0s autopkgtest [09:42:15]: starting date and time: 2024-11-13 09:42:15+0000 0s autopkgtest [09:42:15]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [09:42:15]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.6vjgjnzf/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:python3-defaults,src:python3-stdlib-extensions --apt-upgrade ncbi-acc-download --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=python3-defaults/3.12.7-1 python3-stdlib-extensions/3.12.7-1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-arm64-8.secgroup --name adt-plucky-arm64-ncbi-acc-download-20241113-094214-juju-7f2275-prod-proposed-migration-environment-15-146ac6b7-c581-4a8c-9978-5711656616fd --image adt/ubuntu-plucky-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 82s autopkgtest [09:43:37]: testbed dpkg architecture: arm64 83s autopkgtest [09:43:38]: testbed apt version: 2.9.8 83s autopkgtest [09:43:38]: @@@@@@@@@@@@@@@@@@@@ test bed setup 84s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 84s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [76.4 kB] 84s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.3 kB] 84s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 84s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [849 kB] 84s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [104 kB] 84s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 Packages [50.3 kB] 84s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [601 kB] 85s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [17.1 kB] 85s Fetched 1793 kB in 1s (2073 kB/s) 85s Reading package lists... 88s Reading package lists... 88s Building dependency tree... 88s Reading state information... 89s Calculating upgrade... 89s The following NEW packages will be installed: 89s python3.13-gdbm 89s The following packages will be upgraded: 89s libpython3-stdlib python3 python3-gdbm python3-minimal 89s 4 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 89s Need to get 101 kB of archives. 89s After this operation, 141 kB of additional disk space will be used. 89s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-minimal arm64 3.12.7-1 [27.4 kB] 90s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3 arm64 3.12.7-1 [24.0 kB] 90s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libpython3-stdlib arm64 3.12.7-1 [10.0 kB] 90s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-gdbm arm64 3.13.0-2 [30.7 kB] 90s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-gdbm arm64 3.12.7-1 [8642 B] 90s Fetched 101 kB in 0s (263 kB/s) 90s (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 ... 79924 files and directories currently installed.) 90s Preparing to unpack .../python3-minimal_3.12.7-1_arm64.deb ... 90s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ... 91s Setting up python3-minimal (3.12.7-1) ... 91s (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 ... 79924 files and directories currently installed.) 91s Preparing to unpack .../python3_3.12.7-1_arm64.deb ... 91s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ... 91s Preparing to unpack .../libpython3-stdlib_3.12.7-1_arm64.deb ... 91s Unpacking libpython3-stdlib:arm64 (3.12.7-1) over (3.12.6-0ubuntu1) ... 91s Selecting previously unselected package python3.13-gdbm. 91s Preparing to unpack .../python3.13-gdbm_3.13.0-2_arm64.deb ... 91s Unpacking python3.13-gdbm (3.13.0-2) ... 91s Preparing to unpack .../python3-gdbm_3.12.7-1_arm64.deb ... 91s Unpacking python3-gdbm:arm64 (3.12.7-1) over (3.12.6-1ubuntu1) ... 91s Setting up python3.13-gdbm (3.13.0-2) ... 91s Setting up libpython3-stdlib:arm64 (3.12.7-1) ... 91s Setting up python3 (3.12.7-1) ... 91s Setting up python3-gdbm:arm64 (3.12.7-1) ... 91s Processing triggers for man-db (2.12.1-3) ... 92s Reading package lists... 93s Building dependency tree... 93s Reading state information... 93s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 94s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 95s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 95s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 95s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 96s Reading package lists... 96s Reading package lists... 96s Building dependency tree... 96s Reading state information... 97s Calculating upgrade... 97s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 97s Reading package lists... 98s Building dependency tree... 98s Reading state information... 98s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 106s autopkgtest [09:44:01]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 14:19:41 UTC 2024 106s autopkgtest [09:44:01]: @@@@@@@@@@@@@@@@@@@@ apt-source ncbi-acc-download 108s Get:1 http://ftpmaster.internal/ubuntu plucky/universe ncbi-acc-download 0.2.8-3 (dsc) [2434 B] 108s Get:2 http://ftpmaster.internal/ubuntu plucky/universe ncbi-acc-download 0.2.8-3 (tar) [20.9 kB] 108s Get:3 http://ftpmaster.internal/ubuntu plucky/universe ncbi-acc-download 0.2.8-3 (diff) [4420 B] 108s gpgv: Signature made Thu Aug 1 23:03:26 2024 UTC 108s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 108s gpgv: issuer "tille@debian.org" 108s gpgv: Can't check signature: No public key 108s dpkg-source: warning: cannot verify inline signature for ./ncbi-acc-download_0.2.8-3.dsc: no acceptable signature found 108s autopkgtest [09:44:03]: testing package ncbi-acc-download version 0.2.8-3 109s autopkgtest [09:44:04]: build not needed 110s autopkgtest [09:44:05]: test run-unit-test: preparing testbed 113s Reading package lists... 113s Building dependency tree... 113s Reading state information... 114s Starting pkgProblemResolver with broken count: 0 114s Starting 2 pkgProblemResolver with broken count: 0 114s Done 114s The following additional packages will be installed: 114s fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-urw-base35 114s libblas3 libcairo2 libdeflate0 libfontconfig1 libfontenc1 libgfortran5 114s libgomp1 libgraphite2-3 libharfbuzz0b libimagequant0 libjbig0 libjpeg-turbo8 114s libjpeg8 libjs-jquery libjs-jquery-hotkeys libjs-jquery-isonscreen 114s libjs-jquery-metadata libjs-jquery-tablesorter 114s libjs-jquery-throttle-debounce liblapack3 liblcms2-2 liblerc4 libopenjp2-7 114s libpixman-1-0 libpython3.13-minimal libpython3.13-stdlib libraqm0 114s libsharpyuv0 libtiff6 libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 114s libxcb-shm0 libxrender1 ncbi-acc-download python3-all python3-biopython 114s python3-cairo python3-coverage python3-freetype python3-iniconfig 114s python3-numpy python3-packaging python3-pil python3-pluggy python3-pytest 114s python3-pytest-cov python3-pytest-mock python3-reportlab 114s python3-requests-mock python3-rlpycairo python3.13 python3.13-minimal 114s sgml-base w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core 114s Suggested packages: 114s fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre liblcms2-utils 114s python3-tk bwa clustalo clustalw dialign dssp emboss fasttree mafft muscle3 114s phylip phyml prank probcons python3-mysqldb python3-matplotlib python3-mmtf 114s python3-rdflib python3-psycopg2 python3-scipy raxml samtools t-coffee wise 114s python-coverage-doc gcc gfortran python-numpy-doc python3-dev python-pil-doc 114s python-pytest-mock-doc pdf-viewer python3-egenix-mxtexttools 114s python-reportlab-doc rl-accel rl-renderpm python3.13-venv python3.13-doc 114s binfmt-support sgml-base-doc debhelper 114s Recommended packages: 114s javascript-common python-biopython-doc ncbi-blast+ python3-olefile 114s fonts-dejavu-extra 114s The following NEW packages will be installed: 114s autopkgtest-satdep fontconfig-config fonts-dejavu-core fonts-dejavu-mono 114s fonts-urw-base35 libblas3 libcairo2 libdeflate0 libfontconfig1 libfontenc1 114s libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libimagequant0 libjbig0 114s libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-hotkeys 114s libjs-jquery-isonscreen libjs-jquery-metadata libjs-jquery-tablesorter 114s libjs-jquery-throttle-debounce liblapack3 liblcms2-2 liblerc4 libopenjp2-7 114s libpixman-1-0 libpython3.13-minimal libpython3.13-stdlib libraqm0 114s libsharpyuv0 libtiff6 libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 114s libxcb-shm0 libxrender1 ncbi-acc-download python3-all python3-biopython 114s python3-cairo python3-coverage python3-freetype python3-iniconfig 114s python3-numpy python3-packaging python3-pil python3-pluggy python3-pytest 114s python3-pytest-cov python3-pytest-mock python3-reportlab 114s python3-requests-mock python3-rlpycairo python3.13 python3.13-minimal 114s sgml-base w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core 115s 0 upgraded, 65 newly installed, 0 to remove and 0 not upgraded. 115s Need to get 33.1 MB/33.1 MB of archives. 115s After this operation, 110 MB of additional disk space will be used. 115s Get:1 /tmp/autopkgtest.1Zk6cp/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [760 B] 115s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3.13-minimal arm64 3.13.0-2 [877 kB] 116s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-minimal arm64 3.13.0-2 [2100 kB] 117s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 sgml-base all 1.31 [11.4 kB] 117s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 117s Get:6 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-jquery-hotkeys all 0~20130707+git2d51e3a9+dfsg-2.1 [11.5 kB] 117s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 117s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 117s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 libfontenc1 arm64 1:1.1.8-1build1 [13.9 kB] 117s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 117s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 117s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 xfonts-utils arm64 1:7.7+7 [95.6 kB] 117s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-urw-base35 all 20200910-8 [11.0 MB] 119s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig-config arm64 2.15.0-1.1ubuntu2 [37.4 kB] 119s Get:15 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.0-3build2 [152 kB] 119s Get:16 http://ftpmaster.internal/ubuntu plucky/main arm64 libfontconfig1 arm64 2.15.0-1.1ubuntu2 [142 kB] 119s Get:17 http://ftpmaster.internal/ubuntu plucky/main arm64 libpixman-1-0 arm64 0.44.0-3 [197 kB] 119s Get:18 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-render0 arm64 1.17.0-2 [16.6 kB] 119s Get:19 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-shm0 arm64 1.17.0-2 [5884 B] 119s Get:20 http://ftpmaster.internal/ubuntu plucky/main arm64 libxrender1 arm64 1:0.9.10-1.1build1 [18.8 kB] 119s Get:21 http://ftpmaster.internal/ubuntu plucky/main arm64 libcairo2 arm64 1.18.2-2 [560 kB] 119s Get:22 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate0 arm64 1.22-1 [46.2 kB] 119s Get:23 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 14.2.0-8ubuntu1 [438 kB] 119s Get:24 http://ftpmaster.internal/ubuntu plucky/main arm64 libgomp1 arm64 14.2.0-8ubuntu1 [145 kB] 119s Get:25 http://ftpmaster.internal/ubuntu plucky/main arm64 libgraphite2-3 arm64 1.3.14-2ubuntu1 [70.6 kB] 119s Get:26 http://ftpmaster.internal/ubuntu plucky/main arm64 libharfbuzz0b arm64 10.0.1-1 [487 kB] 119s Get:27 http://ftpmaster.internal/ubuntu plucky/main arm64 libimagequant0 arm64 2.18.0-1build1 [37.1 kB] 119s Get:28 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg-turbo8 arm64 2.1.5-2ubuntu2 [163 kB] 119s Get:29 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 119s Get:30 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-jquery-metadata all 12-4 [6582 B] 119s Get:31 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-jquery-tablesorter all 1:2.31.3+dfsg1-4 [192 kB] 119s Get:32 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-jquery-throttle-debounce all 1.1+dfsg.1-2 [12.5 kB] 119s Get:33 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.0-3build2 [2293 kB] 119s Get:34 http://ftpmaster.internal/ubuntu plucky/main arm64 liblcms2-2 arm64 2.16-2 [170 kB] 119s Get:35 http://ftpmaster.internal/ubuntu plucky/main arm64 liblerc4 arm64 4.0.0+ds-4ubuntu2 [154 kB] 119s Get:36 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3.13-stdlib arm64 3.13.0-2 [2073 kB] 119s Get:37 http://ftpmaster.internal/ubuntu plucky/main arm64 libraqm0 arm64 0.10.1-1build1 [14.7 kB] 119s Get:38 http://ftpmaster.internal/ubuntu plucky/main arm64 libsharpyuv0 arm64 1.4.0-0.1 [16.3 kB] 119s Get:39 http://ftpmaster.internal/ubuntu plucky/main arm64 libjbig0 arm64 2.1-6.1ubuntu2 [29.3 kB] 119s Get:40 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebp7 arm64 1.4.0-0.1 [192 kB] 119s Get:41 http://ftpmaster.internal/ubuntu plucky/main arm64 libtiff6 arm64 4.5.1+git230720-4ubuntu4 [193 kB] 119s Get:42 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebpdemux2 arm64 1.4.0-0.1 [12.3 kB] 119s Get:43 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebpmux3 arm64 1.4.0-0.1 [25.1 kB] 119s Get:44 http://ftpmaster.internal/ubuntu plucky/universe arm64 ncbi-acc-download all 0.2.8-3 [13.3 kB] 119s Get:45 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13 arm64 3.13.0-2 [719 kB] 120s Get:46 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-all arm64 3.12.7-1 [890 B] 120s Get:47 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy arm64 1:1.26.4+ds-11build1 [3654 kB] 120s Get:48 http://ftpmaster.internal/ubuntu plucky/main arm64 libopenjp2-7 arm64 2.5.0-2ubuntu1 [182 kB] 120s Get:49 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-pil arm64 10.4.0-1ubuntu1 [456 kB] 120s Get:50 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-cairo arm64 1.26.1-2 [121 kB] 120s Get:51 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-freetype all 2.5.1-1 [92.3 kB] 120s Get:52 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-rlpycairo all 0.3.0-3 [9130 B] 120s Get:53 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-reportlab all 4.2.5-1 [1107 kB] 120s Get:54 http://ftpmaster.internal/ubuntu plucky/main arm64 xml-core all 0.19 [20.3 kB] 120s Get:55 http://ftpmaster.internal/ubuntu plucky/universe arm64 w3c-sgml-lib all 1.3-3 [280 kB] 120s Get:56 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-biopython arm64 1.84+dfsg-4 [1689 kB] 120s Get:57 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-coverage arm64 7.4.4+dfsg1-0ubuntu2 [148 kB] 120s Get:58 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-iniconfig all 1.1.1-2 [6024 B] 120s Get:59 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-packaging all 24.1-1 [41.4 kB] 120s Get:60 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pluggy all 1.5.0-1 [21.0 kB] 120s Get:61 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pytest all 8.3.3-1 [251 kB] 120s Get:62 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-jquery-isonscreen all 1.2.0-1.1 [3244 B] 120s Get:63 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pytest-cov all 5.0.0-1 [21.3 kB] 120s Get:64 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pytest-mock all 3.14.0-2 [11.7 kB] 120s Get:65 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-requests-mock all 1.12.1-2 [17.8 kB] 121s Fetched 33.1 MB in 6s (5799 kB/s) 121s Selecting previously unselected package libpython3.13-minimal:arm64. 121s (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 ... 79931 files and directories currently installed.) 121s Preparing to unpack .../00-libpython3.13-minimal_3.13.0-2_arm64.deb ... 121s Unpacking libpython3.13-minimal:arm64 (3.13.0-2) ... 121s Selecting previously unselected package python3.13-minimal. 121s Preparing to unpack .../01-python3.13-minimal_3.13.0-2_arm64.deb ... 121s Unpacking python3.13-minimal (3.13.0-2) ... 121s Selecting previously unselected package sgml-base. 121s Preparing to unpack .../02-sgml-base_1.31_all.deb ... 121s Unpacking sgml-base (1.31) ... 121s Selecting previously unselected package libjs-jquery. 121s Preparing to unpack .../03-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 121s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 121s Selecting previously unselected package libjs-jquery-hotkeys. 121s Preparing to unpack .../04-libjs-jquery-hotkeys_0~20130707+git2d51e3a9+dfsg-2.1_all.deb ... 121s Unpacking libjs-jquery-hotkeys (0~20130707+git2d51e3a9+dfsg-2.1) ... 121s Selecting previously unselected package fonts-dejavu-mono. 121s Preparing to unpack .../05-fonts-dejavu-mono_2.37-8_all.deb ... 121s Unpacking fonts-dejavu-mono (2.37-8) ... 121s Selecting previously unselected package fonts-dejavu-core. 121s Preparing to unpack .../06-fonts-dejavu-core_2.37-8_all.deb ... 121s Unpacking fonts-dejavu-core (2.37-8) ... 121s Selecting previously unselected package libfontenc1:arm64. 121s Preparing to unpack .../07-libfontenc1_1%3a1.1.8-1build1_arm64.deb ... 121s Unpacking libfontenc1:arm64 (1:1.1.8-1build1) ... 121s Selecting previously unselected package x11-common. 121s Preparing to unpack .../08-x11-common_1%3a7.7+23ubuntu3_all.deb ... 121s Unpacking x11-common (1:7.7+23ubuntu3) ... 121s Selecting previously unselected package xfonts-encodings. 121s Preparing to unpack .../09-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 121s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 121s Selecting previously unselected package xfonts-utils. 121s Preparing to unpack .../10-xfonts-utils_1%3a7.7+7_arm64.deb ... 121s Unpacking xfonts-utils (1:7.7+7) ... 121s Selecting previously unselected package fonts-urw-base35. 121s Preparing to unpack .../11-fonts-urw-base35_20200910-8_all.deb ... 121s Unpacking fonts-urw-base35 (20200910-8) ... 122s Selecting previously unselected package fontconfig-config. 122s Preparing to unpack .../12-fontconfig-config_2.15.0-1.1ubuntu2_arm64.deb ... 122s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ... 122s Selecting previously unselected package libblas3:arm64. 122s Preparing to unpack .../13-libblas3_3.12.0-3build2_arm64.deb ... 122s Unpacking libblas3:arm64 (3.12.0-3build2) ... 122s Selecting previously unselected package libfontconfig1:arm64. 122s Preparing to unpack .../14-libfontconfig1_2.15.0-1.1ubuntu2_arm64.deb ... 122s Unpacking libfontconfig1:arm64 (2.15.0-1.1ubuntu2) ... 122s Selecting previously unselected package libpixman-1-0:arm64. 122s Preparing to unpack .../15-libpixman-1-0_0.44.0-3_arm64.deb ... 122s Unpacking libpixman-1-0:arm64 (0.44.0-3) ... 122s Selecting previously unselected package libxcb-render0:arm64. 122s Preparing to unpack .../16-libxcb-render0_1.17.0-2_arm64.deb ... 122s Unpacking libxcb-render0:arm64 (1.17.0-2) ... 122s Selecting previously unselected package libxcb-shm0:arm64. 122s Preparing to unpack .../17-libxcb-shm0_1.17.0-2_arm64.deb ... 122s Unpacking libxcb-shm0:arm64 (1.17.0-2) ... 122s Selecting previously unselected package libxrender1:arm64. 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125s Setting up libpixman-1-0:arm64 (0.44.0-3) ... 125s Setting up libsharpyuv0:arm64 (1.4.0-0.1) ... 125s Setting up liblerc4:arm64 (4.0.0+ds-4ubuntu2) ... 125s Setting up libxrender1:arm64 (1:0.9.10-1.1build1) ... 125s Setting up libxcb-render0:arm64 (1.17.0-2) ... 125s Setting up x11-common (1:7.7+23ubuntu3) ... 126s Setting up libdeflate0:arm64 (1.22-1) ... 126s Setting up python3-coverage (7.4.4+dfsg1-0ubuntu2) ... 126s Setting up libxcb-shm0:arm64 (1.17.0-2) ... 126s Setting up libjs-jquery-throttle-debounce (1.1+dfsg.1-2) ... 126s Setting up libgomp1:arm64 (14.2.0-8ubuntu1) ... 126s Setting up python3-freetype (2.5.1-1) ... 126s Setting up libjbig0:arm64 (2.1-6.1ubuntu2) ... 126s Setting up libpython3.13-minimal:arm64 (3.13.0-2) ... 126s Setting up libfontenc1:arm64 (1:1.1.8-1build1) ... 126s Setting up libblas3:arm64 (3.12.0-3build2) ... 126s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 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libpython3.13-stdlib:arm64 (3.13.0-2) ... 128s Setting up libjpeg8:arm64 (8c-2ubuntu11) ... 128s Setting up liblapack3:arm64 (3.12.0-3build2) ... 128s 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 128s Setting up python3.13 (3.13.0-2) ... 129s Setting up fontconfig-config (2.15.0-1.1ubuntu2) ... 129s Setting up python3-pytest (8.3.3-1) ... 130s Setting up libwebpdemux2:arm64 (1.4.0-0.1) ... 130s Setting up python3-all (3.12.7-1) ... 130s Setting up xfonts-utils (1:7.7+7) ... 130s Setting up libjs-jquery-metadata (12-4) ... 130s Setting up libraqm0:arm64 (0.10.1-1build1) ... 130s Setting up libjs-jquery-isonscreen (1.2.0-1.1) ... 130s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 134s Setting up libjs-jquery-tablesorter (1:2.31.3+dfsg1-4) ... 134s Setting up python3-pytest-mock (3.14.0-2) ... 135s Setting up libtiff6:arm64 (4.5.1+git230720-4ubuntu4) ... 135s Setting up xml-core (0.19) ... 135s Setting up libfontconfig1:arm64 (2.15.0-1.1ubuntu2) ... 135s Setting up python3-pytest-cov (5.0.0-1) ... 135s Setting up fonts-urw-base35 (20200910-8) ... 135s Setting up libcairo2:arm64 (1.18.2-2) ... 135s Setting up python3-pil:arm64 (10.4.0-1ubuntu1) ... 136s Setting up python3-cairo (1.26.1-2) ... 136s Setting up python3-rlpycairo (0.3.0-3) ... 136s Setting up python3-reportlab (4.2.5-1) ... 138s Processing triggers for libc-bin (2.40-1ubuntu3) ... 138s Processing triggers for systemd (256.5-2ubuntu4) ... 138s Processing triggers for man-db (2.12.1-3) ... 139s Processing triggers for sgml-base (1.31) ... 139s Setting up w3c-sgml-lib (1.3-3) ... 169s Setting up python3-biopython (1.84+dfsg-4) ... 171s Setting up autopkgtest-satdep (0) ... 178s (Reading database ... 84422 files and directories currently installed.) 178s Removing autopkgtest-satdep (0) ... 179s autopkgtest [09:45:14]: test run-unit-test: [----------------------- 179s /tmp/autopkgtest.1Zk6cp/build.h4H/src/tests /tmp/autopkgtest.1Zk6cp/build.h4H/src 179s Testing with python3.13 in /tmp/autopkgtest.1Zk6cp/build.h4H/src/tests: 180s ============================= test session starts ============================== 180s platform linux -- Python 3.13.0, pytest-8.3.3, pluggy-1.5.0 -- /usr/bin/python3.13 180s cachedir: .pytest_cache 180s rootdir: /tmp/autopkgtest.1Zk6cp/build.h4H/src 180s plugins: mock-3.14.0, cov-5.0.0, requests_mock-1.12.1, typeguard-4.4.1 180s collecting ... collected 32 items 180s 180s test_core.py::test_config PASSED [ 3%] 180s test_core.py::test_config_no_biopython PASSED [ 6%] 180s test_core.py::test_config_have_biopython FAILED [ 9%] 180s test_core.py::test_download_to_file PASSED [ 12%] 180s test_core.py::test_download_to_file_append PASSED [ 15%] 180s test_core.py::test_download_to_file_retry PASSED [ 18%] 180s test_core.py::test_build_params PASSED [ 21%] 180s test_core.py::test_generate_filename PASSED [ 25%] 180s test_core.py::test_validate_and_write_error_pattern_raises PASSED [ 28%] 180s test_core.py::test_validate_and_write_emit PASSED [ 31%] 180s test_core.py::test_validate_and_write_extended_validation FAILED [ 34%] 180s test_core.py::test_get_stream_exception PASSED [ 37%] 180s test_core.py::test_get_stream_bad_status PASSED [ 40%] 180s test_core.py::test_get_stream_too_many_requests PASSED [ 43%] 180s test_core.py::test_generate_url PASSED [ 46%] 180s test_core.py::test_generate_url_with_api_key PASSED [ 50%] 180s test_correct.py::test_download_and_validate_partial_wgs FAILED [ 53%] 180s test_download.py::test_write_stream PASSED [ 56%] 180s test_validate.py::test_run_extended_validation_no_biopython PASSED [ 59%] 181s test_validate.py::test_run_extended_validation_raises FAILED [ 62%] 181s test_validate.py::test_run_extended_validation_loads FAILED [ 65%] 181s test_wgs.py::test_init PASSED [ 68%] 181s test_wgs.py::test_get_ids PASSED [ 71%] 181s test_wgs.py::test_from_string PASSED [ 75%] 181s test_wgs.py::test_download_wgs_parts_no_biopython PASSED [ 78%] 181s test_wgs.py::test_download_wgs_parts_wgs FAILED [ 81%] 181s test_wgs.py::test_download_wgs_parts_wgs_retry FAILED [ 84%] 181s test_wgs.py::test_download_wgs_parts_wgs_scafld FAILED [ 87%] 181s test_wgs.py::test_download_wgs_parts_supercontig FAILED [ 90%] 181s test_wgs.py::test_download_wgs_parts_supercontig_retry FAILED [ 93%] 181s test_wgs.py::test_download_wgs_no_parts FAILED [ 96%] 181s test_wgs.py::test_download_wgs_parts_tsa XFAIL [100%] 181s 181s =================================== FAILURES =================================== 181s __________________________ test_config_have_biopython __________________________ 181s 181s def test_config_have_biopython(): 181s """Test we detect Biopython.""" 181s > assert core.HAVE_BIOPYTHON 181s E assert False 181s E + where False = core.HAVE_BIOPYTHON 181s 181s test_core.py:46: AssertionError 181s _________________ test_validate_and_write_extended_validation __________________ 181s 181s req = 181s 181s def test_validate_and_write_extended_validation(req): 181s """Test extended validation before writing.""" 181s handle = StringIO() 181s req.get('http://fake/', text=u'>foo\nMAGIC') 181s r = requests.get('http://fake/') 181s > config = core.Config(extended_validation='loads', molecule='protein') 181s 181s test_core.py:226: 181s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 181s /usr/lib/python3/dist-packages/ncbi_acc_download/core.py:64: in __init__ 181s self.extended_validation = extended_validation 181s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 181s 181s self = , value = 'loads' 181s 181s @extended_validation.setter 181s def extended_validation(self, value): 181s if value != 'none' and not HAVE_BIOPYTHON: 181s > raise ValueError("Asked for extended validation, but Biopython not available") 181s E ValueError: Asked for extended validation, but Biopython not available 181s 181s /usr/lib/python3/dist-packages/ncbi_acc_download/core.py:96: ValueError 181s ____________________ test_download_and_validate_partial_wgs ____________________ 181s 181s req = 181s 181s def test_download_and_validate_partial_wgs(req): 181s handle = StringIO(open(full_path('partialcontig.gbk'), 'r').read()) 181s > assert validate.run_extended_validation(handle, 'genbank', 'loads') 181s E AssertionError: assert False 181s E + where False = (<_io.StringIO object at 0xea338bb42ec0>, 'genbank', 'loads') 181s E + where = validate.run_extended_validation 181s 181s test_correct.py:15: AssertionError 181s _____________________ test_run_extended_validation_raises ______________________ 181s 181s monkeypatch = <_pytest.monkeypatch.MonkeyPatch object at 0xea338b99bbf0> 181s mocker = 181s 181s def test_run_extended_validation_raises(monkeypatch, mocker): 181s """Test the "seqence loads" validator catches exceptions in SeqIO.parse().""" 181s seqio_mock = mocker.MagicMock() 181s seqio_mock.parse = mocker.MagicMock(side_effect=ValueError) 181s > monkeypatch.setattr(validate, 'SeqIO', seqio_mock) 181s E AttributeError: has no attribute 'SeqIO' 181s 181s test_validate.py:19: AttributeError 181s ______________________ test_run_extended_validation_loads ______________________ 181s 181s def test_run_extended_validation_loads(): 181s """Test the "sequence loads" validator.""" 181s handle = StringIO(u'>foo\nATGC\n>bar\nATGTGA\n') 181s > assert validate.run_extended_validation(handle, 'fasta', 'loads') 181s E AssertionError: assert False 181s E + where False = (<_io.StringIO object at 0xea338bb42680>, 'fasta', 'loads') 181s E + where = validate.run_extended_validation 181s 181s test_validate.py:29: AssertionError 181s _________________________ test_download_wgs_parts_wgs __________________________ 181s 181s req = 181s 181s def test_download_wgs_parts_wgs(req): 181s cfg = Config(format="genbank") 181s wgs_contig = open(full_path('wgs.gbk'), 'rt') 181s req.get( 181s ENTREZ_URL, 181s body=open(full_path('wgs_full.gbk'), 'rb'), 181s headers={"Content-Type": "text/plain; charset=UTF-8"}, 181s ) 181s 181s outhandle = wgs.download_wgs_parts(wgs_contig, cfg) 181s wgs_full = open(full_path('wgs_full.gbk'), 'rt') 181s > assert outhandle.getvalue() == wgs_full.read() 181s E AttributeError: '_io.TextIOWrapper' object has no attribute 'getvalue' 181s 181s test_wgs.py:95: AttributeError 181s ______________________ test_download_wgs_parts_wgs_retry _______________________ 181s 181s req = 181s 181s def test_download_wgs_parts_wgs_retry(req): 181s cfg = Config(format="genbank") 181s wgs_contig = open(full_path('wgs.gbk'), 'rt') 181s req.get(ENTREZ_URL, response_list=[ 181s {"text": u'Whoa, slow down', "status_code": 429, "headers": {"Retry-After": "0"}}, 181s { 181s "body": open(full_path('wgs_full.gbk'), 'rb'), 181s "headers": {"Content-Type": "text/plain; charset=UTF-8"}, 181s }, 181s ]) 181s 181s outhandle = wgs.download_wgs_parts(wgs_contig, cfg) 181s wgs_full = open(full_path('wgs_full.gbk'), 'rt') 181s > assert outhandle.getvalue() == wgs_full.read() 181s E AttributeError: '_io.TextIOWrapper' object has no attribute 'getvalue' 181s 181s test_wgs.py:113: AttributeError 181s ______________________ test_download_wgs_parts_wgs_scafld ______________________ 181s 181s req = 181s 181s def test_download_wgs_parts_wgs_scafld(req): 181s cfg = Config(format="genbank") 181s wgs_contig = open(full_path('wgs_scafld.gbk'), 'rt') 181s with open(full_path('wgs_full.gbk'), 'rt') as handle: 181s full_file = handle.read() 181s req.get(ENTREZ_URL, text=full_file) 181s 181s outhandle = wgs.download_wgs_parts(wgs_contig, cfg) 181s > assert outhandle.getvalue() == full_file 181s E AttributeError: '_io.TextIOWrapper' object has no attribute 'getvalue' 181s 181s test_wgs.py:126: AttributeError 181s _____________________ test_download_wgs_parts_supercontig ______________________ 181s 181s req = 181s 181s def test_download_wgs_parts_supercontig(req): 181s cfg = Config(format="genbank") 181s supercontig = open(full_path('supercontig.gbk'), 'rt') 181s req.get( 181s ENTREZ_URL, 181s body=open(full_path('supercontig_full.gbk'), 'rb'), 181s headers={"Content-Type": "text/plain; charset=UTF-8"}, 181s ) 181s 181s outhandle = wgs.download_wgs_parts(supercontig, cfg) 181s supercontig_full = open(full_path('supercontig_full.gbk'), 'rt') 181s > assert outhandle.getvalue() == supercontig_full.read() 181s E AttributeError: '_io.TextIOWrapper' object has no attribute 'getvalue' 181s 181s test_wgs.py:141: AttributeError 181s __________________ test_download_wgs_parts_supercontig_retry ___________________ 181s 181s req = 181s 181s def test_download_wgs_parts_supercontig_retry(req): 181s cfg = Config(format="genbank") 181s supercontig = open(full_path('supercontig.gbk'), 'rt') 181s req.get(ENTREZ_URL, response_list=[ 181s {"text": u'Whoa, slow down', "status_code": 429, "headers": {"Retry-After": "0"}}, 181s { 181s "body": open(full_path('supercontig_full.gbk'), 'rb'), 181s "headers": {"Content-Type": "text/plain; charset=UTF-8"}, 181s }, 181s ]) 181s 181s outhandle = wgs.download_wgs_parts(supercontig, cfg) 181s supercontig_full = open(full_path('supercontig_full.gbk'), 'rt') 181s > assert outhandle.getvalue() == supercontig_full.read() 181s E AttributeError: '_io.TextIOWrapper' object has no attribute 'getvalue' 181s 181s test_wgs.py:159: AttributeError 181s __________________________ test_download_wgs_no_parts __________________________ 181s 181s req = 181s 181s def test_download_wgs_no_parts(req): 181s cfg = Config(format="genbank") 181s supercontig = open(full_path('supercontig_full.gbk'), 'rt') 181s req.get(ENTREZ_URL, status_code=404) 181s 181s outhandle = wgs.download_wgs_parts(supercontig, cfg) 181s supercontig_full = open(full_path('supercontig_full.gbk'), 'rt') 181s > assert outhandle.getvalue() == supercontig_full.read() 181s E AttributeError: '_io.TextIOWrapper' object has no attribute 'getvalue' 181s 181s test_wgs.py:171: AttributeError 181s =========================== short test summary info ============================ 181s FAILED test_core.py::test_config_have_biopython - assert False 181s FAILED test_core.py::test_validate_and_write_extended_validation - ValueError... 181s FAILED test_correct.py::test_download_and_validate_partial_wgs - AssertionErr... 181s FAILED test_validate.py::test_run_extended_validation_raises - AttributeError... 181s FAILED test_validate.py::test_run_extended_validation_loads - AssertionError:... 181s FAILED test_wgs.py::test_download_wgs_parts_wgs - AttributeError: '_io.TextIO... 181s FAILED test_wgs.py::test_download_wgs_parts_wgs_retry - AttributeError: '_io.... 181s FAILED test_wgs.py::test_download_wgs_parts_wgs_scafld - AttributeError: '_io... 181s FAILED test_wgs.py::test_download_wgs_parts_supercontig - AttributeError: '_i... 181s FAILED test_wgs.py::test_download_wgs_parts_supercontig_retry - AttributeErro... 181s FAILED test_wgs.py::test_download_wgs_no_parts - AttributeError: '_io.TextIOW... 181s =================== 11 failed, 20 passed, 1 xfailed in 0.26s =================== 181s autopkgtest [09:45:16]: test run-unit-test: -----------------------] 182s autopkgtest [09:45:17]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 182s run-unit-test FAIL non-zero exit status 1 183s autopkgtest [09:45:18]: @@@@@@@@@@@@@@@@@@@@ summary 183s run-unit-test FAIL non-zero exit status 1 209s nova [W] Skipping flock in bos03-arm64 209s Creating nova instance adt-plucky-arm64-ncbi-acc-download-20241113-094214-juju-7f2275-prod-proposed-migration-environment-15-146ac6b7-c581-4a8c-9978-5711656616fd from image adt/ubuntu-plucky-arm64-server-20241113.img (UUID 2d7760e6-2439-4200-89d6-5ed33e5c6330)...