0s autopkgtest [05:41:04]: starting date and time: 2025-05-02 05:41:04+0000 0s autopkgtest [05:41:04]: git checkout: 9986aa8c Merge branch 'skia/fix_network_interface' into 'ubuntu/production' 0s autopkgtest [05:41:04]: host juju-7f2275-prod-proposed-migration-environment-21; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.o4fl8j0s/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:setuptools --apt-upgrade python-biopython --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=setuptools/78.1.0-1.2 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-21@bos03-arm64-8.secgroup --name adt-questing-arm64-python-biopython-20250502-054104-juju-7f2275-prod-proposed-migration-environment-21-34c61de2-b690-4c47-a1ad-43e367b48ec0 --image adt/ubuntu-questing-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-21 --net-id=net_prod-proposed-migration -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 133s autopkgtest [05:43:17]: testbed dpkg architecture: arm64 133s autopkgtest [05:43:17]: testbed apt version: 3.0.0 134s autopkgtest [05:43:18]: @@@@@@@@@@@@@@@@@@@@ test bed setup 134s autopkgtest [05:43:18]: testbed release detected to be: None 135s autopkgtest [05:43:19]: updating testbed package index (apt update) 135s Get:1 http://ftpmaster.internal/ubuntu questing-proposed InRelease [110 kB] 135s Hit:2 http://ftpmaster.internal/ubuntu questing InRelease 135s Hit:3 http://ftpmaster.internal/ubuntu questing-updates InRelease 135s Hit:4 http://ftpmaster.internal/ubuntu questing-security InRelease 135s Get:5 http://ftpmaster.internal/ubuntu questing-proposed/main Sources [184 kB] 136s Get:6 http://ftpmaster.internal/ubuntu questing-proposed/universe Sources [2202 kB] 136s Get:7 http://ftpmaster.internal/ubuntu questing-proposed/multiverse Sources [57.4 kB] 136s Get:8 http://ftpmaster.internal/ubuntu questing-proposed/main arm64 Packages [227 kB] 136s Get:9 http://ftpmaster.internal/ubuntu questing-proposed/universe arm64 Packages [1472 kB] 136s Get:10 http://ftpmaster.internal/ubuntu questing-proposed/multiverse arm64 Packages [16.5 kB] 136s Fetched 4269 kB in 1s (3237 kB/s) 137s Reading package lists... 138s autopkgtest [05:43:22]: upgrading testbed (apt dist-upgrade and autopurge) 138s Reading package lists... 138s Building dependency tree... 138s Reading state information... 139s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 139s Starting 2 pkgProblemResolver with broken count: 0 139s Done 140s Entering ResolveByKeep 140s 140s Calculating upgrade... 141s The following packages will be upgraded: 141s python3-pkg-resources python3-setuptools 141s 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 141s Need to get 805 kB of archives. 141s After this operation, 108 kB of additional disk space will be used. 141s Get:1 http://ftpmaster.internal/ubuntu questing-proposed/main arm64 python3-pkg-resources all 78.1.0-1.2 [144 kB] 141s Get:2 http://ftpmaster.internal/ubuntu questing-proposed/main arm64 python3-setuptools all 78.1.0-1.2 [660 kB] 142s Fetched 805 kB in 1s (947 kB/s) 142s (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 ... 117820 files and directories currently installed.) 142s Preparing to unpack .../python3-pkg-resources_78.1.0-1.2_all.deb ... 143s Unpacking python3-pkg-resources (78.1.0-1.2) over (75.8.0-1) ... 143s Preparing to unpack .../python3-setuptools_78.1.0-1.2_all.deb ... 143s Unpacking python3-setuptools (78.1.0-1.2) over (75.8.0-1) ... 143s Setting up python3-pkg-resources (78.1.0-1.2) ... 143s Setting up python3-setuptools (78.1.0-1.2) ... 144s Reading package lists... 145s Building dependency tree... 145s Reading state information... 145s Starting pkgProblemResolver with broken count: 0 145s Starting 2 pkgProblemResolver with broken count: 0 145s Done 145s Solving dependencies... 146s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 148s autopkgtest [05:43:32]: testbed running kernel: Linux 6.14.0-15-generic #15-Ubuntu SMP PREEMPT_DYNAMIC Sun Apr 6 14:37:51 UTC 2025 149s autopkgtest [05:43:33]: @@@@@@@@@@@@@@@@@@@@ apt-source python-biopython 154s Get:1 http://ftpmaster.internal/ubuntu questing/universe python-biopython 1.85+dfsg-2build1 (dsc) [3406 B] 154s Get:2 http://ftpmaster.internal/ubuntu questing/universe python-biopython 1.85+dfsg-2build1 (tar) [14.6 MB] 154s Get:3 http://ftpmaster.internal/ubuntu questing/universe python-biopython 1.85+dfsg-2build1 (diff) [42.8 kB] 155s gpgv: Signature made Tue Mar 4 15:18:59 2025 UTC 155s gpgv: using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2 155s gpgv: Can't check signature: No public key 155s dpkg-source: warning: cannot verify inline signature for ./python-biopython_1.85+dfsg-2build1.dsc: no acceptable signature found 155s autopkgtest [05:43:39]: testing package python-biopython version 1.85+dfsg-2build1 156s autopkgtest [05:43:40]: build not needed 161s autopkgtest [05:43:45]: test dependencies: preparing testbed 161s Reading package lists... 161s Building dependency tree... 161s Reading state information... 162s Starting pkgProblemResolver with broken count: 0 162s Starting 2 pkgProblemResolver with broken count: 0 162s Done 162s The following NEW packages will be installed: 162s fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-urw-base35 162s libblas3 libcairo2 libdeflate0 libfontconfig1 libfontenc1 libgfortran5 162s libgomp1 libgraphite2-3 libharfbuzz0b libimagequant0 libjbig0 libjpeg-turbo8 162s libjpeg8 libjs-jquery libjs-sphinxdoc libjs-underscore liblapack3 liblcms2-2 162s liblerc4 libopenjp2-7 libpixman-1-0 libraqm0 libsharpyuv0 libtiff6 libwebp7 162s libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 libxrender1 162s python-biopython-doc python3-all python3-biopython python3-biopython-sql 162s python3-cairo python3-freetype python3-numpy python3-numpy-dev python3-pil 162s python3-reportlab python3-rlpycairo sgml-base w3c-sgml-lib x11-common 162s xfonts-encodings xfonts-utils xml-core 163s 0 upgraded, 51 newly installed, 0 to remove and 0 not upgraded. 163s Need to get 45.6 MB of archives. 163s After this operation, 124 MB of additional disk space will be used. 163s Get:1 http://ftpmaster.internal/ubuntu questing/main arm64 python3-numpy-dev arm64 1:2.2.3+ds-5 [146 kB] 163s Get:2 http://ftpmaster.internal/ubuntu questing/main arm64 libblas3 arm64 3.12.1-2 [161 kB] 163s Get:3 http://ftpmaster.internal/ubuntu questing/main arm64 libgfortran5 arm64 15-20250404-0ubuntu1 [444 kB] 163s Get:4 http://ftpmaster.internal/ubuntu questing/main arm64 liblapack3 arm64 3.12.1-2 [2307 kB] 163s Get:5 http://ftpmaster.internal/ubuntu questing/main arm64 python3-numpy arm64 1:2.2.3+ds-5 [3981 kB] 164s Get:6 http://ftpmaster.internal/ubuntu questing/main arm64 sgml-base all 1.31 [11.4 kB] 164s Get:7 http://ftpmaster.internal/ubuntu questing/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 164s Get:8 http://ftpmaster.internal/ubuntu questing/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 164s Get:9 http://ftpmaster.internal/ubuntu questing/main arm64 libfontenc1 arm64 1:1.1.8-1build1 [13.9 kB] 164s Get:10 http://ftpmaster.internal/ubuntu questing/main arm64 x11-common all 1:7.7+23ubuntu4 [21.8 kB] 164s Get:11 http://ftpmaster.internal/ubuntu questing/main arm64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 164s Get:12 http://ftpmaster.internal/ubuntu questing/main arm64 xfonts-utils arm64 1:7.7+7 [95.6 kB] 164s Get:13 http://ftpmaster.internal/ubuntu questing/main arm64 fonts-urw-base35 all 20200910-8 [11.0 MB] 165s Get:14 http://ftpmaster.internal/ubuntu questing/main arm64 fontconfig-config arm64 2.15.0-2.2ubuntu1 [37.9 kB] 165s Get:15 http://ftpmaster.internal/ubuntu questing/main arm64 libfontconfig1 arm64 2.15.0-2.2ubuntu1 [144 kB] 165s Get:16 http://ftpmaster.internal/ubuntu questing/main arm64 libpixman-1-0 arm64 0.44.0-3 [197 kB] 165s Get:17 http://ftpmaster.internal/ubuntu questing/main arm64 libxcb-render0 arm64 1.17.0-2 [16.6 kB] 165s Get:18 http://ftpmaster.internal/ubuntu questing/main arm64 libxcb-shm0 arm64 1.17.0-2 [5884 B] 165s Get:19 http://ftpmaster.internal/ubuntu questing/main arm64 libxrender1 arm64 1:0.9.10-1.1build1 [18.8 kB] 165s Get:20 http://ftpmaster.internal/ubuntu questing/main arm64 libcairo2 arm64 1.18.4-1 [560 kB] 165s Get:21 http://ftpmaster.internal/ubuntu questing/main arm64 libdeflate0 arm64 1.23-1 [46.2 kB] 165s Get:22 http://ftpmaster.internal/ubuntu questing/main arm64 libgomp1 arm64 15-20250404-0ubuntu1 [147 kB] 165s Get:23 http://ftpmaster.internal/ubuntu questing/main arm64 libgraphite2-3 arm64 1.3.14-2ubuntu1 [70.6 kB] 165s Get:24 http://ftpmaster.internal/ubuntu questing/main arm64 libharfbuzz0b arm64 10.2.0-1 [490 kB] 165s Get:25 http://ftpmaster.internal/ubuntu questing/main arm64 libimagequant0 arm64 2.18.0-1build1 [37.1 kB] 165s Get:26 http://ftpmaster.internal/ubuntu questing/main arm64 libjpeg-turbo8 arm64 2.1.5-3ubuntu2 [165 kB] 165s Get:27 http://ftpmaster.internal/ubuntu questing/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 165s Get:28 http://ftpmaster.internal/ubuntu questing/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 165s Get:29 http://ftpmaster.internal/ubuntu questing/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 165s Get:30 http://ftpmaster.internal/ubuntu questing/main arm64 libjs-sphinxdoc all 8.1.3-5 [31.0 kB] 165s Get:31 http://ftpmaster.internal/ubuntu questing/main arm64 liblcms2-2 arm64 2.16-2 [170 kB] 165s Get:32 http://ftpmaster.internal/ubuntu questing/main arm64 liblerc4 arm64 4.0.0+ds-5ubuntu1 [167 kB] 165s Get:33 http://ftpmaster.internal/ubuntu questing/main arm64 libraqm0 arm64 0.10.2-1 [14.9 kB] 165s Get:34 http://ftpmaster.internal/ubuntu questing/main arm64 libsharpyuv0 arm64 1.5.0-0.1 [16.9 kB] 165s Get:35 http://ftpmaster.internal/ubuntu questing/main arm64 libjbig0 arm64 2.1-6.1ubuntu2 [29.3 kB] 165s Get:36 http://ftpmaster.internal/ubuntu questing/main arm64 libwebp7 arm64 1.5.0-0.1 [194 kB] 165s Get:37 http://ftpmaster.internal/ubuntu questing/main arm64 libtiff6 arm64 4.5.1+git230720-4ubuntu4 [193 kB] 165s Get:38 http://ftpmaster.internal/ubuntu questing/main arm64 libwebpdemux2 arm64 1.5.0-0.1 [12.5 kB] 165s Get:39 http://ftpmaster.internal/ubuntu questing/main arm64 libwebpmux3 arm64 1.5.0-0.1 [25.4 kB] 165s Get:40 http://ftpmaster.internal/ubuntu questing/universe arm64 python-biopython-doc all 1.85+dfsg-2build1 [18.2 MB] 166s Get:41 http://ftpmaster.internal/ubuntu questing/main arm64 python3-all arm64 3.13.3-1 [880 B] 166s Get:42 http://ftpmaster.internal/ubuntu questing/main arm64 libopenjp2-7 arm64 2.5.3-2 [183 kB] 166s Get:43 http://ftpmaster.internal/ubuntu questing/main arm64 python3-pil arm64 11.1.0-5build1 [463 kB] 166s Get:44 http://ftpmaster.internal/ubuntu questing/main arm64 python3-cairo arm64 1.27.0-2 [122 kB] 166s Get:45 http://ftpmaster.internal/ubuntu questing/universe arm64 python3-freetype all 2.5.1-1 [92.3 kB] 166s Get:46 http://ftpmaster.internal/ubuntu questing/universe arm64 python3-rlpycairo all 0.3.0-3 [9130 B] 166s Get:47 http://ftpmaster.internal/ubuntu questing/universe arm64 python3-reportlab all 4.3.1-1 [1137 kB] 166s Get:48 http://ftpmaster.internal/ubuntu questing/main arm64 xml-core all 0.19 [20.3 kB] 166s Get:49 http://ftpmaster.internal/ubuntu questing/universe arm64 w3c-sgml-lib all 1.3-3 [280 kB] 166s Get:50 http://ftpmaster.internal/ubuntu questing/universe arm64 python3-biopython arm64 1.85+dfsg-2build1 [1711 kB] 166s Get:51 http://ftpmaster.internal/ubuntu questing/universe arm64 python3-biopython-sql all 1.85+dfsg-2build1 [26.4 kB] 166s Fetched 45.6 MB in 3s (14.0 MB/s) 166s Selecting previously unselected package python3-numpy-dev:arm64. 166s (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 ... 117834 files and directories currently installed.) 166s Preparing to unpack .../00-python3-numpy-dev_1%3a2.2.3+ds-5_arm64.deb ... 166s Unpacking python3-numpy-dev:arm64 (1:2.2.3+ds-5) ... 166s Selecting previously unselected package libblas3:arm64. 166s Preparing to unpack .../01-libblas3_3.12.1-2_arm64.deb ... 166s Unpacking libblas3:arm64 (3.12.1-2) ... 166s Selecting previously unselected package libgfortran5:arm64. 166s Preparing to unpack .../02-libgfortran5_15-20250404-0ubuntu1_arm64.deb ... 166s Unpacking libgfortran5:arm64 (15-20250404-0ubuntu1) ... 166s Selecting previously unselected package liblapack3:arm64. 166s Preparing to unpack .../03-liblapack3_3.12.1-2_arm64.deb ... 166s Unpacking liblapack3:arm64 (3.12.1-2) ... 166s Selecting previously unselected package python3-numpy. 167s Preparing to unpack .../04-python3-numpy_1%3a2.2.3+ds-5_arm64.deb ... 167s Unpacking python3-numpy (1:2.2.3+ds-5) ... 167s Selecting previously unselected package sgml-base. 167s Preparing to unpack .../05-sgml-base_1.31_all.deb ... 167s Unpacking sgml-base (1.31) ... 167s Selecting previously unselected package fonts-dejavu-mono. 167s Preparing to unpack .../06-fonts-dejavu-mono_2.37-8_all.deb ... 167s Unpacking fonts-dejavu-mono (2.37-8) ... 167s Selecting previously unselected package fonts-dejavu-core. 167s Preparing to unpack .../07-fonts-dejavu-core_2.37-8_all.deb ... 167s Unpacking fonts-dejavu-core (2.37-8) ... 167s Selecting previously unselected package libfontenc1:arm64. 167s Preparing to unpack .../08-libfontenc1_1%3a1.1.8-1build1_arm64.deb ... 167s Unpacking libfontenc1:arm64 (1:1.1.8-1build1) ... 167s Selecting previously unselected package x11-common. 167s Preparing to unpack .../09-x11-common_1%3a7.7+23ubuntu4_all.deb ... 167s Unpacking x11-common (1:7.7+23ubuntu4) ... 167s Selecting previously unselected package xfonts-encodings. 167s Preparing to unpack .../10-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 167s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 167s Selecting previously unselected package xfonts-utils. 167s Preparing to unpack .../11-xfonts-utils_1%3a7.7+7_arm64.deb ... 167s Unpacking xfonts-utils (1:7.7+7) ... 167s Selecting previously unselected package fonts-urw-base35. 167s Preparing to unpack .../12-fonts-urw-base35_20200910-8_all.deb ... 167s Unpacking fonts-urw-base35 (20200910-8) ... 167s Selecting previously unselected package fontconfig-config. 167s Preparing to unpack .../13-fontconfig-config_2.15.0-2.2ubuntu1_arm64.deb ... 168s Unpacking fontconfig-config (2.15.0-2.2ubuntu1) ... 168s Selecting previously unselected package libfontconfig1:arm64. 168s Preparing to unpack .../14-libfontconfig1_2.15.0-2.2ubuntu1_arm64.deb ... 168s Unpacking libfontconfig1:arm64 (2.15.0-2.2ubuntu1) ... 168s Selecting previously unselected package libpixman-1-0:arm64. 168s Preparing to unpack .../15-libpixman-1-0_0.44.0-3_arm64.deb ... 168s Unpacking libpixman-1-0:arm64 (0.44.0-3) ... 168s Selecting previously unselected package libxcb-render0:arm64. 168s Preparing to unpack .../16-libxcb-render0_1.17.0-2_arm64.deb ... 168s Unpacking libxcb-render0:arm64 (1.17.0-2) ... 168s Selecting previously unselected package libxcb-shm0:arm64. 168s Preparing to unpack .../17-libxcb-shm0_1.17.0-2_arm64.deb ... 168s Unpacking libxcb-shm0:arm64 (1.17.0-2) ... 168s Selecting previously unselected package libxrender1:arm64. 168s Preparing to unpack .../18-libxrender1_1%3a0.9.10-1.1build1_arm64.deb ... 168s Unpacking libxrender1:arm64 (1:0.9.10-1.1build1) ... 168s Selecting previously unselected package libcairo2:arm64. 168s Preparing to unpack .../19-libcairo2_1.18.4-1_arm64.deb ... 168s Unpacking libcairo2:arm64 (1.18.4-1) ... 168s Selecting previously unselected package libdeflate0:arm64. 168s Preparing to unpack .../20-libdeflate0_1.23-1_arm64.deb ... 168s Unpacking libdeflate0:arm64 (1.23-1) ... 168s Selecting previously unselected package libgomp1:arm64. 168s Preparing to unpack .../21-libgomp1_15-20250404-0ubuntu1_arm64.deb ... 168s Unpacking libgomp1:arm64 (15-20250404-0ubuntu1) ... 168s Selecting previously unselected package libgraphite2-3:arm64. 168s Preparing to unpack .../22-libgraphite2-3_1.3.14-2ubuntu1_arm64.deb ... 168s Unpacking libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 168s Selecting previously unselected package libharfbuzz0b:arm64. 168s Preparing to unpack .../23-libharfbuzz0b_10.2.0-1_arm64.deb ... 168s Unpacking libharfbuzz0b:arm64 (10.2.0-1) ... 168s Selecting previously unselected package libimagequant0:arm64. 168s Preparing to unpack .../24-libimagequant0_2.18.0-1build1_arm64.deb ... 168s Unpacking libimagequant0:arm64 (2.18.0-1build1) ... 168s Selecting previously unselected package libjpeg-turbo8:arm64. 168s Preparing to unpack .../25-libjpeg-turbo8_2.1.5-3ubuntu2_arm64.deb ... 168s Unpacking libjpeg-turbo8:arm64 (2.1.5-3ubuntu2) ... 169s Selecting previously unselected package libjpeg8:arm64. 169s Preparing to unpack .../26-libjpeg8_8c-2ubuntu11_arm64.deb ... 169s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 169s Selecting previously unselected package libjs-jquery. 169s Preparing to unpack .../27-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 169s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 169s Selecting previously unselected package libjs-underscore. 169s Preparing to unpack .../28-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 169s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 169s Selecting previously unselected package libjs-sphinxdoc. 169s Preparing to unpack .../29-libjs-sphinxdoc_8.1.3-5_all.deb ... 169s Unpacking libjs-sphinxdoc (8.1.3-5) ... 169s Selecting previously unselected package liblcms2-2:arm64. 169s Preparing to unpack .../30-liblcms2-2_2.16-2_arm64.deb ... 169s Unpacking liblcms2-2:arm64 (2.16-2) ... 169s Selecting previously unselected package liblerc4:arm64. 169s Preparing to unpack .../31-liblerc4_4.0.0+ds-5ubuntu1_arm64.deb ... 169s Unpacking liblerc4:arm64 (4.0.0+ds-5ubuntu1) ... 169s Selecting previously unselected package libraqm0:arm64. 169s Preparing to unpack .../32-libraqm0_0.10.2-1_arm64.deb ... 169s Unpacking libraqm0:arm64 (0.10.2-1) ... 169s Selecting previously unselected package libsharpyuv0:arm64. 169s Preparing to unpack .../33-libsharpyuv0_1.5.0-0.1_arm64.deb ... 169s Unpacking libsharpyuv0:arm64 (1.5.0-0.1) ... 169s Selecting previously unselected package libjbig0:arm64. 169s Preparing to unpack .../34-libjbig0_2.1-6.1ubuntu2_arm64.deb ... 169s Unpacking libjbig0:arm64 (2.1-6.1ubuntu2) ... 169s Selecting previously unselected package libwebp7:arm64. 169s Preparing to unpack .../35-libwebp7_1.5.0-0.1_arm64.deb ... 169s Unpacking libwebp7:arm64 (1.5.0-0.1) ... 169s Selecting previously unselected package libtiff6:arm64. 169s Preparing to unpack .../36-libtiff6_4.5.1+git230720-4ubuntu4_arm64.deb ... 169s Unpacking libtiff6:arm64 (4.5.1+git230720-4ubuntu4) ... 169s Selecting previously unselected package libwebpdemux2:arm64. 169s Preparing to unpack .../37-libwebpdemux2_1.5.0-0.1_arm64.deb ... 169s Unpacking libwebpdemux2:arm64 (1.5.0-0.1) ... 169s Selecting previously unselected package libwebpmux3:arm64. 169s Preparing to unpack .../38-libwebpmux3_1.5.0-0.1_arm64.deb ... 169s Unpacking libwebpmux3:arm64 (1.5.0-0.1) ... 169s Selecting previously unselected package python-biopython-doc. 169s Preparing to unpack .../39-python-biopython-doc_1.85+dfsg-2build1_all.deb ... 169s Unpacking python-biopython-doc (1.85+dfsg-2build1) ... 170s Selecting previously unselected package python3-all. 170s Preparing to unpack .../40-python3-all_3.13.3-1_arm64.deb ... 170s Unpacking python3-all (3.13.3-1) ... 170s Selecting previously unselected package libopenjp2-7:arm64. 170s Preparing to unpack .../41-libopenjp2-7_2.5.3-2_arm64.deb ... 170s Unpacking libopenjp2-7:arm64 (2.5.3-2) ... 170s Selecting previously unselected package python3-pil:arm64. 170s Preparing to unpack .../42-python3-pil_11.1.0-5build1_arm64.deb ... 170s Unpacking python3-pil:arm64 (11.1.0-5build1) ... 170s Selecting previously unselected package python3-cairo. 170s Preparing to unpack .../43-python3-cairo_1.27.0-2_arm64.deb ... 170s Unpacking python3-cairo (1.27.0-2) ... 170s Selecting previously unselected package python3-freetype. 170s Preparing to unpack .../44-python3-freetype_2.5.1-1_all.deb ... 170s Unpacking python3-freetype (2.5.1-1) ... 170s Selecting previously unselected package python3-rlpycairo. 170s Preparing to unpack .../45-python3-rlpycairo_0.3.0-3_all.deb ... 170s Unpacking python3-rlpycairo (0.3.0-3) ... 170s Selecting previously unselected package python3-reportlab. 170s Preparing to unpack .../46-python3-reportlab_4.3.1-1_all.deb ... 170s Unpacking python3-reportlab (4.3.1-1) ... 170s Selecting previously unselected package xml-core. 170s Preparing to unpack .../47-xml-core_0.19_all.deb ... 170s Unpacking xml-core (0.19) ... 170s Selecting previously unselected package w3c-sgml-lib. 170s Preparing to unpack .../48-w3c-sgml-lib_1.3-3_all.deb ... 170s Unpacking w3c-sgml-lib (1.3-3) ... 170s Selecting previously unselected package python3-biopython. 170s Preparing to unpack .../49-python3-biopython_1.85+dfsg-2build1_arm64.deb ... 170s Unpacking python3-biopython (1.85+dfsg-2build1) ... 170s Selecting previously unselected package python3-biopython-sql. 170s Preparing to unpack .../50-python3-biopython-sql_1.85+dfsg-2build1_all.deb ... 170s Unpacking python3-biopython-sql (1.85+dfsg-2build1) ... 171s Setting up libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 171s Setting up liblcms2-2:arm64 (2.16-2) ... 171s Setting up libpixman-1-0:arm64 (0.44.0-3) ... 171s Setting up libsharpyuv0:arm64 (1.5.0-0.1) ... 171s Setting up liblerc4:arm64 (4.0.0+ds-5ubuntu1) ... 171s Setting up libxrender1:arm64 (1:0.9.10-1.1build1) ... 171s Setting up libxcb-render0:arm64 (1.17.0-2) ... 171s Setting up x11-common (1:7.7+23ubuntu4) ... 171s Setting up libdeflate0:arm64 (1.23-1) ... 171s Setting up python3-all (3.13.3-1) ... 171s Setting up libxcb-shm0:arm64 (1.17.0-2) ... 171s Setting up libgomp1:arm64 (15-20250404-0ubuntu1) ... 171s Setting up python3-freetype (2.5.1-1) ... 171s Setting up libjbig0:arm64 (2.1-6.1ubuntu2) ... 171s Setting up libfontenc1:arm64 (1:1.1.8-1build1) ... 171s Setting up libblas3:arm64 (3.12.1-2) ... 171s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode 171s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 171s Setting up libimagequant0:arm64 (2.18.0-1build1) ... 171s Setting up fonts-dejavu-mono (2.37-8) ... 171s Setting up python3-numpy-dev:arm64 (1:2.2.3+ds-5) ... 171s Setting up fonts-dejavu-core (2.37-8) ... 171s Setting up libjpeg-turbo8:arm64 (2.1.5-3ubuntu2) ... 171s Setting up libgfortran5:arm64 (15-20250404-0ubuntu1) ... 171s Setting up libwebp7:arm64 (1.5.0-0.1) ... 171s Setting up libopenjp2-7:arm64 (2.5.3-2) ... 171s Setting up libharfbuzz0b:arm64 (10.2.0-1) ... 171s Setting up sgml-base (1.31) ... 171s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 171s Setting up libwebpmux3:arm64 (1.5.0-0.1) ... 171s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 171s Setting up libjpeg8:arm64 (8c-2ubuntu11) ... 171s Setting up liblapack3:arm64 (3.12.1-2) ... 171s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode 171s Setting up fontconfig-config (2.15.0-2.2ubuntu1) ... 171s Setting up libwebpdemux2:arm64 (1.5.0-0.1) ... 171s Setting up xfonts-utils (1:7.7+7) ... 171s Setting up libraqm0:arm64 (0.10.2-1) ... 171s Setting up python3-numpy (1:2.2.3+ds-5) ... 173s Setting up libjs-sphinxdoc (8.1.3-5) ... 173s Setting up python-biopython-doc (1.85+dfsg-2build1) ... 173s Setting up libtiff6:arm64 (4.5.1+git230720-4ubuntu4) ... 173s Setting up xml-core (0.19) ... 174s Setting up libfontconfig1:arm64 (2.15.0-2.2ubuntu1) ... 174s Setting up fonts-urw-base35 (20200910-8) ... 174s Setting up libcairo2:arm64 (1.18.4-1) ... 174s Setting up python3-pil:arm64 (11.1.0-5build1) ... 174s Setting up python3-cairo (1.27.0-2) ... 174s Setting up python3-rlpycairo (0.3.0-3) ... 174s Setting up python3-reportlab (4.3.1-1) ... 175s Processing triggers for libc-bin (2.41-6ubuntu1) ... 175s Processing triggers for man-db (2.13.0-1) ... 177s Processing triggers for sgml-base (1.31) ... 177s Setting up w3c-sgml-lib (1.3-3) ... 205s Setting up python3-biopython (1.85+dfsg-2build1) ... 206s Setting up python3-biopython-sql (1.85+dfsg-2build1) ... 207s autopkgtest [05:44:31]: test dependencies: sh debian/tests/run-unit-test 207s autopkgtest [05:44:31]: test dependencies: [----------------------- 208s cp: cannot stat '/usr/share/libcifpp/mmcif_pdbx.dic': No such file or directory 208s cp: cannot stat '/usr/share/libcifpp/mmcif_ma.dic': No such file or directory 210s mkdir: created directory 'Bio' 210s mkdir: created directory 'Bio/Align' 210s mkdir: created directory 'Bio/Align/substitution_matrices' 210s mkdir: created directory 'Bio/Align/substitution_matrices/data/' 210s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER22' -> 'Bio/Align/substitution_matrices/data/BENNER22' 210s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER6' -> 'Bio/Align/substitution_matrices/data/BENNER6' 210s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER74' -> 'Bio/Align/substitution_matrices/data/BENNER74' 210s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLASTN' -> 'Bio/Align/substitution_matrices/data/BLASTN' 210s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLASTP' -> 'Bio/Align/substitution_matrices/data/BLASTP' 210s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM45' -> 'Bio/Align/substitution_matrices/data/BLOSUM45' 210s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM50' -> 'Bio/Align/substitution_matrices/data/BLOSUM50' 210s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM62' -> 'Bio/Align/substitution_matrices/data/BLOSUM62' 210s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM80' -> 'Bio/Align/substitution_matrices/data/BLOSUM80' 210s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM90' -> 'Bio/Align/substitution_matrices/data/BLOSUM90' 210s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/DAYHOFF' -> 'Bio/Align/substitution_matrices/data/DAYHOFF' 210s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/FENG' -> 'Bio/Align/substitution_matrices/data/FENG' 210s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/GENETIC' -> 'Bio/Align/substitution_matrices/data/GENETIC' 210s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/GONNET1992' -> 'Bio/Align/substitution_matrices/data/GONNET1992' 210s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/HOXD70' -> 'Bio/Align/substitution_matrices/data/HOXD70' 210s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/JOHNSON' -> 'Bio/Align/substitution_matrices/data/JOHNSON' 210s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/JONES' -> 'Bio/Align/substitution_matrices/data/JONES' 210s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/LEVIN' -> 'Bio/Align/substitution_matrices/data/LEVIN' 210s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MCLACHLAN' -> 'Bio/Align/substitution_matrices/data/MCLACHLAN' 210s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MDM78' -> 'Bio/Align/substitution_matrices/data/MDM78' 210s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MEGABLAST' -> 'Bio/Align/substitution_matrices/data/MEGABLAST' 210s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/NUC.4.4' -> 'Bio/Align/substitution_matrices/data/NUC.4.4' 210s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM250' -> 'Bio/Align/substitution_matrices/data/PAM250' 210s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM30' -> 'Bio/Align/substitution_matrices/data/PAM30' 210s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM70' -> 'Bio/Align/substitution_matrices/data/PAM70' 210s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/RAO' -> 'Bio/Align/substitution_matrices/data/RAO' 210s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/RISLER' -> 'Bio/Align/substitution_matrices/data/RISLER' 210s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/SCHNEIDER' -> 'Bio/Align/substitution_matrices/data/SCHNEIDER' 210s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/STR' -> 'Bio/Align/substitution_matrices/data/STR' 210s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/TRANS' -> 'Bio/Align/substitution_matrices/data/TRANS' 210s test_Ace ... ok 210s test_Affy ... ok 213s test_AlignIO ... ok 213s test_AlignIO_ClustalIO ... ok 213s test_AlignIO_EmbossIO ... ok 213s test_AlignIO_FastaIO ... ok 213s test_AlignIO_MauveIO ... ok 213s test_AlignIO_PhylipIO ... ok 213s test_AlignIO_convert ... ok 213s test_AlignInfo ... ok 213s test_Align_Alignment ... ok 213s test_Align_a2m ... ok 213s test_Align_bed ... ok 213s test_Align_bigbed ... ok 214s test_Align_bigmaf ... ok 214s test_Align_bigpsl ... ok 214s test_Align_chain ... ok 214s test_Align_clustal ... ok 217s test_Align_codonalign ... ok 218s test_Align_emboss ... ok 218s test_Align_exonerate ... ok 218s test_Align_fasta ... ok 218s test_Align_hhr ... ok 219s test_Align_maf ... ok 219s test_Align_mauve ... ok 219s test_Align_msf ... ok 219s test_Align_nexus ... ok 219s test_Align_phylip ... ok 219s test_Align_psl ... ok 220s test_Align_sam ... ok 221s test_Align_stockholm ... ok 222s test_Align_tabular ... ok 222s test_Application ... ok 222s test_BioSQL_MySQLdb_online ... skipping. internet not available 222s test_BioSQL_mysql_connector ... skipping. BioSQL test configuration file biosql.ini missing (see biosql.ini.sample) 222s test_BioSQL_mysql_connector_online ... skipping. internet not available 222s test_BioSQL_psycopg2_online ... skipping. internet not available 227s test_BioSQL_sqlite3 ... ok 227s test_BioSQL_sqlite3_online ... skipping. internet not available 227s test_Blast_Record ... ok 227s test_Blast_parser ... ok 227s test_CAPS ... ok 227s test_Chi2 ... ok 227s test_ClustalOmega_tool ... skipping. Install clustalo if you want to use Clustal Omega from Biopython. 227s test_Clustalw_tool ... skipping. Install clustalw or clustalw2 if you want to use it from Biopython. 228s test_Cluster ... ok 228s test_CodonTable ... ok 228s test_ColorSpiral ... ok 228s test_Compass ... ok 229s test_Consensus ... ok 229s test_Dialign_tool ... skipping. Install DIALIGN2-2 if you want to use the Bio.Align.Applications wrapper. 229s test_EMBL_unittest ... ok 229s test_Emboss ... skipping. $EMBOSS_ROOT='/usr/lib/emboss' which does not exist! 229s test_EmbossPrimer ... ok 233s test_Entrez ... ok 233s test_Entrez_online ... skipping. internet not available 234s test_Entrez_parser ... ok 234s test_Enzyme ... ok 234s test_ExPASy ... skipping. internet not available 234s test_Fasttree_tool ... skipping. Install FastTree and correctly set the file path to the program if you want to use it from Biopython. 234s test_File ... ok 234s test_GenBank ... /usr/lib/python3/dist-packages/Bio/SeqIO/InsdcIO.py:600: BiopythonWarning: Annotation 'Sequence Read Archive: SRX001885, SRX001121, SRX001531, SRX001530, SRX001529' too long 234s warnings.warn(f"Annotation {text!r} too long", BiopythonWarning) 234s ok 236s test_GenomeDiagram ... Warn: Can't find .pfb for face 'Helvetica' 238s ok 238s test_GraphicsChromosome ... ok 239s test_GraphicsDistribution ... ok 239s test_GraphicsGeneral ... ok 240s test_HMMCasino ... ok 240s test_HMMGeneral ... ok 240s test_KEGG ... ok 240s test_KEGG_online ... skipping. internet not available 244s test_KGML_graphics ... ok 244s test_KGML_graphics_online ... skipping. internet not available 245s test_KGML_nographics ... ok 245s test_KeyWList ... ok 245s test_LogisticRegression ... ok 246s test_MafIO_index ... ok 246s test_Mafft_tool ... skipping. Install MAFFT if you want to use the Bio.Align.Applications wrapper. 246s test_MarkovModel ... ok 246s test_Medline ... ok 246s test_Muscle_tool ... skipping. Install MUSCLE if you want to use the Bio.Align.Applications wrapper. 247s test_NCBIXML ... Exception ignored in: 247s Traceback (most recent call last): 247s File "/usr/lib/python3/dist-packages/Bio/Blast/NCBIXML.py", line 1319, in parse 247s expat_parser.Parse(NULL, True) 247s xml.parsers.expat.ExpatError: unclosed token: line 320, column 0 247s ok 247s test_NCBI_BLAST_tools ... skipping. Install the NCBI BLAST+ command line tools if you want to use the Bio.Blast.Applications wrapper. 247s test_NCBI_qblast ... ok 247s test_NMR ... ok 247s test_NaiveBayes ... ok 247s test_Nexus ... ok 248s test_PAML_baseml ... ok 248s test_PAML_codeml ... ok 248s test_PAML_yn00 ... ok 253s test_PDB_CEAligner ... ok 253s test_PDB_DSSP ... ok 253s test_PDB_Dice ... ok 253s test_PDB_Disordered ... ok 253s test_PDB_Exposure ... ok 253s test_PDB_FragmentMapper ... ok 255s test_PDB_KDTree ... ok 255s test_PDB_MMCIF2Dict ... ok 255s test_PDB_MMCIFIO ... ok 256s test_PDB_MMCIFParser ... ok 256s test_PDB_NACCESS ... ok 257s test_PDB_PDBIO ... ok 257s test_PDB_PDBList ... skipping. internet not available 263s test_PDB_PDBMLParser ... ok 263s test_PDB_PDBParser ... ok 263s 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 263s test_PDB_Polypeptide ... ok 263s test_PDB_QCPSuperimposer ... ok 266s test_PDB_SASA ... ok 267s test_PDB_SMCRA ... ok 267s test_PDB_Selection ... ok 267s test_PDB_StructureAlignment ... ok 267s test_PDB_Superimposer ... ok 267s test_PDB_alphafold_db ... skipping. internet not available 267s test_PDB_binary_cif ... skipping. Error: Install msgpack to use Bio.PDB.binaryCIF (e.g. pip install msgpack) 267s 267s test_PDB_internal_coords ... skipping. Error: Install mmtf to use Bio.PDB.mmtf (e.g. pip install mmtf-python) 267s 268s test_PDB_parse_pdb_header ... ok 268s test_PDB_vectors ... ok 268s test_PQR ... ok 268s test_Pathway ... ok 268s test_Phd ... ok 268s test_Phylo ... ok 269s test_PhyloXML ... ok 269s test_Phylo_CDAO ... skipping. Install RDFlib if you want to use the CDAO tree format. 269s test_Phylo_NeXML ... ok 269s test_Phylo_igraph ... skipping. Install igraph if you wish to use it with Bio.Phylo 269s test_Phylo_matplotlib ... skipping. Install matplotlib if you want to use Bio.Phylo._utils. 269s test_Phylo_networkx ... skipping. Install networkx if you wish to use it with Bio.Phylo 269s test_PopGen_GenePop_nodepend ... ok 269s test_Prank_tool ... skipping. Install PRANK if you want to use the Bio.Align.Applications wrapper. 269s test_Probcons_tool ... skipping. Install PROBCONS if you want to use the Bio.Align.Applications wrapper. 269s test_ProtParam ... ok 270s test_RCSBFormats ... ok 270s test_Restriction ... ok 270s test_SCOP_Astral ... ok 270s test_SCOP_Cla ... ok 270s test_SCOP_Des ... ok 270s test_SCOP_Dom ... ok 270s test_SCOP_Hie ... ok 270s test_SCOP_Raf ... ok 270s test_SCOP_Residues ... ok 270s test_SCOP_Scop ... ok 270s test_SVDSuperimposer ... ok 271s test_SearchIO_blast_tab ... ok 271s test_SearchIO_blast_tab_index ... ok 271s test_SearchIO_blast_xml ... ok 272s test_SearchIO_blast_xml_index ... ok 272s test_SearchIO_blat_psl ... ok 272s test_SearchIO_blat_psl_index ... ok 272s test_SearchIO_exonerate ... ok 273s test_SearchIO_exonerate_text_index ... ok 273s test_SearchIO_exonerate_vulgar_index ... ok 273s test_SearchIO_fasta_m10 ... ok 273s test_SearchIO_fasta_m10_index ... ok 273s test_SearchIO_hhsuite2_text ... ok 273s test_SearchIO_hmmer2_text ... ok 273s test_SearchIO_hmmer2_text_index ... ok 273s test_SearchIO_hmmer3_domtab ... ok 273s test_SearchIO_hmmer3_domtab_index ... ok 274s test_SearchIO_hmmer3_tab ... ok 274s test_SearchIO_hmmer3_tab_index ... ok 274s test_SearchIO_hmmer3_text ... ok 274s test_SearchIO_hmmer3_text_index ... ok 274s test_SearchIO_interproscan_xml ... ok 274s test_SearchIO_model ... ok 274s test_SearchIO_write ... ok 274s test_SeqFeature ... ok 289s test_SeqIO ... ok 289s test_SeqIO_AbiIO ... ok 289s test_SeqIO_FastaIO ... ok 289s test_SeqIO_Gck ... ok 289s test_SeqIO_Gfa ... ok 289s test_SeqIO_Insdc ... ok 289s test_SeqIO_NibIO ... ok 291s test_SeqIO_PdbIO ... ok 292s test_SeqIO_QualityIO ... ok 292s test_SeqIO_SeqXML ... ok 292s test_SeqIO_SffIO ... ok 292s test_SeqIO_SnapGene ... ok 293s test_SeqIO_TwoBitIO ... ok 293s test_SeqIO_UniprotIO ... ok 293s test_SeqIO_Xdna ... ok 293s test_SeqIO_features ... ok 306s test_SeqIO_index ... ok 306s test_SeqIO_online ... skipping. internet not available 306s test_SeqIO_write ... ok 306s test_SeqRecord ... ok 306s test_SeqUtils ... ok 308s test_Seq_objs ... ok 308s test_SwissProt ... ok 308s test_TCoffee_tool ... skipping. Install TCOFFEE if you want to use the Bio.Align.Applications wrapper. 308s test_TogoWS ... skipping. internet not available 308s test_TreeConstruction ... ok 308s test_Tutorial ... skipping. Could not find ../Doc/Tutorial/index.rst file 308s test_UniGene ... ok 308s test_UniProt ... skipping. internet not available 309s test_UniProt_GOA ... ok 309s test_align ... ok 309s test_align_substitution_matrices ... ok 311s test_bgzf ... ok 311s test_cellosaurus ... ok 315s test_codonalign ... ok 315s test_geo ... ok 315s test_kNN ... ok 316s test_motifs ... ok 316s test_motifs_online ... skipping. internet not available 316s 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. 316s warnings.warn( 316s ok 316s test_pairwise2_no_C ... ok 316s test_pairwise_aligner ... ok 317s test_pairwise_alignment_map ... ok 323s test_phenotype ... ok 323s test_phenotype_fit ... skipping. Install SciPy if you want to use Bio.phenotype fit functionality. 323s 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. 323s test_prodoc ... ok 324s test_prosite ... ok 324s test_raxml_tool ... skipping. Install RAxML (binary raxmlHPC) if you want to test the Bio.Phylo.Applications wrapper. 324s test_samtools_tool ... skipping. Install samtools and correctly set the file path to the program if you want to use it from Biopython 324s test_seq ... ok 324s test_translate ... ok 324s ---------------------------------------------------------------------- 324s Ran 218 tests in 113.862 seconds 324s 324s Skipping any tests requiring internet access 324s Python version: 3.13.3 (main, Apr 8 2025, 19:55:40) [GCC 14.2.0] 324s Operating system: posix linux 324s :0: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/protein_lib.fa' mode='rt' encoding='UTF-8'> 324s :0: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/nucleotide_lib.fa' mode='rt' encoding='UTF-8'> 325s autopkgtest [05:46:29]: test dependencies: -----------------------] 325s autopkgtest [05:46:29]: test dependencies: - - - - - - - - - - results - - - - - - - - - - 325s dependencies PASS 326s autopkgtest [05:46:30]: test full_suite: preparing testbed 457s autopkgtest [05:48:41]: testbed dpkg architecture: arm64 457s autopkgtest [05:48:41]: testbed apt version: 3.0.0 458s autopkgtest [05:48:42]: @@@@@@@@@@@@@@@@@@@@ test bed setup 458s autopkgtest [05:48:42]: testbed release detected to be: questing 459s autopkgtest [05:48:43]: updating testbed package index (apt update) 459s Get:1 http://ftpmaster.internal/ubuntu questing-proposed InRelease [110 kB] 459s Hit:2 http://ftpmaster.internal/ubuntu questing InRelease 459s Hit:3 http://ftpmaster.internal/ubuntu questing-updates InRelease 460s Hit:4 http://ftpmaster.internal/ubuntu questing-security InRelease 460s Get:5 http://ftpmaster.internal/ubuntu questing-proposed/multiverse Sources [57.4 kB] 460s Get:6 http://ftpmaster.internal/ubuntu questing-proposed/main Sources [184 kB] 460s Get:7 http://ftpmaster.internal/ubuntu questing-proposed/universe Sources [2202 kB] 460s Get:8 http://ftpmaster.internal/ubuntu questing-proposed/main arm64 Packages [227 kB] 461s Get:9 http://ftpmaster.internal/ubuntu questing-proposed/universe arm64 Packages [1472 kB] 461s Get:10 http://ftpmaster.internal/ubuntu questing-proposed/multiverse arm64 Packages [16.5 kB] 461s Fetched 4269 kB in 2s (2078 kB/s) 462s Reading package lists... 463s autopkgtest [05:48:47]: upgrading testbed (apt dist-upgrade and autopurge) 463s Reading package lists... 464s Building dependency tree... 464s Reading state information... 464s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 464s Starting 2 pkgProblemResolver with broken count: 0 464s Done 465s Entering ResolveByKeep 465s 465s Calculating upgrade... 466s The following packages will be upgraded: 466s python3-pkg-resources python3-setuptools 466s 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 466s Need to get 805 kB of archives. 466s After this operation, 108 kB of additional disk space will be used. 466s Get:1 http://ftpmaster.internal/ubuntu questing-proposed/main arm64 python3-pkg-resources all 78.1.0-1.2 [144 kB] 466s Get:2 http://ftpmaster.internal/ubuntu questing-proposed/main arm64 python3-setuptools all 78.1.0-1.2 [660 kB] 467s Fetched 805 kB in 1s (1223 kB/s) 467s (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 ... 117820 files and directories currently installed.) 467s Preparing to unpack .../python3-pkg-resources_78.1.0-1.2_all.deb ... 467s Unpacking python3-pkg-resources (78.1.0-1.2) over (75.8.0-1) ... 467s Preparing to unpack .../python3-setuptools_78.1.0-1.2_all.deb ... 468s Unpacking python3-setuptools (78.1.0-1.2) over (75.8.0-1) ... 468s Setting up python3-pkg-resources (78.1.0-1.2) ... 468s Setting up python3-setuptools (78.1.0-1.2) ... 469s Reading package lists... 469s Building dependency tree... 469s Reading state information... 470s Starting pkgProblemResolver with broken count: 0 470s Starting 2 pkgProblemResolver with broken count: 0 470s Done 470s Solving dependencies... 471s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 474s Reading package lists... 474s Building dependency tree... 474s Reading state information... 475s Starting pkgProblemResolver with broken count: 0 475s Starting 2 pkgProblemResolver with broken count: 0 475s Done 476s The following NEW packages will be installed: 476s autoconf automake autopoint autotools-dev blt build-essential bwa clustalo 476s cpp cpp-14 cpp-14-aarch64-linux-gnu cpp-aarch64-linux-gnu debhelper 476s debugedit dh-autoreconf dh-python dh-strip-nondeterminism dialign 476s docutils-common dssp dwz emboss emboss-data emboss-lib fasttree flex 476s fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-font-awesome 476s fonts-lato fonts-lmodern fonts-lyx fonts-urw-base35 g++ g++-14 476s g++-14-aarch64-linux-gnu g++-aarch64-linux-gnu gcc gcc-14 476s gcc-14-aarch64-linux-gnu gcc-aarch64-linux-gnu gettext ghostscript hevea 476s hicolor-icon-theme imagemagick imagemagick-7-common imagemagick-7.q16 476s intltool-debian libamd3 libaom3 libapache-pom-java libarchive-zip-perl 476s libargtable2-0 libarpack2t64 libasan8 libavahi-client3 libavahi-common-data 476s libavahi-common3 libblas3 libcairo2 libcc1-0 libcifpp-data libcifpp7 476s libcolamd3 libcommons-logging-java libcommons-parent-java libcups2t64 476s libde265-0 libdebhelper-perl libdeflate0 libexpat1-dev libfftw3-double3 476s libfile-stripnondeterminism-perl libfontbox-java libfontconfig1 libfontenc1 476s libgcc-14-dev libgd3 libgfortran5 libglpk40 libgomp1 libgraphite2-3 476s libgs-common libgs10 libgs10-common libharfbuzz0b libheif-plugin-aomdec 476s libheif-plugin-libde265 libheif1 libhpdf-2.3.0 libhwasan0 libice6 libidn12 476s libigraph3t64 libijs-0.35 libimagequant0 libisl23 libitm1 libjbig0 476s libjbig2dec0 libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui 476s libjs-sphinxdoc libjs-underscore libjson-perl libkpathsea6 liblapack3 476s liblbfgsb0 liblcms2-2 liblerc4 liblqr-1-0 liblsan0 libltdl7 476s libmagickcore-7.q16-10 libmagickwand-7.q16-10 libmbedcrypto16 libmbedtls21 476s libmbedx509-7 libmpc3 libmpfi0 libmysqlclient24 libnetpbm11t64 libopenjp2-7 476s libpaper-utils libpaper2 libpdfbox-java libpixman-1-0 libplfit0 libpotrace0 476s libpq5 libptexenc1 libpython3-all-dev libpython3-dev libpython3.13-dev 476s libqhull-r8.0 libraqm0 libraw23t64 libsharpyuv0 libsm6 libstdc++-14-dev 476s libsuitesparseconfig7 libsynctex2 libtcl8.6 libteckit0 libtexlua53-5 476s libtiff6 libtk8.6 libtool libtsan2 libubsan1 libwebp7 libwebpdemux2 476s libwebpmux3 libxaw7 libxcb-render0 libxcb-shm0 libxft2 libxi6 libxmu6 476s libxpm4 libxrender1 libxslt1.1 libxss1 libxt6t64 libzzip-0-13t64 m4 mafft 476s mysql-common ncbi-blast+ ncbi-data netpbm phylip po-debconf poppler-data 476s prank preview-latex-style probcons python-biopython-doc 476s python-matplotlib-data python3-alabaster python3-all python3-all-dev 476s python3-biopython python3-biopython-sql python3-brotli python3-cairo 476s python3-contourpy python3-cycler python3-dateutil python3-decorator 476s python3-defusedxml python3-dev python3-docutils python3-fonttools 476s python3-freetype python3-fs python3-igraph python3-imagesize 476s python3-kiwisolver python3-lxml python3-lz4 python3-matplotlib python3-mmtf 476s python3-mpmath python3-msgpack python3-mysqldb python3-networkx 476s python3-numpy python3-numpy-dev python3-numpydoc python3-packaging 476s python3-pil python3-pil.imagetk python3-platformdirs python3-rdflib 476s python3-reportlab python3-rlpycairo python3-roman python3-scipy 476s python3-snowballstemmer python3-sphinx python3-sphinx-rtd-theme 476s python3-sphinxcontrib.jquery python3-sympy python3-tabulate 476s python3-texttable python3-tk python3-ufolib2 python3.13-dev python3.13-tk 476s sgml-base sphinx-common sphinx-rtd-theme-common t-coffee t1utils tex-common 476s texlive-base texlive-binaries texlive-fonts-recommended texlive-latex-base 476s texlive-latex-extra texlive-latex-recommended texlive-pictures tk8.6-blt2.5 476s unicode-data w3c-sgml-lib wise wise-data x11-common xdg-utils 476s xfonts-encodings xfonts-utils xml-core zlib1g-dev 476s 0 upgraded, 258 newly installed, 0 to remove and 0 not upgraded. 476s Need to get 406 MB of archives. 476s After this operation, 1815 MB of additional disk space will be used. 476s Get:1 http://ftpmaster.internal/ubuntu questing/main arm64 m4 arm64 1.4.19-7 [244 kB] 476s Get:2 http://ftpmaster.internal/ubuntu questing/main arm64 flex arm64 2.6.4-8.2build1 [291 kB] 476s Get:3 http://ftpmaster.internal/ubuntu questing/main arm64 fonts-lato all 2.015-1 [2781 kB] 477s Get:4 http://ftpmaster.internal/ubuntu questing/main arm64 libgomp1 arm64 15-20250404-0ubuntu1 [147 kB] 477s Get:5 http://ftpmaster.internal/ubuntu questing/main arm64 libfftw3-double3 arm64 3.3.10-2fakesync1build1 [392 kB] 477s Get:6 http://ftpmaster.internal/ubuntu questing/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 477s Get:7 http://ftpmaster.internal/ubuntu questing/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 477s Get:8 http://ftpmaster.internal/ubuntu questing/main arm64 libfontenc1 arm64 1:1.1.8-1build1 [13.9 kB] 477s Get:9 http://ftpmaster.internal/ubuntu questing/main arm64 x11-common all 1:7.7+23ubuntu4 [21.8 kB] 477s Get:10 http://ftpmaster.internal/ubuntu questing/main arm64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 477s Get:11 http://ftpmaster.internal/ubuntu questing/main arm64 xfonts-utils arm64 1:7.7+7 [95.6 kB] 477s Get:12 http://ftpmaster.internal/ubuntu questing/main arm64 fonts-urw-base35 all 20200910-8 [11.0 MB] 479s Get:13 http://ftpmaster.internal/ubuntu questing/main arm64 fontconfig-config arm64 2.15.0-2.2ubuntu1 [37.9 kB] 479s Get:14 http://ftpmaster.internal/ubuntu questing/main arm64 libfontconfig1 arm64 2.15.0-2.2ubuntu1 [144 kB] 479s Get:15 http://ftpmaster.internal/ubuntu questing/main arm64 libsharpyuv0 arm64 1.5.0-0.1 [16.9 kB] 479s Get:16 http://ftpmaster.internal/ubuntu questing/main arm64 libaom3 arm64 3.12.0-1 [1828 kB] 479s Get:17 http://ftpmaster.internal/ubuntu questing/main arm64 libheif-plugin-aomdec arm64 1.19.7-1 [11.4 kB] 479s Get:18 http://ftpmaster.internal/ubuntu questing/main arm64 libde265-0 arm64 1.0.15-1build5 [146 kB] 479s Get:19 http://ftpmaster.internal/ubuntu questing/main arm64 libheif-plugin-libde265 arm64 1.19.7-1 [8890 B] 479s Get:20 http://ftpmaster.internal/ubuntu questing/main arm64 libheif1 arm64 1.19.7-1 [371 kB] 479s Get:21 http://ftpmaster.internal/ubuntu questing/main arm64 libjbig0 arm64 2.1-6.1ubuntu2 [29.3 kB] 479s Get:22 http://ftpmaster.internal/ubuntu questing/main arm64 libjpeg-turbo8 arm64 2.1.5-3ubuntu2 [165 kB] 479s Get:23 http://ftpmaster.internal/ubuntu questing/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 479s Get:24 http://ftpmaster.internal/ubuntu questing/main arm64 liblcms2-2 arm64 2.16-2 [170 kB] 479s Get:25 http://ftpmaster.internal/ubuntu questing/universe arm64 liblqr-1-0 arm64 0.4.2-2.1build2 [27.1 kB] 479s Get:26 http://ftpmaster.internal/ubuntu questing/main arm64 libltdl7 arm64 2.5.4-4 [43.0 kB] 479s Get:27 http://ftpmaster.internal/ubuntu questing/main arm64 libopenjp2-7 arm64 2.5.3-2 [183 kB] 479s Get:28 http://ftpmaster.internal/ubuntu questing/main arm64 libraw23t64 arm64 0.21.3-1 [377 kB] 479s Get:29 http://ftpmaster.internal/ubuntu questing/main arm64 libdeflate0 arm64 1.23-1 [46.2 kB] 479s Get:30 http://ftpmaster.internal/ubuntu questing/main arm64 liblerc4 arm64 4.0.0+ds-5ubuntu1 [167 kB] 479s Get:31 http://ftpmaster.internal/ubuntu questing/main arm64 libwebp7 arm64 1.5.0-0.1 [194 kB] 479s Get:32 http://ftpmaster.internal/ubuntu questing/main arm64 libtiff6 arm64 4.5.1+git230720-4ubuntu4 [193 kB] 479s Get:33 http://ftpmaster.internal/ubuntu questing/main arm64 libwebpdemux2 arm64 1.5.0-0.1 [12.5 kB] 479s Get:34 http://ftpmaster.internal/ubuntu questing/main arm64 libwebpmux3 arm64 1.5.0-0.1 [25.4 kB] 479s Get:35 http://ftpmaster.internal/ubuntu questing/universe arm64 imagemagick-7-common all 8:7.1.1.43+dfsg1-1 [69.7 kB] 479s Get:36 http://ftpmaster.internal/ubuntu questing/universe arm64 libmagickcore-7.q16-10 arm64 8:7.1.1.43+dfsg1-1 [1876 kB] 479s Get:37 http://ftpmaster.internal/ubuntu questing/universe arm64 libmagickwand-7.q16-10 arm64 8:7.1.1.43+dfsg1-1 [301 kB] 479s Get:38 http://ftpmaster.internal/ubuntu questing/main arm64 poppler-data all 0.4.12-1 [2060 kB] 479s Get:39 http://ftpmaster.internal/ubuntu questing/main arm64 python3-numpy-dev arm64 1:2.2.3+ds-5 [146 kB] 479s Get:40 http://ftpmaster.internal/ubuntu questing/main arm64 libblas3 arm64 3.12.1-2 [161 kB] 479s Get:41 http://ftpmaster.internal/ubuntu questing/main arm64 libgfortran5 arm64 15-20250404-0ubuntu1 [444 kB] 479s Get:42 http://ftpmaster.internal/ubuntu questing/main arm64 liblapack3 arm64 3.12.1-2 [2307 kB] 479s Get:43 http://ftpmaster.internal/ubuntu questing/main arm64 python3-numpy arm64 1:2.2.3+ds-5 [3981 kB] 479s Get:44 http://ftpmaster.internal/ubuntu questing/main arm64 sgml-base all 1.31 [11.4 kB] 479s Get:45 http://ftpmaster.internal/ubuntu questing/main arm64 autoconf all 2.72-3ubuntu1 [383 kB] 479s Get:46 http://ftpmaster.internal/ubuntu questing/main arm64 autotools-dev all 20220109.1 [44.9 kB] 479s Get:47 http://ftpmaster.internal/ubuntu questing/main arm64 automake all 1:1.17-3ubuntu1 [572 kB] 479s Get:48 http://ftpmaster.internal/ubuntu questing/main arm64 autopoint all 0.23.1-1 [619 kB] 480s Get:49 http://ftpmaster.internal/ubuntu questing/main arm64 libtcl8.6 arm64 8.6.16+dfsg-1 [987 kB] 480s Get:50 http://ftpmaster.internal/ubuntu questing/main arm64 libxrender1 arm64 1:0.9.10-1.1build1 [18.8 kB] 480s Get:51 http://ftpmaster.internal/ubuntu questing/main arm64 libxft2 arm64 2.3.6-1build1 [44.1 kB] 480s Get:52 http://ftpmaster.internal/ubuntu questing/main arm64 libxss1 arm64 1:1.2.3-1build3 [7244 B] 480s Get:53 http://ftpmaster.internal/ubuntu questing/main arm64 libtk8.6 arm64 8.6.16-1 [776 kB] 480s Get:54 http://ftpmaster.internal/ubuntu questing/main arm64 tk8.6-blt2.5 arm64 2.5.3+dfsg-8 [624 kB] 480s Get:55 http://ftpmaster.internal/ubuntu questing/main arm64 blt arm64 2.5.3+dfsg-8 [4824 B] 480s Get:56 http://ftpmaster.internal/ubuntu questing/main arm64 libisl23 arm64 0.27-1 [676 kB] 480s Get:57 http://ftpmaster.internal/ubuntu questing/main arm64 libmpc3 arm64 1.3.1-1build2 [56.8 kB] 480s Get:58 http://ftpmaster.internal/ubuntu questing/main arm64 cpp-14-aarch64-linux-gnu arm64 14.2.0-19ubuntu2 [10.6 MB] 480s Get:59 http://ftpmaster.internal/ubuntu questing/main arm64 cpp-14 arm64 14.2.0-19ubuntu2 [1026 B] 480s Get:60 http://ftpmaster.internal/ubuntu questing/main arm64 cpp-aarch64-linux-gnu arm64 4:14.2.0-1ubuntu1 [5558 B] 480s Get:61 http://ftpmaster.internal/ubuntu questing/main arm64 cpp arm64 4:14.2.0-1ubuntu1 [22.4 kB] 480s Get:62 http://ftpmaster.internal/ubuntu questing/main arm64 libcc1-0 arm64 15-20250404-0ubuntu1 [49.1 kB] 480s Get:63 http://ftpmaster.internal/ubuntu questing/main arm64 libitm1 arm64 15-20250404-0ubuntu1 [27.8 kB] 480s Get:64 http://ftpmaster.internal/ubuntu questing/main arm64 libasan8 arm64 15-20250404-0ubuntu1 [2922 kB] 480s Get:65 http://ftpmaster.internal/ubuntu questing/main arm64 liblsan0 arm64 15-20250404-0ubuntu1 [1318 kB] 480s Get:66 http://ftpmaster.internal/ubuntu questing/main arm64 libtsan2 arm64 15-20250404-0ubuntu1 [2692 kB] 480s Get:67 http://ftpmaster.internal/ubuntu questing/main arm64 libubsan1 arm64 15-20250404-0ubuntu1 [1177 kB] 480s Get:68 http://ftpmaster.internal/ubuntu questing/main arm64 libhwasan0 arm64 15-20250404-0ubuntu1 [1640 kB] 480s Get:69 http://ftpmaster.internal/ubuntu questing/main arm64 libgcc-14-dev arm64 14.2.0-19ubuntu2 [2593 kB] 480s Get:70 http://ftpmaster.internal/ubuntu questing/main arm64 gcc-14-aarch64-linux-gnu arm64 14.2.0-19ubuntu2 [20.9 MB] 481s Get:71 http://ftpmaster.internal/ubuntu questing/main arm64 gcc-14 arm64 14.2.0-19ubuntu2 [529 kB] 481s Get:72 http://ftpmaster.internal/ubuntu questing/main arm64 gcc-aarch64-linux-gnu arm64 4:14.2.0-1ubuntu1 [1200 B] 481s Get:73 http://ftpmaster.internal/ubuntu questing/main arm64 gcc arm64 4:14.2.0-1ubuntu1 [4998 B] 481s Get:74 http://ftpmaster.internal/ubuntu questing/main arm64 libstdc++-14-dev arm64 14.2.0-19ubuntu2 [2501 kB] 481s Get:75 http://ftpmaster.internal/ubuntu questing/main arm64 g++-14-aarch64-linux-gnu arm64 14.2.0-19ubuntu2 [12.1 MB] 481s Get:76 http://ftpmaster.internal/ubuntu questing/main arm64 g++-14 arm64 14.2.0-19ubuntu2 [23.0 kB] 481s Get:77 http://ftpmaster.internal/ubuntu questing/main arm64 g++-aarch64-linux-gnu arm64 4:14.2.0-1ubuntu1 [956 B] 481s Get:78 http://ftpmaster.internal/ubuntu questing/main arm64 g++ arm64 4:14.2.0-1ubuntu1 [1080 B] 481s Get:79 http://ftpmaster.internal/ubuntu questing/main arm64 build-essential arm64 12.12ubuntu1 [5082 B] 481s Get:80 http://ftpmaster.internal/ubuntu questing/universe arm64 bwa arm64 0.7.18-1 [201 kB] 481s Get:81 http://ftpmaster.internal/ubuntu questing/universe arm64 libargtable2-0 arm64 13-3 [15.3 kB] 481s Get:82 http://ftpmaster.internal/ubuntu questing/universe arm64 clustalo arm64 1.2.4-8build1 [190 kB] 481s Get:83 http://ftpmaster.internal/ubuntu questing/main arm64 libdebhelper-perl all 13.24.1ubuntu2 [95.4 kB] 481s Get:84 http://ftpmaster.internal/ubuntu questing/main arm64 libtool all 2.5.4-4 [168 kB] 481s Get:85 http://ftpmaster.internal/ubuntu questing/main arm64 dh-autoreconf all 20 [16.1 kB] 481s Get:86 http://ftpmaster.internal/ubuntu questing/main arm64 libarchive-zip-perl all 1.68-1 [90.2 kB] 481s Get:87 http://ftpmaster.internal/ubuntu questing/main arm64 libfile-stripnondeterminism-perl all 1.14.1-2 [20.3 kB] 481s Get:88 http://ftpmaster.internal/ubuntu questing/main arm64 dh-strip-nondeterminism all 1.14.1-2 [5064 B] 481s Get:89 http://ftpmaster.internal/ubuntu questing/main arm64 debugedit arm64 1:5.1-2 [46.1 kB] 481s Get:90 http://ftpmaster.internal/ubuntu questing/main arm64 dwz arm64 0.15-1build6 [113 kB] 481s Get:91 http://ftpmaster.internal/ubuntu questing/main arm64 gettext arm64 0.23.1-1 [998 kB] 481s Get:92 http://ftpmaster.internal/ubuntu questing/main arm64 intltool-debian all 0.35.0+20060710.6 [23.2 kB] 481s Get:93 http://ftpmaster.internal/ubuntu questing/main arm64 po-debconf all 1.0.21+nmu1 [233 kB] 481s Get:94 http://ftpmaster.internal/ubuntu questing/main arm64 debhelper all 13.24.1ubuntu2 [895 kB] 481s Get:95 http://ftpmaster.internal/ubuntu questing/universe arm64 dh-python all 6.20250308 [118 kB] 481s Get:96 http://ftpmaster.internal/ubuntu questing/universe arm64 dialign arm64 2.2.1-13 [152 kB] 481s Get:97 http://ftpmaster.internal/ubuntu questing/main arm64 xml-core all 0.19 [20.3 kB] 481s Get:98 http://ftpmaster.internal/ubuntu questing/main arm64 docutils-common all 0.21.2+dfsg-2 [131 kB] 481s Get:99 http://ftpmaster.internal/ubuntu questing/universe arm64 libcifpp-data all 7.0.9-1 [481 kB] 482s Get:100 http://ftpmaster.internal/ubuntu questing/universe arm64 libcifpp7 arm64 7.0.9-1 [997 kB] 482s Get:101 http://ftpmaster.internal/ubuntu questing/universe arm64 dssp arm64 4.4.10-1 [753 kB] 482s Get:102 http://ftpmaster.internal/ubuntu questing/main arm64 libimagequant0 arm64 2.18.0-1build1 [37.1 kB] 482s Get:103 http://ftpmaster.internal/ubuntu questing/main arm64 libgraphite2-3 arm64 1.3.14-2ubuntu1 [70.6 kB] 482s Get:104 http://ftpmaster.internal/ubuntu questing/main arm64 libharfbuzz0b arm64 10.2.0-1 [490 kB] 482s Get:105 http://ftpmaster.internal/ubuntu questing/main arm64 libraqm0 arm64 0.10.2-1 [14.9 kB] 482s Get:106 http://ftpmaster.internal/ubuntu questing/main arm64 libxpm4 arm64 1:3.5.17-1build2 [35.1 kB] 482s Get:107 http://ftpmaster.internal/ubuntu questing/main arm64 libgd3 arm64 2.3.3-12ubuntu3 [122 kB] 482s Get:108 http://ftpmaster.internal/ubuntu questing/universe arm64 libhpdf-2.3.0 arm64 2.3.0+dfsg-1build3 [434 kB] 482s Get:109 http://ftpmaster.internal/ubuntu questing/main arm64 mysql-common all 5.8+1.1.1ubuntu1 [6922 B] 482s Get:110 http://ftpmaster.internal/ubuntu questing/main arm64 libmysqlclient24 arm64 8.4.4-0ubuntu2 [1243 kB] 482s Get:111 http://ftpmaster.internal/ubuntu questing/main arm64 libpq5 arm64 17.4-1 [142 kB] 482s Get:112 http://ftpmaster.internal/ubuntu questing/universe arm64 emboss-lib arm64 6.6.0+dfsg-15ubuntu2 [2891 kB] 482s Get:113 http://ftpmaster.internal/ubuntu questing/universe arm64 emboss-data all 6.6.0+dfsg-15ubuntu2 [61.0 MB] 487s Get:114 http://ftpmaster.internal/ubuntu questing/universe arm64 emboss arm64 6.6.0+dfsg-15ubuntu2 [937 kB] 487s Get:115 http://ftpmaster.internal/ubuntu questing/main arm64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB] 487s Get:116 http://ftpmaster.internal/ubuntu questing/universe arm64 fonts-lmodern all 2.005-1 [4799 kB] 487s Get:117 http://ftpmaster.internal/ubuntu questing/universe arm64 fonts-lyx all 2.4.3-1 [171 kB] 487s Get:118 http://ftpmaster.internal/ubuntu questing/main arm64 libgs-common all 10.05.0dfsg1-0ubuntu1 [176 kB] 487s Get:119 http://ftpmaster.internal/ubuntu questing/main arm64 libgs10-common all 10.05.0dfsg1-0ubuntu1 [490 kB] 487s Get:120 http://ftpmaster.internal/ubuntu questing/main arm64 libavahi-common-data arm64 0.8-16ubuntu2 [31.0 kB] 487s Get:121 http://ftpmaster.internal/ubuntu questing/main arm64 libavahi-common3 arm64 0.8-16ubuntu2 [22.9 kB] 487s Get:122 http://ftpmaster.internal/ubuntu questing/main arm64 libavahi-client3 arm64 0.8-16ubuntu2 [26.9 kB] 487s Get:123 http://ftpmaster.internal/ubuntu questing/main arm64 libcups2t64 arm64 2.4.12-0ubuntu1 [272 kB] 487s Get:124 http://ftpmaster.internal/ubuntu questing/main arm64 libidn12 arm64 1.43-1 [58.1 kB] 487s Get:125 http://ftpmaster.internal/ubuntu questing/main arm64 libijs-0.35 arm64 0.35-15.2 [15.4 kB] 487s Get:126 http://ftpmaster.internal/ubuntu questing/main arm64 libjbig2dec0 arm64 0.20-1build3 [63.2 kB] 487s Get:127 http://ftpmaster.internal/ubuntu questing/main arm64 libpaper2 arm64 2.2.5-0.3 [17.3 kB] 487s Get:128 http://ftpmaster.internal/ubuntu questing/main arm64 libice6 arm64 2:1.1.1-1 [42.3 kB] 487s Get:129 http://ftpmaster.internal/ubuntu questing/main arm64 libsm6 arm64 2:1.2.4-1 [16.4 kB] 487s Get:130 http://ftpmaster.internal/ubuntu questing/main arm64 libxt6t64 arm64 1:1.2.1-1.2build1 [168 kB] 487s Get:131 http://ftpmaster.internal/ubuntu questing/main arm64 libgs10 arm64 10.05.0dfsg1-0ubuntu1 [3638 kB] 487s Get:132 http://ftpmaster.internal/ubuntu questing/main arm64 ghostscript arm64 10.05.0dfsg1-0ubuntu1 [43.0 kB] 487s Get:133 http://ftpmaster.internal/ubuntu questing/universe arm64 libnetpbm11t64 arm64 2:11.09.02-2 [114 kB] 487s Get:134 http://ftpmaster.internal/ubuntu questing/universe arm64 netpbm arm64 2:11.09.02-2 [2130 kB] 488s Get:135 http://ftpmaster.internal/ubuntu questing/universe arm64 tex-common all 6.19 [29.8 kB] 488s Get:136 http://ftpmaster.internal/ubuntu questing/main arm64 libpaper-utils arm64 2.2.5-0.3 [15.4 kB] 488s Get:137 http://ftpmaster.internal/ubuntu questing/universe arm64 libkpathsea6 arm64 2024.20240313.70630+ds-6 [64.4 kB] 488s Get:138 http://ftpmaster.internal/ubuntu questing/universe arm64 libptexenc1 arm64 2024.20240313.70630+ds-6 [41.7 kB] 488s Get:139 http://ftpmaster.internal/ubuntu questing/universe arm64 libsynctex2 arm64 2024.20240313.70630+ds-6 [60.4 kB] 488s Get:140 http://ftpmaster.internal/ubuntu questing/universe arm64 libtexlua53-5 arm64 2024.20240313.70630+ds-6 [122 kB] 488s Get:141 http://ftpmaster.internal/ubuntu questing/main arm64 t1utils arm64 1.41-4build3 [61.0 kB] 488s Get:142 http://ftpmaster.internal/ubuntu questing/main arm64 libpixman-1-0 arm64 0.44.0-3 [197 kB] 488s Get:143 http://ftpmaster.internal/ubuntu questing/main arm64 libxcb-render0 arm64 1.17.0-2 [16.6 kB] 488s Get:144 http://ftpmaster.internal/ubuntu questing/main arm64 libxcb-shm0 arm64 1.17.0-2 [5884 B] 488s Get:145 http://ftpmaster.internal/ubuntu questing/main arm64 libcairo2 arm64 1.18.4-1 [560 kB] 488s Get:146 http://ftpmaster.internal/ubuntu questing/universe arm64 libmpfi0 arm64 1.5.4+ds-4 [35.3 kB] 488s Get:147 http://ftpmaster.internal/ubuntu questing/universe arm64 libpotrace0 arm64 1.16-2build1 [16.0 kB] 488s Get:148 http://ftpmaster.internal/ubuntu questing/universe arm64 libteckit0 arm64 2.5.12+ds1-1 [405 kB] 488s Get:149 http://ftpmaster.internal/ubuntu questing/main arm64 libxmu6 arm64 2:1.1.3-3build2 [47.5 kB] 488s Get:150 http://ftpmaster.internal/ubuntu questing/main arm64 libxaw7 arm64 2:1.0.16-1 [184 kB] 488s Get:151 http://ftpmaster.internal/ubuntu questing/main arm64 libxi6 arm64 2:1.8.2-1 [32.4 kB] 488s Get:152 http://ftpmaster.internal/ubuntu questing/universe arm64 libzzip-0-13t64 arm64 0.13.78+dfsg.1-0.1 [30.8 kB] 488s Get:153 http://ftpmaster.internal/ubuntu questing/universe arm64 texlive-binaries arm64 2024.20240313.70630+ds-6 [8349 kB] 488s Get:154 http://ftpmaster.internal/ubuntu questing/main arm64 xdg-utils all 1.2.1-2ubuntu1 [66.0 kB] 488s Get:155 http://ftpmaster.internal/ubuntu questing/universe arm64 texlive-base all 2024.20250309-1 [22.7 MB] 490s Get:156 http://ftpmaster.internal/ubuntu questing/main arm64 hicolor-icon-theme all 0.18-2 [13.3 kB] 490s Get:157 http://ftpmaster.internal/ubuntu questing/universe arm64 imagemagick-7.q16 arm64 8:7.1.1.43+dfsg1-1 [704 kB] 490s Get:158 http://ftpmaster.internal/ubuntu questing/universe arm64 imagemagick arm64 8:7.1.1.43+dfsg1-1 [14.1 kB] 490s Get:159 http://ftpmaster.internal/ubuntu questing/universe arm64 hevea arm64 2.36-2 [2333 kB] 490s Get:160 http://ftpmaster.internal/ubuntu questing/main arm64 libsuitesparseconfig7 arm64 1:7.8.3+dfsg-3 [13.2 kB] 490s Get:161 http://ftpmaster.internal/ubuntu questing/universe arm64 libamd3 arm64 1:7.8.3+dfsg-3 [26.1 kB] 490s Get:162 http://ftpmaster.internal/ubuntu questing/universe arm64 libapache-pom-java all 33-2 [5874 B] 490s Get:163 http://ftpmaster.internal/ubuntu questing/universe arm64 libarpack2t64 arm64 3.9.1-4 [94.4 kB] 490s Get:164 http://ftpmaster.internal/ubuntu questing/main arm64 libcolamd3 arm64 1:7.8.3+dfsg-3 [18.3 kB] 490s Get:165 http://ftpmaster.internal/ubuntu questing/universe arm64 libcommons-parent-java all 56-1 [10.7 kB] 490s Get:166 http://ftpmaster.internal/ubuntu questing/universe arm64 libcommons-logging-java all 1.3.0-1ubuntu1 [63.8 kB] 490s Get:167 http://ftpmaster.internal/ubuntu questing/main arm64 libexpat1-dev arm64 2.7.1-1 [128 kB] 490s Get:168 http://ftpmaster.internal/ubuntu questing/universe arm64 libglpk40 arm64 5.0-1build2 [337 kB] 490s Get:169 http://ftpmaster.internal/ubuntu questing/universe arm64 libplfit0 arm64 0.9.6+ds-2ubuntu1 [35.7 kB] 490s Get:170 http://ftpmaster.internal/ubuntu questing/universe arm64 libigraph3t64 arm64 0.10.15+ds-3 [895 kB] 490s Get:171 http://ftpmaster.internal/ubuntu questing/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 490s Get:172 http://ftpmaster.internal/ubuntu questing/universe arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 490s Get:173 http://ftpmaster.internal/ubuntu questing/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 490s Get:174 http://ftpmaster.internal/ubuntu questing/main arm64 libjs-sphinxdoc all 8.1.3-5 [31.0 kB] 490s Get:175 http://ftpmaster.internal/ubuntu questing/main arm64 libjson-perl all 4.10000-1 [81.9 kB] 490s Get:176 http://ftpmaster.internal/ubuntu questing/universe arm64 liblbfgsb0 arm64 3.0+dfsg.4-1build1 [27.7 kB] 490s Get:177 http://ftpmaster.internal/ubuntu questing/universe arm64 libmbedcrypto16 arm64 3.6.2-3ubuntu1 [258 kB] 490s Get:178 http://ftpmaster.internal/ubuntu questing/universe arm64 libmbedx509-7 arm64 3.6.2-3ubuntu1 [35.7 kB] 490s Get:179 http://ftpmaster.internal/ubuntu questing/universe arm64 libmbedtls21 arm64 3.6.2-3ubuntu1 [122 kB] 490s Get:180 http://ftpmaster.internal/ubuntu questing/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1ubuntu1 [894 kB] 491s Get:181 http://ftpmaster.internal/ubuntu questing/main arm64 libpython3.13-dev arm64 3.13.3-1 [5405 kB] 491s Get:182 http://ftpmaster.internal/ubuntu questing/main arm64 libpython3-dev arm64 3.13.3-1 [10.8 kB] 491s Get:183 http://ftpmaster.internal/ubuntu questing/main arm64 libpython3-all-dev arm64 3.13.3-1 [906 B] 491s Get:184 http://ftpmaster.internal/ubuntu questing/universe arm64 libqhull-r8.0 arm64 2020.2-6build1 [189 kB] 491s Get:185 http://ftpmaster.internal/ubuntu questing/main arm64 libxslt1.1 arm64 1.1.39-0exp1ubuntu4 [168 kB] 491s Get:186 http://ftpmaster.internal/ubuntu questing/universe arm64 mafft arm64 7.505-1 [756 kB] 491s Get:187 http://ftpmaster.internal/ubuntu questing/universe arm64 ncbi-data all 6.1.20170106+dfsg2-5 [3966 kB] 491s Get:188 http://ftpmaster.internal/ubuntu questing/universe arm64 ncbi-blast+ arm64 2.16.0+ds-6build1 [14.8 MB] 492s Get:189 http://ftpmaster.internal/ubuntu questing/universe arm64 phylip arm64 1:3.697+dfsg-4build1 [843 kB] 492s Get:190 http://ftpmaster.internal/ubuntu questing/universe arm64 prank arm64 0.0.170427+dfsg-3 [325 kB] 492s Get:191 http://ftpmaster.internal/ubuntu questing/universe arm64 preview-latex-style all 13.2-1 [347 kB] 492s Get:192 http://ftpmaster.internal/ubuntu questing/universe arm64 probcons arm64 1.12-14 [129 kB] 492s Get:193 http://ftpmaster.internal/ubuntu questing/universe arm64 python-biopython-doc all 1.85+dfsg-2build1 [18.2 MB] 494s Get:194 http://ftpmaster.internal/ubuntu questing/universe arm64 python-matplotlib-data all 3.8.3-7build1 [2934 kB] 494s Get:195 http://ftpmaster.internal/ubuntu questing/main arm64 python3-all arm64 3.13.3-1 [880 B] 494s Get:196 http://ftpmaster.internal/ubuntu questing/main arm64 python3.13-dev arm64 3.13.3-1 [508 kB] 494s Get:197 http://ftpmaster.internal/ubuntu questing/main arm64 python3-dev arm64 3.13.3-1 [26.7 kB] 494s Get:198 http://ftpmaster.internal/ubuntu questing/main arm64 python3-all-dev arm64 3.13.3-1 [904 B] 494s Get:199 http://ftpmaster.internal/ubuntu questing/main arm64 python3.13-tk arm64 3.13.3-1 [106 kB] 494s Get:200 http://ftpmaster.internal/ubuntu questing/main arm64 python3-tk arm64 3.13.3-1 [9856 B] 494s Get:201 http://ftpmaster.internal/ubuntu questing/universe arm64 python3-pil.imagetk arm64 11.1.0-5build1 [9892 B] 494s Get:202 http://ftpmaster.internal/ubuntu questing/main arm64 python3-pil arm64 11.1.0-5build1 [463 kB] 494s Get:203 http://ftpmaster.internal/ubuntu questing/main arm64 python3-cairo arm64 1.27.0-2 [122 kB] 494s Get:204 http://ftpmaster.internal/ubuntu questing/universe arm64 python3-freetype all 2.5.1-1 [92.3 kB] 494s Get:205 http://ftpmaster.internal/ubuntu questing/universe arm64 python3-rlpycairo all 0.3.0-3 [9130 B] 494s Get:206 http://ftpmaster.internal/ubuntu questing/universe arm64 python3-reportlab all 4.3.1-1 [1137 kB] 495s Get:207 http://ftpmaster.internal/ubuntu questing/universe arm64 w3c-sgml-lib all 1.3-3 [280 kB] 495s Get:208 http://ftpmaster.internal/ubuntu questing/universe arm64 python3-biopython arm64 1.85+dfsg-2build1 [1711 kB] 495s Get:209 http://ftpmaster.internal/ubuntu questing/universe arm64 python3-biopython-sql all 1.85+dfsg-2build1 [26.4 kB] 495s Get:210 http://ftpmaster.internal/ubuntu questing/universe arm64 python3-brotli arm64 1.1.0-2build4 [342 kB] 495s Get:211 http://ftpmaster.internal/ubuntu questing/universe arm64 python3-contourpy arm64 1.3.1-1build1 [182 kB] 495s Get:212 http://ftpmaster.internal/ubuntu questing/universe arm64 python3-cycler all 0.12.1-1 [9716 B] 495s Get:213 http://ftpmaster.internal/ubuntu questing/main arm64 python3-dateutil all 2.9.0-4 [80.3 kB] 495s Get:214 http://ftpmaster.internal/ubuntu questing/main arm64 python3-decorator all 5.1.1-5 [10.1 kB] 495s Get:215 http://ftpmaster.internal/ubuntu questing/main arm64 python3-defusedxml all 0.7.1-3 [42.2 kB] 495s Get:216 http://ftpmaster.internal/ubuntu questing/main arm64 python3-roman all 5.0-1 [10.3 kB] 495s Get:217 http://ftpmaster.internal/ubuntu questing/main arm64 python3-docutils all 0.21.2+dfsg-2 [409 kB] 495s Get:218 http://ftpmaster.internal/ubuntu questing/main arm64 python3-platformdirs all 4.3.6-1 [16.8 kB] 495s Get:219 http://ftpmaster.internal/ubuntu questing/universe arm64 python3-fs all 2.4.16-7 [90.8 kB] 495s Get:220 http://ftpmaster.internal/ubuntu questing/main arm64 python3-lxml arm64 5.3.2-1 [1258 kB] 495s Get:221 http://ftpmaster.internal/ubuntu questing/universe arm64 python3-lz4 arm64 4.4.0+dfsg-1build1 [27.1 kB] 495s Get:222 http://ftpmaster.internal/ubuntu questing/universe arm64 python3-scipy arm64 1.14.1-4ubuntu2 [16.7 MB] 495s Get:223 http://ftpmaster.internal/ubuntu questing/universe arm64 python3-mpmath all 1.3.0-1 [425 kB] 495s Get:224 http://ftpmaster.internal/ubuntu questing/universe arm64 python3-sympy all 1.13.3-5 [4229 kB] 496s Get:225 http://ftpmaster.internal/ubuntu questing/universe arm64 python3-ufolib2 all 0.17.0+dfsg1-1 [33.5 kB] 496s Get:226 http://ftpmaster.internal/ubuntu questing/universe arm64 unicode-data all 15.1.0-1 [8878 kB] 496s Get:227 http://ftpmaster.internal/ubuntu questing/universe arm64 python3-fonttools arm64 4.55.3-2build1 [1466 kB] 496s Get:228 http://ftpmaster.internal/ubuntu questing/main arm64 python3-imagesize all 1.4.1-1 [6844 B] 496s Get:229 http://ftpmaster.internal/ubuntu questing/universe arm64 python3-kiwisolver arm64 1.4.7-3build1 [50.7 kB] 496s Get:230 http://ftpmaster.internal/ubuntu questing/main arm64 python3-packaging all 24.2-1 [51.5 kB] 496s Get:231 http://ftpmaster.internal/ubuntu questing/universe arm64 python3-matplotlib arm64 3.8.3-7build1 [17.3 MB] 497s Get:232 http://ftpmaster.internal/ubuntu questing/main arm64 python3-msgpack arm64 1.0.3-3build4 [82.7 kB] 497s Get:233 http://ftpmaster.internal/ubuntu questing/universe arm64 python3-mmtf all 1.1.3-1 [16.2 kB] 497s Get:234 http://ftpmaster.internal/ubuntu questing/main arm64 python3-mysqldb arm64 1.4.6-2build6 [48.8 kB] 497s Get:235 http://ftpmaster.internal/ubuntu questing/main arm64 python3-networkx all 3.2.1-4ubuntu1 [11.5 MB] 498s Get:236 http://ftpmaster.internal/ubuntu questing/main arm64 sphinx-common all 8.1.3-5 [663 kB] 498s Get:237 http://ftpmaster.internal/ubuntu questing/main arm64 python3-alabaster all 0.7.16-0.1 [18.5 kB] 498s Get:238 http://ftpmaster.internal/ubuntu questing/main arm64 python3-snowballstemmer all 2.2.0-4build1 [59.8 kB] 498s Get:239 http://ftpmaster.internal/ubuntu questing/main arm64 python3-sphinx all 8.1.3-5 [474 kB] 498s Get:240 http://ftpmaster.internal/ubuntu questing/main arm64 python3-tabulate all 0.9.0-1 [45.3 kB] 498s Get:241 http://ftpmaster.internal/ubuntu questing/universe arm64 python3-numpydoc all 1.8.0-1 [52.4 kB] 498s Get:242 http://ftpmaster.internal/ubuntu questing/universe arm64 python3-rdflib all 7.1.1-2 [426 kB] 498s Get:243 http://ftpmaster.internal/ubuntu questing/main arm64 sphinx-rtd-theme-common all 3.0.2+dfsg-2 [1014 kB] 498s Get:244 http://ftpmaster.internal/ubuntu questing/universe arm64 python3-sphinxcontrib.jquery all 4.1-5 [6678 B] 498s Get:245 http://ftpmaster.internal/ubuntu questing/universe arm64 python3-sphinx-rtd-theme all 3.0.2+dfsg-2 [23.5 kB] 498s Get:246 http://ftpmaster.internal/ubuntu questing/universe arm64 python3-texttable all 1.7.0-1 [11.2 kB] 498s Get:247 http://ftpmaster.internal/ubuntu questing/universe arm64 t-coffee arm64 13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 [879 kB] 498s Get:248 http://ftpmaster.internal/ubuntu questing/universe arm64 texlive-fonts-recommended all 2024.20250309-1 [4974 kB] 498s Get:249 http://ftpmaster.internal/ubuntu questing/universe arm64 texlive-latex-base all 2024.20250309-1 [1276 kB] 498s Get:250 http://ftpmaster.internal/ubuntu questing/universe arm64 libfontbox-java all 1:1.8.16-5 [208 kB] 498s Get:251 http://ftpmaster.internal/ubuntu questing/universe arm64 libpdfbox-java all 1:1.8.16-5 [5521 kB] 498s Get:252 http://ftpmaster.internal/ubuntu questing/universe arm64 texlive-latex-recommended all 2024.20250309-1 [8727 kB] 499s Get:253 http://ftpmaster.internal/ubuntu questing/universe arm64 texlive-pictures all 2024.20250309-1 [17.0 MB] 499s Get:254 http://ftpmaster.internal/ubuntu questing/universe arm64 texlive-latex-extra all 2024.20250309-2 [24.8 MB] 501s Get:255 http://ftpmaster.internal/ubuntu questing/universe arm64 wise-data all 2.4.1-25 [83.0 kB] 501s Get:256 http://ftpmaster.internal/ubuntu questing/universe arm64 wise arm64 2.4.1-25 [802 kB] 501s Get:257 http://ftpmaster.internal/ubuntu questing/universe arm64 fasttree arm64 2.1.11-2 [164 kB] 501s Get:258 http://ftpmaster.internal/ubuntu questing/universe arm64 python3-igraph arm64 0.11.8+ds-1build1 [345 kB] 501s Preconfiguring packages ... 501s Fetched 406 MB in 25s (16.2 MB/s) 502s Selecting previously unselected package m4. 502s (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 ... 117834 files and directories currently installed.) 502s Preparing to unpack .../000-m4_1.4.19-7_arm64.deb ... 502s Unpacking m4 (1.4.19-7) ... 502s Selecting previously unselected package flex. 502s Preparing to unpack .../001-flex_2.6.4-8.2build1_arm64.deb ... 502s Unpacking flex (2.6.4-8.2build1) ... 502s Selecting previously unselected package fonts-lato. 502s Preparing to unpack .../002-fonts-lato_2.015-1_all.deb ... 502s Unpacking fonts-lato (2.015-1) ... 502s Selecting previously unselected package libgomp1:arm64. 502s Preparing to unpack .../003-libgomp1_15-20250404-0ubuntu1_arm64.deb ... 502s Unpacking libgomp1:arm64 (15-20250404-0ubuntu1) ... 502s Selecting previously unselected package libfftw3-double3:arm64. 502s Preparing to unpack .../004-libfftw3-double3_3.3.10-2fakesync1build1_arm64.deb ... 502s Unpacking libfftw3-double3:arm64 (3.3.10-2fakesync1build1) ... 502s Selecting previously unselected package fonts-dejavu-mono. 502s Preparing to unpack .../005-fonts-dejavu-mono_2.37-8_all.deb ... 502s Unpacking fonts-dejavu-mono (2.37-8) ... 502s Selecting previously unselected package fonts-dejavu-core. 502s Preparing to unpack .../006-fonts-dejavu-core_2.37-8_all.deb ... 502s Unpacking fonts-dejavu-core (2.37-8) ... 502s Selecting previously unselected package libfontenc1:arm64. 502s Preparing to unpack .../007-libfontenc1_1%3a1.1.8-1build1_arm64.deb ... 502s Unpacking libfontenc1:arm64 (1:1.1.8-1build1) ... 502s Selecting previously unselected package x11-common. 502s Preparing to unpack .../008-x11-common_1%3a7.7+23ubuntu4_all.deb ... 502s Unpacking x11-common (1:7.7+23ubuntu4) ... 502s Selecting previously unselected package xfonts-encodings. 502s Preparing to unpack .../009-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 502s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 502s Selecting previously unselected package xfonts-utils. 502s Preparing to unpack .../010-xfonts-utils_1%3a7.7+7_arm64.deb ... 502s Unpacking xfonts-utils (1:7.7+7) ... 502s Selecting previously unselected package fonts-urw-base35. 502s Preparing to unpack .../011-fonts-urw-base35_20200910-8_all.deb ... 503s Unpacking fonts-urw-base35 (20200910-8) ... 503s Selecting previously unselected package fontconfig-config. 503s Preparing to unpack .../012-fontconfig-config_2.15.0-2.2ubuntu1_arm64.deb ... 503s Unpacking fontconfig-config (2.15.0-2.2ubuntu1) ... 503s Selecting previously unselected package libfontconfig1:arm64. 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liblcms2-2:arm64 (2.16-2) ... 504s Selecting previously unselected package liblqr-1-0:arm64. 504s Preparing to unpack .../024-liblqr-1-0_0.4.2-2.1build2_arm64.deb ... 504s Unpacking liblqr-1-0:arm64 (0.4.2-2.1build2) ... 504s Selecting previously unselected package libltdl7:arm64. 504s Preparing to unpack .../025-libltdl7_2.5.4-4_arm64.deb ... 504s Unpacking libltdl7:arm64 (2.5.4-4) ... 504s Selecting previously unselected package libopenjp2-7:arm64. 504s Preparing to unpack .../026-libopenjp2-7_2.5.3-2_arm64.deb ... 504s Unpacking libopenjp2-7:arm64 (2.5.3-2) ... 504s Selecting previously unselected package libraw23t64:arm64. 504s Preparing to unpack .../027-libraw23t64_0.21.3-1_arm64.deb ... 504s Unpacking libraw23t64:arm64 (0.21.3-1) ... 504s Selecting previously unselected package libdeflate0:arm64. 504s Preparing to unpack .../028-libdeflate0_1.23-1_arm64.deb ... 504s Unpacking libdeflate0:arm64 (1.23-1) ... 504s Selecting previously unselected package liblerc4:arm64. 504s Preparing to unpack .../029-liblerc4_4.0.0+ds-5ubuntu1_arm64.deb ... 504s Unpacking liblerc4:arm64 (4.0.0+ds-5ubuntu1) ... 504s Selecting previously unselected package libwebp7:arm64. 504s Preparing to unpack .../030-libwebp7_1.5.0-0.1_arm64.deb ... 504s Unpacking libwebp7:arm64 (1.5.0-0.1) ... 504s Selecting previously unselected package libtiff6:arm64. 504s Preparing to unpack .../031-libtiff6_4.5.1+git230720-4ubuntu4_arm64.deb ... 504s Unpacking libtiff6:arm64 (4.5.1+git230720-4ubuntu4) ... 504s Selecting previously unselected package libwebpdemux2:arm64. 504s Preparing to unpack .../032-libwebpdemux2_1.5.0-0.1_arm64.deb ... 504s Unpacking libwebpdemux2:arm64 (1.5.0-0.1) ... 504s Selecting previously unselected package libwebpmux3:arm64. 504s Preparing to unpack .../033-libwebpmux3_1.5.0-0.1_arm64.deb ... 504s Unpacking libwebpmux3:arm64 (1.5.0-0.1) ... 504s Selecting previously unselected package imagemagick-7-common. 504s Preparing to unpack .../034-imagemagick-7-common_8%3a7.1.1.43+dfsg1-1_all.deb ... 504s Unpacking imagemagick-7-common (8:7.1.1.43+dfsg1-1) ... 504s Selecting previously unselected package libmagickcore-7.q16-10:arm64. 504s Preparing to unpack .../035-libmagickcore-7.q16-10_8%3a7.1.1.43+dfsg1-1_arm64.deb ... 504s Unpacking libmagickcore-7.q16-10:arm64 (8:7.1.1.43+dfsg1-1) ... 505s Selecting previously unselected package libmagickwand-7.q16-10:arm64. 505s Preparing to unpack .../036-libmagickwand-7.q16-10_8%3a7.1.1.43+dfsg1-1_arm64.deb ... 505s Unpacking libmagickwand-7.q16-10:arm64 (8:7.1.1.43+dfsg1-1) ... 505s Selecting previously unselected package poppler-data. 505s Preparing to unpack .../037-poppler-data_0.4.12-1_all.deb ... 505s Unpacking poppler-data (0.4.12-1) ... 505s Selecting previously unselected package python3-numpy-dev:arm64. 505s Preparing to unpack .../038-python3-numpy-dev_1%3a2.2.3+ds-5_arm64.deb ... 505s Unpacking python3-numpy-dev:arm64 (1:2.2.3+ds-5) ... 505s Selecting previously unselected package libblas3:arm64. 505s Preparing to unpack .../039-libblas3_3.12.1-2_arm64.deb ... 505s Unpacking libblas3:arm64 (3.12.1-2) ... 505s Selecting previously unselected package libgfortran5:arm64. 505s Preparing to unpack .../040-libgfortran5_15-20250404-0ubuntu1_arm64.deb ... 505s Unpacking libgfortran5:arm64 (15-20250404-0ubuntu1) ... 505s Selecting previously unselected package liblapack3:arm64. 505s Preparing to unpack .../041-liblapack3_3.12.1-2_arm64.deb ... 505s Unpacking liblapack3:arm64 (3.12.1-2) ... 505s Selecting previously unselected package python3-numpy. 505s Preparing to unpack .../042-python3-numpy_1%3a2.2.3+ds-5_arm64.deb ... 505s Unpacking python3-numpy (1:2.2.3+ds-5) ... 505s Selecting previously unselected package sgml-base. 505s Preparing to unpack .../043-sgml-base_1.31_all.deb ... 505s Unpacking sgml-base (1.31) ... 505s Selecting previously unselected package autoconf. 505s Preparing to unpack .../044-autoconf_2.72-3ubuntu1_all.deb ... 505s 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unselected package libmpc3:arm64. 506s Preparing to unpack .../056-libmpc3_1.3.1-1build2_arm64.deb ... 506s Unpacking libmpc3:arm64 (1.3.1-1build2) ... 506s Selecting previously unselected package cpp-14-aarch64-linux-gnu. 506s Preparing to unpack .../057-cpp-14-aarch64-linux-gnu_14.2.0-19ubuntu2_arm64.deb ... 506s Unpacking cpp-14-aarch64-linux-gnu (14.2.0-19ubuntu2) ... 506s Selecting previously unselected package cpp-14. 506s Preparing to unpack .../058-cpp-14_14.2.0-19ubuntu2_arm64.deb ... 506s Unpacking cpp-14 (14.2.0-19ubuntu2) ... 506s Selecting previously unselected package cpp-aarch64-linux-gnu. 506s Preparing to unpack .../059-cpp-aarch64-linux-gnu_4%3a14.2.0-1ubuntu1_arm64.deb ... 506s Unpacking cpp-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 506s Selecting previously unselected package cpp. 506s Preparing to unpack .../060-cpp_4%3a14.2.0-1ubuntu1_arm64.deb ... 506s Unpacking cpp (4:14.2.0-1ubuntu1) ... 506s Selecting previously unselected package libcc1-0:arm64. 506s 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package libdebhelper-perl. 509s Preparing to unpack .../082-libdebhelper-perl_13.24.1ubuntu2_all.deb ... 509s Unpacking libdebhelper-perl (13.24.1ubuntu2) ... 509s Selecting previously unselected package libtool. 509s Preparing to unpack .../083-libtool_2.5.4-4_all.deb ... 509s Unpacking libtool (2.5.4-4) ... 509s Selecting previously unselected package dh-autoreconf. 509s Preparing to unpack .../084-dh-autoreconf_20_all.deb ... 509s Unpacking dh-autoreconf (20) ... 509s Selecting previously unselected package libarchive-zip-perl. 509s Preparing to unpack .../085-libarchive-zip-perl_1.68-1_all.deb ... 509s Unpacking libarchive-zip-perl (1.68-1) ... 509s Selecting previously unselected package libfile-stripnondeterminism-perl. 509s Preparing to unpack .../086-libfile-stripnondeterminism-perl_1.14.1-2_all.deb ... 509s Unpacking libfile-stripnondeterminism-perl (1.14.1-2) ... 509s Selecting previously unselected package dh-strip-nondeterminism. 509s Preparing to unpack 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libcifpp7:arm64. 510s Preparing to unpack .../099-libcifpp7_7.0.9-1_arm64.deb ... 510s Unpacking libcifpp7:arm64 (7.0.9-1) ... 510s Selecting previously unselected package dssp. 510s Preparing to unpack .../100-dssp_4.4.10-1_arm64.deb ... 510s Unpacking dssp (4.4.10-1) ... 510s Selecting previously unselected package libimagequant0:arm64. 510s Preparing to unpack .../101-libimagequant0_2.18.0-1build1_arm64.deb ... 510s Unpacking libimagequant0:arm64 (2.18.0-1build1) ... 510s Selecting previously unselected package libgraphite2-3:arm64. 510s Preparing to unpack .../102-libgraphite2-3_1.3.14-2ubuntu1_arm64.deb ... 510s Unpacking libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 510s Selecting previously unselected package libharfbuzz0b:arm64. 510s Preparing to unpack .../103-libharfbuzz0b_10.2.0-1_arm64.deb ... 510s Unpacking libharfbuzz0b:arm64 (10.2.0-1) ... 510s Selecting previously unselected package libraqm0:arm64. 510s Preparing to unpack .../104-libraqm0_0.10.2-1_arm64.deb ... 510s Unpacking libraqm0:arm64 (0.10.2-1) ... 510s Selecting previously unselected package libxpm4:arm64. 510s Preparing to unpack .../105-libxpm4_1%3a3.5.17-1build2_arm64.deb ... 510s Unpacking libxpm4:arm64 (1:3.5.17-1build2) ... 510s Selecting previously unselected package libgd3:arm64. 510s Preparing to unpack .../106-libgd3_2.3.3-12ubuntu3_arm64.deb ... 510s Unpacking libgd3:arm64 (2.3.3-12ubuntu3) ... 510s Selecting previously unselected package libhpdf-2.3.0:arm64. 510s Preparing to unpack .../107-libhpdf-2.3.0_2.3.0+dfsg-1build3_arm64.deb ... 510s Unpacking libhpdf-2.3.0:arm64 (2.3.0+dfsg-1build3) ... 510s Selecting previously unselected package mysql-common. 510s Preparing to unpack .../108-mysql-common_5.8+1.1.1ubuntu1_all.deb ... 510s Unpacking mysql-common (5.8+1.1.1ubuntu1) ... 510s Selecting previously unselected package libmysqlclient24:arm64. 510s Preparing to unpack .../109-libmysqlclient24_8.4.4-0ubuntu2_arm64.deb ... 510s Unpacking libmysqlclient24:arm64 (8.4.4-0ubuntu2) ... 510s Selecting previously unselected package libpq5:arm64. 510s Preparing to unpack .../110-libpq5_17.4-1_arm64.deb ... 510s Unpacking libpq5:arm64 (17.4-1) ... 510s Selecting previously unselected package emboss-lib. 510s Preparing to unpack .../111-emboss-lib_6.6.0+dfsg-15ubuntu2_arm64.deb ... 510s Unpacking emboss-lib (6.6.0+dfsg-15ubuntu2) ... 511s Selecting previously unselected package emboss-data. 511s Preparing to unpack .../112-emboss-data_6.6.0+dfsg-15ubuntu2_all.deb ... 511s Unpacking emboss-data (6.6.0+dfsg-15ubuntu2) ... 514s Selecting previously unselected package emboss. 514s Preparing to unpack .../113-emboss_6.6.0+dfsg-15ubuntu2_arm64.deb ... 514s Unpacking emboss (6.6.0+dfsg-15ubuntu2) ... 514s Selecting previously unselected package fonts-font-awesome. 514s Preparing to unpack .../114-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ... 514s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 514s Selecting previously unselected package fonts-lmodern. 514s Preparing to unpack .../115-fonts-lmodern_2.005-1_all.deb ... 514s Unpacking fonts-lmodern (2.005-1) ... 514s Selecting previously unselected package fonts-lyx. 514s Preparing to unpack .../116-fonts-lyx_2.4.3-1_all.deb ... 514s Unpacking fonts-lyx (2.4.3-1) ... 514s Selecting previously unselected package libgs-common. 514s Preparing to unpack .../117-libgs-common_10.05.0dfsg1-0ubuntu1_all.deb ... 514s Unpacking libgs-common (10.05.0dfsg1-0ubuntu1) ... 514s Selecting previously unselected package libgs10-common. 514s Preparing to unpack .../118-libgs10-common_10.05.0dfsg1-0ubuntu1_all.deb ... 514s Unpacking libgs10-common (10.05.0dfsg1-0ubuntu1) ... 514s Selecting previously unselected package libavahi-common-data:arm64. 514s Preparing to unpack .../119-libavahi-common-data_0.8-16ubuntu2_arm64.deb ... 514s Unpacking libavahi-common-data:arm64 (0.8-16ubuntu2) ... 514s Selecting previously unselected package libavahi-common3:arm64. 514s Preparing to unpack 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515s Unpacking libjbig2dec0:arm64 (0.20-1build3) ... 515s Selecting previously unselected package libpaper2:arm64. 515s Preparing to unpack .../126-libpaper2_2.2.5-0.3_arm64.deb ... 515s Unpacking libpaper2:arm64 (2.2.5-0.3) ... 515s Selecting previously unselected package libice6:arm64. 515s Preparing to unpack .../127-libice6_2%3a1.1.1-1_arm64.deb ... 515s Unpacking libice6:arm64 (2:1.1.1-1) ... 515s Selecting previously unselected package libsm6:arm64. 515s Preparing to unpack .../128-libsm6_2%3a1.2.4-1_arm64.deb ... 515s Unpacking libsm6:arm64 (2:1.2.4-1) ... 515s Selecting previously unselected package libxt6t64:arm64. 515s Preparing to unpack .../129-libxt6t64_1%3a1.2.1-1.2build1_arm64.deb ... 515s Unpacking libxt6t64:arm64 (1:1.2.1-1.2build1) ... 515s Selecting previously unselected package libgs10:arm64. 515s Preparing to unpack .../130-libgs10_10.05.0dfsg1-0ubuntu1_arm64.deb ... 515s Unpacking libgs10:arm64 (10.05.0dfsg1-0ubuntu1) ... 515s Selecting previously unselected package ghostscript. 515s Preparing to unpack .../131-ghostscript_10.05.0dfsg1-0ubuntu1_arm64.deb ... 515s Unpacking ghostscript (10.05.0dfsg1-0ubuntu1) ... 515s Selecting previously unselected package libnetpbm11t64:arm64. 515s Preparing to unpack .../132-libnetpbm11t64_2%3a11.09.02-2_arm64.deb ... 515s Unpacking libnetpbm11t64:arm64 (2:11.09.02-2) ... 515s Selecting previously unselected package netpbm. 515s Preparing to unpack .../133-netpbm_2%3a11.09.02-2_arm64.deb ... 515s Unpacking netpbm (2:11.09.02-2) ... 515s Selecting previously unselected package tex-common. 515s Preparing to unpack .../134-tex-common_6.19_all.deb ... 515s Unpacking tex-common (6.19) ... 516s Selecting previously unselected package libpaper-utils. 516s Preparing to unpack .../135-libpaper-utils_2.2.5-0.3_arm64.deb ... 516s Unpacking libpaper-utils (2.2.5-0.3) ... 516s Selecting previously unselected package libkpathsea6:arm64. 516s Preparing to unpack .../136-libkpathsea6_2024.20240313.70630+ds-6_arm64.deb 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516s Selecting previously unselected package libteckit0:arm64. 516s Preparing to unpack .../147-libteckit0_2.5.12+ds1-1_arm64.deb ... 516s Unpacking libteckit0:arm64 (2.5.12+ds1-1) ... 516s Selecting previously unselected package libxmu6:arm64. 516s Preparing to unpack .../148-libxmu6_2%3a1.1.3-3build2_arm64.deb ... 516s Unpacking libxmu6:arm64 (2:1.1.3-3build2) ... 516s Selecting previously unselected package libxaw7:arm64. 516s Preparing to unpack .../149-libxaw7_2%3a1.0.16-1_arm64.deb ... 516s Unpacking libxaw7:arm64 (2:1.0.16-1) ... 516s Selecting previously unselected package libxi6:arm64. 516s Preparing to unpack .../150-libxi6_2%3a1.8.2-1_arm64.deb ... 516s Unpacking libxi6:arm64 (2:1.8.2-1) ... 516s Selecting previously unselected package libzzip-0-13t64:arm64. 516s Preparing to unpack .../151-libzzip-0-13t64_0.13.78+dfsg.1-0.1_arm64.deb ... 516s Unpacking libzzip-0-13t64:arm64 (0.13.78+dfsg.1-0.1) ... 516s Selecting previously unselected package texlive-binaries. 516s 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libarpack2t64:arm64 (3.9.1-4) ... 518s Selecting previously unselected package libcolamd3:arm64. 518s Preparing to unpack .../163-libcolamd3_1%3a7.8.3+dfsg-3_arm64.deb ... 518s Unpacking libcolamd3:arm64 (1:7.8.3+dfsg-3) ... 518s Selecting previously unselected package libcommons-parent-java. 518s Preparing to unpack .../164-libcommons-parent-java_56-1_all.deb ... 518s Unpacking libcommons-parent-java (56-1) ... 518s Selecting previously unselected package libcommons-logging-java. 518s Preparing to unpack .../165-libcommons-logging-java_1.3.0-1ubuntu1_all.deb ... 518s Unpacking libcommons-logging-java (1.3.0-1ubuntu1) ... 518s Selecting previously unselected package libexpat1-dev:arm64. 518s Preparing to unpack .../166-libexpat1-dev_2.7.1-1_arm64.deb ... 518s Unpacking libexpat1-dev:arm64 (2.7.1-1) ... 519s Selecting previously unselected package libglpk40:arm64. 519s Preparing to unpack .../167-libglpk40_5.0-1build2_arm64.deb ... 519s Unpacking libglpk40:arm64 (5.0-1build2) ... 519s Selecting previously unselected package libplfit0:arm64. 519s Preparing to unpack .../168-libplfit0_0.9.6+ds-2ubuntu1_arm64.deb ... 519s Unpacking libplfit0:arm64 (0.9.6+ds-2ubuntu1) ... 519s Selecting previously unselected package libigraph3t64:arm64. 519s Preparing to unpack .../169-libigraph3t64_0.10.15+ds-3_arm64.deb ... 519s Unpacking libigraph3t64:arm64 (0.10.15+ds-3) ... 519s Selecting previously unselected package libjs-jquery. 519s Preparing to unpack .../170-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 519s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 519s Selecting previously unselected package libjs-jquery-ui. 519s Preparing to unpack .../171-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... 519s Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... 519s Selecting previously unselected package libjs-underscore. 519s Preparing to unpack .../172-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 519s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 519s Selecting previously unselected package libjs-sphinxdoc. 519s Preparing to unpack .../173-libjs-sphinxdoc_8.1.3-5_all.deb ... 519s Unpacking libjs-sphinxdoc (8.1.3-5) ... 519s Selecting previously unselected package libjson-perl. 519s Preparing to unpack .../174-libjson-perl_4.10000-1_all.deb ... 519s Unpacking libjson-perl (4.10000-1) ... 519s Selecting previously unselected package liblbfgsb0:arm64. 519s Preparing to unpack .../175-liblbfgsb0_3.0+dfsg.4-1build1_arm64.deb ... 519s Unpacking liblbfgsb0:arm64 (3.0+dfsg.4-1build1) ... 519s Selecting previously unselected package libmbedcrypto16:arm64. 519s Preparing to unpack .../176-libmbedcrypto16_3.6.2-3ubuntu1_arm64.deb ... 519s Unpacking libmbedcrypto16:arm64 (3.6.2-3ubuntu1) ... 519s Selecting previously unselected package libmbedx509-7:arm64. 519s Preparing to unpack .../177-libmbedx509-7_3.6.2-3ubuntu1_arm64.deb ... 519s Unpacking libmbedx509-7:arm64 (3.6.2-3ubuntu1) ... 519s Selecting previously unselected package libmbedtls21:arm64. 519s Preparing to unpack .../178-libmbedtls21_3.6.2-3ubuntu1_arm64.deb ... 519s Unpacking libmbedtls21:arm64 (3.6.2-3ubuntu1) ... 519s Selecting previously unselected package zlib1g-dev:arm64. 519s Preparing to unpack .../179-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1ubuntu1_arm64.deb ... 519s Unpacking zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 519s Selecting previously unselected package libpython3.13-dev:arm64. 519s Preparing to unpack .../180-libpython3.13-dev_3.13.3-1_arm64.deb ... 519s Unpacking libpython3.13-dev:arm64 (3.13.3-1) ... 519s Selecting previously unselected package libpython3-dev:arm64. 519s Preparing to unpack .../181-libpython3-dev_3.13.3-1_arm64.deb ... 519s Unpacking libpython3-dev:arm64 (3.13.3-1) ... 520s Selecting previously unselected package libpython3-all-dev:arm64. 520s Preparing to unpack .../182-libpython3-all-dev_3.13.3-1_arm64.deb ... 520s Unpacking libpython3-all-dev:arm64 (3.13.3-1) ... 520s Selecting previously unselected package libqhull-r8.0:arm64. 520s 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(1:3.697+dfsg-4build1) ... 520s Selecting previously unselected package prank. 520s Preparing to unpack .../189-prank_0.0.170427+dfsg-3_arm64.deb ... 520s Unpacking prank (0.0.170427+dfsg-3) ... 520s Selecting previously unselected package preview-latex-style. 520s Preparing to unpack .../190-preview-latex-style_13.2-1_all.deb ... 520s Unpacking preview-latex-style (13.2-1) ... 520s Selecting previously unselected package probcons. 521s Preparing to unpack .../191-probcons_1.12-14_arm64.deb ... 521s Unpacking probcons (1.12-14) ... 521s Selecting previously unselected package python-biopython-doc. 521s Preparing to unpack .../192-python-biopython-doc_1.85+dfsg-2build1_all.deb ... 521s Unpacking python-biopython-doc (1.85+dfsg-2build1) ... 521s Selecting previously unselected package python-matplotlib-data. 521s Preparing to unpack .../193-python-matplotlib-data_3.8.3-7build1_all.deb ... 521s Unpacking python-matplotlib-data (3.8.3-7build1) ... 521s Selecting previously unselected package python3-all. 521s Preparing to unpack .../194-python3-all_3.13.3-1_arm64.deb ... 521s Unpacking python3-all (3.13.3-1) ... 521s Selecting previously unselected package python3.13-dev. 521s Preparing to unpack .../195-python3.13-dev_3.13.3-1_arm64.deb ... 521s Unpacking python3.13-dev (3.13.3-1) ... 521s Selecting previously unselected package python3-dev. 521s Preparing to unpack .../196-python3-dev_3.13.3-1_arm64.deb ... 521s Unpacking python3-dev (3.13.3-1) ... 521s Selecting previously unselected package python3-all-dev. 521s Preparing to unpack .../197-python3-all-dev_3.13.3-1_arm64.deb ... 521s Unpacking python3-all-dev (3.13.3-1) ... 521s Selecting previously unselected package python3.13-tk. 521s Preparing to unpack .../198-python3.13-tk_3.13.3-1_arm64.deb ... 521s Unpacking python3.13-tk (3.13.3-1) ... 521s Selecting previously unselected package python3-tk:arm64. 521s Preparing to unpack .../199-python3-tk_3.13.3-1_arm64.deb ... 521s Unpacking python3-tk:arm64 (3.13.3-1) ... 521s Selecting previously unselected package python3-pil.imagetk:arm64. 521s Preparing to unpack .../200-python3-pil.imagetk_11.1.0-5build1_arm64.deb ... 521s Unpacking python3-pil.imagetk:arm64 (11.1.0-5build1) ... 521s Selecting previously unselected package python3-pil:arm64. 521s Preparing to unpack .../201-python3-pil_11.1.0-5build1_arm64.deb ... 521s Unpacking python3-pil:arm64 (11.1.0-5build1) ... 521s Selecting previously unselected package python3-cairo. 521s Preparing to unpack .../202-python3-cairo_1.27.0-2_arm64.deb ... 521s Unpacking python3-cairo (1.27.0-2) ... 521s Selecting previously unselected package python3-freetype. 521s Preparing to unpack .../203-python3-freetype_2.5.1-1_all.deb ... 521s Unpacking python3-freetype (2.5.1-1) ... 521s Selecting previously unselected package python3-rlpycairo. 521s Preparing to unpack .../204-python3-rlpycairo_0.3.0-3_all.deb ... 521s Unpacking python3-rlpycairo (0.3.0-3) ... 521s Selecting previously unselected package python3-reportlab. 521s Preparing to unpack .../205-python3-reportlab_4.3.1-1_all.deb ... 521s Unpacking python3-reportlab (4.3.1-1) ... 521s Selecting previously unselected package w3c-sgml-lib. 522s Preparing to unpack .../206-w3c-sgml-lib_1.3-3_all.deb ... 522s Unpacking w3c-sgml-lib (1.3-3) ... 522s Selecting previously unselected package python3-biopython. 522s Preparing to unpack .../207-python3-biopython_1.85+dfsg-2build1_arm64.deb ... 522s Unpacking python3-biopython (1.85+dfsg-2build1) ... 522s Selecting previously unselected package python3-biopython-sql. 522s Preparing to unpack .../208-python3-biopython-sql_1.85+dfsg-2build1_all.deb ... 522s Unpacking python3-biopython-sql (1.85+dfsg-2build1) ... 522s Selecting previously unselected package python3-brotli. 522s Preparing to unpack .../209-python3-brotli_1.1.0-2build4_arm64.deb ... 522s Unpacking python3-brotli (1.1.0-2build4) ... 522s Selecting previously unselected package python3-contourpy. 522s Preparing to unpack .../210-python3-contourpy_1.3.1-1build1_arm64.deb ... 522s Unpacking python3-contourpy (1.3.1-1build1) ... 522s Selecting previously unselected package python3-cycler. 522s Preparing to unpack .../211-python3-cycler_0.12.1-1_all.deb ... 522s Unpacking python3-cycler (0.12.1-1) ... 522s Selecting previously unselected package python3-dateutil. 522s Preparing to unpack .../212-python3-dateutil_2.9.0-4_all.deb ... 522s Unpacking python3-dateutil (2.9.0-4) ... 522s Selecting previously unselected package python3-decorator. 522s Preparing to unpack .../213-python3-decorator_5.1.1-5_all.deb ... 522s Unpacking python3-decorator (5.1.1-5) ... 522s Selecting previously unselected package python3-defusedxml. 522s Preparing to unpack .../214-python3-defusedxml_0.7.1-3_all.deb ... 522s Unpacking python3-defusedxml (0.7.1-3) ... 522s Selecting previously unselected package python3-roman. 522s Preparing to unpack .../215-python3-roman_5.0-1_all.deb ... 522s Unpacking python3-roman (5.0-1) ... 522s Selecting previously unselected package python3-docutils. 522s Preparing to unpack .../216-python3-docutils_0.21.2+dfsg-2_all.deb ... 522s Unpacking python3-docutils (0.21.2+dfsg-2) ... 522s Selecting previously unselected package python3-platformdirs. 522s Preparing to unpack .../217-python3-platformdirs_4.3.6-1_all.deb ... 522s Unpacking python3-platformdirs (4.3.6-1) ... 522s Selecting previously unselected package python3-fs. 522s Preparing to unpack .../218-python3-fs_2.4.16-7_all.deb ... 522s Unpacking python3-fs (2.4.16-7) ... 522s Selecting previously unselected package python3-lxml:arm64. 522s Preparing to unpack .../219-python3-lxml_5.3.2-1_arm64.deb ... 522s Unpacking python3-lxml:arm64 (5.3.2-1) ... 522s Selecting previously unselected package python3-lz4. 522s Preparing to unpack .../220-python3-lz4_4.4.0+dfsg-1build1_arm64.deb ... 522s Unpacking python3-lz4 (4.4.0+dfsg-1build1) ... 522s Selecting previously unselected package python3-scipy. 522s Preparing to unpack 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python3-mmtf. 524s Preparing to unpack .../232-python3-mmtf_1.1.3-1_all.deb ... 524s Unpacking python3-mmtf (1.1.3-1) ... 524s Selecting previously unselected package python3-mysqldb. 524s Preparing to unpack .../233-python3-mysqldb_1.4.6-2build6_arm64.deb ... 524s Unpacking python3-mysqldb (1.4.6-2build6) ... 524s Selecting previously unselected package python3-networkx. 524s Preparing to unpack .../234-python3-networkx_3.2.1-4ubuntu1_all.deb ... 524s Unpacking python3-networkx (3.2.1-4ubuntu1) ... 525s Selecting previously unselected package sphinx-common. 525s Preparing to unpack .../235-sphinx-common_8.1.3-5_all.deb ... 525s Unpacking sphinx-common (8.1.3-5) ... 525s Selecting previously unselected package python3-alabaster. 525s Preparing to unpack .../236-python3-alabaster_0.7.16-0.1_all.deb ... 525s Unpacking python3-alabaster (0.7.16-0.1) ... 525s Selecting previously unselected package python3-snowballstemmer. 525s Preparing to unpack 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libpdfbox-java (1:1.8.16-5) ... 541s Setting up libcolamd3:arm64 (1:7.8.3+dfsg-3) ... 541s Setting up fontconfig-config (2.15.0-2.2ubuntu1) ... 541s Setting up wise (2.4.1-25) ... 541s Setting up preview-latex-style (13.2-1) ... 541s Setting up libwebpdemux2:arm64 (1.5.0-0.1) ... 541s Setting up libcommons-parent-java (56-1) ... 541s Setting up libavahi-common3:arm64 (0.8-16ubuntu2) ... 541s Setting up libcommons-logging-java (1.3.0-1ubuntu1) ... 541s Setting up libcifpp7:arm64 (7.0.9-1) ... 541s Setting up libpaper-utils (2.2.5-0.3) ... 541s Setting up clustalo (1.2.4-8build1) ... 541s Setting up dssp (4.4.10-1) ... 541s Setting up xfonts-utils (1:7.7+7) ... 541s Setting up intltool-debian (0.35.0+20060710.6) ... 541s Setting up libmbedx509-7:arm64 (3.6.2-3ubuntu1) ... 541s Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... 541s Setting up libptexenc1:arm64 (2024.20240313.70630+ds-6) ... 541s Setting up libglpk40:arm64 (5.0-1build2) ... 541s Setting up libraqm0:arm64 (0.10.2-1) ... 541s Setting up libpython3.13-dev:arm64 (3.13.3-1) ... 541s Setting up python3-numpy (1:2.2.3+ds-5) ... 542s Setting up libjs-sphinxdoc (8.1.3-5) ... 542s Setting up libraw23t64:arm64 (0.21.3-1) ... 542s Setting up libmbedtls21:arm64 (3.6.2-3ubuntu1) ... 543s Setting up dh-strip-nondeterminism (1.14.1-2) ... 543s Setting up cpp-14-aarch64-linux-gnu (14.2.0-19ubuntu2) ... 543s Setting up python3-lxml:arm64 (5.3.2-1) ... 543s Setting up python-biopython-doc (1.85+dfsg-2build1) ... 543s Setting up libtiff6:arm64 (4.5.1+git230720-4ubuntu4) ... 543s Setting up xml-core (0.19) ... 543s Setting up python3-contourpy (1.3.1-1build1) ... 543s Setting up libfontconfig1:arm64 (2.15.0-2.2ubuntu1) ... 543s Setting up libgcc-14-dev:arm64 (14.2.0-19ubuntu2) ... 543s Setting up libigraph3t64:arm64 (0.10.15+ds-3) ... 543s Setting up libstdc++-14-dev:arm64 (14.2.0-19ubuntu2) ... 543s Setting up libsm6:arm64 (2:1.2.4-1) ... 543s Setting up libavahi-client3:arm64 (0.8-16ubuntu2) ... 543s Setting up liblbfgsb0:arm64 (3.0+dfsg.4-1build1) ... 543s Setting up libxft2:arm64 (2.3.6-1build1) ... 543s Setting up python3-scipy (1.14.1-4ubuntu2) ... 546s Setting up libpython3-dev:arm64 (3.13.3-1) ... 546s Setting up python3.13-dev (3.13.3-1) ... 546s Setting up po-debconf (1.0.21+nmu1) ... 546s Setting up libtk8.6:arm64 (8.6.16-1) ... 546s Setting up python3-mmtf (1.1.3-1) ... 546s Setting up fonts-urw-base35 (20200910-8) ... 546s Setting up libcairo2:arm64 (1.18.4-1) ... 546s Setting up python3.13-tk (3.13.3-1) ... 547s Setting up ncbi-blast+ (2.16.0+ds-6build1) ... 547s Setting up python3-pil:arm64 (11.1.0-5build1) ... 547s Setting up cpp-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 547s Setting up libpython3-all-dev:arm64 (3.13.3-1) ... 547s Setting up sphinx-common (8.1.3-5) ... 547s Setting up python3-dev (3.13.3-1) ... 547s Setting up libxt6t64:arm64 (1:1.2.1-1.2build1) ... 547s Setting up netpbm (2:11.09.02-2) ... 547s Setting up cpp-14 (14.2.0-19ubuntu2) ... 547s Setting up python3-igraph (0.11.8+ds-1build1) ... 547s Setting up cpp (4:14.2.0-1ubuntu1) ... 547s Setting up gcc-14-aarch64-linux-gnu (14.2.0-19ubuntu2) ... 547s Setting up libcups2t64:arm64 (2.4.12-0ubuntu1) ... 547s Setting up python3-all-dev (3.13.3-1) ... 547s Setting up libgs10-common (10.05.0dfsg1-0ubuntu1) ... 547s Setting up gcc-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 547s Setting up tk8.6-blt2.5 (2.5.3+dfsg-8) ... 547s Setting up libxmu6:arm64 (2:1.1.3-3build2) ... 547s Setting up g++-14-aarch64-linux-gnu (14.2.0-19ubuntu2) ... 547s Setting up python3-cairo (1.27.0-2) ... 547s Setting up blt (2.5.3+dfsg-8) ... 547s Setting up python3-tk:arm64 (3.13.3-1) ... 547s Setting up libxaw7:arm64 (2:1.0.16-1) ... 547s Setting up gcc-14 (14.2.0-19ubuntu2) ... 547s Setting up python3-pil.imagetk:arm64 (11.1.0-5build1) ... 547s Setting up python3-rlpycairo (0.3.0-3) ... 547s Setting up python3-reportlab (4.3.1-1) ... 548s Setting up texlive-binaries (2024.20240313.70630+ds-6) ... 548s update-alternatives: using /usr/bin/xdvi-xaw to provide /usr/bin/xdvi.bin (xdvi.bin) in auto mode 548s update-alternatives: using /usr/bin/bibtex.original to provide /usr/bin/bibtex (bibtex) in auto mode 548s Setting up g++-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 548s Setting up g++-14 (14.2.0-19ubuntu2) ... 548s Setting up texlive-base (2024.20250309-1) ... 549s tl-paper: setting paper size for dvips to a4: /var/lib/texmf/dvips/config/config-paper.ps 549s tl-paper: setting paper size for dvipdfmx to a4: /var/lib/texmf/dvipdfmx/dvipdfmx-paper.cfg 549s tl-paper: setting paper size for xdvi to a4: /var/lib/texmf/xdvi/XDvi-paper 550s tl-paper: setting paper size for pdftex to a4: /var/lib/texmf/tex/generic/tex-ini-files/pdftexconfig.tex 550s Setting up libgs10:arm64 (10.05.0dfsg1-0ubuntu1) ... 550s Setting up libtool (2.5.4-4) ... 550s Setting up ghostscript (10.05.0dfsg1-0ubuntu1) ... 550s Setting up gcc (4:14.2.0-1ubuntu1) ... 550s Setting up dh-autoreconf (20) ... 550s Setting up texlive-latex-base (2024.20250309-1) ... 550s Setting up texlive-latex-recommended (2024.20250309-1) ... 550s Setting up texlive-pictures (2024.20250309-1) ... 550s Setting up g++ (4:14.2.0-1ubuntu1) ... 550s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 550s Setting up texlive-fonts-recommended (2024.20250309-1) ... 550s Setting up build-essential (12.12ubuntu1) ... 550s Setting up debhelper (13.24.1ubuntu2) ... 550s Setting up texlive-latex-extra (2024.20250309-2) ... 550s Setting up python3-ufolib2 (0.17.0+dfsg1-1) ... 550s Setting up libheif-plugin-aomdec:arm64 (1.19.7-1) ... 550s Setting up libheif-plugin-libde265:arm64 (1.19.7-1) ... 550s Setting up libheif1:arm64 (1.19.7-1) ... 550s Setting up python3-fonttools (4.55.3-2build1) ... 551s Setting up libgd3:arm64 (2.3.3-12ubuntu3) ... 551s Setting up libmagickcore-7.q16-10:arm64 (8:7.1.1.43+dfsg1-1) ... 551s Setting up emboss-lib (6.6.0+dfsg-15ubuntu2) ... 551s Setting up python3-matplotlib (3.8.3-7build1) ... 553s Setting up libmagickwand-7.q16-10:arm64 (8:7.1.1.43+dfsg1-1) ... 553s Setting up emboss (6.6.0+dfsg-15ubuntu2) ... 553s Setting up imagemagick-7.q16 (8:7.1.1.43+dfsg1-1) ... 553s update-alternatives: using /usr/bin/compare-im7.q16 to provide /usr/bin/compare (compare) in auto mode 553s update-alternatives: using /usr/bin/compare-im7.q16 to provide /usr/bin/compare-im7 (compare-im7) in auto mode 553s update-alternatives: using /usr/bin/animate-im7.q16 to provide /usr/bin/animate (animate) in auto mode 553s update-alternatives: using /usr/bin/animate-im7.q16 to provide /usr/bin/animate-im7 (animate-im7) in auto mode 553s update-alternatives: using /usr/bin/convert-im7.q16 to provide /usr/bin/convert (convert) in auto mode 553s update-alternatives: using /usr/bin/convert-im7.q16 to provide /usr/bin/convert-im7 (convert-im7) in auto mode 553s update-alternatives: using /usr/bin/composite-im7.q16 to provide /usr/bin/composite (composite) in auto mode 553s update-alternatives: using /usr/bin/composite-im7.q16 to provide /usr/bin/composite-im7 (composite-im7) in auto mode 553s update-alternatives: using /usr/bin/conjure-im7.q16 to provide /usr/bin/conjure (conjure) in auto mode 553s update-alternatives: using /usr/bin/conjure-im7.q16 to provide /usr/bin/conjure-im7 (conjure-im7) in auto mode 553s update-alternatives: using /usr/bin/import-im7.q16 to provide /usr/bin/import (import) in auto mode 553s update-alternatives: using /usr/bin/import-im7.q16 to provide /usr/bin/import-im7 (import-im7) in auto mode 553s update-alternatives: using /usr/bin/identify-im7.q16 to provide /usr/bin/identify (identify) in auto mode 553s update-alternatives: using /usr/bin/identify-im7.q16 to provide /usr/bin/identify-im7 (identify-im7) in auto mode 553s update-alternatives: using /usr/bin/stream-im7.q16 to provide /usr/bin/stream (stream) in auto mode 553s update-alternatives: using /usr/bin/stream-im7.q16 to provide /usr/bin/stream-im7 (stream-im7) in auto mode 553s update-alternatives: using /usr/bin/display-im7.q16 to provide /usr/bin/display (display) in auto mode 553s update-alternatives: using /usr/bin/display-im7.q16 to provide /usr/bin/display-im7 (display-im7) in auto mode 553s update-alternatives: using /usr/bin/montage-im7.q16 to provide /usr/bin/montage (montage) in auto mode 553s update-alternatives: using /usr/bin/montage-im7.q16 to provide /usr/bin/montage-im7 (montage-im7) in auto mode 553s update-alternatives: using /usr/bin/mogrify-im7.q16 to provide /usr/bin/mogrify (mogrify) in auto mode 553s update-alternatives: using /usr/bin/mogrify-im7.q16 to provide /usr/bin/mogrify-im7 (mogrify-im7) in auto mode 553s update-alternatives: using /usr/bin/magick-im7.q16 to provide /usr/bin/magick (magick) in auto mode 553s 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 553s update-alternatives: using /usr/bin/magick-im7.q16 to provide /usr/bin/magick-im7 (magick-im7) in auto mode 553s 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 553s update-alternatives: using /usr/bin/magick-script-im7.q16 to provide /usr/bin/magick-script (magick-script) in auto mode 553s 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 553s update-alternatives: using /usr/bin/magick-script-im7.q16 to provide /usr/bin/magick-script-im7 (magick-script-im7) in auto mode 553s 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 553s Setting up hevea (2.36-2) ... 553s Setting up imagemagick (8:7.1.1.43+dfsg1-1) ... 553s Processing triggers for install-info (7.1.1-1) ... 553s Processing triggers for libc-bin (2.41-6ubuntu1) ... 553s Processing triggers for man-db (2.13.0-1) ... 555s Processing triggers for shared-mime-info (2.4-5build1) ... 555s Processing triggers for sgml-base (1.31) ... 555s Setting up w3c-sgml-lib (1.3-3) ... 581s Setting up docutils-common (0.21.2+dfsg-2) ... 581s Setting up python3-biopython (1.85+dfsg-2build1) ... 582s Setting up python3-biopython-sql (1.85+dfsg-2build1) ... 582s Processing triggers for sgml-base (1.31) ... 582s Setting up python3-docutils (0.21.2+dfsg-2) ... 582s Setting up python3-sphinx (8.1.3-5) ... 583s Setting up python3-sphinxcontrib.jquery (4.1-5) ... 583s Setting up python3-numpydoc (1.8.0-1) ... 583s Setting up python3-sphinx-rtd-theme (3.0.2+dfsg-2) ... 584s Processing triggers for tex-common (6.19) ... 584s Running updmap-sys. This may take some time... done. 584s Running mktexlsr /var/lib/texmf ... done. 584s Building format(s) --all. 658s This may take some time... done. 669s autopkgtest [05:52:13]: test full_suite: sh debian/tests/run-unit-test 669s autopkgtest [05:52:13]: test full_suite: [----------------------- 671s mkdir: created directory 'Bio' 671s mkdir: created directory 'Bio/Align' 671s mkdir: created directory 'Bio/Align/substitution_matrices' 671s mkdir: created directory 'Bio/Align/substitution_matrices/data/' 671s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER22' -> 'Bio/Align/substitution_matrices/data/BENNER22' 671s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER6' -> 'Bio/Align/substitution_matrices/data/BENNER6' 671s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER74' -> 'Bio/Align/substitution_matrices/data/BENNER74' 671s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLASTN' -> 'Bio/Align/substitution_matrices/data/BLASTN' 671s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLASTP' -> 'Bio/Align/substitution_matrices/data/BLASTP' 671s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM45' -> 'Bio/Align/substitution_matrices/data/BLOSUM45' 671s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM50' -> 'Bio/Align/substitution_matrices/data/BLOSUM50' 671s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM62' -> 'Bio/Align/substitution_matrices/data/BLOSUM62' 671s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM80' -> 'Bio/Align/substitution_matrices/data/BLOSUM80' 671s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM90' -> 'Bio/Align/substitution_matrices/data/BLOSUM90' 671s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/DAYHOFF' -> 'Bio/Align/substitution_matrices/data/DAYHOFF' 671s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/FENG' -> 'Bio/Align/substitution_matrices/data/FENG' 671s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/GENETIC' -> 'Bio/Align/substitution_matrices/data/GENETIC' 671s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/GONNET1992' -> 'Bio/Align/substitution_matrices/data/GONNET1992' 671s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/HOXD70' -> 'Bio/Align/substitution_matrices/data/HOXD70' 671s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/JOHNSON' -> 'Bio/Align/substitution_matrices/data/JOHNSON' 671s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/JONES' -> 'Bio/Align/substitution_matrices/data/JONES' 671s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/LEVIN' -> 'Bio/Align/substitution_matrices/data/LEVIN' 671s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MCLACHLAN' -> 'Bio/Align/substitution_matrices/data/MCLACHLAN' 671s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MDM78' -> 'Bio/Align/substitution_matrices/data/MDM78' 671s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MEGABLAST' -> 'Bio/Align/substitution_matrices/data/MEGABLAST' 671s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/NUC.4.4' -> 'Bio/Align/substitution_matrices/data/NUC.4.4' 671s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM250' -> 'Bio/Align/substitution_matrices/data/PAM250' 671s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM30' -> 'Bio/Align/substitution_matrices/data/PAM30' 671s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM70' -> 'Bio/Align/substitution_matrices/data/PAM70' 671s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/RAO' -> 'Bio/Align/substitution_matrices/data/RAO' 671s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/RISLER' -> 'Bio/Align/substitution_matrices/data/RISLER' 671s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/SCHNEIDER' -> 'Bio/Align/substitution_matrices/data/SCHNEIDER' 671s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/STR' -> 'Bio/Align/substitution_matrices/data/STR' 671s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/TRANS' -> 'Bio/Align/substitution_matrices/data/TRANS' 672s test_Ace ... ok 672s test_Affy ... ok 674s test_AlignIO ... ok 674s test_AlignIO_ClustalIO ... ok 674s test_AlignIO_EmbossIO ... ok 674s test_AlignIO_FastaIO ... ok 674s test_AlignIO_MauveIO ... ok 674s test_AlignIO_PhylipIO ... ok 674s test_AlignIO_convert ... ok 674s test_AlignInfo ... ok 675s test_Align_Alignment ... ok 675s test_Align_a2m ... ok 675s test_Align_bed ... ok 675s test_Align_bigbed ... ok 675s test_Align_bigmaf ... ok 676s test_Align_bigpsl ... ok 676s test_Align_chain ... ok 676s test_Align_clustal ... ok 681s test_Align_codonalign ... ok 681s test_Align_emboss ... ok 681s test_Align_exonerate ... ok 681s test_Align_fasta ... ok 681s test_Align_hhr ... ok 682s test_Align_maf ... ok 682s test_Align_mauve ... ok 682s test_Align_msf ... ok 682s test_Align_nexus ... ok 682s test_Align_phylip ... ok 683s test_Align_psl ... ok 683s test_Align_sam ... ok 685s test_Align_stockholm ... ok 685s test_Align_tabular ... ok 685s test_Application ... ok 685s test_BioSQL_MySQLdb_online ... skipping. internet not available 685s test_BioSQL_mysql_connector ... skipping. BioSQL test configuration file biosql.ini missing (see biosql.ini.sample) 685s test_BioSQL_mysql_connector_online ... skipping. internet not available 685s test_BioSQL_psycopg2_online ... skipping. internet not available 689s test_BioSQL_sqlite3 ... ok 689s test_BioSQL_sqlite3_online ... skipping. internet not available 689s test_Blast_Record ... ok 690s test_Blast_parser ... ok 690s test_CAPS ... ok 690s test_Chi2 ... ok 691s test_ClustalOmega_tool ... ok 691s test_Clustalw_tool ... skipping. Install clustalw or clustalw2 if you want to use it from Biopython. 691s test_Cluster ... ok 691s test_CodonTable ... ok 691s test_ColorSpiral ... ok 691s test_Compass ... ok 692s test_Consensus ... ok 694s test_Dialign_tool ... ok 694s test_EMBL_unittest ... ok 700s test_Emboss ... ok 700s test_EmbossPrimer ... ok 704s test_Entrez ... ok 704s test_Entrez_online ... skipping. internet not available 704s test_Entrez_parser ... ok 704s test_Enzyme ... ok 704s test_ExPASy ... skipping. internet not available 704s test_Fasttree_tool ... ok 705s test_File ... ok 705s test_GenBank ... /usr/lib/python3/dist-packages/Bio/SeqIO/InsdcIO.py:600: BiopythonWarning: Annotation 'Sequence Read Archive: SRX001885, SRX001121, SRX001531, SRX001530, SRX001529' too long 705s warnings.warn(f"Annotation {text!r} too long", BiopythonWarning) 705s ok 706s test_GenomeDiagram ... Warn: Can't find .pfb for face 'Helvetica' 708s ok 709s test_GraphicsChromosome ... ok 709s test_GraphicsDistribution ... ok 710s test_GraphicsGeneral ... ok 710s test_HMMCasino ... ok 710s test_HMMGeneral ... ok 710s test_KEGG ... ok 710s test_KEGG_online ... skipping. internet not available 714s test_KGML_graphics ... ok 714s test_KGML_graphics_online ... skipping. internet not available 715s test_KGML_nographics ... ok 715s test_KeyWList ... ok 715s test_LogisticRegression ... ok 716s test_MafIO_index ... ok 718s test_Mafft_tool ... ok 718s test_MarkovModel ... ok 718s test_Medline ... ok 718s test_Muscle_tool ... skipping. Install MUSCLE if you want to use the Bio.Align.Applications wrapper. 719s test_NCBIXML ... Exception ignored in: 719s Traceback (most recent call last): 719s File "/usr/lib/python3/dist-packages/Bio/Blast/NCBIXML.py", line 1319, in parse 719s expat_parser.Parse(NULL, True) 719s xml.parsers.expat.ExpatError: unclosed token: line 320, column 0 719s ok 721s test_NCBI_BLAST_tools ... ok 721s test_NCBI_qblast ... ok 721s test_NMR ... ok 721s test_NaiveBayes ... ok 721s test_Nexus ... ok 721s test_PAML_baseml ... ok 722s test_PAML_codeml ... ok 722s test_PAML_yn00 ... ok 726s test_PDB_CEAligner ... ok 728s test_PDB_DSSP ... ok 728s test_PDB_Dice ... ok 728s test_PDB_Disordered ... ok 729s test_PDB_Exposure ... ok 729s test_PDB_FragmentMapper ... ok 730s test_PDB_KDTree ... ok 730s test_PDB_MMCIF2Dict ... ok 731s test_PDB_MMCIFIO ... ok 732s test_PDB_MMCIFParser ... ok 732s test_PDB_NACCESS ... ok 732s test_PDB_PDBIO ... ok 732s test_PDB_PDBList ... skipping. internet not available 739s test_PDB_PDBMLParser ... ok 739s test_PDB_PDBParser ... ok 739s 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 739s test_PDB_Polypeptide ... ok 739s test_PDB_QCPSuperimposer ... ok 742s test_PDB_SASA ... ok 743s test_PDB_SMCRA ... ok 743s test_PDB_Selection ... ok 743s test_PDB_StructureAlignment ... ok 743s test_PDB_Superimposer ... ok 743s test_PDB_alphafold_db ... skipping. internet not available 746s test_PDB_binary_cif ... /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 1, ' ') redefined at line 7. 746s warnings.warn( 746s /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 15, ' ') redefined at line 144. 746s warnings.warn( 746s /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 15, ' ') redefined at line 153. 746s warnings.warn( 746s /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 1, ' ') redefined at line 0. 746s warnings.warn( 746s /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 15, ' ') redefined at line 0. 746s warnings.warn( 746s ok 753s test_PDB_internal_coords ... ok 753s test_PDB_parse_pdb_header ... ok 754s test_PDB_vectors ... ok 754s test_PQR ... ok 754s test_Pathway ... ok 755s test_Phd ... ok 755s test_Phylo ... ok 756s test_PhyloXML ... ok 756s test_Phylo_CDAO ... ok 756s test_Phylo_NeXML ... ok 758s test_Phylo_igraph ... ok 760s test_Phylo_matplotlib ... ok 761s test_Phylo_networkx ... ok 761s test_PopGen_GenePop_nodepend ... ok 763s test_Prank_tool ... ok 764s test_Probcons_tool ... ok 764s test_ProtParam ... ok 765s test_RCSBFormats ... ok 766s test_Restriction ... ok 766s test_SCOP_Astral ... ok 767s test_SCOP_Cla ... ok 767s test_SCOP_Des ... ok 768s test_SCOP_Dom ... ok 768s test_SCOP_Hie ... ok 769s test_SCOP_Raf ... ok 770s test_SCOP_Residues ... ok 770s test_SCOP_Scop ... ok 771s test_SVDSuperimposer ... ok 771s test_SearchIO_blast_tab ... ok 772s test_SearchIO_blast_tab_index ... ok 773s test_SearchIO_blast_xml ... ok 774s test_SearchIO_blast_xml_index ... ok 775s test_SearchIO_blat_psl ... ok 775s test_SearchIO_blat_psl_index ... ok 776s test_SearchIO_exonerate ... ok 777s test_SearchIO_exonerate_text_index ... ok 777s test_SearchIO_exonerate_vulgar_index ... ok 778s test_SearchIO_fasta_m10 ... ok 778s test_SearchIO_fasta_m10_index ... ok 779s test_SearchIO_hhsuite2_text ... ok 779s test_SearchIO_hmmer2_text ... ok 780s test_SearchIO_hmmer2_text_index ... ok 781s test_SearchIO_hmmer3_domtab ... ok 781s test_SearchIO_hmmer3_domtab_index ... ok 782s test_SearchIO_hmmer3_tab ... ok 782s test_SearchIO_hmmer3_tab_index ... ok 783s test_SearchIO_hmmer3_text ... ok 783s test_SearchIO_hmmer3_text_index ... ok 784s test_SearchIO_interproscan_xml ... ok 785s test_SearchIO_model ... ok 785s test_SearchIO_write ... ok 786s test_SeqFeature ... ok 801s test_SeqIO ... ok 802s test_SeqIO_AbiIO ... ok 802s test_SeqIO_FastaIO ... ok 803s test_SeqIO_Gck ... ok 803s test_SeqIO_Gfa ... ok 804s test_SeqIO_Insdc ... ok 805s test_SeqIO_NibIO ... ok 807s test_SeqIO_PdbIO ... ok 808s test_SeqIO_QualityIO ... ok 808s test_SeqIO_SeqXML ... ok 809s test_SeqIO_SffIO ... ok 810s test_SeqIO_SnapGene ... ok 811s test_SeqIO_TwoBitIO ... ok 812s test_SeqIO_UniprotIO ... ok 812s test_SeqIO_Xdna ... ok 813s test_SeqIO_features ... ok 827s test_SeqIO_index ... ok 827s test_SeqIO_online ... skipping. internet not available 828s test_SeqIO_write ... ok 829s test_SeqRecord ... ok 829s test_SeqUtils ... ok 831s test_Seq_objs ... ok 831s test_SwissProt ... ok 834s test_TCoffee_tool ... ok 835s test_TogoWS ... skipping. internet not available 836s test_TreeConstruction ... ok 836s test_Tutorial ... skipping. Could not find ../Doc/Tutorial/index.rst file 837s test_UniGene ... ok 837s test_UniProt ... skipping. internet not available 838s test_UniProt_GOA ... ok 839s test_align ... ok 839s test_align_substitution_matrices ... ok 842s test_bgzf ... ok 843s test_cellosaurus ... ok 848s test_codonalign ... ok 849s test_geo ... ok 849s test_kNN ... ok 850s test_motifs ... ok 851s test_motifs_online ... skipping. internet not available 852s 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. 852s warnings.warn( 852s ok 852s test_pairwise2_no_C ... ok 853s test_pairwise_aligner ... ok 854s test_pairwise_alignment_map ... ok 861s test_phenotype ... ok 861s test_phenotype_fit ... ok 862s 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. 863s test_prodoc ... ok 863s test_prosite ... ok 864s test_raxml_tool ... skipping. Install RAxML (binary raxmlHPC) if you want to test the Bio.Phylo.Applications wrapper. 864s test_samtools_tool ... skipping. Install samtools and correctly set the file path to the program if you want to use it from Biopython 865s test_seq ... ok 865s test_translate ... ok 866s Skipping any tests requiring internet access 866s Python version: 3.13.3 (main, Apr 8 2025, 19:55:40) [GCC 14.2.0] 866s Operating system: posix linux 866s ---------------------------------------------------------------------- 866s Ran 218 tests in 194.460 seconds 866s 867s :0: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/protein_lib.fa' mode='rt' encoding='UTF-8'> 867s :0: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/nucleotide_lib.fa' mode='rt' encoding='UTF-8'> 868s autopkgtest [05:55:32]: test full_suite: -----------------------] 869s autopkgtest [05:55:33]: test full_suite: - - - - - - - - - - results - - - - - - - - - - 869s full_suite PASS 869s autopkgtest [05:55:33]: @@@@@@@@@@@@@@@@@@@@ summary 869s dependencies PASS 869s full_suite PASS 874s nova [W] Using flock in prodstack6-arm64 874s Creating nova instance adt-questing-arm64-python-biopython-20250502-054104-juju-7f2275-prod-proposed-migration-environment-21-34c61de2-b690-4c47-a1ad-43e367b48ec0 from image adt/ubuntu-questing-arm64-server-20250502.img (UUID a0b7b7fd-ad05-4ea9-97eb-0f52dbbe98e1)... 874s nova [W] Timed out waiting for 087b2483-5db7-4e41-ab58-e203dd78a270 to get deleted. 874s nova [W] Using flock in prodstack6-arm64 874s Creating nova instance adt-questing-arm64-python-biopython-20250502-054104-juju-7f2275-prod-proposed-migration-environment-21-34c61de2-b690-4c47-a1ad-43e367b48ec0 from image adt/ubuntu-questing-arm64-server-20250502.img (UUID a0b7b7fd-ad05-4ea9-97eb-0f52dbbe98e1)... 874s nova [W] Timed out waiting for 5ec2b941-a676-4a98-8656-7beca5efd1a0 to get deleted.