0s autopkgtest [01:01:32]: starting date and time: 2024-11-14 01:01:32+0000 0s autopkgtest [01:01:32]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [01:01:32]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.f67bmq5h/out --timeout-copy=6000 --setup-commands 'ln -s /dev/null /etc/systemd/system/bluetooth.service; printf "http_proxy=http://squid.internal:3128\nhttps_proxy=http://squid.internal:3128\nno_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\n" >> /etc/environment' --apt-pocket=proposed=src:python3-defaults,src:python3-stdlib-extensions --apt-upgrade python-pyfaidx --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=python3-defaults/3.12.7-1 python3-stdlib-extensions/3.12.7-1' -- lxd -r lxd-armhf-10.145.243.27 lxd-armhf-10.145.243.27:autopkgtest/ubuntu/plucky/armhf 53s autopkgtest [01:02:25]: testbed dpkg architecture: armhf 55s autopkgtest [01:02:27]: testbed apt version: 2.9.8 55s autopkgtest [01:02:27]: @@@@@@@@@@@@@@@@@@@@ test bed setup 63s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 64s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [17.2 kB] 64s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [99.6 kB] 64s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 64s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [990 kB] 64s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf Packages [103 kB] 64s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf Packages [667 kB] 65s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf Packages [17.2 kB] 65s Fetched 1975 kB in 2s (1161 kB/s) 65s Reading package lists... 82s tee: /proc/self/fd/2: Permission denied 104s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 104s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 104s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 104s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 105s Reading package lists... 105s Reading package lists... 105s Building dependency tree... 105s Reading state information... 106s Calculating upgrade... 107s The following NEW packages will be installed: 107s python3.13-gdbm 107s The following packages will be upgraded: 107s libgnutls30t64 libjson-glib-1.0-0 libjson-glib-1.0-common libnewt0.52 107s libpython3-stdlib libutempter0 python3 python3-gdbm python3-minimal 107s python3-newt whiptail 107s 11 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 107s Need to get 1207 kB of archives. 107s After this operation, 124 kB of additional disk space will be used. 107s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf python3-minimal armhf 3.12.7-1 [27.4 kB] 107s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf python3 armhf 3.12.7-1 [24.0 kB] 107s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libpython3-stdlib armhf 3.12.7-1 [10.0 kB] 107s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf libgnutls30t64 armhf 3.8.8-2ubuntu1 [955 kB] 107s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf python3-newt armhf 0.52.24-2ubuntu4 [19.7 kB] 107s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf libnewt0.52 armhf 0.52.24-2ubuntu4 [39.2 kB] 107s Get:7 http://ftpmaster.internal/ubuntu plucky/main armhf whiptail armhf 0.52.24-2ubuntu4 [17.2 kB] 107s Get:8 http://ftpmaster.internal/ubuntu plucky/main armhf python3.13-gdbm armhf 3.13.0-2 [29.5 kB] 107s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf python3-gdbm armhf 3.12.7-1 [8642 B] 107s Get:10 http://ftpmaster.internal/ubuntu plucky/main armhf libjson-glib-1.0-common all 1.10.0+ds-3 [5586 B] 107s Get:11 http://ftpmaster.internal/ubuntu plucky/main armhf libjson-glib-1.0-0 armhf 1.10.0+ds-3 [61.7 kB] 107s Get:12 http://ftpmaster.internal/ubuntu plucky/main armhf libutempter0 armhf 1.2.1-4 [9062 B] 108s Fetched 1207 kB in 1s (2210 kB/s) 108s (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 ... 59559 files and directories currently installed.) 108s Preparing to unpack .../python3-minimal_3.12.7-1_armhf.deb ... 108s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ... 108s Setting up python3-minimal (3.12.7-1) ... 108s (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 ... 59559 files and directories currently installed.) 108s Preparing to unpack .../python3_3.12.7-1_armhf.deb ... 108s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ... 108s Preparing to unpack .../libpython3-stdlib_3.12.7-1_armhf.deb ... 108s Unpacking libpython3-stdlib:armhf (3.12.7-1) over (3.12.6-0ubuntu1) ... 108s Preparing to unpack .../libgnutls30t64_3.8.8-2ubuntu1_armhf.deb ... 108s Unpacking libgnutls30t64:armhf (3.8.8-2ubuntu1) over (3.8.6-2ubuntu1) ... 108s Setting up libgnutls30t64:armhf (3.8.8-2ubuntu1) ... 108s (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 ... 59559 files and directories currently installed.) 108s Preparing to unpack .../0-python3-newt_0.52.24-2ubuntu4_armhf.deb ... 108s Unpacking python3-newt:armhf (0.52.24-2ubuntu4) over (0.52.24-2ubuntu3) ... 108s Preparing to unpack .../1-libnewt0.52_0.52.24-2ubuntu4_armhf.deb ... 108s Unpacking libnewt0.52:armhf (0.52.24-2ubuntu4) over (0.52.24-2ubuntu3) ... 108s Preparing to unpack .../2-whiptail_0.52.24-2ubuntu4_armhf.deb ... 108s Unpacking whiptail (0.52.24-2ubuntu4) over (0.52.24-2ubuntu3) ... 108s Selecting previously unselected package python3.13-gdbm. 108s Preparing to unpack .../3-python3.13-gdbm_3.13.0-2_armhf.deb ... 108s Unpacking python3.13-gdbm (3.13.0-2) ... 108s Preparing to unpack .../4-python3-gdbm_3.12.7-1_armhf.deb ... 108s Unpacking python3-gdbm:armhf (3.12.7-1) over (3.12.6-1ubuntu1) ... 108s Preparing to unpack .../5-libjson-glib-1.0-common_1.10.0+ds-3_all.deb ... 108s Unpacking libjson-glib-1.0-common (1.10.0+ds-3) over (1.10.0+ds-2) ... 108s Preparing to unpack .../6-libjson-glib-1.0-0_1.10.0+ds-3_armhf.deb ... 108s Unpacking libjson-glib-1.0-0:armhf (1.10.0+ds-3) over (1.10.0+ds-2) ... 108s Preparing to unpack .../7-libutempter0_1.2.1-4_armhf.deb ... 108s Unpacking libutempter0:armhf (1.2.1-4) over (1.2.1-3build1) ... 108s Setting up libnewt0.52:armhf (0.52.24-2ubuntu4) ... 109s Setting up libutempter0:armhf (1.2.1-4) ... 109s Setting up whiptail (0.52.24-2ubuntu4) ... 109s Setting up libjson-glib-1.0-common (1.10.0+ds-3) ... 109s Setting up python3.13-gdbm (3.13.0-2) ... 109s Setting up libpython3-stdlib:armhf (3.12.7-1) ... 109s Setting up python3 (3.12.7-1) ... 109s Setting up python3-newt:armhf (0.52.24-2ubuntu4) ... 109s Setting up libjson-glib-1.0-0:armhf (1.10.0+ds-3) ... 109s Setting up python3-gdbm:armhf (3.12.7-1) ... 109s Processing triggers for man-db (2.12.1-3) ... 110s Processing triggers for libc-bin (2.40-1ubuntu3) ... 110s Reading package lists... 110s Building dependency tree... 110s Reading state information... 111s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 113s autopkgtest [01:03:25]: rebooting testbed after setup commands that affected boot 179s autopkgtest [01:04:31]: testbed running kernel: Linux 6.8.0-48-generic #48~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Mon Oct 7 11:49:53 UTC 2 206s autopkgtest [01:04:58]: @@@@@@@@@@@@@@@@@@@@ apt-source python-pyfaidx 220s Get:1 http://ftpmaster.internal/ubuntu plucky/universe python-pyfaidx 0.8.1.3-1 (dsc) [2544 B] 220s Get:2 http://ftpmaster.internal/ubuntu plucky/universe python-pyfaidx 0.8.1.3-1 (tar) [96.5 kB] 220s Get:3 http://ftpmaster.internal/ubuntu plucky/universe python-pyfaidx 0.8.1.3-1 (diff) [7096 B] 220s gpgv: Signature made Wed Oct 16 19:20:44 2024 UTC 220s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 220s gpgv: issuer "emollier@debian.org" 220s gpgv: Can't check signature: No public key 220s dpkg-source: warning: cannot verify inline signature for ./python-pyfaidx_0.8.1.3-1.dsc: no acceptable signature found 221s autopkgtest [01:05:13]: testing package python-pyfaidx version 0.8.1.3-1 223s autopkgtest [01:05:15]: build not needed 225s autopkgtest [01:05:17]: test run-unit-test: preparing testbed 236s Reading package lists... 236s Building dependency tree... 236s Reading state information... 237s Starting pkgProblemResolver with broken count: 0 237s Starting 2 pkgProblemResolver with broken count: 0 237s Done 238s The following additional packages will be installed: 238s fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-urw-base35 238s libblas3 libcairo2 libdeflate0 libfontconfig1 libfontenc1 libfreetype6 238s libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libhtscodecs2 238s libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 liblapack3 liblcms2-2 238s liblerc4 libopenjp2-7 libpixman-1-0 libpython3.13-minimal 238s libpython3.13-stdlib libraqm0 libsharpyuv0 libtiff6 libwebp7 libwebpdemux2 238s libwebpmux3 libxcb-render0 libxcb-shm0 libxrender1 python-pyfaidx-examples 238s python3-all python3-biopython python3-cairo python3-freetype 238s python3-importlib-metadata python3-iniconfig python3-numpy python3-packaging 238s python3-pil python3-pluggy python3-pyfaidx python3-pytest python3-reportlab 238s python3-rlpycairo python3.13 python3.13-minimal sgml-base tabix w3c-sgml-lib 238s x11-common xfonts-encodings xfonts-utils xml-core 238s Suggested packages: 238s fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre liblcms2-utils 238s python3-tk bwa clustalo clustalw dialign dssp emboss fasttree mafft muscle3 238s phylip phyml prank probcons python3-mysqldb python3-matplotlib python3-mmtf 238s python3-rdflib python3-psycopg2 python3-scipy raxml samtools t-coffee wise 238s gcc gfortran python-numpy-doc python3-dev python-pil-doc pdf-viewer 238s python3-egenix-mxtexttools python-reportlab-doc rl-accel rl-renderpm 238s python3.13-venv python3.13-doc binfmt-support sgml-base-doc debhelper 238s Recommended packages: 238s python-biopython-doc ncbi-blast+ python3-olefile fonts-dejavu-extra 238s The following NEW packages will be installed: 238s autopkgtest-satdep fontconfig-config fonts-dejavu-core fonts-dejavu-mono 238s fonts-urw-base35 libblas3 libcairo2 libdeflate0 libfontconfig1 libfontenc1 238s libfreetype6 libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b 238s libhtscodecs2 libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 liblapack3 238s liblcms2-2 liblerc4 libopenjp2-7 libpixman-1-0 libpython3.13-minimal 238s libpython3.13-stdlib libraqm0 libsharpyuv0 libtiff6 libwebp7 libwebpdemux2 238s libwebpmux3 libxcb-render0 libxcb-shm0 libxrender1 python-pyfaidx-examples 238s python3-all python3-biopython python3-cairo python3-freetype 238s python3-importlib-metadata python3-iniconfig python3-numpy python3-packaging 238s python3-pil python3-pluggy python3-pyfaidx python3-pytest python3-reportlab 238s python3-rlpycairo python3.13 python3.13-minimal sgml-base tabix w3c-sgml-lib 238s x11-common xfonts-encodings xfonts-utils xml-core 238s 0 upgraded, 60 newly installed, 0 to remove and 0 not upgraded. 238s Need to get 32.1 MB/32.1 MB of archives. 238s After this operation, 94.4 MB of additional disk space will be used. 238s Get:1 /tmp/autopkgtest.HJAeQo/1-autopkgtest-satdep.deb autopkgtest-satdep armhf 0 [752 B] 238s Get:2 http://ftpmaster.internal/ubuntu plucky/main armhf libpython3.13-minimal armhf 3.13.0-2 [866 kB] 239s Get:3 http://ftpmaster.internal/ubuntu plucky/main armhf python3.13-minimal armhf 3.13.0-2 [1854 kB] 239s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf sgml-base all 1.31 [11.4 kB] 239s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-dejavu-mono all 2.37-8 [502 kB] 239s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-dejavu-core all 2.37-8 [835 kB] 239s Get:7 http://ftpmaster.internal/ubuntu plucky/main armhf libfontenc1 armhf 1:1.1.8-1build1 [11.5 kB] 239s Get:8 http://ftpmaster.internal/ubuntu plucky/main armhf libfreetype6 armhf 2.13.3+dfsg-1 [330 kB] 239s Get:9 http://ftpmaster.internal/ubuntu plucky/main armhf x11-common all 1:7.7+23ubuntu3 [21.7 kB] 239s Get:10 http://ftpmaster.internal/ubuntu plucky/main armhf xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 239s Get:11 http://ftpmaster.internal/ubuntu plucky/main armhf xfonts-utils armhf 1:7.7+7 [90.6 kB] 239s Get:12 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-urw-base35 all 20200910-8 [11.0 MB] 240s Get:13 http://ftpmaster.internal/ubuntu plucky/main armhf fontconfig-config armhf 2.15.0-1.1ubuntu2 [37.4 kB] 240s Get:14 http://ftpmaster.internal/ubuntu plucky/main armhf libblas3 armhf 3.12.0-3build2 [126 kB] 240s Get:15 http://ftpmaster.internal/ubuntu plucky/main armhf libfontconfig1 armhf 2.15.0-1.1ubuntu2 [113 kB] 240s Get:16 http://ftpmaster.internal/ubuntu plucky/main armhf libpixman-1-0 armhf 0.44.0-3 [183 kB] 240s Get:17 http://ftpmaster.internal/ubuntu plucky/main armhf libxcb-render0 armhf 1.17.0-2 [15.3 kB] 240s Get:18 http://ftpmaster.internal/ubuntu plucky/main armhf libxcb-shm0 armhf 1.17.0-2 [5774 B] 240s Get:19 http://ftpmaster.internal/ubuntu plucky/main armhf libxrender1 armhf 1:0.9.10-1.1build1 [16.0 kB] 240s Get:20 http://ftpmaster.internal/ubuntu plucky/main armhf libcairo2 armhf 1.18.2-2 [484 kB] 240s Get:21 http://ftpmaster.internal/ubuntu plucky/main armhf libdeflate0 armhf 1.22-1 [38.9 kB] 240s Get:22 http://ftpmaster.internal/ubuntu plucky/main armhf libgfortran5 armhf 14.2.0-8ubuntu1 [311 kB] 240s Get:23 http://ftpmaster.internal/ubuntu plucky/main armhf libgomp1 armhf 14.2.0-8ubuntu1 [125 kB] 240s Get:24 http://ftpmaster.internal/ubuntu plucky/main armhf libgraphite2-3 armhf 1.3.14-2ubuntu1 [64.8 kB] 240s Get:25 http://ftpmaster.internal/ubuntu plucky/main armhf libharfbuzz0b armhf 10.0.1-1 [463 kB] 240s Get:26 http://ftpmaster.internal/ubuntu plucky/universe armhf libhtscodecs2 armhf 1.6.1-1 [67.9 kB] 240s Get:27 http://ftpmaster.internal/ubuntu plucky/main armhf libimagequant0 armhf 2.18.0-1build1 [31.1 kB] 240s Get:28 http://ftpmaster.internal/ubuntu plucky/main armhf libjpeg-turbo8 armhf 2.1.5-2ubuntu2 [125 kB] 240s Get:29 http://ftpmaster.internal/ubuntu plucky/main armhf libjpeg8 armhf 8c-2ubuntu11 [2148 B] 240s Get:30 http://ftpmaster.internal/ubuntu plucky/main armhf liblapack3 armhf 3.12.0-3build2 [2086 kB] 240s Get:31 http://ftpmaster.internal/ubuntu plucky/main armhf liblcms2-2 armhf 2.16-2 [137 kB] 240s Get:32 http://ftpmaster.internal/ubuntu plucky/main armhf liblerc4 armhf 4.0.0+ds-4ubuntu2 [151 kB] 240s Get:33 http://ftpmaster.internal/ubuntu plucky/main armhf libpython3.13-stdlib armhf 3.13.0-2 [1972 kB] 240s Get:34 http://ftpmaster.internal/ubuntu plucky/main armhf libraqm0 armhf 0.10.1-1build1 [12.4 kB] 240s Get:35 http://ftpmaster.internal/ubuntu plucky/main armhf libsharpyuv0 armhf 1.4.0-0.1 [16.3 kB] 240s Get:36 http://ftpmaster.internal/ubuntu plucky/main armhf libjbig0 armhf 2.1-6.1ubuntu2 [24.9 kB] 240s Get:37 http://ftpmaster.internal/ubuntu plucky/main armhf libwebp7 armhf 1.4.0-0.1 [184 kB] 240s Get:38 http://ftpmaster.internal/ubuntu plucky/main armhf libtiff6 armhf 4.5.1+git230720-4ubuntu4 [179 kB] 240s Get:39 http://ftpmaster.internal/ubuntu plucky/main armhf libwebpdemux2 armhf 1.4.0-0.1 [11.8 kB] 240s Get:40 http://ftpmaster.internal/ubuntu plucky/main armhf libwebpmux3 armhf 1.4.0-0.1 [22.5 kB] 240s Get:41 http://ftpmaster.internal/ubuntu plucky/universe armhf python-pyfaidx-examples all 0.8.1.3-1 [38.6 kB] 240s Get:42 http://ftpmaster.internal/ubuntu plucky/main armhf python3.13 armhf 3.13.0-2 [719 kB] 240s Get:43 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf python3-all armhf 3.12.7-1 [890 B] 240s Get:44 http://ftpmaster.internal/ubuntu plucky/main armhf python3-numpy armhf 1:1.26.4+ds-11build1 [3570 kB] 240s Get:45 http://ftpmaster.internal/ubuntu plucky/main armhf libopenjp2-7 armhf 2.5.0-2ubuntu1 [170 kB] 240s Get:46 http://ftpmaster.internal/ubuntu plucky/main armhf python3-pil armhf 10.4.0-1ubuntu1 [428 kB] 240s Get:47 http://ftpmaster.internal/ubuntu plucky/main armhf python3-cairo armhf 1.26.1-2 [114 kB] 240s Get:48 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-freetype all 2.5.1-1 [92.3 kB] 240s Get:49 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-rlpycairo all 0.3.0-3 [9130 B] 240s Get:50 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-reportlab all 4.2.5-1 [1107 kB] 241s Get:51 http://ftpmaster.internal/ubuntu plucky/main armhf xml-core all 0.19 [20.3 kB] 241s Get:52 http://ftpmaster.internal/ubuntu plucky/universe armhf w3c-sgml-lib all 1.3-3 [280 kB] 241s Get:53 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-biopython armhf 1.84+dfsg-4 [1666 kB] 241s Get:54 http://ftpmaster.internal/ubuntu plucky/main armhf python3-importlib-metadata all 8.5.0-1 [20.7 kB] 241s Get:55 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-iniconfig all 1.1.1-2 [6024 B] 241s Get:56 http://ftpmaster.internal/ubuntu plucky/main armhf python3-packaging all 24.1-1 [41.4 kB] 241s Get:57 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pluggy all 1.5.0-1 [21.0 kB] 241s Get:58 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pyfaidx all 0.8.1.3-1 [29.7 kB] 241s Get:59 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pytest all 8.3.3-1 [251 kB] 241s Get:60 http://ftpmaster.internal/ubuntu plucky/universe armhf tabix armhf 1.20+ds-1 [432 kB] 242s Fetched 32.1 MB in 3s (11.3 MB/s) 242s Selecting previously unselected package libpython3.13-minimal:armhf. 242s (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 ... 59567 files and directories currently installed.) 242s Preparing to unpack .../00-libpython3.13-minimal_3.13.0-2_armhf.deb ... 242s Unpacking libpython3.13-minimal:armhf (3.13.0-2) ... 242s Selecting previously unselected package python3.13-minimal. 242s Preparing to unpack .../01-python3.13-minimal_3.13.0-2_armhf.deb ... 242s Unpacking python3.13-minimal (3.13.0-2) ... 242s Selecting previously unselected package sgml-base. 242s Preparing to unpack .../02-sgml-base_1.31_all.deb ... 242s Unpacking sgml-base (1.31) ... 242s Selecting previously unselected package fonts-dejavu-mono. 242s Preparing to unpack .../03-fonts-dejavu-mono_2.37-8_all.deb ... 242s Unpacking fonts-dejavu-mono (2.37-8) ... 242s Selecting previously unselected package fonts-dejavu-core. 242s Preparing to unpack .../04-fonts-dejavu-core_2.37-8_all.deb ... 242s Unpacking fonts-dejavu-core (2.37-8) ... 242s Selecting previously unselected package libfontenc1:armhf. 242s Preparing to unpack .../05-libfontenc1_1%3a1.1.8-1build1_armhf.deb ... 242s Unpacking libfontenc1:armhf (1:1.1.8-1build1) ... 242s Selecting previously unselected package libfreetype6:armhf. 242s Preparing to unpack .../06-libfreetype6_2.13.3+dfsg-1_armhf.deb ... 242s Unpacking libfreetype6:armhf (2.13.3+dfsg-1) ... 242s Selecting previously unselected package x11-common. 242s Preparing to unpack .../07-x11-common_1%3a7.7+23ubuntu3_all.deb ... 242s Unpacking x11-common (1:7.7+23ubuntu3) ... 242s Selecting previously unselected package xfonts-encodings. 242s Preparing to unpack .../08-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 242s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 242s Selecting previously unselected package xfonts-utils. 242s Preparing to unpack .../09-xfonts-utils_1%3a7.7+7_armhf.deb ... 242s Unpacking xfonts-utils (1:7.7+7) ... 242s Selecting previously unselected package fonts-urw-base35. 242s Preparing to unpack .../10-fonts-urw-base35_20200910-8_all.deb ... 242s Unpacking fonts-urw-base35 (20200910-8) ... 243s Selecting previously unselected package fontconfig-config. 243s Preparing to unpack .../11-fontconfig-config_2.15.0-1.1ubuntu2_armhf.deb ... 243s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ... 243s Selecting previously unselected package libblas3:armhf. 243s Preparing to unpack .../12-libblas3_3.12.0-3build2_armhf.deb ... 243s Unpacking libblas3:armhf (3.12.0-3build2) ... 243s Selecting previously unselected package libfontconfig1:armhf. 243s Preparing to unpack .../13-libfontconfig1_2.15.0-1.1ubuntu2_armhf.deb ... 243s Unpacking libfontconfig1:armhf (2.15.0-1.1ubuntu2) ... 243s Selecting previously unselected package libpixman-1-0:armhf. 243s Preparing to unpack .../14-libpixman-1-0_0.44.0-3_armhf.deb ... 243s Unpacking libpixman-1-0:armhf (0.44.0-3) ... 243s Selecting previously unselected package libxcb-render0:armhf. 243s Preparing to unpack .../15-libxcb-render0_1.17.0-2_armhf.deb ... 243s Unpacking libxcb-render0:armhf (1.17.0-2) ... 243s Selecting previously unselected package libxcb-shm0:armhf. 243s Preparing to unpack .../16-libxcb-shm0_1.17.0-2_armhf.deb ... 243s Unpacking libxcb-shm0:armhf (1.17.0-2) ... 243s Selecting previously unselected package libxrender1:armhf. 243s Preparing to unpack .../17-libxrender1_1%3a0.9.10-1.1build1_armhf.deb ... 243s Unpacking libxrender1:armhf (1:0.9.10-1.1build1) ... 243s Selecting previously unselected package libcairo2:armhf. 243s Preparing to unpack .../18-libcairo2_1.18.2-2_armhf.deb ... 243s Unpacking libcairo2:armhf (1.18.2-2) ... 243s Selecting previously unselected package libdeflate0:armhf. 243s Preparing to unpack .../19-libdeflate0_1.22-1_armhf.deb ... 243s Unpacking libdeflate0:armhf (1.22-1) ... 243s Selecting previously unselected package libgfortran5:armhf. 243s Preparing to unpack .../20-libgfortran5_14.2.0-8ubuntu1_armhf.deb ... 243s Unpacking libgfortran5:armhf (14.2.0-8ubuntu1) ... 243s Selecting previously unselected package libgomp1:armhf. 243s Preparing to unpack .../21-libgomp1_14.2.0-8ubuntu1_armhf.deb ... 243s Unpacking libgomp1:armhf (14.2.0-8ubuntu1) ... 243s Selecting previously unselected package libgraphite2-3:armhf. 243s Preparing to unpack .../22-libgraphite2-3_1.3.14-2ubuntu1_armhf.deb ... 243s Unpacking libgraphite2-3:armhf (1.3.14-2ubuntu1) ... 243s Selecting previously unselected package libharfbuzz0b:armhf. 243s Preparing to unpack .../23-libharfbuzz0b_10.0.1-1_armhf.deb ... 243s Unpacking libharfbuzz0b:armhf (10.0.1-1) ... 243s Selecting previously unselected package libhtscodecs2:armhf. 243s Preparing to unpack .../24-libhtscodecs2_1.6.1-1_armhf.deb ... 243s Unpacking libhtscodecs2:armhf (1.6.1-1) ... 243s Selecting previously unselected package libimagequant0:armhf. 243s Preparing to unpack .../25-libimagequant0_2.18.0-1build1_armhf.deb ... 243s Unpacking libimagequant0:armhf (2.18.0-1build1) ... 243s Selecting previously unselected package libjpeg-turbo8:armhf. 243s Preparing to unpack .../26-libjpeg-turbo8_2.1.5-2ubuntu2_armhf.deb ... 243s Unpacking libjpeg-turbo8:armhf (2.1.5-2ubuntu2) ... 243s Selecting previously unselected package libjpeg8:armhf. 243s Preparing to unpack .../27-libjpeg8_8c-2ubuntu11_armhf.deb ... 243s Unpacking libjpeg8:armhf (8c-2ubuntu11) ... 243s Selecting previously unselected package liblapack3:armhf. 243s Preparing to unpack .../28-liblapack3_3.12.0-3build2_armhf.deb ... 243s Unpacking liblapack3:armhf (3.12.0-3build2) ... 243s Selecting previously unselected package liblcms2-2:armhf. 243s Preparing to unpack .../29-liblcms2-2_2.16-2_armhf.deb ... 243s Unpacking liblcms2-2:armhf (2.16-2) ... 243s Selecting previously unselected package liblerc4:armhf. 244s Preparing to unpack .../30-liblerc4_4.0.0+ds-4ubuntu2_armhf.deb ... 244s Unpacking liblerc4:armhf (4.0.0+ds-4ubuntu2) ... 244s Selecting previously unselected package libpython3.13-stdlib:armhf. 244s Preparing to unpack .../31-libpython3.13-stdlib_3.13.0-2_armhf.deb ... 244s Unpacking libpython3.13-stdlib:armhf (3.13.0-2) ... 244s Selecting previously unselected package libraqm0:armhf. 244s Preparing to unpack .../32-libraqm0_0.10.1-1build1_armhf.deb ... 244s Unpacking libraqm0:armhf (0.10.1-1build1) ... 244s Selecting previously unselected package libsharpyuv0:armhf. 244s Preparing to unpack .../33-libsharpyuv0_1.4.0-0.1_armhf.deb ... 244s Unpacking libsharpyuv0:armhf (1.4.0-0.1) ... 244s Selecting previously unselected package libjbig0:armhf. 244s Preparing to unpack .../34-libjbig0_2.1-6.1ubuntu2_armhf.deb ... 244s Unpacking libjbig0:armhf (2.1-6.1ubuntu2) ... 244s Selecting previously unselected package libwebp7:armhf. 244s Preparing to unpack .../35-libwebp7_1.4.0-0.1_armhf.deb ... 244s Unpacking libwebp7:armhf (1.4.0-0.1) ... 244s Selecting previously unselected package libtiff6:armhf. 244s Preparing to unpack .../36-libtiff6_4.5.1+git230720-4ubuntu4_armhf.deb ... 244s Unpacking libtiff6:armhf (4.5.1+git230720-4ubuntu4) ... 244s Selecting previously unselected package libwebpdemux2:armhf. 244s Preparing to unpack .../37-libwebpdemux2_1.4.0-0.1_armhf.deb ... 244s Unpacking libwebpdemux2:armhf (1.4.0-0.1) ... 244s Selecting previously unselected package libwebpmux3:armhf. 244s Preparing to unpack .../38-libwebpmux3_1.4.0-0.1_armhf.deb ... 244s Unpacking libwebpmux3:armhf (1.4.0-0.1) ... 244s Selecting previously unselected package python-pyfaidx-examples. 244s Preparing to unpack .../39-python-pyfaidx-examples_0.8.1.3-1_all.deb ... 244s Unpacking python-pyfaidx-examples (0.8.1.3-1) ... 244s Selecting previously unselected package python3.13. 244s Preparing to unpack .../40-python3.13_3.13.0-2_armhf.deb ... 244s Unpacking python3.13 (3.13.0-2) ... 244s Selecting previously unselected package python3-all. 244s Preparing to unpack .../41-python3-all_3.12.7-1_armhf.deb ... 244s Unpacking python3-all (3.12.7-1) ... 244s Selecting previously unselected package python3-numpy. 244s Preparing to unpack .../42-python3-numpy_1%3a1.26.4+ds-11build1_armhf.deb ... 244s Unpacking python3-numpy (1:1.26.4+ds-11build1) ... 244s Selecting previously unselected package libopenjp2-7:armhf. 244s Preparing to unpack .../43-libopenjp2-7_2.5.0-2ubuntu1_armhf.deb ... 244s Unpacking libopenjp2-7:armhf (2.5.0-2ubuntu1) ... 244s Selecting previously unselected package python3-pil:armhf. 244s Preparing to unpack .../44-python3-pil_10.4.0-1ubuntu1_armhf.deb ... 244s Unpacking python3-pil:armhf (10.4.0-1ubuntu1) ... 244s Selecting previously unselected package python3-cairo. 244s Preparing to unpack .../45-python3-cairo_1.26.1-2_armhf.deb ... 244s Unpacking python3-cairo (1.26.1-2) ... 244s Selecting previously unselected package python3-freetype. 244s Preparing to unpack .../46-python3-freetype_2.5.1-1_all.deb ... 244s Unpacking python3-freetype (2.5.1-1) ... 245s Selecting previously unselected package python3-rlpycairo. 245s Preparing to unpack .../47-python3-rlpycairo_0.3.0-3_all.deb ... 245s Unpacking python3-rlpycairo (0.3.0-3) ... 245s Selecting previously unselected package python3-reportlab. 245s Preparing to unpack .../48-python3-reportlab_4.2.5-1_all.deb ... 245s Unpacking python3-reportlab (4.2.5-1) ... 245s Selecting previously unselected package xml-core. 245s Preparing to unpack .../49-xml-core_0.19_all.deb ... 245s Unpacking xml-core (0.19) ... 245s Selecting previously unselected package w3c-sgml-lib. 245s Preparing to unpack .../50-w3c-sgml-lib_1.3-3_all.deb ... 245s Unpacking w3c-sgml-lib (1.3-3) ... 245s Selecting previously unselected package python3-biopython. 245s Preparing to unpack .../51-python3-biopython_1.84+dfsg-4_armhf.deb ... 245s Unpacking python3-biopython (1.84+dfsg-4) ... 245s Selecting previously unselected package python3-importlib-metadata. 245s Preparing to unpack .../52-python3-importlib-metadata_8.5.0-1_all.deb ... 245s Unpacking python3-importlib-metadata (8.5.0-1) ... 245s Selecting previously unselected package python3-iniconfig. 245s Preparing to unpack .../53-python3-iniconfig_1.1.1-2_all.deb ... 245s Unpacking python3-iniconfig (1.1.1-2) ... 245s Selecting previously unselected package python3-packaging. 245s Preparing to unpack .../54-python3-packaging_24.1-1_all.deb ... 245s Unpacking python3-packaging (24.1-1) ... 245s Selecting previously unselected package python3-pluggy. 245s Preparing to unpack .../55-python3-pluggy_1.5.0-1_all.deb ... 245s Unpacking python3-pluggy (1.5.0-1) ... 245s Selecting previously unselected package python3-pyfaidx. 245s Preparing to unpack .../56-python3-pyfaidx_0.8.1.3-1_all.deb ... 245s Unpacking python3-pyfaidx (0.8.1.3-1) ... 245s Selecting previously unselected package python3-pytest. 245s Preparing to unpack .../57-python3-pytest_8.3.3-1_all.deb ... 245s Unpacking python3-pytest (8.3.3-1) ... 245s Selecting previously unselected package tabix. 245s Preparing to unpack .../58-tabix_1.20+ds-1_armhf.deb ... 245s Unpacking tabix (1.20+ds-1) ... 245s Selecting previously unselected package autopkgtest-satdep. 245s Preparing to unpack .../59-1-autopkgtest-satdep.deb ... 245s Unpacking autopkgtest-satdep (0) ... 245s Setting up libhtscodecs2:armhf (1.6.1-1) ... 245s Setting up libgraphite2-3:armhf (1.3.14-2ubuntu1) ... 245s Setting up liblcms2-2:armhf (2.16-2) ... 245s Setting up python3-iniconfig (1.1.1-2) ... 246s Setting up libpixman-1-0:armhf (0.44.0-3) ... 246s Setting up libsharpyuv0:armhf (1.4.0-0.1) ... 246s Setting up liblerc4:armhf (4.0.0+ds-4ubuntu2) ... 246s Setting up python3-importlib-metadata (8.5.0-1) ... 246s Setting up libxrender1:armhf (1:0.9.10-1.1build1) ... 246s Setting up python-pyfaidx-examples (0.8.1.3-1) ... 246s Setting up libxcb-render0:armhf (1.17.0-2) ... 246s Setting up x11-common (1:7.7+23ubuntu3) ... 246s Setting up libdeflate0:armhf (1.22-1) ... 246s Setting up libxcb-shm0:armhf (1.17.0-2) ... 246s Setting up libgomp1:armhf (14.2.0-8ubuntu1) ... 246s Setting up libjbig0:armhf (2.1-6.1ubuntu2) ... 246s Setting up libpython3.13-minimal:armhf (3.13.0-2) ... 246s Setting up libfontenc1:armhf (1:1.1.8-1build1) ... 246s Setting up libblas3:armhf (3.12.0-3build2) ... 246s update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode 246s Setting up python3-packaging (24.1-1) ... 247s Setting up libfreetype6:armhf (2.13.3+dfsg-1) ... 247s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 247s Setting up libimagequant0:armhf (2.18.0-1build1) ... 247s Setting up fonts-dejavu-mono (2.37-8) ... 247s Setting up fonts-dejavu-core (2.37-8) ... 247s Setting up libjpeg-turbo8:armhf (2.1.5-2ubuntu2) ... 247s Setting up libgfortran5:armhf (14.2.0-8ubuntu1) ... 247s Setting up python3-pluggy (1.5.0-1) ... 247s Setting up libwebp7:armhf (1.4.0-0.1) ... 247s Setting up libopenjp2-7:armhf (2.5.0-2ubuntu1) ... 247s Setting up python3.13-minimal (3.13.0-2) ... 248s Setting up libharfbuzz0b:armhf (10.0.1-1) ... 248s Setting up sgml-base (1.31) ... 248s Setting up libwebpmux3:armhf (1.4.0-0.1) ... 248s Setting up tabix (1.20+ds-1) ... 248s Setting up libpython3.13-stdlib:armhf (3.13.0-2) ... 248s Setting up libjpeg8:armhf (8c-2ubuntu11) ... 248s Setting up python3-pyfaidx (0.8.1.3-1) ... 248s Setting up liblapack3:armhf (3.12.0-3build2) ... 248s update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode 248s Setting up python3.13 (3.13.0-2) ... 250s Setting up fontconfig-config (2.15.0-1.1ubuntu2) ... 250s Setting up python3-pytest (8.3.3-1) ... 251s Setting up libwebpdemux2:armhf (1.4.0-0.1) ... 251s Setting up python3-all (3.12.7-1) ... 251s Setting up python3-freetype (2.5.1-1) ... 251s Setting up xfonts-utils (1:7.7+7) ... 251s Setting up libraqm0:armhf (0.10.1-1build1) ... 251s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 256s Setting up libtiff6:armhf (4.5.1+git230720-4ubuntu4) ... 256s Setting up xml-core (0.19) ... 256s Setting up libfontconfig1:armhf (2.15.0-1.1ubuntu2) ... 256s Setting up fonts-urw-base35 (20200910-8) ... 256s Setting up libcairo2:armhf (1.18.2-2) ... 256s Setting up python3-pil:armhf (10.4.0-1ubuntu1) ... 257s Setting up python3-cairo (1.26.1-2) ... 257s Setting up python3-rlpycairo (0.3.0-3) ... 257s Setting up python3-reportlab (4.2.5-1) ... 259s Processing triggers for libc-bin (2.40-1ubuntu3) ... 259s Processing triggers for systemd (256.5-2ubuntu4) ... 259s Processing triggers for man-db (2.12.1-3) ... 260s Processing triggers for sgml-base (1.31) ... 260s Setting up w3c-sgml-lib (1.3-3) ... 292s Setting up python3-biopython (1.84+dfsg-4) ... 295s Setting up autopkgtest-satdep (0) ... 314s (Reading database ... 63777 files and directories currently installed.) 314s Removing autopkgtest-satdep (0) ... 320s autopkgtest [01:06:52]: test run-unit-test: [----------------------- 322s Testing with python3.13 in /tmp/autopkgtest.HJAeQo/build.cjm/src: 322s ============================= test session starts ============================== 322s platform linux -- Python 3.13.0, pytest-8.3.3, pluggy-1.5.0 -- /usr/bin/python3.13 322s cachedir: .pytest_cache 322s rootdir: /tmp/autopkgtest.HJAeQo/build.cjm/src 322s configfile: pyproject.toml 322s plugins: typeguard-4.4.1 323s collecting ... collected 136 items 323s 323s tests/test_FastaRecord.py::test_sequence_uppercase PASSED [ 0%] 323s tests/test_FastaRecord.py::test_long_names PASSED [ 1%] 323s tests/test_FastaRecord.py::test_issue_62 PASSED [ 2%] 323s tests/test_FastaRecord.py::test_unpadded_length PASSED [ 2%] 323s tests/test_FastaRecord.py::test_numpy_array FAILED [ 3%] 323s tests/test_FastaRecord_iter.py::test_fetch_whole_fasta PASSED [ 4%] 323s tests/test_FastaRecord_iter.py::test_line_len PASSED [ 5%] 323s tests/test_FastaRecord_iter.py::test_reverse_iter PASSED [ 5%] 323s tests/test_FastaVariant.py::test_fetch_variant SKIPPED (pysam not in...) [ 6%] 323s tests/test_FastaVariant.py::test_fetch_hom_variant SKIPPED (pysam no...) [ 7%] 323s tests/test_FastaVariant.py::test_fetch_het_variant SKIPPED (pysam no...) [ 8%] 323s tests/test_FastaVariant.py::test_fetch_chr_not_in_vcf SKIPPED (pysam...) [ 8%] 323s tests/test_FastaVariant.py::test_all_pos SKIPPED (pysam not installed.) [ 9%] 323s tests/test_FastaVariant.py::test_all_diff SKIPPED (pysam not installed.) [ 10%] 323s tests/test_Fasta_bgzip.py::test_build_issue_126 SKIPPED (Biopython i...) [ 11%] 323s tests/test_Fasta_bgzip.py::test_integer_slice PASSED [ 11%] 323s tests/test_Fasta_bgzip.py::test_integer_index PASSED [ 12%] 323s tests/test_Fasta_bgzip.py::test_fetch_whole_fasta PASSED [ 13%] 323s tests/test_Fasta_bgzip.py::test_line_len PASSED [ 13%] 323s tests/test_Fasta_bgzip.py::test_mutable_bgzf PASSED [ 14%] 323s tests/test_Fasta_bgzip.py::test_long_names XFAIL [ 15%] 323s tests/test_Fasta_bgzip.py::test_fetch_whole_entry PASSED [ 16%] 323s tests/test_Fasta_bgzip.py::test_fetch_middle PASSED [ 16%] 323s tests/test_Fasta_bgzip.py::test_fetch_end PASSED [ 17%] 323s tests/test_Fasta_bgzip.py::test_fetch_border PASSED [ 18%] 323s tests/test_Fasta_bgzip.py::test_rev PASSED [ 19%] 323s tests/test_Fasta_bgzip.py::test_fetch_past_bounds PASSED [ 19%] 323s tests/test_Fasta_bgzip.py::test_fetch_negative PASSED [ 20%] 323s tests/test_Fasta_bgzip.py::test_fetch_reversed_coordinates PASSED [ 21%] 323s tests/test_Fasta_bgzip.py::test_fetch_keyerror PASSED [ 22%] 323s tests/test_Fasta_bgzip.py::test_blank_string PASSED [ 22%] 323s tests/test_Fasta_bgzip.py::test_slice_from_beginning PASSED [ 23%] 323s tests/test_Fasta_bgzip.py::test_slice_from_end PASSED [ 24%] 323s tests/test_Fasta_bgzip.py::test_issue_74_start PASSED [ 25%] 323s tests/test_Fasta_bgzip.py::test_issue_74_consistency PASSED [ 25%] 323s tests/test_Fasta_bgzip.py::test_issue_74_end_faidx PASSED [ 26%] 323s tests/test_Fasta_bgzip.py::test_issue_74_end_fasta PASSED [ 27%] 323s tests/test_Fasta_bgzip.py::test_issue_79_fix PASSED [ 27%] 323s tests/test_Fasta_bgzip.py::test_issue_79_fix_negate PASSED [ 28%] 323s tests/test_Fasta_bgzip.py::test_issue_79_fix_one_based_false PASSED [ 29%] 323s tests/test_Fasta_bgzip.py::test_issue_79_fix_one_based_false_negate PASSED [ 30%] 323s tests/test_Fasta_bgzip.py::test_fetch_border_padded PASSED [ 30%] 323s tests/test_Fasta_integer_index.py::test_integer_slice PASSED [ 31%] 323s tests/test_Fasta_integer_index.py::test_integer_index PASSED [ 32%] 323s tests/test_Fasta_synchronization.py::TestFastaIntIndex::test_simultaneous_reads PASSED [ 33%] 324s tests/test_Fasta_synchronization.py::TestFastaIntIndex::test_simultaneous_reads_and_writes PASSED [ 33%] 325s tests/test_Fasta_synchronization.py::TestFastaIntIndex::test_simultaneous_writes PASSED [ 34%] 325s tests/test_Path.py::test_Faidx PASSED [ 35%] 325s tests/test_Path.py::test_Fasta PASSED [ 36%] 325s tests/test_bio_seqio.py::test_fetch_whole_entry SKIPPED (Biopython i...) 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[ 38%] 325s tests/test_faidx.py::test_short_line_lengths PASSED [ 38%] 325s tests/test_faidx.py::test_fetch_whole_file PASSED [ 39%] 325s tests/test_faidx.py::test_split_entry PASSED [ 40%] 325s tests/test_faidx.py::test_fetch_error PASSED [ 41%] 325s tests/test_faidx.py::test_key_warning PASSED [ 41%] 325s tests/test_faidx.py::test_auto_strand PASSED [ 42%] 325s tests/test_faidx.py::test_regexp PASSED [ 43%] 325s tests/test_faidx.py::test_not_regexp PASSED [ 44%] 325s tests/test_faidx.py::test_not_regexp_multi PASSED [ 44%] 325s tests/test_feature_bounds_check.py::test_index_zero_length PASSED [ 45%] 325s tests/test_feature_bounds_check.py::test_fetch_zero_length PASSED [ 46%] 325s tests/test_feature_bounds_check.py::test_as_raw_zero_length_subsequence PASSED [ 47%] 325s tests/test_feature_bounds_check.py::test_zero_length_subsequence PASSED [ 47%] 325s tests/test_feature_bounds_check.py::test_fetch_whole_entry PASSED [ 48%] 325s tests/test_feature_bounds_check.py::test_fetch_middle 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[ 93%] 346s tests/test_sequence_class.py::test_negate PASSED [ 94%] 346s tests/test_sequence_class.py::test_negate_metadata PASSED [ 94%] 346s tests/test_sequence_class.py::test_seq_invalid PASSED [ 95%] 346s tests/test_sequence_class.py::test_integer_index PASSED [ 96%] 347s tests/test_sequence_class.py::test_slice_index PASSED [ 97%] 347s tests/test_sequence_class.py::test_comp_invalid PASSED [ 97%] 347s tests/test_sequence_class.py::test_check_coordinates PASSED [ 98%] 347s tests/test_sequence_class.py::test_comp_valid PASSED [ 99%] 347s tests/test_sequence_class.py::test_comp_empty PASSED [100%] 347s 347s =================================== FAILURES =================================== 347s _______________________________ test_numpy_array _______________________________ 347s 347s """ 347s Contains the core of NumPy: ndarray, ufuncs, dtypes, etc. 347s 347s Please note that this module is private. All functions and objects 347s are available in the main ``numpy`` namespace - use that instead. 347s 347s """ 347s 347s import os 347s import warnings 347s 347s from numpy.version import version as __version__ 347s 347s 347s # disables OpenBLAS affinity setting of the main thread that limits 347s # python threads or processes to one core 347s env_added = [] 347s for envkey in ['OPENBLAS_MAIN_FREE', 'GOTOBLAS_MAIN_FREE']: 347s if envkey not in os.environ: 347s os.environ[envkey] = '1' 347s env_added.append(envkey) 347s 347s try: 347s > from . import multiarray 347s 347s /usr/lib/python3/dist-packages/numpy/core/__init__.py:24: 347s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 347s /usr/lib/python3/dist-packages/numpy/core/multiarray.py:10: in 347s from . import overrides 347s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 347s 347s """Implementation of __array_function__ overrides from NEP-18.""" 347s import collections 347s import functools 347s import os 347s 347s from .._utils import set_module 347s from .._utils._inspect import getargspec 347s > from numpy.core._multiarray_umath import ( 347s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 347s E ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 347s 347s /usr/lib/python3/dist-packages/numpy/core/overrides.py:8: ModuleNotFoundError 347s 347s During handling of the above exception, another exception occurred: 347s 347s """ 347s NumPy 347s ===== 347s 347s Provides 347s 1. An array object of arbitrary homogeneous items 347s 2. Fast mathematical operations over arrays 347s 3. Linear Algebra, Fourier Transforms, Random Number Generation 347s 347s How to use the documentation 347s ---------------------------- 347s Documentation is available in two forms: docstrings provided 347s with the code, and a loose standing reference guide, available from 347s `the NumPy homepage `_. 347s 347s We recommend exploring the docstrings using 347s `IPython `_, an advanced Python shell with 347s TAB-completion and introspection capabilities. See below for further 347s instructions. 347s 347s The docstring examples assume that `numpy` has been imported as ``np``:: 347s 347s >>> import numpy as np 347s 347s Code snippets are indicated by three greater-than signs:: 347s 347s >>> x = 42 347s >>> x = x + 1 347s 347s Use the built-in ``help`` function to view a function's docstring:: 347s 347s >>> help(np.sort) 347s ... # doctest: +SKIP 347s 347s For some objects, ``np.info(obj)`` may provide additional help. This is 347s particularly true if you see the line "Help on ufunc object:" at the top 347s of the help() page. Ufuncs are implemented in C, not Python, for speed. 347s The native Python help() does not know how to view their help, but our 347s np.info() function does. 347s 347s To search for documents containing a keyword, do:: 347s 347s >>> np.lookfor('keyword') 347s ... # doctest: +SKIP 347s 347s General-purpose documents like a glossary and help on the basic concepts 347s of numpy are available under the ``doc`` sub-module:: 347s 347s >>> from numpy import doc 347s >>> help(doc) 347s ... # doctest: +SKIP 347s 347s Available subpackages 347s --------------------- 347s lib 347s Basic functions used by several sub-packages. 347s random 347s Core Random Tools 347s linalg 347s Core Linear Algebra Tools 347s fft 347s Core FFT routines 347s polynomial 347s Polynomial tools 347s testing 347s NumPy testing tools 347s distutils 347s Enhancements to distutils with support for 347s Fortran compilers support and more (for Python <= 3.11). 347s 347s Utilities 347s --------- 347s test 347s Run numpy unittests 347s show_config 347s Show numpy build configuration 347s matlib 347s Make everything matrices. 347s __version__ 347s NumPy version string 347s 347s Viewing documentation using IPython 347s ----------------------------------- 347s 347s Start IPython and import `numpy` usually under the alias ``np``: `import 347s numpy as np`. Then, directly past or use the ``%cpaste`` magic to paste 347s examples into the shell. To see which functions are available in `numpy`, 347s type ``np.`` (where ```` refers to the TAB key), or use 347s ``np.*cos*?`` (where ```` refers to the ENTER key) to narrow 347s down the list. To view the docstring for a function, use 347s ``np.cos?`` (to view the docstring) and ``np.cos??`` (to view 347s the source code). 347s 347s Copies vs. in-place operation 347s ----------------------------- 347s Most of the functions in `numpy` return a copy of the array argument 347s (e.g., `np.sort`). In-place versions of these functions are often 347s available as array methods, i.e. ``x = np.array([1,2,3]); x.sort()``. 347s Exceptions to this rule are documented. 347s 347s """ 347s import sys 347s import warnings 347s 347s from ._globals import _NoValue, _CopyMode 347s # These exceptions were moved in 1.25 and are hidden from __dir__() 347s from .exceptions import ( 347s ComplexWarning, ModuleDeprecationWarning, VisibleDeprecationWarning, 347s TooHardError, AxisError) 347s 347s 347s # If a version with git hash was stored, use that instead 347s from . import version 347s from .version import __version__ 347s 347s # We first need to detect if we're being called as part of the numpy setup 347s # procedure itself in a reliable manner. 347s try: 347s __NUMPY_SETUP__ 347s except NameError: 347s __NUMPY_SETUP__ = False 347s 347s if __NUMPY_SETUP__: 347s sys.stderr.write('Running from numpy source directory.\n') 347s else: 347s # Allow distributors to run custom init code before importing numpy.core 347s from . import _distributor_init 347s 347s try: 347s > from numpy.__config__ import show as show_config 347s 347s /usr/lib/python3/dist-packages/numpy/__init__.py:130: 347s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 347s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 347s from numpy.core._multiarray_umath import ( 347s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 347s 347s """ 347s Contains the core of NumPy: ndarray, ufuncs, dtypes, etc. 347s 347s Please note that this module is private. All functions and objects 347s are available in the main ``numpy`` namespace - use that instead. 347s 347s """ 347s 347s import os 347s import warnings 347s 347s from numpy.version import version as __version__ 347s 347s 347s # disables OpenBLAS affinity setting of the main thread that limits 347s # python threads or processes to one core 347s env_added = [] 347s for envkey in ['OPENBLAS_MAIN_FREE', 'GOTOBLAS_MAIN_FREE']: 347s if envkey not in os.environ: 347s os.environ[envkey] = '1' 347s env_added.append(envkey) 347s 347s try: 347s from . import multiarray 347s except ImportError as exc: 347s import sys 347s msg = """ 347s 347s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 347s 347s Importing the numpy C-extensions failed. This error can happen for 347s many reasons, often due to issues with your setup or how NumPy was 347s installed. 347s 347s We have compiled some common reasons and troubleshooting tips at: 347s 347s https://numpy.org/devdocs/user/troubleshooting-importerror.html 347s 347s Please note and check the following: 347s 347s * The Python version is: Python%d.%d from "%s" 347s * The NumPy version is: "%s" 347s 347s and make sure that they are the versions you expect. 347s Please carefully study the documentation linked above for further help. 347s 347s Original error was: %s 347s """ % (sys.version_info[0], sys.version_info[1], sys.executable, 347s __version__, exc) 347s > raise ImportError(msg) 347s E ImportError: 347s E 347s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 347s E 347s E Importing the numpy C-extensions failed. This error can happen for 347s E many reasons, often due to issues with your setup or how NumPy was 347s E installed. 347s E 347s E We have compiled some common reasons and troubleshooting tips at: 347s E 347s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 347s E 347s E Please note and check the following: 347s E 347s E * The Python version is: Python3.13 from "/usr/bin/python3.13" 347s E * The NumPy version is: "1.26.4" 347s E 347s E and make sure that they are the versions you expect. 347s E Please carefully study the documentation linked above for further help. 347s E 347s E Original error was: No module named 'numpy.core._multiarray_umath' 347s 347s /usr/lib/python3/dist-packages/numpy/core/__init__.py:50: ImportError 347s 347s The above exception was the direct cause of the following exception: 347s 347s remove_index = None 347s 347s def test_numpy_array(remove_index): 347s """ Test the __array_interface__ """ 347s > import numpy 347s 347s /tmp/autopkgtest.HJAeQo/build.cjm/src/tests/test_FastaRecord.py:103: 347s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 347s 347s """ 347s NumPy 347s ===== 347s 347s Provides 347s 1. An array object of arbitrary homogeneous items 347s 2. Fast mathematical operations over arrays 347s 3. Linear Algebra, Fourier Transforms, Random Number Generation 347s 347s How to use the documentation 347s ---------------------------- 347s Documentation is available in two forms: docstrings provided 347s with the code, and a loose standing reference guide, available from 347s `the NumPy homepage `_. 347s 347s We recommend exploring the docstrings using 347s `IPython `_, an advanced Python shell with 347s TAB-completion and introspection capabilities. See below for further 347s instructions. 347s 347s The docstring examples assume that `numpy` has been imported as ``np``:: 347s 347s >>> import numpy as np 347s 347s Code snippets are indicated by three greater-than signs:: 347s 347s >>> x = 42 347s >>> x = x + 1 347s 347s Use the built-in ``help`` function to view a function's docstring:: 347s 347s >>> help(np.sort) 347s ... # doctest: +SKIP 347s 347s For some objects, ``np.info(obj)`` may provide additional help. This is 347s particularly true if you see the line "Help on ufunc object:" at the top 347s of the help() page. Ufuncs are implemented in C, not Python, for speed. 347s The native Python help() does not know how to view their help, but our 347s np.info() function does. 347s 347s To search for documents containing a keyword, do:: 347s 347s >>> np.lookfor('keyword') 347s ... # doctest: +SKIP 347s 347s General-purpose documents like a glossary and help on the basic concepts 347s of numpy are available under the ``doc`` sub-module:: 347s 347s >>> from numpy import doc 347s >>> help(doc) 347s ... # doctest: +SKIP 347s 347s Available subpackages 347s --------------------- 347s lib 347s Basic functions used by several sub-packages. 347s random 347s Core Random Tools 347s linalg 347s Core Linear Algebra Tools 347s fft 347s Core FFT routines 347s polynomial 347s Polynomial tools 347s testing 347s NumPy testing tools 347s distutils 347s Enhancements to distutils with support for 347s Fortran compilers support and more (for Python <= 3.11). 347s 347s Utilities 347s --------- 347s test 347s Run numpy unittests 347s show_config 347s Show numpy build configuration 347s matlib 347s Make everything matrices. 347s __version__ 347s NumPy version string 347s 347s Viewing documentation using IPython 347s ----------------------------------- 347s 347s Start IPython and import `numpy` usually under the alias ``np``: `import 347s numpy as np`. Then, directly past or use the ``%cpaste`` magic to paste 347s examples into the shell. To see which functions are available in `numpy`, 347s type ``np.`` (where ```` refers to the TAB key), or use 347s ``np.*cos*?`` (where ```` refers to the ENTER key) to narrow 347s down the list. To view the docstring for a function, use 347s ``np.cos?`` (to view the docstring) and ``np.cos??`` (to view 347s the source code). 347s 347s Copies vs. in-place operation 347s ----------------------------- 347s Most of the functions in `numpy` return a copy of the array argument 347s (e.g., `np.sort`). In-place versions of these functions are often 347s available as array methods, i.e. ``x = np.array([1,2,3]); x.sort()``. 347s Exceptions to this rule are documented. 347s 347s """ 347s import sys 347s import warnings 347s 347s from ._globals import _NoValue, _CopyMode 347s # These exceptions were moved in 1.25 and are hidden from __dir__() 347s from .exceptions import ( 347s ComplexWarning, ModuleDeprecationWarning, VisibleDeprecationWarning, 347s TooHardError, AxisError) 347s 347s 347s # If a version with git hash was stored, use that instead 347s from . import version 347s from .version import __version__ 347s 347s # We first need to detect if we're being called as part of the numpy setup 347s # procedure itself in a reliable manner. 347s try: 347s __NUMPY_SETUP__ 347s except NameError: 347s __NUMPY_SETUP__ = False 347s 347s if __NUMPY_SETUP__: 347s sys.stderr.write('Running from numpy source directory.\n') 347s else: 347s # Allow distributors to run custom init code before importing numpy.core 347s from . import _distributor_init 347s 347s try: 347s from numpy.__config__ import show as show_config 347s except ImportError as e: 347s msg = """Error importing numpy: you should not try to import numpy from 347s its source directory; please exit the numpy source tree, and relaunch 347s your python interpreter from there.""" 347s > raise ImportError(msg) from e 347s E ImportError: Error importing numpy: you should not try to import numpy from 347s E its source directory; please exit the numpy source tree, and relaunch 347s E your python interpreter from there. 347s 347s /usr/lib/python3/dist-packages/numpy/__init__.py:135: ImportError 347s =========================== short test summary info ============================ 347s FAILED tests/test_FastaRecord.py::test_numpy_array - ImportError: Error impor... 347s ============ 1 failed, 120 passed, 14 skipped, 1 xfailed in 24.17s ============= 347s autopkgtest [01:07:19]: test run-unit-test: -----------------------] 351s autopkgtest [01:07:23]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 351s run-unit-test FAIL non-zero exit status 1 355s autopkgtest [01:07:27]: test autodep8-python3: preparing testbed 410s autopkgtest [01:08:22]: testbed dpkg architecture: armhf 412s autopkgtest [01:08:24]: testbed apt version: 2.9.8 412s autopkgtest [01:08:24]: @@@@@@@@@@@@@@@@@@@@ test bed setup 420s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 420s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 420s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [990 kB] 420s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [17.2 kB] 420s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [99.6 kB] 420s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf Packages [103 kB] 420s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf Packages [667 kB] 420s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf Packages [17.2 kB] 420s Fetched 1975 kB in 1s (1926 kB/s) 421s Reading package lists... 436s tee: /proc/self/fd/2: Permission denied 458s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 458s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 458s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 458s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 460s Reading package lists... 460s Reading package lists... 460s Building dependency tree... 460s Reading state information... 462s Calculating upgrade... 463s The following NEW packages will be installed: 463s python3.13-gdbm 463s The following packages will be upgraded: 463s libgnutls30t64 libjson-glib-1.0-0 libjson-glib-1.0-common libnewt0.52 463s libpython3-stdlib libutempter0 python3 python3-gdbm python3-minimal 463s python3-newt whiptail 463s 11 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 463s Need to get 1207 kB of archives. 463s After this operation, 124 kB of additional disk space will be used. 463s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf python3-minimal armhf 3.12.7-1 [27.4 kB] 463s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf python3 armhf 3.12.7-1 [24.0 kB] 463s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libpython3-stdlib armhf 3.12.7-1 [10.0 kB] 463s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf libgnutls30t64 armhf 3.8.8-2ubuntu1 [955 kB] 464s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf python3-newt armhf 0.52.24-2ubuntu4 [19.7 kB] 464s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf libnewt0.52 armhf 0.52.24-2ubuntu4 [39.2 kB] 464s Get:7 http://ftpmaster.internal/ubuntu plucky/main armhf whiptail armhf 0.52.24-2ubuntu4 [17.2 kB] 464s Get:8 http://ftpmaster.internal/ubuntu plucky/main armhf python3.13-gdbm armhf 3.13.0-2 [29.5 kB] 464s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf python3-gdbm armhf 3.12.7-1 [8642 B] 464s Get:10 http://ftpmaster.internal/ubuntu plucky/main armhf libjson-glib-1.0-common all 1.10.0+ds-3 [5586 B] 464s Get:11 http://ftpmaster.internal/ubuntu plucky/main armhf libjson-glib-1.0-0 armhf 1.10.0+ds-3 [61.7 kB] 464s Get:12 http://ftpmaster.internal/ubuntu plucky/main armhf libutempter0 armhf 1.2.1-4 [9062 B] 464s Fetched 1207 kB in 1s (2176 kB/s) 464s (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 ... 59559 files and directories currently installed.) 464s Preparing to unpack .../python3-minimal_3.12.7-1_armhf.deb ... 464s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ... 464s Setting up python3-minimal (3.12.7-1) ... 465s (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 ... 59559 files and directories currently installed.) 465s Preparing to unpack .../python3_3.12.7-1_armhf.deb ... 465s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ... 465s Preparing to unpack .../libpython3-stdlib_3.12.7-1_armhf.deb ... 465s Unpacking libpython3-stdlib:armhf (3.12.7-1) over (3.12.6-0ubuntu1) ... 465s Preparing to unpack .../libgnutls30t64_3.8.8-2ubuntu1_armhf.deb ... 465s Unpacking libgnutls30t64:armhf (3.8.8-2ubuntu1) over (3.8.6-2ubuntu1) ... 465s Setting up libgnutls30t64:armhf (3.8.8-2ubuntu1) ... 465s (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 ... 59559 files and directories currently installed.) 465s Preparing to unpack .../0-python3-newt_0.52.24-2ubuntu4_armhf.deb ... 465s Unpacking python3-newt:armhf (0.52.24-2ubuntu4) over (0.52.24-2ubuntu3) ... 465s Preparing to unpack .../1-libnewt0.52_0.52.24-2ubuntu4_armhf.deb ... 465s Unpacking libnewt0.52:armhf (0.52.24-2ubuntu4) over (0.52.24-2ubuntu3) ... 465s Preparing to unpack .../2-whiptail_0.52.24-2ubuntu4_armhf.deb ... 465s Unpacking whiptail (0.52.24-2ubuntu4) over (0.52.24-2ubuntu3) ... 465s Selecting previously unselected package python3.13-gdbm. 465s Preparing to unpack .../3-python3.13-gdbm_3.13.0-2_armhf.deb ... 465s Unpacking python3.13-gdbm (3.13.0-2) ... 465s Preparing to unpack .../4-python3-gdbm_3.12.7-1_armhf.deb ... 465s Unpacking python3-gdbm:armhf (3.12.7-1) over (3.12.6-1ubuntu1) ... 465s Preparing to unpack .../5-libjson-glib-1.0-common_1.10.0+ds-3_all.deb ... 465s Unpacking libjson-glib-1.0-common (1.10.0+ds-3) over (1.10.0+ds-2) ... 465s Preparing to unpack .../6-libjson-glib-1.0-0_1.10.0+ds-3_armhf.deb ... 465s Unpacking libjson-glib-1.0-0:armhf (1.10.0+ds-3) over (1.10.0+ds-2) ... 465s Preparing to unpack .../7-libutempter0_1.2.1-4_armhf.deb ... 465s Unpacking libutempter0:armhf (1.2.1-4) over (1.2.1-3build1) ... 465s Setting up libnewt0.52:armhf (0.52.24-2ubuntu4) ... 465s Setting up libutempter0:armhf (1.2.1-4) ... 465s Setting up whiptail (0.52.24-2ubuntu4) ... 465s Setting up libjson-glib-1.0-common (1.10.0+ds-3) ... 465s Setting up python3.13-gdbm (3.13.0-2) ... 465s Setting up libpython3-stdlib:armhf (3.12.7-1) ... 465s Setting up python3 (3.12.7-1) ... 466s Setting up python3-newt:armhf (0.52.24-2ubuntu4) ... 466s Setting up libjson-glib-1.0-0:armhf (1.10.0+ds-3) ... 466s Setting up python3-gdbm:armhf (3.12.7-1) ... 466s Processing triggers for man-db (2.12.1-3) ... 466s Processing triggers for libc-bin (2.40-1ubuntu3) ... 467s Reading package lists... 467s Building dependency tree... 467s Reading state information... 468s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 470s autopkgtest [01:09:22]: rebooting testbed after setup commands that affected boot 571s Reading package lists... 572s Building dependency tree... 572s Reading state information... 572s Starting pkgProblemResolver with broken count: 0 572s Starting 2 pkgProblemResolver with broken count: 0 572s Done 573s The following additional packages will be installed: 573s libpython3.13-minimal libpython3.13-stdlib python3-all 573s python3-importlib-metadata python3-packaging python3-pyfaidx python3.13 573s python3.13-minimal 573s Suggested packages: 573s python3.13-venv python3.13-doc binfmt-support 573s Recommended packages: 573s python3-biopython 573s The following NEW packages will be installed: 573s autopkgtest-satdep libpython3.13-minimal libpython3.13-stdlib python3-all 573s python3-importlib-metadata python3-packaging python3-pyfaidx python3.13 573s python3.13-minimal 573s 0 upgraded, 9 newly installed, 0 to remove and 0 not upgraded. 573s Need to get 5504 kB/5504 kB of archives. 573s After this operation, 19.5 MB of additional disk space will be used. 573s Get:1 /tmp/autopkgtest.HJAeQo/2-autopkgtest-satdep.deb autopkgtest-satdep armhf 0 [712 B] 574s Get:2 http://ftpmaster.internal/ubuntu plucky/main armhf libpython3.13-minimal armhf 3.13.0-2 [866 kB] 574s Get:3 http://ftpmaster.internal/ubuntu plucky/main armhf python3.13-minimal armhf 3.13.0-2 [1854 kB] 574s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf libpython3.13-stdlib armhf 3.13.0-2 [1972 kB] 574s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf python3.13 armhf 3.13.0-2 [719 kB] 574s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf python3-all armhf 3.12.7-1 [890 B] 574s Get:7 http://ftpmaster.internal/ubuntu plucky/main armhf python3-importlib-metadata all 8.5.0-1 [20.7 kB] 574s Get:8 http://ftpmaster.internal/ubuntu plucky/main armhf python3-packaging all 24.1-1 [41.4 kB] 574s Get:9 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pyfaidx all 0.8.1.3-1 [29.7 kB] 575s Fetched 5504 kB in 1s (6920 kB/s) 575s Selecting previously unselected package libpython3.13-minimal:armhf. 575s (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 ... 59567 files and directories currently installed.) 575s Preparing to unpack .../0-libpython3.13-minimal_3.13.0-2_armhf.deb ... 575s Unpacking libpython3.13-minimal:armhf (3.13.0-2) ... 575s Selecting previously unselected package python3.13-minimal. 575s Preparing to unpack .../1-python3.13-minimal_3.13.0-2_armhf.deb ... 575s Unpacking python3.13-minimal (3.13.0-2) ... 575s Selecting previously unselected package libpython3.13-stdlib:armhf. 575s Preparing to unpack .../2-libpython3.13-stdlib_3.13.0-2_armhf.deb ... 575s Unpacking libpython3.13-stdlib:armhf (3.13.0-2) ... 575s Selecting previously unselected package python3.13. 575s Preparing to unpack .../3-python3.13_3.13.0-2_armhf.deb ... 575s Unpacking python3.13 (3.13.0-2) ... 575s Selecting previously unselected package python3-all. 575s Preparing to unpack .../4-python3-all_3.12.7-1_armhf.deb ... 575s Unpacking python3-all (3.12.7-1) ... 575s Selecting previously unselected package python3-importlib-metadata. 575s Preparing to unpack .../5-python3-importlib-metadata_8.5.0-1_all.deb ... 575s Unpacking python3-importlib-metadata (8.5.0-1) ... 575s Selecting previously unselected package python3-packaging. 575s Preparing to unpack .../6-python3-packaging_24.1-1_all.deb ... 575s Unpacking python3-packaging (24.1-1) ... 575s Selecting previously unselected package python3-pyfaidx. 575s Preparing to unpack .../7-python3-pyfaidx_0.8.1.3-1_all.deb ... 575s Unpacking python3-pyfaidx (0.8.1.3-1) ... 575s Selecting previously unselected package autopkgtest-satdep. 575s Preparing to unpack .../8-2-autopkgtest-satdep.deb ... 575s Unpacking autopkgtest-satdep (0) ... 575s Setting up python3-importlib-metadata (8.5.0-1) ... 576s Setting up libpython3.13-minimal:armhf (3.13.0-2) ... 576s Setting up python3-packaging (24.1-1) ... 576s Setting up python3.13-minimal (3.13.0-2) ... 577s Setting up libpython3.13-stdlib:armhf (3.13.0-2) ... 577s Setting up python3-pyfaidx (0.8.1.3-1) ... 577s Setting up python3.13 (3.13.0-2) ... 579s Setting up python3-all (3.12.7-1) ... 579s Setting up autopkgtest-satdep (0) ... 579s Processing triggers for man-db (2.12.1-3) ... 579s Processing triggers for systemd (256.5-2ubuntu4) ... 592s (Reading database ... 60362 files and directories currently installed.) 592s Removing autopkgtest-satdep (0) ... 604s autopkgtest [01:11:36]: test autodep8-python3: set -e ; for py in $(py3versions -r 2>/dev/null) ; do cd "$AUTOPKGTEST_TMP" ; echo "Testing with $py:" ; $py -c "import pyfaidx; print(pyfaidx)" ; done 604s autopkgtest [01:11:36]: test autodep8-python3: [----------------------- 606s Testing with python3.13: 606s 606s Testing with python3.12: 606s 607s autopkgtest [01:11:39]: test autodep8-python3: -----------------------] 611s autopkgtest [01:11:43]: test autodep8-python3: - - - - - - - - - - results - - - - - - - - - - 611s autodep8-python3 PASS (superficial) 615s autopkgtest [01:11:47]: @@@@@@@@@@@@@@@@@@@@ summary 615s run-unit-test FAIL non-zero exit status 1 615s autodep8-python3 PASS (superficial)