0s autopkgtest [12:02:16]: starting date and time: 2024-11-13 12:02:16+0000 0s autopkgtest [12:02:16]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [12:02:16]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.d32wv3su/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-s390x --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-s390x-10.secgroup --name adt-plucky-s390x-ncbi-acc-download-20241113-120216-juju-7f2275-prod-proposed-migration-environment-15-b8a98a0c-c160-4a72-a143-8feb176c94e4 --image adt/ubuntu-plucky-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration-s390x -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/ 101s autopkgtest [12:03:57]: testbed dpkg architecture: s390x 101s autopkgtest [12:03:57]: testbed apt version: 2.9.8 101s autopkgtest [12:03:57]: @@@@@@@@@@@@@@@@@@@@ test bed setup 102s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 102s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [849 kB] 102s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [76.4 kB] 102s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 102s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.3 kB] 102s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x Packages [85.8 kB] 102s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x Packages [565 kB] 102s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x Packages [16.6 kB] 102s Fetched 1689 kB in 1s (2302 kB/s) 103s Reading package lists... 104s Reading package lists... 105s Building dependency tree... 105s Reading state information... 105s Calculating upgrade... 105s The following NEW packages will be installed: 105s python3.13-gdbm 105s The following packages will be upgraded: 105s libgpgme11t64 libpython3-stdlib python3 python3-gdbm python3-minimal 105s 5 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 105s Need to get 252 kB of archives. 105s After this operation, 98.3 kB of additional disk space will be used. 105s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x python3-minimal s390x 3.12.7-1 [27.4 kB] 105s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x python3 s390x 3.12.7-1 [24.0 kB] 105s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libpython3-stdlib s390x 3.12.7-1 [10.0 kB] 105s Get:4 http://ftpmaster.internal/ubuntu plucky/main s390x python3.13-gdbm s390x 3.13.0-2 [31.0 kB] 105s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x python3-gdbm s390x 3.12.7-1 [8642 B] 105s Get:6 http://ftpmaster.internal/ubuntu plucky/main s390x libgpgme11t64 s390x 1.23.2-5ubuntu4 [151 kB] 105s Fetched 252 kB in 0s (574 kB/s) 106s (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 ... 55510 files and directories currently installed.) 106s Preparing to unpack .../python3-minimal_3.12.7-1_s390x.deb ... 106s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ... 106s Setting up python3-minimal (3.12.7-1) ... 106s (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 ... 55510 files and directories currently installed.) 106s Preparing to unpack .../python3_3.12.7-1_s390x.deb ... 106s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ... 106s Preparing to unpack .../libpython3-stdlib_3.12.7-1_s390x.deb ... 106s Unpacking libpython3-stdlib:s390x (3.12.7-1) over (3.12.6-0ubuntu1) ... 106s Selecting previously unselected package python3.13-gdbm. 106s Preparing to unpack .../python3.13-gdbm_3.13.0-2_s390x.deb ... 106s Unpacking python3.13-gdbm (3.13.0-2) ... 106s Preparing to unpack .../python3-gdbm_3.12.7-1_s390x.deb ... 106s Unpacking python3-gdbm:s390x (3.12.7-1) over (3.12.6-1ubuntu1) ... 106s Preparing to unpack .../libgpgme11t64_1.23.2-5ubuntu4_s390x.deb ... 106s Unpacking libgpgme11t64:s390x (1.23.2-5ubuntu4) over (1.18.0-4.1ubuntu4) ... 106s Setting up libgpgme11t64:s390x (1.23.2-5ubuntu4) ... 106s Setting up python3.13-gdbm (3.13.0-2) ... 106s Setting up libpython3-stdlib:s390x (3.12.7-1) ... 106s Setting up python3 (3.12.7-1) ... 106s Setting up python3-gdbm:s390x (3.12.7-1) ... 106s Processing triggers for man-db (2.12.1-3) ... 106s Processing triggers for libc-bin (2.40-1ubuntu3) ... 107s Reading package lists... 107s Building dependency tree... 107s Reading state information... 107s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 107s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 107s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 107s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 107s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 108s Reading package lists... 108s Reading package lists... 108s Building dependency tree... 108s Reading state information... 108s Calculating upgrade... 108s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 108s Reading package lists... 108s Building dependency tree... 108s Reading state information... 109s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 112s autopkgtest [12:04:07]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP Mon Sep 16 12:49:35 UTC 2024 112s autopkgtest [12:04:08]: @@@@@@@@@@@@@@@@@@@@ apt-source ncbi-acc-download 113s Get:1 http://ftpmaster.internal/ubuntu plucky/universe ncbi-acc-download 0.2.8-3 (dsc) [2434 B] 113s Get:2 http://ftpmaster.internal/ubuntu plucky/universe ncbi-acc-download 0.2.8-3 (tar) [20.9 kB] 113s Get:3 http://ftpmaster.internal/ubuntu plucky/universe ncbi-acc-download 0.2.8-3 (diff) [4420 B] 113s gpgv: Signature made Thu Aug 1 23:03:26 2024 UTC 113s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 113s gpgv: issuer "tille@debian.org" 113s gpgv: Can't check signature: No public key 113s dpkg-source: warning: cannot verify inline signature for ./ncbi-acc-download_0.2.8-3.dsc: no acceptable signature found 113s autopkgtest [12:04:09]: testing package ncbi-acc-download version 0.2.8-3 113s autopkgtest [12:04:09]: build not needed 114s autopkgtest [12:04:10]: test run-unit-test: preparing testbed 115s Reading package lists... 116s Building dependency tree... 116s Reading state information... 116s Starting pkgProblemResolver with broken count: 0 116s Starting 2 pkgProblemResolver with broken count: 0 116s Done 116s The following additional packages will be installed: 116s fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-urw-base35 116s libblas3 libcairo2 libdeflate0 libfontconfig1 libfontenc1 libfreetype6 116s libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libimagequant0 libjbig0 116s libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-hotkeys 116s libjs-jquery-isonscreen libjs-jquery-metadata libjs-jquery-tablesorter 116s libjs-jquery-throttle-debounce liblapack3 liblcms2-2 libopenjp2-7 116s libpixman-1-0 libpython3.13-minimal libpython3.13-stdlib libraqm0 116s libsharpyuv0 libtiff6 libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 116s libxcb-shm0 libxrender1 ncbi-acc-download python3-all python3-biopython 116s python3-cairo python3-coverage python3-freetype python3-iniconfig 116s python3-numpy python3-packaging python3-pil python3-pluggy python3-pytest 116s python3-pytest-cov python3-pytest-mock python3-reportlab 116s python3-requests-mock python3-rlpycairo python3.13 python3.13-minimal 116s sgml-base w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core 116s Suggested packages: 116s fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre liblcms2-utils 116s python3-tk bwa clustalo clustalw dialign dssp emboss fasttree mafft muscle3 116s phylip phyml prank probcons python3-mysqldb python3-matplotlib python3-mmtf 116s python3-rdflib python3-psycopg2 python3-scipy raxml samtools t-coffee wise 116s python-coverage-doc gcc gfortran python-numpy-doc python3-dev python-pil-doc 116s python-pytest-mock-doc pdf-viewer python3-egenix-mxtexttools 116s python-reportlab-doc rl-accel rl-renderpm python3.13-venv python3.13-doc 116s binfmt-support sgml-base-doc debhelper 116s Recommended packages: 116s javascript-common python-biopython-doc ncbi-blast+ python3-olefile 116s fonts-dejavu-extra 116s The following NEW packages will be installed: 116s autopkgtest-satdep fontconfig-config fonts-dejavu-core fonts-dejavu-mono 116s fonts-urw-base35 libblas3 libcairo2 libdeflate0 libfontconfig1 libfontenc1 116s libfreetype6 libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b 116s libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 libjs-jquery 116s libjs-jquery-hotkeys libjs-jquery-isonscreen libjs-jquery-metadata 116s libjs-jquery-tablesorter libjs-jquery-throttle-debounce liblapack3 116s liblcms2-2 libopenjp2-7 libpixman-1-0 libpython3.13-minimal 116s libpython3.13-stdlib libraqm0 libsharpyuv0 libtiff6 libwebp7 libwebpdemux2 116s libwebpmux3 libxcb-render0 libxcb-shm0 libxrender1 ncbi-acc-download 116s python3-all python3-biopython python3-cairo python3-coverage 116s python3-freetype python3-iniconfig python3-numpy python3-packaging 116s python3-pil python3-pluggy python3-pytest python3-pytest-cov 116s python3-pytest-mock python3-reportlab python3-requests-mock 116s python3-rlpycairo python3.13 python3.13-minimal sgml-base w3c-sgml-lib 116s x11-common xfonts-encodings xfonts-utils xml-core 116s 0 upgraded, 65 newly installed, 0 to remove and 0 not upgraded. 116s Need to get 35.1 MB/35.1 MB of archives. 116s After this operation, 112 MB of additional disk space will be used. 116s Get:1 /tmp/autopkgtest.c9ORLZ/1-autopkgtest-satdep.deb autopkgtest-satdep s390x 0 [764 B] 116s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x libpython3.13-minimal s390x 3.13.0-2 [877 kB] 117s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x python3.13-minimal s390x 3.13.0-2 [2172 kB] 117s Get:4 http://ftpmaster.internal/ubuntu plucky/main s390x sgml-base all 1.31 [11.4 kB] 117s Get:5 http://ftpmaster.internal/ubuntu plucky/main s390x libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 117s Get:6 http://ftpmaster.internal/ubuntu plucky/universe s390x libjs-jquery-hotkeys all 0~20130707+git2d51e3a9+dfsg-2.1 [11.5 kB] 117s Get:7 http://ftpmaster.internal/ubuntu plucky/main s390x fonts-dejavu-mono all 2.37-8 [502 kB] 117s Get:8 http://ftpmaster.internal/ubuntu plucky/main s390x fonts-dejavu-core all 2.37-8 [835 kB] 117s Get:9 http://ftpmaster.internal/ubuntu plucky/main s390x libfontenc1 s390x 1:1.1.8-1build1 [14.8 kB] 117s Get:10 http://ftpmaster.internal/ubuntu plucky/main s390x libfreetype6 s390x 2.13.3+dfsg-1 [431 kB] 117s Get:11 http://ftpmaster.internal/ubuntu plucky/main s390x x11-common all 1:7.7+23ubuntu3 [21.7 kB] 117s Get:12 http://ftpmaster.internal/ubuntu plucky/main s390x xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 117s Get:13 http://ftpmaster.internal/ubuntu plucky/main s390x xfonts-utils s390x 1:7.7+7 [101 kB] 117s Get:14 http://ftpmaster.internal/ubuntu plucky/main s390x fonts-urw-base35 all 20200910-8 [11.0 MB] 117s Get:15 http://ftpmaster.internal/ubuntu plucky/main s390x fontconfig-config s390x 2.15.0-1.1ubuntu2 [37.4 kB] 117s Get:16 http://ftpmaster.internal/ubuntu plucky/main s390x libblas3 s390x 3.12.0-3build2 [238 kB] 117s Get:17 http://ftpmaster.internal/ubuntu plucky/main s390x libfontconfig1 s390x 2.15.0-1.1ubuntu2 [150 kB] 117s Get:18 http://ftpmaster.internal/ubuntu plucky/main s390x libpixman-1-0 s390x 0.44.0-3 [201 kB] 117s Get:19 http://ftpmaster.internal/ubuntu plucky/main s390x libxcb-render0 s390x 1.17.0-2 [17.0 kB] 117s Get:20 http://ftpmaster.internal/ubuntu plucky/main s390x libxcb-shm0 s390x 1.17.0-2 [5862 B] 117s Get:21 http://ftpmaster.internal/ubuntu plucky/main s390x libxrender1 s390x 1:0.9.10-1.1build1 [20.4 kB] 117s Get:22 http://ftpmaster.internal/ubuntu plucky/main s390x libcairo2 s390x 1.18.2-2 [580 kB] 117s Get:23 http://ftpmaster.internal/ubuntu plucky/main s390x libdeflate0 s390x 1.22-1 [46.1 kB] 117s Get:24 http://ftpmaster.internal/ubuntu plucky/main s390x libgfortran5 s390x 14.2.0-8ubuntu1 [587 kB] 117s Get:25 http://ftpmaster.internal/ubuntu plucky/main s390x libgomp1 s390x 14.2.0-8ubuntu1 [151 kB] 117s Get:26 http://ftpmaster.internal/ubuntu plucky/main s390x libgraphite2-3 s390x 1.3.14-2ubuntu1 [79.8 kB] 117s Get:27 http://ftpmaster.internal/ubuntu plucky/main s390x libharfbuzz0b s390x 10.0.1-1 [536 kB] 117s Get:28 http://ftpmaster.internal/ubuntu plucky/main s390x libimagequant0 s390x 2.18.0-1build1 [43.3 kB] 117s Get:29 http://ftpmaster.internal/ubuntu plucky/main s390x libjpeg-turbo8 s390x 2.1.5-2ubuntu2 [150 kB] 117s Get:30 http://ftpmaster.internal/ubuntu plucky/main s390x libjpeg8 s390x 8c-2ubuntu11 [2146 B] 117s Get:31 http://ftpmaster.internal/ubuntu plucky/universe s390x libjs-jquery-metadata all 12-4 [6582 B] 117s Get:32 http://ftpmaster.internal/ubuntu plucky/universe s390x libjs-jquery-tablesorter all 1:2.31.3+dfsg1-4 [192 kB] 117s Get:33 http://ftpmaster.internal/ubuntu plucky/universe s390x libjs-jquery-throttle-debounce all 1.1+dfsg.1-2 [12.5 kB] 117s Get:34 http://ftpmaster.internal/ubuntu plucky/main s390x liblapack3 s390x 3.12.0-3build2 [2953 kB] 117s Get:35 http://ftpmaster.internal/ubuntu plucky/main s390x liblcms2-2 s390x 2.16-2 [175 kB] 117s Get:36 http://ftpmaster.internal/ubuntu plucky/main s390x libpython3.13-stdlib s390x 3.13.0-2 [2086 kB] 117s Get:37 http://ftpmaster.internal/ubuntu plucky/main s390x libraqm0 s390x 0.10.1-1build1 [16.2 kB] 117s Get:38 http://ftpmaster.internal/ubuntu plucky/main s390x libsharpyuv0 s390x 1.4.0-0.1 [16.2 kB] 117s Get:39 http://ftpmaster.internal/ubuntu plucky/main s390x libjbig0 s390x 2.1-6.1ubuntu2 [33.1 kB] 117s Get:40 http://ftpmaster.internal/ubuntu plucky/main s390x libwebp7 s390x 1.4.0-0.1 [204 kB] 117s Get:41 http://ftpmaster.internal/ubuntu plucky/main s390x libtiff6 s390x 4.5.1+git230720-4ubuntu4 [217 kB] 117s Get:42 http://ftpmaster.internal/ubuntu plucky/main s390x libwebpdemux2 s390x 1.4.0-0.1 [12.2 kB] 117s Get:43 http://ftpmaster.internal/ubuntu plucky/main s390x libwebpmux3 s390x 1.4.0-0.1 [25.3 kB] 117s Get:44 http://ftpmaster.internal/ubuntu plucky/universe s390x ncbi-acc-download all 0.2.8-3 [13.3 kB] 118s Get:45 http://ftpmaster.internal/ubuntu plucky/main s390x python3.13 s390x 3.13.0-2 [719 kB] 118s Get:46 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x python3-all s390x 3.12.7-1 [890 B] 118s Get:47 http://ftpmaster.internal/ubuntu plucky/main s390x python3-numpy s390x 1:1.26.4+ds-11build1 [4113 kB] 118s Get:48 http://ftpmaster.internal/ubuntu plucky/main s390x libopenjp2-7 s390x 2.5.0-2ubuntu1 [208 kB] 118s Get:49 http://ftpmaster.internal/ubuntu plucky/main s390x python3-pil s390x 10.4.0-1ubuntu1 [492 kB] 118s Get:50 http://ftpmaster.internal/ubuntu plucky/main s390x python3-cairo s390x 1.26.1-2 [119 kB] 118s Get:51 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-freetype all 2.5.1-1 [92.3 kB] 118s Get:52 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-rlpycairo all 0.3.0-3 [9130 B] 118s Get:53 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-reportlab all 4.2.5-1 [1107 kB] 118s Get:54 http://ftpmaster.internal/ubuntu plucky/main s390x xml-core all 0.19 [20.3 kB] 118s Get:55 http://ftpmaster.internal/ubuntu plucky/universe s390x w3c-sgml-lib all 1.3-3 [280 kB] 118s Get:56 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-biopython s390x 1.84+dfsg-4 [1721 kB] 118s Get:57 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-coverage s390x 7.4.4+dfsg1-0ubuntu2 [147 kB] 118s Get:58 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-iniconfig all 1.1.1-2 [6024 B] 118s Get:59 http://ftpmaster.internal/ubuntu plucky/main s390x python3-packaging all 24.1-1 [41.4 kB] 118s Get:60 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-pluggy all 1.5.0-1 [21.0 kB] 118s Get:61 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-pytest all 8.3.3-1 [251 kB] 118s Get:62 http://ftpmaster.internal/ubuntu plucky/universe s390x libjs-jquery-isonscreen all 1.2.0-1.1 [3244 B] 118s Get:63 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-pytest-cov all 5.0.0-1 [21.3 kB] 118s Get:64 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-pytest-mock all 3.14.0-2 [11.7 kB] 118s Get:65 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-requests-mock all 1.12.1-2 [17.8 kB] 118s Fetched 35.1 MB in 2s (18.0 MB/s) 118s Selecting previously unselected package libpython3.13-minimal:s390x. 118s (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 ... 55517 files and directories currently installed.) 118s Preparing to unpack .../00-libpython3.13-minimal_3.13.0-2_s390x.deb ... 118s Unpacking libpython3.13-minimal:s390x (3.13.0-2) ... 118s Selecting previously unselected package python3.13-minimal. 118s Preparing to unpack .../01-python3.13-minimal_3.13.0-2_s390x.deb ... 118s Unpacking python3.13-minimal (3.13.0-2) ... 118s Selecting previously unselected package sgml-base. 118s Preparing to unpack .../02-sgml-base_1.31_all.deb ... 118s Unpacking sgml-base (1.31) ... 118s Selecting previously unselected package libjs-jquery. 118s Preparing to unpack .../03-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 118s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 118s Selecting previously unselected package libjs-jquery-hotkeys. 118s Preparing to unpack .../04-libjs-jquery-hotkeys_0~20130707+git2d51e3a9+dfsg-2.1_all.deb ... 118s Unpacking libjs-jquery-hotkeys (0~20130707+git2d51e3a9+dfsg-2.1) ... 118s Selecting previously unselected package fonts-dejavu-mono. 118s Preparing to unpack .../05-fonts-dejavu-mono_2.37-8_all.deb ... 118s Unpacking fonts-dejavu-mono (2.37-8) ... 118s Selecting previously unselected package fonts-dejavu-core. 118s Preparing to unpack .../06-fonts-dejavu-core_2.37-8_all.deb ... 118s Unpacking fonts-dejavu-core (2.37-8) ... 118s Selecting previously unselected package libfontenc1:s390x. 118s Preparing to unpack .../07-libfontenc1_1%3a1.1.8-1build1_s390x.deb ... 118s Unpacking libfontenc1:s390x (1:1.1.8-1build1) ... 118s Selecting previously unselected package libfreetype6:s390x. 118s Preparing to unpack .../08-libfreetype6_2.13.3+dfsg-1_s390x.deb ... 118s Unpacking libfreetype6:s390x (2.13.3+dfsg-1) ... 118s Selecting previously unselected package x11-common. 118s Preparing to unpack .../09-x11-common_1%3a7.7+23ubuntu3_all.deb ... 118s Unpacking x11-common (1:7.7+23ubuntu3) ... 118s Selecting previously unselected package xfonts-encodings. 118s Preparing to unpack .../10-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 118s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 118s Selecting previously unselected package xfonts-utils. 118s Preparing to unpack .../11-xfonts-utils_1%3a7.7+7_s390x.deb ... 118s Unpacking xfonts-utils (1:7.7+7) ... 118s Selecting previously unselected package fonts-urw-base35. 118s Preparing to unpack .../12-fonts-urw-base35_20200910-8_all.deb ... 118s Unpacking fonts-urw-base35 (20200910-8) ... 119s Selecting previously unselected package fontconfig-config. 119s Preparing to unpack .../13-fontconfig-config_2.15.0-1.1ubuntu2_s390x.deb ... 119s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ... 119s Selecting previously unselected package libblas3:s390x. 119s Preparing to unpack .../14-libblas3_3.12.0-3build2_s390x.deb ... 119s Unpacking libblas3:s390x (3.12.0-3build2) ... 119s Selecting previously unselected package libfontconfig1:s390x. 119s Preparing to unpack .../15-libfontconfig1_2.15.0-1.1ubuntu2_s390x.deb ... 119s Unpacking libfontconfig1:s390x (2.15.0-1.1ubuntu2) ... 119s Selecting previously unselected package libpixman-1-0:s390x. 119s Preparing to unpack .../16-libpixman-1-0_0.44.0-3_s390x.deb ... 119s Unpacking libpixman-1-0:s390x (0.44.0-3) ... 119s Selecting previously unselected package libxcb-render0:s390x. 119s Preparing to unpack .../17-libxcb-render0_1.17.0-2_s390x.deb ... 119s Unpacking libxcb-render0:s390x (1.17.0-2) ... 119s Selecting previously unselected package libxcb-shm0:s390x. 119s Preparing to unpack .../18-libxcb-shm0_1.17.0-2_s390x.deb ... 119s Unpacking libxcb-shm0:s390x (1.17.0-2) ... 119s Selecting previously unselected package libxrender1:s390x. 119s Preparing to unpack .../19-libxrender1_1%3a0.9.10-1.1build1_s390x.deb ... 119s Unpacking libxrender1:s390x (1:0.9.10-1.1build1) ... 119s Selecting previously unselected package libcairo2:s390x. 119s Preparing to unpack .../20-libcairo2_1.18.2-2_s390x.deb ... 119s Unpacking libcairo2:s390x (1.18.2-2) ... 119s Selecting previously unselected package libdeflate0:s390x. 119s Preparing to unpack .../21-libdeflate0_1.22-1_s390x.deb ... 119s Unpacking libdeflate0:s390x (1.22-1) ... 119s Selecting previously unselected package libgfortran5:s390x. 119s Preparing to unpack .../22-libgfortran5_14.2.0-8ubuntu1_s390x.deb ... 119s Unpacking libgfortran5:s390x (14.2.0-8ubuntu1) ... 119s Selecting previously unselected package libgomp1:s390x. 119s Preparing to unpack .../23-libgomp1_14.2.0-8ubuntu1_s390x.deb ... 119s Unpacking libgomp1:s390x (14.2.0-8ubuntu1) ... 119s Selecting previously unselected package libgraphite2-3:s390x. 119s Preparing to unpack .../24-libgraphite2-3_1.3.14-2ubuntu1_s390x.deb ... 119s Unpacking libgraphite2-3:s390x (1.3.14-2ubuntu1) ... 119s Selecting previously unselected package libharfbuzz0b:s390x. 119s Preparing to unpack .../25-libharfbuzz0b_10.0.1-1_s390x.deb ... 119s Unpacking libharfbuzz0b:s390x (10.0.1-1) ... 119s Selecting previously unselected package libimagequant0:s390x. 119s Preparing to unpack .../26-libimagequant0_2.18.0-1build1_s390x.deb ... 119s Unpacking libimagequant0:s390x (2.18.0-1build1) ... 119s Selecting previously unselected package libjpeg-turbo8:s390x. 119s Preparing to unpack .../27-libjpeg-turbo8_2.1.5-2ubuntu2_s390x.deb ... 119s Unpacking libjpeg-turbo8:s390x (2.1.5-2ubuntu2) ... 119s Selecting previously unselected package libjpeg8:s390x. 119s Preparing to unpack .../28-libjpeg8_8c-2ubuntu11_s390x.deb ... 119s Unpacking libjpeg8:s390x (8c-2ubuntu11) ... 119s Selecting previously unselected package libjs-jquery-metadata. 119s Preparing to unpack .../29-libjs-jquery-metadata_12-4_all.deb ... 119s Unpacking libjs-jquery-metadata (12-4) ... 119s Selecting previously unselected package libjs-jquery-tablesorter. 119s Preparing to unpack .../30-libjs-jquery-tablesorter_1%3a2.31.3+dfsg1-4_all.deb ... 119s Unpacking libjs-jquery-tablesorter (1:2.31.3+dfsg1-4) ... 119s Selecting previously unselected package libjs-jquery-throttle-debounce. 119s Preparing to unpack .../31-libjs-jquery-throttle-debounce_1.1+dfsg.1-2_all.deb ... 119s Unpacking libjs-jquery-throttle-debounce (1.1+dfsg.1-2) ... 119s Selecting previously unselected package liblapack3:s390x. 119s Preparing to unpack .../32-liblapack3_3.12.0-3build2_s390x.deb ... 119s Unpacking liblapack3:s390x (3.12.0-3build2) ... 119s Selecting previously unselected package liblcms2-2:s390x. 119s Preparing to unpack .../33-liblcms2-2_2.16-2_s390x.deb ... 119s Unpacking liblcms2-2:s390x (2.16-2) ... 119s Selecting previously unselected package libpython3.13-stdlib:s390x. 119s Preparing to unpack .../34-libpython3.13-stdlib_3.13.0-2_s390x.deb ... 119s Unpacking libpython3.13-stdlib:s390x (3.13.0-2) ... 119s Selecting previously unselected package libraqm0:s390x. 119s Preparing to unpack .../35-libraqm0_0.10.1-1build1_s390x.deb ... 119s Unpacking libraqm0:s390x (0.10.1-1build1) ... 119s Selecting previously unselected package libsharpyuv0:s390x. 119s Preparing to unpack .../36-libsharpyuv0_1.4.0-0.1_s390x.deb ... 119s Unpacking libsharpyuv0:s390x (1.4.0-0.1) ... 119s Selecting previously unselected package libjbig0:s390x. 119s Preparing to unpack .../37-libjbig0_2.1-6.1ubuntu2_s390x.deb ... 119s Unpacking libjbig0:s390x (2.1-6.1ubuntu2) ... 119s Selecting previously unselected package libwebp7:s390x. 119s Preparing to unpack .../38-libwebp7_1.4.0-0.1_s390x.deb ... 119s Unpacking libwebp7:s390x (1.4.0-0.1) ... 119s Selecting previously unselected package libtiff6:s390x. 119s Preparing to unpack .../39-libtiff6_4.5.1+git230720-4ubuntu4_s390x.deb ... 119s Unpacking libtiff6:s390x (4.5.1+git230720-4ubuntu4) ... 119s Selecting previously unselected package libwebpdemux2:s390x. 119s Preparing to unpack .../40-libwebpdemux2_1.4.0-0.1_s390x.deb ... 119s Unpacking libwebpdemux2:s390x (1.4.0-0.1) ... 119s Selecting previously unselected package libwebpmux3:s390x. 119s Preparing to unpack .../41-libwebpmux3_1.4.0-0.1_s390x.deb ... 119s Unpacking libwebpmux3:s390x (1.4.0-0.1) ... 119s Selecting previously unselected package ncbi-acc-download. 119s Preparing to unpack .../42-ncbi-acc-download_0.2.8-3_all.deb ... 119s Unpacking ncbi-acc-download (0.2.8-3) ... 119s Selecting previously unselected package python3.13. 119s Preparing to unpack .../43-python3.13_3.13.0-2_s390x.deb ... 119s Unpacking python3.13 (3.13.0-2) ... 119s Selecting previously unselected package python3-all. 119s 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libsharpyuv0:s390x (1.4.0-0.1) ... 120s Setting up libxrender1:s390x (1:0.9.10-1.1build1) ... 120s Setting up libxcb-render0:s390x (1.17.0-2) ... 120s Setting up x11-common (1:7.7+23ubuntu3) ... 120s Setting up libdeflate0:s390x (1.22-1) ... 120s Setting up python3-coverage (7.4.4+dfsg1-0ubuntu2) ... 120s Setting up libxcb-shm0:s390x (1.17.0-2) ... 120s Setting up libjs-jquery-throttle-debounce (1.1+dfsg.1-2) ... 120s Setting up libgomp1:s390x (14.2.0-8ubuntu1) ... 120s Setting up libjbig0:s390x (2.1-6.1ubuntu2) ... 120s Setting up libpython3.13-minimal:s390x (3.13.0-2) ... 120s Setting up libfontenc1:s390x (1:1.1.8-1build1) ... 120s Setting up libblas3:s390x (3.12.0-3build2) ... 120s update-alternatives: using /usr/lib/s390x-linux-gnu/blas/libblas.so.3 to provide /usr/lib/s390x-linux-gnu/libblas.so.3 (libblas.so.3-s390x-linux-gnu) in auto mode 120s Setting up python3-packaging (24.1-1) ... 121s Setting up libfreetype6:s390x (2.13.3+dfsg-1) ... 121s Setting up python3-requests-mock (1.12.1-2) ... 121s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 121s Setting up libimagequant0:s390x (2.18.0-1build1) ... 121s Setting up fonts-dejavu-mono (2.37-8) ... 121s Setting up fonts-dejavu-core (2.37-8) ... 121s Setting up libjpeg-turbo8:s390x (2.1.5-2ubuntu2) ... 121s Setting up libgfortran5:s390x (14.2.0-8ubuntu1) ... 121s Setting up python3-pluggy (1.5.0-1) ... 121s Setting up libwebp7:s390x (1.4.0-0.1) ... 121s Setting up libopenjp2-7:s390x (2.5.0-2ubuntu1) ... 121s Setting up python3.13-minimal (3.13.0-2) ... 122s Setting up ncbi-acc-download (0.2.8-3) ... 122s Setting up libharfbuzz0b:s390x (10.0.1-1) ... 122s Setting up sgml-base (1.31) ... 122s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 122s Setting up libjs-jquery-hotkeys (0~20130707+git2d51e3a9+dfsg-2.1) ... 122s Setting up libwebpmux3:s390x (1.4.0-0.1) ... 122s Setting up libpython3.13-stdlib:s390x (3.13.0-2) ... 122s Setting up libjpeg8:s390x (8c-2ubuntu11) ... 122s Setting up liblapack3:s390x (3.12.0-3build2) ... 122s update-alternatives: using /usr/lib/s390x-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/s390x-linux-gnu/liblapack.so.3 (liblapack.so.3-s390x-linux-gnu) in auto mode 122s Setting up python3.13 (3.13.0-2) ... 123s Setting up fontconfig-config (2.15.0-1.1ubuntu2) ... 123s Setting up python3-pytest (8.3.3-1) ... 123s Setting up libwebpdemux2:s390x (1.4.0-0.1) ... 123s Setting up python3-all (3.12.7-1) ... 123s Setting up python3-freetype (2.5.1-1) ... 124s Setting up xfonts-utils (1:7.7+7) ... 124s Setting up libjs-jquery-metadata (12-4) ... 124s Setting up libraqm0:s390x (0.10.1-1build1) ... 124s Setting up libjs-jquery-isonscreen (1.2.0-1.1) ... 124s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 127s Setting up libjs-jquery-tablesorter (1:2.31.3+dfsg1-4) ... 127s Setting up python3-pytest-mock (3.14.0-2) ... 127s Setting up libtiff6:s390x (4.5.1+git230720-4ubuntu4) ... 127s Setting up xml-core (0.19) ... 128s Setting up libfontconfig1:s390x (2.15.0-1.1ubuntu2) ... 128s Setting up python3-pytest-cov (5.0.0-1) ... 128s Setting up fonts-urw-base35 (20200910-8) ... 128s Setting up libcairo2:s390x (1.18.2-2) ... 128s Setting up python3-pil:s390x (10.4.0-1ubuntu1) ... 128s Setting up python3-cairo (1.26.1-2) ... 128s Setting up python3-rlpycairo (0.3.0-3) ... 129s Setting up python3-reportlab (4.2.5-1) ... 130s Processing triggers for libc-bin (2.40-1ubuntu3) ... 130s Processing triggers for systemd (256.5-2ubuntu4) ... 130s Processing triggers for man-db (2.12.1-3) ... 131s Processing triggers for sgml-base (1.31) ... 131s Setting up w3c-sgml-lib (1.3-3) ... 150s Setting up python3-biopython (1.84+dfsg-4) ... 153s Setting up autopkgtest-satdep (0) ... 155s (Reading database ... 60009 files and directories currently installed.) 155s Removing autopkgtest-satdep (0) ... 156s autopkgtest [12:04:52]: test run-unit-test: [----------------------- 156s /tmp/autopkgtest.c9ORLZ/build.Nyw/src/tests /tmp/autopkgtest.c9ORLZ/build.Nyw/src 156s Testing with python3.13 in /tmp/autopkgtest.c9ORLZ/build.Nyw/src/tests: 156s ============================= test session starts ============================== 156s platform linux -- Python 3.13.0, pytest-8.3.3, pluggy-1.5.0 -- /usr/bin/python3.13 156s cachedir: .pytest_cache 156s rootdir: /tmp/autopkgtest.c9ORLZ/build.Nyw/src 156s plugins: mock-3.14.0, typeguard-4.4.1, cov-5.0.0, requests_mock-1.12.1 157s collecting ... collected 32 items 157s 157s test_core.py::test_config PASSED [ 3%] 157s test_core.py::test_config_no_biopython PASSED [ 6%] 157s test_core.py::test_config_have_biopython FAILED [ 9%] 157s test_core.py::test_download_to_file PASSED [ 12%] 157s test_core.py::test_download_to_file_append PASSED [ 15%] 157s test_core.py::test_download_to_file_retry PASSED [ 18%] 157s test_core.py::test_build_params PASSED [ 21%] 157s test_core.py::test_generate_filename PASSED [ 25%] 157s test_core.py::test_validate_and_write_error_pattern_raises PASSED [ 28%] 157s test_core.py::test_validate_and_write_emit PASSED [ 31%] 157s test_core.py::test_validate_and_write_extended_validation FAILED [ 34%] 157s test_core.py::test_get_stream_exception PASSED [ 37%] 157s test_core.py::test_get_stream_bad_status PASSED [ 40%] 157s test_core.py::test_get_stream_too_many_requests PASSED [ 43%] 157s test_core.py::test_generate_url PASSED [ 46%] 157s test_core.py::test_generate_url_with_api_key PASSED [ 50%] 157s test_correct.py::test_download_and_validate_partial_wgs FAILED [ 53%] 157s test_download.py::test_write_stream PASSED [ 56%] 157s test_validate.py::test_run_extended_validation_no_biopython PASSED [ 59%] 157s test_validate.py::test_run_extended_validation_raises FAILED [ 62%] 157s test_validate.py::test_run_extended_validation_loads FAILED [ 65%] 157s test_wgs.py::test_init PASSED [ 68%] 157s test_wgs.py::test_get_ids PASSED [ 71%] 157s test_wgs.py::test_from_string PASSED [ 75%] 157s test_wgs.py::test_download_wgs_parts_no_biopython PASSED [ 78%] 157s test_wgs.py::test_download_wgs_parts_wgs FAILED [ 81%] 157s test_wgs.py::test_download_wgs_parts_wgs_retry FAILED [ 84%] 157s test_wgs.py::test_download_wgs_parts_wgs_scafld FAILED [ 87%] 157s test_wgs.py::test_download_wgs_parts_supercontig FAILED [ 90%] 157s test_wgs.py::test_download_wgs_parts_supercontig_retry FAILED [ 93%] 157s test_wgs.py::test_download_wgs_no_parts FAILED [ 96%] 157s test_wgs.py::test_download_wgs_parts_tsa XFAIL [100%] 157s 157s =================================== FAILURES =================================== 157s __________________________ test_config_have_biopython __________________________ 157s 157s def test_config_have_biopython(): 157s """Test we detect Biopython.""" 157s > assert core.HAVE_BIOPYTHON 157s E assert False 157s E + where False = core.HAVE_BIOPYTHON 157s 157s test_core.py:46: AssertionError 157s _________________ test_validate_and_write_extended_validation __________________ 157s 157s req = 157s 157s def test_validate_and_write_extended_validation(req): 157s """Test extended validation before writing.""" 157s handle = StringIO() 157s req.get('http://fake/', text=u'>foo\nMAGIC') 157s r = requests.get('http://fake/') 157s > config = core.Config(extended_validation='loads', molecule='protein') 157s 157s test_core.py:226: 157s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 157s /usr/lib/python3/dist-packages/ncbi_acc_download/core.py:64: in __init__ 157s self.extended_validation = extended_validation 157s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 157s 157s self = , value = 'loads' 157s 157s @extended_validation.setter 157s def extended_validation(self, value): 157s if value != 'none' and not HAVE_BIOPYTHON: 157s > raise ValueError("Asked for extended validation, but Biopython not available") 157s E ValueError: Asked for extended validation, but Biopython not available 157s 157s /usr/lib/python3/dist-packages/ncbi_acc_download/core.py:96: ValueError 157s ____________________ test_download_and_validate_partial_wgs ____________________ 157s 157s req = 157s 157s def test_download_and_validate_partial_wgs(req): 157s handle = StringIO(open(full_path('partialcontig.gbk'), 'r').read()) 157s > assert validate.run_extended_validation(handle, 'genbank', 'loads') 157s E AssertionError: assert False 157s E + where False = (<_io.StringIO object at 0x3ffad56eec0>, 'genbank', 'loads') 157s E + where = validate.run_extended_validation 157s 157s test_correct.py:15: AssertionError 157s _____________________ test_run_extended_validation_raises ______________________ 157s 157s monkeypatch = <_pytest.monkeypatch.MonkeyPatch object at 0x3ffad5cbbf0> 157s mocker = 157s 157s def test_run_extended_validation_raises(monkeypatch, mocker): 157s """Test the "seqence loads" validator catches exceptions in SeqIO.parse().""" 157s seqio_mock = mocker.MagicMock() 157s seqio_mock.parse = mocker.MagicMock(side_effect=ValueError) 157s > monkeypatch.setattr(validate, 'SeqIO', seqio_mock) 157s E AttributeError: has no attribute 'SeqIO' 157s 157s test_validate.py:19: AttributeError 157s ______________________ test_run_extended_validation_loads ______________________ 157s 157s def test_run_extended_validation_loads(): 157s """Test the "sequence loads" validator.""" 157s handle = StringIO(u'>foo\nATGC\n>bar\nATGTGA\n') 157s > assert validate.run_extended_validation(handle, 'fasta', 'loads') 157s E AssertionError: assert False 157s E + where False = (<_io.StringIO object at 0x3ffad56e680>, 'fasta', 'loads') 157s E + where = validate.run_extended_validation 157s 157s test_validate.py:29: AssertionError 157s _________________________ test_download_wgs_parts_wgs __________________________ 157s 157s req = 157s 157s def test_download_wgs_parts_wgs(req): 157s cfg = Config(format="genbank") 157s wgs_contig = open(full_path('wgs.gbk'), 'rt') 157s req.get( 157s ENTREZ_URL, 157s body=open(full_path('wgs_full.gbk'), 'rb'), 157s headers={"Content-Type": "text/plain; charset=UTF-8"}, 157s ) 157s 157s outhandle = wgs.download_wgs_parts(wgs_contig, cfg) 157s wgs_full = open(full_path('wgs_full.gbk'), 'rt') 157s > assert outhandle.getvalue() == wgs_full.read() 157s E AttributeError: '_io.TextIOWrapper' object has no attribute 'getvalue' 157s 157s test_wgs.py:95: AttributeError 157s ______________________ test_download_wgs_parts_wgs_retry _______________________ 157s 157s req = 157s 157s def test_download_wgs_parts_wgs_retry(req): 157s cfg = Config(format="genbank") 157s wgs_contig = open(full_path('wgs.gbk'), 'rt') 157s req.get(ENTREZ_URL, response_list=[ 157s {"text": u'Whoa, slow down', "status_code": 429, "headers": {"Retry-After": "0"}}, 157s { 157s "body": open(full_path('wgs_full.gbk'), 'rb'), 157s "headers": {"Content-Type": "text/plain; charset=UTF-8"}, 157s }, 157s ]) 157s 157s outhandle = wgs.download_wgs_parts(wgs_contig, cfg) 157s wgs_full = open(full_path('wgs_full.gbk'), 'rt') 157s > assert outhandle.getvalue() == wgs_full.read() 157s E AttributeError: '_io.TextIOWrapper' object has no attribute 'getvalue' 157s 157s test_wgs.py:113: AttributeError 157s ______________________ test_download_wgs_parts_wgs_scafld ______________________ 157s 157s req = 157s 157s def test_download_wgs_parts_wgs_scafld(req): 157s cfg = Config(format="genbank") 157s wgs_contig = open(full_path('wgs_scafld.gbk'), 'rt') 157s with open(full_path('wgs_full.gbk'), 'rt') as handle: 157s full_file = handle.read() 157s req.get(ENTREZ_URL, text=full_file) 157s 157s outhandle = wgs.download_wgs_parts(wgs_contig, cfg) 157s > assert outhandle.getvalue() == full_file 157s E AttributeError: '_io.TextIOWrapper' object has no attribute 'getvalue' 157s 157s test_wgs.py:126: AttributeError 157s _____________________ test_download_wgs_parts_supercontig ______________________ 157s 157s req = 157s 157s def test_download_wgs_parts_supercontig(req): 157s cfg = Config(format="genbank") 157s supercontig = open(full_path('supercontig.gbk'), 'rt') 157s req.get( 157s ENTREZ_URL, 157s body=open(full_path('supercontig_full.gbk'), 'rb'), 157s headers={"Content-Type": "text/plain; charset=UTF-8"}, 157s ) 157s 157s outhandle = wgs.download_wgs_parts(supercontig, cfg) 157s supercontig_full = open(full_path('supercontig_full.gbk'), 'rt') 157s > assert outhandle.getvalue() == supercontig_full.read() 157s E AttributeError: '_io.TextIOWrapper' object has no attribute 'getvalue' 157s 157s test_wgs.py:141: AttributeError 157s __________________ test_download_wgs_parts_supercontig_retry ___________________ 157s 157s req = 157s 157s def test_download_wgs_parts_supercontig_retry(req): 157s cfg = Config(format="genbank") 157s supercontig = open(full_path('supercontig.gbk'), 'rt') 157s req.get(ENTREZ_URL, response_list=[ 157s {"text": u'Whoa, slow down', "status_code": 429, "headers": {"Retry-After": "0"}}, 157s { 157s "body": open(full_path('supercontig_full.gbk'), 'rb'), 157s "headers": {"Content-Type": "text/plain; charset=UTF-8"}, 157s }, 157s ]) 157s 157s outhandle = wgs.download_wgs_parts(supercontig, cfg) 157s supercontig_full = open(full_path('supercontig_full.gbk'), 'rt') 157s > assert outhandle.getvalue() == supercontig_full.read() 157s E AttributeError: '_io.TextIOWrapper' object has no attribute 'getvalue' 157s 157s test_wgs.py:159: AttributeError 157s __________________________ test_download_wgs_no_parts __________________________ 157s 157s req = 157s 157s def test_download_wgs_no_parts(req): 157s cfg = Config(format="genbank") 157s supercontig = open(full_path('supercontig_full.gbk'), 'rt') 157s req.get(ENTREZ_URL, status_code=404) 157s 157s outhandle = wgs.download_wgs_parts(supercontig, cfg) 157s supercontig_full = open(full_path('supercontig_full.gbk'), 'rt') 157s > assert outhandle.getvalue() == supercontig_full.read() 157s E AttributeError: '_io.TextIOWrapper' object has no attribute 'getvalue' 157s 157s test_wgs.py:171: AttributeError 157s =========================== short test summary info ============================ 157s FAILED test_core.py::test_config_have_biopython - assert False 157s FAILED test_core.py::test_validate_and_write_extended_validation - ValueError... 157s FAILED test_correct.py::test_download_and_validate_partial_wgs - AssertionErr... 157s FAILED test_validate.py::test_run_extended_validation_raises - AttributeError... 157s FAILED test_validate.py::test_run_extended_validation_loads - AssertionError:... 157s FAILED test_wgs.py::test_download_wgs_parts_wgs - AttributeError: '_io.TextIO... 157s FAILED test_wgs.py::test_download_wgs_parts_wgs_retry - AttributeError: '_io.... 157s FAILED test_wgs.py::test_download_wgs_parts_wgs_scafld - AttributeError: '_io... 157s FAILED test_wgs.py::test_download_wgs_parts_supercontig - AttributeError: '_i... 157s FAILED test_wgs.py::test_download_wgs_parts_supercontig_retry - AttributeErro... 157s FAILED test_wgs.py::test_download_wgs_no_parts - AttributeError: '_io.TextIOW... 157s =================== 11 failed, 20 passed, 1 xfailed in 0.16s =================== 157s autopkgtest [12:04:53]: test run-unit-test: -----------------------] 157s autopkgtest [12:04:53]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 157s run-unit-test FAIL non-zero exit status 1 158s autopkgtest [12:04:54]: @@@@@@@@@@@@@@@@@@@@ summary 158s run-unit-test FAIL non-zero exit status 1 170s nova [W] Using flock in prodstack6-s390x 170s flock: timeout while waiting to get lock 170s Creating nova instance adt-plucky-s390x-ncbi-acc-download-20241113-120216-juju-7f2275-prod-proposed-migration-environment-15-b8a98a0c-c160-4a72-a143-8feb176c94e4 from image adt/ubuntu-plucky-s390x-server-20241113.img (UUID e740277e-1f72-40ae-bfbe-46030537c71c)...