0s autopkgtest [22:15:34]: starting date and time: 2026-01-22 22:15:34+0000 0s autopkgtest [22:15:34]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [22:15:34]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.asgq0tsr/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --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 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-cpu2-ram4-disk20-arm64 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@sto01-arm64-15.secgroup --name adt-resolute-arm64-python-biopython-20260122-221534-juju-7f2275-prod-proposed-migration-environment-20-9338cdab-667b-49e6-9a9f-ec7df6f47864 --image adt/ubuntu-resolute-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-autopkgtest-workers-arm64 -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 5s Creating nova instance adt-resolute-arm64-python-biopython-20260122-221534-juju-7f2275-prod-proposed-migration-environment-20-9338cdab-667b-49e6-9a9f-ec7df6f47864 from image adt/ubuntu-resolute-arm64-server-20260122.img (UUID ed27afc7-5f46-4e8b-ad73-864280a0ddbb)... 61s autopkgtest [22:16:35]: testbed dpkg architecture: arm64 62s autopkgtest [22:16:36]: testbed apt version: 3.1.12 62s autopkgtest [22:16:36]: @@@@@@@@@@@@@@@@@@@@ test bed setup 62s autopkgtest [22:16:36]: testbed release detected to be: None 63s autopkgtest [22:16:37]: updating testbed package index (apt update) 63s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 63s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 63s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 63s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 63s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [81.6 kB] 63s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [22.2 kB] 63s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [1011 kB] 64s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [2820 B] 64s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 Packages [101 kB] 64s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 c-n-f Metadata [3424 B] 64s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/restricted arm64 Packages [7876 B] 64s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/restricted arm64 c-n-f Metadata [304 B] 64s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 Packages [727 kB] 64s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 c-n-f Metadata [18.1 kB] 64s Get:15 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse arm64 Packages [7156 B] 64s Get:16 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse arm64 c-n-f Metadata [332 B] 67s Fetched 2107 kB in 1s (1585 kB/s) 68s Reading package lists... 68s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 68s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 68s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 68s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 69s Reading package lists... 69s Reading package lists... 69s Building dependency tree... 69s Reading state information... 70s Calculating upgrade... 70s The following packages were automatically installed and are no longer required: 70s python3.13 python3.13-minimal 70s Use 'sudo apt autoremove' to remove them. 70s The following NEW packages will be installed: 70s libpython3.14-minimal libpython3.14-stdlib python3.14 python3.14-minimal 70s The following packages will be upgraded: 70s libplymouth5 libpython3-stdlib plymouth plymouth-theme-ubuntu-text python3 70s python3-gdbm python3-minimal 70s 7 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. 70s Need to get 6993 kB of archives. 70s After this operation, 26.0 MB of additional disk space will be used. 70s Get:1 http://ftpmaster.internal/ubuntu resolute/main arm64 libpython3.14-minimal arm64 3.14.2-1 [917 kB] 71s Get:2 http://ftpmaster.internal/ubuntu resolute/main arm64 python3.14-minimal arm64 3.14.2-1 [2548 kB] 71s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 python3-gdbm arm64 3.14.2-1 [11.1 kB] 71s Get:4 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 python3-minimal arm64 3.14.2-1 [28.2 kB] 71s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 python3 arm64 3.14.2-1 [22.9 kB] 71s Get:6 http://ftpmaster.internal/ubuntu resolute/main arm64 libpython3.14-stdlib arm64 3.14.2-1 [2351 kB] 71s Get:7 http://ftpmaster.internal/ubuntu resolute/main arm64 python3.14 arm64 3.14.2-1 [816 kB] 71s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 libpython3-stdlib arm64 3.14.2-1 [10.9 kB] 71s Get:9 http://ftpmaster.internal/ubuntu resolute/main arm64 libplymouth5 arm64 24.004.60+git20250831.4a3c171d-0ubuntu4 [141 kB] 71s Get:10 http://ftpmaster.internal/ubuntu resolute/main arm64 plymouth-theme-ubuntu-text arm64 24.004.60+git20250831.4a3c171d-0ubuntu4 [10.0 kB] 71s Get:11 http://ftpmaster.internal/ubuntu resolute/main arm64 plymouth arm64 24.004.60+git20250831.4a3c171d-0ubuntu4 [138 kB] 71s dpkg-preconfigure: unable to re-open stdin: No such file or directory 71s Fetched 6993 kB in 1s (11.3 MB/s) 71s Selecting previously unselected package libpython3.14-minimal:arm64. 72s (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 ... 135223 files and directories currently installed.) 72s Preparing to unpack .../libpython3.14-minimal_3.14.2-1_arm64.deb ... 72s Unpacking libpython3.14-minimal:arm64 (3.14.2-1) ... 72s Selecting previously unselected package python3.14-minimal. 72s Preparing to unpack .../python3.14-minimal_3.14.2-1_arm64.deb ... 72s Unpacking python3.14-minimal (3.14.2-1) ... 72s Preparing to unpack .../python3-gdbm_3.14.2-1_arm64.deb ... 72s Unpacking python3-gdbm (3.14.2-1) over (3.13.9-1) ... 72s Setting up libpython3.14-minimal:arm64 (3.14.2-1) ... 72s Setting up python3.14-minimal (3.14.2-1) ... 73s (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 ... 135565 files and directories currently installed.) 73s Preparing to unpack .../python3-minimal_3.14.2-1_arm64.deb ... 73s Unpacking python3-minimal (3.14.2-1) over (3.13.7-1) ... 73s Setting up python3-minimal (3.14.2-1) ... 74s (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 ... 135565 files and directories currently installed.) 74s Preparing to unpack .../0-python3_3.14.2-1_arm64.deb ... 74s running python pre-rtupdate hooks for python3.14... 74s Unpacking python3 (3.14.2-1) over (3.13.7-1) ... 74s Selecting previously unselected package libpython3.14-stdlib:arm64. 74s Preparing to unpack .../1-libpython3.14-stdlib_3.14.2-1_arm64.deb ... 74s Unpacking libpython3.14-stdlib:arm64 (3.14.2-1) ... 74s Selecting previously unselected package python3.14. 74s Preparing to unpack .../2-python3.14_3.14.2-1_arm64.deb ... 74s Unpacking python3.14 (3.14.2-1) ... 74s Preparing to unpack .../3-libpython3-stdlib_3.14.2-1_arm64.deb ... 74s Unpacking libpython3-stdlib:arm64 (3.14.2-1) over (3.13.7-1) ... 74s Preparing to unpack .../4-libplymouth5_24.004.60+git20250831.4a3c171d-0ubuntu4_arm64.deb ... 74s Unpacking libplymouth5:arm64 (24.004.60+git20250831.4a3c171d-0ubuntu4) over (24.004.60+git20250831.4a3c171d-0ubuntu3) ... 74s Preparing to unpack .../5-plymouth-theme-ubuntu-text_24.004.60+git20250831.4a3c171d-0ubuntu4_arm64.deb ... 74s Unpacking plymouth-theme-ubuntu-text (24.004.60+git20250831.4a3c171d-0ubuntu4) over (24.004.60+git20250831.4a3c171d-0ubuntu3) ... 74s Preparing to unpack .../6-plymouth_24.004.60+git20250831.4a3c171d-0ubuntu4_arm64.deb ... 74s Unpacking plymouth (24.004.60+git20250831.4a3c171d-0ubuntu4) over (24.004.60+git20250831.4a3c171d-0ubuntu3) ... 74s Setting up libpython3.14-stdlib:arm64 (3.14.2-1) ... 74s Setting up libplymouth5:arm64 (24.004.60+git20250831.4a3c171d-0ubuntu4) ... 74s Setting up python3.14 (3.14.2-1) ... 75s Setting up libpython3-stdlib:arm64 (3.14.2-1) ... 75s Setting up python3-gdbm (3.14.2-1) ... 75s Setting up plymouth (24.004.60+git20250831.4a3c171d-0ubuntu4) ... 75s update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults 76s update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults 76s Setting up python3 (3.14.2-1) ... 76s running python rtupdate hooks for python3.14... 76s running python post-rtupdate hooks for python3.14... 76s Processing triggers for libc-bin (2.42-2ubuntu4) ... 76s Processing triggers for systemd (259-1ubuntu2) ... 76s Processing triggers for man-db (2.13.1-1) ... 77s Processing triggers for initramfs-tools (0.150ubuntu7) ... 77s update-initramfs: Generating /boot/initrd.img-6.18.0-9-generic 93s System running in EFI mode, skipping. 93s Setting up plymouth-theme-ubuntu-text (24.004.60+git20250831.4a3c171d-0ubuntu4) ... 93s Processing triggers for initramfs-tools (0.150ubuntu7) ... 93s update-initramfs: Generating /boot/initrd.img-6.18.0-9-generic 106s System running in EFI mode, skipping. 106s autopkgtest [22:17:20]: upgrading testbed (apt dist-upgrade and autopurge) 106s Reading package lists... 106s Building dependency tree... 106s Reading state information... 107s Calculating upgrade... 107s The following packages were automatically installed and are no longer required: 107s python3.13 python3.13-minimal 107s Use 'sudo apt autoremove' to remove them. 107s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 107s Reading package lists... 107s Building dependency tree... 107s Reading state information... 107s Solving dependencies... 108s The following packages will be REMOVED: 108s python3.13* python3.13-minimal* 108s 0 upgraded, 0 newly installed, 2 to remove and 0 not upgraded. 108s After this operation, 7766 kB disk space will be freed. 108s (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 ... 135995 files and directories currently installed.) 108s Removing python3.13 (3.13.11-1) ... 108s Removing python3.13-minimal (3.13.11-1) ... 109s Processing triggers for man-db (2.13.1-1) ... 109s Processing triggers for systemd (259-1ubuntu2) ... 110s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 135968 files and directories currently installed.) 110s Purging configuration files for python3.13-minimal (3.13.11-1) ... 110s autopkgtest [22:17:24]: rebooting testbed after setup commands that affected boot 148s autopkgtest [22:18:02]: testbed running kernel: Linux 6.18.0-9-generic #9-Ubuntu SMP PREEMPT_DYNAMIC Mon Jan 12 16:41:39 UTC 2026 151s autopkgtest [22:18:05]: @@@@@@@@@@@@@@@@@@@@ apt-source python-biopython 153s Get:1 http://ftpmaster.internal/ubuntu resolute/universe python-biopython 1.86+dfsg-1 (dsc) [3562 B] 153s Get:2 http://ftpmaster.internal/ubuntu resolute/universe python-biopython 1.86+dfsg-1 (tar) [14.5 MB] 153s Get:3 http://ftpmaster.internal/ubuntu resolute/universe python-biopython 1.86+dfsg-1 (diff) [41.4 kB] 154s gpgv: Signature made Wed Oct 29 22:41:45 2025 UTC 154s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 154s gpgv: issuer "emollier@debian.org" 154s gpgv: Can't check signature: No public key 154s dpkg-source: warning: cannot verify inline signature for ./python-biopython_1.86+dfsg-1.dsc: no acceptable signature found 154s autopkgtest [22:18:08]: testing package python-biopython version 1.86+dfsg-1 155s autopkgtest [22:18:09]: build not needed 160s autopkgtest [22:18:14]: test dependencies: preparing testbed 161s Reading package lists... 161s Building dependency tree... 161s Reading state information... 161s Solving dependencies... 161s The following NEW packages will be installed: 161s fontconfig-config fonts-dejavu-core fonts-dejavu-extra fonts-dejavu-mono 161s fonts-urw-base35 libblas3 libcairo2 libdeflate0 libfontconfig1 libfontenc1 161s libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libimagequant0 libjbig0 161s libjpeg-turbo8 libjpeg8 libjs-jquery liblapack3 liblcms2-2 liblerc4 161s libopenjp2-7 libpixman-1-0 libraqm0 libsharpyuv0 libtiff6 libwebp7 161s libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 libxrender1 161s python-biopython-doc python3-all python3-biopython python3-biopython-sql 161s python3-cairo python3-charset-normalizer python3-freetype python3-numpy 161s python3-numpy-dev python3-pil python3-reportlab python3-rlpycairo python3.13 161s python3.13-minimal sgml-base w3c-sgml-lib x11-common xfonts-encodings 161s xfonts-utils xml-core 162s 0 upgraded, 53 newly installed, 0 to remove and 0 not upgraded. 162s Need to get 51.4 MB of archives. 162s After this operation, 147 MB of additional disk space will be used. 162s Get:1 http://ftpmaster.internal/ubuntu resolute/main arm64 python3.13-minimal arm64 3.13.11-1 [2346 kB] 162s Get:2 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-numpy-dev arm64 1:2.3.5+ds-3 [366 kB] 162s Get:3 http://ftpmaster.internal/ubuntu resolute/main arm64 libblas3 arm64 3.12.1-7ubuntu1 [181 kB] 162s Get:4 http://ftpmaster.internal/ubuntu resolute/main arm64 libgfortran5 arm64 15.2.0-11ubuntu1 [450 kB] 162s Get:5 http://ftpmaster.internal/ubuntu resolute/main arm64 liblapack3 arm64 3.12.1-7ubuntu1 [2299 kB] 162s Get:6 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-numpy arm64 1:2.3.5+ds-3 [4569 kB] 162s Get:7 http://ftpmaster.internal/ubuntu resolute/main arm64 python3.13 arm64 3.13.11-1 [758 kB] 162s Get:8 http://ftpmaster.internal/ubuntu resolute/main arm64 fonts-dejavu-mono all 2.37-8build1 [502 kB] 162s Get:9 http://ftpmaster.internal/ubuntu resolute/main arm64 fonts-dejavu-core all 2.37-8build1 [834 kB] 162s Get:10 http://ftpmaster.internal/ubuntu resolute/main arm64 libfontenc1 arm64 1:1.1.8-1build2 [13.9 kB] 162s Get:11 http://ftpmaster.internal/ubuntu resolute/main arm64 x11-common all 1:7.7+24ubuntu1 [22.4 kB] 162s Get:12 http://ftpmaster.internal/ubuntu resolute/main arm64 xfonts-encodings all 1:1.0.5-0ubuntu3 [576 kB] 162s Get:13 http://ftpmaster.internal/ubuntu resolute/main arm64 xfonts-utils arm64 1:7.7+7build1 [94.8 kB] 162s Get:14 http://ftpmaster.internal/ubuntu resolute/main arm64 fonts-urw-base35 all 20200910-8build1 [10.9 MB] 163s Get:15 http://ftpmaster.internal/ubuntu resolute/main arm64 fontconfig-config arm64 2.15.0-2.4ubuntu1 [38.2 kB] 163s Get:16 http://ftpmaster.internal/ubuntu resolute/main arm64 fonts-dejavu-extra all 2.37-8build1 [1944 kB] 163s Get:17 http://ftpmaster.internal/ubuntu resolute/main arm64 libfontconfig1 arm64 2.15.0-2.4ubuntu1 [143 kB] 163s Get:18 http://ftpmaster.internal/ubuntu resolute/main arm64 libpixman-1-0 arm64 0.46.4-1 [204 kB] 163s Get:19 http://ftpmaster.internal/ubuntu resolute/main arm64 libxcb-render0 arm64 1.17.0-2build1 [18.1 kB] 163s Get:20 http://ftpmaster.internal/ubuntu resolute/main arm64 libxcb-shm0 arm64 1.17.0-2build1 [6234 B] 163s Get:21 http://ftpmaster.internal/ubuntu resolute/main arm64 libxrender1 arm64 1:0.9.12-1 [19.5 kB] 163s Get:22 http://ftpmaster.internal/ubuntu resolute/main arm64 libcairo2 arm64 1.18.4-3 [556 kB] 163s Get:23 http://ftpmaster.internal/ubuntu resolute/main arm64 libdeflate0 arm64 1.23-2 [46.4 kB] 163s Get:24 http://ftpmaster.internal/ubuntu resolute/main arm64 libgomp1 arm64 15.2.0-11ubuntu1 [147 kB] 163s Get:25 http://ftpmaster.internal/ubuntu resolute/main arm64 libgraphite2-3 arm64 1.3.14-11ubuntu1 [72.1 kB] 163s Get:26 http://ftpmaster.internal/ubuntu resolute/main arm64 libharfbuzz0b arm64 12.3.0-4 [518 kB] 163s Get:27 http://ftpmaster.internal/ubuntu resolute/main arm64 libimagequant0 arm64 2.18.0-1build1 [37.1 kB] 163s Get:28 http://ftpmaster.internal/ubuntu resolute/main arm64 libjpeg-turbo8 arm64 2.1.5-4ubuntu2 [165 kB] 163s Get:29 http://ftpmaster.internal/ubuntu resolute/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 163s Get:30 http://ftpmaster.internal/ubuntu resolute/main arm64 libjs-jquery all 3.7.1+dfsg+~3.5.33-1build1 [321 kB] 163s Get:31 http://ftpmaster.internal/ubuntu resolute/main arm64 liblcms2-2 arm64 2.17-1 [170 kB] 163s Get:32 http://ftpmaster.internal/ubuntu resolute/main arm64 liblerc4 arm64 4.0.0+ds-5ubuntu2 [174 kB] 163s Get:33 http://ftpmaster.internal/ubuntu resolute/main arm64 libraqm0 arm64 0.10.3-1 [15.0 kB] 163s Get:34 http://ftpmaster.internal/ubuntu resolute/main arm64 libsharpyuv0 arm64 1.5.0-0.1build1 [16.7 kB] 163s Get:35 http://ftpmaster.internal/ubuntu resolute/main arm64 libjbig0 arm64 2.1-6.1ubuntu3 [29.2 kB] 163s Get:36 http://ftpmaster.internal/ubuntu resolute/main arm64 libwebp7 arm64 1.5.0-0.1build1 [205 kB] 163s Get:37 http://ftpmaster.internal/ubuntu resolute/main arm64 libtiff6 arm64 4.7.0-3ubuntu3 [196 kB] 163s Get:38 http://ftpmaster.internal/ubuntu resolute/main arm64 libwebpdemux2 arm64 1.5.0-0.1build1 [12.5 kB] 163s Get:39 http://ftpmaster.internal/ubuntu resolute/main arm64 libwebpmux3 arm64 1.5.0-0.1build1 [25.2 kB] 163s Get:40 http://ftpmaster.internal/ubuntu resolute/universe arm64 python-biopython-doc all 1.86+dfsg-1 [18.1 MB] 164s Get:41 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 python3-all arm64 3.14.2-1 [888 B] 164s Get:42 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-charset-normalizer arm64 3.4.4-2 [169 kB] 164s Get:43 http://ftpmaster.internal/ubuntu resolute/main arm64 libopenjp2-7 arm64 2.5.4-1 [180 kB] 164s Get:44 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-pil arm64 12.0.0-1ubuntu1 [486 kB] 164s Get:45 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-cairo arm64 1.27.0-2build1 [141 kB] 164s Get:46 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-freetype all 2.5.1-2 [92.2 kB] 164s Get:47 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-rlpycairo all 0.3.0-4 [9332 B] 164s Get:48 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-reportlab all 4.4.9-1 [1149 kB] 164s Get:49 http://ftpmaster.internal/ubuntu resolute/main arm64 sgml-base all 1.31+nmu1 [11.0 kB] 164s Get:50 http://ftpmaster.internal/ubuntu resolute/main arm64 xml-core all 0.19build1 [20.3 kB] 164s Get:51 http://ftpmaster.internal/ubuntu resolute/universe arm64 w3c-sgml-lib all 1.3-3build1 [278 kB] 164s Get:52 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-biopython arm64 1.86+dfsg-1 [1675 kB] 164s Get:53 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-biopython-sql all 1.86+dfsg-1 [26.4 kB] 164s Fetched 51.4 MB in 2s (23.3 MB/s) 164s Selecting previously unselected package python3.13-minimal. 164s (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 ... 135970 files and directories currently installed.) 164s Preparing to unpack .../00-python3.13-minimal_3.13.11-1_arm64.deb ... 164s Unpacking python3.13-minimal (3.13.11-1) ... 164s Selecting previously unselected package python3-numpy-dev:arm64. 164s Preparing to unpack .../01-python3-numpy-dev_1%3a2.3.5+ds-3_arm64.deb ... 164s Unpacking python3-numpy-dev:arm64 (1:2.3.5+ds-3) ... 164s Selecting previously unselected package libblas3:arm64. 164s Preparing to unpack .../02-libblas3_3.12.1-7ubuntu1_arm64.deb ... 164s Unpacking libblas3:arm64 (3.12.1-7ubuntu1) ... 164s Selecting previously unselected package libgfortran5:arm64. 165s Preparing to unpack .../03-libgfortran5_15.2.0-11ubuntu1_arm64.deb ... 165s Unpacking libgfortran5:arm64 (15.2.0-11ubuntu1) ... 165s Selecting previously unselected package liblapack3:arm64. 165s Preparing to unpack .../04-liblapack3_3.12.1-7ubuntu1_arm64.deb ... 165s Unpacking liblapack3:arm64 (3.12.1-7ubuntu1) ... 165s Selecting previously unselected package python3-numpy. 165s Preparing to unpack .../05-python3-numpy_1%3a2.3.5+ds-3_arm64.deb ... 165s Unpacking python3-numpy (1:2.3.5+ds-3) ... 165s Selecting previously unselected package python3.13. 165s Preparing to unpack .../06-python3.13_3.13.11-1_arm64.deb ... 165s Unpacking python3.13 (3.13.11-1) ... 165s Selecting previously unselected package fonts-dejavu-mono. 165s Preparing to unpack .../07-fonts-dejavu-mono_2.37-8build1_all.deb ... 165s Unpacking fonts-dejavu-mono (2.37-8build1) ... 165s Selecting previously unselected package fonts-dejavu-core. 165s Preparing to unpack .../08-fonts-dejavu-core_2.37-8build1_all.deb ... 165s Unpacking fonts-dejavu-core (2.37-8build1) ... 165s Selecting previously unselected package libfontenc1:arm64. 165s Preparing to unpack .../09-libfontenc1_1%3a1.1.8-1build2_arm64.deb ... 165s Unpacking libfontenc1:arm64 (1:1.1.8-1build2) ... 165s Selecting previously unselected package x11-common. 165s Preparing to unpack .../10-x11-common_1%3a7.7+24ubuntu1_all.deb ... 165s Unpacking x11-common (1:7.7+24ubuntu1) ... 165s Selecting previously unselected package xfonts-encodings. 165s Preparing to unpack .../11-xfonts-encodings_1%3a1.0.5-0ubuntu3_all.deb ... 165s Unpacking xfonts-encodings (1:1.0.5-0ubuntu3) ... 165s Selecting previously unselected package xfonts-utils. 165s Preparing to unpack .../12-xfonts-utils_1%3a7.7+7build1_arm64.deb ... 165s Unpacking xfonts-utils (1:7.7+7build1) ... 165s Selecting previously unselected package fonts-urw-base35. 165s Preparing to unpack .../13-fonts-urw-base35_20200910-8build1_all.deb ... 165s Unpacking fonts-urw-base35 (20200910-8build1) ... 165s Selecting previously unselected package fontconfig-config. 165s Preparing to unpack .../14-fontconfig-config_2.15.0-2.4ubuntu1_arm64.deb ... 166s Unpacking fontconfig-config (2.15.0-2.4ubuntu1) ... 166s Selecting previously unselected package fonts-dejavu-extra. 166s Preparing to unpack .../15-fonts-dejavu-extra_2.37-8build1_all.deb ... 166s Unpacking fonts-dejavu-extra (2.37-8build1) ... 166s Selecting previously unselected package libfontconfig1:arm64. 166s Preparing to unpack .../16-libfontconfig1_2.15.0-2.4ubuntu1_arm64.deb ... 166s Unpacking libfontconfig1:arm64 (2.15.0-2.4ubuntu1) ... 166s Selecting previously unselected package libpixman-1-0:arm64. 166s Preparing to unpack .../17-libpixman-1-0_0.46.4-1_arm64.deb ... 166s Unpacking libpixman-1-0:arm64 (0.46.4-1) ... 166s Selecting previously unselected package libxcb-render0:arm64. 166s Preparing to unpack .../18-libxcb-render0_1.17.0-2build1_arm64.deb ... 166s Unpacking libxcb-render0:arm64 (1.17.0-2build1) ... 166s Selecting previously unselected package libxcb-shm0:arm64. 166s Preparing to unpack .../19-libxcb-shm0_1.17.0-2build1_arm64.deb ... 166s Unpacking libxcb-shm0:arm64 (1.17.0-2build1) ... 166s Selecting previously unselected package libxrender1:arm64. 166s Preparing to unpack .../20-libxrender1_1%3a0.9.12-1_arm64.deb ... 166s Unpacking libxrender1:arm64 (1:0.9.12-1) ... 166s Selecting previously unselected package libcairo2:arm64. 166s Preparing to unpack .../21-libcairo2_1.18.4-3_arm64.deb ... 166s Unpacking libcairo2:arm64 (1.18.4-3) ... 166s Selecting previously unselected package libdeflate0:arm64. 166s Preparing to unpack .../22-libdeflate0_1.23-2_arm64.deb ... 166s Unpacking libdeflate0:arm64 (1.23-2) ... 166s Selecting previously unselected package libgomp1:arm64. 166s Preparing to unpack .../23-libgomp1_15.2.0-11ubuntu1_arm64.deb ... 166s Unpacking libgomp1:arm64 (15.2.0-11ubuntu1) ... 166s Selecting previously unselected package libgraphite2-3:arm64. 166s Preparing to unpack .../24-libgraphite2-3_1.3.14-11ubuntu1_arm64.deb ... 166s Unpacking libgraphite2-3:arm64 (1.3.14-11ubuntu1) ... 166s Selecting previously unselected package libharfbuzz0b:arm64. 166s Preparing to unpack .../25-libharfbuzz0b_12.3.0-4_arm64.deb ... 166s Unpacking libharfbuzz0b:arm64 (12.3.0-4) ... 166s Selecting previously unselected package libimagequant0:arm64. 166s Preparing to unpack .../26-libimagequant0_2.18.0-1build1_arm64.deb ... 166s Unpacking libimagequant0:arm64 (2.18.0-1build1) ... 166s Selecting previously unselected package libjpeg-turbo8:arm64. 166s Preparing to unpack .../27-libjpeg-turbo8_2.1.5-4ubuntu2_arm64.deb ... 166s Unpacking libjpeg-turbo8:arm64 (2.1.5-4ubuntu2) ... 166s Selecting previously unselected package libjpeg8:arm64. 166s Preparing to unpack .../28-libjpeg8_8c-2ubuntu11_arm64.deb ... 166s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 166s Selecting previously unselected package libjs-jquery. 166s Preparing to unpack .../29-libjs-jquery_3.7.1+dfsg+~3.5.33-1build1_all.deb ... 166s Unpacking libjs-jquery (3.7.1+dfsg+~3.5.33-1build1) ... 166s Selecting previously unselected package liblcms2-2:arm64. 167s Preparing to unpack .../30-liblcms2-2_2.17-1_arm64.deb ... 167s Unpacking liblcms2-2:arm64 (2.17-1) ... 167s Selecting previously unselected package liblerc4:arm64. 167s Preparing to unpack .../31-liblerc4_4.0.0+ds-5ubuntu2_arm64.deb ... 167s Unpacking liblerc4:arm64 (4.0.0+ds-5ubuntu2) ... 167s Selecting previously unselected package libraqm0:arm64. 167s Preparing to unpack .../32-libraqm0_0.10.3-1_arm64.deb ... 167s Unpacking libraqm0:arm64 (0.10.3-1) ... 167s Selecting previously unselected package libsharpyuv0:arm64. 167s Preparing to unpack .../33-libsharpyuv0_1.5.0-0.1build1_arm64.deb ... 167s Unpacking libsharpyuv0:arm64 (1.5.0-0.1build1) ... 167s Selecting previously unselected package libjbig0:arm64. 167s Preparing to unpack .../34-libjbig0_2.1-6.1ubuntu3_arm64.deb ... 167s Unpacking libjbig0:arm64 (2.1-6.1ubuntu3) ... 167s Selecting previously unselected package libwebp7:arm64. 167s Preparing to unpack .../35-libwebp7_1.5.0-0.1build1_arm64.deb ... 167s Unpacking libwebp7:arm64 (1.5.0-0.1build1) ... 167s Selecting previously unselected package libtiff6:arm64. 167s Preparing to unpack .../36-libtiff6_4.7.0-3ubuntu3_arm64.deb ... 167s Unpacking libtiff6:arm64 (4.7.0-3ubuntu3) ... 167s Selecting previously unselected package libwebpdemux2:arm64. 167s Preparing to unpack .../37-libwebpdemux2_1.5.0-0.1build1_arm64.deb ... 167s Unpacking libwebpdemux2:arm64 (1.5.0-0.1build1) ... 167s Selecting previously unselected package libwebpmux3:arm64. 167s Preparing to unpack .../38-libwebpmux3_1.5.0-0.1build1_arm64.deb ... 167s Unpacking libwebpmux3:arm64 (1.5.0-0.1build1) ... 167s Selecting previously unselected package python-biopython-doc. 167s Preparing to unpack .../39-python-biopython-doc_1.86+dfsg-1_all.deb ... 167s Unpacking python-biopython-doc (1.86+dfsg-1) ... 167s Selecting previously unselected package python3-all. 167s Preparing to unpack .../40-python3-all_3.14.2-1_arm64.deb ... 167s Unpacking python3-all (3.14.2-1) ... 167s Selecting previously unselected package python3-charset-normalizer. 167s Preparing to unpack .../41-python3-charset-normalizer_3.4.4-2_arm64.deb ... 167s Unpacking python3-charset-normalizer (3.4.4-2) ... 167s Selecting previously unselected package libopenjp2-7:arm64. 167s Preparing to unpack .../42-libopenjp2-7_2.5.4-1_arm64.deb ... 167s Unpacking libopenjp2-7:arm64 (2.5.4-1) ... 167s Selecting previously unselected package python3-pil:arm64. 167s Preparing to unpack .../43-python3-pil_12.0.0-1ubuntu1_arm64.deb ... 167s Unpacking python3-pil:arm64 (12.0.0-1ubuntu1) ... 167s Selecting previously unselected package python3-cairo. 167s Preparing to unpack .../44-python3-cairo_1.27.0-2build1_arm64.deb ... 167s Unpacking python3-cairo (1.27.0-2build1) ... 167s Selecting previously unselected package python3-freetype. 167s Preparing to unpack .../45-python3-freetype_2.5.1-2_all.deb ... 167s Unpacking python3-freetype (2.5.1-2) ... 167s Selecting previously unselected package python3-rlpycairo. 167s Preparing to unpack .../46-python3-rlpycairo_0.3.0-4_all.deb ... 167s Unpacking python3-rlpycairo (0.3.0-4) ... 168s Selecting previously unselected package python3-reportlab. 168s Preparing to unpack .../47-python3-reportlab_4.4.9-1_all.deb ... 168s Unpacking python3-reportlab (4.4.9-1) ... 168s Selecting previously unselected package sgml-base. 168s Preparing to unpack .../48-sgml-base_1.31+nmu1_all.deb ... 168s Unpacking sgml-base (1.31+nmu1) ... 168s Selecting previously unselected package xml-core. 168s Preparing to unpack .../49-xml-core_0.19build1_all.deb ... 168s Unpacking xml-core (0.19build1) ... 168s Selecting previously unselected package w3c-sgml-lib. 168s Preparing to unpack .../50-w3c-sgml-lib_1.3-3build1_all.deb ... 168s Unpacking w3c-sgml-lib (1.3-3build1) ... 168s Selecting previously unselected package python3-biopython. 168s Preparing to unpack .../51-python3-biopython_1.86+dfsg-1_arm64.deb ... 168s Unpacking python3-biopython (1.86+dfsg-1) ... 168s Selecting previously unselected package python3-biopython-sql. 168s Preparing to unpack .../52-python3-biopython-sql_1.86+dfsg-1_all.deb ... 168s Unpacking python3-biopython-sql (1.86+dfsg-1) ... 168s Setting up libgraphite2-3:arm64 (1.3.14-11ubuntu1) ... 168s Setting up liblcms2-2:arm64 (2.17-1) ... 168s Setting up libpixman-1-0:arm64 (0.46.4-1) ... 168s Setting up libsharpyuv0:arm64 (1.5.0-0.1build1) ... 168s Setting up liblerc4:arm64 (4.0.0+ds-5ubuntu2) ... 168s Setting up libxrender1:arm64 (1:0.9.12-1) ... 168s Setting up libxcb-render0:arm64 (1.17.0-2build1) ... 168s Setting up python3-charset-normalizer (3.4.4-2) ... 168s Setting up x11-common (1:7.7+24ubuntu1) ... 169s Setting up libdeflate0:arm64 (1.23-2) ... 169s Setting up libxcb-shm0:arm64 (1.17.0-2build1) ... 169s Setting up libgomp1:arm64 (15.2.0-11ubuntu1) ... 169s Setting up python3-freetype (2.5.1-2) ... 169s Setting up libjbig0:arm64 (2.1-6.1ubuntu3) ... 169s Setting up libfontenc1:arm64 (1:1.1.8-1build2) ... 169s Setting up libblas3:arm64 (3.12.1-7ubuntu1) ... 169s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode 169s Setting up xfonts-encodings (1:1.0.5-0ubuntu3) ... 169s Setting up libimagequant0:arm64 (2.18.0-1build1) ... 169s Setting up fonts-dejavu-mono (2.37-8build1) ... 169s Setting up python3-numpy-dev:arm64 (1:2.3.5+ds-3) ... 169s Setting up fonts-dejavu-core (2.37-8build1) ... 169s Setting up libjpeg-turbo8:arm64 (2.1.5-4ubuntu2) ... 169s Setting up libgfortran5:arm64 (15.2.0-11ubuntu1) ... 169s Setting up libwebp7:arm64 (1.5.0-0.1build1) ... 169s Setting up fonts-dejavu-extra (2.37-8build1) ... 169s Setting up libopenjp2-7:arm64 (2.5.4-1) ... 169s Setting up python3.13-minimal (3.13.11-1) ... 170s Setting up libharfbuzz0b:arm64 (12.3.0-4) ... 170s Setting up sgml-base (1.31+nmu1) ... 170s Setting up libjs-jquery (3.7.1+dfsg+~3.5.33-1build1) ... 170s Setting up libwebpmux3:arm64 (1.5.0-0.1build1) ... 170s Setting up libjpeg8:arm64 (8c-2ubuntu11) ... 170s Setting up liblapack3:arm64 (3.12.1-7ubuntu1) ... 170s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode 170s Setting up python3.13 (3.13.11-1) ... 171s Setting up fontconfig-config (2.15.0-2.4ubuntu1) ... 171s Setting up libwebpdemux2:arm64 (1.5.0-0.1build1) ... 171s Setting up python3-all (3.14.2-1) ... 171s Setting up xfonts-utils (1:7.7+7build1) ... 171s Setting up libraqm0:arm64 (0.10.3-1) ... 171s Setting up python3-numpy (1:2.3.5+ds-3) ... 175s Setting up python-biopython-doc (1.86+dfsg-1) ... 175s Setting up libtiff6:arm64 (4.7.0-3ubuntu3) ... 175s Setting up xml-core (0.19build1) ... 175s Setting up libfontconfig1:arm64 (2.15.0-2.4ubuntu1) ... 175s Setting up fonts-urw-base35 (20200910-8build1) ... 175s Setting up libcairo2:arm64 (1.18.4-3) ... 175s Setting up python3-pil:arm64 (12.0.0-1ubuntu1) ... 176s Setting up python3-cairo (1.27.0-2build1) ... 176s Setting up python3-rlpycairo (0.3.0-4) ... 177s Setting up python3-reportlab (4.4.9-1) ... 178s Processing triggers for libc-bin (2.42-2ubuntu4) ... 178s Processing triggers for systemd (259-1ubuntu2) ... 178s Processing triggers for man-db (2.13.1-1) ... 179s Processing triggers for sgml-base (1.31+nmu1) ... 179s Setting up w3c-sgml-lib (1.3-3build1) ... 205s Setting up python3-biopython (1.86+dfsg-1) ... 207s Setting up python3-biopython-sql (1.86+dfsg-1) ... 208s autopkgtest [22:19:02]: test dependencies: sh debian/tests/run-unit-test 208s autopkgtest [22:19:02]: test dependencies: [----------------------- 208s cp: cannot stat '/usr/share/libcifpp/mmcif_pdbx.dic': No such file or directory 208s cp: cannot stat '/usr/share/libcifpp/mmcif_ma.dic': No such file or directory 210s mkdir: created directory 'Bio' 210s mkdir: created directory 'Bio/Align' 210s mkdir: created directory 'Bio/Align/substitution_matrices' 210s mkdir: created directory 'Bio/Align/substitution_matrices/data/' 210s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER22' -> 'Bio/Align/substitution_matrices/data/BENNER22' 210s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER6' -> 'Bio/Align/substitution_matrices/data/BENNER6' 210s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER74' -> 'Bio/Align/substitution_matrices/data/BENNER74' 210s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLASTN' -> 'Bio/Align/substitution_matrices/data/BLASTN' 210s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLASTP' -> 'Bio/Align/substitution_matrices/data/BLASTP' 210s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM45' -> 'Bio/Align/substitution_matrices/data/BLOSUM45' 210s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM50' -> 'Bio/Align/substitution_matrices/data/BLOSUM50' 210s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM62' -> 'Bio/Align/substitution_matrices/data/BLOSUM62' 210s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM80' -> 'Bio/Align/substitution_matrices/data/BLOSUM80' 210s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM90' -> 'Bio/Align/substitution_matrices/data/BLOSUM90' 210s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/DAYHOFF' -> 'Bio/Align/substitution_matrices/data/DAYHOFF' 210s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/FENG' -> 'Bio/Align/substitution_matrices/data/FENG' 210s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/GENETIC' -> 'Bio/Align/substitution_matrices/data/GENETIC' 210s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/GONNET1992' -> 'Bio/Align/substitution_matrices/data/GONNET1992' 210s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/HOXD70' -> 'Bio/Align/substitution_matrices/data/HOXD70' 210s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/JOHNSON' -> 'Bio/Align/substitution_matrices/data/JOHNSON' 210s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/JONES' -> 'Bio/Align/substitution_matrices/data/JONES' 210s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/LEVIN' -> 'Bio/Align/substitution_matrices/data/LEVIN' 210s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MCLACHLAN' -> 'Bio/Align/substitution_matrices/data/MCLACHLAN' 210s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MDM78' -> 'Bio/Align/substitution_matrices/data/MDM78' 210s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MEGABLAST' -> 'Bio/Align/substitution_matrices/data/MEGABLAST' 210s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/NUC.4.4' -> 'Bio/Align/substitution_matrices/data/NUC.4.4' 210s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM250' -> 'Bio/Align/substitution_matrices/data/PAM250' 210s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM30' -> 'Bio/Align/substitution_matrices/data/PAM30' 210s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM70' -> 'Bio/Align/substitution_matrices/data/PAM70' 210s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/RAO' -> 'Bio/Align/substitution_matrices/data/RAO' 210s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/RISLER' -> 'Bio/Align/substitution_matrices/data/RISLER' 210s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/SCHNEIDER' -> 'Bio/Align/substitution_matrices/data/SCHNEIDER' 210s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/STR' -> 'Bio/Align/substitution_matrices/data/STR' 210s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/TRANS' -> 'Bio/Align/substitution_matrices/data/TRANS' 211s test_Ace ... ok 211s test_Affy ... ok 211s test_AlignIO ... ok 211s test_AlignIO_ClustalIO ... ok 211s test_AlignIO_EmbossIO ... ok 211s test_AlignIO_FastaIO ... ok 211s test_AlignIO_MauveIO ... ok 211s test_AlignIO_PhylipIO ... ok 211s test_AlignIO_convert ... ok 211s test_Align_Alignment ... ok 212s test_Align_a2m ... ok 212s test_Align_bed ... ok 212s test_Align_bigbed ... ok 212s test_Align_bigmaf ... ok 213s test_Align_bigpsl ... ok 213s test_Align_chain ... ok 213s test_Align_clustal ... ok 216s test_Align_codonalign ... ok 216s test_Align_emboss ... ok 216s test_Align_exonerate ... ok 216s test_Align_fasta ... ok 216s test_Align_format_matrix ... ok 217s test_Align_hhr ... ok 218s test_Align_maf ... ok 218s test_Align_mauve ... ok 218s test_Align_msf ... ok 218s test_Align_nexus ... ok 218s test_Align_phylip ... ok 218s test_Align_psl ... ok 218s test_Align_sam ... ok 220s test_Align_stockholm ... ok 220s test_Align_tabular ... ok 221s test_BioSQL_MySQLdb_online ... skipping. internet not available 221s test_BioSQL_mysql_connector ... skipping. BioSQL test configuration file biosql.ini missing (see biosql.ini.sample) 221s test_BioSQL_mysql_connector_online ... skipping. internet not available 221s test_BioSQL_psycopg2_online ... skipping. internet not available 225s test_BioSQL_sqlite3 ... ok 225s test_BioSQL_sqlite3_online ... skipping. internet not available 225s test_Blast_Record ... ok 225s test_Blast_parser ... ok 225s test_CAPS ... ok 225s test_Chi2 ... ok 225s test_Cluster ... ok 225s test_CodonTable ... ok 225s test_ColorSpiral ... ok 225s test_Compass ... ok 226s test_Consensus ... ok 226s test_EMBL_unittest ... ok 226s test_EmbossPrimer ... ok 231s test_Entrez ... ok 231s test_Entrez_online ... skipping. internet not available 231s test_Entrez_parser ... ok 231s test_Enzyme ... ok 231s test_ExPASy ... skipping. internet not available 231s test_File ... ok 231s test_GenBank ... ok 233s test_GenomeDiagram ... Warn: Can't find .pfb for face 'Helvetica' 235s ok 235s test_GraphicsChromosome ... ok 235s test_GraphicsDistribution ... ok 236s test_GraphicsGeneral ... ok 236s test_KEGG ... ok 236s test_KEGG_online ... skipping. internet not available 240s test_KGML_graphics ... ok 240s test_KGML_graphics_online ... skipping. internet not available 241s test_KGML_nographics ... ok 241s test_KeyWList ... ok 242s test_MafIO_index ... ok 242s test_Medline ... ok 243s test_NCBIXML ... Exception ignored in: 243s Traceback (most recent call last): 243s File "/usr/lib/python3/dist-packages/Bio/Blast/NCBIXML.py", line 1319, in parse 243s expat_parser.Parse(NULL, True) 243s xml.parsers.expat.ExpatError: unclosed token: line 320, column 0 243s ok 243s test_NCBI_qblast ... ok 243s test_NMR ... ok 243s test_Nexus ... ok 243s test_PAML_baseml ... ok 244s test_PAML_codeml ... ok 244s test_PAML_yn00 ... ok 248s test_PDB_CEAligner ... ok 248s test_PDB_DSSP ... ok 248s test_PDB_Dice ... ok 248s test_PDB_Disordered ... ok 248s test_PDB_Exposure ... ok 248s test_PDB_FragmentMapper ... ok 250s test_PDB_KDTree ... ok 250s test_PDB_MMCIF2Dict ... ok 250s test_PDB_MMCIFIO ... ok 251s test_PDB_MMCIFParser ... ok 251s test_PDB_NACCESS ... ok 252s test_PDB_PDBIO ... ok 252s test_PDB_PDBList ... skipping. internet not available 258s test_PDB_PDBMLParser ... ok 258s test_PDB_PDBParser ... ok 258s 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 258s test_PDB_Polypeptide ... ok 258s test_PDB_QCPSuperimposer ... ok 261s test_PDB_SASA ... ok 262s test_PDB_SMCRA ... ok 262s test_PDB_Selection ... ok 262s test_PDB_StructureAlignment ... ok 263s test_PDB_Superimposer ... ok 263s test_PDB_alphafold_db ... skipping. internet not available 263s test_PDB_binary_cif ... skipping. Error: Install msgpack to use Bio.PDB.binaryCIF (e.g. pip install msgpack) 263s 263s test_PDB_internal_coords ... skipping. Error: Install mmtf to use Bio.PDB.mmtf (e.g. pip install mmtf-python) 263s 263s test_PDB_parse_pdb_header ... ok 263s test_PDB_vectors ... ok 263s test_PQR ... ok 263s test_Pathway ... ok 263s test_Phd ... ok 263s test_Phylo ... ok 264s test_PhyloXML ... ok 264s test_Phylo_CDAO ... skipping. Install RDFlib if you want to use the CDAO tree format. 264s test_Phylo_NeXML ... ok 264s test_Phylo_igraph ... skipping. Install igraph if you wish to use it with Bio.Phylo 264s test_Phylo_matplotlib ... skipping. Install matplotlib if you want to use Bio.Phylo._utils. 264s test_Phylo_networkx ... skipping. Install networkx if you wish to use it with Bio.Phylo 264s test_PopGen_GenePop_nodepend ... ok 264s test_ProtParam ... ok 265s test_RCSBFormats ... ok 265s test_Restriction ... ok 265s test_SCOP_Astral ... ok 265s test_SCOP_Cla ... ok 265s test_SCOP_Des ... ok 265s test_SCOP_Dom ... ok 265s test_SCOP_Hie ... ok 265s test_SCOP_Raf ... ok 265s test_SCOP_Residues ... ok 265s test_SCOP_Scop ... ok 265s test_SVDSuperimposer ... ok 265s test_SearchIO_blast_tab ... ok 266s test_SearchIO_blast_tab_index ... ok 266s test_SearchIO_blast_xml ... ok 267s test_SearchIO_blast_xml_index ... ok 267s test_SearchIO_blat_psl ... ok 267s test_SearchIO_blat_psl_index ... ok 267s test_SearchIO_exonerate ... ok 267s test_SearchIO_exonerate_text_index ... ok 267s test_SearchIO_exonerate_vulgar_index ... ok 267s test_SearchIO_fasta_m10 ... ok 268s test_SearchIO_fasta_m10_index ... ok 268s test_SearchIO_hhsuite2_text ... ok 268s test_SearchIO_hmmer2_text ... ok 268s test_SearchIO_hmmer2_text_index ... ok 268s test_SearchIO_hmmer3_domtab ... ok 268s test_SearchIO_hmmer3_domtab_index ... ok 268s test_SearchIO_hmmer3_tab ... ok 268s test_SearchIO_hmmer3_tab_index ... ok 268s test_SearchIO_hmmer3_text ... ok 268s test_SearchIO_hmmer3_text_index ... ok 269s test_SearchIO_infernal_tab ... ok 269s test_SearchIO_infernal_tab_index ... ok 269s test_SearchIO_infernal_text ... ok 269s test_SearchIO_infernal_text_index ... ok 269s test_SearchIO_interproscan_xml ... ok 269s test_SearchIO_model ... ok 269s test_SearchIO_write ... ok 269s test_SeqFeature ... ok 286s test_SeqIO ... ok 286s test_SeqIO_AbiIO ... ok 286s test_SeqIO_FastaIO ... ok 286s test_SeqIO_Gck ... ok 286s test_SeqIO_Gfa ... ok 286s test_SeqIO_Insdc ... ok 286s test_SeqIO_NibIO ... ok 288s test_SeqIO_PdbIO ... ok 288s test_SeqIO_QualityIO ... ok 288s test_SeqIO_SeqXML ... ok 289s test_SeqIO_SffIO ... ok 289s test_SeqIO_SnapGene ... ok 289s test_SeqIO_TwoBitIO ... ok 290s test_SeqIO_UniprotIO ... ok 290s test_SeqIO_Xdna ... ok 290s test_SeqIO_features ... ok 303s test_SeqIO_index ... ok 303s test_SeqIO_online ... skipping. internet not available 303s test_SeqIO_write ... ok 303s test_SeqRecord ... ok 303s test_SeqUtils ... ok 304s test_Seq_objs ... ok 304s test_SwissProt ... ok 304s test_TogoWS ... skipping. internet not available 305s test_TreeConstruction ... ok 305s test_Tutorial ... skipping. Could not find ../Doc/Tutorial/index.rst file 305s test_UniGene ... ok 305s test_UniProt ... skipping. internet not available 305s test_UniProt_GOA ... ok 305s test_align ... ok 305s test_align_substitution_matrices ... ok 307s test_bgzf ... ok 308s test_cellosaurus ... ok 311s test_codonalign ... ok 311s test_geo ... ok 312s test_motifs ... ok 312s test_motifs_online ... skipping. internet not available 312s 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. 312s warnings.warn( 312s ok 312s test_pairwise2_no_C ... ok 312s test_pairwise_aligner ... ok 313s test_pairwise_alignment_map ... ok 319s test_phenotype ... ok 319s test_phenotype_fit ... skipping. Install SciPy if you want to use Bio.phenotype fit functionality. 319s test_prodoc ... ok 319s test_prosite ... ok 320s test_seq ... ok 320s test_translate ... ok 320s ---------------------------------------------------------------------- 320s Ran 201 tests in 109.025 seconds 320s 320s Skipping any tests requiring internet access 320s Python version: 3.13.11 (main, Dec 6 2025, 13:15:20) [GCC 15.2.0] 320s Operating system: posix linux 320s :0: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/protein_lib.fa' mode='rt' encoding='UTF-8'> 320s :0: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/nucleotide_lib.fa' mode='rt' encoding='UTF-8'> 321s test_Ace ... ok 321s test_Affy ... ok 321s test_AlignIO ... ok 321s test_AlignIO_ClustalIO ... ok 321s test_AlignIO_EmbossIO ... ok 321s test_AlignIO_FastaIO ... ok 321s test_AlignIO_MauveIO ... ok 321s test_AlignIO_PhylipIO ... ok 321s test_AlignIO_convert ... ok 321s test_Align_Alignment ... ok 321s test_Align_a2m ... ok 322s test_Align_bed ... ok 322s test_Align_bigbed ... ok 322s test_Align_bigmaf ... ok 323s test_Align_bigpsl ... ok 323s test_Align_chain ... ok 323s test_Align_clustal ... ok 326s test_Align_codonalign ... ok 326s test_Align_emboss ... ok 326s test_Align_exonerate ... ok 326s test_Align_fasta ... ok 326s test_Align_format_matrix ... ok 327s test_Align_hhr ... ok 328s test_Align_maf ... ok 328s test_Align_mauve ... ok 328s test_Align_msf ... ok 328s test_Align_nexus ... ok 328s test_Align_phylip ... ok 328s test_Align_psl ... ok 329s test_Align_sam ... ok 330s test_Align_stockholm ... ok 331s test_Align_tabular ... ok 331s test_BioSQL_MySQLdb_online ... skipping. internet not available 331s test_BioSQL_mysql_connector ... skipping. BioSQL test configuration file biosql.ini missing (see biosql.ini.sample) 331s test_BioSQL_mysql_connector_online ... skipping. internet not available 331s test_BioSQL_psycopg2_online ... skipping. internet not available 335s test_BioSQL_sqlite3 ... ok 335s test_BioSQL_sqlite3_online ... skipping. internet not available 335s test_Blast_Record ... ok 336s test_Blast_parser ... ok 336s test_CAPS ... ok 336s test_Chi2 ... ok 336s test_Cluster ... ok 336s test_CodonTable ... ok 336s test_ColorSpiral ... ok 336s test_Compass ... ok 337s test_Consensus ... ok 337s test_EMBL_unittest ... ok 337s test_EmbossPrimer ... ok 341s test_Entrez ... ok 341s test_Entrez_online ... skipping. internet not available 342s test_Entrez_parser ... ok 342s test_Enzyme ... ok 342s test_ExPASy ... skipping. internet not available 342s test_File ... ok 342s test_GenBank ... ok 344s test_GenomeDiagram ... Warn: Can't find .pfb for face 'Helvetica' 346s ok 346s test_GraphicsChromosome ... ok 346s test_GraphicsDistribution ... ok 347s test_GraphicsGeneral ... ok 347s test_KEGG ... ok 347s test_KEGG_online ... skipping. internet not available 351s test_KGML_graphics ... ok 351s test_KGML_graphics_online ... skipping. internet not available 352s test_KGML_nographics ... ok 352s test_KeyWList ... ok 353s test_MafIO_index ... ok 353s test_Medline ... ok 354s test_NCBIXML ... Exception ignored while closing generator : 354s Traceback (most recent call last): 354s File "/usr/lib/python3/dist-packages/Bio/Blast/NCBIXML.py", line 1319, in parse 354s expat_parser.Parse(NULL, True) 354s xml.parsers.expat.ExpatError: unclosed token: line 320, column 0 354s ok 354s test_NCBI_qblast ... ok 354s test_NMR ... ok 354s test_Nexus ... ok 354s test_PAML_baseml ... ok 355s test_PAML_codeml ... ok 355s test_PAML_yn00 ... ok 359s test_PDB_CEAligner ... ok 359s test_PDB_DSSP ... ok 359s test_PDB_Dice ... ok 359s test_PDB_Disordered ... ok 359s test_PDB_Exposure ... ok 359s test_PDB_FragmentMapper ... ok 361s test_PDB_KDTree ... ok 361s test_PDB_MMCIF2Dict ... ok 361s test_PDB_MMCIFIO ... ok 362s test_PDB_MMCIFParser ... ok 362s test_PDB_NACCESS ... ok 363s test_PDB_PDBIO ... ok 363s test_PDB_PDBList ... skipping. internet not available 368s test_PDB_PDBMLParser ... ok 368s test_PDB_PDBParser ... ok 368s 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 368s test_PDB_Polypeptide ... ok 368s test_PDB_QCPSuperimposer ... ok 371s test_PDB_SASA ... ok 371s test_PDB_SMCRA ... ok 371s test_PDB_Selection ... ok 372s test_PDB_StructureAlignment ... ok 373s test_PDB_Superimposer ... ok 373s test_PDB_alphafold_db ... skipping. internet not available 373s test_PDB_binary_cif ... skipping. Error: Install msgpack to use Bio.PDB.binaryCIF (e.g. pip install msgpack) 373s 373s test_PDB_internal_coords ... skipping. Error: Install mmtf to use Bio.PDB.mmtf (e.g. pip install mmtf-python) 373s 373s test_PDB_parse_pdb_header ... ok 373s test_PDB_vectors ... ok 373s test_PQR ... ok 373s test_Pathway ... ok 373s test_Phd ... ok 373s test_Phylo ... ok 374s test_PhyloXML ... ok 374s test_Phylo_CDAO ... skipping. Install RDFlib if you want to use the CDAO tree format. 374s test_Phylo_NeXML ... ok 374s test_Phylo_igraph ... skipping. Install igraph if you wish to use it with Bio.Phylo 374s test_Phylo_matplotlib ... skipping. Install matplotlib if you want to use Bio.Phylo._utils. 374s test_Phylo_networkx ... skipping. Install networkx if you wish to use it with Bio.Phylo 374s test_PopGen_GenePop_nodepend ... ok 375s test_ProtParam ... ok 375s test_RCSBFormats ... ok 375s test_Restriction ... ok 375s test_SCOP_Astral ... ok 375s test_SCOP_Cla ... ok 375s test_SCOP_Des ... ok 375s test_SCOP_Dom ... ok 375s test_SCOP_Hie ... ok 376s test_SCOP_Raf ... ok 376s test_SCOP_Residues ... ok 376s test_SCOP_Scop ... ok 376s test_SVDSuperimposer ... ok 376s test_SearchIO_blast_tab ... ok 376s test_SearchIO_blast_tab_index ... ok 376s test_SearchIO_blast_xml ... ok 378s test_SearchIO_blast_xml_index ... ok 378s test_SearchIO_blat_psl ... ok 378s test_SearchIO_blat_psl_index ... ok 378s test_SearchIO_exonerate ... ok 378s test_SearchIO_exonerate_text_index ... ok 378s test_SearchIO_exonerate_vulgar_index ... ok 378s test_SearchIO_fasta_m10 ... ok 378s test_SearchIO_fasta_m10_index ... ok 379s test_SearchIO_hhsuite2_text ... ok 379s test_SearchIO_hmmer2_text ... ok 379s test_SearchIO_hmmer2_text_index ... ok 379s test_SearchIO_hmmer3_domtab ... ok 379s test_SearchIO_hmmer3_domtab_index ... ok 379s test_SearchIO_hmmer3_tab ... ok 379s test_SearchIO_hmmer3_tab_index ... ok 380s test_SearchIO_hmmer3_text ... ok 380s test_SearchIO_hmmer3_text_index ... ok 380s test_SearchIO_infernal_tab ... ok 380s test_SearchIO_infernal_tab_index ... ok 380s test_SearchIO_infernal_text ... ok 380s test_SearchIO_infernal_text_index ... ok 380s test_SearchIO_interproscan_xml ... ok 380s test_SearchIO_model ... ok 381s test_SearchIO_write ... ok 381s test_SeqFeature ... ok 395s test_SeqIO ... ok 396s test_SeqIO_AbiIO ... ok 396s test_SeqIO_FastaIO ... ok 396s test_SeqIO_Gck ... ok 396s test_SeqIO_Gfa ... ok 396s test_SeqIO_Insdc ... ok 396s test_SeqIO_NibIO ... ok 398s test_SeqIO_PdbIO ... ok 398s test_SeqIO_QualityIO ... ok 398s test_SeqIO_SeqXML ... ok 398s test_SeqIO_SffIO ... ok 398s test_SeqIO_SnapGene ... ok 399s test_SeqIO_TwoBitIO ... ok 399s test_SeqIO_UniprotIO ... ok 400s test_SeqIO_Xdna ... ok 400s test_SeqIO_features ... ok 414s test_SeqIO_index ... ok 414s test_SeqIO_online ... skipping. internet not available 414s test_SeqIO_write ... ok 414s test_SeqRecord ... ok 414s test_SeqUtils ... ok 415s test_Seq_objs ... ok 416s test_SwissProt ... ok 416s test_TogoWS ... skipping. internet not available 416s test_TreeConstruction ... ok 416s test_Tutorial ... skipping. Could not find ../Doc/Tutorial/index.rst file 416s test_UniGene ... ok 416s test_UniProt ... skipping. internet not available 416s test_UniProt_GOA ... ok 416s test_align ... ok 417s test_align_substitution_matrices ... ok 419s test_bgzf ... ok 419s test_cellosaurus ... ok 423s test_codonalign ... ok 423s test_geo ... ok 423s test_motifs ... ok 423s test_motifs_online ... skipping. internet not available 423s 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. 423s warnings.warn( 423s ok 424s test_pairwise2_no_C ... ok 424s test_pairwise_aligner ... ok 424s test_pairwise_alignment_map ... ok 432s test_phenotype ... ok 432s test_phenotype_fit ... skipping. Install SciPy if you want to use Bio.phenotype fit functionality. 432s test_prodoc ... ok 432s test_prosite ... ok 432s test_seq ... ok 432s test_translate ... ok 432s Skipping any tests requiring internet access 432s Python version: 3.14.2 (main, Dec 6 2025, 13:20:08) [GCC 15.2.0] 432s Operating system: posix linux 432s ---------------------------------------------------------------------- 432s Ran 201 tests in 111.610 seconds 432s 432s :0: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/protein_lib.fa' mode='rt' encoding='UTF-8'> 432s :0: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/nucleotide_lib.fa' mode='rt' encoding='UTF-8'> 433s autopkgtest [22:22:47]: test dependencies: -----------------------] 433s dependencies PASS 433s autopkgtest [22:22:47]: test dependencies: - - - - - - - - - - results - - - - - - - - - - 434s autopkgtest [22:22:48]: test full_suite: preparing testbed 455s Creating nova instance adt-resolute-arm64-python-biopython-20260122-221534-juju-7f2275-prod-proposed-migration-environment-20-9338cdab-667b-49e6-9a9f-ec7df6f47864 from image adt/ubuntu-resolute-arm64-server-20260122.img (UUID ed27afc7-5f46-4e8b-ad73-864280a0ddbb)... 517s autopkgtest [22:24:11]: testbed dpkg architecture: arm64 517s autopkgtest [22:24:11]: testbed apt version: 3.1.12 518s autopkgtest [22:24:12]: @@@@@@@@@@@@@@@@@@@@ test bed setup 518s autopkgtest [22:24:12]: testbed release detected to be: resolute 519s autopkgtest [22:24:13]: updating testbed package index (apt update) 520s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 520s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 520s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 520s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 520s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [81.6 kB] 521s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [1011 kB] 521s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [2820 B] 521s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [22.2 kB] 521s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 Packages [101 kB] 521s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 c-n-f Metadata [3424 B] 521s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/restricted arm64 Packages [7876 B] 521s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/restricted arm64 c-n-f Metadata [304 B] 521s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 Packages [727 kB] 521s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 c-n-f Metadata [18.1 kB] 521s Get:15 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse arm64 Packages [7156 B] 521s Get:16 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse arm64 c-n-f Metadata [332 B] 524s Fetched 2107 kB in 2s (1008 kB/s) 524s Reading package lists... 525s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 525s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 525s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 525s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 526s Reading package lists... 526s Reading package lists... 526s Building dependency tree... 526s Reading state information... 526s Calculating upgrade... 527s The following packages were automatically installed and are no longer required: 527s python3.13 python3.13-minimal 527s Use 'sudo apt autoremove' to remove them. 527s The following NEW packages will be installed: 527s libpython3.14-minimal libpython3.14-stdlib python3.14 python3.14-minimal 527s The following packages will be upgraded: 527s libplymouth5 libpython3-stdlib plymouth plymouth-theme-ubuntu-text python3 527s python3-gdbm python3-minimal 527s 7 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. 527s Need to get 6993 kB of archives. 527s After this operation, 26.0 MB of additional disk space will be used. 527s Get:1 http://ftpmaster.internal/ubuntu resolute/main arm64 libpython3.14-minimal arm64 3.14.2-1 [917 kB] 528s Get:2 http://ftpmaster.internal/ubuntu resolute/main arm64 python3.14-minimal arm64 3.14.2-1 [2548 kB] 528s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 python3-gdbm arm64 3.14.2-1 [11.1 kB] 528s Get:4 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 python3-minimal arm64 3.14.2-1 [28.2 kB] 528s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 python3 arm64 3.14.2-1 [22.9 kB] 528s Get:6 http://ftpmaster.internal/ubuntu resolute/main arm64 libpython3.14-stdlib arm64 3.14.2-1 [2351 kB] 528s Get:7 http://ftpmaster.internal/ubuntu resolute/main arm64 python3.14 arm64 3.14.2-1 [816 kB] 528s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 libpython3-stdlib arm64 3.14.2-1 [10.9 kB] 528s Get:9 http://ftpmaster.internal/ubuntu resolute/main arm64 libplymouth5 arm64 24.004.60+git20250831.4a3c171d-0ubuntu4 [141 kB] 528s Get:10 http://ftpmaster.internal/ubuntu resolute/main arm64 plymouth-theme-ubuntu-text arm64 24.004.60+git20250831.4a3c171d-0ubuntu4 [10.0 kB] 528s Get:11 http://ftpmaster.internal/ubuntu resolute/main arm64 plymouth arm64 24.004.60+git20250831.4a3c171d-0ubuntu4 [138 kB] 529s dpkg-preconfigure: unable to re-open stdin: No such file or directory 529s Fetched 6993 kB in 1s (5065 kB/s) 529s Selecting previously unselected package libpython3.14-minimal:arm64. 529s (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 ... 135223 files and directories currently installed.) 529s Preparing to unpack .../libpython3.14-minimal_3.14.2-1_arm64.deb ... 529s Unpacking libpython3.14-minimal:arm64 (3.14.2-1) ... 529s Selecting previously unselected package python3.14-minimal. 529s Preparing to unpack .../python3.14-minimal_3.14.2-1_arm64.deb ... 529s Unpacking python3.14-minimal (3.14.2-1) ... 529s Preparing to unpack .../python3-gdbm_3.14.2-1_arm64.deb ... 529s Unpacking python3-gdbm (3.14.2-1) over (3.13.9-1) ... 529s Setting up libpython3.14-minimal:arm64 (3.14.2-1) ... 529s Setting up python3.14-minimal (3.14.2-1) ... 530s (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 ... 135565 files and directories currently installed.) 530s Preparing to unpack .../python3-minimal_3.14.2-1_arm64.deb ... 531s Unpacking python3-minimal (3.14.2-1) over (3.13.7-1) ... 531s Setting up python3-minimal (3.14.2-1) ... 531s (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 ... 135565 files and directories currently installed.) 531s Preparing to unpack .../0-python3_3.14.2-1_arm64.deb ... 531s running python pre-rtupdate hooks for python3.14... 531s Unpacking python3 (3.14.2-1) over (3.13.7-1) ... 531s Selecting previously unselected package libpython3.14-stdlib:arm64. 531s Preparing to unpack .../1-libpython3.14-stdlib_3.14.2-1_arm64.deb ... 531s Unpacking libpython3.14-stdlib:arm64 (3.14.2-1) ... 531s Selecting previously unselected package python3.14. 531s Preparing to unpack .../2-python3.14_3.14.2-1_arm64.deb ... 531s Unpacking python3.14 (3.14.2-1) ... 531s Preparing to unpack .../3-libpython3-stdlib_3.14.2-1_arm64.deb ... 531s Unpacking libpython3-stdlib:arm64 (3.14.2-1) over (3.13.7-1) ... 531s Preparing to unpack .../4-libplymouth5_24.004.60+git20250831.4a3c171d-0ubuntu4_arm64.deb ... 531s Unpacking libplymouth5:arm64 (24.004.60+git20250831.4a3c171d-0ubuntu4) over (24.004.60+git20250831.4a3c171d-0ubuntu3) ... 531s Preparing to unpack .../5-plymouth-theme-ubuntu-text_24.004.60+git20250831.4a3c171d-0ubuntu4_arm64.deb ... 531s Unpacking plymouth-theme-ubuntu-text (24.004.60+git20250831.4a3c171d-0ubuntu4) over (24.004.60+git20250831.4a3c171d-0ubuntu3) ... 532s Preparing to unpack .../6-plymouth_24.004.60+git20250831.4a3c171d-0ubuntu4_arm64.deb ... 532s Unpacking plymouth (24.004.60+git20250831.4a3c171d-0ubuntu4) over (24.004.60+git20250831.4a3c171d-0ubuntu3) ... 532s Setting up libpython3.14-stdlib:arm64 (3.14.2-1) ... 532s Setting up libplymouth5:arm64 (24.004.60+git20250831.4a3c171d-0ubuntu4) ... 532s Setting up python3.14 (3.14.2-1) ... 533s Setting up libpython3-stdlib:arm64 (3.14.2-1) ... 533s Setting up python3-gdbm (3.14.2-1) ... 533s Setting up plymouth (24.004.60+git20250831.4a3c171d-0ubuntu4) ... 533s update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults 533s update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults 533s Setting up python3 (3.14.2-1) ... 533s running python rtupdate hooks for python3.14... 533s running python post-rtupdate hooks for python3.14... 534s Processing triggers for libc-bin (2.42-2ubuntu4) ... 534s Processing triggers for systemd (259-1ubuntu2) ... 534s Processing triggers for man-db (2.13.1-1) ... 535s Processing triggers for initramfs-tools (0.150ubuntu7) ... 535s update-initramfs: Generating /boot/initrd.img-6.18.0-9-generic 552s System running in EFI mode, skipping. 552s Setting up plymouth-theme-ubuntu-text (24.004.60+git20250831.4a3c171d-0ubuntu4) ... 552s Processing triggers for initramfs-tools (0.150ubuntu7) ... 552s update-initramfs: Generating /boot/initrd.img-6.18.0-9-generic 566s System running in EFI mode, skipping. 566s autopkgtest [22:25:00]: upgrading testbed (apt dist-upgrade and autopurge) 566s Reading package lists... 567s Building dependency tree... 567s Reading state information... 567s Calculating upgrade... 567s The following packages were automatically installed and are no longer required: 567s python3.13 python3.13-minimal 567s Use 'sudo apt autoremove' to remove them. 567s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 567s Reading package lists... 568s Building dependency tree... 568s Reading state information... 568s Solving dependencies... 568s The following packages will be REMOVED: 568s python3.13* python3.13-minimal* 568s 0 upgraded, 0 newly installed, 2 to remove and 0 not upgraded. 568s After this operation, 7766 kB disk space will be freed. 569s (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 ... 135995 files and directories currently installed.) 569s Removing python3.13 (3.13.11-1) ... 569s Removing python3.13-minimal (3.13.11-1) ... 570s Processing triggers for man-db (2.13.1-1) ... 570s Processing triggers for systemd (259-1ubuntu2) ... 570s (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 ... 135968 files and directories currently installed.) 570s Purging configuration files for python3.13-minimal (3.13.11-1) ... 570s autopkgtest [22:25:04]: rebooting testbed after setup commands that affected boot 611s Reading package lists... 611s Building dependency tree... 611s Reading state information... 611s Solving dependencies... 612s The following NEW packages will be installed: 612s autoconf automake autopoint autotools-dev build-essential bwa clustalo cpp 612s cpp-15 cpp-15-aarch64-linux-gnu cpp-aarch64-linux-gnu debhelper debugedit 612s dh-autoreconf dh-python dh-strip-nondeterminism dialign docutils-common dssp 612s dwz emboss emboss-data emboss-lib fasttree flex fontconfig-config 612s fonts-dejavu-core fonts-dejavu-extra fonts-dejavu-mono fonts-font-awesome 612s fonts-lato fonts-lmodern fonts-lyx fonts-urw-base35 g++ g++-15 612s g++-15-aarch64-linux-gnu g++-aarch64-linux-gnu gcc gcc-15 612s gcc-15-aarch64-linux-gnu gcc-aarch64-linux-gnu gettext ghostscript hevea 612s hicolor-icon-theme imagemagick imagemagick-7-common imagemagick-7.q16 612s intltool-debian libamd3 libaom3 libapache-pom-java libarchive-zip-perl 612s libargtable2-0 libarpack2t64 libasan8 libavahi-client3 libavahi-common-data 612s libavahi-common3 libblas3 libcairo2 libcc1-0 libcifpp-data libcifpp9 612s libcolamd3 libcommons-logging-java libcommons-parent-java libcups2t64 612s libde265-0 libdebhelper-perl libdeflate0 libexpat1-dev libfftw3-double3 612s libfile-stripnondeterminism-perl libfontbox-java libfontconfig1 libfontenc1 612s libgcc-15-dev libgd3 libgfortran5 libglpk40 libgomp1 libgraphite2-3 612s libgs-common libgs10 libgs10-common libharfbuzz0b libheif-plugin-aomdec 612s libheif-plugin-libde265 libheif1 libhpdf-2.3.0 libhwasan0 libice6 libidn12 612s libigraph4 libijs-0.35 libimagequant0 libisl23 libitm1 libjbig0 libjbig2dec0 612s libjpeg-turbo8 libjpeg8 libjs-jquery libjson-perl libkpathsea6 liblapack3 612s liblcms2-2 liblerc4 liblqr-1-0 liblsan0 libltdl7 libmagickcore-7.q16-10 612s libmagickwand-7.q16-10 libmbedcrypto16 libmbedtls21 libmbedx509-7 libmpc3 612s libmpfi0 libmysqlclient24 libncbi-vdb3 libnetpbm11t64 libopenjp2-7 612s libpaper-utils libpaper2 libpdfbox-java libpixman-1-0 libplfit0 libpotrace0 612s libpq5 libptexenc1 libpython3-all-dev libpython3-dev libpython3.13-dev 612s libpython3.14 libpython3.14-dev libqhull-r8.0 libraqm0 libraw23t64 612s libsharpyuv0 libsm6 libstdc++-15-dev libsuitesparseconfig7 libsynctex2 612s libtcl8.6 libteckit0 libtexlua53-5 libtiff6 libtk8.6 libtool libtsan2 612s libubsan1 libwebp7 libwebpdemux2 libwebpmux3 libxaw7 libxcb-render0 612s libxcb-shm0 libxft2 libxi6 libxmu6 libxpm4 libxrender1 libxslt1.1 libxss1 612s libxt6t64 libzopfli1 libzzip-0-13t64 lmodern m4 mafft mysql-common 612s ncbi-blast+ ncbi-data ncbi-vdb-data netpbm phylip po-debconf poppler-data 612s prank preview-latex-style probcons python-biopython-doc 612s python-matplotlib-data python3-alabaster python3-all python3-all-dev 612s python3-biopython python3-biopython-sql python3-brotli python3-cairo 612s python3-charset-normalizer python3-contourpy python3-cycler 612s python3-decorator python3-defusedxml python3-dev python3-docutils 612s python3-fonttools python3-freetype python3-igraph python3-imagesize 612s python3-kiwisolver python3-lxml python3-lz4 python3-matplotlib python3-mmtf 612s python3-mpmath python3-msgpack python3-mysqldb python3-networkx 612s python3-numpy python3-numpy-dev python3-numpydoc python3-pil 612s python3-pil.imagetk python3-rdflib python3-reportlab python3-rlpycairo 612s python3-roman-numerals python3-scipy python3-snowballstemmer python3-sphinx 612s python3-sphinx-rtd-theme python3-sphinxcontrib.jquery python3-sympy 612s python3-texttable python3-tk python3-ufolib2 python3-zopfli python3.13 612s python3.13-dev python3.13-minimal python3.13-tk python3.14-dev python3.14-tk 612s sgml-base sphinx-common sphinx-rtd-theme-common t-coffee t1utils tex-common 612s texlive-base texlive-binaries texlive-fonts-recommended texlive-latex-base 612s texlive-latex-extra texlive-latex-recommended texlive-luatex 612s texlive-pictures unicode-data w3c-sgml-lib wise wise-data x11-common 612s xdg-utils xfonts-encodings xfonts-utils xml-core zlib1g-dev 612s 0 upgraded, 261 newly installed, 0 to remove and 0 not upgraded. 612s Need to get 490 MB of archives. 612s After this operation, 2096 MB of additional disk space will be used. 612s Get:1 http://ftpmaster.internal/ubuntu resolute/main arm64 python3.13-minimal arm64 3.13.11-1 [2346 kB] 612s Get:2 http://ftpmaster.internal/ubuntu resolute/main arm64 m4 arm64 1.4.20-2 [213 kB] 612s Get:3 http://ftpmaster.internal/ubuntu resolute/main arm64 flex arm64 2.6.4-8.2build2 [289 kB] 612s Get:4 http://ftpmaster.internal/ubuntu resolute/main arm64 fonts-lato all 2.015-1build1 [2779 kB] 612s Get:5 http://ftpmaster.internal/ubuntu resolute/main arm64 libgomp1 arm64 15.2.0-11ubuntu1 [147 kB] 612s Get:6 http://ftpmaster.internal/ubuntu resolute/main arm64 libfftw3-double3 arm64 3.3.10-2fakesync1build2 [399 kB] 612s Get:7 http://ftpmaster.internal/ubuntu resolute/main arm64 fonts-dejavu-mono all 2.37-8build1 [502 kB] 612s Get:8 http://ftpmaster.internal/ubuntu resolute/main arm64 fonts-dejavu-core all 2.37-8build1 [834 kB] 612s Get:9 http://ftpmaster.internal/ubuntu resolute/main arm64 libfontenc1 arm64 1:1.1.8-1build2 [13.9 kB] 612s Get:10 http://ftpmaster.internal/ubuntu resolute/main arm64 x11-common all 1:7.7+24ubuntu1 [22.4 kB] 612s Get:11 http://ftpmaster.internal/ubuntu resolute/main arm64 xfonts-encodings all 1:1.0.5-0ubuntu3 [576 kB] 612s Get:12 http://ftpmaster.internal/ubuntu resolute/main arm64 xfonts-utils arm64 1:7.7+7build1 [94.8 kB] 613s Get:13 http://ftpmaster.internal/ubuntu resolute/main arm64 fonts-urw-base35 all 20200910-8build1 [10.9 MB] 613s Get:14 http://ftpmaster.internal/ubuntu resolute/main arm64 fontconfig-config arm64 2.15.0-2.4ubuntu1 [38.2 kB] 613s Get:15 http://ftpmaster.internal/ubuntu resolute/main arm64 libfontconfig1 arm64 2.15.0-2.4ubuntu1 [143 kB] 613s Get:16 http://ftpmaster.internal/ubuntu resolute/main arm64 libsharpyuv0 arm64 1.5.0-0.1build1 [16.7 kB] 613s Get:17 http://ftpmaster.internal/ubuntu resolute/main arm64 libaom3 arm64 3.13.1-2 [1773 kB] 613s Get:18 http://ftpmaster.internal/ubuntu resolute/main arm64 libheif-plugin-aomdec arm64 1.21.2-1 [13.9 kB] 613s Get:19 http://ftpmaster.internal/ubuntu resolute/main arm64 libde265-0 arm64 1.0.16-1build1 [148 kB] 613s Get:20 http://ftpmaster.internal/ubuntu resolute/main arm64 libheif-plugin-libde265 arm64 1.21.2-1 [9696 B] 613s Get:21 http://ftpmaster.internal/ubuntu resolute/main arm64 libheif1 arm64 1.21.2-1 [502 kB] 613s Get:22 http://ftpmaster.internal/ubuntu resolute/main arm64 libjbig0 arm64 2.1-6.1ubuntu3 [29.2 kB] 613s Get:23 http://ftpmaster.internal/ubuntu resolute/main arm64 libjpeg-turbo8 arm64 2.1.5-4ubuntu2 [165 kB] 613s Get:24 http://ftpmaster.internal/ubuntu resolute/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 613s Get:25 http://ftpmaster.internal/ubuntu resolute/main arm64 liblcms2-2 arm64 2.17-1 [170 kB] 613s Get:26 http://ftpmaster.internal/ubuntu resolute/universe arm64 liblqr-1-0 arm64 0.4.2-2.2 [27.7 kB] 613s Get:27 http://ftpmaster.internal/ubuntu resolute/main arm64 libltdl7 arm64 2.5.4-9 [43.3 kB] 613s Get:28 http://ftpmaster.internal/ubuntu resolute/main arm64 libopenjp2-7 arm64 2.5.4-1 [180 kB] 613s Get:29 http://ftpmaster.internal/ubuntu resolute/main arm64 libraw23t64 arm64 0.21.4-2 [378 kB] 613s Get:30 http://ftpmaster.internal/ubuntu resolute/main arm64 libdeflate0 arm64 1.23-2 [46.4 kB] 613s Get:31 http://ftpmaster.internal/ubuntu resolute/main arm64 liblerc4 arm64 4.0.0+ds-5ubuntu2 [174 kB] 613s Get:32 http://ftpmaster.internal/ubuntu resolute/main arm64 libwebp7 arm64 1.5.0-0.1build1 [205 kB] 613s Get:33 http://ftpmaster.internal/ubuntu resolute/main arm64 libtiff6 arm64 4.7.0-3ubuntu3 [196 kB] 613s Get:34 http://ftpmaster.internal/ubuntu resolute/main arm64 libwebpdemux2 arm64 1.5.0-0.1build1 [12.5 kB] 613s Get:35 http://ftpmaster.internal/ubuntu resolute/main arm64 libwebpmux3 arm64 1.5.0-0.1build1 [25.2 kB] 613s Get:36 http://ftpmaster.internal/ubuntu resolute/universe arm64 imagemagick-7-common all 8:7.1.2.12+dfsg1-1 [71.8 kB] 613s Get:37 http://ftpmaster.internal/ubuntu resolute/universe arm64 libmagickcore-7.q16-10 arm64 8:7.1.2.12+dfsg1-1 [1856 kB] 613s Get:38 http://ftpmaster.internal/ubuntu resolute/universe arm64 libmagickwand-7.q16-10 arm64 8:7.1.2.12+dfsg1-1 [299 kB] 613s Get:39 http://ftpmaster.internal/ubuntu resolute/main arm64 poppler-data all 0.4.12-1build1 [2000 kB] 613s Get:40 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-numpy-dev arm64 1:2.3.5+ds-3 [366 kB] 613s Get:41 http://ftpmaster.internal/ubuntu resolute/main arm64 libblas3 arm64 3.12.1-7ubuntu1 [181 kB] 613s Get:42 http://ftpmaster.internal/ubuntu resolute/main arm64 libgfortran5 arm64 15.2.0-11ubuntu1 [450 kB] 613s Get:43 http://ftpmaster.internal/ubuntu resolute/main arm64 liblapack3 arm64 3.12.1-7ubuntu1 [2299 kB] 613s Get:44 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-numpy arm64 1:2.3.5+ds-3 [4569 kB] 613s Get:45 http://ftpmaster.internal/ubuntu resolute/main arm64 python3.13 arm64 3.13.11-1 [758 kB] 613s Get:46 http://ftpmaster.internal/ubuntu resolute/main arm64 autoconf all 2.72-3.1ubuntu1 [384 kB] 613s Get:47 http://ftpmaster.internal/ubuntu resolute/main arm64 autotools-dev all 20240727.1 [43.4 kB] 613s Get:48 http://ftpmaster.internal/ubuntu resolute/main arm64 automake all 1:1.18.1-3build1 [582 kB] 613s Get:49 http://ftpmaster.internal/ubuntu resolute/main arm64 autopoint all 0.23.2-1 [620 kB] 613s Get:50 http://ftpmaster.internal/ubuntu resolute/main arm64 libisl23 arm64 0.27-1build1 [676 kB] 613s Get:51 http://ftpmaster.internal/ubuntu resolute/main arm64 libmpc3 arm64 1.3.1-2 [55.6 kB] 613s Get:52 http://ftpmaster.internal/ubuntu resolute/main arm64 cpp-15-aarch64-linux-gnu arm64 15.2.0-11ubuntu1 [11.7 MB] 613s Get:53 http://ftpmaster.internal/ubuntu resolute/main arm64 cpp-15 arm64 15.2.0-11ubuntu1 [1030 B] 613s Get:54 http://ftpmaster.internal/ubuntu resolute/main arm64 cpp-aarch64-linux-gnu arm64 4:15.2.0-4ubuntu1 [5736 B] 613s Get:55 http://ftpmaster.internal/ubuntu resolute/main arm64 cpp arm64 4:15.2.0-4ubuntu1 [22.4 kB] 613s Get:56 http://ftpmaster.internal/ubuntu resolute/main arm64 libcc1-0 arm64 15.2.0-11ubuntu1 [49.0 kB] 613s Get:57 http://ftpmaster.internal/ubuntu resolute/main arm64 libitm1 arm64 15.2.0-11ubuntu1 [28.0 kB] 613s Get:58 http://ftpmaster.internal/ubuntu resolute/main arm64 libasan8 arm64 15.2.0-11ubuntu1 [2920 kB] 613s Get:59 http://ftpmaster.internal/ubuntu resolute/main arm64 liblsan0 arm64 15.2.0-11ubuntu1 [1316 kB] 614s Get:60 http://ftpmaster.internal/ubuntu resolute/main arm64 libtsan2 arm64 15.2.0-11ubuntu1 [2690 kB] 614s Get:61 http://ftpmaster.internal/ubuntu resolute/main arm64 libubsan1 arm64 15.2.0-11ubuntu1 [1176 kB] 614s Get:62 http://ftpmaster.internal/ubuntu resolute/main arm64 libhwasan0 arm64 15.2.0-11ubuntu1 [1638 kB] 614s Get:63 http://ftpmaster.internal/ubuntu resolute/main arm64 libgcc-15-dev arm64 15.2.0-11ubuntu1 [2600 kB] 614s Get:64 http://ftpmaster.internal/ubuntu resolute/main arm64 gcc-15-aarch64-linux-gnu arm64 15.2.0-11ubuntu1 [23.1 MB] 614s Get:65 http://ftpmaster.internal/ubuntu resolute/main arm64 gcc-15 arm64 15.2.0-11ubuntu1 [517 kB] 614s Get:66 http://ftpmaster.internal/ubuntu resolute/main arm64 gcc-aarch64-linux-gnu arm64 4:15.2.0-4ubuntu1 [1206 B] 614s Get:67 http://ftpmaster.internal/ubuntu resolute/main arm64 gcc arm64 4:15.2.0-4ubuntu1 [5016 B] 614s Get:68 http://ftpmaster.internal/ubuntu resolute/main arm64 libstdc++-15-dev arm64 15.2.0-11ubuntu1 [2547 kB] 614s Get:69 http://ftpmaster.internal/ubuntu resolute/main arm64 g++-15-aarch64-linux-gnu arm64 15.2.0-11ubuntu1 [13.2 MB] 614s Get:70 http://ftpmaster.internal/ubuntu resolute/main arm64 g++-15 arm64 15.2.0-11ubuntu1 [24.6 kB] 614s Get:71 http://ftpmaster.internal/ubuntu resolute/main arm64 g++-aarch64-linux-gnu arm64 4:15.2.0-4ubuntu1 [956 B] 614s Get:72 http://ftpmaster.internal/ubuntu resolute/main arm64 g++ arm64 4:15.2.0-4ubuntu1 [1080 B] 614s Get:73 http://ftpmaster.internal/ubuntu resolute/main arm64 build-essential arm64 12.12ubuntu2 [5254 B] 614s Get:74 http://ftpmaster.internal/ubuntu resolute/universe arm64 bwa arm64 0.7.19-1 [202 kB] 615s Get:75 http://ftpmaster.internal/ubuntu resolute/universe arm64 libargtable2-0 arm64 13-4 [15.1 kB] 615s Get:76 http://ftpmaster.internal/ubuntu resolute/universe arm64 clustalo arm64 1.2.4-8build2 [189 kB] 615s Get:77 http://ftpmaster.internal/ubuntu resolute/main arm64 libdebhelper-perl all 13.28ubuntu1 [97.4 kB] 615s Get:78 http://ftpmaster.internal/ubuntu resolute/main arm64 libtool all 2.5.4-9 [169 kB] 615s Get:79 http://ftpmaster.internal/ubuntu resolute/main arm64 dh-autoreconf all 21 [12.5 kB] 615s Get:80 http://ftpmaster.internal/ubuntu resolute/main arm64 libarchive-zip-perl all 1.68-1 [90.2 kB] 615s Get:81 http://ftpmaster.internal/ubuntu resolute/main arm64 libfile-stripnondeterminism-perl all 1.15.0-1build1 [20.6 kB] 615s Get:82 http://ftpmaster.internal/ubuntu resolute/main arm64 dh-strip-nondeterminism all 1.15.0-1build1 [5110 B] 615s Get:83 http://ftpmaster.internal/ubuntu resolute/main arm64 debugedit arm64 1:5.2-3 [49.1 kB] 615s Get:84 http://ftpmaster.internal/ubuntu resolute/main arm64 dwz arm64 0.16-2 [113 kB] 615s Get:85 http://ftpmaster.internal/ubuntu resolute/main arm64 gettext arm64 0.23.2-1 [998 kB] 615s Get:86 http://ftpmaster.internal/ubuntu resolute/main arm64 intltool-debian all 0.35.0+20060710.6build1 [24.1 kB] 615s Get:87 http://ftpmaster.internal/ubuntu resolute/main arm64 po-debconf all 1.0.22 [215 kB] 615s Get:88 http://ftpmaster.internal/ubuntu resolute/main arm64 debhelper all 13.28ubuntu1 [916 kB] 615s Get:89 http://ftpmaster.internal/ubuntu resolute/universe arm64 dh-python all 7.20251231 [122 kB] 615s Get:90 http://ftpmaster.internal/ubuntu resolute/universe arm64 dialign arm64 2.2.1-13build1 [152 kB] 615s Get:91 http://ftpmaster.internal/ubuntu resolute/main arm64 sgml-base all 1.31+nmu1 [11.0 kB] 615s Get:92 http://ftpmaster.internal/ubuntu resolute/main arm64 xml-core all 0.19build1 [20.3 kB] 615s Get:93 http://ftpmaster.internal/ubuntu resolute/main arm64 docutils-common all 0.22.4+dfsg-1 [130 kB] 615s Get:94 http://ftpmaster.internal/ubuntu resolute/universe arm64 libcifpp-data all 9.0.5-2 [483 kB] 615s Get:95 http://ftpmaster.internal/ubuntu resolute/universe arm64 libcifpp9 arm64 9.0.5-2 [958 kB] 615s Get:96 http://ftpmaster.internal/ubuntu resolute/universe arm64 dssp arm64 4.5.7-1 [622 kB] 615s Get:97 http://ftpmaster.internal/ubuntu resolute/main arm64 libimagequant0 arm64 2.18.0-1build1 [37.1 kB] 615s Get:98 http://ftpmaster.internal/ubuntu resolute/main arm64 libxpm4 arm64 1:3.5.17-1build3 [35.5 kB] 615s Get:99 http://ftpmaster.internal/ubuntu resolute/main arm64 libgd3 arm64 2.3.3-13ubuntu1 [124 kB] 615s Get:100 http://ftpmaster.internal/ubuntu resolute/universe arm64 libhpdf-2.3.0 arm64 2.3.0+dfsg-1build4 [435 kB] 615s Get:101 http://ftpmaster.internal/ubuntu resolute/main arm64 mysql-common all 5.8+1.1.1ubuntu2 [7002 B] 615s Get:102 http://ftpmaster.internal/ubuntu resolute/main arm64 libmysqlclient24 arm64 8.4.7-0ubuntu3 [1244 kB] 615s Get:103 http://ftpmaster.internal/ubuntu resolute/main arm64 libpq5 arm64 18.1-2 [151 kB] 615s Get:104 http://ftpmaster.internal/ubuntu resolute/universe arm64 emboss-lib arm64 6.6.0+dfsg-15ubuntu3 [2866 kB] 615s Get:105 http://ftpmaster.internal/ubuntu resolute/universe arm64 emboss-data all 6.6.0+dfsg-15ubuntu3 [61.0 MB] 618s Get:106 http://ftpmaster.internal/ubuntu resolute/universe arm64 emboss arm64 6.6.0+dfsg-15ubuntu3 [932 kB] 618s Get:107 http://ftpmaster.internal/ubuntu resolute/main arm64 fonts-dejavu-extra all 2.37-8build1 [1944 kB] 618s Get:108 http://ftpmaster.internal/ubuntu resolute/main arm64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1build1 [531 kB] 618s Get:109 http://ftpmaster.internal/ubuntu resolute/universe arm64 fonts-lmodern all 2.005-1build1 [4788 kB] 620s Get:110 http://ftpmaster.internal/ubuntu resolute/universe arm64 fonts-lyx all 2.5.0~RC2-3 [171 kB] 620s Get:111 http://ftpmaster.internal/ubuntu resolute/main arm64 libgs-common all 10.05.0dfsg1-0ubuntu4 [176 kB] 620s Get:112 http://ftpmaster.internal/ubuntu resolute/main arm64 libgs10-common all 10.05.0dfsg1-0ubuntu4 [490 kB] 620s Get:113 http://ftpmaster.internal/ubuntu resolute/main arm64 libavahi-common-data arm64 0.8-17ubuntu1 [31.3 kB] 620s Get:114 http://ftpmaster.internal/ubuntu resolute/main arm64 libavahi-common3 arm64 0.8-17ubuntu1 [22.6 kB] 620s Get:115 http://ftpmaster.internal/ubuntu resolute/main arm64 libavahi-client3 arm64 0.8-17ubuntu1 [26.7 kB] 620s Get:116 http://ftpmaster.internal/ubuntu resolute/main arm64 libcups2t64 arm64 2.4.16-1ubuntu1 [271 kB] 620s Get:117 http://ftpmaster.internal/ubuntu resolute/main arm64 libidn12 arm64 1.43-2 [59.6 kB] 620s Get:118 http://ftpmaster.internal/ubuntu resolute/main arm64 libijs-0.35 arm64 0.35-16 [15.3 kB] 620s Get:119 http://ftpmaster.internal/ubuntu resolute/main arm64 libjbig2dec0 arm64 0.20-1build4 [63.4 kB] 620s Get:120 http://ftpmaster.internal/ubuntu resolute/main arm64 libpaper2 arm64 2.2.5-0.3build1 [17.3 kB] 620s Get:121 http://ftpmaster.internal/ubuntu resolute/main arm64 libice6 arm64 2:1.1.1-1build1 [43.0 kB] 620s Get:122 http://ftpmaster.internal/ubuntu resolute/main arm64 libsm6 arm64 2:1.2.6-1 [16.6 kB] 620s Get:123 http://ftpmaster.internal/ubuntu resolute/main arm64 libxt6t64 arm64 1:1.2.1-1.3 [168 kB] 620s Get:124 http://ftpmaster.internal/ubuntu resolute/main arm64 libgs10 arm64 10.05.0dfsg1-0ubuntu4 [3609 kB] 621s Get:125 http://ftpmaster.internal/ubuntu resolute/main arm64 ghostscript arm64 10.05.0dfsg1-0ubuntu4 [43.0 kB] 621s Get:126 http://ftpmaster.internal/ubuntu resolute/universe arm64 libnetpbm11t64 arm64 2:11.10.02-1build1 [115 kB] 621s Get:127 http://ftpmaster.internal/ubuntu resolute/universe arm64 netpbm arm64 2:11.10.02-1build1 [2146 kB] 621s Get:128 http://ftpmaster.internal/ubuntu resolute/universe arm64 tex-common all 6.20 [30.0 kB] 621s Get:129 http://ftpmaster.internal/ubuntu resolute/main arm64 libpaper-utils arm64 2.2.5-0.3build1 [15.4 kB] 621s Get:130 http://ftpmaster.internal/ubuntu resolute/universe arm64 libkpathsea6 arm64 2025.20250727.75242+ds-5build1 [65.4 kB] 621s Get:131 http://ftpmaster.internal/ubuntu resolute/universe arm64 libptexenc1 arm64 2025.20250727.75242+ds-5build1 [46.2 kB] 621s Get:132 http://ftpmaster.internal/ubuntu resolute/universe arm64 libsynctex2 arm64 2025.20250727.75242+ds-5build1 [61.4 kB] 621s Get:133 http://ftpmaster.internal/ubuntu resolute/universe arm64 libtexlua53-5 arm64 2025.20250727.75242+ds-5build1 [122 kB] 621s Get:134 http://ftpmaster.internal/ubuntu resolute/main arm64 t1utils arm64 1.41-4build4 [59.8 kB] 621s Get:135 http://ftpmaster.internal/ubuntu resolute/main arm64 libpixman-1-0 arm64 0.46.4-1 [204 kB] 621s Get:136 http://ftpmaster.internal/ubuntu resolute/main arm64 libxcb-render0 arm64 1.17.0-2build1 [18.1 kB] 621s Get:137 http://ftpmaster.internal/ubuntu resolute/main arm64 libxcb-shm0 arm64 1.17.0-2build1 [6234 B] 621s Get:138 http://ftpmaster.internal/ubuntu resolute/main arm64 libxrender1 arm64 1:0.9.12-1 [19.5 kB] 621s Get:139 http://ftpmaster.internal/ubuntu resolute/main arm64 libcairo2 arm64 1.18.4-3 [556 kB] 621s Get:140 http://ftpmaster.internal/ubuntu resolute/main arm64 libgraphite2-3 arm64 1.3.14-11ubuntu1 [72.1 kB] 621s Get:141 http://ftpmaster.internal/ubuntu resolute/main arm64 libharfbuzz0b arm64 12.3.0-4 [518 kB] 621s Get:142 http://ftpmaster.internal/ubuntu resolute/universe arm64 libmpfi0 arm64 1.5.4+ds-4 [35.3 kB] 621s Get:143 http://ftpmaster.internal/ubuntu resolute/universe arm64 libpotrace0 arm64 1.16-2build2 [16.3 kB] 621s Get:144 http://ftpmaster.internal/ubuntu resolute/universe arm64 libteckit0 arm64 2.5.13+ds-1 [393 kB] 621s Get:145 http://ftpmaster.internal/ubuntu resolute/main arm64 libxmu6 arm64 2:1.1.3-4 [47.6 kB] 621s Get:146 http://ftpmaster.internal/ubuntu resolute/main arm64 libxaw7 arm64 2:1.0.16-1build1 [183 kB] 621s Get:147 http://ftpmaster.internal/ubuntu resolute/main arm64 libxi6 arm64 2:1.8.2-2 [32.4 kB] 621s Get:148 http://ftpmaster.internal/ubuntu resolute/universe arm64 libzzip-0-13t64 arm64 0.13.78+dfsg.1-0.2 [30.7 kB] 621s Get:149 http://ftpmaster.internal/ubuntu resolute/universe arm64 texlive-binaries arm64 2025.20250727.75242+ds-5build1 [8302 kB] 622s Get:150 http://ftpmaster.internal/ubuntu resolute/main arm64 xdg-utils all 1.2.1-2ubuntu2 [66.1 kB] 622s Get:151 http://ftpmaster.internal/ubuntu resolute/universe arm64 texlive-base all 2025.20251127-1 [22.8 MB] 622s Get:152 http://ftpmaster.internal/ubuntu resolute/main arm64 hicolor-icon-theme all 0.18-2build1 [13.2 kB] 622s Get:153 http://ftpmaster.internal/ubuntu resolute/universe arm64 imagemagick-7.q16 arm64 8:7.1.2.12+dfsg1-1 [704 kB] 622s Get:154 http://ftpmaster.internal/ubuntu resolute/universe arm64 imagemagick arm64 8:7.1.2.12+dfsg1-1 [14.1 kB] 622s Get:155 http://ftpmaster.internal/ubuntu resolute/universe arm64 hevea arm64 2.36-2build3 [2636 kB] 622s Get:156 http://ftpmaster.internal/ubuntu resolute/main arm64 libsuitesparseconfig7 arm64 1:7.12.1+dfsg-1 [22.0 kB] 622s Get:157 http://ftpmaster.internal/ubuntu resolute/universe arm64 libamd3 arm64 1:7.12.1+dfsg-1 [34.6 kB] 622s Get:158 http://ftpmaster.internal/ubuntu resolute/universe arm64 libapache-pom-java all 33-2build1 [5976 B] 622s Get:159 http://ftpmaster.internal/ubuntu resolute/universe arm64 libarpack2t64 arm64 3.9.1-6 [94.9 kB] 622s Get:160 http://ftpmaster.internal/ubuntu resolute/main arm64 libcolamd3 arm64 1:7.12.1+dfsg-1 [27.1 kB] 622s Get:161 http://ftpmaster.internal/ubuntu resolute/universe arm64 libcommons-parent-java all 56-1build1 [11.1 kB] 622s Get:162 http://ftpmaster.internal/ubuntu resolute/universe arm64 libcommons-logging-java all 1.3.0-1ubuntu1 [63.8 kB] 622s Get:163 http://ftpmaster.internal/ubuntu resolute/main arm64 libexpat1-dev arm64 2.7.3-1 [131 kB] 622s Get:164 http://ftpmaster.internal/ubuntu resolute/universe arm64 libglpk40 arm64 5.0-2 [347 kB] 622s Get:165 http://ftpmaster.internal/ubuntu resolute/universe arm64 libplfit0 arm64 0.9.6+ds-2ubuntu1 [35.7 kB] 623s Get:166 http://ftpmaster.internal/ubuntu resolute/universe arm64 libigraph4 arm64 1.0.1+ds-3 [1209 kB] 623s Get:167 http://ftpmaster.internal/ubuntu resolute/main arm64 libjs-jquery all 3.7.1+dfsg+~3.5.33-1build1 [321 kB] 623s Get:168 http://ftpmaster.internal/ubuntu resolute/main arm64 libjson-perl all 4.10000-1 [81.9 kB] 623s Get:169 http://ftpmaster.internal/ubuntu resolute/universe arm64 libmbedcrypto16 arm64 3.6.5-0.1ubuntu2 [256 kB] 623s Get:170 http://ftpmaster.internal/ubuntu resolute/universe arm64 libmbedx509-7 arm64 3.6.5-0.1ubuntu2 [35.3 kB] 623s Get:171 http://ftpmaster.internal/ubuntu resolute/universe arm64 libmbedtls21 arm64 3.6.5-0.1ubuntu2 [126 kB] 623s Get:172 http://ftpmaster.internal/ubuntu resolute/universe arm64 ncbi-vdb-data all 3.2.1+dfsg-2 [81.3 kB] 623s Get:173 http://ftpmaster.internal/ubuntu resolute/universe arm64 libncbi-vdb3 arm64 3.2.1+dfsg-2 [1259 kB] 623s Get:174 http://ftpmaster.internal/ubuntu resolute/main arm64 libpython3.14 arm64 3.14.2-1 [2593 kB] 623s Get:175 http://ftpmaster.internal/ubuntu resolute/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1ubuntu2 [899 kB] 623s Get:176 http://ftpmaster.internal/ubuntu resolute/main arm64 libpython3.14-dev arm64 3.14.2-1 [5984 kB] 623s Get:177 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 libpython3-dev arm64 3.14.2-1 [11.2 kB] 623s Get:178 http://ftpmaster.internal/ubuntu resolute/main arm64 libpython3.13-dev arm64 3.13.11-1 [5810 kB] 623s Get:179 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 libpython3-all-dev arm64 3.14.2-1 [916 B] 623s Get:180 http://ftpmaster.internal/ubuntu resolute/universe arm64 libqhull-r8.0 arm64 2020.2-8 [191 kB] 623s Get:181 http://ftpmaster.internal/ubuntu resolute/main arm64 libraqm0 arm64 0.10.3-1 [15.0 kB] 623s Get:182 http://ftpmaster.internal/ubuntu resolute/main arm64 libtcl8.6 arm64 8.6.17+dfsg-1 [1024 kB] 623s Get:183 http://ftpmaster.internal/ubuntu resolute/main arm64 libxft2 arm64 2.3.6-1build2 [43.2 kB] 623s Get:184 http://ftpmaster.internal/ubuntu resolute/main arm64 libxss1 arm64 1:1.2.3-1build4 [7102 B] 623s Get:185 http://ftpmaster.internal/ubuntu resolute/main arm64 libtk8.6 arm64 8.6.17-1 [811 kB] 623s Get:186 http://ftpmaster.internal/ubuntu resolute/main arm64 libxslt1.1 arm64 1.1.43-0.3 [172 kB] 623s Get:187 http://ftpmaster.internal/ubuntu resolute/universe arm64 libzopfli1 arm64 1.0.3-3 [108 kB] 624s Get:188 http://ftpmaster.internal/ubuntu resolute/universe arm64 lmodern all 2.005-1build1 [9538 kB] 624s Get:189 http://ftpmaster.internal/ubuntu resolute/universe arm64 mafft arm64 7.525-1 [826 kB] 624s Get:190 http://ftpmaster.internal/ubuntu resolute/universe arm64 ncbi-data all 6.1.20170106+dfsg2-7 [3969 kB] 624s Get:191 http://ftpmaster.internal/ubuntu resolute/universe arm64 ncbi-blast+ arm64 2.16.0+ds-7 [15.4 MB] 624s Get:192 http://ftpmaster.internal/ubuntu resolute/universe arm64 phylip arm64 1:3.697+dfsg-4build2 [863 kB] 625s Get:193 http://ftpmaster.internal/ubuntu resolute/universe arm64 prank arm64 250331-1 [310 kB] 625s Get:194 http://ftpmaster.internal/ubuntu resolute/universe arm64 preview-latex-style all 13.2-1.1 [347 kB] 625s Get:195 http://ftpmaster.internal/ubuntu resolute/universe arm64 probcons arm64 1.12-15 [139 kB] 625s Get:196 http://ftpmaster.internal/ubuntu resolute/universe arm64 python-biopython-doc all 1.86+dfsg-1 [18.1 MB] 625s Get:197 http://ftpmaster.internal/ubuntu resolute/universe arm64 python-matplotlib-data all 3.10.7+dfsg1-1 [2930 kB] 625s Get:198 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 python3-all arm64 3.14.2-1 [888 B] 625s Get:199 http://ftpmaster.internal/ubuntu resolute/main arm64 python3.14-dev arm64 3.14.2-1 [510 kB] 625s Get:200 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 python3-dev arm64 3.14.2-1 [26.6 kB] 625s Get:201 http://ftpmaster.internal/ubuntu resolute/main arm64 python3.13-dev arm64 3.13.11-1 [508 kB] 625s Get:202 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 python3-all-dev arm64 3.14.2-1 [912 B] 625s Get:203 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-charset-normalizer arm64 3.4.4-2 [169 kB] 625s Get:204 http://ftpmaster.internal/ubuntu resolute/main arm64 python3.13-tk arm64 3.13.11-1 [106 kB] 625s Get:205 http://ftpmaster.internal/ubuntu resolute/main arm64 python3.14-tk arm64 3.14.2-1 [108 kB] 625s Get:206 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 python3-tk arm64 3.14.2-1 [11.2 kB] 625s Get:207 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-pil.imagetk arm64 12.0.0-1ubuntu1 [9532 B] 625s Get:208 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-pil arm64 12.0.0-1ubuntu1 [486 kB] 625s Get:209 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-cairo arm64 1.27.0-2build1 [141 kB] 625s Get:210 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-freetype all 2.5.1-2 [92.2 kB] 625s Get:211 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-rlpycairo all 0.3.0-4 [9332 B] 625s Get:212 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-reportlab all 4.4.9-1 [1149 kB] 625s Get:213 http://ftpmaster.internal/ubuntu resolute/universe arm64 w3c-sgml-lib all 1.3-3build1 [278 kB] 625s Get:214 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-biopython arm64 1.86+dfsg-1 [1675 kB] 625s Get:215 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-biopython-sql all 1.86+dfsg-1 [26.4 kB] 625s Get:216 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-brotli arm64 1.1.0-2build6 [343 kB] 625s Get:217 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-contourpy arm64 1.3.3-1 [245 kB] 625s Get:218 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-cycler all 0.12.1-2 [9850 B] 625s Get:219 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-decorator all 5.2.1-2 [28.1 kB] 625s Get:220 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-defusedxml all 0.7.1-3build1 [42.4 kB] 625s Get:221 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-roman-numerals all 4.1.0-1 [8660 B] 625s Get:222 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-docutils all 0.22.4+dfsg-1 [439 kB] 625s Get:223 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-lxml arm64 6.0.2-1 [2155 kB] 625s Get:224 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-lz4 arm64 4.4.5+dfsg-1 [27.9 kB] 626s Get:225 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-scipy arm64 1.16.3-3 [17.4 MB] 626s Get:226 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-mpmath all 1.3.0-2 [423 kB] 626s Get:227 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-sympy all 1.14.0-2 [4306 kB] 626s Get:228 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-ufolib2 all 0.18.1+dfsg1-1 [33.7 kB] 626s Get:229 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-zopfli arm64 0.4.0-1 [10.8 kB] 626s Get:230 http://ftpmaster.internal/ubuntu resolute/universe arm64 unicode-data all 16.0.0-1build1 [9543 kB] 626s Get:231 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-fonttools arm64 4.61.1-3 [1680 kB] 626s Get:232 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-imagesize all 1.4.1-1build1 [6900 B] 626s Get:233 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-kiwisolver arm64 1.4.10~rc0-1 [60.1 kB] 626s Get:234 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-matplotlib arm64 3.10.7+dfsg1-1 [17.1 MB] 626s Get:235 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-msgpack arm64 1.1.2-1 [102 kB] 626s Get:236 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-mmtf all 1.1.3-1build1 [16.4 kB] 626s Get:237 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-mysqldb arm64 1.4.6-2build7 [52.8 kB] 627s Get:238 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-networkx all 3.2.1-4ubuntu2 [11.8 MB] 627s Get:239 http://ftpmaster.internal/ubuntu resolute/main arm64 sphinx-common all 8.2.3-12 [657 kB] 627s Get:240 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-alabaster all 0.7.16-0.1build1 [18.6 kB] 627s Get:241 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-snowballstemmer all 3.0.1-1 [65.9 kB] 627s Get:242 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-sphinx all 8.2.3-12 [483 kB] 627s Get:243 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-numpydoc all 1.9.0-1 [53.2 kB] 627s Get:244 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-rdflib all 7.1.1-3 [427 kB] 627s Get:245 http://ftpmaster.internal/ubuntu resolute/main arm64 sphinx-rtd-theme-common all 3.0.2+dfsg-3 [1013 kB] 627s Get:246 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-sphinxcontrib.jquery all 4.1-6 [6856 B] 627s Get:247 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-sphinx-rtd-theme all 3.0.2+dfsg-3 [23.5 kB] 627s Get:248 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-texttable all 1.7.0-1 [11.2 kB] 627s Get:249 http://ftpmaster.internal/ubuntu resolute/universe arm64 t-coffee arm64 13.45.0.4846264+really13.41.0.28bdc39+dfsg-1build1 [908 kB] 627s Get:250 http://ftpmaster.internal/ubuntu resolute/universe arm64 texlive-fonts-recommended all 2025.20251127-1 [4972 kB] 627s Get:251 http://ftpmaster.internal/ubuntu resolute/universe arm64 texlive-luatex all 2025.20251127-1 [36.0 MB] 627s Get:252 http://ftpmaster.internal/ubuntu resolute/universe arm64 texlive-latex-base all 2025.20251127-1 [1309 kB] 627s Get:253 http://ftpmaster.internal/ubuntu resolute/universe arm64 libfontbox-java all 1:1.8.16-5 [208 kB] 627s Get:254 http://ftpmaster.internal/ubuntu resolute/universe arm64 libpdfbox-java all 1:1.8.16-5 [5521 kB] 628s Get:255 http://ftpmaster.internal/ubuntu resolute/universe arm64 texlive-latex-recommended all 2025.20251127-1 [8494 kB] 628s Get:256 http://ftpmaster.internal/ubuntu resolute/universe arm64 texlive-pictures all 2025.20251127-1 [23.5 MB] 628s Get:257 http://ftpmaster.internal/ubuntu resolute/universe arm64 texlive-latex-extra all 2025.20251127-2 [32.5 MB] 629s Get:258 http://ftpmaster.internal/ubuntu resolute/universe arm64 wise-data all 2.4.1-27 [83.2 kB] 629s Get:259 http://ftpmaster.internal/ubuntu resolute/universe arm64 wise arm64 2.4.1-27 [791 kB] 629s Get:260 http://ftpmaster.internal/ubuntu resolute/universe arm64 fasttree arm64 2.1.11-2build1 [182 kB] 629s Get:261 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-igraph arm64 1.0.0+ds-1 [347 kB] 629s Preconfiguring packages ... 629s Fetched 490 MB in 17s (29.1 MB/s) 630s Selecting previously unselected package python3.13-minimal. 630s (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 ... 135970 files and directories currently installed.) 630s Preparing to unpack .../000-python3.13-minimal_3.13.11-1_arm64.deb ... 630s Unpacking python3.13-minimal (3.13.11-1) ... 630s Selecting previously unselected package m4. 630s Preparing to unpack .../001-m4_1.4.20-2_arm64.deb ... 630s Unpacking m4 (1.4.20-2) ... 630s Selecting previously unselected package flex. 630s Preparing to unpack .../002-flex_2.6.4-8.2build2_arm64.deb ... 630s Unpacking flex 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Selecting previously unselected package libfontenc1:arm64. 630s Preparing to unpack .../008-libfontenc1_1%3a1.1.8-1build2_arm64.deb ... 630s Unpacking libfontenc1:arm64 (1:1.1.8-1build2) ... 630s Selecting previously unselected package x11-common. 630s Preparing to unpack .../009-x11-common_1%3a7.7+24ubuntu1_all.deb ... 630s Unpacking x11-common (1:7.7+24ubuntu1) ... 630s Selecting previously unselected package xfonts-encodings. 630s Preparing to unpack .../010-xfonts-encodings_1%3a1.0.5-0ubuntu3_all.deb ... 630s Unpacking xfonts-encodings (1:1.0.5-0ubuntu3) ... 630s Selecting previously unselected package xfonts-utils. 631s Preparing to unpack .../011-xfonts-utils_1%3a7.7+7build1_arm64.deb ... 631s Unpacking xfonts-utils (1:7.7+7build1) ... 631s Selecting previously unselected package fonts-urw-base35. 631s Preparing to unpack .../012-fonts-urw-base35_20200910-8build1_all.deb ... 631s Unpacking fonts-urw-base35 (20200910-8build1) ... 631s Selecting previously unselected package fontconfig-config. 631s Preparing to unpack .../013-fontconfig-config_2.15.0-2.4ubuntu1_arm64.deb ... 631s Unpacking fontconfig-config (2.15.0-2.4ubuntu1) ... 631s Selecting previously unselected package libfontconfig1:arm64. 631s Preparing to unpack .../014-libfontconfig1_2.15.0-2.4ubuntu1_arm64.deb ... 631s Unpacking libfontconfig1:arm64 (2.15.0-2.4ubuntu1) ... 631s Selecting previously unselected package libsharpyuv0:arm64. 631s Preparing to unpack .../015-libsharpyuv0_1.5.0-0.1build1_arm64.deb ... 631s Unpacking libsharpyuv0:arm64 (1.5.0-0.1build1) ... 631s Selecting previously unselected package libaom3:arm64. 631s Preparing to unpack .../016-libaom3_3.13.1-2_arm64.deb ... 631s Unpacking libaom3:arm64 (3.13.1-2) ... 631s Selecting previously unselected package libheif-plugin-aomdec:arm64. 631s Preparing to unpack .../017-libheif-plugin-aomdec_1.21.2-1_arm64.deb ... 631s Unpacking libheif-plugin-aomdec:arm64 (1.21.2-1) ... 631s Selecting previously unselected package libde265-0:arm64. 631s Preparing to unpack .../018-libde265-0_1.0.16-1build1_arm64.deb ... 631s Unpacking libde265-0:arm64 (1.0.16-1build1) ... 631s Selecting previously unselected package libheif-plugin-libde265:arm64. 631s Preparing to unpack .../019-libheif-plugin-libde265_1.21.2-1_arm64.deb ... 631s Unpacking libheif-plugin-libde265:arm64 (1.21.2-1) ... 631s Selecting previously unselected package libheif1:arm64. 631s Preparing to unpack .../020-libheif1_1.21.2-1_arm64.deb ... 631s Unpacking libheif1:arm64 (1.21.2-1) ... 631s Selecting previously unselected package libjbig0:arm64. 632s Preparing to unpack .../021-libjbig0_2.1-6.1ubuntu3_arm64.deb ... 632s Unpacking libjbig0:arm64 (2.1-6.1ubuntu3) ... 632s Selecting previously unselected package libjpeg-turbo8:arm64. 632s Preparing to unpack .../022-libjpeg-turbo8_2.1.5-4ubuntu2_arm64.deb ... 632s Unpacking libjpeg-turbo8:arm64 (2.1.5-4ubuntu2) ... 632s Selecting previously unselected package libjpeg8:arm64. 632s Preparing to unpack .../023-libjpeg8_8c-2ubuntu11_arm64.deb ... 632s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 632s Selecting previously unselected package liblcms2-2:arm64. 632s Preparing to unpack .../024-liblcms2-2_2.17-1_arm64.deb ... 632s Unpacking liblcms2-2:arm64 (2.17-1) ... 632s Selecting previously unselected package liblqr-1-0:arm64. 632s Preparing to unpack .../025-liblqr-1-0_0.4.2-2.2_arm64.deb ... 632s Unpacking liblqr-1-0:arm64 (0.4.2-2.2) ... 632s Selecting previously unselected package libltdl7:arm64. 632s Preparing to unpack .../026-libltdl7_2.5.4-9_arm64.deb ... 632s Unpacking libltdl7:arm64 (2.5.4-9) ... 632s Selecting previously unselected package libopenjp2-7:arm64. 632s Preparing to unpack .../027-libopenjp2-7_2.5.4-1_arm64.deb ... 632s Unpacking libopenjp2-7:arm64 (2.5.4-1) ... 632s Selecting previously unselected package libraw23t64:arm64. 632s Preparing to unpack .../028-libraw23t64_0.21.4-2_arm64.deb ... 632s Unpacking libraw23t64:arm64 (0.21.4-2) ... 632s Selecting previously unselected package libdeflate0:arm64. 632s Preparing to unpack .../029-libdeflate0_1.23-2_arm64.deb ... 632s Unpacking libdeflate0:arm64 (1.23-2) ... 632s Selecting previously unselected package liblerc4:arm64. 632s Preparing to unpack .../030-liblerc4_4.0.0+ds-5ubuntu2_arm64.deb ... 632s Unpacking liblerc4:arm64 (4.0.0+ds-5ubuntu2) ... 632s Selecting previously unselected package libwebp7:arm64. 632s Preparing to unpack .../031-libwebp7_1.5.0-0.1build1_arm64.deb ... 632s Unpacking libwebp7:arm64 (1.5.0-0.1build1) ... 632s Selecting previously unselected package libtiff6:arm64. 632s Preparing to unpack .../032-libtiff6_4.7.0-3ubuntu3_arm64.deb ... 632s Unpacking libtiff6:arm64 (4.7.0-3ubuntu3) ... 632s Selecting previously unselected package libwebpdemux2:arm64. 632s Preparing to unpack .../033-libwebpdemux2_1.5.0-0.1build1_arm64.deb ... 632s Unpacking libwebpdemux2:arm64 (1.5.0-0.1build1) ... 632s Selecting previously unselected package libwebpmux3:arm64. 632s Preparing to unpack .../034-libwebpmux3_1.5.0-0.1build1_arm64.deb ... 632s Unpacking libwebpmux3:arm64 (1.5.0-0.1build1) ... 632s Selecting previously unselected package imagemagick-7-common. 632s Preparing to unpack .../035-imagemagick-7-common_8%3a7.1.2.12+dfsg1-1_all.deb ... 632s Unpacking imagemagick-7-common (8:7.1.2.12+dfsg1-1) ... 632s Selecting previously unselected package libmagickcore-7.q16-10:arm64. 632s Preparing to unpack .../036-libmagickcore-7.q16-10_8%3a7.1.2.12+dfsg1-1_arm64.deb ... 632s Unpacking libmagickcore-7.q16-10:arm64 (8:7.1.2.12+dfsg1-1) ... 632s Selecting previously unselected package libmagickwand-7.q16-10:arm64. 632s Preparing to unpack .../037-libmagickwand-7.q16-10_8%3a7.1.2.12+dfsg1-1_arm64.deb ... 632s Unpacking libmagickwand-7.q16-10:arm64 (8:7.1.2.12+dfsg1-1) ... 632s Selecting previously unselected package poppler-data. 632s Preparing to unpack .../038-poppler-data_0.4.12-1build1_all.deb ... 632s Unpacking poppler-data (0.4.12-1build1) ... 632s Selecting previously unselected package python3-numpy-dev:arm64. 632s Preparing to unpack .../039-python3-numpy-dev_1%3a2.3.5+ds-3_arm64.deb ... 632s Unpacking python3-numpy-dev:arm64 (1:2.3.5+ds-3) ... 632s Selecting previously unselected package libblas3:arm64. 632s Preparing to unpack .../040-libblas3_3.12.1-7ubuntu1_arm64.deb ... 632s Unpacking libblas3:arm64 (3.12.1-7ubuntu1) ... 633s Selecting previously unselected package libgfortran5:arm64. 633s Preparing to unpack .../041-libgfortran5_15.2.0-11ubuntu1_arm64.deb ... 633s Unpacking libgfortran5:arm64 (15.2.0-11ubuntu1) ... 633s Selecting previously unselected package liblapack3:arm64. 633s Preparing to unpack .../042-liblapack3_3.12.1-7ubuntu1_arm64.deb ... 633s Unpacking liblapack3:arm64 (3.12.1-7ubuntu1) ... 633s Selecting previously unselected package python3-numpy. 633s Preparing to unpack .../043-python3-numpy_1%3a2.3.5+ds-3_arm64.deb ... 633s Unpacking python3-numpy (1:2.3.5+ds-3) ... 633s Selecting previously unselected package python3.13. 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unselected package libmpc3:arm64. 633s Preparing to unpack .../050-libmpc3_1.3.1-2_arm64.deb ... 633s Unpacking libmpc3:arm64 (1.3.1-2) ... 633s Selecting previously unselected package cpp-15-aarch64-linux-gnu. 633s Preparing to unpack .../051-cpp-15-aarch64-linux-gnu_15.2.0-11ubuntu1_arm64.deb ... 633s Unpacking cpp-15-aarch64-linux-gnu (15.2.0-11ubuntu1) ... 633s Selecting previously unselected package cpp-15. 634s Preparing to unpack .../052-cpp-15_15.2.0-11ubuntu1_arm64.deb ... 634s Unpacking cpp-15 (15.2.0-11ubuntu1) ... 634s Selecting previously unselected package cpp-aarch64-linux-gnu. 634s Preparing to unpack .../053-cpp-aarch64-linux-gnu_4%3a15.2.0-4ubuntu1_arm64.deb ... 634s Unpacking cpp-aarch64-linux-gnu (4:15.2.0-4ubuntu1) ... 634s Selecting previously unselected package cpp. 634s Preparing to unpack .../054-cpp_4%3a15.2.0-4ubuntu1_arm64.deb ... 634s Unpacking cpp (4:15.2.0-4ubuntu1) ... 634s Selecting previously unselected package libcc1-0:arm64. 634s Preparing to unpack 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libubsan1:arm64 (15.2.0-11ubuntu1) ... 634s Selecting previously unselected package libhwasan0:arm64. 634s Preparing to unpack .../061-libhwasan0_15.2.0-11ubuntu1_arm64.deb ... 634s Unpacking libhwasan0:arm64 (15.2.0-11ubuntu1) ... 634s Selecting previously unselected package libgcc-15-dev:arm64. 634s Preparing to unpack .../062-libgcc-15-dev_15.2.0-11ubuntu1_arm64.deb ... 634s Unpacking libgcc-15-dev:arm64 (15.2.0-11ubuntu1) ... 634s Selecting previously unselected package gcc-15-aarch64-linux-gnu. 634s Preparing to unpack .../063-gcc-15-aarch64-linux-gnu_15.2.0-11ubuntu1_arm64.deb ... 634s Unpacking gcc-15-aarch64-linux-gnu (15.2.0-11ubuntu1) ... 635s Selecting previously unselected package gcc-15. 635s Preparing to unpack .../064-gcc-15_15.2.0-11ubuntu1_arm64.deb ... 635s Unpacking gcc-15 (15.2.0-11ubuntu1) ... 635s Selecting previously unselected package gcc-aarch64-linux-gnu. 635s Preparing to unpack .../065-gcc-aarch64-linux-gnu_4%3a15.2.0-4ubuntu1_arm64.deb ... 635s Unpacking gcc-aarch64-linux-gnu (4:15.2.0-4ubuntu1) ... 635s Selecting previously unselected package gcc. 635s Preparing to unpack .../066-gcc_4%3a15.2.0-4ubuntu1_arm64.deb ... 635s Unpacking gcc (4:15.2.0-4ubuntu1) ... 635s Selecting previously unselected package libstdc++-15-dev:arm64. 635s Preparing to unpack .../067-libstdc++-15-dev_15.2.0-11ubuntu1_arm64.deb ... 635s Unpacking libstdc++-15-dev:arm64 (15.2.0-11ubuntu1) ... 635s Selecting previously unselected package g++-15-aarch64-linux-gnu. 635s Preparing to unpack .../068-g++-15-aarch64-linux-gnu_15.2.0-11ubuntu1_arm64.deb ... 635s Unpacking g++-15-aarch64-linux-gnu (15.2.0-11ubuntu1) ... 635s Selecting previously unselected package g++-15. 635s Preparing to unpack .../069-g++-15_15.2.0-11ubuntu1_arm64.deb ... 635s Unpacking g++-15 (15.2.0-11ubuntu1) ... 635s Selecting previously unselected package g++-aarch64-linux-gnu. 635s Preparing to unpack .../070-g++-aarch64-linux-gnu_4%3a15.2.0-4ubuntu1_arm64.deb ... 635s Unpacking g++-aarch64-linux-gnu (4:15.2.0-4ubuntu1) ... 635s Selecting previously unselected package g++. 635s Preparing to unpack .../071-g++_4%3a15.2.0-4ubuntu1_arm64.deb ... 635s Unpacking g++ (4:15.2.0-4ubuntu1) ... 635s Selecting previously unselected package build-essential. 636s Preparing to unpack .../072-build-essential_12.12ubuntu2_arm64.deb ... 636s Unpacking build-essential (12.12ubuntu2) ... 636s Selecting previously unselected package bwa. 636s Preparing to unpack .../073-bwa_0.7.19-1_arm64.deb ... 636s Unpacking bwa (0.7.19-1) ... 636s Selecting previously unselected package libargtable2-0:arm64. 636s Preparing to unpack .../074-libargtable2-0_13-4_arm64.deb ... 636s Unpacking libargtable2-0:arm64 (13-4) ... 636s Selecting previously unselected package clustalo. 636s Preparing to unpack .../075-clustalo_1.2.4-8build2_arm64.deb ... 636s Unpacking clustalo (1.2.4-8build2) ... 636s Selecting previously unselected package libdebhelper-perl. 636s Preparing to unpack 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Unpacking dh-strip-nondeterminism (1.15.0-1build1) ... 636s Selecting previously unselected package debugedit. 636s Preparing to unpack .../082-debugedit_1%3a5.2-3_arm64.deb ... 636s Unpacking debugedit (1:5.2-3) ... 636s Selecting previously unselected package dwz. 636s Preparing to unpack .../083-dwz_0.16-2_arm64.deb ... 636s Unpacking dwz (0.16-2) ... 636s Selecting previously unselected package gettext. 636s Preparing to unpack .../084-gettext_0.23.2-1_arm64.deb ... 636s Unpacking gettext (0.23.2-1) ... 636s Selecting previously unselected package intltool-debian. 636s Preparing to unpack .../085-intltool-debian_0.35.0+20060710.6build1_all.deb ... 636s Unpacking intltool-debian (0.35.0+20060710.6build1) ... 636s Selecting previously unselected package po-debconf. 636s Preparing to unpack .../086-po-debconf_1.0.22_all.deb ... 636s Unpacking po-debconf (1.0.22) ... 636s Selecting previously unselected package debhelper. 636s Preparing to unpack .../087-debhelper_13.28ubuntu1_all.deb 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.../093-libcifpp-data_9.0.5-2_all.deb ... 637s Unpacking libcifpp-data (9.0.5-2) ... 637s Selecting previously unselected package libcifpp9:arm64. 637s Preparing to unpack .../094-libcifpp9_9.0.5-2_arm64.deb ... 637s Unpacking libcifpp9:arm64 (9.0.5-2) ... 637s Selecting previously unselected package dssp. 637s Preparing to unpack .../095-dssp_4.5.7-1_arm64.deb ... 637s Unpacking dssp (4.5.7-1) ... 637s Selecting previously unselected package libimagequant0:arm64. 637s Preparing to unpack .../096-libimagequant0_2.18.0-1build1_arm64.deb ... 637s Unpacking libimagequant0:arm64 (2.18.0-1build1) ... 637s Selecting previously unselected package libxpm4:arm64. 637s Preparing to unpack .../097-libxpm4_1%3a3.5.17-1build3_arm64.deb ... 637s Unpacking libxpm4:arm64 (1:3.5.17-1build3) ... 637s Selecting previously unselected package libgd3:arm64. 637s Preparing to unpack .../098-libgd3_2.3.3-13ubuntu1_arm64.deb ... 637s Unpacking libgd3:arm64 (2.3.3-13ubuntu1) ... 637s Selecting previously unselected package libhpdf-2.3.0:arm64. 637s Preparing to unpack .../099-libhpdf-2.3.0_2.3.0+dfsg-1build4_arm64.deb ... 637s Unpacking libhpdf-2.3.0:arm64 (2.3.0+dfsg-1build4) ... 637s Selecting previously unselected package mysql-common. 637s Preparing to unpack .../100-mysql-common_5.8+1.1.1ubuntu2_all.deb ... 637s Unpacking mysql-common (5.8+1.1.1ubuntu2) ... 637s Selecting previously unselected package libmysqlclient24:arm64. 637s Preparing to unpack .../101-libmysqlclient24_8.4.7-0ubuntu3_arm64.deb ... 637s Unpacking libmysqlclient24:arm64 (8.4.7-0ubuntu3) ... 637s Selecting previously unselected package libpq5:arm64. 637s Preparing to unpack .../102-libpq5_18.1-2_arm64.deb ... 637s Unpacking libpq5:arm64 (18.1-2) ... 637s Selecting previously unselected package emboss-lib. 637s Preparing to unpack .../103-emboss-lib_6.6.0+dfsg-15ubuntu3_arm64.deb ... 637s Unpacking emboss-lib (6.6.0+dfsg-15ubuntu3) ... 637s Selecting previously unselected package emboss-data. 637s Preparing to unpack .../104-emboss-data_6.6.0+dfsg-15ubuntu3_all.deb ... 637s Unpacking emboss-data (6.6.0+dfsg-15ubuntu3) ... 641s Selecting previously unselected package emboss. 641s Preparing to unpack .../105-emboss_6.6.0+dfsg-15ubuntu3_arm64.deb ... 641s Unpacking emboss (6.6.0+dfsg-15ubuntu3) ... 641s Selecting previously unselected package fonts-dejavu-extra. 641s Preparing to unpack .../106-fonts-dejavu-extra_2.37-8build1_all.deb ... 641s Unpacking fonts-dejavu-extra (2.37-8build1) ... 641s Selecting previously unselected package fonts-font-awesome. 641s Preparing to unpack .../107-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1build1_all.deb ... 641s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1build1) ... 641s Selecting previously unselected package fonts-lmodern. 641s Preparing to unpack .../108-fonts-lmodern_2.005-1build1_all.deb ... 641s Unpacking fonts-lmodern (2.005-1build1) ... 641s Selecting previously unselected package fonts-lyx. 641s Preparing to unpack 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libpaper2:arm64 (2.2.5-0.3build1) ... 642s Selecting previously unselected package libice6:arm64. 642s Preparing to unpack .../120-libice6_2%3a1.1.1-1build1_arm64.deb ... 642s Unpacking libice6:arm64 (2:1.1.1-1build1) ... 642s Selecting previously unselected package libsm6:arm64. 642s Preparing to unpack .../121-libsm6_2%3a1.2.6-1_arm64.deb ... 642s Unpacking libsm6:arm64 (2:1.2.6-1) ... 642s Selecting previously unselected package libxt6t64:arm64. 642s Preparing to unpack .../122-libxt6t64_1%3a1.2.1-1.3_arm64.deb ... 642s Unpacking libxt6t64:arm64 (1:1.2.1-1.3) ... 642s Selecting previously unselected package libgs10:arm64. 642s Preparing to unpack .../123-libgs10_10.05.0dfsg1-0ubuntu4_arm64.deb ... 642s Unpacking libgs10:arm64 (10.05.0dfsg1-0ubuntu4) ... 642s Selecting previously unselected package ghostscript. 642s Preparing to unpack .../124-ghostscript_10.05.0dfsg1-0ubuntu4_arm64.deb ... 642s Unpacking ghostscript (10.05.0dfsg1-0ubuntu4) ... 642s Selecting previously unselected package libnetpbm11t64:arm64. 642s Preparing to unpack .../125-libnetpbm11t64_2%3a11.10.02-1build1_arm64.deb ... 642s Unpacking libnetpbm11t64:arm64 (2:11.10.02-1build1) ... 642s Selecting previously unselected package netpbm. 642s Preparing to unpack .../126-netpbm_2%3a11.10.02-1build1_arm64.deb ... 642s Unpacking netpbm (2:11.10.02-1build1) ... 642s Selecting previously unselected package tex-common. 642s Preparing to unpack .../127-tex-common_6.20_all.deb ... 642s Unpacking tex-common (6.20) ... 642s Selecting previously unselected package libpaper-utils. 642s Preparing to unpack .../128-libpaper-utils_2.2.5-0.3build1_arm64.deb ... 642s Unpacking libpaper-utils (2.2.5-0.3build1) ... 642s Selecting previously unselected package libkpathsea6:arm64. 642s Preparing to unpack .../129-libkpathsea6_2025.20250727.75242+ds-5build1_arm64.deb ... 642s Unpacking libkpathsea6:arm64 (2025.20250727.75242+ds-5build1) ... 642s Selecting previously unselected package libptexenc1:arm64. 642s Preparing to unpack .../130-libptexenc1_2025.20250727.75242+ds-5build1_arm64.deb ... 642s Unpacking libptexenc1:arm64 (2025.20250727.75242+ds-5build1) ... 642s Selecting previously unselected package libsynctex2:arm64. 642s Preparing to unpack .../131-libsynctex2_2025.20250727.75242+ds-5build1_arm64.deb ... 642s Unpacking libsynctex2:arm64 (2025.20250727.75242+ds-5build1) ... 642s Selecting previously unselected package libtexlua53-5:arm64. 642s Preparing to unpack .../132-libtexlua53-5_2025.20250727.75242+ds-5build1_arm64.deb ... 642s Unpacking libtexlua53-5:arm64 (2025.20250727.75242+ds-5build1) ... 642s Selecting previously unselected package t1utils. 643s Preparing to unpack .../133-t1utils_1.41-4build4_arm64.deb ... 643s Unpacking t1utils (1.41-4build4) ... 643s Selecting previously unselected package libpixman-1-0:arm64. 643s Preparing to unpack .../134-libpixman-1-0_0.46.4-1_arm64.deb ... 643s Unpacking libpixman-1-0:arm64 (0.46.4-1) ... 643s Selecting previously unselected package libxcb-render0:arm64. 643s Preparing to unpack .../135-libxcb-render0_1.17.0-2build1_arm64.deb ... 643s Unpacking libxcb-render0:arm64 (1.17.0-2build1) ... 643s Selecting previously unselected package libxcb-shm0:arm64. 643s Preparing to unpack .../136-libxcb-shm0_1.17.0-2build1_arm64.deb ... 643s Unpacking libxcb-shm0:arm64 (1.17.0-2build1) ... 643s Selecting previously unselected package libxrender1:arm64. 643s Preparing to unpack .../137-libxrender1_1%3a0.9.12-1_arm64.deb ... 643s Unpacking libxrender1:arm64 (1:0.9.12-1) ... 643s Selecting previously unselected package libcairo2:arm64. 643s Preparing to unpack .../138-libcairo2_1.18.4-3_arm64.deb ... 643s Unpacking libcairo2:arm64 (1.18.4-3) ... 643s Selecting previously unselected package libgraphite2-3:arm64. 643s Preparing to unpack .../139-libgraphite2-3_1.3.14-11ubuntu1_arm64.deb ... 643s Unpacking libgraphite2-3:arm64 (1.3.14-11ubuntu1) ... 643s Selecting previously unselected package libharfbuzz0b:arm64. 643s Preparing to unpack .../140-libharfbuzz0b_12.3.0-4_arm64.deb ... 643s Unpacking libharfbuzz0b:arm64 (12.3.0-4) ... 643s Selecting previously unselected package libmpfi0:arm64. 643s Preparing to unpack .../141-libmpfi0_1.5.4+ds-4_arm64.deb ... 643s Unpacking libmpfi0:arm64 (1.5.4+ds-4) ... 643s Selecting previously unselected package libpotrace0:arm64. 643s Preparing to unpack .../142-libpotrace0_1.16-2build2_arm64.deb ... 643s Unpacking libpotrace0:arm64 (1.16-2build2) ... 643s Selecting previously unselected package libteckit0:arm64. 643s Preparing to unpack .../143-libteckit0_2.5.13+ds-1_arm64.deb ... 643s Unpacking libteckit0:arm64 (2.5.13+ds-1) ... 643s Selecting previously unselected package libxmu6:arm64. 643s Preparing to unpack .../144-libxmu6_2%3a1.1.3-4_arm64.deb ... 643s Unpacking libxmu6:arm64 (2:1.1.3-4) ... 643s Selecting previously unselected package libxaw7:arm64. 643s Preparing to unpack .../145-libxaw7_2%3a1.0.16-1build1_arm64.deb ... 643s Unpacking libxaw7:arm64 (2:1.0.16-1build1) ... 643s Selecting previously unselected package libxi6:arm64. 643s Preparing to unpack .../146-libxi6_2%3a1.8.2-2_arm64.deb ... 643s Unpacking libxi6:arm64 (2:1.8.2-2) ... 643s Selecting previously unselected package libzzip-0-13t64:arm64. 643s Preparing to unpack .../147-libzzip-0-13t64_0.13.78+dfsg.1-0.2_arm64.deb ... 643s Unpacking libzzip-0-13t64:arm64 (0.13.78+dfsg.1-0.2) ... 643s Selecting previously unselected package texlive-binaries. 643s Preparing to unpack .../148-texlive-binaries_2025.20250727.75242+ds-5build1_arm64.deb ... 643s Unpacking texlive-binaries (2025.20250727.75242+ds-5build1) ... 644s Selecting previously unselected package xdg-utils. 644s Preparing to unpack .../149-xdg-utils_1.2.1-2ubuntu2_all.deb ... 644s Unpacking xdg-utils (1.2.1-2ubuntu2) ... 644s Selecting previously unselected package texlive-base. 644s Preparing to unpack .../150-texlive-base_2025.20251127-1_all.deb ... 644s Unpacking texlive-base (2025.20251127-1) ... 645s Selecting previously unselected package hicolor-icon-theme. 645s Preparing to unpack .../151-hicolor-icon-theme_0.18-2build1_all.deb ... 645s Unpacking hicolor-icon-theme (0.18-2build1) ... 645s Selecting previously unselected package imagemagick-7.q16. 645s Preparing to unpack .../152-imagemagick-7.q16_8%3a7.1.2.12+dfsg1-1_arm64.deb ... 645s Unpacking imagemagick-7.q16 (8:7.1.2.12+dfsg1-1) ... 645s Selecting previously unselected package imagemagick. 645s Preparing to unpack .../153-imagemagick_8%3a7.1.2.12+dfsg1-1_arm64.deb ... 645s Unpacking imagemagick (8:7.1.2.12+dfsg1-1) ... 645s Selecting previously unselected package hevea. 645s Preparing to unpack .../154-hevea_2.36-2build3_arm64.deb ... 645s Unpacking hevea (2.36-2build3) ... 645s Selecting previously unselected package libsuitesparseconfig7:arm64. 645s Preparing to unpack .../155-libsuitesparseconfig7_1%3a7.12.1+dfsg-1_arm64.deb ... 645s Unpacking libsuitesparseconfig7:arm64 (1:7.12.1+dfsg-1) ... 645s Selecting previously unselected package libamd3:arm64. 645s Preparing to unpack .../156-libamd3_1%3a7.12.1+dfsg-1_arm64.deb ... 645s Unpacking libamd3:arm64 (1:7.12.1+dfsg-1) ... 645s Selecting previously unselected package libapache-pom-java. 645s Preparing to unpack .../157-libapache-pom-java_33-2build1_all.deb ... 645s Unpacking libapache-pom-java (33-2build1) ... 645s Selecting previously unselected package libarpack2t64:arm64. 645s Preparing to unpack .../158-libarpack2t64_3.9.1-6_arm64.deb ... 645s Unpacking libarpack2t64:arm64 (3.9.1-6) ... 645s Selecting previously unselected package libcolamd3:arm64. 645s Preparing to unpack .../159-libcolamd3_1%3a7.12.1+dfsg-1_arm64.deb ... 645s Unpacking libcolamd3:arm64 (1:7.12.1+dfsg-1) ... 645s Selecting previously unselected package libcommons-parent-java. 645s Preparing to unpack .../160-libcommons-parent-java_56-1build1_all.deb ... 645s Unpacking libcommons-parent-java (56-1build1) ... 645s Selecting previously unselected package libcommons-logging-java. 645s 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.../171-ncbi-vdb-data_3.2.1+dfsg-2_all.deb ... 646s Unpacking ncbi-vdb-data (3.2.1+dfsg-2) ... 646s Selecting previously unselected package libncbi-vdb3:arm64. 646s Preparing to unpack .../172-libncbi-vdb3_3.2.1+dfsg-2_arm64.deb ... 646s Unpacking libncbi-vdb3:arm64 (3.2.1+dfsg-2) ... 646s Selecting previously unselected package libpython3.14:arm64. 646s Preparing to unpack .../173-libpython3.14_3.14.2-1_arm64.deb ... 646s Unpacking libpython3.14:arm64 (3.14.2-1) ... 646s Selecting previously unselected package zlib1g-dev:arm64. 646s Preparing to unpack .../174-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1ubuntu2_arm64.deb ... 646s Unpacking zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1ubuntu2) ... 646s Selecting previously unselected package libpython3.14-dev:arm64. 646s Preparing to unpack .../175-libpython3.14-dev_3.14.2-1_arm64.deb ... 646s Unpacking libpython3.14-dev:arm64 (3.14.2-1) ... 646s Selecting previously unselected package libpython3-dev:arm64. 646s Preparing to unpack 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Unpacking libtcl8.6:arm64 (8.6.17+dfsg-1) ... 647s Selecting previously unselected package libxft2:arm64. 647s Preparing to unpack .../182-libxft2_2.3.6-1build2_arm64.deb ... 647s Unpacking libxft2:arm64 (2.3.6-1build2) ... 647s Selecting previously unselected package libxss1:arm64. 647s Preparing to unpack .../183-libxss1_1%3a1.2.3-1build4_arm64.deb ... 647s Unpacking libxss1:arm64 (1:1.2.3-1build4) ... 647s Selecting previously unselected package libtk8.6:arm64. 647s Preparing to unpack .../184-libtk8.6_8.6.17-1_arm64.deb ... 647s Unpacking libtk8.6:arm64 (8.6.17-1) ... 647s Selecting previously unselected package libxslt1.1:arm64. 647s Preparing to unpack .../185-libxslt1.1_1.1.43-0.3_arm64.deb ... 647s Unpacking libxslt1.1:arm64 (1.1.43-0.3) ... 647s Selecting previously unselected package libzopfli1. 647s Preparing to unpack .../186-libzopfli1_1.0.3-3_arm64.deb ... 647s Unpacking libzopfli1 (1.0.3-3) ... 647s Selecting previously unselected package lmodern. 647s Preparing to unpack .../187-lmodern_2.005-1build1_all.deb ... 647s Unpacking lmodern (2.005-1build1) ... 647s Selecting previously unselected package mafft. 647s Preparing to unpack .../188-mafft_7.525-1_arm64.deb ... 647s Unpacking mafft (7.525-1) ... 647s Selecting previously unselected package ncbi-data. 647s Preparing to unpack .../189-ncbi-data_6.1.20170106+dfsg2-7_all.deb ... 647s Unpacking ncbi-data (6.1.20170106+dfsg2-7) ... 647s Selecting previously unselected package ncbi-blast+. 647s Preparing to unpack .../190-ncbi-blast+_2.16.0+ds-7_arm64.deb ... 647s Unpacking ncbi-blast+ (2.16.0+ds-7) ... 648s Selecting previously unselected package phylip. 648s Preparing to unpack .../191-phylip_1%3a3.697+dfsg-4build2_arm64.deb ... 648s Unpacking phylip (1:3.697+dfsg-4build2) ... 648s Selecting previously unselected package prank. 648s Preparing to unpack .../192-prank_250331-1_arm64.deb ... 648s Unpacking prank (250331-1) ... 648s Selecting previously unselected package preview-latex-style. 648s Preparing to unpack .../193-preview-latex-style_13.2-1.1_all.deb ... 648s Unpacking preview-latex-style (13.2-1.1) ... 648s Selecting previously unselected package probcons. 648s Preparing to unpack .../194-probcons_1.12-15_arm64.deb ... 648s Unpacking probcons (1.12-15) ... 648s Selecting previously unselected package python-biopython-doc. 648s Preparing to unpack .../195-python-biopython-doc_1.86+dfsg-1_all.deb ... 648s Unpacking python-biopython-doc (1.86+dfsg-1) ... 648s Selecting previously unselected package python-matplotlib-data. 648s Preparing to unpack .../196-python-matplotlib-data_3.10.7+dfsg1-1_all.deb ... 648s Unpacking python-matplotlib-data (3.10.7+dfsg1-1) ... 648s Selecting previously unselected package python3-all. 648s Preparing to unpack .../197-python3-all_3.14.2-1_arm64.deb ... 648s Unpacking python3-all (3.14.2-1) ... 648s Selecting previously unselected package python3.14-dev. 648s Preparing to unpack .../198-python3.14-dev_3.14.2-1_arm64.deb ... 648s Unpacking python3.14-dev (3.14.2-1) ... 648s Selecting previously unselected package python3-dev. 649s Preparing to unpack .../199-python3-dev_3.14.2-1_arm64.deb ... 649s Unpacking python3-dev (3.14.2-1) ... 649s Selecting previously unselected package python3.13-dev. 649s Preparing to unpack .../200-python3.13-dev_3.13.11-1_arm64.deb ... 649s Unpacking python3.13-dev (3.13.11-1) ... 649s Selecting previously unselected package python3-all-dev. 649s Preparing to unpack .../201-python3-all-dev_3.14.2-1_arm64.deb ... 649s Unpacking python3-all-dev (3.14.2-1) ... 649s Selecting previously unselected package python3-charset-normalizer. 649s Preparing to unpack .../202-python3-charset-normalizer_3.4.4-2_arm64.deb ... 649s Unpacking python3-charset-normalizer (3.4.4-2) ... 649s Selecting previously unselected package python3.13-tk. 649s Preparing to unpack .../203-python3.13-tk_3.13.11-1_arm64.deb ... 649s Unpacking python3.13-tk (3.13.11-1) ... 649s Selecting previously unselected package python3.14-tk. 649s Preparing to unpack .../204-python3.14-tk_3.14.2-1_arm64.deb ... 649s Unpacking python3.14-tk (3.14.2-1) ... 649s Selecting previously unselected package python3-tk. 649s Preparing to unpack .../205-python3-tk_3.14.2-1_arm64.deb ... 649s Unpacking python3-tk (3.14.2-1) ... 649s Selecting previously unselected package python3-pil.imagetk:arm64. 649s Preparing to unpack .../206-python3-pil.imagetk_12.0.0-1ubuntu1_arm64.deb ... 649s Unpacking python3-pil.imagetk:arm64 (12.0.0-1ubuntu1) ... 649s Selecting previously unselected package python3-pil:arm64. 649s Preparing to unpack .../207-python3-pil_12.0.0-1ubuntu1_arm64.deb ... 649s Unpacking python3-pil:arm64 (12.0.0-1ubuntu1) ... 649s Selecting previously unselected package python3-cairo. 649s Preparing to unpack .../208-python3-cairo_1.27.0-2build1_arm64.deb ... 649s Unpacking python3-cairo (1.27.0-2build1) ... 649s Selecting previously unselected package python3-freetype. 649s Preparing to unpack .../209-python3-freetype_2.5.1-2_all.deb ... 649s Unpacking python3-freetype (2.5.1-2) ... 649s Selecting previously unselected package python3-rlpycairo. 649s Preparing to unpack .../210-python3-rlpycairo_0.3.0-4_all.deb ... 649s Unpacking python3-rlpycairo (0.3.0-4) ... 649s Selecting previously unselected package python3-reportlab. 649s Preparing to unpack .../211-python3-reportlab_4.4.9-1_all.deb ... 649s Unpacking python3-reportlab (4.4.9-1) ... 649s Selecting previously unselected package w3c-sgml-lib. 649s Preparing to unpack .../212-w3c-sgml-lib_1.3-3build1_all.deb ... 649s Unpacking w3c-sgml-lib (1.3-3build1) ... 649s Selecting previously unselected package python3-biopython. 649s Preparing to unpack .../213-python3-biopython_1.86+dfsg-1_arm64.deb ... 649s Unpacking python3-biopython (1.86+dfsg-1) ... 649s Selecting previously unselected package python3-biopython-sql. 649s Preparing to unpack .../214-python3-biopython-sql_1.86+dfsg-1_all.deb ... 649s Unpacking python3-biopython-sql (1.86+dfsg-1) ... 649s Selecting previously unselected package python3-brotli. 650s Preparing to unpack .../215-python3-brotli_1.1.0-2build6_arm64.deb ... 650s Unpacking python3-brotli (1.1.0-2build6) ... 650s Selecting previously unselected package python3-contourpy. 650s Preparing to unpack .../216-python3-contourpy_1.3.3-1_arm64.deb ... 650s Unpacking python3-contourpy (1.3.3-1) ... 650s Selecting previously unselected package python3-cycler. 650s Preparing to unpack .../217-python3-cycler_0.12.1-2_all.deb ... 650s Unpacking python3-cycler (0.12.1-2) ... 650s Selecting previously unselected package python3-decorator. 650s Preparing to unpack .../218-python3-decorator_5.2.1-2_all.deb ... 650s Unpacking python3-decorator (5.2.1-2) ... 650s Selecting previously unselected package python3-defusedxml. 650s Preparing to unpack .../219-python3-defusedxml_0.7.1-3build1_all.deb ... 650s Unpacking python3-defusedxml (0.7.1-3build1) ... 650s Selecting previously unselected package python3-roman-numerals. 650s Preparing to unpack .../220-python3-roman-numerals_4.1.0-1_all.deb ... 650s Unpacking python3-roman-numerals (4.1.0-1) ... 650s Selecting previously unselected package python3-docutils. 650s Preparing to unpack .../221-python3-docutils_0.22.4+dfsg-1_all.deb ... 650s Unpacking python3-docutils (0.22.4+dfsg-1) ... 650s Selecting previously unselected package python3-lxml:arm64. 650s Preparing to unpack .../222-python3-lxml_6.0.2-1_arm64.deb ... 650s Unpacking python3-lxml:arm64 (6.0.2-1) ... 650s Selecting previously unselected package python3-lz4. 650s Preparing to unpack .../223-python3-lz4_4.4.5+dfsg-1_arm64.deb ... 650s Unpacking python3-lz4 (4.4.5+dfsg-1) ... 650s Selecting previously unselected package python3-scipy. 650s Preparing to unpack .../224-python3-scipy_1.16.3-3_arm64.deb ... 650s Unpacking python3-scipy (1.16.3-3) ... 651s Selecting previously unselected package python3-mpmath. 651s Preparing to unpack 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Selecting previously unselected package python3-imagesize. 651s Preparing to unpack .../231-python3-imagesize_1.4.1-1build1_all.deb ... 651s Unpacking python3-imagesize (1.4.1-1build1) ... 651s Selecting previously unselected package python3-kiwisolver. 651s Preparing to unpack .../232-python3-kiwisolver_1.4.10~rc0-1_arm64.deb ... 651s Unpacking python3-kiwisolver (1.4.10~rc0-1) ... 651s Selecting previously unselected package python3-matplotlib. 651s Preparing to unpack .../233-python3-matplotlib_3.10.7+dfsg1-1_arm64.deb ... 651s Unpacking python3-matplotlib (3.10.7+dfsg1-1) ... 652s Selecting previously unselected package python3-msgpack. 652s Preparing to unpack .../234-python3-msgpack_1.1.2-1_arm64.deb ... 652s Unpacking python3-msgpack (1.1.2-1) ... 652s Selecting previously unselected package python3-mmtf. 652s Preparing to unpack .../235-python3-mmtf_1.1.3-1build1_all.deb ... 652s Unpacking python3-mmtf (1.1.3-1build1) ... 652s Selecting previously unselected package python3-mysqldb. 652s Preparing to unpack .../236-python3-mysqldb_1.4.6-2build7_arm64.deb ... 652s Unpacking python3-mysqldb (1.4.6-2build7) ... 652s Selecting previously unselected package python3-networkx. 652s Preparing to unpack .../237-python3-networkx_3.2.1-4ubuntu2_all.deb ... 652s Unpacking python3-networkx (3.2.1-4ubuntu2) ... 652s Selecting previously unselected package sphinx-common. 652s Preparing to unpack .../238-sphinx-common_8.2.3-12_all.deb ... 652s Unpacking sphinx-common (8.2.3-12) ... 653s Selecting previously unselected package python3-alabaster. 653s Preparing to unpack .../239-python3-alabaster_0.7.16-0.1build1_all.deb ... 653s Unpacking python3-alabaster (0.7.16-0.1build1) ... 653s Selecting previously unselected package python3-snowballstemmer. 653s Preparing to unpack .../240-python3-snowballstemmer_3.0.1-1_all.deb ... 653s Unpacking python3-snowballstemmer (3.0.1-1) ... 653s Selecting previously unselected package python3-sphinx. 653s Preparing to unpack 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(8.6.17+dfsg-1) ... 665s Setting up autopoint (0.23.2-1) ... 665s Setting up libmpfi0:arm64 (1.5.4+ds-4) ... 665s Setting up fonts-dejavu-core (2.37-8build1) ... 665s Setting up wise-data (2.4.1-27) ... 665s Setting up libjpeg-turbo8:arm64 (2.1.5-4ubuntu2) ... 665s Setting up libltdl7:arm64 (2.5.4-9) ... 665s Setting up libfftw3-double3:arm64 (3.3.10-2fakesync1build2) ... 665s Setting up libcifpp-data (9.0.5-2) ... 666s Setting up libkpathsea6:arm64 (2025.20250727.75242+ds-5build1) ... 666s Setting up libgfortran5:arm64 (15.2.0-11ubuntu1) ... 666s Setting up autoconf (2.72-3.1ubuntu1) ... 666s Setting up libwebp7:arm64 (1.5.0-0.1build1) ... 666s Setting up libubsan1:arm64 (15.2.0-11ubuntu1) ... 666s Setting up zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1ubuntu2) ... 666s Setting up fonts-dejavu-extra (2.37-8build1) ... 666s Setting up dwz (0.16-2) ... 666s Setting up liblqr-1-0:arm64 (0.4.2-2.2) ... 666s Setting up libhwasan0:arm64 (15.2.0-11ubuntu1) ... 666s Setting up python3-rdflib (7.1.1-3) ... 666s Setting up libasan8:arm64 (15.2.0-11ubuntu1) ... 666s Setting up libjson-perl (4.10000-1) ... 666s Setting up libxslt1.1:arm64 (1.1.43-0.3) ... 666s Setting up libpython3.14:arm64 (3.14.2-1) ... 666s Setting up debugedit (1:5.2-3) ... 666s Setting up fonts-lmodern (2.005-1build1) ... 666s Setting up libsuitesparseconfig7:arm64 (1:7.12.1+dfsg-1) ... 666s Setting up python3-roman-numerals (4.1.0-1) ... 667s Setting up libopenjp2-7:arm64 (2.5.4-1) ... 667s Setting up python3.13-minimal (3.13.11-1) ... 668s Setting up libharfbuzz0b:arm64 (12.3.0-4) ... 668s Setting up ncbi-vdb-data (3.2.1+dfsg-2) ... 668s Setting up fasttree (2.1.11-2build1) ... 668s Setting up libpython3.14-dev:arm64 (3.14.2-1) ... 668s Setting up sgml-base (1.31+nmu1) ... 668s Setting up python3-msgpack (1.1.2-1) ... 668s Setting up libplfit0:arm64 (0.9.6+ds-2ubuntu1) ... 668s Setting up libxss1:arm64 (1:1.2.3-1build4) ... 668s Setting up libmbedcrypto16:arm64 (3.6.5-0.1ubuntu2) ... 668s Setting up libpaper2:arm64 (2.2.5-0.3build1) ... 668s Setting up libtsan2:arm64 (15.2.0-11ubuntu1) ... 668s Setting up libjs-jquery (3.7.1+dfsg+~3.5.33-1build1) ... 668s Setting up python3-mpmath (1.3.0-2) ... 669s Setting up libisl23:arm64 (0.27-1build1) ... 669s Setting up libde265-0:arm64 (1.0.16-1build1) ... 669s Setting up python-matplotlib-data (3.10.7+dfsg1-1) ... 669s Setting up libwebpmux3:arm64 (1.5.0-0.1build1) ... 669s Setting up dialign (2.2.1-13build1) ... 669s Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1build1) ... 669s Setting up sphinx-rtd-theme-common (3.0.2+dfsg-3) ... 669s Setting up xdg-utils (1.2.1-2ubuntu2) ... 669s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode 669s Setting up libcc1-0:arm64 (15.2.0-11ubuntu1) ... 669s Setting up liblsan0:arm64 (15.2.0-11ubuntu1) ... 669s Setting up libitm1:arm64 (15.2.0-11ubuntu1) ... 669s Setting up libsynctex2:arm64 (2025.20250727.75242+ds-5build1) ... 669s Setting up prank (250331-1) ... 669s Setting up libargtable2-0:arm64 (13-4) ... 669s Setting up python3-imagesize (1.4.1-1build1) ... 669s Setting up libpotrace0:arm64 (1.16-2build2) ... 669s Setting up libjpeg8:arm64 (8c-2ubuntu11) ... 669s Setting up automake (1:1.18.1-3build1) ... 669s update-alternatives: using /usr/bin/automake-1.18 to provide /usr/bin/automake (automake) in auto mode 669s Setting up libfile-stripnondeterminism-perl (1.15.0-1build1) ... 669s Setting up python3-sympy (1.14.0-2) ... 682s /usr/lib/python3/dist-packages/sympy/testing/runtests.py:283: SyntaxWarning: 'return' in a 'finally' block 682s return p.returncode 683s Setting up cpp-15-aarch64-linux-gnu (15.2.0-11ubuntu1) ... 683s Setting up libice6:arm64 (2:1.1.1-1build1) ... 683s Setting up flex (2.6.4-8.2build2) ... 683s Setting up liblapack3:arm64 (3.12.1-7ubuntu1) ... 683s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode 683s Setting up gettext (0.23.2-1) ... 683s Setting up libarpack2t64:arm64 (3.9.1-6) ... 683s Setting up libgcc-15-dev:arm64 (15.2.0-11ubuntu1) ... 683s Setting up libpython3-dev:arm64 (3.14.2-1) ... 683s Setting up libamd3:arm64 (1:7.12.1+dfsg-1) ... 683s Setting up libpdfbox-java (1:1.8.16-5) ... 683s Setting up python3.14-dev (3.14.2-1) ... 683s Setting up libcolamd3:arm64 (1:7.12.1+dfsg-1) ... 683s Setting up python3.13 (3.13.11-1) ... 684s Setting up libcifpp9:arm64 (9.0.5-2) ... 684s Setting up fontconfig-config (2.15.0-2.4ubuntu1) ... 684s Setting up wise (2.4.1-27) ... 684s Setting up preview-latex-style (13.2-1.1) ... 684s Setting up libwebpdemux2:arm64 (1.5.0-0.1build1) ... 684s Setting up libcommons-parent-java (56-1build1) ... 684s Setting up libavahi-common3:arm64 (0.8-17ubuntu1) ... 684s Setting up libcommons-logging-java (1.3.0-1ubuntu1) ... 684s Setting up python3-all (3.14.2-1) ... 684s Setting up libpaper-utils (2.2.5-0.3build1) ... 684s Setting up clustalo (1.2.4-8build2) ... 684s Setting up dssp (4.5.7-1) ... 684s Setting up xfonts-utils (1:7.7+7build1) ... 684s Setting up python3-zopfli (0.4.0-1) ... 684s Setting up intltool-debian (0.35.0+20060710.6build1) ... 684s Setting up cpp-aarch64-linux-gnu (4:15.2.0-4ubuntu1) ... 684s Setting up libmbedx509-7:arm64 (3.6.5-0.1ubuntu2) ... 684s Setting up libstdc++-15-dev:arm64 (15.2.0-11ubuntu1) ... 684s Setting up libptexenc1:arm64 (2025.20250727.75242+ds-5build1) ... 684s Setting up libglpk40:arm64 (5.0-2) ... 684s Setting up libraqm0:arm64 (0.10.3-1) ... 684s Setting up libpython3.13-dev:arm64 (3.13.11-1) ... 684s Setting up sphinx-common (8.2.3-12) ... 684s Setting up python3-dev (3.14.2-1) ... 684s Setting up python3-numpy (1:2.3.5+ds-3) ... 688s Setting up libraw23t64:arm64 (0.21.4-2) ... 688s Setting up libmbedtls21:arm64 (3.6.5-0.1ubuntu2) ... 688s Setting up dh-strip-nondeterminism (1.15.0-1build1) ... 688s Setting up cpp-15 (15.2.0-11ubuntu1) ... 688s Setting up python3-lxml:arm64 (6.0.2-1) ... 689s Setting up python-biopython-doc (1.86+dfsg-1) ... 689s Setting up libtiff6:arm64 (4.7.0-3ubuntu3) ... 689s Setting up cpp (4:15.2.0-4ubuntu1) ... 689s Setting up lmodern (2.005-1build1) ... 689s Setting up xml-core (0.19build1) ... 689s Setting up python3-contourpy (1.3.3-1) ... 689s Setting up libfontconfig1:arm64 (2.15.0-2.4ubuntu1) ... 689s Setting up libsm6:arm64 (2:1.2.6-1) ... 689s Setting up libavahi-client3:arm64 (0.8-17ubuntu1) ... 689s Setting up libxft2:arm64 (2.3.6-1build2) ... 689s Setting up gcc-15-aarch64-linux-gnu (15.2.0-11ubuntu1) ... 689s Setting up python3-scipy (1.16.3-3) ... 698s Setting up python3.13-dev (3.13.11-1) ... 698s Setting up libigraph4:arm64 (1.0.1+ds-3) ... 698s Setting up po-debconf (1.0.22) ... 698s Setting up libtk8.6:arm64 (8.6.17-1) ... 698s Setting up libncbi-vdb3:arm64 (3.2.1+dfsg-2) ... 698s Setting up python3-mmtf (1.1.3-1build1) ... 698s Setting up fonts-urw-base35 (20200910-8build1) ... 698s Setting up libcairo2:arm64 (1.18.4-3) ... 698s Setting up python3.13-tk (3.13.11-1) ... 698s Setting up ncbi-blast+ (2.16.0+ds-7) ... 698s Setting up python3-pil:arm64 (12.0.0-1ubuntu1) ... 699s Setting up gcc-15 (15.2.0-11ubuntu1) ... 699s Setting up g++-15-aarch64-linux-gnu (15.2.0-11ubuntu1) ... 699s Setting up libpython3-all-dev:arm64 (3.14.2-1) ... 699s Setting up libxt6t64:arm64 (1:1.2.1-1.3) ... 699s Setting up netpbm (2:11.10.02-1build1) ... 699s Setting up python3-igraph (1.0.0+ds-1) ... 699s Setting up g++-15 (15.2.0-11ubuntu1) ... 699s Setting up libcups2t64:arm64 (2.4.16-1ubuntu1) ... 699s Setting up python3-all-dev (3.14.2-1) ... 699s Setting up libgs10-common (10.05.0dfsg1-0ubuntu4) ... 699s Setting up gcc-aarch64-linux-gnu (4:15.2.0-4ubuntu1) ... 699s Setting up libxmu6:arm64 (2:1.1.3-4) ... 699s Setting up python3.14-tk (3.14.2-1) ... 699s Setting up python3-cairo (1.27.0-2build1) ... 699s Setting up libtool (2.5.4-9) ... 699s Setting up python3-tk (3.14.2-1) ... 699s Setting up libxaw7:arm64 (2:1.0.16-1build1) ... 699s Setting up gcc (4:15.2.0-4ubuntu1) ... 699s Setting up dh-autoreconf (21) ... 699s Setting up python3-pil.imagetk:arm64 (12.0.0-1ubuntu1) ... 700s Setting up python3-rlpycairo (0.3.0-4) ... 700s Setting up python3-reportlab (4.4.9-1) ... 701s Setting up texlive-binaries (2025.20250727.75242+ds-5build1) ... 701s update-alternatives: using /usr/bin/xdvi-xaw to provide /usr/bin/xdvi.bin (xdvi.bin) in auto mode 701s update-alternatives: using /usr/bin/bibtex.original to provide /usr/bin/bibtex (bibtex) in auto mode 701s Setting up g++-aarch64-linux-gnu (4:15.2.0-4ubuntu1) ... 701s Setting up texlive-base (2025.20251127-1) ... 702s tl-paper: setting paper size for dvips to a4: /var/lib/texmf/dvips/config/config-paper.ps 702s tl-paper: setting paper size for dvipdfmx to a4: /var/lib/texmf/dvipdfmx/dvipdfmx-paper.cfg 703s tl-paper: setting paper size for xdvi to a4: /var/lib/texmf/xdvi/XDvi-paper 703s tl-paper: setting paper size for pdftex to a4: /var/lib/texmf/tex/generic/tex-ini-files/pdftexconfig.tex 704s Setting up libgs10:arm64 (10.05.0dfsg1-0ubuntu4) ... 704s Setting up texlive-luatex (2025.20251127-1) ... 704s Setting up debhelper (13.28ubuntu1) ... 704s Setting up ghostscript (10.05.0dfsg1-0ubuntu4) ... 704s Setting up texlive-latex-base (2025.20251127-1) ... 704s Setting up texlive-latex-recommended (2025.20251127-1) ... 704s Setting up texlive-pictures (2025.20251127-1) ... 704s Setting up g++ (4:15.2.0-4ubuntu1) ... 704s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 704s Setting up texlive-fonts-recommended (2025.20251127-1) ... 704s Setting up build-essential (12.12ubuntu2) ... 704s Setting up texlive-latex-extra (2025.20251127-2) ... 704s Setting up python3-ufolib2 (0.18.1+dfsg1-1) ... 704s Setting up libheif-plugin-aomdec:arm64 (1.21.2-1) ... 704s Setting up libheif-plugin-libde265:arm64 (1.21.2-1) ... 704s Setting up libheif1:arm64 (1.21.2-1) ... 704s Setting up python3-fonttools (4.61.1-3) ... 706s Setting up libgd3:arm64 (2.3.3-13ubuntu1) ... 706s Setting up libmagickcore-7.q16-10:arm64 (8:7.1.2.12+dfsg1-1) ... 706s Setting up emboss-lib (6.6.0+dfsg-15ubuntu3) ... 706s Setting up python3-matplotlib (3.10.7+dfsg1-1) ... 709s Setting up libmagickwand-7.q16-10:arm64 (8:7.1.2.12+dfsg1-1) ... 709s Setting up emboss (6.6.0+dfsg-15ubuntu3) ... 709s Setting up imagemagick-7.q16 (8:7.1.2.12+dfsg1-1) ... 709s update-alternatives: using /usr/bin/compare-im7.q16 to provide /usr/bin/compare (compare) in auto mode 709s update-alternatives: using /usr/bin/compare-im7.q16 to provide /usr/bin/compare-im7 (compare-im7) in auto mode 709s update-alternatives: using /usr/bin/animate-im7.q16 to provide /usr/bin/animate (animate) in auto mode 709s update-alternatives: using /usr/bin/animate-im7.q16 to provide /usr/bin/animate-im7 (animate-im7) in auto mode 709s update-alternatives: using /usr/bin/convert-im7.q16 to provide /usr/bin/convert (convert) in auto mode 709s update-alternatives: using /usr/bin/convert-im7.q16 to provide /usr/bin/convert-im7 (convert-im7) in auto mode 709s update-alternatives: using /usr/bin/composite-im7.q16 to provide /usr/bin/composite (composite) in auto mode 709s update-alternatives: using /usr/bin/composite-im7.q16 to provide /usr/bin/composite-im7 (composite-im7) in auto mode 709s update-alternatives: using /usr/bin/conjure-im7.q16 to provide /usr/bin/conjure (conjure) in auto mode 709s update-alternatives: using /usr/bin/conjure-im7.q16 to provide /usr/bin/conjure-im7 (conjure-im7) in auto mode 709s update-alternatives: using /usr/bin/import-im7.q16 to provide /usr/bin/import (import) in auto mode 709s update-alternatives: using /usr/bin/import-im7.q16 to provide /usr/bin/import-im7 (import-im7) in auto mode 709s update-alternatives: using /usr/bin/identify-im7.q16 to provide /usr/bin/identify (identify) in auto mode 709s update-alternatives: using /usr/bin/identify-im7.q16 to provide /usr/bin/identify-im7 (identify-im7) in auto mode 709s update-alternatives: using /usr/bin/stream-im7.q16 to provide /usr/bin/stream (stream) in auto mode 709s update-alternatives: using /usr/bin/stream-im7.q16 to provide /usr/bin/stream-im7 (stream-im7) in auto mode 709s update-alternatives: using /usr/bin/display-im7.q16 to provide /usr/bin/display (display) in auto mode 709s update-alternatives: using /usr/bin/display-im7.q16 to provide /usr/bin/display-im7 (display-im7) in auto mode 709s update-alternatives: using /usr/bin/montage-im7.q16 to provide /usr/bin/montage (montage) in auto mode 709s update-alternatives: using /usr/bin/montage-im7.q16 to provide /usr/bin/montage-im7 (montage-im7) in auto mode 709s update-alternatives: using /usr/bin/mogrify-im7.q16 to provide /usr/bin/mogrify (mogrify) in auto mode 709s update-alternatives: using /usr/bin/mogrify-im7.q16 to provide /usr/bin/mogrify-im7 (mogrify-im7) in auto mode 709s update-alternatives: using /usr/bin/magick-im7.q16 to provide /usr/bin/magick (magick) in auto mode 709s 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 709s update-alternatives: using /usr/bin/magick-im7.q16 to provide /usr/bin/magick-im7 (magick-im7) in auto mode 709s 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 709s update-alternatives: using /usr/bin/magick-script-im7.q16 to provide /usr/bin/magick-script (magick-script) in auto mode 709s 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 709s update-alternatives: using /usr/bin/magick-script-im7.q16 to provide /usr/bin/magick-script-im7 (magick-script-im7) in auto mode 709s 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 709s Setting up hevea (2.36-2build3) ... 709s Setting up imagemagick (8:7.1.2.12+dfsg1-1) ... 709s Processing triggers for install-info (7.2-5) ... 709s Processing triggers for libc-bin (2.42-2ubuntu4) ... 709s Processing triggers for systemd (259-1ubuntu2) ... 710s Processing triggers for man-db (2.13.1-1) ... 711s Processing triggers for shared-mime-info (2.4-5build2) ... 712s Processing triggers for sgml-base (1.31+nmu1) ... 712s Setting up w3c-sgml-lib (1.3-3build1) ... 738s Setting up docutils-common (0.22.4+dfsg-1) ... 738s Setting up python3-biopython (1.86+dfsg-1) ... 740s Setting up python3-biopython-sql (1.86+dfsg-1) ... 740s Processing triggers for sgml-base (1.31+nmu1) ... 740s Setting up python3-docutils (0.22.4+dfsg-1) ... 741s Setting up python3-sphinx (8.2.3-12) ... 743s Setting up python3-sphinxcontrib.jquery (4.1-6) ... 743s Setting up python3-numpydoc (1.9.0-1) ... 743s Setting up python3-sphinx-rtd-theme (3.0.2+dfsg-3) ... 744s Processing triggers for tex-common (6.20) ... 744s Running updmap-sys. This may take some time... done. 744s Running mktexlsr /var/lib/texmf ... done. 744s Building format(s) --all. 797s This may take some time... done. 804s autopkgtest [22:28:58]: test full_suite: sh debian/tests/run-unit-test 804s autopkgtest [22:28:58]: test full_suite: [----------------------- 807s mkdir: created directory 'Bio' 807s mkdir: created directory 'Bio/Align' 807s mkdir: created directory 'Bio/Align/substitution_matrices' 807s mkdir: created directory 'Bio/Align/substitution_matrices/data/' 807s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER22' -> 'Bio/Align/substitution_matrices/data/BENNER22' 807s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER6' -> 'Bio/Align/substitution_matrices/data/BENNER6' 807s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER74' -> 'Bio/Align/substitution_matrices/data/BENNER74' 807s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLASTN' -> 'Bio/Align/substitution_matrices/data/BLASTN' 807s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLASTP' -> 'Bio/Align/substitution_matrices/data/BLASTP' 807s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM45' -> 'Bio/Align/substitution_matrices/data/BLOSUM45' 807s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM50' -> 'Bio/Align/substitution_matrices/data/BLOSUM50' 807s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM62' -> 'Bio/Align/substitution_matrices/data/BLOSUM62' 807s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM80' -> 'Bio/Align/substitution_matrices/data/BLOSUM80' 807s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM90' -> 'Bio/Align/substitution_matrices/data/BLOSUM90' 807s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/DAYHOFF' -> 'Bio/Align/substitution_matrices/data/DAYHOFF' 807s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/FENG' -> 'Bio/Align/substitution_matrices/data/FENG' 807s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/GENETIC' -> 'Bio/Align/substitution_matrices/data/GENETIC' 807s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/GONNET1992' -> 'Bio/Align/substitution_matrices/data/GONNET1992' 807s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/HOXD70' -> 'Bio/Align/substitution_matrices/data/HOXD70' 807s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/JOHNSON' -> 'Bio/Align/substitution_matrices/data/JOHNSON' 807s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/JONES' -> 'Bio/Align/substitution_matrices/data/JONES' 807s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/LEVIN' -> 'Bio/Align/substitution_matrices/data/LEVIN' 807s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MCLACHLAN' -> 'Bio/Align/substitution_matrices/data/MCLACHLAN' 807s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MDM78' -> 'Bio/Align/substitution_matrices/data/MDM78' 807s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MEGABLAST' -> 'Bio/Align/substitution_matrices/data/MEGABLAST' 807s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/NUC.4.4' -> 'Bio/Align/substitution_matrices/data/NUC.4.4' 807s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM250' -> 'Bio/Align/substitution_matrices/data/PAM250' 807s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM30' -> 'Bio/Align/substitution_matrices/data/PAM30' 807s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM70' -> 'Bio/Align/substitution_matrices/data/PAM70' 807s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/RAO' -> 'Bio/Align/substitution_matrices/data/RAO' 807s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/RISLER' -> 'Bio/Align/substitution_matrices/data/RISLER' 807s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/SCHNEIDER' -> 'Bio/Align/substitution_matrices/data/SCHNEIDER' 807s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/STR' -> 'Bio/Align/substitution_matrices/data/STR' 807s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/TRANS' -> 'Bio/Align/substitution_matrices/data/TRANS' 807s test_Ace ... ok 807s test_Affy ... ok 807s test_AlignIO ... ok 807s test_AlignIO_ClustalIO ... ok 807s test_AlignIO_EmbossIO ... ok 808s test_AlignIO_FastaIO ... ok 808s test_AlignIO_MauveIO ... ok 808s test_AlignIO_PhylipIO ... ok 808s test_AlignIO_convert ... ok 808s test_Align_Alignment ... ok 808s test_Align_a2m ... ok 808s test_Align_bed ... ok 808s test_Align_bigbed ... ok 809s test_Align_bigmaf ... ok 809s test_Align_bigpsl ... ok 809s test_Align_chain ... ok 809s test_Align_clustal ... ok 814s test_Align_codonalign ... ok 814s test_Align_emboss ... ok 814s test_Align_exonerate ... ok 815s test_Align_fasta ... ok 815s test_Align_format_matrix ... ok 815s test_Align_hhr ... ok 816s test_Align_maf ... ok 816s test_Align_mauve ... ok 816s test_Align_msf ... ok 816s test_Align_nexus ... ok 816s test_Align_phylip ... ok 817s test_Align_psl ... ok 817s test_Align_sam ... ok 819s test_Align_stockholm ... ok 819s test_Align_tabular ... ok 819s test_BioSQL_MySQLdb_online ... skipping. internet not available 819s test_BioSQL_mysql_connector ... skipping. BioSQL test configuration file biosql.ini missing (see biosql.ini.sample) 819s test_BioSQL_mysql_connector_online ... skipping. internet not available 819s test_BioSQL_psycopg2_online ... skipping. internet not available 823s test_BioSQL_sqlite3 ... ok 823s test_BioSQL_sqlite3_online ... skipping. internet not available 823s test_Blast_Record ... ok 824s test_Blast_parser ... ok 824s test_CAPS ... ok 824s test_Chi2 ... ok 824s test_Cluster ... ok 824s test_CodonTable ... ok 824s test_ColorSpiral ... ok 824s test_Compass ... ok 825s test_Consensus ... ok 825s test_EMBL_unittest ... ok 826s test_EmbossPrimer ... ok 830s test_Entrez ... ok 830s test_Entrez_online ... skipping. internet not available 830s test_Entrez_parser ... ok 830s test_Enzyme ... ok 830s test_ExPASy ... skipping. internet not available 830s test_File ... ok 831s test_GenBank ... ok 832s test_GenomeDiagram ... Warn: Can't find .pfb for face 'Helvetica' 834s ok 835s test_GraphicsChromosome ... ok 835s test_GraphicsDistribution ... ok 835s test_GraphicsGeneral ... ok 835s test_KEGG ... ok 835s test_KEGG_online ... skipping. internet not available 840s test_KGML_graphics ... ok 840s test_KGML_graphics_online ... skipping. internet not available 841s test_KGML_nographics ... ok 841s test_KeyWList ... ok 841s test_MafIO_index ... ok 841s test_Medline ... ok 842s test_NCBIXML ... Exception ignored in: 842s Traceback (most recent call last): 842s File "/usr/lib/python3/dist-packages/Bio/Blast/NCBIXML.py", line 1319, in parse 842s expat_parser.Parse(NULL, True) 842s xml.parsers.expat.ExpatError: unclosed token: line 320, column 0 842s ok 842s test_NCBI_qblast ... ok 842s test_NMR ... ok 842s test_Nexus ... ok 842s test_PAML_baseml ... ok 843s test_PAML_codeml ... ok 843s test_PAML_yn00 ... ok 847s test_PDB_CEAligner ... ok 848s test_PDB_DSSP ... ok 848s test_PDB_Dice ... ok 849s test_PDB_Disordered ... ok 849s test_PDB_Exposure ... ok 849s test_PDB_FragmentMapper ... ok 851s test_PDB_KDTree ... ok 851s test_PDB_MMCIF2Dict ... ok 851s test_PDB_MMCIFIO ... ok 852s test_PDB_MMCIFParser ... ok 852s test_PDB_NACCESS ... ok 852s test_PDB_PDBIO ... ok 852s test_PDB_PDBList ... skipping. internet not available 859s test_PDB_PDBMLParser ... ok 859s test_PDB_PDBParser ... ok 859s 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 859s test_PDB_Polypeptide ... ok 859s test_PDB_QCPSuperimposer ... ok 862s test_PDB_SASA ... ok 862s test_PDB_SMCRA ... ok 862s test_PDB_Selection ... ok 863s test_PDB_StructureAlignment ... ok 863s test_PDB_Superimposer ... ok 863s test_PDB_alphafold_db ... skipping. internet not available 866s test_PDB_binary_cif ... /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 1, ' ') redefined at line 7. 866s warnings.warn( 866s /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 15, ' ') redefined at line 144. 866s warnings.warn( 866s /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 15, ' ') redefined at line 153. 866s warnings.warn( 866s /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 1, ' ') redefined at line 0. 866s warnings.warn( 866s /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 15, ' ') redefined at line 0. 866s warnings.warn( 866s ok 874s test_PDB_internal_coords ... ok 874s test_PDB_parse_pdb_header ... ok 874s test_PDB_vectors ... ok 875s test_PQR ... ok 875s test_Pathway ... ok 875s test_Phd ... ok 876s test_Phylo ... ok 876s test_PhyloXML ... ok 877s test_Phylo_CDAO ... ok 877s test_Phylo_NeXML ... ok 878s test_Phylo_igraph ... ok 881s test_Phylo_matplotlib ... ok 882s test_Phylo_networkx ... ok 883s test_PopGen_GenePop_nodepend ... ok 883s test_ProtParam ... ok 884s test_RCSBFormats ... ok 885s test_Restriction ... ok 885s test_SCOP_Astral ... ok 886s test_SCOP_Cla ... ok 886s test_SCOP_Des ... ok 887s test_SCOP_Dom ... ok 888s test_SCOP_Hie ... ok 888s test_SCOP_Raf ... ok 889s test_SCOP_Residues ... ok 889s test_SCOP_Scop ... ok 890s test_SVDSuperimposer ... ok 891s test_SearchIO_blast_tab ... ok 891s test_SearchIO_blast_tab_index ... ok 892s test_SearchIO_blast_xml ... ok 894s test_SearchIO_blast_xml_index ... ok 894s test_SearchIO_blat_psl ... ok 895s test_SearchIO_blat_psl_index ... ok 896s test_SearchIO_exonerate ... ok 896s test_SearchIO_exonerate_text_index ... ok 897s test_SearchIO_exonerate_vulgar_index ... ok 897s test_SearchIO_fasta_m10 ... ok 898s test_SearchIO_fasta_m10_index ... ok 899s test_SearchIO_hhsuite2_text ... ok 900s test_SearchIO_hmmer2_text ... ok 900s test_SearchIO_hmmer2_text_index ... ok 901s test_SearchIO_hmmer3_domtab ... ok 901s test_SearchIO_hmmer3_domtab_index ... ok 902s test_SearchIO_hmmer3_tab ... ok 902s test_SearchIO_hmmer3_tab_index ... ok 903s test_SearchIO_hmmer3_text ... ok 904s test_SearchIO_hmmer3_text_index ... ok 904s test_SearchIO_infernal_tab ... ok 905s test_SearchIO_infernal_tab_index ... ok 906s test_SearchIO_infernal_text ... ok 906s test_SearchIO_infernal_text_index ... ok 907s test_SearchIO_interproscan_xml ... ok 907s test_SearchIO_model ... ok 908s test_SearchIO_write ... ok 909s test_SeqFeature ... ok 926s test_SeqIO ... ok 927s test_SeqIO_AbiIO ... ok 928s test_SeqIO_FastaIO ... ok 928s test_SeqIO_Gck ... ok 929s test_SeqIO_Gfa ... ok 930s test_SeqIO_Insdc ... ok 930s test_SeqIO_NibIO ... ok 933s test_SeqIO_PdbIO ... ok 933s test_SeqIO_QualityIO ... ok 934s test_SeqIO_SeqXML ... ok 935s test_SeqIO_SffIO ... ok 935s test_SeqIO_SnapGene ... ok 936s test_SeqIO_TwoBitIO ... ok 937s test_SeqIO_UniprotIO ... ok 938s test_SeqIO_Xdna ... ok 939s test_SeqIO_features ... ok 952s test_SeqIO_index ... ok 952s test_SeqIO_online ... skipping. internet not available 953s test_SeqIO_write ... ok 954s test_SeqRecord ... ok 954s test_SeqUtils ... ok 956s test_Seq_objs ... ok 957s test_SwissProt ... ok 957s test_TogoWS ... skipping. internet not available 959s test_TreeConstruction ... ok 959s test_Tutorial ... skipping. Could not find ../Doc/Tutorial/index.rst file 960s test_UniGene ... ok 960s test_UniProt ... skipping. internet not available 961s test_UniProt_GOA ... ok 962s test_align ... ok 962s test_align_substitution_matrices ... ok 965s test_bgzf ... ok 966s test_cellosaurus ... ok 971s test_codonalign ... ok 972s test_geo ... ok 973s test_motifs ... ok 974s test_motifs_online ... skipping. internet not available 974s 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. 974s warnings.warn( 974s ok 975s test_pairwise2_no_C ... ok 976s test_pairwise_aligner ... ok 977s test_pairwise_alignment_map ... ok 984s test_phenotype ... ok 985s test_phenotype_fit ... ok 985s test_prodoc ... ok 986s test_prosite ... ok 987s test_seq ... ok 988s test_translate ... ok 988s Skipping any tests requiring internet access 988s Python version: 3.13.11 (main, Dec 6 2025, 13:15:20) [GCC 15.2.0] 988s Operating system: posix linux 988s ---------------------------------------------------------------------- 988s Ran 201 tests in 181.146 seconds 988s 990s :0: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/protein_lib.fa' mode='rt' encoding='UTF-8'> 990s :0: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/nucleotide_lib.fa' mode='rt' encoding='UTF-8'> 991s test_Ace ... ok 991s test_Affy ... ok 991s test_AlignIO ... ok 991s test_AlignIO_ClustalIO ... ok 991s test_AlignIO_EmbossIO ... ok 991s test_AlignIO_FastaIO ... ok 991s test_AlignIO_MauveIO ... ok 991s test_AlignIO_PhylipIO ... ok 991s test_AlignIO_convert ... ok 992s test_Align_Alignment ... ok 992s test_Align_a2m ... ok 992s test_Align_bed ... ok 992s test_Align_bigbed ... ok 993s test_Align_bigmaf ... ok 993s test_Align_bigpsl ... ok 993s test_Align_chain ... ok 993s test_Align_clustal ... ok 998s test_Align_codonalign ... FAIL 998s test_Align_emboss ... ok 998s test_Align_exonerate ... ok 998s test_Align_fasta ... ok 998s test_Align_format_matrix ... ok 999s test_Align_hhr ... ok 1000s test_Align_maf ... ok 1000s test_Align_mauve ... ok 1000s test_Align_msf ... ok 1000s test_Align_nexus ... ok 1000s test_Align_phylip ... ok 1000s test_Align_psl ... ok 1001s test_Align_sam ... ok 1002s test_Align_stockholm ... ok 1003s test_Align_tabular ... ok 1003s test_BioSQL_MySQLdb_online ... skipping. internet not available 1003s test_BioSQL_mysql_connector ... skipping. BioSQL test configuration file biosql.ini missing (see biosql.ini.sample) 1003s test_BioSQL_mysql_connector_online ... skipping. internet not available 1003s test_BioSQL_psycopg2_online ... skipping. internet not available 1007s test_BioSQL_sqlite3 ... ok 1007s test_BioSQL_sqlite3_online ... skipping. internet not available 1007s test_Blast_Record ... ok 1008s test_Blast_parser ... ok 1008s test_CAPS ... ok 1008s test_Chi2 ... ERROR 1008s test_Cluster ... ok 1008s test_CodonTable ... ok 1009s test_ColorSpiral ... ok 1009s test_Compass ... ok 1009s test_Consensus ... ERROR 1009s test_EMBL_unittest ... ok 1009s test_EmbossPrimer ... ok 1013s test_Entrez ... ok 1013s test_Entrez_online ... skipping. internet not available 1014s test_Entrez_parser ... ok 1014s test_Enzyme ... ok 1014s test_ExPASy ... skipping. internet not available 1014s test_File ... ok 1014s test_GenBank ... ok 1016s test_GenomeDiagram ... Warn: Can't find .pfb for face 'Helvetica' 1018s ok 1018s test_GraphicsChromosome ... ok 1018s test_GraphicsDistribution ... ok 1019s test_GraphicsGeneral ... ok 1019s test_KEGG ... ok 1019s test_KEGG_online ... skipping. internet not available 1023s test_KGML_graphics ... ok 1023s test_KGML_graphics_online ... skipping. internet not available 1024s test_KGML_nographics ... ok 1024s test_KeyWList ... ok 1025s test_MafIO_index ... ok 1025s test_Medline ... ok 1026s test_NCBIXML ... Exception ignored while closing generator : 1026s Traceback (most recent call last): 1026s File "/usr/lib/python3/dist-packages/Bio/Blast/NCBIXML.py", line 1319, in parse 1026s expat_parser.Parse(NULL, True) 1026s xml.parsers.expat.ExpatError: unclosed token: line 320, column 0 1026s ok 1026s test_NCBI_qblast ... ok 1026s test_NMR ... ok 1026s test_Nexus ... ok 1026s test_PAML_baseml ... ERROR 1026s test_PAML_codeml ... ERROR 1027s test_PAML_yn00 ... ERROR 1030s test_PDB_CEAligner ... ok 1032s test_PDB_DSSP ... ok 1032s test_PDB_Dice ... ok 1032s test_PDB_Disordered ... ok 1032s test_PDB_Exposure ... ok 1032s test_PDB_FragmentMapper ... ok 1034s test_PDB_KDTree ... ok 1034s test_PDB_MMCIF2Dict ... ok 1034s test_PDB_MMCIFIO ... ok 1035s test_PDB_MMCIFParser ... ok 1036s test_PDB_NACCESS ... ok 1036s test_PDB_PDBIO ... ok 1036s test_PDB_PDBList ... skipping. internet not available 1042s test_PDB_PDBMLParser ... ok 1042s test_PDB_PDBParser ... ok 1042s 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 1042s test_PDB_Polypeptide ... ok 1042s test_PDB_QCPSuperimposer ... ok 1044s test_PDB_SASA ... ok 1045s test_PDB_SMCRA ... ok 1045s test_PDB_Selection ... ok 1046s test_PDB_StructureAlignment ... ok 1046s test_PDB_Superimposer ... ok 1046s test_PDB_alphafold_db ... skipping. internet not available 1051s test_PDB_binary_cif ... /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 1, ' ') redefined at line 7. 1051s warnings.warn( 1051s /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 15, ' ') redefined at line 144. 1051s warnings.warn( 1051s /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 15, ' ') redefined at line 153. 1051s warnings.warn( 1051s /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 1, ' ') redefined at line 0. 1051s warnings.warn( 1051s /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 15, ' ') redefined at line 0. 1051s warnings.warn( 1051s ok 1056s test_PDB_internal_coords ... ok 1056s test_PDB_parse_pdb_header ... ok 1056s test_PDB_vectors ... ok 1056s test_PQR ... ok 1057s test_Pathway ... ok 1057s test_Phd ... ok 1058s test_Phylo ... ERROR 1058s test_PhyloXML ... ERROR 1058s test_Phylo_CDAO ... ERROR 1058s test_Phylo_NeXML ... ERROR 1058s test_Phylo_igraph ... ERROR 1059s test_Phylo_matplotlib ... ERROR 1059s test_Phylo_networkx ... ERROR 1059s test_PopGen_GenePop_nodepend ... ok 1060s test_ProtParam ... ok 1060s test_RCSBFormats ... ok 1061s test_Restriction ... ok 1061s test_SCOP_Astral ... ok 1061s test_SCOP_Cla ... ok 1061s test_SCOP_Des ... ok 1061s test_SCOP_Dom ... ok 1062s test_SCOP_Hie ... ok 1062s test_SCOP_Raf ... ok 1062s test_SCOP_Residues ... ok 1062s test_SCOP_Scop ... ok 1063s test_SVDSuperimposer ... ok 1063s test_SearchIO_blast_tab ... ok 1063s test_SearchIO_blast_tab_index ... ok 1064s test_SearchIO_blast_xml ... ok 1065s test_SearchIO_blast_xml_index ... ok 1066s test_SearchIO_blat_psl ... ok 1066s test_SearchIO_blat_psl_index ... ok 1066s test_SearchIO_exonerate ... ok 1067s test_SearchIO_exonerate_text_index ... ok 1067s test_SearchIO_exonerate_vulgar_index ... ok 1067s test_SearchIO_fasta_m10 ... ok 1067s test_SearchIO_fasta_m10_index ... ok 1068s test_SearchIO_hhsuite2_text ... ok 1068s test_SearchIO_hmmer2_text ... ok 1069s test_SearchIO_hmmer2_text_index ... ok 1069s test_SearchIO_hmmer3_domtab ... ok 1069s test_SearchIO_hmmer3_domtab_index ... ok 1069s test_SearchIO_hmmer3_tab ... ok 1070s test_SearchIO_hmmer3_tab_index ... ok 1070s test_SearchIO_hmmer3_text ... ok 1070s test_SearchIO_hmmer3_text_index ... ok 1071s test_SearchIO_infernal_tab ... ok 1071s test_SearchIO_infernal_tab_index ... ok 1071s test_SearchIO_infernal_text ... ok 1071s test_SearchIO_infernal_text_index ... ok 1072s test_SearchIO_interproscan_xml ... ok 1072s test_SearchIO_model ... ok 1072s test_SearchIO_write ... ok 1073s test_SeqFeature ... ok 1087s test_SeqIO ... ok 1087s test_SeqIO_AbiIO ... ok 1088s test_SeqIO_FastaIO ... ok 1088s test_SeqIO_Gck ... ok 1088s test_SeqIO_Gfa ... ok 1089s test_SeqIO_Insdc ... ok 1089s test_SeqIO_NibIO ... ok 1091s test_SeqIO_PdbIO ... ok 1091s test_SeqIO_QualityIO ... ok 1091s test_SeqIO_SeqXML ... ok 1092s test_SeqIO_SffIO ... ok 1092s test_SeqIO_SnapGene ... ok 1093s test_SeqIO_TwoBitIO ... ok 1093s test_SeqIO_UniprotIO ... ok 1094s test_SeqIO_Xdna ... ok 1094s test_SeqIO_features ... ok 1107s test_SeqIO_index ... ok 1108s test_SeqIO_online ... skipping. internet not available 1108s test_SeqIO_write ... ok 1108s test_SeqRecord ... ok 1108s test_SeqUtils ... ok 1110s test_Seq_objs ... ok 1110s test_SwissProt ... ok 1110s test_TogoWS ... skipping. internet not available 1111s test_TreeConstruction ... ERROR 1111s test_Tutorial ... skipping. Could not find ../Doc/Tutorial/index.rst file 1111s test_UniGene ... ok 1111s test_UniProt ... skipping. internet not available 1112s test_UniProt_GOA ... ok 1112s test_align ... ok 1113s test_align_substitution_matrices ... ok 1115s test_bgzf ... ok 1115s test_cellosaurus ... ok 1119s test_codonalign ... FAIL 1119s test_geo ... ok 1120s test_motifs ... ok 1120s test_motifs_online ... skipping. internet not available 1120s 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. 1120s warnings.warn( 1120s ok 1121s test_pairwise2_no_C ... ok 1121s test_pairwise_aligner ... ok 1122s test_pairwise_alignment_map ... ok 1129s test_phenotype ... ok 1129s test_phenotype_fit ... ok 1129s test_prodoc ... ok 1130s test_prosite ... ok 1130s test_seq ... ok 1130s test_translate ... ok 1131s ====================================================================== 1131s ERROR: test_dn_ds (test_Align_codonalign.Test_dn_ds.test_dn_ds) 1131s ---------------------------------------------------------------------- 1131s Traceback (most recent call last): 1131s File "/tmp/autopkgtest.kXGLKo/autopkgtest_tmp/Tests/test_Align_codonalign.py", line 8313, in test_dn_ds 1131s dn, ds = calculate_dn_ds_matrix(alignment) 1131s ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^ 1131s File "/usr/lib/python3/dist-packages/Bio/Align/analysis.py", line 1012, in calculate_dn_ds_matrix 1131s from Bio.Phylo.TreeConstruction import DistanceMatrix 1131s File "/usr/lib/python3/dist-packages/Bio/Phylo/__init__.py", line 14, in 1131s from Bio.Phylo._io import convert 1131s File "/usr/lib/python3/dist-packages/Bio/Phylo/_io.py", line 29, in 1131s from Bio.Phylo import CDAOIO 1131s File "/usr/lib/python3/dist-packages/Bio/Phylo/CDAOIO.py", line 37, in 1131s import rdflib 1131s File "/usr/lib/python3/dist-packages/rdflib/__init__.py", line 168, in 1131s from rdflib.graph import ConjunctiveGraph, Dataset, Graph 1131s File "/usr/lib/python3/dist-packages/rdflib/graph.py", line 292, in 1131s from rdflib.resource import Resource 1131s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 296, in 1131s class Resource: 1131s ...<164 lines>... 1131s return "Resource(%s,%s)" % (self._graph, self._identifier) 1131s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 379, in Resource 1131s def value(self, p=RDF.value, o=None, default=None, any=True): 1131s ^^^^^^^^^ 1131s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 285, in __getattr__ 1131s return cls.__getitem__(name) 1131s ~~~~~~~~~~~~~~~^^^^^^ 1131s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 268, in __getitem__ 1131s raise AttributeError(f"term '{name}' not in namespace '{cls._NS}'") 1131s AttributeError: term 'value' not in namespace 'http://www.w3.org/1999/02/22-rdf-syntax-ns#' 1131s 1131s ====================================================================== 1131s ERROR: test_Chi2 1131s ---------------------------------------------------------------------- 1131s Traceback (most recent call last): 1131s File "/tmp/autopkgtest.kXGLKo/autopkgtest_tmp/Tests/run_tests.py", line 245, in runTest 1131s suite = loader.loadTestsFromName(name) 1131s File "/usr/lib/python3.14/unittest/loader.py", line 137, in loadTestsFromName 1131s module = __import__(module_name) 1131s File "/tmp/autopkgtest.kXGLKo/autopkgtest_tmp/Tests/test_Chi2.py", line 10, in 1131s from Bio.Phylo.PAML import chi2 1131s File "/usr/lib/python3/dist-packages/Bio/Phylo/__init__.py", line 14, in 1131s from Bio.Phylo._io import convert 1131s File "/usr/lib/python3/dist-packages/Bio/Phylo/_io.py", line 29, in 1131s from Bio.Phylo import CDAOIO 1131s File "/usr/lib/python3/dist-packages/Bio/Phylo/CDAOIO.py", line 37, in 1131s import rdflib 1131s File "/usr/lib/python3/dist-packages/rdflib/__init__.py", line 168, in 1131s from rdflib.graph import ConjunctiveGraph, Dataset, Graph 1131s File "/usr/lib/python3/dist-packages/rdflib/graph.py", line 292, in 1131s from rdflib.resource import Resource 1131s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 296, in 1131s class Resource: 1131s ...<164 lines>... 1131s return "Resource(%s,%s)" % (self._graph, self._identifier) 1131s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 379, in Resource 1131s def value(self, p=RDF.value, o=None, default=None, any=True): 1131s ^^^^^^^^^ 1131s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 285, in __getattr__ 1131s return cls.__getitem__(name) 1131s ~~~~~~~~~~~~~~~^^^^^^ 1131s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 268, in __getitem__ 1131s raise AttributeError(f"term '{name}' not in namespace '{cls._NS}'") 1131s AttributeError: term 'value' not in namespace 'http://www.w3.org/1999/02/22-rdf-syntax-ns#' 1131s ====================================================================== 1131s ERROR: test_Consensus 1131s ---------------------------------------------------------------------- 1131s Traceback (most recent call last): 1131s File "/tmp/autopkgtest.kXGLKo/autopkgtest_tmp/Tests/run_tests.py", line 245, in runTest 1131s suite = loader.loadTestsFromName(name) 1131s File "/usr/lib/python3.14/unittest/loader.py", line 137, in loadTestsFromName 1131s module = __import__(module_name) 1131s File "/tmp/autopkgtest.kXGLKo/autopkgtest_tmp/Tests/test_Consensus.py", line 15, in 1131s from Bio import Phylo 1131s File "/usr/lib/python3/dist-packages/Bio/Phylo/__init__.py", line 14, in 1131s from Bio.Phylo._io import convert 1131s File "/usr/lib/python3/dist-packages/Bio/Phylo/_io.py", line 29, in 1131s from Bio.Phylo import CDAOIO 1131s File "/usr/lib/python3/dist-packages/Bio/Phylo/CDAOIO.py", line 37, in 1131s import rdflib 1131s File "/usr/lib/python3/dist-packages/rdflib/__init__.py", line 168, in 1131s from rdflib.graph import ConjunctiveGraph, Dataset, Graph 1131s File "/usr/lib/python3/dist-packages/rdflib/graph.py", line 292, in 1131s from rdflib.resource import Resource 1131s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 296, in 1131s class Resource: 1131s ...<164 lines>... 1131s return "Resource(%s,%s)" % (self._graph, self._identifier) 1131s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 379, in Resource 1131s def value(self, p=RDF.value, o=None, default=None, any=True): 1131s ^^^^^^^^^ 1131s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 285, in __getattr__ 1131s return cls.__getitem__(name) 1131s ~~~~~~~~~~~~~~~^^^^^^ 1131s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 268, in __getitem__ 1131s raise AttributeError(f"term '{name}' not in namespace '{cls._NS}'") 1131s AttributeError: term 'value' not in namespace 'http://www.w3.org/1999/02/22-rdf-syntax-ns#' 1131s ====================================================================== 1131s ERROR: test_PAML_baseml 1131s ---------------------------------------------------------------------- 1131s Traceback (most recent call last): 1131s File "/tmp/autopkgtest.kXGLKo/autopkgtest_tmp/Tests/run_tests.py", line 245, in runTest 1131s suite = loader.loadTestsFromName(name) 1131s File "/usr/lib/python3.14/unittest/loader.py", line 137, in loadTestsFromName 1131s module = __import__(module_name) 1131s File "/tmp/autopkgtest.kXGLKo/autopkgtest_tmp/Tests/test_PAML_baseml.py", line 12, in 1131s from Bio.Phylo.PAML import baseml 1131s File "/usr/lib/python3/dist-packages/Bio/Phylo/__init__.py", line 14, in 1131s from Bio.Phylo._io import convert 1131s File "/usr/lib/python3/dist-packages/Bio/Phylo/_io.py", line 29, in 1131s from Bio.Phylo import CDAOIO 1131s File "/usr/lib/python3/dist-packages/Bio/Phylo/CDAOIO.py", line 37, in 1131s import rdflib 1131s File "/usr/lib/python3/dist-packages/rdflib/__init__.py", line 168, in 1131s from rdflib.graph import ConjunctiveGraph, Dataset, Graph 1131s File "/usr/lib/python3/dist-packages/rdflib/graph.py", line 292, in 1131s from rdflib.resource import Resource 1131s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 296, in 1131s class Resource: 1131s ...<164 lines>... 1131s return "Resource(%s,%s)" % (self._graph, self._identifier) 1131s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 379, in Resource 1131s def value(self, p=RDF.value, o=None, default=None, any=True): 1131s ^^^^^^^^^ 1131s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 285, in __getattr__ 1131s return cls.__getitem__(name) 1131s ~~~~~~~~~~~~~~~^^^^^^ 1131s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 268, in __getitem__ 1131s raise AttributeError(f"term '{name}' not in namespace '{cls._NS}'") 1131s AttributeError: term 'value' not in namespace 'http://www.w3.org/1999/02/22-rdf-syntax-ns#' 1131s ====================================================================== 1131s ERROR: test_PAML_codeml 1131s ---------------------------------------------------------------------- 1131s Traceback (most recent call last): 1131s File "/tmp/autopkgtest.kXGLKo/autopkgtest_tmp/Tests/run_tests.py", line 245, in runTest 1131s suite = loader.loadTestsFromName(name) 1131s File "/usr/lib/python3.14/unittest/loader.py", line 137, in loadTestsFromName 1131s module = __import__(module_name) 1131s File "/tmp/autopkgtest.kXGLKo/autopkgtest_tmp/Tests/test_PAML_codeml.py", line 13, in 1131s from Bio.Phylo.PAML import codeml 1131s File "/usr/lib/python3/dist-packages/Bio/Phylo/__init__.py", line 14, in 1131s from Bio.Phylo._io import convert 1131s File "/usr/lib/python3/dist-packages/Bio/Phylo/_io.py", line 29, in 1131s from Bio.Phylo import CDAOIO 1131s File "/usr/lib/python3/dist-packages/Bio/Phylo/CDAOIO.py", line 37, in 1131s import rdflib 1131s File "/usr/lib/python3/dist-packages/rdflib/__init__.py", line 168, in 1131s from rdflib.graph import ConjunctiveGraph, Dataset, Graph 1131s File "/usr/lib/python3/dist-packages/rdflib/graph.py", line 292, in 1131s from rdflib.resource import Resource 1131s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 296, in 1131s class Resource: 1131s ...<164 lines>... 1131s return "Resource(%s,%s)" % (self._graph, self._identifier) 1131s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 379, in Resource 1131s def value(self, p=RDF.value, o=None, default=None, any=True): 1131s ^^^^^^^^^ 1131s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 285, in __getattr__ 1131s return cls.__getitem__(name) 1131s ~~~~~~~~~~~~~~~^^^^^^ 1131s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 268, in __getitem__ 1131s raise AttributeError(f"term '{name}' not in namespace '{cls._NS}'") 1131s AttributeError: term 'value' not in namespace 'http://www.w3.org/1999/02/22-rdf-syntax-ns#' 1131s ====================================================================== 1131s ERROR: test_PAML_yn00 1131s ---------------------------------------------------------------------- 1131s Traceback (most recent call last): 1131s File "/tmp/autopkgtest.kXGLKo/autopkgtest_tmp/Tests/run_tests.py", line 245, in runTest 1131s suite = loader.loadTestsFromName(name) 1131s File "/usr/lib/python3.14/unittest/loader.py", line 137, in loadTestsFromName 1131s module = __import__(module_name) 1131s File "/tmp/autopkgtest.kXGLKo/autopkgtest_tmp/Tests/test_PAML_yn00.py", line 13, in 1131s from Bio.Phylo.PAML import yn00 1131s File "/usr/lib/python3/dist-packages/Bio/Phylo/__init__.py", line 14, in 1131s from Bio.Phylo._io import convert 1131s File "/usr/lib/python3/dist-packages/Bio/Phylo/_io.py", line 29, in 1131s from Bio.Phylo import CDAOIO 1131s File "/usr/lib/python3/dist-packages/Bio/Phylo/CDAOIO.py", line 37, in 1131s import rdflib 1131s File "/usr/lib/python3/dist-packages/rdflib/__init__.py", line 168, in 1131s from rdflib.graph import ConjunctiveGraph, Dataset, Graph 1131s File "/usr/lib/python3/dist-packages/rdflib/graph.py", line 292, in 1131s from rdflib.resource import Resource 1131s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 296, in 1131s class Resource: 1131s ...<164 lines>... 1131s return "Resource(%s,%s)" % (self._graph, self._identifier) 1131s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 379, in Resource 1131s def value(self, p=RDF.value, o=None, default=None, any=True): 1131s ^^^^^^^^^ 1131s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 285, in __getattr__ 1131s return cls.__getitem__(name) 1131s ~~~~~~~~~~~~~~~^^^^^^ 1131s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 268, in __getitem__ 1131s raise AttributeError(f"term '{name}' not in namespace '{cls._NS}'") 1131s AttributeError: term 'value' not in namespace 'http://www.w3.org/1999/02/22-rdf-syntax-ns#' 1131s ====================================================================== 1131s ERROR: test_Phylo 1131s ---------------------------------------------------------------------- 1131s Traceback (most recent call last): 1131s File "/tmp/autopkgtest.kXGLKo/autopkgtest_tmp/Tests/run_tests.py", line 245, in runTest 1131s suite = loader.loadTestsFromName(name) 1131s File "/usr/lib/python3.14/unittest/loader.py", line 137, in loadTestsFromName 1131s module = __import__(module_name) 1131s File "/tmp/autopkgtest.kXGLKo/autopkgtest_tmp/Tests/test_Phylo.py", line 13, in 1131s from Bio import Phylo 1131s File "/usr/lib/python3/dist-packages/Bio/Phylo/__init__.py", line 14, in 1131s from Bio.Phylo._io import convert 1131s File "/usr/lib/python3/dist-packages/Bio/Phylo/_io.py", line 29, in 1131s from Bio.Phylo import CDAOIO 1131s File "/usr/lib/python3/dist-packages/Bio/Phylo/CDAOIO.py", line 37, in 1131s import rdflib 1131s File "/usr/lib/python3/dist-packages/rdflib/__init__.py", line 168, in 1131s from rdflib.graph import ConjunctiveGraph, Dataset, Graph 1131s File "/usr/lib/python3/dist-packages/rdflib/graph.py", line 292, in 1131s from rdflib.resource import Resource 1131s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 296, in 1131s class Resource: 1131s ...<164 lines>... 1131s return "Resource(%s,%s)" % (self._graph, self._identifier) 1131s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 379, in Resource 1131s def value(self, p=RDF.value, o=None, default=None, any=True): 1131s ^^^^^^^^^ 1131s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 285, in __getattr__ 1131s return cls.__getitem__(name) 1131s ~~~~~~~~~~~~~~~^^^^^^ 1131s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 268, in __getitem__ 1131s raise AttributeError(f"term '{name}' not in namespace '{cls._NS}'") 1131s AttributeError: term 'value' not in namespace 'http://www.w3.org/1999/02/22-rdf-syntax-ns#' 1131s ====================================================================== 1131s ERROR: test_PhyloXML 1131s ---------------------------------------------------------------------- 1131s Traceback (most recent call last): 1131s File "/tmp/autopkgtest.kXGLKo/autopkgtest_tmp/Tests/run_tests.py", line 245, in runTest 1131s suite = loader.loadTestsFromName(name) 1131s File "/usr/lib/python3.14/unittest/loader.py", line 137, in loadTestsFromName 1131s module = __import__(module_name) 1131s File "/tmp/autopkgtest.kXGLKo/autopkgtest_tmp/Tests/test_PhyloXML.py", line 17, in 1131s from Bio.Phylo import PhyloXML as PX 1131s File "/usr/lib/python3/dist-packages/Bio/Phylo/__init__.py", line 14, in 1131s from Bio.Phylo._io import convert 1131s File "/usr/lib/python3/dist-packages/Bio/Phylo/_io.py", line 29, in 1131s from Bio.Phylo import CDAOIO 1131s File "/usr/lib/python3/dist-packages/Bio/Phylo/CDAOIO.py", line 37, in 1131s import rdflib 1131s File "/usr/lib/python3/dist-packages/rdflib/__init__.py", line 168, in 1131s from rdflib.graph import ConjunctiveGraph, Dataset, Graph 1131s File "/usr/lib/python3/dist-packages/rdflib/graph.py", line 292, in 1131s from rdflib.resource import Resource 1131s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 296, in 1131s class Resource: 1131s ...<164 lines>... 1131s return "Resource(%s,%s)" % (self._graph, self._identifier) 1131s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 379, in Resource 1131s def value(self, p=RDF.value, o=None, default=None, any=True): 1131s ^^^^^^^^^ 1131s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 285, in __getattr__ 1131s return cls.__getitem__(name) 1131s ~~~~~~~~~~~~~~~^^^^^^ 1131s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 268, in __getitem__ 1131s raise AttributeError(f"term '{name}' not in namespace '{cls._NS}'") 1131s AttributeError: term 'value' not in namespace 'http://www.w3.org/1999/02/22-rdf-syntax-ns#' 1131s ====================================================================== 1131s ERROR: test_Phylo_CDAO 1131s ---------------------------------------------------------------------- 1131s Traceback (most recent call last): 1131s File "/tmp/autopkgtest.kXGLKo/autopkgtest_tmp/Tests/run_tests.py", line 245, in runTest 1131s suite = loader.loadTestsFromName(name) 1131s File "/usr/lib/python3.14/unittest/loader.py", line 137, in loadTestsFromName 1131s module = __import__(module_name) 1131s File "/tmp/autopkgtest.kXGLKo/autopkgtest_tmp/Tests/test_Phylo_CDAO.py", line 13, in 1131s import Bio.Phylo as bp 1131s File "/usr/lib/python3/dist-packages/Bio/Phylo/__init__.py", line 14, in 1131s from Bio.Phylo._io import convert 1131s File "/usr/lib/python3/dist-packages/Bio/Phylo/_io.py", line 29, in 1131s from Bio.Phylo import CDAOIO 1131s File "/usr/lib/python3/dist-packages/Bio/Phylo/CDAOIO.py", line 37, in 1131s import rdflib 1131s File "/usr/lib/python3/dist-packages/rdflib/__init__.py", line 168, in 1131s from rdflib.graph import ConjunctiveGraph, Dataset, Graph 1131s File "/usr/lib/python3/dist-packages/rdflib/graph.py", line 292, in 1131s from rdflib.resource import Resource 1131s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 296, in 1131s class Resource: 1131s ...<164 lines>... 1131s return "Resource(%s,%s)" % (self._graph, self._identifier) 1131s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 379, in Resource 1131s def value(self, p=RDF.value, o=None, default=None, any=True): 1131s ^^^^^^^^^ 1131s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 285, in __getattr__ 1131s return cls.__getitem__(name) 1131s ~~~~~~~~~~~~~~~^^^^^^ 1131s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 268, in __getitem__ 1131s raise AttributeError(f"term '{name}' not in namespace '{cls._NS}'") 1131s AttributeError: term 'value' not in namespace 'http://www.w3.org/1999/02/22-rdf-syntax-ns#' 1131s ====================================================================== 1131s ERROR: test_Phylo_NeXML 1131s ---------------------------------------------------------------------- 1131s Traceback (most recent call last): 1131s File "/tmp/autopkgtest.kXGLKo/autopkgtest_tmp/Tests/run_tests.py", line 245, in runTest 1131s suite = loader.loadTestsFromName(name) 1131s File "/usr/lib/python3.14/unittest/loader.py", line 137, in loadTestsFromName 1131s module = __import__(module_name) 1131s File "/tmp/autopkgtest.kXGLKo/autopkgtest_tmp/Tests/test_Phylo_NeXML.py", line 14, in 1131s from Bio import Phylo 1131s File "/usr/lib/python3/dist-packages/Bio/Phylo/__init__.py", line 14, in 1131s from Bio.Phylo._io import convert 1131s File "/usr/lib/python3/dist-packages/Bio/Phylo/_io.py", line 29, in 1131s from Bio.Phylo import CDAOIO 1131s File "/usr/lib/python3/dist-packages/Bio/Phylo/CDAOIO.py", line 37, in 1131s import rdflib 1131s File "/usr/lib/python3/dist-packages/rdflib/__init__.py", line 168, in 1131s from rdflib.graph import ConjunctiveGraph, Dataset, Graph 1131s File "/usr/lib/python3/dist-packages/rdflib/graph.py", line 292, in 1131s from rdflib.resource import Resource 1131s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 296, in 1131s class Resource: 1131s ...<164 lines>... 1131s return "Resource(%s,%s)" % (self._graph, self._identifier) 1131s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 379, in Resource 1131s def value(self, p=RDF.value, o=None, default=None, any=True): 1131s ^^^^^^^^^ 1131s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 285, in __getattr__ 1131s return cls.__getitem__(name) 1131s ~~~~~~~~~~~~~~~^^^^^^ 1131s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 268, in __getitem__ 1131s raise AttributeError(f"term '{name}' not in namespace '{cls._NS}'") 1131s AttributeError: term 'value' not in namespace 'http://www.w3.org/1999/02/22-rdf-syntax-ns#' 1131s ====================================================================== 1131s ERROR: test_Phylo_igraph 1131s ---------------------------------------------------------------------- 1131s Traceback (most recent call last): 1131s File "/tmp/autopkgtest.kXGLKo/autopkgtest_tmp/Tests/run_tests.py", line 245, in runTest 1131s suite = loader.loadTestsFromName(name) 1131s File "/usr/lib/python3.14/unittest/loader.py", line 137, in loadTestsFromName 1131s module = __import__(module_name) 1131s File "/tmp/autopkgtest.kXGLKo/autopkgtest_tmp/Tests/test_Phylo_igraph.py", line 13, in 1131s from Bio import Phylo 1131s File "/usr/lib/python3/dist-packages/Bio/Phylo/__init__.py", line 14, in 1131s from Bio.Phylo._io import convert 1131s File "/usr/lib/python3/dist-packages/Bio/Phylo/_io.py", line 29, in 1131s from Bio.Phylo import CDAOIO 1131s File "/usr/lib/python3/dist-packages/Bio/Phylo/CDAOIO.py", line 37, in 1131s import rdflib 1131s File "/usr/lib/python3/dist-packages/rdflib/__init__.py", line 168, in 1131s from rdflib.graph import ConjunctiveGraph, Dataset, Graph 1131s File "/usr/lib/python3/dist-packages/rdflib/graph.py", line 292, in 1131s from rdflib.resource import Resource 1131s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 296, in 1131s class Resource: 1131s ...<164 lines>... 1131s return "Resource(%s,%s)" % (self._graph, self._identifier) 1131s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 379, in Resource 1131s def value(self, p=RDF.value, o=None, default=None, any=True): 1131s ^^^^^^^^^ 1131s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 285, in __getattr__ 1131s return cls.__getitem__(name) 1131s ~~~~~~~~~~~~~~~^^^^^^ 1131s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 268, in __getitem__ 1131s raise AttributeError(f"term '{name}' not in namespace '{cls._NS}'") 1131s AttributeError: term 'value' not in namespace 'http://www.w3.org/1999/02/22-rdf-syntax-ns#' 1131s ====================================================================== 1131s ERROR: test_Phylo_matplotlib 1131s ---------------------------------------------------------------------- 1131s Traceback (most recent call last): 1131s File "/tmp/autopkgtest.kXGLKo/autopkgtest_tmp/Tests/run_tests.py", line 245, in runTest 1131s suite = loader.loadTestsFromName(name) 1131s File "/usr/lib/python3.14/unittest/loader.py", line 137, in loadTestsFromName 1131s module = __import__(module_name) 1131s File "/tmp/autopkgtest.kXGLKo/autopkgtest_tmp/Tests/test_Phylo_matplotlib.py", line 13, in 1131s from Bio import Phylo 1131s File "/usr/lib/python3/dist-packages/Bio/Phylo/__init__.py", line 14, in 1131s from Bio.Phylo._io import convert 1131s File "/usr/lib/python3/dist-packages/Bio/Phylo/_io.py", line 29, in 1131s from Bio.Phylo import CDAOIO 1131s File "/usr/lib/python3/dist-packages/Bio/Phylo/CDAOIO.py", line 37, in 1131s import rdflib 1131s File "/usr/lib/python3/dist-packages/rdflib/__init__.py", line 168, in 1131s from rdflib.graph import ConjunctiveGraph, Dataset, Graph 1131s File "/usr/lib/python3/dist-packages/rdflib/graph.py", line 292, in 1131s from rdflib.resource import Resource 1131s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 296, in 1131s class Resource: 1131s ...<164 lines>... 1131s return "Resource(%s,%s)" % (self._graph, self._identifier) 1131s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 379, in Resource 1131s def value(self, p=RDF.value, o=None, default=None, any=True): 1131s ^^^^^^^^^ 1131s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 285, in __getattr__ 1131s return cls.__getitem__(name) 1131s ~~~~~~~~~~~~~~~^^^^^^ 1131s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 268, in __getitem__ 1131s raise AttributeError(f"term '{name}' not in namespace '{cls._NS}'") 1131s AttributeError: term 'value' not in namespace 'http://www.w3.org/1999/02/22-rdf-syntax-ns#' 1131s ====================================================================== 1131s ERROR: test_Phylo_networkx 1131s ---------------------------------------------------------------------- 1131s Traceback (most recent call last): 1131s File "/tmp/autopkgtest.kXGLKo/autopkgtest_tmp/Tests/run_tests.py", line 245, in runTest 1131s suite = loader.loadTestsFromName(name) 1131s File "/usr/lib/python3.14/unittest/loader.py", line 137, in loadTestsFromName 1131s module = __import__(module_name) 1131s File "/tmp/autopkgtest.kXGLKo/autopkgtest_tmp/Tests/test_Phylo_networkx.py", line 12, in 1131s from Bio import Phylo 1131s File "/usr/lib/python3/dist-packages/Bio/Phylo/__init__.py", line 14, in 1131s from Bio.Phylo._io import convert 1131s File "/usr/lib/python3/dist-packages/Bio/Phylo/_io.py", line 29, in 1131s from Bio.Phylo import CDAOIO 1131s File "/usr/lib/python3/dist-packages/Bio/Phylo/CDAOIO.py", line 37, in 1131s import rdflib 1131s File "/usr/lib/python3/dist-packages/rdflib/__init__.py", line 168, in 1131s from rdflib.graph import ConjunctiveGraph, Dataset, Graph 1131s File "/usr/lib/python3/dist-packages/rdflib/graph.py", line 292, in 1131s from rdflib.resource import Resource 1131s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 296, in 1131s class Resource: 1131s ...<164 lines>... 1131s return "Resource(%s,%s)" % (self._graph, self._identifier) 1131s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 379, in Resource 1131s def value(self, p=RDF.value, o=None, default=None, any=True): 1131s ^^^^^^^^^ 1131s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 285, in __getattr__ 1131s return cls.__getitem__(name) 1131s ~~~~~~~~~~~~~~~^^^^^^ 1131s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 268, in __getitem__ 1131s raise AttributeError(f"term '{name}' not in namespace '{cls._NS}'") 1131s AttributeError: term 'value' not in namespace 'http://www.w3.org/1999/02/22-rdf-syntax-ns#' 1131s ====================================================================== 1131s ERROR: test_TreeConstruction 1131s ---------------------------------------------------------------------- 1131s Traceback (most recent call last): 1131s File "/tmp/autopkgtest.kXGLKo/autopkgtest_tmp/Tests/run_tests.py", line 245, in runTest 1131s suite = loader.loadTestsFromName(name) 1131s File "/usr/lib/python3.14/unittest/loader.py", line 137, in loadTestsFromName 1131s module = __import__(module_name) 1131s File "/tmp/autopkgtest.kXGLKo/autopkgtest_tmp/Tests/test_TreeConstruction.py", line 16, in 1131s from Bio import Phylo 1131s File "/usr/lib/python3/dist-packages/Bio/Phylo/__init__.py", line 14, in 1131s from Bio.Phylo._io import convert 1131s File "/usr/lib/python3/dist-packages/Bio/Phylo/_io.py", line 29, in 1131s from Bio.Phylo import CDAOIO 1131s File "/usr/lib/python3/dist-packages/Bio/Phylo/CDAOIO.py", line 37, in 1131s import rdflib 1131s File "/usr/lib/python3/dist-packages/rdflib/__init__.py", line 168, in 1131s from rdflib.graph import ConjunctiveGraph, Dataset, Graph 1131s File "/usr/lib/python3/dist-packages/rdflib/graph.py", line 292, in 1131s from rdflib.resource import Resource 1131s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 296, in 1131s class Resource: 1131s ...<164 lines>... 1131s return "Resource(%s,%s)" % (self._graph, self._identifier) 1131s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 379, in Resource 1131s def value(self, p=RDF.value, o=None, default=None, any=True): 1131s ^^^^^^^^^ 1131s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 285, in __getattr__ 1131s return cls.__getitem__(name) 1131s ~~~~~~~~~~~~~~~^^^^^^ 1131s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 268, in __getitem__ 1131s raise AttributeError(f"term '{name}' not in namespace '{cls._NS}'") 1131s AttributeError: term 'value' not in namespace 'http://www.w3.org/1999/02/22-rdf-syntax-ns#' 1131s ====================================================================== 1131s ERROR: test_dn_ds_matrix (test_codonalign.Test_dn_ds.test_dn_ds_matrix) 1131s ---------------------------------------------------------------------- 1131s Traceback (most recent call last): 1131s File "/tmp/autopkgtest.kXGLKo/autopkgtest_tmp/Tests/test_codonalign.py", line 381, in test_dn_ds_matrix 1131s dn, ds = self.aln.get_dn_ds_matrix() 1131s ~~~~~~~~~~~~~~~~~~~~~~~~~^^ 1131s File "/usr/lib/python3/dist-packages/Bio/codonalign/codonalignment.py", line 159, in get_dn_ds_matrix 1131s from Bio.Phylo.TreeConstruction import DistanceMatrix as DM 1131s File "/usr/lib/python3/dist-packages/Bio/Phylo/__init__.py", line 14, in 1131s from Bio.Phylo._io import convert 1131s File "/usr/lib/python3/dist-packages/Bio/Phylo/_io.py", line 29, in 1131s from Bio.Phylo import CDAOIO 1131s File "/usr/lib/python3/dist-packages/Bio/Phylo/CDAOIO.py", line 37, in 1131s import rdflib 1131s File "/usr/lib/python3/dist-packages/rdflib/__init__.py", line 168, in 1131s from rdflib.graph import ConjunctiveGraph, Dataset, Graph 1131s File "/usr/lib/python3/dist-packages/rdflib/graph.py", line 292, in 1131s from rdflib.resource import Resource 1131s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 296, in 1131s class Resource: 1131s ...<164 lines>... 1131s return "Resource(%s,%s)" % (self._graph, self._identifier) 1131s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 379, in Resource 1131s def value(self, p=RDF.value, o=None, default=None, any=True): 1131s ^^^^^^^^^ 1131s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 285, in __getattr__ 1131s return cls.__getitem__(name) 1131s ~~~~~~~~~~~~~~~^^^^^^ 1131s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 268, in __getitem__ 1131s raise AttributeError(f"term '{name}' not in namespace '{cls._NS}'") 1131s AttributeError: term 'value' not in namespace 'http://www.w3.org/1999/02/22-rdf-syntax-ns#' 1131s 1131s ---------------------------------------------------------------------- 1131s Ran 201 tests in 139.888 seconds 1131s 1131s FAILED (failures = 15) 1131s Skipping any tests requiring internet access 1131s Python version: 3.14.2 (main, Dec 6 2025, 13:20:08) [GCC 15.2.0] 1131s Operating system: posix linux 1131s :0: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/protein_lib.fa' mode='rt' encoding='UTF-8'> 1131s :0: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/nucleotide_lib.fa' mode='rt' encoding='UTF-8'> 1132s autopkgtest [22:34:26]: test full_suite: -----------------------] 1133s autopkgtest [22:34:27]: test full_suite: - - - - - - - - - - results - - - - - - - - - - 1133s full_suite FAIL non-zero exit status 1 1133s autopkgtest [22:34:27]: @@@@@@@@@@@@@@@@@@@@ summary 1133s dependencies PASS 1133s full_suite FAIL non-zero exit status 1