0s autopkgtest [21:19:09]: starting date and time: 2024-11-13 21:19:09+0000 0s autopkgtest [21:19:09]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [21:19:09]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.5856vro_/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-bcbio-gff --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-10.145.243.16 lxd-armhf-10.145.243.16:autopkgtest/ubuntu/plucky/armhf 52s autopkgtest [21:20:01]: testbed dpkg architecture: armhf 54s autopkgtest [21:20:03]: testbed apt version: 2.9.8 54s autopkgtest [21:20:03]: @@@@@@@@@@@@@@@@@@@@ test bed setup 62s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 63s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [970 kB] 63s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [101 kB] 63s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 63s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [17.2 kB] 63s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf Packages [104 kB] 63s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf Packages [662 kB] 63s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf Packages [17.2 kB] 63s Fetched 1951 kB in 1s (2093 kB/s) 63s Reading package lists... 81s tee: /proc/self/fd/2: Permission denied 103s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 103s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 103s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 103s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 104s Reading package lists... 104s Reading package lists... 104s Building dependency tree... 104s Reading state information... 105s 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] 107s Fetched 1207 kB in 1s (2210 kB/s) 107s (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.) 107s Preparing to unpack .../python3-minimal_3.12.7-1_armhf.deb ... 107s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ... 107s Setting up python3-minimal (3.12.7-1) ... 107s (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.) 107s Preparing to unpack .../python3_3.12.7-1_armhf.deb ... 107s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ... 107s Preparing to unpack .../libpython3-stdlib_3.12.7-1_armhf.deb ... 107s Unpacking libpython3-stdlib:armhf (3.12.7-1) over (3.12.6-0ubuntu1) ... 107s Preparing to unpack .../libgnutls30t64_3.8.8-2ubuntu1_armhf.deb ... 107s Unpacking libgnutls30t64:armhf (3.8.8-2ubuntu1) over (3.8.6-2ubuntu1) ... 107s Setting up libgnutls30t64:armhf (3.8.8-2ubuntu1) ... 107s (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.) 107s Preparing to unpack .../0-python3-newt_0.52.24-2ubuntu4_armhf.deb ... 107s Unpacking python3-newt:armhf (0.52.24-2ubuntu4) over (0.52.24-2ubuntu3) ... 107s Preparing to unpack .../1-libnewt0.52_0.52.24-2ubuntu4_armhf.deb ... 107s Unpacking libnewt0.52:armhf (0.52.24-2ubuntu4) over (0.52.24-2ubuntu3) ... 107s Preparing to unpack .../2-whiptail_0.52.24-2ubuntu4_armhf.deb ... 107s Unpacking whiptail (0.52.24-2ubuntu4) over (0.52.24-2ubuntu3) ... 107s Selecting previously unselected package python3.13-gdbm. 107s Preparing to unpack .../3-python3.13-gdbm_3.13.0-2_armhf.deb ... 107s Unpacking python3.13-gdbm (3.13.0-2) ... 107s Preparing to unpack .../4-python3-gdbm_3.12.7-1_armhf.deb ... 107s Unpacking python3-gdbm:armhf (3.12.7-1) over (3.12.6-1ubuntu1) ... 107s Preparing to unpack .../5-libjson-glib-1.0-common_1.10.0+ds-3_all.deb ... 107s Unpacking libjson-glib-1.0-common (1.10.0+ds-3) over (1.10.0+ds-2) ... 107s Preparing to unpack .../6-libjson-glib-1.0-0_1.10.0+ds-3_armhf.deb ... 107s Unpacking libjson-glib-1.0-0:armhf (1.10.0+ds-3) over (1.10.0+ds-2) ... 107s Preparing to unpack .../7-libutempter0_1.2.1-4_armhf.deb ... 107s Unpacking libutempter0:armhf (1.2.1-4) over (1.2.1-3build1) ... 107s Setting up libnewt0.52:armhf (0.52.24-2ubuntu4) ... 107s Setting up libutempter0:armhf (1.2.1-4) ... 107s Setting up whiptail (0.52.24-2ubuntu4) ... 107s Setting up libjson-glib-1.0-common (1.10.0+ds-3) ... 107s Setting up python3.13-gdbm (3.13.0-2) ... 107s Setting up libpython3-stdlib:armhf (3.12.7-1) ... 107s Setting up python3 (3.12.7-1) ... 108s Setting up python3-newt:armhf (0.52.24-2ubuntu4) ... 108s Setting up libjson-glib-1.0-0:armhf (1.10.0+ds-3) ... 108s Setting up python3-gdbm:armhf (3.12.7-1) ... 108s Processing triggers for man-db (2.12.1-3) ... 108s Processing triggers for libc-bin (2.40-1ubuntu3) ... 109s Reading package lists... 109s Building dependency tree... 109s Reading state information... 109s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 111s autopkgtest [21:21:00]: rebooting testbed after setup commands that affected boot 182s autopkgtest [21:22:11]: 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 210s autopkgtest [21:22:39]: @@@@@@@@@@@@@@@@@@@@ apt-source python-bcbio-gff 221s Get:1 http://ftpmaster.internal/ubuntu plucky/universe python-bcbio-gff 0.7.1-2 (dsc) [2386 B] 221s Get:2 http://ftpmaster.internal/ubuntu plucky/universe python-bcbio-gff 0.7.1-2 (tar) [20.1 kB] 221s Get:3 http://ftpmaster.internal/ubuntu plucky/universe python-bcbio-gff 0.7.1-2 (diff) [23.9 kB] 221s gpgv: Signature made Tue Nov 5 22:11:23 2024 UTC 221s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 221s gpgv: issuer "emollier@debian.org" 221s gpgv: Can't check signature: No public key 221s dpkg-source: warning: cannot verify inline signature for ./python-bcbio-gff_0.7.1-2.dsc: no acceptable signature found 221s autopkgtest [21:22:50]: testing package python-bcbio-gff version 0.7.1-2 223s autopkgtest [21:22:52]: build not needed 227s autopkgtest [21:22:56]: test run-unit-test: preparing testbed 239s Reading package lists... 239s Building dependency tree... 239s Reading state information... 240s Starting pkgProblemResolver with broken count: 0 240s Starting 2 pkgProblemResolver with broken count: 0 240s Done 240s The following additional packages will be installed: 240s fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-urw-base35 240s libblas3 libcairo2 libdeflate0 libfontconfig1 libfontenc1 libfreetype6 240s libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libimagequant0 libjbig0 240s libjpeg-turbo8 libjpeg8 liblapack3 liblcms2-2 liblerc4 libopenjp2-7 240s libpixman-1-0 libpython3.13-minimal libpython3.13-stdlib libraqm0 240s libsharpyuv0 libtiff6 libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 240s libxcb-shm0 libxrender1 python3-all python3-bcbio-gff python3-biopython 240s python3-cairo python3-freetype python3-numpy python3-pil python3-reportlab 240s python3-rlpycairo python3-six python3.13 python3.13-minimal sgml-base 240s w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core 240s Suggested packages: 240s fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre liblcms2-utils 240s python3-tk bwa clustalo clustalw dialign dssp emboss fasttree mafft muscle3 240s phylip phyml prank probcons python3-mysqldb python3-matplotlib python3-mmtf 240s python3-rdflib python3-psycopg2 python3-scipy raxml samtools t-coffee wise 240s gcc gfortran python-numpy-doc python3-dev python3-pytest python-pil-doc 240s pdf-viewer python3-egenix-mxtexttools python-reportlab-doc rl-accel 240s rl-renderpm python3.13-venv python3.13-doc binfmt-support sgml-base-doc 240s debhelper 240s Recommended packages: 240s python-biopython-doc ncbi-blast+ python3-olefile fonts-dejavu-extra 240s The following NEW packages will be installed: 240s autopkgtest-satdep fontconfig-config fonts-dejavu-core fonts-dejavu-mono 240s fonts-urw-base35 libblas3 libcairo2 libdeflate0 libfontconfig1 libfontenc1 240s libfreetype6 libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b 240s libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 liblapack3 liblcms2-2 240s liblerc4 libopenjp2-7 libpixman-1-0 libpython3.13-minimal 240s libpython3.13-stdlib libraqm0 libsharpyuv0 libtiff6 libwebp7 libwebpdemux2 240s libwebpmux3 libxcb-render0 libxcb-shm0 libxrender1 python3-all 240s python3-bcbio-gff python3-biopython python3-cairo python3-freetype 240s python3-numpy python3-pil python3-reportlab python3-rlpycairo python3-six 240s python3.13 python3.13-minimal sgml-base w3c-sgml-lib x11-common 240s xfonts-encodings xfonts-utils xml-core 241s 0 upgraded, 53 newly installed, 0 to remove and 0 not upgraded. 241s Need to get 31.2 MB/31.2 MB of archives. 241s After this operation, 90.9 MB of additional disk space will be used. 241s Get:1 /tmp/autopkgtest.1tDfad/1-autopkgtest-satdep.deb autopkgtest-satdep armhf 0 [724 B] 241s Get:2 http://ftpmaster.internal/ubuntu plucky/main armhf libpython3.13-minimal armhf 3.13.0-2 [866 kB] 241s Get:3 http://ftpmaster.internal/ubuntu plucky/main armhf python3.13-minimal armhf 3.13.0-2 [1854 kB] 241s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf sgml-base all 1.31 [11.4 kB] 241s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-dejavu-mono all 2.37-8 [502 kB] 241s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-dejavu-core all 2.37-8 [835 kB] 241s Get:7 http://ftpmaster.internal/ubuntu plucky/main armhf libfontenc1 armhf 1:1.1.8-1build1 [11.5 kB] 241s Get:8 http://ftpmaster.internal/ubuntu plucky/main armhf libfreetype6 armhf 2.13.3+dfsg-1 [330 kB] 241s Get:9 http://ftpmaster.internal/ubuntu plucky/main armhf x11-common all 1:7.7+23ubuntu3 [21.7 kB] 241s Get:10 http://ftpmaster.internal/ubuntu plucky/main armhf xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 241s Get:11 http://ftpmaster.internal/ubuntu plucky/main armhf xfonts-utils armhf 1:7.7+7 [90.6 kB] 241s Get:12 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-urw-base35 all 20200910-8 [11.0 MB] 242s Get:13 http://ftpmaster.internal/ubuntu plucky/main armhf fontconfig-config armhf 2.15.0-1.1ubuntu2 [37.4 kB] 242s Get:14 http://ftpmaster.internal/ubuntu plucky/main armhf libblas3 armhf 3.12.0-3build2 [126 kB] 242s Get:15 http://ftpmaster.internal/ubuntu plucky/main armhf libfontconfig1 armhf 2.15.0-1.1ubuntu2 [113 kB] 242s Get:16 http://ftpmaster.internal/ubuntu plucky/main armhf libpixman-1-0 armhf 0.44.0-3 [183 kB] 242s Get:17 http://ftpmaster.internal/ubuntu plucky/main armhf libxcb-render0 armhf 1.17.0-2 [15.3 kB] 242s Get:18 http://ftpmaster.internal/ubuntu plucky/main armhf libxcb-shm0 armhf 1.17.0-2 [5774 B] 242s Get:19 http://ftpmaster.internal/ubuntu plucky/main armhf libxrender1 armhf 1:0.9.10-1.1build1 [16.0 kB] 242s Get:20 http://ftpmaster.internal/ubuntu plucky/main armhf libcairo2 armhf 1.18.2-2 [484 kB] 242s Get:21 http://ftpmaster.internal/ubuntu plucky/main armhf libdeflate0 armhf 1.22-1 [38.9 kB] 242s Get:22 http://ftpmaster.internal/ubuntu plucky/main armhf libgfortran5 armhf 14.2.0-8ubuntu1 [311 kB] 242s Get:23 http://ftpmaster.internal/ubuntu plucky/main armhf libgomp1 armhf 14.2.0-8ubuntu1 [125 kB] 242s Get:24 http://ftpmaster.internal/ubuntu plucky/main armhf libgraphite2-3 armhf 1.3.14-2ubuntu1 [64.8 kB] 242s Get:25 http://ftpmaster.internal/ubuntu plucky/main armhf libharfbuzz0b armhf 10.0.1-1 [463 kB] 242s Get:26 http://ftpmaster.internal/ubuntu plucky/main armhf libimagequant0 armhf 2.18.0-1build1 [31.1 kB] 242s Get:27 http://ftpmaster.internal/ubuntu plucky/main armhf libjpeg-turbo8 armhf 2.1.5-2ubuntu2 [125 kB] 242s Get:28 http://ftpmaster.internal/ubuntu plucky/main armhf libjpeg8 armhf 8c-2ubuntu11 [2148 B] 242s Get:29 http://ftpmaster.internal/ubuntu plucky/main armhf liblapack3 armhf 3.12.0-3build2 [2086 kB] 242s Get:30 http://ftpmaster.internal/ubuntu plucky/main armhf liblcms2-2 armhf 2.16-2 [137 kB] 242s Get:31 http://ftpmaster.internal/ubuntu plucky/main armhf liblerc4 armhf 4.0.0+ds-4ubuntu2 [151 kB] 242s Get:32 http://ftpmaster.internal/ubuntu plucky/main armhf libpython3.13-stdlib armhf 3.13.0-2 [1972 kB] 242s Get:33 http://ftpmaster.internal/ubuntu plucky/main armhf libraqm0 armhf 0.10.1-1build1 [12.4 kB] 242s Get:34 http://ftpmaster.internal/ubuntu plucky/main armhf libsharpyuv0 armhf 1.4.0-0.1 [16.3 kB] 242s Get:35 http://ftpmaster.internal/ubuntu plucky/main armhf libjbig0 armhf 2.1-6.1ubuntu2 [24.9 kB] 242s Get:36 http://ftpmaster.internal/ubuntu plucky/main armhf libwebp7 armhf 1.4.0-0.1 [184 kB] 242s Get:37 http://ftpmaster.internal/ubuntu plucky/main armhf libtiff6 armhf 4.5.1+git230720-4ubuntu4 [179 kB] 242s Get:38 http://ftpmaster.internal/ubuntu plucky/main armhf libwebpdemux2 armhf 1.4.0-0.1 [11.8 kB] 242s Get:39 http://ftpmaster.internal/ubuntu plucky/main armhf libwebpmux3 armhf 1.4.0-0.1 [22.5 kB] 242s Get:40 http://ftpmaster.internal/ubuntu plucky/main armhf python3.13 armhf 3.13.0-2 [719 kB] 242s Get:41 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf python3-all armhf 3.12.7-1 [890 B] 242s Get:42 http://ftpmaster.internal/ubuntu plucky/main armhf python3-numpy armhf 1:1.26.4+ds-11build1 [3570 kB] 243s Get:43 http://ftpmaster.internal/ubuntu plucky/main armhf libopenjp2-7 armhf 2.5.0-2ubuntu1 [170 kB] 243s Get:44 http://ftpmaster.internal/ubuntu plucky/main armhf python3-pil armhf 10.4.0-1ubuntu1 [428 kB] 243s Get:45 http://ftpmaster.internal/ubuntu plucky/main armhf python3-cairo armhf 1.26.1-2 [114 kB] 243s Get:46 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-freetype all 2.5.1-1 [92.3 kB] 243s Get:47 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-rlpycairo all 0.3.0-3 [9130 B] 243s Get:48 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-reportlab all 4.2.5-1 [1107 kB] 243s Get:49 http://ftpmaster.internal/ubuntu plucky/main armhf xml-core all 0.19 [20.3 kB] 243s Get:50 http://ftpmaster.internal/ubuntu plucky/universe armhf w3c-sgml-lib all 1.3-3 [280 kB] 243s Get:51 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-biopython armhf 1.84+dfsg-4 [1666 kB] 243s Get:52 http://ftpmaster.internal/ubuntu plucky/main armhf python3-six all 1.16.0-7 [13.1 kB] 243s Get:53 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-bcbio-gff all 0.7.1-2 [33.9 kB] 243s Fetched 31.2 MB in 2s (14.1 MB/s) 243s Selecting previously unselected package libpython3.13-minimal:armhf. 243s (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.) 243s Preparing to unpack .../00-libpython3.13-minimal_3.13.0-2_armhf.deb ... 243s Unpacking libpython3.13-minimal:armhf (3.13.0-2) ... 243s Selecting previously unselected package python3.13-minimal. 243s Preparing to unpack .../01-python3.13-minimal_3.13.0-2_armhf.deb ... 243s Unpacking python3.13-minimal (3.13.0-2) ... 243s Selecting previously unselected package sgml-base. 243s Preparing to unpack .../02-sgml-base_1.31_all.deb ... 243s Unpacking sgml-base (1.31) ... 243s Selecting previously unselected package fonts-dejavu-mono. 243s Preparing to unpack .../03-fonts-dejavu-mono_2.37-8_all.deb ... 243s Unpacking fonts-dejavu-mono (2.37-8) ... 243s Selecting previously unselected package fonts-dejavu-core. 243s Preparing to unpack .../04-fonts-dejavu-core_2.37-8_all.deb ... 244s Unpacking fonts-dejavu-core (2.37-8) ... 244s Selecting previously unselected package libfontenc1:armhf. 244s Preparing to unpack .../05-libfontenc1_1%3a1.1.8-1build1_armhf.deb ... 244s Unpacking libfontenc1:armhf (1:1.1.8-1build1) ... 244s Selecting previously unselected package libfreetype6:armhf. 244s Preparing to unpack .../06-libfreetype6_2.13.3+dfsg-1_armhf.deb ... 244s Unpacking libfreetype6:armhf (2.13.3+dfsg-1) ... 244s Selecting previously unselected package x11-common. 244s Preparing to unpack .../07-x11-common_1%3a7.7+23ubuntu3_all.deb ... 244s Unpacking x11-common (1:7.7+23ubuntu3) ... 244s Selecting previously unselected package xfonts-encodings. 244s Preparing to unpack .../08-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 244s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 244s Selecting previously unselected package xfonts-utils. 244s Preparing to unpack .../09-xfonts-utils_1%3a7.7+7_armhf.deb ... 244s Unpacking xfonts-utils (1:7.7+7) ... 244s Selecting previously unselected package fonts-urw-base35. 244s Preparing to unpack .../10-fonts-urw-base35_20200910-8_all.deb ... 244s Unpacking fonts-urw-base35 (20200910-8) ... 244s Selecting previously unselected package fontconfig-config. 244s Preparing to unpack .../11-fontconfig-config_2.15.0-1.1ubuntu2_armhf.deb ... 244s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ... 244s Selecting previously unselected package libblas3:armhf. 244s Preparing to unpack .../12-libblas3_3.12.0-3build2_armhf.deb ... 244s Unpacking libblas3:armhf (3.12.0-3build2) ... 244s Selecting previously unselected package libfontconfig1:armhf. 244s Preparing to unpack .../13-libfontconfig1_2.15.0-1.1ubuntu2_armhf.deb ... 244s Unpacking libfontconfig1:armhf (2.15.0-1.1ubuntu2) ... 244s Selecting previously unselected package libpixman-1-0:armhf. 245s Preparing to unpack .../14-libpixman-1-0_0.44.0-3_armhf.deb ... 245s Unpacking libpixman-1-0:armhf (0.44.0-3) ... 245s Selecting previously unselected package libxcb-render0:armhf. 245s Preparing to unpack .../15-libxcb-render0_1.17.0-2_armhf.deb ... 245s Unpacking libxcb-render0:armhf (1.17.0-2) ... 245s Selecting previously unselected package libxcb-shm0:armhf. 245s Preparing to unpack .../16-libxcb-shm0_1.17.0-2_armhf.deb ... 245s Unpacking libxcb-shm0:armhf (1.17.0-2) ... 245s Selecting previously unselected package libxrender1:armhf. 245s Preparing to unpack .../17-libxrender1_1%3a0.9.10-1.1build1_armhf.deb ... 245s Unpacking libxrender1:armhf (1:0.9.10-1.1build1) ... 245s Selecting previously unselected package libcairo2:armhf. 245s Preparing to unpack .../18-libcairo2_1.18.2-2_armhf.deb ... 245s Unpacking libcairo2:armhf (1.18.2-2) ... 245s Selecting previously unselected package libdeflate0:armhf. 245s Preparing to unpack .../19-libdeflate0_1.22-1_armhf.deb ... 245s Unpacking libdeflate0:armhf (1.22-1) ... 245s Selecting previously unselected package libgfortran5:armhf. 245s Preparing to unpack .../20-libgfortran5_14.2.0-8ubuntu1_armhf.deb ... 245s Unpacking libgfortran5:armhf (14.2.0-8ubuntu1) ... 245s Selecting previously unselected package libgomp1:armhf. 245s Preparing to unpack .../21-libgomp1_14.2.0-8ubuntu1_armhf.deb ... 245s Unpacking libgomp1:armhf (14.2.0-8ubuntu1) ... 245s Selecting previously unselected package libgraphite2-3:armhf. 245s Preparing to unpack .../22-libgraphite2-3_1.3.14-2ubuntu1_armhf.deb ... 245s Unpacking libgraphite2-3:armhf (1.3.14-2ubuntu1) ... 245s Selecting previously unselected package libharfbuzz0b:armhf. 245s Preparing to unpack .../23-libharfbuzz0b_10.0.1-1_armhf.deb ... 245s Unpacking libharfbuzz0b:armhf (10.0.1-1) ... 245s Selecting previously unselected package libimagequant0:armhf. 245s Preparing to unpack .../24-libimagequant0_2.18.0-1build1_armhf.deb ... 245s Unpacking libimagequant0:armhf (2.18.0-1build1) ... 245s Selecting previously unselected package libjpeg-turbo8:armhf. 245s Preparing to unpack .../25-libjpeg-turbo8_2.1.5-2ubuntu2_armhf.deb ... 245s Unpacking libjpeg-turbo8:armhf (2.1.5-2ubuntu2) ... 245s Selecting previously unselected package libjpeg8:armhf. 245s Preparing to unpack .../26-libjpeg8_8c-2ubuntu11_armhf.deb ... 245s Unpacking libjpeg8:armhf (8c-2ubuntu11) ... 245s Selecting previously unselected package liblapack3:armhf. 245s Preparing to unpack .../27-liblapack3_3.12.0-3build2_armhf.deb ... 245s Unpacking liblapack3:armhf (3.12.0-3build2) ... 245s Selecting previously unselected package liblcms2-2:armhf. 245s Preparing to unpack .../28-liblcms2-2_2.16-2_armhf.deb ... 245s Unpacking liblcms2-2:armhf (2.16-2) ... 245s Selecting previously unselected package liblerc4:armhf. 245s Preparing to unpack .../29-liblerc4_4.0.0+ds-4ubuntu2_armhf.deb ... 245s Unpacking liblerc4:armhf (4.0.0+ds-4ubuntu2) ... 245s Selecting previously unselected package libpython3.13-stdlib:armhf. 245s Preparing to unpack .../30-libpython3.13-stdlib_3.13.0-2_armhf.deb ... 245s Unpacking libpython3.13-stdlib:armhf (3.13.0-2) ... 245s Selecting previously unselected package libraqm0:armhf. 245s Preparing to unpack .../31-libraqm0_0.10.1-1build1_armhf.deb ... 245s Unpacking libraqm0:armhf (0.10.1-1build1) ... 245s Selecting previously unselected package libsharpyuv0:armhf. 245s Preparing to unpack .../32-libsharpyuv0_1.4.0-0.1_armhf.deb ... 245s Unpacking libsharpyuv0:armhf (1.4.0-0.1) ... 245s Selecting previously unselected package libjbig0:armhf. 245s Preparing to unpack .../33-libjbig0_2.1-6.1ubuntu2_armhf.deb ... 245s Unpacking libjbig0:armhf (2.1-6.1ubuntu2) ... 245s Selecting previously unselected package libwebp7:armhf. 245s Preparing to unpack .../34-libwebp7_1.4.0-0.1_armhf.deb ... 245s Unpacking libwebp7:armhf (1.4.0-0.1) ... 245s Selecting previously unselected package libtiff6:armhf. 245s Preparing to unpack .../35-libtiff6_4.5.1+git230720-4ubuntu4_armhf.deb ... 245s Unpacking libtiff6:armhf (4.5.1+git230720-4ubuntu4) ... 245s Selecting previously unselected package libwebpdemux2:armhf. 245s Preparing to unpack .../36-libwebpdemux2_1.4.0-0.1_armhf.deb ... 245s Unpacking libwebpdemux2:armhf (1.4.0-0.1) ... 245s Selecting previously unselected package libwebpmux3:armhf. 245s Preparing to unpack .../37-libwebpmux3_1.4.0-0.1_armhf.deb ... 245s Unpacking libwebpmux3:armhf (1.4.0-0.1) ... 245s Selecting previously unselected package python3.13. 245s Preparing to unpack .../38-python3.13_3.13.0-2_armhf.deb ... 245s Unpacking python3.13 (3.13.0-2) ... 245s Selecting previously unselected package python3-all. 245s Preparing to unpack .../39-python3-all_3.12.7-1_armhf.deb ... 245s Unpacking python3-all (3.12.7-1) ... 245s Selecting previously unselected package python3-numpy. 245s Preparing to unpack .../40-python3-numpy_1%3a1.26.4+ds-11build1_armhf.deb ... 245s Unpacking python3-numpy (1:1.26.4+ds-11build1) ... 246s Selecting previously unselected package libopenjp2-7:armhf. 246s Preparing to unpack .../41-libopenjp2-7_2.5.0-2ubuntu1_armhf.deb ... 246s Unpacking libopenjp2-7:armhf (2.5.0-2ubuntu1) ... 246s Selecting previously unselected package python3-pil:armhf. 246s Preparing to unpack .../42-python3-pil_10.4.0-1ubuntu1_armhf.deb ... 246s Unpacking python3-pil:armhf (10.4.0-1ubuntu1) ... 246s Selecting previously unselected package python3-cairo. 246s Preparing to unpack .../43-python3-cairo_1.26.1-2_armhf.deb ... 246s Unpacking python3-cairo (1.26.1-2) ... 246s Selecting previously unselected package python3-freetype. 246s Preparing to unpack .../44-python3-freetype_2.5.1-1_all.deb ... 246s Unpacking python3-freetype (2.5.1-1) ... 246s Selecting previously unselected package python3-rlpycairo. 246s Preparing to unpack .../45-python3-rlpycairo_0.3.0-3_all.deb ... 246s Unpacking python3-rlpycairo (0.3.0-3) ... 246s Selecting previously unselected package python3-reportlab. 246s Preparing to unpack .../46-python3-reportlab_4.2.5-1_all.deb ... 246s Unpacking python3-reportlab (4.2.5-1) ... 246s Selecting previously unselected package xml-core. 246s Preparing to unpack .../47-xml-core_0.19_all.deb ... 246s Unpacking xml-core (0.19) ... 246s Selecting previously unselected package w3c-sgml-lib. 246s Preparing to unpack .../48-w3c-sgml-lib_1.3-3_all.deb ... 246s Unpacking w3c-sgml-lib (1.3-3) ... 246s Selecting previously unselected package python3-biopython. 246s Preparing to unpack .../49-python3-biopython_1.84+dfsg-4_armhf.deb ... 246s Unpacking python3-biopython (1.84+dfsg-4) ... 246s Selecting previously unselected package python3-six. 246s Preparing to unpack .../50-python3-six_1.16.0-7_all.deb ... 246s Unpacking python3-six (1.16.0-7) ... 246s Selecting previously unselected package python3-bcbio-gff. 246s Preparing to unpack .../51-python3-bcbio-gff_0.7.1-2_all.deb ... 246s Unpacking python3-bcbio-gff (0.7.1-2) ... 247s Selecting previously unselected package autopkgtest-satdep. 247s Preparing to unpack .../52-1-autopkgtest-satdep.deb ... 247s Unpacking autopkgtest-satdep (0) ... 247s Setting up libgraphite2-3:armhf (1.3.14-2ubuntu1) ... 247s Setting up liblcms2-2:armhf (2.16-2) ... 247s Setting up libpixman-1-0:armhf (0.44.0-3) ... 247s Setting up libsharpyuv0:armhf (1.4.0-0.1) ... 247s Setting up liblerc4:armhf (4.0.0+ds-4ubuntu2) ... 247s Setting up libxrender1:armhf (1:0.9.10-1.1build1) ... 247s Setting up libxcb-render0:armhf (1.17.0-2) ... 247s Setting up x11-common (1:7.7+23ubuntu3) ... 247s Setting up libdeflate0:armhf (1.22-1) ... 247s Setting up libxcb-shm0:armhf (1.17.0-2) ... 247s Setting up libgomp1:armhf (14.2.0-8ubuntu1) ... 247s Setting up libjbig0:armhf (2.1-6.1ubuntu2) ... 247s Setting up python3-six (1.16.0-7) ... 247s Setting up libpython3.13-minimal:armhf (3.13.0-2) ... 247s Setting up libfontenc1:armhf (1:1.1.8-1build1) ... 247s Setting up libblas3:armhf (3.12.0-3build2) ... 247s 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 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 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 libpython3.13-stdlib:armhf (3.13.0-2) ... 248s Setting up libjpeg8:armhf (8c-2ubuntu11) ... 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) ... 249s Setting up fontconfig-config (2.15.0-1.1ubuntu2) ... 249s Setting up libwebpdemux2:armhf (1.4.0-0.1) ... 249s Setting up python3-all (3.12.7-1) ... 249s Setting up python3-freetype (2.5.1-1) ... 250s Setting up xfonts-utils (1:7.7+7) ... 250s Setting up libraqm0:armhf (0.10.1-1build1) ... 250s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 254s Setting up libtiff6:armhf (4.5.1+git230720-4ubuntu4) ... 254s Setting up xml-core (0.19) ... 254s Setting up libfontconfig1:armhf (2.15.0-1.1ubuntu2) ... 254s Setting up fonts-urw-base35 (20200910-8) ... 254s Setting up libcairo2:armhf (1.18.2-2) ... 254s Setting up python3-pil:armhf (10.4.0-1ubuntu1) ... 255s Setting up python3-cairo (1.26.1-2) ... 255s Setting up python3-rlpycairo (0.3.0-3) ... 255s Setting up python3-reportlab (4.2.5-1) ... 257s Processing triggers for libc-bin (2.40-1ubuntu3) ... 257s Processing triggers for systemd (256.5-2ubuntu4) ... 257s Processing triggers for man-db (2.12.1-3) ... 258s Processing triggers for sgml-base (1.31) ... 258s Setting up w3c-sgml-lib (1.3-3) ... 286s Setting up python3-biopython (1.84+dfsg-4) ... 288s Setting up python3-bcbio-gff (0.7.1-2) ... 288s Setting up autopkgtest-satdep (0) ... 304s (Reading database ... 63579 files and directories currently installed.) 304s Removing autopkgtest-satdep (0) ... 311s autopkgtest [21:24:20]: test run-unit-test: [----------------------- 313s Traceback (most recent call last): 313s File "/tmp/autopkgtest.1tDfad/autopkgtest_tmp/test_GFFSeqIOFeatureAdder.py", line 11, in 313s from Bio import SeqIO 313s File "/usr/lib/python3/dist-packages/Bio/SeqIO/__init__.py", line 401, in 313s from Bio.SeqIO import TwoBitIO 313s File "/usr/lib/python3/dist-packages/Bio/SeqIO/TwoBitIO.py", line 80, in 313s raise MissingPythonDependencyError( 313s ...<2 lines>... 313s ) from None 313s Bio.MissingPythonDependencyError: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 313s autopkgtest [21:24:22]: test run-unit-test: -----------------------] 317s autopkgtest [21:24:26]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 317s run-unit-test FAIL non-zero exit status 1 321s autopkgtest [21:24:30]: test autodep8-python3: preparing testbed 377s autopkgtest [21:25:26]: testbed dpkg architecture: armhf 379s autopkgtest [21:25:28]: testbed apt version: 2.9.8 379s autopkgtest [21:25:28]: @@@@@@@@@@@@@@@@@@@@ test bed setup 388s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 388s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [970 kB] 388s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [101 kB] 388s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [17.2 kB] 388s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 388s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf Packages [104 kB] 388s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf Packages [662 kB] 388s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf Packages [17.2 kB] 388s Fetched 1951 kB in 1s (2215 kB/s) 388s Reading package lists... 404s tee: /proc/self/fd/2: Permission denied 425s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 425s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 426s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 426s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 427s Reading package lists... 427s Reading package lists... 427s Building dependency tree... 427s Reading state information... 428s Calculating upgrade... 428s The following NEW packages will be installed: 428s python3.13-gdbm 428s The following packages will be upgraded: 428s libgnutls30t64 libjson-glib-1.0-0 libjson-glib-1.0-common libnewt0.52 428s libpython3-stdlib libutempter0 python3 python3-gdbm python3-minimal 428s python3-newt whiptail 428s 11 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 428s Need to get 1207 kB of archives. 428s After this operation, 124 kB of additional disk space will be used. 428s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf python3-minimal armhf 3.12.7-1 [27.4 kB] 428s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf python3 armhf 3.12.7-1 [24.0 kB] 428s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libpython3-stdlib armhf 3.12.7-1 [10.0 kB] 428s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf libgnutls30t64 armhf 3.8.8-2ubuntu1 [955 kB] 429s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf python3-newt armhf 0.52.24-2ubuntu4 [19.7 kB] 429s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf libnewt0.52 armhf 0.52.24-2ubuntu4 [39.2 kB] 429s Get:7 http://ftpmaster.internal/ubuntu plucky/main armhf whiptail armhf 0.52.24-2ubuntu4 [17.2 kB] 429s Get:8 http://ftpmaster.internal/ubuntu plucky/main armhf python3.13-gdbm armhf 3.13.0-2 [29.5 kB] 429s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf python3-gdbm armhf 3.12.7-1 [8642 B] 429s Get:10 http://ftpmaster.internal/ubuntu plucky/main armhf libjson-glib-1.0-common all 1.10.0+ds-3 [5586 B] 429s Get:11 http://ftpmaster.internal/ubuntu plucky/main armhf libjson-glib-1.0-0 armhf 1.10.0+ds-3 [61.7 kB] 429s Get:12 http://ftpmaster.internal/ubuntu plucky/main armhf libutempter0 armhf 1.2.1-4 [9062 B] 429s Fetched 1207 kB in 1s (2136 kB/s) 429s (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.) 429s Preparing to unpack .../python3-minimal_3.12.7-1_armhf.deb ... 429s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ... 429s Setting up python3-minimal (3.12.7-1) ... 429s (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.) 429s Preparing to unpack .../python3_3.12.7-1_armhf.deb ... 429s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ... 429s Preparing to unpack .../libpython3-stdlib_3.12.7-1_armhf.deb ... 429s Unpacking libpython3-stdlib:armhf (3.12.7-1) over (3.12.6-0ubuntu1) ... 429s Preparing to unpack .../libgnutls30t64_3.8.8-2ubuntu1_armhf.deb ... 429s Unpacking libgnutls30t64:armhf (3.8.8-2ubuntu1) over (3.8.6-2ubuntu1) ... 429s Setting up libgnutls30t64:armhf (3.8.8-2ubuntu1) ... 429s (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.) 429s Preparing to unpack .../0-python3-newt_0.52.24-2ubuntu4_armhf.deb ... 430s Unpacking python3-newt:armhf (0.52.24-2ubuntu4) over (0.52.24-2ubuntu3) ... 430s Preparing to unpack .../1-libnewt0.52_0.52.24-2ubuntu4_armhf.deb ... 430s Unpacking libnewt0.52:armhf (0.52.24-2ubuntu4) over (0.52.24-2ubuntu3) ... 430s Preparing to unpack .../2-whiptail_0.52.24-2ubuntu4_armhf.deb ... 430s Unpacking whiptail (0.52.24-2ubuntu4) over (0.52.24-2ubuntu3) ... 430s Selecting previously unselected package python3.13-gdbm. 430s Preparing to unpack .../3-python3.13-gdbm_3.13.0-2_armhf.deb ... 430s Unpacking python3.13-gdbm (3.13.0-2) ... 430s Preparing to unpack .../4-python3-gdbm_3.12.7-1_armhf.deb ... 430s Unpacking python3-gdbm:armhf (3.12.7-1) over (3.12.6-1ubuntu1) ... 430s Preparing to unpack .../5-libjson-glib-1.0-common_1.10.0+ds-3_all.deb ... 430s Unpacking libjson-glib-1.0-common (1.10.0+ds-3) over (1.10.0+ds-2) ... 430s Preparing to unpack .../6-libjson-glib-1.0-0_1.10.0+ds-3_armhf.deb ... 430s Unpacking libjson-glib-1.0-0:armhf (1.10.0+ds-3) over (1.10.0+ds-2) ... 430s Preparing to unpack .../7-libutempter0_1.2.1-4_armhf.deb ... 430s Unpacking libutempter0:armhf (1.2.1-4) over (1.2.1-3build1) ... 430s Setting up libnewt0.52:armhf (0.52.24-2ubuntu4) ... 430s Setting up libutempter0:armhf (1.2.1-4) ... 430s Setting up whiptail (0.52.24-2ubuntu4) ... 430s Setting up libjson-glib-1.0-common (1.10.0+ds-3) ... 430s Setting up python3.13-gdbm (3.13.0-2) ... 430s Setting up libpython3-stdlib:armhf (3.12.7-1) ... 430s Setting up python3 (3.12.7-1) ... 430s Setting up python3-newt:armhf (0.52.24-2ubuntu4) ... 430s Setting up libjson-glib-1.0-0:armhf (1.10.0+ds-3) ... 430s Setting up python3-gdbm:armhf (3.12.7-1) ... 430s Processing triggers for man-db (2.12.1-3) ... 431s Processing triggers for libc-bin (2.40-1ubuntu3) ... 431s Reading package lists... 431s Building dependency tree... 431s Reading state information... 432s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 434s autopkgtest [21:26:23]: rebooting testbed after setup commands that affected boot 540s Reading package lists... 540s Building dependency tree... 540s Reading state information... 541s Starting pkgProblemResolver with broken count: 0 541s Starting 2 pkgProblemResolver with broken count: 0 541s Done 542s The following additional packages will be installed: 542s fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-urw-base35 542s libblas3 libcairo2 libdeflate0 libfontconfig1 libfontenc1 libfreetype6 542s libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libimagequant0 libjbig0 542s libjpeg-turbo8 libjpeg8 liblapack3 liblcms2-2 liblerc4 libopenjp2-7 542s libpixman-1-0 libpython3.13-minimal libpython3.13-stdlib libraqm0 542s libsharpyuv0 libtiff6 libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 542s libxcb-shm0 libxrender1 python3-all python3-bcbio-gff python3-biopython 542s python3-cairo python3-freetype python3-numpy python3-pil python3-reportlab 542s python3-rlpycairo python3-six python3.13 python3.13-minimal sgml-base 542s w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core 542s Suggested packages: 542s fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre liblcms2-utils 542s python3-tk bwa clustalo clustalw dialign dssp emboss fasttree mafft muscle3 542s phylip phyml prank probcons python3-mysqldb python3-matplotlib python3-mmtf 542s python3-rdflib python3-psycopg2 python3-scipy raxml samtools t-coffee wise 542s gcc gfortran python-numpy-doc python3-dev python3-pytest python-pil-doc 542s pdf-viewer python3-egenix-mxtexttools python-reportlab-doc rl-accel 542s rl-renderpm python3.13-venv python3.13-doc binfmt-support sgml-base-doc 542s debhelper 542s Recommended packages: 542s python-biopython-doc ncbi-blast+ python3-olefile fonts-dejavu-extra 542s The following NEW packages will be installed: 542s autopkgtest-satdep fontconfig-config fonts-dejavu-core fonts-dejavu-mono 542s fonts-urw-base35 libblas3 libcairo2 libdeflate0 libfontconfig1 libfontenc1 542s libfreetype6 libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b 542s libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 liblapack3 liblcms2-2 542s liblerc4 libopenjp2-7 libpixman-1-0 libpython3.13-minimal 542s libpython3.13-stdlib libraqm0 libsharpyuv0 libtiff6 libwebp7 libwebpdemux2 542s libwebpmux3 libxcb-render0 libxcb-shm0 libxrender1 python3-all 542s python3-bcbio-gff python3-biopython python3-cairo python3-freetype 542s python3-numpy python3-pil python3-reportlab python3-rlpycairo python3-six 542s python3.13 python3.13-minimal sgml-base w3c-sgml-lib x11-common 542s xfonts-encodings xfonts-utils xml-core 542s 0 upgraded, 53 newly installed, 0 to remove and 0 not upgraded. 542s Need to get 31.2 MB/31.2 MB of archives. 542s After this operation, 90.9 MB of additional disk space will be used. 542s Get:1 /tmp/autopkgtest.1tDfad/2-autopkgtest-satdep.deb autopkgtest-satdep armhf 0 [716 B] 542s Get:2 http://ftpmaster.internal/ubuntu plucky/main armhf libpython3.13-minimal armhf 3.13.0-2 [866 kB] 543s Get:3 http://ftpmaster.internal/ubuntu plucky/main armhf python3.13-minimal armhf 3.13.0-2 [1854 kB] 543s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf sgml-base all 1.31 [11.4 kB] 543s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-dejavu-mono all 2.37-8 [502 kB] 543s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-dejavu-core all 2.37-8 [835 kB] 543s Get:7 http://ftpmaster.internal/ubuntu plucky/main armhf libfontenc1 armhf 1:1.1.8-1build1 [11.5 kB] 543s Get:8 http://ftpmaster.internal/ubuntu plucky/main armhf libfreetype6 armhf 2.13.3+dfsg-1 [330 kB] 543s Get:9 http://ftpmaster.internal/ubuntu plucky/main armhf x11-common all 1:7.7+23ubuntu3 [21.7 kB] 543s Get:10 http://ftpmaster.internal/ubuntu plucky/main armhf xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 543s Get:11 http://ftpmaster.internal/ubuntu plucky/main armhf xfonts-utils armhf 1:7.7+7 [90.6 kB] 543s Get:12 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-urw-base35 all 20200910-8 [11.0 MB] 543s Get:13 http://ftpmaster.internal/ubuntu plucky/main armhf fontconfig-config armhf 2.15.0-1.1ubuntu2 [37.4 kB] 543s Get:14 http://ftpmaster.internal/ubuntu plucky/main armhf libblas3 armhf 3.12.0-3build2 [126 kB] 543s Get:15 http://ftpmaster.internal/ubuntu plucky/main armhf libfontconfig1 armhf 2.15.0-1.1ubuntu2 [113 kB] 543s Get:16 http://ftpmaster.internal/ubuntu plucky/main armhf libpixman-1-0 armhf 0.44.0-3 [183 kB] 543s Get:17 http://ftpmaster.internal/ubuntu plucky/main armhf libxcb-render0 armhf 1.17.0-2 [15.3 kB] 543s Get:18 http://ftpmaster.internal/ubuntu plucky/main armhf libxcb-shm0 armhf 1.17.0-2 [5774 B] 543s Get:19 http://ftpmaster.internal/ubuntu plucky/main armhf libxrender1 armhf 1:0.9.10-1.1build1 [16.0 kB] 543s Get:20 http://ftpmaster.internal/ubuntu plucky/main armhf libcairo2 armhf 1.18.2-2 [484 kB] 543s Get:21 http://ftpmaster.internal/ubuntu plucky/main armhf libdeflate0 armhf 1.22-1 [38.9 kB] 543s Get:22 http://ftpmaster.internal/ubuntu plucky/main armhf libgfortran5 armhf 14.2.0-8ubuntu1 [311 kB] 543s Get:23 http://ftpmaster.internal/ubuntu plucky/main armhf libgomp1 armhf 14.2.0-8ubuntu1 [125 kB] 543s Get:24 http://ftpmaster.internal/ubuntu plucky/main armhf libgraphite2-3 armhf 1.3.14-2ubuntu1 [64.8 kB] 543s Get:25 http://ftpmaster.internal/ubuntu plucky/main armhf libharfbuzz0b armhf 10.0.1-1 [463 kB] 543s Get:26 http://ftpmaster.internal/ubuntu plucky/main armhf libimagequant0 armhf 2.18.0-1build1 [31.1 kB] 543s Get:27 http://ftpmaster.internal/ubuntu plucky/main armhf libjpeg-turbo8 armhf 2.1.5-2ubuntu2 [125 kB] 543s Get:28 http://ftpmaster.internal/ubuntu plucky/main armhf libjpeg8 armhf 8c-2ubuntu11 [2148 B] 543s Get:29 http://ftpmaster.internal/ubuntu plucky/main armhf liblapack3 armhf 3.12.0-3build2 [2086 kB] 543s Get:30 http://ftpmaster.internal/ubuntu plucky/main armhf liblcms2-2 armhf 2.16-2 [137 kB] 543s Get:31 http://ftpmaster.internal/ubuntu plucky/main armhf liblerc4 armhf 4.0.0+ds-4ubuntu2 [151 kB] 543s Get:32 http://ftpmaster.internal/ubuntu plucky/main armhf libpython3.13-stdlib armhf 3.13.0-2 [1972 kB] 543s Get:33 http://ftpmaster.internal/ubuntu plucky/main armhf libraqm0 armhf 0.10.1-1build1 [12.4 kB] 543s Get:34 http://ftpmaster.internal/ubuntu plucky/main armhf libsharpyuv0 armhf 1.4.0-0.1 [16.3 kB] 543s Get:35 http://ftpmaster.internal/ubuntu plucky/main armhf libjbig0 armhf 2.1-6.1ubuntu2 [24.9 kB] 543s Get:36 http://ftpmaster.internal/ubuntu plucky/main armhf libwebp7 armhf 1.4.0-0.1 [184 kB] 544s Get:37 http://ftpmaster.internal/ubuntu plucky/main armhf libtiff6 armhf 4.5.1+git230720-4ubuntu4 [179 kB] 544s Get:38 http://ftpmaster.internal/ubuntu plucky/main armhf libwebpdemux2 armhf 1.4.0-0.1 [11.8 kB] 544s Get:39 http://ftpmaster.internal/ubuntu plucky/main armhf libwebpmux3 armhf 1.4.0-0.1 [22.5 kB] 544s Get:40 http://ftpmaster.internal/ubuntu plucky/main armhf python3.13 armhf 3.13.0-2 [719 kB] 544s Get:41 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf python3-all armhf 3.12.7-1 [890 B] 544s Get:42 http://ftpmaster.internal/ubuntu plucky/main armhf python3-numpy armhf 1:1.26.4+ds-11build1 [3570 kB] 544s Get:43 http://ftpmaster.internal/ubuntu plucky/main armhf libopenjp2-7 armhf 2.5.0-2ubuntu1 [170 kB] 544s Get:44 http://ftpmaster.internal/ubuntu plucky/main armhf python3-pil armhf 10.4.0-1ubuntu1 [428 kB] 544s Get:45 http://ftpmaster.internal/ubuntu plucky/main armhf python3-cairo armhf 1.26.1-2 [114 kB] 544s Get:46 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-freetype all 2.5.1-1 [92.3 kB] 544s Get:47 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-rlpycairo all 0.3.0-3 [9130 B] 544s Get:48 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-reportlab all 4.2.5-1 [1107 kB] 544s Get:49 http://ftpmaster.internal/ubuntu plucky/main armhf xml-core all 0.19 [20.3 kB] 544s Get:50 http://ftpmaster.internal/ubuntu plucky/universe armhf w3c-sgml-lib all 1.3-3 [280 kB] 544s Get:51 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-biopython armhf 1.84+dfsg-4 [1666 kB] 544s Get:52 http://ftpmaster.internal/ubuntu plucky/main armhf python3-six all 1.16.0-7 [13.1 kB] 544s Get:53 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-bcbio-gff all 0.7.1-2 [33.9 kB] 544s Fetched 31.2 MB in 2s (15.8 MB/s) 544s Selecting previously unselected package libpython3.13-minimal:armhf. 544s (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.) 544s Preparing to unpack .../00-libpython3.13-minimal_3.13.0-2_armhf.deb ... 544s Unpacking libpython3.13-minimal:armhf (3.13.0-2) ... 545s Selecting previously unselected package python3.13-minimal. 545s Preparing to unpack .../01-python3.13-minimal_3.13.0-2_armhf.deb ... 545s Unpacking python3.13-minimal (3.13.0-2) ... 545s Selecting previously unselected package sgml-base. 545s Preparing to unpack .../02-sgml-base_1.31_all.deb ... 545s Unpacking sgml-base (1.31) ... 545s Selecting previously unselected package fonts-dejavu-mono. 545s Preparing to unpack .../03-fonts-dejavu-mono_2.37-8_all.deb ... 545s Unpacking fonts-dejavu-mono (2.37-8) ... 545s Selecting previously unselected package fonts-dejavu-core. 545s Preparing to unpack .../04-fonts-dejavu-core_2.37-8_all.deb ... 545s Unpacking fonts-dejavu-core (2.37-8) ... 545s Selecting previously unselected package libfontenc1:armhf. 545s Preparing to unpack .../05-libfontenc1_1%3a1.1.8-1build1_armhf.deb ... 545s Unpacking libfontenc1:armhf (1:1.1.8-1build1) ... 545s Selecting previously unselected package libfreetype6:armhf. 545s Preparing to unpack .../06-libfreetype6_2.13.3+dfsg-1_armhf.deb ... 545s Unpacking libfreetype6:armhf (2.13.3+dfsg-1) ... 545s Selecting previously unselected package x11-common. 545s Preparing to unpack .../07-x11-common_1%3a7.7+23ubuntu3_all.deb ... 545s Unpacking x11-common (1:7.7+23ubuntu3) ... 545s Selecting previously unselected package xfonts-encodings. 545s Preparing to unpack .../08-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 545s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 545s Selecting previously unselected package xfonts-utils. 545s Preparing to unpack .../09-xfonts-utils_1%3a7.7+7_armhf.deb ... 545s Unpacking xfonts-utils (1:7.7+7) ... 545s Selecting previously unselected package fonts-urw-base35. 545s Preparing to unpack .../10-fonts-urw-base35_20200910-8_all.deb ... 545s Unpacking fonts-urw-base35 (20200910-8) ... 545s Selecting previously unselected package fontconfig-config. 545s Preparing to unpack .../11-fontconfig-config_2.15.0-1.1ubuntu2_armhf.deb ... 546s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ... 546s Selecting previously unselected package libblas3:armhf. 546s Preparing to unpack .../12-libblas3_3.12.0-3build2_armhf.deb ... 546s Unpacking libblas3:armhf (3.12.0-3build2) ... 546s Selecting previously unselected package libfontconfig1:armhf. 546s Preparing to unpack .../13-libfontconfig1_2.15.0-1.1ubuntu2_armhf.deb ... 546s Unpacking libfontconfig1:armhf (2.15.0-1.1ubuntu2) ... 546s Selecting previously unselected package libpixman-1-0:armhf. 546s Preparing to unpack .../14-libpixman-1-0_0.44.0-3_armhf.deb ... 546s Unpacking libpixman-1-0:armhf (0.44.0-3) ... 546s Selecting previously unselected package libxcb-render0:armhf. 546s Preparing to unpack .../15-libxcb-render0_1.17.0-2_armhf.deb ... 546s Unpacking libxcb-render0:armhf (1.17.0-2) ... 546s Selecting previously unselected package libxcb-shm0:armhf. 546s Preparing to unpack .../16-libxcb-shm0_1.17.0-2_armhf.deb ... 546s Unpacking libxcb-shm0:armhf (1.17.0-2) ... 546s Selecting previously unselected package libxrender1:armhf. 546s Preparing to unpack .../17-libxrender1_1%3a0.9.10-1.1build1_armhf.deb ... 546s Unpacking libxrender1:armhf (1:0.9.10-1.1build1) ... 546s Selecting previously unselected package libcairo2:armhf. 546s Preparing to unpack .../18-libcairo2_1.18.2-2_armhf.deb ... 546s Unpacking libcairo2:armhf (1.18.2-2) ... 546s Selecting previously unselected package libdeflate0:armhf. 546s Preparing to unpack .../19-libdeflate0_1.22-1_armhf.deb ... 546s Unpacking libdeflate0:armhf (1.22-1) ... 546s Selecting previously unselected package libgfortran5:armhf. 546s Preparing to unpack .../20-libgfortran5_14.2.0-8ubuntu1_armhf.deb ... 546s Unpacking libgfortran5:armhf (14.2.0-8ubuntu1) ... 546s Selecting previously unselected package libgomp1:armhf. 546s Preparing to unpack .../21-libgomp1_14.2.0-8ubuntu1_armhf.deb ... 546s Unpacking libgomp1:armhf (14.2.0-8ubuntu1) ... 546s Selecting previously unselected package libgraphite2-3:armhf. 546s Preparing to unpack .../22-libgraphite2-3_1.3.14-2ubuntu1_armhf.deb ... 546s Unpacking libgraphite2-3:armhf (1.3.14-2ubuntu1) ... 546s Selecting previously unselected package libharfbuzz0b:armhf. 546s Preparing to unpack .../23-libharfbuzz0b_10.0.1-1_armhf.deb ... 546s Unpacking libharfbuzz0b:armhf (10.0.1-1) ... 546s Selecting previously unselected package libimagequant0:armhf. 546s Preparing to unpack .../24-libimagequant0_2.18.0-1build1_armhf.deb ... 546s Unpacking libimagequant0:armhf (2.18.0-1build1) ... 546s Selecting previously unselected package libjpeg-turbo8:armhf. 546s Preparing to unpack .../25-libjpeg-turbo8_2.1.5-2ubuntu2_armhf.deb ... 546s Unpacking libjpeg-turbo8:armhf (2.1.5-2ubuntu2) ... 547s Selecting previously unselected package libjpeg8:armhf. 547s Preparing to unpack .../26-libjpeg8_8c-2ubuntu11_armhf.deb ... 547s Unpacking libjpeg8:armhf (8c-2ubuntu11) ... 547s Selecting previously unselected package liblapack3:armhf. 547s Preparing to unpack .../27-liblapack3_3.12.0-3build2_armhf.deb ... 547s Unpacking liblapack3:armhf (3.12.0-3build2) ... 547s Selecting previously unselected package liblcms2-2:armhf. 547s Preparing to unpack .../28-liblcms2-2_2.16-2_armhf.deb ... 547s Unpacking liblcms2-2:armhf (2.16-2) ... 547s Selecting previously unselected package liblerc4:armhf. 547s Preparing to unpack .../29-liblerc4_4.0.0+ds-4ubuntu2_armhf.deb ... 547s Unpacking liblerc4:armhf (4.0.0+ds-4ubuntu2) ... 547s Selecting previously unselected package libpython3.13-stdlib:armhf. 547s Preparing to unpack .../30-libpython3.13-stdlib_3.13.0-2_armhf.deb ... 547s Unpacking libpython3.13-stdlib:armhf (3.13.0-2) ... 547s Selecting previously unselected package libraqm0:armhf. 547s Preparing to unpack .../31-libraqm0_0.10.1-1build1_armhf.deb ... 547s Unpacking libraqm0:armhf (0.10.1-1build1) ... 547s Selecting previously unselected package libsharpyuv0:armhf. 547s Preparing to unpack .../32-libsharpyuv0_1.4.0-0.1_armhf.deb ... 547s Unpacking libsharpyuv0:armhf (1.4.0-0.1) ... 547s Selecting previously unselected package libjbig0:armhf. 547s Preparing to unpack .../33-libjbig0_2.1-6.1ubuntu2_armhf.deb ... 547s Unpacking libjbig0:armhf (2.1-6.1ubuntu2) ... 547s Selecting previously unselected package libwebp7:armhf. 547s Preparing to unpack .../34-libwebp7_1.4.0-0.1_armhf.deb ... 547s Unpacking libwebp7:armhf (1.4.0-0.1) ... 547s Selecting previously unselected package libtiff6:armhf. 547s Preparing to unpack .../35-libtiff6_4.5.1+git230720-4ubuntu4_armhf.deb ... 547s Unpacking libtiff6:armhf (4.5.1+git230720-4ubuntu4) ... 547s Selecting previously unselected package libwebpdemux2:armhf. 547s Preparing to unpack .../36-libwebpdemux2_1.4.0-0.1_armhf.deb ... 547s Unpacking libwebpdemux2:armhf (1.4.0-0.1) ... 547s Selecting previously unselected package libwebpmux3:armhf. 547s Preparing to unpack .../37-libwebpmux3_1.4.0-0.1_armhf.deb ... 547s Unpacking libwebpmux3:armhf (1.4.0-0.1) ... 547s Selecting previously unselected package python3.13. 547s Preparing to unpack .../38-python3.13_3.13.0-2_armhf.deb ... 547s Unpacking python3.13 (3.13.0-2) ... 547s Selecting previously unselected package python3-all. 547s Preparing to unpack .../39-python3-all_3.12.7-1_armhf.deb ... 547s Unpacking python3-all (3.12.7-1) ... 548s Selecting previously unselected package python3-numpy. 548s Preparing to unpack .../40-python3-numpy_1%3a1.26.4+ds-11build1_armhf.deb ... 548s Unpacking python3-numpy (1:1.26.4+ds-11build1) ... 548s Selecting previously unselected package libopenjp2-7:armhf. 548s Preparing to unpack .../41-libopenjp2-7_2.5.0-2ubuntu1_armhf.deb ... 548s Unpacking libopenjp2-7:armhf (2.5.0-2ubuntu1) ... 548s Selecting previously unselected package python3-pil:armhf. 548s Preparing to unpack .../42-python3-pil_10.4.0-1ubuntu1_armhf.deb ... 548s Unpacking python3-pil:armhf (10.4.0-1ubuntu1) ... 548s Selecting previously unselected package python3-cairo. 548s Preparing to unpack .../43-python3-cairo_1.26.1-2_armhf.deb ... 548s Unpacking python3-cairo (1.26.1-2) ... 548s Selecting previously unselected package python3-freetype. 548s Preparing to unpack .../44-python3-freetype_2.5.1-1_all.deb ... 548s Unpacking python3-freetype (2.5.1-1) ... 548s Selecting previously unselected package python3-rlpycairo. 548s Preparing to unpack .../45-python3-rlpycairo_0.3.0-3_all.deb ... 548s Unpacking python3-rlpycairo (0.3.0-3) ... 548s Selecting previously unselected package python3-reportlab. 548s Preparing to unpack .../46-python3-reportlab_4.2.5-1_all.deb ... 548s Unpacking python3-reportlab (4.2.5-1) ... 548s Selecting previously unselected package xml-core. 548s Preparing to unpack .../47-xml-core_0.19_all.deb ... 548s Unpacking xml-core (0.19) ... 548s Selecting previously unselected package w3c-sgml-lib. 548s Preparing to unpack .../48-w3c-sgml-lib_1.3-3_all.deb ... 548s Unpacking w3c-sgml-lib (1.3-3) ... 548s Selecting previously unselected package python3-biopython. 548s Preparing to unpack .../49-python3-biopython_1.84+dfsg-4_armhf.deb ... 548s Unpacking python3-biopython (1.84+dfsg-4) ... 549s Selecting previously unselected package python3-six. 549s Preparing to unpack .../50-python3-six_1.16.0-7_all.deb ... 549s Unpacking python3-six (1.16.0-7) ... 549s Selecting previously unselected package python3-bcbio-gff. 549s Preparing to unpack .../51-python3-bcbio-gff_0.7.1-2_all.deb ... 549s Unpacking python3-bcbio-gff (0.7.1-2) ... 549s Selecting previously unselected package autopkgtest-satdep. 549s Preparing to unpack .../52-2-autopkgtest-satdep.deb ... 549s Unpacking autopkgtest-satdep (0) ... 549s Setting up libgraphite2-3:armhf (1.3.14-2ubuntu1) ... 549s Setting up liblcms2-2:armhf (2.16-2) ... 549s Setting up libpixman-1-0:armhf (0.44.0-3) ... 549s Setting up libsharpyuv0:armhf (1.4.0-0.1) ... 549s Setting up liblerc4:armhf (4.0.0+ds-4ubuntu2) ... 549s Setting up libxrender1:armhf (1:0.9.10-1.1build1) ... 549s Setting up libxcb-render0:armhf (1.17.0-2) ... 549s Setting up x11-common (1:7.7+23ubuntu3) ... 549s Setting up libdeflate0:armhf (1.22-1) ... 549s Setting up libxcb-shm0:armhf (1.17.0-2) ... 549s Setting up libgomp1:armhf (14.2.0-8ubuntu1) ... 549s Setting up libjbig0:armhf (2.1-6.1ubuntu2) ... 549s Setting up python3-six (1.16.0-7) ... 549s Setting up libpython3.13-minimal:armhf (3.13.0-2) ... 549s Setting up libfontenc1:armhf (1:1.1.8-1build1) ... 549s Setting up libblas3:armhf (3.12.0-3build2) ... 549s 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 549s Setting up libfreetype6:armhf (2.13.3+dfsg-1) ... 549s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 549s Setting up libimagequant0:armhf (2.18.0-1build1) ... 549s Setting up fonts-dejavu-mono (2.37-8) ... 549s Setting up fonts-dejavu-core (2.37-8) ... 550s Setting up libjpeg-turbo8:armhf (2.1.5-2ubuntu2) ... 550s Setting up libgfortran5:armhf (14.2.0-8ubuntu1) ... 550s Setting up libwebp7:armhf (1.4.0-0.1) ... 550s Setting up libopenjp2-7:armhf (2.5.0-2ubuntu1) ... 550s Setting up python3.13-minimal (3.13.0-2) ... 550s Setting up libharfbuzz0b:armhf (10.0.1-1) ... 550s Setting up sgml-base (1.31) ... 551s Setting up libwebpmux3:armhf (1.4.0-0.1) ... 551s Setting up libpython3.13-stdlib:armhf (3.13.0-2) ... 551s Setting up libjpeg8:armhf (8c-2ubuntu11) ... 551s Setting up liblapack3:armhf (3.12.0-3build2) ... 551s 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 551s Setting up python3.13 (3.13.0-2) ... 552s Setting up fontconfig-config (2.15.0-1.1ubuntu2) ... 552s Setting up libwebpdemux2:armhf (1.4.0-0.1) ... 552s Setting up python3-all (3.12.7-1) ... 552s Setting up python3-freetype (2.5.1-1) ... 552s Setting up xfonts-utils (1:7.7+7) ... 552s Setting up libraqm0:armhf (0.10.1-1build1) ... 552s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 557s Setting up libtiff6:armhf (4.5.1+git230720-4ubuntu4) ... 557s Setting up xml-core (0.19) ... 557s Setting up libfontconfig1:armhf (2.15.0-1.1ubuntu2) ... 557s Setting up fonts-urw-base35 (20200910-8) ... 558s Setting up libcairo2:armhf (1.18.2-2) ... 558s Setting up python3-pil:armhf (10.4.0-1ubuntu1) ... 559s Setting up python3-cairo (1.26.1-2) ... 559s Setting up python3-rlpycairo (0.3.0-3) ... 559s Setting up python3-reportlab (4.2.5-1) ... 562s Processing triggers for libc-bin (2.40-1ubuntu3) ... 562s Processing triggers for systemd (256.5-2ubuntu4) ... 562s Processing triggers for man-db (2.12.1-3) ... 563s Processing triggers for sgml-base (1.31) ... 563s Setting up w3c-sgml-lib (1.3-3) ... 594s Setting up python3-biopython (1.84+dfsg-4) ... 597s Setting up python3-bcbio-gff (0.7.1-2) ... 597s Setting up autopkgtest-satdep (0) ... 614s (Reading database ... 63579 files and directories currently installed.) 614s Removing autopkgtest-satdep (0) ... 626s autopkgtest [21:29:35]: test autodep8-python3: set -e ; for py in $(py3versions -r 2>/dev/null) ; do cd "$AUTOPKGTEST_TMP" ; echo "Testing with $py:" ; $py -c "import BCBio.GFF; print(BCBio.GFF)" ; done 626s autopkgtest [21:29:35]: test autodep8-python3: [----------------------- 629s Testing with python3.13: 629s Traceback (most recent call last): 629s File "", line 1, in 629s import BCBio.GFF; print(BCBio.GFF) 629s ^^^^^^^^^^^^^^^^ 629s File "/usr/lib/python3/dist-packages/BCBio/GFF/__init__.py", line 3, in 629s from BCBio.GFF.GFFParser import GFFParser, DiscoGFFParser, GFFExaminer, parse, parse_simple 629s File "/usr/lib/python3/dist-packages/BCBio/GFF/GFFParser.py", line 44, in 629s from Bio import SeqIO 629s File "/usr/lib/python3/dist-packages/Bio/SeqIO/__init__.py", line 401, in 629s from Bio.SeqIO import TwoBitIO 629s File "/usr/lib/python3/dist-packages/Bio/SeqIO/TwoBitIO.py", line 80, in 629s raise MissingPythonDependencyError( 629s ...<2 lines>... 629s ) from None 629s Bio.MissingPythonDependencyError: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 629s autopkgtest [21:29:38]: test autodep8-python3: -----------------------] 633s autopkgtest [21:29:42]: test autodep8-python3: - - - - - - - - - - results - - - - - - - - - - 633s autodep8-python3 FAIL non-zero exit status 1 637s autopkgtest [21:29:46]: @@@@@@@@@@@@@@@@@@@@ summary 637s run-unit-test FAIL non-zero exit status 1 637s autodep8-python3 FAIL non-zero exit status 1