0s autopkgtest [13:34:54]: starting date and time: 2025-02-19 13:34:54+0000 0s autopkgtest [13:34:54]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [13:34:54]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.wn5scp96/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:sphinx --apt-upgrade python-biopython --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=sphinx/8.1.3-5 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@bos03-arm64-17.secgroup --name adt-plucky-arm64-python-biopython-20250219-122232-juju-7f2275-prod-proposed-migration-environment-20-b645ef9c-37de-4709-b4ee-d363f84c1666 --image adt/ubuntu-plucky-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --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,radosgw.ps5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 100s autopkgtest [13:36:34]: testbed dpkg architecture: arm64 101s autopkgtest [13:36:35]: testbed apt version: 2.9.29 101s autopkgtest [13:36:35]: @@@@@@@@@@@@@@@@@@@@ test bed setup 101s autopkgtest [13:36:35]: testbed release detected to be: None 102s autopkgtest [13:36:36]: updating testbed package index (apt update) 103s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [110 kB] 103s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 103s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 103s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 103s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [13.9 kB] 103s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [76.1 kB] 103s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [3120 B] 103s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [744 kB] 103s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [103 kB] 103s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 Packages [7960 B] 103s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [692 kB] 103s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [11.2 kB] 104s Fetched 1762 kB in 1s (1616 kB/s) 105s Reading package lists... 105s Reading package lists... 106s Building dependency tree... 106s Reading state information... 106s Calculating upgrade... 107s The following NEW packages will be installed: 107s libapt-pkg7.0 107s The following packages will be upgraded: 107s apt apt-utils iproute2 libgpgme11t64 liblsof0 libp11-kit0 lsof rsyslog 107s sysvinit-utils 107s 9 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 107s Need to get 5019 kB of archives. 107s After this operation, 3410 kB of additional disk space will be used. 107s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 sysvinit-utils arm64 3.14-1ubuntu1 [35.2 kB] 107s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 libapt-pkg7.0 arm64 2.9.30 [1023 kB] 107s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 apt arm64 2.9.30 [1364 kB] 108s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 apt-utils arm64 2.9.30 [207 kB] 108s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 iproute2 arm64 6.13.0-1ubuntu1 [1158 kB] 108s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 libp11-kit0 arm64 0.25.5-2ubuntu3 [280 kB] 108s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 rsyslog arm64 8.2412.0-2ubuntu1 [521 kB] 108s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 lsof arm64 4.99.4+dfsg-1 [236 kB] 108s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 liblsof0 arm64 4.99.4+dfsg-1 [53.9 kB] 108s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 libgpgme11t64 arm64 1.24.2-1ubuntu1 [142 kB] 109s Preconfiguring packages ... 109s Fetched 5019 kB in 1s (4592 kB/s) 109s (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 ... 116620 files and directories currently installed.) 109s Preparing to unpack .../sysvinit-utils_3.14-1ubuntu1_arm64.deb ... 109s Unpacking sysvinit-utils (3.14-1ubuntu1) over (3.08-6ubuntu3) ... 109s Setting up sysvinit-utils (3.14-1ubuntu1) ... 109s Selecting previously unselected package libapt-pkg7.0:arm64. 109s (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 ... 116620 files and directories currently installed.) 109s Preparing to unpack .../libapt-pkg7.0_2.9.30_arm64.deb ... 109s Unpacking libapt-pkg7.0:arm64 (2.9.30) ... 110s Setting up libapt-pkg7.0:arm64 (2.9.30) ... 110s (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 ... 116669 files and directories currently installed.) 110s Preparing to unpack .../archives/apt_2.9.30_arm64.deb ... 110s Unpacking apt (2.9.30) over (2.9.29) ... 110s Setting up apt (2.9.30) ... 111s (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 ... 116669 files and directories currently installed.) 111s Preparing to unpack .../0-apt-utils_2.9.30_arm64.deb ... 111s Unpacking apt-utils (2.9.30) over (2.9.29) ... 111s Preparing to unpack .../1-iproute2_6.13.0-1ubuntu1_arm64.deb ... 111s Unpacking iproute2 (6.13.0-1ubuntu1) over (6.10.0-2ubuntu1) ... 111s Preparing to unpack .../2-libp11-kit0_0.25.5-2ubuntu3_arm64.deb ... 111s Unpacking libp11-kit0:arm64 (0.25.5-2ubuntu3) over (0.25.5-2ubuntu2) ... 111s Preparing to unpack .../3-rsyslog_8.2412.0-2ubuntu1_arm64.deb ... 111s Unpacking rsyslog (8.2412.0-2ubuntu1) over (8.2412.0-1ubuntu1) ... 112s Preparing to unpack .../4-lsof_4.99.4+dfsg-1_arm64.deb ... 112s Unpacking lsof (4.99.4+dfsg-1) over (4.99.3+dfsg-2) ... 112s Preparing to unpack .../5-liblsof0_4.99.4+dfsg-1_arm64.deb ... 112s Unpacking liblsof0 (4.99.4+dfsg-1) over (4.99.3+dfsg-2) ... 112s Preparing to unpack .../6-libgpgme11t64_1.24.2-1ubuntu1_arm64.deb ... 112s Unpacking libgpgme11t64:arm64 (1.24.2-1ubuntu1) over (1.24.1-4ubuntu1) ... 112s Setting up apt-utils (2.9.30) ... 112s Setting up liblsof0 (4.99.4+dfsg-1) ... 112s Setting up iproute2 (6.13.0-1ubuntu1) ... 112s Setting up rsyslog (8.2412.0-2ubuntu1) ... 112s info: The user `syslog' is already a member of `adm'. 113s Setting up libp11-kit0:arm64 (0.25.5-2ubuntu3) ... 113s Setting up lsof (4.99.4+dfsg-1) ... 113s Setting up libgpgme11t64:arm64 (1.24.2-1ubuntu1) ... 113s Processing triggers for man-db (2.13.0-1) ... 116s Processing triggers for libc-bin (2.40-4ubuntu1) ... 117s Reading package lists... 118s Building dependency tree... 118s Reading state information... 119s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 119s autopkgtest [13:36:53]: upgrading testbed (apt dist-upgrade and autopurge) 119s Reading package lists... 119s Building dependency tree... 119s Reading state information... 120s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 120s Starting 2 pkgProblemResolver with broken count: 0 120s Done 121s Entering ResolveByKeep 121s 122s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 122s Reading package lists... 122s Building dependency tree... 122s Reading state information... 123s Starting pkgProblemResolver with broken count: 0 123s Starting 2 pkgProblemResolver with broken count: 0 123s Done 124s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 124s autopkgtest [13:36:58]: rebooting testbed after setup commands that affected boot 158s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 165s autopkgtest [13:37:39]: testbed running kernel: Linux 6.12.0-15-generic #15-Ubuntu SMP PREEMPT_DYNAMIC Tue Feb 4 15:49:33 UTC 2025 168s autopkgtest [13:37:42]: @@@@@@@@@@@@@@@@@@@@ apt-source python-biopython 173s Get:1 http://ftpmaster.internal/ubuntu plucky/universe python-biopython 1.85+dfsg-2 (dsc) [3439 B] 173s Get:2 http://ftpmaster.internal/ubuntu plucky/universe python-biopython 1.85+dfsg-2 (tar) [14.6 MB] 173s Get:3 http://ftpmaster.internal/ubuntu plucky/universe python-biopython 1.85+dfsg-2 (diff) [42.9 kB] 173s gpgv: Signature made Thu Feb 6 14:44:48 2025 UTC 173s gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 173s gpgv: issuer "crusoe@debian.org" 173s gpgv: Can't check signature: No public key 173s dpkg-source: warning: cannot verify inline signature for ./python-biopython_1.85+dfsg-2.dsc: no acceptable signature found 174s autopkgtest [13:37:48]: testing package python-biopython version 1.85+dfsg-2 174s autopkgtest [13:37:48]: build not needed 179s autopkgtest [13:37:53]: test dependencies: preparing testbed 179s Reading package lists... 180s Building dependency tree... 180s Reading state information... 180s Starting pkgProblemResolver with broken count: 0 180s Starting 2 pkgProblemResolver with broken count: 0 180s Done 181s The following NEW packages will be installed: 181s fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-urw-base35 181s libblas3 libcairo2 libdeflate0 libfontconfig1 libfontenc1 libgfortran5 181s libgomp1 libgraphite2-3 libharfbuzz0b libimagequant0 libjbig0 libjpeg-turbo8 181s libjpeg8 libjs-jquery libjs-sphinxdoc libjs-underscore liblapack3 liblcms2-2 181s liblerc4 libopenjp2-7 libpixman-1-0 libraqm0 libsharpyuv0 libtiff6 libwebp7 181s libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 libxrender1 181s python-biopython-doc python3-all python3-biopython python3-biopython-sql 181s python3-cairo python3-freetype python3-numpy python3-pil python3-reportlab 181s python3-rlpycairo python3.12 python3.12-minimal sgml-base w3c-sgml-lib 181s x11-common xfonts-encodings xfonts-utils xml-core 181s 0 upgraded, 52 newly installed, 0 to remove and 0 not upgraded. 181s Need to get 48.5 MB of archives. 181s After this operation, 141 MB of additional disk space will be used. 181s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.12-minimal arm64 3.12.9-1 [2236 kB] 182s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 sgml-base all 1.31 [11.4 kB] 182s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.12 arm64 3.12.9-1 [671 kB] 182s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 182s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 182s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 libfontenc1 arm64 1:1.1.8-1build1 [13.9 kB] 182s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 182s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 182s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 xfonts-utils arm64 1:7.7+7 [95.6 kB] 182s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-urw-base35 all 20200910-8 [11.0 MB] 183s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig-config arm64 2.15.0-2ubuntu1 [37.5 kB] 183s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.1-2 [161 kB] 183s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 libfontconfig1 arm64 2.15.0-2ubuntu1 [144 kB] 183s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 libpixman-1-0 arm64 0.44.0-3 [197 kB] 183s Get:15 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-render0 arm64 1.17.0-2 [16.6 kB] 183s Get:16 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-shm0 arm64 1.17.0-2 [5884 B] 183s Get:17 http://ftpmaster.internal/ubuntu plucky/main arm64 libxrender1 arm64 1:0.9.10-1.1build1 [18.8 kB] 183s Get:18 http://ftpmaster.internal/ubuntu plucky/main arm64 libcairo2 arm64 1.18.2-2 [560 kB] 183s Get:19 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate0 arm64 1.23-1 [46.2 kB] 183s Get:20 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 15-20250213-1ubuntu1 [443 kB] 183s Get:21 http://ftpmaster.internal/ubuntu plucky/main arm64 libgomp1 arm64 15-20250213-1ubuntu1 [146 kB] 183s Get:22 http://ftpmaster.internal/ubuntu plucky/main arm64 libgraphite2-3 arm64 1.3.14-2ubuntu1 [70.6 kB] 183s Get:23 http://ftpmaster.internal/ubuntu plucky/main arm64 libharfbuzz0b arm64 10.2.0-1 [490 kB] 183s Get:24 http://ftpmaster.internal/ubuntu plucky/main arm64 libimagequant0 arm64 2.18.0-1build1 [37.1 kB] 183s Get:25 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg-turbo8 arm64 2.1.5-3ubuntu2 [165 kB] 183s Get:26 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 183s Get:27 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 183s Get:28 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 183s Get:29 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libjs-sphinxdoc all 8.1.3-5 [31.0 kB] 183s Get:30 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.1-2 [2307 kB] 183s Get:31 http://ftpmaster.internal/ubuntu plucky/main arm64 liblcms2-2 arm64 2.16-2 [170 kB] 183s Get:32 http://ftpmaster.internal/ubuntu plucky/main arm64 liblerc4 arm64 4.0.0+ds-5ubuntu1 [167 kB] 183s Get:33 http://ftpmaster.internal/ubuntu plucky/main arm64 libraqm0 arm64 0.10.2-1 [14.9 kB] 183s Get:34 http://ftpmaster.internal/ubuntu plucky/main arm64 libsharpyuv0 arm64 1.5.0-0.1 [16.9 kB] 183s Get:35 http://ftpmaster.internal/ubuntu plucky/main arm64 libjbig0 arm64 2.1-6.1ubuntu2 [29.3 kB] 183s Get:36 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebp7 arm64 1.5.0-0.1 [194 kB] 183s Get:37 http://ftpmaster.internal/ubuntu plucky/main arm64 libtiff6 arm64 4.5.1+git230720-4ubuntu4 [193 kB] 183s Get:38 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebpdemux2 arm64 1.5.0-0.1 [12.5 kB] 183s Get:39 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebpmux3 arm64 1.5.0-0.1 [25.4 kB] 183s Get:40 http://ftpmaster.internal/ubuntu plucky/universe arm64 python-biopython-doc all 1.85+dfsg-2 [18.2 MB] 184s Get:41 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-all arm64 3.13.1-1~exp2 [894 B] 184s Get:42 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy arm64 1:1.26.4+ds-13 [4148 kB] 184s Get:43 http://ftpmaster.internal/ubuntu plucky/main arm64 libopenjp2-7 arm64 2.5.0-2ubuntu3 [182 kB] 184s Get:44 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-pil arm64 11.1.0-5 [491 kB] 184s Get:45 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-cairo arm64 1.26.1-2build1 [139 kB] 184s Get:46 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-freetype all 2.5.1-1 [92.3 kB] 184s Get:47 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-rlpycairo all 0.3.0-3 [9130 B] 184s Get:48 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-reportlab all 4.3.0-1 [1137 kB] 184s Get:49 http://ftpmaster.internal/ubuntu plucky/main arm64 xml-core all 0.19 [20.3 kB] 184s Get:50 http://ftpmaster.internal/ubuntu plucky/universe arm64 w3c-sgml-lib all 1.3-3 [280 kB] 184s Get:51 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-biopython arm64 1.85+dfsg-2 [1718 kB] 184s Get:52 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-biopython-sql all 1.85+dfsg-2 [26.4 kB] 185s Fetched 48.5 MB in 3s (16.6 MB/s) 185s Selecting previously unselected package python3.12-minimal. 185s (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 ... 116670 files and directories currently installed.) 185s Preparing to unpack .../00-python3.12-minimal_3.12.9-1_arm64.deb ... 185s Unpacking python3.12-minimal (3.12.9-1) ... 185s Selecting previously unselected package sgml-base. 185s Preparing to unpack .../01-sgml-base_1.31_all.deb ... 185s Unpacking sgml-base (1.31) ... 185s Selecting previously unselected package python3.12. 185s Preparing to unpack .../02-python3.12_3.12.9-1_arm64.deb ... 185s Unpacking python3.12 (3.12.9-1) ... 186s Selecting previously unselected package fonts-dejavu-mono. 186s Preparing to unpack .../03-fonts-dejavu-mono_2.37-8_all.deb ... 186s Unpacking fonts-dejavu-mono (2.37-8) ... 186s Selecting previously unselected package fonts-dejavu-core. 186s Preparing to unpack .../04-fonts-dejavu-core_2.37-8_all.deb ... 186s Unpacking fonts-dejavu-core (2.37-8) ... 186s Selecting previously unselected package libfontenc1:arm64. 186s Preparing to unpack .../05-libfontenc1_1%3a1.1.8-1build1_arm64.deb ... 186s Unpacking libfontenc1:arm64 (1:1.1.8-1build1) ... 186s Selecting previously unselected package x11-common. 186s Preparing to unpack .../06-x11-common_1%3a7.7+23ubuntu3_all.deb ... 186s Unpacking x11-common (1:7.7+23ubuntu3) ... 186s Selecting previously unselected package xfonts-encodings. 186s Preparing to unpack .../07-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 186s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 186s Selecting previously unselected package xfonts-utils. 186s Preparing to unpack .../08-xfonts-utils_1%3a7.7+7_arm64.deb ... 186s Unpacking xfonts-utils (1:7.7+7) ... 186s Selecting previously unselected package fonts-urw-base35. 186s Preparing to unpack .../09-fonts-urw-base35_20200910-8_all.deb ... 186s Unpacking fonts-urw-base35 (20200910-8) ... 186s Selecting previously unselected package fontconfig-config. 186s Preparing to unpack .../10-fontconfig-config_2.15.0-2ubuntu1_arm64.deb ... 186s Unpacking fontconfig-config (2.15.0-2ubuntu1) ... 186s Selecting previously unselected package libblas3:arm64. 187s Preparing to unpack .../11-libblas3_3.12.1-2_arm64.deb ... 187s Unpacking libblas3:arm64 (3.12.1-2) ... 187s Selecting previously unselected package libfontconfig1:arm64. 187s Preparing to unpack .../12-libfontconfig1_2.15.0-2ubuntu1_arm64.deb ... 187s Unpacking libfontconfig1:arm64 (2.15.0-2ubuntu1) ... 187s Selecting previously unselected package libpixman-1-0:arm64. 187s Preparing to unpack .../13-libpixman-1-0_0.44.0-3_arm64.deb ... 187s Unpacking libpixman-1-0:arm64 (0.44.0-3) ... 187s Selecting previously unselected package libxcb-render0:arm64. 187s Preparing to unpack .../14-libxcb-render0_1.17.0-2_arm64.deb ... 187s Unpacking libxcb-render0:arm64 (1.17.0-2) ... 187s Selecting previously unselected package libxcb-shm0:arm64. 187s Preparing to unpack .../15-libxcb-shm0_1.17.0-2_arm64.deb ... 187s Unpacking libxcb-shm0:arm64 (1.17.0-2) ... 187s Selecting previously unselected package libxrender1:arm64. 187s Preparing to unpack .../16-libxrender1_1%3a0.9.10-1.1build1_arm64.deb ... 187s Unpacking libxrender1:arm64 (1:0.9.10-1.1build1) ... 187s Selecting previously unselected package libcairo2:arm64. 187s Preparing to unpack .../17-libcairo2_1.18.2-2_arm64.deb ... 187s Unpacking libcairo2:arm64 (1.18.2-2) ... 187s Selecting previously unselected package libdeflate0:arm64. 187s Preparing to unpack .../18-libdeflate0_1.23-1_arm64.deb ... 187s Unpacking libdeflate0:arm64 (1.23-1) ... 187s Selecting previously unselected package libgfortran5:arm64. 187s Preparing to unpack .../19-libgfortran5_15-20250213-1ubuntu1_arm64.deb ... 187s Unpacking libgfortran5:arm64 (15-20250213-1ubuntu1) ... 187s Selecting previously unselected package libgomp1:arm64. 187s Preparing to unpack .../20-libgomp1_15-20250213-1ubuntu1_arm64.deb ... 187s Unpacking libgomp1:arm64 (15-20250213-1ubuntu1) ... 187s Selecting previously unselected package libgraphite2-3:arm64. 187s Preparing to unpack .../21-libgraphite2-3_1.3.14-2ubuntu1_arm64.deb ... 187s Unpacking libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 187s Selecting previously unselected package libharfbuzz0b:arm64. 187s Preparing to unpack .../22-libharfbuzz0b_10.2.0-1_arm64.deb ... 187s Unpacking libharfbuzz0b:arm64 (10.2.0-1) ... 187s Selecting previously unselected package libimagequant0:arm64. 187s Preparing to unpack .../23-libimagequant0_2.18.0-1build1_arm64.deb ... 187s Unpacking libimagequant0:arm64 (2.18.0-1build1) ... 187s Selecting previously unselected package libjpeg-turbo8:arm64. 187s Preparing to unpack .../24-libjpeg-turbo8_2.1.5-3ubuntu2_arm64.deb ... 187s Unpacking libjpeg-turbo8:arm64 (2.1.5-3ubuntu2) ... 187s Selecting previously unselected package libjpeg8:arm64. 187s Preparing to unpack .../25-libjpeg8_8c-2ubuntu11_arm64.deb ... 187s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 187s Selecting previously unselected package libjs-jquery. 187s Preparing to unpack .../26-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 187s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 187s Selecting previously unselected package libjs-underscore. 187s Preparing to unpack .../27-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 187s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 188s Selecting previously unselected package libjs-sphinxdoc. 188s Preparing to unpack .../28-libjs-sphinxdoc_8.1.3-5_all.deb ... 188s Unpacking libjs-sphinxdoc (8.1.3-5) ... 188s Selecting previously unselected package liblapack3:arm64. 188s Preparing to unpack .../29-liblapack3_3.12.1-2_arm64.deb ... 188s Unpacking liblapack3:arm64 (3.12.1-2) ... 188s Selecting previously unselected package liblcms2-2:arm64. 188s Preparing to unpack .../30-liblcms2-2_2.16-2_arm64.deb ... 188s Unpacking liblcms2-2:arm64 (2.16-2) ... 188s Selecting previously unselected package liblerc4:arm64. 188s Preparing to unpack .../31-liblerc4_4.0.0+ds-5ubuntu1_arm64.deb ... 188s Unpacking liblerc4:arm64 (4.0.0+ds-5ubuntu1) ... 188s Selecting previously unselected package libraqm0:arm64. 188s Preparing to unpack .../32-libraqm0_0.10.2-1_arm64.deb ... 188s Unpacking libraqm0:arm64 (0.10.2-1) ... 188s Selecting previously unselected package libsharpyuv0:arm64. 188s Preparing to unpack .../33-libsharpyuv0_1.5.0-0.1_arm64.deb ... 188s Unpacking libsharpyuv0:arm64 (1.5.0-0.1) ... 188s Selecting previously unselected package libjbig0:arm64. 188s Preparing to unpack .../34-libjbig0_2.1-6.1ubuntu2_arm64.deb ... 188s Unpacking libjbig0:arm64 (2.1-6.1ubuntu2) ... 188s Selecting previously unselected package libwebp7:arm64. 188s Preparing to unpack .../35-libwebp7_1.5.0-0.1_arm64.deb ... 188s Unpacking libwebp7:arm64 (1.5.0-0.1) ... 188s Selecting previously unselected package libtiff6:arm64. 188s Preparing to unpack .../36-libtiff6_4.5.1+git230720-4ubuntu4_arm64.deb ... 188s Unpacking libtiff6:arm64 (4.5.1+git230720-4ubuntu4) ... 188s Selecting previously unselected package libwebpdemux2:arm64. 188s Preparing to unpack .../37-libwebpdemux2_1.5.0-0.1_arm64.deb ... 188s Unpacking libwebpdemux2:arm64 (1.5.0-0.1) ... 188s Selecting previously unselected package libwebpmux3:arm64. 188s Preparing to unpack .../38-libwebpmux3_1.5.0-0.1_arm64.deb ... 188s Unpacking libwebpmux3:arm64 (1.5.0-0.1) ... 188s Selecting previously unselected package python-biopython-doc. 188s Preparing to unpack .../39-python-biopython-doc_1.85+dfsg-2_all.deb ... 188s Unpacking python-biopython-doc (1.85+dfsg-2) ... 189s Selecting previously unselected package python3-all. 189s Preparing to unpack .../40-python3-all_3.13.1-1~exp2_arm64.deb ... 189s Unpacking python3-all (3.13.1-1~exp2) ... 189s Selecting previously unselected package python3-numpy. 189s Preparing to unpack .../41-python3-numpy_1%3a1.26.4+ds-13_arm64.deb ... 189s Unpacking python3-numpy (1:1.26.4+ds-13) ... 189s Selecting previously unselected package libopenjp2-7:arm64. 189s Preparing to unpack .../42-libopenjp2-7_2.5.0-2ubuntu3_arm64.deb ... 189s Unpacking libopenjp2-7:arm64 (2.5.0-2ubuntu3) ... 189s Selecting previously unselected package python3-pil:arm64. 189s Preparing to unpack .../43-python3-pil_11.1.0-5_arm64.deb ... 189s Unpacking python3-pil:arm64 (11.1.0-5) ... 189s Selecting previously unselected package python3-cairo. 189s Preparing to unpack .../44-python3-cairo_1.26.1-2build1_arm64.deb ... 189s Unpacking python3-cairo (1.26.1-2build1) ... 189s Selecting previously unselected package python3-freetype. 189s Preparing to unpack .../45-python3-freetype_2.5.1-1_all.deb ... 189s Unpacking python3-freetype (2.5.1-1) ... 189s Selecting previously unselected package python3-rlpycairo. 189s Preparing to unpack .../46-python3-rlpycairo_0.3.0-3_all.deb ... 189s Unpacking python3-rlpycairo (0.3.0-3) ... 189s Selecting previously unselected package python3-reportlab. 189s Preparing to unpack .../47-python3-reportlab_4.3.0-1_all.deb ... 189s Unpacking python3-reportlab (4.3.0-1) ... 189s Selecting previously unselected package xml-core. 189s Preparing to unpack .../48-xml-core_0.19_all.deb ... 189s Unpacking xml-core (0.19) ... 189s Selecting previously unselected package w3c-sgml-lib. 189s Preparing to unpack .../49-w3c-sgml-lib_1.3-3_all.deb ... 189s Unpacking w3c-sgml-lib (1.3-3) ... 189s Selecting previously unselected package python3-biopython. 189s Preparing to unpack .../50-python3-biopython_1.85+dfsg-2_arm64.deb ... 189s Unpacking python3-biopython (1.85+dfsg-2) ... 190s Selecting previously unselected package python3-biopython-sql. 190s Preparing to unpack .../51-python3-biopython-sql_1.85+dfsg-2_all.deb ... 190s Unpacking python3-biopython-sql (1.85+dfsg-2) ... 190s Setting up libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 190s Setting up liblcms2-2:arm64 (2.16-2) ... 190s Setting up libpixman-1-0:arm64 (0.44.0-3) ... 190s Setting up python3.12-minimal (3.12.9-1) ... 191s Setting up libsharpyuv0:arm64 (1.5.0-0.1) ... 191s Setting up liblerc4:arm64 (4.0.0+ds-5ubuntu1) ... 191s Setting up libxrender1:arm64 (1:0.9.10-1.1build1) ... 191s Setting up libxcb-render0:arm64 (1.17.0-2) ... 191s Setting up python3.12 (3.12.9-1) ... 192s Setting up x11-common (1:7.7+23ubuntu3) ... 193s Setting up libdeflate0:arm64 (1.23-1) ... 193s Setting up python3-all (3.13.1-1~exp2) ... 193s Setting up libxcb-shm0:arm64 (1.17.0-2) ... 193s Setting up libgomp1:arm64 (15-20250213-1ubuntu1) ... 193s Setting up python3-freetype (2.5.1-1) ... 193s Setting up libjbig0:arm64 (2.1-6.1ubuntu2) ... 193s Setting up libfontenc1:arm64 (1:1.1.8-1build1) ... 193s Setting up libblas3:arm64 (3.12.1-2) ... 193s 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 193s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 193s Setting up libimagequant0:arm64 (2.18.0-1build1) ... 193s Setting up fonts-dejavu-mono (2.37-8) ... 193s Setting up fonts-dejavu-core (2.37-8) ... 193s Setting up libjpeg-turbo8:arm64 (2.1.5-3ubuntu2) ... 193s Setting up libgfortran5:arm64 (15-20250213-1ubuntu1) ... 193s Setting up libwebp7:arm64 (1.5.0-0.1) ... 193s Setting up libopenjp2-7:arm64 (2.5.0-2ubuntu3) ... 193s Setting up libharfbuzz0b:arm64 (10.2.0-1) ... 193s Setting up sgml-base (1.31) ... 193s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 193s Setting up libwebpmux3:arm64 (1.5.0-0.1) ... 193s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 193s Setting up libjpeg8:arm64 (8c-2ubuntu11) ... 193s Setting up liblapack3:arm64 (3.12.1-2) ... 193s 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 193s Setting up fontconfig-config (2.15.0-2ubuntu1) ... 194s Setting up libwebpdemux2:arm64 (1.5.0-0.1) ... 194s Setting up xfonts-utils (1:7.7+7) ... 194s Setting up libraqm0:arm64 (0.10.2-1) ... 194s Setting up python3-numpy (1:1.26.4+ds-13) ... 198s Setting up libjs-sphinxdoc (8.1.3-5) ... 198s Setting up python-biopython-doc (1.85+dfsg-2) ... 198s Setting up libtiff6:arm64 (4.5.1+git230720-4ubuntu4) ... 198s Setting up xml-core (0.19) ... 198s Setting up libfontconfig1:arm64 (2.15.0-2ubuntu1) ... 198s Setting up fonts-urw-base35 (20200910-8) ... 198s Setting up libcairo2:arm64 (1.18.2-2) ... 198s Setting up python3-pil:arm64 (11.1.0-5) ... 199s Setting up python3-cairo (1.26.1-2build1) ... 199s Setting up python3-rlpycairo (0.3.0-3) ... 199s Setting up python3-reportlab (4.3.0-1) ... 201s Processing triggers for libc-bin (2.40-4ubuntu1) ... 201s Processing triggers for systemd (257.2-3ubuntu1) ... 201s Processing triggers for man-db (2.13.0-1) ... 203s Processing triggers for sgml-base (1.31) ... 203s Setting up w3c-sgml-lib (1.3-3) ... 233s Setting up python3-biopython (1.85+dfsg-2) ... 236s Setting up python3-biopython-sql (1.85+dfsg-2) ... 238s autopkgtest [13:38:52]: test dependencies: sh debian/tests/run-unit-test 238s autopkgtest [13:38:52]: test dependencies: [----------------------- 238s cp: cannot stat '/usr/share/libcifpp/mmcif_pdbx.dic': No such file or directory 238s cp: cannot stat '/usr/share/libcifpp/mmcif_ma.dic': No such file or directory 240s mkdir: created directory 'Bio' 240s mkdir: created directory 'Bio/Align' 240s mkdir: created directory 'Bio/Align/substitution_matrices' 240s mkdir: created directory 'Bio/Align/substitution_matrices/data/' 240s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER22' -> 'Bio/Align/substitution_matrices/data/BENNER22' 240s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER6' -> 'Bio/Align/substitution_matrices/data/BENNER6' 240s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER74' -> 'Bio/Align/substitution_matrices/data/BENNER74' 240s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLASTN' -> 'Bio/Align/substitution_matrices/data/BLASTN' 240s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLASTP' -> 'Bio/Align/substitution_matrices/data/BLASTP' 240s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM45' -> 'Bio/Align/substitution_matrices/data/BLOSUM45' 240s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM50' -> 'Bio/Align/substitution_matrices/data/BLOSUM50' 240s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM62' -> 'Bio/Align/substitution_matrices/data/BLOSUM62' 240s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM80' -> 'Bio/Align/substitution_matrices/data/BLOSUM80' 240s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM90' -> 'Bio/Align/substitution_matrices/data/BLOSUM90' 240s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/DAYHOFF' -> 'Bio/Align/substitution_matrices/data/DAYHOFF' 240s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/FENG' -> 'Bio/Align/substitution_matrices/data/FENG' 240s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/GENETIC' -> 'Bio/Align/substitution_matrices/data/GENETIC' 240s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/GONNET1992' -> 'Bio/Align/substitution_matrices/data/GONNET1992' 240s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/HOXD70' -> 'Bio/Align/substitution_matrices/data/HOXD70' 240s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/JOHNSON' -> 'Bio/Align/substitution_matrices/data/JOHNSON' 240s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/JONES' -> 'Bio/Align/substitution_matrices/data/JONES' 240s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/LEVIN' -> 'Bio/Align/substitution_matrices/data/LEVIN' 240s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MCLACHLAN' -> 'Bio/Align/substitution_matrices/data/MCLACHLAN' 240s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MDM78' -> 'Bio/Align/substitution_matrices/data/MDM78' 240s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MEGABLAST' -> 'Bio/Align/substitution_matrices/data/MEGABLAST' 240s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/NUC.4.4' -> 'Bio/Align/substitution_matrices/data/NUC.4.4' 240s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM250' -> 'Bio/Align/substitution_matrices/data/PAM250' 240s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM30' -> 'Bio/Align/substitution_matrices/data/PAM30' 240s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM70' -> 'Bio/Align/substitution_matrices/data/PAM70' 240s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/RAO' -> 'Bio/Align/substitution_matrices/data/RAO' 240s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/RISLER' -> 'Bio/Align/substitution_matrices/data/RISLER' 240s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/SCHNEIDER' -> 'Bio/Align/substitution_matrices/data/SCHNEIDER' 240s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/STR' -> 'Bio/Align/substitution_matrices/data/STR' 240s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/TRANS' -> 'Bio/Align/substitution_matrices/data/TRANS' 241s test_Ace ... ok 241s test_Affy ... ok 244s test_AlignIO ... ok 244s test_AlignIO_ClustalIO ... ok 244s test_AlignIO_EmbossIO ... ok 244s test_AlignIO_FastaIO ... ok 244s test_AlignIO_MauveIO ... ok 244s test_AlignIO_PhylipIO ... ok 244s test_AlignIO_convert ... ok 244s test_AlignInfo ... ok 244s test_Align_Alignment ... ok 244s test_Align_a2m ... ok 245s test_Align_bed ... ok 245s test_Align_bigbed ... ok 245s test_Align_bigmaf ... ok 246s test_Align_bigpsl ... ok 246s test_Align_chain ... ok 246s test_Align_clustal ... ok 249s test_Align_codonalign ... ok 249s test_Align_emboss ... ok 249s test_Align_exonerate ... ok 249s test_Align_fasta ... ok 250s test_Align_hhr ... ok 250s test_Align_maf ... ok 250s test_Align_mauve ... ok 250s test_Align_msf ... ok 250s test_Align_nexus ... ok 251s test_Align_phylip ... ok 251s test_Align_psl ... ok 251s test_Align_sam ... ok 253s test_Align_stockholm ... ok 253s test_Align_tabular ... ok 253s test_Application ... ok 254s test_BioSQL_MySQLdb_online ... skipping. internet not available 254s test_BioSQL_mysql_connector ... skipping. BioSQL test configuration file biosql.ini missing (see biosql.ini.sample) 254s test_BioSQL_mysql_connector_online ... skipping. internet not available 254s test_BioSQL_psycopg2_online ... skipping. internet not available 258s test_BioSQL_sqlite3 ... ok 258s test_BioSQL_sqlite3_online ... skipping. internet not available 258s test_Blast_Record ... ok 259s test_Blast_parser ... ok 259s test_CAPS ... ok 259s test_Chi2 ... ok 259s test_ClustalOmega_tool ... skipping. Install clustalo if you want to use Clustal Omega from Biopython. 259s test_Clustalw_tool ... skipping. Install clustalw or clustalw2 if you want to use it from Biopython. 259s test_Cluster ... ok 259s test_CodonTable ... ok 259s test_ColorSpiral ... ok 259s test_Compass ... ok 261s test_Consensus ... ok 261s test_Dialign_tool ... skipping. Install DIALIGN2-2 if you want to use the Bio.Align.Applications wrapper. 261s test_EMBL_unittest ... ok 261s test_Emboss ... skipping. $EMBOSS_ROOT='/usr/lib/emboss' which does not exist! 261s test_EmbossPrimer ... ok 265s test_Entrez ... ok 265s test_Entrez_online ... skipping. internet not available 266s test_Entrez_parser ... ok 266s test_Enzyme ... ok 266s test_ExPASy ... skipping. internet not available 266s test_Fasttree_tool ... skipping. Install FastTree and correctly set the file path to the program if you want to use it from Biopython. 266s test_File ... ok 266s test_GenBank ... /usr/lib/python3/dist-packages/Bio/SeqIO/InsdcIO.py:600: BiopythonWarning: Annotation 'Sequence Read Archive: SRX001885, SRX001121, SRX001531, SRX001530, SRX001529' too long 266s warnings.warn(f"Annotation {text!r} too long", BiopythonWarning) 266s ok 268s test_GenomeDiagram ... Warn: Can't find .pfb for face 'Helvetica' 270s ok 271s test_GraphicsChromosome ... ok 271s test_GraphicsDistribution ... ok 272s test_GraphicsGeneral ... ok 272s test_HMMCasino ... ok 272s test_HMMGeneral ... ok 272s test_KEGG ... ok 272s test_KEGG_online ... skipping. internet not available 278s test_KGML_graphics ... ok 278s test_KGML_graphics_online ... skipping. internet not available 279s test_KGML_nographics ... ok 280s test_KeyWList ... ok 280s test_LogisticRegression ... ok 281s test_MafIO_index ... ok 281s test_Mafft_tool ... skipping. Install MAFFT if you want to use the Bio.Align.Applications wrapper. 281s test_MarkovModel ... ok 281s test_Medline ... ok 281s test_Muscle_tool ... skipping. Install MUSCLE if you want to use the Bio.Align.Applications wrapper. 282s test_NCBIXML ... Exception ignored in: 282s Traceback (most recent call last): 282s File "/usr/lib/python3/dist-packages/Bio/Blast/NCBIXML.py", line 1319, in parse 282s expat_parser.Parse(NULL, True) 282s xml.parsers.expat.ExpatError: unclosed token: line 320, column 0 282s ok 282s test_NCBI_BLAST_tools ... skipping. Install the NCBI BLAST+ command line tools if you want to use the Bio.Blast.Applications wrapper. 282s test_NCBI_qblast ... ok 282s test_NMR ... ok 282s test_NaiveBayes ... ok 282s test_Nexus ... ok 282s test_PAML_baseml ... ok 283s test_PAML_codeml ... ok 283s test_PAML_yn00 ... ok 288s test_PDB_CEAligner ... ok 288s test_PDB_DSSP ... ok 289s test_PDB_Dice ... ok 289s test_PDB_Disordered ... ok 289s test_PDB_Exposure ... ok 289s test_PDB_FragmentMapper ... ok 291s test_PDB_KDTree ... ok 291s test_PDB_MMCIF2Dict ... ok 291s test_PDB_MMCIFIO ... ok 293s test_PDB_MMCIFParser ... ok 293s test_PDB_NACCESS ... ok 293s test_PDB_PDBIO ... ok 293s test_PDB_PDBList ... skipping. internet not available 301s test_PDB_PDBMLParser ... ok 301s test_PDB_PDBParser ... ok 301s 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 301s test_PDB_Polypeptide ... ok 301s test_PDB_QCPSuperimposer ... ok 304s test_PDB_SASA ... ok 305s test_PDB_SMCRA ... ok 305s test_PDB_Selection ... ok 305s test_PDB_StructureAlignment ... ok 306s test_PDB_Superimposer ... ok 306s test_PDB_alphafold_db ... skipping. internet not available 306s test_PDB_binary_cif ... skipping. Error: Install msgpack to use Bio.PDB.binaryCIF (e.g. pip install msgpack) 306s 306s test_PDB_internal_coords ... skipping. Error: Install mmtf to use Bio.PDB.mmtf (e.g. pip install mmtf-python) 306s 306s test_PDB_parse_pdb_header ... ok 306s test_PDB_vectors ... ok 306s test_PQR ... ok 306s test_Pathway ... ok 306s test_Phd ... ok 307s test_Phylo ... ok 307s test_PhyloXML ... ok 307s test_Phylo_CDAO ... skipping. Install RDFlib if you want to use the CDAO tree format. 307s test_Phylo_NeXML ... ok 307s test_Phylo_igraph ... skipping. Install igraph if you wish to use it with Bio.Phylo 307s test_Phylo_matplotlib ... skipping. Install matplotlib if you want to use Bio.Phylo._utils. 307s test_Phylo_networkx ... skipping. Install networkx if you wish to use it with Bio.Phylo 308s test_PopGen_GenePop_nodepend ... ok 308s test_Prank_tool ... skipping. Install PRANK if you want to use the Bio.Align.Applications wrapper. 308s test_Probcons_tool ... skipping. Install PROBCONS if you want to use the Bio.Align.Applications wrapper. 308s test_ProtParam ... ok 308s test_RCSBFormats ... ok 308s test_Restriction ... ok 309s test_SCOP_Astral ... ok 309s test_SCOP_Cla ... ok 309s test_SCOP_Des ... ok 309s test_SCOP_Dom ... ok 309s test_SCOP_Hie ... ok 309s test_SCOP_Raf ... ok 309s test_SCOP_Residues ... ok 309s test_SCOP_Scop ... ok 309s test_SVDSuperimposer ... ok 309s test_SearchIO_blast_tab ... ok 309s test_SearchIO_blast_tab_index ... ok 310s test_SearchIO_blast_xml ... ok 311s test_SearchIO_blast_xml_index ... ok 311s test_SearchIO_blat_psl ... ok 311s test_SearchIO_blat_psl_index ... ok 311s test_SearchIO_exonerate ... ok 311s test_SearchIO_exonerate_text_index ... ok 311s test_SearchIO_exonerate_vulgar_index ... ok 312s test_SearchIO_fasta_m10 ... ok 312s test_SearchIO_fasta_m10_index ... ok 312s test_SearchIO_hhsuite2_text ... ok 312s test_SearchIO_hmmer2_text ... ok 312s test_SearchIO_hmmer2_text_index ... ok 312s test_SearchIO_hmmer3_domtab ... ok 312s test_SearchIO_hmmer3_domtab_index ... ok 312s test_SearchIO_hmmer3_tab ... ok 312s test_SearchIO_hmmer3_tab_index ... ok 313s test_SearchIO_hmmer3_text ... ok 313s test_SearchIO_hmmer3_text_index ... ok 313s test_SearchIO_interproscan_xml ... ok 313s test_SearchIO_model ... ok 313s test_SearchIO_write ... ok 313s test_SeqFeature ... ok 331s test_SeqIO ... ok 332s test_SeqIO_AbiIO ... ok 332s test_SeqIO_FastaIO ... ok 332s test_SeqIO_Gck ... ok 332s test_SeqIO_Gfa ... ok 332s test_SeqIO_Insdc ... ok 332s test_SeqIO_NibIO ... ok 334s test_SeqIO_PdbIO ... ok 335s test_SeqIO_QualityIO ... ok 335s test_SeqIO_SeqXML ... ok 335s test_SeqIO_SffIO ... ok 335s test_SeqIO_SnapGene ... ok 336s test_SeqIO_TwoBitIO ... ok 336s test_SeqIO_UniprotIO ... ok 336s test_SeqIO_Xdna ... ok 337s test_SeqIO_features ... ok 353s test_SeqIO_index ... ok 353s test_SeqIO_online ... skipping. internet not available 353s test_SeqIO_write ... ok 353s test_SeqRecord ... ok 353s test_SeqUtils ... ok 354s test_Seq_objs ... ok 355s test_SwissProt ... ok 355s test_TCoffee_tool ... skipping. Install TCOFFEE if you want to use the Bio.Align.Applications wrapper. 355s test_TogoWS ... skipping. internet not available 355s test_TreeConstruction ... ok 355s test_Tutorial ... skipping. Could not find ../Doc/Tutorial/index.rst file 355s test_UniGene ... ok 355s test_UniProt ... skipping. internet not available 356s test_UniProt_GOA ... ok 356s test_align ... ok 356s test_align_substitution_matrices ... ok 358s test_bgzf ... ok 359s test_cellosaurus ... ok 363s test_codonalign ... ok 363s test_geo ... ok 363s test_kNN ... ok 364s test_motifs ... ok 364s test_motifs_online ... skipping. internet not available 364s 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. 364s warnings.warn( 364s ok 364s test_pairwise2_no_C ... ok 364s test_pairwise_aligner ... ok 365s test_pairwise_alignment_map ... ok 372s test_phenotype ... ok 372s test_phenotype_fit ... skipping. Install SciPy if you want to use Bio.phenotype fit functionality. 372s 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. 372s test_prodoc ... ok 372s test_prosite ... ok 372s test_raxml_tool ... skipping. Install RAxML (binary raxmlHPC) if you want to test the Bio.Phylo.Applications wrapper. 372s test_samtools_tool ... skipping. Install samtools and correctly set the file path to the program if you want to use it from Biopython 372s test_seq ... ok 373s test_translate ... ok 373s Skipping any tests requiring internet access 373s Python version: 3.12.9 (main, Feb 5 2025, 01:31:18) [GCC 14.2.0] 373s Operating system: posix linux 373s ---------------------------------------------------------------------- 373s Ran 218 tests in 131.787 seconds 373s 373s sys:1: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/protein_lib.fa' mode='rt' encoding='UTF-8'> 373s sys:1: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/nucleotide_lib.fa' mode='rt' encoding='UTF-8'> 374s test_Ace ... ok 374s test_Affy ... ok 377s test_AlignIO ... ok 377s test_AlignIO_ClustalIO ... ok 377s test_AlignIO_EmbossIO ... ok 377s test_AlignIO_FastaIO ... ok 377s test_AlignIO_MauveIO ... ok 377s test_AlignIO_PhylipIO ... ok 377s test_AlignIO_convert ... ok 377s test_AlignInfo ... ok 377s test_Align_Alignment ... ok 377s test_Align_a2m ... ok 377s test_Align_bed ... ok 378s test_Align_bigbed ... ok 378s test_Align_bigmaf ... ok 379s test_Align_bigpsl ... ok 379s test_Align_chain ... ok 379s test_Align_clustal ... ok 382s test_Align_codonalign ... ok 382s test_Align_emboss ... ok 382s test_Align_exonerate ... ok 382s test_Align_fasta ... ok 383s test_Align_hhr ... ok 383s test_Align_maf ... ok 383s test_Align_mauve ... ok 383s test_Align_msf ... ok 384s test_Align_nexus ... ok 384s test_Align_phylip ... ok 384s test_Align_psl ... ok 384s test_Align_sam ... ok 386s test_Align_stockholm ... ok 387s test_Align_tabular ... ok 387s test_Application ... ok 387s test_BioSQL_MySQLdb_online ... skipping. internet not available 387s test_BioSQL_mysql_connector ... skipping. BioSQL test configuration file biosql.ini missing (see biosql.ini.sample) 387s test_BioSQL_mysql_connector_online ... skipping. internet not available 387s test_BioSQL_psycopg2_online ... skipping. internet not available 392s test_BioSQL_sqlite3 ... ok 392s test_BioSQL_sqlite3_online ... skipping. internet not available 392s test_Blast_Record ... ok 392s test_Blast_parser ... ok 393s test_CAPS ... ok 393s test_Chi2 ... ok 393s test_ClustalOmega_tool ... skipping. Install clustalo if you want to use Clustal Omega from Biopython. 393s test_Clustalw_tool ... skipping. Install clustalw or clustalw2 if you want to use it from Biopython. 393s test_Cluster ... ok 393s test_CodonTable ... ok 393s test_ColorSpiral ... ok 393s test_Compass ... ok 394s test_Consensus ... ok 394s test_Dialign_tool ... skipping. Install DIALIGN2-2 if you want to use the Bio.Align.Applications wrapper. 394s test_EMBL_unittest ... ok 394s test_Emboss ... skipping. $EMBOSS_ROOT='/usr/lib/emboss' which does not exist! 394s test_EmbossPrimer ... ok 399s test_Entrez ... ok 399s test_Entrez_online ... skipping. internet not available 399s test_Entrez_parser ... ok 399s test_Enzyme ... ok 399s test_ExPASy ... skipping. internet not available 399s test_Fasttree_tool ... skipping. Install FastTree and correctly set the file path to the program if you want to use it from Biopython. 399s test_File ... ok 400s test_GenBank ... /usr/lib/python3/dist-packages/Bio/SeqIO/InsdcIO.py:600: BiopythonWarning: Annotation 'Sequence Read Archive: SRX001885, SRX001121, SRX001531, SRX001530, SRX001529' too long 400s warnings.warn(f"Annotation {text!r} too long", BiopythonWarning) 400s ok 401s test_GenomeDiagram ... Warn: Can't find .pfb for face 'Helvetica' 403s ok 404s test_GraphicsChromosome ... ok 404s test_GraphicsDistribution ... ok 405s test_GraphicsGeneral ... ok 405s test_HMMCasino ... ok 405s test_HMMGeneral ... ok 405s test_KEGG ... ok 405s test_KEGG_online ... skipping. internet not available 410s test_KGML_graphics ... ok 410s test_KGML_graphics_online ... skipping. internet not available 411s test_KGML_nographics ... ok 411s test_KeyWList ... ok 411s test_LogisticRegression ... ok 412s test_MafIO_index ... ok 412s test_Mafft_tool ... skipping. Install MAFFT if you want to use the Bio.Align.Applications wrapper. 412s test_MarkovModel ... ok 412s test_Medline ... ok 412s test_Muscle_tool ... skipping. Install MUSCLE if you want to use the Bio.Align.Applications wrapper. 413s test_NCBIXML ... Exception ignored in: 413s Traceback (most recent call last): 413s File "/usr/lib/python3/dist-packages/Bio/Blast/NCBIXML.py", line 1319, in parse 413s expat_parser.Parse(NULL, True) 413s xml.parsers.expat.ExpatError: unclosed token: line 320, column 0 413s ok 413s test_NCBI_BLAST_tools ... skipping. Install the NCBI BLAST+ command line tools if you want to use the Bio.Blast.Applications wrapper. 413s test_NCBI_qblast ... ok 413s test_NMR ... ok 413s test_NaiveBayes ... ok 414s test_Nexus ... ok 414s test_PAML_baseml ... ok 414s test_PAML_codeml ... ok 415s test_PAML_yn00 ... ok 419s test_PDB_CEAligner ... ok 420s test_PDB_DSSP ... ok 420s test_PDB_Dice ... ok 420s test_PDB_Disordered ... ok 420s test_PDB_Exposure ... ok 420s test_PDB_FragmentMapper ... ok 422s test_PDB_KDTree ... ok 422s test_PDB_MMCIF2Dict ... ok 422s test_PDB_MMCIFIO ... ok 424s test_PDB_MMCIFParser ... ok 424s test_PDB_NACCESS ... ok 424s test_PDB_PDBIO ... ok 424s test_PDB_PDBList ... skipping. internet not available 431s test_PDB_PDBMLParser ... ok 431s test_PDB_PDBParser ... ok 431s 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 431s test_PDB_Polypeptide ... ok 431s test_PDB_QCPSuperimposer ... ok 435s test_PDB_SASA ... ok 435s test_PDB_SMCRA ... ok 435s test_PDB_Selection ... ok 436s test_PDB_StructureAlignment ... ok 436s test_PDB_Superimposer ... ok 436s test_PDB_alphafold_db ... skipping. internet not available 436s test_PDB_binary_cif ... skipping. Error: Install msgpack to use Bio.PDB.binaryCIF (e.g. pip install msgpack) 436s 436s test_PDB_internal_coords ... skipping. Error: Install mmtf to use Bio.PDB.mmtf (e.g. pip install mmtf-python) 436s 436s test_PDB_parse_pdb_header ... ok 436s test_PDB_vectors ... ok 436s test_PQR ... ok 436s test_Pathway ... ok 436s test_Phd ... ok 437s test_Phylo ... ok 437s test_PhyloXML ... ok 437s test_Phylo_CDAO ... skipping. Install RDFlib if you want to use the CDAO tree format. 437s test_Phylo_NeXML ... ok 438s test_Phylo_igraph ... skipping. Install igraph if you wish to use it with Bio.Phylo 438s test_Phylo_matplotlib ... skipping. Install matplotlib if you want to use Bio.Phylo._utils. 438s test_Phylo_networkx ... skipping. Install networkx if you wish to use it with Bio.Phylo 438s test_PopGen_GenePop_nodepend ... ok 438s test_Prank_tool ... skipping. Install PRANK if you want to use the Bio.Align.Applications wrapper. 438s test_Probcons_tool ... skipping. Install PROBCONS if you want to use the Bio.Align.Applications wrapper. 438s test_ProtParam ... ok 438s test_RCSBFormats ... ok 439s test_Restriction ... ok 439s test_SCOP_Astral ... ok 439s test_SCOP_Cla ... ok 439s test_SCOP_Des ... ok 439s test_SCOP_Dom ... ok 439s test_SCOP_Hie ... ok 439s test_SCOP_Raf ... ok 439s test_SCOP_Residues ... ok 439s test_SCOP_Scop ... ok 439s test_SVDSuperimposer ... ok 439s test_SearchIO_blast_tab ... ok 440s test_SearchIO_blast_tab_index ... ok 440s test_SearchIO_blast_xml ... ok 441s test_SearchIO_blast_xml_index ... ok 441s test_SearchIO_blat_psl ... ok 441s test_SearchIO_blat_psl_index ... ok 441s test_SearchIO_exonerate ... ok 442s test_SearchIO_exonerate_text_index ... ok 442s test_SearchIO_exonerate_vulgar_index ... ok 442s test_SearchIO_fasta_m10 ... ok 442s test_SearchIO_fasta_m10_index ... ok 442s test_SearchIO_hhsuite2_text ... ok 442s test_SearchIO_hmmer2_text ... ok 442s test_SearchIO_hmmer2_text_index ... ok 442s test_SearchIO_hmmer3_domtab ... ok 443s test_SearchIO_hmmer3_domtab_index ... ok 443s test_SearchIO_hmmer3_tab ... ok 443s test_SearchIO_hmmer3_tab_index ... ok 443s test_SearchIO_hmmer3_text ... ok 443s test_SearchIO_hmmer3_text_index ... ok 443s test_SearchIO_interproscan_xml ... ok 443s test_SearchIO_model ... ok 444s test_SearchIO_write ... ok 444s test_SeqFeature ... ok 459s test_SeqIO ... ok 459s test_SeqIO_AbiIO ... ok 459s test_SeqIO_FastaIO ... ok 459s test_SeqIO_Gck ... ok 460s test_SeqIO_Gfa ... ok 460s test_SeqIO_Insdc ... ok 460s test_SeqIO_NibIO ... ok 462s test_SeqIO_PdbIO ... ok 462s test_SeqIO_QualityIO ... ok 462s test_SeqIO_SeqXML ... ok 462s test_SeqIO_SffIO ... ok 462s test_SeqIO_SnapGene ... ok 463s test_SeqIO_TwoBitIO ... ok 464s test_SeqIO_UniprotIO ... ok 464s test_SeqIO_Xdna ... ok 464s test_SeqIO_features ... ok 479s test_SeqIO_index ... ok 479s test_SeqIO_online ... skipping. internet not available 479s test_SeqIO_write ... ok 479s test_SeqRecord ... ok 479s test_SeqUtils ... ok 480s test_Seq_objs ... ok 481s test_SwissProt ... ok 481s test_TCoffee_tool ... skipping. Install TCOFFEE if you want to use the Bio.Align.Applications wrapper. 481s test_TogoWS ... skipping. internet not available 481s test_TreeConstruction ... ok 481s test_Tutorial ... skipping. Could not find ../Doc/Tutorial/index.rst file 481s test_UniGene ... ok 481s test_UniProt ... skipping. internet not available 481s test_UniProt_GOA ... ok 482s test_align ... ok 482s test_align_substitution_matrices ... ok 484s test_bgzf ... ok 484s test_cellosaurus ... ok 488s test_codonalign ... ok 488s test_geo ... ok 489s test_kNN ... ok 489s test_motifs ... ok 489s test_motifs_online ... skipping. internet not available 489s 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. 489s warnings.warn( 489s ok 489s test_pairwise2_no_C ... ok 490s test_pairwise_aligner ... ok 490s test_pairwise_alignment_map ... ok 497s test_phenotype ... ok 497s test_phenotype_fit ... skipping. Install SciPy if you want to use Bio.phenotype fit functionality. 497s 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. 497s test_prodoc ... ok 497s test_prosite ... ok 497s test_raxml_tool ... skipping. Install RAxML (binary raxmlHPC) if you want to test the Bio.Phylo.Applications wrapper. 497s test_samtools_tool ... skipping. Install samtools and correctly set the file path to the program if you want to use it from Biopython 497s test_seq ... ok 498s test_translate ... ok 498s Skipping any tests requiring internet access 498s Python version: 3.13.2 (main, Feb 5 2025, 01:23:35) [GCC 14.2.0] 498s Operating system: posix linux 498s ---------------------------------------------------------------------- 498s Ran 218 tests in 123.634 seconds 498s 498s :0: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/protein_lib.fa' mode='rt' encoding='UTF-8'> 498s :0: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/nucleotide_lib.fa' mode='rt' encoding='UTF-8'> 498s autopkgtest [13:43:12]: test dependencies: -----------------------] 499s autopkgtest [13:43:13]: test dependencies: - - - - - - - - - - results - - - - - - - - - - 499s dependencies PASS 499s autopkgtest [13:43:13]: test full_suite: preparing testbed 593s autopkgtest [13:44:47]: testbed dpkg architecture: arm64 593s autopkgtest [13:44:47]: testbed apt version: 2.9.29 594s autopkgtest [13:44:48]: @@@@@@@@@@@@@@@@@@@@ test bed setup 594s autopkgtest [13:44:48]: testbed release detected to be: plucky 595s autopkgtest [13:44:49]: updating testbed package index (apt update) 595s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [110 kB] 595s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 595s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 595s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 595s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [3120 B] 595s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [13.9 kB] 595s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [76.1 kB] 595s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [744 kB] 596s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [103 kB] 596s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 Packages [7960 B] 596s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [692 kB] 596s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [11.2 kB] 596s Fetched 1762 kB in 1s (1886 kB/s) 597s Reading package lists... 597s Reading package lists... 598s Building dependency tree... 598s Reading state information... 598s Calculating upgrade... 599s The following NEW packages will be installed: 599s libapt-pkg7.0 599s The following packages will be upgraded: 599s apt apt-utils iproute2 libgpgme11t64 liblsof0 libp11-kit0 lsof rsyslog 599s sysvinit-utils 599s 9 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 599s Need to get 5019 kB of archives. 599s After this operation, 3410 kB of additional disk space will be used. 599s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 sysvinit-utils arm64 3.14-1ubuntu1 [35.2 kB] 599s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 libapt-pkg7.0 arm64 2.9.30 [1023 kB] 599s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 apt arm64 2.9.30 [1364 kB] 599s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 apt-utils arm64 2.9.30 [207 kB] 599s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 iproute2 arm64 6.13.0-1ubuntu1 [1158 kB] 599s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 libp11-kit0 arm64 0.25.5-2ubuntu3 [280 kB] 599s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 rsyslog arm64 8.2412.0-2ubuntu1 [521 kB] 599s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 lsof arm64 4.99.4+dfsg-1 [236 kB] 599s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 liblsof0 arm64 4.99.4+dfsg-1 [53.9 kB] 599s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 libgpgme11t64 arm64 1.24.2-1ubuntu1 [142 kB] 600s Preconfiguring packages ... 600s Fetched 5019 kB in 1s (6458 kB/s) 601s (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 ... 116620 files and directories currently installed.) 601s Preparing to unpack .../sysvinit-utils_3.14-1ubuntu1_arm64.deb ... 601s Unpacking sysvinit-utils (3.14-1ubuntu1) over (3.08-6ubuntu3) ... 601s Setting up sysvinit-utils (3.14-1ubuntu1) ... 601s Selecting previously unselected package libapt-pkg7.0:arm64. 601s (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 ... 116620 files and directories currently installed.) 601s Preparing to unpack .../libapt-pkg7.0_2.9.30_arm64.deb ... 601s Unpacking libapt-pkg7.0:arm64 (2.9.30) ... 601s Setting up libapt-pkg7.0:arm64 (2.9.30) ... 601s (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 ... 116669 files and directories currently installed.) 601s Preparing to unpack .../archives/apt_2.9.30_arm64.deb ... 601s Unpacking apt (2.9.30) over (2.9.29) ... 601s Setting up apt (2.9.30) ... 602s (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 ... 116669 files and directories currently installed.) 602s Preparing to unpack .../0-apt-utils_2.9.30_arm64.deb ... 602s Unpacking apt-utils (2.9.30) over (2.9.29) ... 602s Preparing to unpack .../1-iproute2_6.13.0-1ubuntu1_arm64.deb ... 602s Unpacking iproute2 (6.13.0-1ubuntu1) over (6.10.0-2ubuntu1) ... 602s Preparing to unpack .../2-libp11-kit0_0.25.5-2ubuntu3_arm64.deb ... 602s Unpacking libp11-kit0:arm64 (0.25.5-2ubuntu3) over (0.25.5-2ubuntu2) ... 602s Preparing to unpack .../3-rsyslog_8.2412.0-2ubuntu1_arm64.deb ... 602s Unpacking rsyslog (8.2412.0-2ubuntu1) over (8.2412.0-1ubuntu1) ... 602s Preparing to unpack .../4-lsof_4.99.4+dfsg-1_arm64.deb ... 602s Unpacking lsof (4.99.4+dfsg-1) over (4.99.3+dfsg-2) ... 603s Preparing to unpack .../5-liblsof0_4.99.4+dfsg-1_arm64.deb ... 603s Unpacking liblsof0 (4.99.4+dfsg-1) over (4.99.3+dfsg-2) ... 603s Preparing to unpack .../6-libgpgme11t64_1.24.2-1ubuntu1_arm64.deb ... 603s Unpacking libgpgme11t64:arm64 (1.24.2-1ubuntu1) over (1.24.1-4ubuntu1) ... 603s Setting up apt-utils (2.9.30) ... 603s Setting up liblsof0 (4.99.4+dfsg-1) ... 603s Setting up iproute2 (6.13.0-1ubuntu1) ... 603s Setting up rsyslog (8.2412.0-2ubuntu1) ... 603s info: The user `syslog' is already a member of `adm'. 604s Setting up libp11-kit0:arm64 (0.25.5-2ubuntu3) ... 604s Setting up lsof (4.99.4+dfsg-1) ... 604s Setting up libgpgme11t64:arm64 (1.24.2-1ubuntu1) ... 604s Processing triggers for man-db (2.13.0-1) ... 607s Processing triggers for libc-bin (2.40-4ubuntu1) ... 608s Reading package lists... 608s Building dependency tree... 608s Reading state information... 609s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 609s autopkgtest [13:45:03]: upgrading testbed (apt dist-upgrade and autopurge) 609s Reading package lists... 609s Building dependency tree... 609s Reading state information... 610s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 610s Starting 2 pkgProblemResolver with broken count: 0 610s Done 611s Entering ResolveByKeep 611s 612s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 612s Reading package lists... 612s Building dependency tree... 612s Reading state information... 613s Starting pkgProblemResolver with broken count: 0 613s Starting 2 pkgProblemResolver with broken count: 0 613s Done 614s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 614s autopkgtest [13:45:08]: rebooting testbed after setup commands that affected boot 641s Reading package lists... 642s Building dependency tree... 642s Reading state information... 642s Starting pkgProblemResolver with broken count: 0 642s Starting 2 pkgProblemResolver with broken count: 0 642s Done 643s The following NEW packages will be installed: 643s autoconf automake autopoint autotools-dev blt build-essential bwa clustalo 643s cpp cpp-14 cpp-14-aarch64-linux-gnu cpp-aarch64-linux-gnu debhelper 643s debugedit dh-autoreconf dh-python dh-strip-nondeterminism dialign 643s docutils-common dssp dwz emboss emboss-data emboss-lib fasttree flex 643s fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-font-awesome 643s fonts-lato fonts-lmodern fonts-lyx fonts-urw-base35 g++ g++-14 643s g++-14-aarch64-linux-gnu g++-aarch64-linux-gnu gcc gcc-14 643s gcc-14-aarch64-linux-gnu gcc-aarch64-linux-gnu gettext ghostscript hevea 643s hicolor-icon-theme imagemagick imagemagick-7-common imagemagick-7.q16 643s intltool-debian libamd3 libaom3 libapache-pom-java libarchive-zip-perl 643s libargtable2-0 libarpack2t64 libasan8 libavahi-client3 libavahi-common-data 643s libavahi-common3 libblas3 libcairo2 libcc1-0 libcifpp-data libcifpp7 643s libcolamd3 libcommons-logging-java libcommons-parent-java libcups2t64 643s libde265-0 libdebhelper-perl libdeflate0 libexpat1-dev libfftw3-double3 643s libfile-stripnondeterminism-perl libfontbox-java libfontconfig1 libfontenc1 643s libgcc-14-dev libgd3 libgfortran5 libglpk40 libgomp1 libgraphite2-3 643s libgs-common libgs10 libgs10-common libharfbuzz0b libheif-plugin-aomdec 643s libheif-plugin-libde265 libheif1 libhpdf-2.3.0 libhwasan0 libice6 libidn12 643s libigraph3t64 libijs-0.35 libimagequant0 libisl23 libitm1 libjbig0 643s libjbig2dec0 libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui 643s libjs-sphinxdoc libjs-underscore libjson-perl libkpathsea6 liblapack3 643s liblbfgsb0 liblcms2-2 liblerc4 liblqr-1-0 liblsan0 libltdl7 643s libmagickcore-7.q16-10 libmagickwand-7.q16-10 libmbedcrypto16 libmbedtls21 643s libmbedx509-7 libmpc3 libmpfi0 libmysqlclient21 libnetpbm11t64 libopenjp2-7 643s libpaper-utils libpaper2 libpdfbox-java libpixman-1-0 libplfit0 libpotrace0 643s libpq5 libptexenc1 libpython3-all-dev libpython3-dev libpython3.12-dev 643s libpython3.13-dev libqhull-r8.0 libraqm0 libraw23t64 libsharpyuv0 libsm6 643s libstdc++-14-dev libsuitesparseconfig7 libsynctex2 libtcl8.6 libteckit0 643s libtexlua53-5 libtiff6 libtk8.6 libtool libtsan2 libubsan1 libwebp7 643s libwebpdemux2 libwebpmux3 libxaw7 libxcb-render0 libxcb-shm0 libxft2 libxi6 643s libxmu6 libxpm4 libxrender1 libxslt1.1 libxss1 libxt6t64 libzzip-0-13t64 m4 643s mafft mysql-common ncbi-blast+ ncbi-data netpbm phylip po-debconf 643s poppler-data prank preview-latex-style probcons python-biopython-doc 643s python-matplotlib-data python3-alabaster python3-all python3-all-dev 643s python3-biopython python3-biopython-sql python3-brotli python3-cairo 643s python3-contourpy python3-cycler python3-dateutil python3-decorator 643s python3-defusedxml python3-dev python3-docutils python3-fonttools 643s python3-freetype python3-fs python3-igraph python3-imagesize 643s python3-kiwisolver python3-lxml python3-lz4 python3-matplotlib python3-mmtf 643s python3-mpmath python3-msgpack python3-mysqldb python3-networkx 643s python3-numpy python3-numpydoc python3-packaging python3-pil 643s python3-pil.imagetk python3-platformdirs python3-pytz python3-rdflib 643s python3-reportlab python3-rlpycairo python3-roman python3-scipy 643s python3-snowballstemmer python3-sphinx python3-sphinx-rtd-theme 643s python3-sphinxcontrib.jquery python3-sympy python3-tabulate 643s python3-texttable python3-tk python3-tz python3-ufolib2 python3.12 643s python3.12-dev python3.12-minimal python3.12-tk python3.13-dev python3.13-tk 643s sgml-base sphinx-common sphinx-rtd-theme-common t-coffee t1utils tex-common 643s texlive-base texlive-binaries texlive-fonts-recommended texlive-latex-base 643s texlive-latex-extra texlive-latex-recommended texlive-pictures tk8.6-blt2.5 643s unicode-data w3c-sgml-lib wise wise-data x11-common xdg-utils 643s xfonts-encodings xfonts-utils xml-core zlib1g-dev 644s 0 upgraded, 264 newly installed, 0 to remove and 0 not upgraded. 644s Need to get 405 MB of archives. 644s After this operation, 1864 MB of additional disk space will be used. 644s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.12-minimal arm64 3.12.9-1 [2236 kB] 644s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 m4 arm64 1.4.19-5 [244 kB] 644s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 flex arm64 2.6.4-8.2build1 [291 kB] 644s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-lato all 2.015-1 [2781 kB] 644s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 libgomp1 arm64 15-20250213-1ubuntu1 [146 kB] 644s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 libfftw3-double3 arm64 3.3.10-2fakesync1build1 [392 kB] 644s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 644s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 644s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 libfontenc1 arm64 1:1.1.8-1build1 [13.9 kB] 644s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 644s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 644s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 xfonts-utils arm64 1:7.7+7 [95.6 kB] 644s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-urw-base35 all 20200910-8 [11.0 MB] 646s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig-config arm64 2.15.0-2ubuntu1 [37.5 kB] 646s Get:15 http://ftpmaster.internal/ubuntu plucky/main arm64 libfontconfig1 arm64 2.15.0-2ubuntu1 [144 kB] 646s Get:16 http://ftpmaster.internal/ubuntu plucky/main arm64 libsharpyuv0 arm64 1.5.0-0.1 [16.9 kB] 646s Get:17 http://ftpmaster.internal/ubuntu plucky/main arm64 libaom3 arm64 3.12.0-1 [1828 kB] 646s Get:18 http://ftpmaster.internal/ubuntu plucky/main arm64 libheif-plugin-aomdec arm64 1.19.5-1build1 [11.4 kB] 646s Get:19 http://ftpmaster.internal/ubuntu plucky/main arm64 libde265-0 arm64 1.0.15-1build4 [146 kB] 646s Get:20 http://ftpmaster.internal/ubuntu plucky/main arm64 libheif-plugin-libde265 arm64 1.19.5-1build1 [8902 B] 646s Get:21 http://ftpmaster.internal/ubuntu plucky/main arm64 libheif1 arm64 1.19.5-1build1 [369 kB] 646s Get:22 http://ftpmaster.internal/ubuntu plucky/main arm64 libjbig0 arm64 2.1-6.1ubuntu2 [29.3 kB] 646s Get:23 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg-turbo8 arm64 2.1.5-3ubuntu2 [165 kB] 646s Get:24 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 646s Get:25 http://ftpmaster.internal/ubuntu plucky/main arm64 liblcms2-2 arm64 2.16-2 [170 kB] 646s Get:26 http://ftpmaster.internal/ubuntu plucky/universe arm64 liblqr-1-0 arm64 0.4.2-2.1build2 [27.1 kB] 646s Get:27 http://ftpmaster.internal/ubuntu plucky/main arm64 libltdl7 arm64 2.5.4-3build1 [43.0 kB] 646s Get:28 http://ftpmaster.internal/ubuntu plucky/main arm64 libopenjp2-7 arm64 2.5.0-2ubuntu3 [182 kB] 646s Get:29 http://ftpmaster.internal/ubuntu plucky/main arm64 libraw23t64 arm64 0.21.3-1 [377 kB] 646s Get:30 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate0 arm64 1.23-1 [46.2 kB] 646s Get:31 http://ftpmaster.internal/ubuntu plucky/main arm64 liblerc4 arm64 4.0.0+ds-5ubuntu1 [167 kB] 646s Get:32 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebp7 arm64 1.5.0-0.1 [194 kB] 646s Get:33 http://ftpmaster.internal/ubuntu plucky/main arm64 libtiff6 arm64 4.5.1+git230720-4ubuntu4 [193 kB] 646s Get:34 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebpdemux2 arm64 1.5.0-0.1 [12.5 kB] 646s Get:35 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebpmux3 arm64 1.5.0-0.1 [25.4 kB] 646s Get:36 http://ftpmaster.internal/ubuntu plucky/universe arm64 imagemagick-7-common all 8:7.1.1.43+dfsg1-1 [69.7 kB] 646s Get:37 http://ftpmaster.internal/ubuntu plucky/universe arm64 libmagickcore-7.q16-10 arm64 8:7.1.1.43+dfsg1-1 [1876 kB] 646s Get:38 http://ftpmaster.internal/ubuntu plucky/universe arm64 libmagickwand-7.q16-10 arm64 8:7.1.1.43+dfsg1-1 [301 kB] 646s Get:39 http://ftpmaster.internal/ubuntu plucky/main arm64 poppler-data all 0.4.12-1 [2060 kB] 646s Get:40 http://ftpmaster.internal/ubuntu plucky/main arm64 sgml-base all 1.31 [11.4 kB] 646s Get:41 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.12 arm64 3.12.9-1 [671 kB] 646s Get:42 http://ftpmaster.internal/ubuntu plucky/main arm64 autoconf all 2.72-3 [382 kB] 646s Get:43 http://ftpmaster.internal/ubuntu plucky/main arm64 autotools-dev all 20220109.1 [44.9 kB] 646s Get:44 http://ftpmaster.internal/ubuntu plucky/main arm64 automake all 1:1.17-3 [572 kB] 646s Get:45 http://ftpmaster.internal/ubuntu plucky/main arm64 autopoint all 0.23.1-1 [619 kB] 646s Get:46 http://ftpmaster.internal/ubuntu plucky/main arm64 libtcl8.6 arm64 8.6.16+dfsg-1 [987 kB] 646s Get:47 http://ftpmaster.internal/ubuntu plucky/main arm64 libxrender1 arm64 1:0.9.10-1.1build1 [18.8 kB] 646s Get:48 http://ftpmaster.internal/ubuntu plucky/main arm64 libxft2 arm64 2.3.6-1build1 [44.1 kB] 646s Get:49 http://ftpmaster.internal/ubuntu plucky/main arm64 libxss1 arm64 1:1.2.3-1build3 [7244 B] 646s Get:50 http://ftpmaster.internal/ubuntu plucky/main arm64 libtk8.6 arm64 8.6.16-1 [776 kB] 646s Get:51 http://ftpmaster.internal/ubuntu plucky/main arm64 tk8.6-blt2.5 arm64 2.5.3+dfsg-7build1 [618 kB] 646s Get:52 http://ftpmaster.internal/ubuntu plucky/main arm64 blt arm64 2.5.3+dfsg-7build1 [4840 B] 646s Get:53 http://ftpmaster.internal/ubuntu plucky/main arm64 libisl23 arm64 0.27-1 [676 kB] 646s Get:54 http://ftpmaster.internal/ubuntu plucky/main arm64 libmpc3 arm64 1.3.1-1build2 [56.8 kB] 646s Get:55 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp-14-aarch64-linux-gnu arm64 14.2.0-17ubuntu1 [10.6 MB] 646s Get:56 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp-14 arm64 14.2.0-17ubuntu1 [1032 B] 646s Get:57 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp-aarch64-linux-gnu arm64 4:14.2.0-1ubuntu1 [5558 B] 646s Get:58 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp arm64 4:14.2.0-1ubuntu1 [22.4 kB] 646s Get:59 http://ftpmaster.internal/ubuntu plucky/main arm64 libcc1-0 arm64 15-20250213-1ubuntu1 [44.2 kB] 646s Get:60 http://ftpmaster.internal/ubuntu plucky/main arm64 libitm1 arm64 15-20250213-1ubuntu1 [28.0 kB] 646s Get:61 http://ftpmaster.internal/ubuntu plucky/main arm64 libasan8 arm64 15-20250213-1ubuntu1 [2928 kB] 646s Get:62 http://ftpmaster.internal/ubuntu plucky/main arm64 liblsan0 arm64 15-20250213-1ubuntu1 [1319 kB] 646s Get:63 http://ftpmaster.internal/ubuntu plucky/main arm64 libtsan2 arm64 15-20250213-1ubuntu1 [2695 kB] 646s Get:64 http://ftpmaster.internal/ubuntu plucky/main arm64 libubsan1 arm64 15-20250213-1ubuntu1 [1178 kB] 646s Get:65 http://ftpmaster.internal/ubuntu plucky/main arm64 libhwasan0 arm64 15-20250213-1ubuntu1 [1642 kB] 646s Get:66 http://ftpmaster.internal/ubuntu plucky/main arm64 libgcc-14-dev arm64 14.2.0-17ubuntu1 [2593 kB] 646s Get:67 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc-14-aarch64-linux-gnu arm64 14.2.0-17ubuntu1 [20.9 MB] 646s Get:68 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc-14 arm64 14.2.0-17ubuntu1 [526 kB] 646s Get:69 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc-aarch64-linux-gnu arm64 4:14.2.0-1ubuntu1 [1200 B] 646s Get:70 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc arm64 4:14.2.0-1ubuntu1 [4998 B] 646s Get:71 http://ftpmaster.internal/ubuntu plucky/main arm64 libstdc++-14-dev arm64 14.2.0-17ubuntu1 [2499 kB] 647s Get:72 http://ftpmaster.internal/ubuntu plucky/main arm64 g++-14-aarch64-linux-gnu arm64 14.2.0-17ubuntu1 [12.1 MB] 647s Get:73 http://ftpmaster.internal/ubuntu plucky/main arm64 g++-14 arm64 14.2.0-17ubuntu1 [21.8 kB] 647s Get:74 http://ftpmaster.internal/ubuntu plucky/main arm64 g++-aarch64-linux-gnu arm64 4:14.2.0-1ubuntu1 [956 B] 647s Get:75 http://ftpmaster.internal/ubuntu plucky/main arm64 g++ arm64 4:14.2.0-1ubuntu1 [1080 B] 647s Get:76 http://ftpmaster.internal/ubuntu plucky/main arm64 build-essential arm64 12.10ubuntu1 [4932 B] 647s Get:77 http://ftpmaster.internal/ubuntu plucky/universe arm64 bwa arm64 0.7.18-1 [201 kB] 647s Get:78 http://ftpmaster.internal/ubuntu plucky/universe arm64 libargtable2-0 arm64 13-3 [15.3 kB] 647s Get:79 http://ftpmaster.internal/ubuntu plucky/universe arm64 clustalo arm64 1.2.4-8build1 [190 kB] 647s Get:80 http://ftpmaster.internal/ubuntu plucky/main arm64 libdebhelper-perl all 13.24.1ubuntu2 [95.4 kB] 647s Get:81 http://ftpmaster.internal/ubuntu plucky/main arm64 libtool all 2.5.4-3build1 [168 kB] 647s Get:82 http://ftpmaster.internal/ubuntu plucky/main arm64 dh-autoreconf all 20 [16.1 kB] 647s Get:83 http://ftpmaster.internal/ubuntu plucky/main arm64 libarchive-zip-perl all 1.68-1 [90.2 kB] 647s Get:84 http://ftpmaster.internal/ubuntu plucky/main arm64 libfile-stripnondeterminism-perl all 1.14.1-2 [20.3 kB] 647s Get:85 http://ftpmaster.internal/ubuntu plucky/main arm64 dh-strip-nondeterminism all 1.14.1-2 [5064 B] 647s Get:86 http://ftpmaster.internal/ubuntu plucky/main arm64 debugedit arm64 1:5.1-2 [46.1 kB] 647s Get:87 http://ftpmaster.internal/ubuntu plucky/main arm64 dwz arm64 0.15-1build6 [113 kB] 647s Get:88 http://ftpmaster.internal/ubuntu plucky/main arm64 gettext arm64 0.23.1-1 [998 kB] 647s Get:89 http://ftpmaster.internal/ubuntu plucky/main arm64 intltool-debian all 0.35.0+20060710.6 [23.2 kB] 647s Get:90 http://ftpmaster.internal/ubuntu plucky/main arm64 po-debconf all 1.0.21+nmu1 [233 kB] 647s Get:91 http://ftpmaster.internal/ubuntu plucky/main arm64 debhelper all 13.24.1ubuntu2 [895 kB] 647s Get:92 http://ftpmaster.internal/ubuntu plucky/universe arm64 dh-python all 6.20250108 [117 kB] 647s Get:93 http://ftpmaster.internal/ubuntu plucky/universe arm64 dialign arm64 2.2.1-13 [152 kB] 647s Get:94 http://ftpmaster.internal/ubuntu plucky/main arm64 xml-core all 0.19 [20.3 kB] 647s Get:95 http://ftpmaster.internal/ubuntu plucky/main arm64 docutils-common all 0.21.2+dfsg-2 [131 kB] 647s Get:96 http://ftpmaster.internal/ubuntu plucky/universe arm64 libcifpp-data all 7.0.9-1 [481 kB] 647s Get:97 http://ftpmaster.internal/ubuntu plucky/universe arm64 libcifpp7 arm64 7.0.9-1 [997 kB] 647s Get:98 http://ftpmaster.internal/ubuntu plucky/universe arm64 dssp arm64 4.4.10-1 [753 kB] 647s Get:99 http://ftpmaster.internal/ubuntu plucky/main arm64 libimagequant0 arm64 2.18.0-1build1 [37.1 kB] 647s Get:100 http://ftpmaster.internal/ubuntu plucky/main arm64 libgraphite2-3 arm64 1.3.14-2ubuntu1 [70.6 kB] 647s Get:101 http://ftpmaster.internal/ubuntu plucky/main arm64 libharfbuzz0b arm64 10.2.0-1 [490 kB] 648s Get:102 http://ftpmaster.internal/ubuntu plucky/main arm64 libraqm0 arm64 0.10.2-1 [14.9 kB] 648s Get:103 http://ftpmaster.internal/ubuntu plucky/main arm64 libxpm4 arm64 1:3.5.17-1build2 [35.1 kB] 648s Get:104 http://ftpmaster.internal/ubuntu plucky/main arm64 libgd3 arm64 2.3.3-12ubuntu3 [122 kB] 648s Get:105 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhpdf-2.3.0 arm64 2.3.0+dfsg-1build3 [434 kB] 648s Get:106 http://ftpmaster.internal/ubuntu plucky/main arm64 mysql-common all 5.8+1.1.1 [6800 B] 648s Get:107 http://ftpmaster.internal/ubuntu plucky/main arm64 libmysqlclient21 arm64 8.0.40-1 [1241 kB] 648s Get:108 http://ftpmaster.internal/ubuntu plucky/main arm64 libpq5 arm64 17.3-3 [142 kB] 648s Get:109 http://ftpmaster.internal/ubuntu plucky/universe arm64 emboss-lib arm64 6.6.0+dfsg-12ubuntu2 [2853 kB] 648s Get:110 http://ftpmaster.internal/ubuntu plucky/universe arm64 emboss-data all 6.6.0+dfsg-12ubuntu2 [61.0 MB] 652s Get:111 http://ftpmaster.internal/ubuntu plucky/universe arm64 emboss arm64 6.6.0+dfsg-12ubuntu2 [934 kB] 652s Get:112 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB] 652s Get:113 http://ftpmaster.internal/ubuntu plucky/universe arm64 fonts-lmodern all 2.005-1 [4799 kB] 652s Get:114 http://ftpmaster.internal/ubuntu plucky/universe arm64 fonts-lyx all 2.4.3-1 [171 kB] 652s Get:115 http://ftpmaster.internal/ubuntu plucky/main arm64 libgs-common all 10.04.0~dfsg1-2ubuntu1 [176 kB] 652s Get:116 http://ftpmaster.internal/ubuntu plucky/main arm64 libgs10-common all 10.04.0~dfsg1-2ubuntu1 [488 kB] 652s Get:117 http://ftpmaster.internal/ubuntu plucky/main arm64 libavahi-common-data arm64 0.8-14ubuntu1 [30.5 kB] 652s Get:118 http://ftpmaster.internal/ubuntu plucky/main arm64 libavahi-common3 arm64 0.8-14ubuntu1 [23.1 kB] 652s Get:119 http://ftpmaster.internal/ubuntu plucky/main arm64 libavahi-client3 arm64 0.8-14ubuntu1 [27.3 kB] 652s Get:120 http://ftpmaster.internal/ubuntu plucky/main arm64 libcups2t64 arm64 2.4.11-0ubuntu2 [274 kB] 652s Get:121 http://ftpmaster.internal/ubuntu plucky/main arm64 libidn12 arm64 1.42-3 [56.2 kB] 652s Get:122 http://ftpmaster.internal/ubuntu plucky/main arm64 libijs-0.35 arm64 0.35-15.1build1 [15.3 kB] 652s Get:123 http://ftpmaster.internal/ubuntu plucky/main arm64 libjbig2dec0 arm64 0.20-1build3 [63.2 kB] 652s Get:124 http://ftpmaster.internal/ubuntu plucky/main arm64 libpaper2 arm64 2.2.5-0.3 [17.3 kB] 652s Get:125 http://ftpmaster.internal/ubuntu plucky/main arm64 libice6 arm64 2:1.1.1-1 [42.3 kB] 652s Get:126 http://ftpmaster.internal/ubuntu plucky/main arm64 libsm6 arm64 2:1.2.4-1 [16.4 kB] 652s Get:127 http://ftpmaster.internal/ubuntu plucky/main arm64 libxt6t64 arm64 1:1.2.1-1.2build1 [168 kB] 652s Get:128 http://ftpmaster.internal/ubuntu plucky/main arm64 libgs10 arm64 10.04.0~dfsg1-2ubuntu1 [3633 kB] 652s Get:129 http://ftpmaster.internal/ubuntu plucky/main arm64 ghostscript arm64 10.04.0~dfsg1-2ubuntu1 [43.9 kB] 652s Get:130 http://ftpmaster.internal/ubuntu plucky/universe arm64 libnetpbm11t64 arm64 2:11.09.02-2 [114 kB] 652s Get:131 http://ftpmaster.internal/ubuntu plucky/universe arm64 netpbm arm64 2:11.09.02-2 [2130 kB] 652s Get:132 http://ftpmaster.internal/ubuntu plucky/universe arm64 tex-common all 6.18 [32.8 kB] 652s Get:133 http://ftpmaster.internal/ubuntu plucky/main arm64 libpaper-utils arm64 2.2.5-0.3 [15.4 kB] 652s Get:134 http://ftpmaster.internal/ubuntu plucky/main arm64 libkpathsea6 arm64 2024.20240313.70630+ds-5build2 [64.3 kB] 652s Get:135 http://ftpmaster.internal/ubuntu plucky/main arm64 libptexenc1 arm64 2024.20240313.70630+ds-5build2 [41.7 kB] 652s Get:136 http://ftpmaster.internal/ubuntu plucky/main arm64 libsynctex2 arm64 2024.20240313.70630+ds-5build2 [60.3 kB] 652s Get:137 http://ftpmaster.internal/ubuntu plucky/main arm64 libtexlua53-5 arm64 2024.20240313.70630+ds-5build2 [122 kB] 652s Get:138 http://ftpmaster.internal/ubuntu plucky/main arm64 t1utils arm64 1.41-4build3 [61.0 kB] 652s Get:139 http://ftpmaster.internal/ubuntu plucky/main arm64 libpixman-1-0 arm64 0.44.0-3 [197 kB] 652s Get:140 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-render0 arm64 1.17.0-2 [16.6 kB] 652s Get:141 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-shm0 arm64 1.17.0-2 [5884 B] 652s Get:142 http://ftpmaster.internal/ubuntu plucky/main arm64 libcairo2 arm64 1.18.2-2 [560 kB] 652s Get:143 http://ftpmaster.internal/ubuntu plucky/universe arm64 libmpfi0 arm64 1.5.4+ds-4 [35.3 kB] 652s Get:144 http://ftpmaster.internal/ubuntu plucky/universe arm64 libpotrace0 arm64 1.16-2build1 [16.0 kB] 652s Get:145 http://ftpmaster.internal/ubuntu plucky/universe arm64 libteckit0 arm64 2.5.12+ds1-1 [405 kB] 652s Get:146 http://ftpmaster.internal/ubuntu plucky/main arm64 libxmu6 arm64 2:1.1.3-3build2 [47.5 kB] 652s Get:147 http://ftpmaster.internal/ubuntu plucky/main arm64 libxaw7 arm64 2:1.0.16-1 [184 kB] 652s Get:148 http://ftpmaster.internal/ubuntu plucky/main arm64 libxi6 arm64 2:1.8.2-1 [32.4 kB] 652s Get:149 http://ftpmaster.internal/ubuntu plucky/universe arm64 libzzip-0-13t64 arm64 0.13.72+dfsg.1-1.2build1 [29.2 kB] 652s Get:150 http://ftpmaster.internal/ubuntu plucky/universe arm64 texlive-binaries arm64 2024.20240313.70630+ds-5build2 [8328 kB] 653s Get:151 http://ftpmaster.internal/ubuntu plucky/main arm64 xdg-utils all 1.2.1-2ubuntu1 [66.0 kB] 653s Get:152 http://ftpmaster.internal/ubuntu plucky/universe arm64 texlive-base all 2024.20241115-1 [22.5 MB] 654s Get:153 http://ftpmaster.internal/ubuntu plucky/main arm64 hicolor-icon-theme all 0.18-2 [13.3 kB] 654s Get:154 http://ftpmaster.internal/ubuntu plucky/universe arm64 imagemagick-7.q16 arm64 8:7.1.1.43+dfsg1-1 [704 kB] 654s Get:155 http://ftpmaster.internal/ubuntu plucky/universe arm64 imagemagick arm64 8:7.1.1.43+dfsg1-1 [14.1 kB] 654s Get:156 http://ftpmaster.internal/ubuntu plucky/universe arm64 hevea arm64 2.36-2 [2333 kB] 654s Get:157 http://ftpmaster.internal/ubuntu plucky/main arm64 libsuitesparseconfig7 arm64 1:7.8.3+dfsg-3 [13.2 kB] 654s Get:158 http://ftpmaster.internal/ubuntu plucky/universe arm64 libamd3 arm64 1:7.8.3+dfsg-3 [26.1 kB] 654s Get:159 http://ftpmaster.internal/ubuntu plucky/universe arm64 libapache-pom-java all 33-2 [5874 B] 654s Get:160 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.1-2 [161 kB] 654s Get:161 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 15-20250213-1ubuntu1 [443 kB] 654s Get:162 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.1-2 [2307 kB] 654s Get:163 http://ftpmaster.internal/ubuntu plucky/universe arm64 libarpack2t64 arm64 3.9.1-4 [94.4 kB] 654s Get:164 http://ftpmaster.internal/ubuntu plucky/main arm64 libcolamd3 arm64 1:7.8.3+dfsg-3 [18.3 kB] 654s Get:165 http://ftpmaster.internal/ubuntu plucky/universe arm64 libcommons-parent-java all 56-1 [10.7 kB] 654s Get:166 http://ftpmaster.internal/ubuntu plucky/universe arm64 libcommons-logging-java all 1.3.0-1ubuntu1 [63.8 kB] 654s Get:167 http://ftpmaster.internal/ubuntu plucky/main arm64 libexpat1-dev arm64 2.6.4-1 [129 kB] 654s Get:168 http://ftpmaster.internal/ubuntu plucky/universe arm64 libglpk40 arm64 5.0-1build2 [337 kB] 654s Get:169 http://ftpmaster.internal/ubuntu plucky/universe arm64 libplfit0 arm64 0.9.4+ds-1ubuntu5 [35.5 kB] 654s Get:170 http://ftpmaster.internal/ubuntu plucky/universe arm64 libigraph3t64 arm64 0.10.15+ds-2 [895 kB] 654s Get:171 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 654s Get:172 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 654s Get:173 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 654s Get:174 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libjs-sphinxdoc all 8.1.3-5 [31.0 kB] 654s Get:175 http://ftpmaster.internal/ubuntu plucky/main arm64 libjson-perl all 4.10000-1 [81.9 kB] 654s Get:176 http://ftpmaster.internal/ubuntu plucky/universe arm64 liblbfgsb0 arm64 3.0+dfsg.4-1build1 [27.7 kB] 654s Get:177 http://ftpmaster.internal/ubuntu plucky/universe arm64 libmbedcrypto16 arm64 3.6.2-3ubuntu1 [258 kB] 654s Get:178 http://ftpmaster.internal/ubuntu plucky/universe arm64 libmbedx509-7 arm64 3.6.2-3ubuntu1 [35.7 kB] 654s Get:179 http://ftpmaster.internal/ubuntu plucky/universe arm64 libmbedtls21 arm64 3.6.2-3ubuntu1 [122 kB] 654s Get:180 http://ftpmaster.internal/ubuntu plucky/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1ubuntu1 [894 kB] 654s Get:181 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3.13-dev arm64 3.13.2-1 [5399 kB] 654s Get:182 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3-dev arm64 3.13.1-1~exp2 [10.5 kB] 654s Get:183 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3.12-dev arm64 3.12.9-1 [5569 kB] 655s Get:184 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3-all-dev arm64 3.13.1-1~exp2 [922 B] 655s Get:185 http://ftpmaster.internal/ubuntu plucky/universe arm64 libqhull-r8.0 arm64 2020.2-6build1 [189 kB] 655s Get:186 http://ftpmaster.internal/ubuntu plucky/main arm64 libxslt1.1 arm64 1.1.39-0exp1ubuntu2 [168 kB] 655s Get:187 http://ftpmaster.internal/ubuntu plucky/universe arm64 mafft arm64 7.505-1 [756 kB] 655s Get:188 http://ftpmaster.internal/ubuntu plucky/universe arm64 ncbi-data all 6.1.20170106+dfsg2-5 [3966 kB] 655s Get:189 http://ftpmaster.internal/ubuntu plucky/universe arm64 ncbi-blast+ arm64 2.16.0+ds-6build1 [14.8 MB] 655s Get:190 http://ftpmaster.internal/ubuntu plucky/universe arm64 phylip arm64 1:3.697+dfsg-4build1 [843 kB] 655s Get:191 http://ftpmaster.internal/ubuntu plucky/universe arm64 prank arm64 0.0.170427+dfsg-3 [325 kB] 655s Get:192 http://ftpmaster.internal/ubuntu plucky/universe arm64 preview-latex-style all 13.2-1 [347 kB] 655s Get:193 http://ftpmaster.internal/ubuntu plucky/universe arm64 probcons arm64 1.12-14 [129 kB] 655s Get:194 http://ftpmaster.internal/ubuntu plucky/universe arm64 python-biopython-doc all 1.85+dfsg-2 [18.2 MB] 656s Get:195 http://ftpmaster.internal/ubuntu plucky/universe arm64 python-matplotlib-data all 3.8.3-3ubuntu2 [2929 kB] 657s Get:196 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-all arm64 3.13.1-1~exp2 [894 B] 657s Get:197 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-dev arm64 3.13.2-1 [508 kB] 657s Get:198 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-dev arm64 3.13.1-1~exp2 [26.7 kB] 657s Get:199 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.12-dev arm64 3.12.9-1 [505 kB] 657s Get:200 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-all-dev arm64 3.13.1-1~exp2 [918 B] 657s Get:201 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy arm64 1:1.26.4+ds-13 [4148 kB] 657s Get:202 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.12-tk arm64 3.12.9-1 [115 kB] 657s Get:203 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-tk arm64 3.13.2-1 [106 kB] 657s Get:204 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-tk arm64 3.13.1-1 [9770 B] 658s Get:205 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pil.imagetk arm64 11.1.0-5 [9948 B] 658s Get:206 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-pil arm64 11.1.0-5 [491 kB] 658s Get:207 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-cairo arm64 1.26.1-2build1 [139 kB] 658s Get:208 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-freetype all 2.5.1-1 [92.3 kB] 658s Get:209 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-rlpycairo all 0.3.0-3 [9130 B] 658s Get:210 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-reportlab all 4.3.0-1 [1137 kB] 658s Get:211 http://ftpmaster.internal/ubuntu plucky/universe arm64 w3c-sgml-lib all 1.3-3 [280 kB] 658s Get:212 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-biopython arm64 1.85+dfsg-2 [1718 kB] 658s Get:213 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-biopython-sql all 1.85+dfsg-2 [26.4 kB] 658s Get:214 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-brotli arm64 1.1.0-2build3 [342 kB] 658s Get:215 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-contourpy arm64 1.3.1-1 [216 kB] 658s Get:216 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-cycler all 0.12.1-1 [9716 B] 658s Get:217 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-dateutil all 2.9.0-3 [80.2 kB] 658s Get:218 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-decorator all 5.1.1-5 [10.1 kB] 658s Get:219 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-defusedxml all 0.7.1-3 [42.2 kB] 658s Get:220 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-roman all 5.0-1 [10.3 kB] 658s Get:221 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-docutils all 0.21.2+dfsg-2 [409 kB] 658s Get:222 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-pytz all 2025.1-3 [162 kB] 658s Get:223 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-tz all 2025.1-3 [1866 B] 658s Get:224 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-platformdirs all 4.3.6-1 [16.8 kB] 658s Get:225 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-fs all 2.4.16-6 [90.7 kB] 658s Get:226 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-lxml arm64 5.3.1-1 [1600 kB] 658s Get:227 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-lz4 arm64 4.4.0+dfsg-1 [27.3 kB] 658s Get:228 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-scipy arm64 1.14.1-4ubuntu1 [19.5 MB] 660s Get:229 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-mpmath all 1.3.0-1 [425 kB] 660s Get:230 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-sympy all 1.13.3-1 [4228 kB] 660s Get:231 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-ufolib2 all 0.17.0+dfsg1-1 [33.5 kB] 660s Get:232 http://ftpmaster.internal/ubuntu plucky/universe arm64 unicode-data all 15.1.0-1 [8878 kB] 660s Get:233 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-fonttools arm64 4.55.3-2 [1615 kB] 660s Get:234 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-imagesize all 1.4.1-1 [6844 B] 660s Get:235 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-kiwisolver arm64 1.4.7-3 [62.5 kB] 660s Get:236 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-packaging all 24.2-1 [51.5 kB] 660s Get:237 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-matplotlib arm64 3.8.3-3ubuntu2 [4616 kB] 661s Get:238 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-msgpack arm64 1.0.3-3build3 [106 kB] 661s Get:239 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-mmtf all 1.1.3-1 [16.2 kB] 661s Get:240 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-mysqldb arm64 1.4.6-2build4 [50.0 kB] 661s Get:241 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-networkx all 3.2.1-4ubuntu1 [11.5 MB] 661s Get:242 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 sphinx-common all 8.1.3-5 [663 kB] 661s Get:243 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-alabaster all 0.7.16-0.1 [18.5 kB] 661s Get:244 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-snowballstemmer all 2.2.0-4build1 [59.8 kB] 661s Get:245 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-sphinx all 8.1.3-5 [474 kB] 661s Get:246 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-tabulate all 0.9.0-1 [45.3 kB] 661s Get:247 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-numpydoc all 1.8.0-1 [52.4 kB] 661s Get:248 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-rdflib all 7.1.1-2 [426 kB] 661s Get:249 http://ftpmaster.internal/ubuntu plucky/main arm64 sphinx-rtd-theme-common all 3.0.2+dfsg-2 [1014 kB] 661s Get:250 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-sphinxcontrib.jquery all 4.1-5 [6678 B] 661s Get:251 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-sphinx-rtd-theme all 3.0.2+dfsg-2 [23.5 kB] 661s Get:252 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-texttable all 1.7.0-1 [11.2 kB] 661s Get:253 http://ftpmaster.internal/ubuntu plucky/universe arm64 t-coffee arm64 13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 [879 kB] 661s Get:254 http://ftpmaster.internal/ubuntu plucky/universe arm64 texlive-fonts-recommended all 2024.20241115-1 [4973 kB] 661s Get:255 http://ftpmaster.internal/ubuntu plucky/universe arm64 texlive-latex-base all 2024.20241115-1 [1260 kB] 661s Get:256 http://ftpmaster.internal/ubuntu plucky/universe arm64 libfontbox-java all 1:1.8.16-5 [208 kB] 661s Get:257 http://ftpmaster.internal/ubuntu plucky/universe arm64 libpdfbox-java all 1:1.8.16-5 [5521 kB] 662s Get:258 http://ftpmaster.internal/ubuntu plucky/universe arm64 texlive-latex-recommended all 2024.20241115-1 [8739 kB] 662s Get:259 http://ftpmaster.internal/ubuntu plucky/universe arm64 texlive-pictures all 2024.20241115-1 [17.0 MB] 663s Get:260 http://ftpmaster.internal/ubuntu plucky/universe arm64 texlive-latex-extra all 2024.20250114-1 [24.3 MB] 663s Get:261 http://ftpmaster.internal/ubuntu plucky/universe arm64 wise-data all 2.4.1-25 [83.0 kB] 663s Get:262 http://ftpmaster.internal/ubuntu plucky/universe arm64 wise arm64 2.4.1-25 [802 kB] 663s Get:263 http://ftpmaster.internal/ubuntu plucky/universe arm64 fasttree arm64 2.1.11-2 [164 kB] 663s Get:264 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-igraph arm64 0.11.8+ds-1build1 [345 kB] 664s Preconfiguring packages ... 664s Fetched 405 MB in 20s (20.2 MB/s) 664s Selecting previously unselected package python3.12-minimal. 665s (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 ... 116670 files and directories currently installed.) 665s Preparing to unpack .../000-python3.12-minimal_3.12.9-1_arm64.deb ... 665s Unpacking python3.12-minimal (3.12.9-1) ... 665s Selecting previously unselected package m4. 665s Preparing to unpack .../001-m4_1.4.19-5_arm64.deb ... 665s Unpacking m4 (1.4.19-5) ... 665s Selecting previously unselected package flex. 665s Preparing to unpack .../002-flex_2.6.4-8.2build1_arm64.deb ... 665s Unpacking flex (2.6.4-8.2build1) ... 665s Selecting previously unselected package fonts-lato. 665s Preparing to unpack .../003-fonts-lato_2.015-1_all.deb ... 665s Unpacking fonts-lato (2.015-1) ... 665s Selecting previously unselected package libgomp1:arm64. 665s Preparing to unpack .../004-libgomp1_15-20250213-1ubuntu1_arm64.deb ... 665s Unpacking libgomp1:arm64 (15-20250213-1ubuntu1) ... 665s Selecting previously unselected package libfftw3-double3:arm64. 665s Preparing to unpack .../005-libfftw3-double3_3.3.10-2fakesync1build1_arm64.deb ... 665s Unpacking libfftw3-double3:arm64 (3.3.10-2fakesync1build1) ... 665s Selecting previously unselected package fonts-dejavu-mono. 665s Preparing to unpack .../006-fonts-dejavu-mono_2.37-8_all.deb ... 665s Unpacking fonts-dejavu-mono (2.37-8) ... 665s Selecting previously unselected package fonts-dejavu-core. 666s Preparing to unpack .../007-fonts-dejavu-core_2.37-8_all.deb ... 666s Unpacking fonts-dejavu-core (2.37-8) ... 666s Selecting previously unselected package libfontenc1:arm64. 666s Preparing to unpack .../008-libfontenc1_1%3a1.1.8-1build1_arm64.deb ... 666s Unpacking libfontenc1:arm64 (1:1.1.8-1build1) ... 666s Selecting previously unselected package x11-common. 666s Preparing to unpack .../009-x11-common_1%3a7.7+23ubuntu3_all.deb ... 666s Unpacking x11-common (1:7.7+23ubuntu3) ... 666s Selecting previously unselected package xfonts-encodings. 666s Preparing to unpack .../010-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 666s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 666s Selecting previously unselected package xfonts-utils. 666s Preparing to unpack .../011-xfonts-utils_1%3a7.7+7_arm64.deb ... 666s Unpacking xfonts-utils (1:7.7+7) ... 666s Selecting previously unselected package fonts-urw-base35. 666s Preparing to unpack .../012-fonts-urw-base35_20200910-8_all.deb ... 666s Unpacking fonts-urw-base35 (20200910-8) ... 666s Selecting previously unselected package fontconfig-config. 666s Preparing to unpack .../013-fontconfig-config_2.15.0-2ubuntu1_arm64.deb ... 666s Unpacking fontconfig-config (2.15.0-2ubuntu1) ... 666s Selecting previously unselected package libfontconfig1:arm64. 666s Preparing to unpack .../014-libfontconfig1_2.15.0-2ubuntu1_arm64.deb ... 666s Unpacking libfontconfig1:arm64 (2.15.0-2ubuntu1) ... 666s Selecting previously unselected package libsharpyuv0:arm64. 666s Preparing to unpack .../015-libsharpyuv0_1.5.0-0.1_arm64.deb ... 666s Unpacking libsharpyuv0:arm64 (1.5.0-0.1) ... 666s Selecting previously unselected package libaom3:arm64. 667s Preparing to unpack .../016-libaom3_3.12.0-1_arm64.deb ... 667s Unpacking libaom3:arm64 (3.12.0-1) ... 667s Selecting previously unselected package libheif-plugin-aomdec:arm64. 667s Preparing to unpack .../017-libheif-plugin-aomdec_1.19.5-1build1_arm64.deb ... 667s Unpacking libheif-plugin-aomdec:arm64 (1.19.5-1build1) ... 667s Selecting previously unselected package libde265-0:arm64. 667s Preparing to unpack .../018-libde265-0_1.0.15-1build4_arm64.deb ... 667s Unpacking libde265-0:arm64 (1.0.15-1build4) ... 667s Selecting previously unselected package libheif-plugin-libde265:arm64. 667s Preparing to unpack .../019-libheif-plugin-libde265_1.19.5-1build1_arm64.deb ... 667s Unpacking libheif-plugin-libde265:arm64 (1.19.5-1build1) ... 667s Selecting previously unselected package libheif1:arm64. 667s Preparing to unpack .../020-libheif1_1.19.5-1build1_arm64.deb ... 667s Unpacking libheif1:arm64 (1.19.5-1build1) ... 667s Selecting previously unselected package libjbig0:arm64. 667s Preparing to unpack .../021-libjbig0_2.1-6.1ubuntu2_arm64.deb ... 667s Unpacking libjbig0:arm64 (2.1-6.1ubuntu2) ... 667s Selecting previously unselected package libjpeg-turbo8:arm64. 667s Preparing to unpack .../022-libjpeg-turbo8_2.1.5-3ubuntu2_arm64.deb ... 667s Unpacking libjpeg-turbo8:arm64 (2.1.5-3ubuntu2) ... 667s Selecting previously unselected package libjpeg8:arm64. 667s Preparing to unpack .../023-libjpeg8_8c-2ubuntu11_arm64.deb ... 667s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 667s Selecting previously unselected package liblcms2-2:arm64. 667s Preparing to unpack .../024-liblcms2-2_2.16-2_arm64.deb ... 667s Unpacking liblcms2-2:arm64 (2.16-2) ... 667s Selecting previously unselected package liblqr-1-0:arm64. 667s Preparing to unpack .../025-liblqr-1-0_0.4.2-2.1build2_arm64.deb ... 667s Unpacking liblqr-1-0:arm64 (0.4.2-2.1build2) ... 667s Selecting previously unselected package libltdl7:arm64. 667s Preparing to unpack .../026-libltdl7_2.5.4-3build1_arm64.deb ... 667s Unpacking libltdl7:arm64 (2.5.4-3build1) ... 667s Selecting previously unselected package libopenjp2-7:arm64. 667s Preparing to unpack .../027-libopenjp2-7_2.5.0-2ubuntu3_arm64.deb ... 667s Unpacking libopenjp2-7:arm64 (2.5.0-2ubuntu3) ... 667s Selecting previously unselected package libraw23t64:arm64. 667s Preparing to unpack .../028-libraw23t64_0.21.3-1_arm64.deb ... 667s Unpacking libraw23t64:arm64 (0.21.3-1) ... 667s Selecting previously unselected package libdeflate0:arm64. 667s Preparing to unpack .../029-libdeflate0_1.23-1_arm64.deb ... 667s Unpacking libdeflate0:arm64 (1.23-1) ... 667s Selecting previously unselected package liblerc4:arm64. 667s Preparing to unpack .../030-liblerc4_4.0.0+ds-5ubuntu1_arm64.deb ... 667s Unpacking liblerc4:arm64 (4.0.0+ds-5ubuntu1) ... 667s Selecting previously unselected package libwebp7:arm64. 667s Preparing to unpack .../031-libwebp7_1.5.0-0.1_arm64.deb ... 667s Unpacking libwebp7:arm64 (1.5.0-0.1) ... 667s Selecting previously unselected package libtiff6:arm64. 667s Preparing to unpack .../032-libtiff6_4.5.1+git230720-4ubuntu4_arm64.deb ... 667s Unpacking libtiff6:arm64 (4.5.1+git230720-4ubuntu4) ... 667s Selecting previously unselected package libwebpdemux2:arm64. 667s Preparing to unpack .../033-libwebpdemux2_1.5.0-0.1_arm64.deb ... 667s Unpacking libwebpdemux2:arm64 (1.5.0-0.1) ... 667s Selecting previously unselected package libwebpmux3:arm64. 667s Preparing to unpack .../034-libwebpmux3_1.5.0-0.1_arm64.deb ... 667s Unpacking libwebpmux3:arm64 (1.5.0-0.1) ... 667s Selecting previously unselected package imagemagick-7-common. 668s Preparing to unpack .../035-imagemagick-7-common_8%3a7.1.1.43+dfsg1-1_all.deb ... 668s Unpacking imagemagick-7-common (8:7.1.1.43+dfsg1-1) ... 668s Selecting previously unselected package libmagickcore-7.q16-10:arm64. 668s Preparing to unpack .../036-libmagickcore-7.q16-10_8%3a7.1.1.43+dfsg1-1_arm64.deb ... 668s Unpacking libmagickcore-7.q16-10:arm64 (8:7.1.1.43+dfsg1-1) ... 668s Selecting previously unselected package libmagickwand-7.q16-10:arm64. 668s Preparing to unpack .../037-libmagickwand-7.q16-10_8%3a7.1.1.43+dfsg1-1_arm64.deb ... 668s Unpacking libmagickwand-7.q16-10:arm64 (8:7.1.1.43+dfsg1-1) ... 668s Selecting previously unselected package poppler-data. 668s Preparing to unpack .../038-poppler-data_0.4.12-1_all.deb ... 668s Unpacking poppler-data (0.4.12-1) ... 668s Selecting previously unselected package sgml-base. 668s Preparing to unpack .../039-sgml-base_1.31_all.deb ... 668s Unpacking sgml-base (1.31) ... 668s Selecting previously unselected package python3.12. 668s Preparing to unpack .../040-python3.12_3.12.9-1_arm64.deb ... 668s Unpacking python3.12 (3.12.9-1) ... 668s Selecting previously unselected package autoconf. 668s Preparing to unpack .../041-autoconf_2.72-3_all.deb ... 668s Unpacking autoconf (2.72-3) ... 668s Selecting previously unselected package autotools-dev. 668s Preparing to unpack .../042-autotools-dev_20220109.1_all.deb ... 668s Unpacking autotools-dev (20220109.1) ... 668s Selecting previously unselected package automake. 668s Preparing to unpack .../043-automake_1%3a1.17-3_all.deb ... 668s Unpacking automake (1:1.17-3) ... 668s Selecting previously unselected package autopoint. 668s Preparing to unpack .../044-autopoint_0.23.1-1_all.deb ... 668s Unpacking autopoint (0.23.1-1) ... 668s Selecting previously unselected package libtcl8.6:arm64. 668s Preparing to unpack .../045-libtcl8.6_8.6.16+dfsg-1_arm64.deb ... 668s Unpacking libtcl8.6:arm64 (8.6.16+dfsg-1) ... 668s Selecting previously unselected package libxrender1:arm64. 668s Preparing to unpack .../046-libxrender1_1%3a0.9.10-1.1build1_arm64.deb ... 668s Unpacking libxrender1:arm64 (1:0.9.10-1.1build1) ... 668s Selecting previously unselected package libxft2:arm64. 668s Preparing to unpack .../047-libxft2_2.3.6-1build1_arm64.deb ... 668s Unpacking libxft2:arm64 (2.3.6-1build1) ... 668s Selecting previously unselected package libxss1:arm64. 669s Preparing to unpack .../048-libxss1_1%3a1.2.3-1build3_arm64.deb ... 669s Unpacking libxss1:arm64 (1:1.2.3-1build3) ... 669s Selecting previously unselected package libtk8.6:arm64. 669s Preparing to unpack .../049-libtk8.6_8.6.16-1_arm64.deb ... 669s Unpacking libtk8.6:arm64 (8.6.16-1) ... 669s Selecting previously unselected package tk8.6-blt2.5. 669s Preparing to unpack .../050-tk8.6-blt2.5_2.5.3+dfsg-7build1_arm64.deb ... 669s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 669s Selecting previously unselected package blt. 669s Preparing to unpack .../051-blt_2.5.3+dfsg-7build1_arm64.deb ... 669s Unpacking blt (2.5.3+dfsg-7build1) ... 669s Selecting previously unselected package libisl23:arm64. 669s Preparing to unpack .../052-libisl23_0.27-1_arm64.deb ... 669s Unpacking libisl23:arm64 (0.27-1) ... 669s Selecting previously unselected package libmpc3:arm64. 669s Preparing to unpack .../053-libmpc3_1.3.1-1build2_arm64.deb ... 669s Unpacking libmpc3:arm64 (1.3.1-1build2) ... 669s Selecting previously unselected package cpp-14-aarch64-linux-gnu. 669s Preparing to unpack .../054-cpp-14-aarch64-linux-gnu_14.2.0-17ubuntu1_arm64.deb ... 669s Unpacking cpp-14-aarch64-linux-gnu (14.2.0-17ubuntu1) ... 669s Selecting previously unselected package cpp-14. 669s Preparing to unpack .../055-cpp-14_14.2.0-17ubuntu1_arm64.deb ... 669s Unpacking cpp-14 (14.2.0-17ubuntu1) ... 669s Selecting previously unselected package cpp-aarch64-linux-gnu. 669s Preparing to unpack .../056-cpp-aarch64-linux-gnu_4%3a14.2.0-1ubuntu1_arm64.deb ... 669s Unpacking cpp-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 669s Selecting previously unselected package cpp. 669s Preparing to unpack .../057-cpp_4%3a14.2.0-1ubuntu1_arm64.deb ... 669s Unpacking cpp (4:14.2.0-1ubuntu1) ... 669s Selecting previously unselected package libcc1-0:arm64. 669s Preparing to unpack .../058-libcc1-0_15-20250213-1ubuntu1_arm64.deb ... 669s Unpacking libcc1-0:arm64 (15-20250213-1ubuntu1) ... 669s Selecting previously unselected package libitm1:arm64. 669s Preparing to unpack .../059-libitm1_15-20250213-1ubuntu1_arm64.deb ... 669s Unpacking libitm1:arm64 (15-20250213-1ubuntu1) ... 669s Selecting previously unselected package libasan8:arm64. 669s Preparing to unpack .../060-libasan8_15-20250213-1ubuntu1_arm64.deb ... 669s Unpacking libasan8:arm64 (15-20250213-1ubuntu1) ... 670s Selecting previously unselected package liblsan0:arm64. 670s Preparing to unpack .../061-liblsan0_15-20250213-1ubuntu1_arm64.deb ... 670s Unpacking liblsan0:arm64 (15-20250213-1ubuntu1) ... 670s Selecting previously unselected package libtsan2:arm64. 670s Preparing to unpack .../062-libtsan2_15-20250213-1ubuntu1_arm64.deb ... 670s Unpacking libtsan2:arm64 (15-20250213-1ubuntu1) ... 670s Selecting previously unselected package libubsan1:arm64. 670s Preparing to unpack .../063-libubsan1_15-20250213-1ubuntu1_arm64.deb ... 670s Unpacking libubsan1:arm64 (15-20250213-1ubuntu1) ... 670s Selecting previously unselected package libhwasan0:arm64. 670s Preparing to unpack .../064-libhwasan0_15-20250213-1ubuntu1_arm64.deb ... 670s Unpacking libhwasan0:arm64 (15-20250213-1ubuntu1) ... 670s Selecting previously unselected package libgcc-14-dev:arm64. 670s Preparing to unpack .../065-libgcc-14-dev_14.2.0-17ubuntu1_arm64.deb ... 670s Unpacking libgcc-14-dev:arm64 (14.2.0-17ubuntu1) ... 670s Selecting previously unselected package gcc-14-aarch64-linux-gnu. 670s Preparing to unpack .../066-gcc-14-aarch64-linux-gnu_14.2.0-17ubuntu1_arm64.deb ... 670s Unpacking gcc-14-aarch64-linux-gnu (14.2.0-17ubuntu1) ... 670s Selecting previously unselected package gcc-14. 670s Preparing to unpack .../067-gcc-14_14.2.0-17ubuntu1_arm64.deb ... 670s Unpacking gcc-14 (14.2.0-17ubuntu1) ... 670s Selecting previously unselected package gcc-aarch64-linux-gnu. 671s Preparing to unpack .../068-gcc-aarch64-linux-gnu_4%3a14.2.0-1ubuntu1_arm64.deb ... 671s Unpacking gcc-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 671s Selecting previously unselected package gcc. 671s Preparing to unpack .../069-gcc_4%3a14.2.0-1ubuntu1_arm64.deb ... 671s Unpacking gcc (4:14.2.0-1ubuntu1) ... 671s Selecting previously unselected package libstdc++-14-dev:arm64. 671s Preparing to unpack .../070-libstdc++-14-dev_14.2.0-17ubuntu1_arm64.deb ... 671s Unpacking libstdc++-14-dev:arm64 (14.2.0-17ubuntu1) ... 671s Selecting previously unselected package g++-14-aarch64-linux-gnu. 671s Preparing to unpack .../071-g++-14-aarch64-linux-gnu_14.2.0-17ubuntu1_arm64.deb ... 671s Unpacking g++-14-aarch64-linux-gnu (14.2.0-17ubuntu1) ... 671s Selecting previously unselected package g++-14. 671s Preparing to unpack .../072-g++-14_14.2.0-17ubuntu1_arm64.deb ... 671s Unpacking g++-14 (14.2.0-17ubuntu1) ... 671s Selecting previously unselected package g++-aarch64-linux-gnu. 671s Preparing to unpack .../073-g++-aarch64-linux-gnu_4%3a14.2.0-1ubuntu1_arm64.deb ... 671s Unpacking g++-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 671s Selecting previously unselected package g++. 671s Preparing to unpack .../074-g++_4%3a14.2.0-1ubuntu1_arm64.deb ... 671s Unpacking g++ (4:14.2.0-1ubuntu1) ... 671s Selecting previously unselected package build-essential. 671s Preparing to unpack .../075-build-essential_12.10ubuntu1_arm64.deb ... 671s Unpacking build-essential (12.10ubuntu1) ... 671s Selecting previously unselected package bwa. 671s Preparing to unpack .../076-bwa_0.7.18-1_arm64.deb ... 671s Unpacking bwa (0.7.18-1) ... 671s Selecting previously unselected package libargtable2-0. 671s Preparing to unpack .../077-libargtable2-0_13-3_arm64.deb ... 671s Unpacking libargtable2-0 (13-3) ... 671s Selecting previously unselected package clustalo. 671s Preparing to unpack .../078-clustalo_1.2.4-8build1_arm64.deb ... 671s Unpacking clustalo (1.2.4-8build1) ... 671s Selecting previously unselected package libdebhelper-perl. 672s Preparing to unpack .../079-libdebhelper-perl_13.24.1ubuntu2_all.deb ... 672s Unpacking libdebhelper-perl (13.24.1ubuntu2) ... 672s Selecting previously unselected package libtool. 672s Preparing to unpack .../080-libtool_2.5.4-3build1_all.deb ... 672s Unpacking libtool (2.5.4-3build1) ... 672s Selecting previously unselected package dh-autoreconf. 672s Preparing to unpack .../081-dh-autoreconf_20_all.deb ... 672s Unpacking dh-autoreconf (20) ... 672s Selecting previously unselected package libarchive-zip-perl. 672s Preparing to unpack .../082-libarchive-zip-perl_1.68-1_all.deb ... 672s Unpacking libarchive-zip-perl (1.68-1) ... 672s Selecting previously unselected package libfile-stripnondeterminism-perl. 672s Preparing to unpack .../083-libfile-stripnondeterminism-perl_1.14.1-2_all.deb ... 672s Unpacking libfile-stripnondeterminism-perl (1.14.1-2) ... 672s Selecting previously unselected package dh-strip-nondeterminism. 672s Preparing to unpack .../084-dh-strip-nondeterminism_1.14.1-2_all.deb ... 672s Unpacking dh-strip-nondeterminism (1.14.1-2) ... 672s Selecting previously unselected package debugedit. 672s Preparing to unpack .../085-debugedit_1%3a5.1-2_arm64.deb ... 672s Unpacking debugedit (1:5.1-2) ... 672s Selecting previously unselected package dwz. 672s Preparing to unpack .../086-dwz_0.15-1build6_arm64.deb ... 672s Unpacking dwz (0.15-1build6) ... 672s Selecting previously unselected package gettext. 672s Preparing to unpack .../087-gettext_0.23.1-1_arm64.deb ... 672s Unpacking gettext (0.23.1-1) ... 672s Selecting previously unselected package intltool-debian. 672s Preparing to unpack .../088-intltool-debian_0.35.0+20060710.6_all.deb ... 672s Unpacking intltool-debian (0.35.0+20060710.6) ... 672s Selecting previously unselected package po-debconf. 672s Preparing to unpack .../089-po-debconf_1.0.21+nmu1_all.deb ... 672s Unpacking po-debconf (1.0.21+nmu1) ... 672s Selecting previously unselected package debhelper. 672s Preparing to unpack .../090-debhelper_13.24.1ubuntu2_all.deb ... 672s Unpacking debhelper (13.24.1ubuntu2) ... 673s Selecting previously unselected package dh-python. 673s Preparing to unpack .../091-dh-python_6.20250108_all.deb ... 673s Unpacking dh-python (6.20250108) ... 673s Selecting previously unselected package dialign. 673s Preparing to unpack .../092-dialign_2.2.1-13_arm64.deb ... 673s Unpacking dialign (2.2.1-13) ... 673s Selecting previously unselected package xml-core. 673s Preparing to unpack .../093-xml-core_0.19_all.deb ... 673s Unpacking xml-core (0.19) ... 673s Selecting previously unselected package docutils-common. 673s Preparing to unpack .../094-docutils-common_0.21.2+dfsg-2_all.deb ... 673s Unpacking docutils-common (0.21.2+dfsg-2) ... 673s Selecting previously unselected package libcifpp-data. 673s Preparing to unpack .../095-libcifpp-data_7.0.9-1_all.deb ... 673s Unpacking libcifpp-data (7.0.9-1) ... 673s Selecting previously unselected package libcifpp7:arm64. 673s Preparing to unpack .../096-libcifpp7_7.0.9-1_arm64.deb ... 673s Unpacking libcifpp7:arm64 (7.0.9-1) ... 673s Selecting previously unselected package dssp. 673s Preparing to unpack .../097-dssp_4.4.10-1_arm64.deb ... 673s Unpacking dssp (4.4.10-1) ... 673s Selecting previously unselected package libimagequant0:arm64. 673s Preparing to unpack .../098-libimagequant0_2.18.0-1build1_arm64.deb ... 673s Unpacking libimagequant0:arm64 (2.18.0-1build1) ... 673s Selecting previously unselected package libgraphite2-3:arm64. 673s Preparing to unpack .../099-libgraphite2-3_1.3.14-2ubuntu1_arm64.deb ... 673s Unpacking libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 673s Selecting previously unselected package libharfbuzz0b:arm64. 673s Preparing to unpack .../100-libharfbuzz0b_10.2.0-1_arm64.deb ... 673s Unpacking libharfbuzz0b:arm64 (10.2.0-1) ... 673s Selecting previously unselected package libraqm0:arm64. 673s Preparing to unpack .../101-libraqm0_0.10.2-1_arm64.deb ... 673s Unpacking libraqm0:arm64 (0.10.2-1) ... 673s Selecting previously unselected package libxpm4:arm64. 673s Preparing to unpack .../102-libxpm4_1%3a3.5.17-1build2_arm64.deb ... 673s Unpacking libxpm4:arm64 (1:3.5.17-1build2) ... 673s Selecting previously unselected package libgd3:arm64. 673s Preparing to unpack .../103-libgd3_2.3.3-12ubuntu3_arm64.deb ... 673s Unpacking libgd3:arm64 (2.3.3-12ubuntu3) ... 673s Selecting previously unselected package libhpdf-2.3.0:arm64. 673s Preparing to unpack .../104-libhpdf-2.3.0_2.3.0+dfsg-1build3_arm64.deb ... 673s Unpacking libhpdf-2.3.0:arm64 (2.3.0+dfsg-1build3) ... 673s Selecting previously unselected package mysql-common. 673s Preparing to unpack .../105-mysql-common_5.8+1.1.1_all.deb ... 673s Unpacking mysql-common (5.8+1.1.1) ... 673s Selecting previously unselected package libmysqlclient21:arm64. 673s Preparing to unpack .../106-libmysqlclient21_8.0.40-1_arm64.deb ... 673s Unpacking libmysqlclient21:arm64 (8.0.40-1) ... 674s Selecting previously unselected package libpq5:arm64. 674s Preparing to unpack .../107-libpq5_17.3-3_arm64.deb ... 674s Unpacking libpq5:arm64 (17.3-3) ... 674s Selecting previously unselected package emboss-lib. 674s Preparing to unpack .../108-emboss-lib_6.6.0+dfsg-12ubuntu2_arm64.deb ... 674s Unpacking emboss-lib (6.6.0+dfsg-12ubuntu2) ... 674s Selecting previously unselected package emboss-data. 674s Preparing to unpack .../109-emboss-data_6.6.0+dfsg-12ubuntu2_all.deb ... 674s Unpacking emboss-data (6.6.0+dfsg-12ubuntu2) ... 677s Selecting previously unselected package emboss. 677s Preparing to unpack .../110-emboss_6.6.0+dfsg-12ubuntu2_arm64.deb ... 677s Unpacking emboss (6.6.0+dfsg-12ubuntu2) ... 677s Selecting previously unselected package fonts-font-awesome. 677s Preparing to unpack .../111-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ... 678s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 678s Selecting previously unselected package fonts-lmodern. 678s Preparing to unpack .../112-fonts-lmodern_2.005-1_all.deb ... 678s Unpacking fonts-lmodern (2.005-1) ... 678s Selecting previously unselected package fonts-lyx. 678s Preparing to unpack .../113-fonts-lyx_2.4.3-1_all.deb ... 678s Unpacking fonts-lyx (2.4.3-1) ... 678s Selecting previously unselected package libgs-common. 678s Preparing to unpack .../114-libgs-common_10.04.0~dfsg1-2ubuntu1_all.deb ... 678s Unpacking libgs-common (10.04.0~dfsg1-2ubuntu1) ... 678s Selecting previously unselected package libgs10-common. 678s Preparing to unpack .../115-libgs10-common_10.04.0~dfsg1-2ubuntu1_all.deb ... 678s Unpacking libgs10-common (10.04.0~dfsg1-2ubuntu1) ... 678s Selecting previously unselected package libavahi-common-data:arm64. 678s Preparing to unpack .../116-libavahi-common-data_0.8-14ubuntu1_arm64.deb ... 678s Unpacking libavahi-common-data:arm64 (0.8-14ubuntu1) ... 678s Selecting previously unselected package libavahi-common3:arm64. 678s Preparing to unpack .../117-libavahi-common3_0.8-14ubuntu1_arm64.deb ... 678s Unpacking libavahi-common3:arm64 (0.8-14ubuntu1) ... 678s Selecting previously unselected package libavahi-client3:arm64. 678s Preparing to unpack .../118-libavahi-client3_0.8-14ubuntu1_arm64.deb ... 678s Unpacking libavahi-client3:arm64 (0.8-14ubuntu1) ... 678s Selecting previously unselected package libcups2t64:arm64. 678s Preparing to unpack .../119-libcups2t64_2.4.11-0ubuntu2_arm64.deb ... 678s Unpacking libcups2t64:arm64 (2.4.11-0ubuntu2) ... 678s Selecting previously unselected package libidn12:arm64. 678s Preparing to unpack .../120-libidn12_1.42-3_arm64.deb ... 678s Unpacking libidn12:arm64 (1.42-3) ... 678s Selecting previously unselected package libijs-0.35:arm64. 678s Preparing to unpack .../121-libijs-0.35_0.35-15.1build1_arm64.deb ... 678s Unpacking libijs-0.35:arm64 (0.35-15.1build1) ... 678s Selecting previously unselected package libjbig2dec0:arm64. 678s Preparing to unpack .../122-libjbig2dec0_0.20-1build3_arm64.deb ... 678s Unpacking libjbig2dec0:arm64 (0.20-1build3) ... 678s Selecting previously unselected package libpaper2:arm64. 678s Preparing to unpack .../123-libpaper2_2.2.5-0.3_arm64.deb ... 678s Unpacking libpaper2:arm64 (2.2.5-0.3) ... 678s Selecting previously unselected package libice6:arm64. 678s Preparing to unpack .../124-libice6_2%3a1.1.1-1_arm64.deb ... 678s Unpacking libice6:arm64 (2:1.1.1-1) ... 678s Selecting previously unselected package libsm6:arm64. 678s Preparing to unpack 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Unpacking netpbm (2:11.09.02-2) ... 679s Selecting previously unselected package tex-common. 679s Preparing to unpack .../131-tex-common_6.18_all.deb ... 679s Unpacking tex-common (6.18) ... 679s Selecting previously unselected package libpaper-utils. 679s Preparing to unpack .../132-libpaper-utils_2.2.5-0.3_arm64.deb ... 679s Unpacking libpaper-utils (2.2.5-0.3) ... 679s Selecting previously unselected package libkpathsea6:arm64. 679s Preparing to unpack .../133-libkpathsea6_2024.20240313.70630+ds-5build2_arm64.deb ... 679s Unpacking libkpathsea6:arm64 (2024.20240313.70630+ds-5build2) ... 679s Selecting previously unselected package libptexenc1:arm64. 679s Preparing to unpack .../134-libptexenc1_2024.20240313.70630+ds-5build2_arm64.deb ... 679s Unpacking libptexenc1:arm64 (2024.20240313.70630+ds-5build2) ... 679s Selecting previously unselected package libsynctex2:arm64. 679s Preparing to unpack .../135-libsynctex2_2024.20240313.70630+ds-5build2_arm64.deb ... 679s Unpacking libsynctex2:arm64 (2024.20240313.70630+ds-5build2) ... 679s Selecting previously unselected package libtexlua53-5:arm64. 679s Preparing to unpack .../136-libtexlua53-5_2024.20240313.70630+ds-5build2_arm64.deb ... 679s Unpacking libtexlua53-5:arm64 (2024.20240313.70630+ds-5build2) ... 679s Selecting previously unselected package t1utils. 679s Preparing to unpack .../137-t1utils_1.41-4build3_arm64.deb ... 679s Unpacking t1utils (1.41-4build3) ... 679s Selecting previously unselected package libpixman-1-0:arm64. 679s Preparing to unpack .../138-libpixman-1-0_0.44.0-3_arm64.deb ... 679s Unpacking libpixman-1-0:arm64 (0.44.0-3) ... 679s Selecting previously unselected package libxcb-render0:arm64. 679s Preparing to unpack .../139-libxcb-render0_1.17.0-2_arm64.deb ... 679s Unpacking libxcb-render0:arm64 (1.17.0-2) ... 680s Selecting previously unselected package libxcb-shm0:arm64. 680s Preparing to unpack .../140-libxcb-shm0_1.17.0-2_arm64.deb ... 680s Unpacking libxcb-shm0:arm64 (1.17.0-2) ... 680s Selecting previously unselected package libcairo2:arm64. 680s Preparing to unpack .../141-libcairo2_1.18.2-2_arm64.deb ... 680s Unpacking libcairo2:arm64 (1.18.2-2) ... 680s Selecting previously unselected package libmpfi0:arm64. 680s Preparing to unpack .../142-libmpfi0_1.5.4+ds-4_arm64.deb ... 680s Unpacking libmpfi0:arm64 (1.5.4+ds-4) ... 680s Selecting previously unselected package libpotrace0:arm64. 680s Preparing to unpack .../143-libpotrace0_1.16-2build1_arm64.deb ... 680s Unpacking libpotrace0:arm64 (1.16-2build1) ... 680s Selecting previously unselected package libteckit0:arm64. 680s Preparing to unpack .../144-libteckit0_2.5.12+ds1-1_arm64.deb ... 680s Unpacking libteckit0:arm64 (2.5.12+ds1-1) ... 680s Selecting previously unselected package libxmu6:arm64. 680s Preparing to unpack .../145-libxmu6_2%3a1.1.3-3build2_arm64.deb ... 680s Unpacking libxmu6:arm64 (2:1.1.3-3build2) ... 680s Selecting previously unselected package libxaw7:arm64. 680s Preparing to unpack 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libsuitesparseconfig7:arm64 (1:7.8.3+dfsg-3) ... 682s Selecting previously unselected package libamd3:arm64. 682s Preparing to unpack .../157-libamd3_1%3a7.8.3+dfsg-3_arm64.deb ... 682s Unpacking libamd3:arm64 (1:7.8.3+dfsg-3) ... 682s Selecting previously unselected package libapache-pom-java. 682s Preparing to unpack .../158-libapache-pom-java_33-2_all.deb ... 682s Unpacking libapache-pom-java (33-2) ... 682s Selecting previously unselected package libblas3:arm64. 682s Preparing to unpack .../159-libblas3_3.12.1-2_arm64.deb ... 682s Unpacking libblas3:arm64 (3.12.1-2) ... 682s Selecting previously unselected package libgfortran5:arm64. 682s Preparing to unpack .../160-libgfortran5_15-20250213-1ubuntu1_arm64.deb ... 682s Unpacking libgfortran5:arm64 (15-20250213-1ubuntu1) ... 682s Selecting previously unselected package liblapack3:arm64. 682s Preparing to unpack .../161-liblapack3_3.12.1-2_arm64.deb ... 682s Unpacking liblapack3:arm64 (3.12.1-2) ... 682s Selecting previously unselected package libarpack2t64:arm64. 682s Preparing to unpack .../162-libarpack2t64_3.9.1-4_arm64.deb ... 682s Unpacking libarpack2t64:arm64 (3.9.1-4) ... 682s Selecting previously unselected package libcolamd3:arm64. 682s Preparing to unpack .../163-libcolamd3_1%3a7.8.3+dfsg-3_arm64.deb ... 682s Unpacking libcolamd3:arm64 (1:7.8.3+dfsg-3) ... 682s Selecting previously unselected package libcommons-parent-java. 682s Preparing to unpack .../164-libcommons-parent-java_56-1_all.deb ... 682s Unpacking libcommons-parent-java (56-1) ... 682s Selecting previously unselected package libcommons-logging-java. 682s Preparing to unpack .../165-libcommons-logging-java_1.3.0-1ubuntu1_all.deb ... 683s Unpacking libcommons-logging-java (1.3.0-1ubuntu1) ... 683s Selecting previously unselected package libexpat1-dev:arm64. 683s Preparing to unpack .../166-libexpat1-dev_2.6.4-1_arm64.deb ... 683s Unpacking libexpat1-dev:arm64 (2.6.4-1) ... 683s Selecting previously unselected package libglpk40:arm64. 683s Preparing to unpack .../167-libglpk40_5.0-1build2_arm64.deb ... 683s Unpacking libglpk40:arm64 (5.0-1build2) ... 683s Selecting previously unselected package libplfit0:arm64. 683s Preparing to unpack .../168-libplfit0_0.9.4+ds-1ubuntu5_arm64.deb ... 683s Unpacking libplfit0:arm64 (0.9.4+ds-1ubuntu5) ... 683s Selecting previously unselected package libigraph3t64:arm64. 683s Preparing to unpack .../169-libigraph3t64_0.10.15+ds-2_arm64.deb ... 683s Unpacking libigraph3t64:arm64 (0.10.15+ds-2) ... 683s Selecting previously unselected package libjs-jquery. 683s Preparing to unpack .../170-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 683s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 683s Selecting previously unselected package libjs-jquery-ui. 683s Preparing to unpack .../171-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... 683s Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... 683s Selecting previously unselected package libjs-underscore. 683s Preparing to unpack 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.../177-libmbedx509-7_3.6.2-3ubuntu1_arm64.deb ... 683s Unpacking libmbedx509-7:arm64 (3.6.2-3ubuntu1) ... 683s Selecting previously unselected package libmbedtls21:arm64. 683s Preparing to unpack .../178-libmbedtls21_3.6.2-3ubuntu1_arm64.deb ... 683s Unpacking libmbedtls21:arm64 (3.6.2-3ubuntu1) ... 683s Selecting previously unselected package zlib1g-dev:arm64. 683s Preparing to unpack .../179-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1ubuntu1_arm64.deb ... 683s Unpacking zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 683s Selecting previously unselected package libpython3.13-dev:arm64. 683s Preparing to unpack .../180-libpython3.13-dev_3.13.2-1_arm64.deb ... 683s Unpacking libpython3.13-dev:arm64 (3.13.2-1) ... 684s Selecting previously unselected package libpython3-dev:arm64. 684s Preparing to unpack .../181-libpython3-dev_3.13.1-1~exp2_arm64.deb ... 684s Unpacking libpython3-dev:arm64 (3.13.1-1~exp2) ... 684s Selecting previously unselected package libpython3.12-dev:arm64. 684s Preparing to unpack .../182-libpython3.12-dev_3.12.9-1_arm64.deb ... 684s Unpacking libpython3.12-dev:arm64 (3.12.9-1) ... 684s Selecting previously unselected package libpython3-all-dev:arm64. 684s Preparing to unpack .../183-libpython3-all-dev_3.13.1-1~exp2_arm64.deb ... 684s Unpacking libpython3-all-dev:arm64 (3.13.1-1~exp2) ... 684s Selecting previously unselected package libqhull-r8.0:arm64. 684s Preparing to unpack .../184-libqhull-r8.0_2020.2-6build1_arm64.deb ... 684s Unpacking libqhull-r8.0:arm64 (2020.2-6build1) ... 684s Selecting previously unselected package libxslt1.1:arm64. 684s Preparing to unpack .../185-libxslt1.1_1.1.39-0exp1ubuntu2_arm64.deb ... 684s Unpacking libxslt1.1:arm64 (1.1.39-0exp1ubuntu2) ... 684s Selecting previously unselected package mafft. 684s Preparing to unpack .../186-mafft_7.505-1_arm64.deb ... 684s Unpacking mafft (7.505-1) ... 684s Selecting previously unselected package ncbi-data. 684s Preparing to unpack .../187-ncbi-data_6.1.20170106+dfsg2-5_all.deb ... 684s Unpacking ncbi-data (6.1.20170106+dfsg2-5) ... 684s Selecting previously unselected package ncbi-blast+. 684s Preparing to unpack .../188-ncbi-blast+_2.16.0+ds-6build1_arm64.deb ... 684s Unpacking ncbi-blast+ (2.16.0+ds-6build1) ... 685s Selecting previously unselected package phylip. 685s Preparing to unpack .../189-phylip_1%3a3.697+dfsg-4build1_arm64.deb ... 685s Unpacking phylip (1:3.697+dfsg-4build1) ... 685s Selecting previously unselected package prank. 685s Preparing to unpack .../190-prank_0.0.170427+dfsg-3_arm64.deb ... 685s Unpacking prank (0.0.170427+dfsg-3) ... 685s Selecting previously unselected package preview-latex-style. 685s Preparing to unpack .../191-preview-latex-style_13.2-1_all.deb ... 685s Unpacking preview-latex-style (13.2-1) ... 685s Selecting previously unselected package probcons. 685s Preparing to unpack .../192-probcons_1.12-14_arm64.deb ... 685s Unpacking probcons (1.12-14) ... 685s Selecting previously unselected package python-biopython-doc. 685s Preparing to unpack .../193-python-biopython-doc_1.85+dfsg-2_all.deb ... 685s Unpacking python-biopython-doc (1.85+dfsg-2) ... 685s Selecting previously unselected package python-matplotlib-data. 685s Preparing to unpack .../194-python-matplotlib-data_3.8.3-3ubuntu2_all.deb ... 685s Unpacking python-matplotlib-data (3.8.3-3ubuntu2) ... 686s Selecting previously unselected package python3-all. 686s Preparing to unpack .../195-python3-all_3.13.1-1~exp2_arm64.deb ... 686s Unpacking python3-all (3.13.1-1~exp2) ... 686s Selecting previously unselected package python3.13-dev. 686s Preparing to unpack .../196-python3.13-dev_3.13.2-1_arm64.deb ... 686s Unpacking python3.13-dev (3.13.2-1) ... 686s Selecting previously unselected package python3-dev. 686s Preparing to unpack .../197-python3-dev_3.13.1-1~exp2_arm64.deb ... 686s Unpacking python3-dev (3.13.1-1~exp2) ... 686s Selecting previously unselected package python3.12-dev. 686s Preparing to unpack .../198-python3.12-dev_3.12.9-1_arm64.deb ... 686s Unpacking python3.12-dev (3.12.9-1) ... 686s Selecting previously unselected package python3-all-dev. 686s Preparing to unpack .../199-python3-all-dev_3.13.1-1~exp2_arm64.deb ... 686s Unpacking python3-all-dev (3.13.1-1~exp2) ... 686s Selecting previously unselected package python3-numpy. 686s Preparing to unpack .../200-python3-numpy_1%3a1.26.4+ds-13_arm64.deb ... 686s Unpacking python3-numpy (1:1.26.4+ds-13) ... 686s Selecting previously unselected package python3.12-tk. 686s Preparing to unpack .../201-python3.12-tk_3.12.9-1_arm64.deb ... 686s Unpacking python3.12-tk (3.12.9-1) ... 686s Selecting previously unselected package python3.13-tk. 686s Preparing to unpack .../202-python3.13-tk_3.13.2-1_arm64.deb ... 686s Unpacking python3.13-tk (3.13.2-1) ... 686s Selecting previously unselected package python3-tk:arm64. 686s Preparing to unpack .../203-python3-tk_3.13.1-1_arm64.deb ... 686s Unpacking python3-tk:arm64 (3.13.1-1) ... 686s Selecting previously unselected package python3-pil.imagetk:arm64. 686s Preparing to unpack .../204-python3-pil.imagetk_11.1.0-5_arm64.deb ... 686s Unpacking python3-pil.imagetk:arm64 (11.1.0-5) ... 686s Selecting previously unselected package python3-pil:arm64. 686s Preparing to unpack .../205-python3-pil_11.1.0-5_arm64.deb ... 686s Unpacking python3-pil:arm64 (11.1.0-5) ... 686s Selecting previously unselected package python3-cairo. 686s Preparing to unpack .../206-python3-cairo_1.26.1-2build1_arm64.deb ... 686s Unpacking python3-cairo (1.26.1-2build1) ... 686s Selecting previously unselected package python3-freetype. 686s Preparing to unpack .../207-python3-freetype_2.5.1-1_all.deb ... 686s Unpacking python3-freetype (2.5.1-1) ... 686s Selecting previously unselected package python3-rlpycairo. 687s Preparing to unpack .../208-python3-rlpycairo_0.3.0-3_all.deb ... 687s Unpacking python3-rlpycairo (0.3.0-3) ... 687s Selecting previously unselected package python3-reportlab. 687s Preparing to unpack .../209-python3-reportlab_4.3.0-1_all.deb ... 687s Unpacking python3-reportlab (4.3.0-1) ... 687s Selecting previously unselected package w3c-sgml-lib. 687s Preparing to unpack .../210-w3c-sgml-lib_1.3-3_all.deb ... 687s Unpacking w3c-sgml-lib (1.3-3) ... 687s Selecting previously unselected package python3-biopython. 687s Preparing to unpack .../211-python3-biopython_1.85+dfsg-2_arm64.deb ... 687s Unpacking python3-biopython (1.85+dfsg-2) ... 687s Selecting previously unselected package python3-biopython-sql. 687s Preparing to unpack .../212-python3-biopython-sql_1.85+dfsg-2_all.deb ... 687s Unpacking python3-biopython-sql (1.85+dfsg-2) ... 687s Selecting previously unselected package python3-brotli. 687s Preparing to unpack .../213-python3-brotli_1.1.0-2build3_arm64.deb ... 687s Unpacking python3-brotli (1.1.0-2build3) ... 687s Selecting previously unselected package python3-contourpy. 687s Preparing to unpack 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previously unselected package python3-docutils. 687s Preparing to unpack .../220-python3-docutils_0.21.2+dfsg-2_all.deb ... 687s Unpacking python3-docutils (0.21.2+dfsg-2) ... 688s Selecting previously unselected package python3-pytz. 688s Preparing to unpack .../221-python3-pytz_2025.1-3_all.deb ... 688s Unpacking python3-pytz (2025.1-3) ... 688s Selecting previously unselected package python3-tz. 688s Preparing to unpack .../222-python3-tz_2025.1-3_all.deb ... 688s Unpacking python3-tz (2025.1-3) ... 688s Selecting previously unselected package python3-platformdirs. 688s Preparing to unpack .../223-python3-platformdirs_4.3.6-1_all.deb ... 688s Unpacking python3-platformdirs (4.3.6-1) ... 688s Selecting previously unselected package python3-fs. 688s Preparing to unpack .../224-python3-fs_2.4.16-6_all.deb ... 688s Unpacking python3-fs (2.4.16-6) ... 688s Selecting previously unselected package python3-lxml:arm64. 688s Preparing to unpack .../225-python3-lxml_5.3.1-1_arm64.deb ... 688s 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Unpacking python3-matplotlib (3.8.3-3ubuntu2) ... 690s Selecting previously unselected package python3-msgpack. 690s Preparing to unpack .../237-python3-msgpack_1.0.3-3build3_arm64.deb ... 690s Unpacking python3-msgpack (1.0.3-3build3) ... 691s Selecting previously unselected package python3-mmtf. 691s Preparing to unpack .../238-python3-mmtf_1.1.3-1_all.deb ... 691s Unpacking python3-mmtf (1.1.3-1) ... 691s Selecting previously unselected package python3-mysqldb. 691s Preparing to unpack .../239-python3-mysqldb_1.4.6-2build4_arm64.deb ... 691s Unpacking python3-mysqldb (1.4.6-2build4) ... 691s Selecting previously unselected package python3-networkx. 691s Preparing to unpack .../240-python3-networkx_3.2.1-4ubuntu1_all.deb ... 691s Unpacking python3-networkx (3.2.1-4ubuntu1) ... 691s Selecting previously unselected package sphinx-common. 691s Preparing to unpack .../241-sphinx-common_8.1.3-5_all.deb ... 691s Unpacking sphinx-common (8.1.3-5) ... 691s Selecting previously unselected 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(2.6.4-8.2build1) ... 727s Setting up liblapack3:arm64 (3.12.1-2) ... 727s 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 727s Setting up gettext (0.23.1-1) ... 727s Setting up libarpack2t64:arm64 (3.9.1-4) ... 727s Setting up libamd3:arm64 (1:7.8.3+dfsg-3) ... 727s Setting up libpdfbox-java (1:1.8.16-5) ... 727s Setting up libcolamd3:arm64 (1:7.8.3+dfsg-3) ... 727s Setting up fontconfig-config (2.15.0-2ubuntu1) ... 728s Setting up wise (2.4.1-25) ... 728s Setting up preview-latex-style (13.2-1) ... 728s Setting up libwebpdemux2:arm64 (1.5.0-0.1) ... 728s Setting up libcommons-parent-java (56-1) ... 728s Setting up libavahi-common3:arm64 (0.8-14ubuntu1) ... 728s Setting up libcommons-logging-java (1.3.0-1ubuntu1) ... 728s Setting up libcifpp7:arm64 (7.0.9-1) ... 728s Setting up libpython3.12-dev:arm64 (3.12.9-1) ... 728s Setting up libpaper-utils (2.2.5-0.3) ... 728s Setting up clustalo (1.2.4-8build1) ... 728s Setting up dssp (4.4.10-1) ... 728s Setting up xfonts-utils (1:7.7+7) ... 728s Setting up intltool-debian (0.35.0+20060710.6) ... 728s Setting up libmbedx509-7:arm64 (3.6.2-3ubuntu1) ... 728s Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... 728s Setting up libptexenc1:arm64 (2024.20240313.70630+ds-5build2) ... 728s Setting up libglpk40:arm64 (5.0-1build2) ... 728s Setting up libraqm0:arm64 (0.10.2-1) ... 728s Setting up libpython3.13-dev:arm64 (3.13.2-1) ... 728s Setting up python3.12-dev (3.12.9-1) ... 728s Setting up python3-numpy (1:1.26.4+ds-13) ... 732s Setting up libjs-sphinxdoc (8.1.3-5) ... 732s Setting up libraw23t64:arm64 (0.21.3-1) ... 732s Setting up libmbedtls21:arm64 (3.6.2-3ubuntu1) ... 732s Setting up dh-strip-nondeterminism (1.14.1-2) ... 732s Setting up cpp-14-aarch64-linux-gnu (14.2.0-17ubuntu1) ... 732s Setting up python3-lxml:arm64 (5.3.1-1) ... 732s Setting up python-biopython-doc (1.85+dfsg-2) ... 732s Setting up libtiff6:arm64 (4.5.1+git230720-4ubuntu4) ... 732s Setting up xml-core (0.19) ... 732s Setting up python3-contourpy (1.3.1-1) ... 733s Setting up libfontconfig1:arm64 (2.15.0-2ubuntu1) ... 733s Setting up libgcc-14-dev:arm64 (14.2.0-17ubuntu1) ... 733s Setting up libigraph3t64:arm64 (0.10.15+ds-2) ... 733s Setting up libstdc++-14-dev:arm64 (14.2.0-17ubuntu1) ... 733s Setting up libsm6:arm64 (2:1.2.4-1) ... 733s Setting up libavahi-client3:arm64 (0.8-14ubuntu1) ... 733s Setting up liblbfgsb0:arm64 (3.0+dfsg.4-1build1) ... 733s Setting up libxft2:arm64 (2.3.6-1build1) ... 733s Setting up python3-scipy (1.14.1-4ubuntu1) ... 741s Setting up libpython3-dev:arm64 (3.13.1-1~exp2) ... 741s Setting up python3.13-dev (3.13.2-1) ... 741s Setting up po-debconf (1.0.21+nmu1) ... 741s Setting up libtk8.6:arm64 (8.6.16-1) ... 741s Setting up python3.12-tk (3.12.9-1) ... 741s Setting up python3-mmtf (1.1.3-1) ... 741s Setting up fonts-urw-base35 (20200910-8) ... 741s Setting up libcairo2:arm64 (1.18.2-2) ... 741s Setting up python3.13-tk (3.13.2-1) ... 741s Setting up ncbi-blast+ (2.16.0+ds-6build1) ... 741s Setting up python3-pil:arm64 (11.1.0-5) ... 742s Setting up cpp-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 742s Setting up libpython3-all-dev:arm64 (3.13.1-1~exp2) ... 742s Setting up sphinx-common (8.1.3-5) ... 742s Setting up python3-dev (3.13.1-1~exp2) ... 742s Setting up libxt6t64:arm64 (1:1.2.1-1.2build1) ... 742s Setting up netpbm (2:11.09.02-2) ... 742s Setting up cpp-14 (14.2.0-17ubuntu1) ... 742s Setting up python3-igraph (0.11.8+ds-1build1) ... 743s Setting up cpp (4:14.2.0-1ubuntu1) ... 743s Setting up gcc-14-aarch64-linux-gnu (14.2.0-17ubuntu1) ... 743s Setting up libcups2t64:arm64 (2.4.11-0ubuntu2) ... 743s Setting up python3-all-dev (3.13.1-1~exp2) ... 743s Setting up libgs10-common (10.04.0~dfsg1-2ubuntu1) ... 743s Setting up gcc-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 743s Setting up tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 743s Setting up libxmu6:arm64 (2:1.1.3-3build2) ... 743s Setting up g++-14-aarch64-linux-gnu (14.2.0-17ubuntu1) ... 743s Setting up python3-cairo (1.26.1-2build1) ... 743s Setting up blt (2.5.3+dfsg-7build1) ... 743s Setting up python3-tk:arm64 (3.13.1-1) ... 743s Setting up libxaw7:arm64 (2:1.0.16-1) ... 743s Setting up gcc-14 (14.2.0-17ubuntu1) ... 743s Setting up python3-pil.imagetk:arm64 (11.1.0-5) ... 743s Setting up python3-rlpycairo (0.3.0-3) ... 744s Setting up python3-reportlab (4.3.0-1) ... 745s Setting up texlive-binaries (2024.20240313.70630+ds-5build2) ... 745s update-alternatives: using /usr/bin/xdvi-xaw to provide /usr/bin/xdvi.bin (xdvi.bin) in auto mode 745s update-alternatives: using /usr/bin/bibtex.original to provide /usr/bin/bibtex (bibtex) in auto mode 745s Setting up g++-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 745s Setting up g++-14 (14.2.0-17ubuntu1) ... 745s Setting up texlive-base (2024.20241115-1) ... 746s tl-paper: setting paper size for dvips to a4: /var/lib/texmf/dvips/config/config-paper.ps 746s tl-paper: setting paper size for dvipdfmx to a4: /var/lib/texmf/dvipdfmx/dvipdfmx-paper.cfg 747s tl-paper: setting paper size for xdvi to a4: /var/lib/texmf/xdvi/XDvi-paper 747s tl-paper: setting paper size for pdftex to a4: /var/lib/texmf/tex/generic/tex-ini-files/pdftexconfig.tex 748s Setting up libgs10:arm64 (10.04.0~dfsg1-2ubuntu1) ... 748s Setting up libtool (2.5.4-3build1) ... 748s Setting up ghostscript (10.04.0~dfsg1-2ubuntu1) ... 748s Setting up gcc (4:14.2.0-1ubuntu1) ... 748s Setting up dh-autoreconf (20) ... 748s Setting up texlive-latex-base (2024.20241115-1) ... 748s Setting up texlive-latex-recommended (2024.20241115-1) ... 748s Setting up texlive-pictures (2024.20241115-1) ... 748s Setting up g++ (4:14.2.0-1ubuntu1) ... 748s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 748s Setting up texlive-fonts-recommended (2024.20241115-1) ... 748s Setting up build-essential (12.10ubuntu1) ... 748s Setting up debhelper (13.24.1ubuntu2) ... 748s Setting up texlive-latex-extra (2024.20250114-1) ... 748s Setting up python3-ufolib2 (0.17.0+dfsg1-1) ... 748s Setting up libheif-plugin-aomdec:arm64 (1.19.5-1build1) ... 748s Setting up libheif-plugin-libde265:arm64 (1.19.5-1build1) ... 748s Setting up libheif1:arm64 (1.19.5-1build1) ... 748s Setting up python3-fonttools (4.55.3-2) ... 750s Setting up libgd3:arm64 (2.3.3-12ubuntu3) ... 750s Setting up libmagickcore-7.q16-10:arm64 (8:7.1.1.43+dfsg1-1) ... 750s Setting up emboss-lib (6.6.0+dfsg-12ubuntu2) ... 750s Setting up python3-matplotlib (3.8.3-3ubuntu2) ... 754s Setting up libmagickwand-7.q16-10:arm64 (8:7.1.1.43+dfsg1-1) ... 754s Setting up emboss (6.6.0+dfsg-12ubuntu2) ... 754s Setting up imagemagick-7.q16 (8:7.1.1.43+dfsg1-1) ... 754s update-alternatives: using /usr/bin/compare-im7.q16 to provide /usr/bin/compare (compare) in auto mode 754s update-alternatives: using /usr/bin/compare-im7.q16 to provide /usr/bin/compare-im7 (compare-im7) in auto mode 754s update-alternatives: using /usr/bin/animate-im7.q16 to provide /usr/bin/animate (animate) in auto mode 754s update-alternatives: using /usr/bin/animate-im7.q16 to provide /usr/bin/animate-im7 (animate-im7) in auto mode 754s update-alternatives: using /usr/bin/convert-im7.q16 to provide /usr/bin/convert (convert) in auto mode 754s update-alternatives: using /usr/bin/convert-im7.q16 to provide /usr/bin/convert-im7 (convert-im7) in auto mode 754s update-alternatives: using /usr/bin/composite-im7.q16 to provide /usr/bin/composite (composite) in auto mode 754s update-alternatives: using /usr/bin/composite-im7.q16 to provide /usr/bin/composite-im7 (composite-im7) in auto mode 754s update-alternatives: using /usr/bin/conjure-im7.q16 to provide /usr/bin/conjure (conjure) in auto mode 754s update-alternatives: using /usr/bin/conjure-im7.q16 to provide /usr/bin/conjure-im7 (conjure-im7) in auto mode 754s update-alternatives: using /usr/bin/import-im7.q16 to provide /usr/bin/import (import) in auto mode 754s update-alternatives: using /usr/bin/import-im7.q16 to provide /usr/bin/import-im7 (import-im7) in auto mode 754s update-alternatives: using /usr/bin/identify-im7.q16 to provide /usr/bin/identify (identify) in auto mode 754s update-alternatives: using /usr/bin/identify-im7.q16 to provide /usr/bin/identify-im7 (identify-im7) in auto mode 754s update-alternatives: using /usr/bin/stream-im7.q16 to provide /usr/bin/stream (stream) in auto mode 754s update-alternatives: using /usr/bin/stream-im7.q16 to provide /usr/bin/stream-im7 (stream-im7) in auto mode 754s update-alternatives: using /usr/bin/display-im7.q16 to provide /usr/bin/display (display) in auto mode 754s update-alternatives: using /usr/bin/display-im7.q16 to provide /usr/bin/display-im7 (display-im7) in auto mode 754s update-alternatives: using /usr/bin/montage-im7.q16 to provide /usr/bin/montage (montage) in auto mode 754s update-alternatives: using /usr/bin/montage-im7.q16 to provide /usr/bin/montage-im7 (montage-im7) in auto mode 754s update-alternatives: using /usr/bin/mogrify-im7.q16 to provide /usr/bin/mogrify (mogrify) in auto mode 754s update-alternatives: using /usr/bin/mogrify-im7.q16 to provide /usr/bin/mogrify-im7 (mogrify-im7) in auto mode 754s update-alternatives: using /usr/bin/magick-im7.q16 to provide /usr/bin/magick (magick) in auto mode 754s update-alternatives: warning: skip creation of /usr/share/man/man1/magick.1.gz because associated file /usr/share/man/man1/magick-im7.q16.1.gz (of link group magick) doesn't exist 754s update-alternatives: using /usr/bin/magick-im7.q16 to provide /usr/bin/magick-im7 (magick-im7) in auto mode 754s update-alternatives: warning: skip creation of /usr/share/man/man1/magick-im7.1.gz because associated file /usr/share/man/man1/magick-im7.q16.1.gz (of link group magick-im7) doesn't exist 754s update-alternatives: using /usr/bin/magick-script-im7.q16 to provide /usr/bin/magick-script (magick-script) in auto mode 754s update-alternatives: warning: skip creation of /usr/share/man/man1/magick-script.1.gz because associated file /usr/share/man/man1/magick-script-im7.q16.1.gz (of link group magick-script) doesn't exist 754s update-alternatives: using /usr/bin/magick-script-im7.q16 to provide /usr/bin/magick-script-im7 (magick-script-im7) in auto mode 754s update-alternatives: warning: skip creation of /usr/share/man/man1/magick-script-im7.1.gz because associated file /usr/share/man/man1/magick-script-im7.q16.1.gz (of link group magick-script-im7) doesn't exist 754s Setting up hevea (2.36-2) ... 754s Setting up imagemagick (8:7.1.1.43+dfsg1-1) ... 754s Processing triggers for install-info (7.1.1-1) ... 754s Processing triggers for libc-bin (2.40-4ubuntu1) ... 754s Processing triggers for systemd (257.2-3ubuntu1) ... 754s Processing triggers for man-db (2.13.0-1) ... 757s Processing triggers for shared-mime-info (2.4-5) ... 757s Warning: program compiled against libxml 212 using older 209 757s Processing triggers for sgml-base (1.31) ... 757s Setting up w3c-sgml-lib (1.3-3) ... 789s Setting up docutils-common (0.21.2+dfsg-2) ... 789s Setting up python3-biopython (1.85+dfsg-2) ... 792s Setting up python3-biopython-sql (1.85+dfsg-2) ... 792s Processing triggers for sgml-base (1.31) ... 792s Setting up python3-docutils (0.21.2+dfsg-2) ... 793s Setting up python3-sphinx (8.1.3-5) ... 795s Setting up python3-sphinxcontrib.jquery (4.1-5) ... 795s Setting up python3-numpydoc (1.8.0-1) ... 796s Setting up python3-sphinx-rtd-theme (3.0.2+dfsg-2) ... 796s Processing triggers for tex-common (6.18) ... 797s Running updmap-sys. This may take some time... done. 797s Running mktexlsr /var/lib/texmf ... done. 797s Building format(s) --all. 865s This may take some time... done. 877s autopkgtest [13:49:31]: test full_suite: sh debian/tests/run-unit-test 877s autopkgtest [13:49:31]: test full_suite: [----------------------- 880s mkdir: created directory 'Bio' 880s mkdir: created directory 'Bio/Align' 880s mkdir: created directory 'Bio/Align/substitution_matrices' 880s mkdir: created directory 'Bio/Align/substitution_matrices/data/' 880s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER22' -> 'Bio/Align/substitution_matrices/data/BENNER22' 880s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER6' -> 'Bio/Align/substitution_matrices/data/BENNER6' 880s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER74' -> 'Bio/Align/substitution_matrices/data/BENNER74' 880s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLASTN' -> 'Bio/Align/substitution_matrices/data/BLASTN' 880s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLASTP' -> 'Bio/Align/substitution_matrices/data/BLASTP' 880s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM45' -> 'Bio/Align/substitution_matrices/data/BLOSUM45' 880s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM50' -> 'Bio/Align/substitution_matrices/data/BLOSUM50' 880s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM62' -> 'Bio/Align/substitution_matrices/data/BLOSUM62' 880s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM80' -> 'Bio/Align/substitution_matrices/data/BLOSUM80' 880s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM90' -> 'Bio/Align/substitution_matrices/data/BLOSUM90' 880s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/DAYHOFF' -> 'Bio/Align/substitution_matrices/data/DAYHOFF' 880s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/FENG' -> 'Bio/Align/substitution_matrices/data/FENG' 880s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/GENETIC' -> 'Bio/Align/substitution_matrices/data/GENETIC' 880s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/GONNET1992' -> 'Bio/Align/substitution_matrices/data/GONNET1992' 880s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/HOXD70' -> 'Bio/Align/substitution_matrices/data/HOXD70' 880s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/JOHNSON' -> 'Bio/Align/substitution_matrices/data/JOHNSON' 880s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/JONES' -> 'Bio/Align/substitution_matrices/data/JONES' 880s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/LEVIN' -> 'Bio/Align/substitution_matrices/data/LEVIN' 880s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MCLACHLAN' -> 'Bio/Align/substitution_matrices/data/MCLACHLAN' 880s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MDM78' -> 'Bio/Align/substitution_matrices/data/MDM78' 880s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MEGABLAST' -> 'Bio/Align/substitution_matrices/data/MEGABLAST' 880s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/NUC.4.4' -> 'Bio/Align/substitution_matrices/data/NUC.4.4' 880s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM250' -> 'Bio/Align/substitution_matrices/data/PAM250' 880s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM30' -> 'Bio/Align/substitution_matrices/data/PAM30' 880s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM70' -> 'Bio/Align/substitution_matrices/data/PAM70' 880s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/RAO' -> 'Bio/Align/substitution_matrices/data/RAO' 880s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/RISLER' -> 'Bio/Align/substitution_matrices/data/RISLER' 880s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/SCHNEIDER' -> 'Bio/Align/substitution_matrices/data/SCHNEIDER' 880s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/STR' -> 'Bio/Align/substitution_matrices/data/STR' 880s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/TRANS' -> 'Bio/Align/substitution_matrices/data/TRANS' 881s test_Ace ... ok 881s test_Affy ... ok 884s test_AlignIO ... ok 884s test_AlignIO_ClustalIO ... ok 884s test_AlignIO_EmbossIO ... ok 884s test_AlignIO_FastaIO ... ok 884s test_AlignIO_MauveIO ... ok 884s test_AlignIO_PhylipIO ... ok 884s test_AlignIO_convert ... ok 884s test_AlignInfo ... ok 884s test_Align_Alignment ... ok 884s test_Align_a2m ... ok 884s test_Align_bed ... ok 885s test_Align_bigbed ... ok 885s test_Align_bigmaf ... ok 886s test_Align_bigpsl ... ok 886s test_Align_chain ... ok 886s test_Align_clustal ... ok 891s test_Align_codonalign ... ok 891s test_Align_emboss ... ok 891s test_Align_exonerate ... ok 891s test_Align_fasta ... ok 892s test_Align_hhr ... ok 893s test_Align_maf ... ok 893s test_Align_mauve ... ok 893s test_Align_msf ... ok 893s test_Align_nexus ... ok 893s test_Align_phylip ... ok 893s test_Align_psl ... ok 894s test_Align_sam ... ok 896s test_Align_stockholm ... ok 896s test_Align_tabular ... ok 896s test_Application ... ok 896s test_BioSQL_MySQLdb_online ... skipping. internet not available 896s test_BioSQL_mysql_connector ... skipping. BioSQL test configuration file biosql.ini missing (see biosql.ini.sample) 897s test_BioSQL_mysql_connector_online ... skipping. internet not available 897s test_BioSQL_psycopg2_online ... skipping. internet not available 902s test_BioSQL_sqlite3 ... ok 902s test_BioSQL_sqlite3_online ... skipping. internet not available 902s test_Blast_Record ... ok 902s test_Blast_parser ... ok 903s test_CAPS ... ok 903s test_Chi2 ... ok 903s test_ClustalOmega_tool ... ok 903s test_Clustalw_tool ... skipping. Install clustalw or clustalw2 if you want to use it from Biopython. 904s test_Cluster ... ok 904s test_CodonTable ... ok 904s test_ColorSpiral ... ok 904s test_Compass ... ok 905s test_Consensus ... ok 907s test_Dialign_tool ... ok 907s test_EMBL_unittest ... ok 915s test_Emboss ... ok 915s test_EmbossPrimer ... ok 919s test_Entrez ... ok 919s test_Entrez_online ... skipping. internet not available 919s test_Entrez_parser ... ok 920s test_Enzyme ... ok 920s test_ExPASy ... skipping. internet not available 920s test_Fasttree_tool ... ok 920s test_File ... ok 920s test_GenBank ... /usr/lib/python3/dist-packages/Bio/SeqIO/InsdcIO.py:600: BiopythonWarning: Annotation 'Sequence Read Archive: SRX001885, SRX001121, SRX001531, SRX001530, SRX001529' too long 920s warnings.warn(f"Annotation {text!r} too long", BiopythonWarning) 920s ok 922s test_GenomeDiagram ... Warn: Can't find .pfb for face 'Helvetica' 924s ok 925s test_GraphicsChromosome ... ok 925s test_GraphicsDistribution ... ok 926s test_GraphicsGeneral ... ok 926s test_HMMCasino ... ok 926s test_HMMGeneral ... ok 926s test_KEGG ... ok 926s test_KEGG_online ... skipping. internet not available 932s test_KGML_graphics ... ok 932s test_KGML_graphics_online ... skipping. internet not available 933s test_KGML_nographics ... ok 933s test_KeyWList ... ok 933s test_LogisticRegression ... ok 934s test_MafIO_index ... ok 936s test_Mafft_tool ... ok 936s test_MarkovModel ... ok 937s test_Medline ... ok 937s test_Muscle_tool ... skipping. Install MUSCLE if you want to use the Bio.Align.Applications wrapper. 937s test_NCBIXML ... Exception ignored in: 937s Traceback (most recent call last): 937s File "/usr/lib/python3/dist-packages/Bio/Blast/NCBIXML.py", line 1319, in parse 937s expat_parser.Parse(NULL, True) 937s xml.parsers.expat.ExpatError: unclosed token: line 320, column 0 937s ok 940s test_NCBI_BLAST_tools ... ok 940s test_NCBI_qblast ... ok 940s test_NMR ... ok 940s test_NaiveBayes ... ok 940s test_Nexus ... ok 940s test_PAML_baseml ... ok 941s test_PAML_codeml ... ok 941s test_PAML_yn00 ... ok 946s test_PDB_CEAligner ... ok 948s test_PDB_DSSP ... ok 948s test_PDB_Dice ... ok 949s test_PDB_Disordered ... ok 949s test_PDB_Exposure ... ok 949s test_PDB_FragmentMapper ... ok 951s test_PDB_KDTree ... ok 951s test_PDB_MMCIF2Dict ... ok 951s test_PDB_MMCIFIO ... ok 953s test_PDB_MMCIFParser ... ok 953s test_PDB_NACCESS ... ok 953s test_PDB_PDBIO ... ok 953s test_PDB_PDBList ... skipping. internet not available 961s test_PDB_PDBMLParser ... ok 962s test_PDB_PDBParser ... ok 962s 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 962s test_PDB_Polypeptide ... ok 962s test_PDB_QCPSuperimposer ... ok 965s test_PDB_SASA ... ok 966s test_PDB_SMCRA ... ok 966s test_PDB_Selection ... ok 967s test_PDB_StructureAlignment ... ok 967s test_PDB_Superimposer ... ok 967s test_PDB_alphafold_db ... skipping. internet not available 971s test_PDB_binary_cif ... /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 1, ' ') redefined at line 7. 971s warnings.warn( 971s /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 15, ' ') redefined at line 144. 971s warnings.warn( 971s /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 15, ' ') redefined at line 153. 971s warnings.warn( 971s /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 1, ' ') redefined at line 0. 971s warnings.warn( 971s /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 15, ' ') redefined at line 0. 971s warnings.warn( 971s ok 981s test_PDB_internal_coords ... ok 981s test_PDB_parse_pdb_header ... ok 981s test_PDB_vectors ... ok 982s test_PQR ... ok 982s test_Pathway ... ok 982s test_Phd ... ok 983s test_Phylo ... ok 984s test_PhyloXML ... ok 984s test_Phylo_CDAO ... ok 984s test_Phylo_NeXML ... ok 986s test_Phylo_igraph ... ok 989s test_Phylo_matplotlib ... ok 990s test_Phylo_networkx ... ok 991s test_PopGen_GenePop_nodepend ... ok 993s test_Prank_tool ... ok 994s test_Probcons_tool ... ok 994s test_ProtParam ... ok 995s test_RCSBFormats ... ok 996s test_Restriction ... ok 997s test_SCOP_Astral ... ok 998s test_SCOP_Cla ... ok 998s test_SCOP_Des ... ok 999s test_SCOP_Dom ... ok 999s test_SCOP_Hie ... ok 1000s test_SCOP_Raf ... ok 1001s test_SCOP_Residues ... ok 1001s test_SCOP_Scop ... ok 1002s test_SVDSuperimposer ... ok 1003s test_SearchIO_blast_tab ... ok 1004s test_SearchIO_blast_tab_index ... ok 1004s test_SearchIO_blast_xml ... ok 1006s test_SearchIO_blast_xml_index ... ok 1007s test_SearchIO_blat_psl ... ok 1008s test_SearchIO_blat_psl_index ... ok 1008s test_SearchIO_exonerate ... ok 1009s test_SearchIO_exonerate_text_index ... ok 1010s test_SearchIO_exonerate_vulgar_index ... ok 1010s test_SearchIO_fasta_m10 ... ok 1011s test_SearchIO_fasta_m10_index ... ok 1012s test_SearchIO_hhsuite2_text ... ok 1013s test_SearchIO_hmmer2_text ... ok 1013s test_SearchIO_hmmer2_text_index ... ok 1014s test_SearchIO_hmmer3_domtab ... ok 1015s test_SearchIO_hmmer3_domtab_index ... ok 1016s test_SearchIO_hmmer3_tab ... ok 1016s test_SearchIO_hmmer3_tab_index ... ok 1017s test_SearchIO_hmmer3_text ... ok 1018s test_SearchIO_hmmer3_text_index ... ok 1018s test_SearchIO_interproscan_xml ... ok 1019s test_SearchIO_model ... ok 1020s test_SearchIO_write ... ok 1021s test_SeqFeature ... ok 1038s test_SeqIO ... ok 1040s test_SeqIO_AbiIO ... ok 1040s test_SeqIO_FastaIO ... ok 1041s test_SeqIO_Gck ... ok 1042s test_SeqIO_Gfa ... ok 1043s test_SeqIO_Insdc ... ok 1043s test_SeqIO_NibIO ... ok 1046s test_SeqIO_PdbIO ... ok 1047s test_SeqIO_QualityIO ... ok 1048s test_SeqIO_SeqXML ... ok 1049s test_SeqIO_SffIO ... ok 1049s test_SeqIO_SnapGene ... ok 1051s test_SeqIO_TwoBitIO ... ok 1052s test_SeqIO_UniprotIO ... ok 1053s test_SeqIO_Xdna ... ok 1054s test_SeqIO_features ... ok 1071s test_SeqIO_index ... ok 1071s test_SeqIO_online ... skipping. internet not available 1072s test_SeqIO_write ... ok 1073s test_SeqRecord ... ok 1073s test_SeqUtils ... ok 1075s test_Seq_objs ... ok 1076s test_SwissProt ... ok 1079s test_TCoffee_tool ... ok 1080s test_TogoWS ... skipping. internet not available 1081s test_TreeConstruction ... ok 1081s test_Tutorial ... skipping. Could not find ../Doc/Tutorial/index.rst file 1082s test_UniGene ... ok 1083s test_UniProt ... skipping. internet not available 1084s test_UniProt_GOA ... ok 1084s test_align ... ok 1085s test_align_substitution_matrices ... ok 1088s test_bgzf ... ok 1089s test_cellosaurus ... ok 1095s test_codonalign ... ok 1096s test_geo ... ok 1097s test_kNN ... ok 1098s test_motifs ... ok 1099s test_motifs_online ... skipping. internet not available 1099s 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. 1099s warnings.warn( 1100s ok 1100s test_pairwise2_no_C ... ok 1101s test_pairwise_aligner ... ok 1102s test_pairwise_alignment_map ... ok 1110s test_phenotype ... ok 1111s test_phenotype_fit ... ok 1111s 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. 1112s test_prodoc ... ok 1113s test_prosite ... ok 1114s test_raxml_tool ... skipping. Install RAxML (binary raxmlHPC) if you want to test the Bio.Phylo.Applications wrapper. 1114s test_samtools_tool ... skipping. Install samtools and correctly set the file path to the program if you want to use it from Biopython 1115s test_seq ... ok 1116s test_translate ... ok 1117s Skipping any tests requiring internet access 1117s Python version: 3.12.9 (main, Feb 5 2025, 01:31:18) [GCC 14.2.0] 1117s Operating system: posix linux 1117s ---------------------------------------------------------------------- 1117s Ran 218 tests in 236.009 seconds 1117s 1118s sys:1: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/protein_lib.fa' mode='rt' encoding='UTF-8'> 1118s sys:1: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/nucleotide_lib.fa' mode='rt' encoding='UTF-8'> 1119s test_Ace ... ok 1120s test_Affy ... ok 1122s test_AlignIO ... ok 1122s test_AlignIO_ClustalIO ... ok 1122s test_AlignIO_EmbossIO ... ok 1122s test_AlignIO_FastaIO ... ok 1122s test_AlignIO_MauveIO ... ok 1122s test_AlignIO_PhylipIO ... ok 1122s test_AlignIO_convert ... ok 1122s test_AlignInfo ... ok 1123s test_Align_Alignment ... ok 1123s test_Align_a2m ... ok 1123s test_Align_bed ... ok 1123s test_Align_bigbed ... ok 1124s test_Align_bigmaf ... ok 1124s test_Align_bigpsl ... ok 1124s test_Align_chain ... ok 1124s test_Align_clustal ... ok 1129s test_Align_codonalign ... ok 1130s test_Align_emboss ... ok 1130s test_Align_exonerate ... ok 1130s test_Align_fasta ... ok 1130s test_Align_hhr ... ok 1131s test_Align_maf ... ok 1131s test_Align_mauve ... ok 1131s test_Align_msf ... ok 1131s test_Align_nexus ... ok 1131s test_Align_phylip ... ok 1132s test_Align_psl ... ok 1132s test_Align_sam ... ok 1134s test_Align_stockholm ... ok 1134s test_Align_tabular ... ok 1134s test_Application ... ok 1134s test_BioSQL_MySQLdb_online ... skipping. internet not available 1134s test_BioSQL_mysql_connector ... skipping. BioSQL test configuration file biosql.ini missing (see biosql.ini.sample) 1134s test_BioSQL_mysql_connector_online ... skipping. internet not available 1135s test_BioSQL_psycopg2_online ... skipping. internet not available 1139s test_BioSQL_sqlite3 ... ok 1139s test_BioSQL_sqlite3_online ... skipping. internet not available 1139s test_Blast_Record ... ok 1140s test_Blast_parser ... ok 1140s test_CAPS ... ok 1140s test_Chi2 ... ok 1141s test_ClustalOmega_tool ... ok 1141s test_Clustalw_tool ... skipping. Install clustalw or clustalw2 if you want to use it from Biopython. 1141s test_Cluster ... ok 1141s test_CodonTable ... ok 1141s test_ColorSpiral ... ok 1141s test_Compass ... ok 1142s test_Consensus ... ok 1145s test_Dialign_tool ... ok 1145s test_EMBL_unittest ... ok 1152s test_Emboss ... ok 1152s test_EmbossPrimer ... ok 1156s test_Entrez ... ok 1157s test_Entrez_online ... skipping. internet not available 1157s test_Entrez_parser ... ok 1157s test_Enzyme ... ok 1157s test_ExPASy ... skipping. internet not available 1157s test_Fasttree_tool ... ok 1157s test_File ... ok 1158s test_GenBank ... /usr/lib/python3/dist-packages/Bio/SeqIO/InsdcIO.py:600: BiopythonWarning: Annotation 'Sequence Read Archive: SRX001885, SRX001121, SRX001531, SRX001530, SRX001529' too long 1158s warnings.warn(f"Annotation {text!r} too long", BiopythonWarning) 1158s ok 1159s test_GenomeDiagram ... Warn: Can't find .pfb for face 'Helvetica' 1161s ok 1162s test_GraphicsChromosome ... ok 1162s test_GraphicsDistribution ... ok 1163s test_GraphicsGeneral ... ok 1163s test_HMMCasino ... ok 1163s test_HMMGeneral ... ok 1163s test_KEGG ... ok 1163s test_KEGG_online ... skipping. internet not available 1168s test_KGML_graphics ... ok 1168s test_KGML_graphics_online ... skipping. internet not available 1169s test_KGML_nographics ... ok 1169s test_KeyWList ... ok 1169s test_LogisticRegression ... ok 1170s test_MafIO_index ... ok 1172s test_Mafft_tool ... ok 1172s test_MarkovModel ... ok 1172s test_Medline ... ok 1172s test_Muscle_tool ... skipping. Install MUSCLE if you want to use the Bio.Align.Applications wrapper. 1173s test_NCBIXML ... Exception ignored in: 1173s Traceback (most recent call last): 1173s File "/usr/lib/python3/dist-packages/Bio/Blast/NCBIXML.py", line 1319, in parse 1173s expat_parser.Parse(NULL, True) 1173s xml.parsers.expat.ExpatError: unclosed token: line 320, column 0 1173s ok 1175s test_NCBI_BLAST_tools ... ok 1175s test_NCBI_qblast ... ok 1175s test_NMR ... ok 1175s test_NaiveBayes ... ok 1175s test_Nexus ... ok 1175s test_PAML_baseml ... ok 1176s test_PAML_codeml ... ok 1176s test_PAML_yn00 ... ok 1181s test_PDB_CEAligner ... ok 1183s test_PDB_DSSP ... ok 1183s test_PDB_Dice ... ok 1183s test_PDB_Disordered ... ok 1183s test_PDB_Exposure ... ok 1183s test_PDB_FragmentMapper ... ok 1185s test_PDB_KDTree ... ok 1185s test_PDB_MMCIF2Dict ... ok 1186s test_PDB_MMCIFIO ... ok 1187s test_PDB_MMCIFParser ... ok 1187s test_PDB_NACCESS ... ok 1187s test_PDB_PDBIO ... ok 1187s test_PDB_PDBList ... skipping. internet not available 1194s test_PDB_PDBMLParser ... ok 1194s test_PDB_PDBParser ... ok 1194s 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 1194s test_PDB_Polypeptide ... ok 1194s test_PDB_QCPSuperimposer ... ok 1197s test_PDB_SASA ... ok 1198s test_PDB_SMCRA ... ok 1198s test_PDB_Selection ... ok 1198s test_PDB_StructureAlignment ... ok 1198s test_PDB_Superimposer ... ok 1199s test_PDB_alphafold_db ... skipping. internet not available 1202s test_PDB_binary_cif ... /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 1, ' ') redefined at line 7. 1202s warnings.warn( 1202s /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 15, ' ') redefined at line 144. 1202s warnings.warn( 1202s /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 15, ' ') redefined at line 153. 1202s warnings.warn( 1202s /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 1, ' ') redefined at line 0. 1202s warnings.warn( 1202s /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 15, ' ') redefined at line 0. 1202s warnings.warn( 1202s ok 1210s test_PDB_internal_coords ... ok 1210s test_PDB_parse_pdb_header ... ok 1211s test_PDB_vectors ... ok 1211s test_PQR ... ok 1211s test_Pathway ... ok 1211s test_Phd ... ok 1212s test_Phylo ... ok 1212s test_PhyloXML ... ok 1213s test_Phylo_CDAO ... ok 1213s test_Phylo_NeXML ... ok 1214s test_Phylo_igraph ... ok 1217s test_Phylo_matplotlib ... ok 1217s test_Phylo_networkx ... ok 1218s test_PopGen_GenePop_nodepend ... ok 1220s test_Prank_tool ... ok 1221s test_Probcons_tool ... ok 1222s test_ProtParam ... ok 1223s test_RCSBFormats ... ok 1223s test_Restriction ... ok 1224s test_SCOP_Astral ... ok 1225s test_SCOP_Cla ... ok 1225s test_SCOP_Des ... ok 1226s test_SCOP_Dom ... ok 1227s test_SCOP_Hie ... ok 1227s test_SCOP_Raf ... ok 1228s test_SCOP_Residues ... ok 1228s test_SCOP_Scop ... ok 1229s test_SVDSuperimposer ... ok 1230s test_SearchIO_blast_tab ... ok 1231s test_SearchIO_blast_tab_index ... ok 1231s test_SearchIO_blast_xml ... ok 1233s test_SearchIO_blast_xml_index ... ok 1234s test_SearchIO_blat_psl ... ok 1234s test_SearchIO_blat_psl_index ... ok 1235s test_SearchIO_exonerate ... ok 1236s test_SearchIO_exonerate_text_index ... ok 1236s test_SearchIO_exonerate_vulgar_index ... ok 1237s test_SearchIO_fasta_m10 ... ok 1238s test_SearchIO_fasta_m10_index ... ok 1239s test_SearchIO_hhsuite2_text ... ok 1239s test_SearchIO_hmmer2_text ... ok 1240s test_SearchIO_hmmer2_text_index ... ok 1241s test_SearchIO_hmmer3_domtab ... ok 1241s test_SearchIO_hmmer3_domtab_index ... ok 1242s test_SearchIO_hmmer3_tab ... ok 1243s test_SearchIO_hmmer3_tab_index ... ok 1243s test_SearchIO_hmmer3_text ... ok 1244s test_SearchIO_hmmer3_text_index ... ok 1245s test_SearchIO_interproscan_xml ... ok 1246s test_SearchIO_model ... ok 1246s test_SearchIO_write ... ok 1247s test_SeqFeature ... ok 1263s test_SeqIO ... ok 1264s test_SeqIO_AbiIO ... ok 1264s test_SeqIO_FastaIO ... ok 1265s test_SeqIO_Gck ... ok 1266s test_SeqIO_Gfa ... ok 1266s test_SeqIO_Insdc ... ok 1267s test_SeqIO_NibIO ... ok 1269s test_SeqIO_PdbIO ... ok 1270s test_SeqIO_QualityIO ... ok 1271s test_SeqIO_SeqXML ... ok 1272s test_SeqIO_SffIO ... ok 1272s test_SeqIO_SnapGene ... ok 1274s test_SeqIO_TwoBitIO ... ok 1275s test_SeqIO_UniprotIO ... ok 1275s test_SeqIO_Xdna ... ok 1276s test_SeqIO_features ... ok 1291s test_SeqIO_index ... ok 1291s test_SeqIO_online ... skipping. internet not available 1292s test_SeqIO_write ... ok 1293s test_SeqRecord ... ok 1293s test_SeqUtils ... ok 1295s test_Seq_objs ... ok 1296s test_SwissProt ... ok 1299s test_TCoffee_tool ... ok 1299s test_TogoWS ... skipping. internet not available 1300s test_TreeConstruction ... ok 1301s test_Tutorial ... skipping. Could not find ../Doc/Tutorial/index.rst file 1301s test_UniGene ... ok 1302s test_UniProt ... skipping. internet not available 1303s test_UniProt_GOA ... ok 1303s test_align ... ok 1304s test_align_substitution_matrices ... ok 1307s test_bgzf ... ok 1308s test_cellosaurus ... ok 1314s test_codonalign ... ok 1315s test_geo ... ok 1315s test_kNN ... ok 1316s test_motifs ... ok 1317s test_motifs_online ... skipping. internet not available 1317s 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. 1317s warnings.warn( 1317s ok 1318s test_pairwise2_no_C ... ok 1319s test_pairwise_aligner ... ok 1320s test_pairwise_alignment_map ... ok 1327s test_phenotype ... ok 1328s test_phenotype_fit ... ok 1328s 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. 1329s test_prodoc ... ok 1330s test_prosite ... ok 1330s test_raxml_tool ... skipping. Install RAxML (binary raxmlHPC) if you want to test the Bio.Phylo.Applications wrapper. 1331s test_samtools_tool ... skipping. Install samtools and correctly set the file path to the program if you want to use it from Biopython 1332s test_seq ... ok 1332s test_translate ... ok 1333s Skipping any tests requiring internet access 1333s Python version: 3.13.2 (main, Feb 5 2025, 01:23:35) [GCC 14.2.0] 1333s Operating system: posix linux 1333s ---------------------------------------------------------------------- 1333s Ran 218 tests in 213.320 seconds 1333s 1334s :0: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/protein_lib.fa' mode='rt' encoding='UTF-8'> 1334s :0: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/nucleotide_lib.fa' mode='rt' encoding='UTF-8'> 1335s autopkgtest [13:57:09]: test full_suite: -----------------------] 1336s full_suite PASS 1336s autopkgtest [13:57:10]: test full_suite: - - - - - - - - - - results - - - - - - - - - - 1336s autopkgtest [13:57:10]: @@@@@@@@@@@@@@@@@@@@ summary 1336s dependencies PASS 1336s full_suite PASS 1342s nova [W] Using flock in prodstack6-arm64 1342s Creating nova instance adt-plucky-arm64-python-biopython-20250219-122232-juju-7f2275-prod-proposed-migration-environment-20-b645ef9c-37de-4709-b4ee-d363f84c1666 from image adt/ubuntu-plucky-arm64-server-20250219.img (UUID 02c92adb-9d9d-4b0e-b071-488d8ee6210f)... 1342s nova [W] Timed out waiting for f5226432-113e-41b1-86d9-7ae78faf9683 to get deleted. 1342s nova [W] Using flock in prodstack6-arm64 1342s Creating nova instance adt-plucky-arm64-python-biopython-20250219-122232-juju-7f2275-prod-proposed-migration-environment-20-b645ef9c-37de-4709-b4ee-d363f84c1666 from image adt/ubuntu-plucky-arm64-server-20250219.img (UUID 02c92adb-9d9d-4b0e-b071-488d8ee6210f)... 1342s nova [W] Timed out waiting for 1726801d-e6b4-4c8d-83c8-744497b3a775 to get deleted.