1s autopkgtest [11:10:06]: starting date and time: 2024-11-13 11:10:06+0000 1s autopkgtest [11:10:06]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 1s autopkgtest [11:10:06]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.kyi1nz1n/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 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' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-arm64-35.secgroup --name adt-plucky-arm64-seqmagick-20241113-111004-juju-7f2275-prod-proposed-migration-environment-15-6f7f3408-af16-451d-9da5-74b9659b834a --image adt/ubuntu-plucky-arm64-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/ 93s autopkgtest [11:11:38]: testbed dpkg architecture: arm64 94s autopkgtest [11:11:39]: testbed apt version: 2.9.8 94s autopkgtest [11:11:39]: @@@@@@@@@@@@@@@@@@@@ test bed setup 95s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 95s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [849 kB] 95s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 95s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [76.4 kB] 95s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.3 kB] 95s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [104 kB] 95s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 Packages [50.3 kB] 95s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [601 kB] 95s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [17.1 kB] 95s Fetched 1794 kB in 1s (2034 kB/s) 95s Reading package lists... 98s Reading package lists... 99s Building dependency tree... 99s Reading state information... 100s Calculating upgrade... 101s The following NEW packages will be installed: 101s python3.13-gdbm 101s The following packages will be upgraded: 101s libpython3-stdlib python3 python3-gdbm python3-minimal 101s 4 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 101s Need to get 101 kB of archives. 101s After this operation, 141 kB of additional disk space will be used. 101s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-minimal arm64 3.12.7-1 [27.4 kB] 101s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3 arm64 3.12.7-1 [24.0 kB] 101s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libpython3-stdlib arm64 3.12.7-1 [10.0 kB] 101s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-gdbm arm64 3.13.0-2 [30.7 kB] 101s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-gdbm arm64 3.12.7-1 [8642 B] 102s Fetched 101 kB in 0s (281 kB/s) 102s (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 ... 79924 files and directories currently installed.) 102s Preparing to unpack .../python3-minimal_3.12.7-1_arm64.deb ... 102s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ... 102s Setting up python3-minimal (3.12.7-1) ... 103s (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 ... 79924 files and directories currently installed.) 103s Preparing to unpack .../python3_3.12.7-1_arm64.deb ... 103s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ... 103s Preparing to unpack .../libpython3-stdlib_3.12.7-1_arm64.deb ... 103s Unpacking libpython3-stdlib:arm64 (3.12.7-1) over (3.12.6-0ubuntu1) ... 103s Selecting previously unselected package python3.13-gdbm. 103s Preparing to unpack .../python3.13-gdbm_3.13.0-2_arm64.deb ... 103s Unpacking python3.13-gdbm (3.13.0-2) ... 103s Preparing to unpack .../python3-gdbm_3.12.7-1_arm64.deb ... 103s Unpacking python3-gdbm:arm64 (3.12.7-1) over (3.12.6-1ubuntu1) ... 103s Setting up python3.13-gdbm (3.13.0-2) ... 103s Setting up libpython3-stdlib:arm64 (3.12.7-1) ... 103s Setting up python3 (3.12.7-1) ... 103s Setting up python3-gdbm:arm64 (3.12.7-1) ... 103s Processing triggers for man-db (2.12.1-3) ... 104s Reading package lists... 105s Building dependency tree... 105s Reading state information... 107s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 107s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 107s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 107s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 107s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 109s Reading package lists... 109s Reading package lists... 110s Building dependency tree... 110s Reading state information... 111s Calculating upgrade... 112s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 112s Reading package lists... 112s Building dependency tree... 112s Reading state information... 114s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 117s autopkgtest [11:12:02]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 14:19:41 UTC 2024 117s autopkgtest [11:12:02]: @@@@@@@@@@@@@@@@@@@@ apt-source seqmagick 119s Get:1 http://ftpmaster.internal/ubuntu plucky/universe seqmagick 0.8.6-3 (dsc) [2262 B] 119s Get:2 http://ftpmaster.internal/ubuntu plucky/universe seqmagick 0.8.6-3 (tar) [665 kB] 119s Get:3 http://ftpmaster.internal/ubuntu plucky/universe seqmagick 0.8.6-3 (diff) [6012 B] 119s gpgv: Signature made Tue Aug 6 20:16:33 2024 UTC 119s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 119s gpgv: issuer "emollier@debian.org" 119s gpgv: Can't check signature: No public key 119s dpkg-source: warning: cannot verify inline signature for ./seqmagick_0.8.6-3.dsc: no acceptable signature found 120s autopkgtest [11:12:05]: testing package seqmagick version 0.8.6-3 120s autopkgtest [11:12:05]: build not needed 121s autopkgtest [11:12:06]: test run-unit-test: preparing testbed 122s Reading package lists... 123s Building dependency tree... 123s Reading state information... 123s Starting pkgProblemResolver with broken count: 0 124s Starting 2 pkgProblemResolver with broken count: 0 124s Done 125s The following additional packages will be installed: 125s fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-urw-base35 125s libblas3 libcairo2 libdeflate0 libfontconfig1 libfontenc1 libgfortran5 125s libgomp1 libgraphite2-3 libharfbuzz0b libimagequant0 libjbig0 libjpeg-turbo8 125s libjpeg8 liblapack3 liblcms2-2 liblerc4 libopenjp2-7 libpixman-1-0 libraqm0 125s libsharpyuv0 libtiff6 libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 125s libxcb-shm0 libxrender1 python3-biopython python3-cairo python3-freetype 125s python3-numpy python3-pil python3-pygtrie python3-reportlab 125s python3-rlpycairo seqmagick sgml-base w3c-sgml-lib x11-common 125s xfonts-encodings xfonts-utils xml-core 125s Suggested packages: 125s fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre liblcms2-utils 125s python3-tk bwa clustalo clustalw dialign dssp emboss fasttree mafft muscle3 125s phylip phyml prank probcons python3-mysqldb python3-matplotlib python3-mmtf 125s python3-rdflib python3-psycopg2 python3-scipy raxml samtools t-coffee wise 125s gcc gfortran python-numpy-doc python3-dev python3-pytest python-pil-doc 125s python-pygtrie-doc pdf-viewer python3-egenix-mxtexttools 125s python-reportlab-doc rl-accel rl-renderpm sgml-base-doc debhelper 125s Recommended packages: 125s python-biopython-doc ncbi-blast+ python3-olefile fonts-dejavu-extra 125s The following NEW packages will be installed: 125s autopkgtest-satdep fontconfig-config fonts-dejavu-core fonts-dejavu-mono 125s fonts-urw-base35 libblas3 libcairo2 libdeflate0 libfontconfig1 libfontenc1 125s libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libimagequant0 libjbig0 125s libjpeg-turbo8 libjpeg8 liblapack3 liblcms2-2 liblerc4 libopenjp2-7 125s libpixman-1-0 libraqm0 libsharpyuv0 libtiff6 libwebp7 libwebpdemux2 125s libwebpmux3 libxcb-render0 libxcb-shm0 libxrender1 python3-biopython 125s python3-cairo python3-freetype python3-numpy python3-pil python3-pygtrie 125s python3-reportlab python3-rlpycairo seqmagick sgml-base w3c-sgml-lib 125s x11-common xfonts-encodings xfonts-utils xml-core 125s 0 upgraded, 47 newly installed, 0 to remove and 0 not upgraded. 125s Need to get 26.3 MB/26.3 MB of archives. 125s After this operation, 81.5 MB of additional disk space will be used. 125s Get:1 /tmp/autopkgtest.NDSeuo/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [704 B] 125s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 sgml-base all 1.31 [11.4 kB] 125s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 126s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 126s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 libfontenc1 arm64 1:1.1.8-1build1 [13.9 kB] 126s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 126s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 126s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 xfonts-utils arm64 1:7.7+7 [95.6 kB] 126s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-urw-base35 all 20200910-8 [11.0 MB] 126s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig-config arm64 2.15.0-1.1ubuntu2 [37.4 kB] 126s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.0-3build2 [152 kB] 126s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 libfontconfig1 arm64 2.15.0-1.1ubuntu2 [142 kB] 126s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 libpixman-1-0 arm64 0.44.0-3 [197 kB] 126s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-render0 arm64 1.17.0-2 [16.6 kB] 126s Get:15 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-shm0 arm64 1.17.0-2 [5884 B] 126s Get:16 http://ftpmaster.internal/ubuntu plucky/main arm64 libxrender1 arm64 1:0.9.10-1.1build1 [18.8 kB] 126s Get:17 http://ftpmaster.internal/ubuntu plucky/main arm64 libcairo2 arm64 1.18.2-2 [560 kB] 126s Get:18 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate0 arm64 1.22-1 [46.2 kB] 126s Get:19 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 14.2.0-8ubuntu1 [438 kB] 126s Get:20 http://ftpmaster.internal/ubuntu plucky/main arm64 libgomp1 arm64 14.2.0-8ubuntu1 [145 kB] 127s Get:21 http://ftpmaster.internal/ubuntu plucky/main arm64 libgraphite2-3 arm64 1.3.14-2ubuntu1 [70.6 kB] 127s Get:22 http://ftpmaster.internal/ubuntu plucky/main arm64 libharfbuzz0b arm64 10.0.1-1 [487 kB] 127s Get:23 http://ftpmaster.internal/ubuntu plucky/main arm64 libimagequant0 arm64 2.18.0-1build1 [37.1 kB] 127s Get:24 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg-turbo8 arm64 2.1.5-2ubuntu2 [163 kB] 127s Get:25 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 127s Get:26 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.0-3build2 [2293 kB] 127s Get:27 http://ftpmaster.internal/ubuntu plucky/main arm64 liblcms2-2 arm64 2.16-2 [170 kB] 127s Get:28 http://ftpmaster.internal/ubuntu plucky/main arm64 liblerc4 arm64 4.0.0+ds-4ubuntu2 [154 kB] 127s Get:29 http://ftpmaster.internal/ubuntu plucky/main arm64 libraqm0 arm64 0.10.1-1build1 [14.7 kB] 127s Get:30 http://ftpmaster.internal/ubuntu plucky/main arm64 libsharpyuv0 arm64 1.4.0-0.1 [16.3 kB] 127s Get:31 http://ftpmaster.internal/ubuntu plucky/main arm64 libjbig0 arm64 2.1-6.1ubuntu2 [29.3 kB] 127s Get:32 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebp7 arm64 1.4.0-0.1 [192 kB] 127s Get:33 http://ftpmaster.internal/ubuntu plucky/main arm64 libtiff6 arm64 4.5.1+git230720-4ubuntu4 [193 kB] 127s Get:34 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebpdemux2 arm64 1.4.0-0.1 [12.3 kB] 127s Get:35 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebpmux3 arm64 1.4.0-0.1 [25.1 kB] 127s Get:36 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy arm64 1:1.26.4+ds-11build1 [3654 kB] 127s Get:37 http://ftpmaster.internal/ubuntu plucky/main arm64 libopenjp2-7 arm64 2.5.0-2ubuntu1 [182 kB] 127s Get:38 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-pil arm64 10.4.0-1ubuntu1 [456 kB] 127s Get:39 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-cairo arm64 1.26.1-2 [121 kB] 127s Get:40 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-freetype all 2.5.1-1 [92.3 kB] 127s Get:41 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-rlpycairo all 0.3.0-3 [9130 B] 127s Get:42 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-reportlab all 4.2.5-1 [1107 kB] 127s Get:43 http://ftpmaster.internal/ubuntu plucky/main arm64 xml-core all 0.19 [20.3 kB] 127s Get:44 http://ftpmaster.internal/ubuntu plucky/universe arm64 w3c-sgml-lib all 1.3-3 [280 kB] 127s Get:45 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-biopython arm64 1.84+dfsg-4 [1689 kB] 127s Get:46 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pygtrie all 2.2-2 [16.0 kB] 127s Get:47 http://ftpmaster.internal/ubuntu plucky/universe arm64 seqmagick all 0.8.6-3 [38.6 kB] 128s Fetched 26.3 MB in 2s (15.2 MB/s) 128s Selecting previously unselected package sgml-base. 128s (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 ... 79931 files and directories currently installed.) 128s Preparing to unpack .../00-sgml-base_1.31_all.deb ... 128s Unpacking sgml-base (1.31) ... 128s Selecting previously unselected package fonts-dejavu-mono. 128s Preparing to unpack .../01-fonts-dejavu-mono_2.37-8_all.deb ... 128s Unpacking fonts-dejavu-mono (2.37-8) ... 128s Selecting previously unselected package fonts-dejavu-core. 128s Preparing to unpack .../02-fonts-dejavu-core_2.37-8_all.deb ... 128s Unpacking fonts-dejavu-core (2.37-8) ... 128s Selecting previously unselected package libfontenc1:arm64. 128s Preparing to unpack .../03-libfontenc1_1%3a1.1.8-1build1_arm64.deb ... 128s Unpacking libfontenc1:arm64 (1:1.1.8-1build1) ... 128s Selecting previously unselected package x11-common. 128s Preparing to unpack .../04-x11-common_1%3a7.7+23ubuntu3_all.deb ... 128s Unpacking x11-common (1:7.7+23ubuntu3) ... 128s Selecting previously unselected package xfonts-encodings. 128s Preparing to unpack .../05-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 128s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 128s Selecting previously unselected package xfonts-utils. 128s Preparing to unpack .../06-xfonts-utils_1%3a7.7+7_arm64.deb ... 128s Unpacking xfonts-utils (1:7.7+7) ... 128s Selecting previously unselected package fonts-urw-base35. 128s Preparing to unpack .../07-fonts-urw-base35_20200910-8_all.deb ... 129s Unpacking fonts-urw-base35 (20200910-8) ... 129s Selecting previously unselected package fontconfig-config. 129s Preparing to unpack .../08-fontconfig-config_2.15.0-1.1ubuntu2_arm64.deb ... 129s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ... 129s Selecting previously unselected package libblas3:arm64. 129s Preparing to unpack .../09-libblas3_3.12.0-3build2_arm64.deb ... 129s Unpacking libblas3:arm64 (3.12.0-3build2) ... 129s Selecting previously unselected package libfontconfig1:arm64. 129s Preparing to unpack .../10-libfontconfig1_2.15.0-1.1ubuntu2_arm64.deb ... 129s Unpacking libfontconfig1:arm64 (2.15.0-1.1ubuntu2) ... 129s Selecting previously unselected package libpixman-1-0:arm64. 129s Preparing to unpack .../11-libpixman-1-0_0.44.0-3_arm64.deb ... 129s Unpacking libpixman-1-0:arm64 (0.44.0-3) ... 129s Selecting previously unselected package libxcb-render0:arm64. 129s Preparing to unpack .../12-libxcb-render0_1.17.0-2_arm64.deb ... 129s Unpacking libxcb-render0:arm64 (1.17.0-2) ... 129s Selecting previously unselected package libxcb-shm0:arm64. 129s Preparing to unpack .../13-libxcb-shm0_1.17.0-2_arm64.deb ... 129s Unpacking libxcb-shm0:arm64 (1.17.0-2) ... 129s Selecting previously unselected package libxrender1:arm64. 129s Preparing to unpack .../14-libxrender1_1%3a0.9.10-1.1build1_arm64.deb ... 129s Unpacking libxrender1:arm64 (1:0.9.10-1.1build1) ... 129s Selecting previously unselected package libcairo2:arm64. 130s Preparing to unpack .../15-libcairo2_1.18.2-2_arm64.deb ... 130s Unpacking libcairo2:arm64 (1.18.2-2) ... 130s Selecting previously unselected package libdeflate0:arm64. 130s Preparing to unpack .../16-libdeflate0_1.22-1_arm64.deb ... 130s Unpacking libdeflate0:arm64 (1.22-1) ... 130s Selecting previously unselected package libgfortran5:arm64. 130s Preparing to unpack .../17-libgfortran5_14.2.0-8ubuntu1_arm64.deb ... 130s Unpacking libgfortran5:arm64 (14.2.0-8ubuntu1) ... 130s Selecting previously unselected package libgomp1:arm64. 130s Preparing to unpack .../18-libgomp1_14.2.0-8ubuntu1_arm64.deb ... 130s Unpacking libgomp1:arm64 (14.2.0-8ubuntu1) ... 130s Selecting previously unselected package libgraphite2-3:arm64. 130s Preparing to unpack .../19-libgraphite2-3_1.3.14-2ubuntu1_arm64.deb ... 130s Unpacking libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 130s Selecting previously unselected package libharfbuzz0b:arm64. 130s Preparing to unpack .../20-libharfbuzz0b_10.0.1-1_arm64.deb ... 130s Unpacking libharfbuzz0b:arm64 (10.0.1-1) ... 130s Selecting previously unselected package libimagequant0:arm64. 130s Preparing to unpack .../21-libimagequant0_2.18.0-1build1_arm64.deb ... 130s Unpacking libimagequant0:arm64 (2.18.0-1build1) ... 130s Selecting previously unselected package libjpeg-turbo8:arm64. 130s Preparing to unpack .../22-libjpeg-turbo8_2.1.5-2ubuntu2_arm64.deb ... 130s Unpacking libjpeg-turbo8:arm64 (2.1.5-2ubuntu2) ... 130s Selecting previously unselected package libjpeg8:arm64. 130s Preparing to unpack .../23-libjpeg8_8c-2ubuntu11_arm64.deb ... 130s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 130s Selecting previously unselected package liblapack3:arm64. 130s Preparing to unpack .../24-liblapack3_3.12.0-3build2_arm64.deb ... 130s Unpacking liblapack3:arm64 (3.12.0-3build2) ... 130s Selecting previously unselected package liblcms2-2:arm64. 130s Preparing to unpack .../25-liblcms2-2_2.16-2_arm64.deb ... 130s Unpacking liblcms2-2:arm64 (2.16-2) ... 130s Selecting previously unselected package liblerc4:arm64. 130s Preparing to unpack .../26-liblerc4_4.0.0+ds-4ubuntu2_arm64.deb ... 130s Unpacking liblerc4:arm64 (4.0.0+ds-4ubuntu2) ... 130s Selecting previously unselected package libraqm0:arm64. 130s Preparing to unpack .../27-libraqm0_0.10.1-1build1_arm64.deb ... 130s Unpacking libraqm0:arm64 (0.10.1-1build1) ... 130s Selecting previously unselected package libsharpyuv0:arm64. 130s Preparing to unpack .../28-libsharpyuv0_1.4.0-0.1_arm64.deb ... 130s Unpacking libsharpyuv0:arm64 (1.4.0-0.1) ... 130s Selecting previously unselected package libjbig0:arm64. 130s Preparing to unpack .../29-libjbig0_2.1-6.1ubuntu2_arm64.deb ... 130s Unpacking libjbig0:arm64 (2.1-6.1ubuntu2) ... 131s Selecting previously unselected package libwebp7:arm64. 131s Preparing to unpack .../30-libwebp7_1.4.0-0.1_arm64.deb ... 131s Unpacking libwebp7:arm64 (1.4.0-0.1) ... 131s Selecting previously unselected package libtiff6:arm64. 131s Preparing to unpack .../31-libtiff6_4.5.1+git230720-4ubuntu4_arm64.deb ... 131s Unpacking libtiff6:arm64 (4.5.1+git230720-4ubuntu4) ... 131s Selecting previously unselected package libwebpdemux2:arm64. 131s Preparing to unpack .../32-libwebpdemux2_1.4.0-0.1_arm64.deb ... 131s Unpacking libwebpdemux2:arm64 (1.4.0-0.1) ... 131s Selecting previously unselected package libwebpmux3:arm64. 131s Preparing to unpack .../33-libwebpmux3_1.4.0-0.1_arm64.deb ... 131s Unpacking libwebpmux3:arm64 (1.4.0-0.1) ... 131s Selecting previously unselected package python3-numpy. 131s Preparing to unpack .../34-python3-numpy_1%3a1.26.4+ds-11build1_arm64.deb ... 131s Unpacking python3-numpy (1:1.26.4+ds-11build1) ... 131s Selecting previously unselected package libopenjp2-7:arm64. 131s Preparing to unpack .../35-libopenjp2-7_2.5.0-2ubuntu1_arm64.deb ... 131s Unpacking libopenjp2-7:arm64 (2.5.0-2ubuntu1) ... 131s Selecting previously unselected package python3-pil:arm64. 131s Preparing to unpack .../36-python3-pil_10.4.0-1ubuntu1_arm64.deb ... 131s Unpacking python3-pil:arm64 (10.4.0-1ubuntu1) ... 131s Selecting previously unselected package python3-cairo. 131s Preparing to unpack .../37-python3-cairo_1.26.1-2_arm64.deb ... 131s Unpacking python3-cairo (1.26.1-2) ... 131s Selecting previously unselected package python3-freetype. 131s Preparing to unpack .../38-python3-freetype_2.5.1-1_all.deb ... 131s Unpacking python3-freetype (2.5.1-1) ... 131s Selecting previously unselected package python3-rlpycairo. 131s Preparing to unpack .../39-python3-rlpycairo_0.3.0-3_all.deb ... 131s Unpacking python3-rlpycairo (0.3.0-3) ... 131s Selecting previously unselected package python3-reportlab. 131s Preparing to unpack .../40-python3-reportlab_4.2.5-1_all.deb ... 131s Unpacking python3-reportlab (4.2.5-1) ... 132s Selecting previously unselected package xml-core. 132s Preparing to unpack .../41-xml-core_0.19_all.deb ... 132s Unpacking xml-core (0.19) ... 132s Selecting previously unselected package w3c-sgml-lib. 132s Preparing to unpack .../42-w3c-sgml-lib_1.3-3_all.deb ... 132s Unpacking w3c-sgml-lib (1.3-3) ... 132s Selecting previously unselected package python3-biopython. 132s Preparing to unpack .../43-python3-biopython_1.84+dfsg-4_arm64.deb ... 132s Unpacking python3-biopython (1.84+dfsg-4) ... 132s Selecting previously unselected package python3-pygtrie. 132s Preparing to unpack .../44-python3-pygtrie_2.2-2_all.deb ... 132s Unpacking python3-pygtrie (2.2-2) ... 132s Selecting previously unselected package seqmagick. 132s Preparing to unpack .../45-seqmagick_0.8.6-3_all.deb ... 132s Unpacking seqmagick (0.8.6-3) ... 132s Selecting previously unselected package autopkgtest-satdep. 132s Preparing to unpack .../46-1-autopkgtest-satdep.deb ... 132s Unpacking autopkgtest-satdep (0) ... 132s Setting up libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 132s Setting up liblcms2-2:arm64 (2.16-2) ... 132s Setting up libpixman-1-0:arm64 (0.44.0-3) ... 132s Setting up libsharpyuv0:arm64 (1.4.0-0.1) ... 132s Setting up liblerc4:arm64 (4.0.0+ds-4ubuntu2) ... 132s Setting up libxrender1:arm64 (1:0.9.10-1.1build1) ... 132s Setting up libxcb-render0:arm64 (1.17.0-2) ... 132s Setting up x11-common (1:7.7+23ubuntu3) ... 133s Setting up libdeflate0:arm64 (1.22-1) ... 133s Setting up libxcb-shm0:arm64 (1.17.0-2) ... 133s Setting up libgomp1:arm64 (14.2.0-8ubuntu1) ... 133s Setting up python3-freetype (2.5.1-1) ... 133s Setting up libjbig0:arm64 (2.1-6.1ubuntu2) ... 133s Setting up libfontenc1:arm64 (1:1.1.8-1build1) ... 133s Setting up python3-pygtrie (2.2-2) ... 133s Setting up libblas3:arm64 (3.12.0-3build2) ... 133s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode 133s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 133s Setting up libimagequant0:arm64 (2.18.0-1build1) ... 133s Setting up fonts-dejavu-mono (2.37-8) ... 133s Setting up fonts-dejavu-core (2.37-8) ... 133s Setting up libjpeg-turbo8:arm64 (2.1.5-2ubuntu2) ... 133s Setting up libgfortran5:arm64 (14.2.0-8ubuntu1) ... 133s Setting up libwebp7:arm64 (1.4.0-0.1) ... 133s Setting up libopenjp2-7:arm64 (2.5.0-2ubuntu1) ... 133s Setting up libharfbuzz0b:arm64 (10.0.1-1) ... 133s Setting up sgml-base (1.31) ... 133s Setting up libwebpmux3:arm64 (1.4.0-0.1) ... 133s Setting up libjpeg8:arm64 (8c-2ubuntu11) ... 133s Setting up liblapack3:arm64 (3.12.0-3build2) ... 133s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode 133s Setting up fontconfig-config (2.15.0-1.1ubuntu2) ... 134s Setting up libwebpdemux2:arm64 (1.4.0-0.1) ... 134s Setting up xfonts-utils (1:7.7+7) ... 134s Setting up libraqm0:arm64 (0.10.1-1build1) ... 134s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 137s Setting up libtiff6:arm64 (4.5.1+git230720-4ubuntu4) ... 137s Setting up xml-core (0.19) ... 137s Setting up libfontconfig1:arm64 (2.15.0-1.1ubuntu2) ... 137s Setting up fonts-urw-base35 (20200910-8) ... 138s Setting up libcairo2:arm64 (1.18.2-2) ... 138s Setting up python3-pil:arm64 (10.4.0-1ubuntu1) ... 138s Setting up python3-cairo (1.26.1-2) ... 138s Setting up python3-rlpycairo (0.3.0-3) ... 139s Setting up python3-reportlab (4.2.5-1) ... 140s Processing triggers for libc-bin (2.40-1ubuntu3) ... 140s Processing triggers for man-db (2.12.1-3) ... 141s Processing triggers for sgml-base (1.31) ... 141s Setting up w3c-sgml-lib (1.3-3) ... 176s Setting up python3-biopython (1.84+dfsg-4) ... 178s Setting up seqmagick (0.8.6-3) ... 178s Setting up autopkgtest-satdep (0) ... 188s (Reading database ... 83236 files and directories currently installed.) 188s Removing autopkgtest-satdep (0) ... 189s autopkgtest [11:13:14]: test run-unit-test: [----------------------- 190s ++ find examples/ -name '*.sh' 190s + for f in `find examples/ -name '*.sh'` 190s ++ dirname examples/apply-function/run_filter.sh 190s + cd examples/apply-function 190s ++ basename examples/apply-function/run_filter.sh 190s + /bin/bash run_filter.sh 191s + cd - 191s + for f in `find examples/ -name '*.sh'` 191s /tmp/autopkgtest.NDSeuo/autopkgtest_tmp 191s ++ dirname examples/include-from-file/do_filter.sh 191s + cd examples/include-from-file 191s ++ basename examples/include-from-file/do_filter.sh 191s + /bin/bash do_filter.sh 191s + cd - 191s /tmp/autopkgtest.NDSeuo/autopkgtest_tmp 191s PASS 191s + echo PASS 192s autopkgtest [11:13:17]: test run-unit-test: -----------------------] 193s run-unit-test PASS 193s autopkgtest [11:13:18]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 194s autopkgtest [11:13:19]: test pybuild-autopkgtest: preparing testbed 205s Reading package lists... 205s Building dependency tree... 205s Reading state information... 206s Starting pkgProblemResolver with broken count: 0 206s Starting 2 pkgProblemResolver with broken count: 0 206s Done 208s The following additional packages will be installed: 208s autoconf automake autopoint autotools-dev build-essential cpp cpp-14 208s cpp-14-aarch64-linux-gnu cpp-aarch64-linux-gnu debhelper debugedit 208s dh-autoreconf dh-python dh-strip-nondeterminism dwz g++ g++-14 208s g++-14-aarch64-linux-gnu g++-aarch64-linux-gnu gcc gcc-14 208s gcc-14-aarch64-linux-gnu gcc-aarch64-linux-gnu gettext intltool-debian 208s libarchive-zip-perl libasan8 libcc1-0 libdebhelper-perl 208s libfile-stripnondeterminism-perl libgcc-14-dev libhwasan0 libisl23 libitm1 208s liblsan0 libmpc3 libpython3.13-minimal libpython3.13-stdlib libstdc++-14-dev 208s libtool libtsan2 libubsan1 m4 po-debconf pybuild-plugin-autopkgtest 208s python3-all python3-iniconfig python3-packaging python3-pluggy 208s python3-pytest python3.13 python3.13-minimal 208s Suggested packages: 208s autoconf-archive gnu-standards autoconf-doc cpp-doc gcc-14-locales 208s cpp-14-doc dh-make flit python3-build python3-installer python3-wheel 208s gcc-14-doc gcc-multilib manpages-dev flex bison gdb gcc-doc 208s gdb-aarch64-linux-gnu gettext-doc libasprintf-dev libgettextpo-dev 208s libstdc++-14-doc libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc 208s libmail-box-perl python3.13-venv python3.13-doc binfmt-support 208s Recommended packages: 208s libarchive-cpio-perl libltdl-dev libmail-sendmail-perl 208s The following NEW packages will be installed: 208s autoconf automake autopkgtest-satdep autopoint autotools-dev build-essential 208s cpp cpp-14 cpp-14-aarch64-linux-gnu cpp-aarch64-linux-gnu debhelper 208s debugedit dh-autoreconf dh-python dh-strip-nondeterminism dwz g++ g++-14 208s g++-14-aarch64-linux-gnu g++-aarch64-linux-gnu gcc gcc-14 208s gcc-14-aarch64-linux-gnu gcc-aarch64-linux-gnu gettext intltool-debian 208s libarchive-zip-perl libasan8 libcc1-0 libdebhelper-perl 208s libfile-stripnondeterminism-perl libgcc-14-dev libhwasan0 libisl23 libitm1 208s liblsan0 libmpc3 libpython3.13-minimal libpython3.13-stdlib libstdc++-14-dev 208s libtool libtsan2 libubsan1 m4 po-debconf pybuild-plugin-autopkgtest 208s python3-all python3-iniconfig python3-packaging python3-pluggy 208s python3-pytest python3.13 python3.13-minimal 208s 0 upgraded, 53 newly installed, 0 to remove and 0 not upgraded. 208s Need to get 70.4 MB/70.4 MB of archives. 208s After this operation, 245 MB of additional disk space will be used. 208s Get:1 /tmp/autopkgtest.NDSeuo/2-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [796 B] 208s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3.13-minimal arm64 3.13.0-2 [877 kB] 209s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-minimal arm64 3.13.0-2 [2100 kB] 209s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 m4 arm64 1.4.19-4build1 [240 kB] 209s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 autoconf all 2.72-3 [382 kB] 209s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 autotools-dev all 20220109.1 [44.9 kB] 209s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 automake all 1:1.16.5-1.3ubuntu1 [558 kB] 209s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 autopoint all 0.22.5-2 [616 kB] 209s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 libisl23 arm64 0.27-1 [676 kB] 209s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 libmpc3 arm64 1.3.1-1build2 [56.8 kB] 209s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp-14-aarch64-linux-gnu arm64 14.2.0-8ubuntu1 [10.6 MB] 209s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp-14 arm64 14.2.0-8ubuntu1 [1028 B] 209s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp-aarch64-linux-gnu arm64 4:14.1.0-2ubuntu1 [5452 B] 209s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp arm64 4:14.1.0-2ubuntu1 [22.5 kB] 209s Get:15 http://ftpmaster.internal/ubuntu plucky/main arm64 libcc1-0 arm64 14.2.0-8ubuntu1 [49.7 kB] 209s Get:16 http://ftpmaster.internal/ubuntu plucky/main arm64 libitm1 arm64 14.2.0-8ubuntu1 [27.8 kB] 209s Get:17 http://ftpmaster.internal/ubuntu plucky/main arm64 libasan8 arm64 14.2.0-8ubuntu1 [2893 kB] 210s Get:18 http://ftpmaster.internal/ubuntu plucky/main arm64 liblsan0 arm64 14.2.0-8ubuntu1 [1283 kB] 210s Get:19 http://ftpmaster.internal/ubuntu plucky/main arm64 libtsan2 arm64 14.2.0-8ubuntu1 [2686 kB] 210s Get:20 http://ftpmaster.internal/ubuntu plucky/main arm64 libubsan1 arm64 14.2.0-8ubuntu1 [1151 kB] 210s Get:21 http://ftpmaster.internal/ubuntu plucky/main arm64 libhwasan0 arm64 14.2.0-8ubuntu1 [1598 kB] 210s Get:22 http://ftpmaster.internal/ubuntu plucky/main arm64 libgcc-14-dev arm64 14.2.0-8ubuntu1 [2594 kB] 210s Get:23 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc-14-aarch64-linux-gnu arm64 14.2.0-8ubuntu1 [20.9 MB] 210s Get:24 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc-14 arm64 14.2.0-8ubuntu1 [518 kB] 210s Get:25 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc-aarch64-linux-gnu arm64 4:14.1.0-2ubuntu1 [1200 B] 210s Get:26 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc arm64 4:14.1.0-2ubuntu1 [4994 B] 210s Get:27 http://ftpmaster.internal/ubuntu plucky/main arm64 libstdc++-14-dev arm64 14.2.0-8ubuntu1 [2476 kB] 210s Get:28 http://ftpmaster.internal/ubuntu plucky/main arm64 g++-14-aarch64-linux-gnu arm64 14.2.0-8ubuntu1 [12.1 MB] 211s Get:29 http://ftpmaster.internal/ubuntu plucky/main arm64 g++-14 arm64 14.2.0-8ubuntu1 [19.9 kB] 211s Get:30 http://ftpmaster.internal/ubuntu plucky/main arm64 g++-aarch64-linux-gnu arm64 4:14.1.0-2ubuntu1 [958 B] 211s Get:31 http://ftpmaster.internal/ubuntu plucky/main arm64 g++ arm64 4:14.1.0-2ubuntu1 [1080 B] 211s Get:32 http://ftpmaster.internal/ubuntu plucky/main arm64 build-essential arm64 12.10ubuntu1 [4932 B] 211s Get:33 http://ftpmaster.internal/ubuntu plucky/main arm64 libdebhelper-perl all 13.20ubuntu1 [94.2 kB] 211s Get:34 http://ftpmaster.internal/ubuntu plucky/main arm64 libtool all 2.4.7-7build1 [166 kB] 211s Get:35 http://ftpmaster.internal/ubuntu plucky/main arm64 dh-autoreconf all 20 [16.1 kB] 211s Get:36 http://ftpmaster.internal/ubuntu plucky/main arm64 libarchive-zip-perl all 1.68-1 [90.2 kB] 211s Get:37 http://ftpmaster.internal/ubuntu plucky/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [20.1 kB] 211s Get:38 http://ftpmaster.internal/ubuntu plucky/main arm64 dh-strip-nondeterminism all 1.14.0-1 [5058 B] 211s Get:39 http://ftpmaster.internal/ubuntu plucky/main arm64 debugedit arm64 1:5.1-1 [45.9 kB] 211s Get:40 http://ftpmaster.internal/ubuntu plucky/main arm64 dwz arm64 0.15-1build6 [113 kB] 211s Get:41 http://ftpmaster.internal/ubuntu plucky/main arm64 gettext arm64 0.22.5-2 [930 kB] 211s Get:42 http://ftpmaster.internal/ubuntu plucky/main arm64 intltool-debian all 0.35.0+20060710.6 [23.2 kB] 211s Get:43 http://ftpmaster.internal/ubuntu plucky/main arm64 po-debconf all 1.0.21+nmu1 [233 kB] 211s Get:44 http://ftpmaster.internal/ubuntu plucky/main arm64 debhelper all 13.20ubuntu1 [893 kB] 211s Get:45 http://ftpmaster.internal/ubuntu plucky/universe arm64 dh-python all 6.20241024 [112 kB] 211s Get:46 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3.13-stdlib arm64 3.13.0-2 [2073 kB] 211s Get:47 http://ftpmaster.internal/ubuntu plucky/universe arm64 pybuild-plugin-autopkgtest all 6.20241024 [1746 B] 211s Get:48 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13 arm64 3.13.0-2 [719 kB] 211s Get:49 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-all arm64 3.12.7-1 [890 B] 211s Get:50 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-iniconfig all 1.1.1-2 [6024 B] 211s Get:51 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-packaging all 24.1-1 [41.4 kB] 211s Get:52 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pluggy all 1.5.0-1 [21.0 kB] 211s Get:53 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pytest all 8.3.3-1 [251 kB] 211s Fetched 70.4 MB in 3s (25.8 MB/s) 211s Selecting previously unselected package libpython3.13-minimal:arm64. 212s (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 ... 83236 files and directories currently installed.) 212s Preparing to unpack .../00-libpython3.13-minimal_3.13.0-2_arm64.deb ... 212s Unpacking libpython3.13-minimal:arm64 (3.13.0-2) ... 212s Selecting previously unselected package python3.13-minimal. 212s Preparing to unpack .../01-python3.13-minimal_3.13.0-2_arm64.deb ... 212s Unpacking python3.13-minimal (3.13.0-2) ... 212s Selecting previously unselected package m4. 212s Preparing to unpack .../02-m4_1.4.19-4build1_arm64.deb ... 212s Unpacking m4 (1.4.19-4build1) ... 212s Selecting previously unselected package autoconf. 212s Preparing to unpack .../03-autoconf_2.72-3_all.deb ... 212s Unpacking autoconf (2.72-3) ... 212s Selecting previously unselected package autotools-dev. 212s Preparing to unpack .../04-autotools-dev_20220109.1_all.deb ... 212s Unpacking autotools-dev (20220109.1) ... 212s Selecting previously unselected package automake. 212s Preparing to unpack .../05-automake_1%3a1.16.5-1.3ubuntu1_all.deb ... 212s Unpacking automake (1:1.16.5-1.3ubuntu1) ... 212s Selecting previously unselected package autopoint. 212s Preparing to unpack .../06-autopoint_0.22.5-2_all.deb ... 212s Unpacking autopoint (0.22.5-2) ... 212s Selecting previously unselected package libisl23:arm64. 212s Preparing to unpack .../07-libisl23_0.27-1_arm64.deb ... 212s Unpacking libisl23:arm64 (0.27-1) ... 212s Selecting previously unselected package libmpc3:arm64. 212s Preparing to unpack .../08-libmpc3_1.3.1-1build2_arm64.deb ... 212s Unpacking libmpc3:arm64 (1.3.1-1build2) ... 212s Selecting previously unselected package cpp-14-aarch64-linux-gnu. 212s Preparing to unpack .../09-cpp-14-aarch64-linux-gnu_14.2.0-8ubuntu1_arm64.deb ... 212s Unpacking cpp-14-aarch64-linux-gnu (14.2.0-8ubuntu1) ... 213s Selecting previously unselected package cpp-14. 213s Preparing to unpack .../10-cpp-14_14.2.0-8ubuntu1_arm64.deb ... 213s Unpacking cpp-14 (14.2.0-8ubuntu1) ... 213s Selecting previously unselected package cpp-aarch64-linux-gnu. 213s Preparing to unpack .../11-cpp-aarch64-linux-gnu_4%3a14.1.0-2ubuntu1_arm64.deb ... 213s Unpacking cpp-aarch64-linux-gnu (4:14.1.0-2ubuntu1) ... 213s Selecting previously unselected package cpp. 213s Preparing to unpack .../12-cpp_4%3a14.1.0-2ubuntu1_arm64.deb ... 213s Unpacking cpp (4:14.1.0-2ubuntu1) ... 213s Selecting previously unselected package libcc1-0:arm64. 213s Preparing to unpack .../13-libcc1-0_14.2.0-8ubuntu1_arm64.deb ... 213s Unpacking libcc1-0:arm64 (14.2.0-8ubuntu1) ... 213s Selecting previously unselected package libitm1:arm64. 213s Preparing to unpack .../14-libitm1_14.2.0-8ubuntu1_arm64.deb ... 213s Unpacking libitm1:arm64 (14.2.0-8ubuntu1) ... 213s Selecting previously unselected package libasan8:arm64. 213s Preparing to unpack .../15-libasan8_14.2.0-8ubuntu1_arm64.deb ... 213s Unpacking libasan8:arm64 (14.2.0-8ubuntu1) ... 213s Selecting previously unselected package liblsan0:arm64. 213s Preparing to unpack .../16-liblsan0_14.2.0-8ubuntu1_arm64.deb ... 213s Unpacking liblsan0:arm64 (14.2.0-8ubuntu1) ... 214s Selecting previously unselected package libtsan2:arm64. 214s Preparing to unpack .../17-libtsan2_14.2.0-8ubuntu1_arm64.deb ... 214s Unpacking libtsan2:arm64 (14.2.0-8ubuntu1) ... 214s Selecting previously unselected package libubsan1:arm64. 214s Preparing to unpack .../18-libubsan1_14.2.0-8ubuntu1_arm64.deb ... 214s Unpacking libubsan1:arm64 (14.2.0-8ubuntu1) ... 214s Selecting previously unselected package libhwasan0:arm64. 214s Preparing to unpack .../19-libhwasan0_14.2.0-8ubuntu1_arm64.deb ... 214s Unpacking libhwasan0:arm64 (14.2.0-8ubuntu1) ... 214s Selecting previously unselected package libgcc-14-dev:arm64. 214s Preparing to unpack .../20-libgcc-14-dev_14.2.0-8ubuntu1_arm64.deb ... 214s Unpacking libgcc-14-dev:arm64 (14.2.0-8ubuntu1) ... 214s Selecting previously unselected package gcc-14-aarch64-linux-gnu. 214s Preparing to unpack .../21-gcc-14-aarch64-linux-gnu_14.2.0-8ubuntu1_arm64.deb ... 214s Unpacking gcc-14-aarch64-linux-gnu (14.2.0-8ubuntu1) ... 214s Selecting previously unselected package gcc-14. 214s Preparing to unpack .../22-gcc-14_14.2.0-8ubuntu1_arm64.deb ... 214s Unpacking gcc-14 (14.2.0-8ubuntu1) ... 214s Selecting previously unselected package gcc-aarch64-linux-gnu. 214s Preparing to unpack .../23-gcc-aarch64-linux-gnu_4%3a14.1.0-2ubuntu1_arm64.deb ... 214s Unpacking gcc-aarch64-linux-gnu (4:14.1.0-2ubuntu1) ... 214s Selecting previously unselected package gcc. 214s Preparing to unpack .../24-gcc_4%3a14.1.0-2ubuntu1_arm64.deb ... 214s Unpacking gcc (4:14.1.0-2ubuntu1) ... 214s Selecting previously unselected package libstdc++-14-dev:arm64. 214s Preparing to unpack .../25-libstdc++-14-dev_14.2.0-8ubuntu1_arm64.deb ... 214s Unpacking libstdc++-14-dev:arm64 (14.2.0-8ubuntu1) ... 215s Selecting previously unselected package g++-14-aarch64-linux-gnu. 215s Preparing to unpack .../26-g++-14-aarch64-linux-gnu_14.2.0-8ubuntu1_arm64.deb ... 215s Unpacking g++-14-aarch64-linux-gnu (14.2.0-8ubuntu1) ... 215s Selecting previously unselected package g++-14. 215s Preparing to unpack .../27-g++-14_14.2.0-8ubuntu1_arm64.deb ... 215s Unpacking g++-14 (14.2.0-8ubuntu1) ... 215s Selecting previously unselected package g++-aarch64-linux-gnu. 215s Preparing to unpack .../28-g++-aarch64-linux-gnu_4%3a14.1.0-2ubuntu1_arm64.deb ... 215s Unpacking g++-aarch64-linux-gnu (4:14.1.0-2ubuntu1) ... 215s Selecting previously unselected package g++. 215s Preparing to unpack .../29-g++_4%3a14.1.0-2ubuntu1_arm64.deb ... 215s Unpacking g++ (4:14.1.0-2ubuntu1) ... 215s Selecting previously unselected package build-essential. 215s Preparing to unpack .../30-build-essential_12.10ubuntu1_arm64.deb ... 215s Unpacking build-essential (12.10ubuntu1) ... 215s Selecting previously unselected package libdebhelper-perl. 215s Preparing to unpack .../31-libdebhelper-perl_13.20ubuntu1_all.deb ... 215s Unpacking libdebhelper-perl (13.20ubuntu1) ... 215s Selecting previously unselected package libtool. 215s Preparing to unpack .../32-libtool_2.4.7-7build1_all.deb ... 215s Unpacking libtool (2.4.7-7build1) ... 215s Selecting previously unselected package dh-autoreconf. 215s Preparing to unpack .../33-dh-autoreconf_20_all.deb ... 215s Unpacking dh-autoreconf (20) ... 215s Selecting previously unselected package libarchive-zip-perl. 215s Preparing to unpack .../34-libarchive-zip-perl_1.68-1_all.deb ... 215s Unpacking libarchive-zip-perl (1.68-1) ... 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cpp-14-aarch64-linux-gnu (14.2.0-8ubuntu1) ... 222s Setting up libgcc-14-dev:arm64 (14.2.0-8ubuntu1) ... 222s Setting up libstdc++-14-dev:arm64 (14.2.0-8ubuntu1) ... 222s Setting up cpp-aarch64-linux-gnu (4:14.1.0-2ubuntu1) ... 222s Setting up cpp-14 (14.2.0-8ubuntu1) ... 222s Setting up cpp (4:14.1.0-2ubuntu1) ... 222s Setting up gcc-14-aarch64-linux-gnu (14.2.0-8ubuntu1) ... 222s Setting up gcc-aarch64-linux-gnu (4:14.1.0-2ubuntu1) ... 222s Setting up g++-14-aarch64-linux-gnu (14.2.0-8ubuntu1) ... 222s Setting up gcc-14 (14.2.0-8ubuntu1) ... 222s Setting up g++-aarch64-linux-gnu (4:14.1.0-2ubuntu1) ... 222s Setting up g++-14 (14.2.0-8ubuntu1) ... 222s Setting up libtool (2.4.7-7build1) ... 222s Setting up gcc (4:14.1.0-2ubuntu1) ... 222s Setting up dh-autoreconf (20) ... 222s Setting up g++ (4:14.1.0-2ubuntu1) ... 222s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 222s Setting up build-essential (12.10ubuntu1) ... 222s Setting up debhelper (13.20ubuntu1) ... 222s Setting up pybuild-plugin-autopkgtest (6.20241024) ... 222s Setting up autopkgtest-satdep (0) ... 222s Processing triggers for systemd (256.5-2ubuntu4) ... 222s Processing triggers for man-db (2.12.1-3) ... 223s Processing triggers for install-info (7.1.1-1) ... 223s Processing triggers for libc-bin (2.40-1ubuntu3) ... 240s (Reading database ... 86419 files and directories currently installed.) 240s Removing autopkgtest-satdep (0) ... 245s autopkgtest [11:14:10]: test pybuild-autopkgtest: pybuild-autopkgtest 245s autopkgtest [11:14:10]: test pybuild-autopkgtest: [----------------------- 246s # Pull test items that are otherwise uncaught by pybuild-autodep8. 246s mkdir -p ../../autopkgtest_tmp/build/seqmagick 246s cp -r /usr/lib/python3/dist-packages/seqmagick/test \ 246s ../../autopkgtest_tmp/build/seqmagick 246s pybuild-autopkgtest 247s I: pybuild base:311: cd /tmp/autopkgtest.NDSeuo/autopkgtest_tmp/build; python3.13 -m pytest 248s ============================= test session starts ============================== 248s platform linux -- Python 3.13.0, pytest-8.3.3, pluggy-1.5.0 248s rootdir: /tmp/autopkgtest.NDSeuo/autopkgtest_tmp/build 248s plugins: typeguard-4.4.1 248s collected 54 items / 4 errors 248s 248s ==================================== ERRORS ==================================== 248s _____ ERROR collecting seqmagick/test/test_subcommands_backtrans_align.py ______ 248s ImportError while importing test module '/tmp/autopkgtest.NDSeuo/autopkgtest_tmp/build/seqmagick/test/test_subcommands_backtrans_align.py'. 248s Hint: make sure your test modules/packages have valid Python names. 248s Traceback: 248s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 248s return _bootstrap._gcd_import(name[level:], package, level) 248s seqmagick/test/test_subcommands_backtrans_align.py:7: in 248s from seqmagick.subcommands import backtrans_align 248s /usr/lib/python3/dist-packages/seqmagick/subcommands/backtrans_align.py:15: in 248s from Bio import SeqIO 248s /usr/lib/python3/dist-packages/Bio/SeqIO/__init__.py:401: in 248s from Bio.SeqIO import TwoBitIO 248s /usr/lib/python3/dist-packages/Bio/SeqIO/TwoBitIO.py:80: in 248s raise MissingPythonDependencyError( 248s E Bio.MissingPythonDependencyError: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 248s _________ ERROR collecting seqmagick/test/test_subcommands_convert.py __________ 248s ImportError while importing test module '/tmp/autopkgtest.NDSeuo/autopkgtest_tmp/build/seqmagick/test/test_subcommands_convert.py'. 248s Hint: make sure your test modules/packages have valid Python names. 248s Traceback: 248s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 248s return _bootstrap._gcd_import(name[level:], package, level) 248s seqmagick/test/test_subcommands_convert.py:10: in 248s from seqmagick.subcommands import convert 248s /usr/lib/python3/dist-packages/seqmagick/subcommands/convert.py:9: in 248s from Bio import SeqIO 248s /usr/lib/python3/dist-packages/Bio/SeqIO/__init__.py:401: in 248s from Bio.SeqIO import TwoBitIO 248s /usr/lib/python3/dist-packages/Bio/SeqIO/TwoBitIO.py:80: in 248s raise MissingPythonDependencyError( 248s E Bio.MissingPythonDependencyError: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 248s ______ ERROR collecting seqmagick/test/test_subcommands_quality_filter.py ______ 248s ImportError while importing test module '/tmp/autopkgtest.NDSeuo/autopkgtest_tmp/build/seqmagick/test/test_subcommands_quality_filter.py'. 248s Hint: make sure your test modules/packages have valid Python names. 248s Traceback: 248s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 248s return _bootstrap._gcd_import(name[level:], package, level) 248s seqmagick/test/test_subcommands_quality_filter.py:8: in 248s from seqmagick.subcommands import quality_filter 248s /usr/lib/python3/dist-packages/seqmagick/subcommands/quality_filter.py:13: in 248s from Bio import SeqIO 248s /usr/lib/python3/dist-packages/Bio/SeqIO/__init__.py:401: in 248s from Bio.SeqIO import TwoBitIO 248s /usr/lib/python3/dist-packages/Bio/SeqIO/TwoBitIO.py:80: in 248s raise MissingPythonDependencyError( 248s E Bio.MissingPythonDependencyError: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 248s ______________ ERROR collecting seqmagick/test/test_transform.py _______________ 248s ImportError while importing test module '/tmp/autopkgtest.NDSeuo/autopkgtest_tmp/build/seqmagick/test/test_transform.py'. 248s Hint: make sure your test modules/packages have valid Python names. 248s Traceback: 248s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 248s return _bootstrap._gcd_import(name[level:], package, level) 248s seqmagick/test/test_transform.py:10: in 248s from Bio import SeqIO 248s /usr/lib/python3/dist-packages/Bio/SeqIO/__init__.py:401: in 248s from Bio.SeqIO import TwoBitIO 248s /usr/lib/python3/dist-packages/Bio/SeqIO/TwoBitIO.py:80: in 248s raise MissingPythonDependencyError( 248s E Bio.MissingPythonDependencyError: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 248s =========================== short test summary info ============================ 248s ERROR seqmagick/test/test_subcommands_backtrans_align.py 248s ERROR seqmagick/test/test_subcommands_convert.py 248s ERROR seqmagick/test/test_subcommands_quality_filter.py 248s ERROR seqmagick/test/test_transform.py 248s !!!!!!!!!!!!!!!!!!! Interrupted: 4 errors during collection !!!!!!!!!!!!!!!!!!!! 248s ============================== 4 errors in 0.65s =============================== 248s E: pybuild pybuild:389: test: plugin distutils failed with: exit code=2: cd /tmp/autopkgtest.NDSeuo/autopkgtest_tmp/build; python3.13 -m pytest 248s I: pybuild base:311: cd /tmp/autopkgtest.NDSeuo/autopkgtest_tmp/build; python3.12 -m pytest 248s ============================= test session starts ============================== 248s platform linux -- Python 3.12.7, pytest-8.3.3, pluggy-1.5.0 248s rootdir: /tmp/autopkgtest.NDSeuo/autopkgtest_tmp/build 248s plugins: typeguard-4.4.1 248s collected 154 items 248s 249s seqmagick/test/integration/test_convert.py .ss.............. [ 11%] 249s seqmagick/test/integration/test_extract_ids.py ..ss.. [ 14%] 249s seqmagick/test/integration/test_info.py ...s [ 17%] 249s seqmagick/test/integration/test_mogrify.py .s. [ 19%] 249s seqmagick/test/test_subcommands_backtrans_align.py ......... [ 25%] 249s seqmagick/test/test_subcommands_common.py ..................s..... [ 40%] 249s seqmagick/test/test_subcommands_convert.py ...... [ 44%] 249s seqmagick/test/test_subcommands_quality_filter.py ...................... [ 59%] 249s .... [ 61%] 249s seqmagick/test/test_transform.py ....................................... [ 87%] 249s .................... [100%] 249s 249s ======================== 147 passed, 7 skipped in 1.02s ======================== 249s pybuild-autopkgtest: error: pybuild --autopkgtest --test-pytest -i python{version} -p "3.13 3.12" returned exit code 13 249s make: *** [/tmp/5dpWXw7J6o/run:4: pybuild-autopkgtest] Error 25 249s pybuild-autopkgtest: error: /tmp/5dpWXw7J6o/run pybuild-autopkgtest returned exit code 2 250s autopkgtest [11:14:15]: test pybuild-autopkgtest: -----------------------] 251s autopkgtest [11:14:16]: test pybuild-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 251s pybuild-autopkgtest FAIL non-zero exit status 25 252s autopkgtest [11:14:17]: @@@@@@@@@@@@@@@@@@@@ summary 252s run-unit-test PASS 252s pybuild-autopkgtest FAIL non-zero exit status 25 270s nova [W] Skipping flock in bos03-arm64 270s Creating nova instance adt-plucky-arm64-seqmagick-20241113-111004-juju-7f2275-prod-proposed-migration-environment-15-6f7f3408-af16-451d-9da5-74b9659b834a from image adt/ubuntu-plucky-arm64-server-20241113.img (UUID 2d7760e6-2439-4200-89d6-5ed33e5c6330)...