0s autopkgtest [12:48:19]: starting date and time: 2025-02-19 12:48:19+0000 0s autopkgtest [12:48:19]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [12:48:19]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.ghynukxb/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-20@bos03-arm64-26.secgroup --name adt-plucky-arm64-python-pybedtools-20250219-124818-juju-7f2275-prod-proposed-migration-environment-20-04bf6ca8-f553-4706-bada-c30dd3ff0949 --image adt/ubuntu-plucky-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --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/ 124s autopkgtest [12:50:23]: testbed dpkg architecture: arm64 124s autopkgtest [12:50:23]: testbed apt version: 2.9.29 125s autopkgtest [12:50:24]: @@@@@@@@@@@@@@@@@@@@ test bed setup 125s autopkgtest [12:50:24]: testbed release detected to be: None 126s autopkgtest [12:50:25]: updating testbed package index (apt update) 126s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [110 kB] 126s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 126s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 126s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 127s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [750 kB] 127s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [3120 B] 127s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [13.9 kB] 127s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [76.1 kB] 127s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [93.3 kB] 127s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 Packages [7960 B] 127s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [686 kB] 127s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [11.2 kB] 127s Fetched 1752 kB in 1s (1807 kB/s) 128s Reading package lists... 128s Reading package lists... 129s Building dependency tree... 129s Reading state information... 129s Calculating upgrade... 130s The following NEW packages will be installed: 130s libapt-pkg7.0 130s The following packages will be upgraded: 130s apt apt-utils iproute2 liblsof0 libp11-kit0 lsof rsyslog 130s 7 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 130s Need to get 4842 kB of archives. 130s After this operation, 3409 kB of additional disk space will be used. 130s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 libapt-pkg7.0 arm64 2.9.30 [1023 kB] 131s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 apt arm64 2.9.30 [1364 kB] 131s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 apt-utils arm64 2.9.30 [207 kB] 131s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 iproute2 arm64 6.13.0-1ubuntu1 [1158 kB] 131s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 libp11-kit0 arm64 0.25.5-2ubuntu3 [280 kB] 131s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 rsyslog arm64 8.2412.0-2ubuntu1 [521 kB] 131s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 lsof arm64 4.99.4+dfsg-1 [236 kB] 131s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 liblsof0 arm64 4.99.4+dfsg-1 [53.9 kB] 131s Preconfiguring packages ... 132s Fetched 4842 kB in 1s (5384 kB/s) 132s Selecting previously unselected package libapt-pkg7.0:arm64. 132s (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 ... 116620 files and directories currently installed.) 132s Preparing to unpack .../libapt-pkg7.0_2.9.30_arm64.deb ... 132s Unpacking libapt-pkg7.0:arm64 (2.9.30) ... 132s Setting up libapt-pkg7.0:arm64 (2.9.30) ... 132s (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 ... 116669 files and directories currently installed.) 132s Preparing to unpack .../archives/apt_2.9.30_arm64.deb ... 132s Unpacking apt (2.9.30) over (2.9.29) ... 132s Setting up apt (2.9.30) ... 133s (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 ... 116669 files and directories currently installed.) 133s Preparing to unpack .../0-apt-utils_2.9.30_arm64.deb ... 133s Unpacking apt-utils (2.9.30) over (2.9.29) ... 133s Preparing to unpack .../1-iproute2_6.13.0-1ubuntu1_arm64.deb ... 133s Unpacking iproute2 (6.13.0-1ubuntu1) over (6.10.0-2ubuntu1) ... 134s Preparing to unpack .../2-libp11-kit0_0.25.5-2ubuntu3_arm64.deb ... 134s Unpacking libp11-kit0:arm64 (0.25.5-2ubuntu3) over (0.25.5-2ubuntu2) ... 134s Preparing to unpack .../3-rsyslog_8.2412.0-2ubuntu1_arm64.deb ... 134s Unpacking rsyslog (8.2412.0-2ubuntu1) over (8.2412.0-1ubuntu1) ... 134s Preparing to unpack .../4-lsof_4.99.4+dfsg-1_arm64.deb ... 134s Unpacking lsof (4.99.4+dfsg-1) over (4.99.3+dfsg-2) ... 134s Preparing to unpack .../5-liblsof0_4.99.4+dfsg-1_arm64.deb ... 134s Unpacking liblsof0 (4.99.4+dfsg-1) over (4.99.3+dfsg-2) ... 134s Setting up apt-utils (2.9.30) ... 134s Setting up liblsof0 (4.99.4+dfsg-1) ... 134s Setting up iproute2 (6.13.0-1ubuntu1) ... 134s Setting up rsyslog (8.2412.0-2ubuntu1) ... 134s info: The user `syslog' is already a member of `adm'. 136s Setting up libp11-kit0:arm64 (0.25.5-2ubuntu3) ... 136s Setting up lsof (4.99.4+dfsg-1) ... 136s Processing triggers for man-db (2.13.0-1) ... 138s Processing triggers for libc-bin (2.40-4ubuntu1) ... 139s Reading package lists... 140s Building dependency tree... 140s Reading state information... 141s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 141s autopkgtest [12:50:40]: upgrading testbed (apt dist-upgrade and autopurge) 141s Reading package lists... 141s Building dependency tree... 141s Reading state information... 142s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 142s Starting 2 pkgProblemResolver with broken count: 0 142s Done 143s Entering ResolveByKeep 143s 144s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 144s Reading package lists... 144s Building dependency tree... 144s Reading state information... 145s Starting pkgProblemResolver with broken count: 0 145s Starting 2 pkgProblemResolver with broken count: 0 145s Done 146s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 146s autopkgtest [12:50:45]: rebooting testbed after setup commands that affected boot 169s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 176s autopkgtest [12:51:15]: testbed running kernel: Linux 6.12.0-15-generic #15-Ubuntu SMP PREEMPT_DYNAMIC Tue Feb 4 15:49:33 UTC 2025 179s autopkgtest [12:51:18]: @@@@@@@@@@@@@@@@@@@@ apt-source python-pybedtools 183s Get:1 http://ftpmaster.internal/ubuntu plucky/universe python-pybedtools 0.10.0-4 (dsc) [2623 B] 183s Get:2 http://ftpmaster.internal/ubuntu plucky/universe python-pybedtools 0.10.0-4 (tar) [12.0 MB] 183s Get:3 http://ftpmaster.internal/ubuntu plucky/universe python-pybedtools 0.10.0-4 (diff) [33.5 kB] 183s gpgv: Signature made Fri Dec 27 01:57:35 2024 UTC 183s gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 183s gpgv: issuer "crusoe@debian.org" 183s gpgv: Can't check signature: No public key 183s dpkg-source: warning: cannot verify inline signature for ./python-pybedtools_0.10.0-4.dsc: no acceptable signature found 184s autopkgtest [12:51:23]: testing package python-pybedtools version 0.10.0-4 184s autopkgtest [12:51:23]: build not needed 186s autopkgtest [12:51:25]: test pybuild-autopkgtest: preparing testbed 186s Reading package lists... 186s Building dependency tree... 186s Reading state information... 187s Starting pkgProblemResolver with broken count: 0 187s Starting 2 pkgProblemResolver with broken count: 0 187s Done 188s The following NEW packages will be installed: 188s autoconf automake autopoint autotools-dev bedtools blt build-essential cpp 188s cpp-14 cpp-14-aarch64-linux-gnu cpp-aarch64-linux-gnu cython3 debhelper 188s debugedit dh-autoreconf dh-python dh-strip-nondeterminism docutils-common 188s dwz fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono 188s fonts-lyx g++ g++-14 g++-14-aarch64-linux-gnu g++-aarch64-linux-gnu gcc 188s gcc-14 gcc-14-aarch64-linux-gnu gcc-aarch64-linux-gnu gettext 188s intltool-debian libarchive-zip-perl libasan8 libblas3 libcairo2 libcc1-0 188s libdatrie1 libdebhelper-perl libdeflate0 libexpat1-dev 188s libfile-stripnondeterminism-perl libfontconfig1 libgcc-14-dev libgfortran5 188s libgomp1 libgraphite2-3 libharfbuzz0b libhts3t64 libhtscodecs2 libhwasan0 188s libice6 libimagequant0 libisl23 libitm1 libjbig0 libjpeg-turbo8 libjpeg8 188s libjs-jquery libjs-jquery-ui libjs-sphinxdoc libjs-underscore libjson-perl 188s liblapack3 liblbfgsb0 liblcms2-2 liblerc4 liblsan0 libmpc3 libopenjp2-7 188s libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils 188s libpaper2 libpixman-1-0 libpython3-all-dev libpython3-dev libpython3.12-dev 188s libpython3.13-dev libqhull-r8.0 libraqm0 libsharpyuv0 libsm6 188s libstdc++-14-dev libtcl8.6 libthai-data libthai0 libtiff6 libtk8.6 libtool 188s libtsan2 libubsan1 libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 188s libxcb-shm0 libxft2 libxrender1 libxslt1.1 libxss1 libxt6t64 m4 po-debconf 188s pybedtools-bin pybuild-plugin-autopkgtest pybuild-plugin-pyproject 188s python-matplotlib-data python-pybedtools-doc python3-alabaster python3-all 188s python3-all-dev python3-brotli python3-build python3-contourpy 188s python3-cycler python3-dateutil python3-decorator python3-defusedxml 188s python3-dev python3-docutils python3-fonttools python3-fs python3-imagesize 188s python3-iniconfig python3-installer python3-kiwisolver python3-lxml 188s python3-lz4 python3-matplotlib python3-mpmath python3-numpy python3-numpydoc 188s python3-packaging python3-pandas python3-pandas-lib python3-pil 188s python3-pil.imagetk python3-platformdirs python3-pluggy python3-psutil 188s python3-pybedtools python3-pyproject-hooks python3-pysam python3-pytest 188s python3-pytz python3-roman python3-scipy python3-snowballstemmer 188s python3-sphinx python3-sympy python3-tabulate python3-tk python3-toml 188s python3-tz python3-ufolib2 python3-wheel python3.12 python3.12-dev 188s python3.12-minimal python3.12-tk python3.13-dev python3.13-tk r-base-core 188s sgml-base sphinx-common tk8.6-blt2.5 unicode-data unzip x11-common xdg-utils 188s xml-core zip zlib1g-dev 188s 0 upgraded, 177 newly installed, 0 to remove and 0 not upgraded. 188s Need to get 204 MB of archives. 188s After this operation, 793 MB of additional disk space will be used. 188s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.12-minimal arm64 3.12.9-1 [2236 kB] 189s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 sgml-base all 1.31 [11.4 kB] 189s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.12 arm64 3.12.9-1 [671 kB] 189s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 m4 arm64 1.4.19-5 [244 kB] 189s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 autoconf all 2.72-3 [382 kB] 189s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 autotools-dev all 20220109.1 [44.9 kB] 189s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 automake all 1:1.17-3 [572 kB] 189s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 autopoint all 0.23.1-1 [619 kB] 189s Get:9 http://ftpmaster.internal/ubuntu plucky/universe arm64 bedtools arm64 2.31.1+dfsg-2 [636 kB] 189s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 libtcl8.6 arm64 8.6.16+dfsg-1 [987 kB] 189s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 189s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 189s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig-config arm64 2.15.0-2ubuntu1 [37.5 kB] 189s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 libfontconfig1 arm64 2.15.0-2ubuntu1 [144 kB] 189s Get:15 http://ftpmaster.internal/ubuntu plucky/main arm64 libxrender1 arm64 1:0.9.10-1.1build1 [18.8 kB] 189s Get:16 http://ftpmaster.internal/ubuntu plucky/main arm64 libxft2 arm64 2.3.6-1build1 [44.1 kB] 189s Get:17 http://ftpmaster.internal/ubuntu plucky/main arm64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 189s Get:18 http://ftpmaster.internal/ubuntu plucky/main arm64 libxss1 arm64 1:1.2.3-1build3 [7244 B] 189s Get:19 http://ftpmaster.internal/ubuntu plucky/main arm64 libtk8.6 arm64 8.6.16-1 [776 kB] 189s Get:20 http://ftpmaster.internal/ubuntu plucky/main arm64 tk8.6-blt2.5 arm64 2.5.3+dfsg-7build1 [618 kB] 189s Get:21 http://ftpmaster.internal/ubuntu plucky/main arm64 blt arm64 2.5.3+dfsg-7build1 [4840 B] 189s Get:22 http://ftpmaster.internal/ubuntu plucky/main arm64 libisl23 arm64 0.27-1 [676 kB] 189s Get:23 http://ftpmaster.internal/ubuntu plucky/main arm64 libmpc3 arm64 1.3.1-1build2 [56.8 kB] 189s Get:24 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp-14-aarch64-linux-gnu arm64 14.2.0-17ubuntu1 [10.6 MB] 189s Get:25 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp-14 arm64 14.2.0-17ubuntu1 [1032 B] 189s Get:26 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp-aarch64-linux-gnu arm64 4:14.2.0-1ubuntu1 [5558 B] 189s Get:27 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp arm64 4:14.2.0-1ubuntu1 [22.4 kB] 189s Get:28 http://ftpmaster.internal/ubuntu plucky/main arm64 libcc1-0 arm64 15-20250213-1ubuntu1 [44.2 kB] 189s Get:29 http://ftpmaster.internal/ubuntu plucky/main arm64 libgomp1 arm64 15-20250213-1ubuntu1 [146 kB] 189s Get:30 http://ftpmaster.internal/ubuntu plucky/main arm64 libitm1 arm64 15-20250213-1ubuntu1 [28.0 kB] 189s Get:31 http://ftpmaster.internal/ubuntu plucky/main arm64 libasan8 arm64 15-20250213-1ubuntu1 [2928 kB] 190s Get:32 http://ftpmaster.internal/ubuntu plucky/main arm64 liblsan0 arm64 15-20250213-1ubuntu1 [1319 kB] 190s Get:33 http://ftpmaster.internal/ubuntu plucky/main arm64 libtsan2 arm64 15-20250213-1ubuntu1 [2695 kB] 190s Get:34 http://ftpmaster.internal/ubuntu plucky/main arm64 libubsan1 arm64 15-20250213-1ubuntu1 [1178 kB] 190s Get:35 http://ftpmaster.internal/ubuntu plucky/main arm64 libhwasan0 arm64 15-20250213-1ubuntu1 [1642 kB] 190s Get:36 http://ftpmaster.internal/ubuntu plucky/main arm64 libgcc-14-dev arm64 14.2.0-17ubuntu1 [2593 kB] 190s Get:37 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc-14-aarch64-linux-gnu arm64 14.2.0-17ubuntu1 [20.9 MB] 190s Get:38 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc-14 arm64 14.2.0-17ubuntu1 [526 kB] 190s Get:39 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc-aarch64-linux-gnu arm64 4:14.2.0-1ubuntu1 [1200 B] 190s Get:40 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc arm64 4:14.2.0-1ubuntu1 [4998 B] 190s Get:41 http://ftpmaster.internal/ubuntu plucky/main arm64 libstdc++-14-dev arm64 14.2.0-17ubuntu1 [2499 kB] 190s Get:42 http://ftpmaster.internal/ubuntu plucky/main arm64 g++-14-aarch64-linux-gnu arm64 14.2.0-17ubuntu1 [12.1 MB] 191s Get:43 http://ftpmaster.internal/ubuntu plucky/main arm64 g++-14 arm64 14.2.0-17ubuntu1 [21.8 kB] 191s Get:44 http://ftpmaster.internal/ubuntu plucky/main arm64 g++-aarch64-linux-gnu arm64 4:14.2.0-1ubuntu1 [956 B] 191s Get:45 http://ftpmaster.internal/ubuntu plucky/main arm64 g++ arm64 4:14.2.0-1ubuntu1 [1080 B] 191s Get:46 http://ftpmaster.internal/ubuntu plucky/main arm64 build-essential arm64 12.10ubuntu1 [4932 B] 191s Get:47 http://ftpmaster.internal/ubuntu plucky/universe arm64 cython3 arm64 3.0.11+dfsg-2ubuntu1 [2974 kB] 191s Get:48 http://ftpmaster.internal/ubuntu plucky/main arm64 libdebhelper-perl all 13.24.1ubuntu2 [95.4 kB] 191s Get:49 http://ftpmaster.internal/ubuntu plucky/main arm64 libtool all 2.5.4-3build1 [168 kB] 191s Get:50 http://ftpmaster.internal/ubuntu plucky/main arm64 dh-autoreconf all 20 [16.1 kB] 191s Get:51 http://ftpmaster.internal/ubuntu plucky/main arm64 libarchive-zip-perl all 1.68-1 [90.2 kB] 191s Get:52 http://ftpmaster.internal/ubuntu plucky/main arm64 libfile-stripnondeterminism-perl all 1.14.1-2 [20.3 kB] 191s Get:53 http://ftpmaster.internal/ubuntu plucky/main arm64 dh-strip-nondeterminism all 1.14.1-2 [5064 B] 191s Get:54 http://ftpmaster.internal/ubuntu plucky/main arm64 debugedit arm64 1:5.1-2 [46.1 kB] 191s Get:55 http://ftpmaster.internal/ubuntu plucky/main arm64 dwz arm64 0.15-1build6 [113 kB] 191s Get:56 http://ftpmaster.internal/ubuntu plucky/main arm64 gettext arm64 0.23.1-1 [998 kB] 191s Get:57 http://ftpmaster.internal/ubuntu plucky/main arm64 intltool-debian all 0.35.0+20060710.6 [23.2 kB] 191s Get:58 http://ftpmaster.internal/ubuntu plucky/main arm64 po-debconf all 1.0.21+nmu1 [233 kB] 191s Get:59 http://ftpmaster.internal/ubuntu plucky/main arm64 debhelper all 13.24.1ubuntu2 [895 kB] 191s Get:60 http://ftpmaster.internal/ubuntu plucky/universe arm64 dh-python all 6.20250108 [117 kB] 191s Get:61 http://ftpmaster.internal/ubuntu plucky/main arm64 xml-core all 0.19 [20.3 kB] 191s Get:62 http://ftpmaster.internal/ubuntu plucky/main arm64 docutils-common all 0.21.2+dfsg-2 [131 kB] 191s Get:63 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig arm64 2.15.0-2ubuntu1 [191 kB] 191s Get:64 http://ftpmaster.internal/ubuntu plucky/universe arm64 fonts-lyx all 2.4.3-1 [171 kB] 191s Get:65 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.1-2 [161 kB] 191s Get:66 http://ftpmaster.internal/ubuntu plucky/main arm64 libpixman-1-0 arm64 0.44.0-3 [197 kB] 191s Get:67 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-render0 arm64 1.17.0-2 [16.6 kB] 191s Get:68 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-shm0 arm64 1.17.0-2 [5884 B] 191s Get:69 http://ftpmaster.internal/ubuntu plucky/main arm64 libcairo2 arm64 1.18.2-2 [560 kB] 191s Get:70 http://ftpmaster.internal/ubuntu plucky/main arm64 libdatrie1 arm64 0.2.13-3build1 [19.2 kB] 191s Get:71 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate0 arm64 1.23-1 [46.2 kB] 191s Get:72 http://ftpmaster.internal/ubuntu plucky/main arm64 libexpat1-dev arm64 2.6.4-1 [129 kB] 191s Get:73 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 15-20250213-1ubuntu1 [443 kB] 191s Get:74 http://ftpmaster.internal/ubuntu plucky/main arm64 libgraphite2-3 arm64 1.3.14-2ubuntu1 [70.6 kB] 191s Get:75 http://ftpmaster.internal/ubuntu plucky/main arm64 libharfbuzz0b arm64 10.2.0-1 [490 kB] 191s Get:76 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhtscodecs2 arm64 1.6.1-2 [82.7 kB] 191s Get:77 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhts3t64 arm64 1.21+ds-1 [441 kB] 191s Get:78 http://ftpmaster.internal/ubuntu plucky/main arm64 libice6 arm64 2:1.1.1-1 [42.3 kB] 191s Get:79 http://ftpmaster.internal/ubuntu plucky/main arm64 libimagequant0 arm64 2.18.0-1build1 [37.1 kB] 191s Get:80 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg-turbo8 arm64 2.1.5-3ubuntu2 [165 kB] 191s Get:81 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 191s Get:82 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 191s Get:83 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 191s Get:84 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 191s Get:85 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libjs-sphinxdoc all 8.1.3-5 [31.0 kB] 191s Get:86 http://ftpmaster.internal/ubuntu plucky/main arm64 libjson-perl all 4.10000-1 [81.9 kB] 191s Get:87 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.1-2 [2307 kB] 191s Get:88 http://ftpmaster.internal/ubuntu plucky/universe arm64 liblbfgsb0 arm64 3.0+dfsg.4-1build1 [27.7 kB] 191s Get:89 http://ftpmaster.internal/ubuntu plucky/main arm64 liblcms2-2 arm64 2.16-2 [170 kB] 191s Get:90 http://ftpmaster.internal/ubuntu plucky/main arm64 liblerc4 arm64 4.0.0+ds-5ubuntu1 [167 kB] 191s Get:91 http://ftpmaster.internal/ubuntu plucky/main arm64 libthai-data all 0.1.29-2build1 [158 kB] 191s Get:92 http://ftpmaster.internal/ubuntu plucky/main arm64 libthai0 arm64 0.1.29-2build1 [18.2 kB] 191s Get:93 http://ftpmaster.internal/ubuntu plucky/main arm64 libpango-1.0-0 arm64 1.56.1-1 [238 kB] 191s Get:94 http://ftpmaster.internal/ubuntu plucky/main arm64 libpangoft2-1.0-0 arm64 1.56.1-1 [49.6 kB] 191s Get:95 http://ftpmaster.internal/ubuntu plucky/main arm64 libpangocairo-1.0-0 arm64 1.56.1-1 [27.6 kB] 191s Get:96 http://ftpmaster.internal/ubuntu plucky/main arm64 libpaper2 arm64 2.2.5-0.3 [17.3 kB] 191s Get:97 http://ftpmaster.internal/ubuntu plucky/main arm64 libpaper-utils arm64 2.2.5-0.3 [15.4 kB] 191s Get:98 http://ftpmaster.internal/ubuntu plucky/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1ubuntu1 [894 kB] 191s Get:99 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3.13-dev arm64 3.13.2-1 [5399 kB] 192s Get:100 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3-dev arm64 3.13.1-1~exp2 [10.5 kB] 192s Get:101 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3.12-dev arm64 3.12.9-1 [5569 kB] 192s Get:102 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3-all-dev arm64 3.13.1-1~exp2 [922 B] 192s Get:103 http://ftpmaster.internal/ubuntu plucky/universe arm64 libqhull-r8.0 arm64 2020.2-6build1 [189 kB] 192s Get:104 http://ftpmaster.internal/ubuntu plucky/main arm64 libraqm0 arm64 0.10.2-1 [14.9 kB] 192s Get:105 http://ftpmaster.internal/ubuntu plucky/main arm64 libsharpyuv0 arm64 1.5.0-0.1 [16.9 kB] 192s Get:106 http://ftpmaster.internal/ubuntu plucky/main arm64 libsm6 arm64 2:1.2.4-1 [16.4 kB] 192s Get:107 http://ftpmaster.internal/ubuntu plucky/main arm64 libjbig0 arm64 2.1-6.1ubuntu2 [29.3 kB] 192s Get:108 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebp7 arm64 1.5.0-0.1 [194 kB] 192s Get:109 http://ftpmaster.internal/ubuntu plucky/main arm64 libtiff6 arm64 4.5.1+git230720-4ubuntu4 [193 kB] 192s Get:110 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebpdemux2 arm64 1.5.0-0.1 [12.5 kB] 192s Get:111 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebpmux3 arm64 1.5.0-0.1 [25.4 kB] 192s Get:112 http://ftpmaster.internal/ubuntu plucky/main arm64 libxslt1.1 arm64 1.1.39-0exp1ubuntu2 [168 kB] 192s Get:113 http://ftpmaster.internal/ubuntu plucky/main arm64 libxt6t64 arm64 1:1.2.1-1.2build1 [168 kB] 192s Get:114 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy arm64 1:1.26.4+ds-13 [4148 kB] 193s Get:115 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pysam arm64 0.23.0+ds-1 [4080 kB] 193s Get:116 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pybedtools arm64 0.10.0-4 [12.4 MB] 194s Get:117 http://ftpmaster.internal/ubuntu plucky/universe arm64 pybedtools-bin all 0.10.0-4 [3214 B] 194s Get:118 http://ftpmaster.internal/ubuntu plucky/universe arm64 pybuild-plugin-autopkgtest all 6.20250108 [1744 B] 194s Get:119 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-packaging all 24.2-1 [51.5 kB] 194s Get:120 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pyproject-hooks all 1.2.0-1 [10.2 kB] 194s Get:121 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-toml all 0.10.2-1 [16.5 kB] 194s Get:122 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-wheel all 0.45.1-1 [57.7 kB] 194s Get:123 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-build all 1.2.2-1 [31.0 kB] 194s Get:124 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-installer all 0.7.0+dfsg1-3 [17.4 kB] 194s Get:125 http://ftpmaster.internal/ubuntu plucky/universe arm64 pybuild-plugin-pyproject all 6.20250108 [1726 B] 194s Get:126 http://ftpmaster.internal/ubuntu plucky/universe arm64 python-matplotlib-data all 3.8.3-3ubuntu2 [2929 kB] 194s Get:127 http://ftpmaster.internal/ubuntu plucky/universe arm64 python-pybedtools-doc all 0.10.0-4 [269 kB] 194s Get:128 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-all arm64 3.13.1-1~exp2 [894 B] 194s Get:129 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-dev arm64 3.13.2-1 [508 kB] 194s Get:130 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-dev arm64 3.13.1-1~exp2 [26.7 kB] 194s Get:131 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.12-dev arm64 3.12.9-1 [505 kB] 194s Get:132 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-all-dev arm64 3.13.1-1~exp2 [918 B] 194s Get:133 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-brotli arm64 1.1.0-2build3 [342 kB] 194s Get:134 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-contourpy arm64 1.3.1-1 [216 kB] 194s Get:135 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-cycler all 0.12.1-1 [9716 B] 194s Get:136 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-dateutil all 2.9.0-3 [80.2 kB] 194s Get:137 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-decorator all 5.1.1-5 [10.1 kB] 194s Get:138 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-defusedxml all 0.7.1-3 [42.2 kB] 194s Get:139 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-roman all 5.0-1 [10.3 kB] 194s Get:140 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-docutils all 0.21.2+dfsg-2 [409 kB] 194s Get:141 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-pytz all 2025.1-3 [162 kB] 194s Get:142 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-tz all 2025.1-3 [1866 B] 194s Get:143 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-platformdirs all 4.3.6-1 [16.8 kB] 194s Get:144 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-fs all 2.4.16-6 [90.7 kB] 194s Get:145 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-lxml arm64 5.3.1-1 [1600 kB] 194s Get:146 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-lz4 arm64 4.4.0+dfsg-1 [27.3 kB] 194s Get:147 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-scipy arm64 1.14.1-4ubuntu1 [19.5 MB] 195s Get:148 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-mpmath all 1.3.0-1 [425 kB] 195s Get:149 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-sympy all 1.13.3-1 [4228 kB] 196s Get:150 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-ufolib2 all 0.17.0+dfsg1-1 [33.5 kB] 196s Get:151 http://ftpmaster.internal/ubuntu plucky/universe arm64 unicode-data all 15.1.0-1 [8878 kB] 196s Get:152 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-fonttools arm64 4.55.3-2 [1615 kB] 196s Get:153 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-imagesize all 1.4.1-1 [6844 B] 196s Get:154 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-iniconfig all 1.1.1-2 [6024 B] 196s Get:155 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-kiwisolver arm64 1.4.7-3 [62.5 kB] 196s Get:156 http://ftpmaster.internal/ubuntu plucky/main arm64 libopenjp2-7 arm64 2.5.0-2ubuntu3 [182 kB] 196s Get:157 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-pil arm64 11.1.0-5 [491 kB] 196s Get:158 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.12-tk arm64 3.12.9-1 [115 kB] 196s Get:159 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-tk arm64 3.13.2-1 [106 kB] 196s Get:160 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-tk arm64 3.13.1-1 [9770 B] 196s Get:161 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pil.imagetk arm64 11.1.0-5 [9948 B] 196s Get:162 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-matplotlib arm64 3.8.3-3ubuntu2 [4616 kB] 196s Get:163 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 sphinx-common all 8.1.3-5 [663 kB] 196s Get:164 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-alabaster all 0.7.16-0.1 [18.5 kB] 196s Get:165 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-snowballstemmer all 2.2.0-4build1 [59.8 kB] 196s Get:166 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-sphinx all 8.1.3-5 [474 kB] 196s Get:167 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-tabulate all 0.9.0-1 [45.3 kB] 196s Get:168 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-numpydoc all 1.8.0-1 [52.4 kB] 196s Get:169 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pandas-lib arm64 2.2.3+dfsg-8 [6925 kB] 197s Get:170 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pandas all 2.2.3+dfsg-8 [3112 kB] 197s Get:171 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pluggy all 1.5.0-1 [21.0 kB] 197s Get:172 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-psutil arm64 5.9.8-2build3 [196 kB] 197s Get:173 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pytest all 8.3.4-1 [252 kB] 197s Get:174 http://ftpmaster.internal/ubuntu plucky/main arm64 zip arm64 3.0-14ubuntu2 [173 kB] 197s Get:175 http://ftpmaster.internal/ubuntu plucky/main arm64 unzip arm64 6.0-28ubuntu6 [178 kB] 197s Get:176 http://ftpmaster.internal/ubuntu plucky/main arm64 xdg-utils all 1.2.1-2ubuntu1 [66.0 kB] 197s Get:177 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-base-core arm64 4.4.2-1build1 [28.4 MB] 199s Preconfiguring packages ... 199s Fetched 204 MB in 10s (20.0 MB/s) 199s Selecting previously unselected package python3.12-minimal. 199s (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 ... 116670 files and directories currently installed.) 199s Preparing to unpack .../000-python3.12-minimal_3.12.9-1_arm64.deb ... 199s Unpacking python3.12-minimal (3.12.9-1) ... 199s Selecting previously unselected package sgml-base. 199s Preparing to unpack .../001-sgml-base_1.31_all.deb ... 199s Unpacking sgml-base (1.31) ... 199s Selecting previously unselected package python3.12. 199s Preparing to unpack .../002-python3.12_3.12.9-1_arm64.deb ... 199s Unpacking python3.12 (3.12.9-1) ... 200s Selecting previously unselected package m4. 200s Preparing to unpack .../003-m4_1.4.19-5_arm64.deb ... 200s Unpacking m4 (1.4.19-5) ... 200s Selecting previously unselected package autoconf. 200s Preparing to unpack .../004-autoconf_2.72-3_all.deb ... 200s Unpacking autoconf (2.72-3) ... 200s Selecting previously unselected package autotools-dev. 200s Preparing to unpack .../005-autotools-dev_20220109.1_all.deb ... 200s Unpacking autotools-dev (20220109.1) ... 200s Selecting previously unselected package automake. 200s Preparing to unpack .../006-automake_1%3a1.17-3_all.deb ... 200s Unpacking automake (1:1.17-3) ... 200s Selecting previously unselected package autopoint. 200s Preparing to unpack .../007-autopoint_0.23.1-1_all.deb ... 200s Unpacking autopoint (0.23.1-1) ... 200s Selecting previously unselected package bedtools. 200s Preparing to unpack .../008-bedtools_2.31.1+dfsg-2_arm64.deb ... 200s Unpacking bedtools (2.31.1+dfsg-2) ... 200s Selecting previously unselected package libtcl8.6:arm64. 200s Preparing to unpack .../009-libtcl8.6_8.6.16+dfsg-1_arm64.deb ... 200s Unpacking libtcl8.6:arm64 (8.6.16+dfsg-1) ... 200s Selecting previously unselected package fonts-dejavu-mono. 200s Preparing to unpack .../010-fonts-dejavu-mono_2.37-8_all.deb ... 200s Unpacking fonts-dejavu-mono (2.37-8) ... 200s Selecting previously unselected package fonts-dejavu-core. 200s Preparing to unpack .../011-fonts-dejavu-core_2.37-8_all.deb ... 200s Unpacking fonts-dejavu-core (2.37-8) ... 200s Selecting previously unselected package fontconfig-config. 200s Preparing to unpack .../012-fontconfig-config_2.15.0-2ubuntu1_arm64.deb ... 201s Unpacking fontconfig-config (2.15.0-2ubuntu1) ... 201s Selecting previously unselected package libfontconfig1:arm64. 201s Preparing to unpack .../013-libfontconfig1_2.15.0-2ubuntu1_arm64.deb ... 201s Unpacking libfontconfig1:arm64 (2.15.0-2ubuntu1) ... 201s Selecting previously unselected package libxrender1:arm64. 201s Preparing to unpack .../014-libxrender1_1%3a0.9.10-1.1build1_arm64.deb ... 201s Unpacking libxrender1:arm64 (1:0.9.10-1.1build1) ... 201s Selecting previously unselected package libxft2:arm64. 201s Preparing to unpack .../015-libxft2_2.3.6-1build1_arm64.deb ... 201s Unpacking libxft2:arm64 (2.3.6-1build1) ... 201s Selecting previously unselected package x11-common. 201s Preparing to unpack .../016-x11-common_1%3a7.7+23ubuntu3_all.deb ... 201s Unpacking x11-common (1:7.7+23ubuntu3) ... 201s Selecting previously unselected package libxss1:arm64. 201s Preparing to unpack .../017-libxss1_1%3a1.2.3-1build3_arm64.deb ... 201s Unpacking libxss1:arm64 (1:1.2.3-1build3) ... 201s Selecting previously unselected package libtk8.6:arm64. 201s Preparing to unpack .../018-libtk8.6_8.6.16-1_arm64.deb ... 201s Unpacking libtk8.6:arm64 (8.6.16-1) ... 201s Selecting previously unselected package tk8.6-blt2.5. 201s Preparing to unpack .../019-tk8.6-blt2.5_2.5.3+dfsg-7build1_arm64.deb ... 201s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 201s Selecting previously unselected package blt. 201s Preparing to unpack .../020-blt_2.5.3+dfsg-7build1_arm64.deb ... 201s Unpacking blt (2.5.3+dfsg-7build1) ... 201s Selecting previously unselected package libisl23:arm64. 201s Preparing to unpack .../021-libisl23_0.27-1_arm64.deb ... 201s Unpacking libisl23:arm64 (0.27-1) ... 201s Selecting previously unselected package libmpc3:arm64. 201s Preparing to unpack .../022-libmpc3_1.3.1-1build2_arm64.deb ... 201s Unpacking libmpc3:arm64 (1.3.1-1build2) ... 201s Selecting previously unselected package cpp-14-aarch64-linux-gnu. 201s Preparing to unpack .../023-cpp-14-aarch64-linux-gnu_14.2.0-17ubuntu1_arm64.deb ... 201s Unpacking cpp-14-aarch64-linux-gnu (14.2.0-17ubuntu1) ... 202s Selecting previously unselected package cpp-14. 202s Preparing to unpack .../024-cpp-14_14.2.0-17ubuntu1_arm64.deb ... 202s Unpacking cpp-14 (14.2.0-17ubuntu1) ... 202s Selecting previously unselected package cpp-aarch64-linux-gnu. 202s Preparing to unpack .../025-cpp-aarch64-linux-gnu_4%3a14.2.0-1ubuntu1_arm64.deb ... 202s Unpacking cpp-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 202s Selecting previously unselected package cpp. 202s Preparing to unpack .../026-cpp_4%3a14.2.0-1ubuntu1_arm64.deb ... 202s Unpacking cpp (4:14.2.0-1ubuntu1) ... 202s Selecting previously unselected package libcc1-0:arm64. 202s Preparing to unpack .../027-libcc1-0_15-20250213-1ubuntu1_arm64.deb ... 202s Unpacking libcc1-0:arm64 (15-20250213-1ubuntu1) ... 202s Selecting previously unselected package libgomp1:arm64. 202s Preparing to unpack .../028-libgomp1_15-20250213-1ubuntu1_arm64.deb ... 202s Unpacking libgomp1:arm64 (15-20250213-1ubuntu1) ... 202s Selecting previously unselected package libitm1:arm64. 202s Preparing to unpack .../029-libitm1_15-20250213-1ubuntu1_arm64.deb ... 202s Unpacking libitm1:arm64 (15-20250213-1ubuntu1) ... 202s Selecting previously unselected package libasan8:arm64. 202s Preparing to unpack .../030-libasan8_15-20250213-1ubuntu1_arm64.deb ... 202s Unpacking libasan8:arm64 (15-20250213-1ubuntu1) ... 202s Selecting previously unselected package liblsan0:arm64. 202s Preparing to unpack .../031-liblsan0_15-20250213-1ubuntu1_arm64.deb ... 202s Unpacking liblsan0:arm64 (15-20250213-1ubuntu1) ... 202s Selecting previously unselected package libtsan2:arm64. 202s Preparing to unpack .../032-libtsan2_15-20250213-1ubuntu1_arm64.deb ... 202s Unpacking libtsan2:arm64 (15-20250213-1ubuntu1) ... 202s Selecting previously unselected package libubsan1:arm64. 202s Preparing to unpack .../033-libubsan1_15-20250213-1ubuntu1_arm64.deb ... 202s Unpacking libubsan1:arm64 (15-20250213-1ubuntu1) ... 202s Selecting previously unselected package libhwasan0:arm64. 202s Preparing to unpack .../034-libhwasan0_15-20250213-1ubuntu1_arm64.deb ... 202s Unpacking libhwasan0:arm64 (15-20250213-1ubuntu1) ... 202s Selecting previously unselected package libgcc-14-dev:arm64. 202s Preparing to unpack .../035-libgcc-14-dev_14.2.0-17ubuntu1_arm64.deb ... 202s Unpacking libgcc-14-dev:arm64 (14.2.0-17ubuntu1) ... 202s Selecting previously unselected package gcc-14-aarch64-linux-gnu. 202s Preparing to unpack .../036-gcc-14-aarch64-linux-gnu_14.2.0-17ubuntu1_arm64.deb ... 202s Unpacking gcc-14-aarch64-linux-gnu (14.2.0-17ubuntu1) ... 203s Selecting previously unselected package gcc-14. 203s Preparing to unpack .../037-gcc-14_14.2.0-17ubuntu1_arm64.deb ... 203s Unpacking gcc-14 (14.2.0-17ubuntu1) ... 203s Selecting previously unselected package gcc-aarch64-linux-gnu. 203s Preparing to unpack .../038-gcc-aarch64-linux-gnu_4%3a14.2.0-1ubuntu1_arm64.deb ... 203s Unpacking gcc-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 203s Selecting previously unselected package gcc. 203s Preparing to unpack .../039-gcc_4%3a14.2.0-1ubuntu1_arm64.deb ... 203s Unpacking gcc (4:14.2.0-1ubuntu1) ... 203s Selecting previously unselected package libstdc++-14-dev:arm64. 203s Preparing to unpack .../040-libstdc++-14-dev_14.2.0-17ubuntu1_arm64.deb ... 203s Unpacking libstdc++-14-dev:arm64 (14.2.0-17ubuntu1) ... 203s Selecting previously unselected package g++-14-aarch64-linux-gnu. 203s Preparing to unpack .../041-g++-14-aarch64-linux-gnu_14.2.0-17ubuntu1_arm64.deb ... 203s Unpacking g++-14-aarch64-linux-gnu (14.2.0-17ubuntu1) ... 204s Selecting previously unselected package g++-14. 204s Preparing to unpack .../042-g++-14_14.2.0-17ubuntu1_arm64.deb ... 204s Unpacking g++-14 (14.2.0-17ubuntu1) ... 204s Selecting previously unselected package g++-aarch64-linux-gnu. 204s Preparing to unpack .../043-g++-aarch64-linux-gnu_4%3a14.2.0-1ubuntu1_arm64.deb ... 204s Unpacking g++-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 204s Selecting previously unselected package g++. 204s Preparing to unpack .../044-g++_4%3a14.2.0-1ubuntu1_arm64.deb ... 204s Unpacking g++ (4:14.2.0-1ubuntu1) ... 204s Selecting previously unselected package build-essential. 204s Preparing to unpack .../045-build-essential_12.10ubuntu1_arm64.deb ... 204s Unpacking build-essential (12.10ubuntu1) ... 204s Selecting previously unselected package cython3. 204s Preparing to unpack .../046-cython3_3.0.11+dfsg-2ubuntu1_arm64.deb ... 204s Unpacking cython3 (3.0.11+dfsg-2ubuntu1) ... 204s Selecting previously unselected package libdebhelper-perl. 204s Preparing to unpack .../047-libdebhelper-perl_13.24.1ubuntu2_all.deb ... 204s Unpacking libdebhelper-perl (13.24.1ubuntu2) ... 204s Selecting previously unselected package libtool. 204s Preparing to unpack .../048-libtool_2.5.4-3build1_all.deb ... 204s Unpacking libtool (2.5.4-3build1) ... 204s Selecting previously unselected package dh-autoreconf. 204s Preparing to unpack .../049-dh-autoreconf_20_all.deb ... 204s Unpacking dh-autoreconf (20) ... 204s Selecting previously unselected package libarchive-zip-perl. 204s Preparing to unpack .../050-libarchive-zip-perl_1.68-1_all.deb ... 204s Unpacking libarchive-zip-perl (1.68-1) ... 204s Selecting previously unselected package libfile-stripnondeterminism-perl. 204s Preparing to unpack .../051-libfile-stripnondeterminism-perl_1.14.1-2_all.deb ... 204s Unpacking libfile-stripnondeterminism-perl (1.14.1-2) ... 204s Selecting previously unselected package dh-strip-nondeterminism. 204s Preparing to unpack .../052-dh-strip-nondeterminism_1.14.1-2_all.deb ... 204s Unpacking dh-strip-nondeterminism (1.14.1-2) ... 204s Selecting previously unselected package debugedit. 204s Preparing to unpack .../053-debugedit_1%3a5.1-2_arm64.deb ... 204s Unpacking debugedit (1:5.1-2) ... 204s Selecting previously unselected package dwz. 204s Preparing to unpack .../054-dwz_0.15-1build6_arm64.deb ... 204s Unpacking dwz (0.15-1build6) ... 205s Selecting previously unselected package gettext. 205s Preparing to unpack .../055-gettext_0.23.1-1_arm64.deb ... 205s Unpacking gettext (0.23.1-1) ... 205s Selecting previously unselected package intltool-debian. 205s Preparing to unpack .../056-intltool-debian_0.35.0+20060710.6_all.deb ... 205s Unpacking intltool-debian (0.35.0+20060710.6) ... 205s Selecting previously unselected package po-debconf. 205s Preparing to unpack .../057-po-debconf_1.0.21+nmu1_all.deb ... 205s Unpacking po-debconf (1.0.21+nmu1) ... 205s Selecting previously unselected package debhelper. 205s Preparing to unpack .../058-debhelper_13.24.1ubuntu2_all.deb ... 205s Unpacking debhelper (13.24.1ubuntu2) ... 205s Selecting previously unselected package dh-python. 205s Preparing to unpack .../059-dh-python_6.20250108_all.deb ... 205s Unpacking dh-python (6.20250108) ... 205s Selecting previously unselected package xml-core. 205s Preparing to unpack .../060-xml-core_0.19_all.deb ... 205s Unpacking xml-core (0.19) ... 205s Selecting previously unselected package docutils-common. 205s Preparing to unpack .../061-docutils-common_0.21.2+dfsg-2_all.deb ... 205s Unpacking docutils-common (0.21.2+dfsg-2) ... 205s Selecting previously unselected package fontconfig. 205s Preparing to unpack .../062-fontconfig_2.15.0-2ubuntu1_arm64.deb ... 205s Unpacking fontconfig (2.15.0-2ubuntu1) ... 205s Selecting previously unselected package fonts-lyx. 205s Preparing to unpack .../063-fonts-lyx_2.4.3-1_all.deb ... 205s Unpacking fonts-lyx (2.4.3-1) ... 205s Selecting previously unselected package libblas3:arm64. 205s Preparing to unpack .../064-libblas3_3.12.1-2_arm64.deb ... 205s Unpacking libblas3:arm64 (3.12.1-2) ... 205s Selecting previously unselected package libpixman-1-0:arm64. 205s Preparing to unpack .../065-libpixman-1-0_0.44.0-3_arm64.deb ... 205s Unpacking libpixman-1-0:arm64 (0.44.0-3) ... 205s Selecting previously unselected package libxcb-render0:arm64. 205s Preparing to unpack .../066-libxcb-render0_1.17.0-2_arm64.deb ... 205s Unpacking libxcb-render0:arm64 (1.17.0-2) ... 205s Selecting previously unselected package libxcb-shm0:arm64. 205s Preparing to unpack .../067-libxcb-shm0_1.17.0-2_arm64.deb ... 205s Unpacking libxcb-shm0:arm64 (1.17.0-2) ... 205s Selecting previously unselected package libcairo2:arm64. 205s Preparing to unpack .../068-libcairo2_1.18.2-2_arm64.deb ... 205s Unpacking libcairo2:arm64 (1.18.2-2) ... 205s Selecting previously unselected package libdatrie1:arm64. 205s Preparing to unpack .../069-libdatrie1_0.2.13-3build1_arm64.deb ... 205s Unpacking libdatrie1:arm64 (0.2.13-3build1) ... 206s Selecting previously unselected package libdeflate0:arm64. 206s Preparing to unpack .../070-libdeflate0_1.23-1_arm64.deb ... 206s Unpacking libdeflate0:arm64 (1.23-1) ... 206s Selecting previously unselected package libexpat1-dev:arm64. 206s Preparing to unpack .../071-libexpat1-dev_2.6.4-1_arm64.deb ... 206s Unpacking libexpat1-dev:arm64 (2.6.4-1) ... 206s Selecting previously unselected package libgfortran5:arm64. 206s Preparing to unpack .../072-libgfortran5_15-20250213-1ubuntu1_arm64.deb ... 206s Unpacking libgfortran5:arm64 (15-20250213-1ubuntu1) ... 206s Selecting previously unselected package libgraphite2-3:arm64. 206s Preparing to unpack .../073-libgraphite2-3_1.3.14-2ubuntu1_arm64.deb ... 206s Unpacking libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 206s Selecting previously unselected package libharfbuzz0b:arm64. 206s Preparing to unpack .../074-libharfbuzz0b_10.2.0-1_arm64.deb ... 206s Unpacking libharfbuzz0b:arm64 (10.2.0-1) ... 206s Selecting previously unselected package libhtscodecs2:arm64. 206s Preparing to unpack .../075-libhtscodecs2_1.6.1-2_arm64.deb ... 206s Unpacking libhtscodecs2:arm64 (1.6.1-2) ... 206s Selecting previously unselected package libhts3t64:arm64. 206s Preparing to unpack .../076-libhts3t64_1.21+ds-1_arm64.deb ... 206s Unpacking libhts3t64:arm64 (1.21+ds-1) ... 206s Selecting previously unselected package libice6:arm64. 206s Preparing to unpack .../077-libice6_2%3a1.1.1-1_arm64.deb ... 206s Unpacking libice6:arm64 (2:1.1.1-1) ... 206s Selecting previously unselected package libimagequant0:arm64. 206s Preparing to unpack .../078-libimagequant0_2.18.0-1build1_arm64.deb ... 206s Unpacking libimagequant0:arm64 (2.18.0-1build1) ... 206s Selecting previously unselected package libjpeg-turbo8:arm64. 206s Preparing to unpack .../079-libjpeg-turbo8_2.1.5-3ubuntu2_arm64.deb ... 206s Unpacking libjpeg-turbo8:arm64 (2.1.5-3ubuntu2) ... 206s Selecting previously unselected package libjpeg8:arm64. 206s Preparing to unpack .../080-libjpeg8_8c-2ubuntu11_arm64.deb ... 206s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 206s Selecting previously unselected package libjs-jquery. 206s Preparing to unpack .../081-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 206s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 206s Selecting previously unselected package libjs-jquery-ui. 206s Preparing to unpack .../082-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... 206s Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... 206s Selecting previously unselected package libjs-underscore. 206s Preparing to unpack .../083-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 206s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 206s Selecting previously unselected package libjs-sphinxdoc. 207s Preparing to unpack .../084-libjs-sphinxdoc_8.1.3-5_all.deb ... 207s Unpacking libjs-sphinxdoc (8.1.3-5) ... 207s Selecting previously unselected package libjson-perl. 207s Preparing to unpack .../085-libjson-perl_4.10000-1_all.deb ... 207s Unpacking libjson-perl (4.10000-1) ... 207s Selecting previously unselected package liblapack3:arm64. 207s Preparing to unpack .../086-liblapack3_3.12.1-2_arm64.deb ... 207s Unpacking liblapack3:arm64 (3.12.1-2) ... 207s Selecting previously unselected package liblbfgsb0:arm64. 207s Preparing to unpack .../087-liblbfgsb0_3.0+dfsg.4-1build1_arm64.deb ... 207s Unpacking liblbfgsb0:arm64 (3.0+dfsg.4-1build1) ... 207s Selecting previously unselected package liblcms2-2:arm64. 207s Preparing to unpack .../088-liblcms2-2_2.16-2_arm64.deb ... 207s Unpacking liblcms2-2:arm64 (2.16-2) ... 207s Selecting previously unselected package liblerc4:arm64. 207s Preparing to unpack .../089-liblerc4_4.0.0+ds-5ubuntu1_arm64.deb ... 207s Unpacking liblerc4:arm64 (4.0.0+ds-5ubuntu1) ... 207s Selecting previously unselected package libthai-data. 207s Preparing to unpack .../090-libthai-data_0.1.29-2build1_all.deb ... 207s Unpacking libthai-data (0.1.29-2build1) ... 207s Selecting previously unselected package libthai0:arm64. 207s Preparing to unpack .../091-libthai0_0.1.29-2build1_arm64.deb ... 207s Unpacking libthai0:arm64 (0.1.29-2build1) ... 207s Selecting previously unselected package libpango-1.0-0:arm64. 207s Preparing to unpack .../092-libpango-1.0-0_1.56.1-1_arm64.deb ... 207s Unpacking libpango-1.0-0:arm64 (1.56.1-1) ... 207s Selecting previously unselected package libpangoft2-1.0-0:arm64. 207s Preparing to unpack .../093-libpangoft2-1.0-0_1.56.1-1_arm64.deb ... 207s Unpacking libpangoft2-1.0-0:arm64 (1.56.1-1) ... 207s Selecting previously unselected package libpangocairo-1.0-0:arm64. 207s Preparing to unpack .../094-libpangocairo-1.0-0_1.56.1-1_arm64.deb ... 207s Unpacking libpangocairo-1.0-0:arm64 (1.56.1-1) ... 207s Selecting previously unselected package libpaper2:arm64. 208s Preparing to unpack .../095-libpaper2_2.2.5-0.3_arm64.deb ... 208s Unpacking libpaper2:arm64 (2.2.5-0.3) ... 208s Selecting previously unselected package libpaper-utils. 208s Preparing to unpack .../096-libpaper-utils_2.2.5-0.3_arm64.deb ... 208s Unpacking libpaper-utils (2.2.5-0.3) ... 208s Selecting previously unselected package zlib1g-dev:arm64. 208s Preparing to unpack .../097-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1ubuntu1_arm64.deb ... 208s Unpacking zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 208s Selecting previously unselected package libpython3.13-dev:arm64. 208s Preparing to unpack .../098-libpython3.13-dev_3.13.2-1_arm64.deb ... 208s Unpacking libpython3.13-dev:arm64 (3.13.2-1) ... 208s Selecting previously unselected package libpython3-dev:arm64. 208s Preparing to unpack .../099-libpython3-dev_3.13.1-1~exp2_arm64.deb ... 208s Unpacking libpython3-dev:arm64 (3.13.1-1~exp2) ... 208s Selecting previously unselected package libpython3.12-dev:arm64. 208s Preparing to unpack .../100-libpython3.12-dev_3.12.9-1_arm64.deb ... 208s Unpacking libpython3.12-dev:arm64 (3.12.9-1) ... 208s Selecting previously unselected package libpython3-all-dev:arm64. 208s Preparing to unpack .../101-libpython3-all-dev_3.13.1-1~exp2_arm64.deb ... 208s Unpacking libpython3-all-dev:arm64 (3.13.1-1~exp2) ... 208s Selecting previously unselected package libqhull-r8.0:arm64. 208s Preparing to unpack .../102-libqhull-r8.0_2020.2-6build1_arm64.deb ... 208s Unpacking libqhull-r8.0:arm64 (2020.2-6build1) ... 208s Selecting previously unselected package libraqm0:arm64. 208s Preparing to unpack .../103-libraqm0_0.10.2-1_arm64.deb ... 208s Unpacking libraqm0:arm64 (0.10.2-1) ... 208s Selecting previously unselected package libsharpyuv0:arm64. 208s Preparing to unpack .../104-libsharpyuv0_1.5.0-0.1_arm64.deb ... 208s Unpacking libsharpyuv0:arm64 (1.5.0-0.1) ... 208s Selecting previously unselected package libsm6:arm64. 208s Preparing to unpack .../105-libsm6_2%3a1.2.4-1_arm64.deb ... 208s Unpacking libsm6:arm64 (2:1.2.4-1) ... 209s Selecting previously unselected package libjbig0:arm64. 209s Preparing to unpack .../106-libjbig0_2.1-6.1ubuntu2_arm64.deb ... 209s Unpacking libjbig0:arm64 (2.1-6.1ubuntu2) ... 209s Selecting previously unselected package libwebp7:arm64. 209s Preparing to unpack .../107-libwebp7_1.5.0-0.1_arm64.deb ... 209s Unpacking libwebp7:arm64 (1.5.0-0.1) ... 209s Selecting previously unselected package libtiff6:arm64. 209s Preparing to unpack .../108-libtiff6_4.5.1+git230720-4ubuntu4_arm64.deb ... 209s Unpacking libtiff6:arm64 (4.5.1+git230720-4ubuntu4) ... 209s Selecting previously unselected package libwebpdemux2:arm64. 209s Preparing to unpack .../109-libwebpdemux2_1.5.0-0.1_arm64.deb ... 209s Unpacking libwebpdemux2:arm64 (1.5.0-0.1) ... 209s Selecting previously unselected package libwebpmux3:arm64. 209s Preparing to unpack .../110-libwebpmux3_1.5.0-0.1_arm64.deb ... 209s Unpacking libwebpmux3:arm64 (1.5.0-0.1) ... 209s Selecting previously unselected package libxslt1.1:arm64. 209s Preparing to unpack .../111-libxslt1.1_1.1.39-0exp1ubuntu2_arm64.deb ... 209s Unpacking libxslt1.1:arm64 (1.1.39-0exp1ubuntu2) ... 209s Selecting previously unselected package libxt6t64:arm64. 209s Preparing to unpack .../112-libxt6t64_1%3a1.2.1-1.2build1_arm64.deb ... 209s Unpacking libxt6t64:arm64 (1:1.2.1-1.2build1) ... 209s Selecting previously unselected package python3-numpy. 209s Preparing to unpack .../113-python3-numpy_1%3a1.26.4+ds-13_arm64.deb ... 209s Unpacking python3-numpy (1:1.26.4+ds-13) ... 209s Selecting previously unselected package python3-pysam. 209s Preparing to unpack .../114-python3-pysam_0.23.0+ds-1_arm64.deb ... 209s Unpacking python3-pysam (0.23.0+ds-1) ... 210s Selecting previously unselected package python3-pybedtools. 210s Preparing to unpack .../115-python3-pybedtools_0.10.0-4_arm64.deb ... 210s Unpacking python3-pybedtools (0.10.0-4) ... 210s Selecting previously unselected package pybedtools-bin. 210s Preparing to unpack .../116-pybedtools-bin_0.10.0-4_all.deb ... 210s Unpacking pybedtools-bin (0.10.0-4) ... 210s Selecting previously unselected package pybuild-plugin-autopkgtest. 210s Preparing to unpack .../117-pybuild-plugin-autopkgtest_6.20250108_all.deb ... 210s Unpacking pybuild-plugin-autopkgtest (6.20250108) ... 210s Selecting previously unselected package python3-packaging. 210s Preparing to unpack .../118-python3-packaging_24.2-1_all.deb ... 210s Unpacking python3-packaging (24.2-1) ... 210s Selecting previously unselected package python3-pyproject-hooks. 210s Preparing to unpack .../119-python3-pyproject-hooks_1.2.0-1_all.deb ... 210s Unpacking python3-pyproject-hooks (1.2.0-1) ... 210s Selecting previously unselected package python3-toml. 210s Preparing to unpack .../120-python3-toml_0.10.2-1_all.deb ... 210s Unpacking python3-toml (0.10.2-1) ... 210s Selecting previously unselected package python3-wheel. 210s Preparing to unpack .../121-python3-wheel_0.45.1-1_all.deb ... 210s Unpacking python3-wheel (0.45.1-1) ... 210s Selecting previously unselected package python3-build. 210s Preparing to unpack .../122-python3-build_1.2.2-1_all.deb ... 210s Unpacking python3-build (1.2.2-1) ... 210s Selecting previously unselected package python3-installer. 210s Preparing to unpack .../123-python3-installer_0.7.0+dfsg1-3_all.deb ... 210s Unpacking python3-installer (0.7.0+dfsg1-3) ... 210s Selecting previously unselected package pybuild-plugin-pyproject. 210s Preparing to unpack .../124-pybuild-plugin-pyproject_6.20250108_all.deb ... 210s Unpacking pybuild-plugin-pyproject (6.20250108) ... 211s Selecting previously unselected package python-matplotlib-data. 211s Preparing to unpack .../125-python-matplotlib-data_3.8.3-3ubuntu2_all.deb ... 211s Unpacking python-matplotlib-data (3.8.3-3ubuntu2) ... 211s Selecting previously unselected package python-pybedtools-doc. 211s Preparing to unpack .../126-python-pybedtools-doc_0.10.0-4_all.deb ... 211s Unpacking python-pybedtools-doc (0.10.0-4) ... 211s Selecting previously unselected package python3-all. 211s Preparing to unpack .../127-python3-all_3.13.1-1~exp2_arm64.deb ... 211s Unpacking python3-all (3.13.1-1~exp2) ... 211s Selecting previously unselected package python3.13-dev. 211s Preparing to unpack .../128-python3.13-dev_3.13.2-1_arm64.deb ... 211s Unpacking python3.13-dev (3.13.2-1) ... 211s Selecting previously unselected package python3-dev. 211s Preparing to unpack .../129-python3-dev_3.13.1-1~exp2_arm64.deb ... 211s Unpacking python3-dev (3.13.1-1~exp2) ... 211s Selecting previously unselected package python3.12-dev. 211s Preparing to unpack .../130-python3.12-dev_3.12.9-1_arm64.deb ... 211s Unpacking python3.12-dev (3.12.9-1) ... 211s Selecting previously unselected package python3-all-dev. 211s Preparing to unpack .../131-python3-all-dev_3.13.1-1~exp2_arm64.deb ... 211s Unpacking python3-all-dev (3.13.1-1~exp2) ... 211s Selecting previously unselected package python3-brotli. 211s Preparing to unpack .../132-python3-brotli_1.1.0-2build3_arm64.deb ... 211s Unpacking python3-brotli (1.1.0-2build3) ... 211s Selecting previously unselected package python3-contourpy. 211s Preparing to unpack .../133-python3-contourpy_1.3.1-1_arm64.deb ... 211s Unpacking python3-contourpy (1.3.1-1) ... 211s Selecting previously unselected package python3-cycler. 211s Preparing to unpack .../134-python3-cycler_0.12.1-1_all.deb ... 211s Unpacking python3-cycler (0.12.1-1) ... 211s Selecting previously unselected package python3-dateutil. 211s Preparing to unpack .../135-python3-dateutil_2.9.0-3_all.deb ... 211s Unpacking python3-dateutil (2.9.0-3) ... 211s Selecting previously unselected package python3-decorator. 211s Preparing to unpack .../136-python3-decorator_5.1.1-5_all.deb ... 211s Unpacking python3-decorator (5.1.1-5) ... 211s Selecting previously unselected package python3-defusedxml. 211s Preparing to unpack .../137-python3-defusedxml_0.7.1-3_all.deb ... 211s Unpacking python3-defusedxml (0.7.1-3) ... 212s Selecting previously unselected package python3-roman. 212s Preparing to unpack .../138-python3-roman_5.0-1_all.deb ... 212s Unpacking python3-roman (5.0-1) ... 212s Selecting previously unselected package python3-docutils. 212s Preparing to unpack .../139-python3-docutils_0.21.2+dfsg-2_all.deb ... 212s Unpacking python3-docutils (0.21.2+dfsg-2) ... 212s Selecting previously unselected package python3-pytz. 212s Preparing to unpack .../140-python3-pytz_2025.1-3_all.deb ... 212s Unpacking python3-pytz (2025.1-3) ... 212s Selecting previously unselected package python3-tz. 212s Preparing to unpack .../141-python3-tz_2025.1-3_all.deb ... 212s Unpacking python3-tz (2025.1-3) ... 212s Selecting previously unselected package python3-platformdirs. 212s Preparing to unpack .../142-python3-platformdirs_4.3.6-1_all.deb ... 212s Unpacking python3-platformdirs (4.3.6-1) ... 212s Selecting previously unselected package python3-fs. 212s Preparing to unpack .../143-python3-fs_2.4.16-6_all.deb ... 212s Unpacking python3-fs (2.4.16-6) ... 212s Selecting previously unselected package python3-lxml:arm64. 212s Preparing to unpack .../144-python3-lxml_5.3.1-1_arm64.deb ... 212s Unpacking python3-lxml:arm64 (5.3.1-1) ... 212s Selecting previously unselected package python3-lz4. 212s Preparing to unpack .../145-python3-lz4_4.4.0+dfsg-1_arm64.deb ... 212s Unpacking python3-lz4 (4.4.0+dfsg-1) ... 212s Selecting previously unselected package python3-scipy. 212s Preparing to unpack .../146-python3-scipy_1.14.1-4ubuntu1_arm64.deb ... 212s Unpacking python3-scipy (1.14.1-4ubuntu1) ... 213s Selecting previously unselected package python3-mpmath. 213s Preparing to unpack .../147-python3-mpmath_1.3.0-1_all.deb ... 213s Unpacking python3-mpmath (1.3.0-1) ... 213s Selecting previously unselected package python3-sympy. 213s Preparing to unpack .../148-python3-sympy_1.13.3-1_all.deb ... 213s Unpacking python3-sympy (1.13.3-1) ... 214s Selecting previously unselected package python3-ufolib2. 214s Preparing to unpack .../149-python3-ufolib2_0.17.0+dfsg1-1_all.deb ... 214s Unpacking python3-ufolib2 (0.17.0+dfsg1-1) ... 214s Selecting previously unselected package unicode-data. 214s Preparing to unpack .../150-unicode-data_15.1.0-1_all.deb ... 214s Unpacking unicode-data (15.1.0-1) ... 214s Selecting previously unselected package python3-fonttools. 214s Preparing to unpack .../151-python3-fonttools_4.55.3-2_arm64.deb ... 214s Unpacking python3-fonttools (4.55.3-2) ... 214s Selecting previously unselected package python3-imagesize. 214s Preparing to unpack .../152-python3-imagesize_1.4.1-1_all.deb ... 214s Unpacking python3-imagesize (1.4.1-1) ... 214s Selecting previously unselected package python3-iniconfig. 214s Preparing to unpack .../153-python3-iniconfig_1.1.1-2_all.deb ... 214s Unpacking python3-iniconfig (1.1.1-2) ... 215s Selecting previously unselected package python3-kiwisolver. 215s Preparing to unpack .../154-python3-kiwisolver_1.4.7-3_arm64.deb ... 215s Unpacking python3-kiwisolver (1.4.7-3) ... 215s Selecting previously unselected package libopenjp2-7:arm64. 215s Preparing to unpack .../155-libopenjp2-7_2.5.0-2ubuntu3_arm64.deb ... 215s Unpacking libopenjp2-7:arm64 (2.5.0-2ubuntu3) ... 215s Selecting previously unselected package python3-pil:arm64. 215s Preparing to unpack .../156-python3-pil_11.1.0-5_arm64.deb ... 215s Unpacking python3-pil:arm64 (11.1.0-5) ... 215s Selecting previously unselected package python3.12-tk. 215s Preparing to unpack .../157-python3.12-tk_3.12.9-1_arm64.deb ... 215s Unpacking python3.12-tk (3.12.9-1) ... 215s Selecting previously unselected package python3.13-tk. 215s Preparing to unpack .../158-python3.13-tk_3.13.2-1_arm64.deb ... 215s Unpacking python3.13-tk (3.13.2-1) ... 215s Selecting previously unselected package python3-tk:arm64. 215s Preparing to unpack .../159-python3-tk_3.13.1-1_arm64.deb ... 215s Unpacking python3-tk:arm64 (3.13.1-1) ... 215s Selecting previously unselected package python3-pil.imagetk:arm64. 215s Preparing to unpack .../160-python3-pil.imagetk_11.1.0-5_arm64.deb ... 215s Unpacking python3-pil.imagetk:arm64 (11.1.0-5) ... 215s Selecting previously unselected package python3-matplotlib. 215s Preparing to unpack .../161-python3-matplotlib_3.8.3-3ubuntu2_arm64.deb ... 215s Unpacking python3-matplotlib (3.8.3-3ubuntu2) ... 215s Selecting previously unselected package sphinx-common. 215s Preparing to unpack .../162-sphinx-common_8.1.3-5_all.deb ... 215s Unpacking sphinx-common (8.1.3-5) ... 216s Selecting previously unselected package python3-alabaster. 216s Preparing to unpack .../163-python3-alabaster_0.7.16-0.1_all.deb ... 216s Unpacking python3-alabaster (0.7.16-0.1) ... 216s Selecting previously unselected package python3-snowballstemmer. 216s Preparing to unpack .../164-python3-snowballstemmer_2.2.0-4build1_all.deb ... 216s Unpacking python3-snowballstemmer (2.2.0-4build1) ... 216s Selecting previously unselected package python3-sphinx. 216s Preparing to unpack .../165-python3-sphinx_8.1.3-5_all.deb ... 216s Unpacking python3-sphinx (8.1.3-5) ... 216s Selecting previously unselected package python3-tabulate. 216s Preparing to unpack .../166-python3-tabulate_0.9.0-1_all.deb ... 216s Unpacking python3-tabulate (0.9.0-1) ... 216s Selecting previously unselected package python3-numpydoc. 216s Preparing to unpack .../167-python3-numpydoc_1.8.0-1_all.deb ... 216s Unpacking python3-numpydoc (1.8.0-1) ... 216s Selecting previously unselected package python3-pandas-lib:arm64. 216s Preparing to unpack .../168-python3-pandas-lib_2.2.3+dfsg-8_arm64.deb ... 216s Unpacking python3-pandas-lib:arm64 (2.2.3+dfsg-8) ... 216s Selecting previously unselected package python3-pandas. 216s Preparing to unpack .../169-python3-pandas_2.2.3+dfsg-8_all.deb ... 216s Unpacking python3-pandas (2.2.3+dfsg-8) ... 217s Selecting previously unselected package python3-pluggy. 217s Preparing to unpack .../170-python3-pluggy_1.5.0-1_all.deb ... 217s Unpacking python3-pluggy (1.5.0-1) ... 217s Selecting previously unselected package python3-psutil. 217s Preparing to unpack .../171-python3-psutil_5.9.8-2build3_arm64.deb ... 217s Unpacking python3-psutil (5.9.8-2build3) ... 217s Selecting previously unselected package python3-pytest. 217s Preparing to unpack .../172-python3-pytest_8.3.4-1_all.deb ... 217s Unpacking python3-pytest (8.3.4-1) ... 217s Selecting previously unselected package zip. 217s Preparing to unpack .../173-zip_3.0-14ubuntu2_arm64.deb ... 217s Unpacking zip (3.0-14ubuntu2) ... 217s Selecting previously unselected package unzip. 217s Preparing to unpack .../174-unzip_6.0-28ubuntu6_arm64.deb ... 217s Unpacking unzip (6.0-28ubuntu6) ... 217s Selecting previously unselected package xdg-utils. 217s Preparing to unpack .../175-xdg-utils_1.2.1-2ubuntu1_all.deb ... 217s Unpacking xdg-utils (1.2.1-2ubuntu1) ... 217s Selecting previously unselected package r-base-core. 217s Preparing to unpack .../176-r-base-core_4.4.2-1build1_arm64.deb ... 217s Unpacking r-base-core (4.4.2-1build1) ... 218s Setting up libhtscodecs2:arm64 (1.6.1-2) ... 218s Setting up dh-python (6.20250108) ... 218s Setting up libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 218s Setting up liblcms2-2:arm64 (2.16-2) ... 218s Setting up python3-iniconfig (1.1.1-2) ... 218s Setting up libpixman-1-0:arm64 (0.44.0-3) ... 218s Setting up python3.12-minimal (3.12.9-1) ... 219s Setting up libsharpyuv0:arm64 (1.5.0-0.1) ... 219s Setting up liblerc4:arm64 (4.0.0+ds-5ubuntu1) ... 219s Setting up libxrender1:arm64 (1:0.9.10-1.1build1) ... 219s Setting up libdatrie1:arm64 (0.2.13-3build1) ... 219s Setting up python3-lz4 (4.4.0+dfsg-1) ... 220s Setting up libxcb-render0:arm64 (1.17.0-2) ... 220s Setting up python3-defusedxml (0.7.1-3) ... 220s Setting up libarchive-zip-perl (1.68-1) ... 220s Setting up python3-alabaster (0.7.16-0.1) ... 220s Setting up fonts-lyx (2.4.3-1) ... 220s Setting up unzip (6.0-28ubuntu6) ... 220s Setting up libdebhelper-perl (13.24.1ubuntu2) ... 220s Setting up python3.12 (3.12.9-1) ... 222s Setting up x11-common (1:7.7+23ubuntu3) ... 222s Setting up libdeflate0:arm64 (1.23-1) ... 222s Setting up python3-tabulate (0.9.0-1) ... 222s Setting up m4 (1.4.19-5) ... 222s Setting up libqhull-r8.0:arm64 (2020.2-6build1) ... 222s Setting up python3-all (3.13.1-1~exp2) ... 223s Setting up python3-pytz (2025.1-3) ... 223s Setting up libxcb-shm0:arm64 (1.17.0-2) ... 223s Setting up libgomp1:arm64 (15-20250213-1ubuntu1) ... 223s Setting up python3-wheel (0.45.1-1) ... 223s Setting up libjbig0:arm64 (2.1-6.1ubuntu2) ... 223s Setting up python3-platformdirs (4.3.6-1) ... 223s Setting up python3-psutil (5.9.8-2build3) ... 224s Setting up python3-tz (2025.1-3) ... 224s Setting up python3-fs (2.4.16-6) ... 225s Setting up unicode-data (15.1.0-1) ... 225s Setting up python3-roman (5.0-1) ... 225s Setting up python3-decorator (5.1.1-5) ... 225s Setting up zip (3.0-14ubuntu2) ... 225s Setting up autotools-dev (20220109.1) ... 225s Setting up libblas3:arm64 (3.12.1-2) ... 225s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode 225s Setting up python3-packaging (24.2-1) ... 225s Setting up libexpat1-dev:arm64 (2.6.4-1) ... 225s Setting up python3-pyproject-hooks (1.2.0-1) ... 226s Setting up python3-snowballstemmer (2.2.0-4build1) ... 226s Setting up python3-brotli (1.1.0-2build3) ... 227s Setting up python3-cycler (0.12.1-1) ... 227s Setting up libimagequant0:arm64 (2.18.0-1build1) ... 227s Setting up fonts-dejavu-mono (2.37-8) ... 227s Setting up python3-kiwisolver (1.4.7-3) ... 227s Setting up libmpc3:arm64 (1.3.1-1build2) ... 227s Setting up cython3 (3.0.11+dfsg-2ubuntu1) ... 229s Setting up libtcl8.6:arm64 (8.6.16+dfsg-1) ... 229s Setting up autopoint (0.23.1-1) ... 229s Setting up fonts-dejavu-core (2.37-8) ... 229s Setting up libjpeg-turbo8:arm64 (2.1.5-3ubuntu2) ... 229s Setting up python3-toml (0.10.2-1) ... 230s Setting up python3-installer (0.7.0+dfsg1-3) ... 230s Setting up libgfortran5:arm64 (15-20250213-1ubuntu1) ... 230s Setting up autoconf (2.72-3) ... 230s Setting up python3-pluggy (1.5.0-1) ... 230s Setting up libwebp7:arm64 (1.5.0-0.1) ... 230s Setting up libubsan1:arm64 (15-20250213-1ubuntu1) ... 230s Setting up zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 230s Setting up dwz (0.15-1build6) ... 230s Setting up libhwasan0:arm64 (15-20250213-1ubuntu1) ... 230s Setting up libasan8:arm64 (15-20250213-1ubuntu1) ... 230s Setting up libjson-perl (4.10000-1) ... 230s Setting up libxslt1.1:arm64 (1.1.39-0exp1ubuntu2) ... 230s Setting up debugedit (1:5.1-2) ... 230s Setting up libhts3t64:arm64 (1.21+ds-1) ... 230s Setting up libopenjp2-7:arm64 (2.5.0-2ubuntu3) ... 230s Setting up libharfbuzz0b:arm64 (10.2.0-1) ... 230s Setting up libthai-data (0.1.29-2build1) ... 230s Setting up python3-dateutil (2.9.0-3) ... 230s Setting up sgml-base (1.31) ... 230s Setting up libxss1:arm64 (1:1.2.3-1build3) ... 230s Setting up libpaper2:arm64 (2.2.5-0.3) ... 231s Setting up libtsan2:arm64 (15-20250213-1ubuntu1) ... 231s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 231s Setting up python3-mpmath (1.3.0-1) ... 232s Setting up libisl23:arm64 (0.27-1) ... 232s Setting up python3-build (1.2.2-1) ... 232s Setting up python-matplotlib-data (3.8.3-3ubuntu2) ... 232s Setting up libwebpmux3:arm64 (1.5.0-0.1) ... 232s Setting up xdg-utils (1.2.1-2ubuntu1) ... 232s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode 232s Setting up bedtools (2.31.1+dfsg-2) ... 232s Setting up libcc1-0:arm64 (15-20250213-1ubuntu1) ... 232s Setting up liblsan0:arm64 (15-20250213-1ubuntu1) ... 232s Setting up libitm1:arm64 (15-20250213-1ubuntu1) ... 232s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 232s Setting up python3-imagesize (1.4.1-1) ... 232s Setting up libjpeg8:arm64 (8c-2ubuntu11) ... 232s Setting up automake (1:1.17-3) ... 232s update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode 232s Setting up libfile-stripnondeterminism-perl (1.14.1-2) ... 232s Setting up python3-sympy (1.13.3-1) ... 248s Setting up libice6:arm64 (2:1.1.1-1) ... 248s Setting up liblapack3:arm64 (3.12.1-2) ... 248s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode 248s Setting up gettext (0.23.1-1) ... 248s Setting up python3-pysam (0.23.0+ds-1) ... 248s Setting up pybuild-plugin-pyproject (6.20250108) ... 248s Setting up fontconfig-config (2.15.0-2ubuntu1) ... 248s Setting up python3-pytest (8.3.4-1) ... 249s Setting up libwebpdemux2:arm64 (1.5.0-0.1) ... 249s Setting up libpython3.12-dev:arm64 (3.12.9-1) ... 249s Setting up libpaper-utils (2.2.5-0.3) ... 249s Setting up intltool-debian (0.35.0+20060710.6) ... 249s Setting up libthai0:arm64 (0.1.29-2build1) ... 249s Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... 249s Setting up libraqm0:arm64 (0.10.2-1) ... 249s Setting up libpython3.13-dev:arm64 (3.13.2-1) ... 249s Setting up python3.12-dev (3.12.9-1) ... 249s Setting up python3-numpy (1:1.26.4+ds-13) ... 253s Setting up libjs-sphinxdoc (8.1.3-5) ... 253s Setting up dh-strip-nondeterminism (1.14.1-2) ... 253s Setting up cpp-14-aarch64-linux-gnu (14.2.0-17ubuntu1) ... 253s Setting up python3-lxml:arm64 (5.3.1-1) ... 254s Setting up libtiff6:arm64 (4.5.1+git230720-4ubuntu4) ... 254s Setting up xml-core (0.19) ... 254s Setting up python3-contourpy (1.3.1-1) ... 254s Setting up libfontconfig1:arm64 (2.15.0-2ubuntu1) ... 254s Setting up libgcc-14-dev:arm64 (14.2.0-17ubuntu1) ... 254s Setting up libstdc++-14-dev:arm64 (14.2.0-17ubuntu1) ... 254s Setting up libsm6:arm64 (2:1.2.4-1) ... 254s Setting up liblbfgsb0:arm64 (3.0+dfsg.4-1build1) ... 254s Setting up fontconfig (2.15.0-2ubuntu1) ... 256s Regenerating fonts cache... done. 256s Setting up python3-pybedtools (0.10.0-4) ... 257s Setting up libxft2:arm64 (2.3.6-1build1) ... 257s Setting up python3-scipy (1.14.1-4ubuntu1) ... 265s Setting up libpython3-dev:arm64 (3.13.1-1~exp2) ... 265s Setting up python-pybedtools-doc (0.10.0-4) ... 265s Setting up python3.13-dev (3.13.2-1) ... 265s Setting up po-debconf (1.0.21+nmu1) ... 265s Setting up libtk8.6:arm64 (8.6.16-1) ... 265s Setting up python3-pandas-lib:arm64 (2.2.3+dfsg-8) ... 265s Setting up libpango-1.0-0:arm64 (1.56.1-1) ... 265s Setting up python3.12-tk (3.12.9-1) ... 265s Setting up pybedtools-bin (0.10.0-4) ... 265s Setting up libcairo2:arm64 (1.18.2-2) ... 265s Setting up python3.13-tk (3.13.2-1) ... 265s Setting up python3-pil:arm64 (11.1.0-5) ... 266s Setting up cpp-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 266s Setting up python3-pandas (2.2.3+dfsg-8) ... 278s Setting up libpython3-all-dev:arm64 (3.13.1-1~exp2) ... 278s Setting up sphinx-common (8.1.3-5) ... 278s Setting up python3-dev (3.13.1-1~exp2) ... 278s Setting up libxt6t64:arm64 (1:1.2.1-1.2build1) ... 278s Setting up cpp-14 (14.2.0-17ubuntu1) ... 278s Setting up cpp (4:14.2.0-1ubuntu1) ... 278s Setting up gcc-14-aarch64-linux-gnu (14.2.0-17ubuntu1) ... 278s Setting up libpangoft2-1.0-0:arm64 (1.56.1-1) ... 278s Setting up libpangocairo-1.0-0:arm64 (1.56.1-1) ... 278s Setting up python3-all-dev (3.13.1-1~exp2) ... 278s Setting up gcc-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 278s Setting up tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 278s Setting up g++-14-aarch64-linux-gnu (14.2.0-17ubuntu1) ... 278s Setting up blt (2.5.3+dfsg-7build1) ... 278s Setting up python3-tk:arm64 (3.13.1-1) ... 278s Setting up gcc-14 (14.2.0-17ubuntu1) ... 278s Setting up python3-pil.imagetk:arm64 (11.1.0-5) ... 278s Setting up r-base-core (4.4.2-1build1) ... 279s Creating config file /etc/R/Renviron with new version 279s Setting up g++-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 279s Setting up g++-14 (14.2.0-17ubuntu1) ... 279s Setting up libtool (2.5.4-3build1) ... 279s Setting up gcc (4:14.2.0-1ubuntu1) ... 279s Setting up dh-autoreconf (20) ... 279s Setting up g++ (4:14.2.0-1ubuntu1) ... 279s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 279s Setting up build-essential (12.10ubuntu1) ... 279s Setting up debhelper (13.24.1ubuntu2) ... 279s Setting up pybuild-plugin-autopkgtest (6.20250108) ... 279s Setting up python3-ufolib2 (0.17.0+dfsg1-1) ... 279s Setting up python3-fonttools (4.55.3-2) ... 281s Setting up python3-matplotlib (3.8.3-3ubuntu2) ... 285s Processing triggers for libc-bin (2.40-4ubuntu1) ... 285s Processing triggers for systemd (257.2-3ubuntu1) ... 285s Processing triggers for man-db (2.13.0-1) ... 288s Processing triggers for install-info (7.1.1-1) ... 288s Processing triggers for sgml-base (1.31) ... 288s Setting up docutils-common (0.21.2+dfsg-2) ... 288s Processing triggers for sgml-base (1.31) ... 288s Setting up python3-docutils (0.21.2+dfsg-2) ... 289s Setting up python3-sphinx (8.1.3-5) ... 291s Setting up python3-numpydoc (1.8.0-1) ... 293s autopkgtest [12:53:12]: test pybuild-autopkgtest: pybuild-autopkgtest 293s autopkgtest [12:53:12]: test pybuild-autopkgtest: [----------------------- 293s pybuild-autopkgtest 294s I: pybuild base:311: cd /tmp/autopkgtest.2R0Drp/autopkgtest_tmp/build; python3.12 -m pytest -k "not test_chromsizes" --pyargs pybedtools 296s ============================= test session starts ============================== 296s platform linux -- Python 3.12.9, pytest-8.3.4, pluggy-1.5.0 296s rootdir: /tmp/autopkgtest.2R0Drp/autopkgtest_tmp/build 296s configfile: pyproject.toml 296s plugins: typeguard-4.4.1 296s collected 511 items / 2 deselected / 509 selected 296s 302s test/test_1.py ......................................................... [ 11%] 303s ............x..x.x...... [ 15%] 303s test/test_cbedtools.py ....................................... [ 23%] 304s test/test_contrib.py .. [ 23%] 304s test/test_gzip_support.py ........ [ 25%] 304s test/test_helpers.py ...... [ 26%] 307s test/test_issues.py ........................................... [ 35%] 308s test/test_iter.py ...................................................... [ 45%] 308s ........................................................................ [ 59%] 312s ........................................................................ [ 74%] 313s ........................................................................ [ 88%] 313s ......................................................... [ 99%] 313s test/test_pathlib.py ... [100%] 313s 313s ================ 506 passed, 2 deselected, 3 xfailed in 18.63s ================= 313s I: pybuild pybuild:334: cd /tmp/autopkgtest.2R0Drp/build.hHN/src/docs ; PYTHONPATH=/tmp/autopkgtest.2R0Drp/autopkgtest_tmp/build python3.12 -m sphinx -b doctest -d build/doctrees source build/doctest 314s Running Sphinx v8.1.3 314s loading translations [en]... done 315s making output directory... done 315s Converting `source_suffix = '.rst'` to `source_suffix = {'.rst': 'restructuredtext'}`. 315s [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 317s [autosummary] generating autosummary for: /tmp/autopkgtest.2R0Drp/build.hHN/src/docs/source/autodocs/pybedtools.bedtool.BedTool.absolute_distance.rst, /tmp/autopkgtest.2R0Drp/build.hHN/src/docs/source/autodocs/pybedtools.bedtool.BedTool.all_hits.rst, /tmp/autopkgtest.2R0Drp/build.hHN/src/docs/source/autodocs/pybedtools.bedtool.BedTool.annotate.rst, /tmp/autopkgtest.2R0Drp/build.hHN/src/docs/source/autodocs/pybedtools.bedtool.BedTool.any_hits.rst, /tmp/autopkgtest.2R0Drp/build.hHN/src/docs/source/autodocs/pybedtools.bedtool.BedTool.as_intervalfile.rst, /tmp/autopkgtest.2R0Drp/build.hHN/src/docs/source/autodocs/pybedtools.bedtool.BedTool.at.rst, /tmp/autopkgtest.2R0Drp/build.hHN/src/docs/source/autodocs/pybedtools.bedtool.BedTool.bam_to_bed.rst, /tmp/autopkgtest.2R0Drp/build.hHN/src/docs/source/autodocs/pybedtools.bedtool.BedTool.bam_to_fastq.rst, /tmp/autopkgtest.2R0Drp/build.hHN/src/docs/source/autodocs/pybedtools.bedtool.BedTool.bed6.rst, /tmp/autopkgtest.2R0Drp/build.hHN/src/docs/source/autodocs/pybedtools.bedtool.BedTool.bedpe_to_bam.rst, ..., /tmp/autopkgtest.2R0Drp/build.hHN/src/docs/source/autodocs/pybedtools.helpers.set_tempdir.rst, /tmp/autopkgtest.2R0Drp/build.hHN/src/docs/source/autodocs/pybedtools.parallel.parallel_apply.rst, /tmp/autopkgtest.2R0Drp/build.hHN/src/docs/source/pybedtools.featurefuncs.add_color.rst, /tmp/autopkgtest.2R0Drp/build.hHN/src/docs/source/pybedtools.featurefuncs.bedgraph_scale.rst, /tmp/autopkgtest.2R0Drp/build.hHN/src/docs/source/pybedtools.featurefuncs.extend_fields.rst, /tmp/autopkgtest.2R0Drp/build.hHN/src/docs/source/pybedtools.featurefuncs.five_prime.rst, /tmp/autopkgtest.2R0Drp/build.hHN/src/docs/source/pybedtools.featurefuncs.greater_than.rst, /tmp/autopkgtest.2R0Drp/build.hHN/src/docs/source/pybedtools.featurefuncs.less_than.rst, /tmp/autopkgtest.2R0Drp/build.hHN/src/docs/source/pybedtools.featurefuncs.normalized_to_length.rst, /tmp/autopkgtest.2R0Drp/build.hHN/src/docs/source/pybedtools.featurefuncs.three_prime.rst 317s building [mo]: targets for 0 po files that are out of date 317s writing output... 317s building [doctest]: targets for 49 source files that are out of date 317s updating environment: [new config] 157 added, 0 changed, 0 removed 317s reading sources... [ 1%] 3-brief-examples 317s reading sources... [ 1%] FAQs 317s reading sources... [ 2%] autodoc_source 318s /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. 318s self[section] = content 318s /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. 318s self[section] = content 318s reading sources... [ 3%] autodocs/pybedtools.bedtool.BedTool 320s /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. 320s self[section] = content 321s reading sources... [ 3%] autodocs/pybedtools.bedtool.BedTool.absolute_distance 321s reading sources... 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[ 93%] topical-bam-semantics 328s reading sources... [ 94%] topical-comparisons 328s reading sources... [ 94%] topical-create-a-bedtool 328s reading sources... [ 95%] topical-design-principles 328s reading sources... [ 96%] topical-documentation-contents 328s reading sources... [ 96%] topical-genome 328s reading sources... [ 97%] topical-iterators 328s reading sources... [ 97%] topical-low-level-ops 328s reading sources... [ 98%] topical-random 328s reading sources... [ 99%] topical-saving 328s reading sources... [ 99%] topical-wrapping 328s reading sources... [100%] tutorial-contents 328s 328s WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool' with 'bedtool.BedTool'. [autosummary.import_cycle] 328s WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.intersect' with 'bedtool.BedTool.intersect'. 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Replace 'pybedtools.bedtool.BedTool.merge' with 'bedtool.BedTool.merge'. [autosummary.import_cycle] 328s WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.cluster' with 'bedtool.BedTool.cluster'. [autosummary.import_cycle] 328s WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.complement' with 'bedtool.BedTool.complement'. [autosummary.import_cycle] 328s WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.subtract' with 'bedtool.BedTool.subtract'. [autosummary.import_cycle] 328s WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.slop' with 'bedtool.BedTool.slop'. [autosummary.import_cycle] 328s WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.flank' with 'bedtool.BedTool.flank'. [autosummary.import_cycle] 328s WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.sort' with 'bedtool.BedTool.sort'. [autosummary.import_cycle] 328s WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.random' with 'bedtool.BedTool.random'. [autosummary.import_cycle] 328s WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.shuffle' with 'bedtool.BedTool.shuffle'. [autosummary.import_cycle] 328s WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.annotate' with 'bedtool.BedTool.annotate'. [autosummary.import_cycle] 328s WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.multi_intersect' with 'bedtool.BedTool.multi_intersect'. [autosummary.import_cycle] 328s WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.union_bedgraphs' with 'bedtool.BedTool.union_bedgraphs'. [autosummary.import_cycle] 328s WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.pair_to_bed' with 'bedtool.BedTool.pair_to_bed'. [autosummary.import_cycle] 328s WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.pair_to_pair' with 'bedtool.BedTool.pair_to_pair'. [autosummary.import_cycle] 328s WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.bam_to_bed' with 'bedtool.BedTool.bam_to_bed'. [autosummary.import_cycle] 328s WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.to_bam' with 'bedtool.BedTool.to_bam'. [autosummary.import_cycle] 328s WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.bedpe_to_bam' with 'bedtool.BedTool.bedpe_to_bam'. [autosummary.import_cycle] 328s WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.bed6' with 'bedtool.BedTool.bed6'. [autosummary.import_cycle] 328s 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] 328s WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.sequence' with 'bedtool.BedTool.sequence'. [autosummary.import_cycle] 328s WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.mask_fasta' with 'bedtool.BedTool.mask_fasta'. [autosummary.import_cycle] 328s WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.nucleotide_content' with 'bedtool.BedTool.nucleotide_content'. [autosummary.import_cycle] 328s 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] 328s WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.tag_bam' with 'bedtool.BedTool.tag_bam'. [autosummary.import_cycle] 328s WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.jaccard' with 'bedtool.BedTool.jaccard'. [autosummary.import_cycle] 328s WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.reldist' with 'bedtool.BedTool.reldist'. [autosummary.import_cycle] 328s WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.overlap' with 'bedtool.BedTool.overlap'. [autosummary.import_cycle] 328s WARNING: Summarised items should not include the current module. 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[autosummary.import_cycle] 328s /tmp/autopkgtest.2R0Drp/build.hHN/src/docs/source/topical-genome.rst:55: ERROR: Unknown target name: "genomepy". [docutils] 328s looking for now-outdated files... none found 328s pickling environment... done 328s checking consistency... /tmp/autopkgtest.2R0Drp/build.hHN/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 328s /tmp/autopkgtest.2R0Drp/build.hHN/src/docs/source/pybedtools.featurefuncs.rename.rst: document is referenced in multiple toctrees: ['autodoc_source', 'autodoc_source'], selecting: autodoc_source <- pybedtools.featurefuncs.rename 328s done 328s preparing documents... done 328s copying assets... 328s copying assets: done 328s running tests... 329s 329s Document: autodocs/pybedtools.bedtool.BedTool.annotate 329s ------------------------------------------------------ 329s 1 items passed all tests: 329s 3 tests in default 329s 3 tests in 1 items. 329s 3 passed and 0 failed. 329s Test passed. 329s 329s Document: 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tests: 333s 10 tests in default 333s 10 tests in 1 items. 333s 10 passed and 0 failed. 333s Test passed. 333s 333s Document: intersections 333s ----------------------- 333s 1 items passed all tests: 333s 8 tests in default 333s 8 tests in 1 items. 333s 8 passed and 0 failed. 333s Test passed. 333s 333s Document: intervals 333s ------------------- 334s 1 items passed all tests: 334s 50 tests in default 334s 50 tests in 1 items. 334s 50 passed and 0 failed. 334s Test passed. 334s 334s Document: piping 334s ---------------- 334s 1 items passed all tests: 334s 17 tests in default 334s 17 tests in 1 items. 334s 17 passed and 0 failed. 334s Test passed. 334s 334s Document: save-results 334s ---------------------- 334s 1 items passed all tests: 334s 8 tests in default 334s 8 tests in 1 items. 334s 8 passed and 0 failed. 334s Test passed. 334s 334s Document: topical-bam 334s --------------------- 335s 1 items passed all tests: 335s 15 tests in default 335s 15 tests in 1 items. 335s 15 passed and 0 failed. 335s Test passed. 335s 335s Document: topical-create-a-bedtool 335s ---------------------------------- 335s 1 items passed all tests: 335s 10 tests in default 335s 10 tests in 1 items. 335s 10 passed and 0 failed. 335s Test passed. 335s 335s Document: topical-design-principles 335s ----------------------------------- 335s 1 items passed all tests: 335s 15 tests in default 335s 15 tests in 1 items. 335s 15 passed and 0 failed. 335s Test passed. 335s 335s Document: topical-genome 335s ------------------------ 335s 1 items passed all tests: 335s 13 tests in default 335s 13 tests in 1 items. 335s 13 passed and 0 failed. 335s Test passed. 335s 335s Document: topical-iterators 335s --------------------------- 335s 1 items passed all tests: 335s 20 tests in default 335s 20 tests in 1 items. 335s 20 passed and 0 failed. 335s Test passed. 335s 335s Document: topical-low-level-ops 335s ------------------------------- 335s 1 items passed all tests: 335s 6 tests in default 335s 6 tests in 1 items. 335s 6 passed and 0 failed. 335s Test passed. 335s 335s Document: topical-random 335s ------------------------ 337s 1 items passed all tests: 337s 10 tests in default 337s 10 tests in 1 items. 337s 10 passed and 0 failed. 337s Test passed. 337s 337s Document: topical-saving 337s ------------------------ 337s 1 items passed all tests: 337s 14 tests in default 337s 14 tests in 1 items. 337s 14 passed and 0 failed. 337s Test passed. 337s 337s Doctest summary 337s =============== 337s 387 tests 337s 0 failures in tests 337s 0 failures in setup code 337s 0 failures in cleanup code 337s build succeeded, 126 warnings. 337s 337s Testing of doctests in the sources finished, look at the results in build/doctest/output.txt. 338s I: pybuild base:311: cd /tmp/autopkgtest.2R0Drp/autopkgtest_tmp/build; python3.13 -m pytest -k "not test_chromsizes" --pyargs pybedtools 339s ============================= test session starts ============================== 339s platform linux -- Python 3.13.2, pytest-8.3.4, pluggy-1.5.0 339s rootdir: /tmp/autopkgtest.2R0Drp/autopkgtest_tmp/build 339s configfile: pyproject.toml 339s plugins: typeguard-4.4.1 339s collected 511 items / 2 deselected / 509 selected 339s 345s test/test_1.py ......................................................... [ 11%] 346s ............x..x.x...... [ 15%] 347s test/test_cbedtools.py ....................................... [ 23%] 347s test/test_contrib.py .. [ 23%] 347s test/test_gzip_support.py ........ [ 25%] 347s test/test_helpers.py ...... [ 26%] 350s test/test_issues.py ........................................... [ 35%] 350s test/test_iter.py ...................................................... [ 45%] 351s ........................................................................ [ 59%] 355s ........................................................................ [ 74%] 355s ........................................................................ [ 88%] 356s ......................................................... [ 99%] 356s test/test_pathlib.py ... [100%] 356s 356s ================ 506 passed, 2 deselected, 3 xfailed in 17.18s ================= 356s I: pybuild pybuild:334: cd /tmp/autopkgtest.2R0Drp/build.hHN/src/docs ; PYTHONPATH=/tmp/autopkgtest.2R0Drp/autopkgtest_tmp/build python3.13 -m sphinx -b doctest -d build/doctrees source build/doctest 356s Running Sphinx v8.1.3 357s loading translations [en]... done 357s Converting `source_suffix = '.rst'` to `source_suffix = {'.rst': 'restructuredtext'}`. 357s loading pickled environment... done 357s [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 359s building [mo]: targets for 0 po files that are out of date 359s writing output... 359s building [doctest]: targets for 157 source files that are out of date 359s updating environment: 0 added, 0 changed, 0 removed 359s reading sources... 359s looking for now-outdated files... none found 359s preparing documents... done 359s copying assets... 359s copying assets: done 359s running tests... 359s 359s Document: autodocs/pybedtools.bedtool.BedTool.annotate 359s ------------------------------------------------------ 359s 1 item passed all tests: 359s 3 tests in default 359s 3 tests in 1 item. 359s 3 passed. 359s Test passed. 359s 359s Document: autodocs/pybedtools.bedtool.BedTool.cat 359s ------------------------------------------------- 359s 1 item passed all tests: 359s 4 tests in default 359s 4 tests in 1 item. 359s 4 passed. 359s Test passed. 359s 359s Document: autodocs/pybedtools.bedtool.BedTool.complement 359s -------------------------------------------------------- 359s 1 item passed all tests: 359s 2 tests in default 359s 2 tests in 1 item. 359s 2 passed. 359s Test passed. 359s 359s Document: autodocs/pybedtools.bedtool.BedTool.count 359s --------------------------------------------------- 359s 1 item passed all tests: 359s 2 tests in default 359s 2 tests in 1 item. 359s 2 passed. 359s Test passed. 359s 359s Document: autodocs/pybedtools.bedtool.BedTool.coverage 359s ------------------------------------------------------ 359s 1 item passed all tests: 359s 4 tests in default 359s 4 tests in 1 item. 359s 4 passed. 359s Test passed. 359s 359s Document: autodocs/pybedtools.bedtool.BedTool.cut 359s ------------------------------------------------- 359s 1 item passed all tests: 359s 2 tests in default 359s 2 tests in 1 item. 359s 2 passed. 359s Test passed. 359s 359s Document: autodocs/pybedtools.bedtool.BedTool.each 359s -------------------------------------------------- 359s 1 item passed all tests: 359s 4 tests in default 359s 4 tests in 1 item. 359s 4 passed. 359s Test passed. 359s 359s Document: autodocs/pybedtools.bedtool.BedTool.field_count 359s --------------------------------------------------------- 359s 1 item passed all tests: 359s 2 tests in default 359s 2 tests in 1 item. 359s 2 passed. 359s Test passed. 359s 359s Document: autodocs/pybedtools.bedtool.BedTool.file_type 359s ------------------------------------------------------- 359s 1 item passed all tests: 359s 2 tests in default 359s 2 tests in 1 item. 359s 2 passed. 359s Test passed. 359s 359s Document: autodocs/pybedtools.bedtool.BedTool.filter 359s ---------------------------------------------------- 359s 1 item passed all tests: 359s 3 tests in default 359s 3 tests in 1 item. 359s 3 passed. 359s Test passed. 359s 359s Document: autodocs/pybedtools.bedtool.BedTool.flank 359s --------------------------------------------------- 359s 1 item passed all tests: 359s 2 tests in default 359s 2 tests in 1 item. 359s 2 passed. 359s Test passed. 359s 359s Document: autodocs/pybedtools.bedtool.BedTool.genome_coverage 359s ------------------------------------------------------------- 361s 1 item passed all tests: 361s 6 tests in default 361s 6 tests in 1 item. 361s 6 passed. 361s Test passed. 361s 361s Document: autodocs/pybedtools.bedtool.BedTool.groupby 361s ----------------------------------------------------- 361s 1 item passed all tests: 361s 5 tests in default 361s 5 tests in 1 item. 361s 5 passed. 361s Test passed. 361s 361s Document: autodocs/pybedtools.bedtool.BedTool.head 361s -------------------------------------------------- 361s 1 item passed all tests: 361s 2 tests in default 361s 2 tests in 1 item. 361s 2 passed. 361s Test passed. 361s 361s Document: autodocs/pybedtools.bedtool.BedTool.mask_fasta 361s -------------------------------------------------------- 361s 1 item passed all tests: 361s 8 tests in default 361s 8 tests in 1 item. 361s 8 passed. 361s Test passed. 361s 361s Document: autodocs/pybedtools.bedtool.BedTool.merge 361s --------------------------------------------------- 361s 1 item passed all tests: 361s 3 tests in default 361s 3 tests in 1 item. 361s 3 passed. 361s Test passed. 361s 361s Document: autodocs/pybedtools.bedtool.BedTool.moveto 361s ---------------------------------------------------- 361s 1 item passed all tests: 361s 5 tests in default 361s 5 tests in 1 item. 361s 5 passed. 361s Test passed. 361s 361s Document: autodocs/pybedtools.bedtool.BedTool.overlap 361s ----------------------------------------------------- 361s 1 item passed all tests: 361s 4 tests in default 361s 4 tests in 1 item. 361s 4 passed. 361s Test passed. 361s 361s Document: autodocs/pybedtools.bedtool.BedTool.random 361s ---------------------------------------------------- 361s 1 item passed all tests: 361s 2 tests in default 361s 2 tests in 1 item. 361s 2 passed. 361s Test passed. 361s 361s Document: autodocs/pybedtools.bedtool.BedTool.randomintersection 361s ---------------------------------------------------------------- 361s 1 item passed all tests: 361s 6 tests in default 361s 6 tests in 1 item. 361s 6 passed. 361s Test passed. 361s 361s Document: autodocs/pybedtools.bedtool.BedTool.randomstats 361s --------------------------------------------------------- 362s 1 item passed all tests: 362s 4 tests in default 362s 4 tests in 1 item. 362s 4 passed. 362s Test passed. 362s 362s Document: autodocs/pybedtools.bedtool.BedTool.remove_invalid 362s ------------------------------------------------------------ 362s 1 item passed all tests: 362s 2 tests in default 362s 2 tests in 1 item. 362s 2 passed. 362s Test passed. 362s 362s Document: autodocs/pybedtools.bedtool.BedTool.save_seqs 362s ------------------------------------------------------- 362s 1 item passed all tests: 362s 7 tests in default 362s 7 tests in 1 item. 362s 7 passed. 362s Test passed. 362s 362s Document: autodocs/pybedtools.bedtool.BedTool.saveas 362s ---------------------------------------------------- 362s 1 item passed all tests: 362s 7 tests in default 362s 7 tests in 1 item. 362s 7 passed. 362s Test passed. 362s 362s Document: autodocs/pybedtools.bedtool.BedTool.sequence 362s ------------------------------------------------------ 362s 1 item passed all tests: 362s 4 tests in default 362s 4 tests in 1 item. 362s 4 passed. 362s Test passed. 362s 362s Document: autodocs/pybedtools.bedtool.BedTool.set_chromsizes 362s ------------------------------------------------------------ 362s 1 item passed all tests: 362s 4 tests in default 362s 4 tests in 1 item. 362s 4 passed. 362s Test passed. 362s 362s Document: autodocs/pybedtools.bedtool.BedTool.shuffle 362s ----------------------------------------------------- 362s 1 item passed all tests: 362s 4 tests in default 362s 4 tests in 1 item. 362s 4 passed. 362s Test passed. 362s 362s Document: autodocs/pybedtools.bedtool.BedTool.sort 362s -------------------------------------------------- 362s 1 item passed all tests: 362s 2 tests in default 362s 2 tests in 1 item. 362s 2 passed. 362s Test passed. 362s 362s Document: autodocs/pybedtools.bedtool.BedTool.subtract 362s ------------------------------------------------------ 362s 1 item passed all tests: 362s 4 tests in default 362s 4 tests in 1 item. 362s 4 passed. 362s Test passed. 362s 362s Document: autodocs/pybedtools.bedtool.BedTool.total_coverage 362s ------------------------------------------------------------ 362s 1 item passed all tests: 362s 3 tests in default 362s 3 tests in 1 item. 362s 3 passed. 362s Test passed. 362s 362s Document: autodocs/pybedtools.bedtool.BedTool.with_attrs 362s -------------------------------------------------------- 362s 1 item passed all tests: 362s 3 tests in default 362s 3 tests in 1 item. 362s 3 passed. 362s Test passed. 362s 362s Document: autodocs/pybedtools.cbedtools.Interval 362s ------------------------------------------------ 362s 1 item passed all tests: 362s 3 tests in default 362s 3 tests in 1 item. 362s 3 passed. 362s Test passed. 362s 362s Document: autodocs/pybedtools.cbedtools.create_interval_from_list 362s ----------------------------------------------------------------- 362s 1 item passed all tests: 362s 1 test in default 362s 1 test in 1 item. 362s 1 passed. 362s Test passed. 362s 362s Document: autodocs/pybedtools.contrib.long_range_interaction.cis_trans_interactions 362s ----------------------------------------------------------------------------------- 362s 1 item passed all tests: 362s 18 tests in default 362s 18 tests in 1 item. 362s 18 passed. 362s Test passed. 362s 362s Document: autodocs/pybedtools.contrib.plotting.Track 362s ---------------------------------------------------- 362s 1 item passed all tests: 362s 7 tests in default 362s 7 tests in 1 item. 362s 7 passed. 362s Test passed. 362s 362s Document: autodocs/pybedtools.filenames.list_example_files 362s ---------------------------------------------------------- 362s 1 item passed all tests: 362s 5 tests in default 362s 5 tests in 1 item. 362s 5 passed. 362s Test passed. 362s 362s Document: autodocs/pybedtools.helpers.chromsizes 362s ------------------------------------------------ 362s 1 item passed all tests: 362s 2 tests in default 362s 2 tests in 1 item. 362s 2 passed. 362s Test passed. 362s 362s Document: autodocs/pybedtools.parallel.parallel_apply 362s ----------------------------------------------------- 362s 1 item passed all tests: 362s 13 tests in default 362s 13 tests in 1 item. 362s 13 passed. 362s Test passed. 362s 362s Document: default-arguments 362s --------------------------- 362s 1 item passed all tests: 362s 13 tests in default 362s 13 tests in 1 item. 362s 13 passed. 362s Test passed. 362s 362s Document: each 362s -------------- 362s 1 item passed all tests: 362s 6 tests in default 362s 6 tests in 1 item. 362s 6 passed. 362s Test passed. 362s 362s Document: filtering 362s ------------------- 362s 1 item passed all tests: 362s 8 tests in default 362s 8 tests in 1 item. 362s 8 passed. 362s Test passed. 362s 362s Document: history 362s ----------------- 362s 1 item passed all tests: 362s 10 tests in default 362s 10 tests in 1 item. 362s 10 passed. 362s Test passed. 362s 362s Document: intersections 362s ----------------------- 362s 1 item passed all tests: 362s 8 tests in default 362s 8 tests in 1 item. 362s 8 passed. 362s Test passed. 362s 362s Document: intervals 362s ------------------- 362s 1 item passed all tests: 362s 50 tests in default 362s 50 tests in 1 item. 362s 50 passed. 362s Test passed. 362s 362s Document: piping 362s ---------------- 363s 1 item passed all tests: 363s 17 tests in default 363s 17 tests in 1 item. 363s 17 passed. 363s Test passed. 363s 363s Document: save-results 363s ---------------------- 363s 1 item passed all tests: 363s 8 tests in default 363s 8 tests in 1 item. 363s 8 passed. 363s Test passed. 363s 363s Document: topical-bam 363s --------------------- 364s 1 item passed all tests: 364s 15 tests in default 364s 15 tests in 1 item. 364s 15 passed. 364s Test passed. 364s 364s Document: topical-create-a-bedtool 364s ---------------------------------- 364s 1 item passed all tests: 364s 10 tests in default 364s 10 tests in 1 item. 364s 10 passed. 364s Test passed. 364s 364s Document: topical-design-principles 364s ----------------------------------- 364s 1 item passed all tests: 364s 15 tests in default 364s 15 tests in 1 item. 364s 15 passed. 364s Test passed. 364s 364s Document: topical-genome 364s ------------------------ 364s 1 item passed all tests: 364s 13 tests in default 364s 13 tests in 1 item. 364s 13 passed. 364s Test passed. 364s 364s Document: topical-iterators 364s --------------------------- 364s 1 item passed all tests: 364s 20 tests in default 364s 20 tests in 1 item. 364s 20 passed. 364s Test passed. 364s 364s Document: topical-low-level-ops 364s ------------------------------- 364s 1 item passed all tests: 364s 6 tests in default 364s 6 tests in 1 item. 364s 6 passed. 364s Test passed. 364s 364s Document: topical-random 364s ------------------------ 366s 1 item passed all tests: 366s 10 tests in default 366s 10 tests in 1 item. 366s 10 passed. 366s Test passed. 366s 366s Document: topical-saving 366s ------------------------ 366s 1 item passed all tests: 366s 14 tests in default 366s 14 tests in 1 item. 366s 14 passed. 366s Test passed. 366s 366s Doctest summary 366s =============== 366s 387 tests 366s 0 failures in tests 366s 0 failures in setup code 366s 0 failures in cleanup code 366s build succeeded. 366s 366s Testing of doctests in the sources finished, look at the results in build/doctest/output.txt. 367s autopkgtest [12:54:26]: test pybuild-autopkgtest: -----------------------] 367s autopkgtest [12:54:26]: test pybuild-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 367s pybuild-autopkgtest PASS 368s autopkgtest [12:54:27]: @@@@@@@@@@@@@@@@@@@@ summary 368s pybuild-autopkgtest PASS 385s nova [W] Using flock in prodstack6-arm64 385s Creating nova instance adt-plucky-arm64-python-pybedtools-20250219-124818-juju-7f2275-prod-proposed-migration-environment-20-04bf6ca8-f553-4706-bada-c30dd3ff0949 from image adt/ubuntu-plucky-arm64-server-20250219.img (UUID 02c92adb-9d9d-4b0e-b071-488d8ee6210f)... 385s nova [W] Timed out waiting for 685b9366-96ef-4504-85db-9e0fa2524678 to get deleted.