0s autopkgtest [21:33:54]: starting date and time: 2024-11-14 21:33:54+0000 0s autopkgtest [21:33:54]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [21:33:54]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.3jxmaxdz/out --timeout-copy=6000 --setup-commands 'ln -s /dev/null /etc/systemd/system/bluetooth.service; printf "http_proxy=http://squid.internal:3128\nhttps_proxy=http://squid.internal:3128\nno_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com\n" >> /etc/environment' --apt-pocket=proposed=src:python-biopython --apt-upgrade python-biopython --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=python-biopython/1.84+dfsg-4build1 -- lxd -r lxd-armhf-10.145.243.76 lxd-armhf-10.145.243.76:autopkgtest/ubuntu/plucky/armhf 57s autopkgtest [21:34:51]: testbed dpkg architecture: armhf 59s autopkgtest [21:34:53]: testbed apt version: 2.9.8 59s autopkgtest [21:34:53]: @@@@@@@@@@@@@@@@@@@@ test bed setup 67s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 67s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [16.1 kB] 68s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [1037 kB] 68s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 68s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [106 kB] 68s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf Packages [115 kB] 68s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf Packages [741 kB] 68s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf Packages [4136 B] 68s Fetched 2100 kB in 1s (1930 kB/s) 68s Reading package lists... 86s tee: /proc/self/fd/2: Permission denied 108s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 108s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 108s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 109s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 110s Reading package lists... 111s Reading package lists... 111s Building dependency tree... 111s Reading state information... 112s Calculating upgrade... 113s The following packages will be upgraded: 113s libcap-ng0 pastebinit python3-systemd 113s 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 113s Need to get 72.8 kB of archives. 113s After this operation, 89.1 kB of additional disk space will be used. 113s Get:1 http://ftpmaster.internal/ubuntu plucky/main armhf libcap-ng0 armhf 0.8.5-3build1 [13.8 kB] 113s Get:2 http://ftpmaster.internal/ubuntu plucky/main armhf pastebinit all 1.7.1-1 [14.9 kB] 113s Get:3 http://ftpmaster.internal/ubuntu plucky/main armhf python3-systemd armhf 235-1build5 [44.0 kB] 114s Fetched 72.8 kB in 0s (210 kB/s) 114s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 59560 files and directories currently installed.) 114s Preparing to unpack .../libcap-ng0_0.8.5-3build1_armhf.deb ... 114s Unpacking libcap-ng0:armhf (0.8.5-3build1) over (0.8.5-1) ... 114s Setting up libcap-ng0:armhf (0.8.5-3build1) ... 114s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 59560 files and directories currently installed.) 114s Preparing to unpack .../pastebinit_1.7.1-1_all.deb ... 114s Unpacking pastebinit (1.7.1-1) over (1.7.0-1) ... 114s Preparing to unpack .../python3-systemd_235-1build5_armhf.deb ... 115s Unpacking python3-systemd (235-1build5) over (235-1build4) ... 115s Setting up pastebinit (1.7.1-1) ... 115s Setting up python3-systemd (235-1build5) ... 115s Processing triggers for man-db (2.12.1-3) ... 116s Processing triggers for libc-bin (2.40-1ubuntu3) ... 116s Reading package lists... 117s Building dependency tree... 117s Reading state information... 118s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 120s autopkgtest [21:35:54]: rebooting testbed after setup commands that affected boot 187s autopkgtest [21:37:01]: testbed running kernel: Linux 6.8.0-48-generic #48~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Mon Oct 7 11:49:53 UTC 2 214s autopkgtest [21:37:28]: @@@@@@@@@@@@@@@@@@@@ apt-source python-biopython 233s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/universe python-biopython 1.84+dfsg-4build1 (dsc) [3412 B] 233s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/universe python-biopython 1.84+dfsg-4build1 (tar) [14.6 MB] 233s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/universe python-biopython 1.84+dfsg-4build1 (diff) [42.9 kB] 233s gpgv: Signature made Thu Nov 14 18:31:06 2024 UTC 233s gpgv: using RSA key 568BF22A66337CBFC9A6B9B72C83DBC8E9BD0E37 233s gpgv: Can't check signature: No public key 233s dpkg-source: warning: cannot verify inline signature for ./python-biopython_1.84+dfsg-4build1.dsc: no acceptable signature found 234s autopkgtest [21:37:48]: testing package python-biopython version 1.84+dfsg-4build1 236s autopkgtest [21:37:50]: build not needed 242s autopkgtest [21:37:56]: test dependencies: preparing testbed 252s Reading package lists... 253s Building dependency tree... 253s Reading state information... 254s Starting pkgProblemResolver with broken count: 0 254s Starting 2 pkgProblemResolver with broken count: 0 254s Done 255s The following additional packages will be installed: 255s fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-urw-base35 255s libblas3 libcairo2 libdeflate0 libfontconfig1 libfontenc1 libfreetype6 255s libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libimagequant0 libjbig0 255s libjpeg-turbo8 libjpeg8 libjs-jquery libjs-sphinxdoc libjs-underscore 255s liblapack3 liblcms2-2 liblerc4 libopenjp2-7 libpixman-1-0 libraqm0 255s libsharpyuv0 libtiff6 libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 255s libxcb-shm0 libxrender1 python-biopython-doc python3-all python3-biopython 255s python3-biopython-sql python3-cairo python3-freetype python3-numpy 255s python3-pil python3-reportlab python3-rlpycairo sgml-base w3c-sgml-lib 255s x11-common xfonts-encodings xfonts-utils xml-core 255s Suggested packages: 255s fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre liblcms2-utils 255s python3-tk bwa clustalo clustalw dialign dssp emboss fasttree mafft muscle3 255s phylip phyml prank probcons python3-mysqldb python3-matplotlib python3-mmtf 255s python3-rdflib python3-psycopg2 python3-scipy raxml samtools t-coffee wise 255s gcc gfortran python-numpy-doc python3-dev python3-pytest python-pil-doc 255s pdf-viewer python3-egenix-mxtexttools python-reportlab-doc rl-accel 255s rl-renderpm sgml-base-doc debhelper 255s Recommended packages: 255s javascript-common ncbi-blast+ python3-olefile fonts-dejavu-extra 255s The following NEW packages will be installed: 255s autopkgtest-satdep fontconfig-config fonts-dejavu-core fonts-dejavu-mono 255s fonts-urw-base35 libblas3 libcairo2 libdeflate0 libfontconfig1 libfontenc1 255s libfreetype6 libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b 255s libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 libjs-jquery libjs-sphinxdoc 255s libjs-underscore liblapack3 liblcms2-2 liblerc4 libopenjp2-7 libpixman-1-0 255s libraqm0 libsharpyuv0 libtiff6 libwebp7 libwebpdemux2 libwebpmux3 255s libxcb-render0 libxcb-shm0 libxrender1 python-biopython-doc python3-all 255s python3-biopython python3-biopython-sql python3-cairo python3-freetype 255s python3-numpy python3-pil python3-reportlab python3-rlpycairo sgml-base 255s w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core 255s 0 upgraded, 52 newly installed, 0 to remove and 0 not upgraded. 255s Need to get 44.6 MB/44.6 MB of archives. 255s After this operation, 111 MB of additional disk space will be used. 255s Get:1 /tmp/autopkgtest.BXh6wC/1-autopkgtest-satdep.deb autopkgtest-satdep armhf 0 [732 B] 256s Get:2 http://ftpmaster.internal/ubuntu plucky/main armhf sgml-base all 1.31 [11.4 kB] 256s Get:3 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-dejavu-mono all 2.37-8 [502 kB] 256s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-dejavu-core all 2.37-8 [835 kB] 256s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf libfontenc1 armhf 1:1.1.8-1build1 [11.5 kB] 256s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf libfreetype6 armhf 2.13.3+dfsg-1 [330 kB] 256s Get:7 http://ftpmaster.internal/ubuntu plucky/main armhf x11-common all 1:7.7+23ubuntu3 [21.7 kB] 256s Get:8 http://ftpmaster.internal/ubuntu plucky/main armhf xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 256s Get:9 http://ftpmaster.internal/ubuntu plucky/main armhf xfonts-utils armhf 1:7.7+7 [90.6 kB] 256s Get:10 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-urw-base35 all 20200910-8 [11.0 MB] 256s Get:11 http://ftpmaster.internal/ubuntu plucky/main armhf fontconfig-config armhf 2.15.0-1.1ubuntu2 [37.4 kB] 256s Get:12 http://ftpmaster.internal/ubuntu plucky/main armhf libblas3 armhf 3.12.0-3build2 [126 kB] 256s Get:13 http://ftpmaster.internal/ubuntu plucky/main armhf libfontconfig1 armhf 2.15.0-1.1ubuntu2 [113 kB] 256s Get:14 http://ftpmaster.internal/ubuntu plucky/main armhf libpixman-1-0 armhf 0.44.0-3 [183 kB] 256s Get:15 http://ftpmaster.internal/ubuntu plucky/main armhf libxcb-render0 armhf 1.17.0-2 [15.3 kB] 256s Get:16 http://ftpmaster.internal/ubuntu plucky/main armhf libxcb-shm0 armhf 1.17.0-2 [5774 B] 256s Get:17 http://ftpmaster.internal/ubuntu plucky/main armhf libxrender1 armhf 1:0.9.10-1.1build1 [16.0 kB] 256s Get:18 http://ftpmaster.internal/ubuntu plucky/main armhf libcairo2 armhf 1.18.2-2 [484 kB] 256s Get:19 http://ftpmaster.internal/ubuntu plucky/main armhf libdeflate0 armhf 1.22-1 [38.9 kB] 256s Get:20 http://ftpmaster.internal/ubuntu plucky/main armhf libgfortran5 armhf 14.2.0-8ubuntu1 [311 kB] 256s Get:21 http://ftpmaster.internal/ubuntu plucky/main armhf libgomp1 armhf 14.2.0-8ubuntu1 [125 kB] 256s Get:22 http://ftpmaster.internal/ubuntu plucky/main armhf libgraphite2-3 armhf 1.3.14-2ubuntu1 [64.8 kB] 256s Get:23 http://ftpmaster.internal/ubuntu plucky/main armhf libharfbuzz0b armhf 10.0.1-1 [463 kB] 256s Get:24 http://ftpmaster.internal/ubuntu plucky/main armhf libimagequant0 armhf 2.18.0-1build1 [31.1 kB] 256s Get:25 http://ftpmaster.internal/ubuntu plucky/main armhf libjpeg-turbo8 armhf 2.1.5-2ubuntu2 [125 kB] 256s Get:26 http://ftpmaster.internal/ubuntu plucky/main armhf libjpeg8 armhf 8c-2ubuntu11 [2148 B] 256s Get:27 http://ftpmaster.internal/ubuntu plucky/main armhf libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 256s Get:28 http://ftpmaster.internal/ubuntu plucky/main armhf libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 256s Get:29 http://ftpmaster.internal/ubuntu plucky/main armhf libjs-sphinxdoc all 7.4.7-4 [158 kB] 257s Get:30 http://ftpmaster.internal/ubuntu plucky/main armhf liblapack3 armhf 3.12.0-3build2 [2086 kB] 257s Get:31 http://ftpmaster.internal/ubuntu plucky/main armhf liblcms2-2 armhf 2.16-2 [137 kB] 257s Get:32 http://ftpmaster.internal/ubuntu plucky/main armhf liblerc4 armhf 4.0.0+ds-4ubuntu2 [151 kB] 257s Get:33 http://ftpmaster.internal/ubuntu plucky/main armhf libraqm0 armhf 0.10.1-1build1 [12.4 kB] 257s Get:34 http://ftpmaster.internal/ubuntu plucky/main armhf libsharpyuv0 armhf 1.4.0-0.1 [16.3 kB] 257s Get:35 http://ftpmaster.internal/ubuntu plucky/main armhf libjbig0 armhf 2.1-6.1ubuntu2 [24.9 kB] 257s Get:36 http://ftpmaster.internal/ubuntu plucky/main armhf libwebp7 armhf 1.4.0-0.1 [184 kB] 257s Get:37 http://ftpmaster.internal/ubuntu plucky/main armhf libtiff6 armhf 4.5.1+git230720-4ubuntu4 [179 kB] 257s Get:38 http://ftpmaster.internal/ubuntu plucky/main armhf libwebpdemux2 armhf 1.4.0-0.1 [11.8 kB] 257s Get:39 http://ftpmaster.internal/ubuntu plucky/main armhf libwebpmux3 armhf 1.4.0-0.1 [22.5 kB] 257s Get:40 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf python-biopython-doc all 1.84+dfsg-4build1 [18.1 MB] 257s Get:41 http://ftpmaster.internal/ubuntu plucky/main armhf python3-all armhf 3.12.6-0ubuntu1 [886 B] 257s Get:42 http://ftpmaster.internal/ubuntu plucky/main armhf python3-numpy armhf 1:1.26.4+ds-11build1 [3570 kB] 257s Get:43 http://ftpmaster.internal/ubuntu plucky/main armhf libopenjp2-7 armhf 2.5.0-2ubuntu1 [170 kB] 257s Get:44 http://ftpmaster.internal/ubuntu plucky/main armhf python3-pil armhf 10.4.0-1ubuntu1 [428 kB] 257s Get:45 http://ftpmaster.internal/ubuntu plucky/main armhf python3-cairo armhf 1.26.1-2 [114 kB] 257s Get:46 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-freetype all 2.5.1-1 [92.3 kB] 257s Get:47 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-rlpycairo all 0.3.0-3 [9130 B] 257s Get:48 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-reportlab all 4.2.5-1 [1107 kB] 257s Get:49 http://ftpmaster.internal/ubuntu plucky/main armhf xml-core all 0.19 [20.3 kB] 257s Get:50 http://ftpmaster.internal/ubuntu plucky/universe armhf w3c-sgml-lib all 1.3-3 [280 kB] 257s Get:51 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf python3-biopython armhf 1.84+dfsg-4build1 [1672 kB] 257s Get:52 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf python3-biopython-sql all 1.84+dfsg-4build1 [26.4 kB] 258s Fetched 44.6 MB in 2s (22.1 MB/s) 258s Selecting previously unselected package sgml-base. 258s (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 ... 59565 files and directories currently installed.) 258s Preparing to unpack .../00-sgml-base_1.31_all.deb ... 258s Unpacking sgml-base (1.31) ... 258s Selecting previously unselected package fonts-dejavu-mono. 258s Preparing to unpack .../01-fonts-dejavu-mono_2.37-8_all.deb ... 258s Unpacking fonts-dejavu-mono (2.37-8) ... 258s Selecting previously unselected package fonts-dejavu-core. 258s Preparing to unpack .../02-fonts-dejavu-core_2.37-8_all.deb ... 258s Unpacking fonts-dejavu-core (2.37-8) ... 258s Selecting previously unselected package libfontenc1:armhf. 258s Preparing to unpack .../03-libfontenc1_1%3a1.1.8-1build1_armhf.deb ... 258s Unpacking libfontenc1:armhf (1:1.1.8-1build1) ... 258s Selecting previously unselected package libfreetype6:armhf. 258s Preparing to unpack .../04-libfreetype6_2.13.3+dfsg-1_armhf.deb ... 258s Unpacking libfreetype6:armhf (2.13.3+dfsg-1) ... 259s Selecting previously unselected package x11-common. 259s Preparing to unpack .../05-x11-common_1%3a7.7+23ubuntu3_all.deb ... 259s Unpacking x11-common (1:7.7+23ubuntu3) ... 259s Selecting previously unselected package xfonts-encodings. 259s Preparing to unpack .../06-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 259s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 259s Selecting previously unselected package xfonts-utils. 259s Preparing to unpack .../07-xfonts-utils_1%3a7.7+7_armhf.deb ... 259s Unpacking xfonts-utils (1:7.7+7) ... 259s Selecting previously unselected package fonts-urw-base35. 259s Preparing to unpack .../08-fonts-urw-base35_20200910-8_all.deb ... 259s Unpacking fonts-urw-base35 (20200910-8) ... 259s Selecting previously unselected package fontconfig-config. 259s Preparing to unpack .../09-fontconfig-config_2.15.0-1.1ubuntu2_armhf.deb ... 260s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ... 260s Selecting previously unselected package libblas3:armhf. 260s Preparing to unpack .../10-libblas3_3.12.0-3build2_armhf.deb ... 260s Unpacking libblas3:armhf (3.12.0-3build2) ... 260s Selecting previously unselected package libfontconfig1:armhf. 260s Preparing to unpack .../11-libfontconfig1_2.15.0-1.1ubuntu2_armhf.deb ... 260s Unpacking libfontconfig1:armhf (2.15.0-1.1ubuntu2) ... 260s Selecting previously unselected package libpixman-1-0:armhf. 260s Preparing to unpack .../12-libpixman-1-0_0.44.0-3_armhf.deb ... 260s Unpacking libpixman-1-0:armhf (0.44.0-3) ... 260s Selecting previously unselected package libxcb-render0:armhf. 260s Preparing to unpack .../13-libxcb-render0_1.17.0-2_armhf.deb ... 260s Unpacking libxcb-render0:armhf (1.17.0-2) ... 260s Selecting previously unselected package libxcb-shm0:armhf. 260s Preparing to unpack .../14-libxcb-shm0_1.17.0-2_armhf.deb ... 260s Unpacking libxcb-shm0:armhf (1.17.0-2) ... 260s Selecting previously unselected package libxrender1:armhf. 260s Preparing to unpack .../15-libxrender1_1%3a0.9.10-1.1build1_armhf.deb ... 260s Unpacking libxrender1:armhf (1:0.9.10-1.1build1) ... 260s Selecting previously unselected package libcairo2:armhf. 260s Preparing to unpack .../16-libcairo2_1.18.2-2_armhf.deb ... 260s Unpacking libcairo2:armhf (1.18.2-2) ... 260s Selecting previously unselected package libdeflate0:armhf. 260s Preparing to unpack .../17-libdeflate0_1.22-1_armhf.deb ... 260s Unpacking libdeflate0:armhf (1.22-1) ... 260s Selecting previously unselected package libgfortran5:armhf. 260s Preparing to unpack .../18-libgfortran5_14.2.0-8ubuntu1_armhf.deb ... 260s Unpacking libgfortran5:armhf (14.2.0-8ubuntu1) ... 260s Selecting previously unselected package libgomp1:armhf. 260s Preparing to unpack .../19-libgomp1_14.2.0-8ubuntu1_armhf.deb ... 260s Unpacking libgomp1:armhf (14.2.0-8ubuntu1) ... 260s Selecting previously unselected package libgraphite2-3:armhf. 260s Preparing to unpack .../20-libgraphite2-3_1.3.14-2ubuntu1_armhf.deb ... 260s Unpacking libgraphite2-3:armhf (1.3.14-2ubuntu1) ... 260s Selecting previously unselected package libharfbuzz0b:armhf. 260s Preparing to unpack .../21-libharfbuzz0b_10.0.1-1_armhf.deb ... 260s Unpacking libharfbuzz0b:armhf (10.0.1-1) ... 260s Selecting previously unselected package libimagequant0:armhf. 260s Preparing to unpack .../22-libimagequant0_2.18.0-1build1_armhf.deb ... 260s Unpacking libimagequant0:armhf (2.18.0-1build1) ... 260s Selecting previously unselected package libjpeg-turbo8:armhf. 260s Preparing to unpack .../23-libjpeg-turbo8_2.1.5-2ubuntu2_armhf.deb ... 260s Unpacking libjpeg-turbo8:armhf (2.1.5-2ubuntu2) ... 260s Selecting previously unselected package libjpeg8:armhf. 260s Preparing to unpack .../24-libjpeg8_8c-2ubuntu11_armhf.deb ... 260s Unpacking libjpeg8:armhf (8c-2ubuntu11) ... 261s Selecting previously unselected package libjs-jquery. 261s Preparing to unpack .../25-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 261s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 261s Selecting previously unselected package libjs-underscore. 261s Preparing to unpack .../26-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 261s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 261s Selecting previously unselected package libjs-sphinxdoc. 261s Preparing to unpack .../27-libjs-sphinxdoc_7.4.7-4_all.deb ... 261s Unpacking libjs-sphinxdoc (7.4.7-4) ... 261s Selecting previously unselected package liblapack3:armhf. 261s Preparing to unpack .../28-liblapack3_3.12.0-3build2_armhf.deb ... 261s Unpacking liblapack3:armhf (3.12.0-3build2) ... 261s Selecting previously unselected package liblcms2-2:armhf. 261s Preparing to unpack .../29-liblcms2-2_2.16-2_armhf.deb ... 261s Unpacking liblcms2-2:armhf (2.16-2) ... 261s Selecting previously unselected package liblerc4:armhf. 261s Preparing to unpack .../30-liblerc4_4.0.0+ds-4ubuntu2_armhf.deb ... 261s Unpacking liblerc4:armhf (4.0.0+ds-4ubuntu2) ... 261s Selecting previously unselected package libraqm0:armhf. 261s Preparing to unpack .../31-libraqm0_0.10.1-1build1_armhf.deb ... 261s Unpacking libraqm0:armhf (0.10.1-1build1) ... 261s Selecting previously unselected package libsharpyuv0:armhf. 261s Preparing to unpack .../32-libsharpyuv0_1.4.0-0.1_armhf.deb ... 261s Unpacking libsharpyuv0:armhf (1.4.0-0.1) ... 261s Selecting previously unselected package libjbig0:armhf. 261s Preparing to unpack .../33-libjbig0_2.1-6.1ubuntu2_armhf.deb ... 261s Unpacking libjbig0:armhf (2.1-6.1ubuntu2) ... 261s Selecting previously unselected package libwebp7:armhf. 261s Preparing to unpack .../34-libwebp7_1.4.0-0.1_armhf.deb ... 261s Unpacking libwebp7:armhf (1.4.0-0.1) ... 261s Selecting previously unselected package libtiff6:armhf. 261s Preparing to unpack .../35-libtiff6_4.5.1+git230720-4ubuntu4_armhf.deb ... 261s Unpacking libtiff6:armhf (4.5.1+git230720-4ubuntu4) ... 261s Selecting previously unselected package libwebpdemux2:armhf. 261s Preparing to unpack .../36-libwebpdemux2_1.4.0-0.1_armhf.deb ... 261s Unpacking libwebpdemux2:armhf (1.4.0-0.1) ... 261s Selecting previously unselected package libwebpmux3:armhf. 261s Preparing to unpack .../37-libwebpmux3_1.4.0-0.1_armhf.deb ... 261s Unpacking libwebpmux3:armhf (1.4.0-0.1) ... 261s Selecting previously unselected package python-biopython-doc. 261s Preparing to unpack .../38-python-biopython-doc_1.84+dfsg-4build1_all.deb ... 261s Unpacking python-biopython-doc (1.84+dfsg-4build1) ... 262s Selecting previously unselected package python3-all. 262s Preparing to unpack .../39-python3-all_3.12.6-0ubuntu1_armhf.deb ... 262s Unpacking python3-all (3.12.6-0ubuntu1) ... 262s Selecting previously unselected package python3-numpy. 262s Preparing to unpack .../40-python3-numpy_1%3a1.26.4+ds-11build1_armhf.deb ... 262s Unpacking python3-numpy (1:1.26.4+ds-11build1) ... 262s Selecting previously unselected package libopenjp2-7:armhf. 262s Preparing to unpack .../41-libopenjp2-7_2.5.0-2ubuntu1_armhf.deb ... 262s Unpacking libopenjp2-7:armhf (2.5.0-2ubuntu1) ... 262s Selecting previously unselected package python3-pil:armhf. 263s Preparing to unpack .../42-python3-pil_10.4.0-1ubuntu1_armhf.deb ... 263s Unpacking python3-pil:armhf (10.4.0-1ubuntu1) ... 263s Selecting previously unselected package python3-cairo. 263s Preparing to unpack .../43-python3-cairo_1.26.1-2_armhf.deb ... 263s Unpacking python3-cairo (1.26.1-2) ... 263s Selecting previously unselected package python3-freetype. 263s Preparing to unpack .../44-python3-freetype_2.5.1-1_all.deb ... 263s Unpacking python3-freetype (2.5.1-1) ... 263s Selecting previously unselected package python3-rlpycairo. 263s Preparing to unpack .../45-python3-rlpycairo_0.3.0-3_all.deb ... 263s Unpacking python3-rlpycairo (0.3.0-3) ... 263s Selecting previously unselected package python3-reportlab. 263s Preparing to unpack .../46-python3-reportlab_4.2.5-1_all.deb ... 263s Unpacking python3-reportlab (4.2.5-1) ... 263s Selecting previously unselected package xml-core. 263s Preparing to unpack .../47-xml-core_0.19_all.deb ... 263s Unpacking xml-core (0.19) ... 263s Selecting previously unselected package w3c-sgml-lib. 263s Preparing to unpack .../48-w3c-sgml-lib_1.3-3_all.deb ... 263s Unpacking w3c-sgml-lib (1.3-3) ... 263s Selecting previously unselected package python3-biopython. 263s Preparing to unpack .../49-python3-biopython_1.84+dfsg-4build1_armhf.deb ... 263s Unpacking python3-biopython (1.84+dfsg-4build1) ... 264s Selecting previously unselected package python3-biopython-sql. 264s Preparing to unpack .../50-python3-biopython-sql_1.84+dfsg-4build1_all.deb ... 264s Unpacking python3-biopython-sql (1.84+dfsg-4build1) ... 264s Selecting previously unselected package autopkgtest-satdep. 264s Preparing to unpack .../51-1-autopkgtest-satdep.deb ... 264s Unpacking autopkgtest-satdep (0) ... 264s Setting up libgraphite2-3:armhf (1.3.14-2ubuntu1) ... 264s Setting up liblcms2-2:armhf (2.16-2) ... 264s Setting up libpixman-1-0:armhf (0.44.0-3) ... 264s Setting up libsharpyuv0:armhf (1.4.0-0.1) ... 264s Setting up liblerc4:armhf (4.0.0+ds-4ubuntu2) ... 264s Setting up libxrender1:armhf (1:0.9.10-1.1build1) ... 264s Setting up libxcb-render0:armhf (1.17.0-2) ... 264s Setting up x11-common (1:7.7+23ubuntu3) ... 265s Setting up libdeflate0:armhf (1.22-1) ... 265s Setting up python3-all (3.12.6-0ubuntu1) ... 265s Setting up libxcb-shm0:armhf (1.17.0-2) ... 265s Setting up libgomp1:armhf (14.2.0-8ubuntu1) ... 265s Setting up libjbig0:armhf (2.1-6.1ubuntu2) ... 265s Setting up libfontenc1:armhf (1:1.1.8-1build1) ... 265s Setting up libblas3:armhf (3.12.0-3build2) ... 265s 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 265s Setting up libfreetype6:armhf (2.13.3+dfsg-1) ... 265s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 265s Setting up libimagequant0:armhf (2.18.0-1build1) ... 265s Setting up fonts-dejavu-mono (2.37-8) ... 265s Setting up fonts-dejavu-core (2.37-8) ... 265s Setting up libjpeg-turbo8:armhf (2.1.5-2ubuntu2) ... 265s Setting up libgfortran5:armhf (14.2.0-8ubuntu1) ... 265s Setting up libwebp7:armhf (1.4.0-0.1) ... 265s Setting up libopenjp2-7:armhf (2.5.0-2ubuntu1) ... 265s Setting up libharfbuzz0b:armhf (10.0.1-1) ... 265s Setting up sgml-base (1.31) ... 265s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 265s Setting up libwebpmux3:armhf (1.4.0-0.1) ... 265s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 265s Setting up libjpeg8:armhf (8c-2ubuntu11) ... 265s Setting up liblapack3:armhf (3.12.0-3build2) ... 265s 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 265s Setting up fontconfig-config (2.15.0-1.1ubuntu2) ... 265s Setting up libwebpdemux2:armhf (1.4.0-0.1) ... 265s Setting up python3-freetype (2.5.1-1) ... 265s Setting up xfonts-utils (1:7.7+7) ... 265s Setting up libraqm0:armhf (0.10.1-1build1) ... 265s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 268s Setting up libjs-sphinxdoc (7.4.7-4) ... 268s Setting up python-biopython-doc (1.84+dfsg-4build1) ... 268s Setting up libtiff6:armhf (4.5.1+git230720-4ubuntu4) ... 268s Setting up xml-core (0.19) ... 269s Setting up libfontconfig1:armhf (2.15.0-1.1ubuntu2) ... 269s Setting up fonts-urw-base35 (20200910-8) ... 269s Setting up libcairo2:armhf (1.18.2-2) ... 269s Setting up python3-pil:armhf (10.4.0-1ubuntu1) ... 270s Setting up python3-cairo (1.26.1-2) ... 270s Setting up python3-rlpycairo (0.3.0-3) ... 270s Setting up python3-reportlab (4.2.5-1) ... 271s Processing triggers for libc-bin (2.40-1ubuntu3) ... 271s Processing triggers for man-db (2.12.1-3) ... 272s Processing triggers for sgml-base (1.31) ... 272s Setting up w3c-sgml-lib (1.3-3) ... 314s Setting up python3-biopython (1.84+dfsg-4build1) ... 316s Setting up python3-biopython-sql (1.84+dfsg-4build1) ... 316s Setting up autopkgtest-satdep (0) ... 338s (Reading database ... 64988 files and directories currently installed.) 338s Removing autopkgtest-satdep (0) ... 344s autopkgtest [21:39:38]: test dependencies: sh debian/tests/run-unit-test 344s autopkgtest [21:39:38]: test dependencies: [----------------------- 346s cp: cannot stat '/usr/share/libcifpp/mmcif_pdbx.dic': No such file or directory 346s cp: cannot stat '/usr/share/libcifpp/mmcif_ma.dic': No such file or directory 346s cp: cannot stat '/usr/share/doc/python-biopython-doc/Doc/Tutorial': No such file or directory 346s cp: cannot stat '/usr/share/doc/python-biopython-doc/Doc/examples': No such file or directory 350s mkdir: created directory 'Bio' 350s mkdir: created directory 'Bio/Align' 350s mkdir: created directory 'Bio/Align/substitution_matrices' 350s mkdir: created directory 'Bio/Align/substitution_matrices/data/' 350s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER22' -> 'Bio/Align/substitution_matrices/data/BENNER22' 350s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER6' -> 'Bio/Align/substitution_matrices/data/BENNER6' 350s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER74' -> 'Bio/Align/substitution_matrices/data/BENNER74' 350s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLASTN' -> 'Bio/Align/substitution_matrices/data/BLASTN' 350s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLASTP' -> 'Bio/Align/substitution_matrices/data/BLASTP' 350s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM45' -> 'Bio/Align/substitution_matrices/data/BLOSUM45' 350s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM50' -> 'Bio/Align/substitution_matrices/data/BLOSUM50' 350s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM62' -> 'Bio/Align/substitution_matrices/data/BLOSUM62' 350s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM80' -> 'Bio/Align/substitution_matrices/data/BLOSUM80' 350s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM90' -> 'Bio/Align/substitution_matrices/data/BLOSUM90' 350s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/DAYHOFF' -> 'Bio/Align/substitution_matrices/data/DAYHOFF' 350s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/FENG' -> 'Bio/Align/substitution_matrices/data/FENG' 350s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/GENETIC' -> 'Bio/Align/substitution_matrices/data/GENETIC' 350s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/GONNET1992' -> 'Bio/Align/substitution_matrices/data/GONNET1992' 350s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/HOXD70' -> 'Bio/Align/substitution_matrices/data/HOXD70' 350s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/JOHNSON' -> 'Bio/Align/substitution_matrices/data/JOHNSON' 350s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/JONES' -> 'Bio/Align/substitution_matrices/data/JONES' 350s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/LEVIN' -> 'Bio/Align/substitution_matrices/data/LEVIN' 350s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MCLACHLAN' -> 'Bio/Align/substitution_matrices/data/MCLACHLAN' 350s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MDM78' -> 'Bio/Align/substitution_matrices/data/MDM78' 350s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MEGABLAST' -> 'Bio/Align/substitution_matrices/data/MEGABLAST' 350s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/NUC.4.4' -> 'Bio/Align/substitution_matrices/data/NUC.4.4' 350s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM250' -> 'Bio/Align/substitution_matrices/data/PAM250' 350s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM30' -> 'Bio/Align/substitution_matrices/data/PAM30' 350s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM70' -> 'Bio/Align/substitution_matrices/data/PAM70' 350s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/RAO' -> 'Bio/Align/substitution_matrices/data/RAO' 350s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/RISLER' -> 'Bio/Align/substitution_matrices/data/RISLER' 350s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/SCHNEIDER' -> 'Bio/Align/substitution_matrices/data/SCHNEIDER' 350s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/STR' -> 'Bio/Align/substitution_matrices/data/STR' 350s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/TRANS' -> 'Bio/Align/substitution_matrices/data/TRANS' 350s Remove test test_Tutorial.py which is bound to fail 351s test_Ace ... ok 351s test_Affy ... ok 354s test_AlignIO ... ok 354s test_AlignIO_ClustalIO ... ok 354s test_AlignIO_EmbossIO ... ok 354s test_AlignIO_FastaIO ... ok 354s test_AlignIO_MauveIO ... ok 354s test_AlignIO_PhylipIO ... ok 354s test_AlignIO_convert ... ok 354s test_AlignInfo ... ok 355s test_Align_Alignment ... ok 355s test_Align_a2m ... ok 355s test_Align_bed ... ok 355s test_Align_bigbed ... ok 356s test_Align_bigmaf ... ok 356s test_Align_bigpsl ... ok 357s test_Align_chain ... ok 357s test_Align_clustal ... ok 360s test_Align_codonalign ... ok 360s test_Align_emboss ... ok 360s test_Align_exonerate ... ok 360s test_Align_fasta ... ok 361s test_Align_hhr ... ok 362s test_Align_maf ... ok 362s test_Align_mauve ... ok 362s test_Align_msf ... ok 362s test_Align_nexus ... ok 362s test_Align_phylip ... ok 363s test_Align_psl ... ok 363s test_Align_sam ... ok 365s test_Align_stockholm ... ok 366s test_Align_tabular ... ok 366s test_Application ... ok 366s test_BioSQL_MySQLdb_online ... skipping. internet not available 366s test_BioSQL_mysql_connector ... skipping. BioSQL test configuration file biosql.ini missing (see biosql.ini.sample) 366s test_BioSQL_mysql_connector_online ... skipping. internet not available 366s test_BioSQL_psycopg2_online ... skipping. internet not available 372s test_BioSQL_sqlite3 ... ok 372s test_BioSQL_sqlite3_online ... skipping. internet not available 372s test_Blast_Record ... ok 373s test_Blast_parser ... ok 373s test_CAPS ... ok 373s test_Chi2 ... ok 373s test_ClustalOmega_tool ... skipping. Install clustalo if you want to use Clustal Omega from Biopython. 374s test_Clustalw_tool ... skipping. Install clustalw or clustalw2 if you want to use it from Biopython. 374s test_Cluster ... ok 374s test_CodonTable ... ok 374s test_ColorSpiral ... ok 374s test_Compass ... ok 375s test_Consensus ... ok 375s test_Dialign_tool ... skipping. Install DIALIGN2-2 if you want to use the Bio.Align.Applications wrapper. 375s test_EMBL_unittest ... ok 375s test_Emboss ... skipping. $EMBOSS_ROOT='/usr/lib/emboss' which does not exist! 376s test_EmbossPrimer ... ok 380s test_Entrez ... ok 380s test_Entrez_online ... skipping. internet not available 381s test_Entrez_parser ... ok 381s test_Enzyme ... ok 381s test_ExPASy ... skipping. internet not available 381s test_Fasttree_tool ... skipping. Install FastTree and correctly set the file path to the program if you want to use it from Biopython. 381s test_File ... ok 381s test_GenBank ... ok 383s test_GenomeDiagram ... Warn: Can't find .pfb for face 'Helvetica' 386s ok 387s test_GraphicsChromosome ... ok 387s test_GraphicsDistribution ... ok 388s test_GraphicsGeneral ... ok 388s test_HMMCasino ... ok 388s test_HMMGeneral ... ok 388s test_KEGG ... ok 388s test_KEGG_online ... skipping. internet not available 394s test_KGML_graphics ... ok 394s test_KGML_graphics_online ... skipping. internet not available 396s test_KGML_nographics ... ok 396s test_KeyWList ... ok 396s test_LogisticRegression ... ok 397s test_MafIO_index ... ok 397s test_Mafft_tool ... skipping. Install MAFFT if you want to use the Bio.Align.Applications wrapper. 398s test_MarkovModel ... ok 398s test_Medline ... ok 398s test_Muscle_tool ... skipping. Install MUSCLE if you want to use the Bio.Align.Applications wrapper. 399s test_NCBIXML ... ok 399s test_NCBI_BLAST_tools ... skipping. Install the NCBI BLAST+ command line tools if you want to use the Bio.Blast.Applications wrapper. 399s test_NCBI_qblast ... ok 399s test_NMR ... ok 399s test_NaiveBayes ... ok 399s test_Nexus ... ok 400s test_PAML_baseml ... ok 400s test_PAML_codeml ... ok 401s test_PAML_yn00 ... ok 405s test_PDB_CEAligner ... ok 405s test_PDB_DSSP ... ok 405s test_PDB_Dice ... ok 405s test_PDB_Disordered ... ok 406s test_PDB_Exposure ... ok 406s test_PDB_FragmentMapper ... ok 408s test_PDB_KDTree ... ok 408s test_PDB_MMCIF2Dict ... ok 408s test_PDB_MMCIFIO ... ok 410s test_PDB_MMCIFParser ... ok 410s test_PDB_NACCESS ... ok 410s test_PDB_PDBIO ... ok 410s test_PDB_PDBList ... skipping. internet not available 419s test_PDB_PDBMLParser ... ok 419s test_PDB_PDBParser ... ok 419s 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 419s test_PDB_Polypeptide ... ok 420s test_PDB_QCPSuperimposer ... ok 424s test_PDB_SASA ... ok 424s test_PDB_SMCRA ... ok 425s test_PDB_Selection ... ok 425s test_PDB_StructureAlignment ... ok 425s test_PDB_Superimposer ... ok 425s test_PDB_alphafold_db ... skipping. internet not available 425s test_PDB_binary_cif ... skipping. Error: Install msgpack to use Bio.PDB.binaryCIF (e.g. pip install msgpack) 425s 425s test_PDB_internal_coords ... skipping. Error: Install mmtf to use Bio.PDB.mmtf (e.g. pip install mmtf-python) 425s 426s test_PDB_parse_pdb_header ... ok 426s test_PDB_vectors ... ok 426s test_PQR ... ok 426s test_Pathway ... ok 426s test_Phd ... ok 426s test_Phylo ... ok 427s test_PhyloXML ... ok 427s test_Phylo_CDAO ... skipping. Install RDFlib if you want to use the CDAO tree format. 427s test_Phylo_NeXML ... ok 428s test_Phylo_igraph ... skipping. Install igraph if you wish to use it with Bio.Phylo 428s test_Phylo_matplotlib ... skipping. Install matplotlib if you want to use Bio.Phylo._utils. 428s test_Phylo_networkx ... skipping. Install networkx if you wish to use it with Bio.Phylo 428s test_PopGen_GenePop_nodepend ... ok 428s test_Prank_tool ... skipping. Install PRANK if you want to use the Bio.Align.Applications wrapper. 428s test_Probcons_tool ... skipping. Install PROBCONS if you want to use the Bio.Align.Applications wrapper. 428s test_ProtParam ... ok 429s test_RCSBFormats ... ok 429s test_Restriction ... ok 429s test_SCOP_Astral ... ok 429s test_SCOP_Cla ... ok 429s test_SCOP_Des ... ok 429s test_SCOP_Dom ... ok 429s test_SCOP_Hie ... ok 430s test_SCOP_Raf ... ok 430s test_SCOP_Residues ... ok 430s test_SCOP_Scop ... ok 430s test_SVDSuperimposer ... ok 430s test_SearchIO_blast_tab ... ok 430s test_SearchIO_blast_tab_index ... ok 431s test_SearchIO_blast_xml ... ok 432s test_SearchIO_blast_xml_index ... ok 432s test_SearchIO_blat_psl ... ok 432s test_SearchIO_blat_psl_index ... ok 433s test_SearchIO_exonerate ... ok 433s test_SearchIO_exonerate_text_index ... ok 433s test_SearchIO_exonerate_vulgar_index ... ok 433s test_SearchIO_fasta_m10 ... ok 433s test_SearchIO_fasta_m10_index ... ok 433s test_SearchIO_hhsuite2_text ... ok 434s test_SearchIO_hmmer2_text ... ok 434s test_SearchIO_hmmer2_text_index ... ok 434s test_SearchIO_hmmer3_domtab ... ok 434s test_SearchIO_hmmer3_domtab_index ... ok 434s test_SearchIO_hmmer3_tab ... ok 434s test_SearchIO_hmmer3_tab_index ... ok 435s test_SearchIO_hmmer3_text ... ok 435s test_SearchIO_hmmer3_text_index ... ok 435s test_SearchIO_interproscan_xml ... ok 435s test_SearchIO_model ... ok 435s test_SearchIO_write ... ok 436s test_SeqFeature ... ok 455s test_SeqIO ... ok 456s test_SeqIO_AbiIO ... ok 456s test_SeqIO_FastaIO ... ok 456s test_SeqIO_Gck ... ok 456s test_SeqIO_Gfa ... ok 456s test_SeqIO_Insdc ... ok 456s test_SeqIO_NibIO ... ok 459s test_SeqIO_PdbIO ... ok 459s test_SeqIO_QualityIO ... ok 460s test_SeqIO_SeqXML ... ok 460s test_SeqIO_SnapGene ... ok 461s test_SeqIO_TwoBitIO ... ok 461s test_SeqIO_Xdna ... ok 462s test_SeqIO_features ... ok 480s test_SeqIO_index ... ok 480s test_SeqIO_online ... skipping. internet not available 480s test_SeqIO_write ... ok 480s test_SeqRecord ... ok 480s test_SeqUtils ... ok 482s test_Seq_objs ... ok 482s test_SffIO ... ok 482s test_SwissProt ... ok 482s test_TCoffee_tool ... skipping. Install TCOFFEE if you want to use the Bio.Align.Applications wrapper. 482s test_TogoWS ... skipping. internet not available 483s test_TreeConstruction ... ok 483s test_UniGene ... ok 483s test_UniProt ... skipping. internet not available 483s test_UniProt_GOA ... ok 484s test_UniProt_Parser ... ok 484s test_align ... ok 484s test_align_substitution_matrices ... ok 487s test_bgzf ... ok 487s test_cellosaurus ... ok 491s test_codonalign ... ok 492s test_geo ... ok 492s test_kNN ... ok 492s test_motifs ... ok 492s test_motifs_online ... skipping. internet not available 492s 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. 492s warnings.warn( 493s ok 493s test_pairwise2_no_C ... ok 493s test_pairwise_aligner ... ok 493s test_pairwise_alignment_map ... ok 502s test_phenotype ... ok 502s test_phenotype_fit ... skipping. Install SciPy if you want to use Bio.phenotype fit functionality. 502s 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. 503s test_prodoc ... ok 503s test_prosite ... ok 503s test_raxml_tool ... skipping. Install RAxML (binary raxmlHPC) if you want to test the Bio.Phylo.Applications wrapper. 503s test_samtools_tool ... skipping. Install samtools and correctly set the file path to the program if you want to use it from Biopython 503s test_seq ... ok 503s test_translate ... ok 503s Skipping any tests requiring internet access 503s Python version: 3.12.7 (main, Nov 8 2024, 17:55:36) [GCC 14.2.0] 503s Operating system: posix linux 503s ---------------------------------------------------------------------- 503s Ran 217 tests in 152.721 seconds 503s 504s autopkgtest [21:42:18]: test dependencies: -----------------------] 508s autopkgtest [21:42:22]: test dependencies: - - - - - - - - - - results - - - - - - - - - - 508s dependencies PASS 512s autopkgtest [21:42:26]: test full_suite: preparing testbed 567s autopkgtest [21:43:21]: testbed dpkg architecture: armhf 569s autopkgtest [21:43:23]: testbed apt version: 2.9.8 569s autopkgtest [21:43:23]: @@@@@@@@@@@@@@@@@@@@ test bed setup 577s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 577s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [16.1 kB] 577s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 577s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [106 kB] 577s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [1037 kB] 577s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf Packages [115 kB] 577s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf Packages [741 kB] 577s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf Packages [4136 B] 578s Fetched 2100 kB in 1s (2084 kB/s) 578s Reading package lists... 593s tee: /proc/self/fd/2: Permission denied 615s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 615s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 615s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 615s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 617s Reading package lists... 617s Reading package lists... 618s Building dependency tree... 618s Reading state information... 619s Calculating upgrade... 620s The following packages will be upgraded: 620s libcap-ng0 pastebinit python3-systemd 620s 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 620s Need to get 72.8 kB of archives. 620s After this operation, 89.1 kB of additional disk space will be used. 620s Get:1 http://ftpmaster.internal/ubuntu plucky/main armhf libcap-ng0 armhf 0.8.5-3build1 [13.8 kB] 620s Get:2 http://ftpmaster.internal/ubuntu plucky/main armhf pastebinit all 1.7.1-1 [14.9 kB] 620s Get:3 http://ftpmaster.internal/ubuntu plucky/main armhf python3-systemd armhf 235-1build5 [44.0 kB] 621s Fetched 72.8 kB in 0s (209 kB/s) 621s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 59560 files and directories currently installed.) 621s Preparing to unpack .../libcap-ng0_0.8.5-3build1_armhf.deb ... 621s Unpacking libcap-ng0:armhf (0.8.5-3build1) over (0.8.5-1) ... 621s Setting up libcap-ng0:armhf (0.8.5-3build1) ... 621s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 59560 files and directories currently installed.) 621s Preparing to unpack .../pastebinit_1.7.1-1_all.deb ... 621s Unpacking pastebinit (1.7.1-1) over (1.7.0-1) ... 621s Preparing to unpack .../python3-systemd_235-1build5_armhf.deb ... 621s Unpacking python3-systemd (235-1build5) over (235-1build4) ... 621s Setting up pastebinit (1.7.1-1) ... 621s Setting up python3-systemd (235-1build5) ... 621s Processing triggers for man-db (2.12.1-3) ... 622s Processing triggers for libc-bin (2.40-1ubuntu3) ... 622s Reading package lists... 623s Building dependency tree... 623s Reading state information... 624s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 626s autopkgtest [21:44:20]: rebooting testbed after setup commands that affected boot 730s Reading package lists... 730s Building dependency tree... 730s Reading state information... 731s Starting pkgProblemResolver with broken count: 0 731s Starting 2 pkgProblemResolver with broken count: 0 731s Done 732s The following additional packages will be installed: 732s autoconf automake autopoint autotools-dev blt build-essential bwa clustalo 732s cpp cpp-14 cpp-14-arm-linux-gnueabihf cpp-arm-linux-gnueabihf debhelper 732s debugedit dh-autoreconf dh-python dh-strip-nondeterminism dialign 732s docutils-common dssp dwz fasttree flex fontconfig-config fonts-dejavu-core 732s fonts-dejavu-mono fonts-font-awesome fonts-lato fonts-lmodern fonts-lyx 732s fonts-urw-base35 g++ g++-14 g++-14-arm-linux-gnueabihf 732s g++-arm-linux-gnueabihf gcc gcc-14 gcc-14-arm-linux-gnueabihf 732s gcc-arm-linux-gnueabihf gettext ghostscript hevea hicolor-icon-theme 732s imagemagick imagemagick-6-common imagemagick-6.q16 intltool-debian libaom3 732s libapache-pom-java libarchive-zip-perl libargtable2-0 libasan8 732s libavahi-client3 libavahi-common-data libavahi-common3 libblas3 libc-dev-bin 732s libc6-dev libcairo2 libcc1-0 libcifpp-data libcifpp7 libcommons-logging-java 732s libcommons-parent-java libcrypt-dev libcups2t64 libde265-0 libdebhelper-perl 732s libdeflate0 libexpat1-dev libfftw3-double3 libfile-stripnondeterminism-perl 732s libfontbox-java libfontconfig1 libfontenc1 libfreetype6 libgcc-14-dev 732s libgfortran5 libgomp1 libgraphite2-3 libgs-common libgs10 libgs10-common 732s libharfbuzz0b libheif-plugin-aomdec libheif-plugin-libde265 libheif1 libice6 732s libidn12 libijs-0.35 libimagequant0 libisl23 libjbig0 libjbig2dec0 732s libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui libjs-sphinxdoc 732s libjs-underscore libjson-perl libkpathsea6 liblapack3 liblbfgsb0 liblcms2-2 732s liblerc4 liblqr-1-0 libltdl7 libmagickcore-6.q16-7t64 732s libmagickwand-6.q16-7t64 libmbedcrypto7t64 libmbedtls14t64 libmbedx509-1t64 732s libmpc3 libmpfi0 libmysqlclient21 libnetpbm11t64 libopenjp2-7 libpaper-utils 732s libpaper1 libpdfbox-java libpixman-1-0 libpotrace0 libptexenc1 732s libpython3-all-dev libpython3-dev libpython3.12-dev libpython3.12t64 732s libqhull-r8.0 libraqm0 libraw23t64 libsharpyuv0 libsm6 libstdc++-14-dev 732s libsynctex2 libtcl8.6 libteckit0 libtexlua53-5 libtiff6 libtk8.6 libtool 732s libubsan1 libwebp7 libwebpdemux2 libwebpmux3 libxaw7 libxcb-render0 732s libxcb-shm0 libxft2 libxi6 libxmu6 libxpm4 libxrender1 libxslt1.1 libxss1 732s libxt6t64 libzzip-0-13t64 linux-libc-dev m4 mafft mysql-common ncbi-blast+ 732s ncbi-data netpbm phylip po-debconf poppler-data prank preview-latex-style 732s probcons python-biopython-doc python-matplotlib-data python3-alabaster 732s python3-all python3-all-dev python3-appdirs python3-biopython 732s python3-biopython-sql python3-brotli python3-cairo python3-contourpy 732s python3-cycler python3-dateutil python3-decorator python3-defusedxml 732s python3-dev python3-docutils python3-fonttools python3-freetype python3-fs 732s python3-imagesize python3-kiwisolver python3-lxml python3-lz4 732s python3-matplotlib python3-mmtf python3-mpmath python3-msgpack 732s python3-mysqldb python3-networkx python3-numpy python3-numpydoc 732s python3-packaging python3-pil python3-pil.imagetk python3-rdflib 732s python3-reportlab python3-rlpycairo python3-roman python3-scipy python3-six 732s python3-snowballstemmer python3-sphinx python3-sphinx-rtd-theme 732s python3-sphinxcontrib.jquery python3-sympy python3-tabulate python3-tk 732s python3-tz python3-ufolib2 python3.12-dev python3.12-tk rpcsvc-proto 732s sgml-base sphinx-common sphinx-rtd-theme-common t-coffee t1utils tex-common 732s texlive-base texlive-binaries texlive-fonts-recommended texlive-latex-base 732s texlive-latex-extra texlive-latex-recommended texlive-pictures tk8.6-blt2.5 732s unicode-data w3c-sgml-lib wise wise-data x11-common xdg-utils 732s xfonts-encodings xfonts-utils xml-core zlib1g-dev 732s Suggested packages: 732s autoconf-archive gnu-standards autoconf-doc blt-demo samtools cpp-doc 732s gcc-14-locales cpp-14-doc dh-make flit python3-build python3-installer 732s python3-wheel bison flex-doc fonts-freefont-otf | fonts-freefont-ttf 732s fonts-texgyre gcc-14-doc gcc-multilib manpages-dev gdb gcc-doc 732s gdb-arm-linux-gnueabihf gettext-doc libasprintf-dev libgettextpo-dev 732s hevea-doc imagemagick-6-doc autotrace cups-bsd | lpr | lprng enscript ffmpeg 732s gimp gnuplot grads graphviz hp2xx html2ps libwmf-bin mplayer povray radiance 732s sane-utils transfig libraw-bin libc-devtools glibc-doc 732s libavalon-framework-java libexcalibur-logkit-java liblog4j1.2-java 732s cups-common libfftw3-bin libfftw3-dev libheif-plugin-x265 732s libheif-plugin-ffmpegdec libheif-plugin-jpegdec libheif-plugin-jpegenc 732s libheif-plugin-j2kdec libheif-plugin-j2kenc libheif-plugin-kvazaar 732s libheif-plugin-rav1e libheif-plugin-svtenc libjs-jquery-ui-docs 732s liblcms2-utils libmagickcore-6.q16-7-extra libmpfi-doc libstdc++-14-doc 732s tcl8.6 tk8.6 libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc 732s phylip-doc libmail-box-perl poppler-utils fonts-japanese-mincho 732s | fonts-ipafont-mincho fonts-japanese-gothic | fonts-ipafont-gothic 732s fonts-arphic-ukai fonts-arphic-uming fonts-nanum probcons-extra clustalw 732s emboss muscle3 phyml python3-psycopg2 raxml python-cycler-doc docutils-doc 732s fonts-linuxlibertine | ttf-linux-libertine texlive-lang-french 732s python-lxml-doc cm-super-minimal dvipng fonts-staypuft gir1.2-gtk-3.0 732s inkscape ipython3 librsvg2-common python-matplotlib-doc python3-cairocffi 732s python3-gi-cairo python3-gobject python3-pyqt5 python3-sip python3-tornado 732s texlive-extra-utils python-mpmath-doc python3-gmpy2 default-mysql-server 732s | virtual-mysql-server python3-gdal python3-pydot python3-pygraphviz 732s gfortran python-numpy-doc python3-pytest python-pil-doc python-rdflib-doc 732s pdf-viewer python3-egenix-mxtexttools python-reportlab-doc rl-accel 732s rl-renderpm python-scipy-doc python3-stemmer dvisvgm fonts-freefont-otf 732s latexmk libjs-mathjax sphinx-doc tex-gyre texlive-fonts-extra 732s texlive-plain-generic python-sympy-doc tix python3-tk-dbg python3.13-tk 732s sgml-base-doc boxshade seaview t-coffee-examples perl-tk xpdf | pdf-viewer 732s xzdec texlive-binaries-sse2 hintview texlive-fonts-recommended-doc 732s texlive-latex-base-doc wp2latex icc-profiles libfile-which-perl 732s texlive-latex-extra-doc texlive-science texlive-latex-recommended-doc 732s texlive-luatex texlive-pstricks dot2tex prerex texlive-pictures-doc vprerex 732s wise-doc 732s Recommended packages: 732s libfl-dev libmagickcore-6.q16-7-extra manpages manpages-dev 732s libarchive-cpio-perl fonts-droid-fallback libheif-plugin-aomenc 732s javascript-common libjson-xs-perl libltdl-dev blast2 libwww-perl lynx ruby 732s libmail-sendmail-perl python3-bs4 python3-cssselect python3-html5lib 732s python3-olefile python3-html5rdf python3-orjson fonts-dejavu-extra 732s isympy-common amap-align clustalw dialign-tx fsa kalign libsoap-lite-perl 732s libxml-simple-perl muscle mustang poa proda tm-align lmodern dvisvgm 732s tex-gyre tipa default-jre libspreadsheet-parseexcel-perl 732s texlive-plain-generic tk libfile-mimeinfo-perl libnet-dbus-perl 732s libx11-protocol-perl x11-utils x11-xserver-utils 733s The following NEW packages will be installed: 733s autoconf automake autopkgtest-satdep autopoint autotools-dev blt 733s build-essential bwa clustalo cpp cpp-14 cpp-14-arm-linux-gnueabihf 733s cpp-arm-linux-gnueabihf debhelper debugedit dh-autoreconf dh-python 733s dh-strip-nondeterminism dialign docutils-common dssp dwz fasttree flex 733s fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-font-awesome 733s fonts-lato fonts-lmodern fonts-lyx fonts-urw-base35 g++ g++-14 733s g++-14-arm-linux-gnueabihf g++-arm-linux-gnueabihf gcc gcc-14 733s gcc-14-arm-linux-gnueabihf gcc-arm-linux-gnueabihf gettext ghostscript hevea 733s hicolor-icon-theme imagemagick imagemagick-6-common imagemagick-6.q16 733s intltool-debian libaom3 libapache-pom-java libarchive-zip-perl 733s libargtable2-0 libasan8 libavahi-client3 libavahi-common-data 733s libavahi-common3 libblas3 libc-dev-bin libc6-dev libcairo2 libcc1-0 733s libcifpp-data libcifpp7 libcommons-logging-java libcommons-parent-java 733s libcrypt-dev libcups2t64 libde265-0 libdebhelper-perl libdeflate0 733s libexpat1-dev libfftw3-double3 libfile-stripnondeterminism-perl 733s libfontbox-java libfontconfig1 libfontenc1 libfreetype6 libgcc-14-dev 733s libgfortran5 libgomp1 libgraphite2-3 libgs-common libgs10 libgs10-common 733s libharfbuzz0b libheif-plugin-aomdec libheif-plugin-libde265 libheif1 libice6 733s libidn12 libijs-0.35 libimagequant0 libisl23 libjbig0 libjbig2dec0 733s libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui libjs-sphinxdoc 733s libjs-underscore libjson-perl libkpathsea6 liblapack3 liblbfgsb0 liblcms2-2 733s liblerc4 liblqr-1-0 libltdl7 libmagickcore-6.q16-7t64 733s libmagickwand-6.q16-7t64 libmbedcrypto7t64 libmbedtls14t64 libmbedx509-1t64 733s libmpc3 libmpfi0 libmysqlclient21 libnetpbm11t64 libopenjp2-7 libpaper-utils 733s libpaper1 libpdfbox-java libpixman-1-0 libpotrace0 libptexenc1 733s libpython3-all-dev libpython3-dev libpython3.12-dev libpython3.12t64 733s libqhull-r8.0 libraqm0 libraw23t64 libsharpyuv0 libsm6 libstdc++-14-dev 733s libsynctex2 libtcl8.6 libteckit0 libtexlua53-5 libtiff6 libtk8.6 libtool 733s libubsan1 libwebp7 libwebpdemux2 libwebpmux3 libxaw7 libxcb-render0 733s libxcb-shm0 libxft2 libxi6 libxmu6 libxpm4 libxrender1 libxslt1.1 libxss1 733s libxt6t64 libzzip-0-13t64 linux-libc-dev m4 mafft mysql-common ncbi-blast+ 733s ncbi-data netpbm phylip po-debconf poppler-data prank preview-latex-style 733s probcons python-biopython-doc python-matplotlib-data python3-alabaster 733s python3-all python3-all-dev python3-appdirs python3-biopython 733s python3-biopython-sql python3-brotli python3-cairo python3-contourpy 733s python3-cycler python3-dateutil python3-decorator python3-defusedxml 733s python3-dev python3-docutils python3-fonttools python3-freetype python3-fs 733s python3-imagesize python3-kiwisolver python3-lxml python3-lz4 733s python3-matplotlib python3-mmtf python3-mpmath python3-msgpack 733s python3-mysqldb python3-networkx python3-numpy python3-numpydoc 733s python3-packaging python3-pil python3-pil.imagetk python3-rdflib 733s python3-reportlab python3-rlpycairo python3-roman python3-scipy python3-six 733s python3-snowballstemmer python3-sphinx python3-sphinx-rtd-theme 733s python3-sphinxcontrib.jquery python3-sympy python3-tabulate python3-tk 733s python3-tz python3-ufolib2 python3.12-dev python3.12-tk rpcsvc-proto 733s sgml-base sphinx-common sphinx-rtd-theme-common t-coffee t1utils tex-common 733s texlive-base texlive-binaries texlive-fonts-recommended texlive-latex-base 733s texlive-latex-extra texlive-latex-recommended texlive-pictures tk8.6-blt2.5 733s unicode-data w3c-sgml-lib wise wise-data x11-common xdg-utils 733s xfonts-encodings xfonts-utils xml-core zlib1g-dev 733s 0 upgraded, 248 newly installed, 0 to remove and 0 not upgraded. 733s Need to get 312 MB/312 MB of archives. 733s After this operation, 1109 MB of additional disk space will be used. 733s Get:1 /tmp/autopkgtest.BXh6wC/2-autopkgtest-satdep.deb autopkgtest-satdep armhf 0 [996 B] 733s Get:2 http://ftpmaster.internal/ubuntu plucky/main armhf m4 armhf 1.4.19-4build1 [235 kB] 733s Get:3 http://ftpmaster.internal/ubuntu plucky/main armhf flex armhf 2.6.4-8.2build1 [293 kB] 733s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-lato all 2.015-1 [2781 kB] 733s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf libgomp1 armhf 14.2.0-8ubuntu1 [125 kB] 733s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf libfftw3-double3 armhf 3.3.10-1ubuntu4 [368 kB] 733s Get:7 http://ftpmaster.internal/ubuntu plucky/main armhf libfreetype6 armhf 2.13.3+dfsg-1 [330 kB] 733s Get:8 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-dejavu-mono all 2.37-8 [502 kB] 733s Get:9 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-dejavu-core all 2.37-8 [835 kB] 734s Get:10 http://ftpmaster.internal/ubuntu plucky/main armhf libfontenc1 armhf 1:1.1.8-1build1 [11.5 kB] 734s Get:11 http://ftpmaster.internal/ubuntu plucky/main armhf x11-common all 1:7.7+23ubuntu3 [21.7 kB] 734s Get:12 http://ftpmaster.internal/ubuntu plucky/main armhf xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 734s Get:13 http://ftpmaster.internal/ubuntu plucky/main armhf xfonts-utils armhf 1:7.7+7 [90.6 kB] 734s Get:14 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-urw-base35 all 20200910-8 [11.0 MB] 734s Get:15 http://ftpmaster.internal/ubuntu plucky/main armhf fontconfig-config armhf 2.15.0-1.1ubuntu2 [37.4 kB] 734s Get:16 http://ftpmaster.internal/ubuntu plucky/main armhf libfontconfig1 armhf 2.15.0-1.1ubuntu2 [113 kB] 734s Get:17 http://ftpmaster.internal/ubuntu plucky/main armhf libsharpyuv0 armhf 1.4.0-0.1 [16.3 kB] 734s Get:18 http://ftpmaster.internal/ubuntu plucky/main armhf libaom3 armhf 3.11.0~rc1-1 [1762 kB] 734s Get:19 http://ftpmaster.internal/ubuntu plucky/main armhf libheif-plugin-aomdec armhf 1.19.3-1 [11.0 kB] 734s Get:20 http://ftpmaster.internal/ubuntu plucky/main armhf libde265-0 armhf 1.0.15-1build4 [157 kB] 734s Get:21 http://ftpmaster.internal/ubuntu plucky/main armhf libheif-plugin-libde265 armhf 1.19.3-1 [11.5 kB] 734s Get:22 http://ftpmaster.internal/ubuntu plucky/main armhf libheif1 armhf 1.19.3-1 [451 kB] 734s Get:23 http://ftpmaster.internal/ubuntu plucky/main armhf libjbig0 armhf 2.1-6.1ubuntu2 [24.9 kB] 734s Get:24 http://ftpmaster.internal/ubuntu plucky/main armhf libjpeg-turbo8 armhf 2.1.5-2ubuntu2 [125 kB] 734s Get:25 http://ftpmaster.internal/ubuntu plucky/main armhf libjpeg8 armhf 8c-2ubuntu11 [2148 B] 734s Get:26 http://ftpmaster.internal/ubuntu plucky/main armhf liblcms2-2 armhf 2.16-2 [137 kB] 734s Get:27 http://ftpmaster.internal/ubuntu plucky/universe armhf liblqr-1-0 armhf 0.4.2-2.1build2 [23.2 kB] 734s Get:28 http://ftpmaster.internal/ubuntu plucky/main armhf libltdl7 armhf 2.4.7-7build1 [37.6 kB] 734s Get:29 http://ftpmaster.internal/ubuntu plucky/main armhf libopenjp2-7 armhf 2.5.0-2ubuntu1 [170 kB] 734s Get:30 http://ftpmaster.internal/ubuntu plucky/main armhf libraw23t64 armhf 0.21.3-1 [353 kB] 734s Get:31 http://ftpmaster.internal/ubuntu plucky/main armhf libdeflate0 armhf 1.22-1 [38.9 kB] 734s Get:32 http://ftpmaster.internal/ubuntu plucky/main armhf liblerc4 armhf 4.0.0+ds-4ubuntu2 [151 kB] 734s Get:33 http://ftpmaster.internal/ubuntu plucky/main armhf libwebp7 armhf 1.4.0-0.1 [184 kB] 734s Get:34 http://ftpmaster.internal/ubuntu plucky/main armhf libtiff6 armhf 4.5.1+git230720-4ubuntu4 [179 kB] 734s Get:35 http://ftpmaster.internal/ubuntu plucky/main armhf libwebpdemux2 armhf 1.4.0-0.1 [11.8 kB] 734s Get:36 http://ftpmaster.internal/ubuntu plucky/main armhf libwebpmux3 armhf 1.4.0-0.1 [22.5 kB] 734s Get:37 http://ftpmaster.internal/ubuntu plucky/universe armhf imagemagick-6-common all 8:6.9.13.12+dfsg1-1build1 [69.6 kB] 734s Get:38 http://ftpmaster.internal/ubuntu plucky/universe armhf libmagickcore-6.q16-7t64 armhf 8:6.9.13.12+dfsg1-1build1 [1748 kB] 734s Get:39 http://ftpmaster.internal/ubuntu plucky/universe armhf libmagickwand-6.q16-7t64 armhf 8:6.9.13.12+dfsg1-1build1 [336 kB] 734s Get:40 http://ftpmaster.internal/ubuntu plucky/main armhf poppler-data all 0.4.12-1 [2060 kB] 734s Get:41 http://ftpmaster.internal/ubuntu plucky/main armhf sgml-base all 1.31 [11.4 kB] 734s Get:42 http://ftpmaster.internal/ubuntu plucky/main armhf autoconf all 2.72-3 [382 kB] 734s Get:43 http://ftpmaster.internal/ubuntu plucky/main armhf autotools-dev all 20220109.1 [44.9 kB] 734s Get:44 http://ftpmaster.internal/ubuntu plucky/main armhf automake all 1:1.16.5-1.3ubuntu1 [558 kB] 734s Get:45 http://ftpmaster.internal/ubuntu plucky/main armhf autopoint all 0.22.5-2 [616 kB] 734s Get:46 http://ftpmaster.internal/ubuntu plucky/main armhf libtcl8.6 armhf 8.6.15+dfsg-2 [909 kB] 734s Get:47 http://ftpmaster.internal/ubuntu plucky/main armhf libxrender1 armhf 1:0.9.10-1.1build1 [16.0 kB] 734s Get:48 http://ftpmaster.internal/ubuntu plucky/main armhf libxft2 armhf 2.3.6-1build1 [37.4 kB] 734s Get:49 http://ftpmaster.internal/ubuntu plucky/main armhf libxss1 armhf 1:1.2.3-1build3 [6500 B] 734s Get:50 http://ftpmaster.internal/ubuntu plucky/main armhf libtk8.6 armhf 8.6.15-1 [685 kB] 734s Get:51 http://ftpmaster.internal/ubuntu plucky/main armhf tk8.6-blt2.5 armhf 2.5.3+dfsg-7build1 [525 kB] 735s Get:52 http://ftpmaster.internal/ubuntu plucky/main armhf blt armhf 2.5.3+dfsg-7build1 [4840 B] 735s Get:53 http://ftpmaster.internal/ubuntu plucky/main armhf libc-dev-bin armhf 2.40-1ubuntu3 [19.2 kB] 735s Get:54 http://ftpmaster.internal/ubuntu plucky/main armhf linux-libc-dev armhf 6.11.0-8.8 [1628 kB] 735s Get:55 http://ftpmaster.internal/ubuntu plucky/main armhf libcrypt-dev armhf 1:4.4.36-4build1 [120 kB] 735s Get:56 http://ftpmaster.internal/ubuntu plucky/main armhf rpcsvc-proto armhf 1.4.2-0ubuntu7 [62.2 kB] 735s Get:57 http://ftpmaster.internal/ubuntu plucky/main armhf libc6-dev armhf 2.40-1ubuntu3 [1370 kB] 735s Get:58 http://ftpmaster.internal/ubuntu plucky/main armhf libisl23 armhf 0.27-1 [546 kB] 735s Get:59 http://ftpmaster.internal/ubuntu plucky/main armhf libmpc3 armhf 1.3.1-1build2 [47.1 kB] 735s Get:60 http://ftpmaster.internal/ubuntu plucky/main armhf cpp-14-arm-linux-gnueabihf armhf 14.2.0-8ubuntu1 [9219 kB] 735s Get:61 http://ftpmaster.internal/ubuntu plucky/main armhf cpp-14 armhf 14.2.0-8ubuntu1 [1032 B] 735s Get:62 http://ftpmaster.internal/ubuntu plucky/main armhf cpp-arm-linux-gnueabihf armhf 4:14.1.0-2ubuntu1 [5464 B] 735s Get:63 http://ftpmaster.internal/ubuntu plucky/main armhf cpp armhf 4:14.1.0-2ubuntu1 [22.4 kB] 735s Get:64 http://ftpmaster.internal/ubuntu plucky/main armhf libcc1-0 armhf 14.2.0-8ubuntu1 [43.3 kB] 735s Get:65 http://ftpmaster.internal/ubuntu plucky/main armhf libasan8 armhf 14.2.0-8ubuntu1 [2901 kB] 735s Get:66 http://ftpmaster.internal/ubuntu plucky/main armhf libubsan1 armhf 14.2.0-8ubuntu1 [1150 kB] 735s Get:67 http://ftpmaster.internal/ubuntu plucky/main armhf libgcc-14-dev armhf 14.2.0-8ubuntu1 [897 kB] 735s Get:68 http://ftpmaster.internal/ubuntu plucky/main armhf gcc-14-arm-linux-gnueabihf armhf 14.2.0-8ubuntu1 [18.0 MB] 736s Get:69 http://ftpmaster.internal/ubuntu plucky/main armhf gcc-14 armhf 14.2.0-8ubuntu1 [498 kB] 736s Get:70 http://ftpmaster.internal/ubuntu plucky/main armhf gcc-arm-linux-gnueabihf armhf 4:14.1.0-2ubuntu1 [1222 B] 736s Get:71 http://ftpmaster.internal/ubuntu plucky/main armhf gcc armhf 4:14.1.0-2ubuntu1 [5002 B] 736s Get:72 http://ftpmaster.internal/ubuntu plucky/main armhf libstdc++-14-dev armhf 14.2.0-8ubuntu1 [2569 kB] 736s Get:73 http://ftpmaster.internal/ubuntu plucky/main armhf g++-14-arm-linux-gnueabihf armhf 14.2.0-8ubuntu1 [10.5 MB] 736s Get:74 http://ftpmaster.internal/ubuntu plucky/main armhf g++-14 armhf 14.2.0-8ubuntu1 [19.9 kB] 736s Get:75 http://ftpmaster.internal/ubuntu plucky/main armhf g++-arm-linux-gnueabihf armhf 4:14.1.0-2ubuntu1 [968 B] 736s Get:76 http://ftpmaster.internal/ubuntu plucky/main armhf g++ armhf 4:14.1.0-2ubuntu1 [1084 B] 736s Get:77 http://ftpmaster.internal/ubuntu plucky/main armhf build-essential armhf 12.10ubuntu1 [4928 B] 736s Get:78 http://ftpmaster.internal/ubuntu plucky/universe armhf bwa armhf 0.7.18-1 [198 kB] 736s Get:79 http://ftpmaster.internal/ubuntu plucky/universe armhf libargtable2-0 armhf 13-2 [12.2 kB] 736s Get:80 http://ftpmaster.internal/ubuntu plucky/universe armhf clustalo armhf 1.2.4-8build1 [249 kB] 736s Get:81 http://ftpmaster.internal/ubuntu plucky/main armhf libdebhelper-perl all 13.20ubuntu1 [94.2 kB] 736s Get:82 http://ftpmaster.internal/ubuntu plucky/main armhf libtool all 2.4.7-7build1 [166 kB] 736s Get:83 http://ftpmaster.internal/ubuntu plucky/main armhf dh-autoreconf all 20 [16.1 kB] 736s Get:84 http://ftpmaster.internal/ubuntu plucky/main armhf libarchive-zip-perl all 1.68-1 [90.2 kB] 736s Get:85 http://ftpmaster.internal/ubuntu plucky/main armhf libfile-stripnondeterminism-perl all 1.14.0-1 [20.1 kB] 736s Get:86 http://ftpmaster.internal/ubuntu plucky/main armhf dh-strip-nondeterminism all 1.14.0-1 [5058 B] 736s Get:87 http://ftpmaster.internal/ubuntu plucky/main armhf debugedit armhf 1:5.1-1 [46.5 kB] 736s Get:88 http://ftpmaster.internal/ubuntu plucky/main armhf dwz armhf 0.15-1build6 [116 kB] 736s Get:89 http://ftpmaster.internal/ubuntu plucky/main armhf gettext armhf 0.22.5-2 [995 kB] 736s Get:90 http://ftpmaster.internal/ubuntu plucky/main armhf intltool-debian all 0.35.0+20060710.6 [23.2 kB] 736s Get:91 http://ftpmaster.internal/ubuntu plucky/main armhf po-debconf all 1.0.21+nmu1 [233 kB] 736s Get:92 http://ftpmaster.internal/ubuntu plucky/main armhf debhelper all 13.20ubuntu1 [893 kB] 736s Get:93 http://ftpmaster.internal/ubuntu plucky/universe armhf dh-python all 6.20241024 [112 kB] 736s Get:94 http://ftpmaster.internal/ubuntu plucky/universe armhf dialign armhf 2.2.1-13 [156 kB] 736s Get:95 http://ftpmaster.internal/ubuntu plucky/main armhf xml-core all 0.19 [20.3 kB] 736s Get:96 http://ftpmaster.internal/ubuntu plucky/main armhf docutils-common all 0.21.2+dfsg-2 [131 kB] 736s Get:97 http://ftpmaster.internal/ubuntu plucky/universe armhf libcifpp-data all 7.0.7-3 [480 kB] 736s Get:98 http://ftpmaster.internal/ubuntu plucky/universe armhf libcifpp7 armhf 7.0.7-3 [959 kB] 736s Get:99 http://ftpmaster.internal/ubuntu plucky/universe armhf dssp armhf 4.4.10-1 [696 kB] 736s Get:100 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB] 737s Get:101 http://ftpmaster.internal/ubuntu plucky/universe armhf fonts-lmodern all 2.005-1 [4799 kB] 737s Get:102 http://ftpmaster.internal/ubuntu plucky/universe armhf fonts-lyx all 2.4.2.1-1 [171 kB] 737s Get:103 http://ftpmaster.internal/ubuntu plucky/main armhf libgs-common all 10.03.1~dfsg1-0ubuntu3 [175 kB] 737s Get:104 http://ftpmaster.internal/ubuntu plucky/main armhf libgs10-common all 10.03.1~dfsg1-0ubuntu3 [488 kB] 737s Get:105 http://ftpmaster.internal/ubuntu plucky/main armhf libavahi-common-data armhf 0.8-13ubuntu6 [29.7 kB] 737s Get:106 http://ftpmaster.internal/ubuntu plucky/main armhf libavahi-common3 armhf 0.8-13ubuntu6 [20.2 kB] 737s Get:107 http://ftpmaster.internal/ubuntu plucky/main armhf libavahi-client3 armhf 0.8-13ubuntu6 [24.2 kB] 737s Get:108 http://ftpmaster.internal/ubuntu plucky/main armhf libcups2t64 armhf 2.4.10-1ubuntu2 [239 kB] 737s Get:109 http://ftpmaster.internal/ubuntu plucky/main armhf libidn12 armhf 1.42-2 [55.1 kB] 737s Get:110 http://ftpmaster.internal/ubuntu plucky/main armhf libijs-0.35 armhf 0.35-15.1build1 [13.5 kB] 737s Get:111 http://ftpmaster.internal/ubuntu plucky/main armhf libjbig2dec0 armhf 0.20-1build3 [57.6 kB] 737s Get:112 http://ftpmaster.internal/ubuntu plucky/main armhf libpaper1 armhf 1.1.29build1 [12.6 kB] 737s Get:113 http://ftpmaster.internal/ubuntu plucky/main armhf libice6 armhf 2:1.1.1-1 [36.5 kB] 737s Get:114 http://ftpmaster.internal/ubuntu plucky/main armhf libsm6 armhf 2:1.2.4-1 [15.1 kB] 737s Get:115 http://ftpmaster.internal/ubuntu plucky/main armhf libxt6t64 armhf 1:1.2.1-1.2build1 [145 kB] 737s Get:116 http://ftpmaster.internal/ubuntu plucky/main armhf libgs10 armhf 10.03.1~dfsg1-0ubuntu3 [4182 kB] 738s Get:117 http://ftpmaster.internal/ubuntu plucky/main armhf ghostscript armhf 10.03.1~dfsg1-0ubuntu3 [43.4 kB] 738s Get:118 http://ftpmaster.internal/ubuntu plucky/universe armhf libnetpbm11t64 armhf 2:11.08.01-1 [97.5 kB] 738s Get:119 http://ftpmaster.internal/ubuntu plucky/universe armhf netpbm armhf 2:11.08.01-1 [1935 kB] 738s Get:120 http://ftpmaster.internal/ubuntu plucky/universe armhf tex-common all 6.18 [32.8 kB] 738s Get:121 http://ftpmaster.internal/ubuntu plucky/main armhf libpaper-utils armhf 1.1.29build1 [8184 B] 738s Get:122 http://ftpmaster.internal/ubuntu plucky/main armhf libkpathsea6 armhf 2024.20240313.70630+ds-5 [58.8 kB] 738s Get:123 http://ftpmaster.internal/ubuntu plucky/main armhf libptexenc1 armhf 2024.20240313.70630+ds-5 [37.7 kB] 738s Get:124 http://ftpmaster.internal/ubuntu plucky/main armhf libsynctex2 armhf 2024.20240313.70630+ds-5 [48.0 kB] 738s Get:125 http://ftpmaster.internal/ubuntu plucky/main armhf libtexlua53-5 armhf 2024.20240313.70630+ds-5 [98.1 kB] 738s Get:126 http://ftpmaster.internal/ubuntu plucky/main armhf t1utils armhf 1.41-4build3 [51.8 kB] 738s Get:127 http://ftpmaster.internal/ubuntu plucky/main armhf libpixman-1-0 armhf 0.44.0-3 [183 kB] 738s Get:128 http://ftpmaster.internal/ubuntu plucky/main armhf libxcb-render0 armhf 1.17.0-2 [15.3 kB] 738s Get:129 http://ftpmaster.internal/ubuntu plucky/main armhf libxcb-shm0 armhf 1.17.0-2 [5774 B] 738s Get:130 http://ftpmaster.internal/ubuntu plucky/main armhf libcairo2 armhf 1.18.2-2 [484 kB] 738s Get:131 http://ftpmaster.internal/ubuntu plucky/main armhf libgraphite2-3 armhf 1.3.14-2ubuntu1 [64.8 kB] 738s Get:132 http://ftpmaster.internal/ubuntu plucky/main armhf libharfbuzz0b armhf 10.0.1-1 [463 kB] 738s Get:133 http://ftpmaster.internal/ubuntu plucky/universe armhf libmpfi0 armhf 1.5.4+ds-4 [28.0 kB] 738s Get:134 http://ftpmaster.internal/ubuntu plucky/universe armhf libpotrace0 armhf 1.16-2build1 [15.2 kB] 738s Get:135 http://ftpmaster.internal/ubuntu plucky/universe armhf libteckit0 armhf 2.5.12+ds1-1 [323 kB] 738s Get:136 http://ftpmaster.internal/ubuntu plucky/main armhf libxmu6 armhf 2:1.1.3-3build2 [40.4 kB] 738s Get:137 http://ftpmaster.internal/ubuntu plucky/main armhf libxpm4 armhf 1:3.5.17-1build2 [30.1 kB] 738s Get:138 http://ftpmaster.internal/ubuntu plucky/main armhf libxaw7 armhf 2:1.0.16-1 [154 kB] 738s Get:139 http://ftpmaster.internal/ubuntu plucky/main armhf libxi6 armhf 2:1.8.2-1 [26.5 kB] 738s Get:140 http://ftpmaster.internal/ubuntu plucky/universe armhf libzzip-0-13t64 armhf 0.13.72+dfsg.1-1.2build1 [24.4 kB] 738s Get:141 http://ftpmaster.internal/ubuntu plucky/universe armhf texlive-binaries armhf 2024.20240313.70630+ds-5 [7093 kB] 738s Get:142 http://ftpmaster.internal/ubuntu plucky/main armhf xdg-utils all 1.2.1-0ubuntu1 [67.5 kB] 738s Get:143 http://ftpmaster.internal/ubuntu plucky/universe armhf texlive-base all 2024.20241102-1 [22.5 MB] 739s Get:144 http://ftpmaster.internal/ubuntu plucky/main armhf hicolor-icon-theme all 0.18-1 [13.5 kB] 739s Get:145 http://ftpmaster.internal/ubuntu plucky/universe armhf imagemagick-6.q16 armhf 8:6.9.13.12+dfsg1-1build1 [254 kB] 739s Get:146 http://ftpmaster.internal/ubuntu plucky/universe armhf imagemagick armhf 8:6.9.13.12+dfsg1-1build1 [14.2 kB] 739s Get:147 http://ftpmaster.internal/ubuntu plucky/universe armhf hevea armhf 2.36-2 [1938 kB] 739s Get:148 http://ftpmaster.internal/ubuntu plucky/universe armhf libapache-pom-java all 33-2 [5874 B] 739s Get:149 http://ftpmaster.internal/ubuntu plucky/main armhf libblas3 armhf 3.12.0-3build2 [126 kB] 739s Get:150 http://ftpmaster.internal/ubuntu plucky/universe armhf libcommons-parent-java all 56-1 [10.7 kB] 739s Get:151 http://ftpmaster.internal/ubuntu plucky/universe armhf libcommons-logging-java all 1.3.0-1ubuntu1 [63.8 kB] 739s Get:152 http://ftpmaster.internal/ubuntu plucky/main armhf libexpat1-dev armhf 2.6.2-2 [121 kB] 739s Get:153 http://ftpmaster.internal/ubuntu plucky/main armhf libgfortran5 armhf 14.2.0-8ubuntu1 [311 kB] 739s Get:154 http://ftpmaster.internal/ubuntu plucky/main armhf libimagequant0 armhf 2.18.0-1build1 [31.1 kB] 739s Get:155 http://ftpmaster.internal/ubuntu plucky/main armhf libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 739s Get:156 http://ftpmaster.internal/ubuntu plucky/universe armhf libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 739s Get:157 http://ftpmaster.internal/ubuntu plucky/main armhf libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 739s Get:158 http://ftpmaster.internal/ubuntu plucky/main armhf libjs-sphinxdoc all 7.4.7-4 [158 kB] 739s Get:159 http://ftpmaster.internal/ubuntu plucky/main armhf libjson-perl all 4.10000-1 [81.9 kB] 739s Get:160 http://ftpmaster.internal/ubuntu plucky/main armhf liblapack3 armhf 3.12.0-3build2 [2086 kB] 739s Get:161 http://ftpmaster.internal/ubuntu plucky/universe armhf liblbfgsb0 armhf 3.0+dfsg.4-1build1 [27.4 kB] 739s Get:162 http://ftpmaster.internal/ubuntu plucky/universe armhf libmbedcrypto7t64 armhf 2.28.8-1 [182 kB] 739s Get:163 http://ftpmaster.internal/ubuntu plucky/universe armhf libmbedx509-1t64 armhf 2.28.8-1 [43.0 kB] 739s Get:164 http://ftpmaster.internal/ubuntu plucky/universe armhf libmbedtls14t64 armhf 2.28.8-1 [77.2 kB] 739s Get:165 http://ftpmaster.internal/ubuntu plucky/main armhf mysql-common all 5.8+1.1.1 [6800 B] 739s Get:166 http://ftpmaster.internal/ubuntu plucky/main armhf libmysqlclient21 armhf 8.0.40-1 [1234 kB] 739s Get:167 http://ftpmaster.internal/ubuntu plucky/main armhf libpython3.12t64 armhf 3.12.7-3 [2075 kB] 739s Get:168 http://ftpmaster.internal/ubuntu plucky/main armhf zlib1g-dev armhf 1:1.3.dfsg+really1.3.1-1ubuntu1 [880 kB] 739s Get:169 http://ftpmaster.internal/ubuntu plucky/main armhf libpython3.12-dev armhf 3.12.7-3 [4344 kB] 739s Get:170 http://ftpmaster.internal/ubuntu plucky/main armhf libpython3-dev armhf 3.12.6-0ubuntu1 [10.2 kB] 739s Get:171 http://ftpmaster.internal/ubuntu plucky/main armhf libpython3-all-dev armhf 3.12.6-0ubuntu1 [914 B] 739s Get:172 http://ftpmaster.internal/ubuntu plucky/universe armhf libqhull-r8.0 armhf 2020.2-6build1 [173 kB] 739s Get:173 http://ftpmaster.internal/ubuntu plucky/main armhf libraqm0 armhf 0.10.1-1build1 [12.4 kB] 739s Get:174 http://ftpmaster.internal/ubuntu plucky/main armhf libxslt1.1 armhf 1.1.39-0exp1ubuntu1 [150 kB] 739s Get:175 http://ftpmaster.internal/ubuntu plucky/universe armhf mafft armhf 7.505-1 [928 kB] 739s Get:176 http://ftpmaster.internal/ubuntu plucky/universe armhf ncbi-data all 6.1.20170106+dfsg2-5 [3966 kB] 739s Get:177 http://ftpmaster.internal/ubuntu plucky/universe armhf ncbi-blast+ armhf 2.16.0+ds-6 [14.8 MB] 740s Get:178 http://ftpmaster.internal/ubuntu plucky/universe armhf phylip armhf 1:3.697+dfsg-4build1 [876 kB] 740s Get:179 http://ftpmaster.internal/ubuntu plucky/universe armhf prank armhf 0.0.170427+dfsg-3 [340 kB] 740s Get:180 http://ftpmaster.internal/ubuntu plucky/universe armhf preview-latex-style all 13.2-1 [347 kB] 740s Get:181 http://ftpmaster.internal/ubuntu plucky/universe armhf probcons armhf 1.12-14 [120 kB] 740s Get:182 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf python-biopython-doc all 1.84+dfsg-4build1 [18.1 MB] 741s Get:183 http://ftpmaster.internal/ubuntu plucky/universe armhf python-matplotlib-data all 3.8.3-3 [2928 kB] 741s Get:184 http://ftpmaster.internal/ubuntu plucky/main armhf python3-all armhf 3.12.6-0ubuntu1 [886 B] 741s Get:185 http://ftpmaster.internal/ubuntu plucky/main armhf python3.12-dev armhf 3.12.7-3 [505 kB] 741s Get:186 http://ftpmaster.internal/ubuntu plucky/main armhf python3-dev armhf 3.12.6-0ubuntu1 [26.7 kB] 741s Get:187 http://ftpmaster.internal/ubuntu plucky/main armhf python3-all-dev armhf 3.12.6-0ubuntu1 [908 B] 741s Get:188 http://ftpmaster.internal/ubuntu plucky/main armhf python3-appdirs all 1.4.4-4 [10.9 kB] 741s Get:189 http://ftpmaster.internal/ubuntu plucky/main armhf python3-numpy armhf 1:1.26.4+ds-11build1 [3570 kB] 741s Get:190 http://ftpmaster.internal/ubuntu plucky/main armhf python3.12-tk armhf 3.12.7-3 [112 kB] 741s Get:191 http://ftpmaster.internal/ubuntu plucky/main armhf python3-tk armhf 3.12.6-1ubuntu1 [9806 B] 741s Get:192 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pil.imagetk armhf 10.4.0-1ubuntu1 [8848 B] 741s Get:193 http://ftpmaster.internal/ubuntu plucky/main armhf python3-pil armhf 10.4.0-1ubuntu1 [428 kB] 741s Get:194 http://ftpmaster.internal/ubuntu plucky/main armhf python3-cairo armhf 1.26.1-2 [114 kB] 741s Get:195 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-freetype all 2.5.1-1 [92.3 kB] 741s Get:196 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-rlpycairo all 0.3.0-3 [9130 B] 741s Get:197 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-reportlab all 4.2.5-1 [1107 kB] 741s Get:198 http://ftpmaster.internal/ubuntu plucky/universe armhf w3c-sgml-lib all 1.3-3 [280 kB] 741s Get:199 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf python3-biopython armhf 1.84+dfsg-4build1 [1672 kB] 741s Get:200 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf python3-biopython-sql all 1.84+dfsg-4build1 [26.4 kB] 741s Get:201 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-brotli armhf 1.1.0-2build2 [321 kB] 741s Get:202 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-contourpy armhf 1.3.0-2 [192 kB] 741s Get:203 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-cycler all 0.12.1-1 [9716 B] 741s Get:204 http://ftpmaster.internal/ubuntu plucky/main armhf python3-six all 1.16.0-7 [13.1 kB] 741s Get:205 http://ftpmaster.internal/ubuntu plucky/main armhf python3-dateutil all 2.9.0-2 [80.3 kB] 741s Get:206 http://ftpmaster.internal/ubuntu plucky/main armhf python3-decorator all 5.1.1-5 [10.1 kB] 741s Get:207 http://ftpmaster.internal/ubuntu plucky/main armhf python3-defusedxml all 0.7.1-2 [42.0 kB] 741s Get:208 http://ftpmaster.internal/ubuntu plucky/main armhf python3-roman all 4.2-1 [10.0 kB] 741s Get:209 http://ftpmaster.internal/ubuntu plucky/main armhf python3-docutils all 0.21.2+dfsg-2 [409 kB] 741s Get:210 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-scipy armhf 1.13.1-5 [16.4 MB] 742s Get:211 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-ufolib2 all 0.16.1+dfsg1-1 [33.4 kB] 742s Get:212 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-mpmath all 1.3.0-1 [425 kB] 742s Get:213 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-sympy all 1.13.3-1 [4228 kB] 742s Get:214 http://ftpmaster.internal/ubuntu plucky/main armhf python3-tz all 2024.1-2 [31.4 kB] 742s Get:215 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-fs all 2.4.16-4 [91.3 kB] 742s Get:216 http://ftpmaster.internal/ubuntu plucky/main armhf python3-lxml armhf 5.3.0-1 [1234 kB] 742s Get:217 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-lz4 armhf 4.0.2+dfsg-1build4 [24.8 kB] 742s Get:218 http://ftpmaster.internal/ubuntu plucky/universe armhf unicode-data all 15.1.0-1 [8878 kB] 742s Get:219 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-fonttools armhf 4.46.0-1build2 [1402 kB] 742s Get:220 http://ftpmaster.internal/ubuntu plucky/main armhf python3-imagesize all 1.4.1-1 [6844 B] 742s Get:221 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-kiwisolver armhf 1.4.7-2build1 [71.1 kB] 742s Get:222 http://ftpmaster.internal/ubuntu plucky/main armhf python3-packaging all 24.1-1 [41.4 kB] 742s Get:223 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-matplotlib armhf 3.8.3-3 [4500 kB] 743s Get:224 http://ftpmaster.internal/ubuntu plucky/main armhf python3-msgpack armhf 1.0.3-3build2 [76.1 kB] 743s Get:225 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-mmtf all 1.1.3-1 [16.2 kB] 743s Get:226 http://ftpmaster.internal/ubuntu plucky/main armhf python3-mysqldb armhf 1.4.6-2build4 [46.8 kB] 743s Get:227 http://ftpmaster.internal/ubuntu plucky/main armhf python3-networkx all 3.2.1-4ubuntu1 [11.5 MB] 743s Get:228 http://ftpmaster.internal/ubuntu plucky/main armhf sphinx-common all 7.4.7-4 [775 kB] 743s Get:229 http://ftpmaster.internal/ubuntu plucky/main armhf python3-alabaster all 0.7.16-0.1 [18.5 kB] 743s Get:230 http://ftpmaster.internal/ubuntu plucky/main armhf python3-snowballstemmer all 2.2.0-4build1 [59.8 kB] 743s Get:231 http://ftpmaster.internal/ubuntu plucky/main armhf python3-sphinx all 7.4.7-4 [593 kB] 743s Get:232 http://ftpmaster.internal/ubuntu plucky/main armhf python3-tabulate all 0.9.0-1 [45.3 kB] 743s Get:233 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-numpydoc all 1.6.0-2 [50.5 kB] 743s Get:234 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-rdflib all 7.1.1-2 [426 kB] 743s Get:235 http://ftpmaster.internal/ubuntu plucky/main armhf sphinx-rtd-theme-common all 3.0.1+dfsg-1 [1012 kB] 743s Get:236 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-sphinxcontrib.jquery all 4.1-5 [6678 B] 743s Get:237 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-sphinx-rtd-theme all 3.0.1+dfsg-1 [23.5 kB] 743s Get:238 http://ftpmaster.internal/ubuntu plucky/universe armhf t-coffee armhf 13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 [968 kB] 743s Get:239 http://ftpmaster.internal/ubuntu plucky/universe armhf texlive-fonts-recommended all 2024.20241102-1 [4974 kB] 743s Get:240 http://ftpmaster.internal/ubuntu plucky/universe armhf texlive-latex-base all 2024.20241102-1 [1260 kB] 743s Get:241 http://ftpmaster.internal/ubuntu plucky/universe armhf libfontbox-java all 1:1.8.16-5 [208 kB] 743s Get:242 http://ftpmaster.internal/ubuntu plucky/universe armhf libpdfbox-java all 1:1.8.16-5 [5521 kB] 743s Get:243 http://ftpmaster.internal/ubuntu plucky/universe armhf texlive-latex-recommended all 2024.20241102-1 [8739 kB] 744s Get:244 http://ftpmaster.internal/ubuntu plucky/universe armhf texlive-pictures all 2024.20241102-1 [17.0 MB] 744s Get:245 http://ftpmaster.internal/ubuntu plucky/universe armhf texlive-latex-extra all 2024.20241102-1 [24.2 MB] 744s Get:246 http://ftpmaster.internal/ubuntu plucky/universe armhf wise-data all 2.4.1-25 [83.0 kB] 744s Get:247 http://ftpmaster.internal/ubuntu plucky/universe armhf wise armhf 2.4.1-25 [917 kB] 744s Get:248 http://ftpmaster.internal/ubuntu plucky/universe armhf fasttree armhf 2.1.11-2 [162 kB] 746s Preconfiguring packages ... 746s Fetched 312 MB in 12s (26.4 MB/s) 746s Selecting previously unselected package m4. 746s (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 ... 59565 files and directories currently installed.) 746s Preparing to unpack .../000-m4_1.4.19-4build1_armhf.deb ... 746s Unpacking m4 (1.4.19-4build1) ... 746s Selecting previously unselected package flex. 746s Preparing to unpack .../001-flex_2.6.4-8.2build1_armhf.deb ... 746s Unpacking flex (2.6.4-8.2build1) ... 746s Selecting previously unselected package fonts-lato. 746s Preparing to unpack .../002-fonts-lato_2.015-1_all.deb ... 746s Unpacking fonts-lato (2.015-1) ... 746s Selecting previously unselected package libgomp1:armhf. 746s Preparing to unpack .../003-libgomp1_14.2.0-8ubuntu1_armhf.deb ... 746s Unpacking libgomp1:armhf (14.2.0-8ubuntu1) ... 746s Selecting previously unselected package libfftw3-double3:armhf. 746s Preparing to unpack .../004-libfftw3-double3_3.3.10-1ubuntu4_armhf.deb ... 746s Unpacking libfftw3-double3:armhf (3.3.10-1ubuntu4) ... 746s Selecting previously unselected package libfreetype6:armhf. 746s Preparing to unpack .../005-libfreetype6_2.13.3+dfsg-1_armhf.deb ... 746s Unpacking libfreetype6:armhf (2.13.3+dfsg-1) ... 746s Selecting previously unselected package fonts-dejavu-mono. 747s Preparing to unpack .../006-fonts-dejavu-mono_2.37-8_all.deb ... 747s Unpacking fonts-dejavu-mono (2.37-8) ... 747s Selecting previously unselected package fonts-dejavu-core. 747s Preparing to unpack .../007-fonts-dejavu-core_2.37-8_all.deb ... 747s Unpacking fonts-dejavu-core (2.37-8) ... 747s Selecting previously unselected package libfontenc1:armhf. 747s Preparing to unpack .../008-libfontenc1_1%3a1.1.8-1build1_armhf.deb ... 747s Unpacking libfontenc1:armhf (1:1.1.8-1build1) ... 747s Selecting previously unselected package x11-common. 747s Preparing to unpack .../009-x11-common_1%3a7.7+23ubuntu3_all.deb ... 747s Unpacking x11-common (1:7.7+23ubuntu3) ... 747s Selecting previously unselected package xfonts-encodings. 747s Preparing to unpack .../010-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 747s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 747s Selecting previously unselected package xfonts-utils. 747s Preparing to unpack .../011-xfonts-utils_1%3a7.7+7_armhf.deb ... 747s Unpacking xfonts-utils (1:7.7+7) ... 747s Selecting previously unselected package fonts-urw-base35. 747s Preparing to unpack .../012-fonts-urw-base35_20200910-8_all.deb ... 747s Unpacking fonts-urw-base35 (20200910-8) ... 747s Selecting previously unselected package fontconfig-config. 747s Preparing to unpack .../013-fontconfig-config_2.15.0-1.1ubuntu2_armhf.deb ... 748s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ... 748s Selecting previously unselected package libfontconfig1:armhf. 748s Preparing to unpack .../014-libfontconfig1_2.15.0-1.1ubuntu2_armhf.deb ... 748s Unpacking libfontconfig1:armhf (2.15.0-1.1ubuntu2) ... 748s Selecting previously unselected package libsharpyuv0:armhf. 748s Preparing to unpack .../015-libsharpyuv0_1.4.0-0.1_armhf.deb ... 748s Unpacking libsharpyuv0:armhf (1.4.0-0.1) ... 748s Selecting previously unselected package libaom3:armhf. 748s Preparing to unpack .../016-libaom3_3.11.0~rc1-1_armhf.deb ... 748s Unpacking libaom3:armhf (3.11.0~rc1-1) ... 748s Selecting previously unselected package libheif-plugin-aomdec:armhf. 748s Preparing to unpack .../017-libheif-plugin-aomdec_1.19.3-1_armhf.deb ... 748s Unpacking libheif-plugin-aomdec:armhf (1.19.3-1) ... 748s Selecting previously unselected package libde265-0:armhf. 748s Preparing to unpack .../018-libde265-0_1.0.15-1build4_armhf.deb ... 748s Unpacking libde265-0:armhf (1.0.15-1build4) ... 748s Selecting previously unselected package libheif-plugin-libde265:armhf. 748s Preparing to unpack .../019-libheif-plugin-libde265_1.19.3-1_armhf.deb ... 748s Unpacking libheif-plugin-libde265:armhf (1.19.3-1) ... 748s Selecting previously unselected package libheif1:armhf. 748s Preparing to unpack .../020-libheif1_1.19.3-1_armhf.deb ... 748s Unpacking libheif1:armhf (1.19.3-1) ... 748s Selecting previously unselected package libjbig0:armhf. 748s Preparing to unpack .../021-libjbig0_2.1-6.1ubuntu2_armhf.deb ... 748s Unpacking libjbig0:armhf (2.1-6.1ubuntu2) ... 748s Selecting previously unselected package libjpeg-turbo8:armhf. 748s Preparing to unpack .../022-libjpeg-turbo8_2.1.5-2ubuntu2_armhf.deb ... 748s Unpacking libjpeg-turbo8:armhf (2.1.5-2ubuntu2) ... 748s Selecting previously unselected package libjpeg8:armhf. 748s Preparing to unpack .../023-libjpeg8_8c-2ubuntu11_armhf.deb ... 748s Unpacking libjpeg8:armhf (8c-2ubuntu11) ... 748s Selecting previously unselected package liblcms2-2:armhf. 748s Preparing to unpack .../024-liblcms2-2_2.16-2_armhf.deb ... 748s Unpacking liblcms2-2:armhf (2.16-2) ... 748s Selecting previously unselected package liblqr-1-0:armhf. 748s Preparing to unpack .../025-liblqr-1-0_0.4.2-2.1build2_armhf.deb ... 748s Unpacking liblqr-1-0:armhf (0.4.2-2.1build2) ... 748s Selecting previously unselected package libltdl7:armhf. 748s Preparing to unpack .../026-libltdl7_2.4.7-7build1_armhf.deb ... 748s Unpacking libltdl7:armhf (2.4.7-7build1) ... 748s Selecting previously unselected package libopenjp2-7:armhf. 748s Preparing to unpack .../027-libopenjp2-7_2.5.0-2ubuntu1_armhf.deb ... 748s Unpacking libopenjp2-7:armhf (2.5.0-2ubuntu1) ... 748s Selecting previously unselected package libraw23t64:armhf. 748s Preparing to unpack .../028-libraw23t64_0.21.3-1_armhf.deb ... 748s Unpacking libraw23t64:armhf (0.21.3-1) ... 749s Selecting previously unselected package libdeflate0:armhf. 749s Preparing to unpack .../029-libdeflate0_1.22-1_armhf.deb ... 749s Unpacking libdeflate0:armhf (1.22-1) ... 749s Selecting previously unselected package liblerc4:armhf. 749s Preparing to unpack .../030-liblerc4_4.0.0+ds-4ubuntu2_armhf.deb ... 749s Unpacking liblerc4:armhf (4.0.0+ds-4ubuntu2) ... 749s Selecting previously unselected package libwebp7:armhf. 749s Preparing to unpack .../031-libwebp7_1.4.0-0.1_armhf.deb ... 749s Unpacking libwebp7:armhf (1.4.0-0.1) ... 749s Selecting previously unselected package libtiff6:armhf. 749s Preparing to unpack .../032-libtiff6_4.5.1+git230720-4ubuntu4_armhf.deb ... 749s Unpacking libtiff6:armhf (4.5.1+git230720-4ubuntu4) ... 749s Selecting previously unselected package libwebpdemux2:armhf. 749s Preparing to unpack .../033-libwebpdemux2_1.4.0-0.1_armhf.deb ... 749s Unpacking libwebpdemux2:armhf (1.4.0-0.1) ... 749s Selecting previously unselected package libwebpmux3:armhf. 749s Preparing to unpack .../034-libwebpmux3_1.4.0-0.1_armhf.deb ... 749s Unpacking libwebpmux3:armhf (1.4.0-0.1) ... 749s Selecting previously unselected package imagemagick-6-common. 749s Preparing to unpack .../035-imagemagick-6-common_8%3a6.9.13.12+dfsg1-1build1_all.deb ... 749s Unpacking imagemagick-6-common (8:6.9.13.12+dfsg1-1build1) ... 749s Selecting previously unselected package libmagickcore-6.q16-7t64:armhf. 749s Preparing to unpack .../036-libmagickcore-6.q16-7t64_8%3a6.9.13.12+dfsg1-1build1_armhf.deb ... 749s Unpacking libmagickcore-6.q16-7t64:armhf (8:6.9.13.12+dfsg1-1build1) ... 749s Selecting previously unselected package libmagickwand-6.q16-7t64:armhf. 749s Preparing to unpack .../037-libmagickwand-6.q16-7t64_8%3a6.9.13.12+dfsg1-1build1_armhf.deb ... 749s Unpacking libmagickwand-6.q16-7t64:armhf (8:6.9.13.12+dfsg1-1build1) ... 749s Selecting previously unselected package poppler-data. 749s Preparing to unpack .../038-poppler-data_0.4.12-1_all.deb ... 749s Unpacking poppler-data (0.4.12-1) ... 749s Selecting previously unselected package sgml-base. 749s Preparing to unpack .../039-sgml-base_1.31_all.deb ... 749s Unpacking sgml-base (1.31) ... 749s Selecting previously unselected package autoconf. 749s Preparing to unpack .../040-autoconf_2.72-3_all.deb ... 749s Unpacking autoconf (2.72-3) ... 749s Selecting previously unselected package autotools-dev. 750s Preparing to unpack .../041-autotools-dev_20220109.1_all.deb ... 750s Unpacking autotools-dev (20220109.1) ... 750s Selecting previously unselected package automake. 750s Preparing to unpack .../042-automake_1%3a1.16.5-1.3ubuntu1_all.deb ... 750s Unpacking automake (1:1.16.5-1.3ubuntu1) ... 750s Selecting previously unselected package autopoint. 750s Preparing to unpack .../043-autopoint_0.22.5-2_all.deb ... 750s Unpacking autopoint (0.22.5-2) ... 750s Selecting previously unselected package libtcl8.6:armhf. 750s Preparing to unpack .../044-libtcl8.6_8.6.15+dfsg-2_armhf.deb ... 750s Unpacking libtcl8.6:armhf (8.6.15+dfsg-2) ... 750s Selecting previously unselected package libxrender1:armhf. 750s Preparing to unpack .../045-libxrender1_1%3a0.9.10-1.1build1_armhf.deb ... 750s Unpacking libxrender1:armhf (1:0.9.10-1.1build1) ... 750s Selecting previously unselected package libxft2:armhf. 750s Preparing to unpack .../046-libxft2_2.3.6-1build1_armhf.deb ... 750s Unpacking libxft2:armhf (2.3.6-1build1) ... 750s Selecting previously unselected package libxss1:armhf. 750s Preparing to unpack .../047-libxss1_1%3a1.2.3-1build3_armhf.deb ... 750s Unpacking libxss1:armhf (1:1.2.3-1build3) ... 750s Selecting previously unselected package libtk8.6:armhf. 750s Preparing to unpack .../048-libtk8.6_8.6.15-1_armhf.deb ... 750s Unpacking libtk8.6:armhf (8.6.15-1) ... 750s Selecting previously unselected package tk8.6-blt2.5. 750s Preparing to unpack .../049-tk8.6-blt2.5_2.5.3+dfsg-7build1_armhf.deb ... 750s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 750s Selecting previously unselected package blt. 750s Preparing to unpack .../050-blt_2.5.3+dfsg-7build1_armhf.deb ... 750s Unpacking blt (2.5.3+dfsg-7build1) ... 750s Selecting previously unselected package libc-dev-bin. 750s Preparing to unpack .../051-libc-dev-bin_2.40-1ubuntu3_armhf.deb ... 750s Unpacking libc-dev-bin (2.40-1ubuntu3) ... 750s Selecting previously unselected package linux-libc-dev:armhf. 750s Preparing to unpack .../052-linux-libc-dev_6.11.0-8.8_armhf.deb ... 750s Unpacking linux-libc-dev:armhf (6.11.0-8.8) ... 750s Selecting previously unselected package libcrypt-dev:armhf. 751s Preparing to unpack .../053-libcrypt-dev_1%3a4.4.36-4build1_armhf.deb ... 751s Unpacking libcrypt-dev:armhf (1:4.4.36-4build1) ... 751s Selecting previously unselected package rpcsvc-proto. 751s Preparing to unpack .../054-rpcsvc-proto_1.4.2-0ubuntu7_armhf.deb ... 751s Unpacking rpcsvc-proto (1.4.2-0ubuntu7) ... 751s Selecting previously unselected package libc6-dev:armhf. 751s Preparing to unpack .../055-libc6-dev_2.40-1ubuntu3_armhf.deb ... 751s Unpacking libc6-dev:armhf (2.40-1ubuntu3) ... 751s Selecting previously unselected package libisl23:armhf. 751s Preparing to unpack .../056-libisl23_0.27-1_armhf.deb ... 751s Unpacking libisl23:armhf (0.27-1) ... 751s Selecting previously unselected package libmpc3:armhf. 751s Preparing to unpack .../057-libmpc3_1.3.1-1build2_armhf.deb ... 751s Unpacking libmpc3:armhf (1.3.1-1build2) ... 751s Selecting previously unselected package cpp-14-arm-linux-gnueabihf. 751s Preparing to unpack .../058-cpp-14-arm-linux-gnueabihf_14.2.0-8ubuntu1_armhf.deb ... 751s Unpacking cpp-14-arm-linux-gnueabihf (14.2.0-8ubuntu1) ... 751s Selecting previously unselected package cpp-14. 751s Preparing to unpack .../059-cpp-14_14.2.0-8ubuntu1_armhf.deb ... 751s Unpacking cpp-14 (14.2.0-8ubuntu1) ... 751s Selecting previously unselected package cpp-arm-linux-gnueabihf. 751s Preparing to unpack .../060-cpp-arm-linux-gnueabihf_4%3a14.1.0-2ubuntu1_armhf.deb ... 751s Unpacking cpp-arm-linux-gnueabihf (4:14.1.0-2ubuntu1) ... 751s Selecting previously unselected package cpp. 751s Preparing to unpack .../061-cpp_4%3a14.1.0-2ubuntu1_armhf.deb ... 751s Unpacking cpp (4:14.1.0-2ubuntu1) ... 751s Selecting previously unselected package libcc1-0:armhf. 751s Preparing to unpack .../062-libcc1-0_14.2.0-8ubuntu1_armhf.deb ... 751s Unpacking libcc1-0:armhf (14.2.0-8ubuntu1) ... 752s Selecting previously unselected package libasan8:armhf. 752s Preparing to unpack .../063-libasan8_14.2.0-8ubuntu1_armhf.deb ... 752s Unpacking libasan8:armhf (14.2.0-8ubuntu1) ... 752s Selecting previously unselected package libubsan1:armhf. 752s Preparing to unpack .../064-libubsan1_14.2.0-8ubuntu1_armhf.deb ... 752s Unpacking libubsan1:armhf (14.2.0-8ubuntu1) ... 752s Selecting previously unselected package libgcc-14-dev:armhf. 752s Preparing to unpack .../065-libgcc-14-dev_14.2.0-8ubuntu1_armhf.deb ... 752s Unpacking libgcc-14-dev:armhf (14.2.0-8ubuntu1) ... 752s Selecting previously unselected package gcc-14-arm-linux-gnueabihf. 752s Preparing to unpack .../066-gcc-14-arm-linux-gnueabihf_14.2.0-8ubuntu1_armhf.deb ... 752s Unpacking gcc-14-arm-linux-gnueabihf (14.2.0-8ubuntu1) ... 752s Selecting previously unselected package gcc-14. 752s Preparing to unpack .../067-gcc-14_14.2.0-8ubuntu1_armhf.deb ... 752s Unpacking gcc-14 (14.2.0-8ubuntu1) ... 752s Selecting previously unselected package gcc-arm-linux-gnueabihf. 752s Preparing to unpack .../068-gcc-arm-linux-gnueabihf_4%3a14.1.0-2ubuntu1_armhf.deb ... 752s Unpacking gcc-arm-linux-gnueabihf (4:14.1.0-2ubuntu1) ... 752s Selecting previously unselected package gcc. 752s Preparing to unpack .../069-gcc_4%3a14.1.0-2ubuntu1_armhf.deb ... 752s Unpacking gcc (4:14.1.0-2ubuntu1) ... 752s Selecting previously unselected package libstdc++-14-dev:armhf. 753s Preparing to unpack .../070-libstdc++-14-dev_14.2.0-8ubuntu1_armhf.deb ... 753s Unpacking libstdc++-14-dev:armhf (14.2.0-8ubuntu1) ... 753s Selecting previously unselected package g++-14-arm-linux-gnueabihf. 753s Preparing to unpack .../071-g++-14-arm-linux-gnueabihf_14.2.0-8ubuntu1_armhf.deb ... 753s Unpacking g++-14-arm-linux-gnueabihf (14.2.0-8ubuntu1) ... 753s Selecting previously unselected package g++-14. 753s Preparing to unpack .../072-g++-14_14.2.0-8ubuntu1_armhf.deb ... 753s Unpacking g++-14 (14.2.0-8ubuntu1) ... 753s Selecting previously unselected package g++-arm-linux-gnueabihf. 753s Preparing to unpack .../073-g++-arm-linux-gnueabihf_4%3a14.1.0-2ubuntu1_armhf.deb ... 753s Unpacking g++-arm-linux-gnueabihf (4:14.1.0-2ubuntu1) ... 753s Selecting previously unselected package g++. 753s Preparing to unpack .../074-g++_4%3a14.1.0-2ubuntu1_armhf.deb ... 753s Unpacking g++ (4:14.1.0-2ubuntu1) ... 753s Selecting previously unselected package build-essential. 753s Preparing to unpack .../075-build-essential_12.10ubuntu1_armhf.deb ... 753s Unpacking build-essential (12.10ubuntu1) ... 753s Selecting previously unselected package bwa. 753s Preparing to unpack .../076-bwa_0.7.18-1_armhf.deb ... 753s Unpacking bwa (0.7.18-1) ... 753s Selecting previously unselected package libargtable2-0. 753s Preparing to unpack .../077-libargtable2-0_13-2_armhf.deb ... 753s Unpacking libargtable2-0 (13-2) ... 753s Selecting previously unselected package clustalo. 753s Preparing to unpack .../078-clustalo_1.2.4-8build1_armhf.deb ... 753s Unpacking clustalo (1.2.4-8build1) ... 753s Selecting previously unselected package libdebhelper-perl. 753s Preparing to unpack .../079-libdebhelper-perl_13.20ubuntu1_all.deb ... 753s Unpacking libdebhelper-perl (13.20ubuntu1) ... 754s Selecting previously unselected package libtool. 754s Preparing to unpack .../080-libtool_2.4.7-7build1_all.deb ... 754s Unpacking libtool (2.4.7-7build1) ... 754s Selecting previously unselected package dh-autoreconf. 754s Preparing to unpack .../081-dh-autoreconf_20_all.deb ... 754s Unpacking dh-autoreconf (20) ... 754s Selecting previously unselected package libarchive-zip-perl. 754s Preparing to unpack .../082-libarchive-zip-perl_1.68-1_all.deb ... 754s Unpacking libarchive-zip-perl (1.68-1) ... 754s Selecting previously unselected package libfile-stripnondeterminism-perl. 754s Preparing to unpack .../083-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ... 754s Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... 754s Selecting previously unselected package dh-strip-nondeterminism. 754s Preparing to unpack .../084-dh-strip-nondeterminism_1.14.0-1_all.deb ... 754s Unpacking dh-strip-nondeterminism (1.14.0-1) ... 754s Selecting previously unselected package debugedit. 754s Preparing to unpack .../085-debugedit_1%3a5.1-1_armhf.deb ... 754s Unpacking debugedit (1:5.1-1) ... 754s Selecting previously unselected package dwz. 754s Preparing to unpack .../086-dwz_0.15-1build6_armhf.deb ... 754s Unpacking dwz (0.15-1build6) ... 754s Selecting previously unselected package gettext. 754s Preparing to unpack .../087-gettext_0.22.5-2_armhf.deb ... 754s Unpacking gettext (0.22.5-2) ... 754s Selecting previously unselected package intltool-debian. 754s Preparing to unpack .../088-intltool-debian_0.35.0+20060710.6_all.deb ... 754s Unpacking intltool-debian (0.35.0+20060710.6) ... 754s Selecting previously unselected package po-debconf. 754s Preparing to unpack .../089-po-debconf_1.0.21+nmu1_all.deb ... 754s Unpacking po-debconf (1.0.21+nmu1) ... 754s Selecting previously unselected package debhelper. 754s Preparing to unpack .../090-debhelper_13.20ubuntu1_all.deb ... 754s Unpacking debhelper (13.20ubuntu1) ... 754s Selecting previously unselected package dh-python. 754s Preparing to unpack .../091-dh-python_6.20241024_all.deb ... 754s Unpacking dh-python (6.20241024) ... 754s Selecting previously unselected package dialign. 754s Preparing to unpack .../092-dialign_2.2.1-13_armhf.deb ... 754s Unpacking dialign (2.2.1-13) ... 754s Selecting previously unselected package xml-core. 754s Preparing to unpack .../093-xml-core_0.19_all.deb ... 754s Unpacking xml-core (0.19) ... 754s Selecting previously unselected package docutils-common. 754s Preparing to unpack .../094-docutils-common_0.21.2+dfsg-2_all.deb ... 754s Unpacking docutils-common (0.21.2+dfsg-2) ... 754s Selecting previously unselected package libcifpp-data. 754s Preparing to unpack .../095-libcifpp-data_7.0.7-3_all.deb ... 754s Unpacking libcifpp-data (7.0.7-3) ... 755s Selecting previously unselected package libcifpp7:armhf. 755s Preparing to unpack .../096-libcifpp7_7.0.7-3_armhf.deb ... 755s Unpacking libcifpp7:armhf (7.0.7-3) ... 755s Selecting previously unselected package dssp. 755s Preparing to unpack .../097-dssp_4.4.10-1_armhf.deb ... 755s Unpacking dssp (4.4.10-1) ... 755s Selecting previously unselected package fonts-font-awesome. 755s Preparing to unpack .../098-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ... 755s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 755s Selecting previously unselected package fonts-lmodern. 755s Preparing to unpack .../099-fonts-lmodern_2.005-1_all.deb ... 755s Unpacking fonts-lmodern (2.005-1) ... 755s Selecting previously unselected package fonts-lyx. 755s Preparing to unpack .../100-fonts-lyx_2.4.2.1-1_all.deb ... 755s Unpacking fonts-lyx (2.4.2.1-1) ... 755s Selecting previously unselected package libgs-common. 755s Preparing to unpack .../101-libgs-common_10.03.1~dfsg1-0ubuntu3_all.deb ... 755s Unpacking libgs-common (10.03.1~dfsg1-0ubuntu3) ... 755s Selecting previously unselected package libgs10-common. 755s Preparing to unpack .../102-libgs10-common_10.03.1~dfsg1-0ubuntu3_all.deb ... 755s Unpacking libgs10-common (10.03.1~dfsg1-0ubuntu3) ... 755s Selecting previously unselected package libavahi-common-data:armhf. 755s Preparing to unpack .../103-libavahi-common-data_0.8-13ubuntu6_armhf.deb ... 755s Unpacking libavahi-common-data:armhf (0.8-13ubuntu6) ... 755s Selecting previously unselected package libavahi-common3:armhf. 755s Preparing to unpack .../104-libavahi-common3_0.8-13ubuntu6_armhf.deb ... 755s Unpacking libavahi-common3:armhf (0.8-13ubuntu6) ... 755s Selecting previously unselected package libavahi-client3:armhf. 755s Preparing to unpack .../105-libavahi-client3_0.8-13ubuntu6_armhf.deb ... 755s Unpacking libavahi-client3:armhf (0.8-13ubuntu6) ... 755s Selecting previously unselected package libcups2t64:armhf. 755s Preparing to unpack .../106-libcups2t64_2.4.10-1ubuntu2_armhf.deb ... 755s Unpacking libcups2t64:armhf (2.4.10-1ubuntu2) ... 755s Selecting previously unselected package libidn12:armhf. 755s Preparing to unpack .../107-libidn12_1.42-2_armhf.deb ... 755s Unpacking libidn12:armhf (1.42-2) ... 755s Selecting previously unselected package libijs-0.35:armhf. 755s Preparing to unpack .../108-libijs-0.35_0.35-15.1build1_armhf.deb ... 755s Unpacking libijs-0.35:armhf (0.35-15.1build1) ... 756s Selecting previously unselected package libjbig2dec0:armhf. 756s Preparing to unpack .../109-libjbig2dec0_0.20-1build3_armhf.deb ... 756s Unpacking libjbig2dec0:armhf (0.20-1build3) ... 756s Selecting previously unselected package libpaper1:armhf. 756s Preparing to unpack .../110-libpaper1_1.1.29build1_armhf.deb ... 756s Unpacking libpaper1:armhf (1.1.29build1) ... 756s Selecting previously unselected package libice6:armhf. 756s Preparing to unpack .../111-libice6_2%3a1.1.1-1_armhf.deb ... 756s Unpacking libice6:armhf (2:1.1.1-1) ... 756s Selecting previously unselected package libsm6:armhf. 756s Preparing to unpack .../112-libsm6_2%3a1.2.4-1_armhf.deb ... 756s Unpacking libsm6:armhf (2:1.2.4-1) ... 756s Selecting previously unselected package libxt6t64:armhf. 756s Preparing to unpack .../113-libxt6t64_1%3a1.2.1-1.2build1_armhf.deb ... 756s Unpacking libxt6t64:armhf (1:1.2.1-1.2build1) ... 756s Selecting previously unselected package libgs10:armhf. 756s Preparing to unpack .../114-libgs10_10.03.1~dfsg1-0ubuntu3_armhf.deb ... 756s Unpacking libgs10:armhf (10.03.1~dfsg1-0ubuntu3) ... 756s Selecting previously unselected package ghostscript. 756s Preparing to unpack .../115-ghostscript_10.03.1~dfsg1-0ubuntu3_armhf.deb ... 756s Unpacking ghostscript (10.03.1~dfsg1-0ubuntu3) ... 756s Selecting previously unselected package libnetpbm11t64:armhf. 756s Preparing to unpack .../116-libnetpbm11t64_2%3a11.08.01-1_armhf.deb ... 756s Unpacking libnetpbm11t64:armhf (2:11.08.01-1) ... 756s Selecting previously unselected package netpbm. 756s Preparing to unpack .../117-netpbm_2%3a11.08.01-1_armhf.deb ... 756s Unpacking netpbm (2:11.08.01-1) ... 757s Selecting previously unselected package tex-common. 757s Preparing to unpack .../118-tex-common_6.18_all.deb ... 757s Unpacking tex-common (6.18) ... 757s Selecting previously unselected package libpaper-utils. 757s Preparing to unpack .../119-libpaper-utils_1.1.29build1_armhf.deb ... 757s Unpacking libpaper-utils (1.1.29build1) ... 757s Selecting previously unselected package libkpathsea6:armhf. 757s Preparing to unpack .../120-libkpathsea6_2024.20240313.70630+ds-5_armhf.deb ... 757s Unpacking libkpathsea6:armhf (2024.20240313.70630+ds-5) ... 757s Selecting previously unselected package libptexenc1:armhf. 757s Preparing to unpack .../121-libptexenc1_2024.20240313.70630+ds-5_armhf.deb ... 757s Unpacking libptexenc1:armhf (2024.20240313.70630+ds-5) ... 757s Selecting previously unselected package libsynctex2:armhf. 757s Preparing to unpack .../122-libsynctex2_2024.20240313.70630+ds-5_armhf.deb ... 757s Unpacking libsynctex2:armhf (2024.20240313.70630+ds-5) ... 757s Selecting previously unselected package libtexlua53-5:armhf. 757s Preparing to unpack .../123-libtexlua53-5_2024.20240313.70630+ds-5_armhf.deb ... 757s Unpacking libtexlua53-5:armhf (2024.20240313.70630+ds-5) ... 757s Selecting previously unselected package t1utils. 757s Preparing to unpack .../124-t1utils_1.41-4build3_armhf.deb ... 757s Unpacking t1utils (1.41-4build3) ... 757s Selecting previously unselected package libpixman-1-0:armhf. 757s Preparing to unpack .../125-libpixman-1-0_0.44.0-3_armhf.deb ... 757s Unpacking libpixman-1-0:armhf (0.44.0-3) ... 757s Selecting previously unselected package libxcb-render0:armhf. 757s Preparing to unpack .../126-libxcb-render0_1.17.0-2_armhf.deb ... 757s Unpacking libxcb-render0:armhf (1.17.0-2) ... 757s Selecting previously unselected package libxcb-shm0:armhf. 757s Preparing to unpack .../127-libxcb-shm0_1.17.0-2_armhf.deb ... 757s Unpacking libxcb-shm0:armhf (1.17.0-2) ... 757s Selecting previously unselected package libcairo2:armhf. 757s Preparing to unpack .../128-libcairo2_1.18.2-2_armhf.deb ... 757s Unpacking libcairo2:armhf (1.18.2-2) ... 757s Selecting previously unselected package libgraphite2-3:armhf. 757s Preparing to unpack .../129-libgraphite2-3_1.3.14-2ubuntu1_armhf.deb ... 757s Unpacking libgraphite2-3:armhf (1.3.14-2ubuntu1) ... 757s Selecting previously unselected package libharfbuzz0b:armhf. 757s Preparing to unpack .../130-libharfbuzz0b_10.0.1-1_armhf.deb ... 757s Unpacking libharfbuzz0b:armhf (10.0.1-1) ... 757s Selecting previously unselected package libmpfi0:armhf. 757s Preparing to unpack .../131-libmpfi0_1.5.4+ds-4_armhf.deb ... 757s Unpacking libmpfi0:armhf (1.5.4+ds-4) ... 757s Selecting previously unselected package libpotrace0:armhf. 757s Preparing to unpack .../132-libpotrace0_1.16-2build1_armhf.deb ... 757s Unpacking libpotrace0:armhf (1.16-2build1) ... 757s Selecting previously unselected package libteckit0:armhf. 757s Preparing to unpack .../133-libteckit0_2.5.12+ds1-1_armhf.deb ... 757s Unpacking libteckit0:armhf (2.5.12+ds1-1) ... 757s Selecting previously unselected package libxmu6:armhf. 757s Preparing to unpack .../134-libxmu6_2%3a1.1.3-3build2_armhf.deb ... 757s Unpacking libxmu6:armhf (2:1.1.3-3build2) ... 757s Selecting previously unselected package libxpm4:armhf. 758s Preparing to unpack .../135-libxpm4_1%3a3.5.17-1build2_armhf.deb ... 758s Unpacking libxpm4:armhf (1:3.5.17-1build2) ... 758s Selecting previously unselected package libxaw7:armhf. 758s Preparing to unpack .../136-libxaw7_2%3a1.0.16-1_armhf.deb ... 758s Unpacking libxaw7:armhf (2:1.0.16-1) ... 758s Selecting previously unselected package libxi6:armhf. 758s Preparing to unpack .../137-libxi6_2%3a1.8.2-1_armhf.deb ... 758s Unpacking libxi6:armhf (2:1.8.2-1) ... 758s Selecting previously unselected package libzzip-0-13t64:armhf. 758s Preparing to unpack .../138-libzzip-0-13t64_0.13.72+dfsg.1-1.2build1_armhf.deb ... 758s Unpacking libzzip-0-13t64:armhf (0.13.72+dfsg.1-1.2build1) ... 758s Selecting previously unselected package texlive-binaries. 758s Preparing to unpack .../139-texlive-binaries_2024.20240313.70630+ds-5_armhf.deb ... 758s Unpacking texlive-binaries (2024.20240313.70630+ds-5) ... 758s Selecting previously unselected package xdg-utils. 758s Preparing to unpack .../140-xdg-utils_1.2.1-0ubuntu1_all.deb ... 758s Unpacking xdg-utils (1.2.1-0ubuntu1) ... 758s Selecting previously unselected package texlive-base. 758s Preparing to unpack .../141-texlive-base_2024.20241102-1_all.deb ... 758s Unpacking texlive-base (2024.20241102-1) ... 760s Selecting previously unselected package hicolor-icon-theme. 760s Preparing to unpack .../142-hicolor-icon-theme_0.18-1_all.deb ... 760s Unpacking hicolor-icon-theme (0.18-1) ... 760s Selecting previously unselected package imagemagick-6.q16. 760s Preparing to unpack .../143-imagemagick-6.q16_8%3a6.9.13.12+dfsg1-1build1_armhf.deb ... 760s Unpacking imagemagick-6.q16 (8:6.9.13.12+dfsg1-1build1) ... 760s Selecting previously unselected package imagemagick. 760s Preparing to unpack .../144-imagemagick_8%3a6.9.13.12+dfsg1-1build1_armhf.deb ... 760s Unpacking imagemagick (8:6.9.13.12+dfsg1-1build1) ... 760s Selecting previously unselected package hevea. 760s Preparing to unpack .../145-hevea_2.36-2_armhf.deb ... 760s Unpacking hevea (2.36-2) ... 760s Selecting previously unselected package libapache-pom-java. 760s Preparing to unpack .../146-libapache-pom-java_33-2_all.deb ... 760s Unpacking libapache-pom-java (33-2) ... 760s Selecting previously unselected package libblas3:armhf. 760s Preparing to unpack .../147-libblas3_3.12.0-3build2_armhf.deb ... 760s Unpacking libblas3:armhf (3.12.0-3build2) ... 760s Selecting previously unselected package libcommons-parent-java. 760s Preparing to unpack .../148-libcommons-parent-java_56-1_all.deb ... 760s Unpacking libcommons-parent-java (56-1) ... 760s Selecting previously unselected package libcommons-logging-java. 760s Preparing to unpack .../149-libcommons-logging-java_1.3.0-1ubuntu1_all.deb ... 760s Unpacking libcommons-logging-java (1.3.0-1ubuntu1) ... 760s Selecting previously unselected package libexpat1-dev:armhf. 760s Preparing to unpack .../150-libexpat1-dev_2.6.2-2_armhf.deb ... 760s Unpacking libexpat1-dev:armhf (2.6.2-2) ... 760s Selecting previously unselected package libgfortran5:armhf. 760s Preparing to unpack .../151-libgfortran5_14.2.0-8ubuntu1_armhf.deb ... 760s Unpacking libgfortran5:armhf (14.2.0-8ubuntu1) ... 760s Selecting previously unselected package libimagequant0:armhf. 760s Preparing to unpack .../152-libimagequant0_2.18.0-1build1_armhf.deb ... 760s Unpacking libimagequant0:armhf (2.18.0-1build1) ... 760s Selecting previously unselected package libjs-jquery. 760s Preparing to unpack .../153-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 760s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 760s Selecting previously unselected package libjs-jquery-ui. 760s Preparing to unpack .../154-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... 760s Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... 761s Selecting previously unselected package libjs-underscore. 761s Preparing to unpack .../155-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 761s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 761s Selecting previously unselected package libjs-sphinxdoc. 761s Preparing to unpack .../156-libjs-sphinxdoc_7.4.7-4_all.deb ... 761s Unpacking libjs-sphinxdoc (7.4.7-4) ... 761s Selecting previously unselected package libjson-perl. 761s Preparing to unpack .../157-libjson-perl_4.10000-1_all.deb ... 761s Unpacking libjson-perl (4.10000-1) ... 761s Selecting previously unselected package liblapack3:armhf. 761s Preparing to unpack .../158-liblapack3_3.12.0-3build2_armhf.deb ... 761s Unpacking liblapack3:armhf (3.12.0-3build2) ... 761s Selecting previously unselected package liblbfgsb0:armhf. 761s Preparing to unpack .../159-liblbfgsb0_3.0+dfsg.4-1build1_armhf.deb ... 761s Unpacking liblbfgsb0:armhf (3.0+dfsg.4-1build1) ... 761s Selecting previously unselected package libmbedcrypto7t64:armhf. 761s Preparing to unpack .../160-libmbedcrypto7t64_2.28.8-1_armhf.deb ... 761s Unpacking libmbedcrypto7t64:armhf (2.28.8-1) ... 761s Selecting previously unselected package libmbedx509-1t64:armhf. 761s Preparing to unpack .../161-libmbedx509-1t64_2.28.8-1_armhf.deb ... 761s Unpacking libmbedx509-1t64:armhf (2.28.8-1) ... 761s Selecting previously unselected package libmbedtls14t64:armhf. 761s Preparing to unpack .../162-libmbedtls14t64_2.28.8-1_armhf.deb ... 761s Unpacking libmbedtls14t64:armhf (2.28.8-1) ... 761s Selecting previously unselected package mysql-common. 761s Preparing to unpack .../163-mysql-common_5.8+1.1.1_all.deb ... 761s Unpacking mysql-common (5.8+1.1.1) ... 761s Selecting previously unselected package libmysqlclient21:armhf. 761s Preparing to unpack .../164-libmysqlclient21_8.0.40-1_armhf.deb ... 761s Unpacking libmysqlclient21:armhf (8.0.40-1) ... 761s Selecting previously unselected package libpython3.12t64:armhf. 761s Preparing to unpack .../165-libpython3.12t64_3.12.7-3_armhf.deb ... 761s Unpacking libpython3.12t64:armhf (3.12.7-3) ... 761s Selecting previously unselected package zlib1g-dev:armhf. 761s Preparing to unpack .../166-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1ubuntu1_armhf.deb ... 761s Unpacking zlib1g-dev:armhf (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 761s Selecting previously unselected package libpython3.12-dev:armhf. 761s Preparing to unpack .../167-libpython3.12-dev_3.12.7-3_armhf.deb ... 762s Unpacking libpython3.12-dev:armhf (3.12.7-3) ... 762s Selecting previously unselected package libpython3-dev:armhf. 762s Preparing to unpack .../168-libpython3-dev_3.12.6-0ubuntu1_armhf.deb ... 762s Unpacking libpython3-dev:armhf (3.12.6-0ubuntu1) ... 762s Selecting previously unselected package libpython3-all-dev:armhf. 762s Preparing to unpack .../169-libpython3-all-dev_3.12.6-0ubuntu1_armhf.deb ... 762s Unpacking libpython3-all-dev:armhf (3.12.6-0ubuntu1) ... 762s Selecting previously unselected package libqhull-r8.0:armhf. 762s Preparing to unpack .../170-libqhull-r8.0_2020.2-6build1_armhf.deb ... 762s Unpacking libqhull-r8.0:armhf (2020.2-6build1) ... 762s Selecting previously unselected package libraqm0:armhf. 762s Preparing to unpack .../171-libraqm0_0.10.1-1build1_armhf.deb ... 762s Unpacking libraqm0:armhf (0.10.1-1build1) ... 762s Selecting previously unselected package libxslt1.1:armhf. 762s Preparing to unpack .../172-libxslt1.1_1.1.39-0exp1ubuntu1_armhf.deb ... 762s Unpacking libxslt1.1:armhf (1.1.39-0exp1ubuntu1) ... 762s Selecting previously unselected package mafft. 762s Preparing to unpack .../173-mafft_7.505-1_armhf.deb ... 762s Unpacking mafft (7.505-1) ... 762s Selecting previously unselected package ncbi-data. 762s Preparing to unpack .../174-ncbi-data_6.1.20170106+dfsg2-5_all.deb ... 762s Unpacking ncbi-data (6.1.20170106+dfsg2-5) ... 762s Selecting previously unselected package ncbi-blast+. 762s Preparing to unpack .../175-ncbi-blast+_2.16.0+ds-6_armhf.deb ... 762s Unpacking ncbi-blast+ (2.16.0+ds-6) ... 763s Selecting previously unselected package phylip. 763s Preparing to unpack .../176-phylip_1%3a3.697+dfsg-4build1_armhf.deb ... 763s Unpacking phylip (1:3.697+dfsg-4build1) ... 763s Selecting previously unselected package prank. 763s Preparing to unpack .../177-prank_0.0.170427+dfsg-3_armhf.deb ... 763s Unpacking prank (0.0.170427+dfsg-3) ... 763s Selecting previously unselected package preview-latex-style. 763s Preparing to unpack .../178-preview-latex-style_13.2-1_all.deb ... 763s Unpacking preview-latex-style (13.2-1) ... 763s Selecting previously unselected package probcons. 763s Preparing to unpack .../179-probcons_1.12-14_armhf.deb ... 763s Unpacking probcons (1.12-14) ... 763s Selecting previously unselected package python-biopython-doc. 763s Preparing to unpack .../180-python-biopython-doc_1.84+dfsg-4build1_all.deb ... 763s Unpacking python-biopython-doc (1.84+dfsg-4build1) ... 764s Selecting previously unselected package python-matplotlib-data. 764s Preparing to unpack .../181-python-matplotlib-data_3.8.3-3_all.deb ... 764s Unpacking python-matplotlib-data (3.8.3-3) ... 764s Selecting previously unselected package python3-all. 764s Preparing to unpack .../182-python3-all_3.12.6-0ubuntu1_armhf.deb ... 764s Unpacking python3-all (3.12.6-0ubuntu1) ... 764s Selecting previously unselected package python3.12-dev. 764s Preparing to unpack .../183-python3.12-dev_3.12.7-3_armhf.deb ... 764s Unpacking python3.12-dev (3.12.7-3) ... 764s Selecting previously unselected package python3-dev. 764s Preparing to unpack .../184-python3-dev_3.12.6-0ubuntu1_armhf.deb ... 764s Unpacking python3-dev (3.12.6-0ubuntu1) ... 764s Selecting previously unselected package python3-all-dev. 764s Preparing to unpack .../185-python3-all-dev_3.12.6-0ubuntu1_armhf.deb ... 764s Unpacking python3-all-dev (3.12.6-0ubuntu1) ... 764s Selecting previously unselected package python3-appdirs. 764s Preparing to unpack .../186-python3-appdirs_1.4.4-4_all.deb ... 764s Unpacking python3-appdirs (1.4.4-4) ... 764s Selecting previously unselected package python3-numpy. 764s Preparing to unpack .../187-python3-numpy_1%3a1.26.4+ds-11build1_armhf.deb ... 764s Unpacking python3-numpy (1:1.26.4+ds-11build1) ... 765s Selecting previously unselected package python3.12-tk. 765s Preparing to unpack .../188-python3.12-tk_3.12.7-3_armhf.deb ... 765s Unpacking python3.12-tk (3.12.7-3) ... 765s Selecting previously unselected package python3-tk:armhf. 765s Preparing to unpack .../189-python3-tk_3.12.6-1ubuntu1_armhf.deb ... 765s Unpacking python3-tk:armhf (3.12.6-1ubuntu1) ... 765s Selecting previously unselected package python3-pil.imagetk:armhf. 765s Preparing to unpack .../190-python3-pil.imagetk_10.4.0-1ubuntu1_armhf.deb ... 765s Unpacking python3-pil.imagetk:armhf (10.4.0-1ubuntu1) ... 765s Selecting previously unselected package python3-pil:armhf. 765s Preparing to unpack .../191-python3-pil_10.4.0-1ubuntu1_armhf.deb ... 765s Unpacking python3-pil:armhf (10.4.0-1ubuntu1) ... 765s Selecting previously unselected package python3-cairo. 765s Preparing to unpack .../192-python3-cairo_1.26.1-2_armhf.deb ... 765s Unpacking python3-cairo (1.26.1-2) ... 765s Selecting previously unselected package python3-freetype. 765s Preparing to unpack .../193-python3-freetype_2.5.1-1_all.deb ... 765s Unpacking python3-freetype (2.5.1-1) ... 765s Selecting previously unselected package python3-rlpycairo. 765s Preparing to unpack .../194-python3-rlpycairo_0.3.0-3_all.deb ... 765s Unpacking python3-rlpycairo (0.3.0-3) ... 765s Selecting previously unselected package python3-reportlab. 765s Preparing to unpack .../195-python3-reportlab_4.2.5-1_all.deb ... 765s Unpacking python3-reportlab (4.2.5-1) ... 765s Selecting previously unselected package w3c-sgml-lib. 765s Preparing to unpack .../196-w3c-sgml-lib_1.3-3_all.deb ... 765s Unpacking w3c-sgml-lib (1.3-3) ... 766s Selecting previously unselected package python3-biopython. 766s Preparing to unpack .../197-python3-biopython_1.84+dfsg-4build1_armhf.deb ... 766s Unpacking python3-biopython (1.84+dfsg-4build1) ... 766s Selecting previously unselected package python3-biopython-sql. 766s Preparing to unpack .../198-python3-biopython-sql_1.84+dfsg-4build1_all.deb ... 766s Unpacking python3-biopython-sql (1.84+dfsg-4build1) ... 766s Selecting previously unselected package python3-brotli. 766s Preparing to unpack .../199-python3-brotli_1.1.0-2build2_armhf.deb ... 766s Unpacking python3-brotli (1.1.0-2build2) ... 766s Selecting previously unselected package python3-contourpy. 766s Preparing to unpack .../200-python3-contourpy_1.3.0-2_armhf.deb ... 766s Unpacking python3-contourpy (1.3.0-2) ... 766s Selecting previously unselected package python3-cycler. 766s Preparing to unpack .../201-python3-cycler_0.12.1-1_all.deb ... 766s Unpacking python3-cycler (0.12.1-1) ... 766s Selecting previously unselected package python3-six. 766s Preparing to unpack .../202-python3-six_1.16.0-7_all.deb ... 766s Unpacking python3-six (1.16.0-7) ... 766s Selecting previously unselected package python3-dateutil. 766s Preparing to unpack .../203-python3-dateutil_2.9.0-2_all.deb ... 766s Unpacking python3-dateutil (2.9.0-2) ... 766s Selecting previously unselected package python3-decorator. 766s Preparing to unpack .../204-python3-decorator_5.1.1-5_all.deb ... 766s Unpacking python3-decorator (5.1.1-5) ... 766s Selecting previously unselected package python3-defusedxml. 766s Preparing to unpack .../205-python3-defusedxml_0.7.1-2_all.deb ... 766s Unpacking python3-defusedxml (0.7.1-2) ... 766s Selecting previously unselected package python3-roman. 766s Preparing to unpack .../206-python3-roman_4.2-1_all.deb ... 766s Unpacking python3-roman (4.2-1) ... 767s Selecting previously unselected package python3-docutils. 767s Preparing to unpack .../207-python3-docutils_0.21.2+dfsg-2_all.deb ... 767s Unpacking python3-docutils (0.21.2+dfsg-2) ... 767s Selecting previously unselected package python3-scipy. 767s Preparing to unpack .../208-python3-scipy_1.13.1-5_armhf.deb ... 767s Unpacking python3-scipy (1.13.1-5) ... 767s Selecting previously unselected package python3-ufolib2. 767s Preparing to unpack .../209-python3-ufolib2_0.16.1+dfsg1-1_all.deb ... 767s Unpacking python3-ufolib2 (0.16.1+dfsg1-1) ... 767s Selecting previously unselected package python3-mpmath. 767s Preparing to unpack .../210-python3-mpmath_1.3.0-1_all.deb ... 767s Unpacking python3-mpmath (1.3.0-1) ... 768s Selecting previously unselected package python3-sympy. 768s Preparing to unpack .../211-python3-sympy_1.13.3-1_all.deb ... 768s Unpacking python3-sympy (1.13.3-1) ... 768s Selecting previously unselected package python3-tz. 768s Preparing to unpack .../212-python3-tz_2024.1-2_all.deb ... 768s Unpacking python3-tz (2024.1-2) ... 768s Selecting previously unselected package python3-fs. 768s Preparing to unpack .../213-python3-fs_2.4.16-4_all.deb ... 768s Unpacking python3-fs (2.4.16-4) ... 768s Selecting previously unselected package python3-lxml:armhf. 768s Preparing to unpack .../214-python3-lxml_5.3.0-1_armhf.deb ... 768s Unpacking python3-lxml:armhf (5.3.0-1) ... 769s Selecting previously unselected package python3-lz4. 769s Preparing to unpack .../215-python3-lz4_4.0.2+dfsg-1build4_armhf.deb ... 769s Unpacking python3-lz4 (4.0.2+dfsg-1build4) ... 769s Selecting previously unselected package unicode-data. 769s Preparing to unpack .../216-unicode-data_15.1.0-1_all.deb ... 769s Unpacking unicode-data (15.1.0-1) ... 769s Selecting previously unselected package python3-fonttools. 769s Preparing to unpack .../217-python3-fonttools_4.46.0-1build2_armhf.deb ... 769s Unpacking python3-fonttools (4.46.0-1build2) ... 769s Selecting previously unselected package python3-imagesize. 769s Preparing to unpack .../218-python3-imagesize_1.4.1-1_all.deb ... 769s Unpacking python3-imagesize (1.4.1-1) ... 769s Selecting previously unselected package python3-kiwisolver. 769s Preparing to unpack .../219-python3-kiwisolver_1.4.7-2build1_armhf.deb ... 769s Unpacking python3-kiwisolver (1.4.7-2build1) ... 769s Selecting previously unselected package python3-packaging. 769s Preparing to unpack .../220-python3-packaging_24.1-1_all.deb ... 769s Unpacking python3-packaging (24.1-1) ... 769s Selecting previously unselected package python3-matplotlib. 769s Preparing to unpack .../221-python3-matplotlib_3.8.3-3_armhf.deb ... 769s Unpacking python3-matplotlib (3.8.3-3) ... 770s Selecting previously unselected package python3-msgpack. 770s Preparing to unpack .../222-python3-msgpack_1.0.3-3build2_armhf.deb ... 770s Unpacking python3-msgpack (1.0.3-3build2) ... 770s Selecting previously unselected package python3-mmtf. 770s Preparing to unpack .../223-python3-mmtf_1.1.3-1_all.deb ... 770s Unpacking python3-mmtf (1.1.3-1) ... 770s Selecting previously unselected package python3-mysqldb. 770s Preparing to unpack .../224-python3-mysqldb_1.4.6-2build4_armhf.deb ... 770s Unpacking python3-mysqldb (1.4.6-2build4) ... 770s Selecting previously unselected package python3-networkx. 770s Preparing to unpack .../225-python3-networkx_3.2.1-4ubuntu1_all.deb ... 770s Unpacking python3-networkx (3.2.1-4ubuntu1) ... 771s Selecting previously unselected package sphinx-common. 771s Preparing to unpack .../226-sphinx-common_7.4.7-4_all.deb ... 771s Unpacking sphinx-common (7.4.7-4) ... 771s Selecting previously unselected package python3-alabaster. 771s Preparing to unpack .../227-python3-alabaster_0.7.16-0.1_all.deb ... 771s Unpacking python3-alabaster (0.7.16-0.1) ... 771s Selecting previously unselected package python3-snowballstemmer. 771s Preparing to unpack .../228-python3-snowballstemmer_2.2.0-4build1_all.deb ... 771s Unpacking python3-snowballstemmer (2.2.0-4build1) ... 771s Selecting previously unselected package python3-sphinx. 771s Preparing to unpack .../229-python3-sphinx_7.4.7-4_all.deb ... 771s Unpacking python3-sphinx (7.4.7-4) ... 771s Selecting previously unselected package python3-tabulate. 771s Preparing to unpack .../230-python3-tabulate_0.9.0-1_all.deb ... 771s Unpacking python3-tabulate (0.9.0-1) ... 771s Selecting previously unselected package python3-numpydoc. 771s Preparing to unpack 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... 777s Unpacking fasttree (2.1.11-2) ... 777s Selecting previously unselected package autopkgtest-satdep. 777s Preparing to unpack .../247-2-autopkgtest-satdep.deb ... 777s Unpacking autopkgtest-satdep (0) ... 777s Setting up dh-python (6.20241024) ... 778s Setting up libgraphite2-3:armhf (1.3.14-2ubuntu1) ... 778s Setting up liblcms2-2:armhf (2.16-2) ... 778s Setting up ncbi-data (6.1.20170106+dfsg2-5) ... 778s Setting up libpixman-1-0:armhf (0.44.0-3) ... 778s Setting up libsharpyuv0:armhf (1.4.0-0.1) ... 778s Setting up libpaper1:armhf (1.1.29build1) ... 778s 778s Creating config file /etc/papersize with new version 778s Setting up libaom3:armhf (3.11.0~rc1-1) ... 778s Setting up mysql-common (5.8+1.1.1) ... 778s update-alternatives: using /etc/mysql/my.cnf.fallback to provide /etc/mysql/my.cnf (my.cnf) in auto mode 778s Setting up libmysqlclient21:armhf (8.0.40-1) ... 778s Setting up imagemagick-6-common (8:6.9.13.12+dfsg1-1build1) ... 778s Setting up fonts-lato (2.015-1) ... 778s Setting up liblerc4:armhf (4.0.0+ds-4ubuntu2) ... 778s Setting up libxpm4:armhf (1:3.5.17-1build2) ... 778s Setting up hicolor-icon-theme (0.18-1) ... 778s Setting up libxi6:armhf (2:1.8.2-1) ... 778s Setting up probcons (1.12-14) ... 778s Setting up libmbedcrypto7t64:armhf (2.28.8-1) ... 778s Setting up libxrender1:armhf (1:0.9.10-1.1build1) ... 778s Setting up python3-lz4 (4.0.2+dfsg-1build4) ... 778s Setting up libxcb-render0:armhf (1.17.0-2) ... 778s Setting up python3-defusedxml (0.7.1-2) ... 779s Setting up mafft (7.505-1) ... 779s Setting up libarchive-zip-perl (1.68-1) ... 779s Setting up bwa (0.7.18-1) ... 779s Setting up python3-alabaster (0.7.16-0.1) ... 779s Setting up fonts-lyx (2.4.2.1-1) ... 779s Setting up libijs-0.35:armhf (0.35-15.1build1) ... 779s Setting up libdebhelper-perl (13.20ubuntu1) ... 779s Setting up libgs-common (10.03.1~dfsg1-0ubuntu3) ... 779s Setting up libfontbox-java (1:1.8.16-5) ... 779s Setting up phylip (1:3.697+dfsg-4build1) ... 779s Setting up x11-common (1:7.7+23ubuntu3) ... 779s Setting up libdeflate0:armhf (1.22-1) ... 779s Setting up linux-libc-dev:armhf (6.11.0-8.8) ... 779s Setting up python3-tabulate (0.9.0-1) ... 779s Setting up m4 (1.4.19-4build1) ... 779s Setting up libqhull-r8.0:armhf (2020.2-6build1) ... 779s Setting up python3-all (3.12.6-0ubuntu1) ... 779s Setting up libxcb-shm0:armhf (1.17.0-2) ... 779s Setting up libpaper-utils (1.1.29build1) ... 779s Setting up libgomp1:armhf (14.2.0-8ubuntu1) ... 779s Setting up python3-networkx (3.2.1-4ubuntu1) ... 781s Setting up libjbig0:armhf (2.1-6.1ubuntu2) ... 781s Setting up libnetpbm11t64:armhf (2:11.08.01-1) ... 781s Setting up python3-tz (2024.1-2) ... 782s Setting up t-coffee (13.45.0.4846264+really13.41.0.28bdc39+dfsg-1) ... 782s Setting up poppler-data (0.4.12-1) ... 782s Setting up unicode-data (15.1.0-1) ... 782s Setting up python3-mysqldb (1.4.6-2build4) ... 782s Setting up python3-six (1.16.0-7) ... 782s Setting up libpython3.12t64:armhf (3.12.7-3) ... 782s Setting up tex-common (6.18) ... 782s update-language: texlive-base not installed and configured, doing nothing! 782s Setting up python3-roman (4.2-1) ... 783s Setting up python3-decorator (5.1.1-5) ... 783s Setting up libfontenc1:armhf (1:1.1.8-1build1) ... 783s Setting up autotools-dev (20220109.1) ... 783s Setting up libblas3:armhf (3.12.0-3build2) ... 783s 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 783s Setting up python3-packaging (24.1-1) ... 783s Setting up rpcsvc-proto (1.4.2-0ubuntu7) ... 783s Setting up libzzip-0-13t64:armhf (0.13.72+dfsg.1-1.2build1) ... 783s Setting up libfreetype6:armhf (2.13.3+dfsg-1) ... 783s Setting up libjbig2dec0:armhf (0.20-1build3) ... 783s Setting up python3-snowballstemmer (2.2.0-4build1) ... 783s Setting up libteckit0:armhf (2.5.12+ds1-1) ... 783s Setting up python3-brotli (1.1.0-2build2) ... 784s Setting up 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update-alternatives: using /usr/bin/xdvi-xaw to provide /usr/bin/xdvi.bin (xdvi.bin) in auto mode 810s update-alternatives: using /usr/bin/bibtex.original to provide /usr/bin/bibtex (bibtex) in auto mode 810s Setting up build-essential (12.10ubuntu1) ... 810s Setting up texlive-base (2024.20241102-1) ... 811s tl-paper: setting paper size for dvips to a4: /var/lib/texmf/dvips/config/config-paper.ps 811s tl-paper: setting paper size for dvipdfmx to a4: /var/lib/texmf/dvipdfmx/dvipdfmx-paper.cfg 812s tl-paper: setting paper size for xdvi to a4: /var/lib/texmf/xdvi/XDvi-paper 812s tl-paper: setting paper size for pdftex to a4: /var/lib/texmf/tex/generic/tex-ini-files/pdftexconfig.tex 813s Setting up libgs10:armhf (10.03.1~dfsg1-0ubuntu3) ... 813s Setting up libpython3-dev:armhf (3.12.6-0ubuntu1) ... 813s Setting up debhelper (13.20ubuntu1) ... 813s Setting up ghostscript (10.03.1~dfsg1-0ubuntu3) ... 813s Setting up texlive-latex-base (2024.20241102-1) ... 813s Setting up libpython3-all-dev:armhf (3.12.6-0ubuntu1) ... 813s Setting up python3-dev (3.12.6-0ubuntu1) ... 813s Setting up texlive-latex-recommended (2024.20241102-1) ... 813s Setting up texlive-pictures (2024.20241102-1) ... 813s Setting up texlive-fonts-recommended (2024.20241102-1) ... 813s Setting up python3-all-dev (3.12.6-0ubuntu1) ... 813s Setting up texlive-latex-extra (2024.20241102-1) ... 813s Setting up python3-ufolib2 (0.16.1+dfsg1-1) ... 813s Setting up libheif-plugin-aomdec:armhf (1.19.3-1) ... 813s Setting up libheif-plugin-libde265:armhf (1.19.3-1) ... 813s Setting up libheif1:armhf (1.19.3-1) ... 813s Setting up libmagickcore-6.q16-7t64:armhf (8:6.9.13.12+dfsg1-1build1) ... 813s Setting up python3-fonttools (4.46.0-1build2) ... 815s Setting up libmagickwand-6.q16-7t64:armhf (8:6.9.13.12+dfsg1-1build1) ... 815s Setting up imagemagick-6.q16 (8:6.9.13.12+dfsg1-1build1) ... 815s update-alternatives: using /usr/bin/compare-im6.q16 to provide /usr/bin/compare (compare) in auto mode 815s update-alternatives: using /usr/bin/compare-im6.q16 to provide /usr/bin/compare-im6 (compare-im6) in auto mode 815s update-alternatives: using /usr/bin/animate-im6.q16 to provide /usr/bin/animate (animate) in auto mode 815s update-alternatives: using /usr/bin/animate-im6.q16 to provide /usr/bin/animate-im6 (animate-im6) in auto mode 815s update-alternatives: using /usr/bin/convert-im6.q16 to provide /usr/bin/convert (convert) in auto mode 815s update-alternatives: using /usr/bin/convert-im6.q16 to provide /usr/bin/convert-im6 (convert-im6) in auto mode 815s update-alternatives: using /usr/bin/composite-im6.q16 to provide /usr/bin/composite (composite) in auto mode 815s update-alternatives: using /usr/bin/composite-im6.q16 to provide /usr/bin/composite-im6 (composite-im6) in auto mode 815s update-alternatives: using /usr/bin/conjure-im6.q16 to provide /usr/bin/conjure (conjure) in auto mode 815s update-alternatives: using /usr/bin/conjure-im6.q16 to provide /usr/bin/conjure-im6 (conjure-im6) in auto mode 815s update-alternatives: using /usr/bin/import-im6.q16 to provide /usr/bin/import (import) in auto mode 815s update-alternatives: using /usr/bin/import-im6.q16 to provide /usr/bin/import-im6 (import-im6) in auto mode 815s update-alternatives: using /usr/bin/identify-im6.q16 to provide /usr/bin/identify (identify) in auto mode 815s update-alternatives: using /usr/bin/identify-im6.q16 to provide /usr/bin/identify-im6 (identify-im6) in auto mode 815s update-alternatives: using /usr/bin/stream-im6.q16 to provide /usr/bin/stream (stream) in auto mode 815s update-alternatives: using /usr/bin/stream-im6.q16 to provide /usr/bin/stream-im6 (stream-im6) in auto mode 815s update-alternatives: using /usr/bin/display-im6.q16 to provide /usr/bin/display (display) in auto mode 815s update-alternatives: using /usr/bin/display-im6.q16 to provide /usr/bin/display-im6 (display-im6) in auto mode 815s update-alternatives: using /usr/bin/montage-im6.q16 to provide /usr/bin/montage (montage) in auto mode 815s update-alternatives: using /usr/bin/montage-im6.q16 to provide /usr/bin/montage-im6 (montage-im6) in auto mode 815s update-alternatives: using /usr/bin/mogrify-im6.q16 to provide /usr/bin/mogrify (mogrify) in auto mode 815s update-alternatives: using /usr/bin/mogrify-im6.q16 to provide /usr/bin/mogrify-im6 (mogrify-im6) in auto mode 815s Setting up python3-matplotlib (3.8.3-3) ... 817s Setting up hevea (2.36-2) ... 817s Setting up imagemagick (8:6.9.13.12+dfsg1-1build1) ... 817s Processing triggers for install-info (7.1.1-1) ... 817s Processing triggers for libc-bin (2.40-1ubuntu3) ... 817s Processing triggers for man-db (2.12.1-3) ... 819s Processing triggers for sgml-base (1.31) ... 819s Setting up docutils-common (0.21.2+dfsg-2) ... 819s Setting up w3c-sgml-lib (1.3-3) ... 858s Setting up python3-biopython (1.84+dfsg-4build1) ... 860s Setting up python3-biopython-sql (1.84+dfsg-4build1) ... 860s Processing triggers for sgml-base (1.31) ... 860s Setting up python3-docutils (0.21.2+dfsg-2) ... 861s Setting up python3-sphinx (7.4.7-4) ... 862s Setting up python3-sphinxcontrib.jquery (4.1-5) ... 862s Setting up python3-numpydoc (1.6.0-2) ... 863s Setting up python3-sphinx-rtd-theme (3.0.1+dfsg-1) ... 863s Setting up autopkgtest-satdep (0) ... 863s Processing triggers for tex-common (6.18) ... 864s Running updmap-sys. This may take some time... done. 864s Running mktexlsr /var/lib/texmf ... done. 864s Building format(s) --all. 1002s This may take some time... done. 1039s (Reading database ... 105952 files and directories currently installed.) 1039s Removing autopkgtest-satdep (0) ... 1055s autopkgtest [21:51:29]: test full_suite: sh debian/tests/run-unit-test 1055s autopkgtest [21:51:29]: test full_suite: [----------------------- 1057s cp: cannot stat '/usr/share/doc/python-biopython-doc/Doc/Tutorial': No such file or directory 1057s cp: cannot stat '/usr/share/doc/python-biopython-doc/Doc/examples': No such file or directory 1060s mkdir: created directory 'Bio' 1060s mkdir: created directory 'Bio/Align' 1060s mkdir: created directory 'Bio/Align/substitution_matrices' 1060s mkdir: created directory 'Bio/Align/substitution_matrices/data/' 1060s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER22' -> 'Bio/Align/substitution_matrices/data/BENNER22' 1060s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER6' -> 'Bio/Align/substitution_matrices/data/BENNER6' 1060s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER74' -> 'Bio/Align/substitution_matrices/data/BENNER74' 1060s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLASTN' -> 'Bio/Align/substitution_matrices/data/BLASTN' 1060s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLASTP' -> 'Bio/Align/substitution_matrices/data/BLASTP' 1060s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM45' -> 'Bio/Align/substitution_matrices/data/BLOSUM45' 1060s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM50' -> 'Bio/Align/substitution_matrices/data/BLOSUM50' 1060s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM62' -> 'Bio/Align/substitution_matrices/data/BLOSUM62' 1060s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM80' -> 'Bio/Align/substitution_matrices/data/BLOSUM80' 1060s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM90' -> 'Bio/Align/substitution_matrices/data/BLOSUM90' 1060s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/DAYHOFF' -> 'Bio/Align/substitution_matrices/data/DAYHOFF' 1060s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/FENG' -> 'Bio/Align/substitution_matrices/data/FENG' 1060s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/GENETIC' -> 'Bio/Align/substitution_matrices/data/GENETIC' 1060s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/GONNET1992' -> 'Bio/Align/substitution_matrices/data/GONNET1992' 1060s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/HOXD70' -> 'Bio/Align/substitution_matrices/data/HOXD70' 1060s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/JOHNSON' -> 'Bio/Align/substitution_matrices/data/JOHNSON' 1060s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/JONES' -> 'Bio/Align/substitution_matrices/data/JONES' 1060s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/LEVIN' -> 'Bio/Align/substitution_matrices/data/LEVIN' 1060s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MCLACHLAN' -> 'Bio/Align/substitution_matrices/data/MCLACHLAN' 1060s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MDM78' -> 'Bio/Align/substitution_matrices/data/MDM78' 1060s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MEGABLAST' -> 'Bio/Align/substitution_matrices/data/MEGABLAST' 1060s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/NUC.4.4' -> 'Bio/Align/substitution_matrices/data/NUC.4.4' 1060s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM250' -> 'Bio/Align/substitution_matrices/data/PAM250' 1060s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM30' -> 'Bio/Align/substitution_matrices/data/PAM30' 1060s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM70' -> 'Bio/Align/substitution_matrices/data/PAM70' 1060s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/RAO' -> 'Bio/Align/substitution_matrices/data/RAO' 1060s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/RISLER' -> 'Bio/Align/substitution_matrices/data/RISLER' 1060s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/SCHNEIDER' -> 'Bio/Align/substitution_matrices/data/SCHNEIDER' 1060s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/STR' -> 'Bio/Align/substitution_matrices/data/STR' 1060s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/TRANS' -> 'Bio/Align/substitution_matrices/data/TRANS' 1060s Remove test test_Tutorial.py which is bound to fail 1061s test_Ace ... ok 1061s test_Affy ... ok 1064s test_AlignIO ... ok 1064s test_AlignIO_ClustalIO ... ok 1064s test_AlignIO_EmbossIO ... ok 1064s test_AlignIO_FastaIO ... ok 1064s test_AlignIO_MauveIO ... ok 1064s test_AlignIO_PhylipIO ... ok 1064s test_AlignIO_convert ... ok 1064s test_AlignInfo ... ok 1064s test_Align_Alignment ... ok 1065s test_Align_a2m ... ok 1065s test_Align_bed ... ok 1065s test_Align_bigbed ... ok 1065s test_Align_bigmaf ... ok 1066s test_Align_bigpsl ... ok 1066s test_Align_chain ... ok 1066s test_Align_clustal ... ok 1072s test_Align_codonalign ... ok 1072s test_Align_emboss ... ok 1072s test_Align_exonerate ... ok 1072s test_Align_fasta ... ok 1072s test_Align_hhr ... ok 1073s test_Align_maf ... ok 1073s test_Align_mauve ... ok 1073s test_Align_msf ... ok 1073s test_Align_nexus ... ok 1073s test_Align_phylip ... ok 1074s test_Align_psl ... ok 1074s test_Align_sam ... ok 1076s test_Align_stockholm ... ok 1077s test_Align_tabular ... ok 1077s test_Application ... ok 1077s test_BioSQL_MySQLdb_online ... skipping. internet not available 1077s test_BioSQL_mysql_connector ... skipping. BioSQL test configuration file biosql.ini missing (see biosql.ini.sample) 1077s test_BioSQL_mysql_connector_online ... skipping. internet not available 1077s test_BioSQL_psycopg2_online ... skipping. internet not available 1082s test_BioSQL_sqlite3 ... ok 1082s test_BioSQL_sqlite3_online ... skipping. internet not available 1082s test_Blast_Record ... ok 1083s test_Blast_parser ... ok 1083s test_CAPS ... ok 1083s test_Chi2 ... ok 1085s test_ClustalOmega_tool ... ok 1085s test_Clustalw_tool ... skipping. Install clustalw or clustalw2 if you want to use it from Biopython. 1085s test_Cluster ... ok 1085s test_CodonTable ... ok 1085s test_ColorSpiral ... ok 1085s test_Compass ... ok 1086s test_Consensus ... ok 1089s test_Dialign_tool ... ok 1089s test_EMBL_unittest ... ok 1089s test_Emboss ... skipping. $EMBOSS_ROOT='/usr/lib/emboss' which does not exist! 1089s test_EmbossPrimer ... ok 1093s test_Entrez ... ok 1093s test_Entrez_online ... skipping. internet not available 1094s test_Entrez_parser ... ok 1094s test_Enzyme ... ok 1094s test_ExPASy ... skipping. internet not available 1094s test_Fasttree_tool ... ok 1094s test_File ... ok 1094s test_GenBank ... ok 1096s test_GenomeDiagram ... Warn: Can't find .pfb for face 'Helvetica' 1098s ok 1099s test_GraphicsChromosome ... ok 1099s test_GraphicsDistribution ... ok 1100s test_GraphicsGeneral ... ok 1100s test_HMMCasino ... ok 1100s test_HMMGeneral ... ok 1101s test_KEGG ... ok 1101s test_KEGG_online ... skipping. internet not available 1106s test_KGML_graphics ... ok 1106s test_KGML_graphics_online ... skipping. internet not available 1107s test_KGML_nographics ... ok 1107s test_KeyWList ... ok 1107s test_LogisticRegression ... ok 1108s test_MafIO_index ... ok 1110s test_Mafft_tool ... ok 1110s test_MarkovModel ... ok 1110s test_Medline ... ok 1111s test_Muscle_tool ... skipping. Install MUSCLE if you want to use the Bio.Align.Applications wrapper. 1111s test_NCBIXML ... ok 1114s test_NCBI_BLAST_tools ... ok 1115s test_NCBI_qblast ... ok 1115s test_NMR ... ok 1115s test_NaiveBayes ... ok 1115s test_Nexus ... ok 1115s test_PAML_baseml ... ok 1116s test_PAML_codeml ... ok 1116s test_PAML_yn00 ... ok 1119s test_PDB_CEAligner ... ok 1120s test_PDB_DSSP ... /usr/lib/python3/dist-packages/Bio/PDB/DSSP.py:199: UserWarning: 1120s Configuration error: 1120s 1120s The attempt to retrieve compound information for "SO4" failed. 1120s 1120s This information is searched for in a CCD file called components.cif or 1120s components.cif.gz which should be located in one of the following directories: 1120s 1120s "/usr/share/libcifpp" 1120s "/var/cache/libcifpp" 1120s "/tmp/autopkgtest.BXh6wC/autopkgtest_tmp/libcifpp-data" 1120s "/usr/share/libcifpp" 1120s "/usr/share/libcifpp" 1120s 1120s (Note that you can add a directory to the search paths by setting the 1120s LIBCIFPP_DATA_DIR environmental variable) 1120s 1120s On Linux an optional cron script might have been installed that automatically updates 1120s components.cif and mmCIF dictionary files. This script only works when the file 1120s libcifpp.conf contains an uncommented line with the text: 1120s 1120s update=true 1120s 1120s If you do not have a working cron script, you can manually update the files 1120s in /var/cache/libcifpp using the following commands: 1120s 1120s curl -o /var/cache/libcifpp/components.cif https://files.wwpdb.org/pub/pdb/data/monomers/components.cif 1120s curl -o /var/cache/libcifpp/mmcif_pdbx.dic https://mmcif.wwpdb.org/dictionaries/ascii/mmcif_pdbx_v50.dic 1120s curl -o /var/cache/libcifpp/mmcif_ma.dic https://github.com/ihmwg/ModelCIF/raw/master/dist/mmcif_ma.dic 1120s 1120s The current order of compound factory objects is: 1120s 1120s CCD components.cif resource 1120s CCD components.cif resource 1120s Unknown compound: SO4 1120s Missing compound information for SO4 1120s 1120s warnings.warn(err) 1121s ok 1121s test_PDB_Dice ... ok 1121s test_PDB_Disordered ... ok 1122s test_PDB_Exposure ... ok 1122s test_PDB_FragmentMapper ... ok 1124s test_PDB_KDTree ... ok 1124s test_PDB_MMCIF2Dict ... ok 1124s test_PDB_MMCIFIO ... ok 1125s test_PDB_MMCIFParser ... ok 1125s test_PDB_NACCESS ... ok 1126s test_PDB_PDBIO ... ok 1126s test_PDB_PDBList ... skipping. internet not available 1133s test_PDB_PDBMLParser ... ok 1133s test_PDB_PDBParser ... ok 1133s 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 1134s test_PDB_Polypeptide ... ok 1134s test_PDB_QCPSuperimposer ... ok 1137s test_PDB_SASA ... ok 1138s test_PDB_SMCRA ... ok 1138s test_PDB_Selection ... ok 1138s test_PDB_StructureAlignment ... ok 1138s test_PDB_Superimposer ... ok 1138s test_PDB_alphafold_db ... skipping. internet not available 1142s test_PDB_binary_cif ... /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 1, ' ') redefined at line 7. 1142s warnings.warn( 1142s /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 15, ' ') redefined at line 144. 1142s warnings.warn( 1142s /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 15, ' ') redefined at line 153. 1142s warnings.warn( 1142s /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 1, ' ') redefined at line 0. 1142s warnings.warn( 1142s /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 15, ' ') redefined at line 0. 1142s warnings.warn( 1142s ok 1152s test_PDB_internal_coords ... ok 1152s test_PDB_parse_pdb_header ... ok 1152s test_PDB_vectors ... ok 1152s test_PQR ... ok 1153s test_Pathway ... ok 1153s test_Phd ... ok 1153s test_Phylo ... ok 1154s test_PhyloXML ... ok 1154s test_Phylo_CDAO ... ok 1154s test_Phylo_NeXML ... ok 1155s test_Phylo_igraph ... skipping. Install igraph if you wish to use it with Bio.Phylo 1158s test_Phylo_matplotlib ... ok 1159s test_Phylo_networkx ... ok 1160s test_PopGen_GenePop_nodepend ... ok 1161s test_Prank_tool ... ok 1162s test_Probcons_tool ... ok 1163s test_ProtParam ... ok 1164s test_RCSBFormats ... ok 1165s test_Restriction ... ok 1165s test_SCOP_Astral ... ok 1166s test_SCOP_Cla ... ok 1166s test_SCOP_Des ... ok 1167s test_SCOP_Dom ... ok 1167s test_SCOP_Hie ... ok 1168s test_SCOP_Raf ... ok 1169s test_SCOP_Residues ... ok 1169s test_SCOP_Scop ... ok 1170s test_SVDSuperimposer ... ok 1170s test_SearchIO_blast_tab ... ok 1171s test_SearchIO_blast_tab_index ... ok 1172s test_SearchIO_blast_xml ... ok 1174s test_SearchIO_blast_xml_index ... ok 1174s test_SearchIO_blat_psl ... ok 1175s test_SearchIO_blat_psl_index ... ok 1176s test_SearchIO_exonerate ... ok 1176s test_SearchIO_exonerate_text_index ... ok 1177s test_SearchIO_exonerate_vulgar_index ... ok 1177s test_SearchIO_fasta_m10 ... ok 1178s test_SearchIO_fasta_m10_index ... ok 1179s test_SearchIO_hhsuite2_text ... ok 1179s test_SearchIO_hmmer2_text ... ok 1180s test_SearchIO_hmmer2_text_index ... ok 1181s test_SearchIO_hmmer3_domtab ... ok 1181s test_SearchIO_hmmer3_domtab_index ... ok 1182s test_SearchIO_hmmer3_tab ... ok 1182s test_SearchIO_hmmer3_tab_index ... ok 1183s test_SearchIO_hmmer3_text ... ok 1183s test_SearchIO_hmmer3_text_index ... ok 1184s test_SearchIO_interproscan_xml ... ok 1184s test_SearchIO_model ... ok 1185s test_SearchIO_write ... ok 1186s test_SeqFeature ... ok 1203s test_SeqIO ... ok 1204s test_SeqIO_AbiIO ... ok 1205s test_SeqIO_FastaIO ... ok 1205s test_SeqIO_Gck ... ok 1206s test_SeqIO_Gfa ... ok 1206s test_SeqIO_Insdc ... ok 1207s test_SeqIO_NibIO ... ok 1209s test_SeqIO_PdbIO ... ok 1210s test_SeqIO_QualityIO ... ok 1211s test_SeqIO_SeqXML ... ok 1211s test_SeqIO_SnapGene ... ok 1213s test_SeqIO_TwoBitIO ... ok 1213s test_SeqIO_Xdna ... ok 1214s test_SeqIO_features ... ok 1231s test_SeqIO_index ... ok 1231s test_SeqIO_online ... skipping. internet not available 1232s test_SeqIO_write ... ok 1232s test_SeqRecord ... ok 1233s test_SeqUtils ... ok 1235s test_Seq_objs ... ok 1236s test_SffIO ... ok 1237s test_SwissProt ... ok 1241s test_TCoffee_tool ... ok 1241s test_TogoWS ... skipping. internet not available 1242s test_TreeConstruction ... ok 1243s test_UniGene ... ok 1243s test_UniProt ... skipping. internet not available 1244s test_UniProt_GOA ... ok 1244s test_UniProt_Parser ... ok 1245s test_align ... ok 1246s test_align_substitution_matrices ... ok 1249s test_bgzf ... ok 1249s test_cellosaurus ... ok 1256s test_codonalign ... ok 1256s test_geo ... ok 1257s test_kNN ... ok 1258s test_motifs ... ok 1258s test_motifs_online ... skipping. internet not available 1258s 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. 1258s warnings.warn( 1258s ok 1259s test_pairwise2_no_C ... ok 1260s test_pairwise_aligner ... ok 1261s test_pairwise_alignment_map ... ok 1270s test_phenotype ... ok 1270s test_phenotype_fit ... ok 1271s 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. 1271s test_prodoc ... ok 1272s test_prosite ... ok 1272s test_raxml_tool ... skipping. Install RAxML (binary raxmlHPC) if you want to test the Bio.Phylo.Applications wrapper. 1273s test_samtools_tool ... skipping. Install samtools and correctly set the file path to the program if you want to use it from Biopython 1273s test_seq ... ok 1274s test_translate ... ok 1274s Skipping any tests requiring internet access 1274s Python version: 3.12.7 (main, Nov 8 2024, 17:55:36) [GCC 14.2.0] 1274s Operating system: posix linux 1274s ---------------------------------------------------------------------- 1274s Ran 217 tests in 213.436 seconds 1274s 1276s autopkgtest [21:55:10]: test full_suite: -----------------------] 1280s autopkgtest [21:55:14]: test full_suite: - - - - - - - - - - results - - - - - - - - - - 1280s full_suite PASS 1284s autopkgtest [21:55:18]: @@@@@@@@@@@@@@@@@@@@ summary 1284s dependencies PASS 1284s full_suite PASS