 32 http://deb.debian.org/debian trixie/main i386 autoconf all 2.71-3 [332 kB] Get: 33 http://deb.debian.org/debian trixie/main i386 autotools-dev all 20220109.1 [51.6 kB] Get: 34 http://deb.debian.org/debian trixie/main i386 automake all 1:1.16.5-1.3 [823 kB] Get: 35 http://deb.debian.org/debian trixie/main i386 autopoint all 0.21-14 [496 kB] Get: 36 http://deb.debian.org/debian trixie/main i386 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 37 http://deb.debian.org/debian trixie/main i386 libtool all 2.4.7-7 [517 kB] Get: 38 http://deb.debian.org/debian trixie/main i386 dh-autoreconf all 20 [17.1 kB] Get: 39 http://deb.debian.org/debian trixie/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 40 http://deb.debian.org/debian trixie/main i386 libsub-override-perl all 0.10-1 [10.6 kB] Get: 41 http://deb.debian.org/debian trixie/main i386 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 42 http://deb.debian.org/debian trixie/main i386 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 43 http://deb.debian.org/debian trixie/main i386 libelf1 i386 0.190-1+b1 [182 kB] Get: 44 http://deb.debian.org/debian trixie/main i386 dwz i386 0.15-1 [118 kB] Get: 45 http://deb.debian.org/debian trixie/main i386 libicu72 i386 72.1-4+b1 [9549 kB] Get: 46 http://deb.debian.org/debian trixie/main i386 libxml2 i386 2.9.14+dfsg-1.3+b2 [727 kB] Get: 47 http://deb.debian.org/debian trixie/main i386 gettext i386 0.21-14+b1 [1311 kB] Get: 48 http://deb.debian.org/debian trixie/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 49 http://deb.debian.org/debian trixie/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 50 http://deb.debian.org/debian trixie/main i386 debhelper all 13.15.3 [901 kB] Get: 51 http://deb.debian.org/debian trixie/main i386 python3-lib2to3 all 3.11.5-1 [77.5 kB] Get: 52 http://deb.debian.org/debian trixie/main i386 python3-distutils all 3.11.5-1 [131 kB] Get: 53 http://deb.debian.org/debian trixie/main i386 python3-pkg-resources all 68.1.2-2 [241 kB] Get: 54 http://deb.debian.org/debian trixie/main i386 python3-setuptools all 68.1.2-2 [468 kB] Get: 55 http://deb.debian.org/debian trixie/main i386 dh-python all 6.20240310 [106 kB] Get: 56 http://deb.debian.org/debian trixie/main i386 xml-core all 0.19 [20.1 kB] Get: 57 http://deb.debian.org/debian trixie/main i386 docutils-common all 0.20.1+dfsg-3 [128 kB] Get: 58 http://deb.debian.org/debian trixie/main i386 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 59 http://deb.debian.org/debian trixie/main i386 fonts-dejavu-core all 2.37-8 [840 kB] Get: 60 http://deb.debian.org/debian trixie/main i386 libfontenc1 i386 1:1.1.8-1 [23.1 kB] Get: 61 http://deb.debian.org/debian trixie/main i386 libbrotli1 i386 1.1.0-2+b3 [314 kB] Get: 62 http://deb.debian.org/debian trixie/main i386 libpng16-16 i386 1.6.43-1 [285 kB] Get: 63 http://deb.debian.org/debian trixie/main i386 libfreetype6 i386 2.13.2+dfsg-1+b1 [449 kB] Get: 64 http://deb.debian.org/debian trixie/main i386 x11-common all 1:7.7+23 [252 kB] Get: 65 http://deb.debian.org/debian trixie/main i386 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get: 66 http://deb.debian.org/debian trixie/main i386 xfonts-utils i386 1:7.7+6 [95.2 kB] Get: 67 http://deb.debian.org/debian trixie/main i386 fonts-urw-base35 all 20200910-8 [10.8 MB] Get: 68 http://deb.debian.org/debian trixie/main i386 fontconfig-config i386 2.15.0-1.1 [317 kB] Get: 69 http://deb.debian.org/debian trixie/main i386 fonts-dejavu-extra all 2.37-8 [1792 kB] Get: 70 http://deb.debian.org/debian trixie/main i386 libaec0 i386 1.1.3-1 [24.5 kB] Get: 71 http://deb.debian.org/debian trixie/main i386 libblas3 i386 3.12.0-3 [140 kB] Get: 72 http://deb.debian.org/debian trixie/main i386 libbsd0 i386 0.12.2-1 [134 kB] Get: 73 http://deb.debian.org/debian trixie/main i386 libfontconfig1 i386 2.15.0-1.1 [401 kB] Get: 74 http://deb.debian.org/debian trixie/main i386 libpixman-1-0 i386 0.42.2-1+b1 [555 kB] Get: 75 http://deb.debian.org/debian trixie/main i386 libxau6 i386 1:1.0.9-1 [20.0 kB] Get: 76 http://deb.debian.org/debian trixie/main i386 libxdmcp6 i386 1:1.1.2-3 [26.7 kB] Get: 77 http://deb.debian.org/debian trixie/main i386 libxcb1 i386 1.15-1 [148 kB] Get: 78 http://deb.debian.org/debian trixie/main i386 libx11-data all 2:1.8.7-1 [328 kB] Get: 79 http://deb.debian.org/debian trixie/main i386 libx11-6 i386 2:1.8.7-1 [822 kB] Get: 80 http://deb.debian.org/debian trixie/main i386 libxcb-render0 i386 1.15-1 [116 kB] Get: 81 http://deb.debian.org/debian trixie/main i386 libxcb-shm0 i386 1.15-1 [106 kB] Get: 82 http://deb.debian.org/debian trixie/main i386 libxext6 i386 2:1.3.4-1+b1 [55.3 kB] Get: 83 http://deb.debian.org/debian trixie/main i386 libxrender1 i386 1:0.9.10-1.1 [34.1 kB] Get: 84 http://deb.debian.org/debian trixie/main i386 libcairo2 i386 1.18.0-1+b1 [587 kB] Get: 85 http://deb.debian.org/debian trixie/main i386 libsasl2-modules-db i386 2.1.28+dfsg1-4+b1 [20.7 kB] Get: 86 http://deb.debian.org/debian trixie/main i386 libsasl2-2 i386 2.1.28+dfsg1-4+b1 [60.7 kB] Get: 87 http://deb.debian.org/debian trixie/main i386 libldap-2.5-0 i386 2.5.13+dfsg-5+b3 [196 kB] Get: 88 http://deb.debian.org/debian trixie/main i386 libnghttp2-14 i386 1.59.0-1 [82.5 kB] Get: 89 http://deb.debian.org/debian trixie/main i386 libpsl5 i386 0.21.2-1+b1 [59.7 kB] Get: 90 http://deb.debian.org/debian trixie/main i386 librtmp1 i386 2.4+20151223.gitfa8646d.1-2+b2 [64.3 kB] Get: 91 http://deb.debian.org/debian trixie/main i386 libssh2-1 i386 1.11.0-4 [224 kB] Get: 92 http://deb.debian.org/debian trixie/main i386 libcurl3-gnutls i386 8.5.0-2 [454 kB] Get: 93 http://deb.debian.org/debian trixie/main i386 libcurl4 i386 8.5.0-2 [463 kB] Get: 94 http://deb.debian.org/debian trixie/main i386 libdeflate0 i386 1.20-1 [46.9 kB] Get: 95 http://deb.debian.org/debian trixie/main i386 libfribidi0 i386 1.0.13-3+b1 [71.8 kB] Get: 96 http://deb.debian.org/debian trixie/main i386 libgfortran5 i386 14-20240201-3 [733 kB] Get: 97 http://deb.debian.org/debian trixie/main i386 libglib2.0-0 i386 2.78.4-1 [1520 kB] Get: 98 http://deb.debian.org/debian trixie/main i386 libgraphite2-3 i386 1.3.14-2 [77.7 kB] Get: 99 http://deb.debian.org/debian trixie/main i386 libharfbuzz0b i386 8.3.0-2 [2234 kB] Get: 100 http://deb.debian.org/debian trixie/main i386 libsz2 i386 1.1.3-1 [7824 B] Get: 101 http://deb.debian.org/debian trixie/main i386 libhdf5-103-1 i386 1.10.10+repack-3+b1 [1177 kB] Get: 102 http://deb.debian.org/debian trixie/main i386 libhdf5-hl-100 i386 1.10.10+repack-3+b1 [74.3 kB] Get: 103 http://deb.debian.org/debian trixie/main i386 libhtscodecs2 i386 1.6.0-1+b1 [68.5 kB] Get: 104 http://deb.debian.org/debian trixie/main i386 libhts3 i386 1.19+ds-1 [490 kB] Get: 105 http://deb.debian.org/debian trixie/main i386 libimagequant0 i386 2.18.0-1 [35.6 kB] Get: 106 http://deb.debian.org/debian trixie/main i386 libjbig0 i386 2.1-6.1+b1 [31.8 kB] Get: 107 http://deb.debian.org/debian trixie/main i386 libjpeg62-turbo i386 1:2.1.5-2+b2 [169 kB] Get: 108 http://deb.debian.org/debian trixie/main i386 libjs-jquery-isonscreen all 1.2.0-1.1 [3196 B] Get: 109 http://deb.debian.org/debian trixie/main i386 libjs-jquery-metadata all 12-4 [6532 B] Get: 110 http://deb.debian.org/debian trixie/main i386 libjs-jquery-tablesorter all 1:2.31.3+dfsg1-3 [184 kB] Get: 111 http://deb.debian.org/debian trixie/main i386 libjs-jquery-throttle-debounce all 1.1+dfsg.1-2 [12.2 kB] Get: 112 http://deb.debian.org/debian trixie/main i386 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 113 http://deb.debian.org/debian trixie/main i386 libjs-sphinxdoc all 7.2.6-6 [150 kB] Get: 114 http://deb.debian.org/debian trixie/main i386 libjson-perl all 4.10000-1 [87.5 kB] Get: 115 http://deb.debian.org/debian trixie/main i386 liblapack3 i386 3.12.0-3 [2167 kB] Get: 116 http://deb.debian.org/debian trixie/main i386 liblcms2-2 i386 2.14-2+b1 [165 kB] Get: 117 http://deb.debian.org/debian trixie/main i386 liblerc4 i386 4.0.0+ds-4+b1 [180 kB] Get: 118 http://deb.debian.org/debian trixie/main i386 liblzf1 i386 3.6-4 [9756 B] Get: 119 http://deb.debian.org/debian trixie/main i386 libopenjp2-7 i386 2.5.0-2+b2 [197 kB] Get: 120 http://deb.debian.org/debian trixie/main i386 libpython3.12-stdlib i386 3.12.2-1 [1927 kB] Get: 121 http://deb.debian.org/debian trixie/main i386 libraqm0 i386 0.10.1-1+b1 [14.7 kB] Get: 122 http://deb.debian.org/debian trixie/main i386 libsharpyuv0 i386 1.3.2-0.4 [107 kB] Get: 123 http://deb.debian.org/debian trixie/main i386 libwebp7 i386 1.3.2-0.4 [314 kB] Get: 124 http://deb.debian.org/debian trixie/main i386 libtiff6 i386 4.5.1+git230720-4 [338 kB] Get: 125 http://deb.debian.org/debian trixie/main i386 libwebpdemux2 i386 1.3.2-0.4 [108 kB] Get: 126 http://deb.debian.org/debian trixie/main i386 libwebpmux3 i386 1.3.2-0.4 [121 kB] Get: 127 http://deb.debian.org/debian trixie/main i386 python3-six all 1.16.0-6 [16.3 kB] Get: 128 http://deb.debian.org/debian trixie/main i386 python3-typing-extensions all 4.10.0-1 [66.2 kB] Get: 129 http://deb.debian.org/debian trixie/main i386 python3-astroid all 3.0.2-2 [210 kB] Get: 130 http://deb.debian.org/debian trixie/main i386 python3-toml all 0.10.2-1 [16.2 kB] Get: 131 http://deb.debian.org/debian trixie/main i386 python3-isort all 5.6.4-1 [63.2 kB] Get: 132 http://deb.debian.org/debian trixie/main i386 python3-more-itertools all 10.2.0-1 [59.9 kB] Get: 133 http://deb.debian.org/debian trixie/main i386 python3-zipp all 1.0.0-6 [6696 B] Get: 134 http://deb.debian.org/debian trixie/main i386 python3-importlib-metadata all 4.12.0-1 [24.9 kB] Get: 135 http://deb.debian.org/debian trixie/main i386 python3-mypy-extensions all 1.0.0-1 [6064 B] Get: 136 http://deb.debian.org/debian trixie/main i386 python3-logilab-common all 1.9.8-2 [380 kB] Get: 137 http://deb.debian.org/debian trixie/main i386 python3-dill all 0.3.8-1 [81.7 kB] Get: 138 http://deb.debian.org/debian trixie/main i386 python3-mccabe all 0.7.0-1 [10.5 kB] Get: 139 http://deb.debian.org/debian trixie/main i386 python3-platformdirs all 4.2.0-1 [15.9 kB] Get: 140 http://deb.debian.org/debian trixie/main i386 python3-tomlkit all 0.12.4-1 [41.7 kB] Get: 141 http://deb.debian.org/debian trixie/main i386 pylint all 3.0.3-1 [332 kB] Get: 142 http://deb.debian.org/debian trixie/main i386 python-babel-localedata all 2.10.3-3 [5611 kB] Get: 143 http://deb.debian.org/debian trixie/main i386 python3-alabaster all 0.7.12-1 [20.8 kB] Get: 144 http://deb.debian.org/debian trixie/main i386 python3.12 i386 3.12.2-1 [653 kB] Get: 145 http://deb.debian.org/debian trixie/main i386 python3-all i386 3.11.6-1 [1060 B] Get: 146 http://deb.debian.org/debian trixie/main i386 python3-tz all 2024.1-2 [30.9 kB] Get: 147 http://deb.debian.org/debian trixie/main i386 python3-babel all 2.10.3-3 [100.0 kB] Get: 148 http://deb.debian.org/debian trixie/main i386 python3-numpy i386 1:1.24.2-2 [4879 kB] Get: 149 http://deb.debian.org/debian trixie/main i386 python3-chardet all 5.2.0+dfsg-1 [107 kB] Get: 150 http://deb.debian.org/debian trixie/main i386 python3-pil i386 10.2.0-1 [526 kB] Get: 151 http://deb.debian.org/debian trixie/main i386 python3-cairo i386 1.25.1-2 [142 kB] Get: 152 http://deb.debian.org/debian trixie/main i386 python3-freetype all 2.4.0-1 [80.3 kB] Get: 153 http://deb.debian.org/debian trixie/main i386 python3-rlpycairo all 0.3.0-3 [9904 B] Get: 154 http://deb.debian.org/debian trixie/main i386 python3-reportlab all 4.1.0-1 [674 kB] Get: 155 http://deb.debian.org/debian trixie/main i386 w3c-sgml-lib all 1.3-3 [273 kB] Get: 156 http://deb.debian.org/debian trixie/main i386 python3-biopython i386 1.81+dfsg-3 [1616 kB] Get: 157 http://deb.debian.org/debian trixie/main i386 python3-certifi all 2023.11.17-1 [155 kB] Get: 158 http://deb.debian.org/debian trixie/main i386 python3-charset-normalizer all 3.3.2-1 [51.6 kB] Get: 159 http://deb.debian.org/debian trixie/main i386 python3-coverage i386 7.2.7+dfsg1-1+b1 [170 kB] Get: 160 http://deb.debian.org/debian trixie/main i386 python3-roman all 3.3-3 [9880 B] Get: 161 http://deb.debian.org/debian trixie/main i386 python3-docutils all 0.20.1+dfsg-3 [389 kB] Get: 162 http://deb.debian.org/debian trixie/main i386 python3-elementpath all 3.0.2-1 [126 kB] Get: 163 http://deb.debian.org/debian trixie/main i386 python3-execnet all 2.0.2-1 [37.2 kB] Get: 164 http://deb.debian.org/debian trixie/main i386 python3-h5py-serial i386 3.10.0-1 [1399 kB] Get: 165 http://deb.debian.org/debian trixie/main i386 python3-h5py all 3.10.0-1 [14.4 kB] Get: 166 http://deb.debian.org/debian trixie/main i386 python3-idna all 3.6-2 [37.0 kB] Get: 167 http://deb.debian.org/debian trixie/main i386 python3-imagesize all 1.4.1-1 [6688 B] Get: 168 http://deb.debian.org/debian trixie/main i386 python3-iniconfig all 1.1.1-2 [6396 B] Get: 169 http://deb.debian.org/debian trixie/main i386 python3-markupsafe i386 2.1.5-1 [14.4 kB] Get: 170 http://deb.debian.org/debian trixie/main i386 python3-jinja2 all 3.1.3-1 [119 kB] Get: 171 http://deb.debian.org/debian trixie/main i386 python3-packaging all 23.2-1 [44.8 kB] Get: 172 http://deb.debian.org/debian trixie/main i386 python3-pluggy all 1.4.0-1 [26.2 kB] Get: 173 http://deb.debian.org/debian trixie/main i386 python3-pygments all 2.17.2+dfsg-1 [818 kB] Get: 174 http://deb.debian.org/debian trixie/main i386 python3-pysam i386 0.22.0+ds-1+b1 [4120 kB] Get: 175 http://deb.debian.org/debian trixie/main i386 python3-pytest all 7.4.4-3 [239 kB] Get: 176 http://deb.debian.org/debian trixie/main i386 python3-pytest-cov all 4.1.0-1 [26.7 kB] Get: 177 http://deb.debian.org/debian trixie/main i386 python3-pytest-runner all 2.11.1-4 [8432 B] Get: 178 http://deb.debian.org/debian trixie/main i386 python3-pytest-xdist all 3.5.0-1 [42.1 kB] Get: 179 http://deb.debian.org/debian trixie/main i386 python3-urllib3 all 1.26.18-2 [116 kB] Get: 180 http://deb.debian.org/debian trixie/main i386 python3-requests all 2.31.0+dfsg-1 [68.6 kB] Get: 181 http://deb.debian.org/debian trixie/main i386 python3-snowballstemmer all 2.2.0-4 [58.0 kB] Get: 182 http://deb.debian.org/debian trixie/main i386 sphinx-common all 7.2.6-6 [702 kB] Get: 183 http://deb.debian.org/debian trixie/main i386 python3-sphinx all 7.2.6-6 [552 kB] Get: 184 http://deb.debian.org/debian trixie/main i386 python3-uritools all 4.0.1-1 [25.1 kB] Get: 185 http://deb.debian.org/debian trixie/main i386 python3-xmlschema all 1.10.0-7 [177 kB] Fetched 91.2 MB in 2s (59.5 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libjs-jquery. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19876 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:i386. Preparing to unpack .../libpython3.11-minimal_3.11.8-1_i386.deb ... Unpacking libpython3.11-minimal:i386 (3.11.8-1) ... Selecting previously unselected package libexpat1:i386. Preparing to unpack .../libexpat1_2.5.0-2+b2_i386.deb ... Unpacking libexpat1:i386 (2.5.0-2+b2) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.8-1_i386.deb ... Unpacking python3.11-minimal (3.11.8-1) ... Setting up libpython3.11-minimal:i386 (3.11.8-1) ... Setting up libexpat1:i386 (2.5.0-2+b2) ... Setting up python3.11-minimal (3.11.8-1) ... 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 ... 20219 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.6-1_i386.deb ... Unpacking python3-minimal (3.11.6-1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... 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Setting up python3-minimal (3.11.6-1) ... 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 ... 21207 files and directories currently installed.) Preparing to unpack .../000-python3_3.11.6-1_i386.deb ... Unpacking python3 (3.11.6-1) ... Selecting previously unselected package libpython3.12-minimal:i386. Preparing to unpack .../001-libpython3.12-minimal_3.12.2-1_i386.deb ... Unpacking libpython3.12-minimal:i386 (3.12.2-1) ... 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Setting up python3-pil:i386 (10.2.0-1) ... Setting up python3-roman (3.3-3) ... Setting up python3-jinja2 (3.1.3-1) ... Setting up python3-packaging (23.2-1) ... Setting up python3-certifi (2023.11.17-1) ... Setting up python3-snowballstemmer (2.2.0-4) ... Setting up python3-dill (0.3.8-1) ... Setting up python3-idna (3.6-2) ... Setting up python3-elementpath (3.0.2-1) ... Setting up python3-typing-extensions (4.10.0-1) ... Setting up python3-xmlschema (1.10.0-7) ... Setting up python3-toml (0.10.2-1) ... Setting up python3-isort (5.6.4-1) ... Setting up python3-urllib3 (1.26.18-2) ... Setting up python3-pluggy (1.4.0-1) ... Setting up python3-mccabe (0.7.0-1) ... Setting up python3-execnet (2.0.2-1) ... Setting up python3-tomlkit (0.12.4-1) ... Setting up python3-lib2to3 (3.11.5-1) ... Setting up python3-imagesize (1.4.1-1) ... Setting up python3-uritools (4.0.1-1) ... Setting up python3-pkg-resources (68.1.2-2) ... Setting up python3-distutils (3.11.5-1) ... python3.12: can't get files for byte-compilation Setting up python3-more-itertools (10.2.0-1) ... Setting up python3-iniconfig (1.1.1-2) ... Setting up python3-pysam (0.22.0+ds-1+b1) ... Setting up python3-cairo (1.25.1-2) ... Setting up python3-setuptools (68.1.2-2) ... Setting up python3-babel (2.10.3-3) ... update-alternatives: using /usr/bin/pybabel-python3 to provide /usr/bin/pybabel (pybabel) in auto mode Setting up python3-charset-normalizer (3.3.2-1) ... Setting up python3-pytest (7.4.4-3) ... Setting up python3-alabaster (0.7.12-1) ... Setting up python3-mypy-extensions (1.0.0-1) ... Setting up python3-all (3.11.6-1) ... Setting up python3-coverage (7.2.7+dfsg1-1+b1) ... Setting up python3-pytest-cov (4.1.0-1) ... Setting up python3-zipp (1.0.0-6) ... Setting up python3-pygments (2.17.2+dfsg-1) ... Setting up python3-chardet (5.2.0+dfsg-1) ... Setting up python3-rlpycairo (0.3.0-3) ... Setting up python3-requests (2.31.0+dfsg-1) ... Setting up python3-numpy (1:1.24.2-2) ... Setting up python3-reportlab (4.1.0-1) ... Setting up python3-astroid (3.0.2-2) ... Setting up python3-pytest-runner (2.11.1-4) ... Setting up dh-python (6.20240310) ... Setting up python3-importlib-metadata (4.12.0-1) ... Setting up python3-pytest-xdist (3.5.0-1) ... Setting up python3-logilab-common (1.9.8-2) ... Setting up python3-h5py-serial (3.10.0-1) ... Setting up python3-h5py (3.10.0-1) ... Setting up pylint (3.0.3-1) ... Processing triggers for libc-bin (2.37-15) ... Processing triggers for sgml-base (1.31) ... Setting up w3c-sgml-lib (1.3-3) ... Setting up docutils-common (0.20.1+dfsg-3) ... Setting up python3-biopython (1.81+dfsg-3) ... Processing triggers for sgml-base (1.31) ... Setting up python3-docutils (0.20.1+dfsg-3) ... Setting up python3-sphinx (7.2.6-6) ... Processing triggers for ca-certificates (20240203) ... 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-7_source.changes dpkg-buildpackage: info: source package python-pbcore dpkg-buildpackage: info: source version 2.1.2+dfsg-7 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael R. Crusoe dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 debian/rules clean dh clean --buildsystem=pybuild dh_auto_clean -O--buildsystem=pybuild I: pybuild base:305: python3.12 setup.py clean /usr/lib/python3/dist-packages/setuptools/dist.py:744: SetuptoolsDeprecationWarning: Invalid dash-separated options !! ******************************************************************************** Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead. This deprecation is overdue, please update your project and remove deprecated calls to avoid build errors in the future. See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. ******************************************************************************** !! opt = self.warn_dash_deprecation(opt, section) running clean removing '/build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build' (and everything under it) 'build/bdist.linux-i686' does not exist -- can't clean it 'build/scripts-3.12' does not exist -- can't clean it I: pybuild base:305: python3.11 setup.py clean /usr/lib/python3/dist-packages/setuptools/dist.py:744: SetuptoolsDeprecationWarning: Invalid dash-separated options !! ******************************************************************************** Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead. This deprecation is overdue, please update your project and remove deprecated calls to avoid build errors in the future. See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. ******************************************************************************** !! opt = self.warn_dash_deprecation(opt, section) running clean removing '/build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build' (and everything under it) 'build/bdist.linux-i686' does not exist -- can't clean it 'build/scripts-3.11' does not exist -- can't clean it debian/rules execute_after_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/python-pbcore-2.1.2+dfsg' /usr/bin/make clean make[2]: Entering directory '/build/reproducible-path/python-pbcore-2.1.2+dfsg' cd doc && rm -rf _templates _static _build searchindex.js objects.inv rm -rf build/;\ find . -name "*.egg-info" | xargs rm -rf;\ rm -rf dist/;\ find . -name "*.pyc" | xargs rm -f; rm -f nosetests.xml make[2]: Leaving directory '/build/reproducible-path/python-pbcore-2.1.2+dfsg' find . -name __pycache__ | xargs -r rm -rf 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 dh binary --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild I: pybuild base:305: python3.12 setup.py config /usr/lib/python3/dist-packages/setuptools/dist.py:744: SetuptoolsDeprecationWarning: Invalid dash-separated options !! ******************************************************************************** Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead. This deprecation is overdue, please update your project and remove deprecated calls to avoid build errors in the future. See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. ******************************************************************************** !! opt = self.warn_dash_deprecation(opt, section) running config I: pybuild base:305: python3.11 setup.py config /usr/lib/python3/dist-packages/setuptools/dist.py:744: SetuptoolsDeprecationWarning: Invalid dash-separated options !! ******************************************************************************** Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead. This deprecation is overdue, please update your project and remove deprecated calls to avoid build errors in the future. See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. ******************************************************************************** !! opt = self.warn_dash_deprecation(opt, section) running config debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/python-pbcore-2.1.2+dfsg' dh_auto_build I: pybuild base:305: /usr/bin/python3.12 setup.py build /usr/lib/python3/dist-packages/setuptools/dist.py:744: SetuptoolsDeprecationWarning: Invalid dash-separated options !! ******************************************************************************** Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead. This deprecation is overdue, please update your project and remove deprecated calls to avoid build errors in the future. See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. ******************************************************************************** !! opt = self.warn_dash_deprecation(opt, section) running build running build_py creating /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build/pbcore copying pbcore/__init__.py -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build/pbcore copying pbcore/sequence.py -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build/pbcore creating /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build/pbcore/data copying pbcore/data/__init__.py -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build/pbcore/data creating /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build/pbcore/chemistry copying pbcore/chemistry/__init__.py -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build/pbcore/chemistry copying pbcore/chemistry/chemistry.py -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build/pbcore/chemistry creating /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build/pbcore/model copying pbcore/model/baseRegions.py -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build/pbcore/model copying pbcore/model/__init__.py -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build/pbcore/model creating /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build/pbcore/io copying pbcore/io/FastaIO.py -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build/pbcore/io copying pbcore/io/FastqIO.py -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build/pbcore/io copying pbcore/io/GffIO.py -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build/pbcore/io copying pbcore/io/opener.py -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build/pbcore/io copying pbcore/io/_utils.py -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build/pbcore/io copying pbcore/io/__init__.py -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build/pbcore/io copying pbcore/io/FofnIO.py -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build/pbcore/io copying pbcore/io/base.py -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build/pbcore/io copying pbcore/io/VcfIO.py -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build/pbcore/io creating /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build/pbcore/util copying pbcore/util/ToolRunner.py -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build/pbcore/util copying pbcore/util/__init__.py -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build/pbcore/util copying pbcore/util/statistics.py -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build/pbcore/util copying pbcore/util/decorators.py -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build/pbcore/util creating /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/__init__.py -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build/pbcore/data/datasets creating /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build/pbcore/io/align copying pbcore/io/align/_AlignmentMixin.py -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build/pbcore/io/align copying pbcore/io/align/BamIO.py -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build/pbcore/io/align copying pbcore/io/align/BlasrIO.py -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build/pbcore/io/align copying pbcore/io/align/PacBioBamIndex.py -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build/pbcore/io/align copying pbcore/io/align/__init__.py -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build/pbcore/io/align copying pbcore/io/align/BamAlignment.py -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build/pbcore/io/align copying pbcore/io/align/_BamSupport.py -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build/pbcore/io/align creating /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build/pbcore/io/dataset copying pbcore/io/dataset/DataSetIO.py -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build/pbcore/io/dataset copying pbcore/io/dataset/run_split.py -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build/pbcore/io/dataset copying pbcore/io/dataset/DataSetMetaTypes.py -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build/pbcore/io/dataset copying pbcore/io/dataset/DataSetErrors.py -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build/pbcore/io/dataset copying pbcore/io/dataset/DataSetReader.py -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build/pbcore/io/dataset copying pbcore/io/dataset/DataSetWriter.py -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build/pbcore/io/dataset copying pbcore/io/dataset/DataSetMembers.py -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build/pbcore/io/dataset copying pbcore/io/dataset/DataSetValidator.py -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build/pbcore/io/dataset copying pbcore/io/dataset/__init__.py -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build/pbcore/io/dataset copying pbcore/io/dataset/DataSetUtils.py -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build/pbcore/io/dataset copying pbcore/io/dataset/utils.py -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build/pbcore/io/dataset 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:204: _Warning: Package 'pbcore.chemistry.resources' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'pbcore.chemistry.resources' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'pbcore.chemistry.resources' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'pbcore.chemistry.resources' to be distributed and are already explicitly excluding 'pbcore.chemistry.resources' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) copying pbcore/data/Fluidigm_human_amplicons.fasta -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build/pbcore/data copying pbcore/data/Fluidigm_human_amplicons.fasta.fai -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build/pbcore/data copying pbcore/data/Fluidigm_human_amplicons_tiny.fasta -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build/pbcore/data copying pbcore/data/barcodes-ed65-450.fasta -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build/pbcore/data copying pbcore/data/barcodes-ed65-450.fasta.fai -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build/pbcore/data copying pbcore/data/blasr-output.m4 -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build/pbcore/data copying pbcore/data/blasr-output.m5 -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build/pbcore/data copying pbcore/data/chemistry.xml -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build/pbcore/data copying pbcore/data/empty.aligned_subreads.bam -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build/pbcore/data copying pbcore/data/empty.aligned_subreads.bam.pbi -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build/pbcore/data copying pbcore/data/empty.ccs.bam -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build/pbcore/data copying pbcore/data/empty.ccs.bam.pbi -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build/pbcore/data copying pbcore/data/empty2.bam -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build/pbcore/data copying pbcore/data/empty2.bam.pbi -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build/pbcore/data copying pbcore/data/lambdaNEB.fa -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build/pbcore/data copying pbcore/data/lambdaNEB.fa.fai -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_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_3.12_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_3.12_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_3.12_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_3.12_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_3.12_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_3.12_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_3.12_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_3.12_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_3.12_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_3.12_pbcore/build/pbcore/data copying pbcore/data/variants.gff -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build/pbcore/data copying pbcore/data/weird.fa -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build/pbcore/data copying pbcore/data/weird.fa.fai -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build/pbcore/data creating /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build/pbcore/chemistry/resources copying pbcore/chemistry/resources/mapping.xml -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build/pbcore/chemistry/resources copying pbcore/data/datasets/CollectionMetadata.xml -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/alignment.dataset.xml -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/barcode.dataset.xml -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/ccsaligned.dataset.xml -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/ccsread.dataset.xml -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/contig.dataset.xml -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/empty_lambda.aligned.bam -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_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_3.12_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_3.12_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/fofn.fofn -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/lambda.alignmentset.xml -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/lambda.referenceset.xml -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_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_3.12_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_3.12_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_3.12_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_3.12_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_3.12_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/pbalchemysim.alignmentset.xml -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/pbalchemysim0.alignmentset.chunk0contigs.xml -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/pbalchemysim0.alignmentset.chunk1contigs.xml -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/pbalchemysim0.alignmentset.xml -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/pbalchemysim0.pbalign.bam -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/pbalchemysim0.pbalign.bam.bai -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/pbalchemysim0.pbalign.bam.pbi -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/pbalchemysim0.reference.fasta -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/pbalchemysim0.reference.fasta.fai -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/pbalchemysim0.referenceset.xml -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/pbalchemysim0.subreads.bam -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/pbalchemysim0.subreads.bam.bai -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/pbalchemysim0.subreads.bam.pbi -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/pbalchemysim0.subreadset.xml -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/pbalchemysim1.alignmentset.xml -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/pbalchemysim1.pbalign.bam -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/pbalchemysim1.pbalign.bam.bai -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/pbalchemysim1.pbalign.bam.pbi -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/pbalchemysim1.subreads.bam -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/pbalchemysim1.subreads.bam.bai -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/pbalchemysim1.subreads.bam.pbi -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/pbalchemysim1.subreadset.xml -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/reference.dataset.xml -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/subread.dataset.xml -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build/pbcore/data/datasets copying pbcore/data/datasets/subreadSetWithStats.xml -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build/pbcore/data/datasets I: pybuild base:305: /usr/bin/python3 setup.py build /usr/lib/python3/dist-packages/setuptools/dist.py:744: SetuptoolsDeprecationWarning: Invalid dash-separated options !! ******************************************************************************** Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead. This deprecation is overdue, please update your project and remove deprecated calls to avoid build errors in the future. See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. ******************************************************************************** !! opt = self.warn_dash_deprecation(opt, section) running build running build_py creating /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 copying pbcore/sequence.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/chemistry copying pbcore/chemistry/__init__.py -> /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 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/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/GffIO.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 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/__init__.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/VcfIO.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/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/__init__.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 copying pbcore/util/decorators.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/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/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/BamIO.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/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/BamAlignment.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 creating /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/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/DataSetMetaTypes.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/DataSetReader.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/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/__init__.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 copying pbcore/io/dataset/utils.py -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.11_pbcore/build/pbcore/io/dataset running egg_info writing pbcore.egg-info/PKG-INFO writing dependency_links to pbcore.egg-info/dependency_links.txt writing entry points to pbcore.egg-info/entry_points.txt writing requirements to pbcore.egg-info/requires.txt writing top-level names to pbcore.egg-info/top_level.txt reading manifest file 'pbcore.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching '*.txt' warning: no directories found matching 'bin' adding license file 'LICENSE' writing manifest file 'pbcore.egg-info/SOURCES.txt' /usr/lib/python3/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'pbcore.chemistry.resources' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'pbcore.chemistry.resources' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'pbcore.chemistry.resources' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'pbcore.chemistry.resources' to be distributed and are already explicitly excluding 'pbcore.chemistry.resources' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! 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 make[3]: Entering directory '/build/reproducible-path/python-pbcore-2.1.2+dfsg/doc' sphinx-apidoc -o . -d 4 ../pbcore/ sphinx-build -b html -d _build/doctrees . _build/html Running Sphinx v7.2.6 making output directory... done WARNING: The pre-Sphinx 1.0 'intersphinx_mapping' format is deprecated and will be removed in Sphinx 8. Update to the current format as described in the documentation. Hint: "intersphinx_mapping = {'': ('http://docs.python.org/', None)}".https://www.sphinx-doc.org/en/master/usage/extensions/intersphinx.html#confval-intersphinx_mapping 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 writing output... 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... [ 55%] pbcore.data.datasets reading sources... [ 64%] pbcore.io reading sources... [ 73%] pbcore.io.align reading sources... [ 82%] pbcore.io.dataset reading sources... [ 91%] 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 copying assets... copying static files... done copying extra files... done 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... [ 55%] pbcore.data.datasets writing output... [ 64%] pbcore.io writing output... [ 73%] pbcore.io.align writing output... [ 82%] pbcore.io.dataset writing output... [ 91%] 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 dumping search index in English (code: en)... done dumping object inventory... done build succeeded, 10 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' # 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:305: python3.12 setup.py test /usr/lib/python3/dist-packages/setuptools/dist.py:744: SetuptoolsDeprecationWarning: Invalid dash-separated options !! ******************************************************************************** Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead. This deprecation is overdue, please update your project and remove deprecated calls to avoid build errors in the future. See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. ******************************************************************************** !! opt = self.warn_dash_deprecation(opt, section) running pytest /usr/lib/python3/dist-packages/setuptools/dist.py:744: SetuptoolsDeprecationWarning: Invalid dash-separated options !! ******************************************************************************** Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead. This deprecation is overdue, please update your project and remove deprecated calls to avoid build errors in the future. See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. ******************************************************************************** !! opt = self.warn_dash_deprecation(opt, section) /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: EasyInstallDeprecationWarning: easy_install command is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` and ``easy_install``. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://github.com/pypa/setuptools/issues/917 for details. ******************************************************************************** !! self.initialize_options() /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() 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. /usr/lib/python3/dist-packages/setuptools/command/test.py:193: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. !! ******************************************************************************** Requirements should be satisfied by a PEP 517 installer. If you are using pip, you can try `pip install --use-pep517`. ******************************************************************************** !! ir_d = dist.fetch_build_eggs(dist.install_requires) WARNING: The wheel package is not available. /usr/lib/python3/dist-packages/setuptools/command/test.py:194: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. !! ******************************************************************************** Requirements should be satisfied by a PEP 517 installer. If you are using pip, you can try `pip install --use-pep517`. ******************************************************************************** !! tr_d = dist.fetch_build_eggs(dist.tests_require or []) WARNING: The wheel package is not available. /usr/lib/python3/dist-packages/setuptools/command/test.py:195: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. !! ******************************************************************************** Requirements should be satisfied by a PEP 517 installer. If you are using pip, you can try `pip install --use-pep517`. ******************************************************************************** !! er_d = dist.fetch_build_eggs( WARNING: The wheel package is not available. 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 3.12.2, pytest-7.4.4, pluggy-1.4.0 -- /usr/bin/python3.12 cachedir: .pytest_cache rootdir: /build/reproducible-path/python-pbcore-2.1.2+dfsg configfile: pytest.ini plugins: xdist-3.5.0, cov-4.1.0 created: 13/13 workers 13 workers [140 items] scheduling tests via LoadScopeScheduling tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::testIteration tests/test_pbdataset_split.py::TestDataSetSplit::test_split tests/test_pbcore_io_FastqIO.py::TestFastqWriter::test_writeFastq1 tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testBasicOperations tests/test_pbcore_io_FofnIO.py::test_simple tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testBasicOperations tests/test_pbcore_util_sequences.py::TestReverseComplement::test_reverse tests/test_pbindex.py::TestPbIndex::test_pbindex_bam_consistency tests/test_pbdataset_utils.py::TestDataSetUtils::test_get_dataset_uuid [gw9] [ 0%] PASSED tests/test_pbcore_io_FofnIO.py::test_simple tests/test_pbcore_io_FofnIO.py::test_empty_lines tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test__init__ [gw3] [ 1%] PASSED tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test__init__ [gw7] [ 2%] PASSED tests/test_pbcore_util_sequences.py::TestReverseComplement::test_reverse tests/test_pbcore_util_sequences.py::TestReverseComplement::test_complement tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test__init__ [gw6] [ 2%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test__init__ tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test__str__ tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test__str__ [gw3] [ 3%] PASSED tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test__str__ tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test_fromString [gw3] [ 4%] PASSED tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test_fromString tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test_reverse_complement1 [gw3] [ 5%] PASSED tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test_reverse_complement1 tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test_reverse_complement2 [gw3] [ 5%] PASSED tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test_reverse_complement2 tests/test_pbcore_io_GffIO.py::TestGffSorting::test_merge_gffs [gw5] [ 6%] PASSED tests/test_pbcore_io_GffIO.py::TestGffSorting::test_merge_gffs tests/test_pbcore_io_GffIO.py::TestGffSorting::test_merge_gffs_sorted [gw7] [ 7%] PASSED tests/test_pbcore_util_sequences.py::TestReverseComplement::test_complement tests/test_pbcore_util_sequences.py::TestReverseComplement::test_reverseComplement [gw7] [ 7%] PASSED tests/test_pbcore_util_sequences.py::TestReverseComplement::test_reverseComplement tests/test_pbcore_util_sequences.py::TestReverseComplement::test_iupac [gw7] [ 8%] PASSED tests/test_pbcore_util_sequences.py::TestReverseComplement::test_iupac tests/test_pbcore_util_sequences.py::TestReverseComplement::test_complement_error [gw7] [ 9%] PASSED tests/test_pbcore_util_sequences.py::TestReverseComplement::test_complement_error [gw5] [ 10%] PASSED tests/test_pbcore_io_GffIO.py::TestGffSorting::test_merge_gffs_sorted tests/test_pbcore_io_GffIO.py::TestGffSorting::test_sort_gff [gw5] [ 10%] PASSED tests/test_pbcore_io_GffIO.py::TestGffSorting::test_sort_gff [gw4] [ 11%] PASSED tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::testIteration tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::testAccessByName [gw4] [ 12%] PASSED tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::testAccessByName tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::testAccessById tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test_len [gw3] [ 12%] PASSED tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test_len tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test_eq [gw3] [ 13%] PASSED tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test_eq [gw9] [ 14%] PASSED tests/test_pbcore_io_FofnIO.py::test_empty_lines [gw6] [ 15%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test__str__ tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test_fromString [gw6] [ 15%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test_fromString tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test_reverse_complement1 [gw6] [ 16%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test_reverse_complement1 tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test_reverse_complement2 [gw6] [ 17%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test_reverse_complement2 tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test_len [gw6] [ 17%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test_len tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test_eq [gw6] [ 18%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test_eq [gw4] [ 19%] PASSED tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::testAccessById tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::testAccessByPosition [gw4] [ 20%] PASSED tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::testAccessByPosition tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::testSlice [gw2] [ 20%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testBasicOperations tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testStrandOrientation [gw2] [ 21%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testStrandOrientation tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testReadName [gw2] [ 22%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testReadName tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testAlignedRead [gw10] [ 22%] PASSED tests/test_pbdataset_utils.py::TestDataSetUtils::test_get_dataset_uuid tests/test_pbdataset_utils.py::TestDataSetUtils::test_get_dataset_metatype [gw10] [ 23%] PASSED tests/test_pbdataset_utils.py::TestDataSetUtils::test_get_dataset_metatype tests/test_pbdataset_utils.py::TestDataSetUtils::test_dsIdToSuffix [gw11] [ 24%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqWriter::test_writeFastq1 tests/test_pbcore_io_FastqIO.py::TestFastqWriter::test_writeFastq2 [gw11] [ 25%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqWriter::test_writeFastq2 [gw4] [ 25%] PASSED tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::testSlice tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::test_dosLineEndingsFasta [gw1] [ 26%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testBasicOperations tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testStrandOrientation [gw1] [ 27%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testStrandOrientation [gw10] [ 27%] PASSED tests/test_pbdataset_utils.py::TestDataSetUtils::test_dsIdToSuffix [gw2] [ 28%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testAlignedRead tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testUnalignedRead [gw2] [ 29%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testUnalignedRead tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testAlignedReference [gw2] [ 30%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testAlignedReference tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testUnalignedReference [gw2] [ 30%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testUnalignedReference [gw12] [ 31%] PASSED tests/test_pbindex.py::TestPbIndex::test_pbindex_bam_consistency tests/test_pbindex.py::TestPbIndex::test_pbindex_streaming tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testReadName [gw1] [ 32%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testReadName tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testAlignedRead tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testDeletionQV [gw2] [ 32%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testDeletionQV tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testTranscript [gw2] [ 33%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testTranscript tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testClippedAlignments tests/test_pbcore_io_GffIO.py::TestGff3Record::test_str [gw8] [ 34%] PASSED tests/test_pbcore_io_GffIO.py::TestGff3Record::test_str tests/test_pbcore_io_GffIO.py::TestGff3Record::test_modification [gw8] [ 35%] PASSED tests/test_pbcore_io_GffIO.py::TestGff3Record::test_modification tests/test_pbcore_io_GffIO.py::TestGff3Record::test_fromString [gw8] [ 35%] PASSED tests/test_pbcore_io_GffIO.py::TestGff3Record::test_fromString [gw12] [ 36%] PASSED tests/test_pbindex.py::TestPbIndex::test_pbindex_streaming tests/test_pbindex.py::TestPbIndex::test_pbindex_streaming_entire [gw12] [ 37%] PASSED tests/test_pbindex.py::TestPbIndex::test_pbindex_streaming_entire [gw2] [ 37%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testClippedAlignments tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testReadsInRange [gw4] [ 38%] PASSED tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::test_dosLineEndingsFasta [gw1] [ 39%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testAlignedRead tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testUnalignedRead [gw1] [ 40%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testUnalignedRead tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testAlignedReference [gw1] [ 40%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testAlignedReference tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testUnalignedReference [gw1] [ 41%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testUnalignedReference tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testDeletionQV [gw1] [ 42%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testDeletionQV tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testTranscript [gw1] [ 42%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testTranscript tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testClippedAlignments [gw1] [ 43%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testClippedAlignments tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testReadsInRange tests/test_pbcore_io_FofnIO.py::test_absolutifying [gw9] [ 44%] PASSED tests/test_pbcore_io_FofnIO.py::test_absolutifying tests/test_pbcore_io_AlnFileReaders.py::TestCCSBam::testBasicOperations tests/test_pbcore_io_GffIO.py::TestGffSorting::test_empty_file [gw9] [ 45%] SKIPPED tests/test_pbcore_io_AlnFileReaders.py::TestCCSBam::testBasicOperations [gw5] [ 45%] PASSED tests/test_pbcore_io_GffIO.py::TestGffSorting::test_empty_file tests/test_pbcore_io_BlasrIO.py::test_m4 [gw5] [ 46%] PASSED tests/test_pbcore_io_BlasrIO.py::test_m4 tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test_not_equal [gw6] [ 47%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test_not_equal tests/test_pbcore_io_FastaIO.py::TestFastaWriter::test_writeFasta1 [gw6] [ 47%] PASSED tests/test_pbcore_io_FastaIO.py::TestFastaWriter::test_writeFasta1 tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test_not_equal [gw3] [ 48%] PASSED tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test_not_equal tests/test_pbcore_io_FastaIO.py::TestFastaReader::test_readFasta [gw3] [ 49%] PASSED tests/test_pbcore_io_FastaIO.py::TestFastaReader::test_readFasta tests/test_pbcore_util_sequences.py::TestReverseComplement::test_reverse_complement_error [gw7] [ 50%] PASSED tests/test_pbcore_util_sequences.py::TestReverseComplement::test_reverse_complement_error tests/test_pbcore_io_AlnFileReaders.py::TestMultipleReadGroups::test_retrieve_read_group_properties [gw7] [ 50%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestMultipleReadGroups::test_retrieve_read_group_properties tests/test_pbdataset_utils.py::TestDataSetUtils::test_divideKeys_keysToRanges [gw10] [ 51%] PASSED tests/test_pbdataset_utils.py::TestDataSetUtils::test_divideKeys_keysToRanges tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::test_readWeirdFastaIndex tests/test_pbcore_io_FastqIO.py::TestQvConversion::testAsciiFromQvs [gw10] [ 52%] PASSED tests/test_pbcore_io_FastqIO.py::TestQvConversion::testAsciiFromQvs [gw4] [ 52%] PASSED tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::test_readWeirdFastaIndex tests/test_pbcore_io_GffIO.py::TestGffReader::test_headers [gw4] [ 53%] PASSED tests/test_pbcore_io_GffIO.py::TestGffReader::test_headers tests/test_pbcore_io_FastqIO.py::TestFastqWriter::test_writeFastq3 [gw11] [ 54%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqWriter::test_writeFastq3 tests/test_pbcore_io_FastqIO.py::TestFastqReader::test_readFastq1 [gw11] [ 55%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqReader::test_readFastq1 tests/test_pbcore_io_AlnFileReaders.py::TestCCSBam::testQStartEndUnavailable tests/test_pbindex.py::TestPbIndex::test_pbindex_with_zmw_index [gw12] [ 55%] PASSED tests/test_pbindex.py::TestPbIndex::test_pbindex_with_zmw_index tests/test_pbcore_io_unaligned_bam.py::TestUnalignedBam::testInvalidOperations tests/test_pbcore_io_GffIO.py::TestGff3Record::test_get [gw8] [ 56%] PASSED tests/test_pbcore_io_GffIO.py::TestGff3Record::test_get tests/test_pbcore_io_GffIO.py::TestGffWriter::test_writeHeader [gw8] [ 57%] PASSED tests/test_pbcore_io_GffIO.py::TestGffWriter::test_writeHeader [gw12] [ 57%] PASSED tests/test_pbcore_io_unaligned_bam.py::TestUnalignedBam::testInvalidOperations tests/test_pbcore_io_FastaIO.py::TestFastaWriter::test_writeFasta2 [gw6] [ 58%] PASSED tests/test_pbcore_io_FastaIO.py::TestFastaWriter::test_writeFasta2 tests/test_pbcore_io_FastaIO.py::TestFastaReader::test_dosLineEndingsFasta [gw9] [ 59%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestCCSBam::testQStartEndUnavailable tests/test_pbcore_io_AlnFileReaders.py::TestMultipleReadGroups::test_sample_names [gw7] [ 60%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestMultipleReadGroups::test_sample_names tests/test_pbcore_io_AlnFileReaders.py::TestBarcodedBam::test_read_lima_demultiplexed_bam [gw7] [ 60%] SKIPPED tests/test_pbcore_io_AlnFileReaders.py::TestBarcodedBam::test_read_lima_demultiplexed_bam tests/test_pbcore_io_FastqIO.py::TestQvConversion::testQvsFromAscii [gw10] [ 61%] PASSED tests/test_pbcore_io_FastqIO.py::TestQvConversion::testQvsFromAscii tests/test_pbcore_io_lossless_bam.py::TestCase::test_1 [gw10] [ 62%] SKIPPED tests/test_pbcore_io_lossless_bam.py::TestCase::test_1 tests/test_pbcore_io_AlnFileReaders.py::TestTranscriptBam::test_transcript_set_support [gw6] [ 62%] SKIPPED tests/test_pbcore_io_AlnFileReaders.py::TestTranscriptBam::test_transcript_set_support tests/test_pbcore_io_GffIO.py::TestGffReader::test__iter__ [gw4] [ 63%] PASSED tests/test_pbcore_io_GffIO.py::TestGffReader::test__iter__ [gw3] [ 64%] PASSED tests/test_pbcore_io_FastaIO.py::TestFastaReader::test_dosLineEndingsFasta tests/test_pbcore_io_AlnFileReaders.py::TestMissingHeaderM5::test_retrieve_read_group_properties tests/test_pbcore_util.py::TestStatistics::test_accuracy_as_phred_qv [gw9] [ 65%] PASSED tests/test_pbcore_util.py::TestStatistics::test_accuracy_as_phred_qv tests/test_pbcore_io_BlasrIO.py::test_m5 [gw5] [ 65%] PASSED tests/test_pbcore_io_BlasrIO.py::test_m5 tests/test_dataset_run_split.py::test [gw5] [ 66%] SKIPPED tests/test_dataset_run_split.py::test tests/test_pbcore_io_unaligned_bam.py::TestUnalignedBam::testIpd [gw12] [ 67%] PASSED tests/test_pbcore_io_unaligned_bam.py::TestUnalignedBam::testIpd tests/test_pbcore_util.py::TestStatistics::test_phred_qv_as_accuracy [gw9] [ 67%] PASSED tests/test_pbcore_util.py::TestStatistics::test_phred_qv_as_accuracy tests/test_pbcore_io_VcfIO.py::TestVcfSorting::test_merge_vcfs_sorted [gw7] [ 68%] PASSED tests/test_pbcore_io_VcfIO.py::TestVcfSorting::test_merge_vcfs_sorted tests/test_pbcore_io_AlnFileReaders.py::TestEmptyBam::test_empty_bam_reads_in_range [gw6] [ 69%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestEmptyBam::test_empty_bam_reads_in_range tests/test_pbcore_io_FastqIO.py::TestFastqReader::test_readFastq2 [gw11] [ 70%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqReader::test_readFastq2 [gw3] [ 70%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestMissingHeaderM5::test_retrieve_read_group_properties tests/test_pbcore_io_AlnFileReaders.py::TestUpdatedChemistryMapping::test_load_updated_mapping [gw3] [ 71%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestUpdatedChemistryMapping::test_load_updated_mapping tests/test_pbcore_extract_bam_sequence.py::TestCase::test_reverse_complement [gw5] [ 72%] PASSED tests/test_pbcore_extract_bam_sequence.py::TestCase::test_reverse_complement tests/test_pbcore_io_GffIO.py::TestGffWriter::test_writeRecord [gw8] [ 72%] PASSED tests/test_pbcore_io_GffIO.py::TestGffWriter::test_writeRecord [gw2] [ 73%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testReadsInRange tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testReadGroupTable [gw2] [ 74%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testReadGroupTable tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testSequencingChemistry [gw2] [ 75%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testSequencingChemistry tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testSpecVersion [gw2] [ 75%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testSpecVersion tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testReadScore [gw2] [ 76%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testReadScore tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::test_sample_name_default [gw2] [ 77%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::test_sample_name_default tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::test_library_name_default [gw2] [ 77%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::test_library_name_default [gw1] [ 78%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testReadsInRange tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testReadGroupTable [gw1] [ 79%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testReadGroupTable tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testSequencingChemistry [gw1] [ 80%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testSequencingChemistry tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testMapQV [gw1] [ 80%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testMapQV tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testHoleNumbers [gw1] [ 81%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testHoleNumbers tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testErrorCounts [gw1] [ 82%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testErrorCounts tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testReadsByName [gw1] [ 82%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testReadsByName tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::test_empty_bam [gw1] [ 83%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::test_empty_bam tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::test_alignment_identity [gw1] [ 84%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::test_alignment_identity tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::test_alignment_identity_unindexed [gw1] [ 85%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::test_alignment_identity_unindexed [gw0] [ 85%] FAILED tests/test_pbdataset_split.py::TestDataSetSplit::test_split tests/test_pbdataset_split.py::TestDataSetSplit::test_split_zmws [gw0] [ 86%] PASSED tests/test_pbdataset_split.py::TestDataSetSplit::test_split_zmws tests/test_pbdataset_split.py::TestDataSetSplit::test_split_zmws_targetsize [gw0] [ 87%] PASSED tests/test_pbdataset_split.py::TestDataSetSplit::test_split_zmws_targetsize tests/test_pbdataset_split.py::TestDataSetSplit::test_large_split_zmws [gw0] [ 87%] SKIPPED tests/test_pbdataset_split.py::TestDataSetSplit::test_large_split_zmws tests/test_pbdataset_split.py::TestDataSetSplit::test_multi_movie_split_zmws [gw0] [ 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 [gw0] [ 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 [gw0] [ 90%] SKIPPED tests/test_pbdataset_split.py::TestDataSetSplit::test_multi_movie_split_zmws_existing_filters tests/test_pbdataset_split.py::TestDataSetSplit::test_movie_split [gw0] [ 90%] SKIPPED tests/test_pbdataset_split.py::TestDataSetSplit::test_movie_split tests/test_pbdataset_split.py::TestDataSetSplit::test_split_references [gw0] [ 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 [gw0] [ 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 [gw0] [ 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 [gw0] [ 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 [gw0] [ 94%] FAILED tests/test_pbdataset_split.py::TestDataSetSplit::test_split_by_contigs_with_split tests/test_pbdataset_split.py::TestDataSetSplit::test_refWindows [gw0] [ 95%] FAILED tests/test_pbdataset_split.py::TestDataSetSplit::test_refWindows tests/test_pbdataset_split.py::TestDataSetSplit::test_huge_zmw_split [gw0] [ 95%] SKIPPED tests/test_pbdataset_split.py::TestDataSetSplit::test_huge_zmw_split tests/test_pbdataset_split.py::TestDataSetSplit::test_subreadset_split_metadata_element_name [gw0] [ 96%] FAILED tests/test_pbdataset_split.py::TestDataSetSplit::test_subreadset_split_metadata_element_name tests/test_pbdataset_split.py::TestDataSetSplit::test_contigset_split [gw0] [ 97%] PASSED tests/test_pbdataset_split.py::TestDataSetSplit::test_contigset_split tests/test_pbdataset_split.py::TestDataSetSplit::test_isBarcoded [gw0] [ 97%] SKIPPED tests/test_pbdataset_split.py::TestDataSetSplit::test_isBarcoded tests/test_pbdataset_split.py::TestDataSetSplit::test_barcode_split_cornercases [gw0] [ 98%] SKIPPED tests/test_pbdataset_split.py::TestDataSetSplit::test_barcode_split_cornercases tests/test_pbdataset_split.py::TestDataSetSplit::test_barcode_split_maxChunks [gw0] [ 99%] SKIPPED tests/test_pbdataset_split.py::TestDataSetSplit::test_barcode_split_maxChunks tests/test_pbdataset_split.py::TestDataSetSplit::test_split_read_groups [gw0] [100%] SKIPPED tests/test_pbdataset_split.py::TestDataSetSplit::test_split_read_groups =================================== FAILURES =================================== _________________________ TestDataSetSplit.test_split __________________________ [gw0] linux -- Python 3.12.2 /usr/bin/python3.12 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 ________ [gw0] linux -- Python 3.12.2 /usr/bin/python3.12 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 _______________ [gw0] linux -- Python 3.12.2 /usr/bin/python3.12 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 _______________________ [gw0] linux -- Python 3.12.2 /usr/bin/python3.12 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 _________ [gw0] linux -- Python 3.12.2 /usr/bin/python3.12 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 =============================== pbcore/__init__.py:1: 13 warnings /build/reproducible-path/python-pbcore-2.1.2+dfsg/pbcore/__init__.py:1: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html import pkg_resources ../../../usr/lib/python3/dist-packages/pkg_resources/__init__.py:2871: 13 warnings /usr/lib/python3/dist-packages/pkg_resources/__init__.py:2871: DeprecationWarning: Deprecated call to `pkg_resources.declare_namespace('logilab')`. Implementing implicit namespace packages (as specified in PEP 420) is preferred to `pkg_resources.declare_namespace`. See https://setuptools.pypa.io/en/latest/references/keywords.html#keyword-namespace-packages declare_namespace(pkg) 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") tests/test_pbdataset_utils.py: 10 warnings tests/test_pbdataset_split.py: 62 warnings /build/reproducible-path/python-pbcore-2.1.2+dfsg/pbcore/io/dataset/utils.py:24: DeprecationWarning: datetime.datetime.utcnow() is deprecated and scheduled for removal in a future version. Use timezone-aware objects to represent datetimes in UTC: datetime.datetime.now(datetime.UTC). time = datetime.datetime.utcnow().strftime("%y%m%d_%H%M%S%f")[:-3] 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_AlnFileReaders.py: 118 warnings tests/test_pbcore_extract_bam_sequence.py: 1 warning /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_pbdataset_split.py::TestDataSetSplit::test_subreadset_split_metadata_element_name /build/reproducible-path/python-pbcore-2.1.2+dfsg/pbcore/io/dataset/utils.py:30: DeprecationWarning: datetime.datetime.utcnow() is deprecated and scheduled for removal in a future version. Use timezone-aware objects to represent datetimes in UTC: datetime.datetime.now(datetime.UTC). return datetime.datetime.utcnow().strftime("%Y-%m-%dT%H:%M:%S%f")[:-6] -- 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 3.12.2-final-0 ----------- Coverage XML written to file coverage.xml ============================= slowest 20 durations ============================= 0.37s call tests/test_pbdataset_split.py::TestDataSetSplit::test_split_zmws_targetsize 0.36s call tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testReadsInRange 0.32s call tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testReadsInRange 0.22s call tests/test_pbdataset_split.py::TestDataSetSplit::test_split_zmws 0.22s call tests/test_pbdataset_split.py::TestDataSetSplit::test_contigset_split 0.10s call tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::test_alignment_identity_unindexed 0.09s call tests/test_pbindex.py::TestPbIndex::test_pbindex_bam_consistency 0.08s setup tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testBasicOperations 0.05s call tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::test_alignment_identity 0.05s call tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::test_dosLineEndingsFasta 0.04s setup tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testBasicOperations 0.04s call tests/test_pbdataset_split.py::TestDataSetSplit::test_split 0.04s call tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testHoleNumbers 0.02s call tests/test_pbcore_io_FastaIO.py::TestFastaReader::test_dosLineEndingsFasta 0.02s call tests/test_pbdataset_utils.py::TestDataSetUtils::test_get_dataset_uuid 0.02s call tests/test_pbcore_io_AlnFileReaders.py::TestMissingHeaderM5::test_retrieve_read_group_properties 0.02s call tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::testIteration 0.01s call tests/test_pbcore_io_FastqIO.py::TestFastqWriter::test_writeFastq1 0.01s call tests/test_pbdataset_split.py::TestDataSetSplit::test_subreadset_split_metadata_element_name 0.01s call tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testAlignedRead =========================== 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, 291 warnings in 15.12s =========== E: pybuild pybuild:389: test: plugin custom failed with: exit code=1: python3.12 setup.py test I: pybuild base:305: python3.11 setup.py test /usr/lib/python3/dist-packages/setuptools/dist.py:744: SetuptoolsDeprecationWarning: Invalid dash-separated options !! ******************************************************************************** Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead. This deprecation is overdue, please update your project and remove deprecated calls to avoid build errors in the future. See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. ******************************************************************************** !! opt = self.warn_dash_deprecation(opt, section) running pytest /usr/lib/python3/dist-packages/setuptools/dist.py:744: SetuptoolsDeprecationWarning: Invalid dash-separated options !! ******************************************************************************** Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead. This deprecation is overdue, please update your project and remove deprecated calls to avoid build errors in the future. See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. ******************************************************************************** !! opt = self.warn_dash_deprecation(opt, section) /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: EasyInstallDeprecationWarning: easy_install command is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` and ``easy_install``. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://github.com/pypa/setuptools/issues/917 for details. ******************************************************************************** !! self.initialize_options() /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() 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. /usr/lib/python3/dist-packages/setuptools/command/test.py:193: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. !! ******************************************************************************** Requirements should be satisfied by a PEP 517 installer. If you are using pip, you can try `pip install --use-pep517`. ******************************************************************************** !! ir_d = dist.fetch_build_eggs(dist.install_requires) WARNING: The wheel package is not available. /usr/lib/python3/dist-packages/setuptools/command/test.py:194: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. !! ******************************************************************************** Requirements should be satisfied by a PEP 517 installer. If you are using pip, you can try `pip install --use-pep517`. ******************************************************************************** !! tr_d = dist.fetch_build_eggs(dist.tests_require or []) WARNING: The wheel package is not available. /usr/lib/python3/dist-packages/setuptools/command/test.py:195: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. !! ******************************************************************************** Requirements should be satisfied by a PEP 517 installer. If you are using pip, you can try `pip install --use-pep517`. ******************************************************************************** !! er_d = dist.fetch_build_eggs( WARNING: The wheel package is not available. 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 3.11.8, pytest-7.4.4, pluggy-1.4.0 -- /usr/bin/python3.11 cachedir: .pytest_cache rootdir: /build/reproducible-path/python-pbcore-2.1.2+dfsg configfile: pytest.ini plugins: xdist-3.5.0, cov-4.1.0 created: 13/13 workers 13 workers [140 items] scheduling tests via LoadScopeScheduling tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testBasicOperations tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::testIteration tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test__init__ tests/test_pbcore_io_GffIO.py::TestGffSorting::test_merge_gffs tests/test_pbcore_io_FofnIO.py::test_simple tests/test_pbindex.py::TestPbIndex::test_pbindex_bam_consistency [gw12] [ 0%] PASSED tests/test_pbcore_io_FofnIO.py::test_simple tests/test_pbcore_io_FofnIO.py::test_empty_lines tests/test_pbcore_io_FastqIO.py::TestFastqWriter::test_writeFastq1 tests/test_pbcore_io_GffIO.py::TestGff3Record::test_str [gw7] [ 1%] PASSED tests/test_pbcore_io_GffIO.py::TestGff3Record::test_str tests/test_pbcore_io_GffIO.py::TestGff3Record::test_modification [gw7] [ 2%] PASSED tests/test_pbcore_io_GffIO.py::TestGff3Record::test_modification tests/test_pbcore_io_GffIO.py::TestGff3Record::test_fromString [gw7] [ 2%] PASSED tests/test_pbcore_io_GffIO.py::TestGff3Record::test_fromString [gw11] [ 3%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqWriter::test_writeFastq1 [gw1] [ 4%] PASSED tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test__init__ tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test__str__ tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testBasicOperations [gw12] [ 5%] PASSED tests/test_pbcore_io_FofnIO.py::test_empty_lines [gw1] [ 5%] PASSED tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test__str__ [gw6] [ 6%] PASSED tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::testIteration tests/test_pbdataset_utils.py::TestDataSetUtils::test_get_dataset_uuid [gw9] [ 7%] PASSED tests/test_pbdataset_utils.py::TestDataSetUtils::test_get_dataset_uuid tests/test_pbdataset_utils.py::TestDataSetUtils::test_get_dataset_metatype tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::testAccessByName tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test_fromString [gw8] [ 7%] PASSED tests/test_pbcore_io_GffIO.py::TestGffSorting::test_merge_gffs tests/test_pbcore_io_GffIO.py::TestGffSorting::test_merge_gffs_sorted [gw8] [ 8%] PASSED tests/test_pbcore_io_GffIO.py::TestGffSorting::test_merge_gffs_sorted tests/test_pbcore_io_GffIO.py::TestGffSorting::test_sort_gff [gw8] [ 9%] PASSED tests/test_pbcore_io_GffIO.py::TestGffSorting::test_sort_gff [gw1] [ 10%] PASSED tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test_fromString tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test_reverse_complement1 tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test__init__ [gw4] [ 10%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test__init__ tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test__str__ [gw4] [ 11%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test__str__ tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test_fromString [gw4] [ 12%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test_fromString tests/test_pbcore_util_sequences.py::TestReverseComplement::test_reverse [gw5] [ 12%] PASSED tests/test_pbcore_util_sequences.py::TestReverseComplement::test_reverse tests/test_pbcore_util_sequences.py::TestReverseComplement::test_complement [gw5] [ 13%] PASSED tests/test_pbcore_util_sequences.py::TestReverseComplement::test_complement tests/test_pbcore_util_sequences.py::TestReverseComplement::test_reverseComplement [gw5] [ 14%] PASSED tests/test_pbcore_util_sequences.py::TestReverseComplement::test_reverseComplement tests/test_pbcore_util_sequences.py::TestReverseComplement::test_iupac [gw5] [ 15%] PASSED tests/test_pbcore_util_sequences.py::TestReverseComplement::test_iupac tests/test_pbcore_util_sequences.py::TestReverseComplement::test_complement_error [gw5] [ 15%] PASSED tests/test_pbcore_util_sequences.py::TestReverseComplement::test_complement_error tests/test_pbcore_io_FastqIO.py::TestFastqWriter::test_writeFastq2 [gw11] [ 16%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqWriter::test_writeFastq2 tests/test_pbdataset_split.py::TestDataSetSplit::test_split [gw1] [ 17%] PASSED tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test_reverse_complement1 [gw9] [ 17%] PASSED tests/test_pbdataset_utils.py::TestDataSetUtils::test_get_dataset_metatype tests/test_pbdataset_utils.py::TestDataSetUtils::test_dsIdToSuffix tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test_reverse_complement1 [gw4] [ 18%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test_reverse_complement1 tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test_reverse_complement2 [gw6] [ 19%] PASSED tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::testAccessByName tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::testAccessById [gw6] [ 20%] PASSED tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::testAccessById tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::testAccessByPosition tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test_reverse_complement2 [gw1] [ 20%] PASSED tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test_reverse_complement2 tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test_len [gw2] [ 21%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testBasicOperations tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testStrandOrientation [gw2] [ 22%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testStrandOrientation tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testReadName [gw2] [ 22%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testReadName [gw3] [ 23%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testBasicOperations [gw1] [ 24%] PASSED tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test_len tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test_eq [gw1] [ 25%] PASSED tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test_eq [gw6] [ 25%] PASSED tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::testAccessByPosition tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::testSlice [gw6] [ 26%] PASSED tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::testSlice tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::test_dosLineEndingsFasta tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testStrandOrientation [gw3] [ 27%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testStrandOrientation tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testReadName [gw3] [ 27%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testReadName tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testAlignedRead [gw2] [ 28%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testAlignedRead tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testUnalignedRead [gw2] [ 29%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testUnalignedRead [gw4] [ 30%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test_reverse_complement2 tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test_len [gw4] [ 30%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test_len tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test_eq [gw4] [ 31%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test_eq tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testAlignedRead [gw3] [ 32%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testAlignedRead tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testUnalignedRead tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testAlignedReference [gw2] [ 32%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testAlignedReference tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testUnalignedReference [gw2] [ 33%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testUnalignedReference tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testDeletionQV [gw3] [ 34%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testUnalignedRead tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testAlignedReference [gw3] [ 35%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testAlignedReference [gw9] [ 35%] PASSED tests/test_pbdataset_utils.py::TestDataSetUtils::test_dsIdToSuffix tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testUnalignedReference [gw3] [ 36%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testUnalignedReference tests/test_pbcore_io_FofnIO.py::test_absolutifying tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testDeletionQV [gw6] [ 37%] PASSED tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::test_dosLineEndingsFasta [gw12] [ 37%] PASSED tests/test_pbcore_io_FofnIO.py::test_absolutifying [gw2] [ 38%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testDeletionQV tests/test_pbcore_io_AlnFileReaders.py::TestCCSBam::testBasicOperations [gw12] [ 39%] SKIPPED tests/test_pbcore_io_AlnFileReaders.py::TestCCSBam::testBasicOperations tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testTranscript [gw10] [ 40%] PASSED tests/test_pbindex.py::TestPbIndex::test_pbindex_bam_consistency tests/test_pbindex.py::TestPbIndex::test_pbindex_streaming [gw2] [ 40%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testTranscript [gw3] [ 41%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testDeletionQV tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testTranscript tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testClippedAlignments [gw10] [ 42%] PASSED tests/test_pbindex.py::TestPbIndex::test_pbindex_streaming tests/test_pbcore_io_GffIO.py::TestGff3Record::test_get [gw7] [ 42%] PASSED tests/test_pbcore_io_GffIO.py::TestGff3Record::test_get [gw3] [ 43%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testTranscript tests/test_pbindex.py::TestPbIndex::test_pbindex_streaming_entire tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testClippedAlignments tests/test_pbcore_io_AlnFileReaders.py::TestMultipleReadGroups::test_retrieve_read_group_properties [gw2] [ 44%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testClippedAlignments [gw10] [ 45%] PASSED tests/test_pbindex.py::TestPbIndex::test_pbindex_streaming_entire tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testReadsInRange [gw7] [ 45%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestMultipleReadGroups::test_retrieve_read_group_properties tests/test_pbcore_io_GffIO.py::TestGffSorting::test_empty_file [gw3] [ 46%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testClippedAlignments tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testReadsInRange [gw8] [ 47%] PASSED tests/test_pbcore_io_GffIO.py::TestGffSorting::test_empty_file tests/test_pbcore_io_FastqIO.py::TestFastqWriter::test_writeFastq3 tests/test_pbcore_io_BlasrIO.py::test_m4 [gw8] [ 47%] PASSED tests/test_pbcore_io_BlasrIO.py::test_m4 [gw11] [ 48%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqWriter::test_writeFastq3 tests/test_pbcore_io_FastaIO.py::TestFastaWriter::test_writeFasta1 [gw11] [ 49%] PASSED tests/test_pbcore_io_FastaIO.py::TestFastaWriter::test_writeFasta1 tests/test_pbcore_util_sequences.py::TestReverseComplement::test_reverse_complement_error [gw5] [ 50%] PASSED tests/test_pbcore_util_sequences.py::TestReverseComplement::test_reverse_complement_error tests/test_pbcore_io_FastaIO.py::TestFastaReader::test_readFasta [gw5] [ 50%] PASSED tests/test_pbcore_io_FastaIO.py::TestFastaReader::test_readFasta tests/test_pbdataset_utils.py::TestDataSetUtils::test_divideKeys_keysToRanges [gw9] [ 51%] PASSED tests/test_pbdataset_utils.py::TestDataSetUtils::test_divideKeys_keysToRanges tests/test_pbcore_io_FastqIO.py::TestQvConversion::testAsciiFromQvs [gw9] [ 52%] PASSED tests/test_pbcore_io_FastqIO.py::TestQvConversion::testAsciiFromQvs tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test_not_equal [gw1] [ 52%] PASSED tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test_not_equal tests/test_pbcore_io_FastqIO.py::TestFastqReader::test_readFastq1 [gw1] [ 53%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqReader::test_readFastq1 tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test_not_equal [gw4] [ 54%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test_not_equal tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::test_readWeirdFastaIndex [gw6] [ 55%] PASSED tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::test_readWeirdFastaIndex tests/test_pbcore_io_GffIO.py::TestGffReader::test_headers [gw6] [ 55%] PASSED tests/test_pbcore_io_GffIO.py::TestGffReader::test_headers tests/test_pbcore_io_GffIO.py::TestGffWriter::test_writeHeader [gw4] [ 56%] PASSED tests/test_pbcore_io_GffIO.py::TestGffWriter::test_writeHeader tests/test_pbcore_io_AlnFileReaders.py::TestCCSBam::testQStartEndUnavailable tests/test_pbcore_io_AlnFileReaders.py::TestMultipleReadGroups::test_sample_names [gw7] [ 57%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestMultipleReadGroups::test_sample_names tests/test_dataset_run_split.py::test [gw12] [ 57%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestCCSBam::testQStartEndUnavailable tests/test_pbcore_io_unaligned_bam.py::TestUnalignedBam::testInvalidOperations [gw12] [ 58%] PASSED tests/test_pbcore_io_unaligned_bam.py::TestUnalignedBam::testInvalidOperations tests/test_pbcore_io_BlasrIO.py::test_m5 [gw8] [ 59%] PASSED tests/test_pbcore_io_BlasrIO.py::test_m5 tests/test_pbcore_io_AlnFileReaders.py::TestTranscriptBam::test_transcript_set_support tests/test_pbindex.py::TestPbIndex::test_pbindex_with_zmw_index [gw10] [ 60%] PASSED tests/test_pbindex.py::TestPbIndex::test_pbindex_with_zmw_index tests/test_pbcore_util.py::TestStatistics::test_accuracy_as_phred_qv [gw10] [ 60%] PASSED tests/test_pbcore_util.py::TestStatistics::test_accuracy_as_phred_qv [gw7] [ 61%] SKIPPED tests/test_dataset_run_split.py::test tests/test_pbcore_io_FastqIO.py::TestQvConversion::testQvsFromAscii [gw9] [ 62%] PASSED tests/test_pbcore_io_FastqIO.py::TestQvConversion::testQvsFromAscii tests/test_pbcore_io_GffIO.py::TestGffReader::test__iter__ tests/test_pbcore_io_lossless_bam.py::TestCase::test_1 [gw6] [ 62%] PASSED tests/test_pbcore_io_GffIO.py::TestGffReader::test__iter__ tests/test_pbcore_io_GffIO.py::TestGffWriter::test_writeRecord [gw4] [ 63%] PASSED tests/test_pbcore_io_GffIO.py::TestGffWriter::test_writeRecord tests/test_pbcore_extract_bam_sequence.py::TestCase::test_reverse_complement tests/test_pbcore_io_unaligned_bam.py::TestUnalignedBam::testIpd [gw12] [ 64%] PASSED tests/test_pbcore_io_unaligned_bam.py::TestUnalignedBam::testIpd [gw9] [ 65%] SKIPPED tests/test_pbcore_io_lossless_bam.py::TestCase::test_1 [gw8] [ 65%] SKIPPED tests/test_pbcore_io_AlnFileReaders.py::TestTranscriptBam::test_transcript_set_support tests/test_pbcore_io_FastqIO.py::TestFastqReader::test_readFastq2 [gw1] [ 66%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqReader::test_readFastq2 tests/test_pbcore_io_FastaIO.py::TestFastaWriter::test_writeFasta2 [gw11] [ 67%] PASSED tests/test_pbcore_io_FastaIO.py::TestFastaWriter::test_writeFasta2 tests/test_pbcore_io_AlnFileReaders.py::TestMissingHeaderM5::test_retrieve_read_group_properties [gw11] [ 67%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestMissingHeaderM5::test_retrieve_read_group_properties tests/test_pbcore_io_FastaIO.py::TestFastaReader::test_dosLineEndingsFasta [gw5] [ 68%] PASSED tests/test_pbcore_io_FastaIO.py::TestFastaReader::test_dosLineEndingsFasta tests/test_pbcore_io_AlnFileReaders.py::TestBarcodedBam::test_read_lima_demultiplexed_bam [gw5] [ 69%] SKIPPED tests/test_pbcore_io_AlnFileReaders.py::TestBarcodedBam::test_read_lima_demultiplexed_bam tests/test_pbcore_io_AlnFileReaders.py::TestEmptyBam::test_empty_bam_reads_in_range [gw7] [ 70%] PASSED tests/test_pbcore_extract_bam_sequence.py::TestCase::test_reverse_complement [gw8] [ 70%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestEmptyBam::test_empty_bam_reads_in_range tests/test_pbcore_util.py::TestStatistics::test_phred_qv_as_accuracy [gw10] [ 71%] PASSED tests/test_pbcore_util.py::TestStatistics::test_phred_qv_as_accuracy tests/test_pbcore_io_VcfIO.py::TestVcfSorting::test_merge_vcfs_sorted [gw5] [ 72%] PASSED tests/test_pbcore_io_VcfIO.py::TestVcfSorting::test_merge_vcfs_sorted tests/test_pbcore_io_AlnFileReaders.py::TestUpdatedChemistryMapping::test_load_updated_mapping [gw11] [ 72%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestUpdatedChemistryMapping::test_load_updated_mapping [gw3] [ 73%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testReadsInRange tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testReadGroupTable [gw3] [ 74%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testReadGroupTable tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testSequencingChemistry [gw3] [ 75%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testSequencingChemistry tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testSpecVersion [gw3] [ 75%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testSpecVersion tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testReadScore [gw3] [ 76%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testReadScore tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::test_sample_name_default [gw3] [ 77%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::test_sample_name_default tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::test_library_name_default [gw3] [ 77%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::test_library_name_default [gw2] [ 78%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testReadsInRange tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testReadGroupTable [gw2] [ 79%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testReadGroupTable tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testSequencingChemistry [gw2] [ 80%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testSequencingChemistry tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testMapQV [gw2] [ 80%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testMapQV tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testHoleNumbers [gw2] [ 81%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testHoleNumbers tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testErrorCounts [gw2] [ 82%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testErrorCounts tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testReadsByName [gw2] [ 82%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testReadsByName tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::test_empty_bam [gw2] [ 83%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::test_empty_bam tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::test_alignment_identity [gw2] [ 84%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::test_alignment_identity tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::test_alignment_identity_unindexed [gw2] [ 85%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::test_alignment_identity_unindexed [gw0] [ 85%] FAILED tests/test_pbdataset_split.py::TestDataSetSplit::test_split tests/test_pbdataset_split.py::TestDataSetSplit::test_split_zmws [gw0] [ 86%] PASSED tests/test_pbdataset_split.py::TestDataSetSplit::test_split_zmws tests/test_pbdataset_split.py::TestDataSetSplit::test_split_zmws_targetsize [gw0] [ 87%] PASSED tests/test_pbdataset_split.py::TestDataSetSplit::test_split_zmws_targetsize tests/test_pbdataset_split.py::TestDataSetSplit::test_large_split_zmws [gw0] [ 87%] SKIPPED tests/test_pbdataset_split.py::TestDataSetSplit::test_large_split_zmws tests/test_pbdataset_split.py::TestDataSetSplit::test_multi_movie_split_zmws [gw0] [ 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 [gw0] [ 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 [gw0] [ 90%] SKIPPED tests/test_pbdataset_split.py::TestDataSetSplit::test_multi_movie_split_zmws_existing_filters tests/test_pbdataset_split.py::TestDataSetSplit::test_movie_split [gw0] [ 90%] SKIPPED tests/test_pbdataset_split.py::TestDataSetSplit::test_movie_split tests/test_pbdataset_split.py::TestDataSetSplit::test_split_references [gw0] [ 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 [gw0] [ 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 [gw0] [ 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 [gw0] [ 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 [gw0] [ 94%] FAILED tests/test_pbdataset_split.py::TestDataSetSplit::test_split_by_contigs_with_split tests/test_pbdataset_split.py::TestDataSetSplit::test_refWindows [gw0] [ 95%] FAILED tests/test_pbdataset_split.py::TestDataSetSplit::test_refWindows tests/test_pbdataset_split.py::TestDataSetSplit::test_huge_zmw_split [gw0] [ 95%] SKIPPED tests/test_pbdataset_split.py::TestDataSetSplit::test_huge_zmw_split tests/test_pbdataset_split.py::TestDataSetSplit::test_subreadset_split_metadata_element_name [gw0] [ 96%] FAILED tests/test_pbdataset_split.py::TestDataSetSplit::test_subreadset_split_metadata_element_name tests/test_pbdataset_split.py::TestDataSetSplit::test_contigset_split [gw0] [ 97%] PASSED tests/test_pbdataset_split.py::TestDataSetSplit::test_contigset_split tests/test_pbdataset_split.py::TestDataSetSplit::test_isBarcoded [gw0] [ 97%] SKIPPED tests/test_pbdataset_split.py::TestDataSetSplit::test_isBarcoded tests/test_pbdataset_split.py::TestDataSetSplit::test_barcode_split_cornercases [gw0] [ 98%] SKIPPED tests/test_pbdataset_split.py::TestDataSetSplit::test_barcode_split_cornercases tests/test_pbdataset_split.py::TestDataSetSplit::test_barcode_split_maxChunks [gw0] [ 99%] SKIPPED tests/test_pbdataset_split.py::TestDataSetSplit::test_barcode_split_maxChunks tests/test_pbdataset_split.py::TestDataSetSplit::test_split_read_groups [gw0] [100%] SKIPPED tests/test_pbdataset_split.py::TestDataSetSplit::test_split_read_groups =================================== FAILURES =================================== _________________________ TestDataSetSplit.test_split __________________________ [gw0] linux -- Python 3.11.8 /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 ________ [gw0] linux -- Python 3.11.8 /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 _______________ [gw0] linux -- Python 3.11.8 /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 _______________________ [gw0] linux -- Python 3.11.8 /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 _________ [gw0] linux -- Python 3.11.8 /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 =============================== pbcore/__init__.py:1: 13 warnings /build/reproducible-path/python-pbcore-2.1.2+dfsg/pbcore/__init__.py:1: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html import pkg_resources ../../../usr/lib/python3/dist-packages/pkg_resources/__init__.py:2871: 13 warnings /usr/lib/python3/dist-packages/pkg_resources/__init__.py:2871: DeprecationWarning: Deprecated call to `pkg_resources.declare_namespace('logilab')`. Implementing implicit namespace packages (as specified in PEP 420) is preferred to `pkg_resources.declare_namespace`. See https://setuptools.pypa.io/en/latest/references/keywords.html#keyword-namespace-packages declare_namespace(pkg) 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") 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_AlnFileReaders.py: 118 warnings tests/test_pbcore_extract_bam_sequence.py: 1 warning /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") -- 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 3.11.8-final-0 ----------- Coverage XML written to file coverage.xml ============================= slowest 20 durations ============================= 0.37s call tests/test_pbdataset_split.py::TestDataSetSplit::test_split_zmws_targetsize 0.37s call tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testReadsInRange 0.30s call tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testReadsInRange 0.26s call tests/test_pbdataset_split.py::TestDataSetSplit::test_contigset_split 0.24s call tests/test_pbdataset_split.py::TestDataSetSplit::test_split_zmws 0.11s call tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::test_alignment_identity_unindexed 0.10s call tests/test_pbindex.py::TestPbIndex::test_pbindex_bam_consistency 0.06s setup tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testBasicOperations 0.06s call tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::test_alignment_identity 0.05s setup tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testBasicOperations 0.04s call tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testHoleNumbers 0.04s call tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::test_dosLineEndingsFasta 0.03s call tests/test_pbdataset_split.py::TestDataSetSplit::test_split 0.03s call tests/test_pbcore_io_FastaIO.py::TestFastaReader::test_dosLineEndingsFasta 0.03s call tests/test_pbcore_io_AlnFileReaders.py::TestMissingHeaderM5::test_retrieve_read_group_properties 0.02s call tests/test_pbdataset_utils.py::TestDataSetUtils::test_get_dataset_uuid 0.02s call tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::testIteration 0.01s call tests/test_pbdataset_split.py::TestDataSetSplit::test_subreadset_split_metadata_element_name 0.01s call tests/test_pbdataset_utils.py::TestDataSetUtils::test_get_dataset_metatype 0.01s setup tests/test_pbcore_extract_bam_sequence.py::TestCase::test_reverse_complement =========================== 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, 218 warnings in 13.64s =========== E: pybuild pybuild:389: 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 "3.12 3.11" returned exit code 13 make[1]: *** [debian/rules:34: 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/50995 and its subdirectories Tue Apr 2 14:18:44 UTC 2024 W: No second build log, what happened?