Mon Nov 25 15:27:06 UTC 2024 I: starting to build python-pbcore/trixie/armhf on jenkins on '2024-11-25 15:26' Mon Nov 25 15:27:06 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/armhf_31/9003/console.log Mon Nov 25 15:27:06 UTC 2024 I: Downloading source for trixie/python-pbcore=2.1.2+dfsg-9 --2024-11-25 15:27:06-- http://deb.debian.org/debian/pool/main/p/python-pbcore/python-pbcore_2.1.2%2bdfsg-9.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2804 (2.7K) [text/prs.lines.tag] Saving to: ‘python-pbcore_2.1.2+dfsg-9.dsc’ 0K .. 100% 302M=0s 2024-11-25 15:27:06 (302 MB/s) - ‘python-pbcore_2.1.2+dfsg-9.dsc’ saved [2804/2804] Mon Nov 25 15:27:06 UTC 2024 I: python-pbcore_2.1.2+dfsg-9.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-9 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Étienne Mollier Homepage: https://github.com/PacificBiosciences/pbcore Standards-Version: 4.7.0 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 a80cb5556acf7175c012ddd0f4ed37d01827aa35 60264 python-pbcore_2.1.2+dfsg-9.debian.tar.xz Checksums-Sha256: a31283a37b20aa7b327de78a533254c5892c5519fb8214fd3c1a978855351326 2918008 python-pbcore_2.1.2+dfsg.orig.tar.xz f25f24ccfd5c937672b1946ea09c422a75c8b52aef9fcd90baeb3503b64e565b 60264 python-pbcore_2.1.2+dfsg-9.debian.tar.xz Files: b58bb3c6ad20be9ea36bf8a7548bdd84 2918008 python-pbcore_2.1.2+dfsg.orig.tar.xz 3cc7396b7020197ef71b9ef480db84ff 60264 python-pbcore_2.1.2+dfsg-9.debian.tar.xz Dgit: f8fe43ca66d173fca7e1f05138e9f67d181fc8df debian archive/debian/2.1.2+dfsg-9 https://git.dgit.debian.org/python-pbcore -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmcwxuMUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdpDdQ/+K5hihmDeTVcxoZYTQxtXVO3opATd L9frNxJE/HrXNEC02mJpq9LQq832cZfLGiOL6rMb1pao4jb0QBZijYXgRq9FGJNL wzIRNqOXkYH7AQ7zmJTflfvlRjfZYB4+h+u6yUspomNloPMVYevb49G/rUTDciov Riv2XzNjqo+0Efn2TViG0Azgojobkm+H+bQkHbX4pttiuSRhyyqmWyXfQkEvInb7 ONtf+Gb/p798jxoS+XVqhqPfJlDwtUK2yC0rJ69IAllv2gvYd/n6feFYtKDYEObM jQ3xc0SaBTVoV3xEtiLVI9lKolSipxjxfzBiXEt4VW8bAhwgGDxHz7FJGHVbhwnI BnruCLBaho+W+KWdVSoNhHts7+nPJBc21ryLvBJkZzGBbzHZ2jcs+6ytAYmvNny/ 4YYbhyiCH1sUqjetWEDhIx3mrK/F8GvW1nAyrU9I6kU3VjroLaQoUHalosl/0qyn Ocsh3VhCKS/nK3xtoQvi2Eh4yW7vwNdMF7LL3Yt3iuV3vB6Zq0Be1AALUdqpNoGJ ktxM95XQDcRSKF+6eIlN2YTIzBm5aySQ5K7IhTKTd4cBV86uHIQEw5kzft6OdHIa 7cbh/91neQ8FTqPIWNgbaPZrIEPW2G8eQrvfYXda3ikF1uQ1nAdbu7SVf/OKHzBz FxkOvAhlPCSGi60= =e0Z7 -----END PGP SIGNATURE----- Mon Nov 25 15:27:07 UTC 2024 I: Checking whether the package is not for us Mon Nov 25 15:27:07 UTC 2024 I: Starting 1st build on remote node virt64c-armhf-rb.debian.net. Mon Nov 25 15:27:07 UTC 2024 I: Preparing to do remote build '1' on virt64c-armhf-rb.debian.net. Mon Nov 25 15:33:38 UTC 2024 I: Deleting $TMPDIR on virt64c-armhf-rb.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Mon Nov 25 03:27:13 -12 2024 I: pbuilder-time-stamp: 1732548433 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: Copying source file I: copying [python-pbcore_2.1.2+dfsg-9.dsc] I: copying [./python-pbcore_2.1.2+dfsg.orig.tar.xz] I: copying [./python-pbcore_2.1.2+dfsg-9.debian.tar.xz] I: Extracting source gpgv: Signature made Sun Nov 10 14:44:51 2024 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./python-pbcore_2.1.2+dfsg-9.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-9.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/4322/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='armhf' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='armhf' IFS=' ' INVOCATION_ID='e465591d853641af82b151967f0211cd' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='4322' 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.OTHW4VoP/pbuilderrc_9RSy --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.OTHW4VoP/b1 --logfile b1/build.log python-pbcore_2.1.2+dfsg-9.dsc' SUDO_GID='113' SUDO_UID='107' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://10.0.0.15:3142/' I: uname -a Linux virt64c 6.1.0-28-arm64 #1 SMP Debian 6.1.119-1 (2024-11-22) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/4322/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: armhf Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), dh-python, 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 ... 19690 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-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} libcairo2{a} libcom-err2{a} libcurl3t64-gnutls{a} libcurl4t64{a} libdebhelper-perl{a} libdeflate0{a} libelf1t64{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfontenc1{a} libfreetype6{a} libfribidi0{a} libgfortran5{a} libglib2.0-0t64{a} libgraphite2-3{a} libgssapi-krb5-2{a} libharfbuzz0b{a} libhdf5-103-1t64{a} libhdf5-hl-100t64{a} libhts3t64{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} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} liblcms2-2{a} libldap-2.5-0{a} liblerc4{a} liblzf1{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libnghttp3-9{a} libngtcp2-16{a} libngtcp2-crypto-gnutls8{a} libnsl2{a} libopenjp2-7{a} libpipeline1{a} libpixman-1-0{a} libpng16-16t64{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libraqm0{a} libreadline8t64{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsharpyuv0{a} libssh2-1t64{a} libsz2{a} libtiff6{a} libtirpc-common{a} libtirpc3t64{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-autocommand{a} python3-babel{a} python3-biopython{a} python3-cairo{a} python3-certifi{a} python3-chardet{a} python3-charset-normalizer{a} python3-coverage{a} python3-defusedxml{a} python3-dill{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-inflect{a} python3-iniconfig{a} python3-isort{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jinja2{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-snowballstemmer{a} python3-sphinx{a} python3-tomlkit{a} python3-typeguard{a} python3-typing-extensions{a} python3-uritools{a} python3-urllib3{a} python3-xmlschema{a} python3-zipp{a} python3.12{a} python3.12-minimal{a} python3.13{a} python3.13-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 fonts-dejavu-extra javascript-common krb5-locales 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, 194 newly installed, 0 to remove and 0 not upgraded. Need to get 83.6 MB of archives. After unpacking 323 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main armhf libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 2 http://deb.debian.org/debian trixie/main armhf libjs-jquery-hotkeys all 0~20130707+git2d51e3a9+dfsg-2.1 [11.5 kB] Get: 3 http://deb.debian.org/debian trixie/main armhf libpython3.12-minimal armhf 3.12.7-3 [800 kB] Get: 4 http://deb.debian.org/debian trixie/main armhf libexpat1 armhf 2.6.4-1 [83.5 kB] Get: 5 http://deb.debian.org/debian trixie/main armhf python3.12-minimal armhf 3.12.7-3 [1808 kB] Get: 6 http://deb.debian.org/debian trixie/main armhf python3-minimal armhf 3.12.6-1 [26.7 kB] Get: 7 http://deb.debian.org/debian trixie/main armhf media-types all 10.1.0 [26.9 kB] Get: 8 http://deb.debian.org/debian trixie/main armhf netbase all 6.4 [12.8 kB] Get: 9 http://deb.debian.org/debian trixie/main armhf tzdata all 2024b-3 [255 kB] Get: 10 http://deb.debian.org/debian trixie/main armhf libkrb5support0 armhf 1.21.3-3 [30.0 kB] Get: 11 http://deb.debian.org/debian trixie/main armhf libcom-err2 armhf 1.47.1-1+b1 [22.3 kB] Get: 12 http://deb.debian.org/debian trixie/main armhf libk5crypto3 armhf 1.21.3-3 [75.8 kB] Get: 13 http://deb.debian.org/debian trixie/main armhf libkeyutils1 armhf 1.6.3-4 [8096 B] Get: 14 http://deb.debian.org/debian trixie/main armhf libkrb5-3 armhf 1.21.3-3 [283 kB] Get: 15 http://deb.debian.org/debian trixie/main armhf libgssapi-krb5-2 armhf 1.21.3-3 [114 kB] Get: 16 http://deb.debian.org/debian trixie/main armhf libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 17 http://deb.debian.org/debian trixie/main armhf libtirpc3t64 armhf 1.3.4+ds-1.3+b1 [71.3 kB] Get: 18 http://deb.debian.org/debian trixie/main armhf libnsl2 armhf 1.3.0-3+b3 [35.0 kB] Get: 19 http://deb.debian.org/debian trixie/main armhf readline-common all 8.2-5 [69.3 kB] Get: 20 http://deb.debian.org/debian trixie/main armhf libreadline8t64 armhf 8.2-5 [146 kB] Get: 21 http://deb.debian.org/debian trixie/main armhf libpython3.12-stdlib armhf 3.12.7-3 [1819 kB] Get: 22 http://deb.debian.org/debian trixie/main armhf python3.12 armhf 3.12.7-3 [671 kB] Get: 23 http://deb.debian.org/debian trixie/main armhf libpython3-stdlib armhf 3.12.6-1 [9692 B] Get: 24 http://deb.debian.org/debian trixie/main armhf python3 armhf 3.12.6-1 [27.8 kB] Get: 25 http://deb.debian.org/debian trixie/main armhf libpython3.13-minimal armhf 3.13.0-2 [843 kB] Get: 26 http://deb.debian.org/debian trixie/main armhf python3.13-minimal armhf 3.13.0-2 [1691 kB] Get: 27 http://deb.debian.org/debian trixie/main armhf sgml-base all 1.31 [15.4 kB] Get: 28 http://deb.debian.org/debian trixie/main armhf sensible-utils all 0.0.24 [24.8 kB] Get: 29 http://deb.debian.org/debian trixie/main armhf openssl armhf 3.3.2-2 [1348 kB] Get: 30 http://deb.debian.org/debian trixie/main armhf ca-certificates all 20240203 [158 kB] Get: 31 http://deb.debian.org/debian trixie/main armhf libmagic-mgc armhf 1:5.45-3+b1 [314 kB] Get: 32 http://deb.debian.org/debian trixie/main armhf libmagic1t64 armhf 1:5.45-3+b1 [98.5 kB] Get: 33 http://deb.debian.org/debian trixie/main armhf file armhf 1:5.45-3+b1 [42.3 kB] Get: 34 http://deb.debian.org/debian trixie/main armhf gettext-base armhf 0.22.5-2 [195 kB] Get: 35 http://deb.debian.org/debian trixie/main armhf libuchardet0 armhf 0.0.8-1+b2 [65.6 kB] Get: 36 http://deb.debian.org/debian trixie/main armhf groff-base armhf 1.23.0-5 [1091 kB] Get: 37 http://deb.debian.org/debian trixie/main armhf bsdextrautils armhf 2.40.2-11 [83.6 kB] Get: 38 http://deb.debian.org/debian trixie/main armhf libpipeline1 armhf 1.5.8-1 [35.0 kB] Get: 39 http://deb.debian.org/debian trixie/main armhf man-db armhf 2.13.0-1 [1382 kB] Get: 40 http://deb.debian.org/debian trixie/main armhf m4 armhf 1.4.19-4 [264 kB] Get: 41 http://deb.debian.org/debian trixie/main armhf autoconf all 2.72-3 [493 kB] Get: 42 http://deb.debian.org/debian trixie/main armhf autotools-dev all 20220109.1 [51.6 kB] Get: 43 http://deb.debian.org/debian trixie/main armhf automake all 1:1.16.5-1.3 [823 kB] Get: 44 http://deb.debian.org/debian trixie/main armhf autopoint all 0.22.5-2 [723 kB] Get: 45 http://deb.debian.org/debian trixie/main armhf libdebhelper-perl all 13.20 [89.7 kB] Get: 46 http://deb.debian.org/debian trixie/main armhf libtool all 2.4.7-8 [517 kB] Get: 47 http://deb.debian.org/debian trixie/main armhf dh-autoreconf all 20 [17.1 kB] Get: 48 http://deb.debian.org/debian trixie/main armhf libarchive-zip-perl all 1.68-1 [104 kB] Get: 49 http://deb.debian.org/debian trixie/main armhf libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 50 http://deb.debian.org/debian trixie/main armhf dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 51 http://deb.debian.org/debian trixie/main armhf libelf1t64 armhf 0.192-4 [184 kB] Get: 52 http://deb.debian.org/debian trixie/main armhf dwz armhf 0.15-1+b2 [106 kB] Get: 53 http://deb.debian.org/debian trixie/main armhf libicu72 armhf 72.1-5+b1 [9088 kB] Get: 54 http://deb.debian.org/debian trixie/main armhf libxml2 armhf 2.12.7+dfsg+really2.9.14-0.2+b1 [605 kB] Get: 55 http://deb.debian.org/debian trixie/main armhf gettext armhf 0.22.5-2 [1485 kB] Get: 56 http://deb.debian.org/debian trixie/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 57 http://deb.debian.org/debian trixie/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 58 http://deb.debian.org/debian trixie/main armhf debhelper all 13.20 [915 kB] Get: 59 http://deb.debian.org/debian trixie/main armhf python3-autocommand all 2.2.2-3 [13.6 kB] Get: 60 http://deb.debian.org/debian trixie/main armhf python3-more-itertools all 10.5.0-1 [63.8 kB] Get: 61 http://deb.debian.org/debian trixie/main armhf python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 62 http://deb.debian.org/debian trixie/main armhf python3-typeguard all 4.4.1-1 [37.0 kB] Get: 63 http://deb.debian.org/debian trixie/main armhf python3-inflect all 7.3.1-2 [32.4 kB] Get: 64 http://deb.debian.org/debian trixie/main armhf python3-jaraco.context all 6.0.0-1 [7984 B] Get: 65 http://deb.debian.org/debian trixie/main armhf python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 66 http://deb.debian.org/debian trixie/main armhf python3-pkg-resources all 74.1.2-2 [213 kB] Get: 67 http://deb.debian.org/debian trixie/main armhf python3-zipp all 3.21.0-1 [10.6 kB] Get: 68 http://deb.debian.org/debian trixie/main armhf python3-setuptools all 74.1.2-2 [736 kB] Get: 69 http://deb.debian.org/debian trixie/main armhf dh-python all 6.20241024 [109 kB] Get: 70 http://deb.debian.org/debian trixie/main armhf xml-core all 0.19 [20.1 kB] Get: 71 http://deb.debian.org/debian trixie/main armhf docutils-common all 0.21.2+dfsg-2 [128 kB] Get: 72 http://deb.debian.org/debian trixie/main armhf fonts-dejavu-mono all 2.37-8 [489 kB] Get: 73 http://deb.debian.org/debian trixie/main armhf fonts-dejavu-core all 2.37-8 [840 kB] Get: 74 http://deb.debian.org/debian trixie/main armhf libfontenc1 armhf 1:1.1.8-1+b1 [20.8 kB] Get: 75 http://deb.debian.org/debian trixie/main armhf libbrotli1 armhf 1.1.0-2+b6 [282 kB] Get: 76 http://deb.debian.org/debian trixie/main armhf libpng16-16t64 armhf 1.6.44-2 [263 kB] Get: 77 http://deb.debian.org/debian trixie/main armhf libfreetype6 armhf 2.13.3+dfsg-1 [385 kB] Get: 78 http://deb.debian.org/debian trixie/main armhf x11-common all 1:7.7+23.1 [216 kB] Get: 79 http://deb.debian.org/debian trixie/main armhf xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get: 80 http://deb.debian.org/debian trixie/main armhf xfonts-utils armhf 1:7.7+7 [84.2 kB] Get: 81 http://deb.debian.org/debian trixie/main armhf fonts-urw-base35 all 20200910-8 [10.8 MB] Get: 82 http://deb.debian.org/debian trixie/main armhf fontconfig-config armhf 2.15.0-1.1+b1 [318 kB] Get: 83 http://deb.debian.org/debian trixie/main armhf libaec0 armhf 1.1.3-1+b1 [21.9 kB] Get: 84 http://deb.debian.org/debian trixie/main armhf libblas3 armhf 3.12.0-3+b1 [111 kB] Get: 85 http://deb.debian.org/debian trixie/main armhf libfontconfig1 armhf 2.15.0-1.1+b1 [371 kB] Get: 86 http://deb.debian.org/debian trixie/main armhf libpixman-1-0 armhf 0.44.0-3 [164 kB] Get: 87 http://deb.debian.org/debian trixie/main armhf libxau6 armhf 1:1.0.11-1 [19.7 kB] Get: 88 http://deb.debian.org/debian trixie/main armhf libxdmcp6 armhf 1:1.1.5-1 [26.4 kB] Get: 89 http://deb.debian.org/debian trixie/main armhf libxcb1 armhf 1.17.0-2+b1 [140 kB] Get: 90 http://deb.debian.org/debian trixie/main armhf libx11-data all 2:1.8.10-2 [337 kB] Get: 91 http://deb.debian.org/debian trixie/main armhf libx11-6 armhf 2:1.8.10-2 [750 kB] Get: 92 http://deb.debian.org/debian trixie/main armhf libxcb-render0 armhf 1.17.0-2+b1 [114 kB] Get: 93 http://deb.debian.org/debian trixie/main armhf libxcb-shm0 armhf 1.17.0-2+b1 [105 kB] Get: 94 http://deb.debian.org/debian trixie/main armhf libxext6 armhf 2:1.3.4-1+b2 [45.2 kB] Get: 95 http://deb.debian.org/debian trixie/main armhf libxrender1 armhf 1:0.9.10-1.1+b2 [25.0 kB] Get: 96 http://deb.debian.org/debian trixie/main armhf libcairo2 armhf 1.18.2-2 [443 kB] Get: 97 http://deb.debian.org/debian trixie/main armhf libsasl2-modules-db armhf 2.1.28+dfsg1-8 [18.2 kB] Get: 98 http://deb.debian.org/debian trixie/main armhf libsasl2-2 armhf 2.1.28+dfsg1-8 [50.2 kB] Get: 99 http://deb.debian.org/debian trixie/main armhf libldap-2.5-0 armhf 2.5.18+dfsg-3+b1 [163 kB] Get: 100 http://deb.debian.org/debian trixie/main armhf libnghttp2-14 armhf 1.64.0-1 [62.9 kB] Get: 101 http://deb.debian.org/debian trixie/main armhf libnghttp3-9 armhf 1.4.0-1+b1 [55.0 kB] Get: 102 http://deb.debian.org/debian trixie/main armhf libngtcp2-16 armhf 1.6.0-1 [118 kB] Get: 103 http://deb.debian.org/debian trixie/main armhf libngtcp2-crypto-gnutls8 armhf 1.6.0-1 [17.1 kB] Get: 104 http://deb.debian.org/debian trixie/main armhf libpsl5t64 armhf 0.21.2-1.1+b1 [55.8 kB] Get: 105 http://deb.debian.org/debian trixie/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b5 [53.2 kB] Get: 106 http://deb.debian.org/debian trixie/main armhf libssh2-1t64 armhf 1.11.1-1 [227 kB] Get: 107 http://deb.debian.org/debian trixie/main armhf libcurl3t64-gnutls armhf 8.11.0-1 [310 kB] Get: 108 http://deb.debian.org/debian trixie/main armhf libcurl4t64 armhf 8.11.0-1 [303 kB] Get: 109 http://deb.debian.org/debian trixie/main armhf libdeflate0 armhf 1.22-1 [36.3 kB] Get: 110 http://deb.debian.org/debian trixie/main armhf libfribidi0 armhf 1.0.15-1 [70.0 kB] Get: 111 http://deb.debian.org/debian trixie/main armhf libgfortran5 armhf 14.2.0-8 [263 kB] Get: 112 http://deb.debian.org/debian trixie/main armhf libglib2.0-0t64 armhf 2.82.2-2 [1326 kB] Get: 113 http://deb.debian.org/debian trixie/main armhf libgraphite2-3 armhf 1.3.14-2+b1 [63.1 kB] Get: 114 http://deb.debian.org/debian trixie/main armhf libharfbuzz0b armhf 10.0.1-1 [418 kB] Get: 115 http://deb.debian.org/debian trixie/main armhf libsz2 armhf 1.1.3-1+b1 [8036 B] Get: 116 http://deb.debian.org/debian trixie/main armhf libhdf5-103-1t64 armhf 1.10.10+repack-4 [1196 kB] Get: 117 http://deb.debian.org/debian trixie/main armhf libhdf5-hl-100t64 armhf 1.10.10+repack-4 [62.3 kB] Get: 118 http://deb.debian.org/debian trixie/main armhf libhtscodecs2 armhf 1.6.1-1 [63.1 kB] Get: 119 http://deb.debian.org/debian trixie/main armhf libhts3t64 armhf 1.20+ds-2 [401 kB] Get: 120 http://deb.debian.org/debian trixie/main armhf libimagequant0 armhf 2.18.0-1+b2 [30.5 kB] Get: 121 http://deb.debian.org/debian trixie/main armhf libjbig0 armhf 2.1-6.1+b2 [27.3 kB] Get: 122 http://deb.debian.org/debian trixie/main armhf libjpeg62-turbo armhf 1:2.1.5-3+b1 [145 kB] Get: 123 http://deb.debian.org/debian trixie/main armhf libjs-jquery-isonscreen all 1.2.0-1.1 [3196 B] Get: 124 http://deb.debian.org/debian trixie/main armhf libjs-jquery-metadata all 12-4 [6532 B] Get: 125 http://deb.debian.org/debian trixie/main armhf libjs-jquery-tablesorter all 1:2.31.3+dfsg1-4 [184 kB] Get: 126 http://deb.debian.org/debian trixie/main armhf libjs-jquery-throttle-debounce all 1.1+dfsg.1-2 [12.2 kB] Get: 127 http://deb.debian.org/debian trixie/main armhf libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 128 http://deb.debian.org/debian trixie/main armhf libjs-sphinxdoc all 7.4.7-4 [158 kB] Get: 129 http://deb.debian.org/debian trixie/main armhf libjson-perl all 4.10000-1 [87.5 kB] Get: 130 http://deb.debian.org/debian trixie/main armhf liblapack3 armhf 3.12.0-3+b1 [1828 kB] Get: 131 http://deb.debian.org/debian trixie/main armhf liblcms2-2 armhf 2.16-2 [131 kB] Get: 132 http://deb.debian.org/debian trixie/main armhf liblerc4 armhf 4.0.0+ds-5 [146 kB] Get: 133 http://deb.debian.org/debian trixie/main armhf liblzf1 armhf 3.6-4+b2 [9260 B] Get: 134 http://deb.debian.org/debian trixie/main armhf libopenjp2-7 armhf 2.5.0-2+b4 [179 kB] Get: 135 http://deb.debian.org/debian trixie/main armhf libpython3.13-stdlib armhf 3.13.0-2 [1850 kB] Get: 136 http://deb.debian.org/debian trixie/main armhf libraqm0 armhf 0.10.1-1+b2 [11.8 kB] Get: 137 http://deb.debian.org/debian trixie/main armhf libsharpyuv0 armhf 1.4.0-0.1+b1 [111 kB] Get: 138 http://deb.debian.org/debian trixie/main armhf libwebp7 armhf 1.4.0-0.1+b1 [266 kB] Get: 139 http://deb.debian.org/debian trixie/main armhf libtiff6 armhf 4.5.1+git230720-5 [302 kB] Get: 140 http://deb.debian.org/debian trixie/main armhf libwebpdemux2 armhf 1.4.0-0.1+b1 [110 kB] Get: 141 http://deb.debian.org/debian trixie/main armhf libwebpmux3 armhf 1.4.0-0.1+b1 [120 kB] Get: 142 http://deb.debian.org/debian trixie/main armhf python3-astroid all 3.3.5-1 [212 kB] Get: 143 http://deb.debian.org/debian trixie/main armhf python3-isort all 5.13.2-2 [71.7 kB] Get: 144 http://deb.debian.org/debian trixie/main armhf python3-mypy-extensions all 1.0.0-1 [6064 B] Get: 145 http://deb.debian.org/debian trixie/main armhf python3-logilab-common all 2.0.0-1 [343 kB] Get: 146 http://deb.debian.org/debian trixie/main armhf python3-dill all 0.3.9-1 [83.5 kB] Get: 147 http://deb.debian.org/debian trixie/main armhf python3-mccabe all 0.7.0-1 [10.5 kB] Get: 148 http://deb.debian.org/debian trixie/main armhf python3-platformdirs all 4.3.6-1 [16.6 kB] Get: 149 http://deb.debian.org/debian trixie/main armhf python3-tomlkit all 0.13.2-1 [42.7 kB] Get: 150 http://deb.debian.org/debian trixie/main armhf pylint all 3.3.1-2 [340 kB] Get: 151 http://deb.debian.org/debian trixie/main armhf python-babel-localedata all 2.16.0-1 [5696 kB] Get: 152 http://deb.debian.org/debian trixie/main armhf python3-alabaster all 0.7.16-0.1 [27.9 kB] Get: 153 http://deb.debian.org/debian trixie/main armhf python3-all armhf 3.12.6-1 [1040 B] Get: 154 http://deb.debian.org/debian trixie/main armhf python3-babel all 2.16.0-1 [114 kB] Get: 155 http://deb.debian.org/debian trixie/main armhf python3-numpy armhf 1:1.26.4+ds-12 [3676 kB] Get: 156 http://deb.debian.org/debian trixie/main armhf python3-chardet all 5.2.0+dfsg-1 [107 kB] Get: 157 http://deb.debian.org/debian trixie/main armhf python3-pil armhf 10.4.0-1+b1 [478 kB] Get: 158 http://deb.debian.org/debian trixie/main armhf python3-cairo armhf 1.26.1-2+b1 [120 kB] Get: 159 http://deb.debian.org/debian trixie/main armhf python3-freetype all 2.5.1-1 [89.3 kB] Get: 160 http://deb.debian.org/debian trixie/main armhf python3-rlpycairo all 0.3.0-3 [9904 B] Get: 161 http://deb.debian.org/debian trixie/main armhf python3-reportlab all 4.2.5-1 [1117 kB] Get: 162 http://deb.debian.org/debian trixie/main armhf w3c-sgml-lib all 1.3-3 [273 kB] Get: 163 http://deb.debian.org/debian trixie/main armhf python3-biopython armhf 1.84+dfsg-4+b1 [1625 kB] Get: 164 http://deb.debian.org/debian trixie/main armhf python3-certifi all 2024.8.30+dfsg-1 [9576 B] Get: 165 http://deb.debian.org/debian trixie/main armhf python3-charset-normalizer armhf 3.4.0-1+b1 [126 kB] Get: 166 http://deb.debian.org/debian trixie/main armhf python3.13 armhf 3.13.0-2 [730 kB] Get: 167 http://deb.debian.org/debian trixie/main armhf python3-coverage armhf 7.6.0+dfsg1-2+b1 [176 kB] Get: 168 http://deb.debian.org/debian trixie/main armhf python3-defusedxml all 0.7.1-2 [43.3 kB] Get: 169 http://deb.debian.org/debian trixie/main armhf python3-roman all 4.2-1 [10.4 kB] Get: 170 http://deb.debian.org/debian trixie/main armhf python3-docutils all 0.21.2+dfsg-2 [403 kB] Get: 171 http://deb.debian.org/debian trixie/main armhf python3-elementpath all 4.6.0-1 [160 kB] Get: 172 http://deb.debian.org/debian trixie/main armhf python3-execnet all 2.1.1-1 [40.2 kB] Get: 173 http://deb.debian.org/debian trixie/main armhf python3-h5py-serial armhf 3.11.0-5 [900 kB] Get: 174 http://deb.debian.org/debian trixie/main armhf python3-h5py all 3.11.0-5 [14.7 kB] Get: 175 http://deb.debian.org/debian trixie/main armhf python3-idna all 3.8-2 [41.6 kB] Get: 176 http://deb.debian.org/debian trixie/main armhf python3-imagesize all 1.4.1-1 [6688 B] Get: 177 http://deb.debian.org/debian trixie/main armhf python3-iniconfig all 1.1.1-2 [6396 B] Get: 178 http://deb.debian.org/debian trixie/main armhf python3-markupsafe armhf 2.1.5-1+b2 [13.4 kB] Get: 179 http://deb.debian.org/debian trixie/main armhf python3-jinja2 all 3.1.3-1 [119 kB] Get: 180 http://deb.debian.org/debian trixie/main armhf python3-packaging all 24.2-1 [55.3 kB] Get: 181 http://deb.debian.org/debian trixie/main armhf python3-pluggy all 1.5.0-1 [26.9 kB] Get: 182 http://deb.debian.org/debian trixie/main armhf python3-pygments all 2.18.0+dfsg-1 [836 kB] Get: 183 http://deb.debian.org/debian trixie/main armhf python3-pysam armhf 0.22.1+ds-2+b2 [3755 kB] Get: 184 http://deb.debian.org/debian trixie/main armhf python3-pytest all 8.3.3-1 [249 kB] Get: 185 http://deb.debian.org/debian trixie/main armhf python3-pytest-cov all 5.0.0-1 [26.8 kB] Get: 186 http://deb.debian.org/debian trixie/main armhf python3-pytest-runner all 2.11.1-4 [8432 B] Get: 187 http://deb.debian.org/debian trixie/main armhf python3-pytest-xdist all 3.6.1-1 [44.4 kB] Get: 188 http://deb.debian.org/debian trixie/main armhf python3-urllib3 all 2.0.7-2 [111 kB] Get: 189 http://deb.debian.org/debian trixie/main armhf python3-requests all 2.32.3+dfsg-1 [71.9 kB] Get: 190 http://deb.debian.org/debian trixie/main armhf python3-snowballstemmer all 2.2.0-4 [58.0 kB] Get: 191 http://deb.debian.org/debian trixie/main armhf sphinx-common all 7.4.7-4 [731 kB] Get: 192 http://deb.debian.org/debian trixie/main armhf python3-sphinx all 7.4.7-4 [588 kB] Get: 193 http://deb.debian.org/debian trixie/main armhf python3-uritools all 4.0.3-1 [28.6 kB] Get: 194 http://deb.debian.org/debian trixie/main armhf python3-xmlschema all 3.4.3-1 [239 kB] Fetched 83.6 MB in 2s (45.5 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 ... 19690 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 libpython3.12-minimal:armhf. Preparing to unpack .../libpython3.12-minimal_3.12.7-3_armhf.deb ... Unpacking libpython3.12-minimal:armhf (3.12.7-3) ... Selecting previously unselected package libexpat1:armhf. Preparing to unpack .../libexpat1_2.6.4-1_armhf.deb ... Unpacking libexpat1:armhf (2.6.4-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../python3.12-minimal_3.12.7-3_armhf.deb ... Unpacking python3.12-minimal (3.12.7-3) ... Setting up libpython3.12-minimal:armhf (3.12.7-3) ... Setting up libexpat1:armhf (2.6.4-1) ... Setting up python3.12-minimal (3.12.7-3) ... 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 ... 20036 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.12.6-1_armhf.deb ... Unpacking python3-minimal (3.12.6-1) ... Selecting previously unselected package media-types. Preparing to unpack .../01-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../02-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... 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Setting up libarchive-zip-perl (1.68-1) ... Setting up libtirpc-common (1.3.4+ds-1.3) ... Setting up libdebhelper-perl (13.20) ... Setting up libbrotli1:armhf (1.1.0-2+b6) ... Setting up libmagic1t64:armhf (1:5.45-3+b1) ... Setting up x11-common (1:7.7+23.1) ... invoke-rc.d: could not determine current runlevel Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix. Setting up libpsl5t64:armhf (0.21.2-1.1+b1) ... Setting up libnghttp2-14:armhf (1.64.0-1) ... Setting up libdeflate0:armhf (1.22-1) ... Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up libxcb-shm0:armhf (1.17.0-2+b1) ... Setting up libcom-err2:armhf (1.47.1-1+b1) ... Setting up file (1:5.45-3+b1) ... Setting up libjs-jquery-throttle-debounce (1.1+dfsg.1-2) ... Setting up libjbig0:armhf (2.1-6.1+b2) ... Setting up libaec0:armhf (1.1.3-1+b1) ... Setting up libelf1t64:armhf (0.192-4) ... Setting up python-babel-localedata (2.16.0-1) ... Setting up libkrb5support0:armhf (1.21.3-3) ... Setting up libsasl2-modules-db:armhf (2.1.28+dfsg1-8) ... Setting up tzdata (2024b-3) ... Current default time zone: 'Etc/UTC' Local time is now: Mon Nov 25 15:28:35 UTC 2024. Universal Time is now: Mon Nov 25 15:28:35 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libpython3.13-minimal:armhf (3.13.0-2) ... Setting up libfontenc1:armhf (1:1.1.8-1+b1) ... Setting up autotools-dev (20220109.1) ... Setting up libglib2.0-0t64:armhf (2.82.2-2) ... No schema files found: doing nothing. Setting up libblas3:armhf (3.12.0-3+b1) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode Setting up libjpeg62-turbo:armhf (1:2.1.5-3+b1) ... Setting up libx11-data (2:1.8.10-2) ... Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up liblzf1:armhf (3.6-4+b2) ... Setting up xfonts-encodings (1:1.0.4-2.2) ... Setting up libfribidi0:armhf (1.0.15-1) ... Setting up libimagequant0:armhf (2.18.0-1+b2) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libpng16-16t64:armhf (1.6.44-2) ... Setting up autopoint (0.22.5-2) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up libk5crypto3:armhf (1.21.3-3) ... Setting up libsasl2-2:armhf (2.1.28+dfsg1-8) ... Setting up libgfortran5:armhf (14.2.0-8) ... Setting up autoconf (2.72-3) ... Setting up libnghttp3-9:armhf (1.4.0-1+b1) ... Setting up libwebp7:armhf (1.4.0-0.1+b1) ... Setting up dwz (0.15-1+b2) ... Setting up sensible-utils (0.0.24) ... Setting up libtiff6:armhf (4.5.1+git230720-5) ... Setting up libuchardet0:armhf (0.0.8-1+b2) ... Setting up libjson-perl (4.10000-1) ... Setting up libopenjp2-7:armhf (2.5.0-2+b4) ... Setting up python3.13-minimal (3.13.0-2) ... Setting up libx11-6:armhf (2:1.8.10-2) ... Setting up netbase (6.4) ... Setting up libngtcp2-16:armhf (1.6.0-1) ... Setting up sgml-base (1.31) ... Setting up libkrb5-3:armhf (1.21.3-3) ... Setting up libssh2-1t64:armhf (1.11.1-1) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up libjs-jquery-hotkeys (0~20130707+git2d51e3a9+dfsg-2.1) ... Setting up openssl (3.3.2-2) ... Setting up libwebpmux3:armhf (1.4.0-0.1+b1) ... Setting up readline-common (8.2-5) ... Setting up libxml2:armhf (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up libngtcp2-crypto-gnutls8:armhf (1.6.0-1) ... Setting up libsz2:armhf (1.1.3-1+b1) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up liblapack3:armhf (3.12.0-3+b1) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode Setting up gettext (0.22.5-2) ... Setting up libxrender1:armhf (1:0.9.10-1.1+b2) ... Setting up libtool (2.4.7-8) ... Setting up fontconfig-config (2.15.0-1.1+b1) ... Setting up libwebpdemux2:armhf (1.4.0-0.1+b1) ... Setting up libxext6:armhf (2:1.3.4-1+b2) ... Setting up libldap-2.5-0:armhf (2.5.18+dfsg-3+b1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 146 added, 0 removed; done. Setting up libfreetype6:armhf (2.13.3+dfsg-1) ... Setting up libjs-jquery-metadata (12-4) ... Setting up libjs-jquery-isonscreen (1.2.0-1.1) ... Setting up libgssapi-krb5-2:armhf (1.21.3-3) ... Setting up libjs-sphinxdoc (7.4.7-4) ... Setting up libreadline8t64:armhf (8.2-5) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up libjs-jquery-tablesorter (1:2.31.3+dfsg1-4) ... Setting up groff-base (1.23.0-5) ... Setting up xml-core (0.19) ... Setting up libharfbuzz0b:armhf (10.0.1-1) ... Setting up libfontconfig1:armhf (2.15.0-1.1+b1) ... Setting up libpython3.13-stdlib:armhf (3.13.0-2) ... Setting up libcurl4t64:armhf (8.11.0-1) ... Setting up libtirpc3t64:armhf (1.3.4+ds-1.3+b1) ... Setting up python3.13 (3.13.0-2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libcurl3t64-gnutls:armhf (8.11.0-1) ... Setting up xfonts-utils (1:7.7+7) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libcairo2:armhf (1.18.2-2) ... Setting up libraqm0:armhf (0.10.1-1+b2) ... Setting up sphinx-common (7.4.7-4) ... Setting up libnsl2:armhf (1.3.0-3+b3) ... Setting up libhts3t64:armhf (1.20+ds-2) ... Setting up libhdf5-103-1t64:armhf (1.10.10+repack-4) ... Setting up libhdf5-hl-100t64:armhf (1.10.10+repack-4) ... Setting up libpython3.12-stdlib:armhf (3.12.7-3) ... Setting up python3.12 (3.12.7-3) ... Setting up debhelper (13.20) ... Setting up fonts-urw-base35 (20200910-8) ... Setting up libpython3-stdlib:armhf (3.12.6-1) ... Setting up python3 (3.12.6-1) ... Setting up python3-zipp (3.21.0-1) ... Setting up python3-freetype (2.5.1-1) ... Setting up python3-autocommand (2.2.2-3) ... Setting up python3-markupsafe (2.1.5-1+b2) ... Setting up python3-platformdirs (4.3.6-1) ... Setting up python3-pil:armhf (10.4.0-1+b1) ... Setting up python3-roman (4.2-1) ... Setting up python3-jinja2 (3.1.3-1) ... Setting up python3-packaging (24.2-1) ... Setting up python3-certifi (2024.8.30+dfsg-1) ... Setting up python3-snowballstemmer (2.2.0-4) ... Setting up python3-dill (0.3.9-1) ... Setting up python3-idna (3.8-2) ... Setting up python3-elementpath (4.6.0-1) ... Setting up python3-typing-extensions (4.12.2-2) ... Setting up python3-xmlschema (3.4.3-1) ... Setting up python3-isort (5.13.2-2) ... Setting up python3-urllib3 (2.0.7-2) ... Setting up python3-pluggy (1.5.0-1) ... Setting up python3-mccabe (0.7.0-1) ... Setting up python3-execnet (2.1.1-1) ... Setting up python3-tomlkit (0.13.2-1) ... Setting up python3-imagesize (1.4.1-1) ... Setting up python3-uritools (4.0.3-1) ... Setting up python3-more-itertools (10.5.0-1) ... Setting up python3-iniconfig (1.1.1-2) ... Setting up python3-pysam (0.22.1+ds-2+b2) ... Setting up python3-cairo (1.26.1-2+b1) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up python3-jaraco.context (6.0.0-1) ... Setting up python3-defusedxml (0.7.1-2) ... Setting up python3-charset-normalizer (3.4.0-1+b1) ... Setting up python3-pytest (8.3.3-1) ... Setting up python3-alabaster (0.7.16-0.1) ... Setting up python3-mypy-extensions (1.0.0-1) ... Setting up python3-typeguard (4.4.1-1) ... Setting up python3-all (3.12.6-1) ... Setting up python3-coverage (7.6.0+dfsg1-2+b1) ... Setting up python3-pytest-cov (5.0.0-1) ... Setting up python3-inflect (7.3.1-2) ... Setting up python3-rlpycairo (0.3.0-3) ... Setting up python3-pkg-resources (74.1.2-2) ... Setting up python3-setuptools (74.1.2-2) ... Setting up python3-pytest-xdist (3.6.1-1) ... Setting up python3-logilab-common (2.0.0-1) ... Setting up python3-babel (2.16.0-1) ... update-alternatives: using /usr/bin/pybabel-python3 to provide /usr/bin/pybabel (pybabel) in auto mode Setting up python3-pygments (2.18.0+dfsg-1) ... Setting up python3-chardet (5.2.0+dfsg-1) ... Setting up python3-requests (2.32.3+dfsg-1) ... Setting up python3-numpy (1:1.26.4+ds-12) ... Setting up python3-reportlab (4.2.5-1) ... Setting up python3-astroid (3.3.5-1) ... Setting up python3-pytest-runner (2.11.1-4) ... Setting up pylint (3.3.1-2) ... Setting up dh-python (6.20241024) ... Setting up python3-h5py-serial (3.11.0-5) ... Setting up python3-h5py (3.11.0-5) ... Processing triggers for libc-bin (2.40-3) ... Processing triggers for sgml-base (1.31) ... Setting up w3c-sgml-lib (1.3-3) ... Setting up docutils-common (0.21.2+dfsg-2) ... Setting up python3-biopython (1.84+dfsg-4+b1) ... Processing triggers for sgml-base (1.31) ... Setting up python3-docutils (0.21.2+dfsg-2) ... Setting up python3-sphinx (7.4.7-4) ... 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-9_source.changes dpkg-buildpackage: info: source package python-pbcore dpkg-buildpackage: info: source version 2.1.2+dfsg-9 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf debian/rules clean dh clean --buildsystem=pybuild dh_auto_clean -O--buildsystem=pybuild I: pybuild base:311: python3.12 setup.py clean /usr/lib/python3/dist-packages/setuptools/dist.py:452: 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/dist.py:261: UserWarning: Unknown distribution option: 'tests_require' warnings.warn(msg) 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-armv7l' does not exist -- can't clean it 'build/scripts-3.12' 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:311: python3.12 setup.py config /usr/lib/python3/dist-packages/setuptools/dist.py:452: 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/dist.py:261: UserWarning: Unknown distribution option: 'tests_require' warnings.warn(msg) 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:311: /usr/bin/python3 setup.py build /usr/lib/python3/dist-packages/setuptools/dist.py:452: 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/dist.py:261: UserWarning: Unknown distribution option: 'tests_require' warnings.warn(msg) running build running build_py creating /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 copying pbcore/__init__.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/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/FastaIO.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/opener.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 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/_utils.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 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/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/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 copying pbcore/util/__init__.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 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/chemistry.py -> /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 creating /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/_BamSupport.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/_AlignmentMixin.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/BlasrIO.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 creating /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/DataSetMembers.py -> /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/DataSetErrors.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/DataSetMetaTypes.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/DataSetWriter.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/utils.py -> /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build/pbcore/io/dataset 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 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:218: _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 PYTHONPATH=/build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_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 v7.4.7 loading translations [en]... done making output directory... done Converting `source_suffix = '.rst'` to `source_suffix = {'.rst': 'restructuredtext'}`. 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 'main_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 NameResolutionError(": Failed to resolve 'docs.python.org' ([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_3.12_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 copying assets: 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 dh_auto_test I: pybuild base:311: cd /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build; python3.12 -m pytest tests ============================= test session starts ============================== platform linux -- Python 3.12.7, pytest-8.3.3, pluggy-1.5.0 -- /usr/bin/python3.12 cachedir: .pytest_cache rootdir: /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build configfile: pytest.ini plugins: xdist-3.6.1, typeguard-4.4.1, cov-5.0.0 created: 4/4 workers 4 workers [140 items] scheduling tests via LoadScopeScheduling tests/test_pbdataset_split.py::TestDataSetSplit::test_split tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testBasicOperations tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testBasicOperations tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test__init__ [gw3] [ 0%] PASSED tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test__init__ tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test__str__ [gw3] [ 1%] PASSED tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test__str__ tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test_fromString [gw3] [ 2%] PASSED tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test_fromString tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test_reverse_complement1 [gw1] [ 2%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testBasicOperations tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testStrandOrientation [gw1] [ 3%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testStrandOrientation [gw3] [ 4%] 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_FastaIO.py::TestFastaRecord::test_len [gw3] [ 5%] PASSED tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test_len tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test_eq tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testReadName [gw1] [ 6%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testReadName tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testAlignedRead [gw3] [ 7%] PASSED tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test_eq [gw1] [ 7%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testAlignedRead [gw2] [ 8%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testBasicOperations tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testStrandOrientation [gw2] [ 9%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testStrandOrientation tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testReadName [gw2] [ 10%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testReadName tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testAlignedRead tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testUnalignedRead [gw1] [ 10%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testUnalignedRead [gw2] [ 11%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testAlignedRead tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testUnalignedRead [gw2] [ 12%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testUnalignedRead tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testAlignedReference tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testAlignedReference [gw1] [ 12%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testAlignedReference tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testUnalignedReference [gw1] [ 13%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testUnalignedReference tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testDeletionQV [gw1] [ 14%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testDeletionQV tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testTranscript [gw1] [ 15%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testTranscript [gw2] [ 15%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testAlignedReference tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testUnalignedReference [gw2] [ 16%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testUnalignedReference tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testDeletionQV tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testClippedAlignments [gw1] [ 17%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testClippedAlignments tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testReadsInRange tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test_not_equal [gw2] [ 17%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testDeletionQV tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testTranscript [gw3] [ 18%] PASSED tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test_not_equal [gw2] [ 19%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testTranscript tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testClippedAlignments tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test__init__ [gw3] [ 20%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test__init__ tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test__str__ [gw2] [ 20%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testClippedAlignments tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testReadsInRange [gw3] [ 21%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test__str__ tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test_fromString [gw3] [ 22%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test_fromString tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test_reverse_complement1 [gw3] [ 22%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test_reverse_complement1 tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test_reverse_complement2 [gw3] [ 23%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test_reverse_complement2 tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test_len [gw3] [ 24%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test_len tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test_eq [gw3] [ 25%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test_eq tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test_not_equal [gw3] [ 25%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test_not_equal tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::testIteration [gw3] [ 26%] PASSED tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::testIteration tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::testAccessByName [gw3] [ 27%] PASSED tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::testAccessByName tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::testAccessById [gw3] [ 27%] PASSED tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::testAccessById tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::testAccessByPosition [gw3] [ 28%] PASSED tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::testAccessByPosition tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::testSlice [gw3] [ 29%] PASSED tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::testSlice tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::test_dosLineEndingsFasta [gw3] [ 30%] PASSED tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::test_dosLineEndingsFasta tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::test_readWeirdFastaIndex [gw3] [ 30%] PASSED tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::test_readWeirdFastaIndex tests/test_pbcore_util_sequences.py::TestReverseComplement::test_reverse [gw3] [ 31%] PASSED tests/test_pbcore_util_sequences.py::TestReverseComplement::test_reverse tests/test_pbcore_util_sequences.py::TestReverseComplement::test_complement [gw3] [ 32%] PASSED tests/test_pbcore_util_sequences.py::TestReverseComplement::test_complement tests/test_pbcore_util_sequences.py::TestReverseComplement::test_reverseComplement [gw3] [ 32%] PASSED tests/test_pbcore_util_sequences.py::TestReverseComplement::test_reverseComplement tests/test_pbcore_util_sequences.py::TestReverseComplement::test_iupac [gw3] [ 33%] PASSED tests/test_pbcore_util_sequences.py::TestReverseComplement::test_iupac tests/test_pbcore_util_sequences.py::TestReverseComplement::test_complement_error [gw3] [ 34%] PASSED tests/test_pbcore_util_sequences.py::TestReverseComplement::test_complement_error tests/test_pbcore_util_sequences.py::TestReverseComplement::test_reverse_complement_error [gw3] [ 35%] PASSED tests/test_pbcore_util_sequences.py::TestReverseComplement::test_reverse_complement_error tests/test_pbcore_io_GffIO.py::TestGff3Record::test_str [gw3] [ 35%] PASSED tests/test_pbcore_io_GffIO.py::TestGff3Record::test_str tests/test_pbcore_io_GffIO.py::TestGff3Record::test_modification [gw3] [ 36%] PASSED tests/test_pbcore_io_GffIO.py::TestGff3Record::test_modification tests/test_pbcore_io_GffIO.py::TestGff3Record::test_fromString [gw3] [ 37%] PASSED tests/test_pbcore_io_GffIO.py::TestGff3Record::test_fromString tests/test_pbcore_io_GffIO.py::TestGff3Record::test_get [gw3] [ 37%] PASSED tests/test_pbcore_io_GffIO.py::TestGff3Record::test_get tests/test_pbcore_io_GffIO.py::TestGffSorting::test_merge_gffs [gw3] [ 38%] PASSED tests/test_pbcore_io_GffIO.py::TestGffSorting::test_merge_gffs tests/test_pbcore_io_GffIO.py::TestGffSorting::test_merge_gffs_sorted [gw3] [ 39%] PASSED tests/test_pbcore_io_GffIO.py::TestGffSorting::test_merge_gffs_sorted tests/test_pbcore_io_GffIO.py::TestGffSorting::test_sort_gff [gw3] [ 40%] PASSED tests/test_pbcore_io_GffIO.py::TestGffSorting::test_sort_gff tests/test_pbcore_io_GffIO.py::TestGffSorting::test_empty_file [gw3] [ 40%] PASSED tests/test_pbcore_io_GffIO.py::TestGffSorting::test_empty_file tests/test_pbdataset_utils.py::TestDataSetUtils::test_get_dataset_uuid [gw3] [ 41%] PASSED tests/test_pbdataset_utils.py::TestDataSetUtils::test_get_dataset_uuid tests/test_pbdataset_utils.py::TestDataSetUtils::test_get_dataset_metatype [gw3] [ 42%] PASSED tests/test_pbdataset_utils.py::TestDataSetUtils::test_get_dataset_metatype tests/test_pbdataset_utils.py::TestDataSetUtils::test_dsIdToSuffix [gw3] [ 42%] PASSED tests/test_pbdataset_utils.py::TestDataSetUtils::test_dsIdToSuffix tests/test_pbdataset_utils.py::TestDataSetUtils::test_divideKeys_keysToRanges [gw3] [ 43%] PASSED tests/test_pbdataset_utils.py::TestDataSetUtils::test_divideKeys_keysToRanges tests/test_pbindex.py::TestPbIndex::test_pbindex_bam_consistency [gw3] [ 44%] PASSED tests/test_pbindex.py::TestPbIndex::test_pbindex_bam_consistency tests/test_pbindex.py::TestPbIndex::test_pbindex_streaming [gw3] [ 45%] PASSED tests/test_pbindex.py::TestPbIndex::test_pbindex_streaming tests/test_pbindex.py::TestPbIndex::test_pbindex_streaming_entire [gw3] [ 45%] PASSED tests/test_pbindex.py::TestPbIndex::test_pbindex_streaming_entire tests/test_pbindex.py::TestPbIndex::test_pbindex_with_zmw_index [gw3] [ 46%] PASSED tests/test_pbindex.py::TestPbIndex::test_pbindex_with_zmw_index tests/test_pbcore_io_FastqIO.py::TestFastqWriter::test_writeFastq1 [gw3] [ 47%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqWriter::test_writeFastq1 tests/test_pbcore_io_FastqIO.py::TestFastqWriter::test_writeFastq2 [gw3] [ 47%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqWriter::test_writeFastq2 tests/test_pbcore_io_FastqIO.py::TestFastqWriter::test_writeFastq3 [gw3] [ 48%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqWriter::test_writeFastq3 tests/test_pbcore_io_FofnIO.py::test_simple [gw3] [ 49%] PASSED tests/test_pbcore_io_FofnIO.py::test_simple tests/test_pbcore_io_FofnIO.py::test_empty_lines [gw3] [ 50%] PASSED tests/test_pbcore_io_FofnIO.py::test_empty_lines tests/test_pbcore_io_FofnIO.py::test_absolutifying [gw3] [ 50%] PASSED tests/test_pbcore_io_FofnIO.py::test_absolutifying tests/test_pbcore_io_AlnFileReaders.py::TestCCSBam::testBasicOperations [gw3] [ 51%] SKIPPED tests/test_pbcore_io_AlnFileReaders.py::TestCCSBam::testBasicOperations tests/test_pbcore_io_AlnFileReaders.py::TestCCSBam::testQStartEndUnavailable [gw3] [ 52%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestCCSBam::testQStartEndUnavailable tests/test_pbcore_io_AlnFileReaders.py::TestMultipleReadGroups::test_retrieve_read_group_properties [gw3] [ 52%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestMultipleReadGroups::test_retrieve_read_group_properties tests/test_pbcore_io_AlnFileReaders.py::TestMultipleReadGroups::test_sample_names [gw3] [ 53%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestMultipleReadGroups::test_sample_names tests/test_pbcore_io_BlasrIO.py::test_m4 [gw3] [ 54%] PASSED tests/test_pbcore_io_BlasrIO.py::test_m4 tests/test_pbcore_io_BlasrIO.py::test_m5 [gw3] [ 55%] PASSED tests/test_pbcore_io_BlasrIO.py::test_m5 tests/test_pbcore_io_FastaIO.py::TestFastaReader::test_readFasta [gw3] [ 55%] PASSED tests/test_pbcore_io_FastaIO.py::TestFastaReader::test_readFasta tests/test_pbcore_io_FastaIO.py::TestFastaReader::test_dosLineEndingsFasta [gw3] [ 56%] PASSED tests/test_pbcore_io_FastaIO.py::TestFastaReader::test_dosLineEndingsFasta tests/test_pbcore_io_FastaIO.py::TestFastaWriter::test_writeFasta1 [gw3] [ 57%] PASSED tests/test_pbcore_io_FastaIO.py::TestFastaWriter::test_writeFasta1 tests/test_pbcore_io_FastaIO.py::TestFastaWriter::test_writeFasta2 [gw3] [ 57%] PASSED tests/test_pbcore_io_FastaIO.py::TestFastaWriter::test_writeFasta2 tests/test_pbcore_io_FastqIO.py::TestQvConversion::testAsciiFromQvs [gw3] [ 58%] PASSED tests/test_pbcore_io_FastqIO.py::TestQvConversion::testAsciiFromQvs tests/test_pbcore_io_FastqIO.py::TestQvConversion::testQvsFromAscii [gw3] [ 59%] PASSED tests/test_pbcore_io_FastqIO.py::TestQvConversion::testQvsFromAscii tests/test_pbcore_io_FastqIO.py::TestFastqReader::test_readFastq1 [gw2] [ 60%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testReadsInRange tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testReadGroupTable [gw3] [ 60%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqReader::test_readFastq1 tests/test_pbcore_io_FastqIO.py::TestFastqReader::test_readFastq2 [gw3] [ 61%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqReader::test_readFastq2 tests/test_pbcore_io_GffIO.py::TestGffReader::test_headers [gw2] [ 62%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testReadGroupTable [gw3] [ 62%] PASSED tests/test_pbcore_io_GffIO.py::TestGffReader::test_headers tests/test_pbcore_io_GffIO.py::TestGffReader::test__iter__ [gw1] [ 63%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testReadsInRange tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testSequencingChemistry [gw3] [ 64%] PASSED tests/test_pbcore_io_GffIO.py::TestGffReader::test__iter__ [gw2] [ 65%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testSequencingChemistry tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testReadGroupTable [gw1] [ 65%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testReadGroupTable tests/test_pbcore_io_GffIO.py::TestGffWriter::test_writeHeader [gw3] [ 66%] PASSED tests/test_pbcore_io_GffIO.py::TestGffWriter::test_writeHeader tests/test_pbcore_io_GffIO.py::TestGffWriter::test_writeRecord [gw3] [ 67%] PASSED tests/test_pbcore_io_GffIO.py::TestGffWriter::test_writeRecord tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testSequencingChemistry [gw1] [ 67%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testSequencingChemistry tests/test_pbcore_io_unaligned_bam.py::TestUnalignedBam::testInvalidOperations tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testMapQV [gw2] [ 68%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testMapQV tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testHoleNumbers tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testSpecVersion [gw3] [ 69%] PASSED tests/test_pbcore_io_unaligned_bam.py::TestUnalignedBam::testInvalidOperations [gw1] [ 70%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testSpecVersion tests/test_pbcore_io_unaligned_bam.py::TestUnalignedBam::testIpd tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testReadScore [gw3] [ 70%] PASSED tests/test_pbcore_io_unaligned_bam.py::TestUnalignedBam::testIpd [gw1] [ 71%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testReadScore tests/test_pbcore_util.py::TestStatistics::test_accuracy_as_phred_qv [gw3] [ 72%] PASSED tests/test_pbcore_util.py::TestStatistics::test_accuracy_as_phred_qv tests/test_pbcore_util.py::TestStatistics::test_phred_qv_as_accuracy tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::test_sample_name_default [gw1] [ 72%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::test_sample_name_default [gw3] [ 73%] PASSED tests/test_pbcore_util.py::TestStatistics::test_phred_qv_as_accuracy tests/test_dataset_run_split.py::test tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::test_library_name_default [gw3] [ 74%] SKIPPED tests/test_dataset_run_split.py::test tests/test_pbcore_io_AlnFileReaders.py::TestTranscriptBam::test_transcript_set_support [gw3] [ 75%] SKIPPED tests/test_pbcore_io_AlnFileReaders.py::TestTranscriptBam::test_transcript_set_support [gw1] [ 75%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::test_library_name_default tests/test_pbcore_io_AlnFileReaders.py::TestEmptyBam::test_empty_bam_reads_in_range tests/test_pbcore_extract_bam_sequence.py::TestCase::test_reverse_complement [gw3] [ 76%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestEmptyBam::test_empty_bam_reads_in_range tests/test_pbcore_io_AlnFileReaders.py::TestUpdatedChemistryMapping::test_load_updated_mapping [gw1] [ 77%] PASSED tests/test_pbcore_extract_bam_sequence.py::TestCase::test_reverse_complement [gw3] [ 77%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestUpdatedChemistryMapping::test_load_updated_mapping [gw2] [ 78%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testHoleNumbers tests/test_pbcore_io_AlnFileReaders.py::TestBarcodedBam::test_read_lima_demultiplexed_bam tests/test_pbcore_io_AlnFileReaders.py::TestMissingHeaderM5::test_retrieve_read_group_properties [gw3] [ 79%] SKIPPED tests/test_pbcore_io_AlnFileReaders.py::TestBarcodedBam::test_read_lima_demultiplexed_bam tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testErrorCounts [gw2] [ 80%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testErrorCounts tests/test_pbcore_io_lossless_bam.py::TestCase::test_1 [gw3] [ 80%] SKIPPED tests/test_pbcore_io_lossless_bam.py::TestCase::test_1 tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testReadsByName [gw1] [ 81%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestMissingHeaderM5::test_retrieve_read_group_properties tests/test_pbcore_io_VcfIO.py::TestVcfSorting::test_merge_vcfs_sorted [gw1] [ 82%] PASSED tests/test_pbcore_io_VcfIO.py::TestVcfSorting::test_merge_vcfs_sorted [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 3.12.7 /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 3.12.7 /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 3.12.7 /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 3.12.7 /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 3.12.7 /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 pbcore/__init__.py:1 pbcore/__init__.py:1 pbcore/__init__.py:1 pbcore/__init__.py:1 /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build/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:3154 ../../../../../../usr/lib/python3/dist-packages/pkg_resources/__init__.py:3154 ../../../../../../usr/lib/python3/dist-packages/pkg_resources/__init__.py:3154 ../../../../../../usr/lib/python3/dist-packages/pkg_resources/__init__.py:3154 ../../../../../../usr/lib/python3/dist-packages/pkg_resources/__init__.py:3154 /usr/lib/python3/dist-packages/pkg_resources/__init__.py:3154: 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_AlnFileReaders.py: 28 warnings /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build/pbcore/io/align/BamAlignment.py:583: DeprecationWarning: tostring() is deprecated. Use tobytes() instead. return r.tostring().decode("ascii") tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testBasicOperations tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::test_alignment_identity tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::test_alignment_identity_unindexed /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build/pbcore/io/align/PacBioBamIndex.py:159: DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from your array before performing this operation. (Deprecated NumPy 1.25.) ntId = int(peek("u4", 1)) tests/test_pbcore_io_AlnFileReaders.py: 20 warnings /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build/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/.pybuild/cpython3_3.12_pbcore/build/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/.pybuild/cpython3_3.12_pbcore/build/pbcore/io/align/BamAlignment.py:356: DeprecationWarning: tostring() is deprecated. Use tobytes() instead. return _gusfieldTrans[uc].tostring().decode("ascii") tests/test_pbcore_io_FastqIO.py: 11 warnings /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build/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/.pybuild/cpython3_3.12_pbcore/build/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_pbdataset_split.py::TestDataSetSplit::test_subreadset_split_metadata_element_name /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build/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/.pybuild/cpython3_3.12_pbcore/build/nosetests.xml - ---------- coverage: platform linux, python 3.12.7-final-0 ----------- Coverage XML written to file coverage.xml ============================= slowest 20 durations ============================= 1.53s call tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testReadsInRange 1.37s call tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testReadsInRange 0.81s call tests/test_pbdataset_split.py::TestDataSetSplit::test_split_zmws_targetsize 0.51s call tests/test_pbdataset_split.py::TestDataSetSplit::test_split_zmws 0.46s call tests/test_pbdataset_split.py::TestDataSetSplit::test_contigset_split 0.30s call tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::test_alignment_identity_unindexed 0.20s setup tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testBasicOperations 0.19s call tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::test_alignment_identity 0.17s call tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testHoleNumbers 0.13s call tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::test_dosLineEndingsFasta 0.13s setup tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testBasicOperations 0.12s call tests/test_pbindex.py::TestPbIndex::test_pbindex_bam_consistency 0.12s call tests/test_pbdataset_split.py::TestDataSetSplit::test_split 0.05s call tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testReadsByName 0.05s call tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testDeletionQV 0.04s call tests/test_pbdataset_utils.py::TestDataSetUtils::test_get_dataset_uuid 0.04s call tests/test_pbdataset_split.py::TestDataSetSplit::test_subreadset_split_metadata_element_name 0.03s call tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testDeletionQV 0.03s call tests/test_pbcore_io_FastaIO.py::TestFastaReader::test_dosLineEndingsFasta 0.03s 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, 278 warnings in 31.89s =========== E: pybuild pybuild:389: test: plugin distutils failed with: exit code=1: cd /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.12_pbcore/build; python3.12 -m pytest tests dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p 3.12 returned exit code 13 make[1]: *** [debian/rules:39: override_dh_auto_test] Error 25 make[1]: Leaving directory '/build/reproducible-path/python-pbcore-2.1.2+dfsg' make: *** [debian/rules:13: binary] Error 2 dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2 I: copying local configuration E: Failed autobuilding of package I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/4322 and its subdirectories Mon Nov 25 15:33:41 UTC 2024 W: No second build log, what happened?