0s autopkgtest [12:32:10]: starting date and time: 2025-02-19 12:32:10+0000 0s autopkgtest [12:32:10]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [12:32:10]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.fvvdhl7h/out --timeout-copy=6000 --setup-commands 'ln -s /dev/null /etc/systemd/system/bluetooth.service; printf "http_proxy=http://squid.internal:3128\nhttps_proxy=http://squid.internal:3128\nno_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com\n" >> /etc/environment' --apt-pocket=proposed=src:sphinx --apt-upgrade python-biopython --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=sphinx/8.1.3-5 -- lxd -r lxd-armhf-10.145.243.201 lxd-armhf-10.145.243.201:autopkgtest/ubuntu/plucky/armhf 27s autopkgtest [12:32:37]: testbed dpkg architecture: armhf 29s autopkgtest [12:32:39]: testbed apt version: 2.9.30 34s autopkgtest [12:32:44]: @@@@@@@@@@@@@@@@@@@@ test bed setup 36s autopkgtest [12:32:46]: testbed release detected to be: None 45s autopkgtest [12:32:55]: updating testbed package index (apt update) 47s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [110 kB] 47s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 48s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 48s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 48s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [3120 B] 48s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [76.1 kB] 48s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [13.9 kB] 48s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [750 kB] 48s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf Packages [99.0 kB] 48s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted armhf Packages [760 B] 48s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf Packages [636 kB] 49s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf Packages [3116 B] 49s Fetched 1693 kB in 2s (1092 kB/s) 50s Reading package lists... 57s autopkgtest [12:33:07]: upgrading testbed (apt dist-upgrade and autopurge) 59s Reading package lists... 60s Building dependency tree... 60s Reading state information... 60s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 61s Starting 2 pkgProblemResolver with broken count: 0 61s Done 62s Entering ResolveByKeep 62s 63s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 65s Reading package lists... 66s Building dependency tree... 66s Reading state information... 67s Starting pkgProblemResolver with broken count: 0 67s Starting 2 pkgProblemResolver with broken count: 0 67s Done 69s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 71s autopkgtest [12:33:21]: rebooting testbed after setup commands that affected boot 118s autopkgtest [12:34:08]: testbed running kernel: Linux 6.8.0-49-generic #49~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Wed Nov 6 18:12:14 UTC 2 147s autopkgtest [12:34:37]: @@@@@@@@@@@@@@@@@@@@ apt-source python-biopython 168s Get:1 http://ftpmaster.internal/ubuntu plucky/universe python-biopython 1.85+dfsg-2 (dsc) [3439 B] 168s Get:2 http://ftpmaster.internal/ubuntu plucky/universe python-biopython 1.85+dfsg-2 (tar) [14.6 MB] 168s Get:3 http://ftpmaster.internal/ubuntu plucky/universe python-biopython 1.85+dfsg-2 (diff) [42.9 kB] 169s gpgv: Signature made Thu Feb 6 14:44:48 2025 UTC 169s gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 169s gpgv: issuer "crusoe@debian.org" 169s gpgv: Can't check signature: No public key 169s dpkg-source: warning: cannot verify inline signature for ./python-biopython_1.85+dfsg-2.dsc: no acceptable signature found 170s autopkgtest [12:35:00]: testing package python-biopython version 1.85+dfsg-2 172s autopkgtest [12:35:02]: build not needed 178s autopkgtest [12:35:08]: test dependencies: preparing testbed 180s Reading package lists... 180s Building dependency tree... 180s Reading state information... 181s Starting pkgProblemResolver with broken count: 0 181s Starting 2 pkgProblemResolver with broken count: 0 181s Done 182s The following NEW packages will be installed: 182s fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-urw-base35 182s libblas3 libcairo2 libdeflate0 libfontconfig1 libfontenc1 libfreetype6 182s libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libimagequant0 libjbig0 182s libjpeg-turbo8 libjpeg8 libjs-jquery libjs-sphinxdoc libjs-underscore 182s liblapack3 liblcms2-2 liblerc4 libopenjp2-7 libpixman-1-0 libraqm0 182s libsharpyuv0 libtiff6 libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 182s libxcb-shm0 libxrender1 python-biopython-doc python3-all python3-biopython 182s python3-biopython-sql python3-cairo python3-freetype python3-numpy 182s python3-pil python3-reportlab python3-rlpycairo sgml-base w3c-sgml-lib 183s x11-common xfonts-encodings xfonts-utils xml-core 183s 0 upgraded, 51 newly installed, 0 to remove and 0 not upgraded. 183s Need to get 45.1 MB of archives. 183s After this operation, 122 MB of additional disk space will be used. 183s Get:1 http://ftpmaster.internal/ubuntu plucky/main armhf sgml-base all 1.31 [11.4 kB] 183s Get:2 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-dejavu-mono all 2.37-8 [502 kB] 183s Get:3 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-dejavu-core all 2.37-8 [835 kB] 183s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf libfontenc1 armhf 1:1.1.8-1build1 [11.5 kB] 183s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf libfreetype6 armhf 2.13.3+dfsg-1 [330 kB] 183s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf x11-common all 1:7.7+23ubuntu3 [21.7 kB] 183s Get:7 http://ftpmaster.internal/ubuntu plucky/main armhf xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 183s Get:8 http://ftpmaster.internal/ubuntu plucky/main armhf xfonts-utils armhf 1:7.7+7 [90.6 kB] 183s Get:9 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-urw-base35 all 20200910-8 [11.0 MB] 184s Get:10 http://ftpmaster.internal/ubuntu plucky/main armhf fontconfig-config armhf 2.15.0-2ubuntu1 [37.5 kB] 184s Get:11 http://ftpmaster.internal/ubuntu plucky/main armhf libblas3 armhf 3.12.1-2 [132 kB] 184s Get:12 http://ftpmaster.internal/ubuntu plucky/main armhf libfontconfig1 armhf 2.15.0-2ubuntu1 [114 kB] 184s Get:13 http://ftpmaster.internal/ubuntu plucky/main armhf libpixman-1-0 armhf 0.44.0-3 [183 kB] 184s Get:14 http://ftpmaster.internal/ubuntu plucky/main armhf libxcb-render0 armhf 1.17.0-2 [15.3 kB] 184s Get:15 http://ftpmaster.internal/ubuntu plucky/main armhf libxcb-shm0 armhf 1.17.0-2 [5774 B] 184s Get:16 http://ftpmaster.internal/ubuntu plucky/main armhf libxrender1 armhf 1:0.9.10-1.1build1 [16.0 kB] 184s Get:17 http://ftpmaster.internal/ubuntu plucky/main armhf libcairo2 armhf 1.18.2-2 [484 kB] 184s Get:18 http://ftpmaster.internal/ubuntu plucky/main armhf libdeflate0 armhf 1.23-1 [38.5 kB] 184s Get:19 http://ftpmaster.internal/ubuntu plucky/main armhf libgfortran5 armhf 15-20250213-1ubuntu1 [330 kB] 184s Get:20 http://ftpmaster.internal/ubuntu plucky/main armhf libgomp1 armhf 15-20250213-1ubuntu1 [128 kB] 184s Get:21 http://ftpmaster.internal/ubuntu plucky/main armhf libgraphite2-3 armhf 1.3.14-2ubuntu1 [64.8 kB] 184s Get:22 http://ftpmaster.internal/ubuntu plucky/main armhf libharfbuzz0b armhf 10.2.0-1 [464 kB] 184s Get:23 http://ftpmaster.internal/ubuntu plucky/main armhf libimagequant0 armhf 2.18.0-1build1 [31.1 kB] 184s Get:24 http://ftpmaster.internal/ubuntu plucky/main armhf libjpeg-turbo8 armhf 2.1.5-3ubuntu2 [127 kB] 184s Get:25 http://ftpmaster.internal/ubuntu plucky/main armhf libjpeg8 armhf 8c-2ubuntu11 [2148 B] 184s Get:26 http://ftpmaster.internal/ubuntu plucky/main armhf libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 184s Get:27 http://ftpmaster.internal/ubuntu plucky/main armhf libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 184s Get:28 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libjs-sphinxdoc all 8.1.3-5 [31.0 kB] 184s Get:29 http://ftpmaster.internal/ubuntu plucky/main armhf liblapack3 armhf 3.12.1-2 [2091 kB] 184s Get:30 http://ftpmaster.internal/ubuntu plucky/main armhf liblcms2-2 armhf 2.16-2 [137 kB] 184s Get:31 http://ftpmaster.internal/ubuntu plucky/main armhf liblerc4 armhf 4.0.0+ds-5ubuntu1 [160 kB] 184s Get:32 http://ftpmaster.internal/ubuntu plucky/main armhf libraqm0 armhf 0.10.2-1 [12.4 kB] 184s Get:33 http://ftpmaster.internal/ubuntu plucky/main armhf libsharpyuv0 armhf 1.5.0-0.1 [16.4 kB] 184s Get:34 http://ftpmaster.internal/ubuntu plucky/main armhf libjbig0 armhf 2.1-6.1ubuntu2 [24.9 kB] 184s Get:35 http://ftpmaster.internal/ubuntu plucky/main armhf libwebp7 armhf 1.5.0-0.1 [188 kB] 184s Get:36 http://ftpmaster.internal/ubuntu plucky/main armhf libtiff6 armhf 4.5.1+git230720-4ubuntu4 [179 kB] 184s Get:37 http://ftpmaster.internal/ubuntu plucky/main armhf libwebpdemux2 armhf 1.5.0-0.1 [11.5 kB] 184s Get:38 http://ftpmaster.internal/ubuntu plucky/main armhf libwebpmux3 armhf 1.5.0-0.1 [22.4 kB] 184s Get:39 http://ftpmaster.internal/ubuntu plucky/universe armhf python-biopython-doc all 1.85+dfsg-2 [18.2 MB] 185s Get:40 http://ftpmaster.internal/ubuntu plucky/main armhf python3-all armhf 3.13.1-1~exp2 [896 B] 185s Get:41 http://ftpmaster.internal/ubuntu plucky/main armhf python3-numpy armhf 1:1.26.4+ds-13 [3978 kB] 185s Get:42 http://ftpmaster.internal/ubuntu plucky/main armhf libopenjp2-7 armhf 2.5.0-2ubuntu3 [171 kB] 185s Get:43 http://ftpmaster.internal/ubuntu plucky/main armhf python3-pil armhf 11.1.0-5 [453 kB] 185s Get:44 http://ftpmaster.internal/ubuntu plucky/main armhf python3-cairo armhf 1.26.1-2build1 [129 kB] 185s Get:45 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-freetype all 2.5.1-1 [92.3 kB] 185s Get:46 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-rlpycairo all 0.3.0-3 [9130 B] 185s Get:47 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-reportlab all 4.3.0-1 [1137 kB] 185s Get:48 http://ftpmaster.internal/ubuntu plucky/main armhf xml-core all 0.19 [20.3 kB] 185s Get:49 http://ftpmaster.internal/ubuntu plucky/universe armhf w3c-sgml-lib all 1.3-3 [280 kB] 185s Get:50 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-biopython armhf 1.85+dfsg-2 [1696 kB] 185s Get:51 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-biopython-sql all 1.85+dfsg-2 [26.4 kB] 186s Fetched 45.1 MB in 3s (16.7 MB/s) 186s Selecting previously unselected package sgml-base. 186s (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 ... 60727 files and directories currently installed.) 186s Preparing to unpack .../00-sgml-base_1.31_all.deb ... 186s Unpacking sgml-base (1.31) ... 186s Selecting previously unselected package fonts-dejavu-mono. 186s Preparing to unpack .../01-fonts-dejavu-mono_2.37-8_all.deb ... 186s Unpacking fonts-dejavu-mono (2.37-8) ... 186s Selecting previously unselected package fonts-dejavu-core. 186s Preparing to unpack .../02-fonts-dejavu-core_2.37-8_all.deb ... 186s Unpacking fonts-dejavu-core (2.37-8) ... 186s Selecting previously unselected package libfontenc1:armhf. 186s Preparing to unpack .../03-libfontenc1_1%3a1.1.8-1build1_armhf.deb ... 186s Unpacking libfontenc1:armhf (1:1.1.8-1build1) ... 186s Selecting previously unselected package libfreetype6:armhf. 186s Preparing to unpack .../04-libfreetype6_2.13.3+dfsg-1_armhf.deb ... 186s Unpacking libfreetype6:armhf (2.13.3+dfsg-1) ... 186s Selecting previously unselected package x11-common. 186s Preparing to unpack .../05-x11-common_1%3a7.7+23ubuntu3_all.deb ... 186s Unpacking x11-common (1:7.7+23ubuntu3) ... 186s Selecting previously unselected package xfonts-encodings. 186s Preparing to unpack .../06-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 186s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 186s Selecting previously unselected package xfonts-utils. 186s Preparing to unpack .../07-xfonts-utils_1%3a7.7+7_armhf.deb ... 186s Unpacking xfonts-utils (1:7.7+7) ... 186s Selecting previously unselected package fonts-urw-base35. 186s Preparing to unpack .../08-fonts-urw-base35_20200910-8_all.deb ... 186s Unpacking fonts-urw-base35 (20200910-8) ... 187s Selecting previously unselected package fontconfig-config. 187s Preparing to unpack .../09-fontconfig-config_2.15.0-2ubuntu1_armhf.deb ... 187s Unpacking fontconfig-config (2.15.0-2ubuntu1) ... 187s Selecting previously unselected package libblas3:armhf. 187s Preparing to unpack .../10-libblas3_3.12.1-2_armhf.deb ... 187s Unpacking libblas3:armhf (3.12.1-2) ... 187s Selecting previously unselected package libfontconfig1:armhf. 187s Preparing to unpack .../11-libfontconfig1_2.15.0-2ubuntu1_armhf.deb ... 187s Unpacking libfontconfig1:armhf (2.15.0-2ubuntu1) ... 187s Selecting previously unselected package libpixman-1-0:armhf. 187s Preparing to unpack .../12-libpixman-1-0_0.44.0-3_armhf.deb ... 187s Unpacking libpixman-1-0:armhf (0.44.0-3) ... 187s Selecting previously unselected package libxcb-render0:armhf. 187s Preparing to unpack .../13-libxcb-render0_1.17.0-2_armhf.deb ... 187s Unpacking libxcb-render0:armhf (1.17.0-2) ... 187s Selecting previously unselected package libxcb-shm0:armhf. 187s Preparing to unpack .../14-libxcb-shm0_1.17.0-2_armhf.deb ... 187s Unpacking libxcb-shm0:armhf (1.17.0-2) ... 187s Selecting previously unselected package libxrender1:armhf. 187s Preparing to unpack .../15-libxrender1_1%3a0.9.10-1.1build1_armhf.deb ... 187s Unpacking libxrender1:armhf (1:0.9.10-1.1build1) ... 187s Selecting previously unselected package libcairo2:armhf. 187s Preparing to unpack .../16-libcairo2_1.18.2-2_armhf.deb ... 187s Unpacking libcairo2:armhf (1.18.2-2) ... 187s Selecting previously unselected package libdeflate0:armhf. 187s Preparing to unpack .../17-libdeflate0_1.23-1_armhf.deb ... 187s Unpacking libdeflate0:armhf (1.23-1) ... 187s Selecting previously unselected package libgfortran5:armhf. 187s Preparing to unpack .../18-libgfortran5_15-20250213-1ubuntu1_armhf.deb ... 187s Unpacking libgfortran5:armhf (15-20250213-1ubuntu1) ... 187s Selecting previously unselected package libgomp1:armhf. 187s Preparing to unpack .../19-libgomp1_15-20250213-1ubuntu1_armhf.deb ... 187s Unpacking libgomp1:armhf (15-20250213-1ubuntu1) ... 187s Selecting previously unselected package libgraphite2-3:armhf. 187s Preparing to unpack .../20-libgraphite2-3_1.3.14-2ubuntu1_armhf.deb ... 187s Unpacking libgraphite2-3:armhf (1.3.14-2ubuntu1) ... 187s Selecting previously unselected package libharfbuzz0b:armhf. 187s Preparing to unpack .../21-libharfbuzz0b_10.2.0-1_armhf.deb ... 187s Unpacking libharfbuzz0b:armhf (10.2.0-1) ... 187s Selecting previously unselected package libimagequant0:armhf. 187s Preparing to unpack .../22-libimagequant0_2.18.0-1build1_armhf.deb ... 187s Unpacking libimagequant0:armhf (2.18.0-1build1) ... 187s Selecting previously unselected package libjpeg-turbo8:armhf. 187s Preparing to unpack .../23-libjpeg-turbo8_2.1.5-3ubuntu2_armhf.deb ... 187s Unpacking libjpeg-turbo8:armhf (2.1.5-3ubuntu2) ... 187s Selecting previously unselected package libjpeg8:armhf. 187s Preparing to unpack .../24-libjpeg8_8c-2ubuntu11_armhf.deb ... 187s Unpacking libjpeg8:armhf (8c-2ubuntu11) ... 187s Selecting previously unselected package libjs-jquery. 187s Preparing to unpack .../25-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 187s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 188s Selecting previously unselected package libjs-underscore. 188s Preparing to unpack .../26-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 188s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 188s Selecting previously unselected package libjs-sphinxdoc. 188s Preparing to unpack .../27-libjs-sphinxdoc_8.1.3-5_all.deb ... 188s Unpacking libjs-sphinxdoc (8.1.3-5) ... 188s Selecting previously unselected package liblapack3:armhf. 188s Preparing to unpack .../28-liblapack3_3.12.1-2_armhf.deb ... 188s Unpacking liblapack3:armhf (3.12.1-2) ... 188s Selecting previously unselected package liblcms2-2:armhf. 188s Preparing to unpack .../29-liblcms2-2_2.16-2_armhf.deb ... 188s Unpacking liblcms2-2:armhf (2.16-2) ... 188s Selecting previously unselected package liblerc4:armhf. 188s Preparing to unpack .../30-liblerc4_4.0.0+ds-5ubuntu1_armhf.deb ... 188s Unpacking liblerc4:armhf (4.0.0+ds-5ubuntu1) ... 188s Selecting previously unselected package libraqm0:armhf. 188s Preparing to unpack .../31-libraqm0_0.10.2-1_armhf.deb ... 188s Unpacking libraqm0:armhf (0.10.2-1) ... 188s Selecting previously unselected package libsharpyuv0:armhf. 188s Preparing to unpack .../32-libsharpyuv0_1.5.0-0.1_armhf.deb ... 188s Unpacking libsharpyuv0:armhf (1.5.0-0.1) ... 188s Selecting previously unselected package libjbig0:armhf. 188s Preparing to unpack .../33-libjbig0_2.1-6.1ubuntu2_armhf.deb ... 188s Unpacking libjbig0:armhf (2.1-6.1ubuntu2) ... 188s Selecting previously unselected package libwebp7:armhf. 188s Preparing to unpack .../34-libwebp7_1.5.0-0.1_armhf.deb ... 188s Unpacking libwebp7:armhf (1.5.0-0.1) ... 188s Selecting previously unselected package libtiff6:armhf. 188s Preparing to unpack .../35-libtiff6_4.5.1+git230720-4ubuntu4_armhf.deb ... 188s Unpacking libtiff6:armhf (4.5.1+git230720-4ubuntu4) ... 188s Selecting previously unselected package libwebpdemux2:armhf. 188s Preparing to unpack .../36-libwebpdemux2_1.5.0-0.1_armhf.deb ... 188s Unpacking libwebpdemux2:armhf (1.5.0-0.1) ... 188s Selecting previously unselected package libwebpmux3:armhf. 188s Preparing to unpack .../37-libwebpmux3_1.5.0-0.1_armhf.deb ... 188s Unpacking libwebpmux3:armhf (1.5.0-0.1) ... 188s Selecting previously unselected package python-biopython-doc. 188s Preparing to unpack .../38-python-biopython-doc_1.85+dfsg-2_all.deb ... 188s Unpacking python-biopython-doc (1.85+dfsg-2) ... 188s Selecting previously unselected package python3-all. 188s Preparing to unpack .../39-python3-all_3.13.1-1~exp2_armhf.deb ... 188s Unpacking python3-all (3.13.1-1~exp2) ... 189s Selecting previously unselected package python3-numpy. 189s Preparing to unpack .../40-python3-numpy_1%3a1.26.4+ds-13_armhf.deb ... 189s Unpacking python3-numpy (1:1.26.4+ds-13) ... 189s Selecting previously unselected package libopenjp2-7:armhf. 189s Preparing to unpack .../41-libopenjp2-7_2.5.0-2ubuntu3_armhf.deb ... 189s Unpacking libopenjp2-7:armhf (2.5.0-2ubuntu3) ... 189s Selecting previously unselected package python3-pil:armhf. 189s Preparing to unpack .../42-python3-pil_11.1.0-5_armhf.deb ... 189s Unpacking python3-pil:armhf (11.1.0-5) ... 189s Selecting previously unselected package python3-cairo. 189s Preparing to unpack .../43-python3-cairo_1.26.1-2build1_armhf.deb ... 189s Unpacking python3-cairo (1.26.1-2build1) ... 189s Selecting previously unselected package python3-freetype. 189s Preparing to unpack .../44-python3-freetype_2.5.1-1_all.deb ... 189s Unpacking python3-freetype (2.5.1-1) ... 189s Selecting previously unselected package python3-rlpycairo. 189s Preparing to unpack .../45-python3-rlpycairo_0.3.0-3_all.deb ... 189s Unpacking python3-rlpycairo (0.3.0-3) ... 189s Selecting previously unselected package python3-reportlab. 189s Preparing to unpack .../46-python3-reportlab_4.3.0-1_all.deb ... 189s Unpacking python3-reportlab (4.3.0-1) ... 189s Selecting previously unselected package xml-core. 189s Preparing to unpack .../47-xml-core_0.19_all.deb ... 189s Unpacking xml-core (0.19) ... 189s Selecting previously unselected package w3c-sgml-lib. 189s Preparing to unpack .../48-w3c-sgml-lib_1.3-3_all.deb ... 189s Unpacking w3c-sgml-lib (1.3-3) ... 189s Selecting previously unselected package python3-biopython. 189s Preparing to unpack .../49-python3-biopython_1.85+dfsg-2_armhf.deb ... 189s Unpacking python3-biopython (1.85+dfsg-2) ... 189s Selecting previously unselected package python3-biopython-sql. 189s Preparing to unpack .../50-python3-biopython-sql_1.85+dfsg-2_all.deb ... 189s Unpacking python3-biopython-sql (1.85+dfsg-2) ... 190s Setting up libgraphite2-3:armhf (1.3.14-2ubuntu1) ... 190s Setting up liblcms2-2:armhf (2.16-2) ... 190s Setting up libpixman-1-0:armhf (0.44.0-3) ... 190s Setting up libsharpyuv0:armhf (1.5.0-0.1) ... 190s Setting up liblerc4:armhf (4.0.0+ds-5ubuntu1) ... 190s Setting up libxrender1:armhf (1:0.9.10-1.1build1) ... 190s Setting up libxcb-render0:armhf (1.17.0-2) ... 190s Setting up x11-common (1:7.7+23ubuntu3) ... 190s Setting up libdeflate0:armhf (1.23-1) ... 190s Setting up python3-all (3.13.1-1~exp2) ... 190s Setting up libxcb-shm0:armhf (1.17.0-2) ... 190s Setting up libgomp1:armhf (15-20250213-1ubuntu1) ... 190s Setting up libjbig0:armhf (2.1-6.1ubuntu2) ... 190s Setting up libfontenc1:armhf (1:1.1.8-1build1) ... 190s Setting up libblas3:armhf (3.12.1-2) ... 190s 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 190s Setting up libfreetype6:armhf (2.13.3+dfsg-1) ... 190s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 190s Setting up libimagequant0:armhf (2.18.0-1build1) ... 190s Setting up fonts-dejavu-mono (2.37-8) ... 190s Setting up fonts-dejavu-core (2.37-8) ... 190s Setting up libjpeg-turbo8:armhf (2.1.5-3ubuntu2) ... 190s Setting up libgfortran5:armhf (15-20250213-1ubuntu1) ... 190s Setting up libwebp7:armhf (1.5.0-0.1) ... 190s Setting up libopenjp2-7:armhf (2.5.0-2ubuntu3) ... 190s Setting up libharfbuzz0b:armhf (10.2.0-1) ... 190s Setting up sgml-base (1.31) ... 190s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 190s Setting up libwebpmux3:armhf (1.5.0-0.1) ... 190s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 190s Setting up libjpeg8:armhf (8c-2ubuntu11) ... 190s Setting up liblapack3:armhf (3.12.1-2) ... 190s 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 190s Setting up fontconfig-config (2.15.0-2ubuntu1) ... 190s Setting up libwebpdemux2:armhf (1.5.0-0.1) ... 190s Setting up python3-freetype (2.5.1-1) ... 191s Setting up xfonts-utils (1:7.7+7) ... 191s Setting up libraqm0:armhf (0.10.2-1) ... 191s Setting up python3-numpy (1:1.26.4+ds-13) ... 195s Setting up libjs-sphinxdoc (8.1.3-5) ... 195s Setting up python-biopython-doc (1.85+dfsg-2) ... 195s Setting up libtiff6:armhf (4.5.1+git230720-4ubuntu4) ... 195s Setting up xml-core (0.19) ... 195s Setting up libfontconfig1:armhf (2.15.0-2ubuntu1) ... 195s Setting up fonts-urw-base35 (20200910-8) ... 195s Setting up libcairo2:armhf (1.18.2-2) ... 195s Setting up python3-pil:armhf (11.1.0-5) ... 196s Setting up python3-cairo (1.26.1-2build1) ... 196s Setting up python3-rlpycairo (0.3.0-3) ... 196s Setting up python3-reportlab (4.3.0-1) ... 198s Processing triggers for libc-bin (2.40-4ubuntu1) ... 198s Processing triggers for man-db (2.13.0-1) ... 199s Processing triggers for sgml-base (1.31) ... 199s Setting up w3c-sgml-lib (1.3-3) ... 231s Setting up python3-biopython (1.85+dfsg-2) ... 234s Setting up python3-biopython-sql (1.85+dfsg-2) ... 248s autopkgtest [12:36:18]: test dependencies: sh debian/tests/run-unit-test 248s autopkgtest [12:36:18]: test dependencies: [----------------------- 250s cp: cannot stat '/usr/share/libcifpp/mmcif_pdbx.dic': No such file or directory 250s cp: cannot stat '/usr/share/libcifpp/mmcif_ma.dic': No such file or directory 252s mkdir: created directory 'Bio' 252s mkdir: created directory 'Bio/Align' 252s mkdir: created directory 'Bio/Align/substitution_matrices' 252s mkdir: created directory 'Bio/Align/substitution_matrices/data/' 252s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER22' -> 'Bio/Align/substitution_matrices/data/BENNER22' 252s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER6' -> 'Bio/Align/substitution_matrices/data/BENNER6' 252s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER74' -> 'Bio/Align/substitution_matrices/data/BENNER74' 252s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLASTN' -> 'Bio/Align/substitution_matrices/data/BLASTN' 252s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLASTP' -> 'Bio/Align/substitution_matrices/data/BLASTP' 252s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM45' -> 'Bio/Align/substitution_matrices/data/BLOSUM45' 252s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM50' -> 'Bio/Align/substitution_matrices/data/BLOSUM50' 252s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM62' -> 'Bio/Align/substitution_matrices/data/BLOSUM62' 252s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM80' -> 'Bio/Align/substitution_matrices/data/BLOSUM80' 252s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM90' -> 'Bio/Align/substitution_matrices/data/BLOSUM90' 252s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/DAYHOFF' -> 'Bio/Align/substitution_matrices/data/DAYHOFF' 252s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/FENG' -> 'Bio/Align/substitution_matrices/data/FENG' 252s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/GENETIC' -> 'Bio/Align/substitution_matrices/data/GENETIC' 252s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/GONNET1992' -> 'Bio/Align/substitution_matrices/data/GONNET1992' 252s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/HOXD70' -> 'Bio/Align/substitution_matrices/data/HOXD70' 252s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/JOHNSON' -> 'Bio/Align/substitution_matrices/data/JOHNSON' 252s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/JONES' -> 'Bio/Align/substitution_matrices/data/JONES' 252s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/LEVIN' -> 'Bio/Align/substitution_matrices/data/LEVIN' 252s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MCLACHLAN' -> 'Bio/Align/substitution_matrices/data/MCLACHLAN' 252s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MDM78' -> 'Bio/Align/substitution_matrices/data/MDM78' 252s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MEGABLAST' -> 'Bio/Align/substitution_matrices/data/MEGABLAST' 252s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/NUC.4.4' -> 'Bio/Align/substitution_matrices/data/NUC.4.4' 252s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM250' -> 'Bio/Align/substitution_matrices/data/PAM250' 252s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM30' -> 'Bio/Align/substitution_matrices/data/PAM30' 252s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM70' -> 'Bio/Align/substitution_matrices/data/PAM70' 252s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/RAO' -> 'Bio/Align/substitution_matrices/data/RAO' 252s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/RISLER' -> 'Bio/Align/substitution_matrices/data/RISLER' 252s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/SCHNEIDER' -> 'Bio/Align/substitution_matrices/data/SCHNEIDER' 252s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/STR' -> 'Bio/Align/substitution_matrices/data/STR' 252s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/TRANS' -> 'Bio/Align/substitution_matrices/data/TRANS' 253s test_Ace ... ok 253s test_Affy ... ok 256s test_AlignIO ... ok 256s test_AlignIO_ClustalIO ... ok 256s test_AlignIO_EmbossIO ... ok 256s test_AlignIO_FastaIO ... ok 256s test_AlignIO_MauveIO ... ok 256s test_AlignIO_PhylipIO ... ok 256s test_AlignIO_convert ... ok 256s test_AlignInfo ... ok 257s test_Align_Alignment ... ok 257s test_Align_a2m ... ok 257s test_Align_bed ... ok 257s test_Align_bigbed ... ok 258s test_Align_bigmaf ... ok 258s test_Align_bigpsl ... ok 258s test_Align_chain ... ok 258s test_Align_clustal ... ok 262s test_Align_codonalign ... ok 262s test_Align_emboss ... ok 262s test_Align_exonerate ... ok 262s test_Align_fasta ... ok 262s test_Align_hhr ... ok 263s test_Align_maf ... ok 263s test_Align_mauve ... ok 263s test_Align_msf ... ok 263s test_Align_nexus ... ok 264s test_Align_phylip ... ok 264s test_Align_psl ... ok 264s test_Align_sam ... ok 266s test_Align_stockholm ... ok 267s test_Align_tabular ... ok 267s test_Application ... ok 267s test_BioSQL_MySQLdb_online ... skipping. internet not available 267s test_BioSQL_mysql_connector ... skipping. BioSQL test configuration file biosql.ini missing (see biosql.ini.sample) 267s test_BioSQL_mysql_connector_online ... skipping. internet not available 267s test_BioSQL_psycopg2_online ... skipping. internet not available 273s test_BioSQL_sqlite3 ... ok 273s test_BioSQL_sqlite3_online ... skipping. internet not available 273s test_Blast_Record ... ok 274s test_Blast_parser ... ok 274s test_CAPS ... ok 274s test_Chi2 ... ok 274s test_ClustalOmega_tool ... skipping. Install clustalo if you want to use Clustal Omega from Biopython. 274s test_Clustalw_tool ... skipping. Install clustalw or clustalw2 if you want to use it from Biopython. 274s test_Cluster ... ok 274s test_CodonTable ... ok 274s test_ColorSpiral ... ok 274s test_Compass ... ok 276s test_Consensus ... ok 276s test_Dialign_tool ... skipping. Install DIALIGN2-2 if you want to use the Bio.Align.Applications wrapper. 276s test_EMBL_unittest ... ok 276s test_Emboss ... skipping. $EMBOSS_ROOT='/usr/lib/emboss' which does not exist! 276s test_EmbossPrimer ... ok 280s test_Entrez ... ok 280s test_Entrez_online ... skipping. internet not available 281s test_Entrez_parser ... ok 281s test_Enzyme ... ok 281s test_ExPASy ... skipping. internet not available 281s test_Fasttree_tool ... skipping. Install FastTree and correctly set the file path to the program if you want to use it from Biopython. 281s test_File ... ok 281s test_GenBank ... /usr/lib/python3/dist-packages/Bio/SeqIO/InsdcIO.py:600: BiopythonWarning: Annotation 'Sequence Read Archive: SRX001885, SRX001121, SRX001531, SRX001530, SRX001529' too long 281s warnings.warn(f"Annotation {text!r} too long", BiopythonWarning) 281s ok 283s test_GenomeDiagram ... Warn: Can't find .pfb for face 'Helvetica' 285s ok 286s test_GraphicsChromosome ... ok 286s test_GraphicsDistribution ... ok 287s test_GraphicsGeneral ... ok 287s test_HMMCasino ... ok 287s test_HMMGeneral ... ok 287s test_KEGG ... ok 287s test_KEGG_online ... skipping. internet not available 293s test_KGML_graphics ... ok 293s test_KGML_graphics_online ... skipping. internet not available 294s test_KGML_nographics ... ok 294s test_KeyWList ... ok 294s test_LogisticRegression ... ok 295s test_MafIO_index ... ok 295s test_Mafft_tool ... skipping. Install MAFFT if you want to use the Bio.Align.Applications wrapper. 295s test_MarkovModel ... ok 295s test_Medline ... ok 295s test_Muscle_tool ... skipping. Install MUSCLE if you want to use the Bio.Align.Applications wrapper. 296s test_NCBIXML ... Exception ignored in: 296s Traceback (most recent call last): 296s File "/usr/lib/python3/dist-packages/Bio/Blast/NCBIXML.py", line 1319, in parse 296s expat_parser.Parse(NULL, True) 296s xml.parsers.expat.ExpatError: unclosed token: line 320, column 0 296s ok 296s test_NCBI_BLAST_tools ... skipping. Install the NCBI BLAST+ command line tools if you want to use the Bio.Blast.Applications wrapper. 296s test_NCBI_qblast ... ok 296s test_NMR ... ok 296s test_NaiveBayes ... ok 297s test_Nexus ... ok 297s test_PAML_baseml ... ok 297s test_PAML_codeml ... ok 298s test_PAML_yn00 ... ok 303s test_PDB_CEAligner ... ok 303s test_PDB_DSSP ... ok 303s test_PDB_Dice ... ok 303s test_PDB_Disordered ... ok 303s test_PDB_Exposure ... ok 303s test_PDB_FragmentMapper ... ok 305s test_PDB_KDTree ... ok 305s test_PDB_MMCIF2Dict ... ok 306s test_PDB_MMCIFIO ... ok 307s test_PDB_MMCIFParser ... ok 307s test_PDB_NACCESS ... ok 308s test_PDB_PDBIO ... ok 308s test_PDB_PDBList ... skipping. internet not available 316s test_PDB_PDBMLParser ... ok 316s test_PDB_PDBParser ... ok 316s 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 316s test_PDB_Polypeptide ... ok 316s test_PDB_QCPSuperimposer ... ok 320s test_PDB_SASA ... ok 320s test_PDB_SMCRA ... ok 320s test_PDB_Selection ... ok 321s test_PDB_StructureAlignment ... ok 321s test_PDB_Superimposer ... ok 321s test_PDB_alphafold_db ... skipping. internet not available 321s test_PDB_binary_cif ... skipping. Error: Install msgpack to use Bio.PDB.binaryCIF (e.g. pip install msgpack) 321s 321s test_PDB_internal_coords ... skipping. Error: Install mmtf to use Bio.PDB.mmtf (e.g. pip install mmtf-python) 321s 321s test_PDB_parse_pdb_header ... ok 321s test_PDB_vectors ... ok 321s test_PQR ... ok 321s test_Pathway ... ok 321s test_Phd ... ok 322s test_Phylo ... ok 322s test_PhyloXML ... ok 322s test_Phylo_CDAO ... skipping. Install RDFlib if you want to use the CDAO tree format. 322s test_Phylo_NeXML ... ok 322s test_Phylo_igraph ... skipping. Install igraph if you wish to use it with Bio.Phylo 322s test_Phylo_matplotlib ... skipping. Install matplotlib if you want to use Bio.Phylo._utils. 323s test_Phylo_networkx ... skipping. Install networkx if you wish to use it with Bio.Phylo 323s test_PopGen_GenePop_nodepend ... ok 323s test_Prank_tool ... skipping. Install PRANK if you want to use the Bio.Align.Applications wrapper. 323s test_Probcons_tool ... skipping. Install PROBCONS if you want to use the Bio.Align.Applications wrapper. 323s test_ProtParam ... ok 323s test_RCSBFormats ... ok 323s test_Restriction ... ok 323s test_SCOP_Astral ... ok 324s test_SCOP_Cla ... ok 324s test_SCOP_Des ... ok 324s test_SCOP_Dom ... ok 324s test_SCOP_Hie ... ok 324s test_SCOP_Raf ... ok 324s test_SCOP_Residues ... ok 324s test_SCOP_Scop ... ok 324s test_SVDSuperimposer ... ok 324s test_SearchIO_blast_tab ... ok 324s test_SearchIO_blast_tab_index ... ok 324s test_SearchIO_blast_xml ... ok 326s test_SearchIO_blast_xml_index ... ok 326s test_SearchIO_blat_psl ... ok 326s test_SearchIO_blat_psl_index ... ok 326s test_SearchIO_exonerate ... ok 326s test_SearchIO_exonerate_text_index ... ok 326s test_SearchIO_exonerate_vulgar_index ... ok 326s test_SearchIO_fasta_m10 ... ok 326s test_SearchIO_fasta_m10_index ... ok 327s test_SearchIO_hhsuite2_text ... ok 327s test_SearchIO_hmmer2_text ... ok 327s test_SearchIO_hmmer2_text_index ... ok 327s test_SearchIO_hmmer3_domtab ... ok 327s test_SearchIO_hmmer3_domtab_index ... ok 327s test_SearchIO_hmmer3_tab ... ok 327s test_SearchIO_hmmer3_tab_index ... ok 327s test_SearchIO_hmmer3_text ... ok 328s test_SearchIO_hmmer3_text_index ... ok 328s test_SearchIO_interproscan_xml ... ok 328s test_SearchIO_model ... ok 328s test_SearchIO_write ... ok 328s test_SeqFeature ... ok 346s test_SeqIO ... ok 346s test_SeqIO_AbiIO ... ok 346s test_SeqIO_FastaIO ... ok 346s test_SeqIO_Gck ... ok 347s test_SeqIO_Gfa ... ok 347s test_SeqIO_Insdc ... ok 347s test_SeqIO_NibIO ... ok 349s test_SeqIO_PdbIO ... ok 349s test_SeqIO_QualityIO ... ok 349s test_SeqIO_SeqXML ... ok 350s test_SeqIO_SffIO ... ok 350s test_SeqIO_SnapGene ... ok 351s test_SeqIO_TwoBitIO ... ok 351s test_SeqIO_UniprotIO ... ok 351s test_SeqIO_Xdna ... ok 352s test_SeqIO_features ... ok 369s test_SeqIO_index ... ok 369s test_SeqIO_online ... skipping. internet not available 369s test_SeqIO_write ... ok 369s test_SeqRecord ... ok 369s test_SeqUtils ... ok 371s test_Seq_objs ... ok 371s test_SwissProt ... ok 371s test_TCoffee_tool ... skipping. Install TCOFFEE if you want to use the Bio.Align.Applications wrapper. 371s test_TogoWS ... skipping. internet not available 371s test_TreeConstruction ... ok 371s test_Tutorial ... skipping. Could not find ../Doc/Tutorial/index.rst file 372s test_UniGene ... ok 372s test_UniProt ... skipping. internet not available 372s test_UniProt_GOA ... ok 372s test_align ... ok 372s test_align_substitution_matrices ... ok 375s test_bgzf ... ok 375s test_cellosaurus ... ok 379s test_codonalign ... ok 379s test_geo ... ok 379s test_kNN ... ok 380s test_motifs ... ok 380s test_motifs_online ... skipping. internet not available 380s 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. 380s warnings.warn( 380s ok 380s test_pairwise2_no_C ... ok 380s test_pairwise_aligner ... ok 381s test_pairwise_alignment_map ... ok 389s test_phenotype ... ok 390s test_phenotype_fit ... skipping. Install SciPy if you want to use Bio.phenotype fit functionality. 390s 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. 390s test_prodoc ... ok 390s test_prosite ... ok 390s test_raxml_tool ... skipping. Install RAxML (binary raxmlHPC) if you want to test the Bio.Phylo.Applications wrapper. 390s test_samtools_tool ... skipping. Install samtools and correctly set the file path to the program if you want to use it from Biopython 390s test_seq ... ok 390s test_translate ... ok 390s Skipping any tests requiring internet access 390s Python version: 3.12.9 (main, Feb 5 2025, 01:31:18) [GCC 14.2.0] 390s Operating system: posix linux 390s ---------------------------------------------------------------------- 390s Ran 218 tests in 137.098 seconds 390s 390s sys:1: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/protein_lib.fa' mode='rt' encoding='UTF-8'> 390s sys:1: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/nucleotide_lib.fa' mode='rt' encoding='UTF-8'> 391s test_Ace ... ok 391s test_Affy ... ok 394s test_AlignIO ... ok 394s test_AlignIO_ClustalIO ... ok 394s test_AlignIO_EmbossIO ... ok 394s test_AlignIO_FastaIO ... ok 394s test_AlignIO_MauveIO ... ok 394s test_AlignIO_PhylipIO ... ok 394s test_AlignIO_convert ... ok 394s test_AlignInfo ... ok 394s test_Align_Alignment ... ok 394s test_Align_a2m ... ok 394s test_Align_bed ... ok 395s test_Align_bigbed ... ok 395s test_Align_bigmaf ... ok 395s test_Align_bigpsl ... ok 396s test_Align_chain ... ok 396s test_Align_clustal ... ok 399s test_Align_codonalign ... ok 399s test_Align_emboss ... ok 399s test_Align_exonerate ... ok 399s test_Align_fasta ... ok 400s test_Align_hhr ... ok 400s test_Align_maf ... ok 401s test_Align_mauve ... ok 401s test_Align_msf ... ok 401s test_Align_nexus ... ok 401s test_Align_phylip ... ok 401s test_Align_psl ... ok 401s test_Align_sam ... ok 403s test_Align_stockholm ... ok 404s test_Align_tabular ... ok 404s test_Application ... ok 404s test_BioSQL_MySQLdb_online ... skipping. internet not available 404s test_BioSQL_mysql_connector ... skipping. BioSQL test configuration file biosql.ini missing (see biosql.ini.sample) 404s test_BioSQL_mysql_connector_online ... skipping. internet not available 404s test_BioSQL_psycopg2_online ... skipping. internet not available 409s test_BioSQL_sqlite3 ... ok 409s test_BioSQL_sqlite3_online ... skipping. internet not available 409s test_Blast_Record ... ok 410s test_Blast_parser ... ok 410s test_CAPS ... ok 410s test_Chi2 ... ok 410s test_ClustalOmega_tool ... skipping. Install clustalo if you want to use Clustal Omega from Biopython. 410s test_Clustalw_tool ... skipping. Install clustalw or clustalw2 if you want to use it from Biopython. 410s test_Cluster ... ok 410s test_CodonTable ... ok 410s test_ColorSpiral ... ok 410s test_Compass ... ok 411s test_Consensus ... ok 411s test_Dialign_tool ... skipping. Install DIALIGN2-2 if you want to use the Bio.Align.Applications wrapper. 411s test_EMBL_unittest ... ok 411s test_Emboss ... skipping. $EMBOSS_ROOT='/usr/lib/emboss' which does not exist! 411s test_EmbossPrimer ... ok 416s test_Entrez ... ok 416s test_Entrez_online ... skipping. internet not available 416s test_Entrez_parser ... ok 416s test_Enzyme ... ok 416s test_ExPASy ... skipping. internet not available 416s test_Fasttree_tool ... skipping. Install FastTree and correctly set the file path to the program if you want to use it from Biopython. 416s test_File ... ok 417s test_GenBank ... /usr/lib/python3/dist-packages/Bio/SeqIO/InsdcIO.py:600: BiopythonWarning: Annotation 'Sequence Read Archive: SRX001885, SRX001121, SRX001531, SRX001530, SRX001529' too long 417s warnings.warn(f"Annotation {text!r} too long", BiopythonWarning) 417s ok 419s test_GenomeDiagram ... Warn: Can't find .pfb for face 'Helvetica' 421s ok 421s test_GraphicsChromosome ... ok 421s test_GraphicsDistribution ... ok 422s test_GraphicsGeneral ... ok 422s test_HMMCasino ... ok 423s test_HMMGeneral ... ok 423s test_KEGG ... ok 423s test_KEGG_online ... skipping. internet not available 428s test_KGML_graphics ... ok 428s test_KGML_graphics_online ... skipping. internet not available 428s test_KGML_nographics ... ok 429s test_KeyWList ... ok 429s test_LogisticRegression ... ok 430s test_MafIO_index ... ok 430s test_Mafft_tool ... skipping. Install MAFFT if you want to use the Bio.Align.Applications wrapper. 430s test_MarkovModel ... ok 430s test_Medline ... ok 430s test_Muscle_tool ... skipping. Install MUSCLE if you want to use the Bio.Align.Applications wrapper. 431s test_NCBIXML ... Exception ignored in: 431s Traceback (most recent call last): 431s File "/usr/lib/python3/dist-packages/Bio/Blast/NCBIXML.py", line 1319, in parse 431s expat_parser.Parse(NULL, True) 431s xml.parsers.expat.ExpatError: unclosed token: line 320, column 0 431s ok 431s test_NCBI_BLAST_tools ... skipping. Install the NCBI BLAST+ command line tools if you want to use the Bio.Blast.Applications wrapper. 431s test_NCBI_qblast ... ok 431s test_NMR ... ok 431s test_NaiveBayes ... ok 431s test_Nexus ... ok 431s test_PAML_baseml ... ok 432s test_PAML_codeml ... ok 432s test_PAML_yn00 ... ok 437s test_PDB_CEAligner ... ok 437s test_PDB_DSSP ... ok 437s test_PDB_Dice ... ok 438s test_PDB_Disordered ... ok 438s test_PDB_Exposure ... ok 438s test_PDB_FragmentMapper ... ok 440s test_PDB_KDTree ... ok 440s test_PDB_MMCIF2Dict ... ok 440s test_PDB_MMCIFIO ... ok 441s test_PDB_MMCIFParser ... ok 441s test_PDB_NACCESS ... ok 442s test_PDB_PDBIO ... ok 442s test_PDB_PDBList ... skipping. internet not available 448s test_PDB_PDBMLParser ... ok 448s test_PDB_PDBParser ... ok 449s 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 449s test_PDB_Polypeptide ... ok 449s test_PDB_QCPSuperimposer ... ok 452s test_PDB_SASA ... ok 453s test_PDB_SMCRA ... ok 453s test_PDB_Selection ... ok 453s test_PDB_StructureAlignment ... ok 453s test_PDB_Superimposer ... ok 454s test_PDB_alphafold_db ... skipping. internet not available 454s test_PDB_binary_cif ... skipping. Error: Install msgpack to use Bio.PDB.binaryCIF (e.g. pip install msgpack) 454s 454s test_PDB_internal_coords ... skipping. Error: Install mmtf to use Bio.PDB.mmtf (e.g. pip install mmtf-python) 454s 454s test_PDB_parse_pdb_header ... ok 454s test_PDB_vectors ... ok 454s test_PQR ... ok 454s test_Pathway ... ok 454s test_Phd ... ok 454s test_Phylo ... ok 455s test_PhyloXML ... ok 455s test_Phylo_CDAO ... skipping. Install RDFlib if you want to use the CDAO tree format. 455s test_Phylo_NeXML ... ok 455s test_Phylo_igraph ... skipping. Install igraph if you wish to use it with Bio.Phylo 455s test_Phylo_matplotlib ... skipping. Install matplotlib if you want to use Bio.Phylo._utils. 455s test_Phylo_networkx ... skipping. Install networkx if you wish to use it with Bio.Phylo 455s test_PopGen_GenePop_nodepend ... ok 456s test_Prank_tool ... skipping. Install PRANK if you want to use the Bio.Align.Applications wrapper. 456s test_Probcons_tool ... skipping. Install PROBCONS if you want to use the Bio.Align.Applications wrapper. 456s test_ProtParam ... ok 456s test_RCSBFormats ... ok 456s test_Restriction ... ok 456s test_SCOP_Astral ... ok 456s test_SCOP_Cla ... ok 457s test_SCOP_Des ... ok 457s test_SCOP_Dom ... ok 457s test_SCOP_Hie ... ok 457s test_SCOP_Raf ... ok 457s test_SCOP_Residues ... ok 457s test_SCOP_Scop ... ok 457s test_SVDSuperimposer ... ok 457s test_SearchIO_blast_tab ... ok 457s test_SearchIO_blast_tab_index ... ok 458s test_SearchIO_blast_xml ... ok 459s test_SearchIO_blast_xml_index ... ok 459s test_SearchIO_blat_psl ... ok 459s test_SearchIO_blat_psl_index ... ok 459s test_SearchIO_exonerate ... ok 459s test_SearchIO_exonerate_text_index ... ok 459s test_SearchIO_exonerate_vulgar_index ... ok 459s test_SearchIO_fasta_m10 ... ok 460s test_SearchIO_fasta_m10_index ... ok 460s test_SearchIO_hhsuite2_text ... ok 460s test_SearchIO_hmmer2_text ... ok 460s test_SearchIO_hmmer2_text_index ... ok 460s test_SearchIO_hmmer3_domtab ... ok 460s test_SearchIO_hmmer3_domtab_index ... ok 460s test_SearchIO_hmmer3_tab ... ok 460s test_SearchIO_hmmer3_tab_index ... ok 461s test_SearchIO_hmmer3_text ... ok 461s test_SearchIO_hmmer3_text_index ... ok 461s test_SearchIO_interproscan_xml ... ok 461s test_SearchIO_model ... ok 461s test_SearchIO_write ... ok 461s test_SeqFeature ... ok 478s test_SeqIO ... ok 478s test_SeqIO_AbiIO ... ok 478s test_SeqIO_FastaIO ... ok 478s test_SeqIO_Gck ... ok 478s test_SeqIO_Gfa ... ok 478s test_SeqIO_Insdc ... ok 478s test_SeqIO_NibIO ... ok 480s test_SeqIO_PdbIO ... ok 481s test_SeqIO_QualityIO ... ok 481s test_SeqIO_SeqXML ... ok 481s test_SeqIO_SffIO ... ok 481s test_SeqIO_SnapGene ... ok 482s test_SeqIO_TwoBitIO ... ok 482s test_SeqIO_UniprotIO ... ok 482s test_SeqIO_Xdna ... ok 483s test_SeqIO_features ... ok 498s test_SeqIO_index ... ok 498s test_SeqIO_online ... skipping. internet not available 498s test_SeqIO_write ... ok 498s test_SeqRecord ... ok 498s test_SeqUtils ... ok 499s test_Seq_objs ... ok 499s test_SwissProt ... ok 499s test_TCoffee_tool ... skipping. Install TCOFFEE if you want to use the Bio.Align.Applications wrapper. 499s test_TogoWS ... skipping. internet not available 500s test_TreeConstruction ... ok 500s test_Tutorial ... skipping. Could not find ../Doc/Tutorial/index.rst file 500s test_UniGene ... ok 500s test_UniProt ... skipping. internet not available 500s test_UniProt_GOA ... ok 500s test_align ... ok 501s test_align_substitution_matrices ... ok 503s test_bgzf ... ok 503s test_cellosaurus ... ok 508s test_codonalign ... ok 508s test_geo ... ok 508s test_kNN ... ok 508s test_motifs ... ok 508s test_motifs_online ... skipping. internet not available 508s 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. 508s warnings.warn( 508s ok 508s test_pairwise2_no_C ... ok 509s test_pairwise_aligner ... ok 509s test_pairwise_alignment_map ... ok 519s test_phenotype ... ok 519s Skipping any tests requiring internet access 519s Python version: 3.13.2 (main, Feb 5 2025, 01:23:35) [GCC 14.2.0] 519s Operating system: posix linux 519s test_phenotype_fit ... skipping. Install SciPy if you want to use Bio.phenotype fit functionality. 519s 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. 519s test_prodoc ... ok 519s test_prosite ... ok 519s test_raxml_tool ... skipping. Install RAxML (binary raxmlHPC) if you want to test the Bio.Phylo.Applications wrapper. 519s test_samtools_tool ... skipping. Install samtools and correctly set the file path to the program if you want to use it from Biopython 519s test_seq ... ok 519s test_translate ... ok 519s ---------------------------------------------------------------------- 519s Ran 218 tests in 127.609 seconds 519s 519s :0: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/protein_lib.fa' mode='rt' encoding='UTF-8'> 519s :0: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/nucleotide_lib.fa' mode='rt' encoding='UTF-8'> 519s autopkgtest [12:40:49]: test dependencies: -----------------------] 525s autopkgtest [12:40:55]: test dependencies: - - - - - - - - - - results - - - - - - - - - - 525s dependencies PASS 529s autopkgtest [12:40:59]: test full_suite: preparing testbed 557s autopkgtest [12:41:27]: testbed dpkg architecture: armhf 559s autopkgtest [12:41:29]: testbed apt version: 2.9.30 564s autopkgtest [12:41:34]: @@@@@@@@@@@@@@@@@@@@ test bed setup 566s autopkgtest [12:41:36]: testbed release detected to be: plucky 575s autopkgtest [12:41:45]: updating testbed package index (apt update) 578s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [110 kB] 578s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 578s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 578s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 578s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [3120 B] 578s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [13.9 kB] 578s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [750 kB] 578s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [76.1 kB] 578s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf Packages [99.0 kB] 578s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted armhf Packages [760 B] 578s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf Packages [636 kB] 578s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf Packages [3116 B] 579s Fetched 1693 kB in 1s (1713 kB/s) 580s Reading package lists... 587s autopkgtest [12:41:57]: upgrading testbed (apt dist-upgrade and autopurge) 589s Reading package lists... 589s Building dependency tree... 589s Reading state information... 590s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 591s Starting 2 pkgProblemResolver with broken count: 0 591s Done 592s Entering ResolveByKeep 593s 594s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 596s Reading package lists... 597s Building dependency tree... 597s Reading state information... 597s Starting pkgProblemResolver with broken count: 0 597s Starting 2 pkgProblemResolver with broken count: 0 597s Done 599s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 602s autopkgtest [12:42:12]: rebooting testbed after setup commands that affected boot 677s Reading package lists... 677s Building dependency tree... 677s Reading state information... 678s Starting pkgProblemResolver with broken count: 0 678s Starting 2 pkgProblemResolver with broken count: 0 678s Done 679s The following NEW packages will be installed: 679s autoconf automake autopoint autotools-dev blt build-essential bwa clustalo 679s cpp cpp-14 cpp-14-arm-linux-gnueabihf cpp-arm-linux-gnueabihf debhelper 679s debugedit dh-autoreconf dh-python dh-strip-nondeterminism dialign 679s docutils-common dssp dwz fasttree flex fontconfig-config fonts-dejavu-core 679s fonts-dejavu-mono fonts-font-awesome fonts-lato fonts-lmodern fonts-lyx 679s fonts-urw-base35 g++ g++-14 g++-14-arm-linux-gnueabihf 679s g++-arm-linux-gnueabihf gcc gcc-14 gcc-14-arm-linux-gnueabihf 679s gcc-arm-linux-gnueabihf gettext ghostscript hevea hicolor-icon-theme 679s imagemagick imagemagick-7-common imagemagick-7.q16 intltool-debian libamd3 679s libaom3 libapache-pom-java libarchive-zip-perl libargtable2-0 libarpack2t64 679s libasan8 libavahi-client3 libavahi-common-data libavahi-common3 libblas3 679s libc-dev-bin libc6-dev libcairo2 libcc1-0 libcifpp-data libcifpp7 libcolamd3 679s libcommons-logging-java libcommons-parent-java libcrypt-dev libcups2t64 679s libde265-0 libdebhelper-perl libdeflate0 libexpat1-dev libfftw3-double3 679s libfile-stripnondeterminism-perl libfontbox-java libfontconfig1 libfontenc1 679s libfreetype6 libgcc-14-dev libgfortran5 libglpk40 libgomp1 libgraphite2-3 679s libgs-common libgs10 libgs10-common libharfbuzz0b libheif-plugin-aomdec 679s libheif-plugin-libde265 libheif1 libice6 libidn12 libigraph3t64 libijs-0.35 679s libimagequant0 libisl23 libjbig0 libjbig2dec0 libjpeg-turbo8 libjpeg8 679s libjs-jquery libjs-jquery-ui libjs-sphinxdoc libjs-underscore libjson-perl 679s libkpathsea6 liblapack3 liblbfgsb0 liblcms2-2 liblerc4 liblqr-1-0 libltdl7 679s libmagickcore-7.q16-10 libmagickwand-7.q16-10 libmbedcrypto16 libmbedtls21 679s libmbedx509-7 libmpc3 libmpfi0 libmysqlclient21 libnetpbm11t64 libopenjp2-7 679s libpaper-utils libpaper2 libpdfbox-java libpixman-1-0 libplfit0 libpotrace0 679s libptexenc1 libpython3-all-dev libpython3-dev libpython3.12-dev 679s libpython3.12t64 libpython3.13 libpython3.13-dev libqhull-r8.0 libraqm0 679s libraw23t64 libsharpyuv0 libsm6 libstdc++-14-dev libsuitesparseconfig7 679s libsynctex2 libtcl8.6 libteckit0 libtexlua53-5 libtiff6 libtk8.6 libtool 679s libubsan1 libwebp7 libwebpdemux2 libwebpmux3 libxaw7 libxcb-render0 679s libxcb-shm0 libxft2 libxi6 libxmu6 libxpm4 libxrender1 libxslt1.1 libxss1 679s libxt6t64 libzzip-0-13t64 linux-libc-dev m4 mafft mysql-common ncbi-blast+ 679s ncbi-data netpbm phylip po-debconf poppler-data prank preview-latex-style 679s probcons python-biopython-doc python-matplotlib-data python3-alabaster 679s python3-all python3-all-dev python3-biopython python3-biopython-sql 679s python3-brotli python3-cairo python3-contourpy python3-cycler 679s python3-dateutil python3-decorator python3-defusedxml python3-dev 679s python3-docutils python3-fonttools python3-freetype python3-fs 679s python3-igraph python3-imagesize python3-kiwisolver python3-lxml python3-lz4 679s python3-matplotlib python3-mmtf python3-mpmath python3-msgpack 679s python3-mysqldb python3-networkx python3-numpy python3-numpydoc 679s python3-packaging python3-pil python3-pil.imagetk python3-platformdirs 679s python3-pytz python3-rdflib python3-reportlab python3-rlpycairo 679s python3-roman python3-scipy python3-snowballstemmer python3-sphinx 679s python3-sphinx-rtd-theme python3-sphinxcontrib.jquery python3-sympy 679s python3-tabulate python3-texttable python3-tk python3-tz python3-ufolib2 679s python3.12-dev python3.12-tk python3.13-dev python3.13-tk rpcsvc-proto 679s sgml-base sphinx-common sphinx-rtd-theme-common t-coffee t1utils tex-common 679s texlive-base texlive-binaries texlive-fonts-recommended texlive-latex-base 679s texlive-latex-extra texlive-latex-recommended texlive-pictures tk8.6-blt2.5 679s unicode-data w3c-sgml-lib wise wise-data x11-common xdg-utils 679s xfonts-encodings xfonts-utils xml-core zlib1g-dev 679s 0 upgraded, 260 newly installed, 0 to remove and 0 not upgraded. 679s Need to get 326 MB of archives. 679s After this operation, 1223 MB of additional disk space will be used. 679s Get:1 http://ftpmaster.internal/ubuntu plucky/main armhf m4 armhf 1.4.19-5 [238 kB] 680s Get:2 http://ftpmaster.internal/ubuntu plucky/main armhf flex armhf 2.6.4-8.2build1 [293 kB] 680s Get:3 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-lato all 2.015-1 [2781 kB] 680s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf libgomp1 armhf 15-20250213-1ubuntu1 [128 kB] 680s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf libfftw3-double3 armhf 3.3.10-2fakesync1build1 [369 kB] 680s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf libfreetype6 armhf 2.13.3+dfsg-1 [330 kB] 680s Get:7 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-dejavu-mono all 2.37-8 [502 kB] 680s Get:8 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-dejavu-core all 2.37-8 [835 kB] 680s Get:9 http://ftpmaster.internal/ubuntu plucky/main armhf libfontenc1 armhf 1:1.1.8-1build1 [11.5 kB] 680s Get:10 http://ftpmaster.internal/ubuntu plucky/main armhf x11-common all 1:7.7+23ubuntu3 [21.7 kB] 680s Get:11 http://ftpmaster.internal/ubuntu plucky/main armhf xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 680s Get:12 http://ftpmaster.internal/ubuntu plucky/main armhf xfonts-utils armhf 1:7.7+7 [90.6 kB] 680s Get:13 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-urw-base35 all 20200910-8 [11.0 MB] 680s Get:14 http://ftpmaster.internal/ubuntu plucky/main armhf fontconfig-config armhf 2.15.0-2ubuntu1 [37.5 kB] 680s Get:15 http://ftpmaster.internal/ubuntu plucky/main armhf libfontconfig1 armhf 2.15.0-2ubuntu1 [114 kB] 680s Get:16 http://ftpmaster.internal/ubuntu plucky/main armhf libsharpyuv0 armhf 1.5.0-0.1 [16.4 kB] 680s Get:17 http://ftpmaster.internal/ubuntu plucky/main armhf libaom3 armhf 3.12.0-1 [1235 kB] 680s Get:18 http://ftpmaster.internal/ubuntu plucky/main armhf libheif-plugin-aomdec armhf 1.19.5-1build1 [11.0 kB] 680s Get:19 http://ftpmaster.internal/ubuntu plucky/main armhf libde265-0 armhf 1.0.15-1build4 [157 kB] 680s Get:20 http://ftpmaster.internal/ubuntu plucky/main armhf libheif-plugin-libde265 armhf 1.19.5-1build1 [11.7 kB] 680s Get:21 http://ftpmaster.internal/ubuntu plucky/main armhf libheif1 armhf 1.19.5-1build1 [476 kB] 680s Get:22 http://ftpmaster.internal/ubuntu plucky/main armhf libjbig0 armhf 2.1-6.1ubuntu2 [24.9 kB] 680s Get:23 http://ftpmaster.internal/ubuntu plucky/main armhf libjpeg-turbo8 armhf 2.1.5-3ubuntu2 [127 kB] 680s Get:24 http://ftpmaster.internal/ubuntu plucky/main armhf libjpeg8 armhf 8c-2ubuntu11 [2148 B] 680s Get:25 http://ftpmaster.internal/ubuntu plucky/main armhf liblcms2-2 armhf 2.16-2 [137 kB] 680s Get:26 http://ftpmaster.internal/ubuntu plucky/universe armhf liblqr-1-0 armhf 0.4.2-2.1build2 [23.2 kB] 680s Get:27 http://ftpmaster.internal/ubuntu plucky/main armhf libltdl7 armhf 2.5.4-3build1 [39.8 kB] 680s Get:28 http://ftpmaster.internal/ubuntu plucky/main armhf libopenjp2-7 armhf 2.5.0-2ubuntu3 [171 kB] 680s Get:29 http://ftpmaster.internal/ubuntu plucky/main armhf libraw23t64 armhf 0.21.3-1 [353 kB] 680s Get:30 http://ftpmaster.internal/ubuntu plucky/main armhf libdeflate0 armhf 1.23-1 [38.5 kB] 680s Get:31 http://ftpmaster.internal/ubuntu plucky/main armhf liblerc4 armhf 4.0.0+ds-5ubuntu1 [160 kB] 680s Get:32 http://ftpmaster.internal/ubuntu plucky/main armhf libwebp7 armhf 1.5.0-0.1 [188 kB] 680s Get:33 http://ftpmaster.internal/ubuntu plucky/main armhf libtiff6 armhf 4.5.1+git230720-4ubuntu4 [179 kB] 680s Get:34 http://ftpmaster.internal/ubuntu plucky/main armhf libwebpdemux2 armhf 1.5.0-0.1 [11.5 kB] 681s Get:35 http://ftpmaster.internal/ubuntu plucky/main armhf libwebpmux3 armhf 1.5.0-0.1 [22.4 kB] 681s Get:36 http://ftpmaster.internal/ubuntu plucky/universe armhf imagemagick-7-common all 8:7.1.1.43+dfsg1-1 [69.7 kB] 681s Get:37 http://ftpmaster.internal/ubuntu plucky/universe armhf libmagickcore-7.q16-10 armhf 8:7.1.1.43+dfsg1-1 [1810 kB] 681s Get:38 http://ftpmaster.internal/ubuntu plucky/universe armhf libmagickwand-7.q16-10 armhf 8:7.1.1.43+dfsg1-1 [332 kB] 681s Get:39 http://ftpmaster.internal/ubuntu plucky/main armhf poppler-data all 0.4.12-1 [2060 kB] 681s Get:40 http://ftpmaster.internal/ubuntu plucky/main armhf sgml-base all 1.31 [11.4 kB] 681s Get:41 http://ftpmaster.internal/ubuntu plucky/main armhf autoconf all 2.72-3 [382 kB] 681s Get:42 http://ftpmaster.internal/ubuntu plucky/main armhf autotools-dev all 20220109.1 [44.9 kB] 681s Get:43 http://ftpmaster.internal/ubuntu plucky/main armhf automake all 1:1.17-3 [572 kB] 681s Get:44 http://ftpmaster.internal/ubuntu plucky/main armhf autopoint all 0.23.1-1 [619 kB] 681s Get:45 http://ftpmaster.internal/ubuntu plucky/main armhf libtcl8.6 armhf 8.6.16+dfsg-1 [909 kB] 681s Get:46 http://ftpmaster.internal/ubuntu plucky/main armhf libxrender1 armhf 1:0.9.10-1.1build1 [16.0 kB] 681s Get:47 http://ftpmaster.internal/ubuntu plucky/main armhf libxft2 armhf 2.3.6-1build1 [37.4 kB] 681s Get:48 http://ftpmaster.internal/ubuntu plucky/main armhf libxss1 armhf 1:1.2.3-1build3 [6500 B] 681s Get:49 http://ftpmaster.internal/ubuntu plucky/main armhf libtk8.6 armhf 8.6.16-1 [686 kB] 681s Get:50 http://ftpmaster.internal/ubuntu plucky/main armhf tk8.6-blt2.5 armhf 2.5.3+dfsg-7build1 [525 kB] 681s Get:51 http://ftpmaster.internal/ubuntu plucky/main armhf blt armhf 2.5.3+dfsg-7build1 [4840 B] 681s Get:52 http://ftpmaster.internal/ubuntu plucky/main armhf libc-dev-bin armhf 2.40-4ubuntu1 [19.2 kB] 681s Get:53 http://ftpmaster.internal/ubuntu plucky/main armhf linux-libc-dev armhf 6.12.0-15.15 [1697 kB] 681s Get:54 http://ftpmaster.internal/ubuntu plucky/main armhf libcrypt-dev armhf 1:4.4.38-1 [120 kB] 681s Get:55 http://ftpmaster.internal/ubuntu plucky/main armhf rpcsvc-proto armhf 1.4.2-0ubuntu7 [62.2 kB] 681s Get:56 http://ftpmaster.internal/ubuntu plucky/main armhf libc6-dev armhf 2.40-4ubuntu1 [1358 kB] 681s Get:57 http://ftpmaster.internal/ubuntu plucky/main armhf libisl23 armhf 0.27-1 [546 kB] 681s Get:58 http://ftpmaster.internal/ubuntu plucky/main armhf libmpc3 armhf 1.3.1-1build2 [47.1 kB] 681s Get:59 http://ftpmaster.internal/ubuntu plucky/main armhf cpp-14-arm-linux-gnueabihf armhf 14.2.0-17ubuntu1 [9220 kB] 681s Get:60 http://ftpmaster.internal/ubuntu plucky/main armhf cpp-14 armhf 14.2.0-17ubuntu1 [1034 B] 681s Get:61 http://ftpmaster.internal/ubuntu plucky/main armhf cpp-arm-linux-gnueabihf armhf 4:14.2.0-1ubuntu1 [5578 B] 681s Get:62 http://ftpmaster.internal/ubuntu plucky/main armhf cpp armhf 4:14.2.0-1ubuntu1 [22.4 kB] 681s Get:63 http://ftpmaster.internal/ubuntu plucky/main armhf libcc1-0 armhf 15-20250213-1ubuntu1 [38.9 kB] 681s Get:64 http://ftpmaster.internal/ubuntu plucky/main armhf libasan8 armhf 15-20250213-1ubuntu1 [2956 kB] 682s Get:65 http://ftpmaster.internal/ubuntu plucky/main armhf libubsan1 armhf 15-20250213-1ubuntu1 [1190 kB] 682s Get:66 http://ftpmaster.internal/ubuntu plucky/main armhf libgcc-14-dev armhf 14.2.0-17ubuntu1 [897 kB] 682s Get:67 http://ftpmaster.internal/ubuntu plucky/main armhf gcc-14-arm-linux-gnueabihf armhf 14.2.0-17ubuntu1 [18.0 MB] 682s Get:68 http://ftpmaster.internal/ubuntu plucky/main armhf gcc-14 armhf 14.2.0-17ubuntu1 [506 kB] 682s Get:69 http://ftpmaster.internal/ubuntu plucky/main armhf gcc-arm-linux-gnueabihf armhf 4:14.2.0-1ubuntu1 [1218 B] 682s Get:70 http://ftpmaster.internal/ubuntu plucky/main armhf gcc armhf 4:14.2.0-1ubuntu1 [5004 B] 682s Get:71 http://ftpmaster.internal/ubuntu plucky/main armhf libstdc++-14-dev armhf 14.2.0-17ubuntu1 [2573 kB] 683s Get:72 http://ftpmaster.internal/ubuntu plucky/main armhf g++-14-arm-linux-gnueabihf armhf 14.2.0-17ubuntu1 [10.5 MB] 683s Get:73 http://ftpmaster.internal/ubuntu plucky/main armhf g++-14 armhf 14.2.0-17ubuntu1 [21.8 kB] 683s Get:74 http://ftpmaster.internal/ubuntu plucky/main armhf g++-arm-linux-gnueabihf armhf 4:14.2.0-1ubuntu1 [966 B] 683s Get:75 http://ftpmaster.internal/ubuntu plucky/main armhf g++ armhf 4:14.2.0-1ubuntu1 [1084 B] 683s Get:76 http://ftpmaster.internal/ubuntu plucky/main armhf build-essential armhf 12.10ubuntu1 [4928 B] 683s Get:77 http://ftpmaster.internal/ubuntu plucky/universe armhf bwa armhf 0.7.18-1 [198 kB] 683s Get:78 http://ftpmaster.internal/ubuntu plucky/universe armhf libargtable2-0 armhf 13-3 [12.9 kB] 683s Get:79 http://ftpmaster.internal/ubuntu plucky/universe armhf clustalo armhf 1.2.4-8build1 [249 kB] 683s Get:80 http://ftpmaster.internal/ubuntu plucky/main armhf libdebhelper-perl all 13.24.1ubuntu2 [95.4 kB] 683s Get:81 http://ftpmaster.internal/ubuntu plucky/main armhf libtool all 2.5.4-3build1 [168 kB] 683s Get:82 http://ftpmaster.internal/ubuntu plucky/main armhf dh-autoreconf all 20 [16.1 kB] 683s Get:83 http://ftpmaster.internal/ubuntu plucky/main armhf libarchive-zip-perl all 1.68-1 [90.2 kB] 683s Get:84 http://ftpmaster.internal/ubuntu plucky/main armhf libfile-stripnondeterminism-perl all 1.14.1-2 [20.3 kB] 683s Get:85 http://ftpmaster.internal/ubuntu plucky/main armhf dh-strip-nondeterminism all 1.14.1-2 [5064 B] 683s Get:86 http://ftpmaster.internal/ubuntu plucky/main armhf debugedit armhf 1:5.1-2 [46.7 kB] 683s Get:87 http://ftpmaster.internal/ubuntu plucky/main armhf dwz armhf 0.15-1build6 [116 kB] 683s Get:88 http://ftpmaster.internal/ubuntu plucky/main armhf gettext armhf 0.23.1-1 [1053 kB] 683s Get:89 http://ftpmaster.internal/ubuntu plucky/main armhf intltool-debian all 0.35.0+20060710.6 [23.2 kB] 683s Get:90 http://ftpmaster.internal/ubuntu plucky/main armhf po-debconf all 1.0.21+nmu1 [233 kB] 683s Get:91 http://ftpmaster.internal/ubuntu plucky/main armhf debhelper all 13.24.1ubuntu2 [895 kB] 683s Get:92 http://ftpmaster.internal/ubuntu plucky/universe armhf dh-python all 6.20250108 [117 kB] 683s Get:93 http://ftpmaster.internal/ubuntu plucky/universe armhf dialign armhf 2.2.1-13 [156 kB] 683s Get:94 http://ftpmaster.internal/ubuntu plucky/main armhf xml-core all 0.19 [20.3 kB] 683s Get:95 http://ftpmaster.internal/ubuntu plucky/main armhf docutils-common all 0.21.2+dfsg-2 [131 kB] 683s Get:96 http://ftpmaster.internal/ubuntu plucky/universe armhf libcifpp-data all 7.0.9-1 [481 kB] 683s Get:97 http://ftpmaster.internal/ubuntu plucky/universe armhf libcifpp7 armhf 7.0.9-1 [962 kB] 683s Get:98 http://ftpmaster.internal/ubuntu plucky/universe armhf dssp armhf 4.4.10-1 [696 kB] 683s Get:99 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB] 683s Get:100 http://ftpmaster.internal/ubuntu plucky/universe armhf fonts-lmodern all 2.005-1 [4799 kB] 684s Get:101 http://ftpmaster.internal/ubuntu plucky/universe armhf fonts-lyx all 2.4.3-1 [171 kB] 684s Get:102 http://ftpmaster.internal/ubuntu plucky/main armhf libgs-common all 10.04.0~dfsg1-2ubuntu1 [176 kB] 684s Get:103 http://ftpmaster.internal/ubuntu plucky/main armhf libgs10-common all 10.04.0~dfsg1-2ubuntu1 [488 kB] 684s Get:104 http://ftpmaster.internal/ubuntu plucky/main armhf libavahi-common-data armhf 0.8-14ubuntu1 [30.5 kB] 684s Get:105 http://ftpmaster.internal/ubuntu plucky/main armhf libavahi-common3 armhf 0.8-14ubuntu1 [19.5 kB] 684s Get:106 http://ftpmaster.internal/ubuntu plucky/main armhf libavahi-client3 armhf 0.8-14ubuntu1 [23.6 kB] 684s Get:107 http://ftpmaster.internal/ubuntu plucky/main armhf libcups2t64 armhf 2.4.11-0ubuntu2 [243 kB] 684s Get:108 http://ftpmaster.internal/ubuntu plucky/main armhf libidn12 armhf 1.42-3 [54.3 kB] 684s Get:109 http://ftpmaster.internal/ubuntu plucky/main armhf libijs-0.35 armhf 0.35-15.1build1 [13.5 kB] 684s Get:110 http://ftpmaster.internal/ubuntu plucky/main armhf libjbig2dec0 armhf 0.20-1build3 [57.6 kB] 684s Get:111 http://ftpmaster.internal/ubuntu plucky/main armhf libpaper2 armhf 2.2.5-0.3 [16.3 kB] 684s Get:112 http://ftpmaster.internal/ubuntu plucky/main armhf libice6 armhf 2:1.1.1-1 [36.5 kB] 684s Get:113 http://ftpmaster.internal/ubuntu plucky/main armhf libsm6 armhf 2:1.2.4-1 [15.1 kB] 684s Get:114 http://ftpmaster.internal/ubuntu plucky/main armhf libxt6t64 armhf 1:1.2.1-1.2build1 [145 kB] 684s Get:115 http://ftpmaster.internal/ubuntu plucky/main armhf libgs10 armhf 10.04.0~dfsg1-2ubuntu1 [4203 kB] 685s Get:116 http://ftpmaster.internal/ubuntu plucky/main armhf ghostscript armhf 10.04.0~dfsg1-2ubuntu1 [43.6 kB] 685s Get:117 http://ftpmaster.internal/ubuntu plucky/universe armhf libnetpbm11t64 armhf 2:11.09.02-2 [97.7 kB] 685s Get:118 http://ftpmaster.internal/ubuntu plucky/universe armhf netpbm armhf 2:11.09.02-2 [2021 kB] 685s Get:119 http://ftpmaster.internal/ubuntu plucky/universe armhf tex-common all 6.18 [32.8 kB] 685s Get:120 http://ftpmaster.internal/ubuntu plucky/main armhf libpaper-utils armhf 2.2.5-0.3 [14.2 kB] 685s Get:121 http://ftpmaster.internal/ubuntu plucky/main armhf libkpathsea6 armhf 2024.20240313.70630+ds-5build2 [58.9 kB] 685s Get:122 http://ftpmaster.internal/ubuntu plucky/main armhf libptexenc1 armhf 2024.20240313.70630+ds-5build2 [37.8 kB] 685s Get:123 http://ftpmaster.internal/ubuntu plucky/main armhf libsynctex2 armhf 2024.20240313.70630+ds-5build2 [48.5 kB] 685s Get:124 http://ftpmaster.internal/ubuntu plucky/main armhf libtexlua53-5 armhf 2024.20240313.70630+ds-5build2 [98.4 kB] 685s Get:125 http://ftpmaster.internal/ubuntu plucky/main armhf t1utils armhf 1.41-4build3 [51.8 kB] 685s Get:126 http://ftpmaster.internal/ubuntu plucky/main armhf libpixman-1-0 armhf 0.44.0-3 [183 kB] 685s Get:127 http://ftpmaster.internal/ubuntu plucky/main armhf libxcb-render0 armhf 1.17.0-2 [15.3 kB] 685s Get:128 http://ftpmaster.internal/ubuntu plucky/main armhf libxcb-shm0 armhf 1.17.0-2 [5774 B] 685s Get:129 http://ftpmaster.internal/ubuntu plucky/main armhf libcairo2 armhf 1.18.2-2 [484 kB] 685s Get:130 http://ftpmaster.internal/ubuntu plucky/main armhf libgraphite2-3 armhf 1.3.14-2ubuntu1 [64.8 kB] 685s Get:131 http://ftpmaster.internal/ubuntu plucky/main armhf libharfbuzz0b armhf 10.2.0-1 [464 kB] 685s Get:132 http://ftpmaster.internal/ubuntu plucky/universe armhf libmpfi0 armhf 1.5.4+ds-4 [28.0 kB] 685s Get:133 http://ftpmaster.internal/ubuntu plucky/universe armhf libpotrace0 armhf 1.16-2build1 [15.2 kB] 685s Get:134 http://ftpmaster.internal/ubuntu plucky/universe armhf libteckit0 armhf 2.5.12+ds1-1 [323 kB] 685s Get:135 http://ftpmaster.internal/ubuntu plucky/main armhf libxmu6 armhf 2:1.1.3-3build2 [40.4 kB] 685s Get:136 http://ftpmaster.internal/ubuntu plucky/main armhf libxpm4 armhf 1:3.5.17-1build2 [30.1 kB] 685s Get:137 http://ftpmaster.internal/ubuntu plucky/main armhf libxaw7 armhf 2:1.0.16-1 [154 kB] 685s Get:138 http://ftpmaster.internal/ubuntu plucky/main armhf libxi6 armhf 2:1.8.2-1 [26.5 kB] 685s Get:139 http://ftpmaster.internal/ubuntu plucky/universe armhf libzzip-0-13t64 armhf 0.13.72+dfsg.1-1.2build1 [24.4 kB] 685s Get:140 http://ftpmaster.internal/ubuntu plucky/universe armhf texlive-binaries armhf 2024.20240313.70630+ds-5build2 [7070 kB] 685s Get:141 http://ftpmaster.internal/ubuntu plucky/main armhf xdg-utils all 1.2.1-2ubuntu1 [66.0 kB] 685s Get:142 http://ftpmaster.internal/ubuntu plucky/universe armhf texlive-base all 2024.20241115-1 [22.5 MB] 686s Get:143 http://ftpmaster.internal/ubuntu plucky/main armhf hicolor-icon-theme all 0.18-2 [13.3 kB] 686s Get:144 http://ftpmaster.internal/ubuntu plucky/universe armhf imagemagick-7.q16 armhf 8:7.1.1.43+dfsg1-1 [704 kB] 686s Get:145 http://ftpmaster.internal/ubuntu plucky/universe armhf imagemagick armhf 8:7.1.1.43+dfsg1-1 [14.1 kB] 686s Get:146 http://ftpmaster.internal/ubuntu plucky/universe armhf hevea armhf 2.36-2 [1938 kB] 686s Get:147 http://ftpmaster.internal/ubuntu plucky/main armhf libsuitesparseconfig7 armhf 1:7.8.3+dfsg-3 [12.7 kB] 686s Get:148 http://ftpmaster.internal/ubuntu plucky/universe armhf libamd3 armhf 1:7.8.3+dfsg-3 [29.2 kB] 686s Get:149 http://ftpmaster.internal/ubuntu plucky/universe armhf libapache-pom-java all 33-2 [5874 B] 686s Get:150 http://ftpmaster.internal/ubuntu plucky/main armhf libblas3 armhf 3.12.1-2 [132 kB] 686s Get:151 http://ftpmaster.internal/ubuntu plucky/main armhf libgfortran5 armhf 15-20250213-1ubuntu1 [330 kB] 686s Get:152 http://ftpmaster.internal/ubuntu plucky/main armhf liblapack3 armhf 3.12.1-2 [2091 kB] 686s Get:153 http://ftpmaster.internal/ubuntu plucky/universe armhf libarpack2t64 armhf 3.9.1-4 [86.7 kB] 686s Get:154 http://ftpmaster.internal/ubuntu plucky/main armhf libcolamd3 armhf 1:7.8.3+dfsg-3 [19.8 kB] 686s Get:155 http://ftpmaster.internal/ubuntu plucky/universe armhf libcommons-parent-java all 56-1 [10.7 kB] 686s Get:156 http://ftpmaster.internal/ubuntu plucky/universe armhf libcommons-logging-java all 1.3.0-1ubuntu1 [63.8 kB] 686s Get:157 http://ftpmaster.internal/ubuntu plucky/main armhf libexpat1-dev armhf 2.6.4-1 [121 kB] 686s Get:158 http://ftpmaster.internal/ubuntu plucky/universe armhf libglpk40 armhf 5.0-1build2 [326 kB] 686s Get:159 http://ftpmaster.internal/ubuntu plucky/universe armhf libplfit0 armhf 0.9.4+ds-1ubuntu5 [25.5 kB] 686s Get:160 http://ftpmaster.internal/ubuntu plucky/universe armhf libigraph3t64 armhf 0.10.15+ds-2 [847 kB] 686s Get:161 http://ftpmaster.internal/ubuntu plucky/main armhf libimagequant0 armhf 2.18.0-1build1 [31.1 kB] 686s Get:162 http://ftpmaster.internal/ubuntu plucky/main armhf libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 686s Get:163 http://ftpmaster.internal/ubuntu plucky/universe armhf libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 686s Get:164 http://ftpmaster.internal/ubuntu plucky/main armhf libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 686s Get:165 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libjs-sphinxdoc all 8.1.3-5 [31.0 kB] 686s Get:166 http://ftpmaster.internal/ubuntu plucky/main armhf libjson-perl all 4.10000-1 [81.9 kB] 686s Get:167 http://ftpmaster.internal/ubuntu plucky/universe armhf liblbfgsb0 armhf 3.0+dfsg.4-1build1 [27.4 kB] 686s Get:168 http://ftpmaster.internal/ubuntu plucky/universe armhf libmbedcrypto16 armhf 3.6.2-3ubuntu1 [226 kB] 686s Get:169 http://ftpmaster.internal/ubuntu plucky/universe armhf libmbedx509-7 armhf 3.6.2-3ubuntu1 [30.4 kB] 686s Get:170 http://ftpmaster.internal/ubuntu plucky/universe armhf libmbedtls21 armhf 3.6.2-3ubuntu1 [116 kB] 686s Get:171 http://ftpmaster.internal/ubuntu plucky/main armhf mysql-common all 5.8+1.1.1 [6800 B] 686s Get:172 http://ftpmaster.internal/ubuntu plucky/main armhf libmysqlclient21 armhf 8.0.40-1 [1234 kB] 686s Get:173 http://ftpmaster.internal/ubuntu plucky/main armhf libpython3.13 armhf 3.13.2-1 [2075 kB] 686s Get:174 http://ftpmaster.internal/ubuntu plucky/main armhf zlib1g-dev armhf 1:1.3.dfsg+really1.3.1-1ubuntu1 [880 kB] 686s Get:175 http://ftpmaster.internal/ubuntu plucky/main armhf libpython3.13-dev armhf 3.13.2-1 [4264 kB] 687s Get:176 http://ftpmaster.internal/ubuntu plucky/main armhf libpython3-dev armhf 3.13.1-1~exp2 [10.5 kB] 687s Get:177 http://ftpmaster.internal/ubuntu plucky/main armhf libpython3.12t64 armhf 3.12.9-1 [2077 kB] 687s Get:178 http://ftpmaster.internal/ubuntu plucky/main armhf libpython3.12-dev armhf 3.12.9-1 [4345 kB] 687s Get:179 http://ftpmaster.internal/ubuntu plucky/main armhf libpython3-all-dev armhf 3.13.1-1~exp2 [922 B] 687s Get:180 http://ftpmaster.internal/ubuntu plucky/universe armhf libqhull-r8.0 armhf 2020.2-6build1 [173 kB] 687s Get:181 http://ftpmaster.internal/ubuntu plucky/main armhf libraqm0 armhf 0.10.2-1 [12.4 kB] 687s Get:182 http://ftpmaster.internal/ubuntu plucky/main armhf libxslt1.1 armhf 1.1.39-0exp1ubuntu2 [152 kB] 687s Get:183 http://ftpmaster.internal/ubuntu plucky/universe armhf mafft armhf 7.505-1 [928 kB] 687s Get:184 http://ftpmaster.internal/ubuntu plucky/universe armhf ncbi-data all 6.1.20170106+dfsg2-5 [3966 kB] 687s Get:185 http://ftpmaster.internal/ubuntu plucky/universe armhf ncbi-blast+ armhf 2.16.0+ds-6build1 [14.8 MB] 688s Get:186 http://ftpmaster.internal/ubuntu plucky/universe armhf phylip armhf 1:3.697+dfsg-4build1 [876 kB] 688s Get:187 http://ftpmaster.internal/ubuntu plucky/universe armhf prank armhf 0.0.170427+dfsg-3 [340 kB] 688s Get:188 http://ftpmaster.internal/ubuntu plucky/universe armhf preview-latex-style all 13.2-1 [347 kB] 688s Get:189 http://ftpmaster.internal/ubuntu plucky/universe armhf probcons armhf 1.12-14 [120 kB] 688s Get:190 http://ftpmaster.internal/ubuntu plucky/universe armhf python-biopython-doc all 1.85+dfsg-2 [18.2 MB] 688s Get:191 http://ftpmaster.internal/ubuntu plucky/universe armhf python-matplotlib-data all 3.8.3-3ubuntu2 [2929 kB] 688s Get:192 http://ftpmaster.internal/ubuntu plucky/main armhf python3-all armhf 3.13.1-1~exp2 [896 B] 688s Get:193 http://ftpmaster.internal/ubuntu plucky/main armhf python3.13-dev armhf 3.13.2-1 [508 kB] 688s Get:194 http://ftpmaster.internal/ubuntu plucky/main armhf python3-dev armhf 3.13.1-1~exp2 [26.7 kB] 688s Get:195 http://ftpmaster.internal/ubuntu plucky/main armhf python3.12-dev armhf 3.12.9-1 [504 kB] 688s Get:196 http://ftpmaster.internal/ubuntu plucky/main armhf python3-all-dev armhf 3.13.1-1~exp2 [918 B] 688s Get:197 http://ftpmaster.internal/ubuntu plucky/main armhf python3-numpy armhf 1:1.26.4+ds-13 [3978 kB] 689s Get:198 http://ftpmaster.internal/ubuntu plucky/main armhf python3.12-tk armhf 3.12.9-1 [113 kB] 689s Get:199 http://ftpmaster.internal/ubuntu plucky/main armhf python3.13-tk armhf 3.13.2-1 [103 kB] 689s Get:200 http://ftpmaster.internal/ubuntu plucky/main armhf python3-tk armhf 3.13.1-1 [9770 B] 689s Get:201 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pil.imagetk armhf 11.1.0-5 [9208 B] 689s Get:202 http://ftpmaster.internal/ubuntu plucky/main armhf python3-pil armhf 11.1.0-5 [453 kB] 689s Get:203 http://ftpmaster.internal/ubuntu plucky/main armhf python3-cairo armhf 1.26.1-2build1 [129 kB] 689s Get:204 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-freetype all 2.5.1-1 [92.3 kB] 689s Get:205 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-rlpycairo all 0.3.0-3 [9130 B] 689s Get:206 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-reportlab all 4.3.0-1 [1137 kB] 689s Get:207 http://ftpmaster.internal/ubuntu plucky/universe armhf w3c-sgml-lib all 1.3-3 [280 kB] 689s Get:208 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-biopython armhf 1.85+dfsg-2 [1696 kB] 689s Get:209 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-biopython-sql all 1.85+dfsg-2 [26.4 kB] 689s Get:210 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-brotli armhf 1.1.0-2build3 [324 kB] 689s Get:211 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-contourpy armhf 1.3.1-1 [240 kB] 689s Get:212 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-cycler all 0.12.1-1 [9716 B] 689s Get:213 http://ftpmaster.internal/ubuntu plucky/main armhf python3-dateutil all 2.9.0-3 [80.2 kB] 689s Get:214 http://ftpmaster.internal/ubuntu plucky/main armhf python3-decorator all 5.1.1-5 [10.1 kB] 689s Get:215 http://ftpmaster.internal/ubuntu plucky/main armhf python3-defusedxml all 0.7.1-3 [42.2 kB] 689s Get:216 http://ftpmaster.internal/ubuntu plucky/main armhf python3-roman all 5.0-1 [10.3 kB] 689s Get:217 http://ftpmaster.internal/ubuntu plucky/main armhf python3-docutils all 0.21.2+dfsg-2 [409 kB] 689s Get:218 http://ftpmaster.internal/ubuntu plucky/main armhf python3-pytz all 2025.1-3 [162 kB] 689s Get:219 http://ftpmaster.internal/ubuntu plucky/main armhf python3-tz all 2025.1-3 [1866 B] 689s Get:220 http://ftpmaster.internal/ubuntu plucky/main armhf python3-platformdirs all 4.3.6-1 [16.8 kB] 689s Get:221 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-fs all 2.4.16-6 [90.7 kB] 689s Get:222 http://ftpmaster.internal/ubuntu plucky/main armhf python3-lxml armhf 5.3.1-1 [1631 kB] 689s Get:223 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-lz4 armhf 4.4.0+dfsg-1 [25.6 kB] 689s Get:224 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-scipy armhf 1.14.1-4ubuntu1 [19.5 MB] 690s Get:225 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-mpmath all 1.3.0-1 [425 kB] 690s Get:226 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-sympy all 1.13.3-1 [4228 kB] 690s Get:227 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-ufolib2 all 0.17.0+dfsg1-1 [33.5 kB] 690s Get:228 http://ftpmaster.internal/ubuntu plucky/universe armhf unicode-data all 15.1.0-1 [8878 kB] 690s Get:229 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-fonttools armhf 4.55.3-2 [1625 kB] 690s Get:230 http://ftpmaster.internal/ubuntu plucky/main armhf python3-imagesize all 1.4.1-1 [6844 B] 690s Get:231 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-kiwisolver armhf 1.4.7-3 [70.4 kB] 690s Get:232 http://ftpmaster.internal/ubuntu plucky/main armhf python3-packaging all 24.2-1 [51.5 kB] 690s Get:233 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-matplotlib armhf 3.8.3-3ubuntu2 [4598 kB] 691s Get:234 http://ftpmaster.internal/ubuntu plucky/main armhf python3-msgpack armhf 1.0.3-3build3 [106 kB] 691s Get:235 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-mmtf all 1.1.3-1 [16.2 kB] 691s Get:236 http://ftpmaster.internal/ubuntu plucky/main armhf python3-mysqldb armhf 1.4.6-2build4 [46.8 kB] 691s Get:237 http://ftpmaster.internal/ubuntu plucky/main armhf python3-networkx all 3.2.1-4ubuntu1 [11.5 MB] 691s Get:238 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf sphinx-common all 8.1.3-5 [663 kB] 691s Get:239 http://ftpmaster.internal/ubuntu plucky/main armhf python3-alabaster all 0.7.16-0.1 [18.5 kB] 691s Get:240 http://ftpmaster.internal/ubuntu plucky/main armhf python3-snowballstemmer all 2.2.0-4build1 [59.8 kB] 691s Get:241 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf python3-sphinx all 8.1.3-5 [474 kB] 691s Get:242 http://ftpmaster.internal/ubuntu plucky/main armhf python3-tabulate all 0.9.0-1 [45.3 kB] 691s Get:243 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-numpydoc all 1.8.0-1 [52.4 kB] 691s Get:244 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-rdflib all 7.1.1-2 [426 kB] 691s Get:245 http://ftpmaster.internal/ubuntu plucky/main armhf sphinx-rtd-theme-common all 3.0.2+dfsg-2 [1014 kB] 691s Get:246 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-sphinxcontrib.jquery all 4.1-5 [6678 B] 691s Get:247 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-sphinx-rtd-theme all 3.0.2+dfsg-2 [23.5 kB] 691s Get:248 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-texttable all 1.7.0-1 [11.2 kB] 691s Get:249 http://ftpmaster.internal/ubuntu plucky/universe armhf t-coffee armhf 13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 [968 kB] 692s Get:250 http://ftpmaster.internal/ubuntu plucky/universe armhf texlive-fonts-recommended all 2024.20241115-1 [4973 kB] 692s Get:251 http://ftpmaster.internal/ubuntu plucky/universe armhf texlive-latex-base all 2024.20241115-1 [1260 kB] 692s Get:252 http://ftpmaster.internal/ubuntu plucky/universe armhf libfontbox-java all 1:1.8.16-5 [208 kB] 692s Get:253 http://ftpmaster.internal/ubuntu plucky/universe armhf libpdfbox-java all 1:1.8.16-5 [5521 kB] 692s Get:254 http://ftpmaster.internal/ubuntu plucky/universe armhf texlive-latex-recommended all 2024.20241115-1 [8739 kB] 693s Get:255 http://ftpmaster.internal/ubuntu plucky/universe armhf texlive-pictures all 2024.20241115-1 [17.0 MB] 693s Get:256 http://ftpmaster.internal/ubuntu plucky/universe armhf texlive-latex-extra all 2024.20250114-1 [24.3 MB] 695s Get:257 http://ftpmaster.internal/ubuntu plucky/universe armhf wise-data all 2.4.1-25 [83.0 kB] 695s Get:258 http://ftpmaster.internal/ubuntu plucky/universe armhf wise armhf 2.4.1-25 [917 kB] 695s Get:259 http://ftpmaster.internal/ubuntu plucky/universe armhf fasttree armhf 2.1.11-2 [162 kB] 695s Get:260 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-igraph armhf 0.11.8+ds-1build1 [327 kB] 696s Preconfiguring packages ... 696s Fetched 326 MB in 16s (20.3 MB/s) 696s Selecting previously unselected package m4. 696s (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 ... 60727 files and directories currently installed.) 696s Preparing to unpack .../000-m4_1.4.19-5_armhf.deb ... 696s Unpacking m4 (1.4.19-5) ... 696s Selecting previously unselected package flex. 696s Preparing to unpack .../001-flex_2.6.4-8.2build1_armhf.deb ... 696s Unpacking flex (2.6.4-8.2build1) ... 696s Selecting previously unselected package fonts-lato. 696s Preparing to unpack .../002-fonts-lato_2.015-1_all.deb ... 696s Unpacking fonts-lato (2.015-1) ... 697s Selecting previously unselected package libgomp1:armhf. 697s Preparing to unpack .../003-libgomp1_15-20250213-1ubuntu1_armhf.deb ... 697s Unpacking libgomp1:armhf (15-20250213-1ubuntu1) ... 697s Selecting previously unselected package libfftw3-double3:armhf. 697s Preparing to unpack .../004-libfftw3-double3_3.3.10-2fakesync1build1_armhf.deb ... 697s Unpacking libfftw3-double3:armhf (3.3.10-2fakesync1build1) ... 697s Selecting previously unselected package libfreetype6:armhf. 697s Preparing to unpack .../005-libfreetype6_2.13.3+dfsg-1_armhf.deb ... 697s Unpacking libfreetype6:armhf (2.13.3+dfsg-1) ... 697s Selecting previously unselected package fonts-dejavu-mono. 697s Preparing to unpack .../006-fonts-dejavu-mono_2.37-8_all.deb ... 697s Unpacking fonts-dejavu-mono (2.37-8) ... 697s Selecting previously unselected package fonts-dejavu-core. 697s Preparing to unpack .../007-fonts-dejavu-core_2.37-8_all.deb ... 697s Unpacking fonts-dejavu-core (2.37-8) ... 697s Selecting previously unselected package libfontenc1:armhf. 697s Preparing to unpack .../008-libfontenc1_1%3a1.1.8-1build1_armhf.deb ... 697s Unpacking libfontenc1:armhf (1:1.1.8-1build1) ... 697s Selecting previously unselected package x11-common. 697s Preparing to unpack .../009-x11-common_1%3a7.7+23ubuntu3_all.deb ... 697s Unpacking x11-common (1:7.7+23ubuntu3) ... 697s Selecting previously unselected package xfonts-encodings. 697s Preparing to unpack .../010-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 697s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 697s Selecting previously unselected package xfonts-utils. 697s Preparing to unpack .../011-xfonts-utils_1%3a7.7+7_armhf.deb ... 697s Unpacking xfonts-utils (1:7.7+7) ... 697s Selecting previously unselected package fonts-urw-base35. 697s Preparing to unpack .../012-fonts-urw-base35_20200910-8_all.deb ... 697s Unpacking fonts-urw-base35 (20200910-8) ... 697s Selecting previously unselected package fontconfig-config. 697s Preparing to unpack .../013-fontconfig-config_2.15.0-2ubuntu1_armhf.deb ... 698s Unpacking fontconfig-config (2.15.0-2ubuntu1) ... 698s Selecting previously unselected package libfontconfig1:armhf. 698s Preparing to unpack .../014-libfontconfig1_2.15.0-2ubuntu1_armhf.deb ... 698s Unpacking libfontconfig1:armhf (2.15.0-2ubuntu1) ... 698s Selecting previously unselected package libsharpyuv0:armhf. 698s Preparing to unpack .../015-libsharpyuv0_1.5.0-0.1_armhf.deb ... 698s Unpacking libsharpyuv0:armhf (1.5.0-0.1) ... 698s Selecting previously unselected package libaom3:armhf. 698s Preparing to unpack .../016-libaom3_3.12.0-1_armhf.deb ... 698s Unpacking libaom3:armhf (3.12.0-1) ... 698s Selecting previously unselected package libheif-plugin-aomdec:armhf. 698s Preparing to unpack .../017-libheif-plugin-aomdec_1.19.5-1build1_armhf.deb ... 698s Unpacking libheif-plugin-aomdec:armhf (1.19.5-1build1) ... 698s Selecting previously unselected package libde265-0:armhf. 698s Preparing to unpack .../018-libde265-0_1.0.15-1build4_armhf.deb ... 698s Unpacking libde265-0:armhf (1.0.15-1build4) ... 698s Selecting previously unselected package libheif-plugin-libde265:armhf. 698s Preparing to unpack .../019-libheif-plugin-libde265_1.19.5-1build1_armhf.deb ... 698s Unpacking libheif-plugin-libde265:armhf (1.19.5-1build1) ... 698s Selecting previously unselected package libheif1:armhf. 698s Preparing to unpack .../020-libheif1_1.19.5-1build1_armhf.deb ... 698s Unpacking libheif1:armhf (1.19.5-1build1) ... 698s Selecting previously unselected package libjbig0:armhf. 698s Preparing to unpack .../021-libjbig0_2.1-6.1ubuntu2_armhf.deb ... 698s Unpacking libjbig0:armhf (2.1-6.1ubuntu2) ... 698s Selecting previously unselected package libjpeg-turbo8:armhf. 698s Preparing to unpack .../022-libjpeg-turbo8_2.1.5-3ubuntu2_armhf.deb ... 698s Unpacking libjpeg-turbo8:armhf (2.1.5-3ubuntu2) ... 698s Selecting previously unselected package libjpeg8:armhf. 698s Preparing to unpack .../023-libjpeg8_8c-2ubuntu11_armhf.deb ... 698s Unpacking libjpeg8:armhf (8c-2ubuntu11) ... 698s Selecting previously unselected package liblcms2-2:armhf. 698s Preparing to unpack .../024-liblcms2-2_2.16-2_armhf.deb ... 698s Unpacking liblcms2-2:armhf (2.16-2) ... 698s Selecting previously unselected package liblqr-1-0:armhf. 698s Preparing to unpack .../025-liblqr-1-0_0.4.2-2.1build2_armhf.deb ... 698s Unpacking liblqr-1-0:armhf (0.4.2-2.1build2) ... 698s Selecting previously unselected package libltdl7:armhf. 698s Preparing to unpack .../026-libltdl7_2.5.4-3build1_armhf.deb ... 698s Unpacking libltdl7:armhf (2.5.4-3build1) ... 698s Selecting previously unselected package libopenjp2-7:armhf. 698s Preparing to unpack .../027-libopenjp2-7_2.5.0-2ubuntu3_armhf.deb ... 698s Unpacking libopenjp2-7:armhf (2.5.0-2ubuntu3) ... 698s Selecting previously unselected package libraw23t64:armhf. 698s Preparing to unpack .../028-libraw23t64_0.21.3-1_armhf.deb ... 698s Unpacking libraw23t64:armhf (0.21.3-1) ... 699s Selecting previously unselected package libdeflate0:armhf. 699s Preparing to unpack .../029-libdeflate0_1.23-1_armhf.deb ... 699s Unpacking libdeflate0:armhf (1.23-1) ... 699s Selecting previously unselected package liblerc4:armhf. 699s Preparing to unpack .../030-liblerc4_4.0.0+ds-5ubuntu1_armhf.deb ... 699s Unpacking liblerc4:armhf (4.0.0+ds-5ubuntu1) ... 699s Selecting previously unselected package libwebp7:armhf. 699s Preparing to unpack .../031-libwebp7_1.5.0-0.1_armhf.deb ... 699s Unpacking libwebp7:armhf (1.5.0-0.1) ... 699s Selecting previously unselected package libtiff6:armhf. 699s Preparing to unpack .../032-libtiff6_4.5.1+git230720-4ubuntu4_armhf.deb ... 699s Unpacking libtiff6:armhf (4.5.1+git230720-4ubuntu4) ... 699s Selecting previously unselected package libwebpdemux2:armhf. 699s Preparing to unpack .../033-libwebpdemux2_1.5.0-0.1_armhf.deb ... 699s Unpacking libwebpdemux2:armhf (1.5.0-0.1) ... 699s Selecting previously unselected package libwebpmux3:armhf. 699s Preparing to unpack .../034-libwebpmux3_1.5.0-0.1_armhf.deb ... 699s Unpacking libwebpmux3:armhf (1.5.0-0.1) ... 699s Selecting previously unselected package imagemagick-7-common. 699s Preparing to unpack .../035-imagemagick-7-common_8%3a7.1.1.43+dfsg1-1_all.deb ... 699s Unpacking imagemagick-7-common (8:7.1.1.43+dfsg1-1) ... 699s Selecting previously unselected package libmagickcore-7.q16-10:armhf. 699s Preparing to unpack .../036-libmagickcore-7.q16-10_8%3a7.1.1.43+dfsg1-1_armhf.deb ... 699s Unpacking libmagickcore-7.q16-10:armhf (8:7.1.1.43+dfsg1-1) ... 699s Selecting previously unselected package libmagickwand-7.q16-10:armhf. 699s Preparing to unpack .../037-libmagickwand-7.q16-10_8%3a7.1.1.43+dfsg1-1_armhf.deb ... 699s Unpacking libmagickwand-7.q16-10:armhf (8:7.1.1.43+dfsg1-1) ... 699s Selecting previously unselected package poppler-data. 699s Preparing to unpack .../038-poppler-data_0.4.12-1_all.deb ... 699s Unpacking poppler-data (0.4.12-1) ... 699s Selecting previously unselected package sgml-base. 699s Preparing to unpack .../039-sgml-base_1.31_all.deb ... 699s Unpacking sgml-base (1.31) ... 699s Selecting previously unselected package autoconf. 699s Preparing to unpack .../040-autoconf_2.72-3_all.deb ... 699s Unpacking autoconf (2.72-3) ... 699s Selecting previously unselected package autotools-dev. 699s Preparing to unpack .../041-autotools-dev_20220109.1_all.deb ... 699s Unpacking autotools-dev (20220109.1) ... 699s Selecting previously unselected package automake. 699s Preparing to unpack .../042-automake_1%3a1.17-3_all.deb ... 699s Unpacking automake (1:1.17-3) ... 700s Selecting previously unselected package autopoint. 700s Preparing to unpack .../043-autopoint_0.23.1-1_all.deb ... 700s Unpacking autopoint (0.23.1-1) ... 700s Selecting previously unselected package libtcl8.6:armhf. 700s Preparing to unpack .../044-libtcl8.6_8.6.16+dfsg-1_armhf.deb ... 700s Unpacking libtcl8.6:armhf (8.6.16+dfsg-1) ... 700s Selecting previously unselected package libxrender1:armhf. 700s Preparing to unpack .../045-libxrender1_1%3a0.9.10-1.1build1_armhf.deb ... 700s Unpacking libxrender1:armhf (1:0.9.10-1.1build1) ... 700s Selecting previously unselected package libxft2:armhf. 700s Preparing to unpack .../046-libxft2_2.3.6-1build1_armhf.deb ... 700s Unpacking libxft2:armhf (2.3.6-1build1) ... 700s Selecting previously unselected package libxss1:armhf. 700s Preparing to unpack .../047-libxss1_1%3a1.2.3-1build3_armhf.deb ... 700s Unpacking libxss1:armhf (1:1.2.3-1build3) ... 700s Selecting previously unselected package libtk8.6:armhf. 700s Preparing to unpack .../048-libtk8.6_8.6.16-1_armhf.deb ... 700s Unpacking libtk8.6:armhf (8.6.16-1) ... 700s Selecting previously unselected package tk8.6-blt2.5. 700s Preparing to unpack .../049-tk8.6-blt2.5_2.5.3+dfsg-7build1_armhf.deb ... 700s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 700s Selecting previously unselected package blt. 700s Preparing to unpack .../050-blt_2.5.3+dfsg-7build1_armhf.deb ... 700s Unpacking blt (2.5.3+dfsg-7build1) ... 700s Selecting previously unselected package libc-dev-bin. 700s Preparing to unpack .../051-libc-dev-bin_2.40-4ubuntu1_armhf.deb ... 700s Unpacking libc-dev-bin (2.40-4ubuntu1) ... 700s Selecting previously unselected package linux-libc-dev:armhf. 700s Preparing to unpack .../052-linux-libc-dev_6.12.0-15.15_armhf.deb ... 700s Unpacking linux-libc-dev:armhf (6.12.0-15.15) ... 700s Selecting previously unselected package libcrypt-dev:armhf. 700s Preparing to unpack .../053-libcrypt-dev_1%3a4.4.38-1_armhf.deb ... 700s Unpacking libcrypt-dev:armhf (1:4.4.38-1) ... 701s Selecting previously unselected package rpcsvc-proto. 701s Preparing to unpack .../054-rpcsvc-proto_1.4.2-0ubuntu7_armhf.deb ... 701s Unpacking rpcsvc-proto (1.4.2-0ubuntu7) ... 701s Selecting previously unselected package libc6-dev:armhf. 701s Preparing to unpack .../055-libc6-dev_2.40-4ubuntu1_armhf.deb ... 701s Unpacking libc6-dev:armhf (2.40-4ubuntu1) ... 701s Selecting previously unselected package libisl23:armhf. 701s Preparing to unpack .../056-libisl23_0.27-1_armhf.deb ... 701s Unpacking libisl23:armhf (0.27-1) ... 701s Selecting previously unselected package libmpc3:armhf. 701s Preparing to unpack .../057-libmpc3_1.3.1-1build2_armhf.deb ... 701s Unpacking libmpc3:armhf (1.3.1-1build2) ... 701s Selecting previously unselected package cpp-14-arm-linux-gnueabihf. 701s Preparing to unpack .../058-cpp-14-arm-linux-gnueabihf_14.2.0-17ubuntu1_armhf.deb ... 701s Unpacking cpp-14-arm-linux-gnueabihf (14.2.0-17ubuntu1) ... 701s Selecting previously unselected package cpp-14. 701s Preparing to unpack .../059-cpp-14_14.2.0-17ubuntu1_armhf.deb ... 701s Unpacking cpp-14 (14.2.0-17ubuntu1) ... 701s Selecting previously unselected package cpp-arm-linux-gnueabihf. 701s Preparing to unpack .../060-cpp-arm-linux-gnueabihf_4%3a14.2.0-1ubuntu1_armhf.deb ... 701s Unpacking cpp-arm-linux-gnueabihf (4:14.2.0-1ubuntu1) ... 701s Selecting previously unselected package cpp. 701s Preparing to unpack .../061-cpp_4%3a14.2.0-1ubuntu1_armhf.deb ... 701s Unpacking cpp (4:14.2.0-1ubuntu1) ... 701s Selecting previously unselected package libcc1-0:armhf. 701s Preparing to unpack .../062-libcc1-0_15-20250213-1ubuntu1_armhf.deb ... 701s Unpacking libcc1-0:armhf (15-20250213-1ubuntu1) ... 701s Selecting previously unselected package libasan8:armhf. 701s Preparing to unpack .../063-libasan8_15-20250213-1ubuntu1_armhf.deb ... 701s Unpacking libasan8:armhf (15-20250213-1ubuntu1) ... 701s Selecting previously unselected package libubsan1:armhf. 701s Preparing to unpack .../064-libubsan1_15-20250213-1ubuntu1_armhf.deb ... 701s Unpacking libubsan1:armhf (15-20250213-1ubuntu1) ... 702s Selecting previously unselected package libgcc-14-dev:armhf. 702s Preparing to unpack .../065-libgcc-14-dev_14.2.0-17ubuntu1_armhf.deb ... 702s Unpacking libgcc-14-dev:armhf (14.2.0-17ubuntu1) ... 702s Selecting previously unselected package gcc-14-arm-linux-gnueabihf. 702s Preparing to unpack .../066-gcc-14-arm-linux-gnueabihf_14.2.0-17ubuntu1_armhf.deb ... 702s Unpacking gcc-14-arm-linux-gnueabihf (14.2.0-17ubuntu1) ... 702s Selecting previously unselected package gcc-14. 702s Preparing to unpack .../067-gcc-14_14.2.0-17ubuntu1_armhf.deb ... 702s Unpacking gcc-14 (14.2.0-17ubuntu1) ... 702s Selecting previously unselected package gcc-arm-linux-gnueabihf. 702s Preparing to unpack .../068-gcc-arm-linux-gnueabihf_4%3a14.2.0-1ubuntu1_armhf.deb ... 702s Unpacking gcc-arm-linux-gnueabihf (4:14.2.0-1ubuntu1) ... 702s Selecting previously unselected package gcc. 702s Preparing to unpack .../069-gcc_4%3a14.2.0-1ubuntu1_armhf.deb ... 702s Unpacking gcc (4:14.2.0-1ubuntu1) ... 702s Selecting previously unselected package libstdc++-14-dev:armhf. 702s Preparing to unpack .../070-libstdc++-14-dev_14.2.0-17ubuntu1_armhf.deb ... 702s Unpacking libstdc++-14-dev:armhf (14.2.0-17ubuntu1) ... 702s Selecting previously unselected package g++-14-arm-linux-gnueabihf. 702s Preparing to unpack .../071-g++-14-arm-linux-gnueabihf_14.2.0-17ubuntu1_armhf.deb ... 702s Unpacking g++-14-arm-linux-gnueabihf (14.2.0-17ubuntu1) ... 703s Selecting previously unselected package g++-14. 703s Preparing to unpack .../072-g++-14_14.2.0-17ubuntu1_armhf.deb ... 703s Unpacking g++-14 (14.2.0-17ubuntu1) ... 703s Selecting previously unselected package g++-arm-linux-gnueabihf. 703s Preparing to unpack .../073-g++-arm-linux-gnueabihf_4%3a14.2.0-1ubuntu1_armhf.deb ... 703s Unpacking g++-arm-linux-gnueabihf (4:14.2.0-1ubuntu1) ... 703s Selecting previously unselected package g++. 703s Preparing to unpack .../074-g++_4%3a14.2.0-1ubuntu1_armhf.deb ... 703s Unpacking g++ (4:14.2.0-1ubuntu1) ... 703s Selecting previously unselected package build-essential. 703s Preparing to unpack .../075-build-essential_12.10ubuntu1_armhf.deb ... 703s Unpacking build-essential (12.10ubuntu1) ... 703s Selecting previously unselected package bwa. 703s Preparing to unpack .../076-bwa_0.7.18-1_armhf.deb ... 703s Unpacking bwa (0.7.18-1) ... 703s Selecting previously unselected package libargtable2-0. 703s Preparing to unpack .../077-libargtable2-0_13-3_armhf.deb ... 703s Unpacking libargtable2-0 (13-3) ... 703s Selecting previously unselected package clustalo. 703s Preparing to unpack .../078-clustalo_1.2.4-8build1_armhf.deb ... 703s Unpacking clustalo (1.2.4-8build1) ... 703s Selecting previously unselected package libdebhelper-perl. 703s Preparing to unpack .../079-libdebhelper-perl_13.24.1ubuntu2_all.deb ... 703s Unpacking libdebhelper-perl (13.24.1ubuntu2) ... 703s Selecting previously unselected package libtool. 703s Preparing to unpack .../080-libtool_2.5.4-3build1_all.deb ... 703s Unpacking libtool (2.5.4-3build1) ... 703s Selecting previously unselected package dh-autoreconf. 703s Preparing to unpack .../081-dh-autoreconf_20_all.deb ... 703s Unpacking dh-autoreconf (20) ... 703s Selecting previously unselected package libarchive-zip-perl. 703s Preparing to unpack .../082-libarchive-zip-perl_1.68-1_all.deb ... 703s Unpacking libarchive-zip-perl (1.68-1) ... 703s Selecting previously unselected package libfile-stripnondeterminism-perl. 703s Preparing to unpack .../083-libfile-stripnondeterminism-perl_1.14.1-2_all.deb ... 703s Unpacking libfile-stripnondeterminism-perl (1.14.1-2) ... 703s Selecting previously unselected package dh-strip-nondeterminism. 703s Preparing to unpack .../084-dh-strip-nondeterminism_1.14.1-2_all.deb ... 703s Unpacking dh-strip-nondeterminism (1.14.1-2) ... 703s Selecting previously unselected package debugedit. 703s Preparing to unpack .../085-debugedit_1%3a5.1-2_armhf.deb ... 703s Unpacking debugedit (1:5.1-2) ... 703s Selecting previously unselected package dwz. 703s Preparing to unpack .../086-dwz_0.15-1build6_armhf.deb ... 703s Unpacking dwz (0.15-1build6) ... 703s Selecting previously unselected package gettext. 704s Preparing to unpack .../087-gettext_0.23.1-1_armhf.deb 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unselected package fonts-lmodern. 704s Preparing to unpack .../099-fonts-lmodern_2.005-1_all.deb ... 704s Unpacking fonts-lmodern (2.005-1) ... 704s Selecting previously unselected package fonts-lyx. 705s Preparing to unpack .../100-fonts-lyx_2.4.3-1_all.deb ... 705s Unpacking fonts-lyx (2.4.3-1) ... 705s Selecting previously unselected package libgs-common. 705s Preparing to unpack .../101-libgs-common_10.04.0~dfsg1-2ubuntu1_all.deb ... 705s Unpacking libgs-common (10.04.0~dfsg1-2ubuntu1) ... 705s Selecting previously unselected package libgs10-common. 705s Preparing to unpack .../102-libgs10-common_10.04.0~dfsg1-2ubuntu1_all.deb ... 705s Unpacking libgs10-common (10.04.0~dfsg1-2ubuntu1) ... 705s Selecting previously unselected package libavahi-common-data:armhf. 705s Preparing to unpack .../103-libavahi-common-data_0.8-14ubuntu1_armhf.deb ... 705s Unpacking libavahi-common-data:armhf (0.8-14ubuntu1) ... 705s Selecting previously unselected package libavahi-common3:armhf. 705s 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.../109-libjbig2dec0_0.20-1build3_armhf.deb ... 705s Unpacking libjbig2dec0:armhf (0.20-1build3) ... 705s Selecting previously unselected package libpaper2:armhf. 705s Preparing to unpack .../110-libpaper2_2.2.5-0.3_armhf.deb ... 705s Unpacking libpaper2:armhf (2.2.5-0.3) ... 705s Selecting previously unselected package libice6:armhf. 705s Preparing to unpack .../111-libice6_2%3a1.1.1-1_armhf.deb ... 705s Unpacking libice6:armhf (2:1.1.1-1) ... 705s Selecting previously unselected package libsm6:armhf. 705s Preparing to unpack .../112-libsm6_2%3a1.2.4-1_armhf.deb ... 705s Unpacking libsm6:armhf (2:1.2.4-1) ... 705s Selecting previously unselected package libxt6t64:armhf. 705s Preparing to unpack .../113-libxt6t64_1%3a1.2.1-1.2build1_armhf.deb ... 705s Unpacking libxt6t64:armhf (1:1.2.1-1.2build1) ... 705s Selecting previously unselected package libgs10:armhf. 705s Preparing to unpack .../114-libgs10_10.04.0~dfsg1-2ubuntu1_armhf.deb ... 705s Unpacking libgs10:armhf (10.04.0~dfsg1-2ubuntu1) ... 705s Selecting previously unselected package ghostscript. 705s Preparing to unpack .../115-ghostscript_10.04.0~dfsg1-2ubuntu1_armhf.deb ... 705s Unpacking ghostscript (10.04.0~dfsg1-2ubuntu1) ... 705s Selecting previously unselected package libnetpbm11t64:armhf. 706s Preparing to unpack .../116-libnetpbm11t64_2%3a11.09.02-2_armhf.deb ... 706s Unpacking libnetpbm11t64:armhf (2:11.09.02-2) ... 706s Selecting previously unselected package netpbm. 706s Preparing to unpack .../117-netpbm_2%3a11.09.02-2_armhf.deb ... 706s Unpacking netpbm (2:11.09.02-2) ... 706s Selecting previously unselected package tex-common. 706s Preparing to unpack .../118-tex-common_6.18_all.deb ... 706s Unpacking tex-common (6.18) ... 706s Selecting previously unselected package libpaper-utils. 706s Preparing to unpack .../119-libpaper-utils_2.2.5-0.3_armhf.deb ... 706s Unpacking libpaper-utils (2.2.5-0.3) ... 706s Selecting previously unselected package libkpathsea6:armhf. 706s Preparing to unpack .../120-libkpathsea6_2024.20240313.70630+ds-5build2_armhf.deb ... 706s Unpacking libkpathsea6:armhf (2024.20240313.70630+ds-5build2) ... 706s Selecting previously unselected package libptexenc1:armhf. 706s Preparing to unpack .../121-libptexenc1_2024.20240313.70630+ds-5build2_armhf.deb ... 706s Unpacking libptexenc1:armhf (2024.20240313.70630+ds-5build2) ... 706s Selecting previously unselected package libsynctex2:armhf. 706s Preparing to unpack .../122-libsynctex2_2024.20240313.70630+ds-5build2_armhf.deb ... 706s Unpacking libsynctex2:armhf (2024.20240313.70630+ds-5build2) ... 706s Selecting previously unselected package libtexlua53-5:armhf. 706s Preparing to unpack .../123-libtexlua53-5_2024.20240313.70630+ds-5build2_armhf.deb ... 706s Unpacking libtexlua53-5:armhf (2024.20240313.70630+ds-5build2) ... 706s Selecting previously unselected package t1utils. 706s Preparing to unpack .../124-t1utils_1.41-4build3_armhf.deb ... 706s Unpacking t1utils (1.41-4build3) ... 706s Selecting previously unselected package libpixman-1-0:armhf. 706s Preparing to unpack .../125-libpixman-1-0_0.44.0-3_armhf.deb ... 706s Unpacking libpixman-1-0:armhf (0.44.0-3) ... 706s Selecting previously unselected package libxcb-render0:armhf. 706s Preparing to unpack .../126-libxcb-render0_1.17.0-2_armhf.deb ... 706s Unpacking libxcb-render0:armhf (1.17.0-2) ... 706s Selecting previously unselected package libxcb-shm0:armhf. 706s Preparing to unpack .../127-libxcb-shm0_1.17.0-2_armhf.deb ... 706s Unpacking libxcb-shm0:armhf (1.17.0-2) ... 706s Selecting previously unselected package libcairo2:armhf. 706s Preparing to unpack .../128-libcairo2_1.18.2-2_armhf.deb ... 706s Unpacking libcairo2:armhf (1.18.2-2) ... 706s Selecting previously unselected package libgraphite2-3:armhf. 706s Preparing to unpack .../129-libgraphite2-3_1.3.14-2ubuntu1_armhf.deb ... 706s Unpacking libgraphite2-3:armhf (1.3.14-2ubuntu1) ... 706s Selecting previously unselected package libharfbuzz0b:armhf. 706s Preparing to unpack .../130-libharfbuzz0b_10.2.0-1_armhf.deb ... 706s Unpacking libharfbuzz0b:armhf (10.2.0-1) ... 706s Selecting previously unselected package libmpfi0:armhf. 706s Preparing to unpack .../131-libmpfi0_1.5.4+ds-4_armhf.deb ... 706s Unpacking libmpfi0:armhf (1.5.4+ds-4) ... 707s Selecting previously unselected package libpotrace0:armhf. 707s Preparing to unpack .../132-libpotrace0_1.16-2build1_armhf.deb ... 707s Unpacking libpotrace0:armhf (1.16-2build1) ... 707s Selecting previously unselected package libteckit0:armhf. 707s Preparing to unpack .../133-libteckit0_2.5.12+ds1-1_armhf.deb ... 707s Unpacking libteckit0:armhf (2.5.12+ds1-1) ... 707s Selecting previously unselected package libxmu6:armhf. 707s Preparing to unpack .../134-libxmu6_2%3a1.1.3-3build2_armhf.deb ... 707s Unpacking libxmu6:armhf (2:1.1.3-3build2) ... 707s Selecting previously unselected package libxpm4:armhf. 707s Preparing to unpack .../135-libxpm4_1%3a3.5.17-1build2_armhf.deb ... 707s Unpacking libxpm4:armhf (1:3.5.17-1build2) ... 707s Selecting previously unselected package libxaw7:armhf. 707s Preparing to unpack .../136-libxaw7_2%3a1.0.16-1_armhf.deb ... 707s Unpacking libxaw7:armhf (2:1.0.16-1) ... 707s Selecting previously unselected package libxi6:armhf. 707s Preparing to unpack .../137-libxi6_2%3a1.8.2-1_armhf.deb ... 707s Unpacking libxi6:armhf (2:1.8.2-1) ... 707s Selecting previously unselected package libzzip-0-13t64:armhf. 707s Preparing to unpack .../138-libzzip-0-13t64_0.13.72+dfsg.1-1.2build1_armhf.deb ... 707s Unpacking libzzip-0-13t64:armhf (0.13.72+dfsg.1-1.2build1) ... 707s Selecting previously unselected package texlive-binaries. 707s Preparing to unpack .../139-texlive-binaries_2024.20240313.70630+ds-5build2_armhf.deb ... 707s Unpacking texlive-binaries (2024.20240313.70630+ds-5build2) ... 707s Selecting previously unselected package xdg-utils. 707s Preparing to unpack .../140-xdg-utils_1.2.1-2ubuntu1_all.deb ... 707s Unpacking xdg-utils (1.2.1-2ubuntu1) 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Preparing to unpack .../146-libsuitesparseconfig7_1%3a7.8.3+dfsg-3_armhf.deb ... 709s Unpacking libsuitesparseconfig7:armhf (1:7.8.3+dfsg-3) ... 709s Selecting previously unselected package libamd3:armhf. 709s Preparing to unpack .../147-libamd3_1%3a7.8.3+dfsg-3_armhf.deb ... 709s Unpacking libamd3:armhf (1:7.8.3+dfsg-3) ... 709s Selecting previously unselected package libapache-pom-java. 709s Preparing to unpack .../148-libapache-pom-java_33-2_all.deb ... 709s Unpacking libapache-pom-java (33-2) ... 709s Selecting previously unselected package libblas3:armhf. 709s Preparing to unpack .../149-libblas3_3.12.1-2_armhf.deb ... 709s Unpacking libblas3:armhf (3.12.1-2) ... 709s Selecting previously unselected package libgfortran5:armhf. 709s Preparing to unpack .../150-libgfortran5_15-20250213-1ubuntu1_armhf.deb ... 709s Unpacking libgfortran5:armhf (15-20250213-1ubuntu1) ... 709s Selecting previously unselected package liblapack3:armhf. 710s Preparing to unpack .../151-liblapack3_3.12.1-2_armhf.deb ... 710s Unpacking liblapack3:armhf (3.12.1-2) ... 710s Selecting previously unselected package libarpack2t64:armhf. 710s Preparing to unpack .../152-libarpack2t64_3.9.1-4_armhf.deb ... 710s Unpacking libarpack2t64:armhf (3.9.1-4) ... 710s Selecting previously unselected package libcolamd3:armhf. 710s Preparing to unpack .../153-libcolamd3_1%3a7.8.3+dfsg-3_armhf.deb ... 710s Unpacking libcolamd3:armhf (1:7.8.3+dfsg-3) ... 710s Selecting previously unselected package libcommons-parent-java. 710s Preparing to unpack .../154-libcommons-parent-java_56-1_all.deb ... 710s Unpacking libcommons-parent-java (56-1) ... 710s Selecting previously unselected package libcommons-logging-java. 710s Preparing to unpack .../155-libcommons-logging-java_1.3.0-1ubuntu1_all.deb ... 710s Unpacking libcommons-logging-java (1.3.0-1ubuntu1) ... 710s Selecting previously unselected package libexpat1-dev:armhf. 710s Preparing to unpack .../156-libexpat1-dev_2.6.4-1_armhf.deb ... 710s Unpacking libexpat1-dev:armhf (2.6.4-1) ... 710s Selecting previously unselected package libglpk40:armhf. 710s Preparing to unpack .../157-libglpk40_5.0-1build2_armhf.deb ... 710s Unpacking libglpk40:armhf (5.0-1build2) ... 710s Selecting previously unselected package libplfit0:armhf. 710s Preparing to unpack .../158-libplfit0_0.9.4+ds-1ubuntu5_armhf.deb ... 710s Unpacking libplfit0:armhf (0.9.4+ds-1ubuntu5) ... 710s Selecting previously unselected package libigraph3t64:armhf. 710s Preparing to unpack .../159-libigraph3t64_0.10.15+ds-2_armhf.deb ... 710s Unpacking libigraph3t64:armhf (0.10.15+ds-2) ... 710s Selecting previously unselected package libimagequant0:armhf. 710s Preparing to unpack .../160-libimagequant0_2.18.0-1build1_armhf.deb ... 710s Unpacking libimagequant0:armhf (2.18.0-1build1) ... 710s Selecting previously unselected package libjs-jquery. 710s Preparing to unpack .../161-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 710s Unpacking libjs-jquery 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unselected package libmbedcrypto16:armhf. 711s Preparing to unpack .../167-libmbedcrypto16_3.6.2-3ubuntu1_armhf.deb ... 711s Unpacking libmbedcrypto16:armhf (3.6.2-3ubuntu1) ... 711s Selecting previously unselected package libmbedx509-7:armhf. 711s Preparing to unpack .../168-libmbedx509-7_3.6.2-3ubuntu1_armhf.deb ... 711s Unpacking libmbedx509-7:armhf (3.6.2-3ubuntu1) ... 711s Selecting previously unselected package libmbedtls21:armhf. 711s Preparing to unpack .../169-libmbedtls21_3.6.2-3ubuntu1_armhf.deb ... 711s Unpacking libmbedtls21:armhf (3.6.2-3ubuntu1) ... 711s Selecting previously unselected package mysql-common. 711s Preparing to unpack .../170-mysql-common_5.8+1.1.1_all.deb ... 711s Unpacking mysql-common (5.8+1.1.1) ... 711s Selecting previously unselected package libmysqlclient21:armhf. 711s Preparing to unpack .../171-libmysqlclient21_8.0.40-1_armhf.deb ... 711s Unpacking libmysqlclient21:armhf (8.0.40-1) ... 711s Selecting previously unselected package libpython3.13:armhf. 711s Preparing to unpack .../172-libpython3.13_3.13.2-1_armhf.deb ... 711s Unpacking libpython3.13:armhf (3.13.2-1) ... 711s Selecting previously unselected package zlib1g-dev:armhf. 711s Preparing to unpack .../173-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1ubuntu1_armhf.deb ... 711s Unpacking zlib1g-dev:armhf (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 711s Selecting previously unselected package libpython3.13-dev:armhf. 711s Preparing to unpack .../174-libpython3.13-dev_3.13.2-1_armhf.deb ... 711s Unpacking libpython3.13-dev:armhf (3.13.2-1) ... 711s Selecting previously unselected package libpython3-dev:armhf. 711s Preparing to unpack .../175-libpython3-dev_3.13.1-1~exp2_armhf.deb ... 711s Unpacking libpython3-dev:armhf (3.13.1-1~exp2) ... 711s Selecting previously unselected package libpython3.12t64:armhf. 711s Preparing to unpack .../176-libpython3.12t64_3.12.9-1_armhf.deb ... 711s Unpacking libpython3.12t64:armhf (3.12.9-1) ... 712s Selecting previously unselected package libpython3.12-dev:armhf. 712s Preparing to unpack .../177-libpython3.12-dev_3.12.9-1_armhf.deb ... 712s Unpacking libpython3.12-dev:armhf (3.12.9-1) ... 712s Selecting previously unselected package libpython3-all-dev:armhf. 712s Preparing to unpack .../178-libpython3-all-dev_3.13.1-1~exp2_armhf.deb ... 712s Unpacking libpython3-all-dev:armhf (3.13.1-1~exp2) ... 712s Selecting previously unselected package libqhull-r8.0:armhf. 712s Preparing to unpack .../179-libqhull-r8.0_2020.2-6build1_armhf.deb ... 712s Unpacking libqhull-r8.0:armhf (2020.2-6build1) ... 712s Selecting previously unselected package libraqm0:armhf. 712s Preparing to unpack .../180-libraqm0_0.10.2-1_armhf.deb ... 712s Unpacking libraqm0:armhf (0.10.2-1) ... 712s Selecting previously unselected package libxslt1.1:armhf. 712s Preparing to unpack .../181-libxslt1.1_1.1.39-0exp1ubuntu2_armhf.deb ... 712s Unpacking libxslt1.1:armhf (1.1.39-0exp1ubuntu2) ... 712s Selecting previously unselected package mafft. 712s Preparing to unpack .../182-mafft_7.505-1_armhf.deb ... 712s Unpacking mafft (7.505-1) ... 712s Selecting previously unselected package ncbi-data. 712s Preparing to unpack .../183-ncbi-data_6.1.20170106+dfsg2-5_all.deb ... 712s Unpacking ncbi-data (6.1.20170106+dfsg2-5) ... 712s Selecting previously unselected package ncbi-blast+. 712s Preparing to unpack .../184-ncbi-blast+_2.16.0+ds-6build1_armhf.deb ... 712s Unpacking ncbi-blast+ (2.16.0+ds-6build1) ... 713s Selecting previously unselected package phylip. 713s Preparing to unpack .../185-phylip_1%3a3.697+dfsg-4build1_armhf.deb ... 713s Unpacking phylip (1:3.697+dfsg-4build1) ... 713s Selecting previously unselected package prank. 713s Preparing to unpack .../186-prank_0.0.170427+dfsg-3_armhf.deb ... 713s Unpacking prank (0.0.170427+dfsg-3) ... 713s Selecting previously unselected package preview-latex-style. 713s Preparing to unpack .../187-preview-latex-style_13.2-1_all.deb ... 713s Unpacking preview-latex-style (13.2-1) ... 713s Selecting previously unselected package probcons. 713s Preparing to unpack .../188-probcons_1.12-14_armhf.deb ... 713s Unpacking probcons (1.12-14) ... 713s Selecting previously unselected package python-biopython-doc. 713s Preparing to unpack .../189-python-biopython-doc_1.85+dfsg-2_all.deb ... 713s Unpacking python-biopython-doc (1.85+dfsg-2) ... 714s Selecting previously unselected package python-matplotlib-data. 714s Preparing to unpack .../190-python-matplotlib-data_3.8.3-3ubuntu2_all.deb ... 714s Unpacking python-matplotlib-data (3.8.3-3ubuntu2) ... 714s Selecting previously unselected package python3-all. 714s Preparing to unpack .../191-python3-all_3.13.1-1~exp2_armhf.deb ... 714s Unpacking python3-all (3.13.1-1~exp2) ... 714s Selecting previously unselected package python3.13-dev. 714s Preparing to unpack .../192-python3.13-dev_3.13.2-1_armhf.deb ... 714s Unpacking python3.13-dev (3.13.2-1) ... 714s Selecting previously unselected package python3-dev. 714s Preparing to unpack .../193-python3-dev_3.13.1-1~exp2_armhf.deb ... 714s Unpacking python3-dev (3.13.1-1~exp2) ... 714s Selecting previously unselected package python3.12-dev. 714s Preparing to unpack .../194-python3.12-dev_3.12.9-1_armhf.deb ... 714s Unpacking python3.12-dev (3.12.9-1) ... 714s Selecting previously unselected package python3-all-dev. 714s Preparing to unpack .../195-python3-all-dev_3.13.1-1~exp2_armhf.deb ... 714s Unpacking python3-all-dev (3.13.1-1~exp2) ... 714s Selecting previously unselected package python3-numpy. 714s Preparing to unpack .../196-python3-numpy_1%3a1.26.4+ds-13_armhf.deb ... 714s Unpacking python3-numpy (1:1.26.4+ds-13) ... 714s Selecting previously unselected package python3.12-tk. 714s Preparing to unpack .../197-python3.12-tk_3.12.9-1_armhf.deb ... 714s Unpacking python3.12-tk (3.12.9-1) ... 714s Selecting previously unselected package python3.13-tk. 714s Preparing to unpack .../198-python3.13-tk_3.13.2-1_armhf.deb ... 714s Unpacking python3.13-tk (3.13.2-1) ... 714s Selecting previously unselected package python3-tk:armhf. 714s Preparing to unpack .../199-python3-tk_3.13.1-1_armhf.deb ... 714s Unpacking python3-tk:armhf (3.13.1-1) ... 714s Selecting previously unselected package python3-pil.imagetk:armhf. 714s Preparing to unpack .../200-python3-pil.imagetk_11.1.0-5_armhf.deb ... 714s Unpacking python3-pil.imagetk:armhf (11.1.0-5) ... 715s Selecting previously unselected package python3-pil:armhf. 715s Preparing to unpack .../201-python3-pil_11.1.0-5_armhf.deb ... 715s Unpacking python3-pil:armhf (11.1.0-5) ... 715s Selecting previously unselected package python3-cairo. 715s Preparing to unpack .../202-python3-cairo_1.26.1-2build1_armhf.deb ... 715s Unpacking python3-cairo (1.26.1-2build1) ... 715s Selecting previously unselected package python3-freetype. 715s Preparing to unpack .../203-python3-freetype_2.5.1-1_all.deb ... 715s Unpacking python3-freetype (2.5.1-1) ... 715s Selecting previously unselected package python3-rlpycairo. 715s Preparing to unpack .../204-python3-rlpycairo_0.3.0-3_all.deb ... 715s Unpacking python3-rlpycairo (0.3.0-3) ... 715s Selecting previously unselected package python3-reportlab. 715s Preparing to unpack .../205-python3-reportlab_4.3.0-1_all.deb ... 715s Unpacking python3-reportlab (4.3.0-1) ... 715s Selecting previously unselected package w3c-sgml-lib. 715s Preparing to unpack .../206-w3c-sgml-lib_1.3-3_all.deb ... 715s Unpacking w3c-sgml-lib (1.3-3) ... 715s Selecting previously unselected package python3-biopython. 715s Preparing to unpack .../207-python3-biopython_1.85+dfsg-2_armhf.deb ... 715s Unpacking python3-biopython (1.85+dfsg-2) ... 715s Selecting previously unselected package python3-biopython-sql. 715s Preparing to unpack .../208-python3-biopython-sql_1.85+dfsg-2_all.deb ... 715s Unpacking python3-biopython-sql (1.85+dfsg-2) ... 715s Selecting previously unselected package python3-brotli. 715s Preparing to unpack .../209-python3-brotli_1.1.0-2build3_armhf.deb ... 715s Unpacking python3-brotli (1.1.0-2build3) ... 715s Selecting previously unselected package python3-contourpy. 715s Preparing to unpack .../210-python3-contourpy_1.3.1-1_armhf.deb ... 715s Unpacking python3-contourpy (1.3.1-1) ... 715s Selecting previously unselected package python3-cycler. 716s Preparing to unpack .../211-python3-cycler_0.12.1-1_all.deb ... 716s Unpacking python3-cycler (0.12.1-1) ... 716s Selecting previously unselected package python3-dateutil. 716s Preparing to unpack .../212-python3-dateutil_2.9.0-3_all.deb ... 716s Unpacking python3-dateutil (2.9.0-3) ... 716s Selecting previously unselected package python3-decorator. 716s Preparing to unpack .../213-python3-decorator_5.1.1-5_all.deb ... 716s Unpacking python3-decorator (5.1.1-5) ... 716s Selecting previously unselected package python3-defusedxml. 716s Preparing to unpack .../214-python3-defusedxml_0.7.1-3_all.deb ... 716s Unpacking python3-defusedxml (0.7.1-3) ... 716s Selecting previously unselected package python3-roman. 716s Preparing to unpack .../215-python3-roman_5.0-1_all.deb ... 716s Unpacking python3-roman (5.0-1) ... 716s Selecting previously unselected package python3-docutils. 716s Preparing to unpack .../216-python3-docutils_0.21.2+dfsg-2_all.deb ... 716s Unpacking python3-docutils (0.21.2+dfsg-2) ... 716s Selecting previously unselected package python3-pytz. 716s Preparing to unpack .../217-python3-pytz_2025.1-3_all.deb ... 716s Unpacking python3-pytz (2025.1-3) ... 716s Selecting previously unselected package python3-tz. 716s Preparing to unpack .../218-python3-tz_2025.1-3_all.deb ... 716s Unpacking python3-tz (2025.1-3) ... 716s Selecting previously unselected package python3-platformdirs. 716s Preparing to unpack .../219-python3-platformdirs_4.3.6-1_all.deb ... 716s Unpacking python3-platformdirs (4.3.6-1) ... 716s Selecting previously unselected package python3-fs. 716s Preparing to unpack .../220-python3-fs_2.4.16-6_all.deb ... 716s Unpacking python3-fs (2.4.16-6) ... 716s Selecting previously unselected package python3-lxml:armhf. 717s Preparing to unpack .../221-python3-lxml_5.3.1-1_armhf.deb ... 717s Unpacking python3-lxml:armhf (5.3.1-1) ... 717s Selecting previously unselected package python3-lz4. 717s Preparing to unpack .../222-python3-lz4_4.4.0+dfsg-1_armhf.deb ... 717s Unpacking python3-lz4 (4.4.0+dfsg-1) ... 717s Selecting previously unselected package python3-scipy. 717s Preparing to unpack .../223-python3-scipy_1.14.1-4ubuntu1_armhf.deb ... 717s Unpacking python3-scipy (1.14.1-4ubuntu1) ... 718s Selecting previously unselected package python3-mpmath. 718s Preparing to unpack .../224-python3-mpmath_1.3.0-1_all.deb ... 718s Unpacking python3-mpmath (1.3.0-1) ... 718s Selecting previously unselected package python3-sympy. 718s Preparing to unpack .../225-python3-sympy_1.13.3-1_all.deb ... 718s Unpacking python3-sympy (1.13.3-1) ... 719s Selecting previously unselected package python3-ufolib2. 719s Preparing to unpack .../226-python3-ufolib2_0.17.0+dfsg1-1_all.deb ... 719s Unpacking python3-ufolib2 (0.17.0+dfsg1-1) ... 719s Selecting previously unselected package unicode-data. 719s Preparing to unpack .../227-unicode-data_15.1.0-1_all.deb ... 719s Unpacking unicode-data (15.1.0-1) ... 719s Selecting previously unselected package python3-fonttools. 719s Preparing to unpack .../228-python3-fonttools_4.55.3-2_armhf.deb ... 719s Unpacking python3-fonttools (4.55.3-2) ... 719s Selecting previously unselected package python3-imagesize. 719s Preparing to unpack .../229-python3-imagesize_1.4.1-1_all.deb ... 719s Unpacking python3-imagesize (1.4.1-1) ... 719s Selecting previously unselected package python3-kiwisolver. 719s Preparing to unpack .../230-python3-kiwisolver_1.4.7-3_armhf.deb ... 719s Unpacking python3-kiwisolver (1.4.7-3) ... 719s Selecting previously unselected package python3-packaging. 719s Preparing to unpack .../231-python3-packaging_24.2-1_all.deb ... 719s Unpacking python3-packaging (24.2-1) ... 719s Selecting previously unselected package python3-matplotlib. 719s Preparing to unpack .../232-python3-matplotlib_3.8.3-3ubuntu2_armhf.deb ... 719s Unpacking python3-matplotlib (3.8.3-3ubuntu2) ... 720s Selecting previously unselected package python3-msgpack. 720s Preparing to unpack .../233-python3-msgpack_1.0.3-3build3_armhf.deb ... 720s Unpacking python3-msgpack (1.0.3-3build3) ... 720s Selecting previously unselected package python3-mmtf. 720s Preparing to unpack .../234-python3-mmtf_1.1.3-1_all.deb ... 720s Unpacking python3-mmtf (1.1.3-1) ... 720s Selecting previously unselected package python3-mysqldb. 720s Preparing to unpack .../235-python3-mysqldb_1.4.6-2build4_armhf.deb ... 720s Unpacking python3-mysqldb (1.4.6-2build4) ... 720s Selecting previously unselected package python3-networkx. 720s Preparing to unpack .../236-python3-networkx_3.2.1-4ubuntu1_all.deb ... 720s Unpacking python3-networkx (3.2.1-4ubuntu1) ... 721s Selecting previously unselected package sphinx-common. 721s Preparing to unpack .../237-sphinx-common_8.1.3-5_all.deb ... 721s Unpacking sphinx-common (8.1.3-5) ... 721s Selecting previously unselected package python3-alabaster. 721s Preparing to unpack .../238-python3-alabaster_0.7.16-0.1_all.deb ... 721s Unpacking python3-alabaster (0.7.16-0.1) ... 721s Selecting previously unselected package python3-snowballstemmer. 721s Preparing to unpack .../239-python3-snowballstemmer_2.2.0-4build1_all.deb ... 721s Unpacking python3-snowballstemmer (2.2.0-4build1) ... 721s Selecting previously unselected package python3-sphinx. 721s Preparing to unpack .../240-python3-sphinx_8.1.3-5_all.deb ... 721s Unpacking python3-sphinx (8.1.3-5) ... 721s Selecting previously unselected package python3-tabulate. 721s Preparing to unpack .../241-python3-tabulate_0.9.0-1_all.deb ... 721s Unpacking python3-tabulate (0.9.0-1) ... 721s Selecting previously unselected package python3-numpydoc. 721s Preparing to unpack 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/etc/mysql/my.cnf (my.cnf) in auto mode 728s Setting up libmysqlclient21:armhf (8.0.40-1) ... 728s Setting up fonts-lato (2.015-1) ... 728s Setting up liblerc4:armhf (4.0.0+ds-5ubuntu1) ... 728s Setting up libxpm4:armhf (1:3.5.17-1build2) ... 728s Setting up hicolor-icon-theme (0.18-2) ... 728s Setting up libxi6:armhf (2:1.8.2-1) ... 728s Setting up probcons (1.12-14) ... 728s Setting up libxrender1:armhf (1:0.9.10-1.1build1) ... 728s Setting up python3-lz4 (4.4.0+dfsg-1) ... 728s Setting up libxcb-render0:armhf (1.17.0-2) ... 728s Setting up python3-defusedxml (0.7.1-3) ... 728s Setting up mafft (7.505-1) ... 728s Setting up libarchive-zip-perl (1.68-1) ... 728s Setting up imagemagick-7-common (8:7.1.1.43+dfsg1-1) ... 728s Setting up bwa (0.7.18-1) ... 728s Setting up python3-alabaster (0.7.16-0.1) ... 728s Setting up fonts-lyx (2.4.3-1) ... 728s Setting up libijs-0.35:armhf (0.35-15.1build1) ... 728s Setting up libdebhelper-perl (13.24.1ubuntu2) ... 728s Setting up libgs-common (10.04.0~dfsg1-2ubuntu1) ... 728s Setting up libfontbox-java (1:1.8.16-5) ... 728s Setting up phylip (1:3.697+dfsg-4build1) ... 728s Setting up x11-common (1:7.7+23ubuntu3) ... 728s Setting up libdeflate0:armhf (1.23-1) ... 728s Setting up linux-libc-dev:armhf (6.12.0-15.15) ... 728s Setting up python3-tabulate (0.9.0-1) ... 729s Setting up m4 (1.4.19-5) ... 729s Setting up libqhull-r8.0:armhf (2020.2-6build1) ... 729s Setting up python3-all (3.13.1-1~exp2) ... 729s Setting up python3-pytz (2025.1-3) ... 729s Setting up libxcb-shm0:armhf (1.17.0-2) ... 729s Setting up libgomp1:armhf (15-20250213-1ubuntu1) ... 729s Setting up python3-networkx (3.2.1-4ubuntu1) ... 733s Setting up libjbig0:armhf (2.1-6.1ubuntu2) ... 733s Setting up libnetpbm11t64:armhf (2:11.09.02-2) ... 733s Setting up python3-platformdirs (4.3.6-1) ... 733s Setting up python3-tz (2025.1-3) ... 733s Setting up t-coffee (13.45.0.4846264+really13.41.0.28bdc39+dfsg-1) ... 733s Setting up poppler-data (0.4.12-1) ... 733s Setting up python3-fs (2.4.16-6) ... 733s Setting up unicode-data (15.1.0-1) ... 733s Setting up python3-mysqldb (1.4.6-2build4) ... 734s Setting up libpython3.12t64:armhf (3.12.9-1) ... 734s Setting up tex-common (6.18) ... 734s update-language: texlive-base not installed and configured, doing nothing! 734s Setting up python3-roman (5.0-1) ... 734s Setting up python3-decorator (5.1.1-5) ... 734s Setting up libfontenc1:armhf (1:1.1.8-1build1) ... 734s Setting up autotools-dev (20220109.1) ... 734s Setting up libblas3:armhf (3.12.1-2) ... 734s 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 734s Setting up python3-packaging (24.2-1) ... 734s Setting up rpcsvc-proto (1.4.2-0ubuntu7) ... 734s Setting up libzzip-0-13t64:armhf (0.13.72+dfsg.1-1.2build1) ... 734s Setting up libfreetype6:armhf (2.13.3+dfsg-1) ... 734s Setting up libjbig2dec0:armhf (0.20-1build3) ... 734s Setting up python3-snowballstemmer (2.2.0-4build1) ... 735s Setting up libteckit0:armhf (2.5.12+ds1-1) ... 735s Setting up python3-brotli (1.1.0-2build3) ... 735s Setting up libapache-pom-java (33-2) ... 735s Setting up libavahi-common-data:armhf (0.8-14ubuntu1) ... 735s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 735s Setting up t1utils (1.41-4build3) ... 735s Setting up python3-cycler (0.12.1-1) ... 735s Setting up libtexlua53-5:armhf (2024.20240313.70630+ds-5build2) ... 735s Setting up libimagequant0:armhf (2.18.0-1build1) ... 735s Setting up fonts-dejavu-mono (2.37-8) ... 735s Setting up python3-kiwisolver (1.4.7-3) ... 736s Setting up libmpc3:armhf (1.3.1-1build2) ... 736s Setting up libidn12:armhf (1.42-3) ... 736s Setting up libtcl8.6:armhf (8.6.16+dfsg-1) ... 736s Setting up autopoint (0.23.1-1) ... 736s Setting up libmpfi0:armhf (1.5.4+ds-4) ... 736s Setting up fonts-dejavu-core (2.37-8) ... 736s Setting up wise-data (2.4.1-25) ... 736s Setting up libjpeg-turbo8:armhf (2.1.5-3ubuntu2) ... 736s Setting up libltdl7:armhf (2.5.4-3build1) ... 736s Setting up libfftw3-double3:armhf (3.3.10-2fakesync1build1) ... 736s Setting up libcifpp-data (7.0.9-1) ... 736s Setting up libkpathsea6:armhf (2024.20240313.70630+ds-5build2) ... 736s Setting up libgfortran5:armhf (15-20250213-1ubuntu1) ... 736s Setting up autoconf (2.72-3) ... 736s Setting up libwebp7:armhf (1.5.0-0.1) ... 736s Setting up libubsan1:armhf (15-20250213-1ubuntu1) ... 736s Setting up dwz (0.15-1build6) ... 736s Setting up liblqr-1-0:armhf (0.4.2-2.1build2) ... 736s Setting up python3-rdflib (7.1.1-2) ... 737s Setting up libcrypt-dev:armhf (1:4.4.38-1) ... 737s Setting up libasan8:armhf (15-20250213-1ubuntu1) ... 737s Setting up libjson-perl (4.10000-1) ... 737s Setting up libxslt1.1:armhf (1.1.39-0exp1ubuntu2) ... 737s Setting up debugedit (1:5.1-2) ... 737s Setting up fonts-lmodern (2.005-1) ... 737s Setting up libsuitesparseconfig7:armhf (1:7.8.3+dfsg-3) ... 737s Setting up libopenjp2-7:armhf (2.5.0-2ubuntu3) ... 737s Setting up libharfbuzz0b:armhf (10.2.0-1) ... 737s Setting up python3-dateutil (2.9.0-3) ... 737s Setting up fasttree (2.1.11-2) ... 737s Setting up sgml-base (1.31) ... 737s Setting up python3-msgpack (1.0.3-3build3) ... 737s Setting up libplfit0:armhf (0.9.4+ds-1ubuntu5) ... 737s Setting up libxss1:armhf (1:1.2.3-1build3) ... 737s Setting up libmbedcrypto16:armhf (3.6.2-3ubuntu1) ... 737s Setting up libpaper2:armhf (2.2.5-0.3) ... 737s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 738s Setting up libgcc-14-dev:armhf (14.2.0-17ubuntu1) ... 738s Setting up python3-mpmath (1.3.0-1) ... 738s Setting up libisl23:armhf (0.27-1) ... 738s Setting up libde265-0:armhf (1.0.15-1build4) ... 738s Setting up libc-dev-bin (2.40-4ubuntu1) ... 738s Setting up python-matplotlib-data (3.8.3-3ubuntu2) ... 738s Setting up libwebpmux3:armhf (1.5.0-0.1) ... 738s Setting up dialign (2.2.1-13) ... 738s Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 738s Setting up sphinx-rtd-theme-common (3.0.2+dfsg-2) ... 738s Setting up xdg-utils (1.2.1-2ubuntu1) ... 738s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode 738s Setting up libcc1-0:armhf (15-20250213-1ubuntu1) ... 738s Setting up libsynctex2:armhf (2024.20240313.70630+ds-5build2) ... 738s Setting up prank (0.0.170427+dfsg-3) ... 738s Setting up cpp-14-arm-linux-gnueabihf (14.2.0-17ubuntu1) ... 738s Setting up libargtable2-0 (13-3) ... 738s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 738s Setting up python3-imagesize (1.4.1-1) ... 739s Setting up libpotrace0:armhf (1.16-2build1) ... 739s Setting up libjpeg8:armhf (8c-2ubuntu11) ... 739s Setting up automake (1:1.17-3) ... 739s update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode 739s Setting up libfile-stripnondeterminism-perl (1.14.1-2) ... 739s Setting up python3-sympy (1.13.3-1) ... 755s Setting up libice6:armhf (2:1.1.1-1) ... 755s Setting up flex (2.6.4-8.2build1) ... 755s Setting up liblapack3:armhf (3.12.1-2) ... 755s 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 755s Setting up gettext (0.23.1-1) ... 755s Setting up libarpack2t64:armhf (3.9.1-4) ... 755s Setting up libamd3:armhf (1:7.8.3+dfsg-3) ... 755s Setting up libpdfbox-java (1:1.8.16-5) ... 755s Setting up libcolamd3:armhf (1:7.8.3+dfsg-3) ... 755s Setting up fontconfig-config (2.15.0-2ubuntu1) ... 755s Setting up wise (2.4.1-25) ... 755s Setting up preview-latex-style (13.2-1) ... 755s Setting up libwebpdemux2:armhf (1.5.0-0.1) ... 755s Setting up libcommons-parent-java (56-1) ... 755s Setting up libavahi-common3:armhf (0.8-14ubuntu1) ... 755s Setting up libcommons-logging-java (1.3.0-1ubuntu1) ... 755s Setting up gcc-14-arm-linux-gnueabihf (14.2.0-17ubuntu1) ... 755s Setting up libcifpp7:armhf (7.0.9-1) ... 755s Setting up libpaper-utils (2.2.5-0.3) ... 755s Setting up clustalo (1.2.4-8build1) ... 755s Setting up dssp (4.4.10-1) ... 755s Setting up python3-freetype (2.5.1-1) ... 756s Setting up xfonts-utils (1:7.7+7) ... 756s Setting up intltool-debian (0.35.0+20060710.6) ... 756s Setting up libmbedx509-7:armhf (3.6.2-3ubuntu1) ... 756s Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... 756s Setting up libptexenc1:armhf (2024.20240313.70630+ds-5build2) ... 756s Setting up libglpk40:armhf (5.0-1build2) ... 756s Setting up libraqm0:armhf (0.10.2-1) ... 756s Setting up python3-numpy (1:1.26.4+ds-13) ... 761s Setting up libjs-sphinxdoc (8.1.3-5) ... 761s Setting up libraw23t64:armhf (0.21.3-1) ... 761s Setting up cpp-14 (14.2.0-17ubuntu1) ... 761s Setting up libmbedtls21:armhf (3.6.2-3ubuntu1) ... 761s Setting up dh-strip-nondeterminism (1.14.1-2) ... 761s Setting up python3-lxml:armhf (5.3.1-1) ... 762s Setting up python-biopython-doc (1.85+dfsg-2) ... 762s Setting up libtiff6:armhf (4.5.1+git230720-4ubuntu4) ... 762s Setting up xml-core (0.19) ... 762s Setting up libc6-dev:armhf (2.40-4ubuntu1) ... 762s Setting up python3-contourpy (1.3.1-1) ... 762s Setting up libfontconfig1:armhf (2.15.0-2ubuntu1) ... 762s Setting up libigraph3t64:armhf (0.10.15+ds-2) ... 762s Setting up libstdc++-14-dev:armhf (14.2.0-17ubuntu1) ... 762s Setting up libsm6:armhf (2:1.2.4-1) ... 762s Setting up libavahi-client3:armhf (0.8-14ubuntu1) ... 762s Setting up cpp-arm-linux-gnueabihf (4:14.2.0-1ubuntu1) ... 762s Setting up liblbfgsb0:armhf (3.0+dfsg.4-1build1) ... 762s Setting up gcc-arm-linux-gnueabihf (4:14.2.0-1ubuntu1) ... 762s Setting up g++-14-arm-linux-gnueabihf (14.2.0-17ubuntu1) ... 762s Setting up libxft2:armhf (2.3.6-1build1) ... 762s Setting up python3-scipy (1.14.1-4ubuntu1) ... 770s Setting up po-debconf (1.0.21+nmu1) ... 770s Setting up libtk8.6:armhf (8.6.16-1) ... 770s Setting up python3.12-tk (3.12.9-1) ... 770s Setting up python3-mmtf (1.1.3-1) ... 771s Setting up fonts-urw-base35 (20200910-8) ... 771s Setting up libcairo2:armhf (1.18.2-2) ... 771s Setting up python3.13-tk (3.13.2-1) ... 771s Setting up gcc-14 (14.2.0-17ubuntu1) ... 771s Setting up ncbi-blast+ (2.16.0+ds-6build1) ... 771s Setting up python3-pil:armhf (11.1.0-5) ... 773s Setting up libexpat1-dev:armhf (2.6.4-1) ... 773s Setting up sphinx-common (8.1.3-5) ... 773s Setting up libxt6t64:armhf (1:1.2.1-1.2build1) ... 773s Setting up netpbm (2:11.09.02-2) ... 773s Setting up zlib1g-dev:armhf (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 773s Setting up python3-igraph (0.11.8+ds-1build1) ... 773s Setting up cpp (4:14.2.0-1ubuntu1) ... 773s Setting up g++-14 (14.2.0-17ubuntu1) ... 773s Setting up libcups2t64:armhf (2.4.11-0ubuntu2) ... 773s Setting up g++-arm-linux-gnueabihf (4:14.2.0-1ubuntu1) ... 773s Setting up libgs10-common (10.04.0~dfsg1-2ubuntu1) ... 773s Setting up tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 773s Setting up libxmu6:armhf (2:1.1.3-3build2) ... 773s Setting up python3-cairo (1.26.1-2build1) ... 773s Setting up libtool (2.5.4-3build1) ... 773s Setting up blt (2.5.3+dfsg-7build1) ... 773s Setting up python3-tk:armhf (3.13.1-1) ... 773s Setting up libpython3.12-dev:armhf (3.12.9-1) ... 773s Setting up libxaw7:armhf (2:1.0.16-1) ... 773s Setting up gcc (4:14.2.0-1ubuntu1) ... 773s Setting up dh-autoreconf (20) ... 773s Setting up python3-pil.imagetk:armhf (11.1.0-5) ... 773s Setting up python3-rlpycairo (0.3.0-3) ... 774s Setting up libpython3.13-dev:armhf (3.13.2-1) ... 774s Setting up python3.12-dev (3.12.9-1) ... 774s Setting up python3-reportlab (4.3.0-1) ... 775s Setting up g++ (4:14.2.0-1ubuntu1) ... 775s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 775s Setting up texlive-binaries (2024.20240313.70630+ds-5build2) ... 775s update-alternatives: using /usr/bin/xdvi-xaw to provide /usr/bin/xdvi.bin (xdvi.bin) in auto mode 775s update-alternatives: using /usr/bin/bibtex.original to provide /usr/bin/bibtex (bibtex) in auto mode 775s Setting up build-essential (12.10ubuntu1) ... 775s Setting up texlive-base (2024.20241115-1) ... 776s tl-paper: setting paper size for dvips to a4: /var/lib/texmf/dvips/config/config-paper.ps 776s tl-paper: setting paper size for dvipdfmx to a4: /var/lib/texmf/dvipdfmx/dvipdfmx-paper.cfg 777s tl-paper: setting paper size for xdvi to a4: /var/lib/texmf/xdvi/XDvi-paper 777s tl-paper: setting paper size for pdftex to a4: /var/lib/texmf/tex/generic/tex-ini-files/pdftexconfig.tex 778s Setting up libgs10:armhf (10.04.0~dfsg1-2ubuntu1) ... 778s Setting up libpython3-dev:armhf (3.13.1-1~exp2) ... 778s Setting up python3.13-dev (3.13.2-1) ... 778s Setting up debhelper (13.24.1ubuntu2) ... 778s Setting up ghostscript (10.04.0~dfsg1-2ubuntu1) ... 778s Setting up texlive-latex-base (2024.20241115-1) ... 778s Setting up libpython3-all-dev:armhf (3.13.1-1~exp2) ... 778s Setting up python3-dev (3.13.1-1~exp2) ... 778s Setting up texlive-latex-recommended (2024.20241115-1) ... 778s Setting up texlive-pictures (2024.20241115-1) ... 778s Setting up texlive-fonts-recommended (2024.20241115-1) ... 778s Setting up python3-all-dev (3.13.1-1~exp2) ... 778s Setting up texlive-latex-extra (2024.20250114-1) ... 778s Setting up python3-ufolib2 (0.17.0+dfsg1-1) ... 778s Setting up libheif-plugin-aomdec:armhf (1.19.5-1build1) ... 778s Setting up libheif-plugin-libde265:armhf (1.19.5-1build1) ... 778s Setting up libheif1:armhf (1.19.5-1build1) ... 778s Setting up python3-fonttools (4.55.3-2) ... 780s Setting up libmagickcore-7.q16-10:armhf (8:7.1.1.43+dfsg1-1) ... 780s Setting up python3-matplotlib (3.8.3-3ubuntu2) ... 784s Setting up libmagickwand-7.q16-10:armhf (8:7.1.1.43+dfsg1-1) ... 784s Setting up imagemagick-7.q16 (8:7.1.1.43+dfsg1-1) ... 784s update-alternatives: using /usr/bin/compare-im7.q16 to provide /usr/bin/compare (compare) in auto mode 784s update-alternatives: using /usr/bin/compare-im7.q16 to provide /usr/bin/compare-im7 (compare-im7) in auto mode 784s update-alternatives: using /usr/bin/animate-im7.q16 to provide /usr/bin/animate (animate) in auto mode 784s update-alternatives: using /usr/bin/animate-im7.q16 to provide /usr/bin/animate-im7 (animate-im7) in auto mode 784s update-alternatives: using /usr/bin/convert-im7.q16 to provide /usr/bin/convert (convert) in auto mode 784s update-alternatives: using /usr/bin/convert-im7.q16 to provide /usr/bin/convert-im7 (convert-im7) in auto mode 784s update-alternatives: using /usr/bin/composite-im7.q16 to provide /usr/bin/composite (composite) in auto mode 784s update-alternatives: using /usr/bin/composite-im7.q16 to provide /usr/bin/composite-im7 (composite-im7) in auto mode 784s update-alternatives: using /usr/bin/conjure-im7.q16 to provide /usr/bin/conjure (conjure) in auto mode 784s update-alternatives: using /usr/bin/conjure-im7.q16 to provide /usr/bin/conjure-im7 (conjure-im7) in auto mode 784s update-alternatives: using /usr/bin/import-im7.q16 to provide /usr/bin/import (import) in auto mode 784s update-alternatives: using /usr/bin/import-im7.q16 to provide /usr/bin/import-im7 (import-im7) in auto mode 784s update-alternatives: using /usr/bin/identify-im7.q16 to provide /usr/bin/identify (identify) in auto mode 784s update-alternatives: using /usr/bin/identify-im7.q16 to provide /usr/bin/identify-im7 (identify-im7) in auto mode 784s update-alternatives: using /usr/bin/stream-im7.q16 to provide /usr/bin/stream (stream) in auto mode 784s update-alternatives: using /usr/bin/stream-im7.q16 to provide /usr/bin/stream-im7 (stream-im7) in auto mode 784s update-alternatives: using /usr/bin/display-im7.q16 to provide /usr/bin/display (display) in auto mode 784s update-alternatives: using /usr/bin/display-im7.q16 to provide /usr/bin/display-im7 (display-im7) in auto mode 784s update-alternatives: using /usr/bin/montage-im7.q16 to provide /usr/bin/montage (montage) in auto mode 784s update-alternatives: using /usr/bin/montage-im7.q16 to provide /usr/bin/montage-im7 (montage-im7) in auto mode 784s update-alternatives: using /usr/bin/mogrify-im7.q16 to provide /usr/bin/mogrify (mogrify) in auto mode 784s update-alternatives: using /usr/bin/mogrify-im7.q16 to provide /usr/bin/mogrify-im7 (mogrify-im7) in auto mode 784s update-alternatives: using /usr/bin/magick-im7.q16 to provide /usr/bin/magick (magick) in auto mode 784s 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 784s update-alternatives: using /usr/bin/magick-im7.q16 to provide /usr/bin/magick-im7 (magick-im7) in auto mode 784s 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 784s update-alternatives: using /usr/bin/magick-script-im7.q16 to provide /usr/bin/magick-script (magick-script) in auto mode 784s 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 784s update-alternatives: using /usr/bin/magick-script-im7.q16 to provide /usr/bin/magick-script-im7 (magick-script-im7) in auto mode 784s 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 784s Setting up hevea (2.36-2) ... 784s Setting up imagemagick (8:7.1.1.43+dfsg1-1) ... 784s Processing triggers for install-info (7.1.1-1) ... 784s Processing triggers for libc-bin (2.40-4ubuntu1) ... 784s Processing triggers for man-db (2.13.0-1) ... 786s Processing triggers for sgml-base (1.31) ... 786s Setting up docutils-common (0.21.2+dfsg-2) ... 786s Setting up w3c-sgml-lib (1.3-3) ... 820s Setting up python3-biopython (1.85+dfsg-2) ... 823s Setting up python3-biopython-sql (1.85+dfsg-2) ... 823s Processing triggers for sgml-base (1.31) ... 823s Setting up python3-docutils (0.21.2+dfsg-2) ... 824s Setting up python3-sphinx (8.1.3-5) ... 827s Setting up python3-sphinxcontrib.jquery (4.1-5) ... 827s Setting up python3-numpydoc (1.8.0-1) ... 827s Setting up python3-sphinx-rtd-theme (3.0.2+dfsg-2) ... 828s Processing triggers for tex-common (6.18) ... 829s Running updmap-sys. This may take some time... done. 829s Running mktexlsr /var/lib/texmf ... done. 829s Building format(s) --all. 963s This may take some time... done. 995s autopkgtest [12:48:45]: test full_suite: sh debian/tests/run-unit-test 995s autopkgtest [12:48:45]: test full_suite: [----------------------- 1001s mkdir: created directory 'Bio' 1001s mkdir: created directory 'Bio/Align' 1001s mkdir: created directory 'Bio/Align/substitution_matrices' 1001s mkdir: created directory 'Bio/Align/substitution_matrices/data/' 1001s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER22' -> 'Bio/Align/substitution_matrices/data/BENNER22' 1001s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER6' -> 'Bio/Align/substitution_matrices/data/BENNER6' 1001s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER74' -> 'Bio/Align/substitution_matrices/data/BENNER74' 1001s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLASTN' -> 'Bio/Align/substitution_matrices/data/BLASTN' 1001s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLASTP' -> 'Bio/Align/substitution_matrices/data/BLASTP' 1001s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM45' -> 'Bio/Align/substitution_matrices/data/BLOSUM45' 1001s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM50' -> 'Bio/Align/substitution_matrices/data/BLOSUM50' 1001s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM62' -> 'Bio/Align/substitution_matrices/data/BLOSUM62' 1001s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM80' -> 'Bio/Align/substitution_matrices/data/BLOSUM80' 1001s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM90' -> 'Bio/Align/substitution_matrices/data/BLOSUM90' 1001s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/DAYHOFF' -> 'Bio/Align/substitution_matrices/data/DAYHOFF' 1001s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/FENG' -> 'Bio/Align/substitution_matrices/data/FENG' 1001s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/GENETIC' -> 'Bio/Align/substitution_matrices/data/GENETIC' 1001s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/GONNET1992' -> 'Bio/Align/substitution_matrices/data/GONNET1992' 1001s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/HOXD70' -> 'Bio/Align/substitution_matrices/data/HOXD70' 1001s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/JOHNSON' -> 'Bio/Align/substitution_matrices/data/JOHNSON' 1001s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/JONES' -> 'Bio/Align/substitution_matrices/data/JONES' 1001s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/LEVIN' -> 'Bio/Align/substitution_matrices/data/LEVIN' 1001s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MCLACHLAN' -> 'Bio/Align/substitution_matrices/data/MCLACHLAN' 1001s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MDM78' -> 'Bio/Align/substitution_matrices/data/MDM78' 1001s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MEGABLAST' -> 'Bio/Align/substitution_matrices/data/MEGABLAST' 1001s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/NUC.4.4' -> 'Bio/Align/substitution_matrices/data/NUC.4.4' 1001s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM250' -> 'Bio/Align/substitution_matrices/data/PAM250' 1001s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM30' -> 'Bio/Align/substitution_matrices/data/PAM30' 1001s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM70' -> 'Bio/Align/substitution_matrices/data/PAM70' 1001s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/RAO' -> 'Bio/Align/substitution_matrices/data/RAO' 1001s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/RISLER' -> 'Bio/Align/substitution_matrices/data/RISLER' 1001s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/SCHNEIDER' -> 'Bio/Align/substitution_matrices/data/SCHNEIDER' 1001s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/STR' -> 'Bio/Align/substitution_matrices/data/STR' 1001s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/TRANS' -> 'Bio/Align/substitution_matrices/data/TRANS' 1002s test_Ace ... ok 1002s test_Affy ... ok 1005s test_AlignIO ... ok 1005s test_AlignIO_ClustalIO ... ok 1005s test_AlignIO_EmbossIO ... ok 1005s test_AlignIO_FastaIO ... ok 1005s test_AlignIO_MauveIO ... ok 1005s test_AlignIO_PhylipIO ... ok 1005s test_AlignIO_convert ... ok 1005s test_AlignInfo ... ok 1005s test_Align_Alignment ... ok 1005s test_Align_a2m ... ok 1005s test_Align_bed ... ok 1006s test_Align_bigbed ... ok 1006s test_Align_bigmaf ... ok 1007s test_Align_bigpsl ... ok 1007s test_Align_chain ... ok 1007s test_Align_clustal ... ok 1012s test_Align_codonalign ... ok 1012s test_Align_emboss ... ok 1013s test_Align_exonerate ... ok 1013s test_Align_fasta ... ok 1013s test_Align_hhr ... ok 1014s test_Align_maf ... ok 1014s test_Align_mauve ... ok 1014s test_Align_msf ... ok 1014s test_Align_nexus ... ok 1014s test_Align_phylip ... ok 1015s test_Align_psl ... ok 1015s test_Align_sam ... ok 1017s test_Align_stockholm ... ok 1017s test_Align_tabular ... ok 1018s test_Application ... ok 1018s test_BioSQL_MySQLdb_online ... skipping. internet not available 1018s test_BioSQL_mysql_connector ... skipping. BioSQL test configuration file biosql.ini missing (see biosql.ini.sample) 1018s test_BioSQL_mysql_connector_online ... skipping. internet not available 1018s test_BioSQL_psycopg2_online ... skipping. internet not available 1023s test_BioSQL_sqlite3 ... ok 1023s test_BioSQL_sqlite3_online ... skipping. internet not available 1023s test_Blast_Record ... ok 1024s test_Blast_parser ... ok 1024s test_CAPS ... ok 1024s test_Chi2 ... ok 1025s test_ClustalOmega_tool ... ok 1025s test_Clustalw_tool ... skipping. Install clustalw or clustalw2 if you want to use it from Biopython. 1025s test_Cluster ... ok 1025s test_CodonTable ... ok 1025s test_ColorSpiral ... ok 1025s test_Compass ... ok 1027s test_Consensus ... ok 1029s test_Dialign_tool ... ok 1029s test_EMBL_unittest ... ok 1029s test_Emboss ... skipping. $EMBOSS_ROOT='/usr/lib/emboss' which does not exist! 1029s test_EmbossPrimer ... ok 1033s test_Entrez ... ok 1033s test_Entrez_online ... skipping. internet not available 1034s test_Entrez_parser ... ok 1034s test_Enzyme ... ok 1034s test_ExPASy ... skipping. internet not available 1034s test_Fasttree_tool ... ok 1034s test_File ... ok 1034s test_GenBank ... /usr/lib/python3/dist-packages/Bio/SeqIO/InsdcIO.py:600: BiopythonWarning: Annotation 'Sequence Read Archive: SRX001885, SRX001121, SRX001531, SRX001530, SRX001529' too long 1034s warnings.warn(f"Annotation {text!r} too long", BiopythonWarning) 1035s ok 1037s test_GenomeDiagram ... Warn: Can't find .pfb for face 'Helvetica' 1039s ok 1040s test_GraphicsChromosome ... ok 1040s test_GraphicsDistribution ... ok 1041s test_GraphicsGeneral ... ok 1041s test_HMMCasino ... ok 1041s test_HMMGeneral ... ok 1041s test_KEGG ... ok 1041s test_KEGG_online ... skipping. internet not available 1047s test_KGML_graphics ... ok 1047s test_KGML_graphics_online ... skipping. internet not available 1048s test_KGML_nographics ... ok 1048s test_KeyWList ... ok 1049s test_LogisticRegression ... ok 1050s test_MafIO_index ... ok 1052s test_Mafft_tool ... ok 1052s test_MarkovModel ... ok 1052s test_Medline ... ok 1052s test_Muscle_tool ... skipping. Install MUSCLE if you want to use the Bio.Align.Applications wrapper. 1053s test_NCBIXML ... Exception ignored in: 1053s Traceback (most recent call last): 1053s File "/usr/lib/python3/dist-packages/Bio/Blast/NCBIXML.py", line 1319, in parse 1053s expat_parser.Parse(NULL, True) 1053s xml.parsers.expat.ExpatError: unclosed token: line 320, column 0 1053s ok 1056s test_NCBI_BLAST_tools ... ok 1056s test_NCBI_qblast ... ok 1057s test_NMR ... ok 1057s test_NaiveBayes ... ok 1057s test_Nexus ... ok 1057s test_PAML_baseml ... ok 1058s test_PAML_codeml ... ok 1058s test_PAML_yn00 ... ok 1064s test_PDB_CEAligner ... ok 1066s test_PDB_DSSP ... ok 1066s test_PDB_Dice ... ok 1066s test_PDB_Disordered ... ok 1067s test_PDB_Exposure ... ok 1067s test_PDB_FragmentMapper ... ok 1069s test_PDB_KDTree ... ok 1069s test_PDB_MMCIF2Dict ... ok 1069s test_PDB_MMCIFIO ... ok 1071s test_PDB_MMCIFParser ... ok 1071s test_PDB_NACCESS ... ok 1071s test_PDB_PDBIO ... ok 1071s test_PDB_PDBList ... skipping. internet not available 1080s test_PDB_PDBMLParser ... ok 1080s test_PDB_PDBParser ... ok 1080s 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 1080s test_PDB_Polypeptide ... ok 1081s test_PDB_QCPSuperimposer ... ok 1084s test_PDB_SASA ... ok 1085s test_PDB_SMCRA ... ok 1085s test_PDB_Selection ... ok 1086s test_PDB_StructureAlignment ... ok 1086s test_PDB_Superimposer ... ok 1086s test_PDB_alphafold_db ... skipping. internet not available 1090s test_PDB_binary_cif ... /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 1, ' ') redefined at line 7. 1090s warnings.warn( 1090s /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 15, ' ') redefined at line 144. 1090s warnings.warn( 1090s /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 15, ' ') redefined at line 153. 1090s warnings.warn( 1090s /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 1, ' ') redefined at line 0. 1090s warnings.warn( 1090s /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 15, ' ') redefined at line 0. 1090s warnings.warn( 1090s ok 1101s test_PDB_internal_coords ... ok 1101s test_PDB_parse_pdb_header ... ok 1102s test_PDB_vectors ... ok 1102s test_PQR ... ok 1102s test_Pathway ... ok 1103s test_Phd ... ok 1103s test_Phylo ... ok 1104s test_PhyloXML ... ok 1104s test_Phylo_CDAO ... ok 1105s test_Phylo_NeXML ... ok 1106s test_Phylo_igraph ... ok 1110s test_Phylo_matplotlib ... ok 1111s test_Phylo_networkx ... ok 1111s test_PopGen_GenePop_nodepend ... ok 1114s test_Prank_tool ... ok 1116s test_Probcons_tool ... ok 1117s test_ProtParam ... ok 1118s test_RCSBFormats ... ok 1119s test_Restriction ... ok 1121s test_SCOP_Astral ... ok 1122s test_SCOP_Cla ... ok 1123s test_SCOP_Des ... ok 1124s test_SCOP_Dom ... ok 1125s test_SCOP_Hie ... ok 1126s test_SCOP_Raf ... ok 1127s test_SCOP_Residues ... ok 1127s test_SCOP_Scop ... ok 1128s test_SVDSuperimposer ... ok 1129s test_SearchIO_blast_tab ... ok 1130s test_SearchIO_blast_tab_index ... ok 1131s test_SearchIO_blast_xml ... ok 1133s test_SearchIO_blast_xml_index ... ok 1135s test_SearchIO_blat_psl ... ok 1136s test_SearchIO_blat_psl_index ... ok 1137s test_SearchIO_exonerate ... ok 1138s test_SearchIO_exonerate_text_index ... ok 1139s test_SearchIO_exonerate_vulgar_index ... ok 1140s test_SearchIO_fasta_m10 ... ok 1141s test_SearchIO_fasta_m10_index ... ok 1142s test_SearchIO_hhsuite2_text ... ok 1144s test_SearchIO_hmmer2_text ... ok 1145s test_SearchIO_hmmer2_text_index ... ok 1146s test_SearchIO_hmmer3_domtab ... ok 1147s test_SearchIO_hmmer3_domtab_index ... ok 1148s test_SearchIO_hmmer3_tab ... ok 1149s test_SearchIO_hmmer3_tab_index ... ok 1150s test_SearchIO_hmmer3_text ... ok 1151s test_SearchIO_hmmer3_text_index ... ok 1152s test_SearchIO_interproscan_xml ... ok 1153s test_SearchIO_model ... ok 1154s test_SearchIO_write ... ok 1155s test_SeqFeature ... ok 1175s test_SeqIO ... ok 1177s test_SeqIO_AbiIO ... ok 1178s test_SeqIO_FastaIO ... ok 1179s test_SeqIO_Gck ... ok 1180s test_SeqIO_Gfa ... ok 1180s test_SeqIO_Insdc ... ok 1181s test_SeqIO_NibIO ... ok 1184s test_SeqIO_PdbIO ... ok 1186s test_SeqIO_QualityIO ... ok 1187s test_SeqIO_SeqXML ... ok 1188s test_SeqIO_SffIO ... ok 1188s test_SeqIO_SnapGene ... ok 1190s test_SeqIO_TwoBitIO ... ok 1191s test_SeqIO_UniprotIO ... ok 1192s test_SeqIO_Xdna ... ok 1194s test_SeqIO_features ... ok 1213s test_SeqIO_index ... ok 1213s test_SeqIO_online ... skipping. internet not available 1214s test_SeqIO_write ... ok 1215s test_SeqRecord ... ok 1216s test_SeqUtils ... ok 1219s test_Seq_objs ... ok 1220s test_SwissProt ... ok 1223s test_TCoffee_tool ... ok 1224s test_TogoWS ... skipping. internet not available 1225s test_TreeConstruction ... ok 1226s test_Tutorial ... skipping. Could not find ../Doc/Tutorial/index.rst file 1227s test_UniGene ... ok 1227s test_UniProt ... skipping. internet not available 1228s test_UniProt_GOA ... ok 1229s test_align ... ok 1231s test_align_substitution_matrices ... ok 1234s test_bgzf ... ok 1235s test_cellosaurus ... ok 1242s test_codonalign ... ok 1243s test_geo ... ok 1244s test_kNN ... ok 1245s test_motifs ... ok 1246s test_motifs_online ... skipping. internet not available 1246s 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. 1246s warnings.warn( 1247s ok 1247s test_pairwise2_no_C ... ok 1249s test_pairwise_aligner ... ok 1250s test_pairwise_alignment_map ... ok 1259s test_phenotype ... ok 1260s test_phenotype_fit ... ok 1261s 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. 1262s test_prodoc ... ok 1263s test_prosite ... ok 1264s test_raxml_tool ... skipping. Install RAxML (binary raxmlHPC) if you want to test the Bio.Phylo.Applications wrapper. 1265s test_samtools_tool ... skipping. Install samtools and correctly set the file path to the program if you want to use it from Biopython 1266s test_seq ... ok 1267s test_translate ... ok 1268s ---------------------------------------------------------------------- 1268s Ran 218 tests in 266.077 seconds 1268s 1268s Skipping any tests requiring internet access 1268s Python version: 3.12.9 (main, Feb 5 2025, 01:31:18) [GCC 14.2.0] 1268s Operating system: posix linux 1269s sys:1: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/protein_lib.fa' mode='rt' encoding='UTF-8'> 1269s sys:1: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/nucleotide_lib.fa' mode='rt' encoding='UTF-8'> 1271s test_Ace ... ok 1271s test_Affy ... ok 1274s test_AlignIO ... ok 1274s test_AlignIO_ClustalIO ... ok 1274s test_AlignIO_EmbossIO ... ok 1274s test_AlignIO_FastaIO ... ok 1274s test_AlignIO_MauveIO ... ok 1274s test_AlignIO_PhylipIO ... ok 1274s test_AlignIO_convert ... ok 1274s test_AlignInfo ... ok 1274s test_Align_Alignment ... ok 1274s test_Align_a2m ... ok 1275s test_Align_bed ... ok 1275s test_Align_bigbed ... ok 1276s test_Align_bigmaf ... ok 1276s test_Align_bigpsl ... ok 1276s test_Align_chain ... ok 1276s test_Align_clustal ... ok 1282s test_Align_codonalign ... ok 1282s test_Align_emboss ... ok 1282s test_Align_exonerate ... ok 1282s test_Align_fasta ... ok 1283s test_Align_hhr ... ok 1284s test_Align_maf ... ok 1284s test_Align_mauve ... ok 1284s test_Align_msf ... ok 1284s test_Align_nexus ... ok 1284s test_Align_phylip ... ok 1284s test_Align_psl ... ok 1285s test_Align_sam ... ok 1287s test_Align_stockholm ... ok 1287s test_Align_tabular ... ok 1287s test_Application ... ok 1287s test_BioSQL_MySQLdb_online ... skipping. internet not available 1287s test_BioSQL_mysql_connector ... skipping. BioSQL test configuration file biosql.ini missing (see biosql.ini.sample) 1288s test_BioSQL_mysql_connector_online ... skipping. internet not available 1288s test_BioSQL_psycopg2_online ... skipping. internet not available 1293s test_BioSQL_sqlite3 ... ok 1293s test_BioSQL_sqlite3_online ... skipping. internet not available 1293s test_Blast_Record ... ok 1294s test_Blast_parser ... ok 1295s test_CAPS ... ok 1295s test_Chi2 ... ok 1295s test_ClustalOmega_tool ... ok 1296s test_Clustalw_tool ... skipping. Install clustalw or clustalw2 if you want to use it from Biopython. 1296s test_Cluster ... ok 1296s test_CodonTable ... ok 1296s test_ColorSpiral ... ok 1296s test_Compass ... ok 1297s test_Consensus ... ok 1300s test_Dialign_tool ... ok 1300s test_EMBL_unittest ... ok 1300s test_Emboss ... skipping. $EMBOSS_ROOT='/usr/lib/emboss' which does not exist! 1300s test_EmbossPrimer ... ok 1304s test_Entrez ... ok 1304s test_Entrez_online ... skipping. internet not available 1305s test_Entrez_parser ... ok 1305s test_Enzyme ... ok 1305s test_ExPASy ... skipping. internet not available 1305s test_Fasttree_tool ... ok 1305s test_File ... ok 1305s test_GenBank ... /usr/lib/python3/dist-packages/Bio/SeqIO/InsdcIO.py:600: BiopythonWarning: Annotation 'Sequence Read Archive: SRX001885, SRX001121, SRX001531, SRX001530, SRX001529' too long 1305s warnings.warn(f"Annotation {text!r} too long", BiopythonWarning) 1306s ok 1308s test_GenomeDiagram ... Warn: Can't find .pfb for face 'Helvetica' 1310s ok 1310s test_GraphicsChromosome ... ok 1310s test_GraphicsDistribution ... ok 1311s test_GraphicsGeneral ... ok 1311s test_HMMCasino ... ok 1312s test_HMMGeneral ... ok 1312s test_KEGG ... ok 1312s test_KEGG_online ... skipping. internet not available 1317s test_KGML_graphics ... ok 1317s test_KGML_graphics_online ... skipping. internet not available 1318s test_KGML_nographics ... ok 1318s test_KeyWList ... ok 1318s test_LogisticRegression ... ok 1319s test_MafIO_index ... ok 1322s test_Mafft_tool ... ok 1322s test_MarkovModel ... ok 1322s test_Medline ... ok 1322s test_Muscle_tool ... skipping. Install MUSCLE if you want to use the Bio.Align.Applications wrapper. 1323s test_NCBIXML ... Exception ignored in: 1323s Traceback (most recent call last): 1323s File "/usr/lib/python3/dist-packages/Bio/Blast/NCBIXML.py", line 1319, in parse 1323s expat_parser.Parse(NULL, True) 1323s xml.parsers.expat.ExpatError: unclosed token: line 320, column 0 1323s ok 1326s test_NCBI_BLAST_tools ... ok 1327s test_NCBI_qblast ... ok 1327s test_NMR ... ok 1327s test_NaiveBayes ... ok 1327s test_Nexus ... ok 1327s test_PAML_baseml ... ok 1328s test_PAML_codeml ... ok 1328s test_PAML_yn00 ... ok 1334s test_PDB_CEAligner ... ok 1336s test_PDB_DSSP ... ok 1336s test_PDB_Dice ... ok 1336s test_PDB_Disordered ... ok 1336s test_PDB_Exposure ... ok 1337s test_PDB_FragmentMapper ... ok 1339s test_PDB_KDTree ... ok 1339s test_PDB_MMCIF2Dict ... ok 1339s test_PDB_MMCIFIO ... ok 1340s test_PDB_MMCIFParser ... ok 1340s test_PDB_NACCESS ... ok 1341s test_PDB_PDBIO ... ok 1341s test_PDB_PDBList ... skipping. internet not available 1348s test_PDB_PDBMLParser ... ok 1348s test_PDB_PDBParser ... ok 1348s 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 1349s test_PDB_Polypeptide ... ok 1349s test_PDB_QCPSuperimposer ... ok 1352s test_PDB_SASA ... ok 1353s test_PDB_SMCRA ... ok 1354s test_PDB_Selection ... ok 1354s test_PDB_StructureAlignment ... ok 1354s test_PDB_Superimposer ... ok 1354s test_PDB_alphafold_db ... skipping. internet not available 1358s test_PDB_binary_cif ... /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 1, ' ') redefined at line 7. 1358s warnings.warn( 1358s /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 15, ' ') redefined at line 144. 1358s warnings.warn( 1358s /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 15, ' ') redefined at line 153. 1358s warnings.warn( 1358s /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 1, ' ') redefined at line 0. 1358s warnings.warn( 1358s /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 15, ' ') redefined at line 0. 1358s warnings.warn( 1358s ok 1368s test_PDB_internal_coords ... ok 1368s test_PDB_parse_pdb_header ... ok 1368s test_PDB_vectors ... ok 1369s test_PQR ... ok 1369s test_Pathway ... ok 1370s test_Phd ... ok 1370s test_Phylo ... ok 1371s test_PhyloXML ... ok 1372s test_Phylo_CDAO ... ok 1372s test_Phylo_NeXML ... ok 1373s test_Phylo_igraph ... ok 1377s test_Phylo_matplotlib ... ok 1378s test_Phylo_networkx ... ok 1379s test_PopGen_GenePop_nodepend ... ok 1382s test_Prank_tool ... ok 1384s test_Probcons_tool ... ok 1385s test_ProtParam ... ok 1386s test_RCSBFormats ... ok 1387s test_Restriction ... ok 1388s test_SCOP_Astral ... ok 1389s test_SCOP_Cla ... ok 1390s test_SCOP_Des ... ok 1391s test_SCOP_Dom ... ok 1392s test_SCOP_Hie ... ok 1393s test_SCOP_Raf ... ok 1395s test_SCOP_Residues ... ok 1396s test_SCOP_Scop ... ok 1397s test_SVDSuperimposer ... ok 1398s test_SearchIO_blast_tab ... ok 1399s test_SearchIO_blast_tab_index ... ok 1400s test_SearchIO_blast_xml ... ok 1402s test_SearchIO_blast_xml_index ... ok 1403s test_SearchIO_blat_psl ... ok 1405s test_SearchIO_blat_psl_index ... ok 1406s test_SearchIO_exonerate ... ok 1406s test_SearchIO_exonerate_text_index ... ok 1407s test_SearchIO_exonerate_vulgar_index ... ok 1409s test_SearchIO_fasta_m10 ... ok 1410s test_SearchIO_fasta_m10_index ... ok 1411s test_SearchIO_hhsuite2_text ... ok 1412s test_SearchIO_hmmer2_text ... ok 1413s test_SearchIO_hmmer2_text_index ... ok 1414s test_SearchIO_hmmer3_domtab ... ok 1415s test_SearchIO_hmmer3_domtab_index ... ok 1416s test_SearchIO_hmmer3_tab ... ok 1417s test_SearchIO_hmmer3_tab_index ... ok 1418s test_SearchIO_hmmer3_text ... ok 1419s test_SearchIO_hmmer3_text_index ... ok 1420s test_SearchIO_interproscan_xml ... ok 1420s test_SearchIO_model ... ok 1422s test_SearchIO_write ... ok 1423s test_SeqFeature ... ok 1441s test_SeqIO ... ok 1442s test_SeqIO_AbiIO ... ok 1443s test_SeqIO_FastaIO ... ok 1444s test_SeqIO_Gck ... ok 1445s test_SeqIO_Gfa ... ok 1446s test_SeqIO_Insdc ... ok 1447s test_SeqIO_NibIO ... ok 1450s test_SeqIO_PdbIO ... ok 1451s test_SeqIO_QualityIO ... ok 1452s test_SeqIO_SeqXML ... ok 1453s test_SeqIO_SffIO ... ok 1454s test_SeqIO_SnapGene ... ok 1456s test_SeqIO_TwoBitIO ... ok 1457s test_SeqIO_UniprotIO ... ok 1458s test_SeqIO_Xdna ... ok 1460s test_SeqIO_features ... ok 1477s test_SeqIO_index ... ok 1478s test_SeqIO_online ... skipping. internet not available 1479s test_SeqIO_write ... ok 1480s test_SeqRecord ... ok 1481s test_SeqUtils ... ok 1483s test_Seq_objs ... ok 1484s test_SwissProt ... ok 1488s test_TCoffee_tool ... ok 1489s test_TogoWS ... skipping. internet not available 1490s test_TreeConstruction ... ok 1491s test_Tutorial ... skipping. Could not find ../Doc/Tutorial/index.rst file 1492s test_UniGene ... ok 1493s test_UniProt ... skipping. internet not available 1494s test_UniProt_GOA ... ok 1495s test_align ... ok 1497s test_align_substitution_matrices ... ok 1500s test_bgzf ... ok 1501s test_cellosaurus ... ok 1508s test_codonalign ... ok 1509s test_geo ... ok 1510s test_kNN ... ok 1511s test_motifs ... ok 1512s test_motifs_online ... skipping. internet not available 1513s 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. 1513s warnings.warn( 1513s ok 1514s test_pairwise2_no_C ... ok 1515s test_pairwise_aligner ... ok 1516s test_pairwise_alignment_map ... ok 1525s test_phenotype ... ok 1526s test_phenotype_fit ... ok 1527s 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. 1528s test_prodoc ... ok 1529s test_prosite ... ok 1530s test_raxml_tool ... skipping. Install RAxML (binary raxmlHPC) if you want to test the Bio.Phylo.Applications wrapper. 1531s test_samtools_tool ... skipping. Install samtools and correctly set the file path to the program if you want to use it from Biopython 1532s test_seq ... ok 1533s test_translate ... ok 1534s ---------------------------------------------------------------------- 1534s Ran 218 tests in 262.843 seconds 1534s 1534s Skipping any tests requiring internet access 1534s Python version: 3.13.2 (main, Feb 5 2025, 01:23:35) [GCC 14.2.0] 1534s Operating system: posix linux 1535s :0: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/protein_lib.fa' mode='rt' encoding='UTF-8'> 1535s :0: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/nucleotide_lib.fa' mode='rt' encoding='UTF-8'> 1537s autopkgtest [12:57:47]: test full_suite: -----------------------] 1541s full_suite PASS 1541s autopkgtest [12:57:51]: test full_suite: - - - - - - - - - - results - - - - - - - - - - 1546s autopkgtest [12:57:56]: @@@@@@@@@@@@@@@@@@@@ summary 1546s dependencies PASS 1546s full_suite PASS