0s autopkgtest [03:40:12]: starting date and time: 2025-07-12 03:40:12+0000 0s autopkgtest [03:40:12]: git checkout: 508d4a25 a-v-ssh wait_for_ssh: demote "ssh connection failed" to a debug message 0s autopkgtest [03:40:12]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.k0qnu9tk/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,localhost,localdomain,internal,login.ubuntu.com,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com\n" >> /etc/environment' --apt-pocket=proposed=src:python-reportlab --apt-upgrade python-biopython --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=python-reportlab/4.4.2-1 -- lxd -r lxd-armhf-10.145.243.232 lxd-armhf-10.145.243.232:autopkgtest/ubuntu/questing/armhf 28s autopkgtest [03:40:40]: testbed dpkg architecture: armhf 29s autopkgtest [03:40:41]: testbed apt version: 3.1.3 33s autopkgtest [03:40:45]: @@@@@@@@@@@@@@@@@@@@ test bed setup 35s autopkgtest [03:40:47]: testbed release detected to be: None 42s autopkgtest [03:40:54]: updating testbed package index (apt update) 43s Get:1 http://ftpmaster.internal/ubuntu questing-proposed InRelease [249 kB] 44s Hit:2 http://ftpmaster.internal/ubuntu questing InRelease 44s Hit:3 http://ftpmaster.internal/ubuntu questing-updates InRelease 44s Hit:4 http://ftpmaster.internal/ubuntu questing-security InRelease 44s Get:5 http://ftpmaster.internal/ubuntu questing-proposed/main Sources [39.9 kB] 44s Get:6 http://ftpmaster.internal/ubuntu questing-proposed/universe Sources [207 kB] 44s Get:7 http://ftpmaster.internal/ubuntu questing-proposed/multiverse Sources [15.4 kB] 44s Get:8 http://ftpmaster.internal/ubuntu questing-proposed/main armhf Packages [54.2 kB] 44s Get:9 http://ftpmaster.internal/ubuntu questing-proposed/universe armhf Packages [168 kB] 44s Get:10 http://ftpmaster.internal/ubuntu questing-proposed/multiverse armhf Packages [3452 B] 44s Fetched 738 kB in 1s (935 kB/s) 45s Reading package lists... 50s autopkgtest [03:41:02]: upgrading testbed (apt dist-upgrade and autopurge) 52s Reading package lists... 52s Building dependency tree... 52s Reading state information... 52s Calculating upgrade... 53s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 55s Reading package lists... 55s Building dependency tree... 55s Reading state information... 55s Solving dependencies... 55s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 57s autopkgtest [03:41:09]: rebooting testbed after setup commands that affected boot 94s autopkgtest [03:41:46]: testbed running kernel: Linux 6.8.0-58-generic #60~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Fri Mar 28 14:48:37 UTC 2 117s autopkgtest [03:42:09]: @@@@@@@@@@@@@@@@@@@@ apt-source python-biopython 134s Get:1 http://ftpmaster.internal/ubuntu questing/universe python-biopython 1.85+dfsg-4 (dsc) [3070 B] 134s Get:2 http://ftpmaster.internal/ubuntu questing/universe python-biopython 1.85+dfsg-4 (tar) [14.6 MB] 134s Get:3 http://ftpmaster.internal/ubuntu questing/universe python-biopython 1.85+dfsg-4 (diff) [42.8 kB] 134s gpgv: Signature made Fri Apr 11 19:33:28 2025 UTC 134s gpgv: using RSA key D54C3BFAFFB042DE382DA5D741CE7F0B9F1B8B32 134s gpgv: Can't check signature: No public key 134s dpkg-source: warning: cannot verify inline signature for ./python-biopython_1.85+dfsg-4.dsc: no acceptable signature found 135s autopkgtest [03:42:27]: testing package python-biopython version 1.85+dfsg-4 137s autopkgtest [03:42:29]: build not needed 143s autopkgtest [03:42:35]: test dependencies: preparing testbed 144s Reading package lists... 145s Building dependency tree... 145s Reading state information... 145s Solving dependencies... 145s The following NEW packages will be installed: 145s fontconfig-config fonts-urw-base35 libblas3 libcairo2 libdeflate0 145s libfontconfig1 libfontenc1 libfreetype6 libgfortran5 libgomp1 libgraphite2-3 145s libharfbuzz0b libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 libjs-jquery 145s libjs-sphinxdoc libjs-underscore liblapack3 liblcms2-2 liblerc4 libopenjp2-7 145s libpixman-1-0 libraqm0 libsharpyuv0 libtiff6 libwebp7 libwebpdemux2 145s libwebpmux3 libxcb-render0 libxcb-shm0 libxrender1 python-biopython-doc 145s python3-all python3-biopython python3-biopython-sql python3-cairo 145s python3-charset-normalizer python3-freetype python3-numpy python3-numpy-dev 145s python3-pil python3-reportlab python3-rlpycairo sgml-base w3c-sgml-lib 145s x11-common xfonts-encodings xfonts-utils xml-core 145s 0 upgraded, 51 newly installed, 0 to remove and 0 not upgraded. 145s Need to get 43.7 MB of archives. 145s After this operation, 113 MB of additional disk space will be used. 145s Get:1 http://ftpmaster.internal/ubuntu questing/main armhf python3-numpy-dev armhf 1:2.2.4+ds-1ubuntu1 [141 kB] 146s Get:2 http://ftpmaster.internal/ubuntu questing/main armhf libblas3 armhf 3.12.1-2build1 [133 kB] 146s Get:3 http://ftpmaster.internal/ubuntu questing/main armhf libgfortran5 armhf 15.1.0-8ubuntu1 [334 kB] 146s Get:4 http://ftpmaster.internal/ubuntu questing/main armhf liblapack3 armhf 3.12.1-2build1 [2092 kB] 146s Get:5 http://ftpmaster.internal/ubuntu questing/main armhf python3-numpy armhf 1:2.2.4+ds-1ubuntu1 [3724 kB] 146s Get:6 http://ftpmaster.internal/ubuntu questing/main armhf libfontenc1 armhf 1:1.1.8-1build1 [11.5 kB] 146s Get:7 http://ftpmaster.internal/ubuntu questing/main armhf libfreetype6 armhf 2.13.3+dfsg-1 [330 kB] 146s Get:8 http://ftpmaster.internal/ubuntu questing/main armhf x11-common all 1:7.7+24ubuntu1 [22.4 kB] 146s Get:9 http://ftpmaster.internal/ubuntu questing/main armhf xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 146s Get:10 http://ftpmaster.internal/ubuntu questing/main armhf xfonts-utils armhf 1:7.7+7 [90.6 kB] 146s Get:11 http://ftpmaster.internal/ubuntu questing/main armhf fonts-urw-base35 all 20200910-8 [11.0 MB] 146s Get:12 http://ftpmaster.internal/ubuntu questing/main armhf fontconfig-config armhf 2.15.0-2.3ubuntu1 [38.1 kB] 146s Get:13 http://ftpmaster.internal/ubuntu questing/main armhf libfontconfig1 armhf 2.15.0-2.3ubuntu1 [114 kB] 146s Get:14 http://ftpmaster.internal/ubuntu questing/main armhf libpixman-1-0 armhf 0.44.0-3 [183 kB] 146s Get:15 http://ftpmaster.internal/ubuntu questing/main armhf libxcb-render0 armhf 1.17.0-2 [15.3 kB] 146s Get:16 http://ftpmaster.internal/ubuntu questing/main armhf libxcb-shm0 armhf 1.17.0-2 [5774 B] 146s Get:17 http://ftpmaster.internal/ubuntu questing/main armhf libxrender1 armhf 1:0.9.12-1 [16.6 kB] 146s Get:18 http://ftpmaster.internal/ubuntu questing/main armhf libcairo2 armhf 1.18.4-1 [483 kB] 146s Get:19 http://ftpmaster.internal/ubuntu questing/main armhf libdeflate0 armhf 1.23-2 [38.7 kB] 146s Get:20 http://ftpmaster.internal/ubuntu questing/main armhf libgomp1 armhf 15.1.0-8ubuntu1 [129 kB] 146s Get:21 http://ftpmaster.internal/ubuntu questing/main armhf libgraphite2-3 armhf 1.3.14-2ubuntu1 [64.8 kB] 146s Get:22 http://ftpmaster.internal/ubuntu questing/main armhf libharfbuzz0b armhf 10.2.0-1 [464 kB] 147s Get:23 http://ftpmaster.internal/ubuntu questing/main armhf libimagequant0 armhf 2.18.0-1build1 [31.1 kB] 147s Get:24 http://ftpmaster.internal/ubuntu questing/main armhf libjpeg-turbo8 armhf 2.1.5-3ubuntu2 [127 kB] 147s Get:25 http://ftpmaster.internal/ubuntu questing/main armhf libjpeg8 armhf 8c-2ubuntu11 [2148 B] 147s Get:26 http://ftpmaster.internal/ubuntu questing/main armhf libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 147s Get:27 http://ftpmaster.internal/ubuntu questing/main armhf libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 147s Get:28 http://ftpmaster.internal/ubuntu questing/main armhf libjs-sphinxdoc all 8.2.3-1ubuntu2 [28.0 kB] 147s Get:29 http://ftpmaster.internal/ubuntu questing/main armhf liblcms2-2 armhf 2.16-2 [137 kB] 147s Get:30 http://ftpmaster.internal/ubuntu questing/main armhf liblerc4 armhf 4.0.0+ds-5ubuntu1 [160 kB] 147s Get:31 http://ftpmaster.internal/ubuntu questing/main armhf libraqm0 armhf 0.10.2-1 [12.4 kB] 147s Get:32 http://ftpmaster.internal/ubuntu questing/main armhf libsharpyuv0 armhf 1.5.0-0.1 [16.4 kB] 147s Get:33 http://ftpmaster.internal/ubuntu questing/main armhf libjbig0 armhf 2.1-6.1ubuntu2 [24.9 kB] 147s Get:34 http://ftpmaster.internal/ubuntu questing/main armhf libwebp7 armhf 1.5.0-0.1 [188 kB] 147s Get:35 http://ftpmaster.internal/ubuntu questing/main armhf libtiff6 armhf 4.7.0-3ubuntu1 [184 kB] 147s Get:36 http://ftpmaster.internal/ubuntu questing/main armhf libwebpdemux2 armhf 1.5.0-0.1 [11.5 kB] 147s Get:37 http://ftpmaster.internal/ubuntu questing/main armhf libwebpmux3 armhf 1.5.0-0.1 [22.4 kB] 147s Get:38 http://ftpmaster.internal/ubuntu questing/universe armhf python-biopython-doc all 1.85+dfsg-4 [18.2 MB] 147s Get:39 http://ftpmaster.internal/ubuntu questing/main armhf python3-all armhf 3.13.5-1 [882 B] 147s Get:40 http://ftpmaster.internal/ubuntu questing/universe armhf python3-charset-normalizer armhf 3.4.2-1 [122 kB] 147s Get:41 http://ftpmaster.internal/ubuntu questing/main armhf libopenjp2-7 armhf 2.5.3-2 [172 kB] 147s Get:42 http://ftpmaster.internal/ubuntu questing/main armhf python3-pil armhf 11.1.0-5build1 [435 kB] 147s Get:43 http://ftpmaster.internal/ubuntu questing/main armhf python3-cairo armhf 1.27.0-2 [115 kB] 147s Get:44 http://ftpmaster.internal/ubuntu questing/universe armhf python3-freetype all 2.5.1-1 [92.3 kB] 147s Get:45 http://ftpmaster.internal/ubuntu questing/universe armhf python3-rlpycairo all 0.3.0-3 [9130 B] 147s Get:46 http://ftpmaster.internal/ubuntu questing-proposed/universe armhf python3-reportlab all 4.4.2-1 [1145 kB] 147s Get:47 http://ftpmaster.internal/ubuntu questing/main armhf sgml-base all 1.31+nmu1 [11.0 kB] 147s Get:48 http://ftpmaster.internal/ubuntu questing/main armhf xml-core all 0.19 [20.3 kB] 147s Get:49 http://ftpmaster.internal/ubuntu questing/universe armhf w3c-sgml-lib all 1.3-3 [280 kB] 147s Get:50 http://ftpmaster.internal/ubuntu questing/universe armhf python3-biopython armhf 1.85+dfsg-4 [1692 kB] 147s Get:51 http://ftpmaster.internal/ubuntu questing/universe armhf python3-biopython-sql all 1.85+dfsg-4 [26.4 kB] 148s Fetched 43.7 MB in 2s (21.9 MB/s) 148s Selecting previously unselected package python3-numpy-dev:armhf. 148s (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 ... 59841 files and directories currently installed.) 148s Preparing to unpack .../00-python3-numpy-dev_1%3a2.2.4+ds-1ubuntu1_armhf.deb ... 148s Unpacking python3-numpy-dev:armhf (1:2.2.4+ds-1ubuntu1) ... 148s Selecting previously unselected package libblas3:armhf. 148s Preparing to unpack .../01-libblas3_3.12.1-2build1_armhf.deb ... 148s Unpacking libblas3:armhf (3.12.1-2build1) ... 148s Selecting previously unselected package libgfortran5:armhf. 148s Preparing to unpack .../02-libgfortran5_15.1.0-8ubuntu1_armhf.deb ... 148s Unpacking libgfortran5:armhf (15.1.0-8ubuntu1) ... 148s Selecting previously unselected package liblapack3:armhf. 148s Preparing to unpack .../03-liblapack3_3.12.1-2build1_armhf.deb ... 148s Unpacking liblapack3:armhf (3.12.1-2build1) ... 148s Selecting previously unselected package python3-numpy. 148s Preparing to unpack .../04-python3-numpy_1%3a2.2.4+ds-1ubuntu1_armhf.deb ... 148s Unpacking python3-numpy (1:2.2.4+ds-1ubuntu1) ... 148s Selecting previously unselected package libfontenc1:armhf. 148s Preparing to unpack .../05-libfontenc1_1%3a1.1.8-1build1_armhf.deb ... 148s Unpacking libfontenc1:armhf (1:1.1.8-1build1) ... 148s Selecting previously unselected package libfreetype6:armhf. 148s Preparing to unpack .../06-libfreetype6_2.13.3+dfsg-1_armhf.deb ... 148s Unpacking libfreetype6:armhf (2.13.3+dfsg-1) ... 148s Selecting previously unselected package x11-common. 148s Preparing to unpack .../07-x11-common_1%3a7.7+24ubuntu1_all.deb ... 148s Unpacking x11-common (1:7.7+24ubuntu1) ... 148s Selecting previously unselected package xfonts-encodings. 148s Preparing to unpack .../08-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 148s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 148s Selecting previously unselected package xfonts-utils. 148s Preparing to unpack .../09-xfonts-utils_1%3a7.7+7_armhf.deb ... 148s Unpacking xfonts-utils (1:7.7+7) ... 148s Selecting previously unselected package fonts-urw-base35. 148s Preparing to unpack .../10-fonts-urw-base35_20200910-8_all.deb ... 149s Unpacking fonts-urw-base35 (20200910-8) ... 149s Selecting previously unselected package fontconfig-config. 149s Preparing to unpack .../11-fontconfig-config_2.15.0-2.3ubuntu1_armhf.deb ... 149s Unpacking fontconfig-config (2.15.0-2.3ubuntu1) ... 149s Selecting previously unselected package libfontconfig1:armhf. 149s Preparing to unpack .../12-libfontconfig1_2.15.0-2.3ubuntu1_armhf.deb ... 149s Unpacking libfontconfig1:armhf (2.15.0-2.3ubuntu1) ... 149s Selecting previously unselected package libpixman-1-0:armhf. 149s Preparing to unpack .../13-libpixman-1-0_0.44.0-3_armhf.deb ... 149s Unpacking libpixman-1-0:armhf (0.44.0-3) ... 149s Selecting previously unselected package libxcb-render0:armhf. 149s Preparing to unpack .../14-libxcb-render0_1.17.0-2_armhf.deb ... 149s Unpacking libxcb-render0:armhf (1.17.0-2) ... 149s Selecting previously unselected package libxcb-shm0:armhf. 149s Preparing to unpack .../15-libxcb-shm0_1.17.0-2_armhf.deb ... 149s Unpacking libxcb-shm0:armhf (1.17.0-2) ... 149s Selecting previously unselected package libxrender1:armhf. 149s Preparing to unpack .../16-libxrender1_1%3a0.9.12-1_armhf.deb ... 149s Unpacking libxrender1:armhf (1:0.9.12-1) ... 149s Selecting previously unselected package libcairo2:armhf. 149s Preparing to unpack .../17-libcairo2_1.18.4-1_armhf.deb ... 149s Unpacking libcairo2:armhf (1.18.4-1) ... 149s Selecting previously unselected package libdeflate0:armhf. 149s Preparing to unpack .../18-libdeflate0_1.23-2_armhf.deb ... 149s Unpacking libdeflate0:armhf (1.23-2) ... 149s Selecting previously unselected package libgomp1:armhf. 149s Preparing to unpack .../19-libgomp1_15.1.0-8ubuntu1_armhf.deb ... 149s Unpacking libgomp1:armhf (15.1.0-8ubuntu1) ... 149s Selecting previously unselected package libgraphite2-3:armhf. 149s Preparing to unpack .../20-libgraphite2-3_1.3.14-2ubuntu1_armhf.deb ... 149s Unpacking libgraphite2-3:armhf (1.3.14-2ubuntu1) ... 149s Selecting previously unselected package libharfbuzz0b:armhf. 149s Preparing to unpack .../21-libharfbuzz0b_10.2.0-1_armhf.deb ... 149s Unpacking libharfbuzz0b:armhf (10.2.0-1) ... 149s Selecting previously unselected package libimagequant0:armhf. 149s Preparing to unpack .../22-libimagequant0_2.18.0-1build1_armhf.deb ... 149s Unpacking libimagequant0:armhf (2.18.0-1build1) ... 149s Selecting previously unselected package libjpeg-turbo8:armhf. 149s Preparing to unpack .../23-libjpeg-turbo8_2.1.5-3ubuntu2_armhf.deb ... 149s Unpacking libjpeg-turbo8:armhf (2.1.5-3ubuntu2) ... 149s Selecting previously unselected package libjpeg8:armhf. 149s Preparing to unpack .../24-libjpeg8_8c-2ubuntu11_armhf.deb ... 149s Unpacking libjpeg8:armhf (8c-2ubuntu11) ... 149s Selecting previously unselected package libjs-jquery. 149s Preparing to unpack .../25-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 149s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 149s Selecting previously unselected package libjs-underscore. 149s Preparing to unpack .../26-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 149s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 149s Selecting previously unselected package libjs-sphinxdoc. 149s Preparing to unpack .../27-libjs-sphinxdoc_8.2.3-1ubuntu2_all.deb ... 149s Unpacking libjs-sphinxdoc (8.2.3-1ubuntu2) ... 149s Selecting previously unselected package liblcms2-2:armhf. 149s Preparing to unpack .../28-liblcms2-2_2.16-2_armhf.deb ... 149s Unpacking liblcms2-2:armhf (2.16-2) ... 150s Selecting previously unselected package liblerc4:armhf. 150s Preparing to unpack .../29-liblerc4_4.0.0+ds-5ubuntu1_armhf.deb ... 150s Unpacking liblerc4:armhf (4.0.0+ds-5ubuntu1) ... 150s Selecting previously unselected package libraqm0:armhf. 150s Preparing to unpack .../30-libraqm0_0.10.2-1_armhf.deb ... 150s Unpacking libraqm0:armhf (0.10.2-1) ... 150s Selecting previously unselected package libsharpyuv0:armhf. 150s Preparing to unpack .../31-libsharpyuv0_1.5.0-0.1_armhf.deb ... 150s Unpacking libsharpyuv0:armhf (1.5.0-0.1) ... 150s Selecting previously unselected package libjbig0:armhf. 150s Preparing to unpack .../32-libjbig0_2.1-6.1ubuntu2_armhf.deb ... 150s Unpacking libjbig0:armhf (2.1-6.1ubuntu2) ... 150s Selecting previously unselected package libwebp7:armhf. 150s Preparing to unpack .../33-libwebp7_1.5.0-0.1_armhf.deb ... 150s Unpacking libwebp7:armhf (1.5.0-0.1) ... 150s Selecting previously unselected package libtiff6:armhf. 150s Preparing to unpack .../34-libtiff6_4.7.0-3ubuntu1_armhf.deb ... 150s Unpacking libtiff6:armhf (4.7.0-3ubuntu1) ... 150s Selecting previously unselected package libwebpdemux2:armhf. 150s Preparing to unpack .../35-libwebpdemux2_1.5.0-0.1_armhf.deb ... 150s Unpacking libwebpdemux2:armhf (1.5.0-0.1) ... 150s Selecting previously unselected package libwebpmux3:armhf. 150s Preparing to unpack .../36-libwebpmux3_1.5.0-0.1_armhf.deb ... 150s Unpacking libwebpmux3:armhf (1.5.0-0.1) ... 150s Selecting previously unselected package python-biopython-doc. 150s Preparing to unpack .../37-python-biopython-doc_1.85+dfsg-4_all.deb ... 150s Unpacking python-biopython-doc (1.85+dfsg-4) ... 151s Selecting previously unselected package python3-all. 151s Preparing to unpack .../38-python3-all_3.13.5-1_armhf.deb ... 151s Unpacking python3-all (3.13.5-1) ... 151s Selecting previously unselected package python3-charset-normalizer. 151s Preparing to unpack .../39-python3-charset-normalizer_3.4.2-1_armhf.deb ... 151s Unpacking python3-charset-normalizer (3.4.2-1) ... 151s Selecting previously unselected package libopenjp2-7:armhf. 151s Preparing to unpack .../40-libopenjp2-7_2.5.3-2_armhf.deb ... 151s Unpacking libopenjp2-7:armhf (2.5.3-2) ... 151s Selecting previously unselected package python3-pil:armhf. 151s Preparing to unpack .../41-python3-pil_11.1.0-5build1_armhf.deb ... 151s Unpacking python3-pil:armhf (11.1.0-5build1) ... 151s Selecting previously unselected package python3-cairo. 151s Preparing to unpack .../42-python3-cairo_1.27.0-2_armhf.deb ... 151s Unpacking python3-cairo (1.27.0-2) ... 151s Selecting previously unselected package python3-freetype. 151s Preparing to unpack .../43-python3-freetype_2.5.1-1_all.deb ... 151s Unpacking python3-freetype (2.5.1-1) ... 151s Selecting previously unselected package python3-rlpycairo. 151s Preparing to unpack .../44-python3-rlpycairo_0.3.0-3_all.deb ... 151s Unpacking python3-rlpycairo (0.3.0-3) ... 151s Selecting previously unselected package python3-reportlab. 151s Preparing to unpack .../45-python3-reportlab_4.4.2-1_all.deb ... 151s Unpacking python3-reportlab (4.4.2-1) ... 151s Selecting previously unselected package sgml-base. 151s Preparing to unpack .../46-sgml-base_1.31+nmu1_all.deb ... 151s Unpacking sgml-base (1.31+nmu1) ... 151s Selecting previously unselected package xml-core. 151s Preparing to unpack .../47-xml-core_0.19_all.deb ... 151s Unpacking xml-core (0.19) ... 152s Selecting previously unselected package w3c-sgml-lib. 152s Preparing to unpack .../48-w3c-sgml-lib_1.3-3_all.deb ... 152s Unpacking w3c-sgml-lib (1.3-3) ... 152s Selecting previously unselected package python3-biopython. 152s Preparing to unpack .../49-python3-biopython_1.85+dfsg-4_armhf.deb ... 152s Unpacking python3-biopython (1.85+dfsg-4) ... 152s Selecting previously unselected package python3-biopython-sql. 152s Preparing to unpack .../50-python3-biopython-sql_1.85+dfsg-4_all.deb ... 152s Unpacking python3-biopython-sql (1.85+dfsg-4) ... 152s Setting up libgraphite2-3:armhf (1.3.14-2ubuntu1) ... 152s Setting up liblcms2-2:armhf (2.16-2) ... 152s Setting up libpixman-1-0:armhf (0.44.0-3) ... 152s Setting up libsharpyuv0:armhf (1.5.0-0.1) ... 152s Setting up liblerc4:armhf (4.0.0+ds-5ubuntu1) ... 152s Setting up libxrender1:armhf (1:0.9.12-1) ... 152s Setting up libxcb-render0:armhf (1.17.0-2) ... 152s Setting up python3-charset-normalizer (3.4.2-1) ... 152s Setting up x11-common (1:7.7+24ubuntu1) ... 152s Setting up libdeflate0:armhf (1.23-2) ... 152s Setting up python3-all (3.13.5-1) ... 152s Setting up libxcb-shm0:armhf (1.17.0-2) ... 152s Setting up libgomp1:armhf (15.1.0-8ubuntu1) ... 152s Setting up libjbig0:armhf (2.1-6.1ubuntu2) ... 152s Setting up libfontenc1:armhf (1:1.1.8-1build1) ... 152s Setting up libblas3:armhf (3.12.1-2build1) ... 152s 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 152s Setting up libfreetype6:armhf (2.13.3+dfsg-1) ... 152s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 152s Setting up libimagequant0:armhf (2.18.0-1build1) ... 152s Setting up python3-numpy-dev:armhf (1:2.2.4+ds-1ubuntu1) ... 152s Setting up libjpeg-turbo8:armhf (2.1.5-3ubuntu2) ... 152s Setting up libgfortran5:armhf (15.1.0-8ubuntu1) ... 152s Setting up libwebp7:armhf (1.5.0-0.1) ... 152s Setting up libopenjp2-7:armhf (2.5.3-2) ... 152s Setting up libharfbuzz0b:armhf (10.2.0-1) ... 152s Setting up sgml-base (1.31+nmu1) ... 152s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 152s Setting up libwebpmux3:armhf (1.5.0-0.1) ... 152s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 152s Setting up libjpeg8:armhf (8c-2ubuntu11) ... 152s Setting up liblapack3:armhf (3.12.1-2build1) ... 152s 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 152s Setting up libwebpdemux2:armhf (1.5.0-0.1) ... 152s Setting up python3-freetype (2.5.1-1) ... 152s Setting up xfonts-utils (1:7.7+7) ... 152s Setting up libraqm0:armhf (0.10.2-1) ... 152s Setting up python3-numpy (1:2.2.4+ds-1ubuntu1) ... 154s Setting up libjs-sphinxdoc (8.2.3-1ubuntu2) ... 154s Setting up python-biopython-doc (1.85+dfsg-4) ... 154s Setting up libtiff6:armhf (4.7.0-3ubuntu1) ... 154s Setting up xml-core (0.19) ... 154s Setting up fonts-urw-base35 (20200910-8) ... 154s Setting up python3-pil:armhf (11.1.0-5build1) ... 154s Setting up fontconfig-config (2.15.0-2.3ubuntu1) ... 155s Setting up libfontconfig1:armhf (2.15.0-2.3ubuntu1) ... 155s Setting up libcairo2:armhf (1.18.4-1) ... 155s Setting up python3-cairo (1.27.0-2) ... 155s Setting up python3-rlpycairo (0.3.0-3) ... 155s Setting up python3-reportlab (4.4.2-1) ... 156s Processing triggers for libc-bin (2.41-6ubuntu2) ... 156s Processing triggers for man-db (2.13.1-1) ... 157s Processing triggers for sgml-base (1.31+nmu1) ... 157s Setting up w3c-sgml-lib (1.3-3) ... 183s Setting up python3-biopython (1.85+dfsg-4) ... 184s Setting up python3-biopython-sql (1.85+dfsg-4) ... 195s autopkgtest [03:43:27]: test dependencies: sh debian/tests/run-unit-test 195s autopkgtest [03:43:27]: test dependencies: [----------------------- 197s cp: cannot stat '/usr/share/libcifpp/mmcif_pdbx.dic': No such file or directory 197s cp: cannot stat '/usr/share/libcifpp/mmcif_ma.dic': No such file or directory 200s mkdir: created directory 'Bio' 200s mkdir: created directory 'Bio/Align' 200s mkdir: created directory 'Bio/Align/substitution_matrices' 200s mkdir: created directory 'Bio/Align/substitution_matrices/data/' 200s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER22' -> 'Bio/Align/substitution_matrices/data/BENNER22' 200s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER6' -> 'Bio/Align/substitution_matrices/data/BENNER6' 200s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER74' -> 'Bio/Align/substitution_matrices/data/BENNER74' 200s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLASTN' -> 'Bio/Align/substitution_matrices/data/BLASTN' 200s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLASTP' -> 'Bio/Align/substitution_matrices/data/BLASTP' 200s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM45' -> 'Bio/Align/substitution_matrices/data/BLOSUM45' 200s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM50' -> 'Bio/Align/substitution_matrices/data/BLOSUM50' 200s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM62' -> 'Bio/Align/substitution_matrices/data/BLOSUM62' 200s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM80' -> 'Bio/Align/substitution_matrices/data/BLOSUM80' 200s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM90' -> 'Bio/Align/substitution_matrices/data/BLOSUM90' 200s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/DAYHOFF' -> 'Bio/Align/substitution_matrices/data/DAYHOFF' 200s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/FENG' -> 'Bio/Align/substitution_matrices/data/FENG' 200s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/GENETIC' -> 'Bio/Align/substitution_matrices/data/GENETIC' 200s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/GONNET1992' -> 'Bio/Align/substitution_matrices/data/GONNET1992' 200s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/HOXD70' -> 'Bio/Align/substitution_matrices/data/HOXD70' 200s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/JOHNSON' -> 'Bio/Align/substitution_matrices/data/JOHNSON' 200s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/JONES' -> 'Bio/Align/substitution_matrices/data/JONES' 200s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/LEVIN' -> 'Bio/Align/substitution_matrices/data/LEVIN' 200s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MCLACHLAN' -> 'Bio/Align/substitution_matrices/data/MCLACHLAN' 200s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MDM78' -> 'Bio/Align/substitution_matrices/data/MDM78' 200s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MEGABLAST' -> 'Bio/Align/substitution_matrices/data/MEGABLAST' 200s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/NUC.4.4' -> 'Bio/Align/substitution_matrices/data/NUC.4.4' 200s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM250' -> 'Bio/Align/substitution_matrices/data/PAM250' 200s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM30' -> 'Bio/Align/substitution_matrices/data/PAM30' 200s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM70' -> 'Bio/Align/substitution_matrices/data/PAM70' 200s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/RAO' -> 'Bio/Align/substitution_matrices/data/RAO' 200s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/RISLER' -> 'Bio/Align/substitution_matrices/data/RISLER' 200s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/SCHNEIDER' -> 'Bio/Align/substitution_matrices/data/SCHNEIDER' 200s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/STR' -> 'Bio/Align/substitution_matrices/data/STR' 200s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/TRANS' -> 'Bio/Align/substitution_matrices/data/TRANS' 200s test_Ace ... ok 200s test_Affy ... ok 203s test_AlignIO ... ok 203s test_AlignIO_ClustalIO ... ok 203s test_AlignIO_EmbossIO ... ok 203s test_AlignIO_FastaIO ... ok 203s test_AlignIO_MauveIO ... ok 203s test_AlignIO_PhylipIO ... ok 203s test_AlignIO_convert ... ok 203s test_AlignInfo ... ok 203s test_Align_Alignment ... ok 203s test_Align_a2m ... ok 203s test_Align_bed ... ok 205s test_Align_bigbed ... ok 205s test_Align_bigmaf ... ok 205s test_Align_bigpsl ... ok 205s test_Align_chain ... ok 205s test_Align_clustal ... ok 208s test_Align_codonalign ... ok 208s test_Align_emboss ... ok 208s test_Align_exonerate ... ok 208s test_Align_fasta ... ok 208s test_Align_hhr ... ok 209s test_Align_maf ... ok 209s test_Align_mauve ... ok 209s test_Align_msf ... ok 209s test_Align_nexus ... ok 209s test_Align_phylip ... ok 210s test_Align_psl ... ok 210s test_Align_sam ... ok 212s test_Align_stockholm ... ok 212s test_Align_tabular ... ok 212s test_Application ... ok 212s test_BioSQL_MySQLdb_online ... skipping. internet not available 212s test_BioSQL_mysql_connector ... skipping. BioSQL test configuration file biosql.ini missing (see biosql.ini.sample) 212s test_BioSQL_mysql_connector_online ... skipping. internet not available 212s test_BioSQL_psycopg2_online ... skipping. internet not available 219s test_BioSQL_sqlite3 ... ok 219s test_BioSQL_sqlite3_online ... skipping. internet not available 219s test_Blast_Record ... ok 219s test_Blast_parser ... ok 219s test_CAPS ... ok 220s test_Chi2 ... ok 220s test_ClustalOmega_tool ... skipping. Install clustalo if you want to use Clustal Omega from Biopython. 220s test_Clustalw_tool ... skipping. Install clustalw or clustalw2 if you want to use it from Biopython. 220s test_Cluster ... ok 220s test_CodonTable ... ok 220s test_ColorSpiral ... ok 220s test_Compass ... ok 221s test_Consensus ... ok 221s test_Dialign_tool ... skipping. Install DIALIGN2-2 if you want to use the Bio.Align.Applications wrapper. 221s test_EMBL_unittest ... ok 221s test_Emboss ... skipping. $EMBOSS_ROOT='/usr/lib/emboss' which does not exist! 221s test_EmbossPrimer ... ok 226s test_Entrez ... ok 226s test_Entrez_online ... skipping. internet not available 226s test_Entrez_parser ... ok 226s test_Enzyme ... ok 226s test_ExPASy ... skipping. internet not available 226s test_Fasttree_tool ... skipping. Install FastTree and correctly set the file path to the program if you want to use it from Biopython. 226s test_File ... ok 226s test_GenBank ... /usr/lib/python3/dist-packages/Bio/SeqIO/InsdcIO.py:600: BiopythonWarning: Annotation 'Sequence Read Archive: SRX001885, SRX001121, SRX001531, SRX001530, SRX001529' too long 226s warnings.warn(f"Annotation {text!r} too long", BiopythonWarning) 226s ok 228s test_GenomeDiagram ... Warn: Can't find .pfb for face 'Helvetica' 230s ok 231s test_GraphicsChromosome ... ok 231s test_GraphicsDistribution ... ok 231s test_GraphicsGeneral ... ok 232s test_HMMCasino ... ok 232s test_HMMGeneral ... ok 232s test_KEGG ... ok 232s test_KEGG_online ... skipping. internet not available 237s test_KGML_graphics ... ok 237s test_KGML_graphics_online ... skipping. internet not available 237s test_KGML_nographics ... ok 237s test_KeyWList ... ok 237s test_LogisticRegression ... ok 238s test_MafIO_index ... ok 238s test_Mafft_tool ... skipping. Install MAFFT if you want to use the Bio.Align.Applications wrapper. 239s test_MarkovModel ... ok 239s test_Medline ... ok 239s test_Muscle_tool ... skipping. Install MUSCLE if you want to use the Bio.Align.Applications wrapper. 240s test_NCBIXML ... Exception ignored in: 240s Traceback (most recent call last): 240s File "/usr/lib/python3/dist-packages/Bio/Blast/NCBIXML.py", line 1319, in parse 240s expat_parser.Parse(NULL, True) 240s xml.parsers.expat.ExpatError: unclosed token: line 320, column 0 240s ok 240s test_NCBI_BLAST_tools ... skipping. Install the NCBI BLAST+ command line tools if you want to use the Bio.Blast.Applications wrapper. 240s test_NCBI_qblast ... ok 240s test_NMR ... ok 240s test_NaiveBayes ... ok 240s test_Nexus ... ok 240s test_PAML_baseml ... ok 241s test_PAML_codeml ... ok 241s test_PAML_yn00 ... ok 245s test_PDB_CEAligner ... ok 245s test_PDB_DSSP ... ok 246s test_PDB_Dice ... ok 246s test_PDB_Disordered ... ok 246s test_PDB_Exposure ... ok 246s test_PDB_FragmentMapper ... ok 248s test_PDB_KDTree ... ok 248s test_PDB_MMCIF2Dict ... ok 248s test_PDB_MMCIFIO ... ok 249s test_PDB_MMCIFParser ... ok 249s test_PDB_NACCESS ... ok 249s test_PDB_PDBIO ... ok 249s test_PDB_PDBList ... skipping. internet not available 256s test_PDB_PDBMLParser ... ok 256s test_PDB_PDBParser ... ok 256s test_PDB_PSEA ... skipping. Download and install psea from ftp://ftp.lmcp.jussieu.fr/pub/sincris/software/protein/p-sea/. Make sure that psea is on path 256s test_PDB_Polypeptide ... ok 256s test_PDB_QCPSuperimposer ... ok 260s test_PDB_SASA ... ok 260s test_PDB_SMCRA ... ok 260s test_PDB_Selection ... ok 260s test_PDB_StructureAlignment ... ok 261s test_PDB_Superimposer ... ok 261s test_PDB_alphafold_db ... skipping. internet not available 261s test_PDB_binary_cif ... skipping. Error: Install msgpack to use Bio.PDB.binaryCIF (e.g. pip install msgpack) 261s 261s test_PDB_internal_coords ... skipping. Error: Install mmtf to use Bio.PDB.mmtf (e.g. pip install mmtf-python) 261s 261s test_PDB_parse_pdb_header ... ok 261s test_PDB_vectors ... ok 261s test_PQR ... ok 261s test_Pathway ... ok 261s test_Phd ... ok 261s test_Phylo ... ok 262s test_PhyloXML ... ok 262s test_Phylo_CDAO ... skipping. Install RDFlib if you want to use the CDAO tree format. 262s test_Phylo_NeXML ... ok 262s test_Phylo_igraph ... skipping. Install igraph if you wish to use it with Bio.Phylo 262s test_Phylo_matplotlib ... skipping. Install matplotlib if you want to use Bio.Phylo._utils. 262s test_Phylo_networkx ... skipping. Install networkx if you wish to use it with Bio.Phylo 262s test_PopGen_GenePop_nodepend ... ok 262s test_Prank_tool ... skipping. Install PRANK if you want to use the Bio.Align.Applications wrapper. 262s test_Probcons_tool ... skipping. Install PROBCONS if you want to use the Bio.Align.Applications wrapper. 262s test_ProtParam ... ok 263s test_RCSBFormats ... ok 263s test_Restriction ... ok 263s test_SCOP_Astral ... ok 263s test_SCOP_Cla ... ok 263s test_SCOP_Des ... ok 263s test_SCOP_Dom ... ok 263s test_SCOP_Hie ... ok 263s test_SCOP_Raf ... ok 263s test_SCOP_Residues ... ok 263s test_SCOP_Scop ... ok 263s test_SVDSuperimposer ... ok 263s test_SearchIO_blast_tab ... ok 263s test_SearchIO_blast_tab_index ... ok 264s test_SearchIO_blast_xml ... ok 265s test_SearchIO_blast_xml_index ... ok 265s test_SearchIO_blat_psl ... ok 265s test_SearchIO_blat_psl_index ... ok 265s test_SearchIO_exonerate ... ok 265s test_SearchIO_exonerate_text_index ... ok 265s test_SearchIO_exonerate_vulgar_index ... ok 265s test_SearchIO_fasta_m10 ... ok 265s test_SearchIO_fasta_m10_index ... ok 266s test_SearchIO_hhsuite2_text ... ok 266s test_SearchIO_hmmer2_text ... ok 266s test_SearchIO_hmmer2_text_index ... ok 266s test_SearchIO_hmmer3_domtab ... ok 266s test_SearchIO_hmmer3_domtab_index ... ok 266s test_SearchIO_hmmer3_tab ... ok 266s test_SearchIO_hmmer3_tab_index ... ok 266s test_SearchIO_hmmer3_text ... ok 266s test_SearchIO_hmmer3_text_index ... ok 266s test_SearchIO_interproscan_xml ... ok 266s test_SearchIO_model ... ok 267s test_SearchIO_write ... ok 267s test_SeqFeature ... ok 282s test_SeqIO ... ok 282s test_SeqIO_AbiIO ... ok 282s test_SeqIO_FastaIO ... ok 282s test_SeqIO_Gck ... ok 282s test_SeqIO_Gfa ... ok 282s test_SeqIO_Insdc ... ok 282s test_SeqIO_NibIO ... ok 284s test_SeqIO_PdbIO ... ok 285s test_SeqIO_QualityIO ... ok 285s test_SeqIO_SeqXML ... ok 285s test_SeqIO_SffIO ... ok 285s test_SeqIO_SnapGene ... ok 286s test_SeqIO_TwoBitIO ... ok 286s test_SeqIO_UniprotIO ... ok 286s test_SeqIO_Xdna ... ok 286s test_SeqIO_features ... ok 300s test_SeqIO_index ... ok 300s test_SeqIO_online ... skipping. internet not available 301s test_SeqIO_write ... ok 301s test_SeqRecord ... ok 301s test_SeqUtils ... ok 302s test_Seq_objs ... ok 302s test_SwissProt ... ok 302s test_TCoffee_tool ... skipping. Install TCOFFEE if you want to use the Bio.Align.Applications wrapper. 302s test_TogoWS ... skipping. internet not available 303s test_TreeConstruction ... ok 303s test_Tutorial ... skipping. Could not find ../Doc/Tutorial/index.rst file 303s test_UniGene ... ok 303s test_UniProt ... skipping. internet not available 303s test_UniProt_GOA ... ok 303s test_align ... ok 303s test_align_substitution_matrices ... ok 306s test_bgzf ... ok 306s test_cellosaurus ... ok 310s test_codonalign ... ok 310s test_geo ... ok 310s test_kNN ... ok 310s test_motifs ... ok 311s test_motifs_online ... skipping. internet not available 311s test_pairwise2 ... /usr/lib/python3/dist-packages/Bio/pairwise2.py:278: BiopythonDeprecationWarning: Bio.pairwise2 has been deprecated, and we intend to remove it in a future release of Biopython. As an alternative, please consider using Bio.Align.PairwiseAligner as a replacement, and contact the Biopython developers if you still need the Bio.pairwise2 module. 311s warnings.warn( 311s ok 311s test_pairwise2_no_C ... ok 311s test_pairwise_aligner ... ok 311s test_pairwise_alignment_map ... ok 320s test_phenotype ... ok 320s test_phenotype_fit ... skipping. Install SciPy if you want to use Bio.phenotype fit functionality. 320s test_phyml_tool ... skipping. Couldn't find the PhyML software. Install PhyML 3.0 or later if you want to use the Bio.Phylo.Applications wrapper. 320s test_prodoc ... ok 320s test_prosite ... ok 320s test_raxml_tool ... skipping. Install RAxML (binary raxmlHPC) if you want to test the Bio.Phylo.Applications wrapper. 321s test_samtools_tool ... skipping. Install samtools and correctly set the file path to the program if you want to use it from Biopython 321s test_seq ... ok 321s test_translate ... ok 321s ---------------------------------------------------------------------- 321s Ran 218 tests in 120.572 seconds 321s 321s Skipping any tests requiring internet access 321s Python version: 3.13.5 (main, Jun 25 2025, 18:55:22) [GCC 14.3.0] 321s Operating system: posix linux 321s :0: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/protein_lib.fa' mode='rt' encoding='UTF-8'> 321s :0: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/nucleotide_lib.fa' mode='rt' encoding='UTF-8'> 321s autopkgtest [03:45:33]: test dependencies: -----------------------] 326s dependencies PASS 326s autopkgtest [03:45:38]: test dependencies: - - - - - - - - - - results - - - - - - - - - - 329s autopkgtest [03:45:41]: test full_suite: preparing testbed 350s autopkgtest [03:46:02]: testbed dpkg architecture: armhf 352s autopkgtest [03:46:04]: testbed apt version: 3.1.3 355s autopkgtest [03:46:07]: @@@@@@@@@@@@@@@@@@@@ test bed setup 357s autopkgtest [03:46:09]: testbed release detected to be: questing 364s autopkgtest [03:46:16]: updating testbed package index (apt update) 366s Get:1 http://ftpmaster.internal/ubuntu questing-proposed InRelease [249 kB] 366s Hit:2 http://ftpmaster.internal/ubuntu questing InRelease 366s Hit:3 http://ftpmaster.internal/ubuntu questing-updates InRelease 366s Hit:4 http://ftpmaster.internal/ubuntu questing-security InRelease 366s Get:5 http://ftpmaster.internal/ubuntu questing-proposed/main Sources [39.9 kB] 366s Get:6 http://ftpmaster.internal/ubuntu questing-proposed/multiverse Sources [15.4 kB] 366s Get:7 http://ftpmaster.internal/ubuntu questing-proposed/universe Sources [207 kB] 366s Get:8 http://ftpmaster.internal/ubuntu questing-proposed/main armhf Packages [54.2 kB] 366s Get:9 http://ftpmaster.internal/ubuntu questing-proposed/universe armhf Packages [168 kB] 366s Get:10 http://ftpmaster.internal/ubuntu questing-proposed/multiverse armhf Packages [3452 B] 366s Fetched 738 kB in 1s (796 kB/s) 367s Reading package lists... 373s autopkgtest [03:46:25]: upgrading testbed (apt dist-upgrade and autopurge) 374s Reading package lists... 374s Building dependency tree... 374s Reading state information... 375s Calculating upgrade... 375s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 377s Reading package lists... 377s Building dependency tree... 377s Reading state information... 377s Solving dependencies... 378s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 379s autopkgtest [03:46:31]: rebooting testbed after setup commands that affected boot 439s Reading package lists... 439s Building dependency tree... 439s Reading state information... 439s Solving dependencies... 440s The following NEW packages will be installed: 440s autoconf automake autopoint autotools-dev blt build-essential bwa clustalo 440s cpp cpp-14 cpp-14-arm-linux-gnueabihf cpp-arm-linux-gnueabihf debhelper 440s debugedit dh-autoreconf dh-python dh-strip-nondeterminism dialign 440s docutils-common dssp dwz fasttree flex fontconfig-config fonts-dejavu-core 440s fonts-dejavu-mono fonts-font-awesome fonts-lato fonts-lmodern fonts-lyx 440s fonts-urw-base35 g++ g++-14 g++-14-arm-linux-gnueabihf 440s g++-arm-linux-gnueabihf gcc gcc-14 gcc-14-arm-linux-gnueabihf gcc-14-base 440s gcc-arm-linux-gnueabihf gettext ghostscript hevea hicolor-icon-theme 440s imagemagick imagemagick-7-common imagemagick-7.q16 intltool-debian libamd3 440s libaom3 libapache-pom-java libarchive-zip-perl libargtable2-0 libarpack2t64 440s libasan8 libavahi-client3 libavahi-common-data libavahi-common3 libblas3 440s libc-dev-bin libc6-dev libcairo2 libcc1-0 libcifpp-data libcifpp7 libcolamd3 440s libcommons-logging-java libcommons-parent-java libcrypt-dev libcups2t64 440s libde265-0 libdebhelper-perl libdeflate0 libdw1t64 libexpat1-dev 440s libfftw3-double3 libfile-stripnondeterminism-perl libfontbox-java 440s libfontconfig1 libfontenc1 libfreetype6 libgcc-14-dev libgfortran5 libglpk40 440s libgomp1 libgraphite2-3 libgs-common libgs10 libgs10-common libharfbuzz0b 440s libheif-plugin-aomdec libheif-plugin-libde265 libheif1 libice6 libicu76 440s libidn12 libigraph3t64 libijs-0.35 libimagequant0 libisl23 libjbig0 440s libjbig2dec0 libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui 440s libjs-sphinxdoc libjs-underscore libjson-perl libkpathsea6 liblapack3 440s liblcms2-2 liblerc4 liblqr-1-0 libltdl7 libmagickcore-7.q16-10 440s libmagickwand-7.q16-10 libmbedcrypto16 libmbedtls21 libmbedx509-7 libmpc3 440s libmpfi0 libmysqlclient24 libnetpbm11t64 libopenjp2-7 libpaper-utils 440s libpaper2 libpdfbox-java libpixman-1-0 libplfit0 libpotrace0 libptexenc1 440s libpython3-all-dev libpython3-dev libpython3.13 libpython3.13-dev 440s libqhull-r8.0 libraqm0 libraw23t64 libsharpyuv0 libsm6 libstdc++-14-dev 440s libsuitesparseconfig7 libsynctex2 libtcl8.6 libteckit0 libtexlua53-5 440s libtiff6 libtk8.6 libtool libubsan1 libwebp7 libwebpdemux2 libwebpmux3 440s libxaw7 libxcb-render0 libxcb-shm0 libxft2 libxi6 libxmu6 libxpm4 440s libxrender1 libxslt1.1 libxss1 libxt6t64 libzzip-0-13t64 linux-libc-dev m4 440s mafft mysql-common ncbi-blast+ ncbi-data netpbm phylip po-debconf 440s poppler-data prank preview-latex-style probcons python-biopython-doc 440s python-matplotlib-data python3-alabaster python3-all python3-all-dev 440s python3-biopython python3-biopython-sql python3-brotli python3-cairo 440s python3-charset-normalizer python3-contourpy python3-cycler python3-dateutil 440s python3-decorator python3-defusedxml python3-dev python3-docutils 440s python3-fonttools python3-freetype python3-fs python3-igraph 440s python3-imagesize python3-kiwisolver python3-lxml python3-lz4 440s python3-matplotlib python3-mmtf python3-mpmath python3-msgpack 440s python3-mysqldb python3-networkx python3-numpy python3-numpy-dev 440s python3-numpydoc python3-packaging python3-pil python3-pil.imagetk 440s python3-platformdirs python3-rdflib python3-reportlab python3-rlpycairo 440s python3-roman python3-scipy python3-snowballstemmer python3-sphinx 440s python3-sphinx-rtd-theme python3-sphinxcontrib.jquery python3-sympy 440s python3-tabulate python3-texttable python3-tk python3-ufolib2 python3.13-dev 440s python3.13-tk rpcsvc-proto sgml-base sphinx-common sphinx-rtd-theme-common 440s t-coffee t1utils tex-common texlive-base texlive-binaries 440s texlive-fonts-recommended texlive-latex-base texlive-latex-extra 440s texlive-latex-recommended texlive-pictures tk8.6-blt2.5 unicode-data 440s w3c-sgml-lib wise wise-data x11-common xdg-utils xfonts-encodings 440s xfonts-utils xml-core zlib1g-dev 440s 0 upgraded, 258 newly installed, 0 to remove and 0 not upgraded. 440s Need to get 341 MB of archives. 440s After this operation, 1249 MB of additional disk space will be used. 440s Get:1 http://ftpmaster.internal/ubuntu questing/main armhf m4 armhf 1.4.19-8 [238 kB] 440s Get:2 http://ftpmaster.internal/ubuntu questing/main armhf flex armhf 2.6.4-8.2build1 [293 kB] 440s Get:3 http://ftpmaster.internal/ubuntu questing/main armhf fonts-lato all 2.015-1 [2781 kB] 441s Get:4 http://ftpmaster.internal/ubuntu questing/main armhf libgomp1 armhf 15.1.0-8ubuntu1 [129 kB] 441s Get:5 http://ftpmaster.internal/ubuntu questing/main armhf libfftw3-double3 armhf 3.3.10-2fakesync1build1 [369 kB] 441s Get:6 http://ftpmaster.internal/ubuntu questing/main armhf libfreetype6 armhf 2.13.3+dfsg-1 [330 kB] 441s Get:7 http://ftpmaster.internal/ubuntu questing/main armhf fonts-dejavu-mono all 2.37-8 [502 kB] 442s Get:8 http://ftpmaster.internal/ubuntu questing/main armhf fonts-dejavu-core all 2.37-8 [835 kB] 442s Get:9 http://ftpmaster.internal/ubuntu questing/main armhf libfontenc1 armhf 1:1.1.8-1build1 [11.5 kB] 442s Get:10 http://ftpmaster.internal/ubuntu questing/main armhf x11-common all 1:7.7+24ubuntu1 [22.4 kB] 442s Get:11 http://ftpmaster.internal/ubuntu questing/main armhf xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 442s Get:12 http://ftpmaster.internal/ubuntu questing/main armhf xfonts-utils armhf 1:7.7+7 [90.6 kB] 442s Get:13 http://ftpmaster.internal/ubuntu questing/main armhf fonts-urw-base35 all 20200910-8 [11.0 MB] 443s Get:14 http://ftpmaster.internal/ubuntu questing/main armhf fontconfig-config armhf 2.15.0-2.3ubuntu1 [38.1 kB] 443s Get:15 http://ftpmaster.internal/ubuntu questing/main armhf libfontconfig1 armhf 2.15.0-2.3ubuntu1 [114 kB] 443s Get:16 http://ftpmaster.internal/ubuntu questing/main armhf libsharpyuv0 armhf 1.5.0-0.1 [16.4 kB] 443s Get:17 http://ftpmaster.internal/ubuntu questing/main armhf libaom3 armhf 3.12.1-1 [1232 kB] 443s Get:18 http://ftpmaster.internal/ubuntu questing/main armhf libheif-plugin-aomdec armhf 1.19.8-1 [11.0 kB] 443s Get:19 http://ftpmaster.internal/ubuntu questing/main armhf libde265-0 armhf 1.0.16-1 [158 kB] 443s Get:20 http://ftpmaster.internal/ubuntu questing/main armhf libheif-plugin-libde265 armhf 1.19.8-1 [11.7 kB] 443s Get:21 http://ftpmaster.internal/ubuntu questing/main armhf libheif1 armhf 1.19.8-1 [480 kB] 443s Get:22 http://ftpmaster.internal/ubuntu questing/main armhf libjbig0 armhf 2.1-6.1ubuntu2 [24.9 kB] 443s Get:23 http://ftpmaster.internal/ubuntu questing/main armhf libjpeg-turbo8 armhf 2.1.5-3ubuntu2 [127 kB] 443s Get:24 http://ftpmaster.internal/ubuntu questing/main armhf libjpeg8 armhf 8c-2ubuntu11 [2148 B] 443s Get:25 http://ftpmaster.internal/ubuntu questing/main armhf liblcms2-2 armhf 2.16-2 [137 kB] 443s Get:26 http://ftpmaster.internal/ubuntu questing/universe armhf liblqr-1-0 armhf 0.4.2-2.1build2 [23.2 kB] 443s Get:27 http://ftpmaster.internal/ubuntu questing/main armhf libltdl7 armhf 2.5.4-4 [39.8 kB] 443s Get:28 http://ftpmaster.internal/ubuntu questing/main armhf libopenjp2-7 armhf 2.5.3-2 [172 kB] 443s Get:29 http://ftpmaster.internal/ubuntu questing/main armhf libraw23t64 armhf 0.21.4-2 [352 kB] 443s Get:30 http://ftpmaster.internal/ubuntu questing/main armhf libdeflate0 armhf 1.23-2 [38.7 kB] 443s Get:31 http://ftpmaster.internal/ubuntu questing/main armhf liblerc4 armhf 4.0.0+ds-5ubuntu1 [160 kB] 443s Get:32 http://ftpmaster.internal/ubuntu questing/main armhf libwebp7 armhf 1.5.0-0.1 [188 kB] 443s Get:33 http://ftpmaster.internal/ubuntu questing/main armhf libtiff6 armhf 4.7.0-3ubuntu1 [184 kB] 443s Get:34 http://ftpmaster.internal/ubuntu questing/main armhf libwebpdemux2 armhf 1.5.0-0.1 [11.5 kB] 443s Get:35 http://ftpmaster.internal/ubuntu questing/main armhf libwebpmux3 armhf 1.5.0-0.1 [22.4 kB] 443s Get:36 http://ftpmaster.internal/ubuntu questing/universe armhf imagemagick-7-common all 8:7.1.1.43+dfsg1-1ubuntu1 [69.5 kB] 443s Get:37 http://ftpmaster.internal/ubuntu questing/universe armhf libmagickcore-7.q16-10 armhf 8:7.1.1.43+dfsg1-1ubuntu1 [1855 kB] 444s Get:38 http://ftpmaster.internal/ubuntu questing/universe armhf libmagickwand-7.q16-10 armhf 8:7.1.1.43+dfsg1-1ubuntu1 [367 kB] 444s Get:39 http://ftpmaster.internal/ubuntu questing/main armhf poppler-data all 0.4.12-1 [2060 kB] 444s Get:40 http://ftpmaster.internal/ubuntu questing/main armhf python3-numpy-dev armhf 1:2.2.4+ds-1ubuntu1 [141 kB] 444s Get:41 http://ftpmaster.internal/ubuntu questing/main armhf libblas3 armhf 3.12.1-2build1 [133 kB] 444s Get:42 http://ftpmaster.internal/ubuntu questing/main armhf libgfortran5 armhf 15.1.0-8ubuntu1 [334 kB] 444s Get:43 http://ftpmaster.internal/ubuntu questing/main armhf liblapack3 armhf 3.12.1-2build1 [2092 kB] 444s Get:44 http://ftpmaster.internal/ubuntu questing/main armhf python3-numpy armhf 1:2.2.4+ds-1ubuntu1 [3724 kB] 444s Get:45 http://ftpmaster.internal/ubuntu questing/main armhf autoconf all 2.72-3.1ubuntu1 [384 kB] 444s Get:46 http://ftpmaster.internal/ubuntu questing/main armhf autotools-dev all 20240727.1 [43.4 kB] 444s Get:47 http://ftpmaster.internal/ubuntu questing/main armhf automake all 1:1.17-4ubuntu1 [572 kB] 444s Get:48 http://ftpmaster.internal/ubuntu questing/main armhf autopoint all 0.23.1-2build1 [619 kB] 444s Get:49 http://ftpmaster.internal/ubuntu questing/main armhf libtcl8.6 armhf 8.6.16+dfsg-1 [909 kB] 444s Get:50 http://ftpmaster.internal/ubuntu questing/main armhf libxrender1 armhf 1:0.9.12-1 [16.6 kB] 444s Get:51 http://ftpmaster.internal/ubuntu questing/main armhf libxft2 armhf 2.3.6-1build1 [37.4 kB] 444s Get:52 http://ftpmaster.internal/ubuntu questing/main armhf libxss1 armhf 1:1.2.3-1build3 [6500 B] 444s Get:53 http://ftpmaster.internal/ubuntu questing/main armhf libtk8.6 armhf 8.6.16-1 [686 kB] 444s Get:54 http://ftpmaster.internal/ubuntu questing/main armhf tk8.6-blt2.5 armhf 2.5.3+dfsg-8 [527 kB] 444s Get:55 http://ftpmaster.internal/ubuntu questing/main armhf blt armhf 2.5.3+dfsg-8 [4824 B] 444s Get:56 http://ftpmaster.internal/ubuntu questing/main armhf libc-dev-bin armhf 2.41-6ubuntu2 [21.7 kB] 444s Get:57 http://ftpmaster.internal/ubuntu questing/main armhf linux-libc-dev armhf 6.15.0-4.4 [1736 kB] 444s Get:58 http://ftpmaster.internal/ubuntu questing/main armhf libcrypt-dev armhf 1:4.4.38-1 [120 kB] 444s Get:59 http://ftpmaster.internal/ubuntu questing/main armhf rpcsvc-proto armhf 1.4.3-1 [62.3 kB] 444s Get:60 http://ftpmaster.internal/ubuntu questing/main armhf libc6-dev armhf 2.41-6ubuntu2 [1395 kB] 444s Get:61 http://ftpmaster.internal/ubuntu questing/main armhf gcc-14-base armhf 14.3.0-1ubuntu1 [55.7 kB] 444s Get:62 http://ftpmaster.internal/ubuntu questing/main armhf libisl23 armhf 0.27-1 [546 kB] 444s Get:63 http://ftpmaster.internal/ubuntu questing/main armhf libmpc3 armhf 1.3.1-1build2 [47.1 kB] 444s Get:64 http://ftpmaster.internal/ubuntu questing/main armhf cpp-14-arm-linux-gnueabihf armhf 14.3.0-1ubuntu1 [9216 kB] 445s Get:65 http://ftpmaster.internal/ubuntu questing/main armhf cpp-14 armhf 14.3.0-1ubuntu1 [1032 B] 445s Get:66 http://ftpmaster.internal/ubuntu questing/main armhf cpp-arm-linux-gnueabihf armhf 4:14.2.0-1ubuntu1 [5578 B] 445s Get:67 http://ftpmaster.internal/ubuntu questing/main armhf cpp armhf 4:14.2.0-1ubuntu1 [22.4 kB] 445s Get:68 http://ftpmaster.internal/ubuntu questing/main armhf libcc1-0 armhf 15.1.0-8ubuntu1 [43.6 kB] 445s Get:69 http://ftpmaster.internal/ubuntu questing/main armhf libasan8 armhf 15.1.0-8ubuntu1 [2949 kB] 445s Get:70 http://ftpmaster.internal/ubuntu questing/main armhf libubsan1 armhf 15.1.0-8ubuntu1 [1188 kB] 445s Get:71 http://ftpmaster.internal/ubuntu questing/main armhf libgcc-14-dev armhf 14.3.0-1ubuntu1 [896 kB] 445s Get:72 http://ftpmaster.internal/ubuntu questing/main armhf gcc-14-arm-linux-gnueabihf armhf 14.3.0-1ubuntu1 [18.0 MB] 445s Get:73 http://ftpmaster.internal/ubuntu questing/main armhf gcc-14 armhf 14.3.0-1ubuntu1 [518 kB] 445s Get:74 http://ftpmaster.internal/ubuntu questing/main armhf gcc-arm-linux-gnueabihf armhf 4:14.2.0-1ubuntu1 [1218 B] 445s Get:75 http://ftpmaster.internal/ubuntu questing/main armhf gcc armhf 4:14.2.0-1ubuntu1 [5004 B] 445s Get:76 http://ftpmaster.internal/ubuntu questing/main armhf libstdc++-14-dev armhf 14.3.0-1ubuntu1 [2856 kB] 445s Get:77 http://ftpmaster.internal/ubuntu questing/main armhf g++-14-arm-linux-gnueabihf armhf 14.3.0-1ubuntu1 [10.5 MB] 445s Get:78 http://ftpmaster.internal/ubuntu questing/main armhf g++-14 armhf 14.3.0-1ubuntu1 [27.4 kB] 445s Get:79 http://ftpmaster.internal/ubuntu questing/main armhf g++-arm-linux-gnueabihf armhf 4:14.2.0-1ubuntu1 [966 B] 445s Get:80 http://ftpmaster.internal/ubuntu questing/main armhf g++ armhf 4:14.2.0-1ubuntu1 [1084 B] 445s Get:81 http://ftpmaster.internal/ubuntu questing/main armhf build-essential armhf 12.12ubuntu1 [5088 B] 445s Get:82 http://ftpmaster.internal/ubuntu questing/universe armhf bwa armhf 0.7.18-1 [198 kB] 445s Get:83 http://ftpmaster.internal/ubuntu questing/universe armhf libargtable2-0 armhf 13-4 [12.7 kB] 445s Get:84 http://ftpmaster.internal/ubuntu questing/universe armhf clustalo armhf 1.2.4-8build1 [249 kB] 445s Get:85 http://ftpmaster.internal/ubuntu questing/main armhf libdebhelper-perl all 13.24.2ubuntu1 [95.7 kB] 445s Get:86 http://ftpmaster.internal/ubuntu questing/main armhf libtool all 2.5.4-4 [168 kB] 446s Get:87 http://ftpmaster.internal/ubuntu questing/main armhf dh-autoreconf all 20 [16.1 kB] 446s Get:88 http://ftpmaster.internal/ubuntu questing/main armhf libarchive-zip-perl all 1.68-1 [90.2 kB] 446s Get:89 http://ftpmaster.internal/ubuntu questing/main armhf libfile-stripnondeterminism-perl all 1.14.1-2 [20.3 kB] 446s Get:90 http://ftpmaster.internal/ubuntu questing/main armhf dh-strip-nondeterminism all 1.14.1-2 [5064 B] 446s Get:91 http://ftpmaster.internal/ubuntu questing/main armhf libdw1t64 armhf 0.193-1 [248 kB] 446s Get:92 http://ftpmaster.internal/ubuntu questing/main armhf debugedit armhf 1:5.1-2 [46.7 kB] 446s Get:93 http://ftpmaster.internal/ubuntu questing/main armhf dwz armhf 0.15-1build6 [116 kB] 446s Get:94 http://ftpmaster.internal/ubuntu questing/main armhf gettext armhf 0.23.1-2build1 [1508 kB] 446s Get:95 http://ftpmaster.internal/ubuntu questing/main armhf intltool-debian all 0.35.0+20060710.6 [23.2 kB] 446s Get:96 http://ftpmaster.internal/ubuntu questing/main armhf po-debconf all 1.0.21+nmu1 [233 kB] 446s Get:97 http://ftpmaster.internal/ubuntu questing/main armhf debhelper all 13.24.2ubuntu1 [896 kB] 446s Get:98 http://ftpmaster.internal/ubuntu questing/universe armhf dh-python all 6.20250414 [119 kB] 446s Get:99 http://ftpmaster.internal/ubuntu questing/universe armhf dialign armhf 2.2.1-13 [156 kB] 446s Get:100 http://ftpmaster.internal/ubuntu questing/main armhf sgml-base all 1.31+nmu1 [11.0 kB] 446s Get:101 http://ftpmaster.internal/ubuntu questing/main armhf xml-core all 0.19 [20.3 kB] 446s Get:102 http://ftpmaster.internal/ubuntu questing/main armhf docutils-common all 0.21.2+dfsg-2 [131 kB] 446s Get:103 http://ftpmaster.internal/ubuntu questing/universe armhf libcifpp-data all 7.0.9-1 [481 kB] 446s Get:104 http://ftpmaster.internal/ubuntu questing/universe armhf libcifpp7 armhf 7.0.9-1 [962 kB] 446s Get:105 http://ftpmaster.internal/ubuntu questing/universe armhf dssp armhf 4.4.10-1 [696 kB] 446s Get:106 http://ftpmaster.internal/ubuntu questing/main armhf fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB] 446s Get:107 http://ftpmaster.internal/ubuntu questing/universe armhf fonts-lmodern all 2.005-1 [4799 kB] 447s Get:108 http://ftpmaster.internal/ubuntu questing/universe armhf fonts-lyx all 2.4.3-1 [171 kB] 447s Get:109 http://ftpmaster.internal/ubuntu questing/main armhf libgs-common all 10.05.0dfsg1-0ubuntu1 [176 kB] 447s Get:110 http://ftpmaster.internal/ubuntu questing/main armhf libgs10-common all 10.05.0dfsg1-0ubuntu1 [490 kB] 447s Get:111 http://ftpmaster.internal/ubuntu questing/main armhf libavahi-common-data armhf 0.8-16ubuntu2 [31.0 kB] 447s Get:112 http://ftpmaster.internal/ubuntu questing/main armhf libavahi-common3 armhf 0.8-16ubuntu2 [20.2 kB] 447s Get:113 http://ftpmaster.internal/ubuntu questing/main armhf libavahi-client3 armhf 0.8-16ubuntu2 [24.5 kB] 447s Get:114 http://ftpmaster.internal/ubuntu questing/main armhf libcups2t64 armhf 2.4.12-0ubuntu1 [240 kB] 447s Get:115 http://ftpmaster.internal/ubuntu questing/main armhf libidn12 armhf 1.43-1 [56.2 kB] 447s Get:116 http://ftpmaster.internal/ubuntu questing/main armhf libijs-0.35 armhf 0.35-15.3 [13.6 kB] 447s Get:117 http://ftpmaster.internal/ubuntu questing/main armhf libjbig2dec0 armhf 0.20-1build3 [57.6 kB] 447s Get:118 http://ftpmaster.internal/ubuntu questing/main armhf libpaper2 armhf 2.2.5-0.3 [16.3 kB] 447s Get:119 http://ftpmaster.internal/ubuntu questing/main armhf libice6 armhf 2:1.1.1-1 [36.5 kB] 447s Get:120 http://ftpmaster.internal/ubuntu questing/main armhf libsm6 armhf 2:1.2.6-1 [15.3 kB] 447s Get:121 http://ftpmaster.internal/ubuntu questing/main armhf libxt6t64 armhf 1:1.2.1-1.2build1 [145 kB] 447s Get:122 http://ftpmaster.internal/ubuntu questing/main armhf libgs10 armhf 10.05.0dfsg1-0ubuntu1 [4259 kB] 447s Get:123 http://ftpmaster.internal/ubuntu questing/main armhf ghostscript armhf 10.05.0dfsg1-0ubuntu1 [42.7 kB] 447s Get:124 http://ftpmaster.internal/ubuntu questing/universe armhf libnetpbm11t64 armhf 2:11.10.02-1build1 [97.7 kB] 447s Get:125 http://ftpmaster.internal/ubuntu questing/universe armhf netpbm armhf 2:11.10.02-1build1 [2035 kB] 447s Get:126 http://ftpmaster.internal/ubuntu questing/universe armhf tex-common all 6.19 [29.8 kB] 447s Get:127 http://ftpmaster.internal/ubuntu questing/main armhf libpaper-utils armhf 2.2.5-0.3 [14.2 kB] 447s Get:128 http://ftpmaster.internal/ubuntu questing/universe armhf libkpathsea6 armhf 2024.20240313.70630+ds-6 [59.0 kB] 447s Get:129 http://ftpmaster.internal/ubuntu questing/universe armhf libptexenc1 armhf 2024.20240313.70630+ds-6 [37.8 kB] 447s Get:130 http://ftpmaster.internal/ubuntu questing/universe armhf libsynctex2 armhf 2024.20240313.70630+ds-6 [48.6 kB] 447s Get:131 http://ftpmaster.internal/ubuntu questing/universe armhf libtexlua53-5 armhf 2024.20240313.70630+ds-6 [98.5 kB] 447s Get:132 http://ftpmaster.internal/ubuntu questing/main armhf t1utils armhf 1.41-4build3 [51.8 kB] 447s Get:133 http://ftpmaster.internal/ubuntu questing/main armhf libpixman-1-0 armhf 0.44.0-3 [183 kB] 447s Get:134 http://ftpmaster.internal/ubuntu questing/main armhf libxcb-render0 armhf 1.17.0-2 [15.3 kB] 447s Get:135 http://ftpmaster.internal/ubuntu questing/main armhf libxcb-shm0 armhf 1.17.0-2 [5774 B] 447s Get:136 http://ftpmaster.internal/ubuntu questing/main armhf libcairo2 armhf 1.18.4-1 [483 kB] 447s Get:137 http://ftpmaster.internal/ubuntu questing/main armhf libgraphite2-3 armhf 1.3.14-2ubuntu1 [64.8 kB] 447s Get:138 http://ftpmaster.internal/ubuntu questing/main armhf libharfbuzz0b armhf 10.2.0-1 [464 kB] 447s Get:139 http://ftpmaster.internal/ubuntu questing/main armhf libicu76 armhf 76.1-4ubuntu1 [10.7 MB] 448s Get:140 http://ftpmaster.internal/ubuntu questing/universe armhf libmpfi0 armhf 1.5.4+ds-4 [28.0 kB] 448s Get:141 http://ftpmaster.internal/ubuntu questing/universe armhf libpotrace0 armhf 1.16-2build1 [15.2 kB] 448s Get:142 http://ftpmaster.internal/ubuntu questing/universe armhf libteckit0 armhf 2.5.12+ds1-1 [323 kB] 448s Get:143 http://ftpmaster.internal/ubuntu questing/main armhf libxmu6 armhf 2:1.1.3-3build2 [40.4 kB] 448s Get:144 http://ftpmaster.internal/ubuntu questing/main armhf libxpm4 armhf 1:3.5.17-1build2 [30.1 kB] 448s Get:145 http://ftpmaster.internal/ubuntu questing/main armhf libxaw7 armhf 2:1.0.16-1 [154 kB] 448s Get:146 http://ftpmaster.internal/ubuntu questing/main armhf libxi6 armhf 2:1.8.2-1 [26.5 kB] 448s Get:147 http://ftpmaster.internal/ubuntu questing/universe armhf libzzip-0-13t64 armhf 0.13.78+dfsg.1-0.1 [26.1 kB] 448s Get:148 http://ftpmaster.internal/ubuntu questing/universe armhf texlive-binaries armhf 2024.20240313.70630+ds-6 [7065 kB] 448s Get:149 http://ftpmaster.internal/ubuntu questing/main armhf xdg-utils all 1.2.1-2ubuntu1 [66.0 kB] 448s Get:150 http://ftpmaster.internal/ubuntu questing/universe armhf texlive-base all 2024.20250309-1 [22.7 MB] 449s Get:151 http://ftpmaster.internal/ubuntu questing/main armhf hicolor-icon-theme all 0.18-2 [13.3 kB] 449s Get:152 http://ftpmaster.internal/ubuntu questing/universe armhf imagemagick-7.q16 armhf 8:7.1.1.43+dfsg1-1ubuntu1 [704 kB] 449s Get:153 http://ftpmaster.internal/ubuntu questing/universe armhf imagemagick armhf 8:7.1.1.43+dfsg1-1ubuntu1 [14.1 kB] 449s Get:154 http://ftpmaster.internal/ubuntu questing/universe armhf hevea armhf 2.36-2 [1938 kB] 449s Get:155 http://ftpmaster.internal/ubuntu questing/main armhf libsuitesparseconfig7 armhf 1:7.10.1+dfsg-1 [20.9 kB] 449s Get:156 http://ftpmaster.internal/ubuntu questing/universe armhf libamd3 armhf 1:7.10.1+dfsg-1 [37.7 kB] 449s Get:157 http://ftpmaster.internal/ubuntu questing/universe armhf libapache-pom-java all 33-2 [5874 B] 449s Get:158 http://ftpmaster.internal/ubuntu questing/universe armhf libarpack2t64 armhf 3.9.1-6 [88.7 kB] 449s Get:159 http://ftpmaster.internal/ubuntu questing/main armhf libcolamd3 armhf 1:7.10.1+dfsg-1 [28.0 kB] 449s Get:160 http://ftpmaster.internal/ubuntu questing/universe armhf libcommons-parent-java all 56-1 [10.7 kB] 449s Get:161 http://ftpmaster.internal/ubuntu questing/universe armhf libcommons-logging-java all 1.3.0-1ubuntu1 [63.8 kB] 449s Get:162 http://ftpmaster.internal/ubuntu questing/main armhf libexpat1-dev armhf 2.7.1-1 [122 kB] 449s Get:163 http://ftpmaster.internal/ubuntu questing/universe armhf libglpk40 armhf 5.0-1build2 [326 kB] 449s Get:164 http://ftpmaster.internal/ubuntu questing/universe armhf libplfit0 armhf 0.9.6+ds-2ubuntu1 [25.7 kB] 449s Get:165 http://ftpmaster.internal/ubuntu questing/universe armhf libigraph3t64 armhf 0.10.15+ds-3build1 [883 kB] 449s Get:166 http://ftpmaster.internal/ubuntu questing/main armhf libimagequant0 armhf 2.18.0-1build1 [31.1 kB] 449s Get:167 http://ftpmaster.internal/ubuntu questing/main armhf libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 449s Get:168 http://ftpmaster.internal/ubuntu questing/universe armhf libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 449s Get:169 http://ftpmaster.internal/ubuntu questing/main armhf libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 449s Get:170 http://ftpmaster.internal/ubuntu questing/main armhf libjs-sphinxdoc all 8.2.3-1ubuntu2 [28.0 kB] 449s Get:171 http://ftpmaster.internal/ubuntu questing/main armhf libjson-perl all 4.10000-1 [81.9 kB] 449s Get:172 http://ftpmaster.internal/ubuntu questing/universe armhf libmbedcrypto16 armhf 3.6.2-3ubuntu1 [226 kB] 449s Get:173 http://ftpmaster.internal/ubuntu questing/universe armhf libmbedx509-7 armhf 3.6.2-3ubuntu1 [30.4 kB] 449s Get:174 http://ftpmaster.internal/ubuntu questing/universe armhf libmbedtls21 armhf 3.6.2-3ubuntu1 [116 kB] 449s Get:175 http://ftpmaster.internal/ubuntu questing/main armhf mysql-common all 5.8+1.1.1ubuntu1 [6922 B] 449s Get:176 http://ftpmaster.internal/ubuntu questing/main armhf libmysqlclient24 armhf 8.4.5-0ubuntu3 [1264 kB] 449s Get:177 http://ftpmaster.internal/ubuntu questing/main armhf libpython3.13 armhf 3.13.5-2 [2086 kB] 449s Get:178 http://ftpmaster.internal/ubuntu questing/main armhf zlib1g-dev armhf 1:1.3.dfsg+really1.3.1-1ubuntu1 [880 kB] 449s Get:179 http://ftpmaster.internal/ubuntu questing/main armhf libpython3.13-dev armhf 3.13.5-2 [4526 kB] 450s Get:180 http://ftpmaster.internal/ubuntu questing/main armhf libpython3-dev armhf 3.13.5-1 [10.8 kB] 450s Get:181 http://ftpmaster.internal/ubuntu questing/main armhf libpython3-all-dev armhf 3.13.5-1 [906 B] 450s Get:182 http://ftpmaster.internal/ubuntu questing/universe armhf libqhull-r8.0 armhf 2020.2-6build1 [173 kB] 450s Get:183 http://ftpmaster.internal/ubuntu questing/main armhf libraqm0 armhf 0.10.2-1 [12.4 kB] 450s Get:184 http://ftpmaster.internal/ubuntu questing/main armhf libxslt1.1 armhf 1.1.43-0exp1 [144 kB] 450s Get:185 http://ftpmaster.internal/ubuntu questing/universe armhf mafft armhf 7.505-1 [928 kB] 450s Get:186 http://ftpmaster.internal/ubuntu questing/universe armhf ncbi-data all 6.1.20170106+dfsg2-6 [3969 kB] 450s Get:187 http://ftpmaster.internal/ubuntu questing/universe armhf ncbi-blast+ armhf 2.16.0+ds-7 [14.8 MB] 450s Get:188 http://ftpmaster.internal/ubuntu questing/universe armhf phylip armhf 1:3.697+dfsg-4build1 [876 kB] 451s Get:189 http://ftpmaster.internal/ubuntu questing/universe armhf prank armhf 0.0.170427+dfsg-3 [340 kB] 451s Get:190 http://ftpmaster.internal/ubuntu questing/universe armhf preview-latex-style all 13.2-1.1 [347 kB] 451s Get:191 http://ftpmaster.internal/ubuntu questing/universe armhf probcons armhf 1.12-14 [120 kB] 451s Get:192 http://ftpmaster.internal/ubuntu questing/universe armhf python-biopython-doc all 1.85+dfsg-4 [18.2 MB] 451s Get:193 http://ftpmaster.internal/ubuntu questing/universe armhf python-matplotlib-data all 3.10.1+dfsg1-4 [2930 kB] 451s Get:194 http://ftpmaster.internal/ubuntu questing/main armhf python3-all armhf 3.13.5-1 [882 B] 451s Get:195 http://ftpmaster.internal/ubuntu questing/main armhf python3.13-dev armhf 3.13.5-2 [508 kB] 451s Get:196 http://ftpmaster.internal/ubuntu questing/main armhf python3-dev armhf 3.13.5-1 [26.6 kB] 451s Get:197 http://ftpmaster.internal/ubuntu questing/main armhf python3-all-dev armhf 3.13.5-1 [904 B] 451s Get:198 http://ftpmaster.internal/ubuntu questing/universe armhf python3-charset-normalizer armhf 3.4.2-1 [122 kB] 451s Get:199 http://ftpmaster.internal/ubuntu questing/main armhf python3.13-tk armhf 3.13.5-2 [104 kB] 451s Get:200 http://ftpmaster.internal/ubuntu questing/main armhf python3-tk armhf 3.13.4-1 [9884 B] 451s Get:201 http://ftpmaster.internal/ubuntu questing/universe armhf python3-pil.imagetk armhf 11.1.0-5build1 [9226 B] 451s Get:202 http://ftpmaster.internal/ubuntu questing/main armhf python3-pil armhf 11.1.0-5build1 [435 kB] 452s Get:203 http://ftpmaster.internal/ubuntu questing/main armhf python3-cairo armhf 1.27.0-2 [115 kB] 452s Get:204 http://ftpmaster.internal/ubuntu questing/universe armhf python3-freetype all 2.5.1-1 [92.3 kB] 452s Get:205 http://ftpmaster.internal/ubuntu questing/universe armhf python3-rlpycairo all 0.3.0-3 [9130 B] 452s Get:206 http://ftpmaster.internal/ubuntu questing-proposed/universe armhf python3-reportlab all 4.4.2-1 [1145 kB] 452s Get:207 http://ftpmaster.internal/ubuntu questing/universe armhf w3c-sgml-lib all 1.3-3 [280 kB] 452s Get:208 http://ftpmaster.internal/ubuntu questing/universe armhf python3-biopython armhf 1.85+dfsg-4 [1692 kB] 453s Get:209 http://ftpmaster.internal/ubuntu questing/universe armhf python3-biopython-sql all 1.85+dfsg-4 [26.4 kB] 453s Get:210 http://ftpmaster.internal/ubuntu questing/universe armhf python3-brotli armhf 1.1.0-2build4 [322 kB] 453s Get:211 http://ftpmaster.internal/ubuntu questing/universe armhf python3-contourpy armhf 1.3.1-1build1 [195 kB] 453s Get:212 http://ftpmaster.internal/ubuntu questing/universe armhf python3-cycler all 0.12.1-1 [9716 B] 453s Get:213 http://ftpmaster.internal/ubuntu questing/main armhf python3-dateutil all 2.9.0-4 [80.3 kB] 453s Get:214 http://ftpmaster.internal/ubuntu questing/main armhf python3-decorator all 5.2.1-2 [28.1 kB] 453s Get:215 http://ftpmaster.internal/ubuntu questing/main armhf python3-defusedxml all 0.7.1-3 [42.2 kB] 453s Get:216 http://ftpmaster.internal/ubuntu questing/main armhf python3-roman all 5.0-1 [10.3 kB] 453s Get:217 http://ftpmaster.internal/ubuntu questing/main armhf python3-docutils all 0.21.2+dfsg-2 [409 kB] 453s Get:218 http://ftpmaster.internal/ubuntu questing/main armhf python3-platformdirs all 4.3.7-1 [16.9 kB] 453s Get:219 http://ftpmaster.internal/ubuntu questing/universe armhf python3-fs all 2.4.16-7 [90.8 kB] 453s Get:220 http://ftpmaster.internal/ubuntu questing/main armhf python3-lxml armhf 5.4.0-1build1 [1321 kB] 453s Get:221 http://ftpmaster.internal/ubuntu questing/universe armhf python3-lz4 armhf 4.4.0+dfsg-2 [25.2 kB] 453s Get:222 http://ftpmaster.internal/ubuntu questing/universe armhf python3-scipy armhf 1.15.3-1 [16.1 MB] 455s Get:223 http://ftpmaster.internal/ubuntu questing/universe armhf python3-mpmath all 1.3.0-1 [425 kB] 455s Get:224 http://ftpmaster.internal/ubuntu questing/universe armhf python3-sympy all 1.13.3-5 [4229 kB] 455s Get:225 http://ftpmaster.internal/ubuntu questing/universe armhf python3-ufolib2 all 0.17.1+dfsg1-1 [33.5 kB] 455s Get:226 http://ftpmaster.internal/ubuntu questing/universe armhf unicode-data all 15.1.0-1 [8878 kB] 455s Get:227 http://ftpmaster.internal/ubuntu questing/universe armhf python3-fonttools armhf 4.55.3-2build1 [1462 kB] 456s Get:228 http://ftpmaster.internal/ubuntu questing/main armhf python3-imagesize all 1.4.1-1 [6844 B] 456s Get:229 http://ftpmaster.internal/ubuntu questing/universe armhf python3-kiwisolver armhf 1.4.7-3build1 [57.7 kB] 456s Get:230 http://ftpmaster.internal/ubuntu questing/main armhf python3-packaging all 25.0-1 [52.8 kB] 456s Get:231 http://ftpmaster.internal/ubuntu questing/universe armhf python3-matplotlib armhf 3.10.1+dfsg1-4 [18.0 MB] 456s Get:232 http://ftpmaster.internal/ubuntu questing/main armhf python3-msgpack armhf 1.0.3-3build4 [80.6 kB] 456s Get:233 http://ftpmaster.internal/ubuntu questing/universe armhf python3-mmtf all 1.1.3-1 [16.2 kB] 456s Get:234 http://ftpmaster.internal/ubuntu questing/main armhf python3-mysqldb armhf 1.4.6-2build6 [46.3 kB] 456s Get:235 http://ftpmaster.internal/ubuntu questing/main armhf python3-networkx all 3.2.1-4ubuntu1 [11.5 MB] 457s Get:236 http://ftpmaster.internal/ubuntu questing/main armhf sphinx-common all 8.2.3-1ubuntu2 [656 kB] 457s Get:237 http://ftpmaster.internal/ubuntu questing/main armhf python3-alabaster all 0.7.16-0.1 [18.5 kB] 457s Get:238 http://ftpmaster.internal/ubuntu questing/main armhf python3-snowballstemmer all 2.2.0-4build1 [59.8 kB] 457s Get:239 http://ftpmaster.internal/ubuntu questing/main armhf python3-sphinx all 8.2.3-1ubuntu2 [482 kB] 457s Get:240 http://ftpmaster.internal/ubuntu questing/main armhf python3-tabulate all 0.9.0-1 [45.3 kB] 457s Get:241 http://ftpmaster.internal/ubuntu questing/universe armhf python3-numpydoc all 1.8.0-2 [52.4 kB] 457s Get:242 http://ftpmaster.internal/ubuntu questing/universe armhf python3-rdflib all 7.1.1-3 [427 kB] 457s Get:243 http://ftpmaster.internal/ubuntu questing/main armhf sphinx-rtd-theme-common all 3.0.2+dfsg-3 [1013 kB] 457s Get:244 http://ftpmaster.internal/ubuntu questing/universe armhf python3-sphinxcontrib.jquery all 4.1-5 [6678 B] 457s Get:245 http://ftpmaster.internal/ubuntu questing/universe armhf python3-sphinx-rtd-theme all 3.0.2+dfsg-3 [23.5 kB] 457s Get:246 http://ftpmaster.internal/ubuntu questing/universe armhf python3-texttable all 1.7.0-1 [11.2 kB] 457s Get:247 http://ftpmaster.internal/ubuntu questing/universe armhf t-coffee armhf 13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 [968 kB] 457s Get:248 http://ftpmaster.internal/ubuntu questing/universe armhf texlive-fonts-recommended all 2024.20250309-1 [4974 kB] 457s Get:249 http://ftpmaster.internal/ubuntu questing/universe armhf texlive-latex-base all 2024.20250309-1 [1276 kB] 457s Get:250 http://ftpmaster.internal/ubuntu questing/universe armhf libfontbox-java all 1:1.8.16-5 [208 kB] 457s Get:251 http://ftpmaster.internal/ubuntu questing/universe armhf libpdfbox-java all 1:1.8.16-5 [5521 kB] 457s Get:252 http://ftpmaster.internal/ubuntu questing/universe armhf texlive-latex-recommended all 2024.20250309-1 [8727 kB] 458s Get:253 http://ftpmaster.internal/ubuntu questing/universe armhf texlive-pictures all 2024.20250309-1 [17.0 MB] 458s Get:254 http://ftpmaster.internal/ubuntu questing/universe armhf texlive-latex-extra all 2024.20250309-2 [24.8 MB] 460s Get:255 http://ftpmaster.internal/ubuntu questing/universe armhf wise-data all 2.4.1-27 [83.2 kB] 460s Get:256 http://ftpmaster.internal/ubuntu questing/universe armhf wise armhf 2.4.1-27 [916 kB] 460s Get:257 http://ftpmaster.internal/ubuntu questing/universe armhf fasttree armhf 2.1.11-2 [162 kB] 460s Get:258 http://ftpmaster.internal/ubuntu questing/universe armhf python3-igraph armhf 0.11.8+ds-1build1 [327 kB] 461s Preconfiguring packages ... 461s Fetched 341 MB in 20s (17.0 MB/s) 461s Selecting previously unselected package m4. 461s (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 ... 59841 files and directories currently installed.) 461s Preparing to unpack .../000-m4_1.4.19-8_armhf.deb ... 461s Unpacking m4 (1.4.19-8) ... 461s Selecting previously unselected package flex. 461s Preparing to unpack .../001-flex_2.6.4-8.2build1_armhf.deb ... 461s Unpacking flex (2.6.4-8.2build1) ... 461s Selecting previously unselected package fonts-lato. 461s Preparing to unpack .../002-fonts-lato_2.015-1_all.deb ... 461s Unpacking fonts-lato (2.015-1) ... 461s Selecting previously unselected package libgomp1:armhf. 461s Preparing to unpack .../003-libgomp1_15.1.0-8ubuntu1_armhf.deb ... 461s Unpacking libgomp1:armhf (15.1.0-8ubuntu1) ... 461s Selecting previously unselected package libfftw3-double3:armhf. 461s Preparing to unpack .../004-libfftw3-double3_3.3.10-2fakesync1build1_armhf.deb ... 461s Unpacking libfftw3-double3:armhf (3.3.10-2fakesync1build1) ... 461s Selecting previously unselected package libfreetype6:armhf. 461s Preparing to unpack .../005-libfreetype6_2.13.3+dfsg-1_armhf.deb ... 461s Unpacking libfreetype6:armhf (2.13.3+dfsg-1) ... 461s Selecting previously unselected package fonts-dejavu-mono. 461s Preparing to unpack .../006-fonts-dejavu-mono_2.37-8_all.deb ... 461s Unpacking fonts-dejavu-mono (2.37-8) ... 461s Selecting previously unselected package fonts-dejavu-core. 461s Preparing to unpack .../007-fonts-dejavu-core_2.37-8_all.deb ... 461s Unpacking fonts-dejavu-core (2.37-8) ... 461s Selecting previously unselected package libfontenc1:armhf. 461s Preparing to unpack .../008-libfontenc1_1%3a1.1.8-1build1_armhf.deb ... 461s Unpacking libfontenc1:armhf (1:1.1.8-1build1) ... 461s Selecting previously unselected package x11-common. 461s Preparing to unpack .../009-x11-common_1%3a7.7+24ubuntu1_all.deb ... 461s Unpacking x11-common (1:7.7+24ubuntu1) ... 461s Selecting previously unselected package xfonts-encodings. 461s Preparing to unpack .../010-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 461s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 461s Selecting previously unselected package xfonts-utils. 461s Preparing to unpack .../011-xfonts-utils_1%3a7.7+7_armhf.deb ... 461s Unpacking xfonts-utils (1:7.7+7) ... 461s Selecting previously unselected package fonts-urw-base35. 461s Preparing to unpack .../012-fonts-urw-base35_20200910-8_all.deb ... 462s Unpacking fonts-urw-base35 (20200910-8) ... 462s Selecting previously unselected package fontconfig-config. 462s Preparing to unpack .../013-fontconfig-config_2.15.0-2.3ubuntu1_armhf.deb ... 462s Unpacking fontconfig-config (2.15.0-2.3ubuntu1) ... 462s Selecting previously unselected package libfontconfig1:armhf. 462s Preparing to unpack .../014-libfontconfig1_2.15.0-2.3ubuntu1_armhf.deb ... 462s Unpacking libfontconfig1:armhf (2.15.0-2.3ubuntu1) ... 462s Selecting previously unselected package libsharpyuv0:armhf. 462s Preparing to unpack .../015-libsharpyuv0_1.5.0-0.1_armhf.deb ... 462s Unpacking libsharpyuv0:armhf (1.5.0-0.1) ... 462s Selecting previously unselected package libaom3:armhf. 462s Preparing to unpack .../016-libaom3_3.12.1-1_armhf.deb ... 462s Unpacking libaom3:armhf (3.12.1-1) ... 462s Selecting previously unselected package libheif-plugin-aomdec:armhf. 462s Preparing to unpack .../017-libheif-plugin-aomdec_1.19.8-1_armhf.deb ... 462s Unpacking libheif-plugin-aomdec:armhf (1.19.8-1) ... 462s Selecting previously unselected package libde265-0:armhf. 462s Preparing to unpack .../018-libde265-0_1.0.16-1_armhf.deb ... 462s Unpacking libde265-0:armhf (1.0.16-1) ... 462s Selecting previously unselected package libheif-plugin-libde265:armhf. 462s Preparing to unpack .../019-libheif-plugin-libde265_1.19.8-1_armhf.deb ... 462s Unpacking libheif-plugin-libde265:armhf (1.19.8-1) ... 462s Selecting previously unselected package libheif1:armhf. 462s Preparing to unpack .../020-libheif1_1.19.8-1_armhf.deb ... 462s Unpacking libheif1:armhf (1.19.8-1) ... 462s Selecting previously unselected package libjbig0:armhf. 462s Preparing to unpack .../021-libjbig0_2.1-6.1ubuntu2_armhf.deb ... 462s Unpacking libjbig0:armhf (2.1-6.1ubuntu2) ... 462s Selecting previously unselected package libjpeg-turbo8:armhf. 462s Preparing to unpack .../022-libjpeg-turbo8_2.1.5-3ubuntu2_armhf.deb ... 462s Unpacking libjpeg-turbo8:armhf (2.1.5-3ubuntu2) ... 462s Selecting previously unselected package libjpeg8:armhf. 462s Preparing to unpack .../023-libjpeg8_8c-2ubuntu11_armhf.deb ... 462s Unpacking libjpeg8:armhf (8c-2ubuntu11) ... 462s Selecting previously unselected package liblcms2-2:armhf. 462s Preparing to unpack .../024-liblcms2-2_2.16-2_armhf.deb ... 462s Unpacking liblcms2-2:armhf (2.16-2) ... 462s Selecting previously unselected package liblqr-1-0:armhf. 462s Preparing to unpack .../025-liblqr-1-0_0.4.2-2.1build2_armhf.deb ... 462s Unpacking liblqr-1-0:armhf (0.4.2-2.1build2) ... 462s Selecting previously unselected package libltdl7:armhf. 462s Preparing to unpack .../026-libltdl7_2.5.4-4_armhf.deb ... 462s Unpacking libltdl7:armhf (2.5.4-4) ... 462s Selecting previously unselected package libopenjp2-7:armhf. 462s Preparing to unpack .../027-libopenjp2-7_2.5.3-2_armhf.deb ... 462s Unpacking libopenjp2-7:armhf (2.5.3-2) ... 462s Selecting previously unselected package libraw23t64:armhf. 462s Preparing to unpack .../028-libraw23t64_0.21.4-2_armhf.deb ... 462s Unpacking libraw23t64:armhf (0.21.4-2) ... 462s Selecting previously unselected package libdeflate0:armhf. 462s Preparing to unpack .../029-libdeflate0_1.23-2_armhf.deb ... 462s Unpacking libdeflate0:armhf (1.23-2) ... 462s Selecting previously unselected package liblerc4:armhf. 462s Preparing to unpack .../030-liblerc4_4.0.0+ds-5ubuntu1_armhf.deb ... 462s Unpacking liblerc4:armhf (4.0.0+ds-5ubuntu1) ... 462s Selecting previously unselected package libwebp7:armhf. 463s Preparing to unpack .../031-libwebp7_1.5.0-0.1_armhf.deb ... 463s Unpacking libwebp7:armhf (1.5.0-0.1) ... 463s Selecting previously unselected package libtiff6:armhf. 463s Preparing to unpack .../032-libtiff6_4.7.0-3ubuntu1_armhf.deb ... 463s Unpacking libtiff6:armhf (4.7.0-3ubuntu1) ... 463s Selecting previously unselected package libwebpdemux2:armhf. 463s Preparing to unpack .../033-libwebpdemux2_1.5.0-0.1_armhf.deb ... 463s Unpacking libwebpdemux2:armhf (1.5.0-0.1) ... 463s Selecting previously unselected package libwebpmux3:armhf. 463s Preparing to unpack .../034-libwebpmux3_1.5.0-0.1_armhf.deb ... 463s Unpacking libwebpmux3:armhf (1.5.0-0.1) ... 463s Selecting previously unselected package imagemagick-7-common. 463s Preparing to unpack .../035-imagemagick-7-common_8%3a7.1.1.43+dfsg1-1ubuntu1_all.deb ... 463s Unpacking imagemagick-7-common (8:7.1.1.43+dfsg1-1ubuntu1) ... 463s Selecting previously unselected package libmagickcore-7.q16-10:armhf. 463s Preparing to unpack .../036-libmagickcore-7.q16-10_8%3a7.1.1.43+dfsg1-1ubuntu1_armhf.deb ... 463s Unpacking libmagickcore-7.q16-10:armhf (8:7.1.1.43+dfsg1-1ubuntu1) ... 463s Selecting previously unselected package libmagickwand-7.q16-10:armhf. 463s Preparing to unpack .../037-libmagickwand-7.q16-10_8%3a7.1.1.43+dfsg1-1ubuntu1_armhf.deb ... 463s Unpacking libmagickwand-7.q16-10:armhf (8:7.1.1.43+dfsg1-1ubuntu1) ... 463s Selecting previously unselected package poppler-data. 463s Preparing to unpack .../038-poppler-data_0.4.12-1_all.deb ... 463s Unpacking poppler-data (0.4.12-1) ... 463s Selecting previously unselected package python3-numpy-dev:armhf. 463s Preparing to unpack .../039-python3-numpy-dev_1%3a2.2.4+ds-1ubuntu1_armhf.deb ... 463s Unpacking python3-numpy-dev:armhf (1:2.2.4+ds-1ubuntu1) ... 463s Selecting previously unselected package libblas3:armhf. 463s Preparing to unpack .../040-libblas3_3.12.1-2build1_armhf.deb ... 463s Unpacking libblas3:armhf (3.12.1-2build1) ... 463s Selecting previously unselected package libgfortran5:armhf. 463s Preparing to unpack .../041-libgfortran5_15.1.0-8ubuntu1_armhf.deb ... 463s Unpacking libgfortran5:armhf (15.1.0-8ubuntu1) ... 463s Selecting previously unselected package liblapack3:armhf. 463s Preparing to unpack .../042-liblapack3_3.12.1-2build1_armhf.deb ... 463s Unpacking liblapack3:armhf (3.12.1-2build1) ... 463s Selecting previously unselected package python3-numpy. 463s Preparing to unpack .../043-python3-numpy_1%3a2.2.4+ds-1ubuntu1_armhf.deb ... 463s Unpacking python3-numpy (1:2.2.4+ds-1ubuntu1) ... 463s Selecting previously unselected package autoconf. 463s Preparing to unpack .../044-autoconf_2.72-3.1ubuntu1_all.deb ... 463s Unpacking autoconf (2.72-3.1ubuntu1) ... 463s Selecting previously unselected package autotools-dev. 463s Preparing to unpack .../045-autotools-dev_20240727.1_all.deb ... 463s Unpacking autotools-dev (20240727.1) ... 463s Selecting previously unselected package automake. 463s Preparing to unpack .../046-automake_1%3a1.17-4ubuntu1_all.deb ... 463s Unpacking automake (1:1.17-4ubuntu1) ... 463s Selecting previously unselected package autopoint. 463s Preparing to unpack .../047-autopoint_0.23.1-2build1_all.deb ... 463s Unpacking autopoint (0.23.1-2build1) ... 463s Selecting previously unselected package libtcl8.6:armhf. 463s Preparing to unpack .../048-libtcl8.6_8.6.16+dfsg-1_armhf.deb ... 463s Unpacking libtcl8.6:armhf (8.6.16+dfsg-1) ... 464s Selecting previously unselected package libxrender1:armhf. 464s Preparing to unpack .../049-libxrender1_1%3a0.9.12-1_armhf.deb ... 464s Unpacking libxrender1:armhf (1:0.9.12-1) ... 464s Selecting previously unselected package libxft2:armhf. 464s Preparing to unpack .../050-libxft2_2.3.6-1build1_armhf.deb ... 464s Unpacking libxft2:armhf (2.3.6-1build1) ... 464s Selecting previously unselected package libxss1:armhf. 464s Preparing to unpack .../051-libxss1_1%3a1.2.3-1build3_armhf.deb ... 464s Unpacking libxss1:armhf (1:1.2.3-1build3) ... 464s Selecting previously unselected package libtk8.6:armhf. 464s Preparing to unpack .../052-libtk8.6_8.6.16-1_armhf.deb ... 464s Unpacking libtk8.6:armhf (8.6.16-1) ... 464s Selecting previously unselected package tk8.6-blt2.5. 464s Preparing to unpack .../053-tk8.6-blt2.5_2.5.3+dfsg-8_armhf.deb ... 464s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-8) ... 464s Selecting previously unselected package blt. 464s Preparing to unpack .../054-blt_2.5.3+dfsg-8_armhf.deb ... 464s Unpacking blt (2.5.3+dfsg-8) ... 464s Selecting previously unselected package libc-dev-bin. 464s Preparing to unpack .../055-libc-dev-bin_2.41-6ubuntu2_armhf.deb ... 464s Unpacking libc-dev-bin (2.41-6ubuntu2) ... 464s Selecting previously unselected package linux-libc-dev:armhf. 464s Preparing to unpack .../056-linux-libc-dev_6.15.0-4.4_armhf.deb ... 464s Unpacking linux-libc-dev:armhf (6.15.0-4.4) ... 464s Selecting previously unselected package libcrypt-dev:armhf. 464s Preparing to unpack .../057-libcrypt-dev_1%3a4.4.38-1_armhf.deb ... 464s Unpacking libcrypt-dev:armhf (1:4.4.38-1) ... 464s Selecting previously unselected package rpcsvc-proto. 464s Preparing to unpack .../058-rpcsvc-proto_1.4.3-1_armhf.deb ... 464s Unpacking rpcsvc-proto (1.4.3-1) ... 464s Selecting previously unselected package libc6-dev:armhf. 464s Preparing to unpack .../059-libc6-dev_2.41-6ubuntu2_armhf.deb ... 464s Unpacking libc6-dev:armhf (2.41-6ubuntu2) ... 464s Selecting previously unselected package gcc-14-base:armhf. 464s Preparing to unpack .../060-gcc-14-base_14.3.0-1ubuntu1_armhf.deb ... 464s Unpacking gcc-14-base:armhf (14.3.0-1ubuntu1) ... 464s Selecting previously unselected package libisl23:armhf. 464s Preparing to unpack .../061-libisl23_0.27-1_armhf.deb ... 464s Unpacking libisl23:armhf (0.27-1) ... 464s Selecting previously unselected package libmpc3:armhf. 464s Preparing to unpack .../062-libmpc3_1.3.1-1build2_armhf.deb ... 464s Unpacking libmpc3:armhf (1.3.1-1build2) ... 464s Selecting previously unselected package cpp-14-arm-linux-gnueabihf. 464s Preparing to unpack .../063-cpp-14-arm-linux-gnueabihf_14.3.0-1ubuntu1_armhf.deb ... 464s Unpacking cpp-14-arm-linux-gnueabihf (14.3.0-1ubuntu1) ... 464s Selecting previously unselected package cpp-14. 464s Preparing to unpack .../064-cpp-14_14.3.0-1ubuntu1_armhf.deb ... 464s Unpacking cpp-14 (14.3.0-1ubuntu1) ... 464s Selecting previously unselected package cpp-arm-linux-gnueabihf. 464s Preparing to unpack .../065-cpp-arm-linux-gnueabihf_4%3a14.2.0-1ubuntu1_armhf.deb ... 464s Unpacking cpp-arm-linux-gnueabihf (4:14.2.0-1ubuntu1) ... 465s Selecting previously unselected package cpp. 465s Preparing to unpack .../066-cpp_4%3a14.2.0-1ubuntu1_armhf.deb ... 465s Unpacking cpp (4:14.2.0-1ubuntu1) ... 465s Selecting previously unselected package libcc1-0:armhf. 465s Preparing to unpack .../067-libcc1-0_15.1.0-8ubuntu1_armhf.deb ... 465s Unpacking libcc1-0:armhf (15.1.0-8ubuntu1) ... 465s Selecting previously unselected package libasan8:armhf. 465s Preparing to unpack .../068-libasan8_15.1.0-8ubuntu1_armhf.deb ... 465s Unpacking libasan8:armhf (15.1.0-8ubuntu1) ... 465s Selecting previously unselected package libubsan1:armhf. 465s Preparing to unpack .../069-libubsan1_15.1.0-8ubuntu1_armhf.deb ... 465s Unpacking libubsan1:armhf (15.1.0-8ubuntu1) ... 465s Selecting previously unselected package libgcc-14-dev:armhf. 465s Preparing to unpack .../070-libgcc-14-dev_14.3.0-1ubuntu1_armhf.deb ... 465s Unpacking libgcc-14-dev:armhf (14.3.0-1ubuntu1) ... 465s Selecting previously unselected package gcc-14-arm-linux-gnueabihf. 465s Preparing to unpack .../071-gcc-14-arm-linux-gnueabihf_14.3.0-1ubuntu1_armhf.deb ... 465s Unpacking gcc-14-arm-linux-gnueabihf (14.3.0-1ubuntu1) ... 465s Selecting previously unselected package gcc-14. 465s Preparing to unpack .../072-gcc-14_14.3.0-1ubuntu1_armhf.deb ... 465s Unpacking gcc-14 (14.3.0-1ubuntu1) ... 465s Selecting previously unselected package gcc-arm-linux-gnueabihf. 465s Preparing to unpack .../073-gcc-arm-linux-gnueabihf_4%3a14.2.0-1ubuntu1_armhf.deb ... 465s Unpacking gcc-arm-linux-gnueabihf (4:14.2.0-1ubuntu1) ... 465s Selecting previously unselected package gcc. 465s Preparing to unpack .../074-gcc_4%3a14.2.0-1ubuntu1_armhf.deb ... 465s Unpacking gcc (4:14.2.0-1ubuntu1) ... 465s Selecting previously unselected package libstdc++-14-dev:armhf. 465s Preparing to unpack .../075-libstdc++-14-dev_14.3.0-1ubuntu1_armhf.deb ... 465s Unpacking libstdc++-14-dev:armhf (14.3.0-1ubuntu1) ... 465s Selecting previously unselected package g++-14-arm-linux-gnueabihf. 465s Preparing to unpack .../076-g++-14-arm-linux-gnueabihf_14.3.0-1ubuntu1_armhf.deb ... 465s Unpacking g++-14-arm-linux-gnueabihf (14.3.0-1ubuntu1) ... 466s Selecting previously unselected package g++-14. 466s Preparing to unpack .../077-g++-14_14.3.0-1ubuntu1_armhf.deb ... 466s Unpacking g++-14 (14.3.0-1ubuntu1) ... 466s Selecting previously unselected package g++-arm-linux-gnueabihf. 466s Preparing to unpack .../078-g++-arm-linux-gnueabihf_4%3a14.2.0-1ubuntu1_armhf.deb ... 466s Unpacking g++-arm-linux-gnueabihf (4:14.2.0-1ubuntu1) ... 466s Selecting previously unselected package g++. 466s Preparing to unpack .../079-g++_4%3a14.2.0-1ubuntu1_armhf.deb ... 466s Unpacking g++ (4:14.2.0-1ubuntu1) ... 466s Selecting previously unselected package build-essential. 466s Preparing to unpack .../080-build-essential_12.12ubuntu1_armhf.deb ... 466s Unpacking build-essential (12.12ubuntu1) ... 466s Selecting previously unselected package bwa. 466s Preparing to unpack .../081-bwa_0.7.18-1_armhf.deb ... 466s Unpacking bwa (0.7.18-1) ... 466s Selecting previously unselected package libargtable2-0:armhf. 466s Preparing to unpack .../082-libargtable2-0_13-4_armhf.deb ... 466s Unpacking libargtable2-0:armhf (13-4) ... 466s Selecting previously unselected package clustalo. 466s Preparing to unpack .../083-clustalo_1.2.4-8build1_armhf.deb ... 466s Unpacking clustalo (1.2.4-8build1) ... 466s Selecting previously unselected package libdebhelper-perl. 466s Preparing to unpack .../084-libdebhelper-perl_13.24.2ubuntu1_all.deb ... 466s Unpacking libdebhelper-perl (13.24.2ubuntu1) ... 466s Selecting previously unselected package libtool. 466s Preparing to unpack .../085-libtool_2.5.4-4_all.deb ... 466s Unpacking libtool (2.5.4-4) ... 466s Selecting previously unselected package dh-autoreconf. 466s Preparing to unpack .../086-dh-autoreconf_20_all.deb ... 466s Unpacking dh-autoreconf (20) ... 466s Selecting previously unselected package libarchive-zip-perl. 466s Preparing to unpack .../087-libarchive-zip-perl_1.68-1_all.deb ... 466s Unpacking libarchive-zip-perl (1.68-1) ... 466s Selecting previously unselected package libfile-stripnondeterminism-perl. 466s Preparing to unpack .../088-libfile-stripnondeterminism-perl_1.14.1-2_all.deb ... 466s Unpacking libfile-stripnondeterminism-perl (1.14.1-2) ... 466s Selecting previously unselected package dh-strip-nondeterminism. 466s Preparing to unpack .../089-dh-strip-nondeterminism_1.14.1-2_all.deb ... 466s Unpacking dh-strip-nondeterminism (1.14.1-2) ... 466s Selecting previously unselected package libdw1t64:armhf. 466s Preparing to unpack .../090-libdw1t64_0.193-1_armhf.deb ... 466s Unpacking libdw1t64:armhf (0.193-1) ... 466s Selecting previously unselected package debugedit. 466s Preparing to unpack .../091-debugedit_1%3a5.1-2_armhf.deb ... 466s Unpacking debugedit (1:5.1-2) ... 466s Selecting previously unselected package dwz. 466s Preparing to unpack .../092-dwz_0.15-1build6_armhf.deb ... 466s Unpacking dwz (0.15-1build6) ... 466s Selecting previously unselected package gettext. 466s Preparing to unpack .../093-gettext_0.23.1-2build1_armhf.deb ... 466s Unpacking gettext (0.23.1-2build1) ... 466s Selecting previously unselected package intltool-debian. 466s Preparing to unpack .../094-intltool-debian_0.35.0+20060710.6_all.deb ... 466s Unpacking intltool-debian (0.35.0+20060710.6) ... 466s Selecting previously unselected package po-debconf. 466s Preparing to unpack .../095-po-debconf_1.0.21+nmu1_all.deb ... 466s Unpacking po-debconf (1.0.21+nmu1) ... 466s Selecting previously unselected package debhelper. 466s Preparing to unpack .../096-debhelper_13.24.2ubuntu1_all.deb ... 466s Unpacking debhelper (13.24.2ubuntu1) ... 467s Selecting previously unselected package dh-python. 467s Preparing to unpack .../097-dh-python_6.20250414_all.deb ... 467s Unpacking dh-python (6.20250414) ... 467s Selecting previously unselected package dialign. 467s Preparing to unpack .../098-dialign_2.2.1-13_armhf.deb ... 467s Unpacking dialign (2.2.1-13) ... 467s Selecting previously unselected package sgml-base. 467s Preparing to unpack .../099-sgml-base_1.31+nmu1_all.deb ... 467s Unpacking sgml-base (1.31+nmu1) ... 467s Selecting previously unselected package xml-core. 467s Preparing to unpack .../100-xml-core_0.19_all.deb ... 467s Unpacking xml-core (0.19) ... 467s Selecting previously unselected package docutils-common. 467s Preparing to unpack .../101-docutils-common_0.21.2+dfsg-2_all.deb ... 467s Unpacking docutils-common (0.21.2+dfsg-2) ... 467s Selecting previously unselected package libcifpp-data. 467s Preparing to unpack .../102-libcifpp-data_7.0.9-1_all.deb ... 467s Unpacking libcifpp-data (7.0.9-1) ... 467s Selecting previously unselected package libcifpp7:armhf. 467s Preparing to unpack .../103-libcifpp7_7.0.9-1_armhf.deb ... 467s Unpacking libcifpp7:armhf (7.0.9-1) ... 467s Selecting previously unselected package dssp. 467s Preparing to unpack .../104-dssp_4.4.10-1_armhf.deb ... 467s Unpacking dssp (4.4.10-1) ... 467s Selecting previously unselected package fonts-font-awesome. 467s Preparing to unpack .../105-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ... 467s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 467s Selecting previously unselected package fonts-lmodern. 467s Preparing to unpack .../106-fonts-lmodern_2.005-1_all.deb ... 467s Unpacking fonts-lmodern (2.005-1) ... 467s Selecting previously unselected package fonts-lyx. 467s Preparing to unpack .../107-fonts-lyx_2.4.3-1_all.deb ... 467s Unpacking fonts-lyx (2.4.3-1) ... 467s Selecting previously unselected package libgs-common. 467s Preparing to unpack .../108-libgs-common_10.05.0dfsg1-0ubuntu1_all.deb ... 467s Unpacking libgs-common (10.05.0dfsg1-0ubuntu1) ... 467s Selecting previously unselected package libgs10-common. 467s Preparing to unpack .../109-libgs10-common_10.05.0dfsg1-0ubuntu1_all.deb ... 467s Unpacking libgs10-common (10.05.0dfsg1-0ubuntu1) ... 467s Selecting previously unselected package libavahi-common-data:armhf. 467s Preparing to unpack .../110-libavahi-common-data_0.8-16ubuntu2_armhf.deb ... 467s Unpacking libavahi-common-data:armhf (0.8-16ubuntu2) ... 467s Selecting previously unselected package libavahi-common3:armhf. 467s Preparing to unpack .../111-libavahi-common3_0.8-16ubuntu2_armhf.deb ... 467s Unpacking libavahi-common3:armhf (0.8-16ubuntu2) ... 467s Selecting previously unselected package libavahi-client3:armhf. 467s Preparing to unpack .../112-libavahi-client3_0.8-16ubuntu2_armhf.deb ... 467s Unpacking libavahi-client3:armhf (0.8-16ubuntu2) ... 467s Selecting previously unselected package libcups2t64:armhf. 467s Preparing to unpack .../113-libcups2t64_2.4.12-0ubuntu1_armhf.deb ... 467s Unpacking libcups2t64:armhf (2.4.12-0ubuntu1) ... 467s Selecting previously unselected package libidn12:armhf. 467s Preparing to unpack .../114-libidn12_1.43-1_armhf.deb ... 467s Unpacking libidn12:armhf (1.43-1) ... 467s Selecting previously unselected package libijs-0.35:armhf. 467s Preparing to unpack .../115-libijs-0.35_0.35-15.3_armhf.deb ... 467s Unpacking libijs-0.35:armhf (0.35-15.3) ... 467s Selecting previously unselected package libjbig2dec0:armhf. 467s Preparing to unpack .../116-libjbig2dec0_0.20-1build3_armhf.deb ... 467s Unpacking libjbig2dec0:armhf (0.20-1build3) ... 467s Selecting previously unselected package libpaper2:armhf. 467s Preparing to unpack .../117-libpaper2_2.2.5-0.3_armhf.deb ... 467s Unpacking libpaper2:armhf (2.2.5-0.3) ... 468s Selecting previously unselected package libice6:armhf. 468s Preparing to unpack .../118-libice6_2%3a1.1.1-1_armhf.deb ... 468s Unpacking libice6:armhf (2:1.1.1-1) ... 468s Selecting previously unselected package libsm6:armhf. 468s Preparing to unpack .../119-libsm6_2%3a1.2.6-1_armhf.deb ... 468s Unpacking libsm6:armhf (2:1.2.6-1) ... 468s Selecting previously unselected package libxt6t64:armhf. 468s Preparing to unpack .../120-libxt6t64_1%3a1.2.1-1.2build1_armhf.deb ... 468s Unpacking libxt6t64:armhf (1:1.2.1-1.2build1) ... 468s Selecting previously unselected package libgs10:armhf. 468s Preparing to unpack .../121-libgs10_10.05.0dfsg1-0ubuntu1_armhf.deb ... 468s Unpacking libgs10:armhf (10.05.0dfsg1-0ubuntu1) ... 468s Selecting previously unselected package ghostscript. 468s Preparing to unpack .../122-ghostscript_10.05.0dfsg1-0ubuntu1_armhf.deb ... 468s Unpacking ghostscript (10.05.0dfsg1-0ubuntu1) ... 468s Selecting previously unselected package libnetpbm11t64:armhf. 468s Preparing to unpack .../123-libnetpbm11t64_2%3a11.10.02-1build1_armhf.deb ... 468s Unpacking libnetpbm11t64:armhf (2:11.10.02-1build1) ... 468s Selecting previously unselected package netpbm. 468s Preparing to unpack .../124-netpbm_2%3a11.10.02-1build1_armhf.deb ... 468s Unpacking netpbm (2:11.10.02-1build1) ... 468s Selecting previously unselected package tex-common. 468s Preparing to unpack .../125-tex-common_6.19_all.deb ... 468s Unpacking tex-common (6.19) ... 468s Selecting previously unselected package libpaper-utils. 468s Preparing to unpack .../126-libpaper-utils_2.2.5-0.3_armhf.deb ... 468s Unpacking libpaper-utils (2.2.5-0.3) ... 468s Selecting previously unselected package libkpathsea6:armhf. 468s Preparing to unpack .../127-libkpathsea6_2024.20240313.70630+ds-6_armhf.deb ... 468s Unpacking libkpathsea6:armhf (2024.20240313.70630+ds-6) ... 468s Selecting previously unselected package libptexenc1:armhf. 468s Preparing to unpack .../128-libptexenc1_2024.20240313.70630+ds-6_armhf.deb ... 468s Unpacking libptexenc1:armhf (2024.20240313.70630+ds-6) ... 468s Selecting previously unselected package libsynctex2:armhf. 468s Preparing to unpack .../129-libsynctex2_2024.20240313.70630+ds-6_armhf.deb ... 468s Unpacking libsynctex2:armhf (2024.20240313.70630+ds-6) ... 468s Selecting previously unselected package libtexlua53-5:armhf. 468s Preparing to unpack .../130-libtexlua53-5_2024.20240313.70630+ds-6_armhf.deb ... 468s Unpacking libtexlua53-5:armhf (2024.20240313.70630+ds-6) ... 468s Selecting previously unselected package t1utils. 468s Preparing to unpack .../131-t1utils_1.41-4build3_armhf.deb ... 468s Unpacking t1utils (1.41-4build3) ... 468s Selecting previously unselected package libpixman-1-0:armhf. 468s Preparing to unpack .../132-libpixman-1-0_0.44.0-3_armhf.deb ... 468s Unpacking libpixman-1-0:armhf (0.44.0-3) ... 468s Selecting previously unselected package libxcb-render0:armhf. 468s Preparing to unpack .../133-libxcb-render0_1.17.0-2_armhf.deb ... 468s Unpacking libxcb-render0:armhf (1.17.0-2) ... 468s Selecting previously unselected package libxcb-shm0:armhf. 468s Preparing to unpack .../134-libxcb-shm0_1.17.0-2_armhf.deb ... 468s Unpacking libxcb-shm0:armhf (1.17.0-2) ... 468s Selecting previously unselected package libcairo2:armhf. 468s Preparing to unpack .../135-libcairo2_1.18.4-1_armhf.deb ... 468s Unpacking libcairo2:armhf (1.18.4-1) ... 468s Selecting previously unselected package libgraphite2-3:armhf. 468s Preparing to unpack .../136-libgraphite2-3_1.3.14-2ubuntu1_armhf.deb ... 468s Unpacking libgraphite2-3:armhf (1.3.14-2ubuntu1) ... 468s Selecting previously unselected package libharfbuzz0b:armhf. 468s Preparing to unpack .../137-libharfbuzz0b_10.2.0-1_armhf.deb ... 468s Unpacking libharfbuzz0b:armhf (10.2.0-1) ... 468s Selecting previously unselected package libicu76:armhf. 468s Preparing to unpack .../138-libicu76_76.1-4ubuntu1_armhf.deb ... 468s Unpacking libicu76:armhf (76.1-4ubuntu1) ... 469s Selecting previously unselected package libmpfi0:armhf. 469s Preparing to unpack .../139-libmpfi0_1.5.4+ds-4_armhf.deb ... 469s Unpacking libmpfi0:armhf (1.5.4+ds-4) ... 469s Selecting previously unselected package libpotrace0:armhf. 469s Preparing to unpack .../140-libpotrace0_1.16-2build1_armhf.deb ... 469s Unpacking libpotrace0:armhf (1.16-2build1) ... 469s Selecting previously unselected package libteckit0:armhf. 469s Preparing to unpack .../141-libteckit0_2.5.12+ds1-1_armhf.deb ... 469s Unpacking libteckit0:armhf (2.5.12+ds1-1) ... 469s Selecting previously unselected package libxmu6:armhf. 469s Preparing to unpack .../142-libxmu6_2%3a1.1.3-3build2_armhf.deb ... 469s Unpacking libxmu6:armhf (2:1.1.3-3build2) ... 469s Selecting previously unselected package libxpm4:armhf. 469s Preparing to unpack .../143-libxpm4_1%3a3.5.17-1build2_armhf.deb ... 469s Unpacking libxpm4:armhf (1:3.5.17-1build2) ... 469s Selecting previously unselected package libxaw7:armhf. 469s Preparing to unpack .../144-libxaw7_2%3a1.0.16-1_armhf.deb ... 469s Unpacking libxaw7:armhf (2:1.0.16-1) ... 469s Selecting previously unselected package libxi6:armhf. 469s Preparing to unpack .../145-libxi6_2%3a1.8.2-1_armhf.deb ... 469s Unpacking libxi6:armhf (2:1.8.2-1) ... 469s Selecting previously unselected package libzzip-0-13t64:armhf. 469s Preparing to unpack .../146-libzzip-0-13t64_0.13.78+dfsg.1-0.1_armhf.deb ... 469s Unpacking libzzip-0-13t64:armhf (0.13.78+dfsg.1-0.1) ... 469s Selecting previously unselected package texlive-binaries. 469s Preparing to unpack .../147-texlive-binaries_2024.20240313.70630+ds-6_armhf.deb ... 469s Unpacking texlive-binaries (2024.20240313.70630+ds-6) ... 469s Selecting previously unselected package xdg-utils. 469s Preparing to unpack .../148-xdg-utils_1.2.1-2ubuntu1_all.deb ... 469s Unpacking xdg-utils (1.2.1-2ubuntu1) ... 469s Selecting previously unselected package texlive-base. 469s Preparing to unpack .../149-texlive-base_2024.20250309-1_all.deb ... 469s Unpacking texlive-base (2024.20250309-1) ... 470s Selecting previously unselected package hicolor-icon-theme. 470s Preparing to unpack .../150-hicolor-icon-theme_0.18-2_all.deb ... 470s Unpacking hicolor-icon-theme (0.18-2) ... 471s Selecting previously unselected package imagemagick-7.q16. 471s Preparing to unpack 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.../171-libmbedcrypto16_3.6.2-3ubuntu1_armhf.deb ... 471s Unpacking libmbedcrypto16:armhf (3.6.2-3ubuntu1) ... 471s Selecting previously unselected package libmbedx509-7:armhf. 471s Preparing to unpack .../172-libmbedx509-7_3.6.2-3ubuntu1_armhf.deb ... 471s Unpacking libmbedx509-7:armhf (3.6.2-3ubuntu1) ... 471s Selecting previously unselected package libmbedtls21:armhf. 471s Preparing to unpack .../173-libmbedtls21_3.6.2-3ubuntu1_armhf.deb ... 471s Unpacking libmbedtls21:armhf (3.6.2-3ubuntu1) ... 471s Selecting previously unselected package mysql-common. 472s Preparing to unpack .../174-mysql-common_5.8+1.1.1ubuntu1_all.deb ... 472s Unpacking mysql-common (5.8+1.1.1ubuntu1) ... 472s Selecting previously unselected package libmysqlclient24:armhf. 472s Preparing to unpack .../175-libmysqlclient24_8.4.5-0ubuntu3_armhf.deb ... 472s Unpacking libmysqlclient24:armhf (8.4.5-0ubuntu3) ... 472s Selecting previously unselected package libpython3.13:armhf. 472s Preparing to unpack .../176-libpython3.13_3.13.5-2_armhf.deb ... 472s Unpacking libpython3.13:armhf (3.13.5-2) ... 472s Selecting previously unselected package zlib1g-dev:armhf. 472s Preparing to unpack .../177-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1ubuntu1_armhf.deb ... 472s Unpacking zlib1g-dev:armhf (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 472s Selecting previously unselected package libpython3.13-dev:armhf. 472s Preparing to unpack .../178-libpython3.13-dev_3.13.5-2_armhf.deb ... 472s Unpacking libpython3.13-dev:armhf (3.13.5-2) ... 472s Selecting previously unselected package libpython3-dev:armhf. 472s Preparing to unpack .../179-libpython3-dev_3.13.5-1_armhf.deb ... 472s Unpacking libpython3-dev:armhf (3.13.5-1) ... 472s Selecting previously unselected package libpython3-all-dev:armhf. 472s Preparing to unpack .../180-libpython3-all-dev_3.13.5-1_armhf.deb ... 472s Unpacking libpython3-all-dev:armhf (3.13.5-1) ... 472s Selecting previously unselected package libqhull-r8.0:armhf. 472s Preparing to unpack .../181-libqhull-r8.0_2020.2-6build1_armhf.deb ... 472s Unpacking libqhull-r8.0:armhf (2020.2-6build1) ... 472s Selecting previously unselected package libraqm0:armhf. 472s Preparing to unpack .../182-libraqm0_0.10.2-1_armhf.deb ... 472s Unpacking libraqm0:armhf (0.10.2-1) ... 472s Selecting previously unselected package libxslt1.1:armhf. 472s Preparing to unpack .../183-libxslt1.1_1.1.43-0exp1_armhf.deb ... 472s Unpacking libxslt1.1:armhf (1.1.43-0exp1) ... 472s Selecting previously unselected package mafft. 472s Preparing to unpack .../184-mafft_7.505-1_armhf.deb ... 472s Unpacking mafft (7.505-1) ... 472s Selecting previously unselected package ncbi-data. 472s Preparing to unpack .../185-ncbi-data_6.1.20170106+dfsg2-6_all.deb ... 472s Unpacking ncbi-data (6.1.20170106+dfsg2-6) ... 472s Selecting previously unselected package ncbi-blast+. 472s Preparing to unpack .../186-ncbi-blast+_2.16.0+ds-7_armhf.deb ... 472s Unpacking ncbi-blast+ (2.16.0+ds-7) ... 473s Selecting previously unselected package phylip. 473s Preparing to unpack .../187-phylip_1%3a3.697+dfsg-4build1_armhf.deb ... 473s Unpacking phylip (1:3.697+dfsg-4build1) ... 473s Selecting previously unselected package prank. 473s Preparing to unpack .../188-prank_0.0.170427+dfsg-3_armhf.deb ... 473s Unpacking prank (0.0.170427+dfsg-3) ... 473s Selecting previously unselected package preview-latex-style. 473s Preparing to unpack .../189-preview-latex-style_13.2-1.1_all.deb ... 473s Unpacking preview-latex-style (13.2-1.1) ... 473s Selecting previously unselected package probcons. 473s Preparing to unpack .../190-probcons_1.12-14_armhf.deb ... 473s Unpacking probcons (1.12-14) ... 473s Selecting previously unselected package python-biopython-doc. 473s Preparing to unpack .../191-python-biopython-doc_1.85+dfsg-4_all.deb ... 473s Unpacking python-biopython-doc (1.85+dfsg-4) ... 473s Selecting previously unselected package python-matplotlib-data. 473s Preparing to unpack .../192-python-matplotlib-data_3.10.1+dfsg1-4_all.deb ... 473s Unpacking python-matplotlib-data (3.10.1+dfsg1-4) ... 473s Selecting previously unselected package python3-all. 473s Preparing to unpack .../193-python3-all_3.13.5-1_armhf.deb ... 473s Unpacking python3-all (3.13.5-1) ... 473s Selecting previously unselected package python3.13-dev. 474s Preparing to unpack .../194-python3.13-dev_3.13.5-2_armhf.deb ... 474s Unpacking python3.13-dev (3.13.5-2) ... 474s Selecting previously unselected package python3-dev. 474s Preparing to unpack .../195-python3-dev_3.13.5-1_armhf.deb ... 474s Unpacking python3-dev (3.13.5-1) ... 474s Selecting previously unselected package python3-all-dev. 474s Preparing to unpack .../196-python3-all-dev_3.13.5-1_armhf.deb ... 474s Unpacking python3-all-dev (3.13.5-1) ... 474s Selecting previously unselected package python3-charset-normalizer. 474s Preparing to unpack .../197-python3-charset-normalizer_3.4.2-1_armhf.deb ... 474s Unpacking python3-charset-normalizer (3.4.2-1) ... 474s Selecting previously unselected package python3.13-tk. 474s Preparing to unpack .../198-python3.13-tk_3.13.5-2_armhf.deb ... 474s Unpacking python3.13-tk (3.13.5-2) ... 474s Selecting previously unselected package python3-tk:armhf. 474s Preparing to unpack .../199-python3-tk_3.13.4-1_armhf.deb ... 474s Unpacking python3-tk:armhf (3.13.4-1) ... 474s Selecting previously unselected package python3-pil.imagetk:armhf. 474s Preparing to unpack .../200-python3-pil.imagetk_11.1.0-5build1_armhf.deb ... 474s Unpacking python3-pil.imagetk:armhf (11.1.0-5build1) ... 474s Selecting previously unselected package python3-pil:armhf. 474s Preparing to unpack .../201-python3-pil_11.1.0-5build1_armhf.deb ... 474s Unpacking python3-pil:armhf (11.1.0-5build1) ... 474s Selecting previously unselected package python3-cairo. 474s Preparing to unpack .../202-python3-cairo_1.27.0-2_armhf.deb ... 474s Unpacking python3-cairo (1.27.0-2) ... 474s Selecting previously unselected package python3-freetype. 474s Preparing to unpack .../203-python3-freetype_2.5.1-1_all.deb ... 474s Unpacking python3-freetype (2.5.1-1) ... 474s Selecting previously unselected package python3-rlpycairo. 474s Preparing to unpack .../204-python3-rlpycairo_0.3.0-3_all.deb ... 474s Unpacking python3-rlpycairo (0.3.0-3) ... 474s Selecting previously unselected package python3-reportlab. 474s Preparing to unpack .../205-python3-reportlab_4.4.2-1_all.deb ... 474s Unpacking python3-reportlab (4.4.2-1) ... 474s Selecting previously unselected package w3c-sgml-lib. 474s Preparing to unpack .../206-w3c-sgml-lib_1.3-3_all.deb ... 474s Unpacking w3c-sgml-lib (1.3-3) ... 474s Selecting previously unselected package python3-biopython. 474s Preparing to unpack .../207-python3-biopython_1.85+dfsg-4_armhf.deb ... 474s Unpacking python3-biopython (1.85+dfsg-4) ... 474s Selecting previously unselected package python3-biopython-sql. 474s Preparing to unpack .../208-python3-biopython-sql_1.85+dfsg-4_all.deb ... 474s Unpacking python3-biopython-sql (1.85+dfsg-4) ... 474s Selecting previously unselected package python3-brotli. 474s Preparing to unpack .../209-python3-brotli_1.1.0-2build4_armhf.deb ... 474s Unpacking python3-brotli (1.1.0-2build4) ... 474s Selecting previously unselected package python3-contourpy. 474s Preparing to unpack .../210-python3-contourpy_1.3.1-1build1_armhf.deb ... 474s Unpacking python3-contourpy (1.3.1-1build1) ... 474s Selecting previously unselected package python3-cycler. 474s Preparing to unpack .../211-python3-cycler_0.12.1-1_all.deb ... 474s Unpacking python3-cycler (0.12.1-1) ... 474s Selecting previously unselected package python3-dateutil. 474s Preparing to unpack .../212-python3-dateutil_2.9.0-4_all.deb ... 474s Unpacking python3-dateutil (2.9.0-4) ... 474s Selecting previously unselected package python3-decorator. 474s Preparing to unpack .../213-python3-decorator_5.2.1-2_all.deb ... 474s Unpacking python3-decorator (5.2.1-2) ... 474s Selecting previously unselected package python3-defusedxml. 475s Preparing to unpack .../214-python3-defusedxml_0.7.1-3_all.deb ... 475s Unpacking python3-defusedxml (0.7.1-3) ... 475s Selecting previously unselected package python3-roman. 475s Preparing to unpack .../215-python3-roman_5.0-1_all.deb ... 475s Unpacking python3-roman (5.0-1) ... 475s Selecting previously unselected package python3-docutils. 475s Preparing to unpack .../216-python3-docutils_0.21.2+dfsg-2_all.deb ... 475s Unpacking python3-docutils (0.21.2+dfsg-2) ... 475s Selecting previously unselected package python3-platformdirs. 475s Preparing to unpack .../217-python3-platformdirs_4.3.7-1_all.deb ... 475s Unpacking python3-platformdirs (4.3.7-1) ... 475s Selecting previously unselected package python3-fs. 475s Preparing to unpack .../218-python3-fs_2.4.16-7_all.deb ... 475s Unpacking python3-fs (2.4.16-7) ... 475s Selecting previously unselected package python3-lxml:armhf. 475s Preparing to unpack .../219-python3-lxml_5.4.0-1build1_armhf.deb ... 475s Unpacking python3-lxml:armhf (5.4.0-1build1) ... 475s Selecting previously unselected package python3-lz4. 475s Preparing to unpack .../220-python3-lz4_4.4.0+dfsg-2_armhf.deb ... 475s Unpacking python3-lz4 (4.4.0+dfsg-2) ... 475s Selecting previously unselected package python3-scipy. 475s Preparing to unpack .../221-python3-scipy_1.15.3-1_armhf.deb ... 475s Unpacking python3-scipy (1.15.3-1) ... 475s Selecting previously unselected package python3-mpmath. 475s Preparing to unpack .../222-python3-mpmath_1.3.0-1_all.deb ... 475s Unpacking python3-mpmath (1.3.0-1) ... 475s Selecting previously unselected package python3-sympy. 475s Preparing to unpack .../223-python3-sympy_1.13.3-5_all.deb ... 475s Unpacking python3-sympy (1.13.3-5) ... 476s Selecting previously unselected package python3-ufolib2. 476s Preparing to unpack .../224-python3-ufolib2_0.17.1+dfsg1-1_all.deb ... 476s Unpacking python3-ufolib2 (0.17.1+dfsg1-1) ... 476s Selecting previously unselected package unicode-data. 476s Preparing to unpack .../225-unicode-data_15.1.0-1_all.deb ... 476s Unpacking unicode-data (15.1.0-1) ... 476s Selecting previously unselected package python3-fonttools. 476s Preparing to unpack .../226-python3-fonttools_4.55.3-2build1_armhf.deb ... 476s Unpacking python3-fonttools (4.55.3-2build1) ... 476s Selecting previously unselected package python3-imagesize. 476s Preparing to unpack .../227-python3-imagesize_1.4.1-1_all.deb ... 476s Unpacking python3-imagesize (1.4.1-1) ... 476s Selecting previously unselected package python3-kiwisolver. 476s Preparing to unpack .../228-python3-kiwisolver_1.4.7-3build1_armhf.deb ... 476s Unpacking python3-kiwisolver (1.4.7-3build1) ... 476s Selecting previously unselected package python3-packaging. 476s Preparing to unpack .../229-python3-packaging_25.0-1_all.deb ... 476s Unpacking python3-packaging (25.0-1) ... 476s Selecting previously unselected package python3-matplotlib. 476s Preparing to unpack .../230-python3-matplotlib_3.10.1+dfsg1-4_armhf.deb ... 476s Unpacking python3-matplotlib (3.10.1+dfsg1-4) ... 477s Selecting previously unselected package python3-msgpack. 477s Preparing to unpack .../231-python3-msgpack_1.0.3-3build4_armhf.deb ... 477s Unpacking python3-msgpack (1.0.3-3build4) ... 477s Selecting previously unselected package python3-mmtf. 477s Preparing to unpack .../232-python3-mmtf_1.1.3-1_all.deb ... 477s Unpacking python3-mmtf (1.1.3-1) ... 477s Selecting previously unselected package python3-mysqldb. 477s Preparing to unpack .../233-python3-mysqldb_1.4.6-2build6_armhf.deb ... 477s Unpacking python3-mysqldb (1.4.6-2build6) ... 477s Selecting previously unselected package python3-networkx. 477s Preparing to unpack .../234-python3-networkx_3.2.1-4ubuntu1_all.deb ... 477s Unpacking python3-networkx (3.2.1-4ubuntu1) ... 478s Selecting previously unselected package sphinx-common. 478s Preparing to unpack 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tl-paper: setting paper size for dvips to a4: /var/lib/texmf/dvips/config/config-paper.ps 505s tl-paper: setting paper size for dvipdfmx to a4: /var/lib/texmf/dvipdfmx/dvipdfmx-paper.cfg 506s tl-paper: setting paper size for xdvi to a4: /var/lib/texmf/xdvi/XDvi-paper 506s tl-paper: setting paper size for pdftex to a4: /var/lib/texmf/tex/generic/tex-ini-files/pdftexconfig.tex 507s Setting up libgs10:armhf (10.05.0dfsg1-0ubuntu1) ... 507s Setting up libpython3-dev:armhf (3.13.5-1) ... 507s Setting up python3.13-dev (3.13.5-2) ... 507s Setting up debhelper (13.24.2ubuntu1) ... 507s Setting up ghostscript (10.05.0dfsg1-0ubuntu1) ... 507s Setting up texlive-latex-base (2024.20250309-1) ... 507s Setting up libpython3-all-dev:armhf (3.13.5-1) ... 507s Setting up python3-dev (3.13.5-1) ... 507s Setting up texlive-latex-recommended (2024.20250309-1) ... 507s Setting up texlive-pictures (2024.20250309-1) ... 507s Setting up texlive-fonts-recommended (2024.20250309-1) ... 507s Setting up 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using /usr/bin/animate-im7.q16 to provide /usr/bin/animate-im7 (animate-im7) in auto mode 509s update-alternatives: using /usr/bin/convert-im7.q16 to provide /usr/bin/convert (convert) in auto mode 509s update-alternatives: using /usr/bin/convert-im7.q16 to provide /usr/bin/convert-im7 (convert-im7) in auto mode 509s update-alternatives: using /usr/bin/composite-im7.q16 to provide /usr/bin/composite (composite) in auto mode 509s update-alternatives: using /usr/bin/composite-im7.q16 to provide /usr/bin/composite-im7 (composite-im7) in auto mode 509s update-alternatives: using /usr/bin/conjure-im7.q16 to provide /usr/bin/conjure (conjure) in auto mode 509s update-alternatives: using /usr/bin/conjure-im7.q16 to provide /usr/bin/conjure-im7 (conjure-im7) in auto mode 509s update-alternatives: using /usr/bin/import-im7.q16 to provide /usr/bin/import (import) in auto mode 509s update-alternatives: using /usr/bin/import-im7.q16 to provide /usr/bin/import-im7 (import-im7) in auto mode 509s update-alternatives: using /usr/bin/identify-im7.q16 to provide /usr/bin/identify (identify) in auto mode 509s update-alternatives: using /usr/bin/identify-im7.q16 to provide /usr/bin/identify-im7 (identify-im7) in auto mode 509s update-alternatives: using /usr/bin/stream-im7.q16 to provide /usr/bin/stream (stream) in auto mode 509s update-alternatives: using /usr/bin/stream-im7.q16 to provide /usr/bin/stream-im7 (stream-im7) in auto mode 509s update-alternatives: using /usr/bin/display-im7.q16 to provide /usr/bin/display (display) in auto mode 509s update-alternatives: using /usr/bin/display-im7.q16 to provide /usr/bin/display-im7 (display-im7) in auto mode 509s update-alternatives: using /usr/bin/montage-im7.q16 to provide /usr/bin/montage (montage) in auto mode 509s update-alternatives: using /usr/bin/montage-im7.q16 to provide /usr/bin/montage-im7 (montage-im7) in auto mode 509s update-alternatives: using /usr/bin/mogrify-im7.q16 to provide /usr/bin/mogrify (mogrify) in auto mode 509s update-alternatives: using /usr/bin/mogrify-im7.q16 to provide /usr/bin/mogrify-im7 (mogrify-im7) in auto mode 509s update-alternatives: using /usr/bin/magick-im7.q16 to provide /usr/bin/magick (magick) in auto mode 509s update-alternatives: warning: skip creation of /usr/share/man/man1/magick.1.gz because associated file /usr/share/man/man1/magick-im7.q16.1.gz (of link group magick) doesn't exist 509s update-alternatives: using /usr/bin/magick-im7.q16 to provide /usr/bin/magick-im7 (magick-im7) in auto mode 509s update-alternatives: warning: skip creation of /usr/share/man/man1/magick-im7.1.gz because associated file /usr/share/man/man1/magick-im7.q16.1.gz (of link group magick-im7) doesn't exist 509s update-alternatives: using /usr/bin/magick-script-im7.q16 to provide /usr/bin/magick-script (magick-script) in auto mode 509s update-alternatives: warning: skip creation of /usr/share/man/man1/magick-script.1.gz because associated file /usr/share/man/man1/magick-script-im7.q16.1.gz (of link group magick-script) doesn't exist 509s update-alternatives: using /usr/bin/magick-script-im7.q16 to provide /usr/bin/magick-script-im7 (magick-script-im7) in auto mode 509s update-alternatives: warning: skip creation of /usr/share/man/man1/magick-script-im7.1.gz because associated file /usr/share/man/man1/magick-script-im7.q16.1.gz (of link group magick-script-im7) doesn't exist 509s Setting up hevea (2.36-2) ... 509s Setting up imagemagick (8:7.1.1.43+dfsg1-1ubuntu1) ... 509s Processing triggers for install-info (7.1.1-1) ... 510s Processing triggers for libc-bin (2.41-6ubuntu2) ... 510s Processing triggers for man-db (2.13.1-1) ... 511s Processing triggers for sgml-base (1.31+nmu1) ... 511s Setting up docutils-common (0.21.2+dfsg-2) ... 512s Setting up w3c-sgml-lib (1.3-3) ... 538s Setting up python3-biopython (1.85+dfsg-4) ... 539s Setting up python3-biopython-sql (1.85+dfsg-4) ... 539s Processing triggers for sgml-base (1.31+nmu1) ... 539s Setting up python3-docutils (0.21.2+dfsg-2) ... 540s Setting up python3-sphinx (8.2.3-1ubuntu2) ... 540s Setting up python3-sphinxcontrib.jquery (4.1-5) ... 540s Setting up python3-numpydoc (1.8.0-2) ... 541s Setting up python3-sphinx-rtd-theme (3.0.2+dfsg-3) ... 541s Processing triggers for tex-common (6.19) ... 541s Running updmap-sys. This may take some time... done. 541s Running mktexlsr /var/lib/texmf ... done. 542s Building format(s) --all. 685s This may take some time... done. 704s autopkgtest [03:51:56]: test full_suite: sh debian/tests/run-unit-test 704s autopkgtest [03:51:56]: test full_suite: [----------------------- 708s mkdir: created directory 'Bio' 708s mkdir: created directory 'Bio/Align' 708s mkdir: created directory 'Bio/Align/substitution_matrices' 708s mkdir: created directory 'Bio/Align/substitution_matrices/data/' 708s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER22' -> 'Bio/Align/substitution_matrices/data/BENNER22' 708s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER6' -> 'Bio/Align/substitution_matrices/data/BENNER6' 708s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER74' -> 'Bio/Align/substitution_matrices/data/BENNER74' 708s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLASTN' -> 'Bio/Align/substitution_matrices/data/BLASTN' 708s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLASTP' -> 'Bio/Align/substitution_matrices/data/BLASTP' 708s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM45' -> 'Bio/Align/substitution_matrices/data/BLOSUM45' 708s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM50' -> 'Bio/Align/substitution_matrices/data/BLOSUM50' 708s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM62' -> 'Bio/Align/substitution_matrices/data/BLOSUM62' 708s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM80' -> 'Bio/Align/substitution_matrices/data/BLOSUM80' 708s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM90' -> 'Bio/Align/substitution_matrices/data/BLOSUM90' 708s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/DAYHOFF' -> 'Bio/Align/substitution_matrices/data/DAYHOFF' 708s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/FENG' -> 'Bio/Align/substitution_matrices/data/FENG' 708s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/GENETIC' -> 'Bio/Align/substitution_matrices/data/GENETIC' 708s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/GONNET1992' -> 'Bio/Align/substitution_matrices/data/GONNET1992' 708s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/HOXD70' -> 'Bio/Align/substitution_matrices/data/HOXD70' 708s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/JOHNSON' -> 'Bio/Align/substitution_matrices/data/JOHNSON' 708s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/JONES' -> 'Bio/Align/substitution_matrices/data/JONES' 708s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/LEVIN' -> 'Bio/Align/substitution_matrices/data/LEVIN' 708s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MCLACHLAN' -> 'Bio/Align/substitution_matrices/data/MCLACHLAN' 708s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MDM78' -> 'Bio/Align/substitution_matrices/data/MDM78' 708s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MEGABLAST' -> 'Bio/Align/substitution_matrices/data/MEGABLAST' 708s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/NUC.4.4' -> 'Bio/Align/substitution_matrices/data/NUC.4.4' 708s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM250' -> 'Bio/Align/substitution_matrices/data/PAM250' 708s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM30' -> 'Bio/Align/substitution_matrices/data/PAM30' 708s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM70' -> 'Bio/Align/substitution_matrices/data/PAM70' 708s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/RAO' -> 'Bio/Align/substitution_matrices/data/RAO' 708s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/RISLER' -> 'Bio/Align/substitution_matrices/data/RISLER' 708s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/SCHNEIDER' -> 'Bio/Align/substitution_matrices/data/SCHNEIDER' 708s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/STR' -> 'Bio/Align/substitution_matrices/data/STR' 708s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/TRANS' -> 'Bio/Align/substitution_matrices/data/TRANS' 709s test_Ace ... ok 709s test_Affy ... ok 711s test_AlignIO ... ok 711s test_AlignIO_ClustalIO ... ok 711s test_AlignIO_EmbossIO ... ok 711s test_AlignIO_FastaIO ... ok 711s test_AlignIO_MauveIO ... ok 711s test_AlignIO_PhylipIO ... ok 711s test_AlignIO_convert ... ok 711s test_AlignInfo ... ok 712s test_Align_Alignment ... ok 712s test_Align_a2m ... ok 712s test_Align_bed ... ok 712s test_Align_bigbed ... ok 712s test_Align_bigmaf ... ok 713s test_Align_bigpsl ... ok 713s test_Align_chain ... ok 713s test_Align_clustal ... ok 718s test_Align_codonalign ... ok 718s test_Align_emboss ... ok 719s test_Align_exonerate ... ok 719s test_Align_fasta ... ok 719s test_Align_hhr ... ok 720s test_Align_maf ... ok 720s test_Align_mauve ... ok 720s test_Align_msf ... ok 720s test_Align_nexus ... ok 720s test_Align_phylip ... ok 720s test_Align_psl ... ok 721s test_Align_sam ... ok 722s test_Align_stockholm ... ok 723s test_Align_tabular ... ok 723s test_Application ... ok 723s test_BioSQL_MySQLdb_online ... skipping. internet not available 723s test_BioSQL_mysql_connector ... skipping. BioSQL test configuration file biosql.ini missing (see biosql.ini.sample) 723s test_BioSQL_mysql_connector_online ... skipping. internet not available 723s test_BioSQL_psycopg2_online ... skipping. internet not available 728s test_BioSQL_sqlite3 ... ok 728s test_BioSQL_sqlite3_online ... skipping. internet not available 728s test_Blast_Record ... ok 729s test_Blast_parser ... ok 729s test_CAPS ... ok 729s test_Chi2 ... ok 730s test_ClustalOmega_tool ... ok 730s test_Clustalw_tool ... skipping. Install clustalw or clustalw2 if you want to use it from Biopython. 730s test_Cluster ... ok 730s test_CodonTable ... ok 730s test_ColorSpiral ... ok 730s test_Compass ... ok 731s test_Consensus ... ok 733s test_Dialign_tool ... ok 733s test_EMBL_unittest ... ok 733s test_Emboss ... skipping. $EMBOSS_ROOT='/usr/lib/emboss' which does not exist! 733s test_EmbossPrimer ... ok 737s test_Entrez ... ok 737s test_Entrez_online ... skipping. internet not available 738s test_Entrez_parser ... ok 738s test_Enzyme ... ok 738s test_ExPASy ... skipping. internet not available 738s test_Fasttree_tool ... ok 738s test_File ... ok 738s test_GenBank ... /usr/lib/python3/dist-packages/Bio/SeqIO/InsdcIO.py:600: BiopythonWarning: Annotation 'Sequence Read Archive: SRX001885, SRX001121, SRX001531, SRX001530, SRX001529' too long 738s warnings.warn(f"Annotation {text!r} too long", BiopythonWarning) 738s ok 740s test_GenomeDiagram ... Warn: Can't find .pfb for face 'Helvetica' 742s ok 742s test_GraphicsChromosome ... ok 743s test_GraphicsDistribution ... ok 743s test_GraphicsGeneral ... ok 743s test_HMMCasino ... ok 744s test_HMMGeneral ... ok 744s test_KEGG ... ok 744s test_KEGG_online ... skipping. internet not available 748s test_KGML_graphics ... ok 748s test_KGML_graphics_online ... skipping. internet not available 749s test_KGML_nographics ... ok 749s test_KeyWList ... ok 749s test_LogisticRegression ... ok 750s test_MafIO_index ... ok 752s test_Mafft_tool ... ok 752s test_MarkovModel ... ok 752s test_Medline ... ok 752s test_Muscle_tool ... skipping. Install MUSCLE if you want to use the Bio.Align.Applications wrapper. 753s test_NCBIXML ... Exception ignored in: 753s Traceback (most recent call last): 753s File "/usr/lib/python3/dist-packages/Bio/Blast/NCBIXML.py", line 1319, in parse 753s expat_parser.Parse(NULL, True) 753s xml.parsers.expat.ExpatError: unclosed token: line 320, column 0 753s ok 755s test_NCBI_BLAST_tools ... ok 755s test_NCBI_qblast ... ok 755s test_NMR ... ok 755s test_NaiveBayes ... ok 755s test_Nexus ... ok 756s test_PAML_baseml ... ok 756s test_PAML_codeml ... ok 756s test_PAML_yn00 ... ok 761s test_PDB_CEAligner ... ok 763s test_PDB_DSSP ... ok 763s test_PDB_Dice ... ok 763s test_PDB_Disordered ... ok 763s test_PDB_Exposure ... ok 763s test_PDB_FragmentMapper ... ok 765s test_PDB_KDTree ... ok 765s test_PDB_MMCIF2Dict ... ok 765s test_PDB_MMCIFIO ... ok 766s test_PDB_MMCIFParser ... ok 767s test_PDB_NACCESS ... ok 767s test_PDB_PDBIO ... ok 767s test_PDB_PDBList ... skipping. internet not available 773s test_PDB_PDBMLParser ... ok 773s test_PDB_PDBParser ... ok 773s test_PDB_PSEA ... skipping. Download and install psea from ftp://ftp.lmcp.jussieu.fr/pub/sincris/software/protein/p-sea/. Make sure that psea is on path 774s test_PDB_Polypeptide ... ok 774s test_PDB_QCPSuperimposer ... ok 777s test_PDB_SASA ... ok 777s test_PDB_SMCRA ... ok 778s test_PDB_Selection ... ok 778s test_PDB_StructureAlignment ... ok 778s test_PDB_Superimposer ... ok 778s test_PDB_alphafold_db ... skipping. internet not available 781s test_PDB_binary_cif ... /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 1, ' ') redefined at line 7. 781s warnings.warn( 781s /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 15, ' ') redefined at line 144. 781s warnings.warn( 781s /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 15, ' ') redefined at line 153. 781s warnings.warn( 781s /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 1, ' ') redefined at line 0. 781s warnings.warn( 781s /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 15, ' ') redefined at line 0. 781s warnings.warn( 781s ok 788s test_PDB_internal_coords ... ok 789s test_PDB_parse_pdb_header ... ok 789s test_PDB_vectors ... ok 789s test_PQR ... ok 789s test_Pathway ... ok 790s test_Phd ... ok 790s test_Phylo ... ok 790s test_PhyloXML ... ok 791s test_Phylo_CDAO ... ok 791s test_Phylo_NeXML ... ok 792s test_Phylo_igraph ... ok 795s test_Phylo_matplotlib ... ok 796s test_Phylo_networkx ... ok 796s test_PopGen_GenePop_nodepend ... ok 798s test_Prank_tool ... ok 799s test_Probcons_tool ... ok 799s test_ProtParam ... ok 800s test_RCSBFormats ... ok 801s test_Restriction ... ok 801s test_SCOP_Astral ... ok 802s test_SCOP_Cla ... ok 803s test_SCOP_Des ... ok 803s test_SCOP_Dom ... ok 804s test_SCOP_Hie ... ok 804s test_SCOP_Raf ... ok 805s test_SCOP_Residues ... ok 805s test_SCOP_Scop ... ok 806s test_SVDSuperimposer ... ok 807s test_SearchIO_blast_tab ... ok 807s test_SearchIO_blast_tab_index ... ok 808s test_SearchIO_blast_xml ... ok 810s test_SearchIO_blast_xml_index ... ok 810s test_SearchIO_blat_psl ... ok 811s test_SearchIO_blat_psl_index ... ok 811s test_SearchIO_exonerate ... ok 812s test_SearchIO_exonerate_text_index ... ok 813s test_SearchIO_exonerate_vulgar_index ... ok 813s test_SearchIO_fasta_m10 ... ok 814s test_SearchIO_fasta_m10_index ... ok 815s test_SearchIO_hhsuite2_text ... ok 815s test_SearchIO_hmmer2_text ... ok 816s test_SearchIO_hmmer2_text_index ... ok 816s test_SearchIO_hmmer3_domtab ... ok 817s test_SearchIO_hmmer3_domtab_index ... ok 817s test_SearchIO_hmmer3_tab ... ok 818s test_SearchIO_hmmer3_tab_index ... ok 819s test_SearchIO_hmmer3_text ... ok 819s test_SearchIO_hmmer3_text_index ... ok 820s test_SearchIO_interproscan_xml ... ok 820s test_SearchIO_model ... ok 821s test_SearchIO_write ... ok 822s test_SeqFeature ... ok 837s test_SeqIO ... ok 838s test_SeqIO_AbiIO ... ok 838s test_SeqIO_FastaIO ... ok 839s test_SeqIO_Gck ... ok 840s test_SeqIO_Gfa ... ok 840s test_SeqIO_Insdc ... ok 841s test_SeqIO_NibIO ... ok 843s test_SeqIO_PdbIO ... ok 844s test_SeqIO_QualityIO ... ok 844s test_SeqIO_SeqXML ... ok 845s test_SeqIO_SffIO ... ok 846s test_SeqIO_SnapGene ... ok 847s test_SeqIO_TwoBitIO ... ok 848s test_SeqIO_UniprotIO ... ok 848s test_SeqIO_Xdna ... ok 849s test_SeqIO_features ... ok 863s test_SeqIO_index ... ok 864s test_SeqIO_online ... skipping. internet not available 865s test_SeqIO_write ... ok 865s test_SeqRecord ... ok 866s test_SeqUtils ... ok 867s test_Seq_objs ... ok 868s test_SwissProt ... ok 870s test_TCoffee_tool ... ok 871s test_TogoWS ... skipping. internet not available 872s test_TreeConstruction ... ok 872s test_Tutorial ... skipping. Could not find ../Doc/Tutorial/index.rst file 873s test_UniGene ... ok 873s test_UniProt ... skipping. internet not available 874s test_UniProt_GOA ... ok 875s test_align ... ok 876s test_align_substitution_matrices ... ok 878s test_bgzf ... ok 879s test_cellosaurus ... ok 885s test_codonalign ... ok 885s test_geo ... ok 886s test_kNN ... ok 887s test_motifs ... ok 887s test_motifs_online ... skipping. internet not available 888s test_pairwise2 ... /usr/lib/python3/dist-packages/Bio/pairwise2.py:278: BiopythonDeprecationWarning: Bio.pairwise2 has been deprecated, and we intend to remove it in a future release of Biopython. As an alternative, please consider using Bio.Align.PairwiseAligner as a replacement, and contact the Biopython developers if you still need the Bio.pairwise2 module. 888s warnings.warn( 888s ok 889s test_pairwise2_no_C ... ok 889s test_pairwise_aligner ... ok 890s test_pairwise_alignment_map ... ok 900s test_phenotype ... ok 900s test_phenotype_fit ... ok 901s test_phyml_tool ... skipping. Couldn't find the PhyML software. Install PhyML 3.0 or later if you want to use the Bio.Phylo.Applications wrapper. 901s test_prodoc ... ok 902s test_prosite ... ok 902s test_raxml_tool ... skipping. Install RAxML (binary raxmlHPC) if you want to test the Bio.Phylo.Applications wrapper. 903s test_samtools_tool ... skipping. Install samtools and correctly set the file path to the program if you want to use it from Biopython 903s test_seq ... ok 904s test_translate ... ok 905s ---------------------------------------------------------------------- 905s Ran 218 tests in 196.091 seconds 905s 905s Skipping any tests requiring internet access 905s Python version: 3.13.5 (main, Jun 25 2025, 18:55:22) [GCC 14.3.0] 905s Operating system: posix linux 906s :0: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/protein_lib.fa' mode='rt' encoding='UTF-8'> 906s :0: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/nucleotide_lib.fa' mode='rt' encoding='UTF-8'> 907s autopkgtest [03:55:19]: test full_suite: -----------------------] 910s autopkgtest [03:55:22]: test full_suite: - - - - - - - - - - results - - - - - - - - - - 910s full_suite PASS 913s autopkgtest [03:55:25]: @@@@@@@@@@@@@@@@@@@@ summary 913s dependencies PASS 913s full_suite PASS