0s autopkgtest [12:28:08]: starting date and time: 2025-02-19 12:28:08+0000 0s autopkgtest [12:28:08]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [12:28:08]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.fgfwmsbx/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:sphinx --apt-upgrade python-pybedtools --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=sphinx/8.1.3-5 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@lcy02-1.secgroup --name adt-plucky-amd64-python-pybedtools-20250219-122808-juju-7f2275-prod-proposed-migration-environment-2-01b824c0-75da-40fb-8fdb-2fc0f98858f2 --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 40s autopkgtest [12:28:48]: testbed dpkg architecture: amd64 40s autopkgtest [12:28:48]: testbed apt version: 2.9.29 40s autopkgtest [12:28:48]: @@@@@@@@@@@@@@@@@@@@ test bed setup 40s autopkgtest [12:28:48]: testbed release detected to be: None 40s autopkgtest [12:28:48]: updating testbed package index (apt update) 41s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [110 kB] 41s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 41s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 41s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 41s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [3120 B] 41s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [76.1 kB] 41s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [750 kB] 41s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [13.9 kB] 41s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [101 kB] 41s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [81.8 kB] 41s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/restricted i386 Packages [2412 B] 41s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [7984 B] 41s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [265 kB] 41s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [697 kB] 41s Get:15 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [11.5 kB] 41s Get:16 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [3128 B] 41s Fetched 2124 kB in 0s (5728 kB/s) 42s Reading package lists... 43s Reading package lists... 43s Building dependency tree... 43s Reading state information... 43s Calculating upgrade... 44s The following NEW packages will be installed: 44s libapt-pkg7.0 44s The following packages will be upgraded: 44s apt apt-utils iproute2 liblsof0 libp11-kit0 lsof rsyslog 44s 7 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 44s Need to get 5234 kB of archives. 44s After this operation, 4074 kB of additional disk space will be used. 44s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 libapt-pkg7.0 amd64 2.9.30 [1131 kB] 44s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 apt amd64 2.9.30 [1434 kB] 44s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 apt-utils amd64 2.9.30 [222 kB] 44s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 iproute2 amd64 6.13.0-1ubuntu1 [1277 kB] 44s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 libp11-kit0 amd64 0.25.5-2ubuntu3 [311 kB] 44s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 rsyslog amd64 8.2412.0-2ubuntu1 [555 kB] 44s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 lsof amd64 4.99.4+dfsg-1 [245 kB] 44s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 liblsof0 amd64 4.99.4+dfsg-1 [59.6 kB] 44s Preconfiguring packages ... 44s Fetched 5234 kB in 0s (26.7 MB/s) 44s Selecting previously unselected package libapt-pkg7.0:amd64. 45s (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 ... 108925 files and directories currently installed.) 45s Preparing to unpack .../libapt-pkg7.0_2.9.30_amd64.deb ... 45s Unpacking libapt-pkg7.0:amd64 (2.9.30) ... 45s Setting up libapt-pkg7.0:amd64 (2.9.30) ... 45s (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 ... 108974 files and directories currently installed.) 45s Preparing to unpack .../archives/apt_2.9.30_amd64.deb ... 45s Unpacking apt (2.9.30) over (2.9.29) ... 45s Setting up apt (2.9.30) ... 45s (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 ... 108974 files and directories currently installed.) 45s Preparing to unpack .../0-apt-utils_2.9.30_amd64.deb ... 45s Unpacking apt-utils (2.9.30) over (2.9.29) ... 46s Preparing to unpack .../1-iproute2_6.13.0-1ubuntu1_amd64.deb ... 46s Unpacking iproute2 (6.13.0-1ubuntu1) over (6.10.0-2ubuntu1) ... 46s Preparing to unpack .../2-libp11-kit0_0.25.5-2ubuntu3_amd64.deb ... 46s Unpacking libp11-kit0:amd64 (0.25.5-2ubuntu3) over (0.25.5-2ubuntu2) ... 46s Preparing to unpack .../3-rsyslog_8.2412.0-2ubuntu1_amd64.deb ... 46s Unpacking rsyslog (8.2412.0-2ubuntu1) over (8.2412.0-1ubuntu1) ... 46s Preparing to unpack .../4-lsof_4.99.4+dfsg-1_amd64.deb ... 46s Unpacking lsof (4.99.4+dfsg-1) over (4.99.3+dfsg-2) ... 46s Preparing to unpack .../5-liblsof0_4.99.4+dfsg-1_amd64.deb ... 46s Unpacking liblsof0 (4.99.4+dfsg-1) over (4.99.3+dfsg-2) ... 46s Setting up apt-utils (2.9.30) ... 46s Setting up liblsof0 (4.99.4+dfsg-1) ... 46s Setting up iproute2 (6.13.0-1ubuntu1) ... 46s Setting up rsyslog (8.2412.0-2ubuntu1) ... 46s info: The user `syslog' is already a member of `adm'. 47s Setting up libp11-kit0:amd64 (0.25.5-2ubuntu3) ... 47s Setting up lsof (4.99.4+dfsg-1) ... 47s Processing triggers for man-db (2.13.0-1) ... 49s Processing triggers for libc-bin (2.40-4ubuntu1) ... 50s Reading package lists... 51s Building dependency tree... 51s Reading state information... 51s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 51s autopkgtest [12:28:59]: upgrading testbed (apt dist-upgrade and autopurge) 51s Reading package lists... 52s Building dependency tree... 52s Reading state information... 52s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 52s Starting 2 pkgProblemResolver with broken count: 0 52s Done 53s Entering ResolveByKeep 53s 53s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 54s Reading package lists... 54s Building dependency tree... 54s Reading state information... 54s Starting pkgProblemResolver with broken count: 0 54s Starting 2 pkgProblemResolver with broken count: 0 54s Done 55s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 55s autopkgtest [12:29:03]: rebooting testbed after setup commands that affected boot 59s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 70s autopkgtest [12:29:18]: testbed running kernel: Linux 6.12.0-15-generic #15-Ubuntu SMP PREEMPT_DYNAMIC Tue Feb 4 16:02:16 UTC 2025 71s autopkgtest [12:29:19]: @@@@@@@@@@@@@@@@@@@@ apt-source python-pybedtools 73s Get:1 http://ftpmaster.internal/ubuntu plucky/universe python-pybedtools 0.10.0-4 (dsc) [2623 B] 73s Get:2 http://ftpmaster.internal/ubuntu plucky/universe python-pybedtools 0.10.0-4 (tar) [12.0 MB] 73s Get:3 http://ftpmaster.internal/ubuntu plucky/universe python-pybedtools 0.10.0-4 (diff) [33.5 kB] 73s gpgv: Signature made Fri Dec 27 01:57:35 2024 UTC 73s gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 73s gpgv: issuer "crusoe@debian.org" 73s gpgv: Can't check signature: No public key 73s dpkg-source: warning: cannot verify inline signature for ./python-pybedtools_0.10.0-4.dsc: no acceptable signature found 74s autopkgtest [12:29:22]: testing package python-pybedtools version 0.10.0-4 74s autopkgtest [12:29:22]: build not needed 75s autopkgtest [12:29:23]: test pybuild-autopkgtest: preparing testbed 75s Reading package lists... 75s Building dependency tree... 75s Reading state information... 76s Starting pkgProblemResolver with broken count: 0 76s Starting 2 pkgProblemResolver with broken count: 0 76s Done 77s The following NEW packages will be installed: 77s autoconf automake autopoint autotools-dev bedtools blt build-essential cpp 77s cpp-14 cpp-14-x86-64-linux-gnu cpp-x86-64-linux-gnu cython3 debhelper 77s debugedit dh-autoreconf dh-python dh-strip-nondeterminism docutils-common 77s dwz fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono 77s fonts-lyx g++ g++-14 g++-14-x86-64-linux-gnu g++-x86-64-linux-gnu gcc gcc-14 77s gcc-14-x86-64-linux-gnu gcc-x86-64-linux-gnu gettext intltool-debian 77s libarchive-zip-perl libasan8 libblas3 libcairo2 libcc1-0 libdatrie1 77s libdebhelper-perl libdeflate0 libexpat1-dev libfile-stripnondeterminism-perl 77s libfontconfig1 libgcc-14-dev libgfortran5 libgomp1 libgraphite2-3 77s libharfbuzz0b libhts3t64 libhtscodecs2 libhwasan0 libice6 libimagequant0 77s libisl23 libitm1 libjbig0 libjpeg-turbo8 libjpeg8 libjs-jquery 77s libjs-jquery-ui libjs-sphinxdoc libjs-underscore libjson-perl liblapack3 77s liblbfgsb0 liblcms2-2 liblerc4 liblsan0 libmpc3 libopenjp2-7 libpango-1.0-0 77s libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper2 libpixman-1-0 77s libpython3-all-dev libpython3-dev libpython3.12-dev libpython3.13-dev 77s libqhull-r8.0 libquadmath0 libraqm0 libsharpyuv0 libsm6 libstdc++-14-dev 77s libtcl8.6 libthai-data libthai0 libtiff6 libtk8.6 libtool libtsan2 libubsan1 77s libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 libxft2 77s libxrender1 libxslt1.1 libxss1 libxt6t64 m4 po-debconf pybedtools-bin 77s pybuild-plugin-autopkgtest pybuild-plugin-pyproject python-matplotlib-data 77s python-pybedtools-doc python3-alabaster python3-all python3-all-dev 77s python3-brotli python3-build python3-contourpy python3-cycler 77s python3-dateutil python3-decorator python3-defusedxml python3-dev 77s python3-docutils python3-fonttools python3-fs python3-imagesize 77s python3-iniconfig python3-installer python3-kiwisolver python3-lxml 77s python3-lz4 python3-matplotlib python3-mpmath python3-numpy python3-numpydoc 77s python3-packaging python3-pandas python3-pandas-lib python3-pil 77s python3-pil.imagetk python3-platformdirs python3-pluggy python3-psutil 77s python3-pybedtools python3-pyproject-hooks python3-pysam python3-pytest 77s python3-pytz python3-roman python3-scipy python3-snowballstemmer 77s python3-sphinx python3-sympy python3-tabulate python3-tk python3-toml 77s python3-tz python3-ufolib2 python3-wheel python3.12 python3.12-dev 77s python3.12-minimal python3.12-tk python3.13-dev python3.13-tk r-base-core 77s sgml-base sphinx-common tk8.6-blt2.5 unicode-data unzip x11-common xdg-utils 77s xml-core zip zlib1g-dev 77s 0 upgraded, 178 newly installed, 0 to remove and 0 not upgraded. 77s Need to get 221 MB of archives. 77s After this operation, 858 MB of additional disk space will be used. 77s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.12-minimal amd64 3.12.9-1 [2348 kB] 77s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 sgml-base all 1.31 [11.4 kB] 77s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.12 amd64 3.12.9-1 [671 kB] 77s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 m4 amd64 1.4.19-5 [263 kB] 77s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 autoconf all 2.72-3 [382 kB] 77s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 autotools-dev all 20220109.1 [44.9 kB] 77s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 automake all 1:1.17-3 [572 kB] 77s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 autopoint all 0.23.1-1 [619 kB] 77s Get:9 http://ftpmaster.internal/ubuntu plucky/universe amd64 bedtools amd64 2.31.1+dfsg-2 [674 kB] 77s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 libtcl8.6 amd64 8.6.16+dfsg-1 [1086 kB] 77s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB] 77s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-core all 2.37-8 [835 kB] 77s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig-config amd64 2.15.0-2ubuntu1 [37.4 kB] 77s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontconfig1 amd64 2.15.0-2ubuntu1 [164 kB] 77s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 libxrender1 amd64 1:0.9.10-1.1build1 [19.0 kB] 77s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 libxft2 amd64 2.3.6-1build1 [45.3 kB] 77s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 77s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 libxss1 amd64 1:1.2.3-1build3 [7204 B] 77s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 libtk8.6 amd64 8.6.16-1 [868 kB] 77s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-7build1 [630 kB] 77s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 blt amd64 2.5.3+dfsg-7build1 [4840 B] 77s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 libisl23 amd64 0.27-1 [685 kB] 77s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 libmpc3 amd64 1.3.1-1build2 [55.3 kB] 77s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-14-x86-64-linux-gnu amd64 14.2.0-17ubuntu1 [11.9 MB] 77s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-14 amd64 14.2.0-17ubuntu1 [1032 B] 77s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-x86-64-linux-gnu amd64 4:14.2.0-1ubuntu1 [5586 B] 77s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp amd64 4:14.2.0-1ubuntu1 [22.4 kB] 77s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 libcc1-0 amd64 15-20250213-1ubuntu1 [47.0 kB] 77s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 libgomp1 amd64 15-20250213-1ubuntu1 [148 kB] 77s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 libitm1 amd64 15-20250213-1ubuntu1 [28.5 kB] 77s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 libasan8 amd64 15-20250213-1ubuntu1 [3059 kB] 77s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 liblsan0 amd64 15-20250213-1ubuntu1 [1356 kB] 77s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 libtsan2 amd64 15-20250213-1ubuntu1 [2757 kB] 77s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 libubsan1 amd64 15-20250213-1ubuntu1 [1206 kB] 77s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 libhwasan0 amd64 15-20250213-1ubuntu1 [1678 kB] 77s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 libquadmath0 amd64 15-20250213-1ubuntu1 [152 kB] 77s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 libgcc-14-dev amd64 14.2.0-17ubuntu1 [2814 kB] 77s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-14-x86-64-linux-gnu amd64 14.2.0-17ubuntu1 [23.3 MB] 77s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-14 amd64 14.2.0-17ubuntu1 [536 kB] 77s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-x86-64-linux-gnu amd64 4:14.2.0-1ubuntu1 [1208 B] 77s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc amd64 4:14.2.0-1ubuntu1 [5004 B] 77s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 libstdc++-14-dev amd64 14.2.0-17ubuntu1 [2507 kB] 77s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-14-x86-64-linux-gnu amd64 14.2.0-17ubuntu1 [13.4 MB] 77s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-14 amd64 14.2.0-17ubuntu1 [21.8 kB] 77s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-x86-64-linux-gnu amd64 4:14.2.0-1ubuntu1 [968 B] 77s Get:46 http://ftpmaster.internal/ubuntu plucky/main amd64 g++ amd64 4:14.2.0-1ubuntu1 [1100 B] 77s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 build-essential amd64 12.10ubuntu1 [4928 B] 77s Get:48 http://ftpmaster.internal/ubuntu plucky/universe amd64 cython3 amd64 3.0.11+dfsg-2ubuntu1 [3370 kB] 77s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 libdebhelper-perl all 13.24.1ubuntu2 [95.4 kB] 77s Get:50 http://ftpmaster.internal/ubuntu plucky/main amd64 libtool all 2.5.4-3build1 [168 kB] 77s Get:51 http://ftpmaster.internal/ubuntu plucky/main amd64 dh-autoreconf all 20 [16.1 kB] 77s Get:52 http://ftpmaster.internal/ubuntu plucky/main amd64 libarchive-zip-perl all 1.68-1 [90.2 kB] 77s Get:53 http://ftpmaster.internal/ubuntu plucky/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [20.3 kB] 77s Get:54 http://ftpmaster.internal/ubuntu plucky/main amd64 dh-strip-nondeterminism all 1.14.1-2 [5064 B] 77s Get:55 http://ftpmaster.internal/ubuntu plucky/main amd64 debugedit amd64 1:5.1-2 [47.0 kB] 77s Get:56 http://ftpmaster.internal/ubuntu plucky/main amd64 dwz amd64 0.15-1build6 [115 kB] 77s Get:57 http://ftpmaster.internal/ubuntu plucky/main amd64 gettext amd64 0.23.1-1 [1086 kB] 77s Get:58 http://ftpmaster.internal/ubuntu plucky/main amd64 intltool-debian all 0.35.0+20060710.6 [23.2 kB] 77s Get:59 http://ftpmaster.internal/ubuntu plucky/main amd64 po-debconf all 1.0.21+nmu1 [233 kB] 77s Get:60 http://ftpmaster.internal/ubuntu plucky/main amd64 debhelper all 13.24.1ubuntu2 [895 kB] 77s Get:61 http://ftpmaster.internal/ubuntu plucky/universe amd64 dh-python all 6.20250108 [117 kB] 77s Get:62 http://ftpmaster.internal/ubuntu plucky/main amd64 xml-core all 0.19 [20.3 kB] 77s Get:63 http://ftpmaster.internal/ubuntu plucky/main amd64 docutils-common all 0.21.2+dfsg-2 [131 kB] 77s Get:64 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig amd64 2.15.0-2ubuntu1 [180 kB] 77s Get:65 http://ftpmaster.internal/ubuntu plucky/universe amd64 fonts-lyx all 2.4.3-1 [171 kB] 77s Get:66 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.1-2 [359 kB] 77s Get:67 http://ftpmaster.internal/ubuntu plucky/main amd64 libpixman-1-0 amd64 0.44.0-3 [427 kB] 77s Get:68 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-render0 amd64 1.17.0-2 [16.2 kB] 77s Get:69 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-shm0 amd64 1.17.0-2 [5758 B] 77s Get:70 http://ftpmaster.internal/ubuntu plucky/main amd64 libcairo2 amd64 1.18.2-2 [569 kB] 77s Get:71 http://ftpmaster.internal/ubuntu plucky/main amd64 libdatrie1 amd64 0.2.13-3build1 [19.0 kB] 77s Get:72 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate0 amd64 1.23-1 [64.1 kB] 77s Get:73 http://ftpmaster.internal/ubuntu plucky/main amd64 libexpat1-dev amd64 2.6.4-1 [148 kB] 77s Get:74 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 15-20250213-1ubuntu1 [920 kB] 77s Get:75 http://ftpmaster.internal/ubuntu plucky/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB] 77s Get:76 http://ftpmaster.internal/ubuntu plucky/main amd64 libharfbuzz0b amd64 10.2.0-1 [543 kB] 77s Get:77 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhtscodecs2 amd64 1.6.1-2 [132 kB] 77s Get:78 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhts3t64 amd64 1.21+ds-1 [514 kB] 77s Get:79 http://ftpmaster.internal/ubuntu plucky/main amd64 libice6 amd64 2:1.1.1-1 [44.1 kB] 77s Get:80 http://ftpmaster.internal/ubuntu plucky/main amd64 libimagequant0 amd64 2.18.0-1build1 [36.3 kB] 77s Get:81 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg-turbo8 amd64 2.1.5-3ubuntu2 [179 kB] 77s Get:82 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 77s Get:83 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 77s Get:84 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 77s Get:85 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 77s Get:86 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libjs-sphinxdoc all 8.1.3-5 [31.0 kB] 77s Get:87 http://ftpmaster.internal/ubuntu plucky/main amd64 libjson-perl all 4.10000-1 [81.9 kB] 77s Get:88 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.1-2 [3179 kB] 77s Get:89 http://ftpmaster.internal/ubuntu plucky/universe amd64 liblbfgsb0 amd64 3.0+dfsg.4-1build1 [29.9 kB] 77s Get:90 http://ftpmaster.internal/ubuntu plucky/main amd64 liblcms2-2 amd64 2.16-2 [212 kB] 77s Get:91 http://ftpmaster.internal/ubuntu plucky/main amd64 liblerc4 amd64 4.0.0+ds-5ubuntu1 [271 kB] 77s Get:92 http://ftpmaster.internal/ubuntu plucky/main amd64 libthai-data all 0.1.29-2build1 [158 kB] 77s Get:93 http://ftpmaster.internal/ubuntu plucky/main amd64 libthai0 amd64 0.1.29-2build1 [18.9 kB] 77s Get:94 http://ftpmaster.internal/ubuntu plucky/main amd64 libpango-1.0-0 amd64 1.56.1-1 [255 kB] 77s Get:95 http://ftpmaster.internal/ubuntu plucky/main amd64 libpangoft2-1.0-0 amd64 1.56.1-1 [52.6 kB] 77s Get:96 http://ftpmaster.internal/ubuntu plucky/main amd64 libpangocairo-1.0-0 amd64 1.56.1-1 [29.1 kB] 77s Get:97 http://ftpmaster.internal/ubuntu plucky/main amd64 libpaper2 amd64 2.2.5-0.3 [17.4 kB] 77s Get:98 http://ftpmaster.internal/ubuntu plucky/main amd64 libpaper-utils amd64 2.2.5-0.3 [15.5 kB] 77s Get:99 http://ftpmaster.internal/ubuntu plucky/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1ubuntu1 [895 kB] 77s Get:100 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-dev amd64 3.13.2-1 [5501 kB] 77s Get:101 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3-dev amd64 3.13.1-1~exp2 [10.5 kB] 77s Get:102 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.12-dev amd64 3.12.9-1 [5702 kB] 78s Get:103 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3-all-dev amd64 3.13.1-1~exp2 [922 B] 78s Get:104 http://ftpmaster.internal/ubuntu plucky/universe amd64 libqhull-r8.0 amd64 2020.2-6build1 [193 kB] 78s Get:105 http://ftpmaster.internal/ubuntu plucky/main amd64 libraqm0 amd64 0.10.2-1 [17.2 kB] 78s Get:106 http://ftpmaster.internal/ubuntu plucky/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [25.9 kB] 78s Get:107 http://ftpmaster.internal/ubuntu plucky/main amd64 libsm6 amd64 2:1.2.4-1 [17.4 kB] 78s Get:108 http://ftpmaster.internal/ubuntu plucky/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB] 78s Get:109 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebp7 amd64 1.5.0-0.1 [378 kB] 78s Get:110 http://ftpmaster.internal/ubuntu plucky/main amd64 libtiff6 amd64 4.5.1+git230720-4ubuntu4 [200 kB] 78s Get:111 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpdemux2 amd64 1.5.0-0.1 [13.0 kB] 78s Get:112 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpmux3 amd64 1.5.0-0.1 [27.6 kB] 78s Get:113 http://ftpmaster.internal/ubuntu plucky/main amd64 libxslt1.1 amd64 1.1.39-0exp1ubuntu2 [175 kB] 78s Get:114 http://ftpmaster.internal/ubuntu plucky/main amd64 libxt6t64 amd64 1:1.2.1-1.2build1 [171 kB] 78s Get:115 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-numpy amd64 1:1.26.4+ds-13 [5319 kB] 78s Get:116 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pysam amd64 0.23.0+ds-1 [4558 kB] 78s Get:117 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pybedtools amd64 0.10.0-4 [12.4 MB] 78s Get:118 http://ftpmaster.internal/ubuntu plucky/universe amd64 pybedtools-bin all 0.10.0-4 [3214 B] 78s Get:119 http://ftpmaster.internal/ubuntu plucky/universe amd64 pybuild-plugin-autopkgtest all 6.20250108 [1744 B] 78s Get:120 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-packaging all 24.2-1 [51.5 kB] 78s Get:121 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pyproject-hooks all 1.2.0-1 [10.2 kB] 78s Get:122 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-toml all 0.10.2-1 [16.5 kB] 78s Get:123 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-wheel all 0.45.1-1 [57.7 kB] 78s Get:124 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-build all 1.2.2-1 [31.0 kB] 78s Get:125 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-installer all 0.7.0+dfsg1-3 [17.4 kB] 78s Get:126 http://ftpmaster.internal/ubuntu plucky/universe amd64 pybuild-plugin-pyproject all 6.20250108 [1726 B] 78s Get:127 http://ftpmaster.internal/ubuntu plucky/universe amd64 python-matplotlib-data all 3.8.3-3ubuntu2 [2929 kB] 78s Get:128 http://ftpmaster.internal/ubuntu plucky/universe amd64 python-pybedtools-doc all 0.10.0-4 [269 kB] 78s Get:129 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-all amd64 3.13.1-1~exp2 [894 B] 78s Get:130 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-dev amd64 3.13.2-1 [508 kB] 78s Get:131 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-dev amd64 3.13.1-1~exp2 [26.7 kB] 78s Get:132 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.12-dev amd64 3.12.9-1 [505 kB] 78s Get:133 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-all-dev amd64 3.13.1-1~exp2 [918 B] 78s Get:134 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-brotli amd64 1.1.0-2build3 [368 kB] 78s Get:135 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-contourpy amd64 1.3.1-1 [271 kB] 78s Get:136 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-cycler all 0.12.1-1 [9716 B] 78s Get:137 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-dateutil all 2.9.0-3 [80.2 kB] 78s Get:138 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-decorator all 5.1.1-5 [10.1 kB] 78s Get:139 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-defusedxml all 0.7.1-3 [42.2 kB] 78s Get:140 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-roman all 5.0-1 [10.3 kB] 78s Get:141 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-docutils all 0.21.2+dfsg-2 [409 kB] 78s Get:142 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-pytz all 2025.1-3 [162 kB] 78s Get:143 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-tz all 2025.1-3 [1866 B] 78s Get:144 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-platformdirs all 4.3.6-1 [16.8 kB] 78s Get:145 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-fs all 2.4.16-6 [90.7 kB] 78s Get:146 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-lxml amd64 5.3.1-1 [1831 kB] 78s Get:147 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-lz4 amd64 4.4.0+dfsg-1 [27.4 kB] 78s Get:148 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-scipy amd64 1.14.1-4ubuntu1 [22.3 MB] 78s Get:149 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-mpmath all 1.3.0-1 [425 kB] 78s Get:150 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-sympy all 1.13.3-1 [4228 kB] 78s Get:151 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-ufolib2 all 0.17.0+dfsg1-1 [33.5 kB] 78s Get:152 http://ftpmaster.internal/ubuntu plucky/universe amd64 unicode-data all 15.1.0-1 [8878 kB] 78s Get:153 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-fonttools amd64 4.55.3-2 [1755 kB] 78s Get:154 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-imagesize all 1.4.1-1 [6844 B] 78s Get:155 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-iniconfig all 1.1.1-2 [6024 B] 78s Get:156 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-kiwisolver amd64 1.4.7-3 [70.4 kB] 78s Get:157 http://ftpmaster.internal/ubuntu plucky/main amd64 libopenjp2-7 amd64 2.5.0-2ubuntu3 [217 kB] 78s Get:158 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-pil amd64 11.1.0-5 [589 kB] 78s Get:159 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.12-tk amd64 3.12.9-1 [116 kB] 78s Get:160 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-tk amd64 3.13.2-1 [107 kB] 78s Get:161 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-tk amd64 3.13.1-1 [9770 B] 78s Get:162 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pil.imagetk amd64 11.1.0-5 [9936 B] 78s Get:163 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-matplotlib amd64 3.8.3-3ubuntu2 [4697 kB] 79s Get:164 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 sphinx-common all 8.1.3-5 [663 kB] 79s Get:165 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-alabaster all 0.7.16-0.1 [18.5 kB] 79s Get:166 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-snowballstemmer all 2.2.0-4build1 [59.8 kB] 79s Get:167 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-sphinx all 8.1.3-5 [474 kB] 79s Get:168 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-tabulate all 0.9.0-1 [45.3 kB] 79s Get:169 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-numpydoc all 1.8.0-1 [52.4 kB] 79s Get:170 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pandas-lib amd64 2.2.3+dfsg-8 [8248 kB] 79s Get:171 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pandas all 2.2.3+dfsg-8 [3112 kB] 79s Get:172 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pluggy all 1.5.0-1 [21.0 kB] 79s Get:173 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-psutil amd64 5.9.8-2build3 [196 kB] 79s Get:174 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pytest all 8.3.4-1 [252 kB] 79s Get:175 http://ftpmaster.internal/ubuntu plucky/main amd64 zip amd64 3.0-14ubuntu2 [185 kB] 79s Get:176 http://ftpmaster.internal/ubuntu plucky/main amd64 unzip amd64 6.0-28ubuntu6 [181 kB] 79s Get:177 http://ftpmaster.internal/ubuntu plucky/main amd64 xdg-utils all 1.2.1-2ubuntu1 [66.0 kB] 79s Get:178 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-base-core amd64 4.4.2-1build1 [28.9 MB] 80s Preconfiguring packages ... 80s Fetched 221 MB in 3s (87.7 MB/s) 80s Selecting previously unselected package python3.12-minimal. 80s (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 ... 108975 files and directories currently installed.) 80s Preparing to unpack .../000-python3.12-minimal_3.12.9-1_amd64.deb ... 80s Unpacking python3.12-minimal (3.12.9-1) ... 80s Selecting previously unselected package sgml-base. 80s Preparing to unpack .../001-sgml-base_1.31_all.deb ... 80s Unpacking sgml-base (1.31) ... 80s Selecting previously unselected package python3.12. 80s Preparing to unpack .../002-python3.12_3.12.9-1_amd64.deb ... 80s Unpacking python3.12 (3.12.9-1) ... 80s Selecting previously unselected package m4. 80s Preparing to unpack .../003-m4_1.4.19-5_amd64.deb ... 80s Unpacking m4 (1.4.19-5) ... 80s Selecting previously unselected package autoconf. 80s Preparing to unpack .../004-autoconf_2.72-3_all.deb ... 80s Unpacking autoconf (2.72-3) ... 80s Selecting previously unselected package autotools-dev. 80s Preparing to unpack .../005-autotools-dev_20220109.1_all.deb ... 80s Unpacking autotools-dev (20220109.1) ... 80s Selecting previously unselected package automake. 80s Preparing to unpack .../006-automake_1%3a1.17-3_all.deb ... 80s Unpacking automake (1:1.17-3) ... 80s Selecting previously unselected package autopoint. 80s Preparing to unpack .../007-autopoint_0.23.1-1_all.deb ... 80s Unpacking autopoint (0.23.1-1) ... 80s Selecting previously unselected package bedtools. 80s Preparing to unpack .../008-bedtools_2.31.1+dfsg-2_amd64.deb ... 80s Unpacking bedtools (2.31.1+dfsg-2) ... 80s Selecting previously unselected package libtcl8.6:amd64. 80s Preparing to unpack .../009-libtcl8.6_8.6.16+dfsg-1_amd64.deb ... 80s Unpacking libtcl8.6:amd64 (8.6.16+dfsg-1) ... 80s Selecting previously unselected package fonts-dejavu-mono. 80s Preparing to unpack .../010-fonts-dejavu-mono_2.37-8_all.deb ... 80s Unpacking fonts-dejavu-mono (2.37-8) ... 81s Selecting previously unselected package fonts-dejavu-core. 81s Preparing to unpack .../011-fonts-dejavu-core_2.37-8_all.deb ... 81s Unpacking fonts-dejavu-core (2.37-8) ... 81s Selecting previously unselected package fontconfig-config. 81s Preparing to unpack .../012-fontconfig-config_2.15.0-2ubuntu1_amd64.deb ... 81s Unpacking fontconfig-config (2.15.0-2ubuntu1) ... 81s Selecting previously unselected package libfontconfig1:amd64. 81s Preparing to unpack .../013-libfontconfig1_2.15.0-2ubuntu1_amd64.deb ... 81s Unpacking libfontconfig1:amd64 (2.15.0-2ubuntu1) ... 81s Selecting previously unselected package libxrender1:amd64. 81s Preparing to unpack .../014-libxrender1_1%3a0.9.10-1.1build1_amd64.deb ... 81s Unpacking libxrender1:amd64 (1:0.9.10-1.1build1) ... 81s Selecting previously unselected package libxft2:amd64. 81s Preparing to unpack .../015-libxft2_2.3.6-1build1_amd64.deb ... 81s Unpacking libxft2:amd64 (2.3.6-1build1) ... 81s Selecting previously unselected package x11-common. 81s Preparing to unpack .../016-x11-common_1%3a7.7+23ubuntu3_all.deb ... 81s Unpacking x11-common (1:7.7+23ubuntu3) ... 81s Selecting previously unselected package libxss1:amd64. 81s Preparing to unpack .../017-libxss1_1%3a1.2.3-1build3_amd64.deb ... 81s Unpacking libxss1:amd64 (1:1.2.3-1build3) ... 81s Selecting previously unselected package libtk8.6:amd64. 81s Preparing to unpack .../018-libtk8.6_8.6.16-1_amd64.deb ... 81s Unpacking libtk8.6:amd64 (8.6.16-1) ... 81s Selecting previously unselected package tk8.6-blt2.5. 81s Preparing to unpack .../019-tk8.6-blt2.5_2.5.3+dfsg-7build1_amd64.deb ... 81s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 81s Selecting previously unselected package blt. 81s Preparing to unpack .../020-blt_2.5.3+dfsg-7build1_amd64.deb ... 81s Unpacking blt (2.5.3+dfsg-7build1) ... 81s Selecting previously unselected package libisl23:amd64. 81s Preparing to unpack .../021-libisl23_0.27-1_amd64.deb ... 81s Unpacking libisl23:amd64 (0.27-1) ... 81s Selecting previously unselected package libmpc3:amd64. 81s Preparing to unpack .../022-libmpc3_1.3.1-1build2_amd64.deb ... 81s Unpacking libmpc3:amd64 (1.3.1-1build2) ... 81s Selecting previously unselected package cpp-14-x86-64-linux-gnu. 81s Preparing to unpack .../023-cpp-14-x86-64-linux-gnu_14.2.0-17ubuntu1_amd64.deb ... 81s Unpacking cpp-14-x86-64-linux-gnu (14.2.0-17ubuntu1) ... 81s Selecting previously unselected package cpp-14. 81s Preparing to unpack .../024-cpp-14_14.2.0-17ubuntu1_amd64.deb ... 81s Unpacking cpp-14 (14.2.0-17ubuntu1) ... 81s Selecting previously unselected package cpp-x86-64-linux-gnu. 81s Preparing to unpack .../025-cpp-x86-64-linux-gnu_4%3a14.2.0-1ubuntu1_amd64.deb ... 81s Unpacking cpp-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ... 81s Selecting previously unselected package cpp. 81s Preparing to unpack .../026-cpp_4%3a14.2.0-1ubuntu1_amd64.deb ... 81s Unpacking cpp (4:14.2.0-1ubuntu1) ... 81s Selecting previously unselected package libcc1-0:amd64. 81s Preparing to unpack .../027-libcc1-0_15-20250213-1ubuntu1_amd64.deb ... 81s Unpacking libcc1-0:amd64 (15-20250213-1ubuntu1) ... 81s Selecting previously unselected package libgomp1:amd64. 81s Preparing to unpack .../028-libgomp1_15-20250213-1ubuntu1_amd64.deb ... 81s Unpacking libgomp1:amd64 (15-20250213-1ubuntu1) ... 81s Selecting previously unselected package libitm1:amd64. 81s Preparing to unpack .../029-libitm1_15-20250213-1ubuntu1_amd64.deb ... 81s Unpacking libitm1:amd64 (15-20250213-1ubuntu1) ... 82s Selecting previously unselected package libasan8:amd64. 82s Preparing to unpack .../030-libasan8_15-20250213-1ubuntu1_amd64.deb ... 82s Unpacking libasan8:amd64 (15-20250213-1ubuntu1) ... 82s Selecting previously unselected package liblsan0:amd64. 82s Preparing to unpack .../031-liblsan0_15-20250213-1ubuntu1_amd64.deb ... 82s Unpacking liblsan0:amd64 (15-20250213-1ubuntu1) ... 82s Selecting previously unselected package libtsan2:amd64. 82s Preparing to unpack .../032-libtsan2_15-20250213-1ubuntu1_amd64.deb ... 82s Unpacking libtsan2:amd64 (15-20250213-1ubuntu1) ... 82s Selecting previously unselected package libubsan1:amd64. 82s Preparing to unpack .../033-libubsan1_15-20250213-1ubuntu1_amd64.deb ... 82s Unpacking libubsan1:amd64 (15-20250213-1ubuntu1) ... 82s Selecting previously unselected package libhwasan0:amd64. 82s Preparing to unpack .../034-libhwasan0_15-20250213-1ubuntu1_amd64.deb ... 82s Unpacking libhwasan0:amd64 (15-20250213-1ubuntu1) ... 82s Selecting previously unselected package libquadmath0:amd64. 82s Preparing to unpack .../035-libquadmath0_15-20250213-1ubuntu1_amd64.deb ... 82s Unpacking libquadmath0:amd64 (15-20250213-1ubuntu1) ... 82s Selecting previously unselected package libgcc-14-dev:amd64. 82s Preparing to unpack .../036-libgcc-14-dev_14.2.0-17ubuntu1_amd64.deb ... 82s Unpacking libgcc-14-dev:amd64 (14.2.0-17ubuntu1) ... 82s Selecting previously unselected package gcc-14-x86-64-linux-gnu. 82s Preparing to unpack .../037-gcc-14-x86-64-linux-gnu_14.2.0-17ubuntu1_amd64.deb ... 82s Unpacking gcc-14-x86-64-linux-gnu (14.2.0-17ubuntu1) ... 82s Selecting previously unselected package gcc-14. 82s Preparing to unpack .../038-gcc-14_14.2.0-17ubuntu1_amd64.deb ... 82s Unpacking gcc-14 (14.2.0-17ubuntu1) ... 82s Selecting previously unselected package gcc-x86-64-linux-gnu. 82s Preparing to unpack .../039-gcc-x86-64-linux-gnu_4%3a14.2.0-1ubuntu1_amd64.deb ... 82s Unpacking gcc-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ... 82s Selecting previously unselected package gcc. 82s Preparing to unpack .../040-gcc_4%3a14.2.0-1ubuntu1_amd64.deb ... 82s Unpacking gcc (4:14.2.0-1ubuntu1) ... 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package build-essential. 83s Preparing to unpack .../046-build-essential_12.10ubuntu1_amd64.deb ... 83s Unpacking build-essential (12.10ubuntu1) ... 83s Selecting previously unselected package cython3. 83s Preparing to unpack .../047-cython3_3.0.11+dfsg-2ubuntu1_amd64.deb ... 83s Unpacking cython3 (3.0.11+dfsg-2ubuntu1) ... 83s Selecting previously unselected package libdebhelper-perl. 83s Preparing to unpack .../048-libdebhelper-perl_13.24.1ubuntu2_all.deb ... 83s Unpacking libdebhelper-perl (13.24.1ubuntu2) ... 83s Selecting previously unselected package libtool. 83s Preparing to unpack .../049-libtool_2.5.4-3build1_all.deb ... 83s Unpacking libtool (2.5.4-3build1) ... 83s Selecting previously unselected package dh-autoreconf. 83s Preparing to unpack .../050-dh-autoreconf_20_all.deb ... 83s Unpacking dh-autoreconf (20) ... 83s Selecting previously unselected package libarchive-zip-perl. 83s Preparing to unpack .../051-libarchive-zip-perl_1.68-1_all.deb ... 83s Unpacking 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previously unselected package libpaper2:amd64. 85s Preparing to unpack .../096-libpaper2_2.2.5-0.3_amd64.deb ... 85s Unpacking libpaper2:amd64 (2.2.5-0.3) ... 85s Selecting previously unselected package libpaper-utils. 85s Preparing to unpack .../097-libpaper-utils_2.2.5-0.3_amd64.deb ... 85s Unpacking libpaper-utils (2.2.5-0.3) ... 85s Selecting previously unselected package zlib1g-dev:amd64. 85s Preparing to unpack .../098-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1ubuntu1_amd64.deb ... 85s Unpacking zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 85s Selecting previously unselected package libpython3.13-dev:amd64. 85s Preparing to unpack .../099-libpython3.13-dev_3.13.2-1_amd64.deb ... 85s Unpacking libpython3.13-dev:amd64 (3.13.2-1) ... 85s Selecting previously unselected package libpython3-dev:amd64. 85s Preparing to unpack .../100-libpython3-dev_3.13.1-1~exp2_amd64.deb ... 85s Unpacking libpython3-dev:amd64 (3.13.1-1~exp2) ... 85s Selecting previously unselected package 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Selecting previously unselected package python3-roman. 88s Preparing to unpack .../139-python3-roman_5.0-1_all.deb ... 88s Unpacking python3-roman (5.0-1) ... 88s Selecting previously unselected package python3-docutils. 88s Preparing to unpack .../140-python3-docutils_0.21.2+dfsg-2_all.deb ... 88s Unpacking python3-docutils (0.21.2+dfsg-2) ... 88s Selecting previously unselected package python3-pytz. 88s Preparing to unpack .../141-python3-pytz_2025.1-3_all.deb ... 88s Unpacking python3-pytz (2025.1-3) ... 88s Selecting previously unselected package python3-tz. 88s Preparing to unpack .../142-python3-tz_2025.1-3_all.deb ... 88s Unpacking python3-tz (2025.1-3) ... 88s Selecting previously unselected package python3-platformdirs. 88s Preparing to unpack .../143-python3-platformdirs_4.3.6-1_all.deb ... 88s Unpacking python3-platformdirs (4.3.6-1) ... 88s Selecting previously unselected package python3-fs. 88s Preparing to unpack .../144-python3-fs_2.4.16-6_all.deb ... 88s Unpacking python3-fs (2.4.16-6) ... 88s Selecting previously unselected package python3-lxml:amd64. 88s Preparing to unpack .../145-python3-lxml_5.3.1-1_amd64.deb ... 88s Unpacking python3-lxml:amd64 (5.3.1-1) ... 88s Selecting previously unselected package python3-lz4. 88s Preparing to unpack .../146-python3-lz4_4.4.0+dfsg-1_amd64.deb ... 88s Unpacking python3-lz4 (4.4.0+dfsg-1) ... 88s Selecting previously unselected package python3-scipy. 88s Preparing to unpack .../147-python3-scipy_1.14.1-4ubuntu1_amd64.deb ... 88s Unpacking python3-scipy (1.14.1-4ubuntu1) ... 89s Selecting previously unselected package python3-mpmath. 89s Preparing to unpack .../148-python3-mpmath_1.3.0-1_all.deb ... 89s Unpacking python3-mpmath (1.3.0-1) ... 89s Selecting previously unselected package python3-sympy. 89s Preparing to unpack .../149-python3-sympy_1.13.3-1_all.deb ... 89s Unpacking python3-sympy (1.13.3-1) ... 89s Selecting previously unselected package python3-ufolib2. 89s Preparing to unpack .../150-python3-ufolib2_0.17.0+dfsg1-1_all.deb ... 89s Unpacking python3-ufolib2 (0.17.0+dfsg1-1) ... 89s Selecting previously unselected package unicode-data. 89s Preparing to unpack .../151-unicode-data_15.1.0-1_all.deb ... 89s Unpacking unicode-data (15.1.0-1) ... 89s Selecting previously unselected package python3-fonttools. 89s Preparing to unpack .../152-python3-fonttools_4.55.3-2_amd64.deb ... 89s Unpacking python3-fonttools (4.55.3-2) ... 89s Selecting previously unselected package python3-imagesize. 89s Preparing to unpack .../153-python3-imagesize_1.4.1-1_all.deb ... 89s Unpacking python3-imagesize (1.4.1-1) ... 89s Selecting previously unselected package python3-iniconfig. 89s Preparing to unpack .../154-python3-iniconfig_1.1.1-2_all.deb ... 89s Unpacking python3-iniconfig (1.1.1-2) ... 89s Selecting previously unselected package python3-kiwisolver. 90s Preparing to unpack .../155-python3-kiwisolver_1.4.7-3_amd64.deb ... 90s Unpacking python3-kiwisolver (1.4.7-3) ... 90s Selecting previously unselected package libopenjp2-7:amd64. 90s Preparing to unpack .../156-libopenjp2-7_2.5.0-2ubuntu3_amd64.deb ... 90s Unpacking libopenjp2-7:amd64 (2.5.0-2ubuntu3) ... 90s Selecting previously unselected package python3-pil:amd64. 90s Preparing to unpack .../157-python3-pil_11.1.0-5_amd64.deb ... 90s Unpacking python3-pil:amd64 (11.1.0-5) ... 90s Selecting previously unselected package python3.12-tk. 90s Preparing to unpack .../158-python3.12-tk_3.12.9-1_amd64.deb ... 90s Unpacking python3.12-tk (3.12.9-1) ... 90s Selecting previously unselected package python3.13-tk. 90s Preparing to unpack .../159-python3.13-tk_3.13.2-1_amd64.deb ... 90s Unpacking python3.13-tk (3.13.2-1) ... 90s Selecting previously unselected package python3-tk:amd64. 90s Preparing to unpack .../160-python3-tk_3.13.1-1_amd64.deb ... 90s Unpacking python3-tk:amd64 (3.13.1-1) ... 90s Selecting previously unselected package python3-pil.imagetk:amd64. 90s Preparing to unpack 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Unpacking python3-sphinx (8.1.3-5) ... 90s Selecting previously unselected package python3-tabulate. 90s Preparing to unpack .../167-python3-tabulate_0.9.0-1_all.deb ... 90s Unpacking python3-tabulate (0.9.0-1) ... 90s Selecting previously unselected package python3-numpydoc. 90s Preparing to unpack .../168-python3-numpydoc_1.8.0-1_all.deb ... 90s Unpacking python3-numpydoc (1.8.0-1) ... 90s Selecting previously unselected package python3-pandas-lib:amd64. 90s Preparing to unpack .../169-python3-pandas-lib_2.2.3+dfsg-8_amd64.deb ... 90s Unpacking python3-pandas-lib:amd64 (2.2.3+dfsg-8) ... 91s Selecting previously unselected package python3-pandas. 91s Preparing to unpack .../170-python3-pandas_2.2.3+dfsg-8_all.deb ... 91s Unpacking python3-pandas (2.2.3+dfsg-8) ... 91s Selecting previously unselected package python3-pluggy. 91s Preparing to unpack .../171-python3-pluggy_1.5.0-1_all.deb ... 91s Unpacking python3-pluggy (1.5.0-1) ... 91s Selecting previously unselected package 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libdeflate0:amd64 (1.23-1) ... 95s Setting up python3-tabulate (0.9.0-1) ... 95s Setting up m4 (1.4.19-5) ... 95s Setting up libqhull-r8.0:amd64 (2020.2-6build1) ... 95s Setting up python3-all (3.13.1-1~exp2) ... 95s Setting up python3-pytz (2025.1-3) ... 95s Setting up libxcb-shm0:amd64 (1.17.0-2) ... 95s Setting up libgomp1:amd64 (15-20250213-1ubuntu1) ... 95s Setting up python3-wheel (0.45.1-1) ... 95s Setting up libjbig0:amd64 (2.1-6.1ubuntu2) ... 95s Setting up python3-platformdirs (4.3.6-1) ... 96s Setting up python3-psutil (5.9.8-2build3) ... 96s Setting up python3-tz (2025.1-3) ... 96s Setting up python3-fs (2.4.16-6) ... 96s Setting up unicode-data (15.1.0-1) ... 96s Setting up python3-roman (5.0-1) ... 97s Setting up python3-decorator (5.1.1-5) ... 97s Setting up zip (3.0-14ubuntu2) ... 97s Setting up autotools-dev (20220109.1) ... 97s Setting up libblas3:amd64 (3.12.1-2) ... 97s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide 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Setting up libgfortran5:amd64 (15-20250213-1ubuntu1) ... 100s Setting up autoconf (2.72-3) ... 100s Setting up python3-pluggy (1.5.0-1) ... 100s Setting up libwebp7:amd64 (1.5.0-0.1) ... 100s Setting up libubsan1:amd64 (15-20250213-1ubuntu1) ... 100s Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 100s Setting up dwz (0.15-1build6) ... 100s Setting up libhwasan0:amd64 (15-20250213-1ubuntu1) ... 100s Setting up libasan8:amd64 (15-20250213-1ubuntu1) ... 100s Setting up libjson-perl (4.10000-1) ... 100s Setting up libxslt1.1:amd64 (1.1.39-0exp1ubuntu2) ... 100s Setting up debugedit (1:5.1-2) ... 100s Setting up libhts3t64:amd64 (1.21+ds-1) ... 100s Setting up libopenjp2-7:amd64 (2.5.0-2ubuntu3) ... 100s Setting up libharfbuzz0b:amd64 (10.2.0-1) ... 100s Setting up libthai-data (0.1.29-2build1) ... 100s Setting up python3-dateutil (2.9.0-3) ... 100s Setting up sgml-base (1.31) ... 100s Setting up libxss1:amd64 (1:1.2.3-1build3) ... 100s Setting up libpaper2:amd64 (2.2.5-0.3) ... 101s Setting up libtsan2:amd64 (15-20250213-1ubuntu1) ... 101s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 101s Setting up python3-mpmath (1.3.0-1) ... 101s Setting up libisl23:amd64 (0.27-1) ... 101s Setting up python3-build (1.2.2-1) ... 102s Setting up python-matplotlib-data (3.8.3-3ubuntu2) ... 102s Setting up libwebpmux3:amd64 (1.5.0-0.1) ... 102s Setting up xdg-utils (1.2.1-2ubuntu1) ... 102s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode 102s Setting up bedtools (2.31.1+dfsg-2) ... 102s Setting up libcc1-0:amd64 (15-20250213-1ubuntu1) ... 102s Setting up liblsan0:amd64 (15-20250213-1ubuntu1) ... 102s Setting up libitm1:amd64 (15-20250213-1ubuntu1) ... 102s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 102s Setting up python3-imagesize (1.4.1-1) ... 102s Setting up libjpeg8:amd64 (8c-2ubuntu11) ... 102s Setting up automake (1:1.17-3) ... 102s update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode 102s Setting up libfile-stripnondeterminism-perl (1.14.1-2) ... 102s Setting up python3-sympy (1.13.3-1) ... 113s Setting up libice6:amd64 (2:1.1.1-1) ... 113s Setting up liblapack3:amd64 (3.12.1-2) ... 113s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode 113s Setting up gettext (0.23.1-1) ... 113s Setting up python3-pysam (0.23.0+ds-1) ... 113s Setting up pybuild-plugin-pyproject (6.20250108) ... 113s Setting up fontconfig-config (2.15.0-2ubuntu1) ... 113s Setting up python3-pytest (8.3.4-1) ... 114s Setting up libwebpdemux2:amd64 (1.5.0-0.1) ... 114s Setting up libpython3.12-dev:amd64 (3.12.9-1) ... 114s Setting up libpaper-utils (2.2.5-0.3) ... 114s Setting up intltool-debian (0.35.0+20060710.6) ... 114s Setting up libthai0:amd64 (0.1.29-2build1) ... 114s Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... 114s Setting up libraqm0:amd64 (0.10.2-1) ... 114s Setting up libpython3.13-dev:amd64 (3.13.2-1) ... 114s Setting up python3.12-dev (3.12.9-1) ... 114s Setting up cpp-14-x86-64-linux-gnu (14.2.0-17ubuntu1) ... 114s Setting up python3-numpy (1:1.26.4+ds-13) ... 117s Setting up libjs-sphinxdoc (8.1.3-5) ... 117s Setting up cpp-14 (14.2.0-17ubuntu1) ... 117s Setting up dh-strip-nondeterminism (1.14.1-2) ... 117s Setting up python3-lxml:amd64 (5.3.1-1) ... 117s Setting up libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ... 117s Setting up xml-core (0.19) ... 117s Setting up python3-contourpy (1.3.1-1) ... 118s Setting up libfontconfig1:amd64 (2.15.0-2ubuntu1) ... 118s Setting up libgcc-14-dev:amd64 (14.2.0-17ubuntu1) ... 118s Setting up libstdc++-14-dev:amd64 (14.2.0-17ubuntu1) ... 118s Setting up libsm6:amd64 (2:1.2.4-1) ... 118s Setting up liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ... 118s Setting up cpp-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ... 118s Setting up fontconfig (2.15.0-2ubuntu1) ... 120s Regenerating fonts cache... done. 120s Setting up python3-pybedtools (0.10.0-4) ... 120s Setting up libxft2:amd64 (2.3.6-1build1) ... 120s Setting up python3-scipy (1.14.1-4ubuntu1) ... 126s Setting up libpython3-dev:amd64 (3.13.1-1~exp2) ... 126s Setting up python-pybedtools-doc (0.10.0-4) ... 126s Setting up python3.13-dev (3.13.2-1) ... 126s Setting up po-debconf (1.0.21+nmu1) ... 126s Setting up libtk8.6:amd64 (8.6.16-1) ... 126s Setting up python3-pandas-lib:amd64 (2.2.3+dfsg-8) ... 126s Setting up libpango-1.0-0:amd64 (1.56.1-1) ... 126s Setting up python3.12-tk (3.12.9-1) ... 126s Setting up pybedtools-bin (0.10.0-4) ... 126s Setting up libcairo2:amd64 (1.18.2-2) ... 126s Setting up python3.13-tk (3.13.2-1) ... 126s Setting up python3-pil:amd64 (11.1.0-5) ... 127s Setting up python3-pandas (2.2.3+dfsg-8) ... 135s Setting up libpython3-all-dev:amd64 (3.13.1-1~exp2) ... 135s Setting up sphinx-common (8.1.3-5) ... 135s Setting up python3-dev (3.13.1-1~exp2) ... 135s Setting up libxt6t64:amd64 (1:1.2.1-1.2build1) ... 135s Setting up cpp (4:14.2.0-1ubuntu1) ... 135s Setting up gcc-14-x86-64-linux-gnu (14.2.0-17ubuntu1) ... 135s Setting up libpangoft2-1.0-0:amd64 (1.56.1-1) ... 135s Setting up libpangocairo-1.0-0:amd64 (1.56.1-1) ... 135s Setting up python3-all-dev (3.13.1-1~exp2) ... 135s Setting up tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 135s Setting up gcc-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ... 135s Setting up blt (2.5.3+dfsg-7build1) ... 135s Setting up python3-tk:amd64 (3.13.1-1) ... 135s Setting up gcc-14 (14.2.0-17ubuntu1) ... 135s Setting up python3-pil.imagetk:amd64 (11.1.0-5) ... 135s Setting up r-base-core (4.4.2-1build1) ... 136s Creating config file /etc/R/Renviron with new version 136s Setting up g++-14-x86-64-linux-gnu (14.2.0-17ubuntu1) ... 136s Setting up g++-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ... 136s Setting up g++-14 (14.2.0-17ubuntu1) ... 136s Setting up libtool (2.5.4-3build1) ... 136s Setting up gcc (4:14.2.0-1ubuntu1) ... 136s Setting up dh-autoreconf (20) ... 136s Setting up g++ (4:14.2.0-1ubuntu1) ... 136s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 136s Setting up build-essential (12.10ubuntu1) ... 136s Setting up debhelper (13.24.1ubuntu2) ... 136s Setting up pybuild-plugin-autopkgtest (6.20250108) ... 136s Setting up python3-ufolib2 (0.17.0+dfsg1-1) ... 136s Setting up python3-fonttools (4.55.3-2) ... 138s Setting up python3-matplotlib (3.8.3-3ubuntu2) ... 140s Processing triggers for libc-bin (2.40-4ubuntu1) ... 140s Processing triggers for systemd (257.2-3ubuntu1) ... 140s Processing triggers for man-db (2.13.0-1) ... 142s Processing triggers for install-info (7.1.1-1) ... 142s Processing triggers for sgml-base (1.31) ... 142s Setting up docutils-common (0.21.2+dfsg-2) ... 142s Processing triggers for sgml-base (1.31) ... 142s Setting up python3-docutils (0.21.2+dfsg-2) ... 143s Setting up python3-sphinx (8.1.3-5) ... 144s Setting up python3-numpydoc (1.8.0-1) ... 145s autopkgtest [12:30:33]: test pybuild-autopkgtest: pybuild-autopkgtest 145s autopkgtest [12:30:33]: test pybuild-autopkgtest: [----------------------- 145s pybuild-autopkgtest 146s I: pybuild base:311: cd /tmp/autopkgtest.hyO5bx/autopkgtest_tmp/build; python3.12 -m pytest -k "not test_chromsizes" --pyargs pybedtools 147s ============================= test session starts ============================== 147s platform linux -- Python 3.12.9, pytest-8.3.4, pluggy-1.5.0 147s rootdir: /tmp/autopkgtest.hyO5bx/autopkgtest_tmp/build 147s configfile: pyproject.toml 147s plugins: typeguard-4.4.1 147s collected 511 items / 2 deselected / 509 selected 147s 151s test/test_1.py ......................................................... [ 11%] 152s ............x..x.x...... [ 15%] 152s test/test_cbedtools.py ....................................... [ 23%] 152s test/test_contrib.py .. [ 23%] 152s test/test_gzip_support.py ........ [ 25%] 152s test/test_helpers.py ...... [ 26%] 155s test/test_issues.py ........................................... [ 35%] 155s test/test_iter.py ...................................................... [ 45%] 155s ........................................................................ [ 59%] 160s ........................................................................ [ 74%] 161s ........................................................................ [ 88%] 161s ......................................................... [ 99%] 161s test/test_pathlib.py ... [100%] 161s 161s ================ 506 passed, 2 deselected, 3 xfailed in 15.12s ================= 161s I: pybuild pybuild:334: cd /tmp/autopkgtest.hyO5bx/build.vzk/src/docs ; PYTHONPATH=/tmp/autopkgtest.hyO5bx/autopkgtest_tmp/build python3.12 -m sphinx -b doctest -d build/doctrees source build/doctest 162s Running Sphinx v8.1.3 162s loading translations [en]... done 162s making output directory... done 162s Converting `source_suffix = '.rst'` to `source_suffix = {'.rst': 'restructuredtext'}`. 162s [autosummary] generating autosummary for: 3-brief-examples.rst, FAQs.rst, autodoc_source.rst, autodocs/pybedtools.contrib.plotting.Track.rst, changes.rst, create-a-bedtool-tutorial.rst, default-arguments.rst, each.rst, filtering.rst, flow-of-commands.rst, ..., topical-create-a-bedtool.rst, topical-design-principles.rst, topical-documentation-contents.rst, topical-genome.rst, topical-iterators.rst, topical-low-level-ops.rst, topical-random.rst, topical-saving.rst, topical-wrapping.rst, tutorial-contents.rst 164s [autosummary] generating autosummary for: /tmp/autopkgtest.hyO5bx/build.vzk/src/docs/source/autodocs/pybedtools.bedtool.BedTool.absolute_distance.rst, /tmp/autopkgtest.hyO5bx/build.vzk/src/docs/source/autodocs/pybedtools.bedtool.BedTool.all_hits.rst, /tmp/autopkgtest.hyO5bx/build.vzk/src/docs/source/autodocs/pybedtools.bedtool.BedTool.annotate.rst, /tmp/autopkgtest.hyO5bx/build.vzk/src/docs/source/autodocs/pybedtools.bedtool.BedTool.any_hits.rst, /tmp/autopkgtest.hyO5bx/build.vzk/src/docs/source/autodocs/pybedtools.bedtool.BedTool.as_intervalfile.rst, /tmp/autopkgtest.hyO5bx/build.vzk/src/docs/source/autodocs/pybedtools.bedtool.BedTool.at.rst, /tmp/autopkgtest.hyO5bx/build.vzk/src/docs/source/autodocs/pybedtools.bedtool.BedTool.bam_to_bed.rst, /tmp/autopkgtest.hyO5bx/build.vzk/src/docs/source/autodocs/pybedtools.bedtool.BedTool.bam_to_fastq.rst, /tmp/autopkgtest.hyO5bx/build.vzk/src/docs/source/autodocs/pybedtools.bedtool.BedTool.bed6.rst, /tmp/autopkgtest.hyO5bx/build.vzk/src/docs/source/autodocs/pybedtools.bedtool.BedTool.bedpe_to_bam.rst, ..., /tmp/autopkgtest.hyO5bx/build.vzk/src/docs/source/autodocs/pybedtools.helpers.set_tempdir.rst, /tmp/autopkgtest.hyO5bx/build.vzk/src/docs/source/autodocs/pybedtools.parallel.parallel_apply.rst, /tmp/autopkgtest.hyO5bx/build.vzk/src/docs/source/pybedtools.featurefuncs.add_color.rst, /tmp/autopkgtest.hyO5bx/build.vzk/src/docs/source/pybedtools.featurefuncs.bedgraph_scale.rst, /tmp/autopkgtest.hyO5bx/build.vzk/src/docs/source/pybedtools.featurefuncs.extend_fields.rst, /tmp/autopkgtest.hyO5bx/build.vzk/src/docs/source/pybedtools.featurefuncs.five_prime.rst, /tmp/autopkgtest.hyO5bx/build.vzk/src/docs/source/pybedtools.featurefuncs.greater_than.rst, /tmp/autopkgtest.hyO5bx/build.vzk/src/docs/source/pybedtools.featurefuncs.less_than.rst, /tmp/autopkgtest.hyO5bx/build.vzk/src/docs/source/pybedtools.featurefuncs.normalized_to_length.rst, /tmp/autopkgtest.hyO5bx/build.vzk/src/docs/source/pybedtools.featurefuncs.three_prime.rst 164s building [mo]: targets for 0 po files that are out of date 164s writing output... 164s building [doctest]: targets for 49 source files that are out of date 164s updating environment: [new config] 157 added, 0 changed, 0 removed 164s reading sources... [ 1%] 3-brief-examples 164s reading sources... [ 1%] FAQs 164s reading sources... [ 2%] autodoc_source 165s /usr/lib/python3/dist-packages/numpydoc/docscrape.py:421: UserWarning: Unknown section Example in the docstring of decorated in /usr/lib/python3/dist-packages/pybedtools/bedtool.py. 165s self[section] = content 165s /usr/lib/python3/dist-packages/numpydoc/docscrape.py:421: UserWarning: Unknown section Example in the docstring of tag_bedpe in /usr/lib/python3/dist-packages/pybedtools/contrib/long_range_interaction.py. 165s self[section] = content 165s reading sources... [ 3%] autodocs/pybedtools.bedtool.BedTool 166s /usr/lib/python3/dist-packages/numpydoc/docscrape.py:421: UserWarning: Unknown section Example in the docstring of decorated in /usr/lib/python3/dist-packages/pybedtools/bedtool.py. 166s self[section] = content 167s reading sources... [ 3%] autodocs/pybedtools.bedtool.BedTool.absolute_distance 167s reading sources... 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[ 93%] topical-bam-semantics 172s reading sources... [ 94%] topical-comparisons 172s reading sources... [ 94%] topical-create-a-bedtool 172s reading sources... [ 95%] topical-design-principles 172s reading sources... [ 96%] topical-documentation-contents 172s reading sources... [ 96%] topical-genome 172s reading sources... [ 97%] topical-iterators 172s reading sources... [ 97%] topical-low-level-ops 172s reading sources... [ 98%] topical-random 172s reading sources... [ 99%] topical-saving 172s reading sources... [ 99%] topical-wrapping 172s WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool' with 'bedtool.BedTool'. [autosummary.import_cycle] 172s WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.intersect' with 'bedtool.BedTool.intersect'. [autosummary.import_cycle] 172s WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.window' with 'bedtool.BedTool.window'. [autosummary.import_cycle] 172s WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.closest' with 'bedtool.BedTool.closest'. [autosummary.import_cycle] 172s WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.coverage' with 'bedtool.BedTool.coverage'. [autosummary.import_cycle] 172s WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.map' with 'bedtool.BedTool.map'. [autosummary.import_cycle] 172s WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.genome_coverage' with 'bedtool.BedTool.genome_coverage'. [autosummary.import_cycle] 172s WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.merge' with 'bedtool.BedTool.merge'. [autosummary.import_cycle] 172s WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.cluster' with 'bedtool.BedTool.cluster'. [autosummary.import_cycle] 172s WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.complement' with 'bedtool.BedTool.complement'. [autosummary.import_cycle] 172s WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.subtract' with 'bedtool.BedTool.subtract'. [autosummary.import_cycle] 172s reading sources... [100%] tutorial-contents 172s 172s WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.slop' with 'bedtool.BedTool.slop'. [autosummary.import_cycle] 172s WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.flank' with 'bedtool.BedTool.flank'. [autosummary.import_cycle] 172s WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.sort' with 'bedtool.BedTool.sort'. [autosummary.import_cycle] 172s WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.random' with 'bedtool.BedTool.random'. [autosummary.import_cycle] 172s WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.shuffle' with 'bedtool.BedTool.shuffle'. [autosummary.import_cycle] 172s WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.annotate' with 'bedtool.BedTool.annotate'. [autosummary.import_cycle] 172s WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.multi_intersect' with 'bedtool.BedTool.multi_intersect'. [autosummary.import_cycle] 172s WARNING: Summarised items should not include the current module. 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[autosummary.import_cycle] 172s WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.bed6' with 'bedtool.BedTool.bed6'. [autosummary.import_cycle] 172s WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.bam_to_fastq' with 'bedtool.BedTool.bam_to_fastq'. [autosummary.import_cycle] 172s WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.sequence' with 'bedtool.BedTool.sequence'. [autosummary.import_cycle] 172s WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.mask_fasta' with 'bedtool.BedTool.mask_fasta'. [autosummary.import_cycle] 172s WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.nucleotide_content' with 'bedtool.BedTool.nucleotide_content'. [autosummary.import_cycle] 172s WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.multi_bam_coverage' with 'bedtool.BedTool.multi_bam_coverage'. [autosummary.import_cycle] 172s WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.tag_bam' with 'bedtool.BedTool.tag_bam'. [autosummary.import_cycle] 172s WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.jaccard' with 'bedtool.BedTool.jaccard'. [autosummary.import_cycle] 172s WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.reldist' with 'bedtool.BedTool.reldist'. [autosummary.import_cycle] 172s WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.overlap' with 'bedtool.BedTool.overlap'. [autosummary.import_cycle] 172s WARNING: Summarised items should not include the current module. 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[autosummary.import_cycle] 172s /tmp/autopkgtest.hyO5bx/build.vzk/src/docs/source/topical-genome.rst:55: ERROR: Unknown target name: "genomepy". [docutils] 172s looking for now-outdated files... none found 172s pickling environment... done 172s checking consistency... /tmp/autopkgtest.hyO5bx/build.vzk/src/docs/source/pybedtools.featurefuncs.normalized_to_length.rst: document is referenced in multiple toctrees: ['autodoc_source', 'autodoc_source'], selecting: autodoc_source <- pybedtools.featurefuncs.normalized_to_length 172s /tmp/autopkgtest.hyO5bx/build.vzk/src/docs/source/pybedtools.featurefuncs.rename.rst: document is referenced in multiple toctrees: ['autodoc_source', 'autodoc_source'], selecting: autodoc_source <- pybedtools.featurefuncs.rename 172s done 172s preparing documents... done 172s copying assets... 172s copying assets: done 172s running tests... 172s 172s Document: autodocs/pybedtools.bedtool.BedTool.annotate 172s ------------------------------------------------------ 172s 1 items passed all tests: 172s 3 tests in default 172s 3 tests in 1 items. 172s 3 passed and 0 failed. 172s Test passed. 172s 172s Document: 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tests: 176s 10 tests in default 176s 10 tests in 1 items. 176s 10 passed and 0 failed. 176s Test passed. 176s 176s Document: intersections 176s ----------------------- 176s 1 items passed all tests: 176s 8 tests in default 176s 8 tests in 1 items. 176s 8 passed and 0 failed. 176s Test passed. 176s 176s Document: intervals 176s ------------------- 176s 1 items passed all tests: 176s 50 tests in default 176s 50 tests in 1 items. 176s 50 passed and 0 failed. 176s Test passed. 176s 176s Document: piping 176s ---------------- 176s 1 items passed all tests: 176s 17 tests in default 176s 17 tests in 1 items. 176s 17 passed and 0 failed. 176s Test passed. 176s 176s Document: save-results 176s ---------------------- 176s 1 items passed all tests: 176s 8 tests in default 176s 8 tests in 1 items. 176s 8 passed and 0 failed. 176s Test passed. 176s 176s Document: topical-bam 176s --------------------- 178s 1 items passed all tests: 178s 15 tests in default 178s 15 tests in 1 items. 178s 15 passed and 0 failed. 178s Test passed. 178s 178s Document: topical-create-a-bedtool 178s ---------------------------------- 178s 1 items passed all tests: 178s 10 tests in default 178s 10 tests in 1 items. 178s 10 passed and 0 failed. 178s Test passed. 178s 178s Document: topical-design-principles 178s ----------------------------------- 178s 1 items passed all tests: 178s 15 tests in default 178s 15 tests in 1 items. 178s 15 passed and 0 failed. 178s Test passed. 178s 178s Document: topical-genome 178s ------------------------ 178s 1 items passed all tests: 178s 13 tests in default 178s 13 tests in 1 items. 178s 13 passed and 0 failed. 178s Test passed. 178s 178s Document: topical-iterators 178s --------------------------- 178s 1 items passed all tests: 178s 20 tests in default 178s 20 tests in 1 items. 178s 20 passed and 0 failed. 178s Test passed. 178s 178s Document: topical-low-level-ops 178s ------------------------------- 178s 1 items passed all tests: 178s 6 tests in default 178s 6 tests in 1 items. 178s 6 passed and 0 failed. 178s Test passed. 178s 178s Document: topical-random 178s ------------------------ 179s 1 items passed all tests: 179s 10 tests in default 179s 10 tests in 1 items. 179s 10 passed and 0 failed. 179s Test passed. 179s 179s Document: topical-saving 179s ------------------------ 179s 1 items passed all tests: 179s 14 tests in default 179s 14 tests in 1 items. 179s 14 passed and 0 failed. 179s Test passed. 179s 179s Doctest summary 179s =============== 179s 387 tests 179s 0 failures in tests 179s 0 failures in setup code 179s 0 failures in cleanup code 179s build succeeded, 126 warnings. 179s 179s Testing of doctests in the sources finished, look at the results in build/doctest/output.txt. 180s I: pybuild base:311: cd /tmp/autopkgtest.hyO5bx/autopkgtest_tmp/build; python3.13 -m pytest -k "not test_chromsizes" --pyargs pybedtools 180s ============================= test session starts ============================== 180s platform linux -- Python 3.13.2, pytest-8.3.4, pluggy-1.5.0 180s rootdir: /tmp/autopkgtest.hyO5bx/autopkgtest_tmp/build 180s configfile: pyproject.toml 180s plugins: typeguard-4.4.1 180s collected 511 items / 2 deselected / 509 selected 180s 185s test/test_1.py ......................................................... [ 11%] 185s ............x..x.x...... [ 15%] 185s test/test_cbedtools.py ....................................... [ 23%] 186s test/test_contrib.py .. [ 23%] 186s test/test_gzip_support.py ........ [ 25%] 186s test/test_helpers.py ...... [ 26%] 188s test/test_issues.py ........................................... [ 35%] 188s test/test_iter.py ...................................................... [ 45%] 189s ........................................................................ [ 59%] 194s ........................................................................ [ 74%] 195s ........................................................................ [ 88%] 195s ......................................................... [ 99%] 195s test/test_pathlib.py ... [100%] 195s 195s ================ 506 passed, 2 deselected, 3 xfailed in 15.01s ================= 195s I: pybuild pybuild:334: cd /tmp/autopkgtest.hyO5bx/build.vzk/src/docs ; PYTHONPATH=/tmp/autopkgtest.hyO5bx/autopkgtest_tmp/build python3.13 -m sphinx -b doctest -d build/doctrees source build/doctest 195s Running Sphinx v8.1.3 195s loading translations [en]... done 196s Converting `source_suffix = '.rst'` to `source_suffix = {'.rst': 'restructuredtext'}`. 196s loading pickled environment... done 196s [autosummary] generating autosummary for: 3-brief-examples.rst, FAQs.rst, autodoc_source.rst, autodocs/pybedtools.bedtool.BedTool.absolute_distance.rst, autodocs/pybedtools.bedtool.BedTool.all_hits.rst, autodocs/pybedtools.bedtool.BedTool.annotate.rst, autodocs/pybedtools.bedtool.BedTool.any_hits.rst, autodocs/pybedtools.bedtool.BedTool.as_intervalfile.rst, autodocs/pybedtools.bedtool.BedTool.at.rst, autodocs/pybedtools.bedtool.BedTool.bam_to_bed.rst, ..., topical-create-a-bedtool.rst, topical-design-principles.rst, topical-documentation-contents.rst, topical-genome.rst, topical-iterators.rst, topical-low-level-ops.rst, topical-random.rst, topical-saving.rst, topical-wrapping.rst, tutorial-contents.rst 197s building [mo]: targets for 0 po files that are out of date 197s writing output... 197s building [doctest]: targets for 157 source files that are out of date 197s updating environment: 0 added, 0 changed, 0 removed 197s reading sources... 197s looking for now-outdated files... none found 197s preparing documents... done 197s copying assets... 197s copying assets: done 197s running tests... 197s 197s Document: autodocs/pybedtools.bedtool.BedTool.annotate 197s ------------------------------------------------------ 197s 1 item passed all tests: 197s 3 tests in default 197s 3 tests in 1 item. 197s 3 passed. 197s Test passed. 197s 197s Document: autodocs/pybedtools.bedtool.BedTool.cat 197s ------------------------------------------------- 197s 1 item passed all tests: 197s 4 tests in default 197s 4 tests in 1 item. 197s 4 passed. 197s Test passed. 197s 197s Document: autodocs/pybedtools.bedtool.BedTool.complement 197s -------------------------------------------------------- 197s 1 item passed all tests: 197s 2 tests in default 197s 2 tests in 1 item. 197s 2 passed. 197s Test passed. 197s 197s Document: autodocs/pybedtools.bedtool.BedTool.count 197s --------------------------------------------------- 197s 1 item passed all tests: 197s 2 tests in default 197s 2 tests in 1 item. 197s 2 passed. 197s Test passed. 197s 197s Document: autodocs/pybedtools.bedtool.BedTool.coverage 197s ------------------------------------------------------ 197s 1 item passed all tests: 197s 4 tests in default 197s 4 tests in 1 item. 197s 4 passed. 197s Test passed. 197s 197s Document: autodocs/pybedtools.bedtool.BedTool.cut 197s ------------------------------------------------- 197s 1 item passed all tests: 197s 2 tests in default 197s 2 tests in 1 item. 197s 2 passed. 197s Test passed. 197s 197s Document: autodocs/pybedtools.bedtool.BedTool.each 197s -------------------------------------------------- 197s 1 item passed all tests: 197s 4 tests in default 197s 4 tests in 1 item. 197s 4 passed. 197s Test passed. 197s 197s Document: autodocs/pybedtools.bedtool.BedTool.field_count 197s --------------------------------------------------------- 197s 1 item passed all tests: 197s 2 tests in default 197s 2 tests in 1 item. 197s 2 passed. 197s Test passed. 197s 197s Document: autodocs/pybedtools.bedtool.BedTool.file_type 197s ------------------------------------------------------- 197s 1 item passed all tests: 197s 2 tests in default 197s 2 tests in 1 item. 197s 2 passed. 197s Test passed. 197s 197s Document: autodocs/pybedtools.bedtool.BedTool.filter 197s ---------------------------------------------------- 197s 1 item passed all tests: 197s 3 tests in default 197s 3 tests in 1 item. 197s 3 passed. 197s Test passed. 197s 197s Document: autodocs/pybedtools.bedtool.BedTool.flank 197s --------------------------------------------------- 197s 1 item passed all tests: 197s 2 tests in default 197s 2 tests in 1 item. 197s 2 passed. 197s Test passed. 197s 197s Document: autodocs/pybedtools.bedtool.BedTool.genome_coverage 197s ------------------------------------------------------------- 200s 1 item passed all tests: 200s 6 tests in default 200s 6 tests in 1 item. 200s 6 passed. 200s Test passed. 200s 200s Document: autodocs/pybedtools.bedtool.BedTool.groupby 200s ----------------------------------------------------- 200s 1 item passed all tests: 200s 5 tests in default 200s 5 tests in 1 item. 200s 5 passed. 200s Test passed. 200s 200s Document: autodocs/pybedtools.bedtool.BedTool.head 200s -------------------------------------------------- 200s 1 item passed all tests: 200s 2 tests in default 200s 2 tests in 1 item. 200s 2 passed. 200s Test passed. 200s 200s Document: autodocs/pybedtools.bedtool.BedTool.mask_fasta 200s -------------------------------------------------------- 200s 1 item passed all tests: 200s 8 tests in default 200s 8 tests in 1 item. 200s 8 passed. 200s Test passed. 200s 200s Document: autodocs/pybedtools.bedtool.BedTool.merge 200s --------------------------------------------------- 200s 1 item passed all tests: 200s 3 tests in default 200s 3 tests in 1 item. 200s 3 passed. 200s Test passed. 200s 200s Document: autodocs/pybedtools.bedtool.BedTool.moveto 200s ---------------------------------------------------- 200s 1 item passed all tests: 200s 5 tests in default 200s 5 tests in 1 item. 200s 5 passed. 200s Test passed. 200s 200s Document: autodocs/pybedtools.bedtool.BedTool.overlap 200s ----------------------------------------------------- 200s 1 item passed all tests: 200s 4 tests in default 200s 4 tests in 1 item. 200s 4 passed. 200s Test passed. 200s 200s Document: autodocs/pybedtools.bedtool.BedTool.random 200s ---------------------------------------------------- 200s 1 item passed all tests: 200s 2 tests in default 200s 2 tests in 1 item. 200s 2 passed. 200s Test passed. 200s 200s Document: autodocs/pybedtools.bedtool.BedTool.randomintersection 200s ---------------------------------------------------------------- 200s 1 item passed all tests: 200s 6 tests in default 200s 6 tests in 1 item. 200s 6 passed. 200s Test passed. 200s 200s Document: autodocs/pybedtools.bedtool.BedTool.randomstats 200s --------------------------------------------------------- 200s 1 item passed all tests: 200s 4 tests in default 200s 4 tests in 1 item. 200s 4 passed. 200s Test passed. 200s 200s Document: autodocs/pybedtools.bedtool.BedTool.remove_invalid 200s ------------------------------------------------------------ 200s 1 item passed all tests: 200s 2 tests in default 200s 2 tests in 1 item. 200s 2 passed. 200s Test passed. 200s 200s Document: autodocs/pybedtools.bedtool.BedTool.save_seqs 200s ------------------------------------------------------- 200s 1 item passed all tests: 200s 7 tests in default 200s 7 tests in 1 item. 200s 7 passed. 200s Test passed. 200s 200s Document: autodocs/pybedtools.bedtool.BedTool.saveas 200s ---------------------------------------------------- 200s 1 item passed all tests: 200s 7 tests in default 200s 7 tests in 1 item. 200s 7 passed. 200s Test passed. 200s 200s Document: autodocs/pybedtools.bedtool.BedTool.sequence 200s ------------------------------------------------------ 200s 1 item passed all tests: 200s 4 tests in default 200s 4 tests in 1 item. 200s 4 passed. 200s Test passed. 200s 200s Document: autodocs/pybedtools.bedtool.BedTool.set_chromsizes 200s ------------------------------------------------------------ 201s 1 item passed all tests: 201s 4 tests in default 201s 4 tests in 1 item. 201s 4 passed. 201s Test passed. 201s 201s Document: autodocs/pybedtools.bedtool.BedTool.shuffle 201s ----------------------------------------------------- 201s 1 item passed all tests: 201s 4 tests in default 201s 4 tests in 1 item. 201s 4 passed. 201s Test passed. 201s 201s Document: autodocs/pybedtools.bedtool.BedTool.sort 201s -------------------------------------------------- 201s 1 item passed all tests: 201s 2 tests in default 201s 2 tests in 1 item. 201s 2 passed. 201s Test passed. 201s 201s Document: autodocs/pybedtools.bedtool.BedTool.subtract 201s ------------------------------------------------------ 201s 1 item passed all tests: 201s 4 tests in default 201s 4 tests in 1 item. 201s 4 passed. 201s Test passed. 201s 201s Document: autodocs/pybedtools.bedtool.BedTool.total_coverage 201s ------------------------------------------------------------ 201s 1 item passed all tests: 201s 3 tests in default 201s 3 tests in 1 item. 201s 3 passed. 201s Test passed. 201s 201s Document: autodocs/pybedtools.bedtool.BedTool.with_attrs 201s -------------------------------------------------------- 201s 1 item passed all tests: 201s 3 tests in default 201s 3 tests in 1 item. 201s 3 passed. 201s Test passed. 201s 201s Document: autodocs/pybedtools.cbedtools.Interval 201s ------------------------------------------------ 201s 1 item passed all tests: 201s 3 tests in default 201s 3 tests in 1 item. 201s 3 passed. 201s Test passed. 201s 201s Document: autodocs/pybedtools.cbedtools.create_interval_from_list 201s ----------------------------------------------------------------- 201s 1 item passed all tests: 201s 1 test in default 201s 1 test in 1 item. 201s 1 passed. 201s Test passed. 201s 201s Document: autodocs/pybedtools.contrib.long_range_interaction.cis_trans_interactions 201s ----------------------------------------------------------------------------------- 201s 1 item passed all tests: 201s 18 tests in default 201s 18 tests in 1 item. 201s 18 passed. 201s Test passed. 201s 201s Document: autodocs/pybedtools.contrib.plotting.Track 201s ---------------------------------------------------- 201s 1 item passed all tests: 201s 7 tests in default 201s 7 tests in 1 item. 201s 7 passed. 201s Test passed. 201s 201s Document: autodocs/pybedtools.filenames.list_example_files 201s ---------------------------------------------------------- 201s 1 item passed all tests: 201s 5 tests in default 201s 5 tests in 1 item. 201s 5 passed. 201s Test passed. 201s 201s Document: autodocs/pybedtools.helpers.chromsizes 201s ------------------------------------------------ 201s 1 item passed all tests: 201s 2 tests in default 201s 2 tests in 1 item. 201s 2 passed. 201s Test passed. 201s 201s Document: autodocs/pybedtools.parallel.parallel_apply 201s ----------------------------------------------------- 201s 1 item passed all tests: 201s 13 tests in default 201s 13 tests in 1 item. 201s 13 passed. 201s Test passed. 201s 201s Document: default-arguments 201s --------------------------- 201s 1 item passed all tests: 201s 13 tests in default 201s 13 tests in 1 item. 201s 13 passed. 201s Test passed. 201s 201s Document: each 201s -------------- 201s 1 item passed all tests: 201s 6 tests in default 201s 6 tests in 1 item. 201s 6 passed. 201s Test passed. 201s 201s Document: filtering 201s ------------------- 201s 1 item passed all tests: 201s 8 tests in default 201s 8 tests in 1 item. 201s 8 passed. 201s Test passed. 201s 201s Document: history 201s ----------------- 201s 1 item passed all tests: 201s 10 tests in default 201s 10 tests in 1 item. 201s 10 passed. 201s Test passed. 201s 201s Document: intersections 201s ----------------------- 201s 1 item passed all tests: 201s 8 tests in default 201s 8 tests in 1 item. 201s 8 passed. 201s Test passed. 201s 201s Document: intervals 201s ------------------- 201s 1 item passed all tests: 201s 50 tests in default 201s 50 tests in 1 item. 201s 50 passed. 201s Test passed. 201s 201s Document: piping 201s ---------------- 201s 1 item passed all tests: 201s 17 tests in default 201s 17 tests in 1 item. 201s 17 passed. 201s Test passed. 201s 201s Document: save-results 201s ---------------------- 201s 1 item passed all tests: 201s 8 tests in default 201s 8 tests in 1 item. 201s 8 passed. 201s Test passed. 201s 201s Document: topical-bam 201s --------------------- 203s 1 item passed all tests: 203s 15 tests in default 203s 15 tests in 1 item. 203s 15 passed. 203s Test passed. 203s 203s Document: topical-create-a-bedtool 203s ---------------------------------- 203s 1 item passed all tests: 203s 10 tests in default 203s 10 tests in 1 item. 203s 10 passed. 203s Test passed. 203s 203s Document: topical-design-principles 203s ----------------------------------- 203s 1 item passed all tests: 203s 15 tests in default 203s 15 tests in 1 item. 203s 15 passed. 203s Test passed. 203s 203s Document: topical-genome 203s ------------------------ 203s 1 item passed all tests: 203s 13 tests in default 203s 13 tests in 1 item. 203s 13 passed. 203s Test passed. 203s 203s Document: topical-iterators 203s --------------------------- 203s 1 item passed all tests: 203s 20 tests in default 203s 20 tests in 1 item. 203s 20 passed. 203s Test passed. 203s 203s Document: topical-low-level-ops 203s ------------------------------- 203s 1 item passed all tests: 203s 6 tests in default 203s 6 tests in 1 item. 203s 6 passed. 203s Test passed. 203s 203s Document: topical-random 203s ------------------------ 204s 1 item passed all tests: 204s 10 tests in default 204s 10 tests in 1 item. 204s 10 passed. 204s Test passed. 204s 204s Document: topical-saving 204s ------------------------ 204s 1 item passed all tests: 204s 14 tests in default 204s 14 tests in 1 item. 204s 14 passed. 204s Test passed. 204s 204s Doctest summary 204s =============== 204s 387 tests 204s 0 failures in tests 204s 0 failures in setup code 204s 0 failures in cleanup code 204s build succeeded. 204s 204s Testing of doctests in the sources finished, look at the results in build/doctest/output.txt. 205s autopkgtest [12:31:33]: test pybuild-autopkgtest: -----------------------] 205s pybuild-autopkgtest PASS 205s autopkgtest [12:31:33]: test pybuild-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 205s autopkgtest [12:31:33]: @@@@@@@@@@@@@@@@@@@@ summary 205s pybuild-autopkgtest PASS 222s nova [W] Skipping flock for amd64 222s Creating nova instance adt-plucky-amd64-python-pybedtools-20250219-122808-juju-7f2275-prod-proposed-migration-environment-2-01b824c0-75da-40fb-8fdb-2fc0f98858f2 from image adt/ubuntu-plucky-amd64-server-20250218.img (UUID 0c5f6311-785d-4524-a0d8-db541aaf5c09)... 222s nova [W] Timed out waiting for 2250bda7-b5cb-4542-9329-5d351896ed29 to get deleted.