0s autopkgtest [23:04:14]: starting date and time: 2025-05-02 23:04:14+0000 0s autopkgtest [23:04:14]: git checkout: 9986aa8c Merge branch 'skia/fix_network_interface' into 'ubuntu/production' 0s autopkgtest [23:04:14]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.ux4d3g10/out --timeout-copy=6000 --setup-commands 'ln -s /dev/null /etc/systemd/system/bluetooth.service; printf "http_proxy=http://squid.internal:3128\nhttps_proxy=http://squid.internal:3128\nno_proxy=127.0.0.1,127.0.1.1,localhost,localdomain,internal,login.ubuntu.com,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com\n" >> /etc/environment' --apt-pocket=proposed=src:setuptools --apt-upgrade python-biopython --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=setuptools/78.1.0-1.2 -- lxd -r lxd-armhf-10.145.243.149 lxd-armhf-10.145.243.149:autopkgtest/ubuntu/questing/armhf 20s autopkgtest [23:04:34]: testbed dpkg architecture: armhf 22s autopkgtest [23:04:36]: testbed apt version: 3.0.0 26s autopkgtest [23:04:40]: @@@@@@@@@@@@@@@@@@@@ test bed setup 28s autopkgtest [23:04:42]: testbed release detected to be: None 35s autopkgtest [23:04:49]: updating testbed package index (apt update) 37s Get:1 http://ftpmaster.internal/ubuntu questing-proposed InRelease [110 kB] 38s Get:2 http://ftpmaster.internal/ubuntu questing InRelease [110 kB] 38s Get:3 http://ftpmaster.internal/ubuntu questing-updates InRelease [110 kB] 38s Get:4 http://ftpmaster.internal/ubuntu questing-security InRelease [110 kB] 38s Get:5 http://ftpmaster.internal/ubuntu questing-proposed/universe Sources [1947 kB] 38s Get:6 http://ftpmaster.internal/ubuntu questing-proposed/main Sources [168 kB] 38s Get:7 http://ftpmaster.internal/ubuntu questing-proposed/multiverse Sources [43.1 kB] 38s Get:8 http://ftpmaster.internal/ubuntu questing-proposed/main armhf Packages [205 kB] 38s Get:9 http://ftpmaster.internal/ubuntu questing-proposed/universe armhf Packages [1371 kB] 38s Get:10 http://ftpmaster.internal/ubuntu questing-proposed/multiverse armhf Packages [12.9 kB] 38s Get:11 http://ftpmaster.internal/ubuntu questing/main Sources [1397 kB] 38s Get:12 http://ftpmaster.internal/ubuntu questing/universe Sources [21.1 MB] 39s Get:13 http://ftpmaster.internal/ubuntu questing/multiverse Sources [299 kB] 39s Get:14 http://ftpmaster.internal/ubuntu questing/main armhf Packages [1358 kB] 39s Get:15 http://ftpmaster.internal/ubuntu questing/universe armhf Packages [15.4 MB] 40s Get:16 http://ftpmaster.internal/ubuntu questing/multiverse armhf Packages [173 kB] 44s Fetched 43.9 MB in 6s (6864 kB/s) 45s Reading package lists... 51s autopkgtest [23:05:05]: upgrading testbed (apt dist-upgrade and autopurge) 53s Reading package lists... 53s Building dependency tree... 53s Reading state information... 54s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 55s Starting 2 pkgProblemResolver with broken count: 0 55s Done 56s Entering ResolveByKeep 57s 57s Calculating upgrade... 58s The following packages will be upgraded: 58s base-files distro-info-data dpkg dpkg-dev ed fwupd htop libdpkg-perl 58s libftdi1-2 libfwupd3 libnpth0t64 libsensors-config libsensors5 liburcu8t64 58s motd-news-config nano python3-pkg-resources python3-setuptools 58s ubuntu-pro-client ubuntu-pro-client-l10n usb.ids 58s 21 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 58s Need to get 6161 kB of archives. 58s After this operation, 3616 kB disk space will be freed. 58s Get:1 http://ftpmaster.internal/ubuntu questing/main armhf motd-news-config all 13.7ubuntu1 [5260 B] 58s Get:2 http://ftpmaster.internal/ubuntu questing/main armhf base-files armhf 13.7ubuntu1 [75.4 kB] 59s Get:3 http://ftpmaster.internal/ubuntu questing/main armhf dpkg armhf 1.22.18ubuntu3 [1254 kB] 59s Get:4 http://ftpmaster.internal/ubuntu questing/main armhf libnpth0t64 armhf 1.8-3 [7716 B] 59s Get:5 http://ftpmaster.internal/ubuntu questing/main armhf distro-info-data all 0.64 [6664 B] 59s Get:6 http://ftpmaster.internal/ubuntu questing/main armhf ubuntu-pro-client-l10n armhf 35.1ubuntu0 [19.7 kB] 59s Get:7 http://ftpmaster.internal/ubuntu questing/main armhf ubuntu-pro-client armhf 35.1ubuntu0 [258 kB] 59s Get:8 http://ftpmaster.internal/ubuntu questing/main armhf ed armhf 1.21.1-1 [53.0 kB] 59s Get:9 http://ftpmaster.internal/ubuntu questing/main armhf libsensors-config all 1:3.6.2-2 [6756 B] 59s Get:10 http://ftpmaster.internal/ubuntu questing/main armhf libsensors5 armhf 1:3.6.2-2 [26.8 kB] 59s Get:11 http://ftpmaster.internal/ubuntu questing/main armhf liburcu8t64 armhf 0.15.2-2 [57.3 kB] 59s Get:12 http://ftpmaster.internal/ubuntu questing/main armhf nano armhf 8.4-1 [278 kB] 59s Get:13 http://ftpmaster.internal/ubuntu questing/main armhf usb.ids all 2025.04.01-1 [223 kB] 59s Get:14 http://ftpmaster.internal/ubuntu questing/main armhf dpkg-dev all 1.22.18ubuntu3 [1089 kB] 59s Get:15 http://ftpmaster.internal/ubuntu questing/main armhf libdpkg-perl all 1.22.18ubuntu3 [281 kB] 59s Get:16 http://ftpmaster.internal/ubuntu questing/main armhf fwupd armhf 2.0.8-3 [1414 kB] 59s Get:17 http://ftpmaster.internal/ubuntu questing/main armhf libfwupd3 armhf 2.0.8-3 [126 kB] 59s Get:18 http://ftpmaster.internal/ubuntu questing/main armhf htop armhf 3.4.1-4 [147 kB] 59s Get:19 http://ftpmaster.internal/ubuntu questing/main armhf libftdi1-2 armhf 1.5-10 [27.8 kB] 59s Get:20 http://ftpmaster.internal/ubuntu questing-proposed/main armhf python3-pkg-resources all 77.0.3-1 [144 kB] 59s Get:21 http://ftpmaster.internal/ubuntu questing-proposed/main armhf python3-setuptools all 77.0.3-1 [660 kB] 60s Fetched 6161 kB in 1s (7056 kB/s) 60s (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 ... 63953 files and directories currently installed.) 60s Preparing to unpack .../motd-news-config_13.7ubuntu1_all.deb ... 60s Unpacking motd-news-config (13.7ubuntu1) over (13.6ubuntu2) ... 60s Preparing to unpack .../base-files_13.7ubuntu1_armhf.deb ... 60s Unpacking base-files (13.7ubuntu1) over (13.6ubuntu2) ... 60s Setting up base-files (13.7ubuntu1) ... 60s Installing new version of config file /etc/issue ... 60s Installing new version of config file /etc/issue.net ... 60s Installing new version of config file /etc/lsb-release ... 61s motd-news.service is a disabled or a static unit not running, not starting it. 61s (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 ... 63953 files and directories currently installed.) 61s Preparing to unpack .../dpkg_1.22.18ubuntu3_armhf.deb ... 61s Unpacking dpkg (1.22.18ubuntu3) over (1.22.18ubuntu2) ... 62s Setting up dpkg (1.22.18ubuntu3) ... 63s (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 ... 63953 files and directories currently installed.) 63s Preparing to unpack .../libnpth0t64_1.8-3_armhf.deb ... 63s Unpacking libnpth0t64:armhf (1.8-3) over (1.8-2) ... 63s Setting up libnpth0t64:armhf (1.8-3) ... 63s (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 ... 63953 files and directories currently installed.) 63s Preparing to unpack .../00-distro-info-data_0.64_all.deb ... 63s Unpacking distro-info-data (0.64) over (0.63) ... 63s Preparing to unpack .../01-ubuntu-pro-client-l10n_35.1ubuntu0_armhf.deb ... 63s Unpacking ubuntu-pro-client-l10n (35.1ubuntu0) over (35) ... 63s Preparing to unpack .../02-ubuntu-pro-client_35.1ubuntu0_armhf.deb ... 63s Unpacking ubuntu-pro-client (35.1ubuntu0) over (35) ... 63s Preparing to unpack .../03-ed_1.21.1-1_armhf.deb ... 63s Unpacking ed (1.21.1-1) over (1.21-1) ... 63s Preparing to unpack .../04-libsensors-config_1%3a3.6.2-2_all.deb ... 63s Unpacking libsensors-config (1:3.6.2-2) over (1:3.6.0-10) ... 63s Preparing to unpack .../05-libsensors5_1%3a3.6.2-2_armhf.deb ... 63s Unpacking libsensors5:armhf (1:3.6.2-2) over (1:3.6.0-10) ... 63s Preparing to unpack .../06-liburcu8t64_0.15.2-2_armhf.deb ... 63s Unpacking liburcu8t64:armhf (0.15.2-2) over (0.15.1-1) ... 63s Preparing to unpack .../07-nano_8.4-1_armhf.deb ... 63s Unpacking nano (8.4-1) over (8.3-1) ... 63s Preparing to unpack .../08-usb.ids_2025.04.01-1_all.deb ... 63s Unpacking usb.ids (2025.04.01-1) over (2025.01.14-1) ... 63s Preparing to unpack .../09-dpkg-dev_1.22.18ubuntu3_all.deb ... 63s Unpacking dpkg-dev (1.22.18ubuntu3) over (1.22.18ubuntu2) ... 63s Preparing to unpack .../10-libdpkg-perl_1.22.18ubuntu3_all.deb ... 63s Unpacking libdpkg-perl (1.22.18ubuntu3) over (1.22.18ubuntu2) ... 63s Preparing to unpack .../11-fwupd_2.0.8-3_armhf.deb ... 64s Unpacking fwupd (2.0.8-3) over (2.0.7-1) ... 64s dpkg: warning: unable to delete old directory '/etc/grub.d': Directory not empty 64s Preparing to unpack .../12-libfwupd3_2.0.8-3_armhf.deb ... 64s Unpacking libfwupd3:armhf (2.0.8-3) over (2.0.7-1) ... 64s Preparing to unpack .../13-htop_3.4.1-4_armhf.deb ... 64s Unpacking htop (3.4.1-4) over (3.4.0-2) ... 64s Preparing to unpack .../14-libftdi1-2_1.5-10_armhf.deb ... 64s Unpacking libftdi1-2:armhf (1.5-10) over (1.5-8build1) ... 64s Preparing to unpack .../15-python3-pkg-resources_77.0.3-1_all.deb ... 64s Unpacking python3-pkg-resources (77.0.3-1) over (75.8.0-1) ... 64s Preparing to unpack .../16-python3-setuptools_77.0.3-1_all.deb ... 65s Unpacking python3-setuptools (77.0.3-1) over (75.8.0-1) ... 65s Setting up python3-pkg-resources (77.0.3-1) ... 65s Setting up motd-news-config (13.7ubuntu1) ... 65s Setting up liburcu8t64:armhf (0.15.2-2) ... 65s Setting up python3-setuptools (77.0.3-1) ... 66s Setting up distro-info-data (0.64) ... 66s Setting up htop (3.4.1-4) ... 66s Setting up libsensors-config (1:3.6.2-2) ... 66s Installing new version of config file /etc/sensors3.conf ... 66s Setting up libfwupd3:armhf (2.0.8-3) ... 66s Setting up libftdi1-2:armhf (1.5-10) ... 66s Setting up ed (1.21.1-1) ... 66s Setting up usb.ids (2025.04.01-1) ... 66s Setting up libsensors5:armhf (1:3.6.2-2) ... 66s Setting up libdpkg-perl (1.22.18ubuntu3) ... 66s Setting up nano (8.4-1) ... 66s Installing new version of config file /etc/nanorc ... 66s Setting up ubuntu-pro-client (35.1ubuntu0) ... 67s apparmor_parser: Unable to replace "ubuntu_pro_apt_news". apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 67s 67s apparmor_parser: Unable to replace "apt_methods". apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 67s 67s apparmor_parser: Unable to replace "ubuntu_pro_esm_cache". apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 67s 69s Setting up fwupd (2.0.8-3) ... 70s fwupd-refresh.service is a disabled or a static unit not running, not starting it. 70s fwupd.service is a disabled or a static unit not running, not starting it. 70s Setting up ubuntu-pro-client-l10n (35.1ubuntu0) ... 70s Setting up dpkg-dev (1.22.18ubuntu3) ... 70s Processing triggers for dbus (1.16.2-2ubuntu1) ... 70s Processing triggers for install-info (7.1.1-1) ... 70s Processing triggers for libc-bin (2.41-6ubuntu1) ... 70s Processing triggers for man-db (2.13.0-1) ... 72s Processing triggers for plymouth-theme-ubuntu-text (24.004.60-2ubuntu7) ... 72s Processing triggers for initramfs-tools (0.147ubuntu1) ... 74s Reading package lists... 75s Building dependency tree... 75s Reading state information... 76s Starting pkgProblemResolver with broken count: 0 76s Starting 2 pkgProblemResolver with broken count: 0 76s Done 77s Solving dependencies... 78s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 80s autopkgtest [23:05:34]: rebooting testbed after setup commands that affected boot 119s autopkgtest [23:06:13]: testbed running kernel: Linux 6.8.0-58-generic #60~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Fri Mar 28 14:48:37 UTC 2 142s autopkgtest [23:06:36]: @@@@@@@@@@@@@@@@@@@@ apt-source python-biopython 162s Get:1 http://ftpmaster.internal/ubuntu questing/universe python-biopython 1.85+dfsg-2build1 (dsc) [3406 B] 162s Get:2 http://ftpmaster.internal/ubuntu questing/universe python-biopython 1.85+dfsg-2build1 (tar) [14.6 MB] 162s Get:3 http://ftpmaster.internal/ubuntu questing/universe python-biopython 1.85+dfsg-2build1 (diff) [42.8 kB] 162s gpgv: Signature made Tue Mar 4 15:18:59 2025 UTC 162s gpgv: using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2 162s gpgv: Can't check signature: No public key 162s dpkg-source: warning: cannot verify inline signature for ./python-biopython_1.85+dfsg-2build1.dsc: no acceptable signature found 163s autopkgtest [23:06:57]: testing package python-biopython version 1.85+dfsg-2build1 165s autopkgtest [23:06:59]: build not needed 171s autopkgtest [23:07:05]: test dependencies: preparing testbed 173s Reading package lists... 173s Building dependency tree... 173s Reading state information... 174s Starting pkgProblemResolver with broken count: 0 174s Starting 2 pkgProblemResolver with broken count: 0 174s Done 176s The following NEW packages will be installed: 176s fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-urw-base35 176s libblas3 libcairo2 libdeflate0 libfontconfig1 libfontenc1 libfreetype6 176s libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libimagequant0 libjbig0 176s libjpeg-turbo8 libjpeg8 libjs-jquery libjs-sphinxdoc libjs-underscore 176s liblapack3 liblcms2-2 liblerc4 libopenjp2-7 libpixman-1-0 libraqm0 176s libsharpyuv0 libtiff6 libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 176s libxcb-shm0 libxrender1 python-biopython-doc python3-all python3-biopython 176s python3-biopython-sql python3-cairo python3-freetype python3-numpy 176s python3-numpy-dev python3-pil python3-reportlab python3-rlpycairo sgml-base 176s w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core 176s 0 upgraded, 52 newly installed, 0 to remove and 0 not upgraded. 176s Need to get 44.9 MB of archives. 176s After this operation, 116 MB of additional disk space will be used. 176s Get:1 http://ftpmaster.internal/ubuntu questing/main armhf python3-numpy-dev armhf 1:2.2.3+ds-5 [141 kB] 176s Get:2 http://ftpmaster.internal/ubuntu questing/main armhf libblas3 armhf 3.12.1-2 [132 kB] 176s Get:3 http://ftpmaster.internal/ubuntu questing/main armhf libgfortran5 armhf 15-20250404-0ubuntu1 [331 kB] 176s Get:4 http://ftpmaster.internal/ubuntu questing/main armhf liblapack3 armhf 3.12.1-2 [2091 kB] 177s Get:5 http://ftpmaster.internal/ubuntu questing/main armhf python3-numpy armhf 1:2.2.3+ds-5 [3725 kB] 177s Get:6 http://ftpmaster.internal/ubuntu questing/main armhf sgml-base all 1.31 [11.4 kB] 177s Get:7 http://ftpmaster.internal/ubuntu questing/main armhf fonts-dejavu-mono all 2.37-8 [502 kB] 177s Get:8 http://ftpmaster.internal/ubuntu questing/main armhf fonts-dejavu-core all 2.37-8 [835 kB] 177s Get:9 http://ftpmaster.internal/ubuntu questing/main armhf libfontenc1 armhf 1:1.1.8-1build1 [11.5 kB] 177s Get:10 http://ftpmaster.internal/ubuntu questing/main armhf libfreetype6 armhf 2.13.3+dfsg-1 [330 kB] 177s Get:11 http://ftpmaster.internal/ubuntu questing/main armhf x11-common all 1:7.7+23ubuntu4 [21.8 kB] 177s Get:12 http://ftpmaster.internal/ubuntu questing/main armhf xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 177s Get:13 http://ftpmaster.internal/ubuntu questing/main armhf xfonts-utils armhf 1:7.7+7 [90.6 kB] 177s Get:14 http://ftpmaster.internal/ubuntu questing/main armhf fonts-urw-base35 all 20200910-8 [11.0 MB] 178s Get:15 http://ftpmaster.internal/ubuntu questing/main armhf fontconfig-config armhf 2.15.0-2.2ubuntu1 [37.9 kB] 178s Get:16 http://ftpmaster.internal/ubuntu questing/main armhf libfontconfig1 armhf 2.15.0-2.2ubuntu1 [114 kB] 178s Get:17 http://ftpmaster.internal/ubuntu questing/main armhf libpixman-1-0 armhf 0.44.0-3 [183 kB] 178s Get:18 http://ftpmaster.internal/ubuntu questing/main armhf libxcb-render0 armhf 1.17.0-2 [15.3 kB] 178s Get:19 http://ftpmaster.internal/ubuntu questing/main armhf libxcb-shm0 armhf 1.17.0-2 [5774 B] 178s Get:20 http://ftpmaster.internal/ubuntu questing/main armhf libxrender1 armhf 1:0.9.10-1.1build1 [16.0 kB] 178s Get:21 http://ftpmaster.internal/ubuntu questing/main armhf libcairo2 armhf 1.18.4-1 [483 kB] 178s Get:22 http://ftpmaster.internal/ubuntu questing/main armhf libdeflate0 armhf 1.23-1 [38.5 kB] 178s Get:23 http://ftpmaster.internal/ubuntu questing/main armhf libgomp1 armhf 15-20250404-0ubuntu1 [128 kB] 178s Get:24 http://ftpmaster.internal/ubuntu questing/main armhf libgraphite2-3 armhf 1.3.14-2ubuntu1 [64.8 kB] 178s Get:25 http://ftpmaster.internal/ubuntu questing/main armhf libharfbuzz0b armhf 10.2.0-1 [464 kB] 178s Get:26 http://ftpmaster.internal/ubuntu questing/main armhf libimagequant0 armhf 2.18.0-1build1 [31.1 kB] 178s Get:27 http://ftpmaster.internal/ubuntu questing/main armhf libjpeg-turbo8 armhf 2.1.5-3ubuntu2 [127 kB] 178s Get:28 http://ftpmaster.internal/ubuntu questing/main armhf libjpeg8 armhf 8c-2ubuntu11 [2148 B] 178s Get:29 http://ftpmaster.internal/ubuntu questing/main armhf libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 178s Get:30 http://ftpmaster.internal/ubuntu questing/main armhf libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 178s Get:31 http://ftpmaster.internal/ubuntu questing/main armhf libjs-sphinxdoc all 8.1.3-5 [31.0 kB] 178s Get:32 http://ftpmaster.internal/ubuntu questing/main armhf liblcms2-2 armhf 2.16-2 [137 kB] 178s Get:33 http://ftpmaster.internal/ubuntu questing/main armhf liblerc4 armhf 4.0.0+ds-5ubuntu1 [160 kB] 178s Get:34 http://ftpmaster.internal/ubuntu questing/main armhf libraqm0 armhf 0.10.2-1 [12.4 kB] 178s Get:35 http://ftpmaster.internal/ubuntu questing/main armhf libsharpyuv0 armhf 1.5.0-0.1 [16.4 kB] 178s Get:36 http://ftpmaster.internal/ubuntu questing/main armhf libjbig0 armhf 2.1-6.1ubuntu2 [24.9 kB] 178s Get:37 http://ftpmaster.internal/ubuntu questing/main armhf libwebp7 armhf 1.5.0-0.1 [188 kB] 178s Get:38 http://ftpmaster.internal/ubuntu questing/main armhf libtiff6 armhf 4.7.0-3ubuntu1 [184 kB] 178s Get:39 http://ftpmaster.internal/ubuntu questing/main armhf libwebpdemux2 armhf 1.5.0-0.1 [11.5 kB] 178s Get:40 http://ftpmaster.internal/ubuntu questing/main armhf libwebpmux3 armhf 1.5.0-0.1 [22.4 kB] 178s Get:41 http://ftpmaster.internal/ubuntu questing/universe armhf python-biopython-doc all 1.85+dfsg-2build1 [18.2 MB] 179s Get:42 http://ftpmaster.internal/ubuntu questing/main armhf python3-all armhf 3.13.3-1 [880 B] 179s Get:43 http://ftpmaster.internal/ubuntu questing/main armhf libopenjp2-7 armhf 2.5.3-2 [172 kB] 179s Get:44 http://ftpmaster.internal/ubuntu questing/main armhf python3-pil armhf 11.1.0-5build1 [435 kB] 179s Get:45 http://ftpmaster.internal/ubuntu questing/main armhf python3-cairo armhf 1.27.0-2 [115 kB] 179s Get:46 http://ftpmaster.internal/ubuntu questing/universe armhf python3-freetype all 2.5.1-1 [92.3 kB] 179s Get:47 http://ftpmaster.internal/ubuntu questing/universe armhf python3-rlpycairo all 0.3.0-3 [9130 B] 179s Get:48 http://ftpmaster.internal/ubuntu questing/universe armhf python3-reportlab all 4.3.1-1 [1137 kB] 179s Get:49 http://ftpmaster.internal/ubuntu questing/main armhf xml-core all 0.19 [20.3 kB] 179s Get:50 http://ftpmaster.internal/ubuntu questing/universe armhf w3c-sgml-lib all 1.3-3 [280 kB] 179s Get:51 http://ftpmaster.internal/ubuntu questing/universe armhf python3-biopython armhf 1.85+dfsg-2build1 [1692 kB] 179s Get:52 http://ftpmaster.internal/ubuntu questing/universe armhf python3-biopython-sql all 1.85+dfsg-2build1 [26.4 kB] 180s Fetched 44.9 MB in 3s (13.8 MB/s) 180s Selecting previously unselected package python3-numpy-dev:armhf. 180s (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 ... 63965 files and directories currently installed.) 180s Preparing to unpack .../00-python3-numpy-dev_1%3a2.2.3+ds-5_armhf.deb ... 180s Unpacking python3-numpy-dev:armhf (1:2.2.3+ds-5) ... 180s Selecting previously unselected package libblas3:armhf. 180s Preparing to unpack .../01-libblas3_3.12.1-2_armhf.deb ... 180s Unpacking libblas3:armhf (3.12.1-2) ... 180s Selecting previously unselected package libgfortran5:armhf. 180s Preparing to unpack .../02-libgfortran5_15-20250404-0ubuntu1_armhf.deb ... 180s Unpacking libgfortran5:armhf (15-20250404-0ubuntu1) ... 180s Selecting previously unselected package liblapack3:armhf. 180s Preparing to unpack .../03-liblapack3_3.12.1-2_armhf.deb ... 180s Unpacking liblapack3:armhf (3.12.1-2) ... 180s Selecting previously unselected package python3-numpy. 180s Preparing to unpack .../04-python3-numpy_1%3a2.2.3+ds-5_armhf.deb ... 180s Unpacking python3-numpy (1:2.2.3+ds-5) ... 180s Selecting previously unselected package sgml-base. 180s Preparing to unpack .../05-sgml-base_1.31_all.deb ... 181s Unpacking sgml-base (1.31) ... 181s Selecting previously unselected package fonts-dejavu-mono. 181s Preparing to unpack .../06-fonts-dejavu-mono_2.37-8_all.deb ... 181s Unpacking fonts-dejavu-mono (2.37-8) ... 181s Selecting previously unselected package fonts-dejavu-core. 181s Preparing to unpack .../07-fonts-dejavu-core_2.37-8_all.deb ... 181s Unpacking fonts-dejavu-core (2.37-8) ... 181s Selecting previously unselected package libfontenc1:armhf. 181s Preparing to unpack .../08-libfontenc1_1%3a1.1.8-1build1_armhf.deb ... 181s Unpacking libfontenc1:armhf (1:1.1.8-1build1) ... 181s Selecting previously unselected package libfreetype6:armhf. 181s Preparing to unpack .../09-libfreetype6_2.13.3+dfsg-1_armhf.deb ... 181s Unpacking libfreetype6:armhf (2.13.3+dfsg-1) ... 181s Selecting previously unselected package x11-common. 181s Preparing to unpack .../10-x11-common_1%3a7.7+23ubuntu4_all.deb ... 181s Unpacking x11-common (1:7.7+23ubuntu4) ... 181s Selecting previously unselected package xfonts-encodings. 181s Preparing to unpack .../11-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 181s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 181s Selecting previously unselected package xfonts-utils. 181s Preparing to unpack .../12-xfonts-utils_1%3a7.7+7_armhf.deb ... 181s Unpacking xfonts-utils (1:7.7+7) ... 181s Selecting previously unselected package fonts-urw-base35. 181s Preparing to unpack .../13-fonts-urw-base35_20200910-8_all.deb ... 181s Unpacking fonts-urw-base35 (20200910-8) ... 181s Selecting previously unselected package fontconfig-config. 181s Preparing to unpack .../14-fontconfig-config_2.15.0-2.2ubuntu1_armhf.deb ... 182s Unpacking fontconfig-config (2.15.0-2.2ubuntu1) ... 182s Selecting previously unselected package libfontconfig1:armhf. 182s Preparing to unpack .../15-libfontconfig1_2.15.0-2.2ubuntu1_armhf.deb ... 182s Unpacking libfontconfig1:armhf (2.15.0-2.2ubuntu1) ... 182s Selecting previously unselected package libpixman-1-0:armhf. 182s Preparing to unpack .../16-libpixman-1-0_0.44.0-3_armhf.deb ... 182s Unpacking libpixman-1-0:armhf (0.44.0-3) ... 182s Selecting previously unselected package libxcb-render0:armhf. 182s Preparing to unpack .../17-libxcb-render0_1.17.0-2_armhf.deb ... 182s Unpacking libxcb-render0:armhf (1.17.0-2) ... 182s Selecting previously unselected package libxcb-shm0:armhf. 182s Preparing to unpack .../18-libxcb-shm0_1.17.0-2_armhf.deb ... 182s Unpacking libxcb-shm0:armhf (1.17.0-2) ... 182s Selecting previously unselected package libxrender1:armhf. 182s Preparing to unpack .../19-libxrender1_1%3a0.9.10-1.1build1_armhf.deb ... 182s Unpacking libxrender1:armhf (1:0.9.10-1.1build1) ... 182s Selecting previously unselected package libcairo2:armhf. 182s Preparing to unpack .../20-libcairo2_1.18.4-1_armhf.deb ... 182s Unpacking libcairo2:armhf (1.18.4-1) ... 182s Selecting previously unselected package libdeflate0:armhf. 182s Preparing to unpack .../21-libdeflate0_1.23-1_armhf.deb ... 182s Unpacking libdeflate0:armhf (1.23-1) ... 182s Selecting previously unselected package libgomp1:armhf. 182s Preparing to unpack .../22-libgomp1_15-20250404-0ubuntu1_armhf.deb ... 182s Unpacking libgomp1:armhf (15-20250404-0ubuntu1) ... 182s Selecting previously unselected package libgraphite2-3:armhf. 182s Preparing to unpack .../23-libgraphite2-3_1.3.14-2ubuntu1_armhf.deb ... 182s Unpacking libgraphite2-3:armhf (1.3.14-2ubuntu1) ... 182s Selecting previously unselected package libharfbuzz0b:armhf. 182s Preparing to unpack .../24-libharfbuzz0b_10.2.0-1_armhf.deb ... 182s Unpacking libharfbuzz0b:armhf (10.2.0-1) ... 182s Selecting previously unselected package libimagequant0:armhf. 182s Preparing to unpack .../25-libimagequant0_2.18.0-1build1_armhf.deb ... 182s Unpacking libimagequant0:armhf (2.18.0-1build1) ... 182s Selecting previously unselected package libjpeg-turbo8:armhf. 182s Preparing to unpack .../26-libjpeg-turbo8_2.1.5-3ubuntu2_armhf.deb ... 182s Unpacking libjpeg-turbo8:armhf (2.1.5-3ubuntu2) ... 182s Selecting previously unselected package libjpeg8:armhf. 182s Preparing to unpack .../27-libjpeg8_8c-2ubuntu11_armhf.deb ... 182s Unpacking libjpeg8:armhf (8c-2ubuntu11) ... 182s Selecting previously unselected package libjs-jquery. 182s Preparing to unpack .../28-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 182s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 183s Selecting previously unselected package libjs-underscore. 183s Preparing to unpack .../29-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 183s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 183s Selecting previously unselected package libjs-sphinxdoc. 183s Preparing to unpack .../30-libjs-sphinxdoc_8.1.3-5_all.deb ... 183s Unpacking libjs-sphinxdoc (8.1.3-5) ... 183s Selecting previously unselected package liblcms2-2:armhf. 183s Preparing to unpack .../31-liblcms2-2_2.16-2_armhf.deb ... 183s Unpacking liblcms2-2:armhf (2.16-2) ... 183s Selecting previously unselected package liblerc4:armhf. 183s Preparing to unpack .../32-liblerc4_4.0.0+ds-5ubuntu1_armhf.deb ... 183s Unpacking liblerc4:armhf (4.0.0+ds-5ubuntu1) ... 183s Selecting previously unselected package libraqm0:armhf. 183s Preparing to unpack .../33-libraqm0_0.10.2-1_armhf.deb ... 183s Unpacking libraqm0:armhf (0.10.2-1) ... 183s Selecting previously unselected package libsharpyuv0:armhf. 183s Preparing to unpack .../34-libsharpyuv0_1.5.0-0.1_armhf.deb ... 183s Unpacking libsharpyuv0:armhf (1.5.0-0.1) ... 183s Selecting previously unselected package libjbig0:armhf. 183s Preparing to unpack .../35-libjbig0_2.1-6.1ubuntu2_armhf.deb ... 183s Unpacking libjbig0:armhf (2.1-6.1ubuntu2) ... 183s Selecting previously unselected package libwebp7:armhf. 183s Preparing to unpack .../36-libwebp7_1.5.0-0.1_armhf.deb ... 183s Unpacking libwebp7:armhf (1.5.0-0.1) ... 183s Selecting previously unselected package libtiff6:armhf. 183s Preparing to unpack .../37-libtiff6_4.7.0-3ubuntu1_armhf.deb ... 183s Unpacking libtiff6:armhf (4.7.0-3ubuntu1) ... 183s Selecting previously unselected package libwebpdemux2:armhf. 183s Preparing to unpack .../38-libwebpdemux2_1.5.0-0.1_armhf.deb ... 183s Unpacking libwebpdemux2:armhf (1.5.0-0.1) ... 183s Selecting previously unselected package libwebpmux3:armhf. 183s Preparing to unpack .../39-libwebpmux3_1.5.0-0.1_armhf.deb ... 183s Unpacking libwebpmux3:armhf (1.5.0-0.1) ... 183s Selecting previously unselected package python-biopython-doc. 183s Preparing to unpack .../40-python-biopython-doc_1.85+dfsg-2build1_all.deb ... 183s Unpacking python-biopython-doc (1.85+dfsg-2build1) ... 184s Selecting previously unselected package python3-all. 184s Preparing to unpack .../41-python3-all_3.13.3-1_armhf.deb ... 184s Unpacking python3-all (3.13.3-1) ... 184s Selecting previously unselected package libopenjp2-7:armhf. 184s Preparing to unpack .../42-libopenjp2-7_2.5.3-2_armhf.deb ... 184s Unpacking libopenjp2-7:armhf (2.5.3-2) ... 184s Selecting previously unselected package python3-pil:armhf. 184s Preparing to unpack .../43-python3-pil_11.1.0-5build1_armhf.deb ... 184s Unpacking python3-pil:armhf (11.1.0-5build1) ... 184s Selecting previously unselected package python3-cairo. 184s Preparing to unpack .../44-python3-cairo_1.27.0-2_armhf.deb ... 184s Unpacking python3-cairo (1.27.0-2) ... 184s Selecting previously unselected package python3-freetype. 184s Preparing to unpack .../45-python3-freetype_2.5.1-1_all.deb ... 184s Unpacking python3-freetype (2.5.1-1) ... 184s Selecting previously unselected package python3-rlpycairo. 184s Preparing to unpack .../46-python3-rlpycairo_0.3.0-3_all.deb ... 184s Unpacking python3-rlpycairo (0.3.0-3) ... 184s Selecting previously unselected package python3-reportlab. 184s Preparing to unpack .../47-python3-reportlab_4.3.1-1_all.deb ... 184s Unpacking python3-reportlab (4.3.1-1) ... 184s Selecting previously unselected package xml-core. 184s Preparing to unpack .../48-xml-core_0.19_all.deb ... 184s Unpacking xml-core (0.19) ... 184s Selecting previously unselected package w3c-sgml-lib. 184s Preparing to unpack .../49-w3c-sgml-lib_1.3-3_all.deb ... 184s Unpacking w3c-sgml-lib (1.3-3) ... 184s Selecting previously unselected package python3-biopython. 184s Preparing to unpack .../50-python3-biopython_1.85+dfsg-2build1_armhf.deb ... 184s Unpacking python3-biopython (1.85+dfsg-2build1) ... 185s Selecting previously unselected package python3-biopython-sql. 185s Preparing to unpack .../51-python3-biopython-sql_1.85+dfsg-2build1_all.deb ... 185s Unpacking python3-biopython-sql (1.85+dfsg-2build1) ... 185s Setting up libgraphite2-3:armhf (1.3.14-2ubuntu1) ... 185s Setting up liblcms2-2:armhf (2.16-2) ... 185s Setting up libpixman-1-0:armhf (0.44.0-3) ... 185s Setting up libsharpyuv0:armhf (1.5.0-0.1) ... 185s Setting up liblerc4:armhf (4.0.0+ds-5ubuntu1) ... 185s Setting up libxrender1:armhf (1:0.9.10-1.1build1) ... 185s Setting up libxcb-render0:armhf (1.17.0-2) ... 185s Setting up x11-common (1:7.7+23ubuntu4) ... 185s Setting up libdeflate0:armhf (1.23-1) ... 185s Setting up python3-all (3.13.3-1) ... 185s Setting up libxcb-shm0:armhf (1.17.0-2) ... 185s Setting up libgomp1:armhf (15-20250404-0ubuntu1) ... 185s Setting up libjbig0:armhf (2.1-6.1ubuntu2) ... 185s Setting up libfontenc1:armhf (1:1.1.8-1build1) ... 185s Setting up libblas3:armhf (3.12.1-2) ... 185s update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode 185s Setting up libfreetype6:armhf (2.13.3+dfsg-1) ... 185s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 185s Setting up libimagequant0:armhf (2.18.0-1build1) ... 185s Setting up fonts-dejavu-mono (2.37-8) ... 185s Setting up python3-numpy-dev:armhf (1:2.2.3+ds-5) ... 185s Setting up fonts-dejavu-core (2.37-8) ... 185s Setting up libjpeg-turbo8:armhf (2.1.5-3ubuntu2) ... 185s Setting up libgfortran5:armhf (15-20250404-0ubuntu1) ... 185s Setting up libwebp7:armhf (1.5.0-0.1) ... 185s Setting up libopenjp2-7:armhf (2.5.3-2) ... 185s Setting up libharfbuzz0b:armhf (10.2.0-1) ... 185s Setting up sgml-base (1.31) ... 186s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 186s Setting up libwebpmux3:armhf (1.5.0-0.1) ... 186s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 186s Setting up libjpeg8:armhf (8c-2ubuntu11) ... 186s Setting up liblapack3:armhf (3.12.1-2) ... 186s update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode 186s Setting up fontconfig-config (2.15.0-2.2ubuntu1) ... 186s Setting up libwebpdemux2:armhf (1.5.0-0.1) ... 186s Setting up python3-freetype (2.5.1-1) ... 186s Setting up xfonts-utils (1:7.7+7) ... 186s Setting up libraqm0:armhf (0.10.2-1) ... 186s Setting up python3-numpy (1:2.2.3+ds-5) ... 189s Setting up libjs-sphinxdoc (8.1.3-5) ... 189s Setting up python-biopython-doc (1.85+dfsg-2build1) ... 189s Setting up libtiff6:armhf (4.7.0-3ubuntu1) ... 189s Setting up xml-core (0.19) ... 189s Setting up libfontconfig1:armhf (2.15.0-2.2ubuntu1) ... 189s Setting up fonts-urw-base35 (20200910-8) ... 189s Setting up libcairo2:armhf (1.18.4-1) ... 189s Setting up python3-pil:armhf (11.1.0-5build1) ... 190s Setting up python3-cairo (1.27.0-2) ... 190s Setting up python3-rlpycairo (0.3.0-3) ... 190s Setting up python3-reportlab (4.3.1-1) ... 192s Processing triggers for libc-bin (2.41-6ubuntu1) ... 192s Processing triggers for man-db (2.13.0-1) ... 192s Processing triggers for sgml-base (1.31) ... 192s Setting up w3c-sgml-lib (1.3-3) ... 228s Setting up python3-biopython (1.85+dfsg-2build1) ... 230s Setting up python3-biopython-sql (1.85+dfsg-2build1) ... 241s autopkgtest [23:08:15]: test dependencies: sh debian/tests/run-unit-test 241s autopkgtest [23:08:15]: test dependencies: [----------------------- 243s cp: cannot stat '/usr/share/libcifpp/mmcif_pdbx.dic': No such file or directory 243s cp: cannot stat '/usr/share/libcifpp/mmcif_ma.dic': No such file or directory 246s mkdir: created directory 'Bio' 246s mkdir: created directory 'Bio/Align' 246s mkdir: created directory 'Bio/Align/substitution_matrices' 246s mkdir: created directory 'Bio/Align/substitution_matrices/data/' 246s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER22' -> 'Bio/Align/substitution_matrices/data/BENNER22' 246s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER6' -> 'Bio/Align/substitution_matrices/data/BENNER6' 246s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER74' -> 'Bio/Align/substitution_matrices/data/BENNER74' 246s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLASTN' -> 'Bio/Align/substitution_matrices/data/BLASTN' 246s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLASTP' -> 'Bio/Align/substitution_matrices/data/BLASTP' 246s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM45' -> 'Bio/Align/substitution_matrices/data/BLOSUM45' 246s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM50' -> 'Bio/Align/substitution_matrices/data/BLOSUM50' 246s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM62' -> 'Bio/Align/substitution_matrices/data/BLOSUM62' 246s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM80' -> 'Bio/Align/substitution_matrices/data/BLOSUM80' 246s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM90' -> 'Bio/Align/substitution_matrices/data/BLOSUM90' 246s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/DAYHOFF' -> 'Bio/Align/substitution_matrices/data/DAYHOFF' 246s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/FENG' -> 'Bio/Align/substitution_matrices/data/FENG' 246s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/GENETIC' -> 'Bio/Align/substitution_matrices/data/GENETIC' 246s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/GONNET1992' -> 'Bio/Align/substitution_matrices/data/GONNET1992' 246s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/HOXD70' -> 'Bio/Align/substitution_matrices/data/HOXD70' 246s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/JOHNSON' -> 'Bio/Align/substitution_matrices/data/JOHNSON' 246s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/JONES' -> 'Bio/Align/substitution_matrices/data/JONES' 246s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/LEVIN' -> 'Bio/Align/substitution_matrices/data/LEVIN' 246s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MCLACHLAN' -> 'Bio/Align/substitution_matrices/data/MCLACHLAN' 246s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MDM78' -> 'Bio/Align/substitution_matrices/data/MDM78' 246s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MEGABLAST' -> 'Bio/Align/substitution_matrices/data/MEGABLAST' 246s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/NUC.4.4' -> 'Bio/Align/substitution_matrices/data/NUC.4.4' 246s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM250' -> 'Bio/Align/substitution_matrices/data/PAM250' 246s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM30' -> 'Bio/Align/substitution_matrices/data/PAM30' 246s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM70' -> 'Bio/Align/substitution_matrices/data/PAM70' 246s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/RAO' -> 'Bio/Align/substitution_matrices/data/RAO' 246s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/RISLER' -> 'Bio/Align/substitution_matrices/data/RISLER' 246s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/SCHNEIDER' -> 'Bio/Align/substitution_matrices/data/SCHNEIDER' 246s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/STR' -> 'Bio/Align/substitution_matrices/data/STR' 246s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/TRANS' -> 'Bio/Align/substitution_matrices/data/TRANS' 247s test_Ace ... ok 247s test_Affy ... ok 250s test_AlignIO ... ok 250s test_AlignIO_ClustalIO ... ok 250s test_AlignIO_EmbossIO ... ok 250s test_AlignIO_FastaIO ... ok 250s test_AlignIO_MauveIO ... ok 250s test_AlignIO_PhylipIO ... ok 250s test_AlignIO_convert ... ok 250s test_AlignInfo ... ok 251s test_Align_Alignment ... ok 251s test_Align_a2m ... ok 251s test_Align_bed ... ok 251s test_Align_bigbed ... ok 252s test_Align_bigmaf ... ok 252s test_Align_bigpsl ... ok 252s test_Align_chain ... ok 252s test_Align_clustal ... ok 256s test_Align_codonalign ... ok 256s test_Align_emboss ... ok 257s test_Align_exonerate ... ok 257s test_Align_fasta ... ok 257s test_Align_hhr ... ok 258s test_Align_maf ... ok 258s test_Align_mauve ... ok 258s test_Align_msf ... ok 258s test_Align_nexus ... ok 258s test_Align_phylip ... ok 259s test_Align_psl ... ok 259s test_Align_sam ... ok 261s test_Align_stockholm ... ok 262s test_Align_tabular ... ok 262s test_Application ... ok 262s test_BioSQL_MySQLdb_online ... skipping. internet not available 262s test_BioSQL_mysql_connector ... skipping. BioSQL test configuration file biosql.ini missing (see biosql.ini.sample) 262s test_BioSQL_mysql_connector_online ... skipping. internet not available 262s test_BioSQL_psycopg2_online ... skipping. internet not available 268s test_BioSQL_sqlite3 ... ok 268s test_BioSQL_sqlite3_online ... skipping. internet not available 268s test_Blast_Record ... ok 269s test_Blast_parser ... ok 269s test_CAPS ... ok 269s test_Chi2 ... ok 269s test_ClustalOmega_tool ... skipping. Install clustalo if you want to use Clustal Omega from Biopython. 269s test_Clustalw_tool ... skipping. Install clustalw or clustalw2 if you want to use it from Biopython. 269s test_Cluster ... ok 269s test_CodonTable ... ok 270s test_ColorSpiral ... ok 270s test_Compass ... ok 271s test_Consensus ... ok 271s test_Dialign_tool ... skipping. Install DIALIGN2-2 if you want to use the Bio.Align.Applications wrapper. 271s test_EMBL_unittest ... ok 271s test_Emboss ... skipping. $EMBOSS_ROOT='/usr/lib/emboss' which does not exist! 271s test_EmbossPrimer ... ok 275s test_Entrez ... ok 275s test_Entrez_online ... skipping. internet not available 276s test_Entrez_parser ... ok 276s test_Enzyme ... ok 276s test_ExPASy ... skipping. internet not available 276s test_Fasttree_tool ... skipping. Install FastTree and correctly set the file path to the program if you want to use it from Biopython. 276s test_File ... ok 277s test_GenBank ... /usr/lib/python3/dist-packages/Bio/SeqIO/InsdcIO.py:600: BiopythonWarning: Annotation 'Sequence Read Archive: SRX001885, SRX001121, SRX001531, SRX001530, SRX001529' too long 277s warnings.warn(f"Annotation {text!r} too long", BiopythonWarning) 277s ok 279s test_GenomeDiagram ... Warn: Can't find .pfb for face 'Helvetica' 281s ok 282s test_GraphicsChromosome ... ok 282s test_GraphicsDistribution ... ok 283s test_GraphicsGeneral ... ok 283s test_HMMCasino ... ok 283s test_HMMGeneral ... ok 283s test_KEGG ... ok 283s test_KEGG_online ... skipping. internet not available 289s test_KGML_graphics ... ok 289s test_KGML_graphics_online ... skipping. internet not available 290s test_KGML_nographics ... ok 290s test_KeyWList ... ok 290s test_LogisticRegression ... ok 291s test_MafIO_index ... ok 291s test_Mafft_tool ... skipping. Install MAFFT if you want to use the Bio.Align.Applications wrapper. 292s test_MarkovModel ... ok 292s test_Medline ... ok 292s test_Muscle_tool ... skipping. Install MUSCLE if you want to use the Bio.Align.Applications wrapper. 293s test_NCBIXML ... Exception ignored in: 293s Traceback (most recent call last): 293s File "/usr/lib/python3/dist-packages/Bio/Blast/NCBIXML.py", line 1319, in parse 293s expat_parser.Parse(NULL, True) 293s xml.parsers.expat.ExpatError: unclosed token: line 320, column 0 293s ok 293s test_NCBI_BLAST_tools ... skipping. Install the NCBI BLAST+ command line tools if you want to use the Bio.Blast.Applications wrapper. 293s test_NCBI_qblast ... ok 293s test_NMR ... ok 293s test_NaiveBayes ... ok 293s test_Nexus ... ok 294s test_PAML_baseml ... ok 295s test_PAML_codeml ... ok 295s test_PAML_yn00 ... ok 300s test_PDB_CEAligner ... ok 301s test_PDB_DSSP ... ok 301s test_PDB_Dice ... ok 301s test_PDB_Disordered ... ok 301s test_PDB_Exposure ... ok 301s test_PDB_FragmentMapper ... ok 303s test_PDB_KDTree ... ok 304s test_PDB_MMCIF2Dict ... ok 304s test_PDB_MMCIFIO ... ok 305s test_PDB_MMCIFParser ... ok 305s test_PDB_NACCESS ... ok 306s test_PDB_PDBIO ... ok 306s test_PDB_PDBList ... skipping. internet not available 314s test_PDB_PDBMLParser ... ok 314s test_PDB_PDBParser ... ok 314s 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 314s test_PDB_Polypeptide ... ok 314s test_PDB_QCPSuperimposer ... ok 318s test_PDB_SASA ... ok 319s test_PDB_SMCRA ... ok 319s test_PDB_Selection ... ok 319s test_PDB_StructureAlignment ... ok 319s test_PDB_Superimposer ... ok 319s test_PDB_alphafold_db ... skipping. internet not available 319s test_PDB_binary_cif ... skipping. Error: Install msgpack to use Bio.PDB.binaryCIF (e.g. pip install msgpack) 319s 319s test_PDB_internal_coords ... skipping. Error: Install mmtf to use Bio.PDB.mmtf (e.g. pip install mmtf-python) 319s 320s test_PDB_parse_pdb_header ... ok 320s test_PDB_vectors ... ok 320s test_PQR ... ok 320s test_Pathway ... ok 320s test_Phd ... ok 320s test_Phylo ... ok 321s test_PhyloXML ... ok 321s test_Phylo_CDAO ... skipping. Install RDFlib if you want to use the CDAO tree format. 321s test_Phylo_NeXML ... ok 321s test_Phylo_igraph ... skipping. Install igraph if you wish to use it with Bio.Phylo 321s test_Phylo_matplotlib ... skipping. Install matplotlib if you want to use Bio.Phylo._utils. 322s test_Phylo_networkx ... skipping. Install networkx if you wish to use it with Bio.Phylo 322s test_PopGen_GenePop_nodepend ... ok 322s test_Prank_tool ... skipping. Install PRANK if you want to use the Bio.Align.Applications wrapper. 322s test_Probcons_tool ... skipping. Install PROBCONS if you want to use the Bio.Align.Applications wrapper. 322s test_ProtParam ... ok 323s test_RCSBFormats ... ok 323s test_Restriction ... ok 323s test_SCOP_Astral ... ok 323s test_SCOP_Cla ... ok 323s test_SCOP_Des ... ok 323s test_SCOP_Dom ... ok 325s test_SCOP_Hie ... ok 325s test_SCOP_Raf ... ok 325s test_SCOP_Residues ... ok 325s test_SCOP_Scop ... ok 325s test_SVDSuperimposer ... ok 325s test_SearchIO_blast_tab ... ok 325s test_SearchIO_blast_tab_index ... ok 325s test_SearchIO_blast_xml ... ok 325s test_SearchIO_blast_xml_index ... ok 326s test_SearchIO_blat_psl ... ok 326s test_SearchIO_blat_psl_index ... ok 326s test_SearchIO_exonerate ... ok 326s test_SearchIO_exonerate_text_index ... ok 326s test_SearchIO_exonerate_vulgar_index ... ok 326s test_SearchIO_fasta_m10 ... ok 327s test_SearchIO_fasta_m10_index ... ok 327s test_SearchIO_hhsuite2_text ... ok 327s test_SearchIO_hmmer2_text ... ok 327s test_SearchIO_hmmer2_text_index ... ok 327s test_SearchIO_hmmer3_domtab ... ok 327s test_SearchIO_hmmer3_domtab_index ... ok 328s test_SearchIO_hmmer3_tab ... ok 328s test_SearchIO_hmmer3_tab_index ... ok 328s test_SearchIO_hmmer3_text ... ok 328s test_SearchIO_hmmer3_text_index ... ok 328s test_SearchIO_interproscan_xml ... ok 328s test_SearchIO_model ... ok 329s test_SearchIO_write ... ok 329s test_SeqFeature ... ok 348s test_SeqIO ... ok 348s test_SeqIO_AbiIO ... ok 348s test_SeqIO_FastaIO ... ok 348s test_SeqIO_Gck ... ok 348s test_SeqIO_Gfa ... ok 348s test_SeqIO_Insdc ... ok 348s test_SeqIO_NibIO ... ok 351s test_SeqIO_PdbIO ... ok 351s test_SeqIO_QualityIO ... ok 351s test_SeqIO_SeqXML ... ok 351s test_SeqIO_SffIO ... ok 352s test_SeqIO_SnapGene ... ok 353s test_SeqIO_TwoBitIO ... ok 353s test_SeqIO_UniprotIO ... ok 353s test_SeqIO_Xdna ... ok 354s test_SeqIO_features ... ok 371s test_SeqIO_index ... ok 371s test_SeqIO_online ... skipping. internet not available 371s test_SeqIO_write ... ok 371s test_SeqRecord ... ok 371s test_SeqUtils ... ok 372s test_Seq_objs ... ok 373s test_SwissProt ... ok 373s test_TCoffee_tool ... skipping. Install TCOFFEE if you want to use the Bio.Align.Applications wrapper. 373s test_TogoWS ... skipping. internet not available 373s test_TreeConstruction ... ok 374s test_Tutorial ... skipping. Could not find ../Doc/Tutorial/index.rst file 374s test_UniGene ... ok 374s test_UniProt ... skipping. internet not available 374s test_UniProt_GOA ... ok 374s test_align ... ok 375s test_align_substitution_matrices ... ok 377s test_bgzf ... ok 377s test_cellosaurus ... ok 382s test_codonalign ... ok 382s test_geo ... ok 383s test_kNN ... ok 383s test_motifs ... ok 383s test_motifs_online ... skipping. internet not available 383s 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. 383s warnings.warn( 383s ok 383s test_pairwise2_no_C ... ok 384s test_pairwise_aligner ... ok 384s test_pairwise_alignment_map ... ok 394s test_phenotype ... ok 394s test_phenotype_fit ... skipping. Install SciPy if you want to use Bio.phenotype fit functionality. 394s test_phyml_tool ... skipping. Couldn't find the PhyML software. Install PhyML 3.0 or later if you want to use the Bio.Phylo.Applications wrapper. 394s test_prodoc ... ok 394s test_prosite ... ok 394s test_raxml_tool ... skipping. Install RAxML (binary raxmlHPC) if you want to test the Bio.Phylo.Applications wrapper. 394s test_samtools_tool ... skipping. Install samtools and correctly set the file path to the program if you want to use it from Biopython 394s test_seq ... ok 395s test_translate ... ok 395s ---------------------------------------------------------------------- 395s Ran 218 tests in 147.829 seconds 395s 395s Skipping any tests requiring internet access 395s Python version: 3.13.3 (main, Apr 8 2025, 19:55:40) [GCC 14.2.0] 395s Operating system: posix linux 395s :0: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/protein_lib.fa' mode='rt' encoding='UTF-8'> 395s :0: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/nucleotide_lib.fa' mode='rt' encoding='UTF-8'> 396s autopkgtest [23:10:50]: test dependencies: -----------------------] 399s dependencies PASS 399s autopkgtest [23:10:53]: test dependencies: - - - - - - - - - - results - - - - - - - - - - 403s autopkgtest [23:10:57]: test full_suite: preparing testbed 425s autopkgtest [23:11:19]: testbed dpkg architecture: armhf 427s autopkgtest [23:11:21]: testbed apt version: 3.0.0 431s autopkgtest [23:11:25]: @@@@@@@@@@@@@@@@@@@@ test bed setup 433s autopkgtest [23:11:27]: testbed release detected to be: questing 440s autopkgtest [23:11:34]: updating testbed package index (apt update) 442s Get:1 http://ftpmaster.internal/ubuntu questing-proposed InRelease [110 kB] 442s Get:2 http://ftpmaster.internal/ubuntu questing InRelease [110 kB] 442s Get:3 http://ftpmaster.internal/ubuntu questing-updates InRelease [110 kB] 442s Get:4 http://ftpmaster.internal/ubuntu questing-security InRelease [110 kB] 442s Get:5 http://ftpmaster.internal/ubuntu questing-proposed/multiverse Sources [43.1 kB] 442s Get:6 http://ftpmaster.internal/ubuntu questing-proposed/universe Sources [1947 kB] 443s Get:7 http://ftpmaster.internal/ubuntu questing-proposed/main Sources [168 kB] 443s Get:8 http://ftpmaster.internal/ubuntu questing-proposed/main armhf Packages [205 kB] 443s Get:9 http://ftpmaster.internal/ubuntu questing-proposed/universe armhf Packages [1371 kB] 443s Get:10 http://ftpmaster.internal/ubuntu questing-proposed/multiverse armhf Packages [12.9 kB] 443s Get:11 http://ftpmaster.internal/ubuntu questing/universe Sources [21.1 MB] 443s Get:12 http://ftpmaster.internal/ubuntu questing/multiverse Sources [299 kB] 443s Get:13 http://ftpmaster.internal/ubuntu questing/main Sources [1397 kB] 444s Get:14 http://ftpmaster.internal/ubuntu questing/main armhf Packages [1358 kB] 444s Get:15 http://ftpmaster.internal/ubuntu questing/universe armhf Packages [15.4 MB] 444s Get:16 http://ftpmaster.internal/ubuntu questing/multiverse armhf Packages [173 kB] 448s Fetched 43.9 MB in 6s (7399 kB/s) 449s Reading package lists... 455s autopkgtest [23:11:49]: upgrading testbed (apt dist-upgrade and autopurge) 457s Reading package lists... 457s Building dependency tree... 457s Reading state information... 459s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 459s Starting 2 pkgProblemResolver with broken count: 0 459s Done 460s Entering ResolveByKeep 461s 461s Calculating upgrade... 462s The following packages will be upgraded: 462s base-files distro-info-data dpkg dpkg-dev ed fwupd htop libdpkg-perl 462s libftdi1-2 libfwupd3 libnpth0t64 libsensors-config libsensors5 liburcu8t64 462s motd-news-config nano python3-pkg-resources python3-setuptools 462s ubuntu-pro-client ubuntu-pro-client-l10n usb.ids 462s 21 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 462s Need to get 6161 kB of archives. 462s After this operation, 3616 kB disk space will be freed. 462s Get:1 http://ftpmaster.internal/ubuntu questing/main armhf motd-news-config all 13.7ubuntu1 [5260 B] 463s Get:2 http://ftpmaster.internal/ubuntu questing/main armhf base-files armhf 13.7ubuntu1 [75.4 kB] 463s Get:3 http://ftpmaster.internal/ubuntu questing/main armhf dpkg armhf 1.22.18ubuntu3 [1254 kB] 463s Get:4 http://ftpmaster.internal/ubuntu questing/main armhf libnpth0t64 armhf 1.8-3 [7716 B] 463s Get:5 http://ftpmaster.internal/ubuntu questing/main armhf distro-info-data all 0.64 [6664 B] 463s Get:6 http://ftpmaster.internal/ubuntu questing/main armhf ubuntu-pro-client-l10n armhf 35.1ubuntu0 [19.7 kB] 463s Get:7 http://ftpmaster.internal/ubuntu questing/main armhf ubuntu-pro-client armhf 35.1ubuntu0 [258 kB] 463s Get:8 http://ftpmaster.internal/ubuntu questing/main armhf ed armhf 1.21.1-1 [53.0 kB] 463s Get:9 http://ftpmaster.internal/ubuntu questing/main armhf libsensors-config all 1:3.6.2-2 [6756 B] 463s Get:10 http://ftpmaster.internal/ubuntu questing/main armhf libsensors5 armhf 1:3.6.2-2 [26.8 kB] 463s Get:11 http://ftpmaster.internal/ubuntu questing/main armhf liburcu8t64 armhf 0.15.2-2 [57.3 kB] 463s Get:12 http://ftpmaster.internal/ubuntu questing/main armhf nano armhf 8.4-1 [278 kB] 463s Get:13 http://ftpmaster.internal/ubuntu questing/main armhf usb.ids all 2025.04.01-1 [223 kB] 463s Get:14 http://ftpmaster.internal/ubuntu questing/main armhf dpkg-dev all 1.22.18ubuntu3 [1089 kB] 463s Get:15 http://ftpmaster.internal/ubuntu questing/main armhf libdpkg-perl all 1.22.18ubuntu3 [281 kB] 463s Get:16 http://ftpmaster.internal/ubuntu questing/main armhf fwupd armhf 2.0.8-3 [1414 kB] 463s Get:17 http://ftpmaster.internal/ubuntu questing/main armhf libfwupd3 armhf 2.0.8-3 [126 kB] 463s Get:18 http://ftpmaster.internal/ubuntu questing/main armhf htop armhf 3.4.1-4 [147 kB] 463s Get:19 http://ftpmaster.internal/ubuntu questing/main armhf libftdi1-2 armhf 1.5-10 [27.8 kB] 463s Get:20 http://ftpmaster.internal/ubuntu questing-proposed/main armhf python3-pkg-resources all 77.0.3-1 [144 kB] 463s Get:21 http://ftpmaster.internal/ubuntu questing-proposed/main armhf python3-setuptools all 77.0.3-1 [660 kB] 464s Fetched 6161 kB in 1s (7155 kB/s) 464s (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 ... 63953 files and directories currently installed.) 464s Preparing to unpack .../motd-news-config_13.7ubuntu1_all.deb ... 464s Unpacking motd-news-config (13.7ubuntu1) over (13.6ubuntu2) ... 464s Preparing to unpack .../base-files_13.7ubuntu1_armhf.deb ... 464s Unpacking base-files (13.7ubuntu1) over (13.6ubuntu2) ... 464s Setting up base-files (13.7ubuntu1) ... 464s Installing new version of config file /etc/issue ... 464s Installing new version of config file /etc/issue.net ... 464s Installing new version of config file /etc/lsb-release ... 465s motd-news.service is a disabled or a static unit not running, not starting it. 465s (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 ... 63953 files and directories currently installed.) 465s Preparing to unpack .../dpkg_1.22.18ubuntu3_armhf.deb ... 465s Unpacking dpkg (1.22.18ubuntu3) over (1.22.18ubuntu2) ... 466s Setting up dpkg (1.22.18ubuntu3) ... 466s (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 ... 63953 files and directories currently installed.) 466s Preparing to unpack .../libnpth0t64_1.8-3_armhf.deb ... 466s Unpacking libnpth0t64:armhf (1.8-3) over (1.8-2) ... 466s Setting up libnpth0t64:armhf (1.8-3) ... 466s (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 ... 63953 files and directories currently installed.) 466s Preparing to unpack .../00-distro-info-data_0.64_all.deb ... 466s Unpacking distro-info-data (0.64) over (0.63) ... 466s Preparing to unpack .../01-ubuntu-pro-client-l10n_35.1ubuntu0_armhf.deb ... 466s Unpacking ubuntu-pro-client-l10n (35.1ubuntu0) over (35) ... 466s Preparing to unpack .../02-ubuntu-pro-client_35.1ubuntu0_armhf.deb ... 467s Unpacking ubuntu-pro-client (35.1ubuntu0) over (35) ... 467s Preparing to unpack .../03-ed_1.21.1-1_armhf.deb ... 467s Unpacking ed (1.21.1-1) over (1.21-1) ... 467s Preparing to unpack .../04-libsensors-config_1%3a3.6.2-2_all.deb ... 467s Unpacking libsensors-config (1:3.6.2-2) over (1:3.6.0-10) ... 467s Preparing to unpack .../05-libsensors5_1%3a3.6.2-2_armhf.deb ... 467s Unpacking libsensors5:armhf (1:3.6.2-2) over (1:3.6.0-10) ... 467s Preparing to unpack .../06-liburcu8t64_0.15.2-2_armhf.deb ... 467s Unpacking liburcu8t64:armhf (0.15.2-2) over (0.15.1-1) ... 467s Preparing to unpack .../07-nano_8.4-1_armhf.deb ... 467s Unpacking nano (8.4-1) over (8.3-1) ... 467s Preparing to unpack .../08-usb.ids_2025.04.01-1_all.deb ... 467s Unpacking usb.ids (2025.04.01-1) over (2025.01.14-1) ... 467s Preparing to unpack .../09-dpkg-dev_1.22.18ubuntu3_all.deb ... 467s Unpacking dpkg-dev (1.22.18ubuntu3) over (1.22.18ubuntu2) ... 467s Preparing to unpack .../10-libdpkg-perl_1.22.18ubuntu3_all.deb ... 467s Unpacking libdpkg-perl (1.22.18ubuntu3) over (1.22.18ubuntu2) ... 468s Preparing to unpack .../11-fwupd_2.0.8-3_armhf.deb ... 468s Unpacking fwupd (2.0.8-3) over (2.0.7-1) ... 468s dpkg: warning: unable to delete old directory '/etc/grub.d': Directory not empty 468s Preparing to unpack .../12-libfwupd3_2.0.8-3_armhf.deb ... 468s Unpacking libfwupd3:armhf (2.0.8-3) over (2.0.7-1) ... 468s Preparing to unpack .../13-htop_3.4.1-4_armhf.deb ... 468s Unpacking htop (3.4.1-4) over (3.4.0-2) ... 468s Preparing to unpack .../14-libftdi1-2_1.5-10_armhf.deb ... 468s Unpacking libftdi1-2:armhf (1.5-10) over (1.5-8build1) ... 468s Preparing to unpack .../15-python3-pkg-resources_77.0.3-1_all.deb ... 469s Unpacking python3-pkg-resources (77.0.3-1) over (75.8.0-1) ... 469s Preparing to unpack .../16-python3-setuptools_77.0.3-1_all.deb ... 469s Unpacking python3-setuptools (77.0.3-1) over (75.8.0-1) ... 469s Setting up python3-pkg-resources (77.0.3-1) ... 469s Setting up motd-news-config (13.7ubuntu1) ... 469s Setting up liburcu8t64:armhf (0.15.2-2) ... 469s Setting up python3-setuptools (77.0.3-1) ... 471s Setting up distro-info-data (0.64) ... 471s Setting up htop (3.4.1-4) ... 471s Setting up libsensors-config (1:3.6.2-2) ... 471s Installing new version of config file /etc/sensors3.conf ... 471s Setting up libfwupd3:armhf (2.0.8-3) ... 471s Setting up libftdi1-2:armhf (1.5-10) ... 471s Setting up ed (1.21.1-1) ... 471s Setting up usb.ids (2025.04.01-1) ... 471s Setting up libsensors5:armhf (1:3.6.2-2) ... 471s Setting up libdpkg-perl (1.22.18ubuntu3) ... 471s Setting up nano (8.4-1) ... 471s Installing new version of config file /etc/nanorc ... 471s Setting up ubuntu-pro-client (35.1ubuntu0) ... 471s apparmor_parser: Unable to replace "ubuntu_pro_apt_news". apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 471s 471s apparmor_parser: Unable to replace "apt_methods". apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 471s 471s apparmor_parser: Unable to replace "ubuntu_pro_esm_cache". apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 471s 473s Setting up fwupd (2.0.8-3) ... 474s fwupd-refresh.service is a disabled or a static unit not running, not starting it. 474s fwupd.service is a disabled or a static unit not running, not starting it. 474s Setting up ubuntu-pro-client-l10n (35.1ubuntu0) ... 474s Setting up dpkg-dev (1.22.18ubuntu3) ... 474s Processing triggers for dbus (1.16.2-2ubuntu1) ... 474s Processing triggers for install-info (7.1.1-1) ... 474s Processing triggers for libc-bin (2.41-6ubuntu1) ... 474s Processing triggers for man-db (2.13.0-1) ... 476s Processing triggers for plymouth-theme-ubuntu-text (24.004.60-2ubuntu7) ... 476s Processing triggers for initramfs-tools (0.147ubuntu1) ... 479s Reading package lists... 479s Building dependency tree... 479s Reading state information... 480s Starting pkgProblemResolver with broken count: 0 480s Starting 2 pkgProblemResolver with broken count: 0 480s Done 481s Solving dependencies... 482s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 484s autopkgtest [23:12:18]: rebooting testbed after setup commands that affected boot 547s Reading package lists... 547s Building dependency tree... 547s Reading state information... 548s Starting pkgProblemResolver with broken count: 0 548s Starting 2 pkgProblemResolver with broken count: 0 548s Done 550s The following NEW packages will be installed: 550s autoconf automake autopoint autotools-dev blt build-essential bwa clustalo 550s cpp cpp-14 cpp-14-arm-linux-gnueabihf cpp-arm-linux-gnueabihf debhelper 550s debugedit dh-autoreconf dh-python dh-strip-nondeterminism dialign 550s docutils-common dssp dwz fasttree flex fontconfig-config fonts-dejavu-core 550s fonts-dejavu-mono fonts-font-awesome fonts-lato fonts-lmodern fonts-lyx 550s fonts-urw-base35 g++ g++-14 g++-14-arm-linux-gnueabihf 550s g++-arm-linux-gnueabihf gcc gcc-14 gcc-14-arm-linux-gnueabihf 550s gcc-arm-linux-gnueabihf gettext ghostscript hevea hicolor-icon-theme 550s imagemagick imagemagick-7-common imagemagick-7.q16 intltool-debian libamd3 550s libaom3 libapache-pom-java libarchive-zip-perl libargtable2-0 libarpack2t64 550s libasan8 libavahi-client3 libavahi-common-data libavahi-common3 libblas3 550s libc-dev-bin libc6-dev libcairo2 libcc1-0 libcifpp-data libcifpp7 libcolamd3 550s libcommons-logging-java libcommons-parent-java libcrypt-dev libcups2t64 550s libde265-0 libdebhelper-perl libdeflate0 libdw1t64 libexpat1-dev 550s libfftw3-double3 libfile-stripnondeterminism-perl libfontbox-java 550s libfontconfig1 libfontenc1 libfreetype6 libgcc-14-dev libgfortran5 libglpk40 550s libgomp1 libgraphite2-3 libgs-common libgs10 libgs10-common libharfbuzz0b 550s libheif-plugin-aomdec libheif-plugin-libde265 libheif1 libice6 libidn12 550s libigraph3t64 libijs-0.35 libimagequant0 libisl23 libjbig0 libjbig2dec0 550s libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui libjs-sphinxdoc 550s libjs-underscore libjson-perl libkpathsea6 liblapack3 liblbfgsb0 liblcms2-2 550s liblerc4 liblqr-1-0 libltdl7 libmagickcore-7.q16-10 libmagickwand-7.q16-10 550s libmbedcrypto16 libmbedtls21 libmbedx509-7 libmpc3 libmpfi0 libmysqlclient24 550s libnetpbm11t64 libopenjp2-7 libpaper-utils libpaper2 libpdfbox-java 550s libpixman-1-0 libplfit0 libpotrace0 libptexenc1 libpython3-all-dev 550s libpython3-dev libpython3.13 libpython3.13-dev libqhull-r8.0 libraqm0 550s libraw23t64 libsharpyuv0 libsm6 libstdc++-14-dev libsuitesparseconfig7 550s libsynctex2 libtcl8.6 libteckit0 libtexlua53-5 libtiff6 libtk8.6 libtool 550s libubsan1 libwebp7 libwebpdemux2 libwebpmux3 libxaw7 libxcb-render0 550s libxcb-shm0 libxft2 libxi6 libxmu6 libxpm4 libxrender1 libxslt1.1 libxss1 550s libxt6t64 libzzip-0-13t64 linux-libc-dev m4 mafft mysql-common ncbi-blast+ 550s ncbi-data netpbm phylip po-debconf poppler-data prank preview-latex-style 550s probcons python-biopython-doc python-matplotlib-data python3-alabaster 550s python3-all python3-all-dev python3-biopython python3-biopython-sql 550s python3-brotli python3-cairo python3-contourpy python3-cycler 550s python3-decorator python3-defusedxml python3-dev python3-docutils 550s python3-fonttools python3-freetype python3-fs python3-igraph 550s python3-imagesize python3-kiwisolver python3-lxml python3-lz4 550s python3-matplotlib python3-mmtf python3-mpmath python3-msgpack 550s python3-mysqldb python3-networkx python3-numpy python3-numpy-dev 550s python3-numpydoc python3-pil python3-pil.imagetk python3-platformdirs 550s python3-rdflib python3-reportlab python3-rlpycairo python3-roman 550s python3-scipy python3-snowballstemmer python3-sphinx 550s python3-sphinx-rtd-theme python3-sphinxcontrib.jquery python3-sympy 550s python3-tabulate python3-texttable python3-tk python3-ufolib2 python3.13-dev 550s python3.13-tk rpcsvc-proto sgml-base sphinx-common sphinx-rtd-theme-common 550s t-coffee t1utils tex-common texlive-base texlive-binaries 550s texlive-fonts-recommended texlive-latex-base texlive-latex-extra 550s texlive-latex-recommended texlive-pictures tk8.6-blt2.5 unicode-data 550s w3c-sgml-lib wise wise-data x11-common xdg-utils xfonts-encodings 550s xfonts-utils xml-core zlib1g-dev 550s 0 upgraded, 254 newly installed, 0 to remove and 0 not upgraded. 550s Need to get 328 MB of archives. 550s After this operation, 1198 MB of additional disk space will be used. 550s Get:1 http://ftpmaster.internal/ubuntu questing/main armhf m4 armhf 1.4.19-7 [238 kB] 551s Get:2 http://ftpmaster.internal/ubuntu questing/main armhf flex armhf 2.6.4-8.2build1 [293 kB] 551s Get:3 http://ftpmaster.internal/ubuntu questing/main armhf fonts-lato all 2.015-1 [2781 kB] 551s Get:4 http://ftpmaster.internal/ubuntu questing/main armhf libgomp1 armhf 15-20250404-0ubuntu1 [128 kB] 551s Get:5 http://ftpmaster.internal/ubuntu questing/main armhf libfftw3-double3 armhf 3.3.10-2fakesync1build1 [369 kB] 551s Get:6 http://ftpmaster.internal/ubuntu questing/main armhf libfreetype6 armhf 2.13.3+dfsg-1 [330 kB] 551s Get:7 http://ftpmaster.internal/ubuntu questing/main armhf fonts-dejavu-mono all 2.37-8 [502 kB] 551s Get:8 http://ftpmaster.internal/ubuntu questing/main armhf fonts-dejavu-core all 2.37-8 [835 kB] 551s Get:9 http://ftpmaster.internal/ubuntu questing/main armhf libfontenc1 armhf 1:1.1.8-1build1 [11.5 kB] 551s Get:10 http://ftpmaster.internal/ubuntu questing/main armhf x11-common all 1:7.7+23ubuntu4 [21.8 kB] 551s Get:11 http://ftpmaster.internal/ubuntu questing/main armhf xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 551s Get:12 http://ftpmaster.internal/ubuntu questing/main armhf xfonts-utils armhf 1:7.7+7 [90.6 kB] 551s Get:13 http://ftpmaster.internal/ubuntu questing/main armhf fonts-urw-base35 all 20200910-8 [11.0 MB] 551s Get:14 http://ftpmaster.internal/ubuntu questing/main armhf fontconfig-config armhf 2.15.0-2.2ubuntu1 [37.9 kB] 551s Get:15 http://ftpmaster.internal/ubuntu questing/main armhf libfontconfig1 armhf 2.15.0-2.2ubuntu1 [114 kB] 551s Get:16 http://ftpmaster.internal/ubuntu questing/main armhf libsharpyuv0 armhf 1.5.0-0.1 [16.4 kB] 551s Get:17 http://ftpmaster.internal/ubuntu questing/main armhf libaom3 armhf 3.12.0-1 [1235 kB] 551s Get:18 http://ftpmaster.internal/ubuntu questing/main armhf libheif-plugin-aomdec armhf 1.19.7-1 [10.9 kB] 551s Get:19 http://ftpmaster.internal/ubuntu questing/main armhf libde265-0 armhf 1.0.15-1build5 [157 kB] 551s Get:20 http://ftpmaster.internal/ubuntu questing/main armhf libheif-plugin-libde265 armhf 1.19.7-1 [11.7 kB] 551s Get:21 http://ftpmaster.internal/ubuntu questing/main armhf libheif1 armhf 1.19.7-1 [479 kB] 551s Get:22 http://ftpmaster.internal/ubuntu questing/main armhf libjbig0 armhf 2.1-6.1ubuntu2 [24.9 kB] 551s Get:23 http://ftpmaster.internal/ubuntu questing/main armhf libjpeg-turbo8 armhf 2.1.5-3ubuntu2 [127 kB] 551s Get:24 http://ftpmaster.internal/ubuntu questing/main armhf libjpeg8 armhf 8c-2ubuntu11 [2148 B] 551s Get:25 http://ftpmaster.internal/ubuntu questing/main armhf liblcms2-2 armhf 2.16-2 [137 kB] 551s Get:26 http://ftpmaster.internal/ubuntu questing/universe armhf liblqr-1-0 armhf 0.4.2-2.1build2 [23.2 kB] 551s Get:27 http://ftpmaster.internal/ubuntu questing/main armhf libltdl7 armhf 2.5.4-4 [39.8 kB] 551s Get:28 http://ftpmaster.internal/ubuntu questing/main armhf libopenjp2-7 armhf 2.5.3-2 [172 kB] 551s Get:29 http://ftpmaster.internal/ubuntu questing/main armhf libraw23t64 armhf 0.21.3-1 [353 kB] 551s Get:30 http://ftpmaster.internal/ubuntu questing/main armhf libdeflate0 armhf 1.23-1 [38.5 kB] 551s Get:31 http://ftpmaster.internal/ubuntu questing/main armhf liblerc4 armhf 4.0.0+ds-5ubuntu1 [160 kB] 551s Get:32 http://ftpmaster.internal/ubuntu questing/main armhf libwebp7 armhf 1.5.0-0.1 [188 kB] 551s Get:33 http://ftpmaster.internal/ubuntu questing/main armhf libtiff6 armhf 4.7.0-3ubuntu1 [184 kB] 551s Get:34 http://ftpmaster.internal/ubuntu questing/main armhf libwebpdemux2 armhf 1.5.0-0.1 [11.5 kB] 551s Get:35 http://ftpmaster.internal/ubuntu questing/main armhf libwebpmux3 armhf 1.5.0-0.1 [22.4 kB] 551s Get:36 http://ftpmaster.internal/ubuntu questing/universe armhf imagemagick-7-common all 8:7.1.1.43+dfsg1-1 [69.7 kB] 551s Get:37 http://ftpmaster.internal/ubuntu questing/universe armhf libmagickcore-7.q16-10 armhf 8:7.1.1.43+dfsg1-1 [1810 kB] 551s Get:38 http://ftpmaster.internal/ubuntu questing/universe armhf libmagickwand-7.q16-10 armhf 8:7.1.1.43+dfsg1-1 [332 kB] 551s Get:39 http://ftpmaster.internal/ubuntu questing/main armhf poppler-data all 0.4.12-1 [2060 kB] 552s Get:40 http://ftpmaster.internal/ubuntu questing/main armhf python3-numpy-dev armhf 1:2.2.3+ds-5 [141 kB] 552s Get:41 http://ftpmaster.internal/ubuntu questing/main armhf libblas3 armhf 3.12.1-2 [132 kB] 552s Get:42 http://ftpmaster.internal/ubuntu questing/main armhf libgfortran5 armhf 15-20250404-0ubuntu1 [331 kB] 552s Get:43 http://ftpmaster.internal/ubuntu questing/main armhf liblapack3 armhf 3.12.1-2 [2091 kB] 552s Get:44 http://ftpmaster.internal/ubuntu questing/main armhf python3-numpy armhf 1:2.2.3+ds-5 [3725 kB] 552s Get:45 http://ftpmaster.internal/ubuntu questing/main armhf sgml-base all 1.31 [11.4 kB] 552s Get:46 http://ftpmaster.internal/ubuntu questing/main armhf autoconf all 2.72-3ubuntu1 [383 kB] 552s Get:47 http://ftpmaster.internal/ubuntu questing/main armhf autotools-dev all 20220109.1 [44.9 kB] 552s Get:48 http://ftpmaster.internal/ubuntu questing/main armhf automake all 1:1.17-3ubuntu1 [572 kB] 552s Get:49 http://ftpmaster.internal/ubuntu questing/main armhf autopoint all 0.23.1-1 [619 kB] 552s Get:50 http://ftpmaster.internal/ubuntu questing/main armhf libtcl8.6 armhf 8.6.16+dfsg-1 [909 kB] 552s Get:51 http://ftpmaster.internal/ubuntu questing/main armhf libxrender1 armhf 1:0.9.10-1.1build1 [16.0 kB] 552s Get:52 http://ftpmaster.internal/ubuntu questing/main armhf libxft2 armhf 2.3.6-1build1 [37.4 kB] 552s Get:53 http://ftpmaster.internal/ubuntu questing/main armhf libxss1 armhf 1:1.2.3-1build3 [6500 B] 552s Get:54 http://ftpmaster.internal/ubuntu questing/main armhf libtk8.6 armhf 8.6.16-1 [686 kB] 552s Get:55 http://ftpmaster.internal/ubuntu questing/main armhf tk8.6-blt2.5 armhf 2.5.3+dfsg-8 [527 kB] 552s Get:56 http://ftpmaster.internal/ubuntu questing/main armhf blt armhf 2.5.3+dfsg-8 [4824 B] 552s Get:57 http://ftpmaster.internal/ubuntu questing/main armhf libc-dev-bin armhf 2.41-6ubuntu1 [21.7 kB] 552s Get:58 http://ftpmaster.internal/ubuntu questing/main armhf linux-libc-dev armhf 6.14.0-15.15 [1687 kB] 552s Get:59 http://ftpmaster.internal/ubuntu questing/main armhf libcrypt-dev armhf 1:4.4.38-1 [120 kB] 552s Get:60 http://ftpmaster.internal/ubuntu questing/main armhf rpcsvc-proto armhf 1.4.2-0ubuntu7 [62.2 kB] 552s Get:61 http://ftpmaster.internal/ubuntu questing/main armhf libc6-dev armhf 2.41-6ubuntu1 [1396 kB] 552s Get:62 http://ftpmaster.internal/ubuntu questing/main armhf libisl23 armhf 0.27-1 [546 kB] 552s Get:63 http://ftpmaster.internal/ubuntu questing/main armhf libmpc3 armhf 1.3.1-1build2 [47.1 kB] 552s Get:64 http://ftpmaster.internal/ubuntu questing/main armhf cpp-14-arm-linux-gnueabihf armhf 14.2.0-19ubuntu2 [9221 kB] 552s Get:65 http://ftpmaster.internal/ubuntu questing/main armhf cpp-14 armhf 14.2.0-19ubuntu2 [1032 B] 552s Get:66 http://ftpmaster.internal/ubuntu questing/main armhf cpp-arm-linux-gnueabihf armhf 4:14.2.0-1ubuntu1 [5578 B] 552s Get:67 http://ftpmaster.internal/ubuntu questing/main armhf cpp armhf 4:14.2.0-1ubuntu1 [22.4 kB] 552s Get:68 http://ftpmaster.internal/ubuntu questing/main armhf libcc1-0 armhf 15-20250404-0ubuntu1 [43.3 kB] 552s Get:69 http://ftpmaster.internal/ubuntu questing/main armhf libasan8 armhf 15-20250404-0ubuntu1 [2951 kB] 552s Get:70 http://ftpmaster.internal/ubuntu questing/main armhf libubsan1 armhf 15-20250404-0ubuntu1 [1188 kB] 552s Get:71 http://ftpmaster.internal/ubuntu questing/main armhf libgcc-14-dev armhf 14.2.0-19ubuntu2 [897 kB] 552s Get:72 http://ftpmaster.internal/ubuntu questing/main armhf gcc-14-arm-linux-gnueabihf armhf 14.2.0-19ubuntu2 [18.0 MB] 553s Get:73 http://ftpmaster.internal/ubuntu questing/main armhf gcc-14 armhf 14.2.0-19ubuntu2 [510 kB] 553s Get:74 http://ftpmaster.internal/ubuntu questing/main armhf gcc-arm-linux-gnueabihf armhf 4:14.2.0-1ubuntu1 [1218 B] 553s Get:75 http://ftpmaster.internal/ubuntu questing/main armhf gcc armhf 4:14.2.0-1ubuntu1 [5004 B] 553s Get:76 http://ftpmaster.internal/ubuntu questing/main armhf libstdc++-14-dev armhf 14.2.0-19ubuntu2 [2576 kB] 553s Get:77 http://ftpmaster.internal/ubuntu questing/main armhf g++-14-arm-linux-gnueabihf armhf 14.2.0-19ubuntu2 [10.5 MB] 553s Get:78 http://ftpmaster.internal/ubuntu questing/main armhf g++-14 armhf 14.2.0-19ubuntu2 [23.0 kB] 553s Get:79 http://ftpmaster.internal/ubuntu questing/main armhf g++-arm-linux-gnueabihf armhf 4:14.2.0-1ubuntu1 [966 B] 553s Get:80 http://ftpmaster.internal/ubuntu questing/main armhf g++ armhf 4:14.2.0-1ubuntu1 [1084 B] 553s Get:81 http://ftpmaster.internal/ubuntu questing/main armhf build-essential armhf 12.12ubuntu1 [5088 B] 553s Get:82 http://ftpmaster.internal/ubuntu questing/universe armhf bwa armhf 0.7.18-1 [198 kB] 553s Get:83 http://ftpmaster.internal/ubuntu questing/universe armhf libargtable2-0 armhf 13-3 [12.9 kB] 553s Get:84 http://ftpmaster.internal/ubuntu questing/universe armhf clustalo armhf 1.2.4-8build1 [249 kB] 553s Get:85 http://ftpmaster.internal/ubuntu questing/main armhf libdebhelper-perl all 13.24.1ubuntu2 [95.4 kB] 553s Get:86 http://ftpmaster.internal/ubuntu questing/main armhf libtool all 2.5.4-4 [168 kB] 553s Get:87 http://ftpmaster.internal/ubuntu questing/main armhf dh-autoreconf all 20 [16.1 kB] 553s Get:88 http://ftpmaster.internal/ubuntu questing/main armhf libarchive-zip-perl all 1.68-1 [90.2 kB] 553s Get:89 http://ftpmaster.internal/ubuntu questing/main armhf libfile-stripnondeterminism-perl all 1.14.1-2 [20.3 kB] 553s Get:90 http://ftpmaster.internal/ubuntu questing/main armhf dh-strip-nondeterminism all 1.14.1-2 [5064 B] 553s Get:91 http://ftpmaster.internal/ubuntu questing/main armhf libdw1t64 armhf 0.192-4ubuntu1 [244 kB] 553s Get:92 http://ftpmaster.internal/ubuntu questing/main armhf debugedit armhf 1:5.1-2 [46.7 kB] 553s Get:93 http://ftpmaster.internal/ubuntu questing/main armhf dwz armhf 0.15-1build6 [116 kB] 553s Get:94 http://ftpmaster.internal/ubuntu questing/main armhf gettext armhf 0.23.1-1 [1053 kB] 553s Get:95 http://ftpmaster.internal/ubuntu questing/main armhf intltool-debian all 0.35.0+20060710.6 [23.2 kB] 553s Get:96 http://ftpmaster.internal/ubuntu questing/main armhf po-debconf all 1.0.21+nmu1 [233 kB] 553s Get:97 http://ftpmaster.internal/ubuntu questing/main armhf debhelper all 13.24.1ubuntu2 [895 kB] 553s Get:98 http://ftpmaster.internal/ubuntu questing/universe armhf dh-python all 6.20250308 [118 kB] 553s Get:99 http://ftpmaster.internal/ubuntu questing/universe armhf dialign armhf 2.2.1-13 [156 kB] 553s Get:100 http://ftpmaster.internal/ubuntu questing/main armhf xml-core all 0.19 [20.3 kB] 553s Get:101 http://ftpmaster.internal/ubuntu questing/main armhf docutils-common all 0.21.2+dfsg-2 [131 kB] 554s Get:102 http://ftpmaster.internal/ubuntu questing/universe armhf libcifpp-data all 7.0.9-1 [481 kB] 554s Get:103 http://ftpmaster.internal/ubuntu questing/universe armhf libcifpp7 armhf 7.0.9-1 [962 kB] 554s Get:104 http://ftpmaster.internal/ubuntu questing/universe armhf dssp armhf 4.4.10-1 [696 kB] 554s Get:105 http://ftpmaster.internal/ubuntu questing/main armhf fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB] 554s Get:106 http://ftpmaster.internal/ubuntu questing/universe armhf fonts-lmodern all 2.005-1 [4799 kB] 554s Get:107 http://ftpmaster.internal/ubuntu questing/universe armhf fonts-lyx all 2.4.3-1 [171 kB] 554s Get:108 http://ftpmaster.internal/ubuntu questing/main armhf libgs-common all 10.05.0dfsg1-0ubuntu1 [176 kB] 554s Get:109 http://ftpmaster.internal/ubuntu questing/main armhf libgs10-common all 10.05.0dfsg1-0ubuntu1 [490 kB] 554s Get:110 http://ftpmaster.internal/ubuntu questing/main armhf libavahi-common-data armhf 0.8-16ubuntu2 [31.0 kB] 554s Get:111 http://ftpmaster.internal/ubuntu questing/main armhf libavahi-common3 armhf 0.8-16ubuntu2 [20.2 kB] 554s Get:112 http://ftpmaster.internal/ubuntu questing/main armhf libavahi-client3 armhf 0.8-16ubuntu2 [24.5 kB] 554s Get:113 http://ftpmaster.internal/ubuntu questing/main armhf libcups2t64 armhf 2.4.12-0ubuntu1 [240 kB] 554s Get:114 http://ftpmaster.internal/ubuntu questing/main armhf libidn12 armhf 1.43-1 [56.2 kB] 554s Get:115 http://ftpmaster.internal/ubuntu questing/main armhf libijs-0.35 armhf 0.35-15.2 [13.6 kB] 554s Get:116 http://ftpmaster.internal/ubuntu questing/main armhf libjbig2dec0 armhf 0.20-1build3 [57.6 kB] 554s Get:117 http://ftpmaster.internal/ubuntu questing/main armhf libpaper2 armhf 2.2.5-0.3 [16.3 kB] 554s Get:118 http://ftpmaster.internal/ubuntu questing/main armhf libice6 armhf 2:1.1.1-1 [36.5 kB] 554s Get:119 http://ftpmaster.internal/ubuntu questing/main armhf libsm6 armhf 2:1.2.4-1 [15.1 kB] 554s Get:120 http://ftpmaster.internal/ubuntu questing/main armhf libxt6t64 armhf 1:1.2.1-1.2build1 [145 kB] 554s Get:121 http://ftpmaster.internal/ubuntu questing/main armhf libgs10 armhf 10.05.0dfsg1-0ubuntu1 [4259 kB] 554s Get:122 http://ftpmaster.internal/ubuntu questing/main armhf ghostscript armhf 10.05.0dfsg1-0ubuntu1 [42.7 kB] 554s Get:123 http://ftpmaster.internal/ubuntu questing/universe armhf libnetpbm11t64 armhf 2:11.09.02-2 [97.7 kB] 554s Get:124 http://ftpmaster.internal/ubuntu questing/universe armhf netpbm armhf 2:11.09.02-2 [2021 kB] 555s Get:125 http://ftpmaster.internal/ubuntu questing/universe armhf tex-common all 6.19 [29.8 kB] 555s Get:126 http://ftpmaster.internal/ubuntu questing/main armhf libpaper-utils armhf 2.2.5-0.3 [14.2 kB] 555s Get:127 http://ftpmaster.internal/ubuntu questing/universe armhf libkpathsea6 armhf 2024.20240313.70630+ds-6 [59.0 kB] 555s Get:128 http://ftpmaster.internal/ubuntu questing/universe armhf libptexenc1 armhf 2024.20240313.70630+ds-6 [37.8 kB] 555s Get:129 http://ftpmaster.internal/ubuntu questing/universe armhf libsynctex2 armhf 2024.20240313.70630+ds-6 [48.6 kB] 555s Get:130 http://ftpmaster.internal/ubuntu questing/universe armhf libtexlua53-5 armhf 2024.20240313.70630+ds-6 [98.5 kB] 555s Get:131 http://ftpmaster.internal/ubuntu questing/main armhf t1utils armhf 1.41-4build3 [51.8 kB] 555s Get:132 http://ftpmaster.internal/ubuntu questing/main armhf libpixman-1-0 armhf 0.44.0-3 [183 kB] 555s Get:133 http://ftpmaster.internal/ubuntu questing/main armhf libxcb-render0 armhf 1.17.0-2 [15.3 kB] 555s Get:134 http://ftpmaster.internal/ubuntu questing/main armhf libxcb-shm0 armhf 1.17.0-2 [5774 B] 555s Get:135 http://ftpmaster.internal/ubuntu questing/main armhf libcairo2 armhf 1.18.4-1 [483 kB] 555s Get:136 http://ftpmaster.internal/ubuntu questing/main armhf libgraphite2-3 armhf 1.3.14-2ubuntu1 [64.8 kB] 555s Get:137 http://ftpmaster.internal/ubuntu questing/main armhf libharfbuzz0b armhf 10.2.0-1 [464 kB] 555s Get:138 http://ftpmaster.internal/ubuntu questing/universe armhf libmpfi0 armhf 1.5.4+ds-4 [28.0 kB] 555s Get:139 http://ftpmaster.internal/ubuntu questing/universe armhf libpotrace0 armhf 1.16-2build1 [15.2 kB] 555s Get:140 http://ftpmaster.internal/ubuntu questing/universe armhf libteckit0 armhf 2.5.12+ds1-1 [323 kB] 555s Get:141 http://ftpmaster.internal/ubuntu questing/main armhf libxmu6 armhf 2:1.1.3-3build2 [40.4 kB] 555s Get:142 http://ftpmaster.internal/ubuntu questing/main armhf libxpm4 armhf 1:3.5.17-1build2 [30.1 kB] 555s Get:143 http://ftpmaster.internal/ubuntu questing/main armhf libxaw7 armhf 2:1.0.16-1 [154 kB] 555s Get:144 http://ftpmaster.internal/ubuntu questing/main armhf libxi6 armhf 2:1.8.2-1 [26.5 kB] 555s Get:145 http://ftpmaster.internal/ubuntu questing/universe armhf libzzip-0-13t64 armhf 0.13.78+dfsg.1-0.1 [26.1 kB] 555s Get:146 http://ftpmaster.internal/ubuntu questing/universe armhf texlive-binaries armhf 2024.20240313.70630+ds-6 [7065 kB] 555s Get:147 http://ftpmaster.internal/ubuntu questing/main armhf xdg-utils all 1.2.1-2ubuntu1 [66.0 kB] 555s Get:148 http://ftpmaster.internal/ubuntu questing/universe armhf texlive-base all 2024.20250309-1 [22.7 MB] 556s Get:149 http://ftpmaster.internal/ubuntu questing/main armhf hicolor-icon-theme all 0.18-2 [13.3 kB] 556s Get:150 http://ftpmaster.internal/ubuntu questing/universe armhf imagemagick-7.q16 armhf 8:7.1.1.43+dfsg1-1 [704 kB] 556s Get:151 http://ftpmaster.internal/ubuntu questing/universe armhf imagemagick armhf 8:7.1.1.43+dfsg1-1 [14.1 kB] 556s Get:152 http://ftpmaster.internal/ubuntu questing/universe armhf hevea armhf 2.36-2 [1938 kB] 556s Get:153 http://ftpmaster.internal/ubuntu questing/main armhf libsuitesparseconfig7 armhf 1:7.8.3+dfsg-3 [12.7 kB] 556s Get:154 http://ftpmaster.internal/ubuntu questing/universe armhf libamd3 armhf 1:7.8.3+dfsg-3 [29.2 kB] 556s Get:155 http://ftpmaster.internal/ubuntu questing/universe armhf libapache-pom-java all 33-2 [5874 B] 556s Get:156 http://ftpmaster.internal/ubuntu questing/universe armhf libarpack2t64 armhf 3.9.1-4 [86.7 kB] 556s Get:157 http://ftpmaster.internal/ubuntu questing/main armhf libcolamd3 armhf 1:7.8.3+dfsg-3 [19.8 kB] 556s Get:158 http://ftpmaster.internal/ubuntu questing/universe armhf libcommons-parent-java all 56-1 [10.7 kB] 556s Get:159 http://ftpmaster.internal/ubuntu questing/universe armhf libcommons-logging-java all 1.3.0-1ubuntu1 [63.8 kB] 556s Get:160 http://ftpmaster.internal/ubuntu questing/main armhf libexpat1-dev armhf 2.7.1-1 [122 kB] 556s Get:161 http://ftpmaster.internal/ubuntu questing/universe armhf libglpk40 armhf 5.0-1build2 [326 kB] 556s Get:162 http://ftpmaster.internal/ubuntu questing/universe armhf libplfit0 armhf 0.9.6+ds-2ubuntu1 [25.7 kB] 556s Get:163 http://ftpmaster.internal/ubuntu questing/universe armhf libigraph3t64 armhf 0.10.15+ds-3 [847 kB] 556s Get:164 http://ftpmaster.internal/ubuntu questing/main armhf libimagequant0 armhf 2.18.0-1build1 [31.1 kB] 556s Get:165 http://ftpmaster.internal/ubuntu questing/main armhf libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 556s Get:166 http://ftpmaster.internal/ubuntu questing/universe armhf libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 556s Get:167 http://ftpmaster.internal/ubuntu questing/main armhf libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 556s Get:168 http://ftpmaster.internal/ubuntu questing/main armhf libjs-sphinxdoc all 8.1.3-5 [31.0 kB] 556s Get:169 http://ftpmaster.internal/ubuntu questing/main armhf libjson-perl all 4.10000-1 [81.9 kB] 556s Get:170 http://ftpmaster.internal/ubuntu questing/universe armhf liblbfgsb0 armhf 3.0+dfsg.4-1build1 [27.4 kB] 556s Get:171 http://ftpmaster.internal/ubuntu questing/universe armhf libmbedcrypto16 armhf 3.6.2-3ubuntu1 [226 kB] 556s Get:172 http://ftpmaster.internal/ubuntu questing/universe armhf libmbedx509-7 armhf 3.6.2-3ubuntu1 [30.4 kB] 556s Get:173 http://ftpmaster.internal/ubuntu questing/universe armhf libmbedtls21 armhf 3.6.2-3ubuntu1 [116 kB] 556s Get:174 http://ftpmaster.internal/ubuntu questing/main armhf mysql-common all 5.8+1.1.1ubuntu1 [6922 B] 556s Get:175 http://ftpmaster.internal/ubuntu questing/main armhf libmysqlclient24 armhf 8.4.4-0ubuntu2 [1260 kB] 556s Get:176 http://ftpmaster.internal/ubuntu questing/main armhf libpython3.13 armhf 3.13.3-1 [2082 kB] 556s Get:177 http://ftpmaster.internal/ubuntu questing/main armhf zlib1g-dev armhf 1:1.3.dfsg+really1.3.1-1ubuntu1 [880 kB] 556s Get:178 http://ftpmaster.internal/ubuntu questing/main armhf libpython3.13-dev armhf 3.13.3-1 [4276 kB] 556s Get:179 http://ftpmaster.internal/ubuntu questing/main armhf libpython3-dev armhf 3.13.3-1 [10.8 kB] 556s Get:180 http://ftpmaster.internal/ubuntu questing/main armhf libpython3-all-dev armhf 3.13.3-1 [906 B] 556s Get:181 http://ftpmaster.internal/ubuntu questing/universe armhf libqhull-r8.0 armhf 2020.2-6build1 [173 kB] 556s Get:182 http://ftpmaster.internal/ubuntu questing/main armhf libraqm0 armhf 0.10.2-1 [12.4 kB] 556s Get:183 http://ftpmaster.internal/ubuntu questing/main armhf libxslt1.1 armhf 1.1.39-0exp1ubuntu4 [151 kB] 556s Get:184 http://ftpmaster.internal/ubuntu questing/universe armhf mafft armhf 7.505-1 [928 kB] 556s Get:185 http://ftpmaster.internal/ubuntu questing/universe armhf ncbi-data all 6.1.20170106+dfsg2-5 [3966 kB] 556s Get:186 http://ftpmaster.internal/ubuntu questing/universe armhf ncbi-blast+ armhf 2.16.0+ds-6build1 [14.8 MB] 557s Get:187 http://ftpmaster.internal/ubuntu questing/universe armhf phylip armhf 1:3.697+dfsg-4build1 [876 kB] 557s Get:188 http://ftpmaster.internal/ubuntu questing/universe armhf prank armhf 0.0.170427+dfsg-3 [340 kB] 557s Get:189 http://ftpmaster.internal/ubuntu questing/universe armhf preview-latex-style all 13.2-1 [347 kB] 557s Get:190 http://ftpmaster.internal/ubuntu questing/universe armhf probcons armhf 1.12-14 [120 kB] 557s Get:191 http://ftpmaster.internal/ubuntu questing/universe armhf python-biopython-doc all 1.85+dfsg-2build1 [18.2 MB] 558s Get:192 http://ftpmaster.internal/ubuntu questing/universe armhf python-matplotlib-data all 3.8.3-7build1 [2934 kB] 558s Get:193 http://ftpmaster.internal/ubuntu questing/main armhf python3-all armhf 3.13.3-1 [880 B] 558s Get:194 http://ftpmaster.internal/ubuntu questing/main armhf python3.13-dev armhf 3.13.3-1 [508 kB] 558s Get:195 http://ftpmaster.internal/ubuntu questing/main armhf python3-dev armhf 3.13.3-1 [26.7 kB] 558s Get:196 http://ftpmaster.internal/ubuntu questing/main armhf python3-all-dev armhf 3.13.3-1 [904 B] 558s Get:197 http://ftpmaster.internal/ubuntu questing/main armhf python3.13-tk armhf 3.13.3-1 [104 kB] 558s Get:198 http://ftpmaster.internal/ubuntu questing/main armhf python3-tk armhf 3.13.3-1 [9854 B] 558s Get:199 http://ftpmaster.internal/ubuntu questing/universe armhf python3-pil.imagetk armhf 11.1.0-5build1 [9226 B] 558s Get:200 http://ftpmaster.internal/ubuntu questing/main armhf python3-pil armhf 11.1.0-5build1 [435 kB] 558s Get:201 http://ftpmaster.internal/ubuntu questing/main armhf python3-cairo armhf 1.27.0-2 [115 kB] 558s Get:202 http://ftpmaster.internal/ubuntu questing/universe armhf python3-freetype all 2.5.1-1 [92.3 kB] 558s Get:203 http://ftpmaster.internal/ubuntu questing/universe armhf python3-rlpycairo all 0.3.0-3 [9130 B] 558s Get:204 http://ftpmaster.internal/ubuntu questing/universe armhf python3-reportlab all 4.3.1-1 [1137 kB] 559s Get:205 http://ftpmaster.internal/ubuntu questing/universe armhf w3c-sgml-lib all 1.3-3 [280 kB] 559s Get:206 http://ftpmaster.internal/ubuntu questing/universe armhf python3-biopython armhf 1.85+dfsg-2build1 [1692 kB] 559s Get:207 http://ftpmaster.internal/ubuntu questing/universe armhf python3-biopython-sql all 1.85+dfsg-2build1 [26.4 kB] 559s Get:208 http://ftpmaster.internal/ubuntu questing/universe armhf python3-brotli armhf 1.1.0-2build4 [322 kB] 559s Get:209 http://ftpmaster.internal/ubuntu questing/universe armhf python3-contourpy armhf 1.3.1-1build1 [195 kB] 559s Get:210 http://ftpmaster.internal/ubuntu questing/universe armhf python3-cycler all 0.12.1-1 [9716 B] 559s Get:211 http://ftpmaster.internal/ubuntu questing/main armhf python3-decorator all 5.1.1-5 [10.1 kB] 559s Get:212 http://ftpmaster.internal/ubuntu questing/main armhf python3-defusedxml all 0.7.1-3 [42.2 kB] 559s Get:213 http://ftpmaster.internal/ubuntu questing/main armhf python3-roman all 5.0-1 [10.3 kB] 559s Get:214 http://ftpmaster.internal/ubuntu questing/main armhf python3-docutils all 0.21.2+dfsg-2 [409 kB] 559s Get:215 http://ftpmaster.internal/ubuntu questing/main armhf python3-platformdirs all 4.3.6-1 [16.8 kB] 559s Get:216 http://ftpmaster.internal/ubuntu questing/universe armhf python3-fs all 2.4.16-7 [90.8 kB] 559s Get:217 http://ftpmaster.internal/ubuntu questing/main armhf python3-lxml armhf 5.3.2-1 [1281 kB] 559s Get:218 http://ftpmaster.internal/ubuntu questing/universe armhf python3-lz4 armhf 4.4.0+dfsg-1build1 [25.3 kB] 559s Get:219 http://ftpmaster.internal/ubuntu questing/universe armhf python3-scipy armhf 1.14.1-4ubuntu2 [16.7 MB] 560s Get:220 http://ftpmaster.internal/ubuntu questing/universe armhf python3-mpmath all 1.3.0-1 [425 kB] 560s Get:221 http://ftpmaster.internal/ubuntu questing/universe armhf python3-sympy all 1.13.3-5 [4229 kB] 560s Get:222 http://ftpmaster.internal/ubuntu questing/universe armhf python3-ufolib2 all 0.17.0+dfsg1-1 [33.5 kB] 560s Get:223 http://ftpmaster.internal/ubuntu questing/universe armhf unicode-data all 15.1.0-1 [8878 kB] 560s Get:224 http://ftpmaster.internal/ubuntu questing/universe armhf python3-fonttools armhf 4.55.3-2build1 [1462 kB] 560s Get:225 http://ftpmaster.internal/ubuntu questing/main armhf python3-imagesize all 1.4.1-1 [6844 B] 560s Get:226 http://ftpmaster.internal/ubuntu questing/universe armhf python3-kiwisolver armhf 1.4.7-3build1 [57.7 kB] 560s Get:227 http://ftpmaster.internal/ubuntu questing/universe armhf python3-matplotlib armhf 3.8.3-7build1 [17.3 MB] 561s Get:228 http://ftpmaster.internal/ubuntu questing/main armhf python3-msgpack armhf 1.0.3-3build4 [80.6 kB] 561s Get:229 http://ftpmaster.internal/ubuntu questing/universe armhf python3-mmtf all 1.1.3-1 [16.2 kB] 561s Get:230 http://ftpmaster.internal/ubuntu questing/main armhf python3-mysqldb armhf 1.4.6-2build6 [46.3 kB] 561s Get:231 http://ftpmaster.internal/ubuntu questing/main armhf python3-networkx all 3.2.1-4ubuntu1 [11.5 MB] 562s Get:232 http://ftpmaster.internal/ubuntu questing/main armhf sphinx-common all 8.1.3-5 [663 kB] 562s Get:233 http://ftpmaster.internal/ubuntu questing/main armhf python3-alabaster all 0.7.16-0.1 [18.5 kB] 562s Get:234 http://ftpmaster.internal/ubuntu questing/main armhf python3-snowballstemmer all 2.2.0-4build1 [59.8 kB] 562s Get:235 http://ftpmaster.internal/ubuntu questing/main armhf python3-sphinx all 8.1.3-5 [474 kB] 562s Get:236 http://ftpmaster.internal/ubuntu questing/main armhf python3-tabulate all 0.9.0-1 [45.3 kB] 562s Get:237 http://ftpmaster.internal/ubuntu questing/universe armhf python3-numpydoc all 1.8.0-1 [52.4 kB] 562s Get:238 http://ftpmaster.internal/ubuntu questing/universe armhf python3-rdflib all 7.1.1-2 [426 kB] 562s Get:239 http://ftpmaster.internal/ubuntu questing/main armhf sphinx-rtd-theme-common all 3.0.2+dfsg-2 [1014 kB] 562s Get:240 http://ftpmaster.internal/ubuntu questing/universe armhf python3-sphinxcontrib.jquery all 4.1-5 [6678 B] 562s Get:241 http://ftpmaster.internal/ubuntu questing/universe armhf python3-sphinx-rtd-theme all 3.0.2+dfsg-2 [23.5 kB] 562s Get:242 http://ftpmaster.internal/ubuntu questing/universe armhf python3-texttable all 1.7.0-1 [11.2 kB] 562s Get:243 http://ftpmaster.internal/ubuntu questing/universe armhf t-coffee armhf 13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 [968 kB] 562s Get:244 http://ftpmaster.internal/ubuntu questing/universe armhf texlive-fonts-recommended all 2024.20250309-1 [4974 kB] 562s Get:245 http://ftpmaster.internal/ubuntu questing/universe armhf texlive-latex-base all 2024.20250309-1 [1276 kB] 562s Get:246 http://ftpmaster.internal/ubuntu questing/universe armhf libfontbox-java all 1:1.8.16-5 [208 kB] 562s Get:247 http://ftpmaster.internal/ubuntu questing/universe armhf libpdfbox-java all 1:1.8.16-5 [5521 kB] 562s Get:248 http://ftpmaster.internal/ubuntu questing/universe armhf texlive-latex-recommended all 2024.20250309-1 [8727 kB] 563s Get:249 http://ftpmaster.internal/ubuntu questing/universe armhf texlive-pictures all 2024.20250309-1 [17.0 MB] 563s Get:250 http://ftpmaster.internal/ubuntu questing/universe armhf texlive-latex-extra all 2024.20250309-2 [24.8 MB] 564s Get:251 http://ftpmaster.internal/ubuntu questing/universe armhf wise-data all 2.4.1-25 [83.0 kB] 564s Get:252 http://ftpmaster.internal/ubuntu questing/universe armhf wise armhf 2.4.1-25 [917 kB] 564s Get:253 http://ftpmaster.internal/ubuntu questing/universe armhf fasttree armhf 2.1.11-2 [162 kB] 564s Get:254 http://ftpmaster.internal/ubuntu questing/universe armhf python3-igraph armhf 0.11.8+ds-1build1 [327 kB] 565s Preconfiguring packages ... 565s Fetched 328 MB in 14s (23.4 MB/s) 566s Selecting previously unselected package m4. 566s (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 ... 63965 files and directories currently installed.) 566s Preparing to unpack .../000-m4_1.4.19-7_armhf.deb ... 566s Unpacking m4 (1.4.19-7) ... 566s Selecting previously unselected package flex. 566s Preparing to unpack .../001-flex_2.6.4-8.2build1_armhf.deb ... 566s Unpacking flex (2.6.4-8.2build1) ... 566s Selecting previously unselected package fonts-lato. 566s Preparing to unpack .../002-fonts-lato_2.015-1_all.deb ... 566s Unpacking fonts-lato (2.015-1) ... 566s Selecting previously unselected package libgomp1:armhf. 566s Preparing to unpack .../003-libgomp1_15-20250404-0ubuntu1_armhf.deb ... 566s Unpacking libgomp1:armhf (15-20250404-0ubuntu1) ... 566s Selecting previously unselected package libfftw3-double3:armhf. 566s Preparing to unpack .../004-libfftw3-double3_3.3.10-2fakesync1build1_armhf.deb ... 566s Unpacking libfftw3-double3:armhf (3.3.10-2fakesync1build1) ... 566s Selecting previously unselected package libfreetype6:armhf. 566s Preparing to unpack .../005-libfreetype6_2.13.3+dfsg-1_armhf.deb ... 566s Unpacking libfreetype6:armhf (2.13.3+dfsg-1) ... 566s Selecting previously unselected package fonts-dejavu-mono. 566s Preparing to unpack .../006-fonts-dejavu-mono_2.37-8_all.deb ... 566s Unpacking fonts-dejavu-mono (2.37-8) ... 566s Selecting previously unselected package fonts-dejavu-core. 566s Preparing to unpack .../007-fonts-dejavu-core_2.37-8_all.deb ... 566s Unpacking fonts-dejavu-core (2.37-8) ... 566s Selecting previously unselected package libfontenc1:armhf. 566s Preparing to unpack .../008-libfontenc1_1%3a1.1.8-1build1_armhf.deb ... 566s Unpacking libfontenc1:armhf (1:1.1.8-1build1) ... 566s Selecting previously unselected package x11-common. 566s Preparing to unpack .../009-x11-common_1%3a7.7+23ubuntu4_all.deb ... 566s Unpacking x11-common (1:7.7+23ubuntu4) ... 566s Selecting previously unselected package xfonts-encodings. 566s Preparing to unpack .../010-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 566s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 566s Selecting previously unselected package xfonts-utils. 566s Preparing to unpack .../011-xfonts-utils_1%3a7.7+7_armhf.deb ... 566s Unpacking xfonts-utils (1:7.7+7) ... 567s Selecting previously unselected package fonts-urw-base35. 567s Preparing to unpack .../012-fonts-urw-base35_20200910-8_all.deb ... 567s Unpacking fonts-urw-base35 (20200910-8) ... 567s Selecting previously unselected package fontconfig-config. 567s Preparing to unpack .../013-fontconfig-config_2.15.0-2.2ubuntu1_armhf.deb ... 567s Unpacking fontconfig-config (2.15.0-2.2ubuntu1) ... 567s Selecting previously unselected package libfontconfig1:armhf. 567s Preparing to unpack .../014-libfontconfig1_2.15.0-2.2ubuntu1_armhf.deb ... 567s Unpacking libfontconfig1:armhf (2.15.0-2.2ubuntu1) ... 567s Selecting previously unselected package libsharpyuv0:armhf. 567s Preparing to unpack .../015-libsharpyuv0_1.5.0-0.1_armhf.deb ... 567s Unpacking libsharpyuv0:armhf (1.5.0-0.1) ... 567s Selecting previously unselected package libaom3:armhf. 567s Preparing to unpack .../016-libaom3_3.12.0-1_armhf.deb ... 567s Unpacking libaom3:armhf (3.12.0-1) ... 568s Selecting previously unselected package libheif-plugin-aomdec:armhf. 568s Preparing to unpack .../017-libheif-plugin-aomdec_1.19.7-1_armhf.deb ... 568s Unpacking libheif-plugin-aomdec:armhf (1.19.7-1) ... 568s Selecting previously unselected package libde265-0:armhf. 568s Preparing to unpack .../018-libde265-0_1.0.15-1build5_armhf.deb ... 568s Unpacking libde265-0:armhf (1.0.15-1build5) ... 568s Selecting previously unselected package libheif-plugin-libde265:armhf. 568s Preparing to unpack .../019-libheif-plugin-libde265_1.19.7-1_armhf.deb ... 568s Unpacking libheif-plugin-libde265:armhf (1.19.7-1) ... 568s Selecting previously unselected package libheif1:armhf. 568s Preparing to unpack .../020-libheif1_1.19.7-1_armhf.deb ... 568s Unpacking libheif1:armhf (1.19.7-1) ... 568s Selecting previously unselected package libjbig0:armhf. 568s Preparing to unpack .../021-libjbig0_2.1-6.1ubuntu2_armhf.deb ... 568s Unpacking libjbig0:armhf (2.1-6.1ubuntu2) ... 568s Selecting previously unselected package libjpeg-turbo8:armhf. 568s Preparing to unpack .../022-libjpeg-turbo8_2.1.5-3ubuntu2_armhf.deb ... 568s Unpacking libjpeg-turbo8:armhf (2.1.5-3ubuntu2) ... 568s Selecting previously unselected package libjpeg8:armhf. 568s Preparing to unpack .../023-libjpeg8_8c-2ubuntu11_armhf.deb ... 568s Unpacking libjpeg8:armhf (8c-2ubuntu11) ... 568s Selecting previously unselected package liblcms2-2:armhf. 568s Preparing to unpack .../024-liblcms2-2_2.16-2_armhf.deb ... 568s Unpacking liblcms2-2:armhf (2.16-2) ... 568s Selecting previously unselected package liblqr-1-0:armhf. 568s Preparing to unpack .../025-liblqr-1-0_0.4.2-2.1build2_armhf.deb ... 568s Unpacking liblqr-1-0:armhf (0.4.2-2.1build2) ... 568s Selecting previously unselected package libltdl7:armhf. 568s Preparing to unpack .../026-libltdl7_2.5.4-4_armhf.deb ... 568s Unpacking libltdl7:armhf (2.5.4-4) ... 568s Selecting previously unselected package libopenjp2-7:armhf. 568s Preparing to unpack .../027-libopenjp2-7_2.5.3-2_armhf.deb ... 568s Unpacking libopenjp2-7:armhf (2.5.3-2) ... 568s Selecting previously unselected package libraw23t64:armhf. 568s Preparing to unpack .../028-libraw23t64_0.21.3-1_armhf.deb ... 568s Unpacking libraw23t64:armhf (0.21.3-1) ... 568s Selecting previously unselected package libdeflate0:armhf. 568s Preparing to unpack .../029-libdeflate0_1.23-1_armhf.deb ... 568s Unpacking libdeflate0:armhf (1.23-1) ... 568s Selecting previously unselected package liblerc4:armhf. 568s Preparing to unpack .../030-liblerc4_4.0.0+ds-5ubuntu1_armhf.deb ... 568s Unpacking liblerc4:armhf (4.0.0+ds-5ubuntu1) ... 568s Selecting previously unselected package libwebp7:armhf. 568s Preparing to unpack .../031-libwebp7_1.5.0-0.1_armhf.deb ... 568s Unpacking libwebp7:armhf (1.5.0-0.1) ... 568s Selecting previously unselected package libtiff6:armhf. 568s Preparing to unpack .../032-libtiff6_4.7.0-3ubuntu1_armhf.deb ... 568s Unpacking libtiff6:armhf (4.7.0-3ubuntu1) ... 568s Selecting previously unselected package libwebpdemux2:armhf. 568s Preparing to unpack .../033-libwebpdemux2_1.5.0-0.1_armhf.deb ... 568s Unpacking libwebpdemux2:armhf (1.5.0-0.1) ... 568s Selecting previously unselected package libwebpmux3:armhf. 568s Preparing to unpack .../034-libwebpmux3_1.5.0-0.1_armhf.deb ... 568s Unpacking libwebpmux3:armhf (1.5.0-0.1) ... 568s Selecting previously unselected package imagemagick-7-common. 568s Preparing to unpack .../035-imagemagick-7-common_8%3a7.1.1.43+dfsg1-1_all.deb ... 568s Unpacking imagemagick-7-common (8:7.1.1.43+dfsg1-1) ... 569s Selecting previously unselected package libmagickcore-7.q16-10:armhf. 569s Preparing to unpack .../036-libmagickcore-7.q16-10_8%3a7.1.1.43+dfsg1-1_armhf.deb ... 569s Unpacking libmagickcore-7.q16-10:armhf (8:7.1.1.43+dfsg1-1) ... 569s Selecting previously unselected package libmagickwand-7.q16-10:armhf. 569s Preparing to unpack .../037-libmagickwand-7.q16-10_8%3a7.1.1.43+dfsg1-1_armhf.deb ... 569s Unpacking libmagickwand-7.q16-10:armhf (8:7.1.1.43+dfsg1-1) ... 569s Selecting previously unselected package poppler-data. 569s Preparing to unpack .../038-poppler-data_0.4.12-1_all.deb ... 569s Unpacking poppler-data (0.4.12-1) ... 569s Selecting previously unselected package python3-numpy-dev:armhf. 569s Preparing to unpack .../039-python3-numpy-dev_1%3a2.2.3+ds-5_armhf.deb ... 569s Unpacking python3-numpy-dev:armhf (1:2.2.3+ds-5) ... 569s Selecting previously unselected package libblas3:armhf. 569s Preparing to unpack .../040-libblas3_3.12.1-2_armhf.deb ... 569s Unpacking libblas3:armhf (3.12.1-2) ... 569s Selecting previously unselected package libgfortran5:armhf. 569s Preparing to unpack .../041-libgfortran5_15-20250404-0ubuntu1_armhf.deb ... 569s Unpacking libgfortran5:armhf (15-20250404-0ubuntu1) ... 569s Selecting previously unselected package liblapack3:armhf. 569s Preparing to unpack .../042-liblapack3_3.12.1-2_armhf.deb ... 569s Unpacking liblapack3:armhf (3.12.1-2) ... 569s Selecting previously unselected package python3-numpy. 569s Preparing to unpack .../043-python3-numpy_1%3a2.2.3+ds-5_armhf.deb ... 569s Unpacking python3-numpy (1:2.2.3+ds-5) ... 569s Selecting previously unselected package sgml-base. 569s Preparing to unpack .../044-sgml-base_1.31_all.deb ... 569s Unpacking sgml-base (1.31) ... 570s Selecting previously unselected package autoconf. 570s Preparing to unpack .../045-autoconf_2.72-3ubuntu1_all.deb ... 570s Unpacking autoconf (2.72-3ubuntu1) ... 570s Selecting previously unselected package autotools-dev. 570s Preparing to unpack .../046-autotools-dev_20220109.1_all.deb ... 570s Unpacking autotools-dev (20220109.1) ... 570s Selecting previously unselected package automake. 570s Preparing to unpack .../047-automake_1%3a1.17-3ubuntu1_all.deb ... 570s Unpacking automake (1:1.17-3ubuntu1) ... 570s Selecting previously unselected package autopoint. 570s Preparing to unpack .../048-autopoint_0.23.1-1_all.deb ... 570s Unpacking autopoint (0.23.1-1) ... 570s Selecting previously unselected package libtcl8.6:armhf. 570s Preparing to unpack .../049-libtcl8.6_8.6.16+dfsg-1_armhf.deb ... 570s Unpacking libtcl8.6:armhf (8.6.16+dfsg-1) ... 570s Selecting previously unselected package libxrender1:armhf. 570s Preparing to unpack .../050-libxrender1_1%3a0.9.10-1.1build1_armhf.deb ... 570s Unpacking libxrender1:armhf (1:0.9.10-1.1build1) ... 570s Selecting previously unselected package libxft2:armhf. 570s Preparing to unpack .../051-libxft2_2.3.6-1build1_armhf.deb ... 570s Unpacking libxft2:armhf (2.3.6-1build1) ... 570s Selecting previously unselected package libxss1:armhf. 570s Preparing to unpack .../052-libxss1_1%3a1.2.3-1build3_armhf.deb ... 570s Unpacking libxss1:armhf (1:1.2.3-1build3) ... 570s Selecting previously unselected package libtk8.6:armhf. 570s Preparing to unpack .../053-libtk8.6_8.6.16-1_armhf.deb ... 570s Unpacking libtk8.6:armhf (8.6.16-1) ... 570s Selecting previously unselected package tk8.6-blt2.5. 570s Preparing to unpack .../054-tk8.6-blt2.5_2.5.3+dfsg-8_armhf.deb ... 570s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-8) ... 570s Selecting previously unselected package blt. 570s Preparing to unpack .../055-blt_2.5.3+dfsg-8_armhf.deb ... 570s Unpacking blt (2.5.3+dfsg-8) ... 570s Selecting previously unselected package libc-dev-bin. 570s Preparing to unpack .../056-libc-dev-bin_2.41-6ubuntu1_armhf.deb ... 570s Unpacking libc-dev-bin (2.41-6ubuntu1) ... 570s Selecting previously unselected package linux-libc-dev:armhf. 570s Preparing to unpack .../057-linux-libc-dev_6.14.0-15.15_armhf.deb ... 570s Unpacking linux-libc-dev:armhf (6.14.0-15.15) ... 571s Selecting previously unselected package libcrypt-dev:armhf. 571s Preparing to unpack .../058-libcrypt-dev_1%3a4.4.38-1_armhf.deb ... 571s Unpacking libcrypt-dev:armhf (1:4.4.38-1) ... 571s Selecting previously unselected package rpcsvc-proto. 571s Preparing to unpack .../059-rpcsvc-proto_1.4.2-0ubuntu7_armhf.deb ... 571s Unpacking rpcsvc-proto (1.4.2-0ubuntu7) ... 571s Selecting previously unselected package libc6-dev:armhf. 571s Preparing to unpack .../060-libc6-dev_2.41-6ubuntu1_armhf.deb ... 571s Unpacking libc6-dev:armhf (2.41-6ubuntu1) ... 571s Selecting previously unselected package libisl23:armhf. 571s Preparing to unpack .../061-libisl23_0.27-1_armhf.deb ... 571s Unpacking libisl23:armhf (0.27-1) ... 571s Selecting previously unselected package libmpc3:armhf. 571s Preparing to unpack .../062-libmpc3_1.3.1-1build2_armhf.deb ... 571s Unpacking libmpc3:armhf (1.3.1-1build2) ... 571s Selecting previously unselected package cpp-14-arm-linux-gnueabihf. 571s Preparing to unpack .../063-cpp-14-arm-linux-gnueabihf_14.2.0-19ubuntu2_armhf.deb ... 571s Unpacking cpp-14-arm-linux-gnueabihf (14.2.0-19ubuntu2) ... 571s Selecting previously unselected package cpp-14. 571s Preparing to unpack .../064-cpp-14_14.2.0-19ubuntu2_armhf.deb ... 571s Unpacking cpp-14 (14.2.0-19ubuntu2) ... 571s Selecting previously unselected package cpp-arm-linux-gnueabihf. 571s Preparing to unpack .../065-cpp-arm-linux-gnueabihf_4%3a14.2.0-1ubuntu1_armhf.deb ... 571s Unpacking cpp-arm-linux-gnueabihf (4:14.2.0-1ubuntu1) ... 571s Selecting previously unselected package cpp. 571s Preparing to unpack .../066-cpp_4%3a14.2.0-1ubuntu1_armhf.deb ... 571s Unpacking cpp (4:14.2.0-1ubuntu1) ... 571s Selecting previously unselected package libcc1-0:armhf. 571s Preparing to unpack .../067-libcc1-0_15-20250404-0ubuntu1_armhf.deb ... 571s Unpacking libcc1-0:armhf (15-20250404-0ubuntu1) ... 572s Selecting previously unselected package libasan8:armhf. 572s Preparing to unpack .../068-libasan8_15-20250404-0ubuntu1_armhf.deb ... 572s Unpacking libasan8:armhf (15-20250404-0ubuntu1) ... 572s Selecting previously unselected package libubsan1:armhf. 572s Preparing to unpack .../069-libubsan1_15-20250404-0ubuntu1_armhf.deb ... 572s Unpacking libubsan1:armhf (15-20250404-0ubuntu1) ... 572s Selecting previously unselected package libgcc-14-dev:armhf. 572s Preparing to unpack .../070-libgcc-14-dev_14.2.0-19ubuntu2_armhf.deb ... 572s Unpacking libgcc-14-dev:armhf (14.2.0-19ubuntu2) ... 572s Selecting previously unselected package gcc-14-arm-linux-gnueabihf. 572s Preparing to unpack .../071-gcc-14-arm-linux-gnueabihf_14.2.0-19ubuntu2_armhf.deb ... 572s Unpacking gcc-14-arm-linux-gnueabihf (14.2.0-19ubuntu2) ... 572s Selecting previously unselected package gcc-14. 572s Preparing to unpack .../072-gcc-14_14.2.0-19ubuntu2_armhf.deb ... 572s Unpacking gcc-14 (14.2.0-19ubuntu2) ... 572s Selecting previously unselected package gcc-arm-linux-gnueabihf. 572s Preparing to unpack .../073-gcc-arm-linux-gnueabihf_4%3a14.2.0-1ubuntu1_armhf.deb ... 572s Unpacking gcc-arm-linux-gnueabihf (4:14.2.0-1ubuntu1) ... 572s Selecting previously unselected package gcc. 573s Preparing to unpack .../074-gcc_4%3a14.2.0-1ubuntu1_armhf.deb ... 573s Unpacking gcc (4:14.2.0-1ubuntu1) ... 573s Selecting previously unselected package libstdc++-14-dev:armhf. 573s Preparing to unpack .../075-libstdc++-14-dev_14.2.0-19ubuntu2_armhf.deb ... 573s Unpacking libstdc++-14-dev:armhf (14.2.0-19ubuntu2) ... 573s Selecting previously unselected package g++-14-arm-linux-gnueabihf. 573s Preparing to unpack .../076-g++-14-arm-linux-gnueabihf_14.2.0-19ubuntu2_armhf.deb ... 573s Unpacking g++-14-arm-linux-gnueabihf (14.2.0-19ubuntu2) ... 573s Selecting previously unselected package g++-14. 573s Preparing to unpack .../077-g++-14_14.2.0-19ubuntu2_armhf.deb ... 573s Unpacking g++-14 (14.2.0-19ubuntu2) ... 573s Selecting previously unselected package g++-arm-linux-gnueabihf. 573s Preparing to unpack .../078-g++-arm-linux-gnueabihf_4%3a14.2.0-1ubuntu1_armhf.deb ... 573s Unpacking g++-arm-linux-gnueabihf (4:14.2.0-1ubuntu1) ... 573s Selecting previously unselected package g++. 573s Preparing to unpack .../079-g++_4%3a14.2.0-1ubuntu1_armhf.deb ... 573s Unpacking g++ (4:14.2.0-1ubuntu1) ... 573s Selecting previously unselected package build-essential. 573s Preparing to unpack .../080-build-essential_12.12ubuntu1_armhf.deb ... 573s Unpacking build-essential (12.12ubuntu1) ... 573s Selecting previously unselected package bwa. 573s Preparing to unpack .../081-bwa_0.7.18-1_armhf.deb ... 573s Unpacking bwa (0.7.18-1) ... 573s Selecting previously unselected package libargtable2-0. 573s Preparing to unpack .../082-libargtable2-0_13-3_armhf.deb ... 573s Unpacking libargtable2-0 (13-3) ... 573s Selecting previously unselected package clustalo. 573s Preparing to unpack .../083-clustalo_1.2.4-8build1_armhf.deb ... 573s Unpacking clustalo (1.2.4-8build1) ... 574s Selecting previously unselected package libdebhelper-perl. 574s Preparing to unpack .../084-libdebhelper-perl_13.24.1ubuntu2_all.deb ... 574s Unpacking libdebhelper-perl (13.24.1ubuntu2) ... 574s Selecting previously unselected package libtool. 574s Preparing to unpack .../085-libtool_2.5.4-4_all.deb ... 574s Unpacking libtool (2.5.4-4) ... 574s Selecting previously unselected package dh-autoreconf. 574s Preparing to unpack .../086-dh-autoreconf_20_all.deb ... 574s Unpacking dh-autoreconf (20) ... 574s Selecting previously unselected package libarchive-zip-perl. 574s Preparing to unpack .../087-libarchive-zip-perl_1.68-1_all.deb ... 574s Unpacking libarchive-zip-perl (1.68-1) ... 574s Selecting previously unselected package libfile-stripnondeterminism-perl. 574s Preparing to unpack .../088-libfile-stripnondeterminism-perl_1.14.1-2_all.deb ... 574s Unpacking libfile-stripnondeterminism-perl (1.14.1-2) ... 574s Selecting previously unselected package dh-strip-nondeterminism. 574s Preparing to unpack .../089-dh-strip-nondeterminism_1.14.1-2_all.deb ... 574s Unpacking dh-strip-nondeterminism (1.14.1-2) ... 574s Selecting previously unselected package libdw1t64:armhf. 574s Preparing to unpack .../090-libdw1t64_0.192-4ubuntu1_armhf.deb ... 574s Unpacking libdw1t64:armhf (0.192-4ubuntu1) ... 574s Selecting previously unselected package debugedit. 574s Preparing to unpack .../091-debugedit_1%3a5.1-2_armhf.deb ... 574s Unpacking debugedit (1:5.1-2) ... 574s Selecting previously unselected package dwz. 574s Preparing to unpack .../092-dwz_0.15-1build6_armhf.deb ... 574s Unpacking dwz (0.15-1build6) ... 574s Selecting previously unselected package gettext. 574s Preparing to unpack .../093-gettext_0.23.1-1_armhf.deb ... 574s Unpacking gettext (0.23.1-1) ... 574s Selecting previously unselected package intltool-debian. 574s Preparing to unpack .../094-intltool-debian_0.35.0+20060710.6_all.deb ... 574s Unpacking intltool-debian (0.35.0+20060710.6) ... 574s Selecting previously unselected package po-debconf. 574s Preparing to unpack .../095-po-debconf_1.0.21+nmu1_all.deb ... 574s Unpacking po-debconf (1.0.21+nmu1) ... 574s Selecting previously unselected package debhelper. 574s Preparing to unpack .../096-debhelper_13.24.1ubuntu2_all.deb ... 574s Unpacking debhelper (13.24.1ubuntu2) ... 574s Selecting previously unselected package dh-python. 574s Preparing to unpack .../097-dh-python_6.20250308_all.deb ... 574s Unpacking dh-python (6.20250308) ... 574s Selecting previously unselected package dialign. 574s Preparing to unpack .../098-dialign_2.2.1-13_armhf.deb ... 574s Unpacking dialign (2.2.1-13) ... 574s Selecting previously unselected package xml-core. 574s Preparing to unpack .../099-xml-core_0.19_all.deb ... 575s Unpacking xml-core (0.19) ... 575s Selecting previously unselected package docutils-common. 575s Preparing to unpack .../100-docutils-common_0.21.2+dfsg-2_all.deb ... 575s Unpacking docutils-common (0.21.2+dfsg-2) ... 575s Selecting previously unselected package libcifpp-data. 575s Preparing to unpack .../101-libcifpp-data_7.0.9-1_all.deb ... 575s Unpacking libcifpp-data (7.0.9-1) ... 575s Selecting previously unselected package libcifpp7:armhf. 575s Preparing to unpack .../102-libcifpp7_7.0.9-1_armhf.deb ... 575s Unpacking libcifpp7:armhf (7.0.9-1) ... 575s Selecting previously unselected package dssp. 575s Preparing to unpack .../103-dssp_4.4.10-1_armhf.deb ... 575s Unpacking dssp (4.4.10-1) ... 575s Selecting previously unselected package fonts-font-awesome. 575s Preparing to unpack .../104-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ... 575s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 575s Selecting previously unselected package fonts-lmodern. 575s Preparing to unpack .../105-fonts-lmodern_2.005-1_all.deb ... 575s Unpacking fonts-lmodern (2.005-1) ... 575s Selecting previously unselected package fonts-lyx. 575s Preparing to unpack .../106-fonts-lyx_2.4.3-1_all.deb ... 575s Unpacking fonts-lyx (2.4.3-1) ... 575s Selecting previously unselected package libgs-common. 575s Preparing to unpack .../107-libgs-common_10.05.0dfsg1-0ubuntu1_all.deb ... 575s Unpacking libgs-common (10.05.0dfsg1-0ubuntu1) ... 575s Selecting previously unselected package libgs10-common. 575s Preparing to unpack .../108-libgs10-common_10.05.0dfsg1-0ubuntu1_all.deb ... 575s Unpacking libgs10-common (10.05.0dfsg1-0ubuntu1) ... 575s Selecting previously unselected package libavahi-common-data:armhf. 575s Preparing to unpack .../109-libavahi-common-data_0.8-16ubuntu2_armhf.deb ... 575s Unpacking libavahi-common-data:armhf (0.8-16ubuntu2) ... 575s Selecting previously unselected package libavahi-common3:armhf. 575s Preparing to unpack .../110-libavahi-common3_0.8-16ubuntu2_armhf.deb ... 575s Unpacking libavahi-common3:armhf (0.8-16ubuntu2) ... 576s Selecting previously unselected package libavahi-client3:armhf. 576s Preparing to unpack .../111-libavahi-client3_0.8-16ubuntu2_armhf.deb ... 576s Unpacking libavahi-client3:armhf (0.8-16ubuntu2) ... 576s Selecting previously unselected package libcups2t64:armhf. 576s Preparing to unpack .../112-libcups2t64_2.4.12-0ubuntu1_armhf.deb ... 576s Unpacking libcups2t64:armhf (2.4.12-0ubuntu1) ... 576s Selecting previously unselected package libidn12:armhf. 576s Preparing to unpack .../113-libidn12_1.43-1_armhf.deb ... 576s Unpacking libidn12:armhf (1.43-1) ... 576s Selecting previously unselected package libijs-0.35:armhf. 576s Preparing to unpack .../114-libijs-0.35_0.35-15.2_armhf.deb ... 576s Unpacking libijs-0.35:armhf (0.35-15.2) ... 576s Selecting previously unselected package libjbig2dec0:armhf. 576s Preparing to unpack .../115-libjbig2dec0_0.20-1build3_armhf.deb ... 576s Unpacking libjbig2dec0:armhf (0.20-1build3) ... 576s Selecting previously unselected package libpaper2:armhf. 576s Preparing to unpack .../116-libpaper2_2.2.5-0.3_armhf.deb ... 576s Unpacking libpaper2:armhf (2.2.5-0.3) ... 576s Selecting previously unselected package libice6:armhf. 576s Preparing to unpack .../117-libice6_2%3a1.1.1-1_armhf.deb ... 576s Unpacking libice6:armhf (2:1.1.1-1) ... 576s Selecting previously unselected package libsm6:armhf. 576s Preparing to unpack .../118-libsm6_2%3a1.2.4-1_armhf.deb ... 576s Unpacking libsm6:armhf (2:1.2.4-1) ... 576s Selecting previously unselected package libxt6t64:armhf. 576s Preparing to unpack .../119-libxt6t64_1%3a1.2.1-1.2build1_armhf.deb ... 576s Unpacking libxt6t64:armhf (1:1.2.1-1.2build1) ... 576s Selecting previously unselected package libgs10:armhf. 576s Preparing to unpack .../120-libgs10_10.05.0dfsg1-0ubuntu1_armhf.deb ... 576s Unpacking libgs10:armhf (10.05.0dfsg1-0ubuntu1) ... 576s Selecting previously unselected package ghostscript. 576s Preparing to unpack .../121-ghostscript_10.05.0dfsg1-0ubuntu1_armhf.deb ... 576s Unpacking ghostscript (10.05.0dfsg1-0ubuntu1) ... 576s Selecting previously unselected package libnetpbm11t64:armhf. 576s Preparing to unpack .../122-libnetpbm11t64_2%3a11.09.02-2_armhf.deb ... 576s Unpacking libnetpbm11t64:armhf (2:11.09.02-2) ... 576s Selecting previously unselected package netpbm. 576s Preparing to unpack .../123-netpbm_2%3a11.09.02-2_armhf.deb ... 576s Unpacking netpbm (2:11.09.02-2) ... 577s Selecting previously unselected package tex-common. 577s Preparing to unpack .../124-tex-common_6.19_all.deb ... 577s Unpacking tex-common (6.19) ... 577s Selecting previously unselected package libpaper-utils. 577s Preparing to unpack .../125-libpaper-utils_2.2.5-0.3_armhf.deb ... 577s Unpacking libpaper-utils (2.2.5-0.3) ... 577s Selecting previously unselected package libkpathsea6:armhf. 577s Preparing to unpack .../126-libkpathsea6_2024.20240313.70630+ds-6_armhf.deb ... 577s Unpacking libkpathsea6:armhf (2024.20240313.70630+ds-6) ... 577s Selecting previously unselected package libptexenc1:armhf. 577s Preparing to unpack .../127-libptexenc1_2024.20240313.70630+ds-6_armhf.deb ... 577s Unpacking libptexenc1:armhf (2024.20240313.70630+ds-6) ... 577s Selecting previously unselected package libsynctex2:armhf. 577s Preparing to unpack .../128-libsynctex2_2024.20240313.70630+ds-6_armhf.deb ... 577s Unpacking libsynctex2:armhf (2024.20240313.70630+ds-6) ... 577s Selecting previously unselected package libtexlua53-5:armhf. 577s Preparing to unpack .../129-libtexlua53-5_2024.20240313.70630+ds-6_armhf.deb ... 577s Unpacking libtexlua53-5:armhf (2024.20240313.70630+ds-6) ... 577s Selecting previously unselected package t1utils. 577s Preparing to unpack .../130-t1utils_1.41-4build3_armhf.deb ... 577s Unpacking t1utils (1.41-4build3) ... 577s Selecting previously unselected package libpixman-1-0:armhf. 577s Preparing to unpack .../131-libpixman-1-0_0.44.0-3_armhf.deb ... 577s Unpacking libpixman-1-0:armhf (0.44.0-3) ... 577s Selecting previously unselected package libxcb-render0:armhf. 577s Preparing to unpack .../132-libxcb-render0_1.17.0-2_armhf.deb ... 577s Unpacking libxcb-render0:armhf (1.17.0-2) ... 577s Selecting previously unselected package libxcb-shm0:armhf. 577s Preparing to unpack .../133-libxcb-shm0_1.17.0-2_armhf.deb ... 577s Unpacking libxcb-shm0:armhf (1.17.0-2) ... 577s Selecting previously unselected package libcairo2:armhf. 577s Preparing to unpack .../134-libcairo2_1.18.4-1_armhf.deb ... 577s Unpacking libcairo2:armhf (1.18.4-1) ... 577s Selecting previously unselected package libgraphite2-3:armhf. 577s Preparing to unpack .../135-libgraphite2-3_1.3.14-2ubuntu1_armhf.deb ... 577s Unpacking libgraphite2-3:armhf (1.3.14-2ubuntu1) ... 577s Selecting previously unselected package libharfbuzz0b:armhf. 577s Preparing to unpack .../136-libharfbuzz0b_10.2.0-1_armhf.deb ... 577s Unpacking libharfbuzz0b:armhf (10.2.0-1) ... 577s Selecting previously unselected package libmpfi0:armhf. 577s Preparing to unpack .../137-libmpfi0_1.5.4+ds-4_armhf.deb ... 577s Unpacking libmpfi0:armhf (1.5.4+ds-4) ... 577s Selecting previously unselected package libpotrace0:armhf. 577s Preparing to unpack .../138-libpotrace0_1.16-2build1_armhf.deb ... 577s Unpacking libpotrace0:armhf (1.16-2build1) ... 577s Selecting previously unselected package libteckit0:armhf. 577s Preparing to unpack .../139-libteckit0_2.5.12+ds1-1_armhf.deb ... 577s Unpacking libteckit0:armhf (2.5.12+ds1-1) ... 577s Selecting previously unselected package libxmu6:armhf. 577s Preparing to unpack .../140-libxmu6_2%3a1.1.3-3build2_armhf.deb ... 577s Unpacking libxmu6:armhf (2:1.1.3-3build2) ... 578s Selecting previously unselected package libxpm4:armhf. 578s Preparing to unpack .../141-libxpm4_1%3a3.5.17-1build2_armhf.deb ... 578s Unpacking libxpm4:armhf (1:3.5.17-1build2) ... 578s Selecting previously unselected package libxaw7:armhf. 578s Preparing to unpack .../142-libxaw7_2%3a1.0.16-1_armhf.deb ... 578s Unpacking libxaw7:armhf (2:1.0.16-1) ... 578s Selecting previously unselected package libxi6:armhf. 578s Preparing to unpack .../143-libxi6_2%3a1.8.2-1_armhf.deb ... 578s Unpacking libxi6:armhf (2:1.8.2-1) ... 578s Selecting previously unselected package libzzip-0-13t64:armhf. 578s Preparing to unpack .../144-libzzip-0-13t64_0.13.78+dfsg.1-0.1_armhf.deb ... 578s Unpacking libzzip-0-13t64:armhf (0.13.78+dfsg.1-0.1) ... 578s Selecting previously unselected package texlive-binaries. 578s Preparing to unpack .../145-texlive-binaries_2024.20240313.70630+ds-6_armhf.deb ... 578s Unpacking texlive-binaries (2024.20240313.70630+ds-6) ... 578s Selecting previously unselected package xdg-utils. 578s Preparing to unpack .../146-xdg-utils_1.2.1-2ubuntu1_all.deb ... 578s Unpacking xdg-utils (1.2.1-2ubuntu1) ... 578s Selecting previously unselected package texlive-base. 578s Preparing to unpack .../147-texlive-base_2024.20250309-1_all.deb ... 578s Unpacking texlive-base (2024.20250309-1) ... 580s Selecting previously unselected package hicolor-icon-theme. 580s Preparing to unpack .../148-hicolor-icon-theme_0.18-2_all.deb ... 580s Unpacking hicolor-icon-theme (0.18-2) ... 580s Selecting previously unselected package imagemagick-7.q16. 580s Preparing to unpack .../149-imagemagick-7.q16_8%3a7.1.1.43+dfsg1-1_armhf.deb ... 580s Unpacking imagemagick-7.q16 (8:7.1.1.43+dfsg1-1) ... 580s Selecting previously unselected package imagemagick. 580s Preparing to unpack .../150-imagemagick_8%3a7.1.1.43+dfsg1-1_armhf.deb ... 580s Unpacking imagemagick (8:7.1.1.43+dfsg1-1) ... 580s Selecting previously unselected package hevea. 580s Preparing to unpack .../151-hevea_2.36-2_armhf.deb ... 580s Unpacking hevea (2.36-2) ... 580s Selecting previously unselected package libsuitesparseconfig7:armhf. 580s Preparing to unpack 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... 580s Unpacking libcommons-parent-java (56-1) ... 580s Selecting previously unselected package libcommons-logging-java. 580s Preparing to unpack .../158-libcommons-logging-java_1.3.0-1ubuntu1_all.deb ... 580s Unpacking libcommons-logging-java (1.3.0-1ubuntu1) ... 580s Selecting previously unselected package libexpat1-dev:armhf. 580s Preparing to unpack .../159-libexpat1-dev_2.7.1-1_armhf.deb ... 580s Unpacking libexpat1-dev:armhf (2.7.1-1) ... 580s Selecting previously unselected package libglpk40:armhf. 580s Preparing to unpack .../160-libglpk40_5.0-1build2_armhf.deb ... 580s Unpacking libglpk40:armhf (5.0-1build2) ... 580s Selecting previously unselected package libplfit0:armhf. 580s Preparing to unpack .../161-libplfit0_0.9.6+ds-2ubuntu1_armhf.deb ... 580s Unpacking libplfit0:armhf (0.9.6+ds-2ubuntu1) ... 580s Selecting previously unselected package libigraph3t64:armhf. 580s Preparing to unpack .../162-libigraph3t64_0.10.15+ds-3_armhf.deb ... 580s Unpacking libigraph3t64:armhf (0.10.15+ds-3) ... 581s Selecting previously unselected package libimagequant0:armhf. 581s Preparing to unpack .../163-libimagequant0_2.18.0-1build1_armhf.deb ... 581s Unpacking libimagequant0:armhf (2.18.0-1build1) ... 581s Selecting previously unselected package libjs-jquery. 581s Preparing to unpack .../164-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 581s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 581s Selecting previously unselected package libjs-jquery-ui. 581s Preparing to unpack .../165-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... 581s Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... 581s Selecting previously unselected package libjs-underscore. 581s Preparing to unpack .../166-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 581s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 581s Selecting previously unselected package libjs-sphinxdoc. 581s Preparing to unpack .../167-libjs-sphinxdoc_8.1.3-5_all.deb ... 581s Unpacking libjs-sphinxdoc (8.1.3-5) ... 581s Selecting previously unselected package libjson-perl. 581s Preparing to unpack .../168-libjson-perl_4.10000-1_all.deb ... 581s Unpacking libjson-perl (4.10000-1) ... 581s Selecting previously unselected package liblbfgsb0:armhf. 581s Preparing to unpack .../169-liblbfgsb0_3.0+dfsg.4-1build1_armhf.deb ... 581s Unpacking liblbfgsb0:armhf (3.0+dfsg.4-1build1) ... 581s Selecting previously unselected package libmbedcrypto16:armhf. 581s Preparing to unpack .../170-libmbedcrypto16_3.6.2-3ubuntu1_armhf.deb ... 581s Unpacking libmbedcrypto16:armhf (3.6.2-3ubuntu1) ... 581s Selecting previously unselected package libmbedx509-7:armhf. 581s Preparing to unpack .../171-libmbedx509-7_3.6.2-3ubuntu1_armhf.deb ... 581s Unpacking libmbedx509-7:armhf (3.6.2-3ubuntu1) ... 581s Selecting previously unselected package libmbedtls21:armhf. 581s Preparing to unpack .../172-libmbedtls21_3.6.2-3ubuntu1_armhf.deb ... 581s Unpacking libmbedtls21:armhf (3.6.2-3ubuntu1) ... 581s Selecting previously unselected package mysql-common. 581s Preparing to unpack .../173-mysql-common_5.8+1.1.1ubuntu1_all.deb ... 581s Unpacking mysql-common (5.8+1.1.1ubuntu1) ... 581s Selecting previously unselected package libmysqlclient24:armhf. 581s Preparing to unpack .../174-libmysqlclient24_8.4.4-0ubuntu2_armhf.deb ... 581s Unpacking libmysqlclient24:armhf (8.4.4-0ubuntu2) ... 581s Selecting previously unselected package libpython3.13:armhf. 581s Preparing to unpack .../175-libpython3.13_3.13.3-1_armhf.deb ... 581s Unpacking libpython3.13:armhf (3.13.3-1) ... 581s Selecting previously unselected package zlib1g-dev:armhf. 581s Preparing to unpack .../176-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1ubuntu1_armhf.deb ... 581s Unpacking zlib1g-dev:armhf (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 581s Selecting previously unselected package libpython3.13-dev:armhf. 582s Preparing to unpack .../177-libpython3.13-dev_3.13.3-1_armhf.deb ... 582s Unpacking libpython3.13-dev:armhf (3.13.3-1) ... 582s Selecting previously unselected package libpython3-dev:armhf. 582s Preparing to unpack .../178-libpython3-dev_3.13.3-1_armhf.deb ... 582s Unpacking libpython3-dev:armhf (3.13.3-1) ... 582s Selecting previously unselected package libpython3-all-dev:armhf. 582s Preparing to unpack .../179-libpython3-all-dev_3.13.3-1_armhf.deb ... 582s Unpacking libpython3-all-dev:armhf (3.13.3-1) ... 582s Selecting previously unselected package libqhull-r8.0:armhf. 582s Preparing to unpack .../180-libqhull-r8.0_2020.2-6build1_armhf.deb ... 582s Unpacking libqhull-r8.0:armhf (2020.2-6build1) ... 582s Selecting previously unselected package libraqm0:armhf. 582s Preparing to unpack .../181-libraqm0_0.10.2-1_armhf.deb ... 582s Unpacking libraqm0:armhf (0.10.2-1) ... 582s Selecting previously unselected package libxslt1.1:armhf. 582s Preparing to unpack .../182-libxslt1.1_1.1.39-0exp1ubuntu4_armhf.deb ... 582s Unpacking libxslt1.1:armhf (1.1.39-0exp1ubuntu4) ... 582s Selecting previously unselected package mafft. 582s Preparing to unpack .../183-mafft_7.505-1_armhf.deb ... 582s Unpacking mafft (7.505-1) ... 582s Selecting previously unselected package ncbi-data. 582s Preparing to unpack .../184-ncbi-data_6.1.20170106+dfsg2-5_all.deb ... 582s Unpacking ncbi-data (6.1.20170106+dfsg2-5) ... 582s Selecting previously unselected package ncbi-blast+. 582s Preparing to unpack .../185-ncbi-blast+_2.16.0+ds-6build1_armhf.deb ... 582s Unpacking ncbi-blast+ (2.16.0+ds-6build1) ... 583s Selecting previously unselected package phylip. 583s Preparing to unpack .../186-phylip_1%3a3.697+dfsg-4build1_armhf.deb ... 583s Unpacking phylip (1:3.697+dfsg-4build1) ... 583s Selecting previously unselected package prank. 583s Preparing to unpack .../187-prank_0.0.170427+dfsg-3_armhf.deb ... 583s Unpacking prank (0.0.170427+dfsg-3) ... 583s Selecting previously unselected package preview-latex-style. 583s Preparing to unpack .../188-preview-latex-style_13.2-1_all.deb ... 583s Unpacking preview-latex-style (13.2-1) ... 583s Selecting previously unselected package probcons. 583s Preparing to unpack .../189-probcons_1.12-14_armhf.deb ... 583s Unpacking probcons (1.12-14) ... 583s Selecting previously unselected package python-biopython-doc. 583s Preparing to unpack .../190-python-biopython-doc_1.85+dfsg-2build1_all.deb ... 583s Unpacking python-biopython-doc (1.85+dfsg-2build1) ... 584s Selecting previously unselected package python-matplotlib-data. 584s Preparing to unpack .../191-python-matplotlib-data_3.8.3-7build1_all.deb ... 584s Unpacking python-matplotlib-data (3.8.3-7build1) ... 584s Selecting previously unselected package python3-all. 584s Preparing to unpack .../192-python3-all_3.13.3-1_armhf.deb ... 584s Unpacking python3-all (3.13.3-1) ... 584s Selecting previously unselected package python3.13-dev. 584s Preparing to unpack .../193-python3.13-dev_3.13.3-1_armhf.deb ... 584s Unpacking python3.13-dev (3.13.3-1) ... 584s Selecting previously unselected package python3-dev. 584s Preparing to unpack .../194-python3-dev_3.13.3-1_armhf.deb ... 584s Unpacking python3-dev (3.13.3-1) ... 584s Selecting previously unselected package python3-all-dev. 584s Preparing to unpack .../195-python3-all-dev_3.13.3-1_armhf.deb ... 584s Unpacking python3-all-dev (3.13.3-1) ... 584s Selecting previously unselected package python3.13-tk. 584s Preparing to unpack .../196-python3.13-tk_3.13.3-1_armhf.deb ... 584s Unpacking python3.13-tk (3.13.3-1) ... 584s Selecting previously unselected package python3-tk:armhf. 584s Preparing to unpack .../197-python3-tk_3.13.3-1_armhf.deb ... 584s Unpacking python3-tk:armhf (3.13.3-1) ... 584s Selecting previously unselected package python3-pil.imagetk:armhf. 584s Preparing to unpack .../198-python3-pil.imagetk_11.1.0-5build1_armhf.deb ... 584s Unpacking python3-pil.imagetk:armhf (11.1.0-5build1) ... 584s Selecting previously unselected package python3-pil:armhf. 584s Preparing to unpack .../199-python3-pil_11.1.0-5build1_armhf.deb ... 584s Unpacking python3-pil:armhf (11.1.0-5build1) ... 584s Selecting previously unselected package python3-cairo. 584s Preparing to unpack .../200-python3-cairo_1.27.0-2_armhf.deb ... 584s Unpacking python3-cairo (1.27.0-2) ... 584s Selecting previously unselected package python3-freetype. 585s Preparing to unpack .../201-python3-freetype_2.5.1-1_all.deb ... 585s Unpacking python3-freetype (2.5.1-1) ... 585s Selecting previously unselected package python3-rlpycairo. 585s Preparing to unpack .../202-python3-rlpycairo_0.3.0-3_all.deb ... 585s Unpacking python3-rlpycairo (0.3.0-3) ... 585s Selecting previously unselected package python3-reportlab. 585s Preparing to unpack .../203-python3-reportlab_4.3.1-1_all.deb ... 585s Unpacking python3-reportlab (4.3.1-1) ... 585s Selecting previously unselected package w3c-sgml-lib. 585s Preparing to unpack .../204-w3c-sgml-lib_1.3-3_all.deb ... 585s Unpacking w3c-sgml-lib (1.3-3) ... 585s Selecting previously unselected package python3-biopython. 585s Preparing to unpack .../205-python3-biopython_1.85+dfsg-2build1_armhf.deb ... 585s Unpacking python3-biopython (1.85+dfsg-2build1) ... 585s Selecting previously unselected package python3-biopython-sql. 585s Preparing to unpack .../206-python3-biopython-sql_1.85+dfsg-2build1_all.deb ... 585s Unpacking python3-biopython-sql (1.85+dfsg-2build1) ... 585s Selecting previously unselected package python3-brotli. 585s Preparing to unpack .../207-python3-brotli_1.1.0-2build4_armhf.deb ... 585s Unpacking python3-brotli (1.1.0-2build4) ... 585s Selecting previously unselected package python3-contourpy. 585s Preparing to unpack .../208-python3-contourpy_1.3.1-1build1_armhf.deb ... 585s Unpacking python3-contourpy (1.3.1-1build1) ... 585s Selecting previously unselected package python3-cycler. 585s Preparing to unpack .../209-python3-cycler_0.12.1-1_all.deb ... 585s Unpacking python3-cycler (0.12.1-1) ... 585s Selecting previously unselected package python3-decorator. 585s Preparing to unpack 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Selecting previously unselected package python3-lxml:armhf. 586s Preparing to unpack .../216-python3-lxml_5.3.2-1_armhf.deb ... 586s Unpacking python3-lxml:armhf (5.3.2-1) ... 586s Selecting previously unselected package python3-lz4. 586s Preparing to unpack .../217-python3-lz4_4.4.0+dfsg-1build1_armhf.deb ... 586s Unpacking python3-lz4 (4.4.0+dfsg-1build1) ... 586s Selecting previously unselected package python3-scipy. 586s Preparing to unpack .../218-python3-scipy_1.14.1-4ubuntu2_armhf.deb ... 586s Unpacking python3-scipy (1.14.1-4ubuntu2) ... 587s Selecting previously unselected package python3-mpmath. 587s Preparing to unpack .../219-python3-mpmath_1.3.0-1_all.deb ... 587s Unpacking python3-mpmath (1.3.0-1) ... 587s Selecting previously unselected package python3-sympy. 587s Preparing to unpack .../220-python3-sympy_1.13.3-5_all.deb ... 587s Unpacking python3-sympy (1.13.3-5) ... 587s Selecting previously unselected package python3-ufolib2. 587s Preparing to unpack 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Unpacking python3-matplotlib (3.8.3-7build1) ... 589s Selecting previously unselected package python3-msgpack. 589s Preparing to unpack .../227-python3-msgpack_1.0.3-3build4_armhf.deb ... 589s Unpacking python3-msgpack (1.0.3-3build4) ... 589s Selecting previously unselected package python3-mmtf. 589s Preparing to unpack .../228-python3-mmtf_1.1.3-1_all.deb ... 589s Unpacking python3-mmtf (1.1.3-1) ... 589s Selecting previously unselected package python3-mysqldb. 589s Preparing to unpack .../229-python3-mysqldb_1.4.6-2build6_armhf.deb ... 589s Unpacking python3-mysqldb (1.4.6-2build6) ... 589s Selecting previously unselected package python3-networkx. 589s Preparing to unpack .../230-python3-networkx_3.2.1-4ubuntu1_all.deb ... 589s Unpacking python3-networkx (3.2.1-4ubuntu1) ... 590s Selecting previously unselected package sphinx-common. 590s Preparing to unpack .../231-sphinx-common_8.1.3-5_all.deb ... 590s Unpacking sphinx-common (8.1.3-5) ... 590s Selecting previously unselected package python3-alabaster. 590s Preparing to unpack .../232-python3-alabaster_0.7.16-0.1_all.deb ... 590s Unpacking python3-alabaster (0.7.16-0.1) ... 590s Selecting previously unselected package python3-snowballstemmer. 590s Preparing to unpack .../233-python3-snowballstemmer_2.2.0-4build1_all.deb ... 590s Unpacking python3-snowballstemmer (2.2.0-4build1) ... 590s Selecting previously unselected package python3-sphinx. 590s Preparing to unpack .../234-python3-sphinx_8.1.3-5_all.deb ... 590s Unpacking python3-sphinx (8.1.3-5) ... 590s Selecting previously unselected package python3-tabulate. 590s Preparing to unpack .../235-python3-tabulate_0.9.0-1_all.deb ... 590s Unpacking python3-tabulate (0.9.0-1) ... 590s Selecting previously unselected package python3-numpydoc. 590s Preparing to unpack .../236-python3-numpydoc_1.8.0-1_all.deb ... 590s Unpacking python3-numpydoc (1.8.0-1) ... 590s Selecting previously unselected package python3-rdflib. 590s Preparing to unpack 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python3-fonttools (4.55.3-2build1) ... 628s Setting up libmagickcore-7.q16-10:armhf (8:7.1.1.43+dfsg1-1) ... 628s Setting up python3-matplotlib (3.8.3-7build1) ... 631s Setting up libmagickwand-7.q16-10:armhf (8:7.1.1.43+dfsg1-1) ... 631s Setting up imagemagick-7.q16 (8:7.1.1.43+dfsg1-1) ... 631s update-alternatives: using /usr/bin/compare-im7.q16 to provide /usr/bin/compare (compare) in auto mode 631s update-alternatives: using /usr/bin/compare-im7.q16 to provide /usr/bin/compare-im7 (compare-im7) in auto mode 631s update-alternatives: using /usr/bin/animate-im7.q16 to provide /usr/bin/animate (animate) in auto mode 631s update-alternatives: using /usr/bin/animate-im7.q16 to provide /usr/bin/animate-im7 (animate-im7) in auto mode 631s update-alternatives: using /usr/bin/convert-im7.q16 to provide /usr/bin/convert (convert) in auto mode 631s update-alternatives: using /usr/bin/convert-im7.q16 to provide /usr/bin/convert-im7 (convert-im7) in auto mode 631s update-alternatives: using /usr/bin/composite-im7.q16 to provide /usr/bin/composite (composite) in auto mode 631s update-alternatives: using /usr/bin/composite-im7.q16 to provide /usr/bin/composite-im7 (composite-im7) in auto mode 631s update-alternatives: using /usr/bin/conjure-im7.q16 to provide /usr/bin/conjure (conjure) in auto mode 631s update-alternatives: using /usr/bin/conjure-im7.q16 to provide /usr/bin/conjure-im7 (conjure-im7) in auto mode 631s update-alternatives: using /usr/bin/import-im7.q16 to provide /usr/bin/import (import) in auto mode 631s update-alternatives: using /usr/bin/import-im7.q16 to provide /usr/bin/import-im7 (import-im7) in auto mode 631s update-alternatives: using /usr/bin/identify-im7.q16 to provide /usr/bin/identify (identify) in auto mode 631s update-alternatives: using /usr/bin/identify-im7.q16 to provide /usr/bin/identify-im7 (identify-im7) in auto mode 631s update-alternatives: using /usr/bin/stream-im7.q16 to provide /usr/bin/stream (stream) in auto mode 631s update-alternatives: using /usr/bin/stream-im7.q16 to provide /usr/bin/stream-im7 (stream-im7) in auto mode 631s update-alternatives: using /usr/bin/display-im7.q16 to provide /usr/bin/display (display) in auto mode 631s update-alternatives: using /usr/bin/display-im7.q16 to provide /usr/bin/display-im7 (display-im7) in auto mode 631s update-alternatives: using /usr/bin/montage-im7.q16 to provide /usr/bin/montage (montage) in auto mode 631s update-alternatives: using /usr/bin/montage-im7.q16 to provide /usr/bin/montage-im7 (montage-im7) in auto mode 631s update-alternatives: using /usr/bin/mogrify-im7.q16 to provide /usr/bin/mogrify (mogrify) in auto mode 631s update-alternatives: using /usr/bin/mogrify-im7.q16 to provide /usr/bin/mogrify-im7 (mogrify-im7) in auto mode 631s update-alternatives: using /usr/bin/magick-im7.q16 to provide /usr/bin/magick (magick) in auto mode 631s 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 631s update-alternatives: using /usr/bin/magick-im7.q16 to provide /usr/bin/magick-im7 (magick-im7) in auto mode 631s 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 631s update-alternatives: using /usr/bin/magick-script-im7.q16 to provide /usr/bin/magick-script (magick-script) in auto mode 631s 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 631s update-alternatives: using /usr/bin/magick-script-im7.q16 to provide /usr/bin/magick-script-im7 (magick-script-im7) in auto mode 631s 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 631s Setting up hevea (2.36-2) ... 631s Setting up imagemagick (8:7.1.1.43+dfsg1-1) ... 631s Processing triggers for install-info (7.1.1-1) ... 631s Processing triggers for libc-bin (2.41-6ubuntu1) ... 631s Processing triggers for man-db (2.13.0-1) ... 632s Processing triggers for sgml-base (1.31) ... 632s Setting up docutils-common (0.21.2+dfsg-2) ... 632s Setting up w3c-sgml-lib (1.3-3) ... 667s Setting up python3-biopython (1.85+dfsg-2build1) ... 668s Setting up python3-biopython-sql (1.85+dfsg-2build1) ... 669s Processing triggers for sgml-base (1.31) ... 669s Setting up python3-docutils (0.21.2+dfsg-2) ... 669s Setting up python3-sphinx (8.1.3-5) ... 670s Setting up python3-sphinxcontrib.jquery (4.1-5) ... 671s Setting up python3-numpydoc (1.8.0-1) ... 671s Setting up python3-sphinx-rtd-theme (3.0.2+dfsg-2) ... 671s Processing triggers for tex-common (6.19) ... 672s Running updmap-sys. This may take some time... done. 672s Running mktexlsr /var/lib/texmf ... done. 672s Building format(s) --all. 823s This may take some time... done. 844s autopkgtest [23:18:18]: test full_suite: sh debian/tests/run-unit-test 844s autopkgtest [23:18:18]: test full_suite: [----------------------- 849s mkdir: created directory 'Bio' 849s mkdir: created directory 'Bio/Align' 849s mkdir: created directory 'Bio/Align/substitution_matrices' 849s mkdir: created directory 'Bio/Align/substitution_matrices/data/' 849s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER22' -> 'Bio/Align/substitution_matrices/data/BENNER22' 849s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER6' -> 'Bio/Align/substitution_matrices/data/BENNER6' 849s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER74' -> 'Bio/Align/substitution_matrices/data/BENNER74' 849s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLASTN' -> 'Bio/Align/substitution_matrices/data/BLASTN' 849s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLASTP' -> 'Bio/Align/substitution_matrices/data/BLASTP' 849s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM45' -> 'Bio/Align/substitution_matrices/data/BLOSUM45' 849s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM50' -> 'Bio/Align/substitution_matrices/data/BLOSUM50' 849s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM62' -> 'Bio/Align/substitution_matrices/data/BLOSUM62' 849s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM80' -> 'Bio/Align/substitution_matrices/data/BLOSUM80' 849s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM90' -> 'Bio/Align/substitution_matrices/data/BLOSUM90' 849s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/DAYHOFF' -> 'Bio/Align/substitution_matrices/data/DAYHOFF' 849s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/FENG' -> 'Bio/Align/substitution_matrices/data/FENG' 849s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/GENETIC' -> 'Bio/Align/substitution_matrices/data/GENETIC' 849s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/GONNET1992' -> 'Bio/Align/substitution_matrices/data/GONNET1992' 849s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/HOXD70' -> 'Bio/Align/substitution_matrices/data/HOXD70' 849s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/JOHNSON' -> 'Bio/Align/substitution_matrices/data/JOHNSON' 849s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/JONES' -> 'Bio/Align/substitution_matrices/data/JONES' 849s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/LEVIN' -> 'Bio/Align/substitution_matrices/data/LEVIN' 849s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MCLACHLAN' -> 'Bio/Align/substitution_matrices/data/MCLACHLAN' 849s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MDM78' -> 'Bio/Align/substitution_matrices/data/MDM78' 849s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MEGABLAST' -> 'Bio/Align/substitution_matrices/data/MEGABLAST' 849s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/NUC.4.4' -> 'Bio/Align/substitution_matrices/data/NUC.4.4' 849s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM250' -> 'Bio/Align/substitution_matrices/data/PAM250' 849s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM30' -> 'Bio/Align/substitution_matrices/data/PAM30' 849s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM70' -> 'Bio/Align/substitution_matrices/data/PAM70' 849s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/RAO' -> 'Bio/Align/substitution_matrices/data/RAO' 849s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/RISLER' -> 'Bio/Align/substitution_matrices/data/RISLER' 849s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/SCHNEIDER' -> 'Bio/Align/substitution_matrices/data/SCHNEIDER' 849s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/STR' -> 'Bio/Align/substitution_matrices/data/STR' 849s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/TRANS' -> 'Bio/Align/substitution_matrices/data/TRANS' 849s test_Ace ... ok 849s test_Affy ... ok 852s test_AlignIO ... ok 852s test_AlignIO_ClustalIO ... ok 852s test_AlignIO_EmbossIO ... ok 852s test_AlignIO_FastaIO ... ok 852s test_AlignIO_MauveIO ... ok 852s test_AlignIO_PhylipIO ... ok 852s test_AlignIO_convert ... ok 853s test_AlignInfo ... ok 853s test_Align_Alignment ... ok 853s test_Align_a2m ... ok 853s test_Align_bed ... ok 853s test_Align_bigbed ... ok 854s test_Align_bigmaf ... ok 854s test_Align_bigpsl ... ok 855s test_Align_chain ... ok 855s test_Align_clustal ... ok 861s test_Align_codonalign ... ok 861s test_Align_emboss ... ok 861s test_Align_exonerate ... ok 861s test_Align_fasta ... ok 861s test_Align_hhr ... ok 862s test_Align_maf ... ok 862s test_Align_mauve ... ok 863s test_Align_msf ... ok 863s test_Align_nexus ... ok 863s test_Align_phylip ... ok 863s test_Align_psl ... ok 864s test_Align_sam ... ok 866s test_Align_stockholm ... ok 866s test_Align_tabular ... ok 866s test_Application ... ok 866s test_BioSQL_MySQLdb_online ... skipping. internet not available 866s test_BioSQL_mysql_connector ... skipping. BioSQL test configuration file biosql.ini missing (see biosql.ini.sample) 867s test_BioSQL_mysql_connector_online ... skipping. internet not available 867s test_BioSQL_psycopg2_online ... skipping. internet not available 872s test_BioSQL_sqlite3 ... ok 872s test_BioSQL_sqlite3_online ... skipping. internet not available 872s test_Blast_Record ... ok 873s test_Blast_parser ... ok 873s test_CAPS ... ok 873s test_Chi2 ... ok 875s test_ClustalOmega_tool ... ok 875s test_Clustalw_tool ... skipping. Install clustalw or clustalw2 if you want to use it from Biopython. 875s test_Cluster ... ok 875s test_CodonTable ... ok 875s test_ColorSpiral ... ok 875s test_Compass ... ok 876s test_Consensus ... ok 879s test_Dialign_tool ... ok 879s test_EMBL_unittest ... ok 879s test_Emboss ... skipping. $EMBOSS_ROOT='/usr/lib/emboss' which does not exist! 879s test_EmbossPrimer ... ok 883s test_Entrez ... ok 884s test_Entrez_online ... skipping. internet not available 884s test_Entrez_parser ... ok 884s test_Enzyme ... ok 884s test_ExPASy ... skipping. internet not available 885s test_Fasttree_tool ... ok 885s test_File ... ok 885s test_GenBank ... /usr/lib/python3/dist-packages/Bio/SeqIO/InsdcIO.py:600: BiopythonWarning: Annotation 'Sequence Read Archive: SRX001885, SRX001121, SRX001531, SRX001530, SRX001529' too long 885s warnings.warn(f"Annotation {text!r} too long", BiopythonWarning) 885s ok 887s test_GenomeDiagram ... Warn: Can't find .pfb for face 'Helvetica' 889s ok 890s test_GraphicsChromosome ... ok 890s test_GraphicsDistribution ... ok 891s test_GraphicsGeneral ... ok 891s test_HMMCasino ... ok 891s test_HMMGeneral ... ok 892s test_KEGG ... ok 892s test_KEGG_online ... skipping. internet not available 897s test_KGML_graphics ... ok 897s test_KGML_graphics_online ... skipping. internet not available 898s test_KGML_nographics ... ok 898s test_KeyWList ... ok 899s test_LogisticRegression ... ok 900s test_MafIO_index ... ok 902s test_Mafft_tool ... ok 902s test_MarkovModel ... ok 902s test_Medline ... ok 902s test_Muscle_tool ... skipping. Install MUSCLE if you want to use the Bio.Align.Applications wrapper. 903s test_NCBIXML ... Exception ignored in: 903s Traceback (most recent call last): 903s File "/usr/lib/python3/dist-packages/Bio/Blast/NCBIXML.py", line 1319, in parse 903s expat_parser.Parse(NULL, True) 903s xml.parsers.expat.ExpatError: unclosed token: line 320, column 0 903s ok 907s test_NCBI_BLAST_tools ... ok 907s test_NCBI_qblast ... ok 907s test_NMR ... ok 907s test_NaiveBayes ... ok 907s test_Nexus ... ok 908s test_PAML_baseml ... ok 908s test_PAML_codeml ... ok 909s test_PAML_yn00 ... ok 915s test_PDB_CEAligner ... ok 917s test_PDB_DSSP ... ok 917s test_PDB_Dice ... ok 917s test_PDB_Disordered ... ok 917s test_PDB_Exposure ... ok 918s test_PDB_FragmentMapper ... ok 920s test_PDB_KDTree ... ok 920s test_PDB_MMCIF2Dict ... ok 920s test_PDB_MMCIFIO ... ok 922s test_PDB_MMCIFParser ... ok 922s test_PDB_NACCESS ... ok 922s test_PDB_PDBIO ... ok 922s test_PDB_PDBList ... skipping. internet not available 930s test_PDB_PDBMLParser ... ok 930s test_PDB_PDBParser ... ok 930s 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 931s test_PDB_Polypeptide ... ok 931s test_PDB_QCPSuperimposer ... ok 935s test_PDB_SASA ... ok 935s test_PDB_SMCRA ... ok 935s test_PDB_Selection ... ok 936s test_PDB_StructureAlignment ... ok 936s test_PDB_Superimposer ... ok 936s test_PDB_alphafold_db ... skipping. internet not available 939s test_PDB_binary_cif ... /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 1, ' ') redefined at line 7. 939s warnings.warn( 939s /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 15, ' ') redefined at line 144. 939s warnings.warn( 939s /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 15, ' ') redefined at line 153. 939s warnings.warn( 939s /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 1, ' ') redefined at line 0. 939s warnings.warn( 939s /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 15, ' ') redefined at line 0. 939s warnings.warn( 939s ok 949s test_PDB_internal_coords ... ok 949s test_PDB_parse_pdb_header ... ok 950s test_PDB_vectors ... ok 950s test_PQR ... ok 950s test_Pathway ... ok 951s test_Phd ... ok 951s test_Phylo ... ok 952s test_PhyloXML ... ok 953s test_Phylo_CDAO ... ok 953s test_Phylo_NeXML ... ok 955s test_Phylo_igraph ... ok 958s test_Phylo_matplotlib ... ok 959s test_Phylo_networkx ... ok 960s test_PopGen_GenePop_nodepend ... ok 963s test_Prank_tool ... ok 964s test_Probcons_tool ... ok 965s test_ProtParam ... ok 966s test_RCSBFormats ... ok 967s test_Restriction ... ok 968s test_SCOP_Astral ... ok 969s test_SCOP_Cla ... ok 970s test_SCOP_Des ... ok 971s test_SCOP_Dom ... ok 972s test_SCOP_Hie ... ok 973s test_SCOP_Raf ... ok 974s test_SCOP_Residues ... ok 975s test_SCOP_Scop ... ok 976s test_SVDSuperimposer ... ok 977s test_SearchIO_blast_tab ... ok 978s test_SearchIO_blast_tab_index ... ok 979s test_SearchIO_blast_xml ... ok 981s test_SearchIO_blast_xml_index ... ok 982s test_SearchIO_blat_psl ... ok 983s test_SearchIO_blat_psl_index ... ok 984s test_SearchIO_exonerate ... ok 985s test_SearchIO_exonerate_text_index ... ok 986s test_SearchIO_exonerate_vulgar_index ... ok 987s test_SearchIO_fasta_m10 ... ok 988s test_SearchIO_fasta_m10_index ... ok 989s test_SearchIO_hhsuite2_text ... ok 990s test_SearchIO_hmmer2_text ... ok 991s test_SearchIO_hmmer2_text_index ... ok 992s test_SearchIO_hmmer3_domtab ... ok 993s test_SearchIO_hmmer3_domtab_index ... ok 994s test_SearchIO_hmmer3_tab ... ok 995s test_SearchIO_hmmer3_tab_index ... ok 996s test_SearchIO_hmmer3_text ... ok 997s test_SearchIO_hmmer3_text_index ... ok 998s test_SearchIO_interproscan_xml ... ok 999s test_SearchIO_model ... ok 1001s test_SearchIO_write ... ok 1002s test_SeqFeature ... ok 1022s test_SeqIO ... ok 1023s test_SeqIO_AbiIO ... ok 1024s test_SeqIO_FastaIO ... ok 1025s test_SeqIO_Gck ... ok 1026s test_SeqIO_Gfa ... ok 1027s test_SeqIO_Insdc ... ok 1028s test_SeqIO_NibIO ... ok 1031s test_SeqIO_PdbIO ... ok 1033s test_SeqIO_QualityIO ... ok 1034s test_SeqIO_SeqXML ... ok 1035s test_SeqIO_SffIO ... ok 1036s test_SeqIO_SnapGene ... ok 1038s test_SeqIO_TwoBitIO ... ok 1039s test_SeqIO_UniprotIO ... ok 1040s test_SeqIO_Xdna ... ok 1041s test_SeqIO_features ... ok 1059s test_SeqIO_index ... ok 1060s test_SeqIO_online ... skipping. internet not available 1061s test_SeqIO_write ... ok 1062s test_SeqRecord ... ok 1063s test_SeqUtils ... ok 1065s test_Seq_objs ... ok 1066s test_SwissProt ... ok 1069s test_TCoffee_tool ... ok 1070s test_TogoWS ... skipping. internet not available 1071s test_TreeConstruction ... ok 1072s test_Tutorial ... skipping. Could not find ../Doc/Tutorial/index.rst file 1073s test_UniGene ... ok 1074s test_UniProt ... skipping. internet not available 1075s test_UniProt_GOA ... ok 1076s test_align ... ok 1078s test_align_substitution_matrices ... ok 1081s test_bgzf ... ok 1082s test_cellosaurus ... ok 1089s test_codonalign ... ok 1090s test_geo ... ok 1091s test_kNN ... ok 1092s test_motifs ... ok 1093s test_motifs_online ... skipping. internet not available 1094s 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. 1094s warnings.warn( 1094s ok 1095s test_pairwise2_no_C ... ok 1097s test_pairwise_aligner ... ok 1098s test_pairwise_alignment_map ... ok 1108s test_phenotype ... ok 1109s test_phenotype_fit ... ok 1110s test_phyml_tool ... skipping. Couldn't find the PhyML software. Install PhyML 3.0 or later if you want to use the Bio.Phylo.Applications wrapper. 1111s test_prodoc ... ok 1112s test_prosite ... ok 1113s test_raxml_tool ... skipping. Install RAxML (binary raxmlHPC) if you want to test the Bio.Phylo.Applications wrapper. 1114s test_samtools_tool ... skipping. Install samtools and correctly set the file path to the program if you want to use it from Biopython 1115s test_seq ... ok 1116s test_translate ... ok 1117s Skipping any tests requiring internet access 1117s Python version: 3.13.3 (main, Apr 8 2025, 19:55:40) [GCC 14.2.0] 1117s Operating system: posix linux 1117s ---------------------------------------------------------------------- 1117s Ran 218 tests in 267.392 seconds 1117s 1119s :0: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/protein_lib.fa' mode='rt' encoding='UTF-8'> 1119s :0: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/nucleotide_lib.fa' mode='rt' encoding='UTF-8'> 1120s autopkgtest [23:22:54]: test full_suite: -----------------------] 1124s autopkgtest [23:22:58]: test full_suite: - - - - - - - - - - results - - - - - - - - - - 1124s full_suite PASS 1127s autopkgtest [23:23:01]: @@@@@@@@@@@@@@@@@@@@ summary 1127s dependencies PASS 1127s full_suite PASS