0s autopkgtest [05:51:24]: starting date and time: 2024-11-14 05:51:24+0000 0s autopkgtest [05:51:24]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [05:51:24]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.4ojf4h8s/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 seqmagick --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 54s autopkgtest [05:52:18]: testbed dpkg architecture: armhf 56s autopkgtest [05:52:20]: testbed apt version: 2.9.8 56s autopkgtest [05:52:20]: @@@@@@@@@@@@@@@@@@@@ test bed setup 64s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 64s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.4 kB] 64s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [98.6 kB] 64s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 64s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [987 kB] 64s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf Packages [103 kB] 64s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf Packages [684 kB] 64s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf Packages [5040 B] 65s Fetched 1973 kB in 1s (2027 kB/s) 65s Reading package lists... 82s tee: /proc/self/fd/2: Permission denied 104s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 104s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 104s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 104s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 106s Reading package lists... 106s Reading package lists... 107s Building dependency tree... 107s Reading state information... 108s Calculating upgrade... 109s The following NEW packages will be installed: 109s python3.13-gdbm 109s The following packages will be upgraded: 109s libpython3-stdlib python3 python3-gdbm python3-minimal 109s 4 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 109s Need to get 99.6 kB of archives. 109s After this operation, 91.1 kB of additional disk space will be used. 109s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf python3-minimal armhf 3.12.7-1 [27.4 kB] 109s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf python3 armhf 3.12.7-1 [24.0 kB] 109s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libpython3-stdlib armhf 3.12.7-1 [10.0 kB] 109s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf python3.13-gdbm armhf 3.13.0-2 [29.5 kB] 109s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf python3-gdbm armhf 3.12.7-1 [8642 B] 110s Fetched 99.6 kB in 0s (285 kB/s) 110s (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 ... 59560 files and directories currently installed.) 110s Preparing to unpack .../python3-minimal_3.12.7-1_armhf.deb ... 110s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ... 110s Setting up python3-minimal (3.12.7-1) ... 110s (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 ... 59560 files and directories currently installed.) 110s Preparing to unpack .../python3_3.12.7-1_armhf.deb ... 110s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ... 110s Preparing to unpack .../libpython3-stdlib_3.12.7-1_armhf.deb ... 110s Unpacking libpython3-stdlib:armhf (3.12.7-1) over (3.12.6-0ubuntu1) ... 110s Selecting previously unselected package python3.13-gdbm. 110s Preparing to unpack .../python3.13-gdbm_3.13.0-2_armhf.deb ... 110s Unpacking python3.13-gdbm (3.13.0-2) ... 110s Preparing to unpack .../python3-gdbm_3.12.7-1_armhf.deb ... 110s Unpacking python3-gdbm:armhf (3.12.7-1) over (3.12.6-1ubuntu1) ... 110s Setting up python3.13-gdbm (3.13.0-2) ... 110s Setting up libpython3-stdlib:armhf (3.12.7-1) ... 110s Setting up python3 (3.12.7-1) ... 111s Setting up python3-gdbm:armhf (3.12.7-1) ... 111s Processing triggers for man-db (2.12.1-3) ... 112s Reading package lists... 112s Building dependency tree... 112s Reading state information... 113s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 115s autopkgtest [05:53:19]: rebooting testbed after setup commands that affected boot 182s autopkgtest [05:54:26]: 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 [05:54:54]: @@@@@@@@@@@@@@@@@@@@ apt-source seqmagick 221s Get:1 http://ftpmaster.internal/ubuntu plucky/universe seqmagick 0.8.6-3 (dsc) [2262 B] 221s Get:2 http://ftpmaster.internal/ubuntu plucky/universe seqmagick 0.8.6-3 (tar) [665 kB] 221s Get:3 http://ftpmaster.internal/ubuntu plucky/universe seqmagick 0.8.6-3 (diff) [6012 B] 221s gpgv: Signature made Tue Aug 6 20:16:33 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 ./seqmagick_0.8.6-3.dsc: no acceptable signature found 221s autopkgtest [05:55:05]: testing package seqmagick version 0.8.6-3 223s autopkgtest [05:55:07]: build not needed 226s autopkgtest [05:55:10]: test run-unit-test: preparing testbed 236s Reading package lists... 237s Building dependency tree... 237s Reading state information... 238s Starting pkgProblemResolver with broken count: 0 238s Starting 2 pkgProblemResolver with broken count: 0 238s Done 239s The following additional packages will be installed: 239s fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-urw-base35 239s libblas3 libcairo2 libdeflate0 libfontconfig1 libfontenc1 libfreetype6 239s libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libimagequant0 libjbig0 239s libjpeg-turbo8 libjpeg8 liblapack3 liblcms2-2 liblerc4 libopenjp2-7 239s libpixman-1-0 libraqm0 libsharpyuv0 libtiff6 libwebp7 libwebpdemux2 239s libwebpmux3 libxcb-render0 libxcb-shm0 libxrender1 python3-biopython 239s python3-cairo python3-freetype python3-numpy python3-pil python3-pygtrie 239s python3-reportlab python3-rlpycairo seqmagick sgml-base w3c-sgml-lib 239s x11-common xfonts-encodings xfonts-utils xml-core 239s Suggested packages: 239s fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre liblcms2-utils 239s python3-tk bwa clustalo clustalw dialign dssp emboss fasttree mafft muscle3 239s phylip phyml prank probcons python3-mysqldb python3-matplotlib python3-mmtf 239s python3-rdflib python3-psycopg2 python3-scipy raxml samtools t-coffee wise 239s gcc gfortran python-numpy-doc python3-dev python3-pytest python-pil-doc 239s python-pygtrie-doc pdf-viewer python3-egenix-mxtexttools 239s python-reportlab-doc rl-accel rl-renderpm sgml-base-doc debhelper 239s Recommended packages: 239s python-biopython-doc ncbi-blast+ python3-olefile fonts-dejavu-extra 239s The following NEW packages will be installed: 239s autopkgtest-satdep fontconfig-config fonts-dejavu-core fonts-dejavu-mono 239s fonts-urw-base35 libblas3 libcairo2 libdeflate0 libfontconfig1 libfontenc1 239s libfreetype6 libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b 239s libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 liblapack3 liblcms2-2 239s liblerc4 libopenjp2-7 libpixman-1-0 libraqm0 libsharpyuv0 libtiff6 libwebp7 239s libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 libxrender1 239s python3-biopython python3-cairo python3-freetype python3-numpy python3-pil 239s python3-pygtrie python3-reportlab python3-rlpycairo seqmagick sgml-base 239s w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core 239s 0 upgraded, 48 newly installed, 0 to remove and 0 not upgraded. 239s Need to get 25.8 MB/25.8 MB of archives. 239s After this operation, 71.9 MB of additional disk space will be used. 239s Get:1 /tmp/autopkgtest.F5vqCK/1-autopkgtest-satdep.deb autopkgtest-satdep armhf 0 [704 B] 239s Get:2 http://ftpmaster.internal/ubuntu plucky/main armhf sgml-base all 1.31 [11.4 kB] 239s Get:3 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-dejavu-mono all 2.37-8 [502 kB] 239s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-dejavu-core all 2.37-8 [835 kB] 239s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf libfontenc1 armhf 1:1.1.8-1build1 [11.5 kB] 239s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf libfreetype6 armhf 2.13.3+dfsg-1 [330 kB] 239s Get:7 http://ftpmaster.internal/ubuntu plucky/main armhf x11-common all 1:7.7+23ubuntu3 [21.7 kB] 239s Get:8 http://ftpmaster.internal/ubuntu plucky/main armhf xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 239s Get:9 http://ftpmaster.internal/ubuntu plucky/main armhf xfonts-utils armhf 1:7.7+7 [90.6 kB] 239s Get:10 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-urw-base35 all 20200910-8 [11.0 MB] 240s Get:11 http://ftpmaster.internal/ubuntu plucky/main armhf fontconfig-config armhf 2.15.0-1.1ubuntu2 [37.4 kB] 240s Get:12 http://ftpmaster.internal/ubuntu plucky/main armhf libblas3 armhf 3.12.0-3build2 [126 kB] 240s Get:13 http://ftpmaster.internal/ubuntu plucky/main armhf libfontconfig1 armhf 2.15.0-1.1ubuntu2 [113 kB] 240s Get:14 http://ftpmaster.internal/ubuntu plucky/main armhf libpixman-1-0 armhf 0.44.0-3 [183 kB] 240s Get:15 http://ftpmaster.internal/ubuntu plucky/main armhf libxcb-render0 armhf 1.17.0-2 [15.3 kB] 240s Get:16 http://ftpmaster.internal/ubuntu plucky/main armhf libxcb-shm0 armhf 1.17.0-2 [5774 B] 240s Get:17 http://ftpmaster.internal/ubuntu plucky/main armhf libxrender1 armhf 1:0.9.10-1.1build1 [16.0 kB] 240s Get:18 http://ftpmaster.internal/ubuntu plucky/main armhf libcairo2 armhf 1.18.2-2 [484 kB] 240s Get:19 http://ftpmaster.internal/ubuntu plucky/main armhf libdeflate0 armhf 1.22-1 [38.9 kB] 240s Get:20 http://ftpmaster.internal/ubuntu plucky/main armhf libgfortran5 armhf 14.2.0-8ubuntu1 [311 kB] 240s Get:21 http://ftpmaster.internal/ubuntu plucky/main armhf libgomp1 armhf 14.2.0-8ubuntu1 [125 kB] 240s Get:22 http://ftpmaster.internal/ubuntu plucky/main armhf libgraphite2-3 armhf 1.3.14-2ubuntu1 [64.8 kB] 240s Get:23 http://ftpmaster.internal/ubuntu plucky/main armhf libharfbuzz0b armhf 10.0.1-1 [463 kB] 240s Get:24 http://ftpmaster.internal/ubuntu plucky/main armhf libimagequant0 armhf 2.18.0-1build1 [31.1 kB] 240s Get:25 http://ftpmaster.internal/ubuntu plucky/main armhf libjpeg-turbo8 armhf 2.1.5-2ubuntu2 [125 kB] 240s Get:26 http://ftpmaster.internal/ubuntu plucky/main armhf libjpeg8 armhf 8c-2ubuntu11 [2148 B] 240s Get:27 http://ftpmaster.internal/ubuntu plucky/main armhf liblapack3 armhf 3.12.0-3build2 [2086 kB] 240s Get:28 http://ftpmaster.internal/ubuntu plucky/main armhf liblcms2-2 armhf 2.16-2 [137 kB] 240s Get:29 http://ftpmaster.internal/ubuntu plucky/main armhf liblerc4 armhf 4.0.0+ds-4ubuntu2 [151 kB] 240s Get:30 http://ftpmaster.internal/ubuntu plucky/main armhf libraqm0 armhf 0.10.1-1build1 [12.4 kB] 240s Get:31 http://ftpmaster.internal/ubuntu plucky/main armhf libsharpyuv0 armhf 1.4.0-0.1 [16.3 kB] 240s Get:32 http://ftpmaster.internal/ubuntu plucky/main armhf libjbig0 armhf 2.1-6.1ubuntu2 [24.9 kB] 240s Get:33 http://ftpmaster.internal/ubuntu plucky/main armhf libwebp7 armhf 1.4.0-0.1 [184 kB] 240s Get:34 http://ftpmaster.internal/ubuntu plucky/main armhf libtiff6 armhf 4.5.1+git230720-4ubuntu4 [179 kB] 240s Get:35 http://ftpmaster.internal/ubuntu plucky/main armhf libwebpdemux2 armhf 1.4.0-0.1 [11.8 kB] 240s Get:36 http://ftpmaster.internal/ubuntu plucky/main armhf libwebpmux3 armhf 1.4.0-0.1 [22.5 kB] 240s Get:37 http://ftpmaster.internal/ubuntu plucky/main armhf python3-numpy armhf 1:1.26.4+ds-11build1 [3570 kB] 240s Get:38 http://ftpmaster.internal/ubuntu plucky/main armhf libopenjp2-7 armhf 2.5.0-2ubuntu1 [170 kB] 240s Get:39 http://ftpmaster.internal/ubuntu plucky/main armhf python3-pil armhf 10.4.0-1ubuntu1 [428 kB] 240s Get:40 http://ftpmaster.internal/ubuntu plucky/main armhf python3-cairo armhf 1.26.1-2 [114 kB] 240s Get:41 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-freetype all 2.5.1-1 [92.3 kB] 240s Get:42 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-rlpycairo all 0.3.0-3 [9130 B] 240s Get:43 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-reportlab all 4.2.5-1 [1107 kB] 240s Get:44 http://ftpmaster.internal/ubuntu plucky/main armhf xml-core all 0.19 [20.3 kB] 240s Get:45 http://ftpmaster.internal/ubuntu plucky/universe armhf w3c-sgml-lib all 1.3-3 [280 kB] 240s Get:46 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-biopython armhf 1.84+dfsg-4 [1666 kB] 240s Get:47 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pygtrie all 2.2-2 [16.0 kB] 240s Get:48 http://ftpmaster.internal/ubuntu plucky/universe armhf seqmagick all 0.8.6-3 [38.6 kB] 241s Fetched 25.8 MB in 2s (15.7 MB/s) 241s Selecting previously unselected package sgml-base. 241s (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.) 241s Preparing to unpack .../00-sgml-base_1.31_all.deb ... 241s Unpacking sgml-base (1.31) ... 241s Selecting previously unselected package fonts-dejavu-mono. 241s Preparing to unpack .../01-fonts-dejavu-mono_2.37-8_all.deb ... 241s Unpacking fonts-dejavu-mono (2.37-8) ... 241s Selecting previously unselected package fonts-dejavu-core. 241s Preparing to unpack .../02-fonts-dejavu-core_2.37-8_all.deb ... 241s Unpacking fonts-dejavu-core (2.37-8) ... 241s Selecting previously unselected package libfontenc1:armhf. 241s Preparing to unpack .../03-libfontenc1_1%3a1.1.8-1build1_armhf.deb ... 241s Unpacking libfontenc1:armhf (1:1.1.8-1build1) ... 241s Selecting previously unselected package libfreetype6:armhf. 241s Preparing to unpack .../04-libfreetype6_2.13.3+dfsg-1_armhf.deb ... 241s Unpacking libfreetype6:armhf (2.13.3+dfsg-1) ... 241s Selecting previously unselected package x11-common. 241s Preparing to unpack .../05-x11-common_1%3a7.7+23ubuntu3_all.deb ... 241s Unpacking x11-common (1:7.7+23ubuntu3) ... 241s Selecting previously unselected package xfonts-encodings. 241s Preparing to unpack .../06-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 241s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 241s Selecting previously unselected package xfonts-utils. 241s Preparing to unpack .../07-xfonts-utils_1%3a7.7+7_armhf.deb ... 241s Unpacking xfonts-utils (1:7.7+7) ... 241s Selecting previously unselected package fonts-urw-base35. 241s Preparing to unpack .../08-fonts-urw-base35_20200910-8_all.deb ... 242s Unpacking fonts-urw-base35 (20200910-8) ... 243s Selecting previously unselected package fontconfig-config. 243s Preparing to unpack .../09-fontconfig-config_2.15.0-1.1ubuntu2_armhf.deb ... 243s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ... 243s Selecting previously unselected package libblas3:armhf. 243s Preparing to unpack .../10-libblas3_3.12.0-3build2_armhf.deb ... 243s Unpacking libblas3:armhf (3.12.0-3build2) ... 243s Selecting previously unselected package libfontconfig1:armhf. 243s Preparing to unpack .../11-libfontconfig1_2.15.0-1.1ubuntu2_armhf.deb ... 243s Unpacking libfontconfig1:armhf (2.15.0-1.1ubuntu2) ... 243s Selecting previously unselected package libpixman-1-0:armhf. 243s Preparing to unpack .../12-libpixman-1-0_0.44.0-3_armhf.deb ... 243s Unpacking libpixman-1-0:armhf (0.44.0-3) ... 243s Selecting previously unselected package libxcb-render0:armhf. 243s Preparing to unpack .../13-libxcb-render0_1.17.0-2_armhf.deb ... 243s Unpacking libxcb-render0:armhf (1.17.0-2) ... 243s Selecting previously unselected package libxcb-shm0:armhf. 243s Preparing to unpack .../14-libxcb-shm0_1.17.0-2_armhf.deb ... 243s Unpacking libxcb-shm0:armhf (1.17.0-2) ... 243s Selecting previously unselected package libxrender1:armhf. 243s Preparing to unpack .../15-libxrender1_1%3a0.9.10-1.1build1_armhf.deb ... 243s Unpacking libxrender1:armhf (1:0.9.10-1.1build1) ... 243s Selecting previously unselected package libcairo2:armhf. 243s Preparing to unpack .../16-libcairo2_1.18.2-2_armhf.deb ... 243s Unpacking libcairo2:armhf (1.18.2-2) ... 243s Selecting previously unselected package libdeflate0:armhf. 243s Preparing to unpack .../17-libdeflate0_1.22-1_armhf.deb ... 243s Unpacking libdeflate0:armhf (1.22-1) ... 243s Selecting previously unselected package libgfortran5:armhf. 243s Preparing to unpack .../18-libgfortran5_14.2.0-8ubuntu1_armhf.deb ... 243s Unpacking libgfortran5:armhf (14.2.0-8ubuntu1) ... 243s Selecting previously unselected package libgomp1:armhf. 243s Preparing to unpack .../19-libgomp1_14.2.0-8ubuntu1_armhf.deb ... 243s Unpacking libgomp1:armhf (14.2.0-8ubuntu1) ... 243s Selecting previously unselected package libgraphite2-3:armhf. 243s Preparing to unpack .../20-libgraphite2-3_1.3.14-2ubuntu1_armhf.deb ... 243s Unpacking libgraphite2-3:armhf (1.3.14-2ubuntu1) ... 243s Selecting previously unselected package libharfbuzz0b:armhf. 243s Preparing to unpack .../21-libharfbuzz0b_10.0.1-1_armhf.deb ... 243s Unpacking libharfbuzz0b:armhf (10.0.1-1) ... 243s Selecting previously unselected package libimagequant0:armhf. 243s Preparing to unpack .../22-libimagequant0_2.18.0-1build1_armhf.deb ... 243s Unpacking libimagequant0:armhf (2.18.0-1build1) ... 243s Selecting previously unselected package libjpeg-turbo8:armhf. 243s Preparing to unpack .../23-libjpeg-turbo8_2.1.5-2ubuntu2_armhf.deb ... 243s Unpacking libjpeg-turbo8:armhf (2.1.5-2ubuntu2) ... 243s Selecting previously unselected package libjpeg8:armhf. 243s Preparing to unpack .../24-libjpeg8_8c-2ubuntu11_armhf.deb ... 243s Unpacking libjpeg8:armhf (8c-2ubuntu11) ... 243s Selecting previously unselected package liblapack3:armhf. 243s Preparing to unpack .../25-liblapack3_3.12.0-3build2_armhf.deb ... 243s Unpacking liblapack3:armhf (3.12.0-3build2) ... 243s Selecting previously unselected package liblcms2-2:armhf. 243s Preparing to unpack .../26-liblcms2-2_2.16-2_armhf.deb ... 243s Unpacking liblcms2-2:armhf (2.16-2) ... 243s Selecting previously unselected package liblerc4:armhf. 243s Preparing to unpack .../27-liblerc4_4.0.0+ds-4ubuntu2_armhf.deb ... 243s Unpacking liblerc4:armhf (4.0.0+ds-4ubuntu2) ... 243s Selecting previously unselected package libraqm0:armhf. 243s Preparing to unpack .../28-libraqm0_0.10.1-1build1_armhf.deb ... 243s Unpacking libraqm0:armhf (0.10.1-1build1) ... 243s Selecting previously unselected package libsharpyuv0:armhf. 243s Preparing to unpack .../29-libsharpyuv0_1.4.0-0.1_armhf.deb ... 243s Unpacking libsharpyuv0:armhf (1.4.0-0.1) ... 243s Selecting previously unselected package libjbig0:armhf. 243s Preparing to unpack .../30-libjbig0_2.1-6.1ubuntu2_armhf.deb ... 243s Unpacking libjbig0:armhf (2.1-6.1ubuntu2) ... 243s Selecting previously unselected package libwebp7:armhf. 243s Preparing to unpack .../31-libwebp7_1.4.0-0.1_armhf.deb ... 243s Unpacking libwebp7:armhf (1.4.0-0.1) ... 243s Selecting previously unselected package libtiff6:armhf. 243s Preparing to unpack .../32-libtiff6_4.5.1+git230720-4ubuntu4_armhf.deb ... 243s Unpacking libtiff6:armhf (4.5.1+git230720-4ubuntu4) ... 243s Selecting previously unselected package libwebpdemux2:armhf. 243s Preparing to unpack .../33-libwebpdemux2_1.4.0-0.1_armhf.deb ... 243s Unpacking libwebpdemux2:armhf (1.4.0-0.1) ... 243s Selecting previously unselected package libwebpmux3:armhf. 243s Preparing to unpack .../34-libwebpmux3_1.4.0-0.1_armhf.deb ... 243s Unpacking libwebpmux3:armhf (1.4.0-0.1) ... 243s Selecting previously unselected package python3-numpy. 243s Preparing to unpack .../35-python3-numpy_1%3a1.26.4+ds-11build1_armhf.deb ... 243s Unpacking python3-numpy (1:1.26.4+ds-11build1) ... 243s Selecting previously unselected package libopenjp2-7:armhf. 243s Preparing to unpack .../36-libopenjp2-7_2.5.0-2ubuntu1_armhf.deb ... 243s Unpacking libopenjp2-7:armhf (2.5.0-2ubuntu1) ... 243s Selecting previously unselected package python3-pil:armhf. 243s Preparing to unpack .../37-python3-pil_10.4.0-1ubuntu1_armhf.deb ... 243s Unpacking python3-pil:armhf (10.4.0-1ubuntu1) ... 243s Selecting previously unselected package python3-cairo. 243s Preparing to unpack .../38-python3-cairo_1.26.1-2_armhf.deb ... 243s Unpacking python3-cairo (1.26.1-2) ... 243s Selecting previously unselected package python3-freetype. 244s Preparing to unpack .../39-python3-freetype_2.5.1-1_all.deb ... 244s Unpacking python3-freetype (2.5.1-1) ... 244s Selecting previously unselected package python3-rlpycairo. 244s Preparing to unpack .../40-python3-rlpycairo_0.3.0-3_all.deb ... 244s Unpacking python3-rlpycairo (0.3.0-3) ... 244s Selecting previously unselected package python3-reportlab. 244s Preparing to unpack .../41-python3-reportlab_4.2.5-1_all.deb ... 244s Unpacking python3-reportlab (4.2.5-1) ... 244s Selecting previously unselected package xml-core. 244s Preparing to unpack .../42-xml-core_0.19_all.deb ... 244s Unpacking xml-core (0.19) ... 244s Selecting previously unselected package w3c-sgml-lib. 244s Preparing to unpack .../43-w3c-sgml-lib_1.3-3_all.deb ... 244s Unpacking w3c-sgml-lib (1.3-3) ... 244s Selecting previously unselected package python3-biopython. 244s Preparing to unpack .../44-python3-biopython_1.84+dfsg-4_armhf.deb ... 244s Unpacking python3-biopython (1.84+dfsg-4) ... 244s Selecting previously unselected package python3-pygtrie. 244s Preparing to unpack .../45-python3-pygtrie_2.2-2_all.deb ... 244s Unpacking python3-pygtrie (2.2-2) ... 244s Selecting previously unselected package seqmagick. 244s Preparing to unpack .../46-seqmagick_0.8.6-3_all.deb ... 244s Unpacking seqmagick (0.8.6-3) ... 244s Selecting previously unselected package autopkgtest-satdep. 244s Preparing to unpack .../47-1-autopkgtest-satdep.deb ... 244s Unpacking autopkgtest-satdep (0) ... 244s Setting up libgraphite2-3:armhf (1.3.14-2ubuntu1) ... 244s Setting up liblcms2-2:armhf (2.16-2) ... 244s Setting up libpixman-1-0:armhf (0.44.0-3) ... 244s Setting up libsharpyuv0:armhf (1.4.0-0.1) ... 244s Setting up liblerc4:armhf (4.0.0+ds-4ubuntu2) ... 244s Setting up libxrender1:armhf (1:0.9.10-1.1build1) ... 244s Setting up libxcb-render0:armhf (1.17.0-2) ... 244s Setting up x11-common (1:7.7+23ubuntu3) ... 245s Setting up libdeflate0:armhf (1.22-1) ... 245s Setting up libxcb-shm0:armhf (1.17.0-2) ... 245s Setting up libgomp1:armhf (14.2.0-8ubuntu1) ... 245s Setting up libjbig0:armhf (2.1-6.1ubuntu2) ... 245s Setting up libfontenc1:armhf (1:1.1.8-1build1) ... 245s Setting up python3-pygtrie (2.2-2) ... 245s Setting up libblas3:armhf (3.12.0-3build2) ... 245s 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 245s Setting up libfreetype6:armhf (2.13.3+dfsg-1) ... 245s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 245s Setting up libimagequant0:armhf (2.18.0-1build1) ... 245s Setting up fonts-dejavu-mono (2.37-8) ... 245s Setting up fonts-dejavu-core (2.37-8) ... 245s Setting up libjpeg-turbo8:armhf (2.1.5-2ubuntu2) ... 245s Setting up libgfortran5:armhf (14.2.0-8ubuntu1) ... 245s Setting up libwebp7:armhf (1.4.0-0.1) ... 245s Setting up libopenjp2-7:armhf (2.5.0-2ubuntu1) ... 245s Setting up libharfbuzz0b:armhf (10.0.1-1) ... 245s Setting up sgml-base (1.31) ... 245s Setting up libwebpmux3:armhf (1.4.0-0.1) ... 245s Setting up libjpeg8:armhf (8c-2ubuntu11) ... 245s Setting up liblapack3:armhf (3.12.0-3build2) ... 245s 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 245s Setting up fontconfig-config (2.15.0-1.1ubuntu2) ... 245s Setting up libwebpdemux2:armhf (1.4.0-0.1) ... 245s Setting up python3-freetype (2.5.1-1) ... 245s Setting up xfonts-utils (1:7.7+7) ... 245s Setting up libraqm0:armhf (0.10.1-1build1) ... 245s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 248s Setting up libtiff6:armhf (4.5.1+git230720-4ubuntu4) ... 248s Setting up xml-core (0.19) ... 248s Setting up libfontconfig1:armhf (2.15.0-1.1ubuntu2) ... 248s Setting up fonts-urw-base35 (20200910-8) ... 248s Setting up libcairo2:armhf (1.18.2-2) ... 248s Setting up python3-pil:armhf (10.4.0-1ubuntu1) ... 249s Setting up python3-cairo (1.26.1-2) ... 249s Setting up python3-rlpycairo (0.3.0-3) ... 249s Setting up python3-reportlab (4.2.5-1) ... 250s Processing triggers for libc-bin (2.40-1ubuntu3) ... 250s Processing triggers for man-db (2.12.1-3) ... 251s Processing triggers for sgml-base (1.31) ... 251s Setting up w3c-sgml-lib (1.3-3) ... 283s Setting up python3-biopython (1.84+dfsg-4) ... 285s Setting up seqmagick (0.8.6-3) ... 285s Setting up autopkgtest-satdep (0) ... 302s (Reading database ... 62879 files and directories currently installed.) 302s Removing autopkgtest-satdep (0) ... 308s autopkgtest [05:56:32]: test run-unit-test: [----------------------- 310s ++ find examples/ -name '*.sh' 310s + for f in `find examples/ -name '*.sh'` 310s ++ dirname examples/apply-function/run_filter.sh 310s + cd examples/apply-function 310s ++ basename examples/apply-function/run_filter.sh 310s + /bin/bash run_filter.sh 311s + cd - 311s + for f in `find examples/ -name '*.sh'` 311s /tmp/autopkgtest.F5vqCK/autopkgtest_tmp 311s ++ dirname examples/include-from-file/do_filter.sh 311s + cd examples/include-from-file 311s ++ basename examples/include-from-file/do_filter.sh 311s + /bin/bash do_filter.sh 312s /tmp/autopkgtest.F5vqCK/autopkgtest_tmp 312s PASS 312s + cd - 312s + echo PASS 312s autopkgtest [05:56:36]: test run-unit-test: -----------------------] 316s autopkgtest [05:56:40]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 316s run-unit-test PASS 321s autopkgtest [05:56:45]: test pybuild-autopkgtest: preparing testbed 331s Reading package lists... 331s Building dependency tree... 331s Reading state information... 332s Starting pkgProblemResolver with broken count: 0 332s Starting 2 pkgProblemResolver with broken count: 0 332s Done 333s The following additional packages will be installed: 333s autoconf automake autopoint autotools-dev build-essential cpp cpp-14 333s cpp-14-arm-linux-gnueabihf cpp-arm-linux-gnueabihf debhelper debugedit 333s dh-autoreconf dh-python dh-strip-nondeterminism dwz g++ g++-14 333s g++-14-arm-linux-gnueabihf g++-arm-linux-gnueabihf gcc gcc-14 333s gcc-14-arm-linux-gnueabihf gcc-arm-linux-gnueabihf gettext intltool-debian 333s libarchive-zip-perl libasan8 libc-dev-bin libc6-dev libcc1-0 libcrypt-dev 333s libdebhelper-perl libfile-stripnondeterminism-perl libgcc-14-dev libisl23 333s libmpc3 libpython3.13-minimal libpython3.13-stdlib libstdc++-14-dev libtool 333s libubsan1 linux-libc-dev m4 po-debconf pybuild-plugin-autopkgtest 333s python3-all python3-iniconfig python3-packaging python3-pluggy 333s python3-pytest python3.13 python3.13-minimal rpcsvc-proto 333s Suggested packages: 333s autoconf-archive gnu-standards autoconf-doc cpp-doc gcc-14-locales 333s cpp-14-doc dh-make flit python3-build python3-installer python3-wheel 333s gcc-14-doc gcc-multilib manpages-dev flex bison gdb gcc-doc 333s gdb-arm-linux-gnueabihf gettext-doc libasprintf-dev libgettextpo-dev 333s libc-devtools glibc-doc libstdc++-14-doc libtool-doc gfortran 333s | fortran95-compiler gcj-jdk m4-doc libmail-box-perl python3.13-venv 333s python3.13-doc binfmt-support 333s Recommended packages: 333s manpages manpages-dev libarchive-cpio-perl libltdl-dev libmail-sendmail-perl 333s The following NEW packages will be installed: 333s autoconf automake autopkgtest-satdep autopoint autotools-dev build-essential 333s cpp cpp-14 cpp-14-arm-linux-gnueabihf cpp-arm-linux-gnueabihf debhelper 333s debugedit dh-autoreconf dh-python dh-strip-nondeterminism dwz g++ g++-14 333s g++-14-arm-linux-gnueabihf g++-arm-linux-gnueabihf gcc gcc-14 333s gcc-14-arm-linux-gnueabihf gcc-arm-linux-gnueabihf gettext intltool-debian 333s libarchive-zip-perl libasan8 libc-dev-bin libc6-dev libcc1-0 libcrypt-dev 333s libdebhelper-perl libfile-stripnondeterminism-perl libgcc-14-dev libisl23 333s libmpc3 libpython3.13-minimal libpython3.13-stdlib libstdc++-14-dev libtool 333s libubsan1 linux-libc-dev m4 po-debconf pybuild-plugin-autopkgtest 333s python3-all python3-iniconfig python3-packaging python3-pluggy 333s python3-pytest python3.13 python3.13-minimal rpcsvc-proto 334s 0 upgraded, 54 newly installed, 0 to remove and 0 not upgraded. 334s Need to get 60.0 MB/60.0 MB of archives. 334s After this operation, 178 MB of additional disk space will be used. 334s Get:1 /tmp/autopkgtest.F5vqCK/2-autopkgtest-satdep.deb autopkgtest-satdep armhf 0 [796 B] 334s Get:2 http://ftpmaster.internal/ubuntu plucky/main armhf libpython3.13-minimal armhf 3.13.0-2 [866 kB] 334s Get:3 http://ftpmaster.internal/ubuntu plucky/main armhf python3.13-minimal armhf 3.13.0-2 [1854 kB] 334s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf m4 armhf 1.4.19-4build1 [235 kB] 334s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf autoconf all 2.72-3 [382 kB] 334s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf autotools-dev all 20220109.1 [44.9 kB] 334s Get:7 http://ftpmaster.internal/ubuntu plucky/main armhf automake all 1:1.16.5-1.3ubuntu1 [558 kB] 334s Get:8 http://ftpmaster.internal/ubuntu plucky/main armhf autopoint all 0.22.5-2 [616 kB] 334s Get:9 http://ftpmaster.internal/ubuntu plucky/main armhf libc-dev-bin armhf 2.40-1ubuntu3 [19.2 kB] 334s Get:10 http://ftpmaster.internal/ubuntu plucky/main armhf linux-libc-dev armhf 6.11.0-8.8 [1628 kB] 334s Get:11 http://ftpmaster.internal/ubuntu plucky/main armhf libcrypt-dev armhf 1:4.4.36-4build1 [120 kB] 334s Get:12 http://ftpmaster.internal/ubuntu plucky/main armhf rpcsvc-proto armhf 1.4.2-0ubuntu7 [62.2 kB] 334s Get:13 http://ftpmaster.internal/ubuntu plucky/main armhf libc6-dev armhf 2.40-1ubuntu3 [1370 kB] 334s Get:14 http://ftpmaster.internal/ubuntu plucky/main armhf libisl23 armhf 0.27-1 [546 kB] 334s Get:15 http://ftpmaster.internal/ubuntu plucky/main armhf libmpc3 armhf 1.3.1-1build2 [47.1 kB] 334s Get:16 http://ftpmaster.internal/ubuntu plucky/main armhf cpp-14-arm-linux-gnueabihf armhf 14.2.0-8ubuntu1 [9219 kB] 335s Get:17 http://ftpmaster.internal/ubuntu plucky/main armhf cpp-14 armhf 14.2.0-8ubuntu1 [1032 B] 335s Get:18 http://ftpmaster.internal/ubuntu plucky/main armhf cpp-arm-linux-gnueabihf armhf 4:14.1.0-2ubuntu1 [5464 B] 335s Get:19 http://ftpmaster.internal/ubuntu plucky/main armhf cpp armhf 4:14.1.0-2ubuntu1 [22.4 kB] 335s Get:20 http://ftpmaster.internal/ubuntu plucky/main armhf libcc1-0 armhf 14.2.0-8ubuntu1 [43.3 kB] 335s Get:21 http://ftpmaster.internal/ubuntu plucky/main armhf libasan8 armhf 14.2.0-8ubuntu1 [2901 kB] 335s Get:22 http://ftpmaster.internal/ubuntu plucky/main armhf libubsan1 armhf 14.2.0-8ubuntu1 [1150 kB] 335s Get:23 http://ftpmaster.internal/ubuntu plucky/main armhf libgcc-14-dev armhf 14.2.0-8ubuntu1 [897 kB] 335s Get:24 http://ftpmaster.internal/ubuntu plucky/main armhf gcc-14-arm-linux-gnueabihf armhf 14.2.0-8ubuntu1 [18.0 MB] 335s Get:25 http://ftpmaster.internal/ubuntu plucky/main armhf gcc-14 armhf 14.2.0-8ubuntu1 [498 kB] 335s Get:26 http://ftpmaster.internal/ubuntu plucky/main armhf gcc-arm-linux-gnueabihf armhf 4:14.1.0-2ubuntu1 [1222 B] 335s Get:27 http://ftpmaster.internal/ubuntu plucky/main armhf gcc armhf 4:14.1.0-2ubuntu1 [5002 B] 335s Get:28 http://ftpmaster.internal/ubuntu plucky/main armhf libstdc++-14-dev armhf 14.2.0-8ubuntu1 [2569 kB] 335s Get:29 http://ftpmaster.internal/ubuntu plucky/main armhf g++-14-arm-linux-gnueabihf armhf 14.2.0-8ubuntu1 [10.5 MB] 336s Get:30 http://ftpmaster.internal/ubuntu plucky/main armhf g++-14 armhf 14.2.0-8ubuntu1 [19.9 kB] 336s Get:31 http://ftpmaster.internal/ubuntu plucky/main armhf g++-arm-linux-gnueabihf armhf 4:14.1.0-2ubuntu1 [968 B] 336s Get:32 http://ftpmaster.internal/ubuntu plucky/main armhf g++ armhf 4:14.1.0-2ubuntu1 [1084 B] 336s Get:33 http://ftpmaster.internal/ubuntu plucky/main armhf build-essential armhf 12.10ubuntu1 [4928 B] 336s Get:34 http://ftpmaster.internal/ubuntu plucky/main armhf libdebhelper-perl all 13.20ubuntu1 [94.2 kB] 336s Get:35 http://ftpmaster.internal/ubuntu plucky/main armhf libtool all 2.4.7-7build1 [166 kB] 336s Get:36 http://ftpmaster.internal/ubuntu plucky/main armhf dh-autoreconf all 20 [16.1 kB] 336s Get:37 http://ftpmaster.internal/ubuntu plucky/main armhf libarchive-zip-perl all 1.68-1 [90.2 kB] 336s Get:38 http://ftpmaster.internal/ubuntu plucky/main armhf libfile-stripnondeterminism-perl all 1.14.0-1 [20.1 kB] 336s Get:39 http://ftpmaster.internal/ubuntu plucky/main armhf dh-strip-nondeterminism all 1.14.0-1 [5058 B] 336s Get:40 http://ftpmaster.internal/ubuntu plucky/main armhf debugedit armhf 1:5.1-1 [46.5 kB] 336s Get:41 http://ftpmaster.internal/ubuntu plucky/main armhf dwz armhf 0.15-1build6 [116 kB] 336s Get:42 http://ftpmaster.internal/ubuntu plucky/main armhf gettext armhf 0.22.5-2 [995 kB] 336s Get:43 http://ftpmaster.internal/ubuntu plucky/main armhf intltool-debian all 0.35.0+20060710.6 [23.2 kB] 336s Get:44 http://ftpmaster.internal/ubuntu plucky/main armhf po-debconf all 1.0.21+nmu1 [233 kB] 336s Get:45 http://ftpmaster.internal/ubuntu plucky/main armhf debhelper all 13.20ubuntu1 [893 kB] 336s Get:46 http://ftpmaster.internal/ubuntu plucky/universe armhf dh-python all 6.20241024 [112 kB] 336s Get:47 http://ftpmaster.internal/ubuntu plucky/main armhf libpython3.13-stdlib armhf 3.13.0-2 [1972 kB] 336s Get:48 http://ftpmaster.internal/ubuntu plucky/universe armhf pybuild-plugin-autopkgtest all 6.20241024 [1746 B] 336s Get:49 http://ftpmaster.internal/ubuntu plucky/main armhf python3.13 armhf 3.13.0-2 [719 kB] 336s Get:50 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf python3-all armhf 3.12.7-1 [890 B] 336s Get:51 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-iniconfig all 1.1.1-2 [6024 B] 336s Get:52 http://ftpmaster.internal/ubuntu plucky/main armhf python3-packaging all 24.1-1 [41.4 kB] 336s Get:53 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pluggy all 1.5.0-1 [21.0 kB] 336s Get:54 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pytest all 8.3.3-1 [251 kB] 337s Fetched 60.0 MB in 2s (24.4 MB/s) 337s Selecting previously unselected package libpython3.13-minimal:armhf. 337s (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 ... 62879 files and directories currently installed.) 337s Preparing to unpack .../00-libpython3.13-minimal_3.13.0-2_armhf.deb ... 337s Unpacking libpython3.13-minimal:armhf (3.13.0-2) ... 337s Selecting previously unselected package python3.13-minimal. 337s Preparing to unpack .../01-python3.13-minimal_3.13.0-2_armhf.deb ... 337s Unpacking python3.13-minimal (3.13.0-2) ... 337s Selecting previously unselected package m4. 337s Preparing to unpack .../02-m4_1.4.19-4build1_armhf.deb ... 337s Unpacking m4 (1.4.19-4build1) ... 337s Selecting previously unselected package autoconf. 337s Preparing to unpack .../03-autoconf_2.72-3_all.deb ... 337s Unpacking autoconf (2.72-3) ... 337s Selecting previously unselected package autotools-dev. 337s Preparing to unpack .../04-autotools-dev_20220109.1_all.deb ... 337s Unpacking autotools-dev (20220109.1) ... 337s Selecting previously unselected package automake. 337s Preparing to unpack .../05-automake_1%3a1.16.5-1.3ubuntu1_all.deb ... 337s Unpacking automake (1:1.16.5-1.3ubuntu1) ... 337s Selecting previously unselected package autopoint. 337s Preparing to unpack .../06-autopoint_0.22.5-2_all.deb ... 337s Unpacking autopoint (0.22.5-2) ... 337s Selecting previously unselected package libc-dev-bin. 337s Preparing to unpack .../07-libc-dev-bin_2.40-1ubuntu3_armhf.deb ... 337s Unpacking libc-dev-bin (2.40-1ubuntu3) ... 337s Selecting previously unselected package linux-libc-dev:armhf. 337s Preparing to unpack .../08-linux-libc-dev_6.11.0-8.8_armhf.deb ... 337s Unpacking linux-libc-dev:armhf (6.11.0-8.8) ... 337s Selecting previously unselected package libcrypt-dev:armhf. 337s Preparing to unpack .../09-libcrypt-dev_1%3a4.4.36-4build1_armhf.deb ... 337s Unpacking libcrypt-dev:armhf (1:4.4.36-4build1) ... 337s Selecting previously unselected package rpcsvc-proto. 337s Preparing to unpack .../10-rpcsvc-proto_1.4.2-0ubuntu7_armhf.deb ... 337s Unpacking rpcsvc-proto (1.4.2-0ubuntu7) ... 337s Selecting previously unselected package libc6-dev:armhf. 337s Preparing to unpack .../11-libc6-dev_2.40-1ubuntu3_armhf.deb ... 337s Unpacking libc6-dev:armhf (2.40-1ubuntu3) ... 338s Selecting previously unselected package libisl23:armhf. 338s Preparing to unpack .../12-libisl23_0.27-1_armhf.deb ... 338s Unpacking libisl23:armhf (0.27-1) ... 338s Selecting previously unselected package libmpc3:armhf. 338s Preparing to unpack .../13-libmpc3_1.3.1-1build2_armhf.deb ... 338s Unpacking libmpc3:armhf (1.3.1-1build2) ... 338s Selecting previously unselected package cpp-14-arm-linux-gnueabihf. 338s Preparing to unpack .../14-cpp-14-arm-linux-gnueabihf_14.2.0-8ubuntu1_armhf.deb ... 338s Unpacking cpp-14-arm-linux-gnueabihf (14.2.0-8ubuntu1) ... 338s Selecting previously unselected package cpp-14. 338s Preparing to unpack .../15-cpp-14_14.2.0-8ubuntu1_armhf.deb ... 338s Unpacking cpp-14 (14.2.0-8ubuntu1) ... 338s Selecting previously unselected package cpp-arm-linux-gnueabihf. 338s Preparing to unpack .../16-cpp-arm-linux-gnueabihf_4%3a14.1.0-2ubuntu1_armhf.deb ... 338s Unpacking cpp-arm-linux-gnueabihf (4:14.1.0-2ubuntu1) ... 338s Selecting previously unselected package cpp. 338s Preparing to unpack .../17-cpp_4%3a14.1.0-2ubuntu1_armhf.deb ... 338s Unpacking cpp (4:14.1.0-2ubuntu1) ... 338s Selecting previously unselected package libcc1-0:armhf. 338s Preparing to unpack .../18-libcc1-0_14.2.0-8ubuntu1_armhf.deb ... 338s Unpacking libcc1-0:armhf (14.2.0-8ubuntu1) ... 338s Selecting previously unselected package libasan8:armhf. 338s Preparing to unpack .../19-libasan8_14.2.0-8ubuntu1_armhf.deb ... 338s Unpacking libasan8:armhf (14.2.0-8ubuntu1) ... 338s Selecting previously unselected package libubsan1:armhf. 338s Preparing to unpack .../20-libubsan1_14.2.0-8ubuntu1_armhf.deb ... 338s Unpacking libubsan1:armhf (14.2.0-8ubuntu1) ... 338s Selecting previously unselected package libgcc-14-dev:armhf. 338s Preparing to unpack .../21-libgcc-14-dev_14.2.0-8ubuntu1_armhf.deb ... 338s Unpacking libgcc-14-dev:armhf (14.2.0-8ubuntu1) ... 338s Selecting previously unselected package gcc-14-arm-linux-gnueabihf. 338s Preparing to unpack .../22-gcc-14-arm-linux-gnueabihf_14.2.0-8ubuntu1_armhf.deb ... 338s Unpacking gcc-14-arm-linux-gnueabihf (14.2.0-8ubuntu1) ... 339s Selecting previously unselected package gcc-14. 339s Preparing to unpack .../23-gcc-14_14.2.0-8ubuntu1_armhf.deb ... 339s Unpacking gcc-14 (14.2.0-8ubuntu1) ... 339s Selecting previously unselected package gcc-arm-linux-gnueabihf. 339s Preparing to unpack .../24-gcc-arm-linux-gnueabihf_4%3a14.1.0-2ubuntu1_armhf.deb ... 339s Unpacking gcc-arm-linux-gnueabihf (4:14.1.0-2ubuntu1) ... 339s Selecting previously unselected package gcc. 339s Preparing to unpack .../25-gcc_4%3a14.1.0-2ubuntu1_armhf.deb ... 339s Unpacking gcc (4:14.1.0-2ubuntu1) ... 339s Selecting previously unselected package libstdc++-14-dev:armhf. 339s Preparing to unpack .../26-libstdc++-14-dev_14.2.0-8ubuntu1_armhf.deb ... 339s Unpacking libstdc++-14-dev:armhf (14.2.0-8ubuntu1) ... 339s Selecting previously unselected package g++-14-arm-linux-gnueabihf. 339s Preparing to unpack .../27-g++-14-arm-linux-gnueabihf_14.2.0-8ubuntu1_armhf.deb ... 339s Unpacking g++-14-arm-linux-gnueabihf (14.2.0-8ubuntu1) ... 340s Selecting previously unselected package g++-14. 340s Preparing to unpack .../28-g++-14_14.2.0-8ubuntu1_armhf.deb ... 340s Unpacking g++-14 (14.2.0-8ubuntu1) ... 340s Selecting previously unselected package g++-arm-linux-gnueabihf. 340s Preparing to unpack .../29-g++-arm-linux-gnueabihf_4%3a14.1.0-2ubuntu1_armhf.deb ... 340s Unpacking g++-arm-linux-gnueabihf (4:14.1.0-2ubuntu1) ... 340s Selecting previously unselected package g++. 340s Preparing to unpack .../30-g++_4%3a14.1.0-2ubuntu1_armhf.deb ... 340s Unpacking g++ (4:14.1.0-2ubuntu1) ... 340s Selecting previously unselected package build-essential. 340s Preparing to unpack .../31-build-essential_12.10ubuntu1_armhf.deb ... 340s Unpacking build-essential (12.10ubuntu1) ... 340s Selecting previously unselected package libdebhelper-perl. 340s Preparing to unpack .../32-libdebhelper-perl_13.20ubuntu1_all.deb ... 340s Unpacking libdebhelper-perl (13.20ubuntu1) ... 340s Selecting previously unselected package libtool. 340s Preparing to unpack .../33-libtool_2.4.7-7build1_all.deb ... 340s Unpacking libtool (2.4.7-7build1) ... 340s Selecting previously unselected package dh-autoreconf. 340s Preparing to unpack .../34-dh-autoreconf_20_all.deb ... 340s Unpacking dh-autoreconf (20) ... 340s Selecting previously unselected package libarchive-zip-perl. 340s Preparing to unpack .../35-libarchive-zip-perl_1.68-1_all.deb ... 340s Unpacking libarchive-zip-perl (1.68-1) ... 340s Selecting previously unselected package libfile-stripnondeterminism-perl. 340s Preparing to unpack .../36-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ... 340s Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... 340s Selecting previously unselected package dh-strip-nondeterminism. 340s Preparing to unpack .../37-dh-strip-nondeterminism_1.14.0-1_all.deb ... 340s Unpacking dh-strip-nondeterminism (1.14.0-1) ... 340s Selecting previously unselected package debugedit. 340s Preparing to unpack .../38-debugedit_1%3a5.1-1_armhf.deb ... 340s Unpacking debugedit (1:5.1-1) ... 340s Selecting previously unselected package dwz. 340s Preparing to unpack .../39-dwz_0.15-1build6_armhf.deb ... 340s Unpacking dwz (0.15-1build6) ... 340s Selecting previously unselected package gettext. 340s Preparing to unpack .../40-gettext_0.22.5-2_armhf.deb ... 340s Unpacking gettext (0.22.5-2) ... 340s Selecting previously unselected package intltool-debian. 340s Preparing to unpack .../41-intltool-debian_0.35.0+20060710.6_all.deb ... 340s Unpacking intltool-debian (0.35.0+20060710.6) ... 340s Selecting previously unselected package po-debconf. 340s Preparing to unpack .../42-po-debconf_1.0.21+nmu1_all.deb ... 340s Unpacking po-debconf (1.0.21+nmu1) ... 340s Selecting previously unselected package debhelper. 340s Preparing to unpack .../43-debhelper_13.20ubuntu1_all.deb ... 340s Unpacking debhelper (13.20ubuntu1) ... 340s Selecting previously unselected package dh-python. 340s Preparing to unpack .../44-dh-python_6.20241024_all.deb ... 340s Unpacking dh-python (6.20241024) ... 340s Selecting previously unselected package libpython3.13-stdlib:armhf. 340s Preparing to unpack .../45-libpython3.13-stdlib_3.13.0-2_armhf.deb ... 340s Unpacking libpython3.13-stdlib:armhf (3.13.0-2) ... 340s Selecting previously unselected package pybuild-plugin-autopkgtest. 340s Preparing to unpack .../46-pybuild-plugin-autopkgtest_6.20241024_all.deb ... 340s Unpacking pybuild-plugin-autopkgtest (6.20241024) ... 341s Selecting previously unselected package python3.13. 341s Preparing to unpack .../47-python3.13_3.13.0-2_armhf.deb ... 341s Unpacking python3.13 (3.13.0-2) ... 341s Selecting previously unselected package python3-all. 341s Preparing to unpack .../48-python3-all_3.12.7-1_armhf.deb ... 341s Unpacking python3-all (3.12.7-1) ... 341s Selecting previously unselected package python3-iniconfig. 341s Preparing to unpack .../49-python3-iniconfig_1.1.1-2_all.deb ... 341s Unpacking python3-iniconfig (1.1.1-2) ... 341s Selecting previously unselected package python3-packaging. 341s Preparing to unpack .../50-python3-packaging_24.1-1_all.deb ... 341s Unpacking python3-packaging (24.1-1) ... 341s Selecting previously unselected package python3-pluggy. 341s Preparing to unpack .../51-python3-pluggy_1.5.0-1_all.deb ... 341s Unpacking python3-pluggy (1.5.0-1) ... 341s Selecting previously unselected package python3-pytest. 341s Preparing to unpack .../52-python3-pytest_8.3.3-1_all.deb ... 341s Unpacking python3-pytest (8.3.3-1) ... 341s Selecting previously unselected package autopkgtest-satdep. 341s Preparing to unpack .../53-2-autopkgtest-satdep.deb ... 341s Unpacking autopkgtest-satdep (0) ... 341s Setting up dh-python (6.20241024) ... 341s Setting up python3-iniconfig (1.1.1-2) ... 341s Setting up gettext (0.22.5-2) ... 341s Setting up libarchive-zip-perl (1.68-1) ... 341s Setting up libdebhelper-perl (13.20ubuntu1) ... 341s Setting up linux-libc-dev:armhf (6.11.0-8.8) ... 341s Setting up m4 (1.4.19-4build1) ... 341s Setting up intltool-debian (0.35.0+20060710.6) ... 341s Setting up libpython3.13-minimal:armhf (3.13.0-2) ... 341s Setting up autotools-dev (20220109.1) ... 341s Setting up python3-packaging (24.1-1) ... 342s Setting up rpcsvc-proto (1.4.2-0ubuntu7) ... 342s Setting up libmpc3:armhf (1.3.1-1build2) ... 342s Setting up autopoint (0.22.5-2) ... 342s Setting up autoconf (2.72-3) ... 342s Setting up python3-pluggy (1.5.0-1) ... 342s Setting up libubsan1:armhf (14.2.0-8ubuntu1) ... 342s Setting up dwz (0.15-1build6) ... 342s Setting up libcrypt-dev:armhf (1:4.4.36-4build1) ... 342s Setting up libasan8:armhf (14.2.0-8ubuntu1) ... 342s Setting up debugedit (1:5.1-1) ... 342s Setting up python3.13-minimal (3.13.0-2) ... 343s Setting up libgcc-14-dev:armhf (14.2.0-8ubuntu1) ... 343s Setting up libisl23:armhf (0.27-1) ... 343s Setting up libc-dev-bin (2.40-1ubuntu3) ... 343s Setting up libpython3.13-stdlib:armhf (3.13.0-2) ... 343s Setting up libcc1-0:armhf (14.2.0-8ubuntu1) ... 343s Setting up cpp-14-arm-linux-gnueabihf (14.2.0-8ubuntu1) ... 343s Setting up automake (1:1.16.5-1.3ubuntu1) ... 343s update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode 343s Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... 343s Setting up python3.13 (3.13.0-2) ... 344s Setting up python3-pytest (8.3.3-1) ... 345s Setting up po-debconf (1.0.21+nmu1) ... 345s Setting up gcc-14-arm-linux-gnueabihf (14.2.0-8ubuntu1) ... 345s Setting up python3-all (3.12.7-1) ... 345s Setting up cpp-14 (14.2.0-8ubuntu1) ... 345s Setting up dh-strip-nondeterminism (1.14.0-1) ... 345s Setting up libc6-dev:armhf (2.40-1ubuntu3) ... 345s Setting up libstdc++-14-dev:armhf (14.2.0-8ubuntu1) ... 345s Setting up cpp-arm-linux-gnueabihf (4:14.1.0-2ubuntu1) ... 345s Setting up gcc-arm-linux-gnueabihf (4:14.1.0-2ubuntu1) ... 345s Setting up g++-14-arm-linux-gnueabihf (14.2.0-8ubuntu1) ... 345s Setting up gcc-14 (14.2.0-8ubuntu1) ... 345s Setting up cpp (4:14.1.0-2ubuntu1) ... 345s Setting up g++-14 (14.2.0-8ubuntu1) ... 345s Setting up g++-arm-linux-gnueabihf (4:14.1.0-2ubuntu1) ... 345s Setting up libtool (2.4.7-7build1) ... 345s Setting up gcc (4:14.1.0-2ubuntu1) ... 345s Setting up dh-autoreconf (20) ... 345s Setting up g++ (4:14.1.0-2ubuntu1) ... 345s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 345s Setting up build-essential (12.10ubuntu1) ... 345s Setting up debhelper (13.20ubuntu1) ... 345s Setting up pybuild-plugin-autopkgtest (6.20241024) ... 345s Setting up autopkgtest-satdep (0) ... 345s Processing triggers for systemd (256.5-2ubuntu4) ... 345s Processing triggers for man-db (2.12.1-3) ... 346s Processing triggers for install-info (7.1.1-1) ... 347s Processing triggers for libc-bin (2.40-1ubuntu3) ... 360s (Reading database ... 67635 files and directories currently installed.) 360s Removing autopkgtest-satdep (0) ... 365s autopkgtest [05:57:29]: test pybuild-autopkgtest: pybuild-autopkgtest 365s autopkgtest [05:57:29]: test pybuild-autopkgtest: [----------------------- 368s # Pull test items that are otherwise uncaught by pybuild-autodep8. 368s mkdir -p ../../autopkgtest_tmp/build/seqmagick 368s cp -r /usr/lib/python3/dist-packages/seqmagick/test \ 368s ../../autopkgtest_tmp/build/seqmagick 368s pybuild-autopkgtest 368s I: pybuild base:311: cd /tmp/autopkgtest.F5vqCK/autopkgtest_tmp/build; python3.13 -m pytest 369s ============================= test session starts ============================== 369s platform linux -- Python 3.13.0, pytest-8.3.3, pluggy-1.5.0 369s rootdir: /tmp/autopkgtest.F5vqCK/autopkgtest_tmp/build 369s plugins: typeguard-4.4.1 369s collected 54 items / 4 errors 369s 369s ==================================== ERRORS ==================================== 369s _____ ERROR collecting seqmagick/test/test_subcommands_backtrans_align.py ______ 369s ImportError while importing test module '/tmp/autopkgtest.F5vqCK/autopkgtest_tmp/build/seqmagick/test/test_subcommands_backtrans_align.py'. 369s Hint: make sure your test modules/packages have valid Python names. 369s Traceback: 369s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 369s return _bootstrap._gcd_import(name[level:], package, level) 369s seqmagick/test/test_subcommands_backtrans_align.py:7: in 369s from seqmagick.subcommands import backtrans_align 369s /usr/lib/python3/dist-packages/seqmagick/subcommands/backtrans_align.py:15: in 369s from Bio import SeqIO 369s /usr/lib/python3/dist-packages/Bio/SeqIO/__init__.py:401: in 369s from Bio.SeqIO import TwoBitIO 369s /usr/lib/python3/dist-packages/Bio/SeqIO/TwoBitIO.py:80: in 369s raise MissingPythonDependencyError( 369s E Bio.MissingPythonDependencyError: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 369s _________ ERROR collecting seqmagick/test/test_subcommands_convert.py __________ 369s ImportError while importing test module '/tmp/autopkgtest.F5vqCK/autopkgtest_tmp/build/seqmagick/test/test_subcommands_convert.py'. 369s Hint: make sure your test modules/packages have valid Python names. 369s Traceback: 369s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 369s return _bootstrap._gcd_import(name[level:], package, level) 369s seqmagick/test/test_subcommands_convert.py:10: in 369s from seqmagick.subcommands import convert 369s /usr/lib/python3/dist-packages/seqmagick/subcommands/convert.py:9: in 369s from Bio import SeqIO 369s /usr/lib/python3/dist-packages/Bio/SeqIO/__init__.py:401: in 369s from Bio.SeqIO import TwoBitIO 369s /usr/lib/python3/dist-packages/Bio/SeqIO/TwoBitIO.py:80: in 369s raise MissingPythonDependencyError( 369s E Bio.MissingPythonDependencyError: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 369s ______ ERROR collecting seqmagick/test/test_subcommands_quality_filter.py ______ 369s ImportError while importing test module '/tmp/autopkgtest.F5vqCK/autopkgtest_tmp/build/seqmagick/test/test_subcommands_quality_filter.py'. 369s Hint: make sure your test modules/packages have valid Python names. 369s Traceback: 369s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 369s return _bootstrap._gcd_import(name[level:], package, level) 369s seqmagick/test/test_subcommands_quality_filter.py:8: in 369s from seqmagick.subcommands import quality_filter 369s /usr/lib/python3/dist-packages/seqmagick/subcommands/quality_filter.py:13: in 369s from Bio import SeqIO 369s /usr/lib/python3/dist-packages/Bio/SeqIO/__init__.py:401: in 369s from Bio.SeqIO import TwoBitIO 369s /usr/lib/python3/dist-packages/Bio/SeqIO/TwoBitIO.py:80: in 369s raise MissingPythonDependencyError( 369s E Bio.MissingPythonDependencyError: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 369s ______________ ERROR collecting seqmagick/test/test_transform.py _______________ 369s ImportError while importing test module '/tmp/autopkgtest.F5vqCK/autopkgtest_tmp/build/seqmagick/test/test_transform.py'. 369s Hint: make sure your test modules/packages have valid Python names. 369s Traceback: 369s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 369s return _bootstrap._gcd_import(name[level:], package, level) 369s seqmagick/test/test_transform.py:10: in 369s from Bio import SeqIO 369s /usr/lib/python3/dist-packages/Bio/SeqIO/__init__.py:401: in 369s from Bio.SeqIO import TwoBitIO 369s /usr/lib/python3/dist-packages/Bio/SeqIO/TwoBitIO.py:80: in 369s raise MissingPythonDependencyError( 369s E Bio.MissingPythonDependencyError: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 369s =========================== short test summary info ============================ 369s ERROR seqmagick/test/test_subcommands_backtrans_align.py 369s ERROR seqmagick/test/test_subcommands_convert.py 369s ERROR seqmagick/test/test_subcommands_quality_filter.py 369s ERROR seqmagick/test/test_transform.py 369s !!!!!!!!!!!!!!!!!!! Interrupted: 4 errors during collection !!!!!!!!!!!!!!!!!!!! 369s ============================== 4 errors in 0.71s =============================== 369s E: pybuild pybuild:389: test: plugin distutils failed with: exit code=2: cd /tmp/autopkgtest.F5vqCK/autopkgtest_tmp/build; python3.13 -m pytest 369s I: pybuild base:311: cd /tmp/autopkgtest.F5vqCK/autopkgtest_tmp/build; python3.12 -m pytest 370s ============================= test session starts ============================== 370s platform linux -- Python 3.12.7, pytest-8.3.3, pluggy-1.5.0 370s rootdir: /tmp/autopkgtest.F5vqCK/autopkgtest_tmp/build 370s plugins: typeguard-4.4.1 370s collected 154 items 370s 370s seqmagick/test/integration/test_convert.py .ss.............. [ 11%] 370s seqmagick/test/integration/test_extract_ids.py ..ss.. [ 14%] 370s seqmagick/test/integration/test_info.py ...s [ 17%] 370s seqmagick/test/integration/test_mogrify.py .s. [ 19%] 370s seqmagick/test/test_subcommands_backtrans_align.py ......... [ 25%] 370s seqmagick/test/test_subcommands_common.py ..................s..... [ 40%] 370s seqmagick/test/test_subcommands_convert.py ...... [ 44%] 370s seqmagick/test/test_subcommands_quality_filter.py ...................... [ 59%] 370s .... [ 61%] 371s seqmagick/test/test_transform.py ....................................... [ 87%] 371s .................... [100%] 371s 371s ======================== 147 passed, 7 skipped in 1.07s ======================== 371s pybuild-autopkgtest: error: pybuild --autopkgtest --test-pytest -i python{version} -p "3.13 3.12" returned exit code 13 371s make: *** [/tmp/jQDP3Q_mpA/run:4: pybuild-autopkgtest] Error 25 371s pybuild-autopkgtest: error: /tmp/jQDP3Q_mpA/run pybuild-autopkgtest returned exit code 2 371s autopkgtest [05:57:35]: test pybuild-autopkgtest: -----------------------] 375s autopkgtest [05:57:39]: test pybuild-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 375s pybuild-autopkgtest FAIL non-zero exit status 25 379s autopkgtest [05:57:43]: @@@@@@@@@@@@@@@@@@@@ summary 379s run-unit-test PASS 379s pybuild-autopkgtest FAIL non-zero exit status 25