0s autopkgtest [09:43:22]: starting date and time: 2024-10-30 09:43:22+0000 0s autopkgtest [09:43:22]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [09:43:22]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.szuum32_/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:setuptools --apt-upgrade python-biopython --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=setuptools/75.2.0-1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-arm64-44.secgroup --name adt-plucky-arm64-python-biopython-20241030-094321-juju-7f2275-prod-proposed-migration-environment-2-6a0cdafa-ee97-43f4-819f-e38913519adb --image adt/ubuntu-plucky-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 72s autopkgtest [09:44:34]: testbed dpkg architecture: arm64 72s autopkgtest [09:44:34]: testbed apt version: 2.9.8 72s autopkgtest [09:44:34]: @@@@@@@@@@@@@@@@@@@@ test bed setup 73s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 73s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [212 kB] 74s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [2840 B] 74s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [28.1 kB] 74s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 74s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [59.3 kB] 74s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 Packages [50.3 kB] 74s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [249 kB] 74s Fetched 682 kB in 1s (1038 kB/s) 74s Reading package lists... 76s Reading package lists... 77s Building dependency tree... 77s Reading state information... 77s Calculating upgrade... 78s The following NEW packages will be installed: 78s python3-jaraco.text 78s The following packages will be upgraded: 78s libkeyutils1 python3-pkg-resources python3-setuptools 78s 3 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 78s Need to get 812 kB of archives. 78s After this operation, 13.3 kB of additional disk space will be used. 78s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 libkeyutils1 arm64 1.6.3-4ubuntu2 [10.2 kB] 78s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-jaraco.text all 4.0.0-1 [11.5 kB] 78s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-pkg-resources all 75.2.0-1 [134 kB] 78s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-setuptools all 75.2.0-1 [657 kB] 79s Fetched 812 kB in 1s (1485 kB/s) 79s (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 ... 79697 files and directories currently installed.) 79s Preparing to unpack .../libkeyutils1_1.6.3-4ubuntu2_arm64.deb ... 79s Unpacking libkeyutils1:arm64 (1.6.3-4ubuntu2) over (1.6.3-3build1) ... 79s Selecting previously unselected package python3-jaraco.text. 79s Preparing to unpack .../python3-jaraco.text_4.0.0-1_all.deb ... 79s Unpacking python3-jaraco.text (4.0.0-1) ... 79s Preparing to unpack .../python3-pkg-resources_75.2.0-1_all.deb ... 79s Unpacking python3-pkg-resources (75.2.0-1) over (74.1.2-1) ... 79s Preparing to unpack .../python3-setuptools_75.2.0-1_all.deb ... 80s Unpacking python3-setuptools (75.2.0-1) over (74.1.2-1) ... 80s Setting up python3-pkg-resources (75.2.0-1) ... 80s Setting up libkeyutils1:arm64 (1.6.3-4ubuntu2) ... 80s Setting up python3-jaraco.text (4.0.0-1) ... 80s Setting up python3-setuptools (75.2.0-1) ... 81s Processing triggers for libc-bin (2.40-1ubuntu3) ... 81s Reading package lists... 81s Building dependency tree... 81s Reading state information... 82s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 83s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 83s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 83s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 83s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 84s Reading package lists... 84s Reading package lists... 84s Building dependency tree... 84s Reading state information... 85s Calculating upgrade... 85s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 85s Reading package lists... 85s Building dependency tree... 85s Reading state information... 86s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 89s autopkgtest [09:44:51]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 14:19:41 UTC 2024 89s autopkgtest [09:44:51]: @@@@@@@@@@@@@@@@@@@@ apt-source python-biopython 93s Get:1 http://ftpmaster.internal/ubuntu plucky/universe python-biopython 1.83+dfsg1-3 (dsc) [3437 B] 93s Get:2 http://ftpmaster.internal/ubuntu plucky/universe python-biopython 1.83+dfsg1-3 (tar) [11.5 MB] 93s Get:3 http://ftpmaster.internal/ubuntu plucky/universe python-biopython 1.83+dfsg1-3 (diff) [21.7 kB] 93s gpgv: Signature made Wed May 22 13:59:24 2024 UTC 93s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 93s gpgv: issuer "emollier@debian.org" 93s gpgv: Can't check signature: No public key 93s dpkg-source: warning: cannot verify inline signature for ./python-biopython_1.83+dfsg1-3.dsc: no acceptable signature found 94s autopkgtest [09:44:56]: testing package python-biopython version 1.83+dfsg1-3 94s autopkgtest [09:44:56]: build not needed 99s autopkgtest [09:45:01]: test dependencies: preparing testbed 100s Reading package lists... 101s Building dependency tree... 101s Reading state information... 101s Starting pkgProblemResolver with broken count: 0 101s Starting 2 pkgProblemResolver with broken count: 0 101s Done 102s The following additional packages will be installed: 102s fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-urw-base35 102s libblas3 libcairo2 libdeflate0 libfontconfig1 libfontenc1 libgfortran5 102s libgomp1 libgraphite2-3 libharfbuzz0b libimagequant0 libjbig0 libjpeg-turbo8 102s libjpeg8 liblapack3 liblcms2-2 liblerc4 libopenjp2-7 libpixman-1-0 libraqm0 102s libsharpyuv0 libtiff6 libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 102s libxcb-shm0 libxrender1 python-biopython-doc python3-all python3-biopython 102s python3-biopython-sql python3-cairo python3-freetype python3-numpy 102s python3-pil python3-reportlab python3-rlpycairo sgml-base w3c-sgml-lib 102s x11-common xfonts-encodings xfonts-utils xml-core 102s Suggested packages: 102s fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre liblcms2-utils 102s python3-tk bwa clustalo clustalw dialign dssp emboss fasttree mafft muscle3 102s phylip phyml prank probcons python3-mysqldb python3-matplotlib python3-mmtf 102s python3-rdflib python3-psycopg2 python3-scipy raxml samtools t-coffee wise 102s gcc gfortran python-numpy-doc python3-dev python3-pytest python-pil-doc 102s pdf-viewer python3-egenix-mxtexttools python-reportlab-doc rl-accel 102s rl-renderpm sgml-base-doc debhelper 102s Recommended packages: 102s ncbi-blast+ python3-olefile fonts-dejavu-extra 102s The following NEW packages will be installed: 102s autopkgtest-satdep fontconfig-config fonts-dejavu-core fonts-dejavu-mono 102s fonts-urw-base35 libblas3 libcairo2 libdeflate0 libfontconfig1 libfontenc1 102s libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libimagequant0 libjbig0 102s libjpeg-turbo8 libjpeg8 liblapack3 liblcms2-2 liblerc4 libopenjp2-7 102s libpixman-1-0 libraqm0 libsharpyuv0 libtiff6 libwebp7 libwebpdemux2 102s libwebpmux3 libxcb-render0 libxcb-shm0 libxrender1 python-biopython-doc 102s python3-all python3-biopython python3-biopython-sql python3-cairo 102s python3-freetype python3-numpy python3-pil python3-reportlab 102s python3-rlpycairo sgml-base w3c-sgml-lib x11-common xfonts-encodings 102s xfonts-utils xml-core 102s 0 upgraded, 48 newly installed, 0 to remove and 0 not upgraded. 102s Need to get 43.6 MB/43.7 MB of archives. 102s After this operation, 102 MB of additional disk space will be used. 102s Get:1 /tmp/autopkgtest.sA24HF/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [736 B] 102s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 sgml-base all 1.31 [11.4 kB] 102s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 102s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 103s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 libfontenc1 arm64 1:1.1.8-1build1 [13.9 kB] 103s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 103s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 103s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 xfonts-utils arm64 1:7.7+7 [95.6 kB] 103s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-urw-base35 all 20200910-8 [11.0 MB] 103s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig-config arm64 2.15.0-1.1ubuntu2 [37.4 kB] 103s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.0-3build2 [152 kB] 103s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 libfontconfig1 arm64 2.15.0-1.1ubuntu2 [142 kB] 103s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 libpixman-1-0 arm64 0.42.2-1build1 [204 kB] 103s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-render0 arm64 1.17.0-2 [16.6 kB] 103s Get:15 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-shm0 arm64 1.17.0-2 [5884 B] 103s Get:16 http://ftpmaster.internal/ubuntu plucky/main arm64 libxrender1 arm64 1:0.9.10-1.1build1 [18.8 kB] 103s Get:17 http://ftpmaster.internal/ubuntu plucky/main arm64 libcairo2 arm64 1.18.2-2 [560 kB] 103s Get:18 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate0 arm64 1.21-1 [46.2 kB] 103s Get:19 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 14.2.0-7ubuntu1 [438 kB] 103s Get:20 http://ftpmaster.internal/ubuntu plucky/main arm64 libgomp1 arm64 14.2.0-7ubuntu1 [145 kB] 103s Get:21 http://ftpmaster.internal/ubuntu plucky/main arm64 libgraphite2-3 arm64 1.3.14-2ubuntu1 [70.6 kB] 103s Get:22 http://ftpmaster.internal/ubuntu plucky/main arm64 libharfbuzz0b arm64 9.0.0-1 [486 kB] 103s Get:23 http://ftpmaster.internal/ubuntu plucky/main arm64 libimagequant0 arm64 2.18.0-1build1 [37.1 kB] 103s Get:24 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg-turbo8 arm64 2.1.5-2ubuntu2 [163 kB] 103s Get:25 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 103s Get:26 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.0-3build2 [2293 kB] 103s Get:27 http://ftpmaster.internal/ubuntu plucky/main arm64 liblcms2-2 arm64 2.14-2build1 [161 kB] 103s Get:28 http://ftpmaster.internal/ubuntu plucky/main arm64 liblerc4 arm64 4.0.0+ds-4ubuntu2 [154 kB] 103s Get:29 http://ftpmaster.internal/ubuntu plucky/main arm64 libraqm0 arm64 0.10.1-1build1 [14.7 kB] 103s Get:30 http://ftpmaster.internal/ubuntu plucky/main arm64 libsharpyuv0 arm64 1.4.0-0.1 [16.3 kB] 103s Get:31 http://ftpmaster.internal/ubuntu plucky/main arm64 libjbig0 arm64 2.1-6.1ubuntu2 [29.3 kB] 103s Get:32 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebp7 arm64 1.4.0-0.1 [192 kB] 103s Get:33 http://ftpmaster.internal/ubuntu plucky/main arm64 libtiff6 arm64 4.5.1+git230720-4ubuntu4 [193 kB] 103s Get:34 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebpdemux2 arm64 1.4.0-0.1 [12.3 kB] 103s Get:35 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebpmux3 arm64 1.4.0-0.1 [25.1 kB] 103s Get:36 http://ftpmaster.internal/ubuntu plucky/universe arm64 python-biopython-doc all 1.83+dfsg1-3 [17.4 MB] 104s Get:37 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-all arm64 3.12.6-0ubuntu1 [886 B] 104s Get:38 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy arm64 1:1.26.4+ds-11build1 [3654 kB] 104s Get:39 http://ftpmaster.internal/ubuntu plucky/main arm64 libopenjp2-7 arm64 2.5.0-2ubuntu1 [182 kB] 104s Get:40 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-pil arm64 10.4.0-1ubuntu1 [456 kB] 105s Get:41 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-cairo arm64 1.26.1-2 [121 kB] 105s Get:42 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-freetype all 2.4.0-2 [81.3 kB] 105s Get:43 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-rlpycairo all 0.3.0-3 [9130 B] 105s Get:44 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-reportlab all 4.2.2-1 [1130 kB] 105s Get:45 http://ftpmaster.internal/ubuntu plucky/main arm64 xml-core all 0.19 [20.3 kB] 105s Get:46 http://ftpmaster.internal/ubuntu plucky/universe arm64 w3c-sgml-lib all 1.3-3 [280 kB] 105s Get:47 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-biopython arm64 1.83+dfsg1-3 [1646 kB] 105s Get:48 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-biopython-sql all 1.83+dfsg1-3 [25.7 kB] 105s Fetched 43.6 MB in 3s (16.4 MB/s) 105s Selecting previously unselected package sgml-base. 105s (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 ... 79706 files and directories currently installed.) 105s Preparing to unpack .../00-sgml-base_1.31_all.deb ... 105s Unpacking sgml-base (1.31) ... 105s Selecting previously unselected package fonts-dejavu-mono. 105s Preparing to unpack .../01-fonts-dejavu-mono_2.37-8_all.deb ... 105s Unpacking fonts-dejavu-mono (2.37-8) ... 105s Selecting previously unselected package fonts-dejavu-core. 105s Preparing to unpack .../02-fonts-dejavu-core_2.37-8_all.deb ... 105s Unpacking fonts-dejavu-core (2.37-8) ... 105s Selecting previously unselected package libfontenc1:arm64. 105s Preparing to unpack .../03-libfontenc1_1%3a1.1.8-1build1_arm64.deb ... 105s Unpacking libfontenc1:arm64 (1:1.1.8-1build1) ... 105s Selecting previously unselected package x11-common. 105s Preparing to unpack .../04-x11-common_1%3a7.7+23ubuntu3_all.deb ... 105s Unpacking x11-common (1:7.7+23ubuntu3) ... 106s Selecting previously unselected package xfonts-encodings. 106s Preparing to unpack .../05-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 106s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 106s Selecting previously unselected package xfonts-utils. 106s Preparing to unpack .../06-xfonts-utils_1%3a7.7+7_arm64.deb ... 106s Unpacking xfonts-utils (1:7.7+7) ... 106s Selecting previously unselected package fonts-urw-base35. 106s Preparing to unpack .../07-fonts-urw-base35_20200910-8_all.deb ... 106s Unpacking fonts-urw-base35 (20200910-8) ... 106s Selecting previously unselected package fontconfig-config. 106s Preparing to unpack .../08-fontconfig-config_2.15.0-1.1ubuntu2_arm64.deb ... 106s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ... 106s Selecting previously unselected package libblas3:arm64. 106s Preparing to unpack .../09-libblas3_3.12.0-3build2_arm64.deb ... 106s Unpacking libblas3:arm64 (3.12.0-3build2) ... 106s Selecting previously unselected package libfontconfig1:arm64. 106s Preparing to unpack .../10-libfontconfig1_2.15.0-1.1ubuntu2_arm64.deb ... 106s Unpacking libfontconfig1:arm64 (2.15.0-1.1ubuntu2) ... 106s Selecting previously unselected package libpixman-1-0:arm64. 106s Preparing to unpack .../11-libpixman-1-0_0.42.2-1build1_arm64.deb ... 106s Unpacking libpixman-1-0:arm64 (0.42.2-1build1) ... 106s Selecting previously unselected package libxcb-render0:arm64. 106s Preparing to unpack .../12-libxcb-render0_1.17.0-2_arm64.deb ... 106s Unpacking libxcb-render0:arm64 (1.17.0-2) ... 106s Selecting previously unselected package libxcb-shm0:arm64. 106s Preparing to unpack .../13-libxcb-shm0_1.17.0-2_arm64.deb ... 106s Unpacking libxcb-shm0:arm64 (1.17.0-2) ... 106s Selecting previously unselected package libxrender1:arm64. 106s Preparing to unpack .../14-libxrender1_1%3a0.9.10-1.1build1_arm64.deb ... 106s Unpacking libxrender1:arm64 (1:0.9.10-1.1build1) ... 106s Selecting previously unselected package libcairo2:arm64. 106s Preparing to unpack .../15-libcairo2_1.18.2-2_arm64.deb ... 106s Unpacking libcairo2:arm64 (1.18.2-2) ... 106s Selecting previously unselected package libdeflate0:arm64. 106s Preparing to unpack .../16-libdeflate0_1.21-1_arm64.deb ... 106s Unpacking libdeflate0:arm64 (1.21-1) ... 106s Selecting previously unselected package libgfortran5:arm64. 106s Preparing to unpack .../17-libgfortran5_14.2.0-7ubuntu1_arm64.deb ... 106s Unpacking libgfortran5:arm64 (14.2.0-7ubuntu1) ... 106s Selecting previously unselected package libgomp1:arm64. 107s Preparing to unpack .../18-libgomp1_14.2.0-7ubuntu1_arm64.deb ... 107s Unpacking libgomp1:arm64 (14.2.0-7ubuntu1) ... 107s Selecting previously unselected package libgraphite2-3:arm64. 107s Preparing to unpack .../19-libgraphite2-3_1.3.14-2ubuntu1_arm64.deb ... 107s Unpacking libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 107s Selecting previously unselected package libharfbuzz0b:arm64. 107s Preparing to unpack .../20-libharfbuzz0b_9.0.0-1_arm64.deb ... 107s Unpacking libharfbuzz0b:arm64 (9.0.0-1) ... 107s Selecting previously unselected package libimagequant0:arm64. 107s Preparing to unpack .../21-libimagequant0_2.18.0-1build1_arm64.deb ... 107s Unpacking libimagequant0:arm64 (2.18.0-1build1) ... 107s Selecting previously unselected package libjpeg-turbo8:arm64. 107s Preparing to unpack .../22-libjpeg-turbo8_2.1.5-2ubuntu2_arm64.deb ... 107s Unpacking libjpeg-turbo8:arm64 (2.1.5-2ubuntu2) ... 107s Selecting previously unselected package libjpeg8:arm64. 107s Preparing to unpack .../23-libjpeg8_8c-2ubuntu11_arm64.deb ... 107s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 107s Selecting previously unselected package liblapack3:arm64. 107s Preparing to unpack .../24-liblapack3_3.12.0-3build2_arm64.deb ... 107s Unpacking liblapack3:arm64 (3.12.0-3build2) ... 107s Selecting previously unselected package liblcms2-2:arm64. 107s Preparing to unpack .../25-liblcms2-2_2.14-2build1_arm64.deb ... 107s Unpacking liblcms2-2:arm64 (2.14-2build1) ... 107s Selecting previously unselected package liblerc4:arm64. 107s Preparing to unpack .../26-liblerc4_4.0.0+ds-4ubuntu2_arm64.deb ... 107s Unpacking liblerc4:arm64 (4.0.0+ds-4ubuntu2) ... 107s Selecting previously unselected package libraqm0:arm64. 107s Preparing to unpack .../27-libraqm0_0.10.1-1build1_arm64.deb ... 107s Unpacking libraqm0:arm64 (0.10.1-1build1) ... 107s Selecting previously unselected package libsharpyuv0:arm64. 107s Preparing to unpack .../28-libsharpyuv0_1.4.0-0.1_arm64.deb ... 107s Unpacking libsharpyuv0:arm64 (1.4.0-0.1) ... 107s Selecting previously unselected package libjbig0:arm64. 107s Preparing to unpack .../29-libjbig0_2.1-6.1ubuntu2_arm64.deb ... 107s Unpacking libjbig0:arm64 (2.1-6.1ubuntu2) ... 107s Selecting previously unselected package libwebp7:arm64. 107s Preparing to unpack .../30-libwebp7_1.4.0-0.1_arm64.deb ... 107s Unpacking libwebp7:arm64 (1.4.0-0.1) ... 107s Selecting previously unselected package libtiff6:arm64. 107s Preparing to unpack .../31-libtiff6_4.5.1+git230720-4ubuntu4_arm64.deb ... 107s Unpacking libtiff6:arm64 (4.5.1+git230720-4ubuntu4) ... 107s Selecting previously unselected package libwebpdemux2:arm64. 107s Preparing to unpack .../32-libwebpdemux2_1.4.0-0.1_arm64.deb ... 107s Unpacking libwebpdemux2:arm64 (1.4.0-0.1) ... 107s Selecting previously unselected package libwebpmux3:arm64. 107s Preparing to unpack .../33-libwebpmux3_1.4.0-0.1_arm64.deb ... 107s Unpacking libwebpmux3:arm64 (1.4.0-0.1) ... 107s Selecting previously unselected package python-biopython-doc. 107s Preparing to unpack .../34-python-biopython-doc_1.83+dfsg1-3_all.deb ... 107s Unpacking python-biopython-doc (1.83+dfsg1-3) ... 107s Selecting previously unselected package python3-all. 107s Preparing to unpack .../35-python3-all_3.12.6-0ubuntu1_arm64.deb ... 107s Unpacking python3-all (3.12.6-0ubuntu1) ... 107s Selecting previously unselected package python3-numpy. 107s Preparing to unpack .../36-python3-numpy_1%3a1.26.4+ds-11build1_arm64.deb ... 107s Unpacking python3-numpy (1:1.26.4+ds-11build1) ... 108s Selecting previously unselected package libopenjp2-7:arm64. 108s Preparing to unpack .../37-libopenjp2-7_2.5.0-2ubuntu1_arm64.deb ... 108s Unpacking libopenjp2-7:arm64 (2.5.0-2ubuntu1) ... 108s Selecting previously unselected package python3-pil:arm64. 108s Preparing to unpack .../38-python3-pil_10.4.0-1ubuntu1_arm64.deb ... 108s Unpacking python3-pil:arm64 (10.4.0-1ubuntu1) ... 108s Selecting previously unselected package python3-cairo. 108s Preparing to unpack .../39-python3-cairo_1.26.1-2_arm64.deb ... 108s Unpacking python3-cairo (1.26.1-2) ... 108s Selecting previously unselected package python3-freetype. 108s Preparing to unpack .../40-python3-freetype_2.4.0-2_all.deb ... 108s Unpacking python3-freetype (2.4.0-2) ... 108s Selecting previously unselected package python3-rlpycairo. 108s Preparing to unpack .../41-python3-rlpycairo_0.3.0-3_all.deb ... 108s Unpacking python3-rlpycairo (0.3.0-3) ... 108s Selecting previously unselected package python3-reportlab. 108s Preparing to unpack .../42-python3-reportlab_4.2.2-1_all.deb ... 108s Unpacking python3-reportlab (4.2.2-1) ... 108s Selecting previously unselected package xml-core. 108s Preparing to unpack .../43-xml-core_0.19_all.deb ... 108s Unpacking xml-core (0.19) ... 108s Selecting previously unselected package w3c-sgml-lib. 108s Preparing to unpack .../44-w3c-sgml-lib_1.3-3_all.deb ... 108s Unpacking w3c-sgml-lib (1.3-3) ... 108s Selecting previously unselected package python3-biopython. 108s Preparing to unpack .../45-python3-biopython_1.83+dfsg1-3_arm64.deb ... 108s Unpacking python3-biopython (1.83+dfsg1-3) ... 108s Selecting previously unselected package python3-biopython-sql. 108s Preparing to unpack .../46-python3-biopython-sql_1.83+dfsg1-3_all.deb ... 108s Unpacking python3-biopython-sql (1.83+dfsg1-3) ... 108s Selecting previously unselected package autopkgtest-satdep. 108s Preparing to unpack .../47-1-autopkgtest-satdep.deb ... 108s Unpacking autopkgtest-satdep (0) ... 108s Setting up libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 108s Setting up liblcms2-2:arm64 (2.14-2build1) ... 108s Setting up libpixman-1-0:arm64 (0.42.2-1build1) ... 108s Setting up libsharpyuv0:arm64 (1.4.0-0.1) ... 108s Setting up liblerc4:arm64 (4.0.0+ds-4ubuntu2) ... 108s Setting up libxrender1:arm64 (1:0.9.10-1.1build1) ... 108s Setting up libxcb-render0:arm64 (1.17.0-2) ... 108s Setting up x11-common (1:7.7+23ubuntu3) ... 109s Setting up libdeflate0:arm64 (1.21-1) ... 109s Setting up python3-all (3.12.6-0ubuntu1) ... 109s Setting up libxcb-shm0:arm64 (1.17.0-2) ... 109s Setting up libgomp1:arm64 (14.2.0-7ubuntu1) ... 109s Setting up python3-freetype (2.4.0-2) ... 109s Setting up libjbig0:arm64 (2.1-6.1ubuntu2) ... 109s Setting up libfontenc1:arm64 (1:1.1.8-1build1) ... 109s Setting up libblas3:arm64 (3.12.0-3build2) ... 109s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode 109s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 109s Setting up libimagequant0:arm64 (2.18.0-1build1) ... 109s Setting up fonts-dejavu-mono (2.37-8) ... 109s Setting up fonts-dejavu-core (2.37-8) ... 109s Setting up libjpeg-turbo8:arm64 (2.1.5-2ubuntu2) ... 109s Setting up libgfortran5:arm64 (14.2.0-7ubuntu1) ... 109s Setting up libwebp7:arm64 (1.4.0-0.1) ... 109s Setting up python-biopython-doc (1.83+dfsg1-3) ... 109s Setting up libopenjp2-7:arm64 (2.5.0-2ubuntu1) ... 109s Setting up libharfbuzz0b:arm64 (9.0.0-1) ... 109s Setting up sgml-base (1.31) ... 109s Setting up libwebpmux3:arm64 (1.4.0-0.1) ... 109s Setting up libjpeg8:arm64 (8c-2ubuntu11) ... 109s Setting up liblapack3:arm64 (3.12.0-3build2) ... 109s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode 109s Setting up fontconfig-config (2.15.0-1.1ubuntu2) ... 109s Setting up libwebpdemux2:arm64 (1.4.0-0.1) ... 109s Setting up xfonts-utils (1:7.7+7) ... 109s Setting up libraqm0:arm64 (0.10.1-1build1) ... 109s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 111s Setting up libtiff6:arm64 (4.5.1+git230720-4ubuntu4) ... 111s Setting up xml-core (0.19) ... 111s Setting up libfontconfig1:arm64 (2.15.0-1.1ubuntu2) ... 111s Setting up fonts-urw-base35 (20200910-8) ... 111s Setting up libcairo2:arm64 (1.18.2-2) ... 111s Setting up python3-pil:arm64 (10.4.0-1ubuntu1) ... 112s Setting up python3-cairo (1.26.1-2) ... 112s Setting up python3-rlpycairo (0.3.0-3) ... 112s Setting up python3-reportlab (4.2.2-1) ... 113s Processing triggers for libc-bin (2.40-1ubuntu3) ... 113s Processing triggers for man-db (2.12.1-3) ... 114s Processing triggers for sgml-base (1.31) ... 114s Setting up w3c-sgml-lib (1.3-3) ... 147s Setting up python3-biopython (1.83+dfsg1-3) ... 149s Setting up python3-biopython-sql (1.83+dfsg1-3) ... 149s Setting up autopkgtest-satdep (0) ... 154s (Reading database ... 84721 files and directories currently installed.) 154s Removing autopkgtest-satdep (0) ... 154s autopkgtest [09:45:56]: test dependencies: sh debian/tests/run-unit-test 154s autopkgtest [09:45:56]: test dependencies: [----------------------- 156s mkdir: created directory 'Bio' 156s mkdir: created directory 'Bio/Align' 156s mkdir: created directory 'Bio/Align/substitution_matrices' 156s mkdir: created directory 'Bio/Align/substitution_matrices/data/' 156s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER22' -> 'Bio/Align/substitution_matrices/data/BENNER22' 156s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER6' -> 'Bio/Align/substitution_matrices/data/BENNER6' 156s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER74' -> 'Bio/Align/substitution_matrices/data/BENNER74' 156s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLASTN' -> 'Bio/Align/substitution_matrices/data/BLASTN' 156s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLASTP' -> 'Bio/Align/substitution_matrices/data/BLASTP' 156s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM45' -> 'Bio/Align/substitution_matrices/data/BLOSUM45' 156s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM50' -> 'Bio/Align/substitution_matrices/data/BLOSUM50' 156s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM62' -> 'Bio/Align/substitution_matrices/data/BLOSUM62' 156s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM80' -> 'Bio/Align/substitution_matrices/data/BLOSUM80' 156s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM90' -> 'Bio/Align/substitution_matrices/data/BLOSUM90' 156s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/DAYHOFF' -> 'Bio/Align/substitution_matrices/data/DAYHOFF' 156s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/FENG' -> 'Bio/Align/substitution_matrices/data/FENG' 156s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/GENETIC' -> 'Bio/Align/substitution_matrices/data/GENETIC' 156s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/GONNET1992' -> 'Bio/Align/substitution_matrices/data/GONNET1992' 156s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/HOXD70' -> 'Bio/Align/substitution_matrices/data/HOXD70' 156s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/JOHNSON' -> 'Bio/Align/substitution_matrices/data/JOHNSON' 156s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/JONES' -> 'Bio/Align/substitution_matrices/data/JONES' 156s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/LEVIN' -> 'Bio/Align/substitution_matrices/data/LEVIN' 156s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MCLACHLAN' -> 'Bio/Align/substitution_matrices/data/MCLACHLAN' 156s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MDM78' -> 'Bio/Align/substitution_matrices/data/MDM78' 156s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MEGABLAST' -> 'Bio/Align/substitution_matrices/data/MEGABLAST' 156s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/NUC.4.4' -> 'Bio/Align/substitution_matrices/data/NUC.4.4' 156s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM250' -> 'Bio/Align/substitution_matrices/data/PAM250' 156s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM30' -> 'Bio/Align/substitution_matrices/data/PAM30' 156s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM70' -> 'Bio/Align/substitution_matrices/data/PAM70' 156s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/RAO' -> 'Bio/Align/substitution_matrices/data/RAO' 156s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/RISLER' -> 'Bio/Align/substitution_matrices/data/RISLER' 156s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/SCHNEIDER' -> 'Bio/Align/substitution_matrices/data/SCHNEIDER' 156s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/STR' -> 'Bio/Align/substitution_matrices/data/STR' 156s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/TRANS' -> 'Bio/Align/substitution_matrices/data/TRANS' 156s Remove test test_Tutorial.py which is bound to fail 157s test_Ace ... ok 157s test_Affy ... ok 160s test_AlignIO ... ok 160s test_AlignIO_ClustalIO ... ok 160s test_AlignIO_EmbossIO ... ok 160s test_AlignIO_FastaIO ... ok 160s test_AlignIO_MauveIO ... ok 160s test_AlignIO_PhylipIO ... ok 160s test_AlignIO_convert ... ok 160s test_AlignInfo ... ok 161s test_Align_Alignment ... ok 161s test_Align_a2m ... ok 161s test_Align_bed ... ok 161s test_Align_bigbed ... ok 162s test_Align_bigmaf ... ok 162s test_Align_bigpsl ... ok 162s test_Align_chain ... ok 162s test_Align_clustal ... ok 165s test_Align_codonalign ... ok 165s test_Align_emboss ... ok 166s test_Align_exonerate ... ok 166s test_Align_fasta ... ok 166s test_Align_hhr ... ok 166s test_Align_maf ... ok 166s test_Align_mauve ... ok 166s test_Align_msf ... ok 167s test_Align_nexus ... ok 167s test_Align_phylip ... ok 167s test_Align_psl ... ok 167s test_Align_sam ... ok 169s test_Align_stockholm ... ok 170s test_Align_tabular ... ok 170s test_Application ... ok 170s test_BioSQL_MySQLdb_online ... skipping. internet not available 170s test_BioSQL_mysql_connector ... skipping. BioSQL test configuration file biosql.ini missing (see biosql.ini.sample) 170s test_BioSQL_mysql_connector_online ... skipping. internet not available 170s test_BioSQL_psycopg2_online ... skipping. internet not available 174s test_BioSQL_sqlite3 ... ok 175s test_BioSQL_sqlite3_online ... skipping. internet not available 175s test_Blast_Record ... ok 175s test_CAPS ... ok 175s test_Chi2 ... ok 175s test_ClustalOmega_tool ... skipping. Install clustalo if you want to use Clustal Omega from Biopython. 175s test_Clustalw_tool ... skipping. Install clustalw or clustalw2 if you want to use it from Biopython. 175s test_Cluster ... ok 175s test_CodonTable ... ok 175s test_ColorSpiral ... ok 175s test_Compass ... ok 176s test_Consensus ... ok 177s test_Dialign_tool ... skipping. Install DIALIGN2-2 if you want to use the Bio.Align.Applications wrapper. 177s test_EMBL_unittest ... ok 177s test_Emboss ... skipping. $EMBOSS_ROOT='/usr/lib/emboss' which does not exist! 177s test_EmbossPrimer ... ok 181s test_Entrez ... ok 181s test_Entrez_online ... skipping. internet not available 181s test_Entrez_parser ... ok 182s test_Enzyme ... ok 182s test_ExPASy ... skipping. internet not available 182s test_Fasttree_tool ... skipping. Install FastTree and correctly set the file path to the program if you want to use it from Biopython. 182s test_File ... ok 182s test_GenBank ... ok 184s test_GenomeDiagram ... Warn: Can't find .pfb for face 'Helvetica' 186s ok 187s test_GraphicsChromosome ... ok 187s test_GraphicsDistribution ... ok 187s test_GraphicsGeneral ... ok 188s test_HMMCasino ... ok 188s test_HMMGeneral ... ok 188s test_KEGG ... ok 188s test_KEGG_online ... skipping. internet not available 193s test_KGML_graphics ... ok 193s test_KGML_graphics_online ... skipping. internet not available 194s test_KGML_nographics ... ok 194s test_KeyWList ... ok 194s test_LogisticRegression ... ok 195s test_MafIO_index ... ok 195s test_Mafft_tool ... skipping. Install MAFFT if you want to use the Bio.Align.Applications wrapper. 196s test_MarkovModel ... ok 196s test_Medline ... ok 196s test_Muscle_tool ... skipping. Install MUSCLE if you want to use the Bio.Align.Applications wrapper. 196s test_NCBIXML ... ok 196s test_NCBI_BLAST_tools ... skipping. Install the NCBI BLAST+ command line tools if you want to use the Bio.Blast.Applications wrapper. 196s test_NCBI_qblast ... ok 196s test_NMR ... ok 197s test_NaiveBayes ... ok 197s test_Nexus ... ok 197s test_PAML_baseml ... ok 198s test_PAML_codeml ... ok 198s test_PAML_yn00 ... ok 198s test_PDBList ... skipping. internet not available 200s test_PDB_CEAligner ... ok 201s test_PDB_DSSP ... ok 201s test_PDB_Dice ... ok 201s test_PDB_Disordered ... ok 201s test_PDB_Exposure ... ok 201s test_PDB_FragmentMapper ... ok 203s test_PDB_KDTree ... ok 203s test_PDB_MMCIF2Dict ... ok 203s test_PDB_MMCIFIO ... ok 204s test_PDB_MMCIFParser ... ok 205s test_PDB_NACCESS ... ok 205s test_PDB_PDBIO ... ok 205s test_PDB_PDBParser ... ok 205s 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 205s test_PDB_Polypeptide ... ok 205s test_PDB_QCPSuperimposer ... ok 208s test_PDB_SASA ... ok 209s test_PDB_SMCRA ... ok 209s test_PDB_Selection ... ok 209s test_PDB_StructureAlignment ... ok 209s test_PDB_Superimposer ... ok 209s test_PDB_internal_coords ... skipping. Error: Install mmtf to use Bio.PDB.mmtf (e.g. pip install mmtf-python) 209s 209s test_PDB_parse_pdb_header ... ok 209s test_PDB_vectors ... ok 209s test_PQR ... ok 210s test_Pathway ... ok 210s test_Phd ... ok 210s test_Phylo ... ok 211s test_PhyloXML ... ok 211s test_Phylo_CDAO ... skipping. Install RDFlib if you want to use the CDAO tree format. 211s test_Phylo_NeXML ... ok 211s test_Phylo_matplotlib ... skipping. Install matplotlib if you want to use Bio.Phylo._utils. 211s test_Phylo_networkx ... skipping. Install networkx if you wish to use it with Bio.Phylo 211s test_PopGen_GenePop_nodepend ... ok 211s test_Prank_tool ... skipping. Install PRANK if you want to use the Bio.Align.Applications wrapper. 211s test_Probcons_tool ... skipping. Install PROBCONS if you want to use the Bio.Align.Applications wrapper. 211s test_ProtParam ... ok 212s test_RCSBFormats ... ok 212s test_Restriction ... ok 212s test_SCOP_Astral ... ok 212s test_SCOP_Cla ... ok 212s test_SCOP_Des ... ok 212s test_SCOP_Dom ... ok 212s test_SCOP_Hie ... ok 212s test_SCOP_Raf ... ok 212s test_SCOP_Residues ... ok 212s test_SCOP_Scop ... ok 212s test_SCOP_online ... skipping. internet not available 213s test_SVDSuperimposer ... ok 213s test_SearchIO_blast_tab ... ok 213s test_SearchIO_blast_tab_index ... ok 213s test_SearchIO_blast_xml ... ok 214s test_SearchIO_blast_xml_index ... ok 214s test_SearchIO_blat_psl ... ok 214s test_SearchIO_blat_psl_index ... ok 215s test_SearchIO_exonerate ... ok 215s test_SearchIO_exonerate_text_index ... ok 215s test_SearchIO_exonerate_vulgar_index ... ok 215s test_SearchIO_fasta_m10 ... ok 215s test_SearchIO_fasta_m10_index ... ok 215s test_SearchIO_hhsuite2_text ... ok 215s test_SearchIO_hmmer2_text ... ok 215s test_SearchIO_hmmer2_text_index ... ok 216s test_SearchIO_hmmer3_domtab ... ok 216s test_SearchIO_hmmer3_domtab_index ... ok 216s test_SearchIO_hmmer3_tab ... ok 216s test_SearchIO_hmmer3_tab_index ... ok 216s test_SearchIO_hmmer3_text ... ok 216s test_SearchIO_hmmer3_text_index ... ok 216s test_SearchIO_interproscan_xml ... ok 216s test_SearchIO_model ... ok 217s test_SearchIO_write ... ok 217s test_SeqFeature ... /usr/lib/python3/dist-packages/Bio/SeqFeature.py:1040: BiopythonParserWarning: Attempting to fix invalid location '3..2' as it looks like incorrect origin wrapping. Please fix input file, this could have unintended behavior. 217s warnings.warn( 217s ok 233s test_SeqIO ... ok 234s test_SeqIO_AbiIO ... ok 234s test_SeqIO_FastaIO ... ok 234s test_SeqIO_Gck ... ok 234s test_SeqIO_Insdc ... ok 234s test_SeqIO_NibIO ... ok 236s test_SeqIO_PdbIO ... ok 237s test_SeqIO_QualityIO ... ok 237s test_SeqIO_SeqXML ... ok 237s test_SeqIO_SnapGene ... ok 238s test_SeqIO_TwoBitIO ... ok 238s test_SeqIO_Xdna ... ok 238s test_SeqIO_features ... /usr/lib/python3/dist-packages/Bio/SeqIO/InsdcIO.py:549: BiopythonWarning: Annotation 'swissprot: locus SCX3_BUTOC, accession P01485; class: standard. created: Jul 21, 1986. sequence updated: Jul 21, 1986. annotation updated: Oct 16, 2001. xrefs: gi: gi: 69530 xrefs (non-sequence databases): HSSP P01484, InterPro IPR003614, InterPro IPR002061, InterPro IPR001219, Pfam PF00537, PRINTS PR00284, ProDom PD000908, SMART SM00505' too long for 'DBSOURCE' line 238s warnings.warn( 238s ok 254s test_SeqIO_index ... ok 254s test_SeqIO_online ... skipping. internet not available 254s test_SeqIO_write ... ok 254s test_SeqRecord ... ok 254s test_SeqUtils ... ok 255s test_Seq_objs ... ok 256s test_SffIO ... ok 256s test_SwissProt ... ok 256s test_TCoffee_tool ... skipping. Install TCOFFEE if you want to use the Bio.Align.Applications wrapper. 256s test_TogoWS ... skipping. internet not available 256s test_TreeConstruction ... ok 256s test_UniGene ... ok 257s test_UniProt_GOA ... ok 257s test_Uniprot ... ok 257s test_align ... ok 257s test_align_substitution_matrices ... ok 260s test_bgzf ... ok 260s test_cellosaurus ... ok 264s test_codonalign ... ok 264s test_geo ... ok 264s test_kNN ... ok 264s test_motifs ... ok 265s test_motifs_online ... skipping. internet not available 265s 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. 265s warnings.warn( 265s ok 265s test_pairwise2_no_C ... ok 265s test_pairwise_aligner ... ok 265s test_pairwise_alignment_map ... ok 272s test_phenotype ... ok 272s test_phenotype_fit ... skipping. Install SciPy if you want to use Bio.phenotype fit functionality. 272s 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. 272s test_prodoc ... ok 273s test_prosite ... ok 273s test_raxml_tool ... skipping. Install RAxML (binary raxmlHPC) if you want to test the Bio.Phylo.Applications wrapper. 273s test_samtools_tool ... skipping. Install samtools and correctly set the file path to the program if you want to use it from Biopython 273s test_seq ... ok 273s test_translate ... ok 273s Skipping any tests requiring internet access 273s Python version: 3.12.7 (main, Oct 3 2024, 15:15:22) [GCC 14.2.0] 273s Operating system: posix linux 273s ---------------------------------------------------------------------- 273s Ran 211 tests in 116.152 seconds 273s 274s autopkgtest [09:47:56]: test dependencies: -----------------------] 274s autopkgtest [09:47:56]: test dependencies: - - - - - - - - - - results - - - - - - - - - - 274s dependencies PASS 275s autopkgtest [09:47:57]: test full_suite: preparing testbed 372s autopkgtest [09:49:34]: testbed dpkg architecture: arm64 373s autopkgtest [09:49:35]: testbed apt version: 2.9.8 373s autopkgtest [09:49:35]: @@@@@@@@@@@@@@@@@@@@ test bed setup 373s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 374s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [28.1 kB] 374s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [2840 B] 374s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 374s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [212 kB] 374s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [59.3 kB] 374s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 Packages [50.3 kB] 374s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [249 kB] 374s Fetched 682 kB in 1s (1020 kB/s) 374s Reading package lists... 376s Reading package lists... 377s Building dependency tree... 377s Reading state information... 377s Calculating upgrade... 378s The following NEW packages will be installed: 378s python3-jaraco.text 378s The following packages will be upgraded: 378s libkeyutils1 python3-pkg-resources python3-setuptools 378s 3 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 378s Need to get 812 kB of archives. 378s After this operation, 13.3 kB of additional disk space will be used. 378s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 libkeyutils1 arm64 1.6.3-4ubuntu2 [10.2 kB] 378s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-jaraco.text all 4.0.0-1 [11.5 kB] 378s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-pkg-resources all 75.2.0-1 [134 kB] 378s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-setuptools all 75.2.0-1 [657 kB] 379s Fetched 812 kB in 1s (1471 kB/s) 379s (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 ... 79697 files and directories currently installed.) 379s Preparing to unpack .../libkeyutils1_1.6.3-4ubuntu2_arm64.deb ... 379s Unpacking libkeyutils1:arm64 (1.6.3-4ubuntu2) over (1.6.3-3build1) ... 379s Selecting previously unselected package python3-jaraco.text. 379s Preparing to unpack .../python3-jaraco.text_4.0.0-1_all.deb ... 379s Unpacking python3-jaraco.text (4.0.0-1) ... 379s Preparing to unpack .../python3-pkg-resources_75.2.0-1_all.deb ... 379s Unpacking python3-pkg-resources (75.2.0-1) over (74.1.2-1) ... 379s Preparing to unpack .../python3-setuptools_75.2.0-1_all.deb ... 379s Unpacking python3-setuptools (75.2.0-1) over (74.1.2-1) ... 380s Setting up python3-pkg-resources (75.2.0-1) ... 380s Setting up libkeyutils1:arm64 (1.6.3-4ubuntu2) ... 380s Setting up python3-jaraco.text (4.0.0-1) ... 380s Setting up python3-setuptools (75.2.0-1) ... 381s Processing triggers for libc-bin (2.40-1ubuntu3) ... 381s Reading package lists... 381s Building dependency tree... 381s Reading state information... 382s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 382s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 383s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 383s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 383s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 384s Reading package lists... 384s Reading package lists... 384s Building dependency tree... 384s Reading state information... 384s Calculating upgrade... 385s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 385s Reading package lists... 385s Building dependency tree... 385s Reading state information... 386s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 390s Reading package lists... 391s Building dependency tree... 391s Reading state information... 391s Starting pkgProblemResolver with broken count: 0 391s Starting 2 pkgProblemResolver with broken count: 0 391s Done 392s The following additional packages will be installed: 392s autoconf automake autopoint autotools-dev blt build-essential bwa clustalo 392s cpp cpp-14 cpp-14-aarch64-linux-gnu cpp-aarch64-linux-gnu debhelper 392s debugedit dh-autoreconf dh-python dh-strip-nondeterminism dialign dssp dwz 392s emboss emboss-data emboss-lib fasttree flex fontconfig-config 392s fonts-dejavu-core fonts-dejavu-mono fonts-lmodern fonts-lyx fonts-urw-base35 392s g++ g++-14 g++-14-aarch64-linux-gnu g++-aarch64-linux-gnu gcc gcc-14 392s gcc-14-aarch64-linux-gnu gcc-aarch64-linux-gnu gettext ghostscript hevea 392s hicolor-icon-theme imagemagick imagemagick-6-common imagemagick-6.q16 392s intltool-debian libaom3 libapache-pom-java libarchive-zip-perl 392s libargtable2-0 libasan8 libavahi-client3 libavahi-common-data 392s libavahi-common3 libblas3 libcairo2 libcc1-0 libcifpp-data libcifpp5 392s libcommons-logging-java libcommons-parent-java libcups2t64 libde265-0 392s libdebhelper-perl libdeflate0 libexpat1-dev libfftw3-double3 392s libfile-stripnondeterminism-perl libfontbox-java libfontconfig1 libfontenc1 392s libgcc-14-dev libgd3 libgfortran5 libgomp1 libgraphite2-3 libgs-common 392s libgs10 libgs10-common libharfbuzz0b libheif-plugin-aomdec 392s libheif-plugin-libde265 libheif1 libhpdf-2.3.0 libhwasan0 libice6 libidn12 392s libijs-0.35 libimagequant0 libisl23 libitm1 libjbig0 libjbig2dec0 392s libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui libjs-sphinxdoc 392s libjs-underscore libkpathsea6 liblapack3 liblbfgsb0 liblcms2-2 liblerc4 392s liblqr-1-0 liblsan0 libltdl7 libmagickcore-6.q16-7t64 392s libmagickwand-6.q16-7t64 libmbedcrypto7t64 libmbedtls14t64 libmbedx509-1t64 392s libmpc3 libmpfi0 libmysqlclient21 libnetpbm11t64 libopenjp2-7 libpaper-utils 392s libpaper1 libpdfbox-java libpixman-1-0 libpotrace0 libpq5 libptexenc1 392s libpython3-all-dev libpython3-dev libpython3.12-dev libqhull-r8.0 libraqm0 392s libraw23t64 libsharpyuv0 libsm6 libstdc++-14-dev libsynctex2 libtcl8.6 392s libteckit0 libtexlua53-5 libtiff6 libtk8.6 libtool libtsan2 libubsan1 392s libwebp7 libwebpdemux2 libwebpmux3 libxaw7 libxcb-render0 libxcb-shm0 392s libxft2 libxi6 libxmu6 libxpm4 libxrender1 libxslt1.1 libxss1 libxt6t64 392s libzzip-0-13t64 m4 mafft mysql-common ncbi-blast+ ncbi-data netpbm phylip 392s po-debconf poppler-data prank preview-latex-style probcons 392s python-biopython-doc python-matplotlib-data python3-all python3-all-dev 392s python3-appdirs python3-biopython python3-biopython-sql python3-brotli 392s python3-cairo python3-contourpy python3-cycler python3-dateutil 392s python3-decorator python3-dev python3-fonttools python3-freetype python3-fs 392s python3-isodate python3-kiwisolver python3-lxml python3-lz4 392s python3-matplotlib python3-mmtf python3-mpmath python3-msgpack 392s python3-mysqldb python3-networkx python3-numpy python3-packaging python3-pil 392s python3-pil.imagetk python3-rdflib python3-reportlab python3-rlpycairo 392s python3-scipy python3-six python3-sympy python3-tk python3-tz 392s python3-ufolib2 python3.12-dev python3.12-tk sgml-base t-coffee t1utils 392s tex-common texlive-base texlive-binaries texlive-fonts-recommended 392s texlive-latex-base texlive-latex-extra texlive-latex-recommended 392s texlive-pictures tk8.6-blt2.5 unicode-data w3c-sgml-lib wise wise-data 392s x11-common xdg-utils xfonts-encodings xfonts-utils xml-core zlib1g-dev 392s Suggested packages: 392s autoconf-archive gnu-standards autoconf-doc blt-demo samtools cpp-doc 392s gcc-14-locales cpp-14-doc dh-make flit python3-build python3-installer 392s python3-wheel emboss-doc emboss-test embassy clustalw bison flex-doc 392s fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre gcc-14-doc 392s gcc-multilib manpages-dev gdb gcc-doc gdb-aarch64-linux-gnu gettext-doc 392s libasprintf-dev libgettextpo-dev hevea-doc imagemagick-6-doc autotrace 392s cups-bsd | lpr | lprng enscript ffmpeg gimp gnuplot grads graphviz hp2xx 392s html2ps libwmf-bin mplayer povray radiance sane-utils transfig libraw-bin 392s libavalon-framework-java libexcalibur-logkit-java liblog4j1.2-java 392s cups-common libfftw3-bin libfftw3-dev libgd-tools libheif-plugin-x265 392s libheif-plugin-ffmpegdec libheif-plugin-jpegdec libheif-plugin-jpegenc 392s libheif-plugin-j2kdec libheif-plugin-j2kenc libheif-plugin-kvazaar 392s libheif-plugin-rav1e libheif-plugin-svtenc libjs-jquery-ui-docs 392s liblcms2-utils libmagickcore-6.q16-7-extra libmpfi-doc libstdc++-14-doc 392s tcl8.6 tk8.6 libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc 392s phylip-doc libmail-box-perl poppler-utils fonts-japanese-mincho 392s | fonts-ipafont-mincho fonts-japanese-gothic | fonts-ipafont-gothic 392s fonts-arphic-ukai fonts-arphic-uming fonts-nanum probcons-extra muscle3 392s phyml python3-psycopg2 raxml python-cycler-doc python-lxml-doc 392s cm-super-minimal dvipng fonts-staypuft gir1.2-gtk-3.0 inkscape ipython3 392s librsvg2-common python-matplotlib-doc python3-cairocffi python3-gi-cairo 392s python3-gobject python3-pyqt5 python3-sip python3-tornado 392s texlive-extra-utils python-mpmath-doc python3-gmpy2 default-mysql-server 392s | virtual-mysql-server python3-gdal python3-pydot python3-pygraphviz 392s gfortran python-numpy-doc python3-pytest python-pil-doc python-rdflib-doc 392s pdf-viewer python3-egenix-mxtexttools python-reportlab-doc rl-accel 392s rl-renderpm python-scipy-doc texlive-fonts-extra python-sympy-doc tix 392s python3-tk-dbg python3.13-tk sgml-base-doc boxshade seaview 392s t-coffee-examples perl-tk xpdf | pdf-viewer xzdec texlive-binaries-sse2 392s hintview texlive-fonts-recommended-doc texlive-latex-base-doc wp2latex 392s icc-profiles libfile-which-perl texlive-latex-extra-doc texlive-science 392s texlive-latex-recommended-doc texlive-luatex texlive-pstricks dot2tex prerex 392s texlive-pictures-doc vprerex wise-doc 392s Recommended packages: 392s primer3 libfl-dev libmagickcore-6.q16-7-extra libarchive-cpio-perl 392s fonts-droid-fallback libheif-plugin-aomenc javascript-common libltdl-dev 392s blast2 libwww-perl lynx ruby libmail-sendmail-perl python3-bs4 392s python3-cssselect python3-html5lib python3-olefile python3-sparqlwrapper 392s fonts-dejavu-extra isympy-common amap-align clustalw dialign-tx fsa kalign 392s libsoap-lite-perl libxml-simple-perl muscle mustang poa proda tm-align 392s lmodern dvisvgm tex-gyre tipa default-jre libspreadsheet-parseexcel-perl 392s texlive-plain-generic tk libfile-mimeinfo-perl libnet-dbus-perl 392s libx11-protocol-perl x11-utils x11-xserver-utils 392s The following NEW packages will be installed: 392s autoconf automake autopkgtest-satdep autopoint autotools-dev blt 392s build-essential bwa clustalo cpp cpp-14 cpp-14-aarch64-linux-gnu 392s cpp-aarch64-linux-gnu debhelper debugedit dh-autoreconf dh-python 392s dh-strip-nondeterminism dialign dssp dwz emboss emboss-data emboss-lib 392s fasttree flex fontconfig-config fonts-dejavu-core fonts-dejavu-mono 392s fonts-lmodern fonts-lyx fonts-urw-base35 g++ g++-14 g++-14-aarch64-linux-gnu 392s g++-aarch64-linux-gnu gcc gcc-14 gcc-14-aarch64-linux-gnu 392s gcc-aarch64-linux-gnu gettext ghostscript hevea hicolor-icon-theme 392s imagemagick imagemagick-6-common imagemagick-6.q16 intltool-debian libaom3 392s libapache-pom-java libarchive-zip-perl libargtable2-0 libasan8 392s libavahi-client3 libavahi-common-data libavahi-common3 libblas3 libcairo2 392s libcc1-0 libcifpp-data libcifpp5 libcommons-logging-java 392s libcommons-parent-java libcups2t64 libde265-0 libdebhelper-perl libdeflate0 392s libexpat1-dev libfftw3-double3 libfile-stripnondeterminism-perl 392s libfontbox-java libfontconfig1 libfontenc1 libgcc-14-dev libgd3 libgfortran5 392s libgomp1 libgraphite2-3 libgs-common libgs10 libgs10-common libharfbuzz0b 392s libheif-plugin-aomdec libheif-plugin-libde265 libheif1 libhpdf-2.3.0 392s libhwasan0 libice6 libidn12 libijs-0.35 libimagequant0 libisl23 libitm1 392s libjbig0 libjbig2dec0 libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui 392s libjs-sphinxdoc libjs-underscore libkpathsea6 liblapack3 liblbfgsb0 392s liblcms2-2 liblerc4 liblqr-1-0 liblsan0 libltdl7 libmagickcore-6.q16-7t64 392s libmagickwand-6.q16-7t64 libmbedcrypto7t64 libmbedtls14t64 libmbedx509-1t64 392s libmpc3 libmpfi0 libmysqlclient21 libnetpbm11t64 libopenjp2-7 libpaper-utils 392s libpaper1 libpdfbox-java libpixman-1-0 libpotrace0 libpq5 libptexenc1 392s libpython3-all-dev libpython3-dev libpython3.12-dev libqhull-r8.0 libraqm0 392s libraw23t64 libsharpyuv0 libsm6 libstdc++-14-dev libsynctex2 libtcl8.6 392s libteckit0 libtexlua53-5 libtiff6 libtk8.6 libtool libtsan2 libubsan1 392s libwebp7 libwebpdemux2 libwebpmux3 libxaw7 libxcb-render0 libxcb-shm0 392s libxft2 libxi6 libxmu6 libxpm4 libxrender1 libxslt1.1 libxss1 libxt6t64 392s libzzip-0-13t64 m4 mafft mysql-common ncbi-blast+ ncbi-data netpbm phylip 392s po-debconf poppler-data prank preview-latex-style probcons 392s python-biopython-doc python-matplotlib-data python3-all python3-all-dev 392s python3-appdirs python3-biopython python3-biopython-sql python3-brotli 392s python3-cairo python3-contourpy python3-cycler python3-dateutil 392s python3-decorator python3-dev python3-fonttools python3-freetype python3-fs 392s python3-isodate python3-kiwisolver python3-lxml python3-lz4 392s python3-matplotlib python3-mmtf python3-mpmath python3-msgpack 392s python3-mysqldb python3-networkx python3-numpy python3-packaging python3-pil 392s python3-pil.imagetk python3-rdflib python3-reportlab python3-rlpycairo 392s python3-scipy python3-six python3-sympy python3-tk python3-tz 392s python3-ufolib2 python3.12-dev python3.12-tk sgml-base t-coffee t1utils 392s tex-common texlive-base texlive-binaries texlive-fonts-recommended 392s texlive-latex-base texlive-latex-extra texlive-latex-recommended 392s texlive-pictures tk8.6-blt2.5 unicode-data w3c-sgml-lib wise wise-data 392s x11-common xdg-utils xfonts-encodings xfonts-utils xml-core zlib1g-dev 392s 0 upgraded, 235 newly installed, 0 to remove and 0 not upgraded. 392s Need to get 376 MB/376 MB of archives. 392s After this operation, 1709 MB of additional disk space will be used. 392s Get:1 /tmp/autopkgtest.sA24HF/2-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [980 B] 392s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 m4 arm64 1.4.19-4build1 [240 kB] 392s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 flex arm64 2.6.4-8.2build1 [291 kB] 393s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 libgomp1 arm64 14.2.0-7ubuntu1 [145 kB] 393s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 libfftw3-double3 arm64 3.3.10-1ubuntu4 [392 kB] 393s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 393s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 393s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 libfontenc1 arm64 1:1.1.8-1build1 [13.9 kB] 393s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 393s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 393s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 xfonts-utils arm64 1:7.7+7 [95.6 kB] 393s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-urw-base35 all 20200910-8 [11.0 MB] 393s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig-config arm64 2.15.0-1.1ubuntu2 [37.4 kB] 393s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 libfontconfig1 arm64 2.15.0-1.1ubuntu2 [142 kB] 393s Get:15 http://ftpmaster.internal/ubuntu plucky/main arm64 libsharpyuv0 arm64 1.4.0-0.1 [16.3 kB] 393s Get:16 http://ftpmaster.internal/ubuntu plucky/main arm64 libaom3 arm64 3.9.1-1 [1651 kB] 393s Get:17 http://ftpmaster.internal/ubuntu plucky/main arm64 libheif-plugin-aomdec arm64 1.18.1-2 [10.9 kB] 393s Get:18 http://ftpmaster.internal/ubuntu plucky/main arm64 libde265-0 arm64 1.0.15-1build4 [146 kB] 393s Get:19 http://ftpmaster.internal/ubuntu plucky/main arm64 libheif-plugin-libde265 arm64 1.18.1-2 [8612 B] 393s Get:20 http://ftpmaster.internal/ubuntu plucky/main arm64 libheif1 arm64 1.18.1-2 [274 kB] 393s Get:21 http://ftpmaster.internal/ubuntu plucky/main arm64 libjbig0 arm64 2.1-6.1ubuntu2 [29.3 kB] 393s Get:22 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg-turbo8 arm64 2.1.5-2ubuntu2 [163 kB] 393s Get:23 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 393s Get:24 http://ftpmaster.internal/ubuntu plucky/main arm64 liblcms2-2 arm64 2.14-2build1 [161 kB] 393s Get:25 http://ftpmaster.internal/ubuntu plucky/universe arm64 liblqr-1-0 arm64 0.4.2-2.1build2 [27.1 kB] 393s Get:26 http://ftpmaster.internal/ubuntu plucky/main arm64 libltdl7 arm64 2.4.7-7build1 [40.4 kB] 393s Get:27 http://ftpmaster.internal/ubuntu plucky/main arm64 libopenjp2-7 arm64 2.5.0-2ubuntu1 [182 kB] 393s Get:28 http://ftpmaster.internal/ubuntu plucky/main arm64 libraw23t64 arm64 0.21.2-2.1build1 [382 kB] 393s Get:29 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate0 arm64 1.21-1 [46.2 kB] 393s Get:30 http://ftpmaster.internal/ubuntu plucky/main arm64 liblerc4 arm64 4.0.0+ds-4ubuntu2 [154 kB] 393s Get:31 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebp7 arm64 1.4.0-0.1 [192 kB] 393s Get:32 http://ftpmaster.internal/ubuntu plucky/main arm64 libtiff6 arm64 4.5.1+git230720-4ubuntu4 [193 kB] 393s Get:33 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebpdemux2 arm64 1.4.0-0.1 [12.3 kB] 393s Get:34 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebpmux3 arm64 1.4.0-0.1 [25.1 kB] 393s Get:35 http://ftpmaster.internal/ubuntu plucky/universe arm64 imagemagick-6-common all 8:6.9.13.12+dfsg1-1build1 [69.6 kB] 393s Get:36 http://ftpmaster.internal/ubuntu plucky/universe arm64 libmagickcore-6.q16-7t64 arm64 8:6.9.13.12+dfsg1-1build1 [1760 kB] 393s Get:37 http://ftpmaster.internal/ubuntu plucky/universe arm64 libmagickwand-6.q16-7t64 arm64 8:6.9.13.12+dfsg1-1build1 [276 kB] 393s Get:38 http://ftpmaster.internal/ubuntu plucky/main arm64 poppler-data all 0.4.12-1 [2060 kB] 393s Get:39 http://ftpmaster.internal/ubuntu plucky/main arm64 sgml-base all 1.31 [11.4 kB] 393s Get:40 http://ftpmaster.internal/ubuntu plucky/main arm64 autoconf all 2.72-3 [382 kB] 393s Get:41 http://ftpmaster.internal/ubuntu plucky/main arm64 autotools-dev all 20220109.1 [44.9 kB] 393s Get:42 http://ftpmaster.internal/ubuntu plucky/main arm64 automake all 1:1.16.5-1.3ubuntu1 [558 kB] 393s Get:43 http://ftpmaster.internal/ubuntu plucky/main arm64 autopoint all 0.22.5-2 [616 kB] 393s Get:44 http://ftpmaster.internal/ubuntu plucky/main arm64 libtcl8.6 arm64 8.6.14+dfsg-1build1 [978 kB] 393s Get:45 http://ftpmaster.internal/ubuntu plucky/main arm64 libxrender1 arm64 1:0.9.10-1.1build1 [18.8 kB] 393s Get:46 http://ftpmaster.internal/ubuntu plucky/main arm64 libxft2 arm64 2.3.6-1build1 [44.1 kB] 393s Get:47 http://ftpmaster.internal/ubuntu plucky/main arm64 libxss1 arm64 1:1.2.3-1build3 [7244 B] 393s Get:48 http://ftpmaster.internal/ubuntu plucky/main arm64 libtk8.6 arm64 8.6.14-1build1 [767 kB] 393s Get:49 http://ftpmaster.internal/ubuntu plucky/main arm64 tk8.6-blt2.5 arm64 2.5.3+dfsg-7build1 [618 kB] 393s Get:50 http://ftpmaster.internal/ubuntu plucky/main arm64 blt arm64 2.5.3+dfsg-7build1 [4840 B] 393s Get:51 http://ftpmaster.internal/ubuntu plucky/main arm64 libisl23 arm64 0.27-1 [676 kB] 394s Get:52 http://ftpmaster.internal/ubuntu plucky/main arm64 libmpc3 arm64 1.3.1-1build2 [56.8 kB] 394s Get:53 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp-14-aarch64-linux-gnu arm64 14.2.0-7ubuntu1 [10.6 MB] 394s Get:54 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp-14 arm64 14.2.0-7ubuntu1 [1030 B] 394s Get:55 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp-aarch64-linux-gnu arm64 4:14.1.0-2ubuntu1 [5452 B] 394s Get:56 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp arm64 4:14.1.0-2ubuntu1 [22.5 kB] 394s Get:57 http://ftpmaster.internal/ubuntu plucky/main arm64 libcc1-0 arm64 14.2.0-7ubuntu1 [49.7 kB] 394s Get:58 http://ftpmaster.internal/ubuntu plucky/main arm64 libitm1 arm64 14.2.0-7ubuntu1 [27.8 kB] 394s Get:59 http://ftpmaster.internal/ubuntu plucky/main arm64 libasan8 arm64 14.2.0-7ubuntu1 [2893 kB] 394s Get:60 http://ftpmaster.internal/ubuntu plucky/main arm64 liblsan0 arm64 14.2.0-7ubuntu1 [1283 kB] 394s Get:61 http://ftpmaster.internal/ubuntu plucky/main arm64 libtsan2 arm64 14.2.0-7ubuntu1 [2691 kB] 394s Get:62 http://ftpmaster.internal/ubuntu plucky/main arm64 libubsan1 arm64 14.2.0-7ubuntu1 [1151 kB] 394s Get:63 http://ftpmaster.internal/ubuntu plucky/main arm64 libhwasan0 arm64 14.2.0-7ubuntu1 [1599 kB] 394s Get:64 http://ftpmaster.internal/ubuntu plucky/main arm64 libgcc-14-dev arm64 14.2.0-7ubuntu1 [2594 kB] 394s Get:65 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc-14-aarch64-linux-gnu arm64 14.2.0-7ubuntu1 [20.9 MB] 395s Get:66 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc-14 arm64 14.2.0-7ubuntu1 [515 kB] 395s Get:67 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc-aarch64-linux-gnu arm64 4:14.1.0-2ubuntu1 [1200 B] 395s Get:68 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc arm64 4:14.1.0-2ubuntu1 [4994 B] 395s Get:69 http://ftpmaster.internal/ubuntu plucky/main arm64 libstdc++-14-dev arm64 14.2.0-7ubuntu1 [2474 kB] 395s Get:70 http://ftpmaster.internal/ubuntu plucky/main arm64 g++-14-aarch64-linux-gnu arm64 14.2.0-7ubuntu1 [12.1 MB] 395s Get:71 http://ftpmaster.internal/ubuntu plucky/main arm64 g++-14 arm64 14.2.0-7ubuntu1 [19.8 kB] 395s Get:72 http://ftpmaster.internal/ubuntu plucky/main arm64 g++-aarch64-linux-gnu arm64 4:14.1.0-2ubuntu1 [958 B] 395s Get:73 http://ftpmaster.internal/ubuntu plucky/main arm64 g++ arm64 4:14.1.0-2ubuntu1 [1080 B] 395s Get:74 http://ftpmaster.internal/ubuntu plucky/main arm64 build-essential arm64 12.10ubuntu1 [4932 B] 395s Get:75 http://ftpmaster.internal/ubuntu plucky/universe arm64 bwa arm64 0.7.17-7 [192 kB] 395s Get:76 http://ftpmaster.internal/ubuntu plucky/universe arm64 libargtable2-0 arm64 13-2 [14.7 kB] 395s Get:77 http://ftpmaster.internal/ubuntu plucky/universe arm64 clustalo arm64 1.2.4-8build1 [190 kB] 395s Get:78 http://ftpmaster.internal/ubuntu plucky/main arm64 libdebhelper-perl all 13.20ubuntu1 [94.2 kB] 395s Get:79 http://ftpmaster.internal/ubuntu plucky/main arm64 libtool all 2.4.7-7build1 [166 kB] 395s Get:80 http://ftpmaster.internal/ubuntu plucky/main arm64 dh-autoreconf all 20 [16.1 kB] 395s Get:81 http://ftpmaster.internal/ubuntu plucky/main arm64 libarchive-zip-perl all 1.68-1 [90.2 kB] 395s Get:82 http://ftpmaster.internal/ubuntu plucky/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [20.1 kB] 395s Get:83 http://ftpmaster.internal/ubuntu plucky/main arm64 dh-strip-nondeterminism all 1.14.0-1 [5058 B] 395s Get:84 http://ftpmaster.internal/ubuntu plucky/main arm64 debugedit arm64 1:5.0-6 [45.4 kB] 395s Get:85 http://ftpmaster.internal/ubuntu plucky/main arm64 dwz arm64 0.15-1build6 [113 kB] 395s Get:86 http://ftpmaster.internal/ubuntu plucky/main arm64 gettext arm64 0.22.5-2 [930 kB] 395s Get:87 http://ftpmaster.internal/ubuntu plucky/main arm64 intltool-debian all 0.35.0+20060710.6 [23.2 kB] 395s Get:88 http://ftpmaster.internal/ubuntu plucky/main arm64 po-debconf all 1.0.21+nmu1 [233 kB] 395s Get:89 http://ftpmaster.internal/ubuntu plucky/main arm64 debhelper all 13.20ubuntu1 [893 kB] 395s Get:90 http://ftpmaster.internal/ubuntu plucky/universe arm64 dh-python all 6.20240824 [112 kB] 395s Get:91 http://ftpmaster.internal/ubuntu plucky/universe arm64 dialign arm64 2.2.1-13 [152 kB] 395s Get:92 http://ftpmaster.internal/ubuntu plucky/universe arm64 libcifpp-data all 5.0.7.1-3build1 [450 kB] 395s Get:93 http://ftpmaster.internal/ubuntu plucky/universe arm64 libcifpp5 arm64 5.0.7.1-3build1 [867 kB] 395s Get:94 http://ftpmaster.internal/ubuntu plucky/universe arm64 dssp arm64 4.2.2-2 [659 kB] 395s Get:95 http://ftpmaster.internal/ubuntu plucky/main arm64 libimagequant0 arm64 2.18.0-1build1 [37.1 kB] 395s Get:96 http://ftpmaster.internal/ubuntu plucky/main arm64 libgraphite2-3 arm64 1.3.14-2ubuntu1 [70.6 kB] 395s Get:97 http://ftpmaster.internal/ubuntu plucky/main arm64 libharfbuzz0b arm64 9.0.0-1 [486 kB] 395s Get:98 http://ftpmaster.internal/ubuntu plucky/main arm64 libraqm0 arm64 0.10.1-1build1 [14.7 kB] 395s Get:99 http://ftpmaster.internal/ubuntu plucky/main arm64 libxpm4 arm64 1:3.5.17-1build2 [35.1 kB] 395s Get:100 http://ftpmaster.internal/ubuntu plucky/main arm64 libgd3 arm64 2.3.3-12ubuntu3 [122 kB] 395s Get:101 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhpdf-2.3.0 arm64 2.3.0+dfsg-1build3 [434 kB] 395s Get:102 http://ftpmaster.internal/ubuntu plucky/main arm64 mysql-common all 5.8+1.1.1 [6800 B] 395s Get:103 http://ftpmaster.internal/ubuntu plucky/main arm64 libmysqlclient21 arm64 8.0.39-1 [1239 kB] 396s Get:104 http://ftpmaster.internal/ubuntu plucky/main arm64 libpq5 arm64 17.0-1 [248 kB] 396s Get:105 http://ftpmaster.internal/ubuntu plucky/universe arm64 emboss-lib arm64 6.6.0+dfsg-12ubuntu2 [2853 kB] 397s Get:106 http://ftpmaster.internal/ubuntu plucky/universe arm64 emboss-data all 6.6.0+dfsg-12ubuntu2 [61.0 MB] 402s Get:107 http://ftpmaster.internal/ubuntu plucky/universe arm64 emboss arm64 6.6.0+dfsg-12ubuntu2 [934 kB] 402s Get:108 http://ftpmaster.internal/ubuntu plucky/universe arm64 fonts-lmodern all 2.005-1 [4799 kB] 402s Get:109 http://ftpmaster.internal/ubuntu plucky/universe arm64 fonts-lyx all 2.4.1-2 [171 kB] 402s Get:110 http://ftpmaster.internal/ubuntu plucky/main arm64 libgs-common all 10.03.1~dfsg1-0ubuntu2 [175 kB] 402s Get:111 http://ftpmaster.internal/ubuntu plucky/main arm64 libgs10-common all 10.03.1~dfsg1-0ubuntu2 [488 kB] 402s Get:112 http://ftpmaster.internal/ubuntu plucky/main arm64 libavahi-common-data arm64 0.8-13ubuntu6 [29.6 kB] 402s Get:113 http://ftpmaster.internal/ubuntu plucky/main arm64 libavahi-common3 arm64 0.8-13ubuntu6 [23.3 kB] 402s Get:114 http://ftpmaster.internal/ubuntu plucky/main arm64 libavahi-client3 arm64 0.8-13ubuntu6 [27.2 kB] 402s Get:115 http://ftpmaster.internal/ubuntu plucky/main arm64 libcups2t64 arm64 2.4.10-1ubuntu2 [271 kB] 402s Get:116 http://ftpmaster.internal/ubuntu plucky/main arm64 libidn12 arm64 1.42-2 [56.9 kB] 402s Get:117 http://ftpmaster.internal/ubuntu plucky/main arm64 libijs-0.35 arm64 0.35-15.1build1 [15.3 kB] 402s Get:118 http://ftpmaster.internal/ubuntu plucky/main arm64 libjbig2dec0 arm64 0.20-1build3 [63.2 kB] 402s Get:119 http://ftpmaster.internal/ubuntu plucky/main arm64 libpaper1 arm64 1.1.29build1 [13.4 kB] 402s Get:120 http://ftpmaster.internal/ubuntu plucky/main arm64 libice6 arm64 2:1.0.10-1build3 [41.1 kB] 402s Get:121 http://ftpmaster.internal/ubuntu plucky/main arm64 libsm6 arm64 2:1.2.3-1build3 [15.6 kB] 402s Get:122 http://ftpmaster.internal/ubuntu plucky/main arm64 libxt6t64 arm64 1:1.2.1-1.2build1 [168 kB] 402s Get:123 http://ftpmaster.internal/ubuntu plucky/main arm64 libgs10 arm64 10.03.1~dfsg1-0ubuntu2 [3579 kB] 402s Get:124 http://ftpmaster.internal/ubuntu plucky/main arm64 ghostscript arm64 10.03.1~dfsg1-0ubuntu2 [43.6 kB] 402s Get:125 http://ftpmaster.internal/ubuntu plucky/universe arm64 libnetpbm11t64 arm64 2:11.07.00-2 [113 kB] 402s Get:126 http://ftpmaster.internal/ubuntu plucky/universe arm64 netpbm arm64 2:11.07.00-2 [2106 kB] 402s Get:127 http://ftpmaster.internal/ubuntu plucky/universe arm64 tex-common all 6.18 [32.8 kB] 402s Get:128 http://ftpmaster.internal/ubuntu plucky/main arm64 libpaper-utils arm64 1.1.29build1 [8490 B] 402s Get:129 http://ftpmaster.internal/ubuntu plucky/main arm64 libkpathsea6 arm64 2024.20240313.70630+ds-4 [64.0 kB] 402s Get:130 http://ftpmaster.internal/ubuntu plucky/main arm64 libptexenc1 arm64 2024.20240313.70630+ds-4 [41.6 kB] 402s Get:131 http://ftpmaster.internal/ubuntu plucky/main arm64 libsynctex2 arm64 2024.20240313.70630+ds-4 [60.0 kB] 402s Get:132 http://ftpmaster.internal/ubuntu plucky/main arm64 libtexlua53-5 arm64 2024.20240313.70630+ds-4 [121 kB] 402s Get:133 http://ftpmaster.internal/ubuntu plucky/main arm64 t1utils arm64 1.41-4build3 [61.0 kB] 402s Get:134 http://ftpmaster.internal/ubuntu plucky/main arm64 libpixman-1-0 arm64 0.42.2-1build1 [204 kB] 402s Get:135 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-render0 arm64 1.17.0-2 [16.6 kB] 402s Get:136 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-shm0 arm64 1.17.0-2 [5884 B] 402s Get:137 http://ftpmaster.internal/ubuntu plucky/main arm64 libcairo2 arm64 1.18.2-2 [560 kB] 402s Get:138 http://ftpmaster.internal/ubuntu plucky/universe arm64 libmpfi0 arm64 1.5.4+ds-3 [34.9 kB] 402s Get:139 http://ftpmaster.internal/ubuntu plucky/universe arm64 libpotrace0 arm64 1.16-2build1 [16.0 kB] 402s Get:140 http://ftpmaster.internal/ubuntu plucky/universe arm64 libteckit0 arm64 2.5.12+ds1-1 [405 kB] 402s Get:141 http://ftpmaster.internal/ubuntu plucky/main arm64 libxmu6 arm64 2:1.1.3-3build2 [47.5 kB] 402s Get:142 http://ftpmaster.internal/ubuntu plucky/main arm64 libxaw7 arm64 2:1.0.14-1build2 [183 kB] 402s Get:143 http://ftpmaster.internal/ubuntu plucky/main arm64 libxi6 arm64 2:1.8.2-1 [32.4 kB] 402s Get:144 http://ftpmaster.internal/ubuntu plucky/universe arm64 libzzip-0-13t64 arm64 0.13.72+dfsg.1-1.2build1 [29.2 kB] 402s Get:145 http://ftpmaster.internal/ubuntu plucky/universe arm64 texlive-binaries arm64 2024.20240313.70630+ds-4 [8319 kB] 403s Get:146 http://ftpmaster.internal/ubuntu plucky/main arm64 xdg-utils all 1.2.1-0ubuntu1 [67.5 kB] 403s Get:147 http://ftpmaster.internal/ubuntu plucky/universe arm64 texlive-base all 2024.20240706-1 [22.5 MB] 404s Get:148 http://ftpmaster.internal/ubuntu plucky/main arm64 hicolor-icon-theme all 0.18-1 [13.5 kB] 404s Get:149 http://ftpmaster.internal/ubuntu plucky/universe arm64 imagemagick-6.q16 arm64 8:6.9.13.12+dfsg1-1build1 [254 kB] 404s Get:150 http://ftpmaster.internal/ubuntu plucky/universe arm64 imagemagick arm64 8:6.9.13.12+dfsg1-1build1 [14.2 kB] 404s Get:151 http://ftpmaster.internal/ubuntu plucky/universe arm64 hevea arm64 2.36-2 [2333 kB] 404s Get:152 http://ftpmaster.internal/ubuntu plucky/universe arm64 libapache-pom-java all 29-2 [5284 B] 404s Get:153 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.0-3build2 [152 kB] 404s Get:154 http://ftpmaster.internal/ubuntu plucky/universe arm64 libcommons-parent-java all 56-1 [10.7 kB] 404s Get:155 http://ftpmaster.internal/ubuntu plucky/universe arm64 libcommons-logging-java all 1.3.0-1ubuntu1 [63.8 kB] 404s Get:156 http://ftpmaster.internal/ubuntu plucky/main arm64 libexpat1-dev arm64 2.6.2-2 [128 kB] 404s Get:157 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 14.2.0-7ubuntu1 [438 kB] 404s Get:158 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 404s Get:159 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 404s Get:160 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 404s Get:161 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-sphinxdoc all 7.4.7-3 [157 kB] 404s Get:162 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.0-3build2 [2293 kB] 404s Get:163 http://ftpmaster.internal/ubuntu plucky/universe arm64 liblbfgsb0 arm64 3.0+dfsg.4-1build1 [27.7 kB] 404s Get:164 http://ftpmaster.internal/ubuntu plucky/universe arm64 libmbedcrypto7t64 arm64 2.28.8-1 [209 kB] 404s Get:165 http://ftpmaster.internal/ubuntu plucky/universe arm64 libmbedx509-1t64 arm64 2.28.8-1 [47.2 kB] 404s Get:166 http://ftpmaster.internal/ubuntu plucky/universe arm64 libmbedtls14t64 arm64 2.28.8-1 [82.2 kB] 404s Get:167 http://ftpmaster.internal/ubuntu plucky/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1ubuntu1 [894 kB] 404s Get:168 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3.12-dev arm64 3.12.7-1 [5568 kB] 404s Get:169 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3-dev arm64 3.12.6-0ubuntu1 [10.2 kB] 404s Get:170 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3-all-dev arm64 3.12.6-0ubuntu1 [916 B] 404s Get:171 http://ftpmaster.internal/ubuntu plucky/universe arm64 libqhull-r8.0 arm64 2020.2-6build1 [189 kB] 404s Get:172 http://ftpmaster.internal/ubuntu plucky/main arm64 libxslt1.1 arm64 1.1.39-0exp1ubuntu1 [167 kB] 404s Get:173 http://ftpmaster.internal/ubuntu plucky/universe arm64 mafft arm64 7.505-1 [756 kB] 405s Get:174 http://ftpmaster.internal/ubuntu plucky/universe arm64 ncbi-data all 6.1.20170106+dfsg2-3 [3966 kB] 405s Get:175 http://ftpmaster.internal/ubuntu plucky/universe arm64 ncbi-blast+ arm64 2.16.0+ds-6 [14.7 MB] 405s Get:176 http://ftpmaster.internal/ubuntu plucky/universe arm64 phylip arm64 1:3.697+dfsg-4build1 [843 kB] 405s Get:177 http://ftpmaster.internal/ubuntu plucky/universe arm64 prank arm64 0.0.170427+dfsg-3 [325 kB] 405s Get:178 http://ftpmaster.internal/ubuntu plucky/universe arm64 preview-latex-style all 13.2-1 [347 kB] 405s Get:179 http://ftpmaster.internal/ubuntu plucky/universe arm64 probcons arm64 1.12-14 [129 kB] 405s Get:180 http://ftpmaster.internal/ubuntu plucky/universe arm64 python-biopython-doc all 1.83+dfsg1-3 [17.4 MB] 406s Get:181 http://ftpmaster.internal/ubuntu plucky/universe arm64 python-matplotlib-data all 3.8.3-3 [2928 kB] 406s Get:182 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-all arm64 3.12.6-0ubuntu1 [886 B] 406s Get:183 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.12-dev arm64 3.12.7-1 [505 kB] 406s Get:184 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-dev arm64 3.12.6-0ubuntu1 [26.7 kB] 406s Get:185 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-all-dev arm64 3.12.6-0ubuntu1 [908 B] 406s Get:186 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-appdirs all 1.4.4-4 [10.9 kB] 406s Get:187 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy arm64 1:1.26.4+ds-11build1 [3654 kB] 406s Get:188 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.12-tk arm64 3.12.7-1 [114 kB] 406s Get:189 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-tk arm64 3.12.6-1ubuntu1 [9806 B] 406s Get:190 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pil.imagetk arm64 10.4.0-1ubuntu1 [9504 B] 406s Get:191 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-pil arm64 10.4.0-1ubuntu1 [456 kB] 406s Get:192 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-cairo arm64 1.26.1-2 [121 kB] 406s Get:193 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-freetype all 2.4.0-2 [81.3 kB] 406s Get:194 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-rlpycairo all 0.3.0-3 [9130 B] 406s Get:195 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-reportlab all 4.2.2-1 [1130 kB] 406s Get:196 http://ftpmaster.internal/ubuntu plucky/main arm64 xml-core all 0.19 [20.3 kB] 406s Get:197 http://ftpmaster.internal/ubuntu plucky/universe arm64 w3c-sgml-lib all 1.3-3 [280 kB] 406s Get:198 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-biopython arm64 1.83+dfsg1-3 [1646 kB] 406s Get:199 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-biopython-sql all 1.83+dfsg1-3 [25.7 kB] 406s Get:200 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-brotli arm64 1.1.0-2build2 [340 kB] 406s Get:201 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-contourpy arm64 1.2.1-1 [173 kB] 406s Get:202 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-cycler all 0.12.1-1 [9716 B] 406s Get:203 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-six all 1.16.0-7 [13.1 kB] 406s Get:204 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-dateutil all 2.9.0-2 [80.3 kB] 406s Get:205 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-decorator all 5.1.1-5 [10.1 kB] 406s Get:206 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-scipy arm64 1.13.1-3 [16.3 MB] 407s Get:207 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-ufolib2 all 0.16.0+dfsg1-1 [33.5 kB] 407s Get:208 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-mpmath all 1.3.0-1 [425 kB] 407s Get:209 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-sympy all 1.13.1-1 [4228 kB] 407s Get:210 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-tz all 2024.1-2 [31.4 kB] 407s Get:211 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-fs all 2.4.16-4 [91.3 kB] 407s Get:212 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-lxml arm64 5.3.0-1 [1205 kB] 407s Get:213 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-lz4 arm64 4.0.2+dfsg-1build4 [26.7 kB] 407s Get:214 http://ftpmaster.internal/ubuntu plucky/universe arm64 unicode-data all 15.1.0-1 [8878 kB] 408s Get:215 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-fonttools arm64 4.46.0-1build2 [1398 kB] 408s Get:216 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-isodate all 0.6.1-3 [24.3 kB] 408s Get:217 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-kiwisolver arm64 1.4.5-1 [48.9 kB] 408s Get:218 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-packaging all 24.1-1 [41.4 kB] 408s Get:219 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-matplotlib arm64 3.8.3-3 [4515 kB] 408s Get:220 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-msgpack arm64 1.0.3-3build2 [77.9 kB] 408s Get:221 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-mmtf all 1.1.3-1 [16.2 kB] 408s Get:222 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-mysqldb arm64 1.4.6-2build3 [47.5 kB] 408s Get:223 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-networkx all 3.2.1-4ubuntu1 [11.5 MB] 408s Get:224 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-rdflib all 7.0.0-1 [405 kB] 408s Get:225 http://ftpmaster.internal/ubuntu plucky/universe arm64 t-coffee arm64 13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 [879 kB] 408s Get:226 http://ftpmaster.internal/ubuntu plucky/universe arm64 texlive-fonts-recommended all 2024.20240706-1 [4973 kB] 409s Get:227 http://ftpmaster.internal/ubuntu plucky/universe arm64 texlive-latex-base all 2024.20240706-1 [1256 kB] 409s Get:228 http://ftpmaster.internal/ubuntu plucky/universe arm64 libfontbox-java all 1:1.8.16-5 [208 kB] 409s Get:229 http://ftpmaster.internal/ubuntu plucky/universe arm64 libpdfbox-java all 1:1.8.16-5 [5521 kB] 409s Get:230 http://ftpmaster.internal/ubuntu plucky/universe arm64 texlive-latex-recommended all 2024.20240706-1 [8830 kB] 409s Get:231 http://ftpmaster.internal/ubuntu plucky/universe arm64 texlive-pictures all 2024.20240706-1 [17.0 MB] 410s Get:232 http://ftpmaster.internal/ubuntu plucky/universe arm64 texlive-latex-extra all 2024.20240706-2 [19.6 MB] 410s Get:233 http://ftpmaster.internal/ubuntu plucky/universe arm64 wise-data all 2.4.1-25 [83.0 kB] 410s Get:234 http://ftpmaster.internal/ubuntu plucky/universe arm64 wise arm64 2.4.1-25 [802 kB] 410s Get:235 http://ftpmaster.internal/ubuntu plucky/universe arm64 fasttree arm64 2.1.11-2 [164 kB] 411s Preconfiguring packages ... 411s Fetched 376 MB in 18s (20.4 MB/s) 411s Selecting previously unselected package m4. 411s (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 ... 79706 files and directories currently installed.) 411s Preparing to unpack .../000-m4_1.4.19-4build1_arm64.deb ... 411s Unpacking m4 (1.4.19-4build1) ... 411s Selecting previously unselected package flex. 411s Preparing to unpack .../001-flex_2.6.4-8.2build1_arm64.deb ... 411s Unpacking flex (2.6.4-8.2build1) ... 411s Selecting previously unselected package libgomp1:arm64. 411s Preparing to unpack .../002-libgomp1_14.2.0-7ubuntu1_arm64.deb ... 411s Unpacking libgomp1:arm64 (14.2.0-7ubuntu1) ... 411s Selecting previously unselected package libfftw3-double3:arm64. 411s Preparing to unpack .../003-libfftw3-double3_3.3.10-1ubuntu4_arm64.deb ... 411s Unpacking libfftw3-double3:arm64 (3.3.10-1ubuntu4) ... 411s Selecting previously unselected package fonts-dejavu-mono. 411s Preparing to unpack .../004-fonts-dejavu-mono_2.37-8_all.deb ... 411s Unpacking fonts-dejavu-mono (2.37-8) ... 412s Selecting previously unselected package fonts-dejavu-core. 412s Preparing to unpack .../005-fonts-dejavu-core_2.37-8_all.deb ... 412s Unpacking fonts-dejavu-core (2.37-8) ... 412s Selecting previously unselected package libfontenc1:arm64. 412s Preparing to unpack .../006-libfontenc1_1%3a1.1.8-1build1_arm64.deb ... 412s Unpacking libfontenc1:arm64 (1:1.1.8-1build1) ... 412s Selecting previously unselected package x11-common. 412s Preparing to unpack .../007-x11-common_1%3a7.7+23ubuntu3_all.deb ... 412s Unpacking x11-common (1:7.7+23ubuntu3) ... 412s Selecting previously unselected package xfonts-encodings. 412s Preparing to unpack .../008-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 412s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 412s Selecting previously unselected package xfonts-utils. 412s Preparing to unpack .../009-xfonts-utils_1%3a7.7+7_arm64.deb ... 412s Unpacking xfonts-utils (1:7.7+7) ... 412s Selecting previously unselected package fonts-urw-base35. 412s Preparing to unpack .../010-fonts-urw-base35_20200910-8_all.deb ... 412s Unpacking fonts-urw-base35 (20200910-8) ... 412s Selecting previously unselected package fontconfig-config. 412s Preparing to unpack .../011-fontconfig-config_2.15.0-1.1ubuntu2_arm64.deb ... 412s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ... 412s Selecting previously unselected package libfontconfig1:arm64. 412s Preparing to unpack .../012-libfontconfig1_2.15.0-1.1ubuntu2_arm64.deb ... 412s Unpacking libfontconfig1:arm64 (2.15.0-1.1ubuntu2) ... 412s Selecting previously unselected package libsharpyuv0:arm64. 412s Preparing to unpack .../013-libsharpyuv0_1.4.0-0.1_arm64.deb ... 412s Unpacking libsharpyuv0:arm64 (1.4.0-0.1) ... 412s Selecting previously unselected package libaom3:arm64. 412s Preparing to unpack .../014-libaom3_3.9.1-1_arm64.deb ... 412s Unpacking libaom3:arm64 (3.9.1-1) ... 412s Selecting previously unselected package libheif-plugin-aomdec:arm64. 412s Preparing to unpack .../015-libheif-plugin-aomdec_1.18.1-2_arm64.deb ... 412s Unpacking libheif-plugin-aomdec:arm64 (1.18.1-2) ... 412s Selecting previously unselected package libde265-0:arm64. 413s Preparing to unpack .../016-libde265-0_1.0.15-1build4_arm64.deb ... 413s Unpacking libde265-0:arm64 (1.0.15-1build4) ... 413s Selecting previously unselected package libheif-plugin-libde265:arm64. 413s Preparing to unpack .../017-libheif-plugin-libde265_1.18.1-2_arm64.deb ... 413s Unpacking libheif-plugin-libde265:arm64 (1.18.1-2) ... 413s Selecting previously unselected package libheif1:arm64. 413s Preparing to unpack .../018-libheif1_1.18.1-2_arm64.deb ... 413s Unpacking libheif1:arm64 (1.18.1-2) ... 413s Selecting previously unselected package libjbig0:arm64. 413s Preparing to unpack .../019-libjbig0_2.1-6.1ubuntu2_arm64.deb ... 413s Unpacking libjbig0:arm64 (2.1-6.1ubuntu2) ... 413s Selecting previously unselected package libjpeg-turbo8:arm64. 413s Preparing to unpack .../020-libjpeg-turbo8_2.1.5-2ubuntu2_arm64.deb ... 413s Unpacking libjpeg-turbo8:arm64 (2.1.5-2ubuntu2) ... 413s Selecting previously unselected package libjpeg8:arm64. 413s Preparing to unpack .../021-libjpeg8_8c-2ubuntu11_arm64.deb ... 413s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 413s Selecting previously unselected package liblcms2-2:arm64. 413s Preparing to unpack .../022-liblcms2-2_2.14-2build1_arm64.deb ... 413s Unpacking liblcms2-2:arm64 (2.14-2build1) ... 413s Selecting previously unselected package liblqr-1-0:arm64. 413s Preparing to unpack .../023-liblqr-1-0_0.4.2-2.1build2_arm64.deb ... 413s Unpacking liblqr-1-0:arm64 (0.4.2-2.1build2) ... 413s Selecting previously unselected package libltdl7:arm64. 413s Preparing to unpack .../024-libltdl7_2.4.7-7build1_arm64.deb ... 413s Unpacking libltdl7:arm64 (2.4.7-7build1) ... 413s Selecting previously unselected package libopenjp2-7:arm64. 413s Preparing to unpack .../025-libopenjp2-7_2.5.0-2ubuntu1_arm64.deb ... 413s Unpacking libopenjp2-7:arm64 (2.5.0-2ubuntu1) ... 413s Selecting previously unselected package libraw23t64:arm64. 413s Preparing to unpack .../026-libraw23t64_0.21.2-2.1build1_arm64.deb ... 413s Unpacking libraw23t64:arm64 (0.21.2-2.1build1) ... 413s Selecting previously unselected package libdeflate0:arm64. 413s Preparing to unpack .../027-libdeflate0_1.21-1_arm64.deb ... 413s Unpacking libdeflate0:arm64 (1.21-1) ... 413s Selecting previously unselected package liblerc4:arm64. 413s Preparing to unpack .../028-liblerc4_4.0.0+ds-4ubuntu2_arm64.deb ... 413s Unpacking liblerc4:arm64 (4.0.0+ds-4ubuntu2) ... 413s Selecting previously unselected package libwebp7:arm64. 413s Preparing to unpack .../029-libwebp7_1.4.0-0.1_arm64.deb ... 413s Unpacking libwebp7:arm64 (1.4.0-0.1) ... 413s Selecting previously unselected package libtiff6:arm64. 413s Preparing to unpack .../030-libtiff6_4.5.1+git230720-4ubuntu4_arm64.deb ... 413s Unpacking libtiff6:arm64 (4.5.1+git230720-4ubuntu4) ... 413s Selecting previously unselected package libwebpdemux2:arm64. 413s Preparing to unpack .../031-libwebpdemux2_1.4.0-0.1_arm64.deb ... 413s Unpacking libwebpdemux2:arm64 (1.4.0-0.1) ... 413s Selecting previously unselected package libwebpmux3:arm64. 413s Preparing to unpack .../032-libwebpmux3_1.4.0-0.1_arm64.deb ... 413s Unpacking libwebpmux3:arm64 (1.4.0-0.1) ... 413s Selecting previously unselected package imagemagick-6-common. 414s Preparing to unpack .../033-imagemagick-6-common_8%3a6.9.13.12+dfsg1-1build1_all.deb ... 414s Unpacking imagemagick-6-common (8:6.9.13.12+dfsg1-1build1) ... 414s Selecting previously unselected package libmagickcore-6.q16-7t64:arm64. 414s Preparing to unpack .../034-libmagickcore-6.q16-7t64_8%3a6.9.13.12+dfsg1-1build1_arm64.deb ... 414s Unpacking libmagickcore-6.q16-7t64:arm64 (8:6.9.13.12+dfsg1-1build1) ... 414s Selecting previously unselected package libmagickwand-6.q16-7t64:arm64. 414s Preparing to unpack .../035-libmagickwand-6.q16-7t64_8%3a6.9.13.12+dfsg1-1build1_arm64.deb ... 414s Unpacking libmagickwand-6.q16-7t64:arm64 (8:6.9.13.12+dfsg1-1build1) ... 414s Selecting previously unselected package poppler-data. 414s Preparing to unpack .../036-poppler-data_0.4.12-1_all.deb ... 414s Unpacking poppler-data (0.4.12-1) ... 414s Selecting previously unselected package sgml-base. 414s Preparing to unpack .../037-sgml-base_1.31_all.deb ... 414s Unpacking sgml-base (1.31) ... 414s Selecting previously unselected package autoconf. 414s Preparing to unpack .../038-autoconf_2.72-3_all.deb ... 414s Unpacking autoconf (2.72-3) ... 414s Selecting previously unselected package autotools-dev. 414s Preparing to unpack .../039-autotools-dev_20220109.1_all.deb ... 414s Unpacking autotools-dev (20220109.1) ... 414s Selecting previously unselected package automake. 414s Preparing to unpack .../040-automake_1%3a1.16.5-1.3ubuntu1_all.deb ... 414s Unpacking automake (1:1.16.5-1.3ubuntu1) ... 414s Selecting previously unselected package autopoint. 414s Preparing to unpack .../041-autopoint_0.22.5-2_all.deb ... 414s Unpacking autopoint (0.22.5-2) ... 415s Selecting previously unselected package libtcl8.6:arm64. 415s Preparing to unpack .../042-libtcl8.6_8.6.14+dfsg-1build1_arm64.deb ... 415s Unpacking libtcl8.6:arm64 (8.6.14+dfsg-1build1) ... 415s Selecting previously unselected package libxrender1:arm64. 415s Preparing to unpack .../043-libxrender1_1%3a0.9.10-1.1build1_arm64.deb ... 415s Unpacking libxrender1:arm64 (1:0.9.10-1.1build1) ... 415s Selecting previously unselected package libxft2:arm64. 415s Preparing to unpack .../044-libxft2_2.3.6-1build1_arm64.deb ... 415s Unpacking libxft2:arm64 (2.3.6-1build1) ... 415s Selecting previously unselected package libxss1:arm64. 415s Preparing to unpack .../045-libxss1_1%3a1.2.3-1build3_arm64.deb ... 415s Unpacking libxss1:arm64 (1:1.2.3-1build3) ... 415s Selecting previously unselected package libtk8.6:arm64. 415s Preparing to unpack .../046-libtk8.6_8.6.14-1build1_arm64.deb ... 415s Unpacking libtk8.6:arm64 (8.6.14-1build1) ... 415s Selecting previously unselected package tk8.6-blt2.5. 415s Preparing to unpack .../047-tk8.6-blt2.5_2.5.3+dfsg-7build1_arm64.deb ... 415s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 415s Selecting previously unselected package blt. 415s Preparing to unpack .../048-blt_2.5.3+dfsg-7build1_arm64.deb ... 415s Unpacking blt (2.5.3+dfsg-7build1) ... 415s Selecting previously unselected package libisl23:arm64. 415s Preparing to unpack .../049-libisl23_0.27-1_arm64.deb ... 415s Unpacking libisl23:arm64 (0.27-1) ... 415s Selecting previously unselected package libmpc3:arm64. 415s Preparing to unpack .../050-libmpc3_1.3.1-1build2_arm64.deb ... 415s Unpacking libmpc3:arm64 (1.3.1-1build2) ... 415s Selecting previously unselected package cpp-14-aarch64-linux-gnu. 415s Preparing to unpack .../051-cpp-14-aarch64-linux-gnu_14.2.0-7ubuntu1_arm64.deb ... 415s Unpacking cpp-14-aarch64-linux-gnu (14.2.0-7ubuntu1) ... 415s Selecting previously unselected package cpp-14. 415s Preparing to unpack .../052-cpp-14_14.2.0-7ubuntu1_arm64.deb ... 415s Unpacking cpp-14 (14.2.0-7ubuntu1) ... 415s Selecting previously unselected package cpp-aarch64-linux-gnu. 415s Preparing to unpack .../053-cpp-aarch64-linux-gnu_4%3a14.1.0-2ubuntu1_arm64.deb ... 415s Unpacking cpp-aarch64-linux-gnu (4:14.1.0-2ubuntu1) ... 415s Selecting previously unselected package cpp. 415s Preparing to unpack .../054-cpp_4%3a14.1.0-2ubuntu1_arm64.deb ... 415s Unpacking cpp (4:14.1.0-2ubuntu1) ... 415s Selecting previously unselected package libcc1-0:arm64. 415s Preparing to unpack .../055-libcc1-0_14.2.0-7ubuntu1_arm64.deb ... 415s Unpacking libcc1-0:arm64 (14.2.0-7ubuntu1) ... 415s Selecting previously unselected package libitm1:arm64. 415s Preparing to unpack .../056-libitm1_14.2.0-7ubuntu1_arm64.deb ... 415s Unpacking libitm1:arm64 (14.2.0-7ubuntu1) ... 416s Selecting previously unselected package libasan8:arm64. 416s Preparing to unpack .../057-libasan8_14.2.0-7ubuntu1_arm64.deb ... 416s Unpacking libasan8:arm64 (14.2.0-7ubuntu1) ... 416s Selecting previously unselected package liblsan0:arm64. 416s Preparing to unpack .../058-liblsan0_14.2.0-7ubuntu1_arm64.deb ... 416s Unpacking liblsan0:arm64 (14.2.0-7ubuntu1) ... 416s Selecting previously unselected package libtsan2:arm64. 416s Preparing to unpack .../059-libtsan2_14.2.0-7ubuntu1_arm64.deb ... 416s Unpacking libtsan2:arm64 (14.2.0-7ubuntu1) ... 416s Selecting previously unselected package libubsan1:arm64. 416s Preparing to unpack .../060-libubsan1_14.2.0-7ubuntu1_arm64.deb ... 416s Unpacking libubsan1:arm64 (14.2.0-7ubuntu1) ... 416s Selecting previously unselected package libhwasan0:arm64. 416s Preparing to unpack .../061-libhwasan0_14.2.0-7ubuntu1_arm64.deb ... 416s Unpacking libhwasan0:arm64 (14.2.0-7ubuntu1) ... 416s Selecting previously unselected package libgcc-14-dev:arm64. 416s Preparing to unpack .../062-libgcc-14-dev_14.2.0-7ubuntu1_arm64.deb ... 416s Unpacking libgcc-14-dev:arm64 (14.2.0-7ubuntu1) ... 416s Selecting previously unselected package gcc-14-aarch64-linux-gnu. 416s Preparing to unpack .../063-gcc-14-aarch64-linux-gnu_14.2.0-7ubuntu1_arm64.deb ... 416s Unpacking gcc-14-aarch64-linux-gnu (14.2.0-7ubuntu1) ... 417s Selecting previously unselected package gcc-14. 417s Preparing to unpack .../064-gcc-14_14.2.0-7ubuntu1_arm64.deb ... 417s Unpacking gcc-14 (14.2.0-7ubuntu1) ... 417s Selecting previously unselected package gcc-aarch64-linux-gnu. 417s Preparing to unpack .../065-gcc-aarch64-linux-gnu_4%3a14.1.0-2ubuntu1_arm64.deb ... 417s Unpacking gcc-aarch64-linux-gnu (4:14.1.0-2ubuntu1) ... 417s Selecting previously unselected package gcc. 417s Preparing to unpack .../066-gcc_4%3a14.1.0-2ubuntu1_arm64.deb ... 417s Unpacking gcc (4:14.1.0-2ubuntu1) ... 417s Selecting previously unselected package libstdc++-14-dev:arm64. 417s Preparing to unpack .../067-libstdc++-14-dev_14.2.0-7ubuntu1_arm64.deb ... 417s Unpacking libstdc++-14-dev:arm64 (14.2.0-7ubuntu1) ... 417s Selecting previously unselected package g++-14-aarch64-linux-gnu. 417s Preparing to unpack .../068-g++-14-aarch64-linux-gnu_14.2.0-7ubuntu1_arm64.deb ... 417s Unpacking g++-14-aarch64-linux-gnu (14.2.0-7ubuntu1) ... 417s Selecting previously unselected package g++-14. 417s Preparing to unpack .../069-g++-14_14.2.0-7ubuntu1_arm64.deb ... 417s Unpacking g++-14 (14.2.0-7ubuntu1) ... 417s Selecting previously unselected package g++-aarch64-linux-gnu. 417s Preparing to unpack .../070-g++-aarch64-linux-gnu_4%3a14.1.0-2ubuntu1_arm64.deb ... 417s Unpacking g++-aarch64-linux-gnu (4:14.1.0-2ubuntu1) ... 417s Selecting previously unselected package g++. 417s Preparing to unpack .../071-g++_4%3a14.1.0-2ubuntu1_arm64.deb ... 417s Unpacking g++ (4:14.1.0-2ubuntu1) ... 417s Selecting previously unselected package build-essential. 417s Preparing to unpack .../072-build-essential_12.10ubuntu1_arm64.deb ... 417s Unpacking build-essential (12.10ubuntu1) ... 417s Selecting previously unselected package bwa. 417s Preparing to unpack .../073-bwa_0.7.17-7_arm64.deb ... 417s Unpacking bwa (0.7.17-7) ... 417s Selecting previously unselected package libargtable2-0. 417s Preparing to unpack .../074-libargtable2-0_13-2_arm64.deb ... 417s Unpacking libargtable2-0 (13-2) ... 417s Selecting previously unselected package clustalo. 417s Preparing to unpack .../075-clustalo_1.2.4-8build1_arm64.deb ... 417s Unpacking clustalo (1.2.4-8build1) ... 417s Selecting previously unselected package libdebhelper-perl. 417s Preparing to unpack .../076-libdebhelper-perl_13.20ubuntu1_all.deb ... 417s Unpacking libdebhelper-perl (13.20ubuntu1) ... 418s Selecting previously unselected package libtool. 418s Preparing to unpack .../077-libtool_2.4.7-7build1_all.deb ... 418s Unpacking libtool (2.4.7-7build1) ... 418s Selecting previously unselected package dh-autoreconf. 418s Preparing to unpack .../078-dh-autoreconf_20_all.deb ... 418s Unpacking dh-autoreconf (20) ... 418s Selecting previously unselected package libarchive-zip-perl. 418s Preparing to unpack .../079-libarchive-zip-perl_1.68-1_all.deb ... 418s Unpacking libarchive-zip-perl (1.68-1) ... 418s Selecting previously unselected package libfile-stripnondeterminism-perl. 418s Preparing to unpack .../080-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ... 418s Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... 418s Selecting previously unselected package dh-strip-nondeterminism. 418s Preparing to unpack .../081-dh-strip-nondeterminism_1.14.0-1_all.deb ... 418s Unpacking dh-strip-nondeterminism (1.14.0-1) ... 418s Selecting previously unselected package debugedit. 418s Preparing to unpack .../082-debugedit_1%3a5.0-6_arm64.deb ... 418s Unpacking debugedit (1:5.0-6) ... 418s Selecting previously unselected package dwz. 418s Preparing to unpack .../083-dwz_0.15-1build6_arm64.deb ... 418s Unpacking dwz (0.15-1build6) ... 418s Selecting previously unselected package gettext. 418s Preparing to unpack .../084-gettext_0.22.5-2_arm64.deb ... 418s Unpacking gettext (0.22.5-2) ... 418s Selecting previously unselected package intltool-debian. 418s Preparing to unpack .../085-intltool-debian_0.35.0+20060710.6_all.deb ... 418s Unpacking intltool-debian (0.35.0+20060710.6) ... 418s Selecting previously unselected package po-debconf. 418s Preparing to unpack .../086-po-debconf_1.0.21+nmu1_all.deb ... 418s Unpacking po-debconf (1.0.21+nmu1) ... 418s Selecting previously unselected package debhelper. 418s Preparing to unpack .../087-debhelper_13.20ubuntu1_all.deb ... 418s Unpacking debhelper (13.20ubuntu1) ... 418s Selecting previously unselected package dh-python. 418s Preparing to unpack .../088-dh-python_6.20240824_all.deb ... 418s Unpacking dh-python (6.20240824) ... 418s Selecting previously unselected package dialign. 418s Preparing to unpack .../089-dialign_2.2.1-13_arm64.deb ... 418s Unpacking dialign (2.2.1-13) ... 418s Selecting previously unselected package libcifpp-data. 418s Preparing to unpack .../090-libcifpp-data_5.0.7.1-3build1_all.deb ... 418s Unpacking libcifpp-data (5.0.7.1-3build1) ... 418s Selecting previously unselected package libcifpp5:arm64. 418s Preparing to unpack .../091-libcifpp5_5.0.7.1-3build1_arm64.deb ... 418s Unpacking libcifpp5:arm64 (5.0.7.1-3build1) ... 418s Selecting previously unselected package dssp. 418s Preparing to unpack .../092-dssp_4.2.2-2_arm64.deb ... 418s Unpacking dssp (4.2.2-2) ... 419s Selecting previously unselected package libimagequant0:arm64. 419s Preparing to unpack .../093-libimagequant0_2.18.0-1build1_arm64.deb ... 419s Unpacking libimagequant0:arm64 (2.18.0-1build1) ... 419s Selecting previously unselected package libgraphite2-3:arm64. 419s Preparing to unpack .../094-libgraphite2-3_1.3.14-2ubuntu1_arm64.deb ... 419s Unpacking libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 419s Selecting previously unselected package libharfbuzz0b:arm64. 419s Preparing to unpack .../095-libharfbuzz0b_9.0.0-1_arm64.deb ... 419s Unpacking libharfbuzz0b:arm64 (9.0.0-1) ... 419s Selecting previously unselected package libraqm0:arm64. 419s Preparing to unpack .../096-libraqm0_0.10.1-1build1_arm64.deb ... 419s Unpacking libraqm0:arm64 (0.10.1-1build1) ... 419s Selecting previously unselected package libxpm4:arm64. 419s Preparing to unpack .../097-libxpm4_1%3a3.5.17-1build2_arm64.deb ... 419s Unpacking libxpm4:arm64 (1:3.5.17-1build2) ... 419s Selecting previously unselected package libgd3:arm64. 419s Preparing to unpack .../098-libgd3_2.3.3-12ubuntu3_arm64.deb ... 419s Unpacking libgd3:arm64 (2.3.3-12ubuntu3) ... 419s Selecting previously unselected package libhpdf-2.3.0:arm64. 419s Preparing to unpack .../099-libhpdf-2.3.0_2.3.0+dfsg-1build3_arm64.deb ... 419s Unpacking libhpdf-2.3.0:arm64 (2.3.0+dfsg-1build3) ... 419s Selecting previously unselected package mysql-common. 419s Preparing to unpack .../100-mysql-common_5.8+1.1.1_all.deb ... 419s Unpacking mysql-common (5.8+1.1.1) ... 419s Selecting previously unselected package libmysqlclient21:arm64. 419s Preparing to unpack .../101-libmysqlclient21_8.0.39-1_arm64.deb ... 419s Unpacking libmysqlclient21:arm64 (8.0.39-1) ... 419s Selecting previously unselected package libpq5:arm64. 419s Preparing to unpack .../102-libpq5_17.0-1_arm64.deb ... 419s Unpacking libpq5:arm64 (17.0-1) ... 419s Selecting previously unselected package emboss-lib. 419s Preparing to unpack .../103-emboss-lib_6.6.0+dfsg-12ubuntu2_arm64.deb ... 419s Unpacking emboss-lib (6.6.0+dfsg-12ubuntu2) ... 419s Selecting previously unselected package emboss-data. 419s Preparing to unpack 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libidn12:arm64 (1.42-2) ... 424s Selecting previously unselected package libijs-0.35:arm64. 424s Preparing to unpack .../115-libijs-0.35_0.35-15.1build1_arm64.deb ... 424s Unpacking libijs-0.35:arm64 (0.35-15.1build1) ... 424s Selecting previously unselected package libjbig2dec0:arm64. 424s Preparing to unpack .../116-libjbig2dec0_0.20-1build3_arm64.deb ... 424s Unpacking libjbig2dec0:arm64 (0.20-1build3) ... 424s Selecting previously unselected package libpaper1:arm64. 424s Preparing to unpack .../117-libpaper1_1.1.29build1_arm64.deb ... 424s Unpacking libpaper1:arm64 (1.1.29build1) ... 424s Selecting previously unselected package libice6:arm64. 424s Preparing to unpack .../118-libice6_2%3a1.0.10-1build3_arm64.deb ... 424s Unpacking libice6:arm64 (2:1.0.10-1build3) ... 424s Selecting previously unselected package libsm6:arm64. 424s Preparing to unpack .../119-libsm6_2%3a1.2.3-1build3_arm64.deb ... 424s Unpacking libsm6:arm64 (2:1.2.3-1build3) ... 424s Selecting previously unselected package libxt6t64:arm64. 424s Preparing to unpack .../120-libxt6t64_1%3a1.2.1-1.2build1_arm64.deb ... 424s Unpacking libxt6t64:arm64 (1:1.2.1-1.2build1) ... 424s Selecting previously unselected package libgs10:arm64. 424s Preparing to unpack .../121-libgs10_10.03.1~dfsg1-0ubuntu2_arm64.deb ... 424s Unpacking libgs10:arm64 (10.03.1~dfsg1-0ubuntu2) ... 424s Selecting previously unselected package ghostscript. 424s Preparing to unpack .../122-ghostscript_10.03.1~dfsg1-0ubuntu2_arm64.deb ... 424s Unpacking ghostscript (10.03.1~dfsg1-0ubuntu2) ... 424s Selecting previously unselected package libnetpbm11t64:arm64. 424s Preparing to unpack .../123-libnetpbm11t64_2%3a11.07.00-2_arm64.deb ... 424s Unpacking libnetpbm11t64:arm64 (2:11.07.00-2) ... 424s Selecting previously unselected package netpbm. 424s Preparing to unpack .../124-netpbm_2%3a11.07.00-2_arm64.deb ... 424s Unpacking netpbm (2:11.07.00-2) ... 424s Selecting previously unselected package tex-common. 424s Preparing to unpack .../125-tex-common_6.18_all.deb ... 424s Unpacking tex-common (6.18) ... 425s Selecting previously unselected package libpaper-utils. 425s Preparing to unpack .../126-libpaper-utils_1.1.29build1_arm64.deb ... 425s Unpacking libpaper-utils (1.1.29build1) ... 425s Selecting previously unselected package libkpathsea6:arm64. 425s Preparing to unpack .../127-libkpathsea6_2024.20240313.70630+ds-4_arm64.deb ... 425s Unpacking libkpathsea6:arm64 (2024.20240313.70630+ds-4) ... 425s Selecting previously unselected package libptexenc1:arm64. 425s Preparing to unpack .../128-libptexenc1_2024.20240313.70630+ds-4_arm64.deb ... 425s Unpacking libptexenc1:arm64 (2024.20240313.70630+ds-4) ... 425s Selecting previously unselected package libsynctex2:arm64. 425s Preparing to unpack .../129-libsynctex2_2024.20240313.70630+ds-4_arm64.deb ... 425s Unpacking libsynctex2:arm64 (2024.20240313.70630+ds-4) ... 425s Selecting previously unselected package libtexlua53-5:arm64. 425s Preparing to unpack .../130-libtexlua53-5_2024.20240313.70630+ds-4_arm64.deb ... 425s Unpacking libtexlua53-5:arm64 (2024.20240313.70630+ds-4) ... 425s Selecting previously unselected package t1utils. 425s Preparing to unpack .../131-t1utils_1.41-4build3_arm64.deb ... 425s Unpacking t1utils (1.41-4build3) ... 425s Selecting previously unselected package libpixman-1-0:arm64. 425s Preparing to unpack .../132-libpixman-1-0_0.42.2-1build1_arm64.deb ... 425s Unpacking libpixman-1-0:arm64 (0.42.2-1build1) ... 425s Selecting previously unselected package libxcb-render0:arm64. 425s Preparing to unpack .../133-libxcb-render0_1.17.0-2_arm64.deb ... 425s Unpacking libxcb-render0:arm64 (1.17.0-2) ... 425s Selecting previously unselected package libxcb-shm0:arm64. 425s Preparing to unpack .../134-libxcb-shm0_1.17.0-2_arm64.deb ... 425s Unpacking libxcb-shm0:arm64 (1.17.0-2) ... 425s Selecting previously unselected package libcairo2:arm64. 425s Preparing to unpack .../135-libcairo2_1.18.2-2_arm64.deb ... 425s Unpacking libcairo2:arm64 (1.18.2-2) ... 425s Selecting previously unselected package libmpfi0:arm64. 425s Preparing to unpack .../136-libmpfi0_1.5.4+ds-3_arm64.deb ... 425s Unpacking libmpfi0:arm64 (1.5.4+ds-3) ... 425s Selecting previously unselected package libpotrace0:arm64. 425s Preparing to unpack .../137-libpotrace0_1.16-2build1_arm64.deb ... 425s Unpacking libpotrace0:arm64 (1.16-2build1) ... 425s Selecting previously unselected package libteckit0:arm64. 425s Preparing to unpack .../138-libteckit0_2.5.12+ds1-1_arm64.deb ... 425s Unpacking libteckit0:arm64 (2.5.12+ds1-1) ... 425s Selecting previously unselected package libxmu6:arm64. 425s Preparing to unpack .../139-libxmu6_2%3a1.1.3-3build2_arm64.deb ... 425s Unpacking libxmu6:arm64 (2:1.1.3-3build2) ... 425s Selecting previously unselected package libxaw7:arm64. 425s Preparing to unpack .../140-libxaw7_2%3a1.0.14-1build2_arm64.deb ... 425s Unpacking libxaw7:arm64 (2:1.0.14-1build2) ... 425s Selecting previously unselected package libxi6:arm64. 425s Preparing to unpack .../141-libxi6_2%3a1.8.2-1_arm64.deb ... 425s Unpacking libxi6:arm64 (2:1.8.2-1) ... 425s Selecting previously unselected package libzzip-0-13t64:arm64. 425s Preparing to unpack .../142-libzzip-0-13t64_0.13.72+dfsg.1-1.2build1_arm64.deb ... 425s Unpacking libzzip-0-13t64:arm64 (0.13.72+dfsg.1-1.2build1) ... 425s Selecting previously unselected package texlive-binaries. 425s Preparing to unpack .../143-texlive-binaries_2024.20240313.70630+ds-4_arm64.deb ... 425s Unpacking texlive-binaries (2024.20240313.70630+ds-4) ... 426s Selecting previously unselected package xdg-utils. 426s Preparing to unpack .../144-xdg-utils_1.2.1-0ubuntu1_all.deb ... 426s Unpacking xdg-utils (1.2.1-0ubuntu1) ... 426s Selecting previously unselected package texlive-base. 426s Preparing to unpack .../145-texlive-base_2024.20240706-1_all.deb ... 426s Unpacking texlive-base (2024.20240706-1) ... 427s Selecting previously unselected package hicolor-icon-theme. 427s Preparing to unpack .../146-hicolor-icon-theme_0.18-1_all.deb ... 427s Unpacking hicolor-icon-theme (0.18-1) ... 427s Selecting previously unselected package imagemagick-6.q16. 427s Preparing to unpack .../147-imagemagick-6.q16_8%3a6.9.13.12+dfsg1-1build1_arm64.deb ... 427s Unpacking imagemagick-6.q16 (8:6.9.13.12+dfsg1-1build1) ... 427s Selecting previously unselected package imagemagick. 427s Preparing to unpack .../148-imagemagick_8%3a6.9.13.12+dfsg1-1build1_arm64.deb ... 427s Unpacking imagemagick (8:6.9.13.12+dfsg1-1build1) ... 427s Selecting previously unselected package hevea. 427s Preparing to unpack .../149-hevea_2.36-2_arm64.deb ... 427s Unpacking hevea (2.36-2) ... 427s Selecting previously unselected package libapache-pom-java. 427s Preparing to unpack .../150-libapache-pom-java_29-2_all.deb ... 427s Unpacking libapache-pom-java (29-2) ... 427s Selecting previously unselected package libblas3:arm64. 427s Preparing to unpack .../151-libblas3_3.12.0-3build2_arm64.deb ... 427s Unpacking libblas3:arm64 (3.12.0-3build2) ... 427s Selecting previously unselected package libcommons-parent-java. 427s Preparing to unpack .../152-libcommons-parent-java_56-1_all.deb ... 427s Unpacking libcommons-parent-java (56-1) ... 427s Selecting previously unselected package libcommons-logging-java. 427s Preparing to unpack .../153-libcommons-logging-java_1.3.0-1ubuntu1_all.deb ... 427s Unpacking libcommons-logging-java (1.3.0-1ubuntu1) ... 427s Selecting previously unselected package libexpat1-dev:arm64. 427s Preparing to unpack .../154-libexpat1-dev_2.6.2-2_arm64.deb ... 427s Unpacking libexpat1-dev:arm64 (2.6.2-2) ... 427s Selecting previously unselected package libgfortran5:arm64. 427s Preparing to unpack .../155-libgfortran5_14.2.0-7ubuntu1_arm64.deb ... 427s Unpacking libgfortran5:arm64 (14.2.0-7ubuntu1) ... 427s Selecting previously unselected package libjs-jquery. 427s Preparing to unpack .../156-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 427s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 427s Selecting previously unselected package libjs-jquery-ui. 427s Preparing to unpack .../157-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... 427s Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... 427s Selecting previously unselected package libjs-underscore. 427s Preparing to unpack .../158-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 427s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 427s Selecting previously unselected package libjs-sphinxdoc. 427s Preparing to unpack .../159-libjs-sphinxdoc_7.4.7-3_all.deb ... 427s Unpacking libjs-sphinxdoc (7.4.7-3) ... 427s Selecting previously unselected package liblapack3:arm64. 427s Preparing to unpack .../160-liblapack3_3.12.0-3build2_arm64.deb ... 427s Unpacking liblapack3:arm64 (3.12.0-3build2) ... 428s Selecting previously unselected package liblbfgsb0:arm64. 428s Preparing to unpack .../161-liblbfgsb0_3.0+dfsg.4-1build1_arm64.deb ... 428s Unpacking liblbfgsb0:arm64 (3.0+dfsg.4-1build1) ... 428s Selecting previously unselected package libmbedcrypto7t64:arm64. 428s Preparing to unpack .../162-libmbedcrypto7t64_2.28.8-1_arm64.deb ... 428s Unpacking libmbedcrypto7t64:arm64 (2.28.8-1) ... 428s Selecting previously unselected package libmbedx509-1t64:arm64. 428s Preparing to unpack .../163-libmbedx509-1t64_2.28.8-1_arm64.deb ... 428s Unpacking libmbedx509-1t64:arm64 (2.28.8-1) ... 428s Selecting previously unselected package libmbedtls14t64:arm64. 428s Preparing to unpack .../164-libmbedtls14t64_2.28.8-1_arm64.deb ... 428s Unpacking libmbedtls14t64:arm64 (2.28.8-1) ... 428s Selecting previously unselected package zlib1g-dev:arm64. 428s Preparing to unpack .../165-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1ubuntu1_arm64.deb ... 428s Unpacking zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 428s Selecting previously unselected package libpython3.12-dev:arm64. 428s Preparing to unpack .../166-libpython3.12-dev_3.12.7-1_arm64.deb ... 428s Unpacking libpython3.12-dev:arm64 (3.12.7-1) ... 428s Selecting previously unselected package libpython3-dev:arm64. 428s Preparing to unpack .../167-libpython3-dev_3.12.6-0ubuntu1_arm64.deb ... 428s Unpacking libpython3-dev:arm64 (3.12.6-0ubuntu1) ... 428s Selecting previously unselected package libpython3-all-dev:arm64. 428s Preparing to unpack .../168-libpython3-all-dev_3.12.6-0ubuntu1_arm64.deb ... 428s Unpacking libpython3-all-dev:arm64 (3.12.6-0ubuntu1) ... 428s Selecting previously unselected package libqhull-r8.0:arm64. 428s Preparing to unpack .../169-libqhull-r8.0_2020.2-6build1_arm64.deb ... 428s Unpacking libqhull-r8.0:arm64 (2020.2-6build1) ... 428s Selecting previously unselected package libxslt1.1:arm64. 428s Preparing to unpack .../170-libxslt1.1_1.1.39-0exp1ubuntu1_arm64.deb ... 428s Unpacking libxslt1.1:arm64 (1.1.39-0exp1ubuntu1) ... 428s Selecting previously unselected package mafft. 428s Preparing to unpack .../171-mafft_7.505-1_arm64.deb ... 428s Unpacking mafft (7.505-1) ... 428s Selecting previously unselected package ncbi-data. 428s Preparing to unpack .../172-ncbi-data_6.1.20170106+dfsg2-3_all.deb ... 428s Unpacking ncbi-data (6.1.20170106+dfsg2-3) ... 428s Selecting previously unselected package ncbi-blast+. 428s Preparing to unpack .../173-ncbi-blast+_2.16.0+ds-6_arm64.deb ... 428s Unpacking ncbi-blast+ (2.16.0+ds-6) ... 429s Selecting previously unselected package phylip. 429s Preparing to unpack .../174-phylip_1%3a3.697+dfsg-4build1_arm64.deb ... 429s Unpacking phylip (1:3.697+dfsg-4build1) ... 429s Selecting previously unselected package prank. 429s Preparing to unpack .../175-prank_0.0.170427+dfsg-3_arm64.deb ... 429s Unpacking prank (0.0.170427+dfsg-3) ... 429s Selecting previously unselected package preview-latex-style. 429s Preparing to unpack .../176-preview-latex-style_13.2-1_all.deb ... 429s Unpacking preview-latex-style (13.2-1) ... 429s Selecting previously unselected package probcons. 429s Preparing to unpack .../177-probcons_1.12-14_arm64.deb ... 429s Unpacking probcons (1.12-14) ... 429s Selecting previously unselected package python-biopython-doc. 429s Preparing to unpack .../178-python-biopython-doc_1.83+dfsg1-3_all.deb ... 429s Unpacking python-biopython-doc (1.83+dfsg1-3) ... 429s Selecting previously unselected package python-matplotlib-data. 429s Preparing to unpack .../179-python-matplotlib-data_3.8.3-3_all.deb ... 429s Unpacking python-matplotlib-data (3.8.3-3) ... 429s Selecting previously unselected package python3-all. 429s Preparing to unpack .../180-python3-all_3.12.6-0ubuntu1_arm64.deb ... 429s Unpacking python3-all (3.12.6-0ubuntu1) ... 429s Selecting previously unselected package python3.12-dev. 429s Preparing to unpack .../181-python3.12-dev_3.12.7-1_arm64.deb ... 429s Unpacking python3.12-dev (3.12.7-1) ... 429s Selecting previously unselected package python3-dev. 429s Preparing to unpack .../182-python3-dev_3.12.6-0ubuntu1_arm64.deb ... 429s Unpacking python3-dev (3.12.6-0ubuntu1) ... 430s Selecting previously unselected package python3-all-dev. 430s Preparing to unpack .../183-python3-all-dev_3.12.6-0ubuntu1_arm64.deb ... 430s Unpacking python3-all-dev (3.12.6-0ubuntu1) ... 430s Selecting previously unselected package python3-appdirs. 430s Preparing to unpack .../184-python3-appdirs_1.4.4-4_all.deb ... 430s Unpacking python3-appdirs (1.4.4-4) ... 430s Selecting previously unselected package python3-numpy. 430s Preparing to unpack .../185-python3-numpy_1%3a1.26.4+ds-11build1_arm64.deb ... 430s Unpacking python3-numpy (1:1.26.4+ds-11build1) ... 430s Selecting previously unselected package python3.12-tk. 430s Preparing to unpack .../186-python3.12-tk_3.12.7-1_arm64.deb ... 430s Unpacking python3.12-tk (3.12.7-1) ... 430s Selecting previously unselected package python3-tk:arm64. 430s Preparing to unpack .../187-python3-tk_3.12.6-1ubuntu1_arm64.deb ... 430s Unpacking python3-tk:arm64 (3.12.6-1ubuntu1) ... 430s Selecting previously unselected package python3-pil.imagetk:arm64. 430s Preparing to unpack .../188-python3-pil.imagetk_10.4.0-1ubuntu1_arm64.deb ... 430s Unpacking python3-pil.imagetk:arm64 (10.4.0-1ubuntu1) ... 430s Selecting previously unselected package python3-pil:arm64. 430s Preparing to unpack .../189-python3-pil_10.4.0-1ubuntu1_arm64.deb ... 430s Unpacking python3-pil:arm64 (10.4.0-1ubuntu1) ... 430s Selecting previously unselected package python3-cairo. 430s Preparing to unpack .../190-python3-cairo_1.26.1-2_arm64.deb ... 430s Unpacking python3-cairo (1.26.1-2) ... 430s Selecting previously unselected package python3-freetype. 430s Preparing to unpack .../191-python3-freetype_2.4.0-2_all.deb ... 430s Unpacking python3-freetype (2.4.0-2) ... 430s Selecting previously unselected package python3-rlpycairo. 430s Preparing to unpack .../192-python3-rlpycairo_0.3.0-3_all.deb ... 430s Unpacking python3-rlpycairo (0.3.0-3) ... 430s Selecting previously unselected package python3-reportlab. 430s Preparing to unpack .../193-python3-reportlab_4.2.2-1_all.deb ... 430s Unpacking python3-reportlab (4.2.2-1) ... 430s Selecting previously unselected package xml-core. 430s Preparing to unpack .../194-xml-core_0.19_all.deb ... 430s Unpacking xml-core (0.19) ... 430s Selecting previously unselected package w3c-sgml-lib. 430s Preparing to unpack .../195-w3c-sgml-lib_1.3-3_all.deb ... 430s Unpacking w3c-sgml-lib (1.3-3) ... 430s Selecting previously unselected package python3-biopython. 430s Preparing to unpack .../196-python3-biopython_1.83+dfsg1-3_arm64.deb ... 430s Unpacking python3-biopython (1.83+dfsg1-3) ... 430s Selecting previously unselected package python3-biopython-sql. 430s Preparing to unpack .../197-python3-biopython-sql_1.83+dfsg1-3_all.deb ... 430s Unpacking python3-biopython-sql (1.83+dfsg1-3) ... 430s Selecting previously unselected package python3-brotli. 430s Preparing to unpack .../198-python3-brotli_1.1.0-2build2_arm64.deb ... 430s Unpacking python3-brotli (1.1.0-2build2) ... 431s Selecting previously unselected package python3-contourpy. 431s 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Selecting previously unselected package python3-ufolib2. 431s Preparing to unpack .../205-python3-ufolib2_0.16.0+dfsg1-1_all.deb ... 431s Unpacking python3-ufolib2 (0.16.0+dfsg1-1) ... 431s Selecting previously unselected package python3-mpmath. 431s Preparing to unpack .../206-python3-mpmath_1.3.0-1_all.deb ... 431s Unpacking python3-mpmath (1.3.0-1) ... 431s Selecting previously unselected package python3-sympy. 431s Preparing to unpack .../207-python3-sympy_1.13.1-1_all.deb ... 431s Unpacking python3-sympy (1.13.1-1) ... 432s Selecting previously unselected package python3-tz. 432s Preparing to unpack .../208-python3-tz_2024.1-2_all.deb ... 432s Unpacking python3-tz (2024.1-2) ... 432s Selecting previously unselected package python3-fs. 432s Preparing to unpack .../209-python3-fs_2.4.16-4_all.deb ... 432s Unpacking python3-fs (2.4.16-4) ... 432s Selecting previously unselected package python3-lxml:arm64. 432s Preparing to unpack .../210-python3-lxml_5.3.0-1_arm64.deb ... 432s Unpacking python3-lxml:arm64 (5.3.0-1) ... 432s Selecting previously unselected package python3-lz4. 432s Preparing to unpack .../211-python3-lz4_4.0.2+dfsg-1build4_arm64.deb ... 432s Unpacking python3-lz4 (4.0.2+dfsg-1build4) ... 432s Selecting previously unselected package unicode-data. 432s Preparing to unpack .../212-unicode-data_15.1.0-1_all.deb ... 432s Unpacking unicode-data (15.1.0-1) ... 432s Selecting previously unselected package python3-fonttools. 432s Preparing to unpack .../213-python3-fonttools_4.46.0-1build2_arm64.deb ... 432s Unpacking python3-fonttools (4.46.0-1build2) ... 432s Selecting previously unselected package python3-isodate. 432s Preparing to unpack .../214-python3-isodate_0.6.1-3_all.deb ... 432s Unpacking python3-isodate (0.6.1-3) ... 432s Selecting previously unselected package python3-kiwisolver. 432s Preparing to unpack .../215-python3-kiwisolver_1.4.5-1_arm64.deb ... 432s Unpacking python3-kiwisolver (1.4.5-1) ... 432s Selecting previously unselected package python3-packaging. 432s Preparing to unpack .../216-python3-packaging_24.1-1_all.deb ... 432s Unpacking python3-packaging (24.1-1) ... 432s Selecting previously unselected package python3-matplotlib. 432s Preparing to unpack .../217-python3-matplotlib_3.8.3-3_arm64.deb ... 432s Unpacking python3-matplotlib (3.8.3-3) ... 432s Selecting previously unselected package python3-msgpack. 432s Preparing to unpack .../218-python3-msgpack_1.0.3-3build2_arm64.deb ... 432s Unpacking python3-msgpack (1.0.3-3build2) ... 433s Selecting previously unselected package python3-mmtf. 433s Preparing to unpack .../219-python3-mmtf_1.1.3-1_all.deb ... 433s Unpacking python3-mmtf (1.1.3-1) ... 433s Selecting previously unselected package python3-mysqldb. 433s Preparing to unpack .../220-python3-mysqldb_1.4.6-2build3_arm64.deb ... 433s Unpacking python3-mysqldb (1.4.6-2build3) ... 433s Selecting previously unselected package python3-networkx. 433s Preparing to unpack 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libaom3:arm64 (3.9.1-1) ... 438s Setting up mysql-common (5.8+1.1.1) ... 438s update-alternatives: using /etc/mysql/my.cnf.fallback to provide /etc/mysql/my.cnf (my.cnf) in auto mode 438s Setting up libmysqlclient21:arm64 (8.0.39-1) ... 438s Setting up imagemagick-6-common (8:6.9.13.12+dfsg1-1build1) ... 438s Setting up libhpdf-2.3.0:arm64 (2.3.0+dfsg-1build3) ... 438s Setting up liblerc4:arm64 (4.0.0+ds-4ubuntu2) ... 438s Setting up libxpm4:arm64 (1:3.5.17-1build2) ... 438s Setting up hicolor-icon-theme (0.18-1) ... 438s Setting up libxi6:arm64 (2:1.8.2-1) ... 438s Setting up probcons (1.12-14) ... 438s Setting up libmbedcrypto7t64:arm64 (2.28.8-1) ... 438s Setting up libxrender1:arm64 (1:0.9.10-1.1build1) ... 438s Setting up python3-lz4 (4.0.2+dfsg-1build4) ... 438s Setting up libxcb-render0:arm64 (1.17.0-2) ... 438s Setting up mafft (7.505-1) ... 438s Setting up libarchive-zip-perl (1.68-1) ... 438s Setting up bwa (0.7.17-7) ... 438s Setting up fonts-lyx (2.4.1-2) ... 438s Setting up libijs-0.35:arm64 (0.35-15.1build1) ... 438s Setting up libdebhelper-perl (13.20ubuntu1) ... 438s Setting up libgs-common (10.03.1~dfsg1-0ubuntu2) ... 438s Setting up libfontbox-java (1:1.8.16-5) ... 438s Setting up phylip (1:3.697+dfsg-4build1) ... 438s Setting up x11-common (1:7.7+23ubuntu3) ... 439s Setting up libpq5:arm64 (17.0-1) ... 439s Setting up libdeflate0:arm64 (1.21-1) ... 439s Setting up m4 (1.4.19-4build1) ... 439s Setting up libqhull-r8.0:arm64 (2020.2-6build1) ... 439s Setting up python3-all (3.12.6-0ubuntu1) ... 439s Setting up libxcb-shm0:arm64 (1.17.0-2) ... 439s Setting up libpaper-utils (1.1.29build1) ... 439s Setting up libgomp1:arm64 (14.2.0-7ubuntu1) ... 439s Setting up python3-freetype (2.4.0-2) ... 439s Setting up emboss-data (6.6.0+dfsg-12ubuntu2) ... 439s Setting up python3-networkx (3.2.1-4ubuntu1) ... 440s Setting up libjbig0:arm64 (2.1-6.1ubuntu2) ... 440s Setting up libnetpbm11t64:arm64 (2:11.07.00-2) ... 440s Setting up python3-tz (2024.1-2) ... 440s Setting up t-coffee (13.45.0.4846264+really13.41.0.28bdc39+dfsg-1) ... 440s Setting up poppler-data (0.4.12-1) ... 440s Setting up unicode-data (15.1.0-1) ... 440s Setting up python3-mysqldb (1.4.6-2build3) ... 440s Setting up python3-six (1.16.0-7) ... 441s Setting up tex-common (6.18) ... 441s update-language: texlive-base not installed and configured, doing nothing! 441s Setting up python3-isodate (0.6.1-3) ... 441s Setting up python3-decorator (5.1.1-5) ... 441s Setting up libfontenc1:arm64 (1:1.1.8-1build1) ... 441s Setting up autotools-dev (20220109.1) ... 441s Setting up libblas3:arm64 (3.12.0-3build2) ... 441s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode 441s Setting up python3-packaging (24.1-1) ... 441s Setting up libexpat1-dev:arm64 (2.6.2-2) ... 441s Setting up libzzip-0-13t64:arm64 (0.13.72+dfsg.1-1.2build1) ... 441s Setting up libjbig2dec0:arm64 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libharfbuzz0b:arm64 (9.0.0-1) ... 442s Setting up python3-dateutil (2.9.0-2) ... 442s Setting up fasttree (2.1.11-2) ... 442s Setting up sgml-base (1.31) ... 442s Setting up python3-msgpack (1.0.3-3build2) ... 443s Setting up libxss1:arm64 (1:1.2.3-1build3) ... 443s Setting up libtsan2:arm64 (14.2.0-7ubuntu1) ... 443s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 443s Setting up python3-mpmath (1.3.0-1) ... 443s Setting up libisl23:arm64 (0.27-1) ... 443s Setting up libde265-0:arm64 (1.0.15-1build4) ... 443s Setting up python-matplotlib-data (3.8.3-3) ... 443s Setting up libwebpmux3:arm64 (1.4.0-0.1) ... 443s Setting up python3-appdirs (1.4.4-4) ... 443s Setting up dialign (2.2.1-13) ... 443s Setting up xdg-utils (1.2.1-0ubuntu1) ... 443s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode 443s Setting up libcc1-0:arm64 (14.2.0-7ubuntu1) ... 443s Setting up liblsan0:arm64 (14.2.0-7ubuntu1) ... 443s Setting up libitm1:arm64 (14.2.0-7ubuntu1) ... 443s Setting up libsynctex2:arm64 (2024.20240313.70630+ds-4) ... 443s Setting up prank (0.0.170427+dfsg-3) ... 443s Setting up libargtable2-0 (13-2) ... 443s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 443s Setting up libpotrace0:arm64 (1.16-2build1) ... 443s Setting up libjpeg8:arm64 (8c-2ubuntu11) ... 443s Setting up automake (1:1.16.5-1.3ubuntu1) ... 443s update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode 443s Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... 443s Setting up python3-sympy (1.13.1-1) ... 451s Setting up libice6:arm64 (2:1.0.10-1build3) ... 451s Setting up flex (2.6.4-8.2build1) ... 451s Setting up liblapack3:arm64 (3.12.0-3build2) ... 451s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode 451s Setting up gettext (0.22.5-2) ... 451s Setting up libmbedx509-1t64:arm64 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Setting up libjs-sphinxdoc (7.4.7-3) ... 453s Setting up libraw23t64:arm64 (0.21.2-2.1build1) ... 453s Setting up dh-strip-nondeterminism (1.14.0-1) ... 453s Setting up cpp-14-aarch64-linux-gnu (14.2.0-7ubuntu1) ... 453s Setting up libmbedtls14t64:arm64 (2.28.8-1) ... 453s Setting up python3-lxml:arm64 (5.3.0-1) ... 453s Setting up libtiff6:arm64 (4.5.1+git230720-4ubuntu4) ... 453s Setting up xml-core (0.19) ... 454s Setting up python3-contourpy (1.2.1-1) ... 454s Setting up libfontconfig1:arm64 (2.15.0-1.1ubuntu2) ... 454s Setting up libgcc-14-dev:arm64 (14.2.0-7ubuntu1) ... 454s Setting up libstdc++-14-dev:arm64 (14.2.0-7ubuntu1) ... 454s Setting up libsm6:arm64 (2:1.2.3-1build3) ... 454s Setting up libavahi-client3:arm64 (0.8-13ubuntu6) ... 454s Setting up liblbfgsb0:arm64 (3.0+dfsg.4-1build1) ... 454s Setting up libxft2:arm64 (2.3.6-1build1) ... 454s Setting up python3-scipy (1.13.1-3) ... 458s Setting up libpython3-dev:arm64 (3.12.6-0ubuntu1) ... 458s Setting up po-debconf (1.0.21+nmu1) ... 458s Setting up libtk8.6:arm64 (8.6.14-1build1) ... 458s Setting up python3.12-tk (3.12.7-1) ... 458s Setting up python3-mmtf (1.1.3-1) ... 458s Setting up fonts-urw-base35 (20200910-8) ... 458s Setting up dssp (4.2.2-2) ... 458s Setting up libcairo2:arm64 (1.18.2-2) ... 458s Setting up ncbi-blast+ (2.16.0+ds-6) ... 458s Setting up python3-pil:arm64 (10.4.0-1ubuntu1) ... 458s Setting up cpp-aarch64-linux-gnu (4:14.1.0-2ubuntu1) ... 458s Setting up libpython3-all-dev:arm64 (3.12.6-0ubuntu1) ... 458s Setting up python3-dev (3.12.6-0ubuntu1) ... 459s Setting up libxt6t64:arm64 (1:1.2.1-1.2build1) ... 459s Setting up netpbm (2:11.07.00-2) ... 459s Setting up cpp-14 (14.2.0-7ubuntu1) ... 459s Setting up cpp (4:14.1.0-2ubuntu1) ... 459s Setting up gcc-14-aarch64-linux-gnu (14.2.0-7ubuntu1) ... 459s Setting up libcups2t64:arm64 (2.4.10-1ubuntu2) ... 459s Setting up python3-all-dev (3.12.6-0ubuntu1) ... 459s Setting up libgs10-common (10.03.1~dfsg1-0ubuntu2) ... 459s Setting up gcc-aarch64-linux-gnu (4:14.1.0-2ubuntu1) ... 459s Setting up tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 459s Setting up libxmu6:arm64 (2:1.1.3-3build2) ... 459s Setting up g++-14-aarch64-linux-gnu (14.2.0-7ubuntu1) ... 459s Setting up python3-cairo (1.26.1-2) ... 459s Setting up blt (2.5.3+dfsg-7build1) ... 459s Setting up python3-tk:arm64 (3.12.6-1ubuntu1) ... 459s Setting up libxaw7:arm64 (2:1.0.14-1build2) ... 459s Setting up gcc-14 (14.2.0-7ubuntu1) ... 459s Setting up python3-pil.imagetk:arm64 (10.4.0-1ubuntu1) ... 459s Setting up python3-rlpycairo (0.3.0-3) ... 459s Setting up python3-reportlab (4.2.2-1) ... 460s Setting up texlive-binaries (2024.20240313.70630+ds-4) ... 460s update-alternatives: using /usr/bin/xdvi-xaw to provide /usr/bin/xdvi.bin (xdvi.bin) in auto mode 460s update-alternatives: using /usr/bin/bibtex.original to provide /usr/bin/bibtex (bibtex) in auto mode 460s Setting up g++-aarch64-linux-gnu (4:14.1.0-2ubuntu1) ... 460s Setting up g++-14 (14.2.0-7ubuntu1) ... 460s Setting up texlive-base (2024.20240706-1) ... 460s tl-paper: setting paper size for dvips to a4: /var/lib/texmf/dvips/config/config-paper.ps 461s tl-paper: setting paper size for dvipdfmx to a4: /var/lib/texmf/dvipdfmx/dvipdfmx-paper.cfg 461s tl-paper: setting paper size for xdvi to a4: /var/lib/texmf/xdvi/XDvi-paper 461s tl-paper: setting paper size for pdftex to a4: /var/lib/texmf/tex/generic/tex-ini-files/pdftexconfig.tex 462s Setting up libgs10:arm64 (10.03.1~dfsg1-0ubuntu2) ... 462s Setting up libtool (2.4.7-7build1) ... 462s Setting up ghostscript (10.03.1~dfsg1-0ubuntu2) ... 462s Setting up gcc (4:14.1.0-2ubuntu1) ... 462s Setting up dh-autoreconf (20) ... 462s Setting up texlive-latex-base (2024.20240706-1) ... 462s Setting up texlive-latex-recommended (2024.20240706-1) ... 462s Setting up texlive-pictures (2024.20240706-1) ... 462s Setting up g++ (4:14.1.0-2ubuntu1) ... 462s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 462s Setting up texlive-fonts-recommended (2024.20240706-1) ... 462s Setting up build-essential (12.10ubuntu1) ... 462s Setting up debhelper (13.20ubuntu1) ... 462s Setting up texlive-latex-extra (2024.20240706-2) ... 462s Setting up python3-ufolib2 (0.16.0+dfsg1-1) ... 462s Setting up libheif-plugin-aomdec:arm64 (1.18.1-2) ... 462s Setting up libheif-plugin-libde265:arm64 (1.18.1-2) ... 462s Setting up libheif1:arm64 (1.18.1-2) ... 462s Setting up libmagickcore-6.q16-7t64:arm64 (8:6.9.13.12+dfsg1-1build1) ... 462s Setting up python3-fonttools (4.46.0-1build2) ... 463s Setting up libmagickwand-6.q16-7t64:arm64 (8:6.9.13.12+dfsg1-1build1) ... 463s Setting up libgd3:arm64 (2.3.3-12ubuntu3) ... 463s Setting up imagemagick-6.q16 (8:6.9.13.12+dfsg1-1build1) ... 463s update-alternatives: using /usr/bin/compare-im6.q16 to provide /usr/bin/compare (compare) in auto mode 463s update-alternatives: using /usr/bin/compare-im6.q16 to provide /usr/bin/compare-im6 (compare-im6) in auto mode 463s update-alternatives: using /usr/bin/animate-im6.q16 to provide /usr/bin/animate (animate) in auto mode 463s update-alternatives: using /usr/bin/animate-im6.q16 to provide /usr/bin/animate-im6 (animate-im6) in auto mode 463s update-alternatives: using /usr/bin/convert-im6.q16 to provide /usr/bin/convert (convert) in auto mode 463s update-alternatives: using /usr/bin/convert-im6.q16 to provide /usr/bin/convert-im6 (convert-im6) in auto mode 463s update-alternatives: using /usr/bin/composite-im6.q16 to provide /usr/bin/composite (composite) in auto mode 463s update-alternatives: using /usr/bin/composite-im6.q16 to provide /usr/bin/composite-im6 (composite-im6) in auto mode 463s update-alternatives: using /usr/bin/conjure-im6.q16 to provide /usr/bin/conjure (conjure) in auto mode 463s update-alternatives: using /usr/bin/conjure-im6.q16 to provide /usr/bin/conjure-im6 (conjure-im6) in auto mode 463s update-alternatives: using /usr/bin/import-im6.q16 to provide /usr/bin/import (import) in auto mode 463s update-alternatives: using /usr/bin/import-im6.q16 to provide /usr/bin/import-im6 (import-im6) in auto mode 463s update-alternatives: using /usr/bin/identify-im6.q16 to provide /usr/bin/identify (identify) in auto mode 463s update-alternatives: using /usr/bin/identify-im6.q16 to provide /usr/bin/identify-im6 (identify-im6) in auto mode 463s update-alternatives: using /usr/bin/stream-im6.q16 to provide /usr/bin/stream (stream) in auto mode 463s update-alternatives: using /usr/bin/stream-im6.q16 to provide /usr/bin/stream-im6 (stream-im6) in auto mode 463s update-alternatives: using /usr/bin/display-im6.q16 to provide /usr/bin/display (display) in auto mode 463s update-alternatives: using /usr/bin/display-im6.q16 to provide /usr/bin/display-im6 (display-im6) in auto mode 463s update-alternatives: using /usr/bin/montage-im6.q16 to provide /usr/bin/montage (montage) in auto mode 463s update-alternatives: using /usr/bin/montage-im6.q16 to provide /usr/bin/montage-im6 (montage-im6) in auto mode 463s update-alternatives: using /usr/bin/mogrify-im6.q16 to provide /usr/bin/mogrify (mogrify) in auto mode 463s update-alternatives: using /usr/bin/mogrify-im6.q16 to provide /usr/bin/mogrify-im6 (mogrify-im6) in auto mode 463s Setting up emboss-lib (6.6.0+dfsg-12ubuntu2) ... 463s Setting up python3-matplotlib (3.8.3-3) ... 465s Setting up emboss (6.6.0+dfsg-12ubuntu2) ... 465s Setting up hevea (2.36-2) ... 465s Setting up imagemagick (8:6.9.13.12+dfsg1-1build1) ... 465s Processing triggers for install-info (7.1.1-1) ... 465s Processing triggers for libc-bin (2.40-1ubuntu3) ... 465s Processing triggers for man-db (2.12.1-3) ... 467s Processing triggers for shared-mime-info (2.4-5) ... 468s Processing triggers for sgml-base (1.31) ... 468s Setting up w3c-sgml-lib (1.3-3) ... 495s Setting up python3-biopython (1.83+dfsg1-3) ... 497s Setting up python3-biopython-sql (1.83+dfsg1-3) ... 497s Setting up autopkgtest-satdep (0) ... 497s Processing triggers for tex-common (6.18) ... 497s Running updmap-sys. This may take some time... done. 497s Running mktexlsr /var/lib/texmf ... done. 498s Building format(s) --all. 569s This may take some time... done. 579s (Reading database ... 124328 files and directories currently installed.) 579s Removing autopkgtest-satdep (0) ... 596s autopkgtest [09:53:18]: test full_suite: sh debian/tests/run-unit-test 596s autopkgtest [09:53:18]: test full_suite: [----------------------- 598s mkdir: created directory 'Bio' 598s mkdir: created directory 'Bio/Align' 598s mkdir: created directory 'Bio/Align/substitution_matrices' 598s mkdir: created directory 'Bio/Align/substitution_matrices/data/' 598s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER22' -> 'Bio/Align/substitution_matrices/data/BENNER22' 598s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER6' -> 'Bio/Align/substitution_matrices/data/BENNER6' 598s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER74' -> 'Bio/Align/substitution_matrices/data/BENNER74' 598s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLASTN' -> 'Bio/Align/substitution_matrices/data/BLASTN' 598s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLASTP' -> 'Bio/Align/substitution_matrices/data/BLASTP' 598s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM45' -> 'Bio/Align/substitution_matrices/data/BLOSUM45' 598s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM50' -> 'Bio/Align/substitution_matrices/data/BLOSUM50' 598s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM62' -> 'Bio/Align/substitution_matrices/data/BLOSUM62' 598s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM80' -> 'Bio/Align/substitution_matrices/data/BLOSUM80' 598s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM90' -> 'Bio/Align/substitution_matrices/data/BLOSUM90' 598s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/DAYHOFF' -> 'Bio/Align/substitution_matrices/data/DAYHOFF' 598s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/FENG' -> 'Bio/Align/substitution_matrices/data/FENG' 598s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/GENETIC' -> 'Bio/Align/substitution_matrices/data/GENETIC' 598s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/GONNET1992' -> 'Bio/Align/substitution_matrices/data/GONNET1992' 598s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/HOXD70' -> 'Bio/Align/substitution_matrices/data/HOXD70' 598s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/JOHNSON' -> 'Bio/Align/substitution_matrices/data/JOHNSON' 598s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/JONES' -> 'Bio/Align/substitution_matrices/data/JONES' 598s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/LEVIN' -> 'Bio/Align/substitution_matrices/data/LEVIN' 598s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MCLACHLAN' -> 'Bio/Align/substitution_matrices/data/MCLACHLAN' 598s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MDM78' -> 'Bio/Align/substitution_matrices/data/MDM78' 598s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MEGABLAST' -> 'Bio/Align/substitution_matrices/data/MEGABLAST' 598s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/NUC.4.4' -> 'Bio/Align/substitution_matrices/data/NUC.4.4' 598s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM250' -> 'Bio/Align/substitution_matrices/data/PAM250' 598s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM30' -> 'Bio/Align/substitution_matrices/data/PAM30' 598s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM70' -> 'Bio/Align/substitution_matrices/data/PAM70' 598s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/RAO' -> 'Bio/Align/substitution_matrices/data/RAO' 598s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/RISLER' -> 'Bio/Align/substitution_matrices/data/RISLER' 598s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/SCHNEIDER' -> 'Bio/Align/substitution_matrices/data/SCHNEIDER' 598s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/STR' -> 'Bio/Align/substitution_matrices/data/STR' 598s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/TRANS' -> 'Bio/Align/substitution_matrices/data/TRANS' 598s Remove test test_Tutorial.py which is bound to fail 599s test_Ace ... ok 599s test_Affy ... ok 602s test_AlignIO ... ok 602s test_AlignIO_ClustalIO ... ok 602s test_AlignIO_EmbossIO ... ok 602s test_AlignIO_FastaIO ... ok 602s test_AlignIO_MauveIO ... ok 602s test_AlignIO_PhylipIO ... ok 602s test_AlignIO_convert ... ok 602s test_AlignInfo ... ok 602s test_Align_Alignment ... ok 602s test_Align_a2m ... ok 602s test_Align_bed ... ok 603s test_Align_bigbed ... ok 603s test_Align_bigmaf ... ok 603s test_Align_bigpsl ... ok 604s test_Align_chain ... ok 604s test_Align_clustal ... ok 609s test_Align_codonalign ... ok 609s test_Align_emboss ... ok 609s test_Align_exonerate ... ok 609s test_Align_fasta ... ok 609s test_Align_hhr ... ok 610s test_Align_maf ... ok 610s test_Align_mauve ... ok 610s test_Align_msf ... ok 610s test_Align_nexus ... ok 610s test_Align_phylip ... ok 610s test_Align_psl ... ok 611s test_Align_sam ... ok 612s test_Align_stockholm ... ok 613s test_Align_tabular ... ok 613s test_Application ... ok 613s test_BioSQL_MySQLdb_online ... skipping. internet not available 613s test_BioSQL_mysql_connector ... skipping. BioSQL test configuration file biosql.ini missing (see biosql.ini.sample) 613s test_BioSQL_mysql_connector_online ... skipping. internet not available 613s test_BioSQL_psycopg2_online ... skipping. internet not available 617s test_BioSQL_sqlite3 ... ok 617s test_BioSQL_sqlite3_online ... skipping. internet not available 617s test_Blast_Record ... ok 618s test_CAPS ... ok 618s test_Chi2 ... ok 618s test_ClustalOmega_tool ... ok 618s test_Clustalw_tool ... skipping. Install clustalw or clustalw2 if you want to use it from Biopython. 618s test_Cluster ... ok 618s test_CodonTable ... ok 619s test_ColorSpiral ... ok 619s test_Compass ... ok 620s test_Consensus ... ok 622s test_Dialign_tool ... ok 622s test_EMBL_unittest ... ok 629s test_Emboss ... ok 629s test_EmbossPrimer ... ok 633s test_Entrez ... ok 633s test_Entrez_online ... skipping. internet not available 634s test_Entrez_parser ... ok 634s test_Enzyme ... ok 634s test_ExPASy ... skipping. internet not available 634s test_Fasttree_tool ... ok 634s test_File ... ok 634s test_GenBank ... ok 636s test_GenomeDiagram ... Warn: Can't find .pfb for face 'Helvetica' 638s ok 639s test_GraphicsChromosome ... ok 639s test_GraphicsDistribution ... ok 640s test_GraphicsGeneral ... ok 640s test_HMMCasino ... ok 640s test_HMMGeneral ... ok 640s test_KEGG ... ok 640s test_KEGG_online ... skipping. internet not available 645s test_KGML_graphics ... ok 645s test_KGML_graphics_online ... skipping. internet not available 647s test_KGML_nographics ... ok 647s test_KeyWList ... ok 647s test_LogisticRegression ... ok 648s test_MafIO_index ... ok 649s test_Mafft_tool ... ok 649s test_MarkovModel ... ok 649s test_Medline ... ok 649s test_Muscle_tool ... skipping. Install MUSCLE if you want to use the Bio.Align.Applications wrapper. 650s test_NCBIXML ... ok 653s test_NCBI_BLAST_tools ... ok 653s test_NCBI_qblast ... ok 653s test_NMR ... ok 653s test_NaiveBayes ... ok 653s test_Nexus ... ok 654s test_PAML_baseml ... ok 654s test_PAML_codeml ... ok 654s test_PAML_yn00 ... ok 655s test_PDBList ... skipping. internet not available 657s test_PDB_CEAligner ... ok 659s test_PDB_DSSP ... ok 659s test_PDB_Dice ... ok 659s test_PDB_Disordered ... ok 660s test_PDB_Exposure ... ok 660s test_PDB_FragmentMapper ... ok 661s test_PDB_KDTree ... ok 661s test_PDB_MMCIF2Dict ... ok 662s test_PDB_MMCIFIO ... ok 663s test_PDB_MMCIFParser ... ok 663s test_PDB_NACCESS ... ok 663s test_PDB_PDBIO ... ok 663s test_PDB_PDBParser ... ok 664s 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 664s test_PDB_Polypeptide ... ok 664s test_PDB_QCPSuperimposer ... ok 667s test_PDB_SASA ... ok 667s test_PDB_SMCRA ... ok 667s test_PDB_Selection ... ok 668s test_PDB_StructureAlignment ... ok 668s test_PDB_Superimposer ... ok 677s test_PDB_internal_coords ... ok 677s test_PDB_parse_pdb_header ... ok 677s test_PDB_vectors ... ok 678s test_PQR ... ok 678s test_Pathway ... ok 678s test_Phd ... ok 679s test_Phylo ... ok 680s test_PhyloXML ... ok 680s test_Phylo_CDAO ... ok 681s test_Phylo_NeXML ... ok 684s test_Phylo_matplotlib ... ok 685s test_Phylo_networkx ... ok 686s test_PopGen_GenePop_nodepend ... ok 687s test_Prank_tool ... ok 688s test_Probcons_tool ... ok 689s test_ProtParam ... ok 690s test_RCSBFormats ... ok 691s test_Restriction ... ok 691s test_SCOP_Astral ... ok 692s test_SCOP_Cla ... ok 693s test_SCOP_Des ... ok 693s test_SCOP_Dom ... ok 694s test_SCOP_Hie ... ok 695s test_SCOP_Raf ... ok 695s test_SCOP_Residues ... ok 696s test_SCOP_Scop ... ok 696s test_SCOP_online ... skipping. internet not available 697s test_SVDSuperimposer ... ok 698s test_SearchIO_blast_tab ... ok 699s test_SearchIO_blast_tab_index ... ok 699s test_SearchIO_blast_xml ... ok 701s test_SearchIO_blast_xml_index ... ok 702s test_SearchIO_blat_psl ... ok 702s test_SearchIO_blat_psl_index ... ok 703s test_SearchIO_exonerate ... ok 704s test_SearchIO_exonerate_text_index ... ok 705s test_SearchIO_exonerate_vulgar_index ... ok 705s test_SearchIO_fasta_m10 ... ok 706s test_SearchIO_fasta_m10_index ... ok 707s test_SearchIO_hhsuite2_text ... ok 708s test_SearchIO_hmmer2_text ... ok 708s test_SearchIO_hmmer2_text_index ... ok 709s test_SearchIO_hmmer3_domtab ... ok 710s test_SearchIO_hmmer3_domtab_index ... ok 710s test_SearchIO_hmmer3_tab ... ok 711s test_SearchIO_hmmer3_tab_index ... ok 712s test_SearchIO_hmmer3_text ... ok 713s test_SearchIO_hmmer3_text_index ... ok 714s test_SearchIO_interproscan_xml ... ok 714s test_SearchIO_model ... ok 715s test_SearchIO_write ... ok 716s test_SeqFeature ... /usr/lib/python3/dist-packages/Bio/SeqFeature.py:1040: BiopythonParserWarning: Attempting to fix invalid location '3..2' as it looks like incorrect origin wrapping. Please fix input file, this could have unintended behavior. 716s warnings.warn( 716s ok 733s test_SeqIO ... ok 734s test_SeqIO_AbiIO ... ok 735s test_SeqIO_FastaIO ... ok 735s test_SeqIO_Gck ... ok 736s test_SeqIO_Insdc ... ok 737s test_SeqIO_NibIO ... ok 739s test_SeqIO_PdbIO ... ok 740s test_SeqIO_QualityIO ... ok 741s test_SeqIO_SeqXML ... ok 742s test_SeqIO_SnapGene ... ok 743s test_SeqIO_TwoBitIO ... ok 744s test_SeqIO_Xdna ... ok 745s test_SeqIO_features ... /usr/lib/python3/dist-packages/Bio/SeqIO/InsdcIO.py:549: BiopythonWarning: Annotation 'swissprot: locus SCX3_BUTOC, accession P01485; class: standard. created: Jul 21, 1986. sequence updated: Jul 21, 1986. annotation updated: Oct 16, 2001. xrefs: gi: gi: 69530 xrefs (non-sequence databases): HSSP P01484, InterPro IPR003614, InterPro IPR002061, InterPro IPR001219, Pfam PF00537, PRINTS PR00284, ProDom PD000908, SMART SM00505' too long for 'DBSOURCE' line 745s warnings.warn( 745s ok 761s test_SeqIO_index ... ok 762s test_SeqIO_online ... skipping. internet not available 763s test_SeqIO_write ... ok 763s test_SeqRecord ... ok 764s test_SeqUtils ... ok 766s test_Seq_objs ... ok 767s test_SffIO ... ok 767s test_SwissProt ... ok 770s test_TCoffee_tool ... ok 771s test_TogoWS ... skipping. internet not available 772s test_TreeConstruction ... ok 772s test_UniGene ... ok 773s test_UniProt_GOA ... ok 774s test_Uniprot ... ok 774s test_align ... ok 775s test_align_substitution_matrices ... ok 778s test_bgzf ... ok 779s test_cellosaurus ... ok 785s test_codonalign ... ok 786s test_geo ... ok 786s test_kNN ... ok 787s test_motifs ... ok 788s test_motifs_online ... skipping. internet not available 789s 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. 789s warnings.warn( 789s ok 789s test_pairwise2_no_C ... ok 790s test_pairwise_aligner ... ok 791s test_pairwise_alignment_map ... ok 798s test_phenotype ... ok 799s test_phenotype_fit ... ok 800s 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. 800s test_prodoc ... ok 801s test_prosite ... ok 802s test_raxml_tool ... skipping. Install RAxML (binary raxmlHPC) if you want to test the Bio.Phylo.Applications wrapper. 802s test_samtools_tool ... skipping. Install samtools and correctly set the file path to the program if you want to use it from Biopython 803s test_seq ... ok 804s test_translate ... ok 804s Skipping any tests requiring internet access 804s Python version: 3.12.7 (main, Oct 3 2024, 15:15:22) [GCC 14.2.0] 804s Operating system: posix linux 804s ---------------------------------------------------------------------- 804s Ran 211 tests in 205.567 seconds 804s 806s autopkgtest [09:56:48]: test full_suite: -----------------------] 807s autopkgtest [09:56:49]: test full_suite: - - - - - - - - - - results - - - - - - - - - - 807s full_suite PASS 807s autopkgtest [09:56:49]: @@@@@@@@@@@@@@@@@@@@ summary 807s dependencies PASS 807s full_suite PASS 820s nova [W] Skipping flock in bos03-arm64 820s Creating nova instance adt-plucky-arm64-python-biopython-20241030-094321-juju-7f2275-prod-proposed-migration-environment-2-6a0cdafa-ee97-43f4-819f-e38913519adb from image adt/ubuntu-plucky-arm64-server-20241029.img (UUID b10dda10-7c97-4e89-a4a8-9b73e189f96e)... 820s nova [W] Skipping flock in bos03-arm64 820s Creating nova instance adt-plucky-arm64-python-biopython-20241030-094321-juju-7f2275-prod-proposed-migration-environment-2-6a0cdafa-ee97-43f4-819f-e38913519adb from image adt/ubuntu-plucky-arm64-server-20241029.img (UUID b10dda10-7c97-4e89-a4a8-9b73e189f96e)...