0s autopkgtest [20:54:15]: starting date and time: 2026-01-22 20:54:15+0000 0s autopkgtest [20:54:15]: git checkout: 508d4a25 a-v-ssh wait_for_ssh: demote "ssh connection failed" to a debug message 0s autopkgtest [20:54:15]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.qvp2uiqs/out --timeout-copy=6000 --setup-commands 'ln -s /dev/null /etc/systemd/system/bluetooth.service; printf "http_proxy=http://squid.internal:3128\nhttps_proxy=http://squid.internal:3128\nno_proxy=127.0.0.1,127.0.1.1,localhost,localdomain,internal,login.ubuntu.com,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com\n" >> /etc/environment' --apt-pocket=proposed=src:python3-defaults --apt-upgrade python-biopython --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=python3-defaults/3.14.2-1 -- lxd -r lxd-armhf-10.145.243.197 lxd-armhf-10.145.243.197:autopkgtest/ubuntu/resolute/armhf 23s autopkgtest [20:54:38]: testbed dpkg architecture: armhf 25s autopkgtest [20:54:40]: testbed apt version: 3.1.12 29s autopkgtest [20:54:44]: @@@@@@@@@@@@@@@@@@@@ test bed setup 30s autopkgtest [20:54:45]: testbed release detected to be: None 38s autopkgtest [20:54:53]: updating testbed package index (apt update) 41s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 41s Get:2 http://ftpmaster.internal/ubuntu resolute InRelease [124 kB] 41s Get:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease [124 kB] 42s Get:4 http://ftpmaster.internal/ubuntu resolute-security InRelease [124 kB] 42s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [81.6 kB] 42s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [22.2 kB] 42s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [2820 B] 42s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [1011 kB] 44s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf Packages [95.3 kB] 44s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/universe armhf Packages [658 kB] 45s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse armhf Packages [4896 B] 45s Get:12 http://ftpmaster.internal/ubuntu resolute/main Sources [1398 kB] 49s Get:13 http://ftpmaster.internal/ubuntu resolute/universe Sources [21.4 MB] 84s Get:14 http://ftpmaster.internal/ubuntu resolute/multiverse Sources [310 kB] 85s Get:15 http://ftpmaster.internal/ubuntu resolute/main armhf Packages [1371 kB] 87s Get:16 http://ftpmaster.internal/ubuntu resolute/universe armhf Packages [15.2 MB] 112s Get:17 http://ftpmaster.internal/ubuntu resolute/multiverse armhf Packages [175 kB] 114s Fetched 42.2 MB in 1min 13s (577 kB/s) 115s Reading package lists... 121s autopkgtest [20:56:16]: upgrading testbed (apt dist-upgrade and autopurge) 122s Reading package lists... 123s Building dependency tree... 123s Reading state information... 123s Calculating upgrade... 124s The following packages were automatically installed and are no longer required: 124s libpython3.13-minimal libpython3.13-stdlib python3.13 python3.13-minimal 124s Use 'apt autoremove' to remove them. 124s The following NEW packages will be installed: 124s libpython3.14-minimal libpython3.14-stdlib python3.14 python3.14-minimal 124s The following packages will be upgraded: 124s libplymouth5 libpython3-stdlib plymouth plymouth-theme-ubuntu-text python3 124s python3-gdbm python3-minimal 124s 7 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. 124s Need to get 6525 kB of archives. 124s After this operation, 22.5 MB of additional disk space will be used. 124s Get:1 http://ftpmaster.internal/ubuntu resolute/main armhf libpython3.14-minimal armhf 3.14.2-1 [905 kB] 126s Get:2 http://ftpmaster.internal/ubuntu resolute/main armhf python3.14-minimal armhf 3.14.2-1 [2155 kB] 130s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf python3-gdbm armhf 3.14.2-1 [11.1 kB] 130s Get:4 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf python3-minimal armhf 3.14.2-1 [28.2 kB] 130s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf python3 armhf 3.14.2-1 [22.9 kB] 130s Get:6 http://ftpmaster.internal/ubuntu resolute/main armhf libpython3.14-stdlib armhf 3.14.2-1 [2270 kB] 134s Get:7 http://ftpmaster.internal/ubuntu resolute/main armhf python3.14 armhf 3.14.2-1 [816 kB] 136s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf libpython3-stdlib armhf 3.14.2-1 [10.9 kB] 136s Get:9 http://ftpmaster.internal/ubuntu resolute/main armhf libplymouth5 armhf 24.004.60+git20250831.4a3c171d-0ubuntu4 [147 kB] 136s Get:10 http://ftpmaster.internal/ubuntu resolute/main armhf plymouth-theme-ubuntu-text armhf 24.004.60+git20250831.4a3c171d-0ubuntu4 [10.0 kB] 136s Get:11 http://ftpmaster.internal/ubuntu resolute/main armhf plymouth armhf 24.004.60+git20250831.4a3c171d-0ubuntu4 [150 kB] 137s Fetched 6525 kB in 13s (521 kB/s) 137s Selecting previously unselected package libpython3.14-minimal:armhf. 137s (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 ... 66485 files and directories currently installed.) 137s Preparing to unpack .../libpython3.14-minimal_3.14.2-1_armhf.deb ... 137s Unpacking libpython3.14-minimal:armhf (3.14.2-1) ... 137s Selecting previously unselected package python3.14-minimal. 137s Preparing to unpack .../python3.14-minimal_3.14.2-1_armhf.deb ... 137s Unpacking python3.14-minimal (3.14.2-1) ... 137s Preparing to unpack .../python3-gdbm_3.14.2-1_armhf.deb ... 137s Unpacking python3-gdbm (3.14.2-1) over (3.13.9-1) ... 137s Setting up libpython3.14-minimal:armhf (3.14.2-1) ... 137s Setting up python3.14-minimal (3.14.2-1) ... 139s (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 ... 66827 files and directories currently installed.) 139s Preparing to unpack .../python3-minimal_3.14.2-1_armhf.deb ... 139s Unpacking python3-minimal (3.14.2-1) over (3.13.7-1) ... 139s Setting up python3-minimal (3.14.2-1) ... 139s (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 ... 66827 files and directories currently installed.) 139s Preparing to unpack .../0-python3_3.14.2-1_armhf.deb ... 139s Unpacking python3 (3.14.2-1) over (3.13.7-1) ... 139s Selecting previously unselected package libpython3.14-stdlib:armhf. 139s Preparing to unpack .../1-libpython3.14-stdlib_3.14.2-1_armhf.deb ... 139s Unpacking libpython3.14-stdlib:armhf (3.14.2-1) ... 140s Selecting previously unselected package python3.14. 140s Preparing to unpack .../2-python3.14_3.14.2-1_armhf.deb ... 140s Unpacking python3.14 (3.14.2-1) ... 140s Preparing to unpack .../3-libpython3-stdlib_3.14.2-1_armhf.deb ... 140s Unpacking libpython3-stdlib:armhf (3.14.2-1) over (3.13.7-1) ... 140s Preparing to unpack .../4-libplymouth5_24.004.60+git20250831.4a3c171d-0ubuntu4_armhf.deb ... 140s Unpacking libplymouth5:armhf (24.004.60+git20250831.4a3c171d-0ubuntu4) over (24.004.60+git20250831.4a3c171d-0ubuntu3) ... 140s Preparing to unpack .../5-plymouth-theme-ubuntu-text_24.004.60+git20250831.4a3c171d-0ubuntu4_armhf.deb ... 140s Unpacking plymouth-theme-ubuntu-text (24.004.60+git20250831.4a3c171d-0ubuntu4) over (24.004.60+git20250831.4a3c171d-0ubuntu3) ... 140s Preparing to unpack .../6-plymouth_24.004.60+git20250831.4a3c171d-0ubuntu4_armhf.deb ... 140s Unpacking plymouth (24.004.60+git20250831.4a3c171d-0ubuntu4) over (24.004.60+git20250831.4a3c171d-0ubuntu3) ... 140s Setting up libpython3.14-stdlib:armhf (3.14.2-1) ... 140s Setting up libplymouth5:armhf (24.004.60+git20250831.4a3c171d-0ubuntu4) ... 140s Setting up python3.14 (3.14.2-1) ... 141s Setting up libpython3-stdlib:armhf (3.14.2-1) ... 141s Setting up python3-gdbm (3.14.2-1) ... 141s Setting up plymouth (24.004.60+git20250831.4a3c171d-0ubuntu4) ... 141s update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults 142s update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults 142s Setting up python3 (3.14.2-1) ... 142s Processing triggers for libc-bin (2.42-2ubuntu4) ... 143s Processing triggers for systemd (259-1ubuntu2) ... 143s Processing triggers for man-db (2.13.1-1) ... 144s Processing triggers for initramfs-tools (0.150ubuntu7) ... 144s Setting up plymouth-theme-ubuntu-text (24.004.60+git20250831.4a3c171d-0ubuntu4) ... 144s Processing triggers for initramfs-tools (0.150ubuntu7) ... 146s Reading package lists... 146s Building dependency tree... 146s Reading state information... 146s Solving dependencies... 147s The following packages will be REMOVED: 147s libpython3.13-minimal* libpython3.13-stdlib* python3.13* python3.13-minimal* 147s 0 upgraded, 0 newly installed, 4 to remove and 0 not upgraded. 147s After this operation, 21.3 MB disk space will be freed. 147s (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 ... 67257 files and directories currently installed.) 147s Removing python3.13 (3.13.11-1) ... 148s Removing libpython3.13-stdlib:armhf (3.13.11-1) ... 148s Removing python3.13-minimal (3.13.11-1) ... 149s Removing libpython3.13-minimal:armhf (3.13.11-1) ... 149s Processing triggers for man-db (2.13.1-1) ... 149s Processing triggers for systemd (259-1ubuntu2) ... 149s (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 ... 66518 files and directories currently installed.) 149s Purging configuration files for libpython3.13-minimal:armhf (3.13.11-1) ... 149s Purging configuration files for python3.13-minimal (3.13.11-1) ... 151s autopkgtest [20:56:46]: rebooting testbed after setup commands that affected boot 196s autopkgtest [20:57:31]: testbed running kernel: Linux 6.8.0-87-generic #88~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Tue Oct 14 14:00:09 UTC 2 223s autopkgtest [20:57:58]: @@@@@@@@@@@@@@@@@@@@ apt-source python-biopython 263s Get:1 http://ftpmaster.internal/ubuntu resolute/universe python-biopython 1.86+dfsg-1 (dsc) [3562 B] 263s Get:2 http://ftpmaster.internal/ubuntu resolute/universe python-biopython 1.86+dfsg-1 (tar) [14.5 MB] 263s Get:3 http://ftpmaster.internal/ubuntu resolute/universe python-biopython 1.86+dfsg-1 (diff) [41.4 kB] 263s gpgv: Signature made Wed Oct 29 22:41:45 2025 UTC 263s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 263s gpgv: issuer "emollier@debian.org" 263s gpgv: Can't check signature: No public key 263s dpkg-source: warning: cannot verify inline signature for ./python-biopython_1.86+dfsg-1.dsc: no acceptable signature found 264s autopkgtest [20:58:39]: testing package python-biopython version 1.86+dfsg-1 267s autopkgtest [20:58:42]: build not needed 275s autopkgtest [20:58:50]: test dependencies: preparing testbed 276s Reading package lists... 277s Building dependency tree... 277s Reading state information... 277s Solving dependencies... 277s The following NEW packages will be installed: 277s fontconfig-config fonts-dejavu-core fonts-dejavu-extra fonts-dejavu-mono 277s fonts-urw-base35 libblas3 libcairo2 libdeflate0 libfontconfig1 libfontenc1 277s libfreetype6 libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b 277s libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 libjs-jquery liblapack3 277s liblcms2-2 liblerc4 libopenjp2-7 libpixman-1-0 libpython3.13-minimal 277s libpython3.13-stdlib libraqm0 libsharpyuv0 libtiff6 libwebp7 libwebpdemux2 277s libwebpmux3 libxcb-render0 libxcb-shm0 libxrender1 python-biopython-doc 277s python3-all python3-biopython python3-biopython-sql python3-cairo 277s python3-charset-normalizer python3-freetype python3-numpy python3-numpy-dev 277s python3-pil python3-reportlab python3-rlpycairo python3.13 278s python3.13-minimal sgml-base w3c-sgml-lib x11-common xfonts-encodings 278s xfonts-utils xml-core 278s 0 upgraded, 56 newly installed, 0 to remove and 0 not upgraded. 278s Need to get 53.5 MB of archives. 278s After this operation, 152 MB of additional disk space will be used. 278s Get:1 http://ftpmaster.internal/ubuntu resolute/main armhf libpython3.13-minimal armhf 3.13.11-1 [875 kB] 279s Get:2 http://ftpmaster.internal/ubuntu resolute/main armhf python3.13-minimal armhf 3.13.11-1 [2055 kB] 282s Get:3 http://ftpmaster.internal/ubuntu resolute/main armhf python3-numpy-dev armhf 1:2.3.5+ds-3 [141 kB] 282s Get:4 http://ftpmaster.internal/ubuntu resolute/main armhf libblas3 armhf 3.12.1-7ubuntu1 [133 kB] 282s Get:5 http://ftpmaster.internal/ubuntu resolute/main armhf libgfortran5 armhf 15.2.0-11ubuntu1 [334 kB] 283s Get:6 http://ftpmaster.internal/ubuntu resolute/main armhf liblapack3 armhf 3.12.1-7ubuntu1 [2090 kB] 285s Get:7 http://ftpmaster.internal/ubuntu resolute/main armhf python3-numpy armhf 1:2.3.5+ds-3 [4729 kB] 291s Get:8 http://ftpmaster.internal/ubuntu resolute/main armhf libpython3.13-stdlib armhf 3.13.11-1 [1960 kB] 294s Get:9 http://ftpmaster.internal/ubuntu resolute/main armhf python3.13 armhf 3.13.11-1 [758 kB] 295s Get:10 http://ftpmaster.internal/ubuntu resolute/main armhf fonts-dejavu-mono all 2.37-8build1 [502 kB] 295s Get:11 http://ftpmaster.internal/ubuntu resolute/main armhf fonts-dejavu-core all 2.37-8build1 [834 kB] 296s Get:12 http://ftpmaster.internal/ubuntu resolute/main armhf libfontenc1 armhf 1:1.1.8-1build2 [11.7 kB] 296s Get:13 http://ftpmaster.internal/ubuntu resolute/main armhf libfreetype6 armhf 2.14.1+dfsg-2 [345 kB] 297s Get:14 http://ftpmaster.internal/ubuntu resolute/main armhf x11-common all 1:7.7+24ubuntu1 [22.4 kB] 297s Get:15 http://ftpmaster.internal/ubuntu resolute/main armhf xfonts-encodings all 1:1.0.5-0ubuntu3 [576 kB] 298s Get:16 http://ftpmaster.internal/ubuntu resolute/main armhf xfonts-utils armhf 1:7.7+7build1 [91.0 kB] 298s Get:17 http://ftpmaster.internal/ubuntu resolute/main armhf fonts-urw-base35 all 20200910-8build1 [10.9 MB] 310s Get:18 http://ftpmaster.internal/ubuntu resolute/main armhf fontconfig-config armhf 2.15.0-2.4ubuntu1 [38.2 kB] 310s Get:19 http://ftpmaster.internal/ubuntu resolute/main armhf fonts-dejavu-extra all 2.37-8build1 [1944 kB] 312s Get:20 http://ftpmaster.internal/ubuntu resolute/main armhf libfontconfig1 armhf 2.15.0-2.4ubuntu1 [116 kB] 312s Get:21 http://ftpmaster.internal/ubuntu resolute/main armhf libpixman-1-0 armhf 0.46.4-1 [196 kB] 313s Get:22 http://ftpmaster.internal/ubuntu resolute/main armhf libxcb-render0 armhf 1.17.0-2build1 [15.5 kB] 313s Get:23 http://ftpmaster.internal/ubuntu resolute/main armhf libxcb-shm0 armhf 1.17.0-2build1 [5962 B] 313s Get:24 http://ftpmaster.internal/ubuntu resolute/main armhf libxrender1 armhf 1:0.9.12-1 [16.6 kB] 313s Get:25 http://ftpmaster.internal/ubuntu resolute/main armhf libcairo2 armhf 1.18.4-3 [489 kB] 313s Get:26 http://ftpmaster.internal/ubuntu resolute/main armhf libdeflate0 armhf 1.23-2 [38.7 kB] 313s Get:27 http://ftpmaster.internal/ubuntu resolute/main armhf libgomp1 armhf 15.2.0-11ubuntu1 [129 kB] 313s Get:28 http://ftpmaster.internal/ubuntu resolute/main armhf libgraphite2-3 armhf 1.3.14-11ubuntu1 [65.2 kB] 313s Get:29 http://ftpmaster.internal/ubuntu resolute/main armhf libharfbuzz0b armhf 12.3.0-4 [507 kB] 314s Get:30 http://ftpmaster.internal/ubuntu resolute/main armhf libimagequant0 armhf 2.18.0-1build1 [31.1 kB] 314s Get:31 http://ftpmaster.internal/ubuntu resolute/main armhf libjpeg-turbo8 armhf 2.1.5-4ubuntu2 [127 kB] 314s Get:32 http://ftpmaster.internal/ubuntu resolute/main armhf libjpeg8 armhf 8c-2ubuntu11 [2148 B] 314s Get:33 http://ftpmaster.internal/ubuntu resolute/main armhf libjs-jquery all 3.7.1+dfsg+~3.5.33-1build1 [321 kB] 314s Get:34 http://ftpmaster.internal/ubuntu resolute/main armhf liblcms2-2 armhf 2.17-1 [139 kB] 314s Get:35 http://ftpmaster.internal/ubuntu resolute/main armhf liblerc4 armhf 4.0.0+ds-5ubuntu2 [162 kB] 315s Get:36 http://ftpmaster.internal/ubuntu resolute/main armhf libraqm0 armhf 0.10.3-1 [12.7 kB] 315s Get:37 http://ftpmaster.internal/ubuntu resolute/main armhf libsharpyuv0 armhf 1.5.0-0.1build1 [16.3 kB] 315s Get:38 http://ftpmaster.internal/ubuntu resolute/main armhf libjbig0 armhf 2.1-6.1ubuntu3 [25.3 kB] 315s Get:39 http://ftpmaster.internal/ubuntu resolute/main armhf libwebp7 armhf 1.5.0-0.1build1 [189 kB] 315s Get:40 http://ftpmaster.internal/ubuntu resolute/main armhf libtiff6 armhf 4.7.0-3ubuntu3 [188 kB] 315s Get:41 http://ftpmaster.internal/ubuntu resolute/main armhf libwebpdemux2 armhf 1.5.0-0.1build1 [11.7 kB] 315s Get:42 http://ftpmaster.internal/ubuntu resolute/main armhf libwebpmux3 armhf 1.5.0-0.1build1 [22.4 kB] 315s Get:43 http://ftpmaster.internal/ubuntu resolute/universe armhf python-biopython-doc all 1.86+dfsg-1 [18.1 MB] 337s Get:44 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf python3-all armhf 3.14.2-1 [888 B] 337s Get:45 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-charset-normalizer armhf 3.4.4-2 [167 kB] 337s Get:46 http://ftpmaster.internal/ubuntu resolute/main armhf libopenjp2-7 armhf 2.5.4-1 [175 kB] 337s Get:47 http://ftpmaster.internal/ubuntu resolute/main armhf python3-pil armhf 12.0.0-1ubuntu1 [462 kB] 338s Get:48 http://ftpmaster.internal/ubuntu resolute/main armhf python3-cairo armhf 1.27.0-2build1 [135 kB] 338s Get:49 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-freetype all 2.5.1-2 [92.2 kB] 338s Get:50 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-rlpycairo all 0.3.0-4 [9332 B] 338s Get:51 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-reportlab all 4.4.9-1 [1149 kB] 339s Get:52 http://ftpmaster.internal/ubuntu resolute/main armhf sgml-base all 1.31+nmu1 [11.0 kB] 339s Get:53 http://ftpmaster.internal/ubuntu resolute/main armhf xml-core all 0.19build1 [20.3 kB] 339s Get:54 http://ftpmaster.internal/ubuntu resolute/universe armhf w3c-sgml-lib all 1.3-3build1 [278 kB] 340s Get:55 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-biopython armhf 1.86+dfsg-1 [1652 kB] 341s Get:56 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-biopython-sql all 1.86+dfsg-1 [26.4 kB] 342s Fetched 53.5 MB in 1min 4s (836 kB/s) 342s Selecting previously unselected package libpython3.13-minimal:armhf. 342s (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 ... 66518 files and directories currently installed.) 342s Preparing to unpack .../00-libpython3.13-minimal_3.13.11-1_armhf.deb ... 342s Unpacking libpython3.13-minimal:armhf (3.13.11-1) ... 342s Selecting previously unselected package python3.13-minimal. 342s Preparing to unpack .../01-python3.13-minimal_3.13.11-1_armhf.deb ... 342s Unpacking python3.13-minimal (3.13.11-1) ... 342s Selecting previously unselected package python3-numpy-dev:armhf. 342s Preparing to unpack .../02-python3-numpy-dev_1%3a2.3.5+ds-3_armhf.deb ... 342s Unpacking python3-numpy-dev:armhf (1:2.3.5+ds-3) ... 342s Selecting previously unselected package libblas3:armhf. 342s Preparing to unpack .../03-libblas3_3.12.1-7ubuntu1_armhf.deb ... 342s Unpacking libblas3:armhf (3.12.1-7ubuntu1) ... 342s Selecting previously unselected package libgfortran5:armhf. 342s Preparing to unpack .../04-libgfortran5_15.2.0-11ubuntu1_armhf.deb ... 342s Unpacking libgfortran5:armhf (15.2.0-11ubuntu1) ... 342s Selecting previously unselected package liblapack3:armhf. 342s Preparing to unpack .../05-liblapack3_3.12.1-7ubuntu1_armhf.deb ... 342s Unpacking liblapack3:armhf (3.12.1-7ubuntu1) ... 343s Selecting previously unselected package python3-numpy. 343s Preparing to unpack .../06-python3-numpy_1%3a2.3.5+ds-3_armhf.deb ... 343s Unpacking python3-numpy (1:2.3.5+ds-3) ... 343s Selecting previously unselected package libpython3.13-stdlib:armhf. 343s Preparing to unpack .../07-libpython3.13-stdlib_3.13.11-1_armhf.deb ... 343s Unpacking libpython3.13-stdlib:armhf (3.13.11-1) ... 343s Selecting previously unselected package python3.13. 343s Preparing to unpack .../08-python3.13_3.13.11-1_armhf.deb ... 343s Unpacking python3.13 (3.13.11-1) ... 343s Selecting previously unselected package fonts-dejavu-mono. 343s Preparing to unpack .../09-fonts-dejavu-mono_2.37-8build1_all.deb ... 343s Unpacking fonts-dejavu-mono (2.37-8build1) ... 343s Selecting previously unselected package fonts-dejavu-core. 343s Preparing to unpack .../10-fonts-dejavu-core_2.37-8build1_all.deb ... 343s Unpacking fonts-dejavu-core (2.37-8build1) ... 343s Selecting previously unselected package libfontenc1:armhf. 343s Preparing to unpack .../11-libfontenc1_1%3a1.1.8-1build2_armhf.deb ... 343s Unpacking libfontenc1:armhf (1:1.1.8-1build2) ... 343s Selecting previously unselected package libfreetype6:armhf. 343s Preparing to unpack .../12-libfreetype6_2.14.1+dfsg-2_armhf.deb ... 343s Unpacking libfreetype6:armhf (2.14.1+dfsg-2) ... 343s Selecting previously unselected package x11-common. 343s Preparing to unpack .../13-x11-common_1%3a7.7+24ubuntu1_all.deb ... 343s Unpacking x11-common (1:7.7+24ubuntu1) ... 343s Selecting previously unselected package xfonts-encodings. 343s Preparing to unpack .../14-xfonts-encodings_1%3a1.0.5-0ubuntu3_all.deb ... 343s Unpacking xfonts-encodings (1:1.0.5-0ubuntu3) ... 343s Selecting previously unselected package xfonts-utils. 343s Preparing to unpack .../15-xfonts-utils_1%3a7.7+7build1_armhf.deb ... 343s Unpacking xfonts-utils (1:7.7+7build1) ... 343s Selecting previously unselected package fonts-urw-base35. 343s Preparing to unpack .../16-fonts-urw-base35_20200910-8build1_all.deb ... 344s Unpacking fonts-urw-base35 (20200910-8build1) ... 344s Selecting previously unselected package fontconfig-config. 344s Preparing to unpack .../17-fontconfig-config_2.15.0-2.4ubuntu1_armhf.deb ... 344s Unpacking fontconfig-config (2.15.0-2.4ubuntu1) ... 344s Selecting previously unselected package fonts-dejavu-extra. 344s Preparing to unpack .../18-fonts-dejavu-extra_2.37-8build1_all.deb ... 344s Unpacking fonts-dejavu-extra (2.37-8build1) ... 344s Selecting previously unselected package libfontconfig1:armhf. 344s Preparing to unpack .../19-libfontconfig1_2.15.0-2.4ubuntu1_armhf.deb ... 344s Unpacking libfontconfig1:armhf (2.15.0-2.4ubuntu1) ... 344s Selecting previously unselected package libpixman-1-0:armhf. 344s Preparing to unpack .../20-libpixman-1-0_0.46.4-1_armhf.deb ... 344s Unpacking libpixman-1-0:armhf (0.46.4-1) ... 344s Selecting previously unselected package libxcb-render0:armhf. 344s Preparing to unpack .../21-libxcb-render0_1.17.0-2build1_armhf.deb ... 344s Unpacking libxcb-render0:armhf (1.17.0-2build1) ... 344s Selecting previously unselected package libxcb-shm0:armhf. 344s Preparing to unpack .../22-libxcb-shm0_1.17.0-2build1_armhf.deb ... 344s Unpacking libxcb-shm0:armhf (1.17.0-2build1) ... 344s Selecting previously unselected package libxrender1:armhf. 344s Preparing to unpack .../23-libxrender1_1%3a0.9.12-1_armhf.deb ... 344s Unpacking libxrender1:armhf (1:0.9.12-1) ... 344s Selecting previously unselected package libcairo2:armhf. 344s Preparing to unpack .../24-libcairo2_1.18.4-3_armhf.deb ... 344s Unpacking libcairo2:armhf (1.18.4-3) ... 344s Selecting previously unselected package libdeflate0:armhf. 344s Preparing to unpack .../25-libdeflate0_1.23-2_armhf.deb ... 344s Unpacking libdeflate0:armhf (1.23-2) ... 344s Selecting previously unselected package libgomp1:armhf. 344s Preparing to unpack .../26-libgomp1_15.2.0-11ubuntu1_armhf.deb ... 344s Unpacking libgomp1:armhf (15.2.0-11ubuntu1) ... 344s Selecting previously unselected package libgraphite2-3:armhf. 345s Preparing to unpack .../27-libgraphite2-3_1.3.14-11ubuntu1_armhf.deb ... 345s Unpacking libgraphite2-3:armhf (1.3.14-11ubuntu1) ... 345s Selecting previously unselected package libharfbuzz0b:armhf. 345s Preparing to unpack .../28-libharfbuzz0b_12.3.0-4_armhf.deb ... 345s Unpacking libharfbuzz0b:armhf (12.3.0-4) ... 345s Selecting previously unselected package libimagequant0:armhf. 345s Preparing to unpack .../29-libimagequant0_2.18.0-1build1_armhf.deb ... 345s Unpacking libimagequant0:armhf (2.18.0-1build1) ... 345s Selecting previously unselected package libjpeg-turbo8:armhf. 345s Preparing to unpack .../30-libjpeg-turbo8_2.1.5-4ubuntu2_armhf.deb ... 345s Unpacking libjpeg-turbo8:armhf (2.1.5-4ubuntu2) ... 345s Selecting previously unselected package libjpeg8:armhf. 345s Preparing to unpack .../31-libjpeg8_8c-2ubuntu11_armhf.deb ... 345s Unpacking libjpeg8:armhf (8c-2ubuntu11) ... 345s Selecting previously unselected package libjs-jquery. 345s Preparing to unpack .../32-libjs-jquery_3.7.1+dfsg+~3.5.33-1build1_all.deb ... 345s Unpacking libjs-jquery (3.7.1+dfsg+~3.5.33-1build1) ... 345s Selecting previously unselected package liblcms2-2:armhf. 345s Preparing to unpack .../33-liblcms2-2_2.17-1_armhf.deb ... 345s Unpacking liblcms2-2:armhf (2.17-1) ... 345s Selecting previously unselected package liblerc4:armhf. 345s Preparing to unpack .../34-liblerc4_4.0.0+ds-5ubuntu2_armhf.deb ... 345s Unpacking liblerc4:armhf (4.0.0+ds-5ubuntu2) ... 345s Selecting previously unselected package libraqm0:armhf. 345s Preparing to unpack .../35-libraqm0_0.10.3-1_armhf.deb ... 345s Unpacking libraqm0:armhf (0.10.3-1) ... 345s Selecting previously unselected package libsharpyuv0:armhf. 345s Preparing to unpack .../36-libsharpyuv0_1.5.0-0.1build1_armhf.deb ... 345s Unpacking libsharpyuv0:armhf (1.5.0-0.1build1) ... 345s Selecting previously unselected package libjbig0:armhf. 345s Preparing to unpack .../37-libjbig0_2.1-6.1ubuntu3_armhf.deb ... 345s Unpacking libjbig0:armhf (2.1-6.1ubuntu3) ... 345s Selecting previously unselected package libwebp7:armhf. 345s Preparing to unpack .../38-libwebp7_1.5.0-0.1build1_armhf.deb ... 345s Unpacking libwebp7:armhf (1.5.0-0.1build1) ... 345s Selecting previously unselected package libtiff6:armhf. 345s Preparing to unpack .../39-libtiff6_4.7.0-3ubuntu3_armhf.deb ... 345s Unpacking libtiff6:armhf (4.7.0-3ubuntu3) ... 345s Selecting previously unselected package libwebpdemux2:armhf. 345s Preparing to unpack .../40-libwebpdemux2_1.5.0-0.1build1_armhf.deb ... 345s Unpacking libwebpdemux2:armhf (1.5.0-0.1build1) ... 345s Selecting previously unselected package libwebpmux3:armhf. 345s Preparing to unpack .../41-libwebpmux3_1.5.0-0.1build1_armhf.deb ... 345s Unpacking libwebpmux3:armhf (1.5.0-0.1build1) ... 345s Selecting previously unselected package python-biopython-doc. 345s Preparing to unpack .../42-python-biopython-doc_1.86+dfsg-1_all.deb ... 345s Unpacking python-biopython-doc (1.86+dfsg-1) ... 346s Selecting previously unselected package python3-all. 346s Preparing to unpack .../43-python3-all_3.14.2-1_armhf.deb ... 346s Unpacking python3-all (3.14.2-1) ... 346s Selecting previously unselected package python3-charset-normalizer. 346s Preparing to unpack .../44-python3-charset-normalizer_3.4.4-2_armhf.deb ... 346s Unpacking python3-charset-normalizer (3.4.4-2) ... 346s Selecting previously unselected package libopenjp2-7:armhf. 346s Preparing to unpack .../45-libopenjp2-7_2.5.4-1_armhf.deb ... 346s Unpacking libopenjp2-7:armhf (2.5.4-1) ... 346s Selecting previously unselected package python3-pil:armhf. 346s Preparing to unpack .../46-python3-pil_12.0.0-1ubuntu1_armhf.deb ... 346s Unpacking python3-pil:armhf (12.0.0-1ubuntu1) ... 346s Selecting previously unselected package python3-cairo. 346s Preparing to unpack .../47-python3-cairo_1.27.0-2build1_armhf.deb ... 346s Unpacking python3-cairo (1.27.0-2build1) ... 346s Selecting previously unselected package python3-freetype. 346s Preparing to unpack .../48-python3-freetype_2.5.1-2_all.deb ... 346s Unpacking python3-freetype (2.5.1-2) ... 346s Selecting previously unselected package python3-rlpycairo. 346s Preparing to unpack .../49-python3-rlpycairo_0.3.0-4_all.deb ... 346s Unpacking python3-rlpycairo (0.3.0-4) ... 346s Selecting previously unselected package python3-reportlab. 346s Preparing to unpack .../50-python3-reportlab_4.4.9-1_all.deb ... 346s Unpacking python3-reportlab (4.4.9-1) ... 346s Selecting previously unselected package sgml-base. 346s Preparing to unpack .../51-sgml-base_1.31+nmu1_all.deb ... 346s Unpacking sgml-base (1.31+nmu1) ... 346s Selecting previously unselected package xml-core. 346s Preparing to unpack .../52-xml-core_0.19build1_all.deb ... 346s Unpacking xml-core (0.19build1) ... 346s Selecting previously unselected package w3c-sgml-lib. 346s Preparing to unpack .../53-w3c-sgml-lib_1.3-3build1_all.deb ... 346s Unpacking w3c-sgml-lib (1.3-3build1) ... 346s Selecting previously unselected package python3-biopython. 346s Preparing to unpack .../54-python3-biopython_1.86+dfsg-1_armhf.deb ... 346s Unpacking python3-biopython (1.86+dfsg-1) ... 347s Selecting previously unselected package python3-biopython-sql. 347s Preparing to unpack .../55-python3-biopython-sql_1.86+dfsg-1_all.deb ... 347s Unpacking python3-biopython-sql (1.86+dfsg-1) ... 347s Setting up libgraphite2-3:armhf (1.3.14-11ubuntu1) ... 347s Setting up liblcms2-2:armhf (2.17-1) ... 347s Setting up libpixman-1-0:armhf (0.46.4-1) ... 347s Setting up libsharpyuv0:armhf (1.5.0-0.1build1) ... 347s Setting up liblerc4:armhf (4.0.0+ds-5ubuntu2) ... 347s Setting up libxrender1:armhf (1:0.9.12-1) ... 347s Setting up libxcb-render0:armhf (1.17.0-2build1) ... 347s Setting up python3-charset-normalizer (3.4.4-2) ... 347s Setting up x11-common (1:7.7+24ubuntu1) ... 347s Setting up libdeflate0:armhf (1.23-2) ... 347s Setting up libxcb-shm0:armhf (1.17.0-2build1) ... 347s Setting up libgomp1:armhf (15.2.0-11ubuntu1) ... 347s Setting up libjbig0:armhf (2.1-6.1ubuntu3) ... 347s Setting up libpython3.13-minimal:armhf (3.13.11-1) ... 347s Setting up libfontenc1:armhf (1:1.1.8-1build2) ... 347s Setting up libblas3:armhf (3.12.1-7ubuntu1) ... 347s update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode 347s Setting up libfreetype6:armhf (2.14.1+dfsg-2) ... 347s Setting up xfonts-encodings (1:1.0.5-0ubuntu3) ... 347s Setting up libimagequant0:armhf (2.18.0-1build1) ... 347s Setting up fonts-dejavu-mono (2.37-8build1) ... 347s Setting up python3-numpy-dev:armhf (1:2.3.5+ds-3) ... 347s Setting up fonts-dejavu-core (2.37-8build1) ... 347s Setting up libjpeg-turbo8:armhf (2.1.5-4ubuntu2) ... 347s Setting up libgfortran5:armhf (15.2.0-11ubuntu1) ... 347s Setting up libwebp7:armhf (1.5.0-0.1build1) ... 347s Setting up fonts-dejavu-extra (2.37-8build1) ... 347s Setting up libopenjp2-7:armhf (2.5.4-1) ... 347s Setting up python3.13-minimal (3.13.11-1) ... 348s Setting up libharfbuzz0b:armhf (12.3.0-4) ... 348s Setting up sgml-base (1.31+nmu1) ... 348s Setting up libjs-jquery (3.7.1+dfsg+~3.5.33-1build1) ... 348s Setting up libwebpmux3:armhf (1.5.0-0.1build1) ... 348s Setting up libpython3.13-stdlib:armhf (3.13.11-1) ... 348s Setting up libjpeg8:armhf (8c-2ubuntu11) ... 348s Setting up liblapack3:armhf (3.12.1-7ubuntu1) ... 348s update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode 348s Setting up python3.13 (3.13.11-1) ... 350s Setting up fontconfig-config (2.15.0-2.4ubuntu1) ... 350s Setting up libwebpdemux2:armhf (1.5.0-0.1build1) ... 350s Setting up python3-all (3.14.2-1) ... 350s Setting up python3-freetype (2.5.1-2) ... 350s Setting up xfonts-utils (1:7.7+7build1) ... 350s Setting up libraqm0:armhf (0.10.3-1) ... 350s Setting up python3-numpy (1:2.3.5+ds-3) ... 355s Setting up python-biopython-doc (1.86+dfsg-1) ... 355s Setting up libtiff6:armhf (4.7.0-3ubuntu3) ... 355s Setting up xml-core (0.19build1) ... 355s Setting up libfontconfig1:armhf (2.15.0-2.4ubuntu1) ... 355s Setting up fonts-urw-base35 (20200910-8build1) ... 355s Setting up libcairo2:armhf (1.18.4-3) ... 355s Setting up python3-pil:armhf (12.0.0-1ubuntu1) ... 356s Setting up python3-cairo (1.27.0-2build1) ... 357s Setting up python3-rlpycairo (0.3.0-4) ... 357s Setting up python3-reportlab (4.4.9-1) ... 359s Processing triggers for libc-bin (2.42-2ubuntu4) ... 359s Processing triggers for systemd (259-1ubuntu2) ... 359s Processing triggers for man-db (2.13.1-1) ... 360s Processing triggers for sgml-base (1.31+nmu1) ... 360s Setting up w3c-sgml-lib (1.3-3build1) ... 391s Setting up python3-biopython (1.86+dfsg-1) ... 394s Setting up python3-biopython-sql (1.86+dfsg-1) ... 406s autopkgtest [21:01:01]: test dependencies: sh debian/tests/run-unit-test 406s autopkgtest [21:01:01]: test dependencies: [----------------------- 409s cp: cannot stat '/usr/share/libcifpp/mmcif_pdbx.dic': No such file or directory 409s cp: cannot stat '/usr/share/libcifpp/mmcif_ma.dic': No such file or directory 413s mkdir: created directory 'Bio' 413s mkdir: created directory 'Bio/Align' 413s mkdir: created directory 'Bio/Align/substitution_matrices' 413s mkdir: created directory 'Bio/Align/substitution_matrices/data/' 413s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER22' -> 'Bio/Align/substitution_matrices/data/BENNER22' 413s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER6' -> 'Bio/Align/substitution_matrices/data/BENNER6' 413s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER74' -> 'Bio/Align/substitution_matrices/data/BENNER74' 413s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLASTN' -> 'Bio/Align/substitution_matrices/data/BLASTN' 413s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLASTP' -> 'Bio/Align/substitution_matrices/data/BLASTP' 413s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM45' -> 'Bio/Align/substitution_matrices/data/BLOSUM45' 413s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM50' -> 'Bio/Align/substitution_matrices/data/BLOSUM50' 413s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM62' -> 'Bio/Align/substitution_matrices/data/BLOSUM62' 413s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM80' -> 'Bio/Align/substitution_matrices/data/BLOSUM80' 413s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM90' -> 'Bio/Align/substitution_matrices/data/BLOSUM90' 413s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/DAYHOFF' -> 'Bio/Align/substitution_matrices/data/DAYHOFF' 413s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/FENG' -> 'Bio/Align/substitution_matrices/data/FENG' 413s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/GENETIC' -> 'Bio/Align/substitution_matrices/data/GENETIC' 413s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/GONNET1992' -> 'Bio/Align/substitution_matrices/data/GONNET1992' 413s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/HOXD70' -> 'Bio/Align/substitution_matrices/data/HOXD70' 413s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/JOHNSON' -> 'Bio/Align/substitution_matrices/data/JOHNSON' 413s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/JONES' -> 'Bio/Align/substitution_matrices/data/JONES' 413s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/LEVIN' -> 'Bio/Align/substitution_matrices/data/LEVIN' 413s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MCLACHLAN' -> 'Bio/Align/substitution_matrices/data/MCLACHLAN' 413s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MDM78' -> 'Bio/Align/substitution_matrices/data/MDM78' 413s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MEGABLAST' -> 'Bio/Align/substitution_matrices/data/MEGABLAST' 413s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/NUC.4.4' -> 'Bio/Align/substitution_matrices/data/NUC.4.4' 413s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM250' -> 'Bio/Align/substitution_matrices/data/PAM250' 413s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM30' -> 'Bio/Align/substitution_matrices/data/PAM30' 413s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM70' -> 'Bio/Align/substitution_matrices/data/PAM70' 413s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/RAO' -> 'Bio/Align/substitution_matrices/data/RAO' 413s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/RISLER' -> 'Bio/Align/substitution_matrices/data/RISLER' 413s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/SCHNEIDER' -> 'Bio/Align/substitution_matrices/data/SCHNEIDER' 413s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/STR' -> 'Bio/Align/substitution_matrices/data/STR' 413s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/TRANS' -> 'Bio/Align/substitution_matrices/data/TRANS' 414s test_Ace ... ok 414s test_Affy ... ok 415s test_AlignIO ... ok 415s test_AlignIO_ClustalIO ... ok 415s test_AlignIO_EmbossIO ... ok 415s test_AlignIO_FastaIO ... ok 415s test_AlignIO_MauveIO ... ok 415s test_AlignIO_PhylipIO ... ok 415s test_AlignIO_convert ... ok 416s test_Align_Alignment ... ok 416s test_Align_a2m ... ok 416s test_Align_bed ... ok 417s test_Align_bigbed ... ok 418s test_Align_bigmaf ... ok 418s test_Align_bigpsl ... ok 419s test_Align_chain ... ok 419s test_Align_clustal ... ok 423s test_Align_codonalign ... ok 423s test_Align_emboss ... ok 423s test_Align_exonerate ... ok 423s test_Align_fasta ... ok 423s test_Align_format_matrix ... ok 424s test_Align_hhr ... ok 426s test_Align_maf ... ok 426s test_Align_mauve ... ok 426s test_Align_msf ... ok 426s test_Align_nexus ... ok 426s test_Align_phylip ... ok 427s test_Align_psl ... ok 427s test_Align_sam ... ok 429s test_Align_stockholm ... ok 430s test_Align_tabular ... ok 430s test_BioSQL_MySQLdb_online ... skipping. internet not available 430s test_BioSQL_mysql_connector ... skipping. BioSQL test configuration file biosql.ini missing (see biosql.ini.sample) 431s test_BioSQL_mysql_connector_online ... skipping. internet not available 431s test_BioSQL_psycopg2_online ... skipping. internet not available 436s test_BioSQL_sqlite3 ... ok 436s test_BioSQL_sqlite3_online ... skipping. internet not available 437s test_Blast_Record ... ok 437s test_Blast_parser ... ok 437s test_CAPS ... ok 437s test_Chi2 ... ok 438s test_Cluster ... ok 438s test_CodonTable ... ok 438s test_ColorSpiral ... ok 438s test_Compass ... ok 439s test_Consensus ... ok 439s test_EMBL_unittest ... ok 439s test_EmbossPrimer ... ok 443s test_Entrez ... ok 443s test_Entrez_online ... skipping. internet not available 444s test_Entrez_parser ... ok 444s test_Enzyme ... ok 444s test_ExPASy ... skipping. internet not available 444s test_File ... ok 445s test_GenBank ... ok 447s test_GenomeDiagram ... Warn: Can't find .pfb for face 'Helvetica' 449s ok 450s test_GraphicsChromosome ... ok 450s test_GraphicsDistribution ... ok 451s test_GraphicsGeneral ... ok 451s test_KEGG ... ok 452s test_KEGG_online ... skipping. internet not available 458s test_KGML_graphics ... ok 458s test_KGML_graphics_online ... skipping. internet not available 459s test_KGML_nographics ... ok 459s test_KeyWList ... ok 460s test_MafIO_index ... ok 461s test_Medline ... ok 462s test_NCBIXML ... Exception ignored in: 462s Traceback (most recent call last): 462s File "/usr/lib/python3/dist-packages/Bio/Blast/NCBIXML.py", line 1319, in parse 462s expat_parser.Parse(NULL, True) 462s xml.parsers.expat.ExpatError: unclosed token: line 320, column 0 462s ok 462s test_NCBI_qblast ... ok 462s test_NMR ... ok 463s test_Nexus ... ok 463s test_PAML_baseml ... ok 464s test_PAML_codeml ... ok 464s test_PAML_yn00 ... ok 471s test_PDB_CEAligner ... ok 472s test_PDB_DSSP ... ok 472s test_PDB_Dice ... ok 472s test_PDB_Disordered ... ok 472s test_PDB_Exposure ... ok 472s test_PDB_FragmentMapper ... ok 475s test_PDB_KDTree ... ok 475s test_PDB_MMCIF2Dict ... ok 475s test_PDB_MMCIFIO ... ok 477s test_PDB_MMCIFParser ... ok 477s test_PDB_NACCESS ... ok 477s test_PDB_PDBIO ... ok 478s test_PDB_PDBList ... skipping. internet not available 487s test_PDB_PDBMLParser ... ok 487s test_PDB_PDBParser ... ok 487s 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 487s test_PDB_Polypeptide ... ok 488s test_PDB_QCPSuperimposer ... ok 492s test_PDB_SASA ... ok 493s test_PDB_SMCRA ... ok 493s test_PDB_Selection ... ok 494s test_PDB_StructureAlignment ... ok 494s test_PDB_Superimposer ... ok 494s test_PDB_alphafold_db ... skipping. internet not available 494s test_PDB_binary_cif ... skipping. Error: Install msgpack to use Bio.PDB.binaryCIF (e.g. pip install msgpack) 494s 495s test_PDB_internal_coords ... skipping. Error: Install mmtf to use Bio.PDB.mmtf (e.g. pip install mmtf-python) 495s 495s test_PDB_parse_pdb_header ... ok 495s test_PDB_vectors ... ok 495s test_PQR ... ok 495s test_Pathway ... ok 495s test_Phd ... ok 496s test_Phylo ... ok 497s test_PhyloXML ... ok 497s test_Phylo_CDAO ... skipping. Install RDFlib if you want to use the CDAO tree format. 497s test_Phylo_NeXML ... ok 497s test_Phylo_igraph ... skipping. Install igraph if you wish to use it with Bio.Phylo 497s test_Phylo_matplotlib ... skipping. Install matplotlib if you want to use Bio.Phylo._utils. 498s test_Phylo_networkx ... skipping. Install networkx if you wish to use it with Bio.Phylo 498s test_PopGen_GenePop_nodepend ... ok 498s test_ProtParam ... ok 499s test_RCSBFormats ... ok 499s test_Restriction ... ok 499s test_SCOP_Astral ... ok 499s test_SCOP_Cla ... ok 499s test_SCOP_Des ... ok 499s test_SCOP_Dom ... ok 500s test_SCOP_Hie ... ok 500s test_SCOP_Raf ... ok 500s test_SCOP_Residues ... ok 500s test_SCOP_Scop ... ok 500s test_SVDSuperimposer ... ok 500s test_SearchIO_blast_tab ... ok 501s test_SearchIO_blast_tab_index ... ok 501s test_SearchIO_blast_xml ... ok 503s test_SearchIO_blast_xml_index ... ok 503s test_SearchIO_blat_psl ... ok 503s test_SearchIO_blat_psl_index ... ok 503s test_SearchIO_exonerate ... ok 504s test_SearchIO_exonerate_text_index ... ok 504s test_SearchIO_exonerate_vulgar_index ... ok 504s test_SearchIO_fasta_m10 ... ok 504s test_SearchIO_fasta_m10_index ... ok 505s test_SearchIO_hhsuite2_text ... ok 505s test_SearchIO_hmmer2_text ... ok 505s test_SearchIO_hmmer2_text_index ... ok 505s test_SearchIO_hmmer3_domtab ... ok 506s test_SearchIO_hmmer3_domtab_index ... ok 506s test_SearchIO_hmmer3_tab ... ok 506s test_SearchIO_hmmer3_tab_index ... ok 506s test_SearchIO_hmmer3_text ... ok 506s test_SearchIO_hmmer3_text_index ... ok 507s test_SearchIO_infernal_tab ... ok 507s test_SearchIO_infernal_tab_index ... ok 507s test_SearchIO_infernal_text ... ok 507s test_SearchIO_infernal_text_index ... ok 507s test_SearchIO_interproscan_xml ... ok 508s test_SearchIO_model ... ok 508s test_SearchIO_write ... ok 508s test_SeqFeature ... ok 537s test_SeqIO ... ok 538s test_SeqIO_AbiIO ... ok 538s test_SeqIO_FastaIO ... ok 538s test_SeqIO_Gck ... ok 538s test_SeqIO_Gfa ... ok 538s test_SeqIO_Insdc ... ok 538s test_SeqIO_NibIO ... ok 541s test_SeqIO_PdbIO ... ok 542s test_SeqIO_QualityIO ... ok 542s test_SeqIO_SeqXML ... ok 542s test_SeqIO_SffIO ... ok 542s test_SeqIO_SnapGene ... ok 544s test_SeqIO_TwoBitIO ... ok 544s test_SeqIO_UniprotIO ... ok 544s test_SeqIO_Xdna ... ok 545s test_SeqIO_features ... ok 566s test_SeqIO_index ... ok 567s test_SeqIO_online ... skipping. internet not available 567s test_SeqIO_write ... ok 567s test_SeqRecord ... ok 567s test_SeqUtils ... ok 569s test_Seq_objs ... ok 569s test_SwissProt ... ok 569s test_TogoWS ... skipping. internet not available 570s test_TreeConstruction ... ok 570s test_Tutorial ... skipping. Could not find ../Doc/Tutorial/index.rst file 570s test_UniGene ... ok 571s test_UniProt ... skipping. internet not available 571s test_UniProt_GOA ... ok 571s test_align ... ok 572s test_align_substitution_matrices ... ok 575s test_bgzf ... ok 575s test_cellosaurus ... ok 580s test_codonalign ... ok 580s test_geo ... ok 581s test_motifs ... ok 581s test_motifs_online ... skipping. internet not available 581s 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. 581s warnings.warn( 581s ok 581s test_pairwise2_no_C ... ok 582s test_pairwise_aligner ... ok 583s test_pairwise_alignment_map ... ok 592s test_phenotype ... ok 592s test_phenotype_fit ... skipping. Install SciPy if you want to use Bio.phenotype fit functionality. 593s test_prodoc ... ok 593s test_prosite ... ok 593s test_seq ... ok 593s test_translate ... ok 593s ---------------------------------------------------------------------- 593s Ran 201 tests in 178.955 seconds 593s 593s Skipping any tests requiring internet access 593s Python version: 3.13.11 (main, Dec 6 2025, 13:15:20) [GCC 15.2.0] 593s Operating system: posix linux 593s :0: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/protein_lib.fa' mode='rt' encoding='UTF-8'> 593s :0: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/nucleotide_lib.fa' mode='rt' encoding='UTF-8'> 595s test_Ace ... ok 595s test_Affy ... ok 595s test_AlignIO ... ok 595s test_AlignIO_ClustalIO ... ok 595s test_AlignIO_EmbossIO ... ok 595s test_AlignIO_FastaIO ... ok 596s test_AlignIO_MauveIO ... ok 596s test_AlignIO_PhylipIO ... ok 596s test_AlignIO_convert ... ok 596s test_Align_Alignment ... ok 597s test_Align_a2m ... ok 597s test_Align_bed ... ok 597s test_Align_bigbed ... ok 598s test_Align_bigmaf ... ok 599s test_Align_bigpsl ... ok 600s test_Align_chain ... ok 600s test_Align_clustal ... ok 604s test_Align_codonalign ... ok 604s test_Align_emboss ... ok 604s test_Align_exonerate ... ok 604s test_Align_fasta ... ok 604s test_Align_format_matrix ... ok 605s test_Align_hhr ... ok 607s test_Align_maf ... ok 607s test_Align_mauve ... ok 607s test_Align_msf ... ok 607s test_Align_nexus ... ok 608s test_Align_phylip ... ok 608s test_Align_psl ... ok 608s test_Align_sam ... ok 610s test_Align_stockholm ... ok 611s test_Align_tabular ... ok 611s test_BioSQL_MySQLdb_online ... skipping. internet not available 611s test_BioSQL_mysql_connector ... skipping. BioSQL test configuration file biosql.ini missing (see biosql.ini.sample) 611s test_BioSQL_mysql_connector_online ... skipping. internet not available 611s test_BioSQL_psycopg2_online ... skipping. internet not available 617s test_BioSQL_sqlite3 ... ok 617s test_BioSQL_sqlite3_online ... skipping. internet not available 617s test_Blast_Record ... ok 618s test_Blast_parser ... ok 618s test_CAPS ... ok 618s test_Chi2 ... ok 618s test_Cluster ... ok 618s test_CodonTable ... ok 618s test_ColorSpiral ... ok 618s test_Compass ... ok 620s test_Consensus ... ok 620s test_EMBL_unittest ... ok 620s test_EmbossPrimer ... ok 624s test_Entrez ... ok 624s test_Entrez_online ... skipping. internet not available 625s test_Entrez_parser ... ok 625s test_Enzyme ... ok 625s test_ExPASy ... skipping. internet not available 625s test_File ... ok 625s test_GenBank ... ok 627s test_GenomeDiagram ... Warn: Can't find .pfb for face 'Helvetica' 629s ok 630s test_GraphicsChromosome ... ok 630s test_GraphicsDistribution ... ok 631s test_GraphicsGeneral ... ok 631s test_KEGG ... ok 631s test_KEGG_online ... skipping. internet not available 636s test_KGML_graphics ... ok 636s test_KGML_graphics_online ... skipping. internet not available 637s test_KGML_nographics ... ok 637s test_KeyWList ... ok 638s test_MafIO_index ... ok 638s test_Medline ... ok 639s test_NCBIXML ... Exception ignored while closing generator : 639s Traceback (most recent call last): 639s File "/usr/lib/python3/dist-packages/Bio/Blast/NCBIXML.py", line 1319, in parse 639s expat_parser.Parse(NULL, True) 639s xml.parsers.expat.ExpatError: unclosed token: line 320, column 0 639s ok 639s test_NCBI_qblast ... ok 639s test_NMR ... ok 640s test_Nexus ... ok 640s test_PAML_baseml ... ok 641s test_PAML_codeml ... ok 641s test_PAML_yn00 ... ok 646s test_PDB_CEAligner ... ok 646s test_PDB_DSSP ... ok 646s test_PDB_Dice ... ok 646s test_PDB_Disordered ... ok 647s test_PDB_Exposure ... ok 647s test_PDB_FragmentMapper ... ok 649s test_PDB_KDTree ... ok 649s test_PDB_MMCIF2Dict ... ok 649s test_PDB_MMCIFIO ... ok 650s test_PDB_MMCIFParser ... ok 651s test_PDB_NACCESS ... ok 651s test_PDB_PDBIO ... ok 651s test_PDB_PDBList ... skipping. internet not available 657s test_PDB_PDBMLParser ... ok 657s test_PDB_PDBParser ... ok 657s 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 658s test_PDB_Polypeptide ... ok 658s test_PDB_QCPSuperimposer ... ok 661s test_PDB_SASA ... ok 662s test_PDB_SMCRA ... ok 662s test_PDB_Selection ... ok 663s test_PDB_StructureAlignment ... ok 664s test_PDB_Superimposer ... ok 664s test_PDB_alphafold_db ... skipping. internet not available 664s test_PDB_binary_cif ... skipping. Error: Install msgpack to use Bio.PDB.binaryCIF (e.g. pip install msgpack) 664s 664s test_PDB_internal_coords ... skipping. Error: Install mmtf to use Bio.PDB.mmtf (e.g. pip install mmtf-python) 664s 665s test_PDB_parse_pdb_header ... ok 665s test_PDB_vectors ... ok 665s test_PQR ... ok 665s test_Pathway ... ok 666s test_Phd ... ok 666s test_Phylo ... ok 667s test_PhyloXML ... ok 667s test_Phylo_CDAO ... skipping. Install RDFlib if you want to use the CDAO tree format. 668s test_Phylo_NeXML ... ok 668s test_Phylo_igraph ... skipping. Install igraph if you wish to use it with Bio.Phylo 668s test_Phylo_matplotlib ... skipping. Install matplotlib if you want to use Bio.Phylo._utils. 668s test_Phylo_networkx ... skipping. Install networkx if you wish to use it with Bio.Phylo 669s test_PopGen_GenePop_nodepend ... ok 669s test_ProtParam ... ok 670s test_RCSBFormats ... ok 670s test_Restriction ... ok 670s test_SCOP_Astral ... ok 670s test_SCOP_Cla ... ok 671s test_SCOP_Des ... ok 671s test_SCOP_Dom ... ok 671s test_SCOP_Hie ... ok 671s test_SCOP_Raf ... ok 672s test_SCOP_Residues ... ok 672s test_SCOP_Scop ... ok 672s test_SVDSuperimposer ... ok 672s test_SearchIO_blast_tab ... ok 673s test_SearchIO_blast_tab_index ... ok 673s test_SearchIO_blast_xml ... ok 675s test_SearchIO_blast_xml_index ... ok 675s test_SearchIO_blat_psl ... ok 675s test_SearchIO_blat_psl_index ... ok 676s test_SearchIO_exonerate ... ok 676s test_SearchIO_exonerate_text_index ... ok 676s test_SearchIO_exonerate_vulgar_index ... ok 677s test_SearchIO_fasta_m10 ... ok 677s test_SearchIO_fasta_m10_index ... ok 677s test_SearchIO_hhsuite2_text ... ok 678s test_SearchIO_hmmer2_text ... ok 678s test_SearchIO_hmmer2_text_index ... ok 678s test_SearchIO_hmmer3_domtab ... ok 679s test_SearchIO_hmmer3_domtab_index ... ok 679s test_SearchIO_hmmer3_tab ... ok 680s test_SearchIO_hmmer3_tab_index ... ok 680s test_SearchIO_hmmer3_text ... ok 680s test_SearchIO_hmmer3_text_index ... ok 680s test_SearchIO_infernal_tab ... ok 681s test_SearchIO_infernal_tab_index ... ok 681s test_SearchIO_infernal_text ... ok 681s test_SearchIO_infernal_text_index ... ok 681s test_SearchIO_interproscan_xml ... ok 682s test_SearchIO_model ... ok 682s test_SearchIO_write ... ok 682s test_SeqFeature ... ok 702s test_SeqIO ... ok 702s test_SeqIO_AbiIO ... ok 702s test_SeqIO_FastaIO ... ok 702s test_SeqIO_Gck ... ok 702s test_SeqIO_Gfa ... ok 702s test_SeqIO_Insdc ... ok 703s test_SeqIO_NibIO ... ok 704s test_SeqIO_PdbIO ... ok 705s test_SeqIO_QualityIO ... ok 705s test_SeqIO_SeqXML ... ok 705s test_SeqIO_SffIO ... ok 705s test_SeqIO_SnapGene ... ok 707s test_SeqIO_TwoBitIO ... ok 707s test_SeqIO_UniprotIO ... ok 707s test_SeqIO_Xdna ... ok 708s test_SeqIO_features ... ok 726s test_SeqIO_index ... ok 726s test_SeqIO_online ... skipping. internet not available 727s test_SeqIO_write ... ok 727s test_SeqRecord ... ok 727s test_SeqUtils ... ok 729s test_Seq_objs ... ok 729s test_SwissProt ... ok 729s test_TogoWS ... skipping. internet not available 730s test_TreeConstruction ... ok 730s test_Tutorial ... skipping. Could not find ../Doc/Tutorial/index.rst file 731s test_UniGene ... ok 731s test_UniProt ... skipping. internet not available 731s test_UniProt_GOA ... ok 731s test_align ... ok 732s test_align_substitution_matrices ... ok 734s test_bgzf ... ok 734s test_cellosaurus ... ok 739s test_codonalign ... ok 739s test_geo ... ok 739s test_motifs ... ok 739s test_motifs_online ... skipping. internet not available 739s 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. 739s warnings.warn( 739s ok 740s test_pairwise2_no_C ... ok 740s test_pairwise_aligner ... ok 740s test_pairwise_alignment_map ... ok 749s test_phenotype ... ok 749s test_phenotype_fit ... skipping. Install SciPy if you want to use Bio.phenotype fit functionality. 750s test_prodoc ... ok 750s test_prosite ... ok 750s test_seq ... ok 750s test_translate ... ok 750s ---------------------------------------------------------------------- 750s Ran 201 tests in 155.678 seconds 750s 750s Skipping any tests requiring internet access 750s Python version: 3.14.2 (main, Dec 6 2025, 13:20:08) [GCC 15.2.0] 750s Operating system: posix linux 750s :0: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/protein_lib.fa' mode='rt' encoding='UTF-8'> 750s :0: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/nucleotide_lib.fa' mode='rt' encoding='UTF-8'> 751s autopkgtest [21:06:46]: test dependencies: -----------------------] 755s autopkgtest [21:06:50]: test dependencies: - - - - - - - - - - results - - - - - - - - - - 755s dependencies PASS 760s autopkgtest [21:06:55]: test full_suite: preparing testbed 786s autopkgtest [21:07:21]: testbed dpkg architecture: armhf 788s autopkgtest [21:07:23]: testbed apt version: 3.1.12 792s autopkgtest [21:07:27]: @@@@@@@@@@@@@@@@@@@@ test bed setup 796s autopkgtest [21:07:31]: testbed release detected to be: resolute 804s autopkgtest [21:07:39]: updating testbed package index (apt update) 806s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 807s Get:2 http://ftpmaster.internal/ubuntu resolute InRelease [124 kB] 807s Get:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease [124 kB] 807s Get:4 http://ftpmaster.internal/ubuntu resolute-security InRelease [124 kB] 807s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [1011 kB] 809s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [2820 B] 809s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [22.2 kB] 809s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [81.6 kB] 809s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf Packages [95.3 kB] 809s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/universe armhf Packages [658 kB] 810s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse armhf Packages [4896 B] 810s Get:12 http://ftpmaster.internal/ubuntu resolute/main Sources [1398 kB] 811s Get:13 http://ftpmaster.internal/ubuntu resolute/universe Sources [21.4 MB] 837s Get:14 http://ftpmaster.internal/ubuntu resolute/multiverse Sources [310 kB] 837s Get:15 http://ftpmaster.internal/ubuntu resolute/main armhf Packages [1371 kB] 839s Get:16 http://ftpmaster.internal/ubuntu resolute/universe armhf Packages [15.2 MB] 856s Get:17 http://ftpmaster.internal/ubuntu resolute/multiverse armhf Packages [175 kB] 858s Fetched 42.2 MB in 52s (815 kB/s) 860s Reading package lists... 866s autopkgtest [21:08:41]: upgrading testbed (apt dist-upgrade and autopurge) 868s Reading package lists... 868s Building dependency tree... 868s Reading state information... 869s Calculating upgrade... 869s The following packages were automatically installed and are no longer required: 869s libpython3.13-minimal libpython3.13-stdlib python3.13 python3.13-minimal 869s Use 'apt autoremove' to remove them. 869s The following NEW packages will be installed: 869s libpython3.14-minimal libpython3.14-stdlib python3.14 python3.14-minimal 869s The following packages will be upgraded: 869s libplymouth5 libpython3-stdlib plymouth plymouth-theme-ubuntu-text python3 869s python3-gdbm python3-minimal 870s 7 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. 870s Need to get 6525 kB of archives. 870s After this operation, 22.5 MB of additional disk space will be used. 870s Get:1 http://ftpmaster.internal/ubuntu resolute/main armhf libpython3.14-minimal armhf 3.14.2-1 [905 kB] 871s Get:2 http://ftpmaster.internal/ubuntu resolute/main armhf python3.14-minimal armhf 3.14.2-1 [2155 kB] 873s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf python3-gdbm armhf 3.14.2-1 [11.1 kB] 873s Get:4 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf python3-minimal armhf 3.14.2-1 [28.2 kB] 873s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf python3 armhf 3.14.2-1 [22.9 kB] 873s Get:6 http://ftpmaster.internal/ubuntu resolute/main armhf libpython3.14-stdlib armhf 3.14.2-1 [2270 kB] 875s Get:7 http://ftpmaster.internal/ubuntu resolute/main armhf python3.14 armhf 3.14.2-1 [816 kB] 876s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf libpython3-stdlib armhf 3.14.2-1 [10.9 kB] 876s Get:9 http://ftpmaster.internal/ubuntu resolute/main armhf libplymouth5 armhf 24.004.60+git20250831.4a3c171d-0ubuntu4 [147 kB] 876s Get:10 http://ftpmaster.internal/ubuntu resolute/main armhf plymouth-theme-ubuntu-text armhf 24.004.60+git20250831.4a3c171d-0ubuntu4 [10.0 kB] 876s Get:11 http://ftpmaster.internal/ubuntu resolute/main armhf plymouth armhf 24.004.60+git20250831.4a3c171d-0ubuntu4 [150 kB] 877s Fetched 6525 kB in 7s (975 kB/s) 877s Selecting previously unselected package libpython3.14-minimal:armhf. 877s (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 ... 66485 files and directories currently installed.) 877s Preparing to unpack .../libpython3.14-minimal_3.14.2-1_armhf.deb ... 877s Unpacking libpython3.14-minimal:armhf (3.14.2-1) ... 877s Selecting previously unselected package python3.14-minimal. 877s Preparing to unpack .../python3.14-minimal_3.14.2-1_armhf.deb ... 877s Unpacking python3.14-minimal (3.14.2-1) ... 877s Preparing to unpack .../python3-gdbm_3.14.2-1_armhf.deb ... 877s Unpacking python3-gdbm (3.14.2-1) over (3.13.9-1) ... 877s Setting up libpython3.14-minimal:armhf (3.14.2-1) ... 877s Setting up python3.14-minimal (3.14.2-1) ... 879s (Reading database ... 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(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 ... 66827 files and directories currently installed.) 879s Preparing to unpack .../0-python3_3.14.2-1_armhf.deb ... 880s Unpacking python3 (3.14.2-1) over (3.13.7-1) ... 880s Selecting previously unselected package libpython3.14-stdlib:armhf. 880s Preparing to unpack .../1-libpython3.14-stdlib_3.14.2-1_armhf.deb ... 880s Unpacking libpython3.14-stdlib:armhf (3.14.2-1) ... 880s Selecting previously unselected package python3.14. 880s Preparing to unpack .../2-python3.14_3.14.2-1_armhf.deb ... 880s Unpacking python3.14 (3.14.2-1) ... 880s Preparing to unpack .../3-libpython3-stdlib_3.14.2-1_armhf.deb ... 880s Unpacking libpython3-stdlib:armhf (3.14.2-1) over (3.13.7-1) ... 880s Preparing to unpack .../4-libplymouth5_24.004.60+git20250831.4a3c171d-0ubuntu4_armhf.deb ... 880s Unpacking libplymouth5:armhf (24.004.60+git20250831.4a3c171d-0ubuntu4) over (24.004.60+git20250831.4a3c171d-0ubuntu3) ... 880s Preparing to unpack .../5-plymouth-theme-ubuntu-text_24.004.60+git20250831.4a3c171d-0ubuntu4_armhf.deb ... 880s Unpacking plymouth-theme-ubuntu-text (24.004.60+git20250831.4a3c171d-0ubuntu4) over (24.004.60+git20250831.4a3c171d-0ubuntu3) ... 880s Preparing to unpack .../6-plymouth_24.004.60+git20250831.4a3c171d-0ubuntu4_armhf.deb ... 880s Unpacking plymouth (24.004.60+git20250831.4a3c171d-0ubuntu4) over (24.004.60+git20250831.4a3c171d-0ubuntu3) ... 880s Setting up libpython3.14-stdlib:armhf (3.14.2-1) ... 880s Setting up libplymouth5:armhf (24.004.60+git20250831.4a3c171d-0ubuntu4) ... 880s Setting up python3.14 (3.14.2-1) ... 882s Setting up libpython3-stdlib:armhf (3.14.2-1) ... 882s Setting up python3-gdbm (3.14.2-1) ... 882s Setting up plymouth (24.004.60+git20250831.4a3c171d-0ubuntu4) ... 882s update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults 882s update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults 882s Setting up python3 (3.14.2-1) ... 883s Processing triggers for libc-bin (2.42-2ubuntu4) ... 883s Processing triggers for systemd (259-1ubuntu2) ... 883s Processing triggers for man-db (2.13.1-1) ... 884s Processing triggers for initramfs-tools (0.150ubuntu7) ... 884s Setting up plymouth-theme-ubuntu-text (24.004.60+git20250831.4a3c171d-0ubuntu4) ... 884s Processing triggers for initramfs-tools (0.150ubuntu7) ... 886s Reading package lists... 887s Building dependency tree... 887s Reading state information... 887s Solving dependencies... 888s The following packages will be REMOVED: 888s libpython3.13-minimal* libpython3.13-stdlib* python3.13* python3.13-minimal* 889s 0 upgraded, 0 newly installed, 4 to remove and 0 not upgraded. 889s After this operation, 21.3 MB disk space will be freed. 889s (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 ... 67257 files and directories currently installed.) 889s Removing python3.13 (3.13.11-1) ... 889s Removing libpython3.13-stdlib:armhf (3.13.11-1) ... 889s Removing python3.13-minimal (3.13.11-1) ... 890s Removing libpython3.13-minimal:armhf (3.13.11-1) ... 890s Processing triggers for man-db (2.13.1-1) ... 890s Processing triggers for systemd (259-1ubuntu2) ... 891s (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 ... 66518 files and directories currently installed.) 891s Purging configuration files for libpython3.13-minimal:armhf (3.13.11-1) ... 891s Purging configuration files for python3.13-minimal (3.13.11-1) ... 893s autopkgtest [21:09:08]: rebooting testbed after setup commands that affected boot 960s Reading package lists... 960s Building dependency tree... 960s Reading state information... 960s Solving dependencies... 961s The following NEW packages will be installed: 961s autoconf automake autopoint autotools-dev build-essential bwa clustalo cpp 961s cpp-15 cpp-15-arm-linux-gnueabihf cpp-arm-linux-gnueabihf debhelper 961s debugedit dh-autoreconf dh-python dh-strip-nondeterminism dialign 961s docutils-common dssp dwz fasttree flex fontconfig-config fonts-dejavu-core 961s fonts-dejavu-extra fonts-dejavu-mono fonts-font-awesome fonts-lato 961s fonts-lmodern fonts-lyx fonts-urw-base35 g++ g++-15 961s g++-15-arm-linux-gnueabihf g++-arm-linux-gnueabihf gcc gcc-15 961s gcc-15-arm-linux-gnueabihf gcc-arm-linux-gnueabihf gettext ghostscript hevea 961s hicolor-icon-theme imagemagick imagemagick-7-common imagemagick-7.q16 961s intltool-debian libamd3 libaom3 libapache-pom-java libarchive-zip-perl 961s libargtable2-0 libarpack2t64 libasan8 libavahi-client3 libavahi-common-data 961s libavahi-common3 libblas3 libc-dev-bin libc6-dev libcairo2 libcc1-0 961s libcifpp-data libcifpp9 libcolamd3 libcommons-logging-java 961s libcommons-parent-java libcrypt-dev libcups2t64 libde265-0 libdebhelper-perl 961s libdeflate0 libdw1t64 libexpat1-dev libfftw3-double3 961s libfile-stripnondeterminism-perl libfontbox-java libfontconfig1 libfontenc1 961s libfreetype6 libgcc-15-dev libgfortran5 libglpk40 libgomp1 libgraphite2-3 961s libgs-common libgs10 libgs10-common libharfbuzz0b libheif-plugin-aomdec 961s libheif-plugin-libde265 libheif1 libice6 libidn12 libigraph4 libijs-0.35 961s libimagequant0 libisl23 libjbig0 libjbig2dec0 libjpeg-turbo8 libjpeg8 961s libjs-jquery libjson-perl libkpathsea6 liblapack3 liblcms2-2 liblerc4 961s liblqr-1-0 libltdl7 libmagickcore-7.q16-10 libmagickwand-7.q16-10 961s libmbedcrypto16 libmbedtls21 libmbedx509-7 libmpc3 libmpfi0 libmysqlclient24 961s libnetpbm11t64 libopenjp2-7 libpaper-utils libpaper2 libpdfbox-java 961s libpixman-1-0 libplfit0 libpotrace0 libptexenc1 libpython3-all-dev 961s libpython3-dev libpython3.13 libpython3.13-dev libpython3.13-minimal 961s libpython3.13-stdlib libpython3.14 libpython3.14-dev libqhull-r8.0 libraqm0 961s libraw23t64 libsharpyuv0 libsm6 libstdc++-15-dev libstdlib-ocaml 961s libsuitesparseconfig7 libsynctex2 libtcl8.6 libteckit0 libtexlua53-5 961s libtiff6 libtk8.6 libtool libubsan1 libwebp7 libwebpdemux2 libwebpmux3 961s libxaw7 libxcb-render0 libxcb-shm0 libxft2 libxi6 libxmu6 libxpm4 961s libxrender1 libxslt1.1 libxss1 libxt6t64 libzopfli1 libzzip-0-13t64 961s linux-libc-dev lmodern m4 mafft mysql-common ncbi-blast+ ncbi-data netpbm 961s ocaml-base phylip po-debconf poppler-data prank preview-latex-style probcons 961s python-biopython-doc python-matplotlib-data python3-alabaster python3-all 961s python3-all-dev python3-biopython python3-biopython-sql python3-brotli 961s python3-cairo python3-charset-normalizer python3-contourpy python3-cycler 961s python3-decorator python3-defusedxml python3-dev python3-docutils 961s python3-fonttools python3-freetype python3-igraph python3-imagesize 961s python3-kiwisolver python3-lxml python3-lz4 python3-matplotlib python3-mmtf 961s python3-mpmath python3-msgpack python3-mysqldb python3-networkx 961s python3-numpy python3-numpy-dev python3-numpydoc python3-pil 961s python3-pil.imagetk python3-rdflib python3-reportlab python3-rlpycairo 961s python3-roman-numerals python3-scipy python3-snowballstemmer python3-sphinx 961s python3-sphinx-rtd-theme python3-sphinxcontrib.jquery python3-sympy 961s python3-texttable python3-tk python3-ufolib2 python3-zopfli python3.13 961s python3.13-dev python3.13-minimal python3.13-tk python3.14-dev python3.14-tk 961s rpcsvc-proto sgml-base sphinx-common sphinx-rtd-theme-common t-coffee 961s t1utils tex-common texlive-base texlive-binaries texlive-fonts-recommended 961s texlive-latex-base texlive-latex-extra texlive-latex-recommended 961s texlive-luatex texlive-pictures unicode-data w3c-sgml-lib wise wise-data 961s x11-common xdg-utils xfonts-encodings xfonts-utils xml-core zlib1g-dev 961s 0 upgraded, 261 newly installed, 0 to remove and 0 not upgraded. 961s Need to get 412 MB of archives. 961s After this operation, 1445 MB of additional disk space will be used. 961s Get:1 http://ftpmaster.internal/ubuntu resolute/main armhf libpython3.13-minimal armhf 3.13.11-1 [875 kB] 962s Get:2 http://ftpmaster.internal/ubuntu resolute/main armhf python3.13-minimal armhf 3.13.11-1 [2055 kB] 964s Get:3 http://ftpmaster.internal/ubuntu resolute/main armhf m4 armhf 1.4.20-2 [212 kB] 964s Get:4 http://ftpmaster.internal/ubuntu resolute/main armhf flex armhf 2.6.4-8.2build2 [290 kB] 965s Get:5 http://ftpmaster.internal/ubuntu resolute/main armhf fonts-lato all 2.015-1build1 [2779 kB] 968s Get:6 http://ftpmaster.internal/ubuntu resolute/main armhf libgomp1 armhf 15.2.0-11ubuntu1 [129 kB] 968s Get:7 http://ftpmaster.internal/ubuntu resolute/main armhf libfftw3-double3 armhf 3.3.10-2fakesync1build2 [368 kB] 968s Get:8 http://ftpmaster.internal/ubuntu resolute/main armhf libfreetype6 armhf 2.14.1+dfsg-2 [345 kB] 968s Get:9 http://ftpmaster.internal/ubuntu resolute/main armhf fonts-dejavu-mono all 2.37-8build1 [502 kB] 969s Get:10 http://ftpmaster.internal/ubuntu resolute/main armhf fonts-dejavu-core all 2.37-8build1 [834 kB] 970s Get:11 http://ftpmaster.internal/ubuntu resolute/main armhf libfontenc1 armhf 1:1.1.8-1build2 [11.7 kB] 970s Get:12 http://ftpmaster.internal/ubuntu resolute/main armhf x11-common all 1:7.7+24ubuntu1 [22.4 kB] 970s Get:13 http://ftpmaster.internal/ubuntu resolute/main armhf xfonts-encodings all 1:1.0.5-0ubuntu3 [576 kB] 970s Get:14 http://ftpmaster.internal/ubuntu resolute/main armhf xfonts-utils armhf 1:7.7+7build1 [91.0 kB] 970s Get:15 http://ftpmaster.internal/ubuntu resolute/main armhf fonts-urw-base35 all 20200910-8build1 [10.9 MB] 979s Get:16 http://ftpmaster.internal/ubuntu resolute/main armhf fontconfig-config armhf 2.15.0-2.4ubuntu1 [38.2 kB] 979s Get:17 http://ftpmaster.internal/ubuntu resolute/main armhf libfontconfig1 armhf 2.15.0-2.4ubuntu1 [116 kB] 980s Get:18 http://ftpmaster.internal/ubuntu resolute/main armhf libsharpyuv0 armhf 1.5.0-0.1build1 [16.3 kB] 980s Get:19 http://ftpmaster.internal/ubuntu resolute/main armhf libaom3 armhf 3.13.1-2 [1258 kB] 981s Get:20 http://ftpmaster.internal/ubuntu resolute/main armhf libheif-plugin-aomdec armhf 1.21.2-1 [13.0 kB] 981s Get:21 http://ftpmaster.internal/ubuntu resolute/main armhf libde265-0 armhf 1.0.16-1build1 [159 kB] 981s Get:22 http://ftpmaster.internal/ubuntu resolute/main armhf libheif-plugin-libde265 armhf 1.21.2-1 [13.6 kB] 981s Get:23 http://ftpmaster.internal/ubuntu resolute/main armhf libheif1 armhf 1.21.2-1 [597 kB] 981s Get:24 http://ftpmaster.internal/ubuntu resolute/main armhf libjbig0 armhf 2.1-6.1ubuntu3 [25.3 kB] 981s Get:25 http://ftpmaster.internal/ubuntu resolute/main armhf libjpeg-turbo8 armhf 2.1.5-4ubuntu2 [127 kB] 981s Get:26 http://ftpmaster.internal/ubuntu resolute/main armhf libjpeg8 armhf 8c-2ubuntu11 [2148 B] 981s Get:27 http://ftpmaster.internal/ubuntu resolute/main armhf liblcms2-2 armhf 2.17-1 [139 kB] 982s Get:28 http://ftpmaster.internal/ubuntu resolute/universe armhf liblqr-1-0 armhf 0.4.2-2.2 [24.1 kB] 982s Get:29 http://ftpmaster.internal/ubuntu resolute/main armhf libltdl7 armhf 2.5.4-9 [40.4 kB] 982s Get:30 http://ftpmaster.internal/ubuntu resolute/main armhf libopenjp2-7 armhf 2.5.4-1 [175 kB] 982s Get:31 http://ftpmaster.internal/ubuntu resolute/main armhf libraw23t64 armhf 0.21.4-2 [352 kB] 982s Get:32 http://ftpmaster.internal/ubuntu resolute/main armhf libdeflate0 armhf 1.23-2 [38.7 kB] 982s Get:33 http://ftpmaster.internal/ubuntu resolute/main armhf liblerc4 armhf 4.0.0+ds-5ubuntu2 [162 kB] 982s Get:34 http://ftpmaster.internal/ubuntu resolute/main armhf libwebp7 armhf 1.5.0-0.1build1 [189 kB] 982s Get:35 http://ftpmaster.internal/ubuntu resolute/main armhf libtiff6 armhf 4.7.0-3ubuntu3 [188 kB] 983s Get:36 http://ftpmaster.internal/ubuntu resolute/main armhf libwebpdemux2 armhf 1.5.0-0.1build1 [11.7 kB] 983s Get:37 http://ftpmaster.internal/ubuntu resolute/main armhf libwebpmux3 armhf 1.5.0-0.1build1 [22.4 kB] 983s Get:38 http://ftpmaster.internal/ubuntu resolute/universe armhf imagemagick-7-common all 8:7.1.2.12+dfsg1-1 [71.8 kB] 983s Get:39 http://ftpmaster.internal/ubuntu resolute/universe armhf libmagickcore-7.q16-10 armhf 8:7.1.2.12+dfsg1-1 [1874 kB] 985s Get:40 http://ftpmaster.internal/ubuntu resolute/universe armhf libmagickwand-7.q16-10 armhf 8:7.1.2.12+dfsg1-1 [365 kB] 985s Get:41 http://ftpmaster.internal/ubuntu resolute/main armhf poppler-data all 0.4.12-1build1 [2000 kB] 987s Get:42 http://ftpmaster.internal/ubuntu resolute/main armhf python3-numpy-dev armhf 1:2.3.5+ds-3 [141 kB] 987s Get:43 http://ftpmaster.internal/ubuntu resolute/main armhf libblas3 armhf 3.12.1-7ubuntu1 [133 kB] 987s Get:44 http://ftpmaster.internal/ubuntu resolute/main armhf libgfortran5 armhf 15.2.0-11ubuntu1 [334 kB] 988s Get:45 http://ftpmaster.internal/ubuntu resolute/main armhf liblapack3 armhf 3.12.1-7ubuntu1 [2090 kB] 990s Get:46 http://ftpmaster.internal/ubuntu resolute/main armhf python3-numpy armhf 1:2.3.5+ds-3 [4729 kB] 995s Get:47 http://ftpmaster.internal/ubuntu resolute/main armhf libpython3.13-stdlib armhf 3.13.11-1 [1960 kB] 997s Get:48 http://ftpmaster.internal/ubuntu resolute/main armhf python3.13 armhf 3.13.11-1 [758 kB] 998s Get:49 http://ftpmaster.internal/ubuntu resolute/main armhf autoconf all 2.72-3.1ubuntu1 [384 kB] 998s Get:50 http://ftpmaster.internal/ubuntu resolute/main armhf autotools-dev all 20240727.1 [43.4 kB] 998s Get:51 http://ftpmaster.internal/ubuntu resolute/main armhf automake all 1:1.18.1-3build1 [582 kB] 999s Get:52 http://ftpmaster.internal/ubuntu resolute/main armhf autopoint all 0.23.2-1 [620 kB] 999s Get:53 http://ftpmaster.internal/ubuntu resolute/main armhf libc-dev-bin armhf 2.42-2ubuntu4 [21.8 kB] 999s Get:54 http://ftpmaster.internal/ubuntu resolute/main armhf linux-libc-dev armhf 6.18.0-9.9 [1819 kB] 1001s Get:55 http://ftpmaster.internal/ubuntu resolute/main armhf libcrypt-dev armhf 1:4.5.1-1 [128 kB] 1001s Get:56 http://ftpmaster.internal/ubuntu resolute/main armhf rpcsvc-proto armhf 1.4.3-1 [62.3 kB] 1001s Get:57 http://ftpmaster.internal/ubuntu resolute/main armhf libc6-dev armhf 2.42-2ubuntu4 [1416 kB] 1003s Get:58 http://ftpmaster.internal/ubuntu resolute/main armhf libisl23 armhf 0.27-1build1 [553 kB] 1003s Get:59 http://ftpmaster.internal/ubuntu resolute/main armhf libmpc3 armhf 1.3.1-2 [47.0 kB] 1003s Get:60 http://ftpmaster.internal/ubuntu resolute/main armhf cpp-15-arm-linux-gnueabihf armhf 15.2.0-11ubuntu1 [10.1 MB] 1012s Get:61 http://ftpmaster.internal/ubuntu resolute/main armhf cpp-15 armhf 15.2.0-11ubuntu1 [1032 B] 1012s Get:62 http://ftpmaster.internal/ubuntu resolute/main armhf cpp-arm-linux-gnueabihf armhf 4:15.2.0-4ubuntu1 [5756 B] 1012s Get:63 http://ftpmaster.internal/ubuntu resolute/main armhf cpp armhf 4:15.2.0-4ubuntu1 [22.4 kB] 1012s Get:64 http://ftpmaster.internal/ubuntu resolute/main armhf libcc1-0 armhf 15.2.0-11ubuntu1 [43.5 kB] 1012s Get:65 http://ftpmaster.internal/ubuntu resolute/main armhf libasan8 armhf 15.2.0-11ubuntu1 [2947 kB] 1015s Get:66 http://ftpmaster.internal/ubuntu resolute/main armhf libubsan1 armhf 15.2.0-11ubuntu1 [1187 kB] 1016s Get:67 http://ftpmaster.internal/ubuntu resolute/main armhf libgcc-15-dev armhf 15.2.0-11ubuntu1 [898 kB] 1017s Get:68 http://ftpmaster.internal/ubuntu resolute/main armhf gcc-15-arm-linux-gnueabihf armhf 15.2.0-11ubuntu1 [19.5 MB] 1032s Get:69 http://ftpmaster.internal/ubuntu resolute/main armhf gcc-15 armhf 15.2.0-11ubuntu1 [497 kB] 1032s Get:70 http://ftpmaster.internal/ubuntu resolute/main armhf gcc-arm-linux-gnueabihf armhf 4:15.2.0-4ubuntu1 [1220 B] 1032s Get:71 http://ftpmaster.internal/ubuntu resolute/main armhf gcc armhf 4:15.2.0-4ubuntu1 [5022 B] 1032s Get:72 http://ftpmaster.internal/ubuntu resolute/main armhf libstdc++-15-dev armhf 15.2.0-11ubuntu1 [2638 kB] 1034s Get:73 http://ftpmaster.internal/ubuntu resolute/main armhf g++-15-arm-linux-gnueabihf armhf 15.2.0-11ubuntu1 [11.4 MB] 1042s Get:74 http://ftpmaster.internal/ubuntu resolute/main armhf g++-15 armhf 15.2.0-11ubuntu1 [24.6 kB] 1042s Get:75 http://ftpmaster.internal/ubuntu resolute/main armhf g++-arm-linux-gnueabihf armhf 4:15.2.0-4ubuntu1 [968 B] 1042s Get:76 http://ftpmaster.internal/ubuntu resolute/main armhf g++ armhf 4:15.2.0-4ubuntu1 [1086 B] 1042s Get:77 http://ftpmaster.internal/ubuntu resolute/main armhf build-essential armhf 12.12ubuntu2 [5256 B] 1042s Get:78 http://ftpmaster.internal/ubuntu resolute/universe armhf bwa armhf 0.7.19-1 [199 kB] 1042s Get:79 http://ftpmaster.internal/ubuntu resolute/universe armhf libargtable2-0 armhf 13-4 [12.7 kB] 1042s Get:80 http://ftpmaster.internal/ubuntu resolute/universe armhf clustalo armhf 1.2.4-8build2 [250 kB] 1042s Get:81 http://ftpmaster.internal/ubuntu resolute/main armhf libdebhelper-perl all 13.28ubuntu1 [97.4 kB] 1042s Get:82 http://ftpmaster.internal/ubuntu resolute/main armhf libtool all 2.5.4-9 [169 kB] 1042s Get:83 http://ftpmaster.internal/ubuntu resolute/main armhf dh-autoreconf all 21 [12.5 kB] 1042s Get:84 http://ftpmaster.internal/ubuntu resolute/main armhf libarchive-zip-perl all 1.68-1 [90.2 kB] 1042s Get:85 http://ftpmaster.internal/ubuntu resolute/main armhf libfile-stripnondeterminism-perl all 1.15.0-1build1 [20.6 kB] 1042s Get:86 http://ftpmaster.internal/ubuntu resolute/main armhf dh-strip-nondeterminism all 1.15.0-1build1 [5110 B] 1042s Get:87 http://ftpmaster.internal/ubuntu resolute/main armhf libdw1t64 armhf 0.194-1 [254 kB] 1043s Get:88 http://ftpmaster.internal/ubuntu resolute/main armhf debugedit armhf 1:5.2-3 [48.9 kB] 1043s Get:89 http://ftpmaster.internal/ubuntu resolute/main armhf dwz armhf 0.16-2 [114 kB] 1043s Get:90 http://ftpmaster.internal/ubuntu resolute/main armhf gettext armhf 0.23.2-1 [1059 kB] 1043s Get:91 http://ftpmaster.internal/ubuntu resolute/main armhf intltool-debian all 0.35.0+20060710.6build1 [24.1 kB] 1043s Get:92 http://ftpmaster.internal/ubuntu resolute/main armhf po-debconf all 1.0.22 [215 kB] 1044s Get:93 http://ftpmaster.internal/ubuntu resolute/main armhf debhelper all 13.28ubuntu1 [916 kB] 1044s Get:94 http://ftpmaster.internal/ubuntu resolute/universe armhf dh-python all 7.20251231 [122 kB] 1044s Get:95 http://ftpmaster.internal/ubuntu resolute/universe armhf dialign armhf 2.2.1-13build1 [154 kB] 1044s Get:96 http://ftpmaster.internal/ubuntu resolute/main armhf sgml-base all 1.31+nmu1 [11.0 kB] 1044s Get:97 http://ftpmaster.internal/ubuntu resolute/main armhf xml-core all 0.19build1 [20.3 kB] 1044s Get:98 http://ftpmaster.internal/ubuntu resolute/main armhf docutils-common all 0.22.4+dfsg-1 [130 kB] 1045s Get:99 http://ftpmaster.internal/ubuntu resolute/universe armhf libcifpp-data all 9.0.5-2 [483 kB] 1045s Get:100 http://ftpmaster.internal/ubuntu resolute/universe armhf libcifpp9 armhf 9.0.5-2 [954 kB] 1046s Get:101 http://ftpmaster.internal/ubuntu resolute/universe armhf dssp armhf 4.5.7-1 [636 kB] 1046s Get:102 http://ftpmaster.internal/ubuntu resolute/main armhf fonts-dejavu-extra all 2.37-8build1 [1944 kB] 1049s Get:103 http://ftpmaster.internal/ubuntu resolute/main armhf fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1build1 [531 kB] 1049s Get:104 http://ftpmaster.internal/ubuntu resolute/universe armhf fonts-lmodern all 2.005-1build1 [4788 kB] 1053s Get:105 http://ftpmaster.internal/ubuntu resolute/universe armhf fonts-lyx all 2.5.0~RC2-3 [171 kB] 1053s Get:106 http://ftpmaster.internal/ubuntu resolute/main armhf libgs-common all 10.05.0dfsg1-0ubuntu4 [176 kB] 1054s Get:107 http://ftpmaster.internal/ubuntu resolute/main armhf libgs10-common all 10.05.0dfsg1-0ubuntu4 [490 kB] 1054s Get:108 http://ftpmaster.internal/ubuntu resolute/main armhf libavahi-common-data armhf 0.8-17ubuntu1 [31.3 kB] 1054s Get:109 http://ftpmaster.internal/ubuntu resolute/main armhf libavahi-common3 armhf 0.8-17ubuntu1 [20.4 kB] 1054s Get:110 http://ftpmaster.internal/ubuntu resolute/main armhf libavahi-client3 armhf 0.8-17ubuntu1 [24.3 kB] 1054s Get:111 http://ftpmaster.internal/ubuntu resolute/main armhf libcups2t64 armhf 2.4.16-1ubuntu1 [242 kB] 1054s Get:112 http://ftpmaster.internal/ubuntu resolute/main armhf libidn12 armhf 1.43-2 [56.7 kB] 1054s Get:113 http://ftpmaster.internal/ubuntu resolute/main armhf libijs-0.35 armhf 0.35-16 [13.7 kB] 1054s Get:114 http://ftpmaster.internal/ubuntu resolute/main armhf libjbig2dec0 armhf 0.20-1build4 [59.0 kB] 1054s Get:115 http://ftpmaster.internal/ubuntu resolute/main armhf libpaper2 armhf 2.2.5-0.3build1 [16.3 kB] 1054s Get:116 http://ftpmaster.internal/ubuntu resolute/main armhf libice6 armhf 2:1.1.1-1build1 [37.5 kB] 1054s Get:117 http://ftpmaster.internal/ubuntu resolute/main armhf libsm6 armhf 2:1.2.6-1 [15.3 kB] 1054s Get:118 http://ftpmaster.internal/ubuntu resolute/main armhf libxt6t64 armhf 1:1.2.1-1.3 [145 kB] 1055s Get:119 http://ftpmaster.internal/ubuntu resolute/main armhf libgs10 armhf 10.05.0dfsg1-0ubuntu4 [4291 kB] 1058s Get:120 http://ftpmaster.internal/ubuntu resolute/main armhf ghostscript armhf 10.05.0dfsg1-0ubuntu4 [42.7 kB] 1058s Get:121 http://ftpmaster.internal/ubuntu resolute/universe armhf libnetpbm11t64 armhf 2:11.10.02-1build1 [97.7 kB] 1058s Get:122 http://ftpmaster.internal/ubuntu resolute/universe armhf netpbm armhf 2:11.10.02-1build1 [2035 kB] 1060s Get:123 http://ftpmaster.internal/ubuntu resolute/universe armhf tex-common all 6.20 [30.0 kB] 1060s Get:124 http://ftpmaster.internal/ubuntu resolute/main armhf libpaper-utils armhf 2.2.5-0.3build1 [14.2 kB] 1060s Get:125 http://ftpmaster.internal/ubuntu resolute/universe armhf libkpathsea6 armhf 2025.20250727.75242+ds-5build1 [62.7 kB] 1060s Get:126 http://ftpmaster.internal/ubuntu resolute/universe armhf libptexenc1 armhf 2025.20250727.75242+ds-5build1 [44.5 kB] 1060s Get:127 http://ftpmaster.internal/ubuntu resolute/universe armhf libsynctex2 armhf 2025.20250727.75242+ds-5build1 [56.1 kB] 1060s Get:128 http://ftpmaster.internal/ubuntu resolute/universe armhf libtexlua53-5 armhf 2025.20250727.75242+ds-5build1 [107 kB] 1060s Get:129 http://ftpmaster.internal/ubuntu resolute/main armhf t1utils armhf 1.41-4build4 [52.4 kB] 1060s Get:130 http://ftpmaster.internal/ubuntu resolute/main armhf libpixman-1-0 armhf 0.46.4-1 [196 kB] 1060s Get:131 http://ftpmaster.internal/ubuntu resolute/main armhf libxcb-render0 armhf 1.17.0-2build1 [15.5 kB] 1060s Get:132 http://ftpmaster.internal/ubuntu resolute/main armhf libxcb-shm0 armhf 1.17.0-2build1 [5962 B] 1060s Get:133 http://ftpmaster.internal/ubuntu resolute/main armhf libxrender1 armhf 1:0.9.12-1 [16.6 kB] 1060s Get:134 http://ftpmaster.internal/ubuntu resolute/main armhf libcairo2 armhf 1.18.4-3 [489 kB] 1061s Get:135 http://ftpmaster.internal/ubuntu resolute/main armhf libgraphite2-3 armhf 1.3.14-11ubuntu1 [65.2 kB] 1061s Get:136 http://ftpmaster.internal/ubuntu resolute/main armhf libharfbuzz0b armhf 12.3.0-4 [507 kB] 1061s Get:137 http://ftpmaster.internal/ubuntu resolute/universe armhf libmpfi0 armhf 1.5.4+ds-4 [28.0 kB] 1061s Get:138 http://ftpmaster.internal/ubuntu resolute/universe armhf libpotrace0 armhf 1.16-2build2 [15.3 kB] 1061s Get:139 http://ftpmaster.internal/ubuntu resolute/universe armhf libteckit0 armhf 2.5.13+ds-1 [343 kB] 1061s Get:140 http://ftpmaster.internal/ubuntu resolute/main armhf libxmu6 armhf 2:1.1.3-4 [41.2 kB] 1061s Get:141 http://ftpmaster.internal/ubuntu resolute/main armhf libxpm4 armhf 1:3.5.17-1build3 [31.1 kB] 1061s Get:142 http://ftpmaster.internal/ubuntu resolute/main armhf libxaw7 armhf 2:1.0.16-1build1 [156 kB] 1062s Get:143 http://ftpmaster.internal/ubuntu resolute/main armhf libxi6 armhf 2:1.8.2-2 [26.7 kB] 1062s Get:144 http://ftpmaster.internal/ubuntu resolute/universe armhf libzzip-0-13t64 armhf 0.13.78+dfsg.1-0.2 [26.2 kB] 1062s Get:145 http://ftpmaster.internal/ubuntu resolute/universe armhf texlive-binaries armhf 2025.20250727.75242+ds-5build1 [8010 kB] 1069s Get:146 http://ftpmaster.internal/ubuntu resolute/main armhf xdg-utils all 1.2.1-2ubuntu2 [66.1 kB] 1069s Get:147 http://ftpmaster.internal/ubuntu resolute/universe armhf texlive-base all 2025.20251127-1 [22.8 MB] 1092s Get:148 http://ftpmaster.internal/ubuntu resolute/main armhf hicolor-icon-theme all 0.18-2build1 [13.2 kB] 1092s Get:149 http://ftpmaster.internal/ubuntu resolute/universe armhf imagemagick-7.q16 armhf 8:7.1.2.12+dfsg1-1 [703 kB] 1093s Get:150 http://ftpmaster.internal/ubuntu resolute/universe armhf imagemagick armhf 8:7.1.2.12+dfsg1-1 [14.1 kB] 1093s Get:151 http://ftpmaster.internal/ubuntu resolute/universe armhf libstdlib-ocaml armhf 5.4.0-1ubuntu1 [303 kB] 1093s Get:152 http://ftpmaster.internal/ubuntu resolute/universe armhf ocaml-base armhf 5.4.0-1ubuntu1 [282 kB] 1093s Get:153 http://ftpmaster.internal/ubuntu resolute/universe armhf hevea armhf 2.36-2build3 [919 kB] 1094s Get:154 http://ftpmaster.internal/ubuntu resolute/main armhf libsuitesparseconfig7 armhf 1:7.12.1+dfsg-1 [21.4 kB] 1094s Get:155 http://ftpmaster.internal/ubuntu resolute/universe armhf libamd3 armhf 1:7.12.1+dfsg-1 [37.5 kB] 1094s Get:156 http://ftpmaster.internal/ubuntu resolute/universe armhf libapache-pom-java all 33-2build1 [5976 B] 1094s Get:157 http://ftpmaster.internal/ubuntu resolute/universe armhf libarpack2t64 armhf 3.9.1-6 [88.7 kB] 1094s Get:158 http://ftpmaster.internal/ubuntu resolute/main armhf libcolamd3 armhf 1:7.12.1+dfsg-1 [28.2 kB] 1094s Get:159 http://ftpmaster.internal/ubuntu resolute/universe armhf libcommons-parent-java all 56-1build1 [11.1 kB] 1094s Get:160 http://ftpmaster.internal/ubuntu resolute/universe armhf libcommons-logging-java all 1.3.0-1ubuntu1 [63.8 kB] 1094s Get:161 http://ftpmaster.internal/ubuntu resolute/main armhf libexpat1-dev armhf 2.7.3-1 [126 kB] 1094s Get:162 http://ftpmaster.internal/ubuntu resolute/universe armhf libglpk40 armhf 5.0-2 [325 kB] 1094s Get:163 http://ftpmaster.internal/ubuntu resolute/universe armhf libplfit0 armhf 0.9.6+ds-2ubuntu1 [25.7 kB] 1094s Get:164 http://ftpmaster.internal/ubuntu resolute/universe armhf libigraph4 armhf 1.0.1+ds-3 [1173 kB] 1095s Get:165 http://ftpmaster.internal/ubuntu resolute/main armhf libimagequant0 armhf 2.18.0-1build1 [31.1 kB] 1096s Get:166 http://ftpmaster.internal/ubuntu resolute/main armhf libjs-jquery all 3.7.1+dfsg+~3.5.33-1build1 [321 kB] 1096s Get:167 http://ftpmaster.internal/ubuntu resolute/main armhf libjson-perl all 4.10000-1 [81.9 kB] 1096s Get:168 http://ftpmaster.internal/ubuntu resolute/universe armhf libmbedcrypto16 armhf 3.6.5-0.1ubuntu2 [230 kB] 1096s Get:169 http://ftpmaster.internal/ubuntu resolute/universe armhf libmbedx509-7 armhf 3.6.5-0.1ubuntu2 [30.5 kB] 1096s Get:170 http://ftpmaster.internal/ubuntu resolute/universe armhf libmbedtls21 armhf 3.6.5-0.1ubuntu2 [121 kB] 1096s Get:171 http://ftpmaster.internal/ubuntu resolute/main armhf mysql-common all 5.8+1.1.1ubuntu2 [7002 B] 1096s Get:172 http://ftpmaster.internal/ubuntu resolute/main armhf libmysqlclient24 armhf 8.4.7-0ubuntu3 [1266 kB] 1097s Get:173 http://ftpmaster.internal/ubuntu resolute/main armhf libpython3.14 armhf 3.14.2-1 [2213 kB] 1100s Get:174 http://ftpmaster.internal/ubuntu resolute/main armhf zlib1g-dev armhf 1:1.3.dfsg+really1.3.1-1ubuntu2 [881 kB] 1100s Get:175 http://ftpmaster.internal/ubuntu resolute/main armhf libpython3.14-dev armhf 3.14.2-1 [4504 kB] 1104s Get:176 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf libpython3-dev armhf 3.14.2-1 [11.2 kB] 1104s Get:177 http://ftpmaster.internal/ubuntu resolute/main armhf libpython3.13 armhf 3.13.11-1 [2124 kB] 1107s Get:178 http://ftpmaster.internal/ubuntu resolute/main armhf libpython3.13-dev armhf 3.13.11-1 [4564 kB] 1111s Get:179 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf libpython3-all-dev armhf 3.14.2-1 [916 B] 1111s Get:180 http://ftpmaster.internal/ubuntu resolute/universe armhf libqhull-r8.0 armhf 2020.2-8 [175 kB] 1112s Get:181 http://ftpmaster.internal/ubuntu resolute/main armhf libraqm0 armhf 0.10.3-1 [12.7 kB] 1112s Get:182 http://ftpmaster.internal/ubuntu resolute/main armhf libtcl8.6 armhf 8.6.17+dfsg-1 [918 kB] 1112s Get:183 http://ftpmaster.internal/ubuntu resolute/main armhf libxft2 armhf 2.3.6-1build2 [37.2 kB] 1112s Get:184 http://ftpmaster.internal/ubuntu resolute/main armhf libxss1 armhf 1:1.2.3-1build4 [6328 B] 1112s Get:185 http://ftpmaster.internal/ubuntu resolute/main armhf libtk8.6 armhf 8.6.17-1 [694 kB] 1113s Get:186 http://ftpmaster.internal/ubuntu resolute/main armhf libxslt1.1 armhf 1.1.43-0.3 [146 kB] 1113s Get:187 http://ftpmaster.internal/ubuntu resolute/universe armhf libzopfli1 armhf 1.0.3-3 [91.7 kB] 1113s Get:188 http://ftpmaster.internal/ubuntu resolute/universe armhf lmodern all 2.005-1build1 [9538 kB] 1121s Get:189 http://ftpmaster.internal/ubuntu resolute/universe armhf mafft armhf 7.525-1 [950 kB] 1122s Get:190 http://ftpmaster.internal/ubuntu resolute/universe armhf ncbi-data all 6.1.20170106+dfsg2-7 [3969 kB] 1125s Get:191 http://ftpmaster.internal/ubuntu resolute/universe armhf ncbi-blast+ armhf 2.16.0+ds-7 [14.8 MB] 1137s Get:192 http://ftpmaster.internal/ubuntu resolute/universe armhf phylip armhf 1:3.697+dfsg-4build2 [883 kB] 1138s Get:193 http://ftpmaster.internal/ubuntu resolute/universe armhf prank armhf 250331-1 [371 kB] 1138s Get:194 http://ftpmaster.internal/ubuntu resolute/universe armhf preview-latex-style all 13.2-1.1 [347 kB] 1139s Get:195 http://ftpmaster.internal/ubuntu resolute/universe armhf probcons armhf 1.12-15 [125 kB] 1139s Get:196 http://ftpmaster.internal/ubuntu resolute/universe armhf python-biopython-doc all 1.86+dfsg-1 [18.1 MB] 1154s Get:197 http://ftpmaster.internal/ubuntu resolute/universe armhf python-matplotlib-data all 3.10.7+dfsg1-1 [2930 kB] 1157s Get:198 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf python3-all armhf 3.14.2-1 [888 B] 1157s Get:199 http://ftpmaster.internal/ubuntu resolute/main armhf python3.14-dev armhf 3.14.2-1 [512 kB] 1157s Get:200 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf python3-dev armhf 3.14.2-1 [26.6 kB] 1157s Get:201 http://ftpmaster.internal/ubuntu resolute/main armhf python3.13-dev armhf 3.13.11-1 [508 kB] 1158s Get:202 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf python3-all-dev armhf 3.14.2-1 [912 B] 1158s Get:203 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-charset-normalizer armhf 3.4.4-2 [167 kB] 1158s Get:204 http://ftpmaster.internal/ubuntu resolute/main armhf python3.13-tk armhf 3.13.11-1 [104 kB] 1158s Get:205 http://ftpmaster.internal/ubuntu resolute/main armhf python3.14-tk armhf 3.14.2-1 [105 kB] 1158s Get:206 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf python3-tk armhf 3.14.2-1 [11.2 kB] 1158s Get:207 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-pil.imagetk armhf 12.0.0-1ubuntu1 [9168 B] 1158s Get:208 http://ftpmaster.internal/ubuntu resolute/main armhf python3-pil armhf 12.0.0-1ubuntu1 [462 kB] 1159s Get:209 http://ftpmaster.internal/ubuntu resolute/main armhf python3-cairo armhf 1.27.0-2build1 [135 kB] 1159s Get:210 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-freetype all 2.5.1-2 [92.2 kB] 1159s Get:211 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-rlpycairo all 0.3.0-4 [9332 B] 1159s Get:212 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-reportlab all 4.4.9-1 [1149 kB] 1160s Get:213 http://ftpmaster.internal/ubuntu resolute/universe armhf w3c-sgml-lib all 1.3-3build1 [278 kB] 1160s Get:214 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-biopython armhf 1.86+dfsg-1 [1652 kB] 1161s Get:215 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-biopython-sql all 1.86+dfsg-1 [26.4 kB] 1161s Get:216 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-brotli armhf 1.1.0-2build6 [327 kB] 1162s Get:217 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-contourpy armhf 1.3.3-1 [268 kB] 1162s Get:218 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-cycler all 0.12.1-2 [9850 B] 1162s Get:219 http://ftpmaster.internal/ubuntu resolute/main armhf python3-decorator all 5.2.1-2 [28.1 kB] 1162s Get:220 http://ftpmaster.internal/ubuntu resolute/main armhf python3-defusedxml all 0.7.1-3build1 [42.4 kB] 1162s Get:221 http://ftpmaster.internal/ubuntu resolute/main armhf python3-roman-numerals all 4.1.0-1 [8660 B] 1162s Get:222 http://ftpmaster.internal/ubuntu resolute/main armhf python3-docutils all 0.22.4+dfsg-1 [439 kB] 1162s Get:223 http://ftpmaster.internal/ubuntu resolute/main armhf python3-lxml armhf 6.0.2-1 [2260 kB] 1164s Get:224 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-lz4 armhf 4.4.5+dfsg-1 [26.1 kB] 1164s Get:225 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-scipy armhf 1.16.3-3 [18.2 MB] 1176s Get:226 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-mpmath all 1.3.0-2 [423 kB] 1176s Get:227 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-sympy all 1.14.0-2 [4306 kB] 1180s Get:228 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-ufolib2 all 0.18.1+dfsg1-1 [33.7 kB] 1180s Get:229 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-zopfli armhf 0.4.0-1 [10.5 kB] 1180s Get:230 http://ftpmaster.internal/ubuntu resolute/universe armhf unicode-data all 16.0.0-1build1 [9543 kB] 1187s Get:231 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-fonttools armhf 4.61.1-3 [1697 kB] 1190s Get:232 http://ftpmaster.internal/ubuntu resolute/main armhf python3-imagesize all 1.4.1-1build1 [6900 B] 1190s Get:233 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-kiwisolver armhf 1.4.10~rc0-1 [77.8 kB] 1190s Get:234 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-matplotlib armhf 3.10.7+dfsg1-1 [17.2 MB] 1203s Get:235 http://ftpmaster.internal/ubuntu resolute/main armhf python3-msgpack armhf 1.1.2-1 [107 kB] 1203s Get:236 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-mmtf all 1.1.3-1build1 [16.4 kB] 1203s Get:237 http://ftpmaster.internal/ubuntu resolute/main armhf python3-mysqldb armhf 1.4.6-2build7 [49.9 kB] 1203s Get:238 http://ftpmaster.internal/ubuntu resolute/main armhf python3-networkx all 3.2.1-4ubuntu2 [11.8 MB] 1212s Get:239 http://ftpmaster.internal/ubuntu resolute/main armhf sphinx-common all 8.2.3-12 [657 kB] 1212s Get:240 http://ftpmaster.internal/ubuntu resolute/main armhf python3-alabaster all 0.7.16-0.1build1 [18.6 kB] 1212s Get:241 http://ftpmaster.internal/ubuntu resolute/main armhf python3-snowballstemmer all 3.0.1-1 [65.9 kB] 1212s Get:242 http://ftpmaster.internal/ubuntu resolute/main armhf python3-sphinx all 8.2.3-12 [483 kB] 1213s Get:243 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-numpydoc all 1.9.0-1 [53.2 kB] 1213s Get:244 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-rdflib all 7.1.1-3 [427 kB] 1213s Get:245 http://ftpmaster.internal/ubuntu resolute/main armhf sphinx-rtd-theme-common all 3.0.2+dfsg-3 [1013 kB] 1214s Get:246 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-sphinxcontrib.jquery all 4.1-6 [6856 B] 1214s Get:247 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-sphinx-rtd-theme all 3.0.2+dfsg-3 [23.5 kB] 1214s Get:248 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-texttable all 1.7.0-1 [11.2 kB] 1214s Get:249 http://ftpmaster.internal/ubuntu resolute/universe armhf t-coffee armhf 13.45.0.4846264+really13.41.0.28bdc39+dfsg-1build1 [977 kB] 1214s Get:250 http://ftpmaster.internal/ubuntu resolute/universe armhf texlive-fonts-recommended all 2025.20251127-1 [4972 kB] 1217s Get:251 http://ftpmaster.internal/ubuntu resolute/universe armhf texlive-luatex all 2025.20251127-1 [36.0 MB] 1231s Get:252 http://ftpmaster.internal/ubuntu resolute/universe armhf texlive-latex-base all 2025.20251127-1 [1309 kB] 1231s Get:253 http://ftpmaster.internal/ubuntu resolute/universe armhf libfontbox-java all 1:1.8.16-5 [208 kB] 1231s Get:254 http://ftpmaster.internal/ubuntu resolute/universe armhf libpdfbox-java all 1:1.8.16-5 [5521 kB] 1231s Get:255 http://ftpmaster.internal/ubuntu resolute/universe armhf texlive-latex-recommended all 2025.20251127-1 [8494 kB] 1232s Get:256 http://ftpmaster.internal/ubuntu resolute/universe armhf texlive-pictures all 2025.20251127-1 [23.5 MB] 1232s Get:257 http://ftpmaster.internal/ubuntu resolute/universe armhf texlive-latex-extra all 2025.20251127-2 [32.5 MB] 1233s Get:258 http://ftpmaster.internal/ubuntu resolute/universe armhf wise-data all 2.4.1-27 [83.2 kB] 1233s Get:259 http://ftpmaster.internal/ubuntu resolute/universe armhf wise armhf 2.4.1-27 [916 kB] 1233s Get:260 http://ftpmaster.internal/ubuntu resolute/universe armhf fasttree armhf 2.1.11-2build1 [173 kB] 1233s Get:261 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-igraph armhf 1.0.0+ds-1 [333 kB] 1234s Preconfiguring packages ... 1235s Fetched 412 MB in 4min 32s (1514 kB/s) 1235s Selecting previously unselected package libpython3.13-minimal:armhf. 1235s (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 ... 66518 files and directories currently installed.) 1235s Preparing to unpack .../000-libpython3.13-minimal_3.13.11-1_armhf.deb ... 1235s Unpacking libpython3.13-minimal:armhf (3.13.11-1) ... 1235s Selecting previously unselected package python3.13-minimal. 1235s Preparing to unpack .../001-python3.13-minimal_3.13.11-1_armhf.deb ... 1235s Unpacking python3.13-minimal (3.13.11-1) ... 1235s Selecting previously unselected package m4. 1235s Preparing to unpack .../002-m4_1.4.20-2_armhf.deb ... 1235s Unpacking m4 (1.4.20-2) ... 1235s Selecting previously unselected package flex. 1235s Preparing to unpack .../003-flex_2.6.4-8.2build2_armhf.deb ... 1235s Unpacking flex (2.6.4-8.2build2) ... 1235s Selecting previously unselected package fonts-lato. 1235s Preparing to unpack .../004-fonts-lato_2.015-1build1_all.deb ... 1235s Unpacking fonts-lato (2.015-1build1) ... 1235s Selecting previously unselected package libgomp1:armhf. 1235s Preparing to unpack .../005-libgomp1_15.2.0-11ubuntu1_armhf.deb ... 1235s Unpacking libgomp1:armhf (15.2.0-11ubuntu1) ... 1235s Selecting previously unselected package libfftw3-double3:armhf. 1235s Preparing to unpack .../006-libfftw3-double3_3.3.10-2fakesync1build2_armhf.deb ... 1235s Unpacking libfftw3-double3:armhf (3.3.10-2fakesync1build2) ... 1235s Selecting previously unselected package libfreetype6:armhf. 1235s Preparing to unpack .../007-libfreetype6_2.14.1+dfsg-2_armhf.deb ... 1235s Unpacking libfreetype6:armhf (2.14.1+dfsg-2) ... 1235s Selecting previously unselected package fonts-dejavu-mono. 1235s Preparing to unpack .../008-fonts-dejavu-mono_2.37-8build1_all.deb ... 1235s Unpacking fonts-dejavu-mono (2.37-8build1) ... 1235s Selecting previously unselected package fonts-dejavu-core. 1236s Preparing to unpack .../009-fonts-dejavu-core_2.37-8build1_all.deb ... 1236s Unpacking fonts-dejavu-core (2.37-8build1) ... 1236s Selecting previously unselected package libfontenc1:armhf. 1236s Preparing to unpack .../010-libfontenc1_1%3a1.1.8-1build2_armhf.deb ... 1236s Unpacking libfontenc1:armhf (1:1.1.8-1build2) ... 1236s Selecting previously unselected package x11-common. 1236s Preparing to unpack .../011-x11-common_1%3a7.7+24ubuntu1_all.deb ... 1236s Unpacking x11-common (1:7.7+24ubuntu1) ... 1236s Selecting previously unselected package xfonts-encodings. 1236s Preparing to unpack .../012-xfonts-encodings_1%3a1.0.5-0ubuntu3_all.deb ... 1236s Unpacking xfonts-encodings 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libsharpyuv0:armhf (1.5.0-0.1build1) ... 1237s Selecting previously unselected package libaom3:armhf. 1237s Preparing to unpack .../018-libaom3_3.13.1-2_armhf.deb ... 1237s Unpacking libaom3:armhf (3.13.1-2) ... 1237s Selecting previously unselected package libheif-plugin-aomdec:armhf. 1237s Preparing to unpack .../019-libheif-plugin-aomdec_1.21.2-1_armhf.deb ... 1237s Unpacking libheif-plugin-aomdec:armhf (1.21.2-1) ... 1237s Selecting previously unselected package libde265-0:armhf. 1237s Preparing to unpack .../020-libde265-0_1.0.16-1build1_armhf.deb ... 1237s Unpacking libde265-0:armhf (1.0.16-1build1) ... 1237s Selecting previously unselected package libheif-plugin-libde265:armhf. 1237s Preparing to unpack .../021-libheif-plugin-libde265_1.21.2-1_armhf.deb ... 1237s Unpacking libheif-plugin-libde265:armhf (1.21.2-1) ... 1237s Selecting previously unselected package libheif1:armhf. 1237s Preparing to unpack .../022-libheif1_1.21.2-1_armhf.deb ... 1237s Unpacking libheif1:armhf 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libltdl7:armhf. 1237s Preparing to unpack .../028-libltdl7_2.5.4-9_armhf.deb ... 1237s Unpacking libltdl7:armhf (2.5.4-9) ... 1237s Selecting previously unselected package libopenjp2-7:armhf. 1237s Preparing to unpack .../029-libopenjp2-7_2.5.4-1_armhf.deb ... 1237s Unpacking libopenjp2-7:armhf (2.5.4-1) ... 1237s Selecting previously unselected package libraw23t64:armhf. 1237s Preparing to unpack .../030-libraw23t64_0.21.4-2_armhf.deb ... 1237s Unpacking libraw23t64:armhf (0.21.4-2) ... 1237s Selecting previously unselected package libdeflate0:armhf. 1237s Preparing to unpack .../031-libdeflate0_1.23-2_armhf.deb ... 1237s Unpacking libdeflate0:armhf (1.23-2) ... 1237s Selecting previously unselected package liblerc4:armhf. 1237s Preparing to unpack .../032-liblerc4_4.0.0+ds-5ubuntu2_armhf.deb ... 1237s Unpacking liblerc4:armhf (4.0.0+ds-5ubuntu2) ... 1238s Selecting previously unselected package libwebp7:armhf. 1238s Preparing to unpack .../033-libwebp7_1.5.0-0.1build1_armhf.deb ... 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package libgfortran5:armhf. 1238s Preparing to unpack .../043-libgfortran5_15.2.0-11ubuntu1_armhf.deb ... 1238s Unpacking libgfortran5:armhf (15.2.0-11ubuntu1) ... 1238s Selecting previously unselected package liblapack3:armhf. 1238s Preparing to unpack .../044-liblapack3_3.12.1-7ubuntu1_armhf.deb ... 1238s Unpacking liblapack3:armhf (3.12.1-7ubuntu1) ... 1239s Selecting previously unselected package python3-numpy. 1239s Preparing to unpack .../045-python3-numpy_1%3a2.3.5+ds-3_armhf.deb ... 1239s Unpacking python3-numpy (1:2.3.5+ds-3) ... 1239s Selecting previously unselected package libpython3.13-stdlib:armhf. 1239s Preparing to unpack .../046-libpython3.13-stdlib_3.13.11-1_armhf.deb ... 1239s Unpacking libpython3.13-stdlib:armhf (3.13.11-1) ... 1239s Selecting previously unselected package python3.13. 1239s Preparing to unpack .../047-python3.13_3.13.11-1_armhf.deb ... 1239s Unpacking python3.13 (3.13.11-1) ... 1239s Selecting previously unselected package autoconf. 1239s Preparing 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unpack .../059-cpp-15-arm-linux-gnueabihf_15.2.0-11ubuntu1_armhf.deb ... 1241s Unpacking cpp-15-arm-linux-gnueabihf (15.2.0-11ubuntu1) ... 1241s Selecting previously unselected package cpp-15. 1241s Preparing to unpack .../060-cpp-15_15.2.0-11ubuntu1_armhf.deb ... 1241s Unpacking cpp-15 (15.2.0-11ubuntu1) ... 1241s Selecting previously unselected package cpp-arm-linux-gnueabihf. 1241s Preparing to unpack .../061-cpp-arm-linux-gnueabihf_4%3a15.2.0-4ubuntu1_armhf.deb ... 1241s Unpacking cpp-arm-linux-gnueabihf (4:15.2.0-4ubuntu1) ... 1241s Selecting previously unselected package cpp. 1241s Preparing to unpack .../062-cpp_4%3a15.2.0-4ubuntu1_armhf.deb ... 1241s Unpacking cpp (4:15.2.0-4ubuntu1) ... 1241s Selecting previously unselected package libcc1-0:armhf. 1241s Preparing to unpack .../063-libcc1-0_15.2.0-11ubuntu1_armhf.deb ... 1241s Unpacking libcc1-0:armhf (15.2.0-11ubuntu1) ... 1241s Selecting previously unselected package libasan8:armhf. 1241s Preparing to unpack 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unselected package dh-strip-nondeterminism. 1244s Preparing to unpack .../085-dh-strip-nondeterminism_1.15.0-1build1_all.deb ... 1244s Unpacking dh-strip-nondeterminism (1.15.0-1build1) ... 1244s Selecting previously unselected package libdw1t64:armhf. 1244s Preparing to unpack .../086-libdw1t64_0.194-1_armhf.deb ... 1244s Unpacking libdw1t64:armhf (0.194-1) ... 1244s Selecting previously unselected package debugedit. 1244s Preparing to unpack .../087-debugedit_1%3a5.2-3_armhf.deb ... 1244s Unpacking debugedit (1:5.2-3) ... 1244s Selecting previously unselected package dwz. 1244s Preparing to unpack .../088-dwz_0.16-2_armhf.deb ... 1244s Unpacking dwz (0.16-2) ... 1244s Selecting previously unselected package gettext. 1244s Preparing to unpack .../089-gettext_0.23.2-1_armhf.deb ... 1244s Unpacking gettext (0.23.2-1) ... 1244s Selecting previously unselected package intltool-debian. 1244s Preparing to unpack .../090-intltool-debian_0.35.0+20060710.6build1_all.deb ... 1244s Unpacking intltool-debian (0.35.0+20060710.6build1) ... 1244s Selecting previously unselected package po-debconf. 1244s Preparing to unpack .../091-po-debconf_1.0.22_all.deb ... 1244s Unpacking po-debconf (1.0.22) ... 1244s Selecting previously unselected package debhelper. 1244s Preparing to unpack .../092-debhelper_13.28ubuntu1_all.deb ... 1244s Unpacking debhelper (13.28ubuntu1) ... 1244s Selecting previously unselected package dh-python. 1244s Preparing to unpack .../093-dh-python_7.20251231_all.deb ... 1244s Unpacking dh-python (7.20251231) ... 1244s Selecting previously unselected package dialign. 1244s Preparing to unpack .../094-dialign_2.2.1-13build1_armhf.deb ... 1244s Unpacking dialign (2.2.1-13build1) ... 1244s Selecting previously unselected package sgml-base. 1244s Preparing to unpack .../095-sgml-base_1.31+nmu1_all.deb ... 1244s Unpacking sgml-base (1.31+nmu1) ... 1244s Selecting previously unselected package xml-core. 1244s Preparing to unpack .../096-xml-core_0.19build1_all.deb ... 1244s Unpacking xml-core (0.19build1) ... 1244s Selecting previously unselected package docutils-common. 1244s Preparing to unpack .../097-docutils-common_0.22.4+dfsg-1_all.deb ... 1245s Unpacking docutils-common (0.22.4+dfsg-1) ... 1245s Selecting previously unselected package libcifpp-data. 1245s Preparing to unpack .../098-libcifpp-data_9.0.5-2_all.deb ... 1245s Unpacking libcifpp-data (9.0.5-2) ... 1245s Selecting previously unselected package libcifpp9:armhf. 1245s Preparing to unpack .../099-libcifpp9_9.0.5-2_armhf.deb ... 1245s Unpacking libcifpp9:armhf (9.0.5-2) ... 1245s Selecting previously unselected package dssp. 1245s Preparing to unpack .../100-dssp_4.5.7-1_armhf.deb ... 1245s Unpacking dssp (4.5.7-1) ... 1245s Selecting previously unselected package fonts-dejavu-extra. 1245s Preparing to unpack .../101-fonts-dejavu-extra_2.37-8build1_all.deb ... 1245s Unpacking fonts-dejavu-extra (2.37-8build1) ... 1245s Selecting previously unselected package fonts-font-awesome. 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libavahi-common-data:armhf. 1246s Preparing to unpack .../107-libavahi-common-data_0.8-17ubuntu1_armhf.deb ... 1246s Unpacking libavahi-common-data:armhf (0.8-17ubuntu1) ... 1246s Selecting previously unselected package libavahi-common3:armhf. 1246s Preparing to unpack .../108-libavahi-common3_0.8-17ubuntu1_armhf.deb ... 1246s Unpacking libavahi-common3:armhf (0.8-17ubuntu1) ... 1246s Selecting previously unselected package libavahi-client3:armhf. 1246s Preparing to unpack .../109-libavahi-client3_0.8-17ubuntu1_armhf.deb ... 1246s Unpacking libavahi-client3:armhf (0.8-17ubuntu1) ... 1246s Selecting previously unselected package libcups2t64:armhf. 1246s Preparing to unpack .../110-libcups2t64_2.4.16-1ubuntu1_armhf.deb ... 1246s Unpacking libcups2t64:armhf (2.4.16-1ubuntu1) ... 1246s Selecting previously unselected package libidn12:armhf. 1246s Preparing to unpack .../111-libidn12_1.43-2_armhf.deb ... 1246s Unpacking libidn12:armhf (1.43-2) ... 1246s Selecting previously unselected package libijs-0.35:armhf. 1246s Preparing to unpack .../112-libijs-0.35_0.35-16_armhf.deb ... 1246s Unpacking libijs-0.35:armhf (0.35-16) ... 1246s Selecting previously unselected package libjbig2dec0:armhf. 1246s Preparing to unpack .../113-libjbig2dec0_0.20-1build4_armhf.deb ... 1246s Unpacking libjbig2dec0:armhf (0.20-1build4) ... 1246s Selecting previously unselected package libpaper2:armhf. 1246s Preparing to unpack .../114-libpaper2_2.2.5-0.3build1_armhf.deb ... 1246s Unpacking libpaper2:armhf (2.2.5-0.3build1) ... 1246s Selecting previously unselected package libice6:armhf. 1246s Preparing to unpack .../115-libice6_2%3a1.1.1-1build1_armhf.deb ... 1246s Unpacking libice6:armhf (2:1.1.1-1build1) ... 1246s Selecting previously unselected package libsm6:armhf. 1246s Preparing to unpack .../116-libsm6_2%3a1.2.6-1_armhf.deb ... 1246s Unpacking libsm6:armhf (2:1.2.6-1) ... 1246s Selecting previously unselected package libxt6t64:armhf. 1246s Preparing to unpack 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unpack .../132-libxrender1_1%3a0.9.12-1_armhf.deb ... 1248s Unpacking libxrender1:armhf (1:0.9.12-1) ... 1248s Selecting previously unselected package libcairo2:armhf. 1248s Preparing to unpack .../133-libcairo2_1.18.4-3_armhf.deb ... 1248s Unpacking libcairo2:armhf (1.18.4-3) ... 1248s Selecting previously unselected package libgraphite2-3:armhf. 1248s Preparing to unpack .../134-libgraphite2-3_1.3.14-11ubuntu1_armhf.deb ... 1248s Unpacking libgraphite2-3:armhf (1.3.14-11ubuntu1) ... 1248s Selecting previously unselected package libharfbuzz0b:armhf. 1248s Preparing to unpack .../135-libharfbuzz0b_12.3.0-4_armhf.deb ... 1248s Unpacking libharfbuzz0b:armhf (12.3.0-4) ... 1248s Selecting previously unselected package libmpfi0:armhf. 1248s Preparing to unpack .../136-libmpfi0_1.5.4+ds-4_armhf.deb ... 1248s Unpacking libmpfi0:armhf (1.5.4+ds-4) ... 1248s Selecting previously unselected package libpotrace0:armhf. 1248s Preparing to unpack .../137-libpotrace0_1.16-2build2_armhf.deb ... 1248s 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package libzzip-0-13t64:armhf. 1248s Preparing to unpack .../143-libzzip-0-13t64_0.13.78+dfsg.1-0.2_armhf.deb ... 1248s Unpacking libzzip-0-13t64:armhf (0.13.78+dfsg.1-0.2) ... 1248s Selecting previously unselected package texlive-binaries. 1248s Preparing to unpack .../144-texlive-binaries_2025.20250727.75242+ds-5build1_armhf.deb ... 1248s Unpacking texlive-binaries (2025.20250727.75242+ds-5build1) ... 1249s Selecting previously unselected package xdg-utils. 1249s Preparing to unpack .../145-xdg-utils_1.2.1-2ubuntu2_all.deb ... 1249s Unpacking xdg-utils (1.2.1-2ubuntu2) ... 1249s Selecting previously unselected package texlive-base. 1249s Preparing to unpack .../146-texlive-base_2025.20251127-1_all.deb ... 1249s Unpacking texlive-base (2025.20251127-1) ... 1250s Selecting previously unselected package hicolor-icon-theme. 1250s Preparing to unpack .../147-hicolor-icon-theme_0.18-2build1_all.deb ... 1250s Unpacking hicolor-icon-theme (0.18-2build1) ... 1250s Selecting previously unselected package imagemagick-7.q16. 1250s Preparing to unpack .../148-imagemagick-7.q16_8%3a7.1.2.12+dfsg1-1_armhf.deb ... 1250s Unpacking imagemagick-7.q16 (8:7.1.2.12+dfsg1-1) ... 1250s Selecting previously unselected package imagemagick. 1250s Preparing to unpack .../149-imagemagick_8%3a7.1.2.12+dfsg1-1_armhf.deb ... 1250s Unpacking imagemagick (8:7.1.2.12+dfsg1-1) ... 1250s Selecting previously unselected package libstdlib-ocaml. 1250s Preparing to unpack .../150-libstdlib-ocaml_5.4.0-1ubuntu1_armhf.deb ... 1250s Unpacking libstdlib-ocaml (5.4.0-1ubuntu1) ... 1250s Selecting previously unselected package ocaml-base. 1250s Preparing to unpack .../151-ocaml-base_5.4.0-1ubuntu1_armhf.deb ... 1250s Unpacking ocaml-base (5.4.0-1ubuntu1) ... 1250s Selecting previously unselected package hevea. 1250s Preparing to unpack .../152-hevea_2.36-2build3_armhf.deb ... 1250s Unpacking hevea (2.36-2build3) ... 1250s Selecting previously unselected package libsuitesparseconfig7:armhf. 1250s 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unpack .../158-libcommons-parent-java_56-1build1_all.deb ... 1251s Unpacking libcommons-parent-java (56-1build1) ... 1251s Selecting previously unselected package libcommons-logging-java. 1251s Preparing to unpack .../159-libcommons-logging-java_1.3.0-1ubuntu1_all.deb ... 1251s Unpacking libcommons-logging-java (1.3.0-1ubuntu1) ... 1251s Selecting previously unselected package libexpat1-dev:armhf. 1251s Preparing to unpack .../160-libexpat1-dev_2.7.3-1_armhf.deb ... 1251s Unpacking libexpat1-dev:armhf (2.7.3-1) ... 1251s Selecting previously unselected package libglpk40:armhf. 1251s Preparing to unpack .../161-libglpk40_5.0-2_armhf.deb ... 1251s Unpacking libglpk40:armhf (5.0-2) ... 1251s Selecting previously unselected package libplfit0:armhf. 1251s Preparing to unpack .../162-libplfit0_0.9.6+ds-2ubuntu1_armhf.deb ... 1251s Unpacking libplfit0:armhf (0.9.6+ds-2ubuntu1) ... 1251s Selecting previously unselected package libigraph4:armhf. 1251s Preparing to unpack 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1253s Unpacking libxss1:armhf (1:1.2.3-1build4) ... 1253s Selecting previously unselected package libtk8.6:armhf. 1253s Preparing to unpack .../184-libtk8.6_8.6.17-1_armhf.deb ... 1253s Unpacking libtk8.6:armhf (8.6.17-1) ... 1253s Selecting previously unselected package libxslt1.1:armhf. 1253s Preparing to unpack .../185-libxslt1.1_1.1.43-0.3_armhf.deb ... 1253s Unpacking libxslt1.1:armhf (1.1.43-0.3) ... 1253s Selecting previously unselected package libzopfli1. 1253s Preparing to unpack .../186-libzopfli1_1.0.3-3_armhf.deb ... 1253s Unpacking libzopfli1 (1.0.3-3) ... 1253s Selecting previously unselected package lmodern. 1253s Preparing to unpack .../187-lmodern_2.005-1build1_all.deb ... 1253s Unpacking lmodern (2.005-1build1) ... 1254s Selecting previously unselected package mafft. 1254s Preparing to unpack .../188-mafft_7.525-1_armhf.deb ... 1254s Unpacking mafft (7.525-1) ... 1254s Selecting previously unselected package ncbi-data. 1254s Preparing to unpack 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unselected package python-biopython-doc. 1255s Preparing to unpack .../195-python-biopython-doc_1.86+dfsg-1_all.deb ... 1255s Unpacking python-biopython-doc (1.86+dfsg-1) ... 1256s Selecting previously unselected package python-matplotlib-data. 1256s Preparing to unpack .../196-python-matplotlib-data_3.10.7+dfsg1-1_all.deb ... 1256s Unpacking python-matplotlib-data (3.10.7+dfsg1-1) ... 1256s Selecting previously unselected package python3-all. 1256s Preparing to unpack .../197-python3-all_3.14.2-1_armhf.deb ... 1256s Unpacking python3-all (3.14.2-1) ... 1256s Selecting previously unselected package python3.14-dev. 1256s Preparing to unpack .../198-python3.14-dev_3.14.2-1_armhf.deb ... 1256s Unpacking python3.14-dev (3.14.2-1) ... 1256s Selecting previously unselected package python3-dev. 1256s Preparing to unpack .../199-python3-dev_3.14.2-1_armhf.deb ... 1256s Unpacking python3-dev (3.14.2-1) ... 1256s Selecting previously unselected package python3.13-dev. 1256s Preparing to unpack .../200-python3.13-dev_3.13.11-1_armhf.deb ... 1256s Unpacking python3.13-dev (3.13.11-1) ... 1256s Selecting previously unselected package python3-all-dev. 1256s Preparing to unpack .../201-python3-all-dev_3.14.2-1_armhf.deb ... 1256s Unpacking python3-all-dev (3.14.2-1) ... 1256s Selecting previously unselected package python3-charset-normalizer. 1256s Preparing to unpack .../202-python3-charset-normalizer_3.4.4-2_armhf.deb ... 1256s Unpacking python3-charset-normalizer (3.4.4-2) ... 1256s Selecting previously unselected package python3.13-tk. 1256s Preparing to unpack .../203-python3.13-tk_3.13.11-1_armhf.deb ... 1256s Unpacking python3.13-tk (3.13.11-1) ... 1256s Selecting previously unselected package python3.14-tk. 1256s Preparing to unpack .../204-python3.14-tk_3.14.2-1_armhf.deb ... 1256s Unpacking python3.14-tk (3.14.2-1) ... 1256s Selecting previously unselected package python3-tk. 1256s Preparing to unpack .../205-python3-tk_3.14.2-1_armhf.deb ... 1256s Unpacking python3-tk (3.14.2-1) ... 1257s Selecting previously unselected package python3-pil.imagetk:armhf. 1257s Preparing to unpack .../206-python3-pil.imagetk_12.0.0-1ubuntu1_armhf.deb ... 1257s Unpacking python3-pil.imagetk:armhf (12.0.0-1ubuntu1) ... 1257s Selecting previously unselected package python3-pil:armhf. 1257s Preparing to unpack .../207-python3-pil_12.0.0-1ubuntu1_armhf.deb ... 1257s Unpacking python3-pil:armhf (12.0.0-1ubuntu1) ... 1257s Selecting previously unselected package python3-cairo. 1257s Preparing to unpack .../208-python3-cairo_1.27.0-2build1_armhf.deb ... 1257s Unpacking python3-cairo (1.27.0-2build1) ... 1257s Selecting previously unselected package python3-freetype. 1257s Preparing to unpack .../209-python3-freetype_2.5.1-2_all.deb ... 1257s Unpacking python3-freetype (2.5.1-2) ... 1257s Selecting previously unselected package python3-rlpycairo. 1257s Preparing to unpack .../210-python3-rlpycairo_0.3.0-4_all.deb ... 1257s Unpacking python3-rlpycairo (0.3.0-4) ... 1257s Selecting previously unselected package python3-reportlab. 1257s Preparing to unpack .../211-python3-reportlab_4.4.9-1_all.deb ... 1257s Unpacking python3-reportlab (4.4.9-1) ... 1257s Selecting previously unselected package w3c-sgml-lib. 1257s Preparing to unpack .../212-w3c-sgml-lib_1.3-3build1_all.deb ... 1257s Unpacking w3c-sgml-lib (1.3-3build1) ... 1257s Selecting previously unselected package python3-biopython. 1257s Preparing to unpack .../213-python3-biopython_1.86+dfsg-1_armhf.deb ... 1257s Unpacking python3-biopython (1.86+dfsg-1) ... 1257s Selecting previously unselected package python3-biopython-sql. 1257s Preparing to unpack .../214-python3-biopython-sql_1.86+dfsg-1_all.deb ... 1257s Unpacking python3-biopython-sql (1.86+dfsg-1) ... 1257s Selecting previously unselected package python3-brotli. 1257s Preparing to unpack .../215-python3-brotli_1.1.0-2build6_armhf.deb ... 1257s Unpacking python3-brotli (1.1.0-2build6) ... 1258s Selecting previously unselected package python3-contourpy. 1258s Preparing to unpack .../216-python3-contourpy_1.3.3-1_armhf.deb ... 1258s Unpacking python3-contourpy (1.3.3-1) ... 1258s Selecting previously unselected package python3-cycler. 1258s Preparing to unpack .../217-python3-cycler_0.12.1-2_all.deb ... 1258s Unpacking python3-cycler (0.12.1-2) ... 1258s Selecting previously unselected package python3-decorator. 1258s Preparing to unpack .../218-python3-decorator_5.2.1-2_all.deb ... 1258s Unpacking python3-decorator (5.2.1-2) ... 1258s Selecting previously unselected package python3-defusedxml. 1258s Preparing to unpack .../219-python3-defusedxml_0.7.1-3build1_all.deb ... 1258s Unpacking python3-defusedxml (0.7.1-3build1) ... 1258s Selecting previously unselected package python3-roman-numerals. 1258s Preparing to unpack .../220-python3-roman-numerals_4.1.0-1_all.deb ... 1258s Unpacking python3-roman-numerals (4.1.0-1) ... 1258s Selecting previously unselected package python3-docutils. 1258s Preparing to unpack .../221-python3-docutils_0.22.4+dfsg-1_all.deb ... 1258s Unpacking python3-docutils (0.22.4+dfsg-1) ... 1258s Selecting previously unselected package python3-lxml:armhf. 1258s Preparing to unpack .../222-python3-lxml_6.0.2-1_armhf.deb ... 1258s Unpacking python3-lxml:armhf (6.0.2-1) ... 1258s Selecting previously unselected package python3-lz4. 1258s Preparing to unpack .../223-python3-lz4_4.4.5+dfsg-1_armhf.deb ... 1258s Unpacking python3-lz4 (4.4.5+dfsg-1) ... 1258s Selecting previously unselected package python3-scipy. 1258s Preparing to unpack .../224-python3-scipy_1.16.3-3_armhf.deb ... 1258s Unpacking python3-scipy (1.16.3-3) ... 1259s Selecting previously unselected package python3-mpmath. 1259s Preparing to unpack .../225-python3-mpmath_1.3.0-2_all.deb ... 1259s Unpacking python3-mpmath (1.3.0-2) ... 1259s Selecting previously unselected package python3-sympy. 1259s Preparing to unpack .../226-python3-sympy_1.14.0-2_all.deb ... 1259s Unpacking python3-sympy (1.14.0-2) ... 1260s Selecting previously unselected package python3-ufolib2. 1260s Preparing to unpack .../227-python3-ufolib2_0.18.1+dfsg1-1_all.deb ... 1260s Unpacking python3-ufolib2 (0.18.1+dfsg1-1) ... 1260s Selecting previously unselected package python3-zopfli. 1260s Preparing to unpack .../228-python3-zopfli_0.4.0-1_armhf.deb ... 1260s Unpacking python3-zopfli (0.4.0-1) ... 1260s Selecting previously unselected package unicode-data. 1260s Preparing to unpack .../229-unicode-data_16.0.0-1build1_all.deb ... 1260s Unpacking unicode-data (16.0.0-1build1) ... 1260s Selecting previously unselected package python3-fonttools. 1260s Preparing to unpack .../230-python3-fonttools_4.61.1-3_armhf.deb ... 1260s Unpacking python3-fonttools (4.61.1-3) ... 1260s Selecting previously unselected package python3-imagesize. 1260s Preparing to unpack .../231-python3-imagesize_1.4.1-1build1_all.deb ... 1260s Unpacking python3-imagesize (1.4.1-1build1) ... 1260s Selecting previously unselected package python3-kiwisolver. 1260s Preparing to unpack .../232-python3-kiwisolver_1.4.10~rc0-1_armhf.deb ... 1260s Unpacking python3-kiwisolver (1.4.10~rc0-1) ... 1260s Selecting previously unselected package python3-matplotlib. 1260s Preparing to unpack .../233-python3-matplotlib_3.10.7+dfsg1-1_armhf.deb ... 1260s Unpacking python3-matplotlib (3.10.7+dfsg1-1) ... 1261s Selecting previously unselected package python3-msgpack. 1261s Preparing to unpack .../234-python3-msgpack_1.1.2-1_armhf.deb ... 1261s Unpacking python3-msgpack (1.1.2-1) ... 1261s Selecting previously unselected package python3-mmtf. 1261s Preparing to unpack .../235-python3-mmtf_1.1.3-1build1_all.deb ... 1261s Unpacking python3-mmtf (1.1.3-1build1) ... 1261s Selecting previously unselected package python3-mysqldb. 1261s Preparing to unpack .../236-python3-mysqldb_1.4.6-2build7_armhf.deb ... 1261s Unpacking python3-mysqldb (1.4.6-2build7) ... 1261s Selecting previously unselected package python3-networkx. 1261s Preparing to unpack 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(4.10000-1) ... 1279s Setting up libxslt1.1:armhf (1.1.43-0.3) ... 1279s Setting up libpython3.14:armhf (3.14.2-1) ... 1279s Setting up debugedit (1:5.2-3) ... 1279s Setting up fonts-lmodern (2.005-1build1) ... 1279s Setting up libsuitesparseconfig7:armhf (1:7.12.1+dfsg-1) ... 1279s Setting up python3-roman-numerals (4.1.0-1) ... 1279s Setting up libopenjp2-7:armhf (2.5.4-1) ... 1279s Setting up python3.13-minimal (3.13.11-1) ... 1280s Setting up libharfbuzz0b:armhf (12.3.0-4) ... 1280s Setting up fasttree (2.1.11-2build1) ... 1280s Setting up sgml-base (1.31+nmu1) ... 1280s Setting up python3-msgpack (1.1.2-1) ... 1280s Setting up libplfit0:armhf (0.9.6+ds-2ubuntu1) ... 1280s Setting up libxss1:armhf (1:1.2.3-1build4) ... 1280s Setting up libmbedcrypto16:armhf (3.6.5-0.1ubuntu2) ... 1280s Setting up libpaper2:armhf (2.2.5-0.3build1) ... 1281s Setting up libjs-jquery (3.7.1+dfsg+~3.5.33-1build1) ... 1281s Setting up python3-mpmath (1.3.0-2) ... 1282s Setting up libisl23:armhf (0.27-1build1) ... 1282s Setting up libde265-0:armhf (1.0.16-1build1) ... 1282s Setting up libc-dev-bin (2.42-2ubuntu4) ... 1282s Setting up python-matplotlib-data (3.10.7+dfsg1-1) ... 1282s Setting up libwebpmux3:armhf (1.5.0-0.1build1) ... 1282s Setting up cpp-15-arm-linux-gnueabihf (15.2.0-11ubuntu1) ... 1282s Setting up dialign (2.2.1-13build1) ... 1282s Setting up libpython3.13-stdlib:armhf (3.13.11-1) ... 1282s Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1build1) ... 1282s Setting up sphinx-rtd-theme-common (3.0.2+dfsg-3) ... 1282s Setting up xdg-utils (1.2.1-2ubuntu2) ... 1282s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode 1282s Setting up libcc1-0:armhf (15.2.0-11ubuntu1) ... 1282s Setting up cpp-arm-linux-gnueabihf (4:15.2.0-4ubuntu1) ... 1282s Setting up libsynctex2:armhf (2025.20250727.75242+ds-5build1) ... 1282s Setting up prank (250331-1) ... 1282s Setting up libargtable2-0:armhf (13-4) ... 1282s Setting up python3-imagesize (1.4.1-1build1) ... 1282s Setting up libpotrace0:armhf (1.16-2build2) ... 1282s Setting up libpython3.13:armhf (3.13.11-1) ... 1282s Setting up libjpeg8:armhf (8c-2ubuntu11) ... 1282s Setting up automake (1:1.18.1-3build1) ... 1282s update-alternatives: using /usr/bin/automake-1.18 to provide /usr/bin/automake (automake) in auto mode 1282s Setting up libfile-stripnondeterminism-perl (1.15.0-1build1) ... 1282s Setting up python3-sympy (1.14.0-2) ... 1290s /usr/lib/python3/dist-packages/sympy/testing/runtests.py:283: SyntaxWarning: 'return' in a 'finally' block 1290s return p.returncode 1298s Setting up libice6:armhf (2:1.1.1-1build1) ... 1298s Setting up flex (2.6.4-8.2build2) ... 1298s Setting up liblapack3:armhf (3.12.1-7ubuntu1) ... 1298s update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode 1298s Setting up gettext (0.23.2-1) ... 1298s Setting up libarpack2t64:armhf (3.9.1-6) ... 1298s Setting up libgcc-15-dev:armhf (15.2.0-11ubuntu1) ... 1298s Setting up libamd3:armhf (1:7.12.1+dfsg-1) ... 1298s Setting up libpdfbox-java (1:1.8.16-5) ... 1298s Setting up gcc-15-arm-linux-gnueabihf (15.2.0-11ubuntu1) ... 1298s Setting up libcolamd3:armhf (1:7.12.1+dfsg-1) ... 1298s Setting up python3.13 (3.13.11-1) ... 1300s Setting up libcifpp9:armhf (9.0.5-2) ... 1300s Setting up fontconfig-config (2.15.0-2.4ubuntu1) ... 1300s Setting up wise (2.4.1-27) ... 1300s Setting up preview-latex-style (13.2-1.1) ... 1300s Setting up libwebpdemux2:armhf (1.5.0-0.1build1) ... 1300s Setting up libcommons-parent-java (56-1build1) ... 1300s Setting up libavahi-common3:armhf (0.8-17ubuntu1) ... 1300s Setting up libcommons-logging-java (1.3.0-1ubuntu1) ... 1300s Setting up python3-all (3.14.2-1) ... 1300s Setting up libpaper-utils (2.2.5-0.3build1) ... 1300s Setting up clustalo (1.2.4-8build2) ... 1300s Setting up dssp (4.5.7-1) ... 1300s Setting up python3-freetype (2.5.1-2) ... 1300s Setting up xfonts-utils (1:7.7+7build1) ... 1300s Setting up python3-zopfli (0.4.0-1) ... 1301s Setting up intltool-debian (0.35.0+20060710.6build1) ... 1301s Setting up libmbedx509-7:armhf (3.6.5-0.1ubuntu2) ... 1301s Setting up libptexenc1:armhf (2025.20250727.75242+ds-5build1) ... 1301s Setting up libglpk40:armhf (5.0-2) ... 1301s Setting up libraqm0:armhf (0.10.3-1) ... 1301s Setting up sphinx-common (8.2.3-12) ... 1301s Setting up python3-numpy (1:2.3.5+ds-3) ... 1305s Setting up libraw23t64:armhf (0.21.4-2) ... 1305s Setting up libmbedtls21:armhf (3.6.5-0.1ubuntu2) ... 1305s Setting up dh-strip-nondeterminism (1.15.0-1build1) ... 1305s Setting up cpp-15 (15.2.0-11ubuntu1) ... 1305s Setting up python3-lxml:armhf (6.0.2-1) ... 1306s Setting up python-biopython-doc (1.86+dfsg-1) ... 1306s Setting up libtiff6:armhf (4.7.0-3ubuntu3) ... 1306s Setting up cpp (4:15.2.0-4ubuntu1) ... 1306s Setting up lmodern (2.005-1build1) ... 1306s Setting up xml-core (0.19build1) ... 1306s Setting up libc6-dev:armhf (2.42-2ubuntu4) ... 1306s Setting up python3-contourpy (1.3.3-1) ... 1306s Setting up libfontconfig1:armhf (2.15.0-2.4ubuntu1) ... 1306s Setting up libsm6:armhf (2:1.2.6-1) ... 1306s Setting up libavahi-client3:armhf (0.8-17ubuntu1) ... 1306s Setting up gcc-arm-linux-gnueabihf (4:15.2.0-4ubuntu1) ... 1306s Setting up libxft2:armhf (2.3.6-1build2) ... 1306s Setting up python3-scipy (1.16.3-3) ... 1316s Setting up libigraph4:armhf (1.0.1+ds-3) ... 1316s Setting up po-debconf (1.0.22) ... 1316s Setting up libtk8.6:armhf (8.6.17-1) ... 1316s Setting up python3-mmtf (1.1.3-1build1) ... 1317s Setting up fonts-urw-base35 (20200910-8build1) ... 1317s Setting up libcairo2:armhf (1.18.4-3) ... 1317s Setting up python3.13-tk (3.13.11-1) ... 1317s Setting up ncbi-blast+ (2.16.0+ds-7) ... 1317s Setting up python3-pil:armhf (12.0.0-1ubuntu1) ... 1318s Setting up gcc-15 (15.2.0-11ubuntu1) ... 1318s Setting up libstdc++-15-dev:armhf (15.2.0-11ubuntu1) ... 1318s Setting up libexpat1-dev:armhf (2.7.3-1) ... 1318s Setting up libxt6t64:armhf (1:1.2.1-1.3) ... 1318s Setting up netpbm (2:11.10.02-1build1) ... 1318s Setting up zlib1g-dev:armhf (1:1.3.dfsg+really1.3.1-1ubuntu2) ... 1318s Setting up python3-igraph (1.0.0+ds-1) ... 1319s Setting up libpython3.14-dev:armhf (3.14.2-1) ... 1319s Setting up libcups2t64:armhf (2.4.16-1ubuntu1) ... 1319s Setting up libgs10-common (10.05.0dfsg1-0ubuntu4) ... 1319s Setting up libxmu6:armhf (2:1.1.3-4) ... 1319s Setting up python3.14-tk (3.14.2-1) ... 1319s Setting up libpython3-dev:armhf (3.14.2-1) ... 1319s Setting up python3-cairo (1.27.0-2build1) ... 1319s Setting up python3.14-dev (3.14.2-1) ... 1319s Setting up libtool (2.5.4-9) ... 1319s Setting up g++-15-arm-linux-gnueabihf (15.2.0-11ubuntu1) ... 1319s Setting up python3-tk (3.14.2-1) ... 1319s Setting up libxaw7:armhf (2:1.0.16-1build1) ... 1319s Setting up gcc (4:15.2.0-4ubuntu1) ... 1319s Setting up dh-autoreconf (21) ... 1319s Setting up python3-pil.imagetk:armhf (12.0.0-1ubuntu1) ... 1319s Setting up python3-rlpycairo (0.3.0-4) ... 1320s Setting up libpython3.13-dev:armhf (3.13.11-1) ... 1320s Setting up python3-dev (3.14.2-1) ... 1320s Setting up python3-reportlab (4.4.9-1) ... 1322s Setting up texlive-binaries (2025.20250727.75242+ds-5build1) ... 1322s update-alternatives: using /usr/bin/xdvi-xaw to provide /usr/bin/xdvi.bin (xdvi.bin) in auto mode 1322s update-alternatives: using /usr/bin/bibtex.original to provide /usr/bin/bibtex (bibtex) in auto mode 1322s Setting up texlive-base (2025.20251127-1) ... 1323s tl-paper: setting paper size for dvips to a4: /var/lib/texmf/dvips/config/config-paper.ps 1323s tl-paper: setting paper size for dvipdfmx to a4: /var/lib/texmf/dvipdfmx/dvipdfmx-paper.cfg 1323s tl-paper: setting paper size for xdvi to a4: /var/lib/texmf/xdvi/XDvi-paper 1324s tl-paper: setting paper size for pdftex to a4: /var/lib/texmf/tex/generic/tex-ini-files/pdftexconfig.tex 1324s Setting up g++-15 (15.2.0-11ubuntu1) ... 1324s Setting up libgs10:armhf (10.05.0dfsg1-0ubuntu4) ... 1324s Setting up g++-arm-linux-gnueabihf (4:15.2.0-4ubuntu1) ... 1324s Setting up texlive-luatex (2025.20251127-1) ... 1324s Setting up python3.13-dev (3.13.11-1) ... 1324s Setting up debhelper (13.28ubuntu1) ... 1324s Setting up ghostscript (10.05.0dfsg1-0ubuntu4) ... 1324s Setting up texlive-latex-base (2025.20251127-1) ... 1324s Setting up libpython3-all-dev:armhf (3.14.2-1) ... 1324s Setting up texlive-latex-recommended (2025.20251127-1) ... 1324s Setting up texlive-pictures (2025.20251127-1) ... 1324s Setting up g++ (4:15.2.0-4ubuntu1) ... 1324s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 1324s Setting up texlive-fonts-recommended (2025.20251127-1) ... 1324s Setting up build-essential (12.12ubuntu2) ... 1324s Setting up python3-all-dev (3.14.2-1) ... 1324s Setting up texlive-latex-extra (2025.20251127-2) ... 1325s Setting up python3-ufolib2 (0.18.1+dfsg1-1) ... 1325s Setting up libheif-plugin-aomdec:armhf (1.21.2-1) ... 1325s Setting up libheif-plugin-libde265:armhf (1.21.2-1) ... 1325s Setting up libheif1:armhf (1.21.2-1) ... 1325s Setting up python3-fonttools (4.61.1-3) ... 1327s Setting up libmagickcore-7.q16-10:armhf (8:7.1.2.12+dfsg1-1) ... 1327s Setting up python3-matplotlib (3.10.7+dfsg1-1) ... 1332s Setting up libmagickwand-7.q16-10:armhf (8:7.1.2.12+dfsg1-1) ... 1332s Setting up imagemagick-7.q16 (8:7.1.2.12+dfsg1-1) ... 1332s update-alternatives: using /usr/bin/compare-im7.q16 to provide /usr/bin/compare (compare) in auto mode 1332s update-alternatives: using /usr/bin/compare-im7.q16 to provide /usr/bin/compare-im7 (compare-im7) in auto mode 1332s update-alternatives: using /usr/bin/animate-im7.q16 to provide /usr/bin/animate (animate) in auto mode 1332s update-alternatives: using /usr/bin/animate-im7.q16 to provide /usr/bin/animate-im7 (animate-im7) in auto mode 1332s update-alternatives: using /usr/bin/convert-im7.q16 to provide /usr/bin/convert (convert) in auto mode 1332s update-alternatives: using /usr/bin/convert-im7.q16 to provide /usr/bin/convert-im7 (convert-im7) in auto mode 1332s update-alternatives: using /usr/bin/composite-im7.q16 to provide /usr/bin/composite (composite) in auto mode 1332s update-alternatives: using /usr/bin/composite-im7.q16 to provide /usr/bin/composite-im7 (composite-im7) in auto mode 1332s update-alternatives: using /usr/bin/conjure-im7.q16 to provide /usr/bin/conjure (conjure) in auto mode 1332s update-alternatives: using /usr/bin/conjure-im7.q16 to provide /usr/bin/conjure-im7 (conjure-im7) in auto mode 1332s update-alternatives: using /usr/bin/import-im7.q16 to provide /usr/bin/import (import) in auto mode 1332s update-alternatives: using /usr/bin/import-im7.q16 to provide /usr/bin/import-im7 (import-im7) in auto mode 1332s update-alternatives: using /usr/bin/identify-im7.q16 to provide /usr/bin/identify (identify) in auto mode 1332s update-alternatives: using /usr/bin/identify-im7.q16 to provide /usr/bin/identify-im7 (identify-im7) in auto mode 1332s update-alternatives: using /usr/bin/stream-im7.q16 to provide /usr/bin/stream (stream) in auto mode 1332s update-alternatives: using /usr/bin/stream-im7.q16 to provide /usr/bin/stream-im7 (stream-im7) in auto mode 1332s update-alternatives: using /usr/bin/display-im7.q16 to provide /usr/bin/display (display) in auto mode 1332s update-alternatives: using /usr/bin/display-im7.q16 to provide /usr/bin/display-im7 (display-im7) in auto mode 1332s update-alternatives: using /usr/bin/montage-im7.q16 to provide /usr/bin/montage (montage) in auto mode 1332s update-alternatives: using /usr/bin/montage-im7.q16 to provide /usr/bin/montage-im7 (montage-im7) in auto mode 1332s update-alternatives: using /usr/bin/mogrify-im7.q16 to provide /usr/bin/mogrify (mogrify) in auto mode 1332s update-alternatives: using /usr/bin/mogrify-im7.q16 to provide /usr/bin/mogrify-im7 (mogrify-im7) in auto mode 1332s update-alternatives: using /usr/bin/magick-im7.q16 to provide /usr/bin/magick (magick) in auto mode 1332s 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 1332s update-alternatives: using /usr/bin/magick-im7.q16 to provide /usr/bin/magick-im7 (magick-im7) in auto mode 1332s 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 1332s update-alternatives: using /usr/bin/magick-script-im7.q16 to provide /usr/bin/magick-script (magick-script) in auto mode 1332s 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 1332s update-alternatives: using /usr/bin/magick-script-im7.q16 to provide /usr/bin/magick-script-im7 (magick-script-im7) in auto mode 1332s 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 1332s Setting up hevea (2.36-2build3) ... 1332s Setting up imagemagick (8:7.1.2.12+dfsg1-1) ... 1332s Processing triggers for install-info (7.2-5) ... 1332s Processing triggers for libc-bin (2.42-2ubuntu4) ... 1332s Processing triggers for systemd (259-1ubuntu2) ... 1332s Processing triggers for man-db (2.13.1-1) ... 1334s Processing triggers for sgml-base (1.31+nmu1) ... 1334s Setting up docutils-common (0.22.4+dfsg-1) ... 1334s Setting up w3c-sgml-lib (1.3-3build1) ... 1365s Setting up python3-biopython (1.86+dfsg-1) ... 1368s Setting up python3-biopython-sql (1.86+dfsg-1) ... 1369s Processing triggers for sgml-base (1.31+nmu1) ... 1369s Setting up python3-docutils (0.22.4+dfsg-1) ... 1370s Setting up python3-sphinx (8.2.3-12) ... 1372s Setting up python3-sphinxcontrib.jquery (4.1-6) ... 1372s Setting up python3-numpydoc (1.9.0-1) ... 1372s Setting up python3-sphinx-rtd-theme (3.0.2+dfsg-3) ... 1372s Processing triggers for tex-common (6.20) ... 1373s Running updmap-sys. This may take some time... done. 1373s Running mktexlsr /var/lib/texmf ... done. 1374s Building format(s) --all. 1444s This may take some time... done. 1472s autopkgtest [21:18:47]: test full_suite: sh debian/tests/run-unit-test 1472s autopkgtest [21:18:47]: test full_suite: [----------------------- 1477s mkdir: created directory 'Bio' 1477s mkdir: created directory 'Bio/Align' 1477s mkdir: created directory 'Bio/Align/substitution_matrices' 1477s mkdir: created directory 'Bio/Align/substitution_matrices/data/' 1477s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER22' -> 'Bio/Align/substitution_matrices/data/BENNER22' 1477s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER6' -> 'Bio/Align/substitution_matrices/data/BENNER6' 1477s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER74' -> 'Bio/Align/substitution_matrices/data/BENNER74' 1477s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLASTN' -> 'Bio/Align/substitution_matrices/data/BLASTN' 1477s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLASTP' -> 'Bio/Align/substitution_matrices/data/BLASTP' 1477s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM45' -> 'Bio/Align/substitution_matrices/data/BLOSUM45' 1477s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM50' -> 'Bio/Align/substitution_matrices/data/BLOSUM50' 1477s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM62' -> 'Bio/Align/substitution_matrices/data/BLOSUM62' 1477s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM80' -> 'Bio/Align/substitution_matrices/data/BLOSUM80' 1477s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM90' -> 'Bio/Align/substitution_matrices/data/BLOSUM90' 1477s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/DAYHOFF' -> 'Bio/Align/substitution_matrices/data/DAYHOFF' 1477s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/FENG' -> 'Bio/Align/substitution_matrices/data/FENG' 1477s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/GENETIC' -> 'Bio/Align/substitution_matrices/data/GENETIC' 1477s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/GONNET1992' -> 'Bio/Align/substitution_matrices/data/GONNET1992' 1477s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/HOXD70' -> 'Bio/Align/substitution_matrices/data/HOXD70' 1477s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/JOHNSON' -> 'Bio/Align/substitution_matrices/data/JOHNSON' 1477s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/JONES' -> 'Bio/Align/substitution_matrices/data/JONES' 1477s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/LEVIN' -> 'Bio/Align/substitution_matrices/data/LEVIN' 1477s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MCLACHLAN' -> 'Bio/Align/substitution_matrices/data/MCLACHLAN' 1477s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MDM78' -> 'Bio/Align/substitution_matrices/data/MDM78' 1477s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MEGABLAST' -> 'Bio/Align/substitution_matrices/data/MEGABLAST' 1477s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/NUC.4.4' -> 'Bio/Align/substitution_matrices/data/NUC.4.4' 1477s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM250' -> 'Bio/Align/substitution_matrices/data/PAM250' 1477s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM30' -> 'Bio/Align/substitution_matrices/data/PAM30' 1477s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM70' -> 'Bio/Align/substitution_matrices/data/PAM70' 1477s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/RAO' -> 'Bio/Align/substitution_matrices/data/RAO' 1477s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/RISLER' -> 'Bio/Align/substitution_matrices/data/RISLER' 1477s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/SCHNEIDER' -> 'Bio/Align/substitution_matrices/data/SCHNEIDER' 1477s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/STR' -> 'Bio/Align/substitution_matrices/data/STR' 1477s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/TRANS' -> 'Bio/Align/substitution_matrices/data/TRANS' 1478s test_Ace ... ok 1478s test_Affy ... ok 1478s test_AlignIO ... ok 1478s test_AlignIO_ClustalIO ... ok 1478s test_AlignIO_EmbossIO ... ok 1478s test_AlignIO_FastaIO ... ok 1479s test_AlignIO_MauveIO ... ok 1479s test_AlignIO_PhylipIO ... ok 1479s test_AlignIO_convert ... ok 1479s test_Align_Alignment ... ok 1479s test_Align_a2m ... ok 1479s test_Align_bed ... ok 1479s test_Align_bigbed ... ok 1480s test_Align_bigmaf ... ok 1480s test_Align_bigpsl ... ok 1481s test_Align_chain ... ok 1481s test_Align_clustal ... ok 1487s test_Align_codonalign ... ok 1487s test_Align_emboss ... ok 1487s test_Align_exonerate ... ok 1487s test_Align_fasta ... ok 1487s test_Align_format_matrix ... ok 1488s test_Align_hhr ... ok 1489s test_Align_maf ... ok 1489s test_Align_mauve ... ok 1489s test_Align_msf ... ok 1489s test_Align_nexus ... ok 1489s test_Align_phylip ... ok 1490s test_Align_psl ... ok 1490s test_Align_sam ... ok 1492s test_Align_stockholm ... ok 1492s test_Align_tabular ... ok 1493s test_BioSQL_MySQLdb_online ... skipping. internet not available 1493s test_BioSQL_mysql_connector ... skipping. BioSQL test configuration file biosql.ini missing (see biosql.ini.sample) 1493s test_BioSQL_mysql_connector_online ... skipping. internet not available 1493s test_BioSQL_psycopg2_online ... skipping. internet not available 1498s test_BioSQL_sqlite3 ... ok 1498s test_BioSQL_sqlite3_online ... skipping. internet not available 1498s test_Blast_Record ... ok 1499s test_Blast_parser ... ok 1499s test_CAPS ... ok 1499s test_Chi2 ... ok 1499s test_Cluster ... ok 1499s test_CodonTable ... ok 1500s test_ColorSpiral ... ok 1500s test_Compass ... ok 1501s test_Consensus ... ok 1501s test_EMBL_unittest ... ok 1501s test_EmbossPrimer ... ok 1505s test_Entrez ... ok 1505s test_Entrez_online ... skipping. internet not available 1506s test_Entrez_parser ... ok 1506s test_Enzyme ... ok 1507s test_ExPASy ... skipping. internet not available 1507s test_File ... ok 1507s test_GenBank ... ok 1509s test_GenomeDiagram ... Warn: Can't find .pfb for face 'Helvetica' 1512s ok 1512s test_GraphicsChromosome ... ok 1513s test_GraphicsDistribution ... ok 1513s test_GraphicsGeneral ... ok 1514s test_KEGG ... ok 1514s test_KEGG_online ... skipping. internet not available 1519s test_KGML_graphics ... ok 1519s test_KGML_graphics_online ... skipping. internet not available 1520s test_KGML_nographics ... ok 1520s test_KeyWList ... ok 1521s test_MafIO_index ... ok 1521s test_Medline ... ok 1522s test_NCBIXML ... Exception ignored in: 1522s Traceback (most recent call last): 1522s File "/usr/lib/python3/dist-packages/Bio/Blast/NCBIXML.py", line 1319, in parse 1522s expat_parser.Parse(NULL, True) 1522s xml.parsers.expat.ExpatError: unclosed token: line 320, column 0 1522s ok 1522s test_NCBI_qblast ... ok 1522s test_NMR ... ok 1522s test_Nexus ... ok 1522s test_PAML_baseml ... ok 1523s test_PAML_codeml ... ok 1523s test_PAML_yn00 ... ok 1529s test_PDB_CEAligner ... ok 1530s test_PDB_DSSP ... ok 1530s test_PDB_Dice ... ok 1530s test_PDB_Disordered ... ok 1531s test_PDB_Exposure ... ok 1531s test_PDB_FragmentMapper ... ok 1533s test_PDB_KDTree ... ok 1533s test_PDB_MMCIF2Dict ... ok 1533s test_PDB_MMCIFIO ... ok 1535s test_PDB_MMCIFParser ... ok 1535s test_PDB_NACCESS ... ok 1535s test_PDB_PDBIO ... ok 1535s test_PDB_PDBList ... skipping. internet not available 1542s test_PDB_PDBMLParser ... ok 1542s test_PDB_PDBParser ... ok 1542s 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 1543s test_PDB_Polypeptide ... ok 1543s test_PDB_QCPSuperimposer ... ok 1546s test_PDB_SASA ... ok 1547s test_PDB_SMCRA ... ok 1547s test_PDB_Selection ... ok 1548s test_PDB_StructureAlignment ... ok 1548s test_PDB_Superimposer ... ok 1548s test_PDB_alphafold_db ... skipping. internet not available 1552s test_PDB_binary_cif ... /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 1, ' ') redefined at line 7. 1552s warnings.warn( 1552s /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 15, ' ') redefined at line 144. 1552s warnings.warn( 1552s /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 15, ' ') redefined at line 153. 1552s warnings.warn( 1552s /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 1, ' ') redefined at line 0. 1552s warnings.warn( 1552s /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 15, ' ') redefined at line 0. 1552s warnings.warn( 1552s ok 1561s test_PDB_internal_coords ... ok 1562s test_PDB_parse_pdb_header ... ok 1562s test_PDB_vectors ... ok 1562s test_PQR ... ok 1562s test_Pathway ... ok 1563s test_Phd ... ok 1563s test_Phylo ... ok 1564s test_PhyloXML ... ok 1564s test_Phylo_CDAO ... ok 1565s test_Phylo_NeXML ... ok 1567s test_Phylo_igraph ... ok 1570s test_Phylo_matplotlib ... ok 1571s test_Phylo_networkx ... ok 1572s test_PopGen_GenePop_nodepend ... ok 1572s test_ProtParam ... ok 1574s test_RCSBFormats ... ok 1574s test_Restriction ... ok 1575s test_SCOP_Astral ... ok 1576s test_SCOP_Cla ... ok 1577s test_SCOP_Des ... ok 1577s test_SCOP_Dom ... ok 1578s test_SCOP_Hie ... ok 1579s test_SCOP_Raf ... ok 1579s test_SCOP_Residues ... ok 1580s test_SCOP_Scop ... ok 1581s test_SVDSuperimposer ... ok 1582s test_SearchIO_blast_tab ... ok 1582s test_SearchIO_blast_tab_index ... ok 1583s test_SearchIO_blast_xml ... ok 1585s test_SearchIO_blast_xml_index ... ok 1586s test_SearchIO_blat_psl ... ok 1587s test_SearchIO_blat_psl_index ... ok 1588s test_SearchIO_exonerate ... ok 1588s test_SearchIO_exonerate_text_index ... ok 1589s test_SearchIO_exonerate_vulgar_index ... ok 1590s test_SearchIO_fasta_m10 ... ok 1591s test_SearchIO_fasta_m10_index ... ok 1592s test_SearchIO_hhsuite2_text ... ok 1592s test_SearchIO_hmmer2_text ... ok 1593s test_SearchIO_hmmer2_text_index ... ok 1594s test_SearchIO_hmmer3_domtab ... ok 1595s test_SearchIO_hmmer3_domtab_index ... ok 1595s test_SearchIO_hmmer3_tab ... ok 1596s test_SearchIO_hmmer3_tab_index ... ok 1597s test_SearchIO_hmmer3_text ... ok 1598s test_SearchIO_hmmer3_text_index ... ok 1598s test_SearchIO_infernal_tab ... ok 1599s test_SearchIO_infernal_tab_index ... ok 1600s test_SearchIO_infernal_text ... ok 1601s test_SearchIO_infernal_text_index ... ok 1601s test_SearchIO_interproscan_xml ... ok 1602s test_SearchIO_model ... ok 1603s test_SearchIO_write ... ok 1604s test_SeqFeature ... ok 1625s test_SeqIO ... ok 1626s test_SeqIO_AbiIO ... ok 1626s test_SeqIO_FastaIO ... ok 1627s test_SeqIO_Gck ... ok 1628s test_SeqIO_Gfa ... ok 1628s test_SeqIO_Insdc ... ok 1629s test_SeqIO_NibIO ... ok 1632s test_SeqIO_PdbIO ... ok 1633s test_SeqIO_QualityIO ... ok 1633s test_SeqIO_SeqXML ... ok 1634s test_SeqIO_SffIO ... ok 1635s test_SeqIO_SnapGene ... ok 1636s test_SeqIO_TwoBitIO ... ok 1637s test_SeqIO_UniprotIO ... ok 1638s test_SeqIO_Xdna ... ok 1639s test_SeqIO_features ... ok 1656s test_SeqIO_index ... ok 1656s test_SeqIO_online ... skipping. internet not available 1657s test_SeqIO_write ... ok 1657s test_SeqRecord ... ok 1658s test_SeqUtils ... ok 1660s test_Seq_objs ... ok 1661s test_SwissProt ... ok 1661s test_TogoWS ... skipping. internet not available 1662s test_TreeConstruction ... ok 1663s test_Tutorial ... skipping. Could not find ../Doc/Tutorial/index.rst file 1664s test_UniGene ... ok 1664s test_UniProt ... skipping. internet not available 1665s test_UniProt_GOA ... ok 1666s test_align ... ok 1667s test_align_substitution_matrices ... ok 1670s test_bgzf ... ok 1671s test_cellosaurus ... ok 1677s test_codonalign ... ok 1678s test_geo ... ok 1679s test_motifs ... ok 1680s test_motifs_online ... skipping. internet not available 1680s 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. 1680s warnings.warn( 1680s ok 1681s test_pairwise2_no_C ... ok 1682s test_pairwise_aligner ... ok 1683s test_pairwise_alignment_map ... ok 1693s test_phenotype ... ok 1694s test_phenotype_fit ... ok 1694s test_prodoc ... ok 1695s test_prosite ... ok 1696s test_seq ... ok 1697s test_translate ... ok 1697s ---------------------------------------------------------------------- 1697s Ran 201 tests in 219.396 seconds 1697s 1697s Skipping any tests requiring internet access 1697s Python version: 3.13.11 (main, Dec 6 2025, 13:15:20) [GCC 15.2.0] 1697s Operating system: posix linux 1699s :0: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/protein_lib.fa' mode='rt' encoding='UTF-8'> 1699s :0: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/nucleotide_lib.fa' mode='rt' encoding='UTF-8'> 1700s test_Ace ... ok 1700s test_Affy ... ok 1700s test_AlignIO ... ok 1700s test_AlignIO_ClustalIO ... ok 1700s test_AlignIO_EmbossIO ... ok 1700s test_AlignIO_FastaIO ... ok 1701s test_AlignIO_MauveIO ... ok 1701s test_AlignIO_PhylipIO ... ok 1701s test_AlignIO_convert ... ok 1701s test_Align_Alignment ... ok 1701s test_Align_a2m ... ok 1701s test_Align_bed ... ok 1702s test_Align_bigbed ... ok 1702s test_Align_bigmaf ... ok 1703s test_Align_bigpsl ... ok 1703s test_Align_chain ... ok 1703s test_Align_clustal ... ok 1708s test_Align_codonalign ... FAIL 1708s test_Align_emboss ... ok 1709s test_Align_exonerate ... ok 1709s test_Align_fasta ... ok 1709s test_Align_format_matrix ... ok 1709s test_Align_hhr ... ok 1711s test_Align_maf ... ok 1711s test_Align_mauve ... ok 1711s test_Align_msf ... ok 1711s test_Align_nexus ... ok 1711s test_Align_phylip ... ok 1712s test_Align_psl ... ok 1712s test_Align_sam ... ok 1714s test_Align_stockholm ... ok 1715s test_Align_tabular ... ok 1715s test_BioSQL_MySQLdb_online ... skipping. internet not available 1715s test_BioSQL_mysql_connector ... skipping. BioSQL test configuration file biosql.ini missing (see biosql.ini.sample) 1715s test_BioSQL_mysql_connector_online ... skipping. internet not available 1715s test_BioSQL_psycopg2_online ... skipping. internet not available 1720s test_BioSQL_sqlite3 ... ok 1720s test_BioSQL_sqlite3_online ... skipping. internet not available 1720s test_Blast_Record ... ok 1721s test_Blast_parser ... ok 1721s test_CAPS ... ok 1722s test_Chi2 ... ERROR 1722s test_Cluster ... ok 1722s test_CodonTable ... ok 1722s test_ColorSpiral ... ok 1722s test_Compass ... ok 1722s test_Consensus ... ERROR 1722s test_EMBL_unittest ... ok 1722s test_EmbossPrimer ... ok 1726s test_Entrez ... ok 1727s test_Entrez_online ... skipping. internet not available 1727s test_Entrez_parser ... ok 1727s test_Enzyme ... ok 1727s test_ExPASy ... skipping. internet not available 1727s test_File ... ok 1728s test_GenBank ... ok 1730s test_GenomeDiagram ... Warn: Can't find .pfb for face 'Helvetica' 1732s ok 1733s test_GraphicsChromosome ... ok 1733s test_GraphicsDistribution ... ok 1734s test_GraphicsGeneral ... ok 1734s test_KEGG ... ok 1734s test_KEGG_online ... skipping. internet not available 1739s test_KGML_graphics ... ok 1739s test_KGML_graphics_online ... skipping. internet not available 1739s test_KGML_nographics ... ok 1740s test_KeyWList ... ok 1741s test_MafIO_index ... ok 1741s test_Medline ... ok 1742s test_NCBIXML ... Exception ignored while closing generator : 1742s Traceback (most recent call last): 1742s File "/usr/lib/python3/dist-packages/Bio/Blast/NCBIXML.py", line 1319, in parse 1742s expat_parser.Parse(NULL, True) 1742s xml.parsers.expat.ExpatError: unclosed token: line 320, column 0 1742s ok 1742s test_NCBI_qblast ... ok 1742s test_NMR ... ok 1742s test_Nexus ... ok 1742s test_PAML_baseml ... ERROR 1742s test_PAML_codeml ... ERROR 1742s test_PAML_yn00 ... ERROR 1747s test_PDB_CEAligner ... ok 1749s test_PDB_DSSP ... ok 1749s test_PDB_Dice ... ok 1749s test_PDB_Disordered ... ok 1749s test_PDB_Exposure ... ok 1749s test_PDB_FragmentMapper ... ok 1751s test_PDB_KDTree ... ok 1751s test_PDB_MMCIF2Dict ... ok 1752s test_PDB_MMCIFIO ... ok 1753s test_PDB_MMCIFParser ... ok 1753s test_PDB_NACCESS ... ok 1753s test_PDB_PDBIO ... ok 1753s test_PDB_PDBList ... skipping. internet not available 1759s test_PDB_PDBMLParser ... ok 1760s test_PDB_PDBParser ... ok 1760s 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 1760s test_PDB_Polypeptide ... ok 1760s test_PDB_QCPSuperimposer ... ok 1763s test_PDB_SASA ... ok 1764s test_PDB_SMCRA ... ok 1764s test_PDB_Selection ... ok 1765s test_PDB_StructureAlignment ... ok 1765s test_PDB_Superimposer ... ok 1765s test_PDB_alphafold_db ... skipping. internet not available 1769s test_PDB_binary_cif ... /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 1, ' ') redefined at line 7. 1769s warnings.warn( 1769s /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 15, ' ') redefined at line 144. 1769s warnings.warn( 1769s /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 15, ' ') redefined at line 153. 1769s warnings.warn( 1769s /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 1, ' ') redefined at line 0. 1769s warnings.warn( 1769s /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 15, ' ') redefined at line 0. 1769s warnings.warn( 1769s ok 1777s test_PDB_internal_coords ... ok 1777s test_PDB_parse_pdb_header ... ok 1778s test_PDB_vectors ... ok 1778s test_PQR ... ok 1778s test_Pathway ... ok 1779s test_Phd ... ok 1779s test_Phylo ... ERROR 1779s test_PhyloXML ... ERROR 1779s test_Phylo_CDAO ... ERROR 1780s test_Phylo_NeXML ... ERROR 1780s test_Phylo_igraph ... ERROR 1780s test_Phylo_matplotlib ... ERROR 1781s test_Phylo_networkx ... ERROR 1781s test_PopGen_GenePop_nodepend ... ok 1781s test_ProtParam ... ok 1782s test_RCSBFormats ... ok 1782s test_Restriction ... ok 1783s test_SCOP_Astral ... ok 1783s test_SCOP_Cla ... ok 1783s test_SCOP_Des ... ok 1783s test_SCOP_Dom ... ok 1784s test_SCOP_Hie ... ok 1784s test_SCOP_Raf ... ok 1784s test_SCOP_Residues ... ok 1784s test_SCOP_Scop ... ok 1785s test_SVDSuperimposer ... ok 1785s test_SearchIO_blast_tab ... ok 1785s test_SearchIO_blast_tab_index ... ok 1786s test_SearchIO_blast_xml ... ok 1787s test_SearchIO_blast_xml_index ... ok 1788s test_SearchIO_blat_psl ... ok 1788s test_SearchIO_blat_psl_index ... ok 1788s test_SearchIO_exonerate ... ok 1789s test_SearchIO_exonerate_text_index ... ok 1789s test_SearchIO_exonerate_vulgar_index ... ok 1789s test_SearchIO_fasta_m10 ... ok 1790s test_SearchIO_fasta_m10_index ... ok 1790s test_SearchIO_hhsuite2_text ... ok 1790s test_SearchIO_hmmer2_text ... ok 1791s test_SearchIO_hmmer2_text_index ... ok 1791s test_SearchIO_hmmer3_domtab ... ok 1791s test_SearchIO_hmmer3_domtab_index ... ok 1792s test_SearchIO_hmmer3_tab ... ok 1792s test_SearchIO_hmmer3_tab_index ... ok 1792s test_SearchIO_hmmer3_text ... ok 1793s test_SearchIO_hmmer3_text_index ... ok 1793s test_SearchIO_infernal_tab ... ok 1793s test_SearchIO_infernal_tab_index ... ok 1793s test_SearchIO_infernal_text ... ok 1794s test_SearchIO_infernal_text_index ... ok 1794s test_SearchIO_interproscan_xml ... ok 1794s test_SearchIO_model ... ok 1795s test_SearchIO_write ... ok 1795s test_SeqFeature ... ok 1812s test_SeqIO ... ok 1813s test_SeqIO_AbiIO ... ok 1813s test_SeqIO_FastaIO ... ok 1813s test_SeqIO_Gck ... ok 1813s test_SeqIO_Gfa ... ok 1814s test_SeqIO_Insdc ... ok 1814s test_SeqIO_NibIO ... ok 1816s test_SeqIO_PdbIO ... ok 1817s test_SeqIO_QualityIO ... ok 1817s test_SeqIO_SeqXML ... ok 1817s test_SeqIO_SffIO ... ok 1817s test_SeqIO_SnapGene ... ok 1819s test_SeqIO_TwoBitIO ... ok 1819s test_SeqIO_UniprotIO ... ok 1819s test_SeqIO_Xdna ... ok 1820s test_SeqIO_features ... ok 1836s test_SeqIO_index ... ok 1837s test_SeqIO_online ... skipping. internet not available 1837s test_SeqIO_write ... ok 1837s test_SeqRecord ... ok 1838s test_SeqUtils ... ok 1839s test_Seq_objs ... ok 1840s test_SwissProt ... ok 1840s test_TogoWS ... skipping. internet not available 1840s test_TreeConstruction ... ERROR 1840s test_Tutorial ... skipping. Could not find ../Doc/Tutorial/index.rst file 1841s test_UniGene ... ok 1841s test_UniProt ... skipping. internet not available 1841s test_UniProt_GOA ... ok 1842s test_align ... ok 1842s test_align_substitution_matrices ... ok 1845s test_bgzf ... ok 1845s test_cellosaurus ... ok 1850s test_codonalign ... FAIL 1850s test_geo ... ok 1851s test_motifs ... ok 1851s test_motifs_online ... skipping. internet not available 1851s 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. 1851s warnings.warn( 1851s ok 1852s test_pairwise2_no_C ... ok 1853s test_pairwise_aligner ... ok 1853s test_pairwise_alignment_map ... ok 1862s test_phenotype ... ok 1863s test_phenotype_fit ... ok 1863s test_prodoc ... ok 1863s test_prosite ... ok 1864s test_seq ... ok 1864s test_translate ... ok 1864s ====================================================================== 1864s ERROR: test_dn_ds (test_Align_codonalign.Test_dn_ds.test_dn_ds) 1864s ---------------------------------------------------------------------- 1864s Traceback (most recent call last): 1864s File "/tmp/autopkgtest.3Ugg4H/autopkgtest_tmp/Tests/test_Align_codonalign.py", line 8313, in test_dn_ds 1864s dn, ds = calculate_dn_ds_matrix(alignment) 1864s ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^ 1864s File "/usr/lib/python3/dist-packages/Bio/Align/analysis.py", line 1012, in calculate_dn_ds_matrix 1864s from Bio.Phylo.TreeConstruction import DistanceMatrix 1864s File "/usr/lib/python3/dist-packages/Bio/Phylo/__init__.py", line 14, in 1864s from Bio.Phylo._io import convert 1864s File "/usr/lib/python3/dist-packages/Bio/Phylo/_io.py", line 29, in 1864s from Bio.Phylo import CDAOIO 1864s File "/usr/lib/python3/dist-packages/Bio/Phylo/CDAOIO.py", line 37, in 1864s import rdflib 1864s File "/usr/lib/python3/dist-packages/rdflib/__init__.py", line 168, in 1864s from rdflib.graph import ConjunctiveGraph, Dataset, Graph 1864s File "/usr/lib/python3/dist-packages/rdflib/graph.py", line 292, in 1864s from rdflib.resource import Resource 1864s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 296, in 1864s class Resource: 1864s ...<164 lines>... 1864s return "Resource(%s,%s)" % (self._graph, self._identifier) 1864s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 379, in Resource 1864s def value(self, p=RDF.value, o=None, default=None, any=True): 1864s ^^^^^^^^^ 1864s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 285, in __getattr__ 1864s return cls.__getitem__(name) 1864s ~~~~~~~~~~~~~~~^^^^^^ 1864s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 268, in __getitem__ 1864s raise AttributeError(f"term '{name}' not in namespace '{cls._NS}'") 1864s AttributeError: term 'value' not in namespace 'http://www.w3.org/1999/02/22-rdf-syntax-ns#' 1864s 1864s ====================================================================== 1864s ERROR: test_Chi2 1864s ---------------------------------------------------------------------- 1864s Traceback (most recent call last): 1864s File "/tmp/autopkgtest.3Ugg4H/autopkgtest_tmp/Tests/run_tests.py", line 245, in runTest 1864s suite = loader.loadTestsFromName(name) 1864s File "/usr/lib/python3.14/unittest/loader.py", line 137, in loadTestsFromName 1864s module = __import__(module_name) 1864s File "/tmp/autopkgtest.3Ugg4H/autopkgtest_tmp/Tests/test_Chi2.py", line 10, in 1864s from Bio.Phylo.PAML import chi2 1864s File "/usr/lib/python3/dist-packages/Bio/Phylo/__init__.py", line 14, in 1864s from Bio.Phylo._io import convert 1864s File "/usr/lib/python3/dist-packages/Bio/Phylo/_io.py", line 29, in 1864s from Bio.Phylo import CDAOIO 1864s File "/usr/lib/python3/dist-packages/Bio/Phylo/CDAOIO.py", line 37, in 1864s import rdflib 1864s File "/usr/lib/python3/dist-packages/rdflib/__init__.py", line 168, in 1864s from rdflib.graph import ConjunctiveGraph, Dataset, Graph 1864s File "/usr/lib/python3/dist-packages/rdflib/graph.py", line 292, in 1864s from rdflib.resource import Resource 1864s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 296, in 1864s class Resource: 1864s ...<164 lines>... 1864s return "Resource(%s,%s)" % (self._graph, self._identifier) 1864s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 379, in Resource 1864s def value(self, p=RDF.value, o=None, default=None, any=True): 1864s ^^^^^^^^^ 1864s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 285, in __getattr__ 1864s return cls.__getitem__(name) 1864s ~~~~~~~~~~~~~~~^^^^^^ 1864s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 268, in __getitem__ 1864s raise AttributeError(f"term '{name}' not in namespace '{cls._NS}'") 1864s AttributeError: term 'value' not in namespace 'http://www.w3.org/1999/02/22-rdf-syntax-ns#' 1864s ====================================================================== 1864s ERROR: test_Consensus 1864s ---------------------------------Skipping any tests requiring internet access 1864s Python version: 3.14.2 (main, Dec 6 2025, 13:20:08) [GCC 15.2.0] 1864s Operating system: posix linux 1864s ------------------------------------- 1864s Traceback (most recent call last): 1864s File "/tmp/autopkgtest.3Ugg4H/autopkgtest_tmp/Tests/run_tests.py", line 245, in runTest 1864s suite = loader.loadTestsFromName(name) 1864s File "/usr/lib/python3.14/unittest/loader.py", line 137, in loadTestsFromName 1864s module = __import__(module_name) 1864s File "/tmp/autopkgtest.3Ugg4H/autopkgtest_tmp/Tests/test_Consensus.py", line 15, in 1864s from Bio import Phylo 1864s File "/usr/lib/python3/dist-packages/Bio/Phylo/__init__.py", line 14, in 1864s from Bio.Phylo._io import convert 1864s File "/usr/lib/python3/dist-packages/Bio/Phylo/_io.py", line 29, in 1864s from Bio.Phylo import CDAOIO 1864s File "/usr/lib/python3/dist-packages/Bio/Phylo/CDAOIO.py", line 37, in 1864s import rdflib 1864s File "/usr/lib/python3/dist-packages/rdflib/__init__.py", line 168, in 1864s from rdflib.graph import ConjunctiveGraph, Dataset, Graph 1864s File "/usr/lib/python3/dist-packages/rdflib/graph.py", line 292, in 1864s from rdflib.resource import Resource 1864s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 296, in 1864s class Resource: 1864s ...<164 lines>... 1864s return "Resource(%s,%s)" % (self._graph, self._identifier) 1864s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 379, in Resource 1864s def value(self, p=RDF.value, o=None, default=None, any=True): 1864s ^^^^^^^^^ 1864s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 285, in __getattr__ 1864s return cls.__getitem__(name) 1864s ~~~~~~~~~~~~~~~^^^^^^ 1864s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 268, in __getitem__ 1864s raise AttributeError(f"term '{name}' not in namespace '{cls._NS}'") 1864s AttributeError: term 'value' not in namespace 'http://www.w3.org/1999/02/22-rdf-syntax-ns#' 1864s ====================================================================== 1864s ERROR: test_PAML_baseml 1864s ---------------------------------------------------------------------- 1864s Traceback (most recent call last): 1864s File "/tmp/autopkgtest.3Ugg4H/autopkgtest_tmp/Tests/run_tests.py", line 245, in runTest 1864s suite = loader.loadTestsFromName(name) 1864s File "/usr/lib/python3.14/unittest/loader.py", line 137, in loadTestsFromName 1864s module = __import__(module_name) 1864s File "/tmp/autopkgtest.3Ugg4H/autopkgtest_tmp/Tests/test_PAML_baseml.py", line 12, in 1864s from Bio.Phylo.PAML import baseml 1864s File "/usr/lib/python3/dist-packages/Bio/Phylo/__init__.py", line 14, in 1864s from Bio.Phylo._io import convert 1864s File "/usr/lib/python3/dist-packages/Bio/Phylo/_io.py", line 29, in 1864s from Bio.Phylo import CDAOIO 1864s File "/usr/lib/python3/dist-packages/Bio/Phylo/CDAOIO.py", line 37, in 1864s import rdflib 1864s File "/usr/lib/python3/dist-packages/rdflib/__init__.py", line 168, in 1864s from rdflib.graph import ConjunctiveGraph, Dataset, Graph 1864s File "/usr/lib/python3/dist-packages/rdflib/graph.py", line 292, in 1864s from rdflib.resource import Resource 1864s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 296, in 1864s class Resource: 1864s ...<164 lines>... 1864s return "Resource(%s,%s)" % (self._graph, self._identifier) 1864s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 379, in Resource 1864s def value(self, p=RDF.value, o=None, default=None, any=True): 1864s ^^^^^^^^^ 1864s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 285, in __getattr__ 1864s return cls.__getitem__(name) 1864s ~~~~~~~~~~~~~~~^^^^^^ 1864s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 268, in __getitem__ 1864s raise AttributeError(f"term '{name}' not in namespace '{cls._NS}'") 1864s AttributeError: term 'value' not in namespace 'http://www.w3.org/1999/02/22-rdf-syntax-ns#' 1864s ====================================================================== 1864s ERROR: test_PAML_codeml 1864s ---------------------------------------------------------------------- 1864s Traceback (most recent call last): 1864s File "/tmp/autopkgtest.3Ugg4H/autopkgtest_tmp/Tests/run_tests.py", line 245, in runTest 1864s suite = loader.loadTestsFromName(name) 1864s File "/usr/lib/python3.14/unittest/loader.py", line 137, in loadTestsFromName 1864s module = __import__(module_name) 1864s File "/tmp/autopkgtest.3Ugg4H/autopkgtest_tmp/Tests/test_PAML_codeml.py", line 13, in 1864s from Bio.Phylo.PAML import codeml 1864s File "/usr/lib/python3/dist-packages/Bio/Phylo/__init__.py", line 14, in 1864s from Bio.Phylo._io import convert 1864s File "/usr/lib/python3/dist-packages/Bio/Phylo/_io.py", line 29, in 1864s from Bio.Phylo import CDAOIO 1864s File "/usr/lib/python3/dist-packages/Bio/Phylo/CDAOIO.py", line 37, in 1864s import rdflib 1864s File "/usr/lib/python3/dist-packages/rdflib/__init__.py", line 168, in 1864s from rdflib.graph import ConjunctiveGraph, Dataset, Graph 1864s File "/usr/lib/python3/dist-packages/rdflib/graph.py", line 292, in 1864s from rdflib.resource import Resource 1864s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 296, in 1864s class Resource: 1864s ...<164 lines>... 1864s return "Resource(%s,%s)" % (self._graph, self._identifier) 1864s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 379, in Resource 1864s def value(self, p=RDF.value, o=None, default=None, any=True): 1864s ^^^^^^^^^ 1864s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 285, in __getattr__ 1864s return cls.__getitem__(name) 1864s ~~~~~~~~~~~~~~~^^^^^^ 1864s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 268, in __getitem__ 1864s raise AttributeError(f"term '{name}' not in namespace '{cls._NS}'") 1864s AttributeError: term 'value' not in namespace 'http://www.w3.org/1999/02/22-rdf-syntax-ns#' 1864s ====================================================================== 1864s ERROR: test_PAML_yn00 1864s ---------------------------------------------------------------------- 1864s Traceback (most recent call last): 1864s File "/tmp/autopkgtest.3Ugg4H/autopkgtest_tmp/Tests/run_tests.py", line 245, in runTest 1864s suite = loader.loadTestsFromName(name) 1864s File "/usr/lib/python3.14/unittest/loader.py", line 137, in loadTestsFromName 1864s module = __import__(module_name) 1864s File "/tmp/autopkgtest.3Ugg4H/autopkgtest_tmp/Tests/test_PAML_yn00.py", line 13, in 1864s from Bio.Phylo.PAML import yn00 1864s File "/usr/lib/python3/dist-packages/Bio/Phylo/__init__.py", line 14, in 1864s from Bio.Phylo._io import convert 1864s File "/usr/lib/python3/dist-packages/Bio/Phylo/_io.py", line 29, in 1864s from Bio.Phylo import CDAOIO 1864s File "/usr/lib/python3/dist-packages/Bio/Phylo/CDAOIO.py", line 37, in 1864s import rdflib 1864s File "/usr/lib/python3/dist-packages/rdflib/__init__.py", line 168, in 1864s from rdflib.graph import ConjunctiveGraph, Dataset, Graph 1864s File "/usr/lib/python3/dist-packages/rdflib/graph.py", line 292, in 1864s from rdflib.resource import Resource 1864s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 296, in 1864s class Resource: 1864s ...<164 lines>... 1864s return "Resource(%s,%s)" % (self._graph, self._identifier) 1864s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 379, in Resource 1864s def value(self, p=RDF.value, o=None, default=None, any=True): 1864s ^^^^^^^^^ 1864s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 285, in __getattr__ 1864s return cls.__getitem__(name) 1864s ~~~~~~~~~~~~~~~^^^^^^ 1864s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 268, in __getitem__ 1864s raise AttributeError(f"term '{name}' not in namespace '{cls._NS}'") 1864s AttributeError: term 'value' not in namespace 'http://www.w3.org/1999/02/22-rdf-syntax-ns#' 1864s ====================================================================== 1864s ERROR: test_Phylo 1864s ---------------------------------------------------------------------- 1864s Traceback (most recent call last): 1864s File "/tmp/autopkgtest.3Ugg4H/autopkgtest_tmp/Tests/run_tests.py", line 245, in runTest 1864s suite = loader.loadTestsFromName(name) 1864s File "/usr/lib/python3.14/unittest/loader.py", line 137, in loadTestsFromName 1864s module = __import__(module_name) 1864s File "/tmp/autopkgtest.3Ugg4H/autopkgtest_tmp/Tests/test_Phylo.py", line 13, in 1864s from Bio import Phylo 1864s File "/usr/lib/python3/dist-packages/Bio/Phylo/__init__.py", line 14, in 1864s from Bio.Phylo._io import convert 1864s File "/usr/lib/python3/dist-packages/Bio/Phylo/_io.py", line 29, in 1864s from Bio.Phylo import CDAOIO 1864s File "/usr/lib/python3/dist-packages/Bio/Phylo/CDAOIO.py", line 37, in 1864s import rdflib 1864s File "/usr/lib/python3/dist-packages/rdflib/__init__.py", line 168, in 1864s from rdflib.graph import ConjunctiveGraph, Dataset, Graph 1864s File "/usr/lib/python3/dist-packages/rdflib/graph.py", line 292, in 1864s from rdflib.resource import Resource 1864s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 296, in 1864s class Resource: 1864s ...<164 lines>... 1864s return "Resource(%s,%s)" % (self._graph, self._identifier) 1864s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 379, in Resource 1864s def value(self, p=RDF.value, o=None, default=None, any=True): 1864s ^^^^^^^^^ 1864s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 285, in __getattr__ 1864s return cls.__getitem__(name) 1864s ~~~~~~~~~~~~~~~^^^^^^ 1864s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 268, in __getitem__ 1864s raise AttributeError(f"term '{name}' not in namespace '{cls._NS}'") 1864s AttributeError: term 'value' not in namespace 'http://www.w3.org/1999/02/22-rdf-syntax-ns#' 1864s ====================================================================== 1864s ERROR: test_PhyloXML 1864s ---------------------------------------------------------------------- 1864s Traceback (most recent call last): 1864s File "/tmp/autopkgtest.3Ugg4H/autopkgtest_tmp/Tests/run_tests.py", line 245, in runTest 1864s suite = loader.loadTestsFromName(name) 1864s File "/usr/lib/python3.14/unittest/loader.py", line 137, in loadTestsFromName 1864s module = __import__(module_name) 1864s File "/tmp/autopkgtest.3Ugg4H/autopkgtest_tmp/Tests/test_PhyloXML.py", line 17, in 1864s from Bio.Phylo import PhyloXML as PX 1864s File "/usr/lib/python3/dist-packages/Bio/Phylo/__init__.py", line 14, in 1864s from Bio.Phylo._io import convert 1864s File "/usr/lib/python3/dist-packages/Bio/Phylo/_io.py", line 29, in 1864s from Bio.Phylo import CDAOIO 1864s File "/usr/lib/python3/dist-packages/Bio/Phylo/CDAOIO.py", line 37, in 1864s import rdflib 1864s File "/usr/lib/python3/dist-packages/rdflib/__init__.py", line 168, in 1864s from rdflib.graph import ConjunctiveGraph, Dataset, Graph 1864s File "/usr/lib/python3/dist-packages/rdflib/graph.py", line 292, in 1864s from rdflib.resource import Resource 1864s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 296, in 1864s class Resource: 1864s ...<164 lines>... 1864s return "Resource(%s,%s)" % (self._graph, self._identifier) 1864s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 379, in Resource 1864s def value(self, p=RDF.value, o=None, default=None, any=True): 1864s ^^^^^^^^^ 1864s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 285, in __getattr__ 1864s return cls.__getitem__(name) 1864s ~~~~~~~~~~~~~~~^^^^^^ 1864s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 268, in __getitem__ 1864s raise AttributeError(f"term '{name}' not in namespace '{cls._NS}'") 1864s AttributeError: term 'value' not in namespace 'http://www.w3.org/1999/02/22-rdf-syntax-ns#' 1864s ====================================================================== 1864s ERROR: test_Phylo_CDAO 1864s ---------------------------------------------------------------------- 1864s Traceback (most recent call last): 1864s File "/tmp/autopkgtest.3Ugg4H/autopkgtest_tmp/Tests/run_tests.py", line 245, in runTest 1864s suite = loader.loadTestsFromName(name) 1864s File "/usr/lib/python3.14/unittest/loader.py", line 137, in loadTestsFromName 1864s module = __import__(module_name) 1864s File "/tmp/autopkgtest.3Ugg4H/autopkgtest_tmp/Tests/test_Phylo_CDAO.py", line 13, in 1864s import Bio.Phylo as bp 1864s File "/usr/lib/python3/dist-packages/Bio/Phylo/__init__.py", line 14, in 1864s from Bio.Phylo._io import convert 1864s File "/usr/lib/python3/dist-packages/Bio/Phylo/_io.py", line 29, in 1864s from Bio.Phylo import CDAOIO 1864s File "/usr/lib/python3/dist-packages/Bio/Phylo/CDAOIO.py", line 37, in 1864s import rdflib 1864s File "/usr/lib/python3/dist-packages/rdflib/__init__.py", line 168, in 1864s from rdflib.graph import ConjunctiveGraph, Dataset, Graph 1864s File "/usr/lib/python3/dist-packages/rdflib/graph.py", line 292, in 1864s from rdflib.resource import Resource 1864s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 296, in 1864s class Resource: 1864s ...<164 lines>... 1864s return "Resource(%s,%s)" % (self._graph, self._identifier) 1864s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 379, in Resource 1864s def value(self, p=RDF.value, o=None, default=None, any=True): 1864s ^^^^^^^^^ 1864s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 285, in __getattr__ 1864s return cls.__getitem__(name) 1864s ~~~~~~~~~~~~~~~^^^^^^ 1864s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 268, in __getitem__ 1864s raise AttributeError(f"term '{name}' not in namespace '{cls._NS}'") 1864s AttributeError: term 'value' not in namespace 'http://www.w3.org/1999/02/22-rdf-syntax-ns#' 1864s ====================================================================== 1864s ERROR: test_Phylo_NeXML 1864s ---------------------------------------------------------------------- 1864s Traceback (most recent call last): 1864s File "/tmp/autopkgtest.3Ugg4H/autopkgtest_tmp/Tests/run_tests.py", line 245, in runTest 1864s suite = loader.loadTestsFromName(name) 1864s File "/usr/lib/python3.14/unittest/loader.py", line 137, in loadTestsFromName 1864s module = __import__(module_name) 1864s File "/tmp/autopkgtest.3Ugg4H/autopkgtest_tmp/Tests/test_Phylo_NeXML.py", line 14, in 1864s from Bio import Phylo 1864s File "/usr/lib/python3/dist-packages/Bio/Phylo/__init__.py", line 14, in 1864s from Bio.Phylo._io import convert 1864s File "/usr/lib/python3/dist-packages/Bio/Phylo/_io.py", line 29, in 1864s from Bio.Phylo import CDAOIO 1864s File "/usr/lib/python3/dist-packages/Bio/Phylo/CDAOIO.py", line 37, in 1864s import rdflib 1864s File "/usr/lib/python3/dist-packages/rdflib/__init__.py", line 168, in 1864s from rdflib.graph import ConjunctiveGraph, Dataset, Graph 1864s File "/usr/lib/python3/dist-packages/rdflib/graph.py", line 292, in 1864s from rdflib.resource import Resource 1864s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 296, in 1864s class Resource: 1864s ...<164 lines>... 1864s return "Resource(%s,%s)" % (self._graph, self._identifier) 1864s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 379, in Resource 1864s def value(self, p=RDF.value, o=None, default=None, any=True): 1864s ^^^^^^^^^ 1864s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 285, in __getattr__ 1864s return cls.__getitem__(name) 1864s ~~~~~~~~~~~~~~~^^^^^^ 1864s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 268, in __getitem__ 1864s raise AttributeError(f"term '{name}' not in namespace '{cls._NS}'") 1864s AttributeError: term 'value' not in namespace 'http://www.w3.org/1999/02/22-rdf-syntax-ns#' 1864s ====================================================================== 1864s ERROR: test_Phylo_igraph 1864s ---------------------------------------------------------------------- 1864s Traceback (most recent call last): 1864s File "/tmp/autopkgtest.3Ugg4H/autopkgtest_tmp/Tests/run_tests.py", line 245, in runTest 1864s suite = loader.loadTestsFromName(name) 1864s File "/usr/lib/python3.14/unittest/loader.py", line 137, in loadTestsFromName 1864s module = __import__(module_name) 1864s File "/tmp/autopkgtest.3Ugg4H/autopkgtest_tmp/Tests/test_Phylo_igraph.py", line 13, in 1864s from Bio import Phylo 1864s File "/usr/lib/python3/dist-packages/Bio/Phylo/__init__.py", line 14, in 1864s from Bio.Phylo._io import convert 1864s File "/usr/lib/python3/dist-packages/Bio/Phylo/_io.py", line 29, in 1864s from Bio.Phylo import CDAOIO 1864s File "/usr/lib/python3/dist-packages/Bio/Phylo/CDAOIO.py", line 37, in 1864s import rdflib 1864s File "/usr/lib/python3/dist-packages/rdflib/__init__.py", line 168, in 1864s from rdflib.graph import ConjunctiveGraph, Dataset, Graph 1864s File "/usr/lib/python3/dist-packages/rdflib/graph.py", line 292, in 1864s from rdflib.resource import Resource 1864s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 296, in 1864s class Resource: 1864s ...<164 lines>... 1864s return "Resource(%s,%s)" % (self._graph, self._identifier) 1864s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 379, in Resource 1864s def value(self, p=RDF.value, o=None, default=None, any=True): 1864s ^^^^^^^^^ 1864s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 285, in __getattr__ 1864s return cls.__getitem__(name) 1864s ~~~~~~~~~~~~~~~^^^^^^ 1864s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 268, in __getitem__ 1864s raise AttributeError(f"term '{name}' not in namespace '{cls._NS}'") 1864s AttributeError: term 'value' not in namespace 'http://www.w3.org/1999/02/22-rdf-syntax-ns#' 1864s ====================================================================== 1864s ERROR: test_Phylo_matplotlib 1864s ---------------------------------------------------------------------- 1864s Traceback (most recent call last): 1864s File "/tmp/autopkgtest.3Ugg4H/autopkgtest_tmp/Tests/run_tests.py", line 245, in runTest 1864s suite = loader.loadTestsFromName(name) 1864s File "/usr/lib/python3.14/unittest/loader.py", line 137, in loadTestsFromName 1864s module = __import__(module_name) 1864s File "/tmp/autopkgtest.3Ugg4H/autopkgtest_tmp/Tests/test_Phylo_matplotlib.py", line 13, in 1864s from Bio import Phylo 1864s File "/usr/lib/python3/dist-packages/Bio/Phylo/__init__.py", line 14, in 1864s from Bio.Phylo._io import convert 1864s File "/usr/lib/python3/dist-packages/Bio/Phylo/_io.py", line 29, in 1864s from Bio.Phylo import CDAOIO 1864s File "/usr/lib/python3/dist-packages/Bio/Phylo/CDAOIO.py", line 37, in 1864s import rdflib 1864s File "/usr/lib/python3/dist-packages/rdflib/__init__.py", line 168, in 1864s from rdflib.graph import ConjunctiveGraph, Dataset, Graph 1864s File "/usr/lib/python3/dist-packages/rdflib/graph.py", line 292, in 1864s from rdflib.resource import Resource 1864s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 296, in 1864s class Resource: 1864s ...<164 lines>... 1864s return "Resource(%s,%s)" % (self._graph, self._identifier) 1864s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 379, in Resource 1864s def value(self, p=RDF.value, o=None, default=None, any=True): 1864s ^^^^^^^^^ 1864s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 285, in __getattr__ 1864s return cls.__getitem__(name) 1864s ~~~~~~~~~~~~~~~^^^^^^ 1864s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 268, in __getitem__ 1864s raise AttributeError(f"term '{name}' not in namespace '{cls._NS}'") 1864s AttributeError: term 'value' not in namespace 'http://www.w3.org/1999/02/22-rdf-syntax-ns#' 1864s ====================================================================== 1864s ERROR: test_Phylo_networkx 1864s ---------------------------------------------------------------------- 1864s Traceback (most recent call last): 1864s File "/tmp/autopkgtest.3Ugg4H/autopkgtest_tmp/Tests/run_tests.py", line 245, in runTest 1864s suite = loader.loadTestsFromName(name) 1864s File "/usr/lib/python3.14/unittest/loader.py", line 137, in loadTestsFromName 1864s module = __import__(module_name) 1864s File "/tmp/autopkgtest.3Ugg4H/autopkgtest_tmp/Tests/test_Phylo_networkx.py", line 12, in 1864s from Bio import Phylo 1864s File "/usr/lib/python3/dist-packages/Bio/Phylo/__init__.py", line 14, in 1864s from Bio.Phylo._io import convert 1864s File "/usr/lib/python3/dist-packages/Bio/Phylo/_io.py", line 29, in 1864s from Bio.Phylo import CDAOIO 1864s File "/usr/lib/python3/dist-packages/Bio/Phylo/CDAOIO.py", line 37, in 1864s import rdflib 1864s File "/usr/lib/python3/dist-packages/rdflib/__init__.py", line 168, in 1864s from rdflib.graph import ConjunctiveGraph, Dataset, Graph 1864s File "/usr/lib/python3/dist-packages/rdflib/graph.py", line 292, in 1864s from rdflib.resource import Resource 1864s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 296, in 1864s class Resource: 1864s ...<164 lines>... 1864s return "Resource(%s,%s)" % (self._graph, self._identifier) 1864s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 379, in Resource 1864s def value(self, p=RDF.value, o=None, default=None, any=True): 1864s ^^^^^^^^^ 1864s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 285, in __getattr__ 1864s return cls.__getitem__(name) 1864s ~~~~~~~~~~~~~~~^^^^^^ 1864s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 268, in __getitem__ 1864s raise AttributeError(f"term '{name}' not in namespace '{cls._NS}'") 1864s AttributeError: term 'value' not in namespace 'http://www.w3.org/1999/02/22-rdf-syntax-ns#' 1864s ====================================================================== 1864s ERROR: test_TreeConstruction 1864s ---------------------------------------------------------------------- 1864s Traceback (most recent call last): 1864s File "/tmp/autopkgtest.3Ugg4H/autopkgtest_tmp/Tests/run_tests.py", line 245, in runTest 1864s suite = loader.loadTestsFromName(name) 1864s File "/usr/lib/python3.14/unittest/loader.py", line 137, in loadTestsFromName 1864s module = __import__(module_name) 1864s File "/tmp/autopkgtest.3Ugg4H/autopkgtest_tmp/Tests/test_TreeConstruction.py", line 16, in 1864s from Bio import Phylo 1864s File "/usr/lib/python3/dist-packages/Bio/Phylo/__init__.py", line 14, in 1864s from Bio.Phylo._io import convert 1864s File "/usr/lib/python3/dist-packages/Bio/Phylo/_io.py", line 29, in 1864s from Bio.Phylo import CDAOIO 1864s File "/usr/lib/python3/dist-packages/Bio/Phylo/CDAOIO.py", line 37, in 1864s import rdflib 1864s File "/usr/lib/python3/dist-packages/rdflib/__init__.py", line 168, in 1864s from rdflib.graph import ConjunctiveGraph, Dataset, Graph 1864s File "/usr/lib/python3/dist-packages/rdflib/graph.py", line 292, in 1864s from rdflib.resource import Resource 1864s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 296, in 1864s class Resource: 1864s ...<164 lines>... 1864s return "Resource(%s,%s)" % (self._graph, self._identifier) 1864s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 379, in Resource 1864s def value(self, p=RDF.value, o=None, default=None, any=True): 1864s ^^^^^^^^^ 1864s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 285, in __getattr__ 1864s return cls.__getitem__(name) 1864s ~~~~~~~~~~~~~~~^^^^^^ 1864s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 268, in __getitem__ 1864s raise AttributeError(f"term '{name}' not in namespace '{cls._NS}'") 1864s AttributeError: term 'value' not in namespace 'http://www.w3.org/1999/02/22-rdf-syntax-ns#' 1864s ====================================================================== 1864s ERROR: test_dn_ds_matrix (test_codonalign.Test_dn_ds.test_dn_ds_matrix) 1864s ---------------------------------------------------------------------- 1864s Traceback (most recent call last): 1864s File "/tmp/autopkgtest.3Ugg4H/autopkgtest_tmp/Tests/test_codonalign.py", line 381, in test_dn_ds_matrix 1864s dn, ds = self.aln.get_dn_ds_matrix() 1864s ~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1864s File "/usr/lib/python3/dist-packages/Bio/codonalign/codonalignment.py", line 159, in get_dn_ds_matrix 1864s from Bio.Phylo.TreeConstruction import DistanceMatrix as DM 1864s File "/usr/lib/python3/dist-packages/Bio/Phylo/__init__.py", line 14, in 1864s from Bio.Phylo._io import convert 1864s File "/usr/lib/python3/dist-packages/Bio/Phylo/_io.py", line 29, in 1864s from Bio.Phylo import CDAOIO 1864s File "/usr/lib/python3/dist-packages/Bio/Phylo/CDAOIO.py", line 37, in 1864s import rdflib 1864s File "/usr/lib/python3/dist-packages/rdflib/__init__.py", line 168, in 1864s from rdflib.graph import ConjunctiveGraph, Dataset, Graph 1864s File "/usr/lib/python3/dist-packages/rdflib/graph.py", line 292, in 1864s from rdflib.resource import Resource 1864s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 296, in 1864s class Resource: 1864s ...<164 lines>... 1864s return "Resource(%s,%s)" % (self._graph, self._identifier) 1864s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 379, in Resource 1864s def value(self, p=RDF.value, o=None, default=None, any=True): 1864s ^^^^^^^^^ 1864s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 285, in __getattr__ 1864s return cls.__getitem__(name) 1864s ~~~~~~~~~~~~~~~^^^^^^ 1864s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 268, in __getitem__ 1864s raise AttributeError(f"term '{name}' not in namespace '{cls._NS}'") 1864s AttributeError: term 'value' not in namespace 'http://www.w3.org/1999/02/22-rdf-syntax-ns#' 1864s 1864s ---------------------------------------------------------------------- 1864s Ran 201 tests in 164.147 seconds 1864s 1864s FAILED (failures = 15) 1865s :0: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/protein_lib.fa' mode='rt' encoding='UTF-8'> 1865s :0: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/nucleotide_lib.fa' mode='rt' encoding='UTF-8'> 1866s autopkgtest [21:25:21]: test full_suite: -----------------------] 1870s autopkgtest [21:25:25]: test full_suite: - - - - - - - - - - results - - - - - - - - - - 1870s full_suite FAIL non-zero exit status 1 1874s autopkgtest [21:25:29]: @@@@@@@@@@@@@@@@@@@@ summary 1874s dependencies PASS 1874s full_suite FAIL non-zero exit status 1