0s autopkgtest [18:26:12]: starting date and time: 2024-11-13 18:26:12+0000 0s autopkgtest [18:26:12]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [18:26:12]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.wofnblbx/out --timeout-copy=6000 --setup-commands 'ln -s /dev/null /etc/systemd/system/bluetooth.service; printf "http_proxy=http://squid.internal:3128\nhttps_proxy=http://squid.internal:3128\nno_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\n" >> /etc/environment' --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' -- lxd -r lxd-armhf-10.145.243.149 lxd-armhf-10.145.243.149:autopkgtest/ubuntu/plucky/armhf 53s autopkgtest [18:27:05]: testbed dpkg architecture: armhf 55s autopkgtest [18:27:07]: testbed apt version: 2.9.8 55s autopkgtest [18:27:07]: @@@@@@@@@@@@@@@@@@@@ test bed setup 63s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 63s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [971 kB] 63s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [104 kB] 63s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 63s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [17.2 kB] 63s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf Packages [106 kB] 63s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf Packages [647 kB] 63s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf Packages [17.2 kB] 64s Fetched 1943 kB in 1s (2248 kB/s) 64s Reading package lists... 82s tee: /proc/self/fd/2: Permission denied 103s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 103s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 103s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 104s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 105s Reading package lists... 106s Reading package lists... 106s Building dependency tree... 106s Reading state information... 106s Calculating upgrade... 106s The following NEW packages will be installed: 106s python3.13-gdbm 106s The following packages will be upgraded: 106s libgnutls30t64 libjson-glib-1.0-0 libjson-glib-1.0-common libpython3-stdlib 106s libutempter0 python3 python3-gdbm python3-minimal 106s 8 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 106s Need to get 1131 kB of archives. 106s After this operation, 95.2 kB of additional disk space will be used. 106s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf python3-minimal armhf 3.12.7-1 [27.4 kB] 107s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf python3 armhf 3.12.7-1 [24.0 kB] 107s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libpython3-stdlib armhf 3.12.7-1 [10.0 kB] 107s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf libgnutls30t64 armhf 3.8.8-2ubuntu1 [955 kB] 107s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf python3.13-gdbm armhf 3.13.0-2 [29.5 kB] 107s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf python3-gdbm armhf 3.12.7-1 [8642 B] 107s Get:7 http://ftpmaster.internal/ubuntu plucky/main armhf libjson-glib-1.0-common all 1.10.0+ds-3 [5586 B] 107s Get:8 http://ftpmaster.internal/ubuntu plucky/main armhf libjson-glib-1.0-0 armhf 1.10.0+ds-3 [61.7 kB] 107s Get:9 http://ftpmaster.internal/ubuntu plucky/main armhf libutempter0 armhf 1.2.1-4 [9062 B] 107s Fetched 1131 kB in 1s (2032 kB/s) 107s (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 ... 59559 files and directories currently installed.) 107s Preparing to unpack .../python3-minimal_3.12.7-1_armhf.deb ... 107s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ... 107s Setting up python3-minimal (3.12.7-1) ... 108s (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 ... 59559 files and directories currently installed.) 108s Preparing to unpack .../python3_3.12.7-1_armhf.deb ... 108s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ... 108s Preparing to unpack .../libpython3-stdlib_3.12.7-1_armhf.deb ... 108s Unpacking libpython3-stdlib:armhf (3.12.7-1) over (3.12.6-0ubuntu1) ... 108s Preparing to unpack .../libgnutls30t64_3.8.8-2ubuntu1_armhf.deb ... 108s Unpacking libgnutls30t64:armhf (3.8.8-2ubuntu1) over (3.8.6-2ubuntu1) ... 108s Setting up libgnutls30t64:armhf (3.8.8-2ubuntu1) ... 108s Selecting previously unselected package python3.13-gdbm. 108s (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 ... 59559 files and directories currently installed.) 108s Preparing to unpack .../python3.13-gdbm_3.13.0-2_armhf.deb ... 108s Unpacking python3.13-gdbm (3.13.0-2) ... 108s Preparing to unpack .../python3-gdbm_3.12.7-1_armhf.deb ... 108s Unpacking python3-gdbm:armhf (3.12.7-1) over (3.12.6-1ubuntu1) ... 108s Preparing to unpack .../libjson-glib-1.0-common_1.10.0+ds-3_all.deb ... 108s Unpacking libjson-glib-1.0-common (1.10.0+ds-3) over (1.10.0+ds-2) ... 108s Preparing to unpack .../libjson-glib-1.0-0_1.10.0+ds-3_armhf.deb ... 108s Unpacking libjson-glib-1.0-0:armhf (1.10.0+ds-3) over (1.10.0+ds-2) ... 108s Preparing to unpack .../libutempter0_1.2.1-4_armhf.deb ... 108s Unpacking libutempter0:armhf (1.2.1-4) over (1.2.1-3build1) ... 108s Setting up libutempter0:armhf (1.2.1-4) ... 108s Setting up libjson-glib-1.0-common (1.10.0+ds-3) ... 108s Setting up python3.13-gdbm (3.13.0-2) ... 108s Setting up libpython3-stdlib:armhf (3.12.7-1) ... 108s Setting up python3 (3.12.7-1) ... 108s Setting up libjson-glib-1.0-0:armhf (1.10.0+ds-3) ... 108s Setting up python3-gdbm:armhf (3.12.7-1) ... 108s Processing triggers for man-db (2.12.1-3) ... 109s Processing triggers for libc-bin (2.40-1ubuntu3) ... 109s Reading package lists... 110s Building dependency tree... 110s Reading state information... 110s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 113s autopkgtest [18:28:05]: rebooting testbed after setup commands that affected boot 182s autopkgtest [18:29:14]: testbed running kernel: Linux 6.8.0-48-generic #48~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Mon Oct 7 11:49:53 UTC 2 211s autopkgtest [18:29:43]: @@@@@@@@@@@@@@@@@@@@ apt-source ncbi-acc-download 221s Get:1 http://ftpmaster.internal/ubuntu plucky/universe ncbi-acc-download 0.2.8-3 (dsc) [2434 B] 221s Get:2 http://ftpmaster.internal/ubuntu plucky/universe ncbi-acc-download 0.2.8-3 (tar) [20.9 kB] 221s Get:3 http://ftpmaster.internal/ubuntu plucky/universe ncbi-acc-download 0.2.8-3 (diff) [4420 B] 221s gpgv: Signature made Thu Aug 1 23:03:26 2024 UTC 221s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 221s gpgv: issuer "tille@debian.org" 221s gpgv: Can't check signature: No public key 221s dpkg-source: warning: cannot verify inline signature for ./ncbi-acc-download_0.2.8-3.dsc: no acceptable signature found 221s autopkgtest [18:29:53]: testing package ncbi-acc-download version 0.2.8-3 224s autopkgtest [18:29:56]: build not needed 226s autopkgtest [18:29:58]: test run-unit-test: preparing testbed 238s Reading package lists... 238s Building dependency tree... 238s Reading state information... 238s Starting pkgProblemResolver with broken count: 0 238s Starting 2 pkgProblemResolver with broken count: 0 238s Done 239s The following additional packages will be installed: 239s fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-urw-base35 239s libblas3 libcairo2 libdeflate0 libfontconfig1 libfontenc1 libfreetype6 239s libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libimagequant0 libjbig0 239s libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-hotkeys 239s libjs-jquery-isonscreen libjs-jquery-metadata libjs-jquery-tablesorter 239s libjs-jquery-throttle-debounce liblapack3 liblcms2-2 liblerc4 libopenjp2-7 239s libpixman-1-0 libpython3.13-minimal libpython3.13-stdlib libraqm0 239s libsharpyuv0 libtiff6 libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 239s libxcb-shm0 libxrender1 ncbi-acc-download python3-all python3-biopython 239s python3-cairo python3-coverage python3-freetype python3-iniconfig 239s python3-numpy python3-packaging python3-pil python3-pluggy python3-pytest 239s python3-pytest-cov python3-pytest-mock python3-reportlab 239s python3-requests-mock python3-rlpycairo python3.13 python3.13-minimal 239s sgml-base w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core 239s Suggested packages: 239s fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre liblcms2-utils 239s python3-tk bwa clustalo clustalw dialign dssp emboss fasttree mafft muscle3 239s phylip phyml prank probcons python3-mysqldb python3-matplotlib python3-mmtf 239s python3-rdflib python3-psycopg2 python3-scipy raxml samtools t-coffee wise 239s python-coverage-doc gcc gfortran python-numpy-doc python3-dev python-pil-doc 239s python-pytest-mock-doc pdf-viewer python3-egenix-mxtexttools 239s python-reportlab-doc rl-accel rl-renderpm python3.13-venv python3.13-doc 239s binfmt-support sgml-base-doc debhelper 239s Recommended packages: 239s javascript-common python-biopython-doc ncbi-blast+ python3-olefile 239s fonts-dejavu-extra 239s The following NEW packages will be installed: 239s autopkgtest-satdep fontconfig-config fonts-dejavu-core fonts-dejavu-mono 239s fonts-urw-base35 libblas3 libcairo2 libdeflate0 libfontconfig1 libfontenc1 239s libfreetype6 libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b 239s libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 libjs-jquery 239s libjs-jquery-hotkeys libjs-jquery-isonscreen libjs-jquery-metadata 239s libjs-jquery-tablesorter libjs-jquery-throttle-debounce liblapack3 239s liblcms2-2 liblerc4 libopenjp2-7 libpixman-1-0 libpython3.13-minimal 239s libpython3.13-stdlib libraqm0 libsharpyuv0 libtiff6 libwebp7 libwebpdemux2 239s libwebpmux3 libxcb-render0 libxcb-shm0 libxrender1 ncbi-acc-download 239s python3-all python3-biopython python3-cairo python3-coverage 239s python3-freetype python3-iniconfig python3-numpy python3-packaging 239s python3-pil python3-pluggy python3-pytest python3-pytest-cov 239s python3-pytest-mock python3-reportlab python3-requests-mock 239s python3-rlpycairo python3.13 python3.13-minimal sgml-base w3c-sgml-lib 239s x11-common xfonts-encodings xfonts-utils xml-core 239s 0 upgraded, 66 newly installed, 0 to remove and 0 not upgraded. 239s Need to get 32.3 MB/32.3 MB of archives. 239s After this operation, 95.5 MB of additional disk space will be used. 239s Get:1 /tmp/autopkgtest.TiOFkh/1-autopkgtest-satdep.deb autopkgtest-satdep armhf 0 [756 B] 239s Get:2 http://ftpmaster.internal/ubuntu plucky/main armhf libpython3.13-minimal armhf 3.13.0-2 [866 kB] 240s Get:3 http://ftpmaster.internal/ubuntu plucky/main armhf python3.13-minimal armhf 3.13.0-2 [1854 kB] 240s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf sgml-base all 1.31 [11.4 kB] 240s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 240s Get:6 http://ftpmaster.internal/ubuntu plucky/universe armhf libjs-jquery-hotkeys all 0~20130707+git2d51e3a9+dfsg-2.1 [11.5 kB] 240s Get:7 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-dejavu-mono all 2.37-8 [502 kB] 240s Get:8 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-dejavu-core all 2.37-8 [835 kB] 240s Get:9 http://ftpmaster.internal/ubuntu plucky/main armhf libfontenc1 armhf 1:1.1.8-1build1 [11.5 kB] 240s Get:10 http://ftpmaster.internal/ubuntu plucky/main armhf libfreetype6 armhf 2.13.3+dfsg-1 [330 kB] 240s Get:11 http://ftpmaster.internal/ubuntu plucky/main armhf x11-common all 1:7.7+23ubuntu3 [21.7 kB] 240s Get:12 http://ftpmaster.internal/ubuntu plucky/main armhf xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 240s Get:13 http://ftpmaster.internal/ubuntu plucky/main armhf xfonts-utils armhf 1:7.7+7 [90.6 kB] 240s Get:14 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-urw-base35 all 20200910-8 [11.0 MB] 240s Get:15 http://ftpmaster.internal/ubuntu plucky/main armhf fontconfig-config armhf 2.15.0-1.1ubuntu2 [37.4 kB] 240s Get:16 http://ftpmaster.internal/ubuntu plucky/main armhf libblas3 armhf 3.12.0-3build2 [126 kB] 240s Get:17 http://ftpmaster.internal/ubuntu plucky/main armhf libfontconfig1 armhf 2.15.0-1.1ubuntu2 [113 kB] 240s Get:18 http://ftpmaster.internal/ubuntu plucky/main armhf libpixman-1-0 armhf 0.44.0-3 [183 kB] 240s Get:19 http://ftpmaster.internal/ubuntu plucky/main armhf libxcb-render0 armhf 1.17.0-2 [15.3 kB] 240s Get:20 http://ftpmaster.internal/ubuntu plucky/main armhf libxcb-shm0 armhf 1.17.0-2 [5774 B] 240s Get:21 http://ftpmaster.internal/ubuntu plucky/main armhf libxrender1 armhf 1:0.9.10-1.1build1 [16.0 kB] 240s Get:22 http://ftpmaster.internal/ubuntu plucky/main armhf libcairo2 armhf 1.18.2-2 [484 kB] 240s Get:23 http://ftpmaster.internal/ubuntu plucky/main armhf libdeflate0 armhf 1.22-1 [38.9 kB] 241s Get:24 http://ftpmaster.internal/ubuntu plucky/main armhf libgfortran5 armhf 14.2.0-8ubuntu1 [311 kB] 241s Get:25 http://ftpmaster.internal/ubuntu plucky/main armhf libgomp1 armhf 14.2.0-8ubuntu1 [125 kB] 241s Get:26 http://ftpmaster.internal/ubuntu plucky/main armhf libgraphite2-3 armhf 1.3.14-2ubuntu1 [64.8 kB] 241s Get:27 http://ftpmaster.internal/ubuntu plucky/main armhf libharfbuzz0b armhf 10.0.1-1 [463 kB] 241s Get:28 http://ftpmaster.internal/ubuntu plucky/main armhf libimagequant0 armhf 2.18.0-1build1 [31.1 kB] 241s Get:29 http://ftpmaster.internal/ubuntu plucky/main armhf libjpeg-turbo8 armhf 2.1.5-2ubuntu2 [125 kB] 241s Get:30 http://ftpmaster.internal/ubuntu plucky/main armhf libjpeg8 armhf 8c-2ubuntu11 [2148 B] 241s Get:31 http://ftpmaster.internal/ubuntu plucky/universe armhf libjs-jquery-metadata all 12-4 [6582 B] 241s Get:32 http://ftpmaster.internal/ubuntu plucky/universe armhf libjs-jquery-tablesorter all 1:2.31.3+dfsg1-4 [192 kB] 241s Get:33 http://ftpmaster.internal/ubuntu plucky/universe armhf libjs-jquery-throttle-debounce all 1.1+dfsg.1-2 [12.5 kB] 241s Get:34 http://ftpmaster.internal/ubuntu plucky/main armhf liblapack3 armhf 3.12.0-3build2 [2086 kB] 241s Get:35 http://ftpmaster.internal/ubuntu plucky/main armhf liblcms2-2 armhf 2.16-2 [137 kB] 241s Get:36 http://ftpmaster.internal/ubuntu plucky/main armhf liblerc4 armhf 4.0.0+ds-4ubuntu2 [151 kB] 241s Get:37 http://ftpmaster.internal/ubuntu plucky/main armhf libpython3.13-stdlib armhf 3.13.0-2 [1972 kB] 241s Get:38 http://ftpmaster.internal/ubuntu plucky/main armhf libraqm0 armhf 0.10.1-1build1 [12.4 kB] 241s Get:39 http://ftpmaster.internal/ubuntu plucky/main armhf libsharpyuv0 armhf 1.4.0-0.1 [16.3 kB] 241s Get:40 http://ftpmaster.internal/ubuntu plucky/main armhf libjbig0 armhf 2.1-6.1ubuntu2 [24.9 kB] 241s Get:41 http://ftpmaster.internal/ubuntu plucky/main armhf libwebp7 armhf 1.4.0-0.1 [184 kB] 241s Get:42 http://ftpmaster.internal/ubuntu plucky/main armhf libtiff6 armhf 4.5.1+git230720-4ubuntu4 [179 kB] 241s Get:43 http://ftpmaster.internal/ubuntu plucky/main armhf libwebpdemux2 armhf 1.4.0-0.1 [11.8 kB] 241s Get:44 http://ftpmaster.internal/ubuntu plucky/main armhf libwebpmux3 armhf 1.4.0-0.1 [22.5 kB] 241s Get:45 http://ftpmaster.internal/ubuntu plucky/universe armhf ncbi-acc-download all 0.2.8-3 [13.3 kB] 241s Get:46 http://ftpmaster.internal/ubuntu plucky/main armhf python3.13 armhf 3.13.0-2 [719 kB] 241s Get:47 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf python3-all armhf 3.12.7-1 [890 B] 241s Get:48 http://ftpmaster.internal/ubuntu plucky/main armhf python3-numpy armhf 1:1.26.4+ds-11build1 [3570 kB] 241s Get:49 http://ftpmaster.internal/ubuntu plucky/main armhf libopenjp2-7 armhf 2.5.0-2ubuntu1 [170 kB] 241s Get:50 http://ftpmaster.internal/ubuntu plucky/main armhf python3-pil armhf 10.4.0-1ubuntu1 [428 kB] 241s Get:51 http://ftpmaster.internal/ubuntu plucky/main armhf python3-cairo armhf 1.26.1-2 [114 kB] 241s Get:52 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-freetype all 2.5.1-1 [92.3 kB] 241s Get:53 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-rlpycairo all 0.3.0-3 [9130 B] 241s Get:54 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-reportlab all 4.2.5-1 [1107 kB] 241s Get:55 http://ftpmaster.internal/ubuntu plucky/main armhf xml-core all 0.19 [20.3 kB] 241s Get:56 http://ftpmaster.internal/ubuntu plucky/universe armhf w3c-sgml-lib all 1.3-3 [280 kB] 241s Get:57 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-biopython armhf 1.84+dfsg-4 [1666 kB] 241s Get:58 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-coverage armhf 7.4.4+dfsg1-0ubuntu2 [146 kB] 241s Get:59 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-iniconfig all 1.1.1-2 [6024 B] 241s Get:60 http://ftpmaster.internal/ubuntu plucky/main armhf python3-packaging all 24.1-1 [41.4 kB] 241s Get:61 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pluggy all 1.5.0-1 [21.0 kB] 241s Get:62 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pytest all 8.3.3-1 [251 kB] 241s Get:63 http://ftpmaster.internal/ubuntu plucky/universe armhf libjs-jquery-isonscreen all 1.2.0-1.1 [3244 B] 241s Get:64 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pytest-cov all 5.0.0-1 [21.3 kB] 241s Get:65 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pytest-mock all 3.14.0-2 [11.7 kB] 241s Get:66 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-requests-mock all 1.12.1-2 [17.8 kB] 242s Fetched 32.3 MB in 2s (16.5 MB/s) 242s Selecting previously unselected package libpython3.13-minimal:armhf. 242s (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 ... 59566 files and directories currently installed.) 242s Preparing to unpack .../00-libpython3.13-minimal_3.13.0-2_armhf.deb ... 242s Unpacking libpython3.13-minimal:armhf (3.13.0-2) ... 242s Selecting previously unselected package python3.13-minimal. 242s Preparing to unpack .../01-python3.13-minimal_3.13.0-2_armhf.deb ... 242s Unpacking python3.13-minimal (3.13.0-2) ... 242s Selecting previously unselected package sgml-base. 242s Preparing to unpack .../02-sgml-base_1.31_all.deb ... 242s Unpacking sgml-base (1.31) ... 242s Selecting previously unselected package libjs-jquery. 242s Preparing to unpack .../03-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 242s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 242s Selecting previously unselected package libjs-jquery-hotkeys. 242s Preparing to unpack .../04-libjs-jquery-hotkeys_0~20130707+git2d51e3a9+dfsg-2.1_all.deb ... 242s Unpacking libjs-jquery-hotkeys (0~20130707+git2d51e3a9+dfsg-2.1) ... 242s Selecting previously unselected package fonts-dejavu-mono. 242s Preparing to unpack .../05-fonts-dejavu-mono_2.37-8_all.deb ... 242s Unpacking fonts-dejavu-mono (2.37-8) ... 242s Selecting previously unselected package fonts-dejavu-core. 242s Preparing to unpack .../06-fonts-dejavu-core_2.37-8_all.deb ... 242s Unpacking fonts-dejavu-core (2.37-8) ... 242s Selecting previously unselected package libfontenc1:armhf. 242s Preparing to unpack .../07-libfontenc1_1%3a1.1.8-1build1_armhf.deb ... 242s Unpacking libfontenc1:armhf (1:1.1.8-1build1) ... 242s Selecting previously unselected package libfreetype6:armhf. 242s Preparing to unpack .../08-libfreetype6_2.13.3+dfsg-1_armhf.deb ... 242s Unpacking libfreetype6:armhf (2.13.3+dfsg-1) ... 242s Selecting previously unselected package x11-common. 242s Preparing to unpack .../09-x11-common_1%3a7.7+23ubuntu3_all.deb ... 242s Unpacking x11-common (1:7.7+23ubuntu3) ... 242s Selecting previously unselected package xfonts-encodings. 242s Preparing to unpack .../10-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 242s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 242s Selecting previously unselected package xfonts-utils. 242s Preparing to unpack .../11-xfonts-utils_1%3a7.7+7_armhf.deb ... 242s Unpacking xfonts-utils (1:7.7+7) ... 242s Selecting previously unselected package fonts-urw-base35. 242s Preparing to unpack .../12-fonts-urw-base35_20200910-8_all.deb ... 242s Unpacking fonts-urw-base35 (20200910-8) ... 242s Selecting previously unselected package fontconfig-config. 242s Preparing to unpack .../13-fontconfig-config_2.15.0-1.1ubuntu2_armhf.deb ... 243s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ... 243s Selecting previously unselected package libblas3:armhf. 243s Preparing to unpack .../14-libblas3_3.12.0-3build2_armhf.deb ... 243s Unpacking libblas3:armhf (3.12.0-3build2) ... 243s Selecting previously unselected package libfontconfig1:armhf. 243s Preparing to unpack .../15-libfontconfig1_2.15.0-1.1ubuntu2_armhf.deb ... 243s Unpacking libfontconfig1:armhf (2.15.0-1.1ubuntu2) ... 243s Selecting previously unselected package libpixman-1-0:armhf. 243s Preparing to unpack .../16-libpixman-1-0_0.44.0-3_armhf.deb ... 243s Unpacking libpixman-1-0:armhf (0.44.0-3) ... 243s Selecting previously unselected package libxcb-render0:armhf. 243s Preparing to unpack .../17-libxcb-render0_1.17.0-2_armhf.deb ... 243s Unpacking libxcb-render0:armhf (1.17.0-2) ... 243s Selecting previously unselected package libxcb-shm0:armhf. 243s Preparing to unpack .../18-libxcb-shm0_1.17.0-2_armhf.deb ... 243s Unpacking libxcb-shm0:armhf (1.17.0-2) ... 243s Selecting previously unselected package libxrender1:armhf. 243s Preparing to unpack .../19-libxrender1_1%3a0.9.10-1.1build1_armhf.deb ... 243s Unpacking libxrender1:armhf (1:0.9.10-1.1build1) ... 243s Selecting previously unselected package libcairo2:armhf. 243s Preparing to unpack .../20-libcairo2_1.18.2-2_armhf.deb ... 243s Unpacking libcairo2:armhf (1.18.2-2) ... 243s Selecting previously unselected package libdeflate0:armhf. 243s Preparing to unpack .../21-libdeflate0_1.22-1_armhf.deb ... 243s Unpacking libdeflate0:armhf (1.22-1) ... 243s Selecting previously unselected package libgfortran5:armhf. 243s Preparing to unpack .../22-libgfortran5_14.2.0-8ubuntu1_armhf.deb ... 243s Unpacking libgfortran5:armhf (14.2.0-8ubuntu1) ... 243s Selecting previously unselected package libgomp1:armhf. 243s Preparing to unpack .../23-libgomp1_14.2.0-8ubuntu1_armhf.deb ... 243s Unpacking libgomp1:armhf (14.2.0-8ubuntu1) ... 243s Selecting previously unselected package libgraphite2-3:armhf. 243s Preparing to unpack .../24-libgraphite2-3_1.3.14-2ubuntu1_armhf.deb ... 243s Unpacking libgraphite2-3:armhf (1.3.14-2ubuntu1) ... 243s Selecting previously unselected package libharfbuzz0b:armhf. 243s Preparing to unpack .../25-libharfbuzz0b_10.0.1-1_armhf.deb ... 243s Unpacking libharfbuzz0b:armhf (10.0.1-1) ... 243s Selecting previously unselected package libimagequant0:armhf. 243s Preparing to unpack .../26-libimagequant0_2.18.0-1build1_armhf.deb ... 243s Unpacking libimagequant0:armhf (2.18.0-1build1) ... 243s Selecting previously unselected package libjpeg-turbo8:armhf. 243s Preparing to unpack .../27-libjpeg-turbo8_2.1.5-2ubuntu2_armhf.deb ... 243s Unpacking libjpeg-turbo8:armhf (2.1.5-2ubuntu2) ... 243s Selecting previously unselected package libjpeg8:armhf. 243s Preparing to unpack .../28-libjpeg8_8c-2ubuntu11_armhf.deb ... 243s Unpacking libjpeg8:armhf (8c-2ubuntu11) ... 243s Selecting previously unselected package libjs-jquery-metadata. 243s Preparing to unpack .../29-libjs-jquery-metadata_12-4_all.deb ... 243s Unpacking libjs-jquery-metadata (12-4) ... 243s Selecting previously unselected package libjs-jquery-tablesorter. 243s Preparing to unpack .../30-libjs-jquery-tablesorter_1%3a2.31.3+dfsg1-4_all.deb ... 243s Unpacking libjs-jquery-tablesorter (1:2.31.3+dfsg1-4) ... 243s Selecting previously unselected package libjs-jquery-throttle-debounce. 243s Preparing to unpack .../31-libjs-jquery-throttle-debounce_1.1+dfsg.1-2_all.deb ... 243s Unpacking libjs-jquery-throttle-debounce (1.1+dfsg.1-2) ... 243s Selecting previously unselected package liblapack3:armhf. 243s Preparing to unpack .../32-liblapack3_3.12.0-3build2_armhf.deb ... 243s Unpacking liblapack3:armhf (3.12.0-3build2) ... 243s Selecting previously unselected package liblcms2-2:armhf. 243s Preparing to unpack .../33-liblcms2-2_2.16-2_armhf.deb ... 243s Unpacking liblcms2-2:armhf (2.16-2) ... 243s Selecting previously unselected package liblerc4:armhf. 243s Preparing to unpack .../34-liblerc4_4.0.0+ds-4ubuntu2_armhf.deb ... 243s Unpacking liblerc4:armhf (4.0.0+ds-4ubuntu2) ... 243s Selecting previously unselected package libpython3.13-stdlib:armhf. 243s Preparing to unpack .../35-libpython3.13-stdlib_3.13.0-2_armhf.deb ... 243s Unpacking libpython3.13-stdlib:armhf (3.13.0-2) ... 244s Selecting previously unselected package libraqm0:armhf. 244s Preparing to unpack .../36-libraqm0_0.10.1-1build1_armhf.deb ... 244s Unpacking libraqm0:armhf (0.10.1-1build1) ... 244s Selecting previously unselected package libsharpyuv0:armhf. 244s Preparing to unpack .../37-libsharpyuv0_1.4.0-0.1_armhf.deb ... 244s Unpacking libsharpyuv0:armhf (1.4.0-0.1) ... 244s Selecting previously unselected package libjbig0:armhf. 244s Preparing to unpack .../38-libjbig0_2.1-6.1ubuntu2_armhf.deb ... 244s Unpacking libjbig0:armhf (2.1-6.1ubuntu2) ... 244s Selecting previously unselected package libwebp7:armhf. 244s Preparing to unpack .../39-libwebp7_1.4.0-0.1_armhf.deb ... 244s Unpacking libwebp7:armhf (1.4.0-0.1) ... 244s Selecting previously unselected package libtiff6:armhf. 244s Preparing to unpack .../40-libtiff6_4.5.1+git230720-4ubuntu4_armhf.deb ... 244s Unpacking libtiff6:armhf (4.5.1+git230720-4ubuntu4) ... 244s Selecting previously unselected package libwebpdemux2:armhf. 244s Preparing to unpack .../41-libwebpdemux2_1.4.0-0.1_armhf.deb ... 244s Unpacking libwebpdemux2:armhf (1.4.0-0.1) ... 244s Selecting previously unselected package libwebpmux3:armhf. 244s Preparing to unpack .../42-libwebpmux3_1.4.0-0.1_armhf.deb ... 244s Unpacking libwebpmux3:armhf (1.4.0-0.1) ... 244s Selecting previously unselected package ncbi-acc-download. 244s Preparing to unpack .../43-ncbi-acc-download_0.2.8-3_all.deb ... 244s Unpacking ncbi-acc-download (0.2.8-3) ... 244s Selecting previously unselected package python3.13. 244s Preparing to unpack .../44-python3.13_3.13.0-2_armhf.deb ... 244s Unpacking python3.13 (3.13.0-2) ... 244s Selecting previously unselected package python3-all. 244s Preparing to unpack .../45-python3-all_3.12.7-1_armhf.deb ... 244s Unpacking python3-all (3.12.7-1) ... 244s Selecting previously unselected package python3-numpy. 244s Preparing to unpack .../46-python3-numpy_1%3a1.26.4+ds-11build1_armhf.deb ... 244s Unpacking python3-numpy (1:1.26.4+ds-11build1) ... 244s Selecting previously unselected package libopenjp2-7:armhf. 244s Preparing to unpack .../47-libopenjp2-7_2.5.0-2ubuntu1_armhf.deb ... 244s Unpacking libopenjp2-7:armhf (2.5.0-2ubuntu1) ... 244s Selecting previously unselected package python3-pil:armhf. 244s Preparing to unpack .../48-python3-pil_10.4.0-1ubuntu1_armhf.deb ... 244s Unpacking python3-pil:armhf (10.4.0-1ubuntu1) ... 245s Selecting previously unselected package python3-cairo. 245s Preparing to unpack .../49-python3-cairo_1.26.1-2_armhf.deb ... 245s Unpacking python3-cairo (1.26.1-2) ... 245s Selecting previously unselected package python3-freetype. 245s Preparing to unpack .../50-python3-freetype_2.5.1-1_all.deb ... 245s Unpacking python3-freetype (2.5.1-1) ... 245s Selecting previously unselected package python3-rlpycairo. 245s Preparing to unpack .../51-python3-rlpycairo_0.3.0-3_all.deb ... 245s Unpacking python3-rlpycairo (0.3.0-3) ... 245s Selecting previously unselected package python3-reportlab. 245s Preparing to unpack .../52-python3-reportlab_4.2.5-1_all.deb ... 245s Unpacking python3-reportlab (4.2.5-1) ... 245s Selecting previously unselected package xml-core. 245s Preparing to unpack .../53-xml-core_0.19_all.deb ... 245s Unpacking xml-core (0.19) ... 245s Selecting previously unselected package w3c-sgml-lib. 245s Preparing to unpack .../54-w3c-sgml-lib_1.3-3_all.deb ... 245s Unpacking w3c-sgml-lib (1.3-3) ... 245s Selecting previously unselected package python3-biopython. 245s Preparing to unpack .../55-python3-biopython_1.84+dfsg-4_armhf.deb ... 245s Unpacking python3-biopython (1.84+dfsg-4) ... 245s Selecting previously unselected package python3-coverage. 245s Preparing to unpack .../56-python3-coverage_7.4.4+dfsg1-0ubuntu2_armhf.deb ... 245s Unpacking python3-coverage (7.4.4+dfsg1-0ubuntu2) ... 245s Selecting previously unselected package python3-iniconfig. 245s Preparing to unpack .../57-python3-iniconfig_1.1.1-2_all.deb ... 245s Unpacking python3-iniconfig (1.1.1-2) ... 245s Selecting previously unselected package python3-packaging. 245s Preparing to unpack .../58-python3-packaging_24.1-1_all.deb ... 245s Unpacking python3-packaging (24.1-1) ... 245s Selecting previously unselected package python3-pluggy. 245s Preparing to unpack .../59-python3-pluggy_1.5.0-1_all.deb ... 245s Unpacking python3-pluggy (1.5.0-1) ... 245s Selecting previously unselected package python3-pytest. 245s Preparing to unpack .../60-python3-pytest_8.3.3-1_all.deb ... 245s Unpacking python3-pytest (8.3.3-1) ... 245s Selecting previously unselected package libjs-jquery-isonscreen. 245s Preparing to unpack .../61-libjs-jquery-isonscreen_1.2.0-1.1_all.deb ... 245s Unpacking libjs-jquery-isonscreen (1.2.0-1.1) ... 245s Selecting previously unselected package python3-pytest-cov. 245s Preparing to unpack .../62-python3-pytest-cov_5.0.0-1_all.deb ... 245s Unpacking python3-pytest-cov (5.0.0-1) ... 245s Selecting previously unselected package python3-pytest-mock. 245s Preparing to unpack .../63-python3-pytest-mock_3.14.0-2_all.deb ... 245s Unpacking python3-pytest-mock (3.14.0-2) ... 245s Selecting previously unselected package python3-requests-mock. 245s Preparing to unpack .../64-python3-requests-mock_1.12.1-2_all.deb ... 245s Unpacking python3-requests-mock (1.12.1-2) ... 245s Selecting previously unselected package autopkgtest-satdep. 245s Preparing to unpack .../65-1-autopkgtest-satdep.deb ... 245s Unpacking autopkgtest-satdep (0) ... 246s Setting up libgraphite2-3:armhf (1.3.14-2ubuntu1) ... 246s Setting up liblcms2-2:armhf (2.16-2) ... 246s Setting up python3-iniconfig (1.1.1-2) ... 246s Setting up libpixman-1-0:armhf (0.44.0-3) ... 246s Setting up libsharpyuv0:armhf (1.4.0-0.1) ... 246s Setting up liblerc4:armhf (4.0.0+ds-4ubuntu2) ... 246s Setting up libxrender1:armhf (1:0.9.10-1.1build1) ... 246s Setting up libxcb-render0:armhf (1.17.0-2) ... 246s Setting up x11-common (1:7.7+23ubuntu3) ... 246s Setting up libdeflate0:armhf (1.22-1) ... 246s Setting up python3-coverage (7.4.4+dfsg1-0ubuntu2) ... 247s Setting up libxcb-shm0:armhf (1.17.0-2) ... 247s Setting up libjs-jquery-throttle-debounce (1.1+dfsg.1-2) ... 247s Setting up libgomp1:armhf (14.2.0-8ubuntu1) ... 247s Setting up libjbig0:armhf (2.1-6.1ubuntu2) ... 247s Setting up libpython3.13-minimal:armhf (3.13.0-2) ... 247s Setting up libfontenc1:armhf (1:1.1.8-1build1) ... 247s Setting up libblas3:armhf (3.12.0-3build2) ... 247s update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode 247s Setting up python3-packaging (24.1-1) ... 247s Setting up libfreetype6:armhf (2.13.3+dfsg-1) ... 247s Setting up python3-requests-mock (1.12.1-2) ... 247s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 247s Setting up libimagequant0:armhf (2.18.0-1build1) ... 247s Setting up fonts-dejavu-mono (2.37-8) ... 247s Setting up fonts-dejavu-core (2.37-8) ... 247s Setting up libjpeg-turbo8:armhf (2.1.5-2ubuntu2) ... 247s Setting up libgfortran5:armhf (14.2.0-8ubuntu1) ... 247s Setting up python3-pluggy (1.5.0-1) ... 247s Setting up libwebp7:armhf (1.4.0-0.1) ... 247s Setting up libopenjp2-7:armhf (2.5.0-2ubuntu1) ... 247s Setting up python3.13-minimal (3.13.0-2) ... 248s Setting up ncbi-acc-download (0.2.8-3) ... 248s Setting up libharfbuzz0b:armhf (10.0.1-1) ... 248s Setting up sgml-base (1.31) ... 248s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 248s Setting up libjs-jquery-hotkeys (0~20130707+git2d51e3a9+dfsg-2.1) ... 248s Setting up libwebpmux3:armhf (1.4.0-0.1) ... 248s Setting up libpython3.13-stdlib:armhf (3.13.0-2) ... 248s Setting up libjpeg8:armhf (8c-2ubuntu11) ... 248s Setting up liblapack3:armhf (3.12.0-3build2) ... 248s update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode 248s Setting up python3.13 (3.13.0-2) ... 250s Setting up fontconfig-config (2.15.0-1.1ubuntu2) ... 250s Setting up python3-pytest (8.3.3-1) ... 250s Setting up libwebpdemux2:armhf (1.4.0-0.1) ... 250s Setting up python3-all (3.12.7-1) ... 250s Setting up python3-freetype (2.5.1-1) ... 251s Setting up xfonts-utils (1:7.7+7) ... 251s Setting up libjs-jquery-metadata (12-4) ... 251s Setting up libraqm0:armhf (0.10.1-1build1) ... 251s Setting up libjs-jquery-isonscreen (1.2.0-1.1) ... 251s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 255s Setting up libjs-jquery-tablesorter (1:2.31.3+dfsg1-4) ... 255s Setting up python3-pytest-mock (3.14.0-2) ... 255s Setting up libtiff6:armhf (4.5.1+git230720-4ubuntu4) ... 255s Setting up xml-core (0.19) ... 255s Setting up libfontconfig1:armhf (2.15.0-1.1ubuntu2) ... 255s Setting up python3-pytest-cov (5.0.0-1) ... 255s Setting up fonts-urw-base35 (20200910-8) ... 255s Setting up libcairo2:armhf (1.18.2-2) ... 255s Setting up python3-pil:armhf (10.4.0-1ubuntu1) ... 256s Setting up python3-cairo (1.26.1-2) ... 256s Setting up python3-rlpycairo (0.3.0-3) ... 256s Setting up python3-reportlab (4.2.5-1) ... 258s Processing triggers for libc-bin (2.40-1ubuntu3) ... 258s Processing triggers for systemd (256.5-2ubuntu4) ... 258s Processing triggers for man-db (2.12.1-3) ... 259s Processing triggers for sgml-base (1.31) ... 259s Setting up w3c-sgml-lib (1.3-3) ... 285s Setting up python3-biopython (1.84+dfsg-4) ... 288s Setting up autopkgtest-satdep (0) ... 307s (Reading database ... 64064 files and directories currently installed.) 307s Removing autopkgtest-satdep (0) ... 313s autopkgtest [18:31:25]: test run-unit-test: [----------------------- 316s /tmp/autopkgtest.TiOFkh/build.xuN/src/tests /tmp/autopkgtest.TiOFkh/build.xuN/src 316s Testing with python3.13 in /tmp/autopkgtest.TiOFkh/build.xuN/src/tests: 316s ============================= test session starts ============================== 316s platform linux -- Python 3.13.0, pytest-8.3.3, pluggy-1.5.0 -- /usr/bin/python3.13 316s cachedir: .pytest_cache 316s rootdir: /tmp/autopkgtest.TiOFkh/build.xuN/src 316s plugins: typeguard-4.4.1, cov-5.0.0, mock-3.14.0, requests_mock-1.12.1 316s collecting ... collected 32 items 316s 316s test_core.py::test_config PASSED [ 3%] 316s test_core.py::test_config_no_biopython PASSED [ 6%] 316s test_core.py::test_config_have_biopython FAILED [ 9%] 316s test_core.py::test_download_to_file PASSED [ 12%] 317s test_core.py::test_download_to_file_append PASSED [ 15%] 317s test_core.py::test_download_to_file_retry PASSED [ 18%] 317s test_core.py::test_build_params PASSED [ 21%] 317s test_core.py::test_generate_filename PASSED [ 25%] 317s test_core.py::test_validate_and_write_error_pattern_raises PASSED [ 28%] 317s test_core.py::test_validate_and_write_emit PASSED [ 31%] 317s test_core.py::test_validate_and_write_extended_validation FAILED [ 34%] 317s test_core.py::test_get_stream_exception PASSED [ 37%] 317s test_core.py::test_get_stream_bad_status PASSED [ 40%] 317s test_core.py::test_get_stream_too_many_requests PASSED [ 43%] 317s test_core.py::test_generate_url PASSED [ 46%] 317s test_core.py::test_generate_url_with_api_key PASSED [ 50%] 317s test_correct.py::test_download_and_validate_partial_wgs FAILED [ 53%] 317s test_download.py::test_write_stream PASSED [ 56%] 317s test_validate.py::test_run_extended_validation_no_biopython PASSED [ 59%] 317s test_validate.py::test_run_extended_validation_raises FAILED [ 62%] 317s test_validate.py::test_run_extended_validation_loads FAILED [ 65%] 317s test_wgs.py::test_init PASSED [ 68%] 317s test_wgs.py::test_get_ids PASSED [ 71%] 317s test_wgs.py::test_from_string PASSED [ 75%] 317s test_wgs.py::test_download_wgs_parts_no_biopython PASSED [ 78%] 317s test_wgs.py::test_download_wgs_parts_wgs FAILED [ 81%] 317s test_wgs.py::test_download_wgs_parts_wgs_retry FAILED [ 84%] 317s test_wgs.py::test_download_wgs_parts_wgs_scafld FAILED [ 87%] 317s test_wgs.py::test_download_wgs_parts_supercontig FAILED [ 90%] 317s test_wgs.py::test_download_wgs_parts_supercontig_retry FAILED [ 93%] 317s test_wgs.py::test_download_wgs_no_parts FAILED [ 96%] 317s test_wgs.py::test_download_wgs_parts_tsa XFAIL [100%] 317s 317s =================================== FAILURES =================================== 317s __________________________ test_config_have_biopython __________________________ 317s 317s def test_config_have_biopython(): 317s """Test we detect Biopython.""" 317s > assert core.HAVE_BIOPYTHON 317s E assert False 317s E + where False = core.HAVE_BIOPYTHON 317s 317s test_core.py:46: AssertionError 317s _________________ test_validate_and_write_extended_validation __________________ 317s 317s req = 317s 317s def test_validate_and_write_extended_validation(req): 317s """Test extended validation before writing.""" 317s handle = StringIO() 317s req.get('http://fake/', text=u'>foo\nMAGIC') 317s r = requests.get('http://fake/') 317s > config = core.Config(extended_validation='loads', molecule='protein') 317s 317s test_core.py:226: 317s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 317s /usr/lib/python3/dist-packages/ncbi_acc_download/core.py:64: in __init__ 317s self.extended_validation = extended_validation 317s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 317s 317s self = , value = 'loads' 317s 317s @extended_validation.setter 317s def extended_validation(self, value): 317s if value != 'none' and not HAVE_BIOPYTHON: 317s > raise ValueError("Asked for extended validation, but Biopython not available") 317s E ValueError: Asked for extended validation, but Biopython not available 317s 317s /usr/lib/python3/dist-packages/ncbi_acc_download/core.py:96: ValueError 317s ____________________ test_download_and_validate_partial_wgs ____________________ 317s 317s req = 317s 317s def test_download_and_validate_partial_wgs(req): 317s handle = StringIO(open(full_path('partialcontig.gbk'), 'r').read()) 317s > assert validate.run_extended_validation(handle, 'genbank', 'loads') 317s E AssertionError: assert False 317s E + where False = (<_io.StringIO object at 0xf13fe6a8>, 'genbank', 'loads') 317s E + where = validate.run_extended_validation 317s 317s test_correct.py:15: AssertionError 317s _____________________ test_run_extended_validation_raises ______________________ 317s 317s monkeypatch = <_pytest.monkeypatch.MonkeyPatch object at 0xf13ea3f0> 317s mocker = 317s 317s def test_run_extended_validation_raises(monkeypatch, mocker): 317s """Test the "seqence loads" validator catches exceptions in SeqIO.parse().""" 317s seqio_mock = mocker.MagicMock() 317s seqio_mock.parse = mocker.MagicMock(side_effect=ValueError) 317s > monkeypatch.setattr(validate, 'SeqIO', seqio_mock) 317s E AttributeError: has no attribute 'SeqIO' 317s 317s test_validate.py:19: AttributeError 317s ______________________ test_run_extended_validation_loads ______________________ 317s 317s def test_run_extended_validation_loads(): 317s """Test the "sequence loads" validator.""" 317s handle = StringIO(u'>foo\nATGC\n>bar\nATGTGA\n') 317s > assert validate.run_extended_validation(handle, 'fasta', 'loads') 317s E AssertionError: assert False 317s E + where False = (<_io.StringIO object at 0xf13fe438>, 'fasta', 'loads') 317s E + where = validate.run_extended_validation 317s 317s test_validate.py:29: AssertionError 317s _________________________ test_download_wgs_parts_wgs __________________________ 317s 317s req = 317s 317s def test_download_wgs_parts_wgs(req): 317s cfg = Config(format="genbank") 317s wgs_contig = open(full_path('wgs.gbk'), 'rt') 317s req.get( 317s ENTREZ_URL, 317s body=open(full_path('wgs_full.gbk'), 'rb'), 317s headers={"Content-Type": "text/plain; charset=UTF-8"}, 317s ) 317s 317s outhandle = wgs.download_wgs_parts(wgs_contig, cfg) 317s wgs_full = open(full_path('wgs_full.gbk'), 'rt') 317s > assert outhandle.getvalue() == wgs_full.read() 317s E AttributeError: '_io.TextIOWrapper' object has no attribute 'getvalue' 317s 317s test_wgs.py:95: AttributeError 317s ______________________ test_download_wgs_parts_wgs_retry _______________________ 317s 317s req = 317s 317s def test_download_wgs_parts_wgs_retry(req): 317s cfg = Config(format="genbank") 317s wgs_contig = open(full_path('wgs.gbk'), 'rt') 317s req.get(ENTREZ_URL, response_list=[ 317s {"text": u'Whoa, slow down', "status_code": 429, "headers": {"Retry-After": "0"}}, 317s { 317s "body": open(full_path('wgs_full.gbk'), 'rb'), 317s "headers": {"Content-Type": "text/plain; charset=UTF-8"}, 317s }, 317s ]) 317s 317s outhandle = wgs.download_wgs_parts(wgs_contig, cfg) 317s wgs_full = open(full_path('wgs_full.gbk'), 'rt') 317s > assert outhandle.getvalue() == wgs_full.read() 317s E AttributeError: '_io.TextIOWrapper' object has no attribute 'getvalue' 317s 317s test_wgs.py:113: AttributeError 317s ______________________ test_download_wgs_parts_wgs_scafld ______________________ 317s 317s req = 317s 317s def test_download_wgs_parts_wgs_scafld(req): 317s cfg = Config(format="genbank") 317s wgs_contig = open(full_path('wgs_scafld.gbk'), 'rt') 317s with open(full_path('wgs_full.gbk'), 'rt') as handle: 317s full_file = handle.read() 317s req.get(ENTREZ_URL, text=full_file) 317s 317s outhandle = wgs.download_wgs_parts(wgs_contig, cfg) 317s > assert outhandle.getvalue() == full_file 317s E AttributeError: '_io.TextIOWrapper' object has no attribute 'getvalue' 317s 317s test_wgs.py:126: AttributeError 317s _____________________ test_download_wgs_parts_supercontig ______________________ 317s 317s req = 317s 317s def test_download_wgs_parts_supercontig(req): 317s cfg = Config(format="genbank") 317s supercontig = open(full_path('supercontig.gbk'), 'rt') 317s req.get( 317s ENTREZ_URL, 317s body=open(full_path('supercontig_full.gbk'), 'rb'), 317s headers={"Content-Type": "text/plain; charset=UTF-8"}, 317s ) 317s 317s outhandle = wgs.download_wgs_parts(supercontig, cfg) 317s supercontig_full = open(full_path('supercontig_full.gbk'), 'rt') 317s > assert outhandle.getvalue() == supercontig_full.read() 317s E AttributeError: '_io.TextIOWrapper' object has no attribute 'getvalue' 317s 317s test_wgs.py:141: AttributeError 317s __________________ test_download_wgs_parts_supercontig_retry ___________________ 317s 317s req = 317s 317s def test_download_wgs_parts_supercontig_retry(req): 317s cfg = Config(format="genbank") 317s supercontig = open(full_path('supercontig.gbk'), 'rt') 317s req.get(ENTREZ_URL, response_list=[ 317s {"text": u'Whoa, slow down', "status_code": 429, "headers": {"Retry-After": "0"}}, 317s { 317s "body": open(full_path('supercontig_full.gbk'), 'rb'), 317s "headers": {"Content-Type": "text/plain; charset=UTF-8"}, 317s }, 317s ]) 317s 317s outhandle = wgs.download_wgs_parts(supercontig, cfg) 317s supercontig_full = open(full_path('supercontig_full.gbk'), 'rt') 317s > assert outhandle.getvalue() == supercontig_full.read() 317s E AttributeError: '_io.TextIOWrapper' object has no attribute 'getvalue' 317s 317s test_wgs.py:159: AttributeError 317s __________________________ test_download_wgs_no_parts __________________________ 317s 317s req = 317s 317s def test_download_wgs_no_parts(req): 317s cfg = Config(format="genbank") 317s supercontig = open(full_path('supercontig_full.gbk'), 'rt') 317s req.get(ENTREZ_URL, status_code=404) 317s 317s outhandle = wgs.download_wgs_parts(supercontig, cfg) 317s supercontig_full = open(full_path('supercontig_full.gbk'), 'rt') 317s > assert outhandle.getvalue() == supercontig_full.read() 317s E AttributeError: '_io.TextIOWrapper' object has no attribute 'getvalue' 317s 317s test_wgs.py:171: AttributeError 317s =========================== short test summary info ============================ 317s FAILED test_core.py::test_config_have_biopython - assert False 317s FAILED test_core.py::test_validate_and_write_extended_validation - ValueError... 317s FAILED test_correct.py::test_download_and_validate_partial_wgs - AssertionErr... 317s FAILED test_validate.py::test_run_extended_validation_raises - AttributeError... 317s FAILED test_validate.py::test_run_extended_validation_loads - AssertionError:... 317s FAILED test_wgs.py::test_download_wgs_parts_wgs - AttributeError: '_io.TextIO... 317s FAILED test_wgs.py::test_download_wgs_parts_wgs_retry - AttributeError: '_io.... 317s FAILED test_wgs.py::test_download_wgs_parts_wgs_scafld - AttributeError: '_io... 317s FAILED test_wgs.py::test_download_wgs_parts_supercontig - AttributeError: '_i... 317s FAILED test_wgs.py::test_download_wgs_parts_supercontig_retry - AttributeErro... 317s FAILED test_wgs.py::test_download_wgs_no_parts - AttributeError: '_io.TextIOW... 317s =================== 11 failed, 20 passed, 1 xfailed in 0.26s =================== 317s autopkgtest [18:31:29]: test run-unit-test: -----------------------] 321s autopkgtest [18:31:33]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 321s run-unit-test FAIL non-zero exit status 1 326s autopkgtest [18:31:38]: @@@@@@@@@@@@@@@@@@@@ summary 326s run-unit-test FAIL non-zero exit status 1