0s autopkgtest [11:30:06]: starting date and time: 2024-11-13 11:30:06+0000 0s autopkgtest [11:30:06]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [11:30:06]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.5sh_pqn_/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --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' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@lcy02-9.secgroup --name adt-plucky-amd64-python-bcbio-gff-20241113-113005-juju-7f2275-prod-proposed-migration-environment-15-cfa4fb35-dc67-47a1-9fae-3f2454c7b3b7 --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 65s autopkgtest [11:31:10]: testbed dpkg architecture: amd64 66s autopkgtest [11:31:12]: testbed apt version: 2.9.8 66s autopkgtest [11:31:12]: @@@@@@@@@@@@@@@@@@@@ test bed setup 67s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 67s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 67s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [76.4 kB] 67s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [849 kB] 67s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.3 kB] 67s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [111 kB] 67s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [65.2 kB] 67s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [32.6 kB] 67s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [639 kB] 67s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [255 kB] 67s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [37.7 kB] 67s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [13.0 kB] 67s Fetched 2175 kB in 0s (5222 kB/s) 67s Reading package lists... 87s Reading package lists... 88s Building dependency tree... 88s Reading state information... 88s Calculating upgrade... 88s The following NEW packages will be installed: 88s python3.13-gdbm 88s The following packages will be upgraded: 88s libgpgme11t64 libpython3-stdlib python3 python3-gdbm python3-minimal 89s 5 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 89s Need to get 253 kB of archives. 89s After this operation, 147 kB of additional disk space will be used. 89s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-minimal amd64 3.12.7-1 [27.4 kB] 89s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3 amd64 3.12.7-1 [24.0 kB] 89s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libpython3-stdlib amd64 3.12.7-1 [10.0 kB] 89s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-gdbm amd64 3.13.0-2 [31.3 kB] 89s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-gdbm amd64 3.12.7-1 [8642 B] 89s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 libgpgme11t64 amd64 1.23.2-5ubuntu4 [152 kB] 89s Fetched 253 kB in 0s (3000 kB/s) 89s (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 ... 75541 files and directories currently installed.) 89s Preparing to unpack .../python3-minimal_3.12.7-1_amd64.deb ... 89s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ... 89s Setting up python3-minimal (3.12.7-1) ... 90s (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 ... 75541 files and directories currently installed.) 90s Preparing to unpack .../python3_3.12.7-1_amd64.deb ... 90s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ... 90s Preparing to unpack .../libpython3-stdlib_3.12.7-1_amd64.deb ... 90s Unpacking libpython3-stdlib:amd64 (3.12.7-1) over (3.12.6-0ubuntu1) ... 90s Selecting previously unselected package python3.13-gdbm. 90s Preparing to unpack .../python3.13-gdbm_3.13.0-2_amd64.deb ... 90s Unpacking python3.13-gdbm (3.13.0-2) ... 90s Preparing to unpack .../python3-gdbm_3.12.7-1_amd64.deb ... 90s Unpacking python3-gdbm:amd64 (3.12.7-1) over (3.12.6-1ubuntu1) ... 90s Preparing to unpack .../libgpgme11t64_1.23.2-5ubuntu4_amd64.deb ... 90s Unpacking libgpgme11t64:amd64 (1.23.2-5ubuntu4) over (1.18.0-4.1ubuntu4) ... 90s Setting up libgpgme11t64:amd64 (1.23.2-5ubuntu4) ... 90s Setting up python3.13-gdbm (3.13.0-2) ... 90s Setting up libpython3-stdlib:amd64 (3.12.7-1) ... 90s Setting up python3 (3.12.7-1) ... 90s Setting up python3-gdbm:amd64 (3.12.7-1) ... 90s Processing triggers for man-db (2.12.1-3) ... 91s Processing triggers for libc-bin (2.40-1ubuntu3) ... 91s Reading package lists... 92s Building dependency tree... 92s Reading state information... 92s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 118s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 118s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 118s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 118s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 120s Reading package lists... 120s Reading package lists... 120s Building dependency tree... 120s Reading state information... 121s Calculating upgrade... 122s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 126s Reading package lists... 126s Building dependency tree... 126s Reading state information... 129s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 153s autopkgtest [11:32:39]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 13:41:20 UTC 2024 154s autopkgtest [11:32:40]: @@@@@@@@@@@@@@@@@@@@ apt-source python-bcbio-gff 156s Get:1 http://ftpmaster.internal/ubuntu plucky/universe python-bcbio-gff 0.7.1-2 (dsc) [2386 B] 156s Get:2 http://ftpmaster.internal/ubuntu plucky/universe python-bcbio-gff 0.7.1-2 (tar) [20.1 kB] 156s Get:3 http://ftpmaster.internal/ubuntu plucky/universe python-bcbio-gff 0.7.1-2 (diff) [23.9 kB] 156s gpgv: Signature made Tue Nov 5 22:11:23 2024 UTC 156s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 156s gpgv: issuer "emollier@debian.org" 156s gpgv: Can't check signature: No public key 156s dpkg-source: warning: cannot verify inline signature for ./python-bcbio-gff_0.7.1-2.dsc: no acceptable signature found 156s autopkgtest [11:32:42]: testing package python-bcbio-gff version 0.7.1-2 158s autopkgtest [11:32:44]: build not needed 161s autopkgtest [11:32:47]: test run-unit-test: preparing testbed 164s Reading package lists... 164s Building dependency tree... 164s Reading state information... 165s Starting pkgProblemResolver with broken count: 0 165s Starting 2 pkgProblemResolver with broken count: 0 165s Done 165s The following additional packages will be installed: 165s fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-urw-base35 165s libblas3 libcairo2 libdeflate0 libfontconfig1 libfontenc1 libgfortran5 165s libgomp1 libgraphite2-3 libharfbuzz0b libimagequant0 libjbig0 libjpeg-turbo8 165s libjpeg8 liblapack3 liblcms2-2 liblerc4 libopenjp2-7 libpixman-1-0 165s libpython3.13-minimal libpython3.13-stdlib libraqm0 libsharpyuv0 libtiff6 165s libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 libxrender1 165s python3-all python3-bcbio-gff python3-biopython python3-cairo 165s python3-freetype python3-numpy python3-pil python3-reportlab 165s python3-rlpycairo python3-six python3.13 python3.13-minimal sgml-base 165s w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core 165s Suggested packages: 165s fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre liblcms2-utils 165s python3-tk bwa clustalo clustalw dialign dssp emboss fasttree mafft muscle3 165s phylip phyml prank probcons python3-mysqldb python3-matplotlib python3-mmtf 165s python3-rdflib python3-psycopg2 python3-scipy raxml samtools t-coffee wise 165s gcc gfortran python-numpy-doc python3-dev python3-pytest python-pil-doc 165s pdf-viewer python3-egenix-mxtexttools python-reportlab-doc rl-accel 165s rl-renderpm python3.13-venv python3.13-doc binfmt-support sgml-base-doc 165s debhelper 165s Recommended packages: 165s python-biopython-doc ncbi-blast+ python3-olefile fonts-dejavu-extra 165s The following NEW packages will be installed: 165s autopkgtest-satdep fontconfig-config fonts-dejavu-core fonts-dejavu-mono 165s fonts-urw-base35 libblas3 libcairo2 libdeflate0 libfontconfig1 libfontenc1 165s libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libimagequant0 libjbig0 165s libjpeg-turbo8 libjpeg8 liblapack3 liblcms2-2 liblerc4 libopenjp2-7 165s libpixman-1-0 libpython3.13-minimal libpython3.13-stdlib libraqm0 165s libsharpyuv0 libtiff6 libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 165s libxcb-shm0 libxrender1 python3-all python3-bcbio-gff python3-biopython 165s python3-cairo python3-freetype python3-numpy python3-pil python3-reportlab 165s python3-rlpycairo python3-six python3.13 python3.13-minimal sgml-base 165s w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core 165s 0 upgraded, 52 newly installed, 0 to remove and 0 not upgraded. 165s Need to get 34.4 MB/34.4 MB of archives. 165s After this operation, 112 MB of additional disk space will be used. 165s Get:1 /tmp/autopkgtest.tLZRRY/1-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [720 B] 165s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-minimal amd64 3.13.0-2 [879 kB] 165s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-minimal amd64 3.13.0-2 [2188 kB] 165s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 sgml-base all 1.31 [11.4 kB] 165s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB] 165s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-core all 2.37-8 [835 kB] 165s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontenc1 amd64 1:1.1.8-1build1 [14.0 kB] 165s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 165s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 165s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 xfonts-utils amd64 1:7.7+7 [97.1 kB] 165s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-urw-base35 all 20200910-8 [11.0 MB] 165s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig-config amd64 2.15.0-1.1ubuntu2 [37.3 kB] 165s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.0-3build2 [247 kB] 165s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontconfig1 amd64 2.15.0-1.1ubuntu2 [139 kB] 165s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 libpixman-1-0 amd64 0.44.0-3 [427 kB] 165s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-render0 amd64 1.17.0-2 [16.2 kB] 165s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-shm0 amd64 1.17.0-2 [5758 B] 165s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 libxrender1 amd64 1:0.9.10-1.1build1 [19.0 kB] 165s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 libcairo2 amd64 1.18.2-2 [569 kB] 165s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate0 amd64 1.22-1 [64.5 kB] 165s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 14.2.0-8ubuntu1 [909 kB] 166s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 libgomp1 amd64 14.2.0-8ubuntu1 [148 kB] 166s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB] 166s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 libharfbuzz0b amd64 10.0.1-1 [540 kB] 166s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 libimagequant0 amd64 2.18.0-1build1 [36.3 kB] 166s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg-turbo8 amd64 2.1.5-2ubuntu2 [150 kB] 166s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 166s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.0-3build2 [2668 kB] 166s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 liblcms2-2 amd64 2.16-2 [212 kB] 166s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 liblerc4 amd64 4.0.0+ds-4ubuntu2 [179 kB] 166s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-stdlib amd64 3.13.0-2 [2107 kB] 166s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 libraqm0 amd64 0.10.1-1build1 [15.0 kB] 166s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 libsharpyuv0 amd64 1.4.0-0.1 [17.5 kB] 166s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB] 166s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebp7 amd64 1.4.0-0.1 [231 kB] 166s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 libtiff6 amd64 4.5.1+git230720-4ubuntu4 [200 kB] 166s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpdemux2 amd64 1.4.0-0.1 [12.4 kB] 166s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpmux3 amd64 1.4.0-0.1 [25.8 kB] 166s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13 amd64 3.13.0-2 [719 kB] 166s Get:40 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-all amd64 3.12.7-1 [890 B] 166s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-numpy amd64 1:1.26.4+ds-11build1 [4479 kB] 166s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 libopenjp2-7 amd64 2.5.0-2ubuntu1 [184 kB] 166s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-pil amd64 10.4.0-1ubuntu1 [463 kB] 166s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-cairo amd64 1.26.1-2 [119 kB] 166s Get:45 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-freetype all 2.5.1-1 [92.3 kB] 166s Get:46 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-rlpycairo all 0.3.0-3 [9130 B] 166s Get:47 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-reportlab all 4.2.5-1 [1107 kB] 166s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 xml-core all 0.19 [20.3 kB] 166s Get:49 http://ftpmaster.internal/ubuntu plucky/universe amd64 w3c-sgml-lib all 1.3-3 [280 kB] 166s Get:50 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-biopython amd64 1.84+dfsg-4 [1714 kB] 166s Get:51 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-six all 1.16.0-7 [13.1 kB] 166s Get:52 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-bcbio-gff all 0.7.1-2 [33.9 kB] 166s Fetched 34.4 MB in 0s (79.6 MB/s) 166s Selecting previously unselected package libpython3.13-minimal:amd64. 166s (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 ... 75548 files and directories currently installed.) 166s Preparing to unpack .../00-libpython3.13-minimal_3.13.0-2_amd64.deb ... 166s Unpacking libpython3.13-minimal:amd64 (3.13.0-2) ... 166s Selecting previously unselected package python3.13-minimal. 166s Preparing to unpack .../01-python3.13-minimal_3.13.0-2_amd64.deb ... 166s Unpacking python3.13-minimal (3.13.0-2) ... 166s Selecting previously unselected package sgml-base. 166s Preparing to unpack .../02-sgml-base_1.31_all.deb ... 166s Unpacking sgml-base (1.31) ... 167s Selecting previously unselected package fonts-dejavu-mono. 167s Preparing to unpack .../03-fonts-dejavu-mono_2.37-8_all.deb ... 167s Unpacking fonts-dejavu-mono (2.37-8) ... 167s Selecting previously unselected package fonts-dejavu-core. 167s Preparing to unpack .../04-fonts-dejavu-core_2.37-8_all.deb ... 167s Unpacking fonts-dejavu-core (2.37-8) ... 167s Selecting previously unselected package libfontenc1:amd64. 167s Preparing to unpack .../05-libfontenc1_1%3a1.1.8-1build1_amd64.deb ... 167s Unpacking libfontenc1:amd64 (1:1.1.8-1build1) ... 167s Selecting previously unselected package x11-common. 167s Preparing to unpack .../06-x11-common_1%3a7.7+23ubuntu3_all.deb ... 167s Unpacking x11-common (1:7.7+23ubuntu3) ... 167s Selecting previously unselected package xfonts-encodings. 167s Preparing to unpack .../07-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 167s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 167s Selecting previously unselected package xfonts-utils. 167s Preparing to unpack .../08-xfonts-utils_1%3a7.7+7_amd64.deb ... 167s Unpacking xfonts-utils (1:7.7+7) ... 167s Selecting previously unselected package fonts-urw-base35. 167s Preparing to unpack .../09-fonts-urw-base35_20200910-8_all.deb ... 167s Unpacking fonts-urw-base35 (20200910-8) ... 167s Selecting previously unselected package fontconfig-config. 167s Preparing to unpack .../10-fontconfig-config_2.15.0-1.1ubuntu2_amd64.deb ... 167s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ... 167s Selecting previously unselected package libblas3:amd64. 167s Preparing to unpack .../11-libblas3_3.12.0-3build2_amd64.deb ... 167s Unpacking libblas3:amd64 (3.12.0-3build2) ... 167s Selecting previously unselected package libfontconfig1:amd64. 167s Preparing to unpack .../12-libfontconfig1_2.15.0-1.1ubuntu2_amd64.deb ... 167s Unpacking libfontconfig1:amd64 (2.15.0-1.1ubuntu2) ... 167s Selecting previously unselected package libpixman-1-0:amd64. 167s Preparing to unpack .../13-libpixman-1-0_0.44.0-3_amd64.deb ... 167s Unpacking libpixman-1-0:amd64 (0.44.0-3) ... 167s Selecting previously unselected package libxcb-render0:amd64. 167s Preparing to unpack .../14-libxcb-render0_1.17.0-2_amd64.deb ... 167s Unpacking libxcb-render0:amd64 (1.17.0-2) ... 167s Selecting previously unselected package libxcb-shm0:amd64. 167s Preparing to unpack .../15-libxcb-shm0_1.17.0-2_amd64.deb ... 167s Unpacking libxcb-shm0:amd64 (1.17.0-2) ... 167s Selecting previously unselected package libxrender1:amd64. 167s Preparing to unpack .../16-libxrender1_1%3a0.9.10-1.1build1_amd64.deb ... 167s Unpacking libxrender1:amd64 (1:0.9.10-1.1build1) ... 167s Selecting previously unselected package libcairo2:amd64. 167s Preparing to unpack .../17-libcairo2_1.18.2-2_amd64.deb ... 167s Unpacking libcairo2:amd64 (1.18.2-2) ... 167s Selecting previously unselected package libdeflate0:amd64. 167s Preparing to unpack .../18-libdeflate0_1.22-1_amd64.deb ... 167s Unpacking libdeflate0:amd64 (1.22-1) ... 167s Selecting previously unselected package libgfortran5:amd64. 167s Preparing to unpack .../19-libgfortran5_14.2.0-8ubuntu1_amd64.deb ... 167s Unpacking libgfortran5:amd64 (14.2.0-8ubuntu1) ... 167s Selecting previously unselected package libgomp1:amd64. 167s Preparing to unpack .../20-libgomp1_14.2.0-8ubuntu1_amd64.deb ... 167s Unpacking libgomp1:amd64 (14.2.0-8ubuntu1) ... 167s Selecting previously unselected package libgraphite2-3:amd64. 167s Preparing to unpack .../21-libgraphite2-3_1.3.14-2ubuntu1_amd64.deb ... 167s Unpacking libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 167s Selecting previously unselected package libharfbuzz0b:amd64. 167s Preparing to unpack .../22-libharfbuzz0b_10.0.1-1_amd64.deb ... 167s Unpacking libharfbuzz0b:amd64 (10.0.1-1) ... 167s Selecting previously unselected package libimagequant0:amd64. 167s Preparing to unpack .../23-libimagequant0_2.18.0-1build1_amd64.deb ... 167s Unpacking libimagequant0:amd64 (2.18.0-1build1) ... 168s Selecting previously unselected package libjpeg-turbo8:amd64. 168s Preparing to unpack .../24-libjpeg-turbo8_2.1.5-2ubuntu2_amd64.deb ... 168s Unpacking libjpeg-turbo8:amd64 (2.1.5-2ubuntu2) ... 168s Selecting previously unselected package libjpeg8:amd64. 168s Preparing to unpack .../25-libjpeg8_8c-2ubuntu11_amd64.deb ... 168s Unpacking libjpeg8:amd64 (8c-2ubuntu11) ... 168s Selecting previously unselected package liblapack3:amd64. 168s Preparing to unpack .../26-liblapack3_3.12.0-3build2_amd64.deb ... 168s Unpacking liblapack3:amd64 (3.12.0-3build2) ... 168s Selecting previously unselected package liblcms2-2:amd64. 168s Preparing to unpack .../27-liblcms2-2_2.16-2_amd64.deb ... 168s Unpacking liblcms2-2:amd64 (2.16-2) ... 168s Selecting previously unselected package liblerc4:amd64. 168s Preparing to unpack .../28-liblerc4_4.0.0+ds-4ubuntu2_amd64.deb ... 168s Unpacking liblerc4:amd64 (4.0.0+ds-4ubuntu2) ... 168s Selecting previously unselected package libpython3.13-stdlib:amd64. 168s Preparing to unpack .../29-libpython3.13-stdlib_3.13.0-2_amd64.deb ... 168s Unpacking libpython3.13-stdlib:amd64 (3.13.0-2) ... 168s Selecting previously unselected package libraqm0:amd64. 168s Preparing to unpack .../30-libraqm0_0.10.1-1build1_amd64.deb ... 168s Unpacking libraqm0:amd64 (0.10.1-1build1) ... 168s Selecting previously unselected package libsharpyuv0:amd64. 168s Preparing to unpack .../31-libsharpyuv0_1.4.0-0.1_amd64.deb ... 168s Unpacking libsharpyuv0:amd64 (1.4.0-0.1) ... 168s Selecting previously unselected package libjbig0:amd64. 168s Preparing to unpack .../32-libjbig0_2.1-6.1ubuntu2_amd64.deb ... 168s Unpacking libjbig0:amd64 (2.1-6.1ubuntu2) ... 168s Selecting previously unselected package libwebp7:amd64. 168s Preparing to unpack .../33-libwebp7_1.4.0-0.1_amd64.deb ... 168s Unpacking libwebp7:amd64 (1.4.0-0.1) ... 168s Selecting previously unselected package libtiff6:amd64. 168s Preparing to unpack .../34-libtiff6_4.5.1+git230720-4ubuntu4_amd64.deb ... 168s Unpacking libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ... 168s Selecting previously unselected package libwebpdemux2:amd64. 168s Preparing to unpack .../35-libwebpdemux2_1.4.0-0.1_amd64.deb ... 168s Unpacking libwebpdemux2:amd64 (1.4.0-0.1) ... 168s Selecting previously unselected package libwebpmux3:amd64. 168s Preparing to unpack .../36-libwebpmux3_1.4.0-0.1_amd64.deb ... 168s Unpacking libwebpmux3:amd64 (1.4.0-0.1) ... 168s Selecting previously unselected package python3.13. 168s Preparing to unpack .../37-python3.13_3.13.0-2_amd64.deb ... 168s Unpacking python3.13 (3.13.0-2) ... 168s Selecting previously unselected package python3-all. 168s Preparing to unpack .../38-python3-all_3.12.7-1_amd64.deb ... 168s Unpacking python3-all (3.12.7-1) ... 168s Selecting previously unselected package python3-numpy. 168s Preparing to unpack .../39-python3-numpy_1%3a1.26.4+ds-11build1_amd64.deb ... 168s Unpacking python3-numpy (1:1.26.4+ds-11build1) ... 169s Selecting previously unselected package libopenjp2-7:amd64. 169s Preparing to unpack .../40-libopenjp2-7_2.5.0-2ubuntu1_amd64.deb ... 169s Unpacking libopenjp2-7:amd64 (2.5.0-2ubuntu1) ... 169s Selecting previously unselected package python3-pil:amd64. 169s Preparing to unpack .../41-python3-pil_10.4.0-1ubuntu1_amd64.deb ... 169s Unpacking python3-pil:amd64 (10.4.0-1ubuntu1) ... 169s Selecting previously unselected package python3-cairo. 169s Preparing to unpack .../42-python3-cairo_1.26.1-2_amd64.deb ... 169s Unpacking python3-cairo (1.26.1-2) ... 169s Selecting previously unselected package python3-freetype. 169s Preparing to unpack .../43-python3-freetype_2.5.1-1_all.deb ... 169s Unpacking python3-freetype (2.5.1-1) ... 169s Selecting previously unselected package python3-rlpycairo. 169s Preparing to unpack .../44-python3-rlpycairo_0.3.0-3_all.deb ... 169s Unpacking python3-rlpycairo (0.3.0-3) ... 169s Selecting previously unselected package python3-reportlab. 169s Preparing to unpack .../45-python3-reportlab_4.2.5-1_all.deb ... 169s Unpacking python3-reportlab (4.2.5-1) ... 169s Selecting previously unselected package xml-core. 169s Preparing to unpack .../46-xml-core_0.19_all.deb ... 169s Unpacking xml-core (0.19) ... 169s Selecting previously unselected package w3c-sgml-lib. 169s Preparing to unpack .../47-w3c-sgml-lib_1.3-3_all.deb ... 169s Unpacking w3c-sgml-lib (1.3-3) ... 169s Selecting previously unselected package python3-biopython. 169s Preparing to unpack .../48-python3-biopython_1.84+dfsg-4_amd64.deb ... 169s Unpacking python3-biopython (1.84+dfsg-4) ... 169s Selecting previously unselected package python3-six. 169s Preparing to unpack .../49-python3-six_1.16.0-7_all.deb ... 169s Unpacking python3-six (1.16.0-7) ... 169s Selecting previously unselected package python3-bcbio-gff. 169s Preparing to unpack .../50-python3-bcbio-gff_0.7.1-2_all.deb ... 169s Unpacking python3-bcbio-gff (0.7.1-2) ... 169s Selecting previously unselected package autopkgtest-satdep. 169s Preparing to unpack .../51-1-autopkgtest-satdep.deb ... 169s Unpacking autopkgtest-satdep (0) ... 169s Setting up libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 169s Setting up liblcms2-2:amd64 (2.16-2) ... 169s Setting up libpixman-1-0:amd64 (0.44.0-3) ... 169s Setting up libsharpyuv0:amd64 (1.4.0-0.1) ... 169s Setting up liblerc4:amd64 (4.0.0+ds-4ubuntu2) ... 169s Setting up libxrender1:amd64 (1:0.9.10-1.1build1) ... 169s Setting up libxcb-render0:amd64 (1.17.0-2) ... 169s Setting up x11-common (1:7.7+23ubuntu3) ... 170s Setting up libdeflate0:amd64 (1.22-1) ... 170s Setting up libxcb-shm0:amd64 (1.17.0-2) ... 170s Setting up libgomp1:amd64 (14.2.0-8ubuntu1) ... 170s Setting up python3-freetype (2.5.1-1) ... 170s Setting up libjbig0:amd64 (2.1-6.1ubuntu2) ... 170s Setting up python3-six (1.16.0-7) ... 170s Setting up libpython3.13-minimal:amd64 (3.13.0-2) ... 170s Setting up libfontenc1:amd64 (1:1.1.8-1build1) ... 170s Setting up libblas3:amd64 (3.12.0-3build2) ... 170s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode 170s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 170s Setting up libimagequant0:amd64 (2.18.0-1build1) ... 170s Setting up fonts-dejavu-mono (2.37-8) ... 170s Setting up fonts-dejavu-core (2.37-8) ... 170s Setting up libjpeg-turbo8:amd64 (2.1.5-2ubuntu2) ... 170s Setting up libgfortran5:amd64 (14.2.0-8ubuntu1) ... 170s Setting up libwebp7:amd64 (1.4.0-0.1) ... 170s Setting up libopenjp2-7:amd64 (2.5.0-2ubuntu1) ... 170s Setting up python3.13-minimal (3.13.0-2) ... 171s Setting up libharfbuzz0b:amd64 (10.0.1-1) ... 171s Setting up sgml-base (1.31) ... 171s Setting up libwebpmux3:amd64 (1.4.0-0.1) ... 171s Setting up libpython3.13-stdlib:amd64 (3.13.0-2) ... 171s Setting up libjpeg8:amd64 (8c-2ubuntu11) ... 171s Setting up liblapack3:amd64 (3.12.0-3build2) ... 171s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode 171s Setting up python3.13 (3.13.0-2) ... 172s Setting up fontconfig-config (2.15.0-1.1ubuntu2) ... 173s Setting up libwebpdemux2:amd64 (1.4.0-0.1) ... 173s Setting up python3-all (3.12.7-1) ... 173s Setting up xfonts-utils (1:7.7+7) ... 173s Setting up libraqm0:amd64 (0.10.1-1build1) ... 173s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 177s Setting up libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ... 177s Setting up xml-core (0.19) ... 177s Setting up libfontconfig1:amd64 (2.15.0-1.1ubuntu2) ... 177s Setting up fonts-urw-base35 (20200910-8) ... 177s Setting up libcairo2:amd64 (1.18.2-2) ... 177s Setting up python3-pil:amd64 (10.4.0-1ubuntu1) ... 178s Setting up python3-cairo (1.26.1-2) ... 178s Setting up python3-rlpycairo (0.3.0-3) ... 179s Setting up python3-reportlab (4.2.5-1) ... 181s Processing triggers for libc-bin (2.40-1ubuntu3) ... 181s Processing triggers for systemd (256.5-2ubuntu4) ... 181s Processing triggers for man-db (2.12.1-3) ... 182s Processing triggers for sgml-base (1.31) ... 182s Setting up w3c-sgml-lib (1.3-3) ... 216s Setting up python3-biopython (1.84+dfsg-4) ... 219s Setting up python3-bcbio-gff (0.7.1-2) ... 219s Setting up autopkgtest-satdep (0) ... 223s (Reading database ... 79553 files and directories currently installed.) 223s Removing autopkgtest-satdep (0) ... 223s autopkgtest [11:33:49]: test run-unit-test: [----------------------- 223s Traceback (most recent call last): 223s File "/tmp/autopkgtest.tLZRRY/autopkgtest_tmp/test_GFFSeqIOFeatureAdder.py", line 11, in 223s from Bio import SeqIO 223s File "/usr/lib/python3/dist-packages/Bio/SeqIO/__init__.py", line 401, in 223s from Bio.SeqIO import TwoBitIO 223s File "/usr/lib/python3/dist-packages/Bio/SeqIO/TwoBitIO.py", line 80, in 223s raise MissingPythonDependencyError( 223s ...<2 lines>... 223s ) from None 223s Bio.MissingPythonDependencyError: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 223s autopkgtest [11:33:49]: test run-unit-test: -----------------------] 224s autopkgtest [11:33:50]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 224s run-unit-test FAIL non-zero exit status 1 224s autopkgtest [11:33:50]: test autodep8-python3: preparing testbed 286s autopkgtest [11:34:52]: testbed dpkg architecture: amd64 286s autopkgtest [11:34:52]: testbed apt version: 2.9.8 286s autopkgtest [11:34:52]: @@@@@@@@@@@@@@@@@@@@ test bed setup 287s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 287s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [76.4 kB] 287s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 287s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.3 kB] 287s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [849 kB] 287s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [111 kB] 287s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [65.2 kB] 287s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [32.6 kB] 287s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [255 kB] 287s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [639 kB] 287s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [13.0 kB] 287s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [37.7 kB] 287s Fetched 2175 kB in 0s (6400 kB/s) 287s Reading package lists... 289s Reading package lists... 289s Building dependency tree... 289s Reading state information... 290s Calculating upgrade... 290s The following NEW packages will be installed: 290s python3.13-gdbm 290s The following packages will be upgraded: 290s libgpgme11t64 libpython3-stdlib python3 python3-gdbm python3-minimal 290s 5 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 290s Need to get 253 kB of archives. 290s After this operation, 147 kB of additional disk space will be used. 290s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-minimal amd64 3.12.7-1 [27.4 kB] 290s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3 amd64 3.12.7-1 [24.0 kB] 290s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libpython3-stdlib amd64 3.12.7-1 [10.0 kB] 290s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-gdbm amd64 3.13.0-2 [31.3 kB] 290s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-gdbm amd64 3.12.7-1 [8642 B] 290s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 libgpgme11t64 amd64 1.23.2-5ubuntu4 [152 kB] 290s Fetched 253 kB in 0s (8668 kB/s) 290s (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 ... 75541 files and directories currently installed.) 290s Preparing to unpack .../python3-minimal_3.12.7-1_amd64.deb ... 290s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ... 291s Setting up python3-minimal (3.12.7-1) ... 291s (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 ... 75541 files and directories currently installed.) 291s Preparing to unpack .../python3_3.12.7-1_amd64.deb ... 291s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ... 291s Preparing to unpack .../libpython3-stdlib_3.12.7-1_amd64.deb ... 291s Unpacking libpython3-stdlib:amd64 (3.12.7-1) over (3.12.6-0ubuntu1) ... 291s Selecting previously unselected package python3.13-gdbm. 291s Preparing to unpack .../python3.13-gdbm_3.13.0-2_amd64.deb ... 291s Unpacking python3.13-gdbm (3.13.0-2) ... 291s Preparing to unpack .../python3-gdbm_3.12.7-1_amd64.deb ... 291s Unpacking python3-gdbm:amd64 (3.12.7-1) over (3.12.6-1ubuntu1) ... 291s Preparing to unpack .../libgpgme11t64_1.23.2-5ubuntu4_amd64.deb ... 291s Unpacking libgpgme11t64:amd64 (1.23.2-5ubuntu4) over (1.18.0-4.1ubuntu4) ... 291s Setting up libgpgme11t64:amd64 (1.23.2-5ubuntu4) ... 291s Setting up python3.13-gdbm (3.13.0-2) ... 291s Setting up libpython3-stdlib:amd64 (3.12.7-1) ... 291s Setting up python3 (3.12.7-1) ... 291s Setting up python3-gdbm:amd64 (3.12.7-1) ... 291s Processing triggers for man-db (2.12.1-3) ... 292s Processing triggers for libc-bin (2.40-1ubuntu3) ... 292s Reading package lists... 293s Building dependency tree... 293s Reading state information... 293s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 294s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 294s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 294s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 294s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 295s Reading package lists... 295s Reading package lists... 295s Building dependency tree... 295s Reading state information... 296s Calculating upgrade... 296s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 296s Reading package lists... 296s Building dependency tree... 296s Reading state information... 297s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 299s Reading package lists... 299s Building dependency tree... 299s Reading state information... 299s Starting pkgProblemResolver with broken count: 0 299s Starting 2 pkgProblemResolver with broken count: 0 299s Done 300s The following additional packages will be installed: 300s fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-urw-base35 300s libblas3 libcairo2 libdeflate0 libfontconfig1 libfontenc1 libgfortran5 300s libgomp1 libgraphite2-3 libharfbuzz0b libimagequant0 libjbig0 libjpeg-turbo8 300s libjpeg8 liblapack3 liblcms2-2 liblerc4 libopenjp2-7 libpixman-1-0 300s libpython3.13-minimal libpython3.13-stdlib libraqm0 libsharpyuv0 libtiff6 300s libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 libxrender1 300s python3-all python3-bcbio-gff python3-biopython python3-cairo 300s python3-freetype python3-numpy python3-pil python3-reportlab 300s python3-rlpycairo python3-six python3.13 python3.13-minimal sgml-base 300s w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core 300s Suggested packages: 300s fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre liblcms2-utils 300s python3-tk bwa clustalo clustalw dialign dssp emboss fasttree mafft muscle3 300s phylip phyml prank probcons python3-mysqldb python3-matplotlib python3-mmtf 300s python3-rdflib python3-psycopg2 python3-scipy raxml samtools t-coffee wise 300s gcc gfortran python-numpy-doc python3-dev python3-pytest python-pil-doc 300s pdf-viewer python3-egenix-mxtexttools python-reportlab-doc rl-accel 300s rl-renderpm python3.13-venv python3.13-doc binfmt-support sgml-base-doc 300s debhelper 300s Recommended packages: 300s python-biopython-doc ncbi-blast+ python3-olefile fonts-dejavu-extra 300s The following NEW packages will be installed: 300s autopkgtest-satdep fontconfig-config fonts-dejavu-core fonts-dejavu-mono 300s fonts-urw-base35 libblas3 libcairo2 libdeflate0 libfontconfig1 libfontenc1 300s libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libimagequant0 libjbig0 300s libjpeg-turbo8 libjpeg8 liblapack3 liblcms2-2 liblerc4 libopenjp2-7 300s libpixman-1-0 libpython3.13-minimal libpython3.13-stdlib libraqm0 300s libsharpyuv0 libtiff6 libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 300s libxcb-shm0 libxrender1 python3-all python3-bcbio-gff python3-biopython 300s python3-cairo python3-freetype python3-numpy python3-pil python3-reportlab 300s python3-rlpycairo python3-six python3.13 python3.13-minimal sgml-base 300s w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core 300s 0 upgraded, 52 newly installed, 0 to remove and 0 not upgraded. 300s Need to get 34.4 MB/34.4 MB of archives. 300s After this operation, 112 MB of additional disk space will be used. 300s Get:1 /tmp/autopkgtest.tLZRRY/2-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [716 B] 300s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-minimal amd64 3.13.0-2 [879 kB] 300s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-minimal amd64 3.13.0-2 [2188 kB] 300s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 sgml-base all 1.31 [11.4 kB] 300s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB] 300s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-core all 2.37-8 [835 kB] 300s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontenc1 amd64 1:1.1.8-1build1 [14.0 kB] 300s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 300s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 300s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 xfonts-utils amd64 1:7.7+7 [97.1 kB] 300s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-urw-base35 all 20200910-8 [11.0 MB] 300s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig-config amd64 2.15.0-1.1ubuntu2 [37.3 kB] 300s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.0-3build2 [247 kB] 300s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontconfig1 amd64 2.15.0-1.1ubuntu2 [139 kB] 300s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 libpixman-1-0 amd64 0.44.0-3 [427 kB] 300s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-render0 amd64 1.17.0-2 [16.2 kB] 300s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-shm0 amd64 1.17.0-2 [5758 B] 300s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 libxrender1 amd64 1:0.9.10-1.1build1 [19.0 kB] 300s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 libcairo2 amd64 1.18.2-2 [569 kB] 300s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate0 amd64 1.22-1 [64.5 kB] 300s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 14.2.0-8ubuntu1 [909 kB] 300s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 libgomp1 amd64 14.2.0-8ubuntu1 [148 kB] 300s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB] 300s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 libharfbuzz0b amd64 10.0.1-1 [540 kB] 300s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 libimagequant0 amd64 2.18.0-1build1 [36.3 kB] 300s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg-turbo8 amd64 2.1.5-2ubuntu2 [150 kB] 300s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 300s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.0-3build2 [2668 kB] 300s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 liblcms2-2 amd64 2.16-2 [212 kB] 300s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 liblerc4 amd64 4.0.0+ds-4ubuntu2 [179 kB] 300s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-stdlib amd64 3.13.0-2 [2107 kB] 300s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 libraqm0 amd64 0.10.1-1build1 [15.0 kB] 300s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 libsharpyuv0 amd64 1.4.0-0.1 [17.5 kB] 300s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB] 300s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebp7 amd64 1.4.0-0.1 [231 kB] 300s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 libtiff6 amd64 4.5.1+git230720-4ubuntu4 [200 kB] 301s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpdemux2 amd64 1.4.0-0.1 [12.4 kB] 301s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpmux3 amd64 1.4.0-0.1 [25.8 kB] 301s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13 amd64 3.13.0-2 [719 kB] 301s Get:40 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-all amd64 3.12.7-1 [890 B] 301s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-numpy amd64 1:1.26.4+ds-11build1 [4479 kB] 301s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 libopenjp2-7 amd64 2.5.0-2ubuntu1 [184 kB] 301s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-pil amd64 10.4.0-1ubuntu1 [463 kB] 301s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-cairo amd64 1.26.1-2 [119 kB] 301s Get:45 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-freetype all 2.5.1-1 [92.3 kB] 301s Get:46 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-rlpycairo all 0.3.0-3 [9130 B] 301s Get:47 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-reportlab all 4.2.5-1 [1107 kB] 301s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 xml-core all 0.19 [20.3 kB] 301s Get:49 http://ftpmaster.internal/ubuntu plucky/universe amd64 w3c-sgml-lib all 1.3-3 [280 kB] 301s Get:50 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-biopython amd64 1.84+dfsg-4 [1714 kB] 301s Get:51 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-six all 1.16.0-7 [13.1 kB] 301s Get:52 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-bcbio-gff all 0.7.1-2 [33.9 kB] 301s Fetched 34.4 MB in 0s (77.3 MB/s) 301s Selecting previously unselected package libpython3.13-minimal:amd64. 301s (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 ... 75548 files and directories currently installed.) 301s Preparing to unpack .../00-libpython3.13-minimal_3.13.0-2_amd64.deb ... 301s Unpacking libpython3.13-minimal:amd64 (3.13.0-2) ... 301s Selecting previously unselected package python3.13-minimal. 301s Preparing to unpack .../01-python3.13-minimal_3.13.0-2_amd64.deb ... 301s Unpacking python3.13-minimal (3.13.0-2) ... 301s Selecting previously unselected package sgml-base. 301s Preparing to unpack .../02-sgml-base_1.31_all.deb ... 301s Unpacking sgml-base (1.31) ... 301s Selecting previously unselected package fonts-dejavu-mono. 301s Preparing to unpack .../03-fonts-dejavu-mono_2.37-8_all.deb ... 301s Unpacking fonts-dejavu-mono (2.37-8) ... 301s Selecting previously unselected package fonts-dejavu-core. 301s Preparing to unpack .../04-fonts-dejavu-core_2.37-8_all.deb ... 301s Unpacking fonts-dejavu-core (2.37-8) ... 301s Selecting previously unselected package libfontenc1:amd64. 301s Preparing to unpack .../05-libfontenc1_1%3a1.1.8-1build1_amd64.deb ... 301s Unpacking libfontenc1:amd64 (1:1.1.8-1build1) ... 301s Selecting previously unselected package x11-common. 301s Preparing to unpack .../06-x11-common_1%3a7.7+23ubuntu3_all.deb ... 301s Unpacking x11-common (1:7.7+23ubuntu3) ... 301s Selecting previously unselected package xfonts-encodings. 301s Preparing to unpack .../07-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 301s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 301s Selecting previously unselected package xfonts-utils. 301s Preparing to unpack .../08-xfonts-utils_1%3a7.7+7_amd64.deb ... 301s Unpacking xfonts-utils (1:7.7+7) ... 302s Selecting previously unselected package fonts-urw-base35. 302s Preparing to unpack .../09-fonts-urw-base35_20200910-8_all.deb ... 302s Unpacking fonts-urw-base35 (20200910-8) ... 302s Selecting previously unselected package fontconfig-config. 302s Preparing to unpack .../10-fontconfig-config_2.15.0-1.1ubuntu2_amd64.deb ... 302s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ... 302s Selecting previously unselected package libblas3:amd64. 302s Preparing to unpack .../11-libblas3_3.12.0-3build2_amd64.deb ... 302s Unpacking libblas3:amd64 (3.12.0-3build2) ... 302s Selecting previously unselected package libfontconfig1:amd64. 302s Preparing to unpack .../12-libfontconfig1_2.15.0-1.1ubuntu2_amd64.deb ... 302s Unpacking libfontconfig1:amd64 (2.15.0-1.1ubuntu2) ... 302s Selecting previously unselected package libpixman-1-0:amd64. 302s Preparing to unpack .../13-libpixman-1-0_0.44.0-3_amd64.deb ... 302s Unpacking libpixman-1-0:amd64 (0.44.0-3) ... 302s Selecting previously unselected package libxcb-render0:amd64. 302s Preparing to unpack .../14-libxcb-render0_1.17.0-2_amd64.deb ... 302s Unpacking libxcb-render0:amd64 (1.17.0-2) ... 302s Selecting previously unselected package libxcb-shm0:amd64. 302s Preparing to unpack .../15-libxcb-shm0_1.17.0-2_amd64.deb ... 302s Unpacking libxcb-shm0:amd64 (1.17.0-2) ... 302s Selecting previously unselected package libxrender1:amd64. 302s Preparing to unpack .../16-libxrender1_1%3a0.9.10-1.1build1_amd64.deb ... 302s Unpacking libxrender1:amd64 (1:0.9.10-1.1build1) ... 302s Selecting previously unselected package libcairo2:amd64. 302s Preparing to unpack .../17-libcairo2_1.18.2-2_amd64.deb ... 302s Unpacking libcairo2:amd64 (1.18.2-2) ... 302s Selecting previously unselected package libdeflate0:amd64. 302s Preparing to unpack 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.../34-libtiff6_4.5.1+git230720-4ubuntu4_amd64.deb ... 303s Unpacking libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ... 303s Selecting previously unselected package libwebpdemux2:amd64. 303s Preparing to unpack .../35-libwebpdemux2_1.4.0-0.1_amd64.deb ... 303s Unpacking libwebpdemux2:amd64 (1.4.0-0.1) ... 303s Selecting previously unselected package libwebpmux3:amd64. 303s Preparing to unpack .../36-libwebpmux3_1.4.0-0.1_amd64.deb ... 303s Unpacking libwebpmux3:amd64 (1.4.0-0.1) ... 303s Selecting previously unselected package python3.13. 303s Preparing to unpack .../37-python3.13_3.13.0-2_amd64.deb ... 303s Unpacking python3.13 (3.13.0-2) ... 303s Selecting previously unselected package python3-all. 303s Preparing to unpack .../38-python3-all_3.12.7-1_amd64.deb ... 303s Unpacking python3-all (3.12.7-1) ... 303s Selecting previously unselected package python3-numpy. 303s Preparing to unpack .../39-python3-numpy_1%3a1.26.4+ds-11build1_amd64.deb ... 303s Unpacking python3-numpy (1:1.26.4+ds-11build1) ... 303s Selecting previously unselected package libopenjp2-7:amd64. 303s Preparing to unpack .../40-libopenjp2-7_2.5.0-2ubuntu1_amd64.deb ... 303s Unpacking libopenjp2-7:amd64 (2.5.0-2ubuntu1) ... 303s Selecting previously unselected package python3-pil:amd64. 303s Preparing to unpack .../41-python3-pil_10.4.0-1ubuntu1_amd64.deb ... 303s Unpacking python3-pil:amd64 (10.4.0-1ubuntu1) ... 304s Selecting previously unselected package python3-cairo. 304s Preparing to unpack .../42-python3-cairo_1.26.1-2_amd64.deb ... 304s Unpacking python3-cairo (1.26.1-2) ... 304s Selecting previously unselected package python3-freetype. 304s Preparing to unpack .../43-python3-freetype_2.5.1-1_all.deb ... 304s Unpacking python3-freetype (2.5.1-1) ... 304s Selecting previously unselected package python3-rlpycairo. 304s Preparing to unpack .../44-python3-rlpycairo_0.3.0-3_all.deb ... 304s Unpacking python3-rlpycairo (0.3.0-3) ... 304s Selecting previously unselected package python3-reportlab. 304s Preparing to unpack .../45-python3-reportlab_4.2.5-1_all.deb ... 304s Unpacking python3-reportlab (4.2.5-1) ... 304s Selecting previously unselected package xml-core. 304s Preparing to unpack .../46-xml-core_0.19_all.deb ... 304s Unpacking xml-core (0.19) ... 304s Selecting previously unselected package w3c-sgml-lib. 304s Preparing to unpack .../47-w3c-sgml-lib_1.3-3_all.deb ... 304s Unpacking w3c-sgml-lib (1.3-3) ... 304s Selecting previously unselected package python3-biopython. 304s Preparing to unpack .../48-python3-biopython_1.84+dfsg-4_amd64.deb ... 304s Unpacking python3-biopython (1.84+dfsg-4) ... 304s Selecting previously unselected package python3-six. 304s Preparing to unpack .../49-python3-six_1.16.0-7_all.deb ... 304s Unpacking python3-six (1.16.0-7) ... 304s Selecting previously unselected package python3-bcbio-gff. 304s Preparing to unpack .../50-python3-bcbio-gff_0.7.1-2_all.deb ... 304s Unpacking python3-bcbio-gff (0.7.1-2) ... 304s Selecting previously unselected package autopkgtest-satdep. 304s Preparing to unpack .../51-2-autopkgtest-satdep.deb ... 304s Unpacking autopkgtest-satdep (0) ... 304s Setting up libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 304s Setting up liblcms2-2:amd64 (2.16-2) ... 304s Setting up libpixman-1-0:amd64 (0.44.0-3) ... 304s Setting up libsharpyuv0:amd64 (1.4.0-0.1) ... 304s Setting up liblerc4:amd64 (4.0.0+ds-4ubuntu2) ... 304s Setting up libxrender1:amd64 (1:0.9.10-1.1build1) ... 304s Setting up libxcb-render0:amd64 (1.17.0-2) ... 304s Setting up x11-common (1:7.7+23ubuntu3) ... 305s Setting up libdeflate0:amd64 (1.22-1) ... 305s Setting up libxcb-shm0:amd64 (1.17.0-2) ... 305s Setting up libgomp1:amd64 (14.2.0-8ubuntu1) ... 305s Setting up python3-freetype (2.5.1-1) ... 305s Setting up libjbig0:amd64 (2.1-6.1ubuntu2) ... 305s Setting up python3-six (1.16.0-7) ... 305s Setting up libpython3.13-minimal:amd64 (3.13.0-2) ... 305s Setting up libfontenc1:amd64 (1:1.1.8-1build1) ... 305s Setting up libblas3:amd64 (3.12.0-3build2) ... 305s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode 305s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 305s Setting up libimagequant0:amd64 (2.18.0-1build1) ... 305s Setting up fonts-dejavu-mono (2.37-8) ... 305s Setting up fonts-dejavu-core (2.37-8) ... 305s Setting up libjpeg-turbo8:amd64 (2.1.5-2ubuntu2) ... 305s Setting up libgfortran5:amd64 (14.2.0-8ubuntu1) ... 305s Setting up libwebp7:amd64 (1.4.0-0.1) ... 305s Setting up libopenjp2-7:amd64 (2.5.0-2ubuntu1) ... 305s Setting up python3.13-minimal (3.13.0-2) ... 306s Setting up libharfbuzz0b:amd64 (10.0.1-1) ... 306s Setting up sgml-base (1.31) ... 306s Setting up libwebpmux3:amd64 (1.4.0-0.1) ... 306s Setting up libpython3.13-stdlib:amd64 (3.13.0-2) ... 306s Setting up libjpeg8:amd64 (8c-2ubuntu11) ... 306s Setting up liblapack3:amd64 (3.12.0-3build2) ... 306s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode 306s Setting up python3.13 (3.13.0-2) ... 307s Setting up fontconfig-config (2.15.0-1.1ubuntu2) ... 307s Setting up libwebpdemux2:amd64 (1.4.0-0.1) ... 307s Setting up python3-all (3.12.7-1) ... 307s Setting up xfonts-utils (1:7.7+7) ... 307s Setting up libraqm0:amd64 (0.10.1-1build1) ... 307s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 311s Setting up libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ... 311s Setting up xml-core (0.19) ... 311s Setting up libfontconfig1:amd64 (2.15.0-1.1ubuntu2) ... 311s Setting up fonts-urw-base35 (20200910-8) ... 311s Setting up libcairo2:amd64 (1.18.2-2) ... 311s Setting up python3-pil:amd64 (10.4.0-1ubuntu1) ... 312s Setting up python3-cairo (1.26.1-2) ... 312s Setting up python3-rlpycairo (0.3.0-3) ... 313s Setting up python3-reportlab (4.2.5-1) ... 314s Processing triggers for libc-bin (2.40-1ubuntu3) ... 314s Processing triggers for systemd (256.5-2ubuntu4) ... 314s Processing triggers for man-db (2.12.1-3) ... 315s Processing triggers for sgml-base (1.31) ... 315s Setting up w3c-sgml-lib (1.3-3) ... 348s Setting up python3-biopython (1.84+dfsg-4) ... 350s Setting up python3-bcbio-gff (0.7.1-2) ... 351s Setting up autopkgtest-satdep (0) ... 354s (Reading database ... 79553 files and directories currently installed.) 354s Removing autopkgtest-satdep (0) ... 355s autopkgtest [11:36:01]: 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 355s autopkgtest [11:36:01]: test autodep8-python3: [----------------------- 355s Testing with python3.13: 355s Traceback (most recent call last): 355s File "", line 1, in 355s import BCBio.GFF; print(BCBio.GFF) 355s ^^^^^^^^^^^^^^^^ 355s File "/usr/lib/python3/dist-packages/BCBio/GFF/__init__.py", line 3, in 355s from BCBio.GFF.GFFParser import GFFParser, DiscoGFFParser, GFFExaminer, parse, parse_simple 355s File "/usr/lib/python3/dist-packages/BCBio/GFF/GFFParser.py", line 44, in 355s from Bio import SeqIO 355s File "/usr/lib/python3/dist-packages/Bio/SeqIO/__init__.py", line 401, in 355s from Bio.SeqIO import TwoBitIO 355s File "/usr/lib/python3/dist-packages/Bio/SeqIO/TwoBitIO.py", line 80, in 355s raise MissingPythonDependencyError( 355s ...<2 lines>... 355s ) from None 355s Bio.MissingPythonDependencyError: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 355s autopkgtest [11:36:01]: test autodep8-python3: -----------------------] 356s autopkgtest [11:36:02]: test autodep8-python3: - - - - - - - - - - results - - - - - - - - - - 356s autodep8-python3 FAIL non-zero exit status 1 356s autopkgtest [11:36:02]: @@@@@@@@@@@@@@@@@@@@ summary 356s run-unit-test FAIL non-zero exit status 1 356s autodep8-python3 FAIL non-zero exit status 1 367s nova [W] Skipping flock for amd64 367s Creating nova instance adt-plucky-amd64-python-bcbio-gff-20241113-113005-juju-7f2275-prod-proposed-migration-environment-15-cfa4fb35-dc67-47a1-9fae-3f2454c7b3b7 from image adt/ubuntu-plucky-amd64-server-20241113.img (UUID 76b850f9-98f4-4b79-af06-fa11000b95b2)... 367s nova [W] Skipping flock for amd64 367s Creating nova instance adt-plucky-amd64-python-bcbio-gff-20241113-113005-juju-7f2275-prod-proposed-migration-environment-15-cfa4fb35-dc67-47a1-9fae-3f2454c7b3b7 from image adt/ubuntu-plucky-amd64-server-20241113.img (UUID 76b850f9-98f4-4b79-af06-fa11000b95b2)...