0s autopkgtest [04:52:19]: starting date and time: 2025-07-12 04:52:19+0000 0s autopkgtest [04:52:19]: git checkout: 508d4a25 a-v-ssh wait_for_ssh: demote "ssh connection failed" to a debug message 0s autopkgtest [04:52:19]: host juju-7f2275-prod-proposed-migration-environment-21; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.0_lv24mq/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:python-reportlab --apt-upgrade python-biopython --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=python-reportlab/4.4.2-1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-cpu2-ram4-disk20-amd64 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-21@sto01-9.secgroup --name adt-questing-amd64-python-biopython-20250712-034006-juju-7f2275-prod-proposed-migration-environment-21-167aed06-24ab-4e99-8290-12a0844b6ffb --image adt/ubuntu-questing-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-21 --net-id=net_prod-autopkgtest-workers-amd64 -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 3s Creating nova instance adt-questing-amd64-python-biopython-20250712-034006-juju-7f2275-prod-proposed-migration-environment-21-167aed06-24ab-4e99-8290-12a0844b6ffb from image adt/ubuntu-questing-amd64-server-20250712.img (UUID a3af3852-4aad-4db5-9ffd-e1ae3f54f6b0)... 38s autopkgtest [04:52:57]: testbed dpkg architecture: amd64 38s autopkgtest [04:52:57]: testbed apt version: 3.1.3 39s autopkgtest [04:52:58]: @@@@@@@@@@@@@@@@@@@@ test bed setup 39s autopkgtest [04:52:58]: testbed release detected to be: None 39s autopkgtest [04:52:58]: updating testbed package index (apt update) 40s Get:1 http://ftpmaster.internal/ubuntu questing-proposed InRelease [249 kB] 40s Get:2 http://ftpmaster.internal/ubuntu questing InRelease [249 kB] 40s Get:3 http://ftpmaster.internal/ubuntu questing-updates InRelease [110 kB] 40s Get:4 http://ftpmaster.internal/ubuntu questing-security InRelease [110 kB] 40s Get:5 http://ftpmaster.internal/ubuntu questing-proposed/main Sources [39.3 kB] 40s Get:6 http://ftpmaster.internal/ubuntu questing-proposed/universe Sources [207 kB] 40s Get:7 http://ftpmaster.internal/ubuntu questing-proposed/multiverse Sources [15.4 kB] 40s Get:8 http://ftpmaster.internal/ubuntu questing-proposed/main amd64 Packages [60.3 kB] 40s Get:9 http://ftpmaster.internal/ubuntu questing-proposed/main i386 Packages [44.1 kB] 40s Get:10 http://ftpmaster.internal/ubuntu questing-proposed/universe i386 Packages [110 kB] 40s Get:11 http://ftpmaster.internal/ubuntu questing-proposed/universe amd64 Packages [197 kB] 40s Get:12 http://ftpmaster.internal/ubuntu questing-proposed/multiverse amd64 Packages [16.6 kB] 40s Get:13 http://ftpmaster.internal/ubuntu questing-proposed/multiverse i386 Packages [8592 B] 40s Fetched 1419 kB in 1s (1799 kB/s) 41s Reading package lists... 41s autopkgtest [04:53:00]: upgrading testbed (apt dist-upgrade and autopurge) 42s Reading package lists... 42s Building dependency tree... 42s Reading state information... 42s Calculating upgrade... 42s The following packages will be upgraded: 42s htop 42s 1 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 42s Need to get 176 kB of archives. 42s After this operation, 0 B of additional disk space will be used. 42s Get:1 http://ftpmaster.internal/ubuntu questing/main amd64 htop amd64 3.4.1-5 [176 kB] 42s Fetched 176 kB in 0s (0 B/s) 42s (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 ... 121132 files and directories currently installed.) 42s Preparing to unpack .../htop_3.4.1-5_amd64.deb ... 42s Unpacking htop (3.4.1-5) over (3.4.1-4) ... 42s Setting up htop (3.4.1-5) ... 42s Processing triggers for man-db (2.13.1-1) ... 43s Reading package lists... 43s Building dependency tree... 43s Reading state information... 43s Solving dependencies... 43s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 46s autopkgtest [04:53:05]: testbed running kernel: Linux 6.15.0-4-generic #4-Ubuntu SMP PREEMPT_DYNAMIC Fri Jul 4 14:41:53 UTC 2025 46s autopkgtest [04:53:05]: @@@@@@@@@@@@@@@@@@@@ apt-source python-biopython 49s Get:1 http://ftpmaster.internal/ubuntu questing/universe python-biopython 1.85+dfsg-4 (dsc) [3070 B] 49s Get:2 http://ftpmaster.internal/ubuntu questing/universe python-biopython 1.85+dfsg-4 (tar) [14.6 MB] 49s Get:3 http://ftpmaster.internal/ubuntu questing/universe python-biopython 1.85+dfsg-4 (diff) [42.8 kB] 49s gpgv: Signature made Fri Apr 11 19:33:28 2025 UTC 49s gpgv: using RSA key D54C3BFAFFB042DE382DA5D741CE7F0B9F1B8B32 49s gpgv: Can't check signature: No public key 49s dpkg-source: warning: cannot verify inline signature for ./python-biopython_1.85+dfsg-4.dsc: no acceptable signature found 50s autopkgtest [04:53:09]: testing package python-biopython version 1.85+dfsg-4 50s autopkgtest [04:53:09]: build not needed 55s autopkgtest [04:53:14]: test dependencies: preparing testbed 55s Reading package lists... 55s Building dependency tree... 55s Reading state information... 55s Solving dependencies... 55s The following NEW packages will be installed: 55s fontconfig-config fonts-urw-base35 libblas3 libcairo2 libdeflate0 55s libfontconfig1 libfontenc1 libgfortran5 libgomp1 libgraphite2-3 55s libharfbuzz0b libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 libjs-jquery 55s libjs-sphinxdoc libjs-underscore liblapack3 liblcms2-2 liblerc4 libopenjp2-7 55s libpixman-1-0 libraqm0 libsharpyuv0 libtiff6 libwebp7 libwebpdemux2 55s libwebpmux3 libxcb-render0 libxcb-shm0 libxrender1 python-biopython-doc 55s python3-all python3-biopython python3-biopython-sql python3-cairo 55s python3-charset-normalizer python3-freetype python3-numpy python3-numpy-dev 55s python3-pil python3-reportlab python3-rlpycairo sgml-base w3c-sgml-lib 55s x11-common xfonts-encodings xfonts-utils xml-core 55s 0 upgraded, 50 newly installed, 0 to remove and 0 not upgraded. 55s Need to get 47.7 MB of archives. 55s After this operation, 133 MB of additional disk space will be used. 55s Get:1 http://ftpmaster.internal/ubuntu questing/main amd64 python3-numpy-dev amd64 1:2.2.4+ds-1ubuntu1 [147 kB] 55s Get:2 http://ftpmaster.internal/ubuntu questing/main amd64 libblas3 amd64 3.12.1-2build1 [262 kB] 56s Get:3 http://ftpmaster.internal/ubuntu questing/main amd64 libgfortran5 amd64 15.1.0-8ubuntu1 [940 kB] 56s Get:4 http://ftpmaster.internal/ubuntu questing/main amd64 liblapack3 amd64 3.12.1-2build1 [2672 kB] 56s Get:5 http://ftpmaster.internal/ubuntu questing/main amd64 python3-numpy amd64 1:2.2.4+ds-1ubuntu1 [5377 kB] 57s Get:6 http://ftpmaster.internal/ubuntu questing/main amd64 libfontenc1 amd64 1:1.1.8-1build1 [14.0 kB] 57s Get:7 http://ftpmaster.internal/ubuntu questing/main amd64 x11-common all 1:7.7+24ubuntu1 [22.4 kB] 57s Get:8 http://ftpmaster.internal/ubuntu questing/main amd64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 57s Get:9 http://ftpmaster.internal/ubuntu questing/main amd64 xfonts-utils amd64 1:7.7+7 [97.1 kB] 57s Get:10 http://ftpmaster.internal/ubuntu questing/main amd64 fonts-urw-base35 all 20200910-8 [11.0 MB] 57s Get:11 http://ftpmaster.internal/ubuntu questing/main amd64 fontconfig-config amd64 2.15.0-2.3ubuntu1 [38.0 kB] 57s Get:12 http://ftpmaster.internal/ubuntu questing/main amd64 libfontconfig1 amd64 2.15.0-2.3ubuntu1 [141 kB] 57s Get:13 http://ftpmaster.internal/ubuntu questing/main amd64 libpixman-1-0 amd64 0.44.0-3 [427 kB] 57s Get:14 http://ftpmaster.internal/ubuntu questing/main amd64 libxcb-render0 amd64 1.17.0-2 [16.2 kB] 57s Get:15 http://ftpmaster.internal/ubuntu questing/main amd64 libxcb-shm0 amd64 1.17.0-2 [5758 B] 57s Get:16 http://ftpmaster.internal/ubuntu questing/main amd64 libxrender1 amd64 1:0.9.12-1 [19.8 kB] 57s Get:17 http://ftpmaster.internal/ubuntu questing/main amd64 libcairo2 amd64 1.18.4-1 [662 kB] 57s Get:18 http://ftpmaster.internal/ubuntu questing/main amd64 libdeflate0 amd64 1.23-2 [49.9 kB] 57s Get:19 http://ftpmaster.internal/ubuntu questing/main amd64 libgomp1 amd64 15.1.0-8ubuntu1 [151 kB] 57s Get:20 http://ftpmaster.internal/ubuntu questing/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB] 57s Get:21 http://ftpmaster.internal/ubuntu questing/main amd64 libharfbuzz0b amd64 10.2.0-1 [543 kB] 57s Get:22 http://ftpmaster.internal/ubuntu questing/main amd64 libimagequant0 amd64 2.18.0-1build1 [36.3 kB] 57s Get:23 http://ftpmaster.internal/ubuntu questing/main amd64 libjpeg-turbo8 amd64 2.1.5-3ubuntu2 [179 kB] 57s Get:24 http://ftpmaster.internal/ubuntu questing/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 57s Get:25 http://ftpmaster.internal/ubuntu questing/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 57s Get:26 http://ftpmaster.internal/ubuntu questing/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 57s Get:27 http://ftpmaster.internal/ubuntu questing/main amd64 libjs-sphinxdoc all 8.2.3-1ubuntu2 [28.0 kB] 57s Get:28 http://ftpmaster.internal/ubuntu questing/main amd64 liblcms2-2 amd64 2.16-2 [212 kB] 57s Get:29 http://ftpmaster.internal/ubuntu questing/main amd64 liblerc4 amd64 4.0.0+ds-5ubuntu1 [271 kB] 57s Get:30 http://ftpmaster.internal/ubuntu questing/main amd64 libraqm0 amd64 0.10.2-1 [17.2 kB] 57s Get:31 http://ftpmaster.internal/ubuntu questing/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [25.9 kB] 57s Get:32 http://ftpmaster.internal/ubuntu questing/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB] 57s Get:33 http://ftpmaster.internal/ubuntu questing/main amd64 libwebp7 amd64 1.5.0-0.1 [378 kB] 57s Get:34 http://ftpmaster.internal/ubuntu questing/main amd64 libtiff6 amd64 4.7.0-3ubuntu1 [204 kB] 57s Get:35 http://ftpmaster.internal/ubuntu questing/main amd64 libwebpdemux2 amd64 1.5.0-0.1 [13.0 kB] 57s Get:36 http://ftpmaster.internal/ubuntu questing/main amd64 libwebpmux3 amd64 1.5.0-0.1 [27.6 kB] 57s Get:37 http://ftpmaster.internal/ubuntu questing/universe amd64 python-biopython-doc all 1.85+dfsg-4 [18.2 MB] 58s Get:38 http://ftpmaster.internal/ubuntu questing/main amd64 python3-all amd64 3.13.5-1 [884 B] 58s Get:39 http://ftpmaster.internal/ubuntu questing/universe amd64 python3-charset-normalizer amd64 3.4.2-1 [129 kB] 58s Get:40 http://ftpmaster.internal/ubuntu questing/main amd64 libopenjp2-7 amd64 2.5.3-2 [218 kB] 58s Get:41 http://ftpmaster.internal/ubuntu questing/main amd64 python3-pil amd64 11.1.0-5build1 [583 kB] 58s Get:42 http://ftpmaster.internal/ubuntu questing/main amd64 python3-cairo amd64 1.27.0-2 [124 kB] 58s Get:43 http://ftpmaster.internal/ubuntu questing/universe amd64 python3-freetype all 2.5.1-1 [92.3 kB] 58s Get:44 http://ftpmaster.internal/ubuntu questing/universe amd64 python3-rlpycairo all 0.3.0-3 [9130 B] 58s Get:45 http://ftpmaster.internal/ubuntu questing-proposed/universe amd64 python3-reportlab all 4.4.2-1 [1145 kB] 58s Get:46 http://ftpmaster.internal/ubuntu questing/main amd64 sgml-base all 1.31+nmu1 [11.0 kB] 58s Get:47 http://ftpmaster.internal/ubuntu questing/main amd64 xml-core all 0.19 [20.3 kB] 58s Get:48 http://ftpmaster.internal/ubuntu questing/universe amd64 w3c-sgml-lib all 1.3-3 [280 kB] 58s Get:49 http://ftpmaster.internal/ubuntu questing/universe amd64 python3-biopython amd64 1.85+dfsg-4 [1719 kB] 58s Get:50 http://ftpmaster.internal/ubuntu questing/universe amd64 python3-biopython-sql all 1.85+dfsg-4 [26.4 kB] 58s Fetched 47.7 MB in 2s (19.5 MB/s) 58s Selecting previously unselected package python3-numpy-dev:amd64. 58s (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 ... 121132 files and directories currently installed.) 58s Preparing to unpack .../00-python3-numpy-dev_1%3a2.2.4+ds-1ubuntu1_amd64.deb ... 58s Unpacking python3-numpy-dev:amd64 (1:2.2.4+ds-1ubuntu1) ... 58s Selecting previously unselected package libblas3:amd64. 58s Preparing to unpack .../01-libblas3_3.12.1-2build1_amd64.deb ... 58s Unpacking libblas3:amd64 (3.12.1-2build1) ... 58s Selecting previously unselected package libgfortran5:amd64. 58s Preparing to unpack .../02-libgfortran5_15.1.0-8ubuntu1_amd64.deb ... 58s Unpacking libgfortran5:amd64 (15.1.0-8ubuntu1) ... 58s Selecting previously unselected package liblapack3:amd64. 58s Preparing to unpack .../03-liblapack3_3.12.1-2build1_amd64.deb ... 58s Unpacking liblapack3:amd64 (3.12.1-2build1) ... 58s Selecting previously unselected package python3-numpy. 58s Preparing to unpack .../04-python3-numpy_1%3a2.2.4+ds-1ubuntu1_amd64.deb ... 58s Unpacking python3-numpy (1:2.2.4+ds-1ubuntu1) ... 59s Selecting previously unselected package libfontenc1:amd64. 59s Preparing to unpack .../05-libfontenc1_1%3a1.1.8-1build1_amd64.deb ... 59s Unpacking libfontenc1:amd64 (1:1.1.8-1build1) ... 59s Selecting previously unselected package x11-common. 59s Preparing to unpack .../06-x11-common_1%3a7.7+24ubuntu1_all.deb ... 59s Unpacking x11-common (1:7.7+24ubuntu1) ... 59s Selecting previously unselected package xfonts-encodings. 59s Preparing to unpack .../07-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 59s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 59s Selecting previously unselected package xfonts-utils. 59s Preparing to unpack .../08-xfonts-utils_1%3a7.7+7_amd64.deb ... 59s Unpacking xfonts-utils (1:7.7+7) ... 59s Selecting previously unselected package fonts-urw-base35. 59s Preparing to unpack .../09-fonts-urw-base35_20200910-8_all.deb ... 59s Unpacking fonts-urw-base35 (20200910-8) ... 59s Selecting previously unselected package fontconfig-config. 59s Preparing to unpack .../10-fontconfig-config_2.15.0-2.3ubuntu1_amd64.deb ... 59s Unpacking fontconfig-config (2.15.0-2.3ubuntu1) ... 59s Selecting previously unselected package libfontconfig1:amd64. 59s Preparing to unpack .../11-libfontconfig1_2.15.0-2.3ubuntu1_amd64.deb ... 59s Unpacking libfontconfig1:amd64 (2.15.0-2.3ubuntu1) ... 59s Selecting previously unselected package libpixman-1-0:amd64. 59s Preparing to unpack .../12-libpixman-1-0_0.44.0-3_amd64.deb ... 59s Unpacking libpixman-1-0:amd64 (0.44.0-3) ... 59s Selecting previously unselected package libxcb-render0:amd64. 59s Preparing to unpack .../13-libxcb-render0_1.17.0-2_amd64.deb ... 59s Unpacking libxcb-render0:amd64 (1.17.0-2) ... 59s Selecting previously unselected package libxcb-shm0:amd64. 59s Preparing to unpack .../14-libxcb-shm0_1.17.0-2_amd64.deb ... 59s Unpacking libxcb-shm0:amd64 (1.17.0-2) ... 59s Selecting previously unselected package libxrender1:amd64. 59s Preparing to unpack .../15-libxrender1_1%3a0.9.12-1_amd64.deb ... 59s Unpacking libxrender1:amd64 (1:0.9.12-1) ... 59s Selecting previously unselected package libcairo2:amd64. 59s Preparing to unpack .../16-libcairo2_1.18.4-1_amd64.deb ... 59s Unpacking libcairo2:amd64 (1.18.4-1) ... 59s Selecting previously unselected package libdeflate0:amd64. 59s Preparing to unpack .../17-libdeflate0_1.23-2_amd64.deb ... 59s Unpacking libdeflate0:amd64 (1.23-2) ... 59s Selecting previously unselected package libgomp1:amd64. 59s Preparing to unpack .../18-libgomp1_15.1.0-8ubuntu1_amd64.deb ... 59s Unpacking libgomp1:amd64 (15.1.0-8ubuntu1) ... 59s Selecting previously unselected package libgraphite2-3:amd64. 59s Preparing to unpack .../19-libgraphite2-3_1.3.14-2ubuntu1_amd64.deb ... 59s Unpacking libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 59s Selecting previously unselected package libharfbuzz0b:amd64. 59s Preparing to unpack .../20-libharfbuzz0b_10.2.0-1_amd64.deb ... 59s Unpacking libharfbuzz0b:amd64 (10.2.0-1) ... 59s Selecting previously unselected package libimagequant0:amd64. 59s Preparing to unpack .../21-libimagequant0_2.18.0-1build1_amd64.deb ... 59s Unpacking libimagequant0:amd64 (2.18.0-1build1) ... 59s Selecting previously unselected package libjpeg-turbo8:amd64. 59s Preparing to unpack .../22-libjpeg-turbo8_2.1.5-3ubuntu2_amd64.deb ... 59s Unpacking libjpeg-turbo8:amd64 (2.1.5-3ubuntu2) ... 59s Selecting previously unselected package libjpeg8:amd64. 59s Preparing to unpack .../23-libjpeg8_8c-2ubuntu11_amd64.deb ... 59s Unpacking libjpeg8:amd64 (8c-2ubuntu11) ... 59s Selecting previously unselected package libjs-jquery. 59s Preparing to unpack .../24-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 59s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 59s Selecting previously unselected package libjs-underscore. 59s Preparing to unpack .../25-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 59s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 59s Selecting previously unselected package libjs-sphinxdoc. 59s Preparing to unpack .../26-libjs-sphinxdoc_8.2.3-1ubuntu2_all.deb ... 59s Unpacking libjs-sphinxdoc (8.2.3-1ubuntu2) ... 59s Selecting previously unselected package liblcms2-2:amd64. 59s Preparing to unpack .../27-liblcms2-2_2.16-2_amd64.deb ... 59s Unpacking liblcms2-2:amd64 (2.16-2) ... 59s Selecting previously unselected package liblerc4:amd64. 59s Preparing to unpack .../28-liblerc4_4.0.0+ds-5ubuntu1_amd64.deb ... 59s Unpacking liblerc4:amd64 (4.0.0+ds-5ubuntu1) ... 59s Selecting previously unselected package libraqm0:amd64. 59s Preparing to unpack .../29-libraqm0_0.10.2-1_amd64.deb ... 59s Unpacking libraqm0:amd64 (0.10.2-1) ... 59s Selecting previously unselected package libsharpyuv0:amd64. 59s Preparing to unpack .../30-libsharpyuv0_1.5.0-0.1_amd64.deb ... 59s Unpacking libsharpyuv0:amd64 (1.5.0-0.1) ... 59s Selecting previously unselected package libjbig0:amd64. 59s Preparing to unpack .../31-libjbig0_2.1-6.1ubuntu2_amd64.deb ... 59s Unpacking libjbig0:amd64 (2.1-6.1ubuntu2) ... 59s Selecting previously unselected package libwebp7:amd64. 59s Preparing to unpack .../32-libwebp7_1.5.0-0.1_amd64.deb ... 59s Unpacking libwebp7:amd64 (1.5.0-0.1) ... 59s Selecting previously unselected package libtiff6:amd64. 59s Preparing to unpack .../33-libtiff6_4.7.0-3ubuntu1_amd64.deb ... 59s Unpacking libtiff6:amd64 (4.7.0-3ubuntu1) ... 59s Selecting previously unselected package libwebpdemux2:amd64. 59s Preparing to unpack .../34-libwebpdemux2_1.5.0-0.1_amd64.deb ... 59s Unpacking libwebpdemux2:amd64 (1.5.0-0.1) ... 59s Selecting previously unselected package libwebpmux3:amd64. 59s Preparing to unpack .../35-libwebpmux3_1.5.0-0.1_amd64.deb ... 59s Unpacking libwebpmux3:amd64 (1.5.0-0.1) ... 59s Selecting previously unselected package python-biopython-doc. 59s Preparing to unpack .../36-python-biopython-doc_1.85+dfsg-4_all.deb ... 59s Unpacking python-biopython-doc (1.85+dfsg-4) ... 60s Selecting previously unselected package python3-all. 60s Preparing to unpack .../37-python3-all_3.13.5-1_amd64.deb ... 60s Unpacking python3-all (3.13.5-1) ... 60s Selecting previously unselected package python3-charset-normalizer. 60s Preparing to unpack .../38-python3-charset-normalizer_3.4.2-1_amd64.deb ... 60s Unpacking python3-charset-normalizer (3.4.2-1) ... 60s Selecting previously unselected package libopenjp2-7:amd64. 60s Preparing to unpack .../39-libopenjp2-7_2.5.3-2_amd64.deb ... 60s Unpacking libopenjp2-7:amd64 (2.5.3-2) ... 60s Selecting previously unselected package python3-pil:amd64. 60s Preparing to unpack .../40-python3-pil_11.1.0-5build1_amd64.deb ... 60s Unpacking python3-pil:amd64 (11.1.0-5build1) ... 60s Selecting previously unselected package python3-cairo. 60s Preparing to unpack .../41-python3-cairo_1.27.0-2_amd64.deb ... 60s Unpacking python3-cairo (1.27.0-2) ... 60s Selecting previously unselected package python3-freetype. 60s Preparing to unpack .../42-python3-freetype_2.5.1-1_all.deb ... 60s Unpacking python3-freetype (2.5.1-1) ... 60s Selecting previously unselected package python3-rlpycairo. 60s Preparing to unpack .../43-python3-rlpycairo_0.3.0-3_all.deb ... 60s Unpacking python3-rlpycairo (0.3.0-3) ... 60s Selecting previously unselected package python3-reportlab. 60s Preparing to unpack .../44-python3-reportlab_4.4.2-1_all.deb ... 60s Unpacking python3-reportlab (4.4.2-1) ... 60s Selecting previously unselected package sgml-base. 60s Preparing to unpack .../45-sgml-base_1.31+nmu1_all.deb ... 60s Unpacking sgml-base (1.31+nmu1) ... 60s Selecting previously unselected package xml-core. 60s Preparing to unpack .../46-xml-core_0.19_all.deb ... 60s Unpacking xml-core (0.19) ... 60s Selecting previously unselected package w3c-sgml-lib. 60s Preparing to unpack .../47-w3c-sgml-lib_1.3-3_all.deb ... 60s Unpacking w3c-sgml-lib (1.3-3) ... 60s Selecting previously unselected package python3-biopython. 60s Preparing to unpack .../48-python3-biopython_1.85+dfsg-4_amd64.deb ... 60s Unpacking python3-biopython (1.85+dfsg-4) ... 60s Selecting previously unselected package python3-biopython-sql. 60s Preparing to unpack .../49-python3-biopython-sql_1.85+dfsg-4_all.deb ... 60s Unpacking python3-biopython-sql (1.85+dfsg-4) ... 60s Setting up libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 60s Setting up liblcms2-2:amd64 (2.16-2) ... 60s Setting up libpixman-1-0:amd64 (0.44.0-3) ... 60s Setting up libsharpyuv0:amd64 (1.5.0-0.1) ... 60s Setting up liblerc4:amd64 (4.0.0+ds-5ubuntu1) ... 60s Setting up libxrender1:amd64 (1:0.9.12-1) ... 60s Setting up libxcb-render0:amd64 (1.17.0-2) ... 60s Setting up python3-charset-normalizer (3.4.2-1) ... 60s Setting up x11-common (1:7.7+24ubuntu1) ... 61s Setting up libdeflate0:amd64 (1.23-2) ... 61s Setting up python3-all (3.13.5-1) ... 61s Setting up libxcb-shm0:amd64 (1.17.0-2) ... 61s Setting up libgomp1:amd64 (15.1.0-8ubuntu1) ... 61s Setting up python3-freetype (2.5.1-1) ... 61s Setting up libjbig0:amd64 (2.1-6.1ubuntu2) ... 61s Setting up libfontenc1:amd64 (1:1.1.8-1build1) ... 61s Setting up libblas3:amd64 (3.12.1-2build1) ... 61s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode 61s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 61s Setting up libimagequant0:amd64 (2.18.0-1build1) ... 61s Setting up python3-numpy-dev:amd64 (1:2.2.4+ds-1ubuntu1) ... 61s Setting up libjpeg-turbo8:amd64 (2.1.5-3ubuntu2) ... 61s Setting up libgfortran5:amd64 (15.1.0-8ubuntu1) ... 61s Setting up libwebp7:amd64 (1.5.0-0.1) ... 61s Setting up libopenjp2-7:amd64 (2.5.3-2) ... 61s Setting up libharfbuzz0b:amd64 (10.2.0-1) ... 61s Setting up sgml-base (1.31+nmu1) ... 61s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 61s Setting up libwebpmux3:amd64 (1.5.0-0.1) ... 61s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 61s Setting up libjpeg8:amd64 (8c-2ubuntu11) ... 61s Setting up liblapack3:amd64 (3.12.1-2build1) ... 61s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode 61s Setting up libwebpdemux2:amd64 (1.5.0-0.1) ... 61s Setting up xfonts-utils (1:7.7+7) ... 61s Setting up libraqm0:amd64 (0.10.2-1) ... 61s Setting up python3-numpy (1:2.2.4+ds-1ubuntu1) ... 62s Setting up libjs-sphinxdoc (8.2.3-1ubuntu2) ... 62s Setting up python-biopython-doc (1.85+dfsg-4) ... 62s Setting up libtiff6:amd64 (4.7.0-3ubuntu1) ... 62s Setting up xml-core (0.19) ... 62s Setting up fonts-urw-base35 (20200910-8) ... 62s Setting up python3-pil:amd64 (11.1.0-5build1) ... 63s Setting up fontconfig-config (2.15.0-2.3ubuntu1) ... 63s Setting up libfontconfig1:amd64 (2.15.0-2.3ubuntu1) ... 63s Setting up libcairo2:amd64 (1.18.4-1) ... 63s Setting up python3-cairo (1.27.0-2) ... 63s Setting up python3-rlpycairo (0.3.0-3) ... 63s Setting up python3-reportlab (4.4.2-1) ... 63s Processing triggers for libc-bin (2.41-6ubuntu2) ... 63s Processing triggers for man-db (2.13.1-1) ... 64s Processing triggers for sgml-base (1.31+nmu1) ... 64s Setting up w3c-sgml-lib (1.3-3) ... 84s Setting up python3-biopython (1.85+dfsg-4) ... 85s Setting up python3-biopython-sql (1.85+dfsg-4) ... 86s autopkgtest [04:53:45]: test dependencies: sh debian/tests/run-unit-test 86s autopkgtest [04:53:45]: test dependencies: [----------------------- 87s cp: cannot stat '/usr/share/libcifpp/mmcif_pdbx.dic': No such file or directory 87s cp: cannot stat '/usr/share/libcifpp/mmcif_ma.dic': No such file or directory 88s mkdir: created directory 'Bio' 88s mkdir: created directory 'Bio/Align' 88s mkdir: created directory 'Bio/Align/substitution_matrices' 88s mkdir: created directory 'Bio/Align/substitution_matrices/data/' 88s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER22' -> 'Bio/Align/substitution_matrices/data/BENNER22' 88s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER6' -> 'Bio/Align/substitution_matrices/data/BENNER6' 88s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER74' -> 'Bio/Align/substitution_matrices/data/BENNER74' 88s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLASTN' -> 'Bio/Align/substitution_matrices/data/BLASTN' 88s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLASTP' -> 'Bio/Align/substitution_matrices/data/BLASTP' 88s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM45' -> 'Bio/Align/substitution_matrices/data/BLOSUM45' 88s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM50' -> 'Bio/Align/substitution_matrices/data/BLOSUM50' 88s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM62' -> 'Bio/Align/substitution_matrices/data/BLOSUM62' 88s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM80' -> 'Bio/Align/substitution_matrices/data/BLOSUM80' 88s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM90' -> 'Bio/Align/substitution_matrices/data/BLOSUM90' 88s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/DAYHOFF' -> 'Bio/Align/substitution_matrices/data/DAYHOFF' 88s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/FENG' -> 'Bio/Align/substitution_matrices/data/FENG' 88s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/GENETIC' -> 'Bio/Align/substitution_matrices/data/GENETIC' 88s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/GONNET1992' -> 'Bio/Align/substitution_matrices/data/GONNET1992' 88s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/HOXD70' -> 'Bio/Align/substitution_matrices/data/HOXD70' 88s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/JOHNSON' -> 'Bio/Align/substitution_matrices/data/JOHNSON' 88s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/JONES' -> 'Bio/Align/substitution_matrices/data/JONES' 88s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/LEVIN' -> 'Bio/Align/substitution_matrices/data/LEVIN' 88s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MCLACHLAN' -> 'Bio/Align/substitution_matrices/data/MCLACHLAN' 88s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MDM78' -> 'Bio/Align/substitution_matrices/data/MDM78' 88s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MEGABLAST' -> 'Bio/Align/substitution_matrices/data/MEGABLAST' 88s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/NUC.4.4' -> 'Bio/Align/substitution_matrices/data/NUC.4.4' 88s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM250' -> 'Bio/Align/substitution_matrices/data/PAM250' 88s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM30' -> 'Bio/Align/substitution_matrices/data/PAM30' 88s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM70' -> 'Bio/Align/substitution_matrices/data/PAM70' 88s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/RAO' -> 'Bio/Align/substitution_matrices/data/RAO' 88s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/RISLER' -> 'Bio/Align/substitution_matrices/data/RISLER' 88s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/SCHNEIDER' -> 'Bio/Align/substitution_matrices/data/SCHNEIDER' 88s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/STR' -> 'Bio/Align/substitution_matrices/data/STR' 88s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/TRANS' -> 'Bio/Align/substitution_matrices/data/TRANS' 88s test_Ace ... ok 88s test_Affy ... ok 90s test_AlignIO ... ok 90s test_AlignIO_ClustalIO ... ok 90s test_AlignIO_EmbossIO ... ok 90s test_AlignIO_FastaIO ... ok 91s test_AlignIO_MauveIO ... ok 91s test_AlignIO_PhylipIO ... ok 91s test_AlignIO_convert ... ok 91s test_AlignInfo ... ok 91s test_Align_Alignment ... ok 91s test_Align_a2m ... ok 91s test_Align_bed ... ok 91s test_Align_bigbed ... ok 91s test_Align_bigmaf ... ok 92s test_Align_bigpsl ... ok 92s test_Align_chain ... ok 92s test_Align_clustal ... ok 94s test_Align_codonalign ... ok 94s test_Align_emboss ... ok 94s test_Align_exonerate ... ok 94s test_Align_fasta ... ok 95s test_Align_hhr ... ok 95s test_Align_maf ... ok 95s test_Align_mauve ... ok 95s test_Align_msf ... ok 95s test_Align_nexus ... ok 95s test_Align_phylip ... ok 95s test_Align_psl ... ok 96s test_Align_sam ... ok 96s test_Align_stockholm ... ok 97s test_Align_tabular ... ok 97s test_Application ... ok 97s test_BWA_tool ... skipping. Install bwa and correctly set the file path to the program if you want to use it from Biopython 97s test_BioSQL_MySQLdb_online ... skipping. internet not available 97s test_BioSQL_mysql_connector ... skipping. BioSQL test configuration file biosql.ini missing (see biosql.ini.sample) 97s test_BioSQL_mysql_connector_online ... skipping. internet not available 97s test_BioSQL_psycopg2_online ... skipping. internet not available 100s test_BioSQL_sqlite3 ... ok 100s test_BioSQL_sqlite3_online ... skipping. internet not available 100s test_Blast_Record ... ok 101s test_Blast_parser ... ok 101s test_CAPS ... ok 101s test_Chi2 ... ok 101s test_ClustalOmega_tool ... skipping. Install clustalo if you want to use Clustal Omega from Biopython. 101s test_Clustalw_tool ... skipping. Install clustalw or clustalw2 if you want to use it from Biopython. 101s test_Cluster ... ok 101s test_CodonTable ... ok 101s test_ColorSpiral ... ok 101s test_Compass ... ok 102s test_Consensus ... ok 102s test_Dialign_tool ... skipping. Install DIALIGN2-2 if you want to use the Bio.Align.Applications wrapper. 102s test_EMBL_unittest ... ok 102s test_Emboss ... skipping. $EMBOSS_ROOT='/usr/lib/emboss' which does not exist! 102s test_EmbossPrimer ... ok 1306s autopkgtest-virt-ssh [05:14:05]: ------- nova console-log 3bc789b8-4447-48c5-a7e4-cd972740ef02 (adt-questing-amd64-python-biopython-20250712-034006-juju-7f2275-prod-proposed-migration-environment-21-167aed06-24ab-4e99-8290-12a0844b6ffb) ------ 1306s ERROR (CommandError): No server with a name or ID of '3bc789b8-4447-48c5-a7e4-cd972740ef02' exists. 1306s --------------------------------------------------- 1306s ------- nova show 3bc789b8-4447-48c5-a7e4-cd972740ef02 (adt-questing-amd64-python-biopython-20250712-034006-juju-7f2275-prod-proposed-migration-environment-21-167aed06-24ab-4e99-8290-12a0844b6ffb) ------ 1306s ERROR (CommandError): No server with a name or ID of '3bc789b8-4447-48c5-a7e4-cd972740ef02' exists. 1306s --------------------------------------------------- 1306s 1849s autopkgtest [05:23:08]: ERROR: testbed failure: testbed auxverb failed with exit code 255