0s autopkgtest [09:02:16]: starting date and time: 2024-11-13 09:02:16+0000 0s autopkgtest [09:02:16]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [09:02:16]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.lusvdpc0/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-20@lcy02-6.secgroup --name adt-plucky-amd64-ncbi-acc-download-20241113-090216-juju-7f2275-prod-proposed-migration-environment-20-912eab36-7770-43e8-aca0-91e5ce3cdd59 --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --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/ 63s autopkgtest [09:03:19]: testbed dpkg architecture: amd64 63s autopkgtest [09:03:19]: testbed apt version: 2.9.8 63s autopkgtest [09:03:19]: @@@@@@@@@@@@@@@@@@@@ test bed setup 64s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 64s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [76.4 kB] 64s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [849 kB] 64s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 64s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.3 kB] 64s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [111 kB] 64s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [65.2 kB] 64s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [32.6 kB] 64s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [255 kB] 64s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [637 kB] 64s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [13.0 kB] 64s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [37.7 kB] 64s Fetched 2173 kB in 0s (6618 kB/s) 64s Reading package lists... 66s Reading package lists... 66s Building dependency tree... 66s Reading state information... 66s Calculating upgrade... 67s The following NEW packages will be installed: 67s python3.13-gdbm 67s The following packages will be upgraded: 67s libgpgme11t64 libpython3-stdlib python3 python3-gdbm python3-minimal 67s 5 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 67s Need to get 253 kB of archives. 67s After this operation, 147 kB of additional disk space will be used. 67s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-minimal amd64 3.12.7-1 [27.4 kB] 67s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3 amd64 3.12.7-1 [24.0 kB] 67s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libpython3-stdlib amd64 3.12.7-1 [10.0 kB] 67s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-gdbm amd64 3.13.0-2 [31.3 kB] 67s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-gdbm amd64 3.12.7-1 [8642 B] 67s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 libgpgme11t64 amd64 1.23.2-5ubuntu4 [152 kB] 67s Fetched 253 kB in 0s (5563 kB/s) 67s (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 ... 75541 files and directories currently installed.) 67s Preparing to unpack .../python3-minimal_3.12.7-1_amd64.deb ... 67s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ... 67s Setting up python3-minimal (3.12.7-1) ... 67s (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 ... 75541 files and directories currently installed.) 67s Preparing to unpack .../python3_3.12.7-1_amd64.deb ... 67s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ... 67s Preparing to unpack .../libpython3-stdlib_3.12.7-1_amd64.deb ... 67s Unpacking libpython3-stdlib:amd64 (3.12.7-1) over (3.12.6-0ubuntu1) ... 67s Selecting previously unselected package python3.13-gdbm. 67s Preparing to unpack .../python3.13-gdbm_3.13.0-2_amd64.deb ... 67s Unpacking python3.13-gdbm (3.13.0-2) ... 68s Preparing to unpack .../python3-gdbm_3.12.7-1_amd64.deb ... 68s Unpacking python3-gdbm:amd64 (3.12.7-1) over (3.12.6-1ubuntu1) ... 68s Preparing to unpack .../libgpgme11t64_1.23.2-5ubuntu4_amd64.deb ... 68s Unpacking libgpgme11t64:amd64 (1.23.2-5ubuntu4) over (1.18.0-4.1ubuntu4) ... 68s Setting up libgpgme11t64:amd64 (1.23.2-5ubuntu4) ... 68s Setting up python3.13-gdbm (3.13.0-2) ... 68s Setting up libpython3-stdlib:amd64 (3.12.7-1) ... 68s Setting up python3 (3.12.7-1) ... 68s Setting up python3-gdbm:amd64 (3.12.7-1) ... 68s Processing triggers for man-db (2.12.1-3) ... 69s Processing triggers for libc-bin (2.40-1ubuntu3) ... 69s Reading package lists... 69s Building dependency tree... 69s Reading state information... 69s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 69s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 69s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 69s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 69s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 71s Reading package lists... 71s Reading package lists... 71s Building dependency tree... 71s Reading state information... 71s Calculating upgrade... 72s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 72s Reading package lists... 72s Building dependency tree... 72s Reading state information... 72s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 73s autopkgtest [09:03:29]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 13:41:20 UTC 2024 73s autopkgtest [09:03:29]: @@@@@@@@@@@@@@@@@@@@ apt-source ncbi-acc-download 74s Get:1 http://ftpmaster.internal/ubuntu plucky/universe ncbi-acc-download 0.2.8-3 (dsc) [2434 B] 74s Get:2 http://ftpmaster.internal/ubuntu plucky/universe ncbi-acc-download 0.2.8-3 (tar) [20.9 kB] 74s Get:3 http://ftpmaster.internal/ubuntu plucky/universe ncbi-acc-download 0.2.8-3 (diff) [4420 B] 74s gpgv: Signature made Thu Aug 1 23:03:26 2024 UTC 74s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 74s gpgv: issuer "tille@debian.org" 74s gpgv: Can't check signature: No public key 74s dpkg-source: warning: cannot verify inline signature for ./ncbi-acc-download_0.2.8-3.dsc: no acceptable signature found 74s autopkgtest [09:03:30]: testing package ncbi-acc-download version 0.2.8-3 75s autopkgtest [09:03:31]: build not needed 75s autopkgtest [09:03:31]: test run-unit-test: preparing testbed 76s Reading package lists... 76s Building dependency tree... 76s Reading state information... 77s Starting pkgProblemResolver with broken count: 0 77s Starting 2 pkgProblemResolver with broken count: 0 77s Done 77s The following additional packages will be installed: 77s fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-urw-base35 77s libblas3 libcairo2 libdeflate0 libfontconfig1 libfontenc1 libgfortran5 77s libgomp1 libgraphite2-3 libharfbuzz0b libimagequant0 libjbig0 libjpeg-turbo8 77s libjpeg8 libjs-jquery libjs-jquery-hotkeys libjs-jquery-isonscreen 77s libjs-jquery-metadata libjs-jquery-tablesorter 77s libjs-jquery-throttle-debounce liblapack3 liblcms2-2 liblerc4 libopenjp2-7 77s libpixman-1-0 libpython3.13-minimal libpython3.13-stdlib libraqm0 77s libsharpyuv0 libtiff6 libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 77s libxcb-shm0 libxrender1 ncbi-acc-download python3-all python3-biopython 77s python3-cairo python3-coverage python3-freetype python3-iniconfig 77s python3-numpy python3-packaging python3-pil python3-pluggy python3-pytest 77s python3-pytest-cov python3-pytest-mock python3-reportlab 77s python3-requests-mock python3-rlpycairo python3.13 python3.13-minimal 77s sgml-base w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core 77s Suggested packages: 77s fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre liblcms2-utils 77s python3-tk bwa clustalo clustalw dialign dssp emboss fasttree mafft muscle3 77s phylip phyml prank probcons python3-mysqldb python3-matplotlib python3-mmtf 77s python3-rdflib python3-psycopg2 python3-scipy raxml samtools t-coffee wise 77s python-coverage-doc gcc gfortran python-numpy-doc python3-dev python-pil-doc 77s python-pytest-mock-doc pdf-viewer python3-egenix-mxtexttools 77s python-reportlab-doc rl-accel rl-renderpm python3.13-venv python3.13-doc 77s binfmt-support sgml-base-doc debhelper 77s Recommended packages: 77s javascript-common python-biopython-doc ncbi-blast+ python3-olefile 77s fonts-dejavu-extra 77s The following NEW packages will be installed: 77s autopkgtest-satdep fontconfig-config fonts-dejavu-core fonts-dejavu-mono 77s fonts-urw-base35 libblas3 libcairo2 libdeflate0 libfontconfig1 libfontenc1 77s libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libimagequant0 libjbig0 77s libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-hotkeys 77s libjs-jquery-isonscreen libjs-jquery-metadata libjs-jquery-tablesorter 77s libjs-jquery-throttle-debounce liblapack3 liblcms2-2 liblerc4 libopenjp2-7 77s libpixman-1-0 libpython3.13-minimal libpython3.13-stdlib libraqm0 77s libsharpyuv0 libtiff6 libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 77s libxcb-shm0 libxrender1 ncbi-acc-download python3-all python3-biopython 77s python3-cairo python3-coverage python3-freetype python3-iniconfig 77s python3-numpy python3-packaging python3-pil python3-pluggy python3-pytest 77s python3-pytest-cov python3-pytest-mock python3-reportlab 77s python3-requests-mock python3-rlpycairo python3.13 python3.13-minimal 77s sgml-base w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core 77s 0 upgraded, 65 newly installed, 0 to remove and 0 not upgraded. 77s Need to get 35.4 MB/35.4 MB of archives. 77s After this operation, 116 MB of additional disk space will be used. 77s Get:1 /tmp/autopkgtest.vVcyaG/1-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [756 B] 77s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-minimal amd64 3.13.0-2 [879 kB] 77s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-minimal amd64 3.13.0-2 [2188 kB] 77s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 sgml-base all 1.31 [11.4 kB] 77s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 77s Get:6 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-jquery-hotkeys all 0~20130707+git2d51e3a9+dfsg-2.1 [11.5 kB] 77s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB] 77s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-core all 2.37-8 [835 kB] 77s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontenc1 amd64 1:1.1.8-1build1 [14.0 kB] 77s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 77s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 77s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 xfonts-utils amd64 1:7.7+7 [97.1 kB] 77s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-urw-base35 all 20200910-8 [11.0 MB] 77s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig-config amd64 2.15.0-1.1ubuntu2 [37.3 kB] 77s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.0-3build2 [247 kB] 77s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontconfig1 amd64 2.15.0-1.1ubuntu2 [139 kB] 77s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 libpixman-1-0 amd64 0.44.0-3 [427 kB] 77s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-render0 amd64 1.17.0-2 [16.2 kB] 77s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-shm0 amd64 1.17.0-2 [5758 B] 77s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 libxrender1 amd64 1:0.9.10-1.1build1 [19.0 kB] 77s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 libcairo2 amd64 1.18.2-2 [569 kB] 77s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate0 amd64 1.22-1 [64.5 kB] 77s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 14.2.0-8ubuntu1 [909 kB] 77s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 libgomp1 amd64 14.2.0-8ubuntu1 [148 kB] 77s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB] 77s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 libharfbuzz0b amd64 10.0.1-1 [540 kB] 77s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 libimagequant0 amd64 2.18.0-1build1 [36.3 kB] 77s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg-turbo8 amd64 2.1.5-2ubuntu2 [150 kB] 77s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 77s Get:30 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-jquery-metadata all 12-4 [6582 B] 77s Get:31 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-jquery-tablesorter all 1:2.31.3+dfsg1-4 [192 kB] 77s Get:32 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-jquery-throttle-debounce all 1.1+dfsg.1-2 [12.5 kB] 77s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.0-3build2 [2668 kB] 77s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 liblcms2-2 amd64 2.16-2 [212 kB] 77s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 liblerc4 amd64 4.0.0+ds-4ubuntu2 [179 kB] 77s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-stdlib amd64 3.13.0-2 [2107 kB] 77s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 libraqm0 amd64 0.10.1-1build1 [15.0 kB] 77s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 libsharpyuv0 amd64 1.4.0-0.1 [17.5 kB] 77s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB] 78s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebp7 amd64 1.4.0-0.1 [231 kB] 78s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 libtiff6 amd64 4.5.1+git230720-4ubuntu4 [200 kB] 78s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpdemux2 amd64 1.4.0-0.1 [12.4 kB] 78s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpmux3 amd64 1.4.0-0.1 [25.8 kB] 78s Get:44 http://ftpmaster.internal/ubuntu plucky/universe amd64 ncbi-acc-download all 0.2.8-3 [13.3 kB] 78s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13 amd64 3.13.0-2 [719 kB] 78s Get:46 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-all amd64 3.12.7-1 [890 B] 78s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-numpy amd64 1:1.26.4+ds-11build1 [4479 kB] 78s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 libopenjp2-7 amd64 2.5.0-2ubuntu1 [184 kB] 78s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-pil amd64 10.4.0-1ubuntu1 [463 kB] 78s Get:50 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-cairo amd64 1.26.1-2 [119 kB] 78s Get:51 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-freetype all 2.5.1-1 [92.3 kB] 78s Get:52 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-rlpycairo all 0.3.0-3 [9130 B] 78s Get:53 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-reportlab all 4.2.5-1 [1107 kB] 78s Get:54 http://ftpmaster.internal/ubuntu plucky/main amd64 xml-core all 0.19 [20.3 kB] 78s Get:55 http://ftpmaster.internal/ubuntu plucky/universe amd64 w3c-sgml-lib all 1.3-3 [280 kB] 78s Get:56 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-biopython amd64 1.84+dfsg-4 [1714 kB] 78s Get:57 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-coverage amd64 7.4.4+dfsg1-0ubuntu2 [147 kB] 78s Get:58 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-iniconfig all 1.1.1-2 [6024 B] 78s Get:59 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-packaging all 24.1-1 [41.4 kB] 78s Get:60 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pluggy all 1.5.0-1 [21.0 kB] 78s Get:61 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pytest all 8.3.3-1 [251 kB] 78s Get:62 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-jquery-isonscreen all 1.2.0-1.1 [3244 B] 78s Get:63 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pytest-cov all 5.0.0-1 [21.3 kB] 78s Get:64 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pytest-mock all 3.14.0-2 [11.7 kB] 78s Get:65 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-requests-mock all 1.12.1-2 [17.8 kB] 78s Fetched 35.4 MB in 1s (66.8 MB/s) 78s Selecting previously unselected package libpython3.13-minimal:amd64. 78s (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 ... 75548 files and directories currently installed.) 78s Preparing to unpack .../00-libpython3.13-minimal_3.13.0-2_amd64.deb ... 78s Unpacking libpython3.13-minimal:amd64 (3.13.0-2) ... 78s Selecting previously unselected package python3.13-minimal. 78s Preparing to unpack .../01-python3.13-minimal_3.13.0-2_amd64.deb ... 78s Unpacking python3.13-minimal (3.13.0-2) ... 78s Selecting previously unselected package sgml-base. 78s Preparing to unpack .../02-sgml-base_1.31_all.deb ... 78s Unpacking sgml-base (1.31) ... 78s Selecting previously unselected package libjs-jquery. 78s Preparing to unpack .../03-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 78s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 78s Selecting previously unselected package libjs-jquery-hotkeys. 78s Preparing to unpack .../04-libjs-jquery-hotkeys_0~20130707+git2d51e3a9+dfsg-2.1_all.deb ... 78s Unpacking libjs-jquery-hotkeys (0~20130707+git2d51e3a9+dfsg-2.1) ... 78s Selecting previously unselected package fonts-dejavu-mono. 78s Preparing to unpack .../05-fonts-dejavu-mono_2.37-8_all.deb ... 78s Unpacking fonts-dejavu-mono (2.37-8) ... 78s Selecting previously unselected package fonts-dejavu-core. 78s Preparing to unpack .../06-fonts-dejavu-core_2.37-8_all.deb ... 78s Unpacking fonts-dejavu-core (2.37-8) ... 78s Selecting previously unselected package libfontenc1:amd64. 78s Preparing to unpack .../07-libfontenc1_1%3a1.1.8-1build1_amd64.deb ... 78s Unpacking libfontenc1:amd64 (1:1.1.8-1build1) ... 78s Selecting previously unselected package x11-common. 78s Preparing to unpack .../08-x11-common_1%3a7.7+23ubuntu3_all.deb ... 78s Unpacking x11-common (1:7.7+23ubuntu3) ... 78s Selecting previously unselected package xfonts-encodings. 78s Preparing to unpack .../09-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 78s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 78s Selecting previously unselected package xfonts-utils. 78s Preparing to unpack .../10-xfonts-utils_1%3a7.7+7_amd64.deb ... 78s Unpacking xfonts-utils (1:7.7+7) ... 78s Selecting previously unselected package fonts-urw-base35. 78s Preparing to unpack .../11-fonts-urw-base35_20200910-8_all.deb ... 79s Unpacking fonts-urw-base35 (20200910-8) ... 79s Selecting previously unselected package fontconfig-config. 79s Preparing to unpack .../12-fontconfig-config_2.15.0-1.1ubuntu2_amd64.deb ... 79s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ... 79s Selecting previously unselected package libblas3:amd64. 79s Preparing to unpack .../13-libblas3_3.12.0-3build2_amd64.deb ... 79s Unpacking libblas3:amd64 (3.12.0-3build2) ... 79s Selecting previously unselected package libfontconfig1:amd64. 79s Preparing to unpack .../14-libfontconfig1_2.15.0-1.1ubuntu2_amd64.deb ... 79s Unpacking libfontconfig1:amd64 (2.15.0-1.1ubuntu2) ... 79s Selecting previously unselected package libpixman-1-0:amd64. 79s Preparing to unpack .../15-libpixman-1-0_0.44.0-3_amd64.deb ... 79s Unpacking libpixman-1-0:amd64 (0.44.0-3) ... 79s Selecting previously unselected package libxcb-render0:amd64. 79s Preparing to unpack .../16-libxcb-render0_1.17.0-2_amd64.deb ... 79s Unpacking libxcb-render0:amd64 (1.17.0-2) ... 79s Selecting previously unselected package libxcb-shm0:amd64. 79s Preparing to unpack .../17-libxcb-shm0_1.17.0-2_amd64.deb ... 79s Unpacking libxcb-shm0:amd64 (1.17.0-2) ... 79s Selecting previously unselected package libxrender1:amd64. 79s Preparing to unpack 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81s Setting up x11-common (1:7.7+23ubuntu3) ... 82s Setting up libdeflate0:amd64 (1.22-1) ... 82s Setting up python3-coverage (7.4.4+dfsg1-0ubuntu2) ... 82s Setting up libxcb-shm0:amd64 (1.17.0-2) ... 82s Setting up libjs-jquery-throttle-debounce (1.1+dfsg.1-2) ... 82s Setting up libgomp1:amd64 (14.2.0-8ubuntu1) ... 82s Setting up python3-freetype (2.5.1-1) ... 82s Setting up libjbig0:amd64 (2.1-6.1ubuntu2) ... 82s Setting up libpython3.13-minimal:amd64 (3.13.0-2) ... 82s Setting up libfontenc1:amd64 (1:1.1.8-1build1) ... 82s Setting up libblas3:amd64 (3.12.0-3build2) ... 82s 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 82s Setting up python3-packaging (24.1-1) ... 82s Setting up python3-requests-mock (1.12.1-2) ... 83s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 83s Setting up libimagequant0:amd64 (2.18.0-1build1) ... 83s Setting up fonts-dejavu-mono (2.37-8) 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mode 84s Setting up python3.13 (3.13.0-2) ... 85s Setting up fontconfig-config (2.15.0-1.1ubuntu2) ... 85s Setting up python3-pytest (8.3.3-1) ... 85s Setting up libwebpdemux2:amd64 (1.4.0-0.1) ... 85s Setting up python3-all (3.12.7-1) ... 85s Setting up xfonts-utils (1:7.7+7) ... 85s Setting up libjs-jquery-metadata (12-4) ... 85s Setting up libraqm0:amd64 (0.10.1-1build1) ... 85s Setting up libjs-jquery-isonscreen (1.2.0-1.1) ... 85s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 89s Setting up libjs-jquery-tablesorter (1:2.31.3+dfsg1-4) ... 89s Setting up python3-pytest-mock (3.14.0-2) ... 89s Setting up libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ... 89s Setting up xml-core (0.19) ... 89s Setting up libfontconfig1:amd64 (2.15.0-1.1ubuntu2) ... 89s Setting up python3-pytest-cov (5.0.0-1) ... 89s Setting up fonts-urw-base35 (20200910-8) ... 89s Setting up libcairo2:amd64 (1.18.2-2) ... 89s Setting up python3-pil:amd64 (10.4.0-1ubuntu1) ... 90s Setting up python3-cairo (1.26.1-2) ... 90s Setting up python3-rlpycairo (0.3.0-3) ... 90s Setting up python3-reportlab (4.2.5-1) ... 92s Processing triggers for libc-bin (2.40-1ubuntu3) ... 92s Processing triggers for systemd (256.5-2ubuntu4) ... 92s Processing triggers for man-db (2.12.1-3) ... 93s Processing triggers for sgml-base (1.31) ... 93s Setting up w3c-sgml-lib (1.3-3) ... 119s Setting up python3-biopython (1.84+dfsg-4) ... 121s Setting up autopkgtest-satdep (0) ... 124s (Reading database ... 80039 files and directories currently installed.) 124s Removing autopkgtest-satdep (0) ... 124s autopkgtest [09:04:20]: test run-unit-test: [----------------------- 124s /tmp/autopkgtest.vVcyaG/build.hA4/src/tests /tmp/autopkgtest.vVcyaG/build.hA4/src 124s Testing with python3.13 in /tmp/autopkgtest.vVcyaG/build.hA4/src/tests: 125s ============================= test session starts ============================== 125s platform linux -- Python 3.13.0, pytest-8.3.3, pluggy-1.5.0 -- /usr/bin/python3.13 125s cachedir: .pytest_cache 125s rootdir: /tmp/autopkgtest.vVcyaG/build.hA4/src 125s plugins: requests_mock-1.12.1, cov-5.0.0, mock-3.14.0, typeguard-4.4.1 125s collecting ... collected 32 items 125s 125s test_core.py::test_config PASSED [ 3%] 125s test_core.py::test_config_no_biopython PASSED [ 6%] 125s test_core.py::test_config_have_biopython FAILED [ 9%] 125s test_core.py::test_download_to_file PASSED [ 12%] 125s test_core.py::test_download_to_file_append PASSED [ 15%] 125s test_core.py::test_download_to_file_retry PASSED [ 18%] 125s test_core.py::test_build_params PASSED [ 21%] 125s test_core.py::test_generate_filename PASSED [ 25%] 125s test_core.py::test_validate_and_write_error_pattern_raises PASSED [ 28%] 125s test_core.py::test_validate_and_write_emit PASSED [ 31%] 125s test_core.py::test_validate_and_write_extended_validation FAILED [ 34%] 125s test_core.py::test_get_stream_exception PASSED [ 37%] 125s test_core.py::test_get_stream_bad_status PASSED [ 40%] 125s test_core.py::test_get_stream_too_many_requests PASSED [ 43%] 125s test_core.py::test_generate_url PASSED [ 46%] 125s test_core.py::test_generate_url_with_api_key PASSED [ 50%] 125s test_correct.py::test_download_and_validate_partial_wgs FAILED [ 53%] 125s test_download.py::test_write_stream PASSED [ 56%] 125s test_validate.py::test_run_extended_validation_no_biopython PASSED [ 59%] 125s test_validate.py::test_run_extended_validation_raises FAILED [ 62%] 125s test_validate.py::test_run_extended_validation_loads FAILED [ 65%] 125s test_wgs.py::test_init PASSED [ 68%] 125s test_wgs.py::test_get_ids PASSED [ 71%] 125s test_wgs.py::test_from_string PASSED [ 75%] 125s test_wgs.py::test_download_wgs_parts_no_biopython PASSED [ 78%] 125s test_wgs.py::test_download_wgs_parts_wgs FAILED [ 81%] 125s test_wgs.py::test_download_wgs_parts_wgs_retry FAILED [ 84%] 125s test_wgs.py::test_download_wgs_parts_wgs_scafld FAILED [ 87%] 125s test_wgs.py::test_download_wgs_parts_supercontig FAILED [ 90%] 125s test_wgs.py::test_download_wgs_parts_supercontig_retry FAILED [ 93%] 125s test_wgs.py::test_download_wgs_no_parts FAILED [ 96%] 125s test_wgs.py::test_download_wgs_parts_tsa XFAIL [100%] 125s 125s =================================== FAILURES =================================== 125s __________________________ test_config_have_biopython __________________________ 125s 125s def test_config_have_biopython(): 125s """Test we detect Biopython.""" 125s > assert core.HAVE_BIOPYTHON 125s E assert False 125s E + where False = core.HAVE_BIOPYTHON 125s 125s test_core.py:46: AssertionError 125s _________________ test_validate_and_write_extended_validation __________________ 125s 125s req = 125s 125s def test_validate_and_write_extended_validation(req): 125s """Test extended validation before writing.""" 125s handle = StringIO() 125s req.get('http://fake/', text=u'>foo\nMAGIC') 125s r = requests.get('http://fake/') 125s > config = core.Config(extended_validation='loads', molecule='protein') 125s 125s test_core.py:226: 125s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 125s /usr/lib/python3/dist-packages/ncbi_acc_download/core.py:64: in __init__ 125s self.extended_validation = extended_validation 125s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 125s 125s self = , value = 'loads' 125s 125s @extended_validation.setter 125s def extended_validation(self, value): 125s if value != 'none' and not HAVE_BIOPYTHON: 125s > raise ValueError("Asked for extended validation, but Biopython not available") 125s E ValueError: Asked for extended validation, but Biopython not available 125s 125s /usr/lib/python3/dist-packages/ncbi_acc_download/core.py:96: ValueError 125s ____________________ test_download_and_validate_partial_wgs ____________________ 125s 125s req = 125s 125s def test_download_and_validate_partial_wgs(req): 125s handle = StringIO(open(full_path('partialcontig.gbk'), 'r').read()) 125s > assert validate.run_extended_validation(handle, 'genbank', 'loads') 125s E AssertionError: assert False 125s E + where False = (<_io.StringIO object at 0x79962c9daec0>, 'genbank', 'loads') 125s E + where = validate.run_extended_validation 125s 125s test_correct.py:15: AssertionError 125s _____________________ test_run_extended_validation_raises ______________________ 125s 125s monkeypatch = <_pytest.monkeypatch.MonkeyPatch object at 0x79962ca33bf0> 125s mocker = 125s 125s def test_run_extended_validation_raises(monkeypatch, mocker): 125s """Test the "seqence loads" validator catches exceptions in SeqIO.parse().""" 125s seqio_mock = mocker.MagicMock() 125s seqio_mock.parse = mocker.MagicMock(side_effect=ValueError) 125s > monkeypatch.setattr(validate, 'SeqIO', seqio_mock) 125s E AttributeError: has no attribute 'SeqIO' 125s 125s test_validate.py:19: AttributeError 125s ______________________ test_run_extended_validation_loads ______________________ 125s 125s def test_run_extended_validation_loads(): 125s """Test the "sequence loads" validator.""" 125s handle = StringIO(u'>foo\nATGC\n>bar\nATGTGA\n') 125s > assert validate.run_extended_validation(handle, 'fasta', 'loads') 125s E AssertionError: assert False 125s E + where False = (<_io.StringIO object at 0x79962c9da680>, 'fasta', 'loads') 125s E + where = validate.run_extended_validation 125s 125s test_validate.py:29: AssertionError 125s _________________________ test_download_wgs_parts_wgs __________________________ 125s 125s req = 125s 125s def test_download_wgs_parts_wgs(req): 125s cfg = Config(format="genbank") 125s wgs_contig = open(full_path('wgs.gbk'), 'rt') 125s req.get( 125s ENTREZ_URL, 125s body=open(full_path('wgs_full.gbk'), 'rb'), 125s headers={"Content-Type": "text/plain; charset=UTF-8"}, 125s ) 125s 125s outhandle = wgs.download_wgs_parts(wgs_contig, cfg) 125s wgs_full = open(full_path('wgs_full.gbk'), 'rt') 125s > assert outhandle.getvalue() == wgs_full.read() 125s E AttributeError: '_io.TextIOWrapper' object has no attribute 'getvalue' 125s 125s test_wgs.py:95: AttributeError 125s ______________________ test_download_wgs_parts_wgs_retry _______________________ 125s 125s req = 125s 125s def test_download_wgs_parts_wgs_retry(req): 125s cfg = Config(format="genbank") 125s wgs_contig = open(full_path('wgs.gbk'), 'rt') 125s req.get(ENTREZ_URL, response_list=[ 125s {"text": u'Whoa, slow down', "status_code": 429, "headers": {"Retry-After": "0"}}, 125s { 125s "body": open(full_path('wgs_full.gbk'), 'rb'), 125s "headers": {"Content-Type": "text/plain; charset=UTF-8"}, 125s }, 125s ]) 125s 125s outhandle = wgs.download_wgs_parts(wgs_contig, cfg) 125s wgs_full = open(full_path('wgs_full.gbk'), 'rt') 125s > assert outhandle.getvalue() == wgs_full.read() 125s E AttributeError: '_io.TextIOWrapper' object has no attribute 'getvalue' 125s 125s test_wgs.py:113: AttributeError 125s ______________________ test_download_wgs_parts_wgs_scafld ______________________ 125s 125s req = 125s 125s def test_download_wgs_parts_wgs_scafld(req): 125s cfg = Config(format="genbank") 125s wgs_contig = open(full_path('wgs_scafld.gbk'), 'rt') 125s with open(full_path('wgs_full.gbk'), 'rt') as handle: 125s full_file = handle.read() 125s req.get(ENTREZ_URL, text=full_file) 125s 125s outhandle = wgs.download_wgs_parts(wgs_contig, cfg) 125s > assert outhandle.getvalue() == full_file 125s E AttributeError: '_io.TextIOWrapper' object has no attribute 'getvalue' 125s 125s test_wgs.py:126: AttributeError 125s _____________________ test_download_wgs_parts_supercontig ______________________ 125s 125s req = 125s 125s def test_download_wgs_parts_supercontig(req): 125s cfg = Config(format="genbank") 125s supercontig = open(full_path('supercontig.gbk'), 'rt') 125s req.get( 125s ENTREZ_URL, 125s body=open(full_path('supercontig_full.gbk'), 'rb'), 125s headers={"Content-Type": "text/plain; charset=UTF-8"}, 125s ) 125s 125s outhandle = wgs.download_wgs_parts(supercontig, cfg) 125s supercontig_full = open(full_path('supercontig_full.gbk'), 'rt') 125s > assert outhandle.getvalue() == supercontig_full.read() 125s E AttributeError: '_io.TextIOWrapper' object has no attribute 'getvalue' 125s 125s test_wgs.py:141: AttributeError 125s __________________ test_download_wgs_parts_supercontig_retry ___________________ 125s 125s req = 125s 125s def test_download_wgs_parts_supercontig_retry(req): 125s cfg = Config(format="genbank") 125s supercontig = open(full_path('supercontig.gbk'), 'rt') 125s req.get(ENTREZ_URL, response_list=[ 125s {"text": u'Whoa, slow down', "status_code": 429, "headers": {"Retry-After": "0"}}, 125s { 125s "body": open(full_path('supercontig_full.gbk'), 'rb'), 125s "headers": {"Content-Type": "text/plain; charset=UTF-8"}, 125s }, 125s ]) 125s 125s outhandle = wgs.download_wgs_parts(supercontig, cfg) 125s supercontig_full = open(full_path('supercontig_full.gbk'), 'rt') 125s > assert outhandle.getvalue() == supercontig_full.read() 125s E AttributeError: '_io.TextIOWrapper' object has no attribute 'getvalue' 125s 125s test_wgs.py:159: AttributeError 125s __________________________ test_download_wgs_no_parts __________________________ 125s 125s req = 125s 125s def test_download_wgs_no_parts(req): 125s cfg = Config(format="genbank") 125s supercontig = open(full_path('supercontig_full.gbk'), 'rt') 125s req.get(ENTREZ_URL, status_code=404) 125s 125s outhandle = wgs.download_wgs_parts(supercontig, cfg) 125s supercontig_full = open(full_path('supercontig_full.gbk'), 'rt') 125s > assert outhandle.getvalue() == supercontig_full.read() 125s E AttributeError: '_io.TextIOWrapper' object has no attribute 'getvalue' 125s 125s test_wgs.py:171: AttributeError 125s =========================== short test summary info ============================ 125s FAILED test_core.py::test_config_have_biopython - assert False 125s FAILED test_core.py::test_validate_and_write_extended_validation - ValueError... 125s FAILED test_correct.py::test_download_and_validate_partial_wgs - AssertionErr... 125s FAILED test_validate.py::test_run_extended_validation_raises - AttributeError... 125s FAILED test_validate.py::test_run_extended_validation_loads - AssertionError:... 125s FAILED test_wgs.py::test_download_wgs_parts_wgs - AttributeError: '_io.TextIO... 125s FAILED test_wgs.py::test_download_wgs_parts_wgs_retry - AttributeError: '_io.... 125s FAILED test_wgs.py::test_download_wgs_parts_wgs_scafld - AttributeError: '_io... 125s FAILED test_wgs.py::test_download_wgs_parts_supercontig - AttributeError: '_i... 125s FAILED test_wgs.py::test_download_wgs_parts_supercontig_retry - AttributeErro... 125s FAILED test_wgs.py::test_download_wgs_no_parts - AttributeError: '_io.TextIOW... 125s =================== 11 failed, 20 passed, 1 xfailed in 0.21s =================== 126s autopkgtest [09:04:22]: test run-unit-test: -----------------------] 126s autopkgtest [09:04:22]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 126s run-unit-test FAIL non-zero exit status 1 126s autopkgtest [09:04:22]: @@@@@@@@@@@@@@@@@@@@ summary 126s run-unit-test FAIL non-zero exit status 1 137s nova [W] Skipping flock for amd64 137s Creating nova instance adt-plucky-amd64-ncbi-acc-download-20241113-090216-juju-7f2275-prod-proposed-migration-environment-20-912eab36-7770-43e8-aca0-91e5ce3cdd59 from image adt/ubuntu-plucky-amd64-server-20241113.img (UUID 76b850f9-98f4-4b79-af06-fa11000b95b2)...