0s autopkgtest [18:46:50]: starting date and time: 2024-11-13 18:46:50+0000 0s autopkgtest [18:46:50]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [18:46:50]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.pk51_yld/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-ppc64el --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@bos03-ppc64el-21.secgroup --name adt-plucky-ppc64el-ncbi-acc-download-20241113-184649-juju-7f2275-prod-proposed-migration-environment-20-35f6eeed-cbc2-4946-83d5-481856f3696a --image adt/ubuntu-plucky-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-proposed-migration-ppc64el -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/ 118s autopkgtest [18:48:48]: testbed dpkg architecture: ppc64el 118s autopkgtest [18:48:48]: testbed apt version: 2.9.8 118s autopkgtest [18:48:48]: @@@@@@@@@@@@@@@@@@@@ test bed setup 119s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 119s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 119s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [17.2 kB] 119s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [104 kB] 119s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [971 kB] 119s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el Packages [113 kB] 119s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe ppc64el Packages [672 kB] 119s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse ppc64el Packages [20.8 kB] 119s Fetched 1978 kB in 1s (2008 kB/s) 120s Reading package lists... 122s Reading package lists... 122s Building dependency tree... 122s Reading state information... 123s Calculating upgrade... 123s The following NEW packages will be installed: 123s python3.13-gdbm 123s The following packages will be upgraded: 123s libgnutls30t64 libjson-glib-1.0-0 libjson-glib-1.0-common libpython3-stdlib 123s libutempter0 python3 python3-gdbm python3-minimal 123s 8 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 123s Need to get 1265 kB of archives. 123s After this operation, 141 kB of additional disk space will be used. 123s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el python3-minimal ppc64el 3.12.7-1 [27.4 kB] 123s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el python3 ppc64el 3.12.7-1 [24.0 kB] 123s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el libpython3-stdlib ppc64el 3.12.7-1 [10.0 kB] 123s Get:4 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgnutls30t64 ppc64el 3.8.8-2ubuntu1 [1072 kB] 123s Get:5 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3.13-gdbm ppc64el 3.13.0-2 [31.5 kB] 123s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el python3-gdbm ppc64el 3.12.7-1 [8640 B] 123s Get:7 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjson-glib-1.0-common all 1.10.0+ds-3 [5586 B] 123s Get:8 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjson-glib-1.0-0 ppc64el 1.10.0+ds-3 [76.0 kB] 123s Get:9 http://ftpmaster.internal/ubuntu plucky/main ppc64el libutempter0 ppc64el 1.2.1-4 [9850 B] 124s Fetched 1265 kB in 1s (2163 kB/s) 124s (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 ... 73767 files and directories currently installed.) 124s Preparing to unpack .../python3-minimal_3.12.7-1_ppc64el.deb ... 124s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ... 124s Setting up python3-minimal (3.12.7-1) ... 124s (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 ... 73767 files and directories currently installed.) 124s Preparing to unpack .../python3_3.12.7-1_ppc64el.deb ... 124s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ... 124s Preparing to unpack .../libpython3-stdlib_3.12.7-1_ppc64el.deb ... 124s Unpacking libpython3-stdlib:ppc64el (3.12.7-1) over (3.12.6-0ubuntu1) ... 124s Preparing to unpack .../libgnutls30t64_3.8.8-2ubuntu1_ppc64el.deb ... 124s Unpacking libgnutls30t64:ppc64el (3.8.8-2ubuntu1) over (3.8.6-2ubuntu1) ... 124s Setting up libgnutls30t64:ppc64el (3.8.8-2ubuntu1) ... 124s Selecting previously unselected package python3.13-gdbm. 124s (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 ... 73767 files and directories currently installed.) 124s Preparing to unpack .../python3.13-gdbm_3.13.0-2_ppc64el.deb ... 124s Unpacking python3.13-gdbm (3.13.0-2) ... 124s Preparing to unpack .../python3-gdbm_3.12.7-1_ppc64el.deb ... 124s Unpacking python3-gdbm:ppc64el (3.12.7-1) over (3.12.6-1ubuntu1) ... 124s Preparing to unpack .../libjson-glib-1.0-common_1.10.0+ds-3_all.deb ... 124s Unpacking libjson-glib-1.0-common (1.10.0+ds-3) over (1.10.0+ds-2) ... 125s Preparing to unpack .../libjson-glib-1.0-0_1.10.0+ds-3_ppc64el.deb ... 125s Unpacking libjson-glib-1.0-0:ppc64el (1.10.0+ds-3) over (1.10.0+ds-2) ... 125s Preparing to unpack .../libutempter0_1.2.1-4_ppc64el.deb ... 125s Unpacking libutempter0:ppc64el (1.2.1-4) over (1.2.1-3build1) ... 125s Setting up libutempter0:ppc64el (1.2.1-4) ... 125s Setting up libjson-glib-1.0-common (1.10.0+ds-3) ... 125s Setting up python3.13-gdbm (3.13.0-2) ... 125s Setting up libpython3-stdlib:ppc64el (3.12.7-1) ... 125s Setting up python3 (3.12.7-1) ... 125s Setting up libjson-glib-1.0-0:ppc64el (1.10.0+ds-3) ... 125s Setting up python3-gdbm:ppc64el (3.12.7-1) ... 125s Processing triggers for man-db (2.12.1-3) ... 126s Processing triggers for libc-bin (2.40-1ubuntu3) ... 126s Reading package lists... 126s Building dependency tree... 126s Reading state information... 126s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 127s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 127s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 127s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 127s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 128s Reading package lists... 128s Reading package lists... 128s Building dependency tree... 128s Reading state information... 129s Calculating upgrade... 129s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 129s Reading package lists... 129s Building dependency tree... 129s Reading state information... 129s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 132s autopkgtest [18:49:02]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP Mon Sep 16 13:49:23 UTC 2024 132s autopkgtest [18:49:02]: @@@@@@@@@@@@@@@@@@@@ apt-source ncbi-acc-download 134s Get:1 http://ftpmaster.internal/ubuntu plucky/universe ncbi-acc-download 0.2.8-3 (dsc) [2434 B] 134s Get:2 http://ftpmaster.internal/ubuntu plucky/universe ncbi-acc-download 0.2.8-3 (tar) [20.9 kB] 134s Get:3 http://ftpmaster.internal/ubuntu plucky/universe ncbi-acc-download 0.2.8-3 (diff) [4420 B] 134s gpgv: Signature made Thu Aug 1 23:03:26 2024 UTC 134s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 134s gpgv: issuer "tille@debian.org" 134s gpgv: Can't check signature: No public key 134s dpkg-source: warning: cannot verify inline signature for ./ncbi-acc-download_0.2.8-3.dsc: no acceptable signature found 134s autopkgtest [18:49:04]: testing package ncbi-acc-download version 0.2.8-3 134s autopkgtest [18:49:04]: build not needed 134s autopkgtest [18:49:04]: test run-unit-test: preparing testbed 136s Reading package lists... 136s Building dependency tree... 136s Reading state information... 137s Starting pkgProblemResolver with broken count: 0 137s Starting 2 pkgProblemResolver with broken count: 0 137s Done 137s The following additional packages will be installed: 137s fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-urw-base35 137s libblas3 libcairo2 libdeflate0 libfontconfig1 libfontenc1 libgfortran5 137s libgomp1 libgraphite2-3 libharfbuzz0b libimagequant0 libjbig0 libjpeg-turbo8 137s libjpeg8 libjs-jquery libjs-jquery-hotkeys libjs-jquery-isonscreen 137s libjs-jquery-metadata libjs-jquery-tablesorter 137s libjs-jquery-throttle-debounce liblapack3 liblcms2-2 liblerc4 libopenjp2-7 137s libpixman-1-0 libpython3.13-minimal libpython3.13-stdlib libraqm0 137s libsharpyuv0 libtiff6 libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 137s libxcb-shm0 libxrender1 ncbi-acc-download python3-all python3-biopython 137s python3-cairo python3-coverage python3-freetype python3-iniconfig 137s python3-numpy python3-packaging python3-pil python3-pluggy python3-pytest 137s python3-pytest-cov python3-pytest-mock python3-reportlab 137s python3-requests-mock python3-rlpycairo python3.13 python3.13-minimal 137s sgml-base w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core 137s Suggested packages: 137s fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre liblcms2-utils 137s python3-tk bwa clustalo clustalw dialign dssp emboss fasttree mafft muscle3 137s phylip phyml prank probcons python3-mysqldb python3-matplotlib python3-mmtf 137s python3-rdflib python3-psycopg2 python3-scipy raxml samtools t-coffee wise 137s python-coverage-doc gcc gfortran python-numpy-doc python3-dev python-pil-doc 137s python-pytest-mock-doc pdf-viewer python3-egenix-mxtexttools 137s python-reportlab-doc rl-accel rl-renderpm python3.13-venv python3.13-doc 137s binfmt-support sgml-base-doc debhelper 137s Recommended packages: 137s javascript-common python-biopython-doc ncbi-blast+ python3-olefile 137s fonts-dejavu-extra 137s The following NEW packages will be installed: 137s autopkgtest-satdep fontconfig-config fonts-dejavu-core fonts-dejavu-mono 137s fonts-urw-base35 libblas3 libcairo2 libdeflate0 libfontconfig1 libfontenc1 137s libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libimagequant0 libjbig0 137s libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-hotkeys 137s libjs-jquery-isonscreen libjs-jquery-metadata libjs-jquery-tablesorter 137s libjs-jquery-throttle-debounce liblapack3 liblcms2-2 liblerc4 libopenjp2-7 137s libpixman-1-0 libpython3.13-minimal libpython3.13-stdlib libraqm0 137s libsharpyuv0 libtiff6 libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 137s libxcb-shm0 libxrender1 ncbi-acc-download python3-all python3-biopython 137s python3-cairo python3-coverage python3-freetype python3-iniconfig 137s python3-numpy python3-packaging python3-pil python3-pluggy python3-pytest 137s python3-pytest-cov python3-pytest-mock python3-reportlab 137s python3-requests-mock python3-rlpycairo python3.13 python3.13-minimal 137s sgml-base w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core 137s 0 upgraded, 65 newly installed, 0 to remove and 0 not upgraded. 137s Need to get 36.2 MB/36.2 MB of archives. 137s After this operation, 123 MB of additional disk space will be used. 137s Get:1 /tmp/autopkgtest.kkeWl4/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [760 B] 137s Get:2 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpython3.13-minimal ppc64el 3.13.0-2 [881 kB] 138s Get:3 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3.13-minimal ppc64el 3.13.0-2 [2302 kB] 138s Get:4 http://ftpmaster.internal/ubuntu plucky/main ppc64el sgml-base all 1.31 [11.4 kB] 138s Get:5 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 138s Get:6 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libjs-jquery-hotkeys all 0~20130707+git2d51e3a9+dfsg-2.1 [11.5 kB] 138s Get:7 http://ftpmaster.internal/ubuntu plucky/main ppc64el fonts-dejavu-mono all 2.37-8 [502 kB] 138s Get:8 http://ftpmaster.internal/ubuntu plucky/main ppc64el fonts-dejavu-core all 2.37-8 [835 kB] 138s Get:9 http://ftpmaster.internal/ubuntu plucky/main ppc64el libfontenc1 ppc64el 1:1.1.8-1build1 [15.8 kB] 138s Get:10 http://ftpmaster.internal/ubuntu plucky/main ppc64el x11-common all 1:7.7+23ubuntu3 [21.7 kB] 138s Get:11 http://ftpmaster.internal/ubuntu plucky/main ppc64el xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 138s Get:12 http://ftpmaster.internal/ubuntu plucky/main ppc64el xfonts-utils ppc64el 1:7.7+7 [114 kB] 138s Get:13 http://ftpmaster.internal/ubuntu plucky/main ppc64el fonts-urw-base35 all 20200910-8 [11.0 MB] 138s Get:14 http://ftpmaster.internal/ubuntu plucky/main ppc64el fontconfig-config ppc64el 2.15.0-1.1ubuntu2 [37.4 kB] 138s Get:15 http://ftpmaster.internal/ubuntu plucky/main ppc64el libblas3 ppc64el 3.12.0-3build2 [222 kB] 138s Get:16 http://ftpmaster.internal/ubuntu plucky/main ppc64el libfontconfig1 ppc64el 2.15.0-1.1ubuntu2 [190 kB] 138s Get:17 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpixman-1-0 ppc64el 0.44.0-3 [334 kB] 138s Get:18 http://ftpmaster.internal/ubuntu plucky/main ppc64el libxcb-render0 ppc64el 1.17.0-2 [17.2 kB] 138s Get:19 http://ftpmaster.internal/ubuntu plucky/main ppc64el libxcb-shm0 ppc64el 1.17.0-2 [5980 B] 138s Get:20 http://ftpmaster.internal/ubuntu plucky/main ppc64el libxrender1 ppc64el 1:0.9.10-1.1build1 [23.1 kB] 138s Get:21 http://ftpmaster.internal/ubuntu plucky/main ppc64el libcairo2 ppc64el 1.18.2-2 [747 kB] 138s Get:22 http://ftpmaster.internal/ubuntu plucky/main ppc64el libdeflate0 ppc64el 1.22-1 [63.3 kB] 138s Get:23 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgfortran5 ppc64el 14.2.0-8ubuntu1 [571 kB] 138s Get:24 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgomp1 ppc64el 14.2.0-8ubuntu1 [161 kB] 138s Get:25 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgraphite2-3 ppc64el 1.3.14-2ubuntu1 [84.6 kB] 139s Get:26 http://ftpmaster.internal/ubuntu plucky/main ppc64el libharfbuzz0b ppc64el 10.0.1-1 [596 kB] 139s Get:27 http://ftpmaster.internal/ubuntu plucky/main ppc64el libimagequant0 ppc64el 2.18.0-1build1 [43.2 kB] 139s Get:28 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjpeg-turbo8 ppc64el 2.1.5-2ubuntu2 [219 kB] 139s Get:29 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjpeg8 ppc64el 8c-2ubuntu11 [2148 B] 139s Get:30 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libjs-jquery-metadata all 12-4 [6582 B] 139s Get:31 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libjs-jquery-tablesorter all 1:2.31.3+dfsg1-4 [192 kB] 139s Get:32 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libjs-jquery-throttle-debounce all 1.1+dfsg.1-2 [12.5 kB] 139s Get:33 http://ftpmaster.internal/ubuntu plucky/main ppc64el liblapack3 ppc64el 3.12.0-3build2 [2806 kB] 139s Get:34 http://ftpmaster.internal/ubuntu plucky/main ppc64el liblcms2-2 ppc64el 2.16-2 [243 kB] 139s Get:35 http://ftpmaster.internal/ubuntu plucky/main ppc64el liblerc4 ppc64el 4.0.0+ds-4ubuntu2 [270 kB] 139s Get:36 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpython3.13-stdlib ppc64el 3.13.0-2 [2148 kB] 139s Get:37 http://ftpmaster.internal/ubuntu plucky/main ppc64el libraqm0 ppc64el 0.10.1-1build1 [19.4 kB] 139s Get:38 http://ftpmaster.internal/ubuntu plucky/main ppc64el libsharpyuv0 ppc64el 1.4.0-0.1 [22.0 kB] 139s Get:39 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjbig0 ppc64el 2.1-6.1ubuntu2 [35.9 kB] 139s Get:40 http://ftpmaster.internal/ubuntu plucky/main ppc64el libwebp7 ppc64el 1.4.0-0.1 [309 kB] 139s Get:41 http://ftpmaster.internal/ubuntu plucky/main ppc64el libtiff6 ppc64el 4.5.1+git230720-4ubuntu4 [272 kB] 139s Get:42 http://ftpmaster.internal/ubuntu plucky/main ppc64el libwebpdemux2 ppc64el 1.4.0-0.1 [14.1 kB] 139s Get:43 http://ftpmaster.internal/ubuntu plucky/main ppc64el libwebpmux3 ppc64el 1.4.0-0.1 [31.4 kB] 139s Get:44 http://ftpmaster.internal/ubuntu plucky/universe ppc64el ncbi-acc-download all 0.2.8-3 [13.3 kB] 139s Get:45 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3.13 ppc64el 3.13.0-2 [719 kB] 139s Get:46 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el python3-all ppc64el 3.12.7-1 [888 B] 139s Get:47 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-numpy ppc64el 1:1.26.4+ds-11build1 [4434 kB] 139s Get:48 http://ftpmaster.internal/ubuntu plucky/main ppc64el libopenjp2-7 ppc64el 2.5.0-2ubuntu1 [246 kB] 139s Get:49 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-pil ppc64el 10.4.0-1ubuntu1 [581 kB] 139s Get:50 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-cairo ppc64el 1.26.1-2 [129 kB] 139s Get:51 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-freetype all 2.5.1-1 [92.3 kB] 139s Get:52 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-rlpycairo all 0.3.0-3 [9130 B] 139s Get:53 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-reportlab all 4.2.5-1 [1107 kB] 139s Get:54 http://ftpmaster.internal/ubuntu plucky/main ppc64el xml-core all 0.19 [20.3 kB] 139s Get:55 http://ftpmaster.internal/ubuntu plucky/universe ppc64el w3c-sgml-lib all 1.3-3 [280 kB] 139s Get:56 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-biopython ppc64el 1.84+dfsg-4 [1738 kB] 139s Get:57 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-coverage ppc64el 7.4.4+dfsg1-0ubuntu2 [149 kB] 139s Get:58 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-iniconfig all 1.1.1-2 [6024 B] 139s Get:59 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-packaging all 24.1-1 [41.4 kB] 139s Get:60 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-pluggy all 1.5.0-1 [21.0 kB] 139s Get:61 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-pytest all 8.3.3-1 [251 kB] 139s Get:62 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libjs-jquery-isonscreen all 1.2.0-1.1 [3244 B] 139s Get:63 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-pytest-cov all 5.0.0-1 [21.3 kB] 139s Get:64 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-pytest-mock all 3.14.0-2 [11.7 kB] 139s Get:65 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-requests-mock all 1.12.1-2 [17.8 kB] 140s Fetched 36.2 MB in 2s (16.3 MB/s) 140s Selecting previously unselected package libpython3.13-minimal:ppc64el. 140s (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 ... 73774 files and directories currently installed.) 140s Preparing to unpack .../00-libpython3.13-minimal_3.13.0-2_ppc64el.deb ... 140s Unpacking libpython3.13-minimal:ppc64el (3.13.0-2) ... 140s Selecting previously unselected package python3.13-minimal. 140s Preparing to unpack .../01-python3.13-minimal_3.13.0-2_ppc64el.deb ... 140s Unpacking python3.13-minimal (3.13.0-2) ... 140s Selecting previously unselected package sgml-base. 140s Preparing to 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libgraphite2-3:ppc64el (1.3.14-2ubuntu1) ... 142s Setting up liblcms2-2:ppc64el (2.16-2) ... 142s Setting up python3-iniconfig (1.1.1-2) ... 143s Setting up libpixman-1-0:ppc64el (0.44.0-3) ... 143s Setting up libsharpyuv0:ppc64el (1.4.0-0.1) ... 143s Setting up liblerc4:ppc64el (4.0.0+ds-4ubuntu2) ... 143s Setting up libxrender1:ppc64el (1:0.9.10-1.1build1) ... 143s Setting up libxcb-render0:ppc64el (1.17.0-2) ... 143s Setting up x11-common (1:7.7+23ubuntu3) ... 143s Setting up libdeflate0:ppc64el (1.22-1) ... 143s Setting up python3-coverage (7.4.4+dfsg1-0ubuntu2) ... 144s Setting up libxcb-shm0:ppc64el (1.17.0-2) ... 144s Setting up libjs-jquery-throttle-debounce (1.1+dfsg.1-2) ... 144s Setting up libgomp1:ppc64el (14.2.0-8ubuntu1) ... 144s Setting up python3-freetype (2.5.1-1) ... 144s Setting up libjbig0:ppc64el (2.1-6.1ubuntu2) ... 144s Setting up libpython3.13-minimal:ppc64el (3.13.0-2) ... 144s Setting up libfontenc1:ppc64el (1:1.1.8-1build1) ... 144s Setting up libblas3:ppc64el (3.12.0-3build2) ... 144s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/blas/libblas.so.3 to provide /usr/lib/powerpc64le-linux-gnu/libblas.so.3 (libblas.so.3-powerpc64le-linux-gnu) in auto mode 144s Setting up python3-packaging (24.1-1) ... 144s Setting up python3-requests-mock (1.12.1-2) ... 144s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 144s Setting up libimagequant0:ppc64el (2.18.0-1build1) ... 144s Setting up fonts-dejavu-mono (2.37-8) ... 144s Setting up fonts-dejavu-core (2.37-8) ... 144s Setting up libjpeg-turbo8:ppc64el (2.1.5-2ubuntu2) ... 144s Setting up libgfortran5:ppc64el (14.2.0-8ubuntu1) ... 144s Setting up python3-pluggy (1.5.0-1) ... 144s Setting up libwebp7:ppc64el (1.4.0-0.1) ... 144s Setting up libopenjp2-7:ppc64el (2.5.0-2ubuntu1) ... 144s Setting up python3.13-minimal (3.13.0-2) ... 145s Setting up ncbi-acc-download (0.2.8-3) ... 146s Setting up libharfbuzz0b:ppc64el (10.0.1-1) ... 146s Setting up sgml-base (1.31) ... 146s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 146s Setting up libjs-jquery-hotkeys (0~20130707+git2d51e3a9+dfsg-2.1) ... 146s Setting up libwebpmux3:ppc64el (1.4.0-0.1) ... 146s Setting up libpython3.13-stdlib:ppc64el (3.13.0-2) ... 146s Setting up libjpeg8:ppc64el (8c-2ubuntu11) ... 146s Setting up liblapack3:ppc64el (3.12.0-3build2) ... 146s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/powerpc64le-linux-gnu/liblapack.so.3 (liblapack.so.3-powerpc64le-linux-gnu) in auto mode 146s Setting up python3.13 (3.13.0-2) ... 147s Setting up fontconfig-config (2.15.0-1.1ubuntu2) ... 147s Setting up python3-pytest (8.3.3-1) ... 148s Setting up libwebpdemux2:ppc64el (1.4.0-0.1) ... 148s Setting up python3-all (3.12.7-1) ... 148s Setting up xfonts-utils (1:7.7+7) ... 148s Setting up libjs-jquery-metadata (12-4) ... 148s Setting up libraqm0:ppc64el (0.10.1-1build1) ... 148s Setting up libjs-jquery-isonscreen (1.2.0-1.1) ... 148s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 153s Setting up libjs-jquery-tablesorter (1:2.31.3+dfsg1-4) ... 153s Setting up python3-pytest-mock (3.14.0-2) ... 153s Setting up libtiff6:ppc64el (4.5.1+git230720-4ubuntu4) ... 153s Setting up xml-core (0.19) ... 153s Setting up libfontconfig1:ppc64el (2.15.0-1.1ubuntu2) ... 153s Setting up python3-pytest-cov (5.0.0-1) ... 153s Setting up fonts-urw-base35 (20200910-8) ... 154s Setting up libcairo2:ppc64el (1.18.2-2) ... 154s Setting up python3-pil:ppc64el (10.4.0-1ubuntu1) ... 154s Setting up python3-cairo (1.26.1-2) ... 155s Setting up python3-rlpycairo (0.3.0-3) ... 155s Setting up python3-reportlab (4.2.5-1) ... 157s Processing triggers for libc-bin (2.40-1ubuntu3) ... 157s Processing triggers for systemd (256.5-2ubuntu4) ... 157s Processing triggers for man-db (2.12.1-3) ... 158s Processing triggers for sgml-base (1.31) ... 158s Setting up w3c-sgml-lib (1.3-3) ... 196s Setting up python3-biopython (1.84+dfsg-4) ... 199s Setting up autopkgtest-satdep (0) ... 202s (Reading database ... 78265 files and directories currently installed.) 202s Removing autopkgtest-satdep (0) ... 203s autopkgtest [18:50:13]: test run-unit-test: [----------------------- 203s /tmp/autopkgtest.kkeWl4/build.19v/src/tests /tmp/autopkgtest.kkeWl4/build.19v/src 203s Testing with python3.13 in /tmp/autopkgtest.kkeWl4/build.19v/src/tests: 204s ============================= test session starts ============================== 204s platform linux -- Python 3.13.0, pytest-8.3.3, pluggy-1.5.0 -- /usr/bin/python3.13 204s cachedir: .pytest_cache 204s rootdir: /tmp/autopkgtest.kkeWl4/build.19v/src 204s plugins: mock-3.14.0, cov-5.0.0, requests_mock-1.12.1, typeguard-4.4.1 205s collecting ... collected 32 items 205s 205s test_core.py::test_config PASSED [ 3%] 205s test_core.py::test_config_no_biopython PASSED [ 6%] 205s test_core.py::test_config_have_biopython FAILED [ 9%] 205s test_core.py::test_download_to_file PASSED [ 12%] 205s test_core.py::test_download_to_file_append PASSED [ 15%] 205s test_core.py::test_download_to_file_retry PASSED [ 18%] 205s test_core.py::test_build_params PASSED [ 21%] 205s test_core.py::test_generate_filename PASSED [ 25%] 205s test_core.py::test_validate_and_write_error_pattern_raises PASSED [ 28%] 205s test_core.py::test_validate_and_write_emit PASSED [ 31%] 205s test_core.py::test_validate_and_write_extended_validation FAILED [ 34%] 205s test_core.py::test_get_stream_exception PASSED [ 37%] 205s test_core.py::test_get_stream_bad_status PASSED [ 40%] 205s test_core.py::test_get_stream_too_many_requests PASSED [ 43%] 205s test_core.py::test_generate_url PASSED [ 46%] 205s test_core.py::test_generate_url_with_api_key PASSED [ 50%] 205s test_correct.py::test_download_and_validate_partial_wgs FAILED [ 53%] 205s test_download.py::test_write_stream PASSED [ 56%] 205s test_validate.py::test_run_extended_validation_no_biopython PASSED [ 59%] 205s test_validate.py::test_run_extended_validation_raises FAILED [ 62%] 205s test_validate.py::test_run_extended_validation_loads FAILED [ 65%] 205s test_wgs.py::test_init PASSED [ 68%] 205s test_wgs.py::test_get_ids PASSED [ 71%] 205s test_wgs.py::test_from_string PASSED [ 75%] 205s test_wgs.py::test_download_wgs_parts_no_biopython PASSED [ 78%] 205s test_wgs.py::test_download_wgs_parts_wgs FAILED [ 81%] 205s test_wgs.py::test_download_wgs_parts_wgs_retry FAILED [ 84%] 205s test_wgs.py::test_download_wgs_parts_wgs_scafld FAILED [ 87%] 205s test_wgs.py::test_download_wgs_parts_supercontig FAILED [ 90%] 205s test_wgs.py::test_download_wgs_parts_supercontig_retry FAILED [ 93%] 205s test_wgs.py::test_download_wgs_no_parts FAILED [ 96%] 205s test_wgs.py::test_download_wgs_parts_tsa XFAIL [100%] 205s 205s =================================== FAILURES =================================== 205s __________________________ test_config_have_biopython __________________________ 205s 205s def test_config_have_biopython(): 205s """Test we detect Biopython.""" 205s > assert core.HAVE_BIOPYTHON 205s E assert False 205s E + where False = core.HAVE_BIOPYTHON 205s 205s test_core.py:46: AssertionError 205s _________________ test_validate_and_write_extended_validation __________________ 205s 205s req = 205s 205s def test_validate_and_write_extended_validation(req): 205s """Test extended validation before writing.""" 205s handle = StringIO() 205s req.get('http://fake/', text=u'>foo\nMAGIC') 205s r = requests.get('http://fake/') 205s > config = core.Config(extended_validation='loads', molecule='protein') 205s 205s test_core.py:226: 205s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 205s /usr/lib/python3/dist-packages/ncbi_acc_download/core.py:64: in __init__ 205s self.extended_validation = extended_validation 205s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 205s 205s self = , value = 'loads' 205s 205s @extended_validation.setter 205s def extended_validation(self, value): 205s if value != 'none' and not HAVE_BIOPYTHON: 205s > raise ValueError("Asked for extended validation, but Biopython not available") 205s E ValueError: Asked for extended validation, but Biopython not available 205s 205s /usr/lib/python3/dist-packages/ncbi_acc_download/core.py:96: ValueError 205s ____________________ test_download_and_validate_partial_wgs ____________________ 205s 205s req = 205s 205s def test_download_and_validate_partial_wgs(req): 205s handle = StringIO(open(full_path('partialcontig.gbk'), 'r').read()) 205s > assert validate.run_extended_validation(handle, 'genbank', 'loads') 205s E AssertionError: assert False 205s E + where False = (<_io.StringIO object at 0x67de86ffaec0>, 'genbank', 'loads') 205s E + where = validate.run_extended_validation 205s 205s test_correct.py:15: AssertionError 205s _____________________ test_run_extended_validation_raises ______________________ 205s 205s monkeypatch = <_pytest.monkeypatch.MonkeyPatch object at 0x67de8704fbf0> 205s mocker = 205s 205s def test_run_extended_validation_raises(monkeypatch, mocker): 205s """Test the "seqence loads" validator catches exceptions in SeqIO.parse().""" 205s seqio_mock = mocker.MagicMock() 205s seqio_mock.parse = mocker.MagicMock(side_effect=ValueError) 205s > monkeypatch.setattr(validate, 'SeqIO', seqio_mock) 205s E AttributeError: has no attribute 'SeqIO' 205s 205s test_validate.py:19: AttributeError 205s ______________________ test_run_extended_validation_loads ______________________ 205s 205s def test_run_extended_validation_loads(): 205s """Test the "sequence loads" validator.""" 205s handle = StringIO(u'>foo\nATGC\n>bar\nATGTGA\n') 205s > assert validate.run_extended_validation(handle, 'fasta', 'loads') 205s E AssertionError: assert False 205s E + where False = (<_io.StringIO object at 0x67de86ffa680>, 'fasta', 'loads') 205s E + where = validate.run_extended_validation 205s 205s test_validate.py:29: AssertionError 205s _________________________ test_download_wgs_parts_wgs __________________________ 205s 205s req = 205s 205s def test_download_wgs_parts_wgs(req): 205s cfg = Config(format="genbank") 205s wgs_contig = open(full_path('wgs.gbk'), 'rt') 205s req.get( 205s ENTREZ_URL, 205s body=open(full_path('wgs_full.gbk'), 'rb'), 205s headers={"Content-Type": "text/plain; charset=UTF-8"}, 205s ) 205s 205s outhandle = wgs.download_wgs_parts(wgs_contig, cfg) 205s wgs_full = open(full_path('wgs_full.gbk'), 'rt') 205s > assert outhandle.getvalue() == wgs_full.read() 205s E AttributeError: '_io.TextIOWrapper' object has no attribute 'getvalue' 205s 205s test_wgs.py:95: AttributeError 205s ______________________ test_download_wgs_parts_wgs_retry _______________________ 205s 205s req = 205s 205s def test_download_wgs_parts_wgs_retry(req): 205s cfg = Config(format="genbank") 205s wgs_contig = open(full_path('wgs.gbk'), 'rt') 205s req.get(ENTREZ_URL, response_list=[ 205s {"text": u'Whoa, slow down', "status_code": 429, "headers": {"Retry-After": "0"}}, 205s { 205s "body": open(full_path('wgs_full.gbk'), 'rb'), 205s "headers": {"Content-Type": "text/plain; charset=UTF-8"}, 205s }, 205s ]) 205s 205s outhandle = wgs.download_wgs_parts(wgs_contig, cfg) 205s wgs_full = open(full_path('wgs_full.gbk'), 'rt') 205s > assert outhandle.getvalue() == wgs_full.read() 205s E AttributeError: '_io.TextIOWrapper' object has no attribute 'getvalue' 205s 205s test_wgs.py:113: AttributeError 205s ______________________ test_download_wgs_parts_wgs_scafld ______________________ 205s 205s req = 205s 205s def test_download_wgs_parts_wgs_scafld(req): 205s cfg = Config(format="genbank") 205s wgs_contig = open(full_path('wgs_scafld.gbk'), 'rt') 205s with open(full_path('wgs_full.gbk'), 'rt') as handle: 205s full_file = handle.read() 205s req.get(ENTREZ_URL, text=full_file) 205s 205s outhandle = wgs.download_wgs_parts(wgs_contig, cfg) 205s > assert outhandle.getvalue() == full_file 205s E AttributeError: '_io.TextIOWrapper' object has no attribute 'getvalue' 205s 205s test_wgs.py:126: AttributeError 205s _____________________ test_download_wgs_parts_supercontig ______________________ 205s 205s req = 205s 205s def test_download_wgs_parts_supercontig(req): 205s cfg = Config(format="genbank") 205s supercontig = open(full_path('supercontig.gbk'), 'rt') 205s req.get( 205s ENTREZ_URL, 205s body=open(full_path('supercontig_full.gbk'), 'rb'), 205s headers={"Content-Type": "text/plain; charset=UTF-8"}, 205s ) 205s 205s outhandle = wgs.download_wgs_parts(supercontig, cfg) 205s supercontig_full = open(full_path('supercontig_full.gbk'), 'rt') 205s > assert outhandle.getvalue() == supercontig_full.read() 205s E AttributeError: '_io.TextIOWrapper' object has no attribute 'getvalue' 205s 205s test_wgs.py:141: AttributeError 205s __________________ test_download_wgs_parts_supercontig_retry ___________________ 205s 205s req = 205s 205s def test_download_wgs_parts_supercontig_retry(req): 205s cfg = Config(format="genbank") 205s supercontig = open(full_path('supercontig.gbk'), 'rt') 205s req.get(ENTREZ_URL, response_list=[ 205s {"text": u'Whoa, slow down', "status_code": 429, "headers": {"Retry-After": "0"}}, 205s { 205s "body": open(full_path('supercontig_full.gbk'), 'rb'), 205s "headers": {"Content-Type": "text/plain; charset=UTF-8"}, 205s }, 205s ]) 205s 205s outhandle = wgs.download_wgs_parts(supercontig, cfg) 205s supercontig_full = open(full_path('supercontig_full.gbk'), 'rt') 205s > assert outhandle.getvalue() == supercontig_full.read() 205s E AttributeError: '_io.TextIOWrapper' object has no attribute 'getvalue' 205s 205s test_wgs.py:159: AttributeError 205s __________________________ test_download_wgs_no_parts __________________________ 205s 205s req = 205s 205s def test_download_wgs_no_parts(req): 205s cfg = Config(format="genbank") 205s supercontig = open(full_path('supercontig_full.gbk'), 'rt') 205s req.get(ENTREZ_URL, status_code=404) 205s 205s outhandle = wgs.download_wgs_parts(supercontig, cfg) 205s supercontig_full = open(full_path('supercontig_full.gbk'), 'rt') 205s > assert outhandle.getvalue() == supercontig_full.read() 205s E AttributeError: '_io.TextIOWrapper' object has no attribute 'getvalue' 205s 205s test_wgs.py:171: AttributeError 205s =========================== short test summary info ============================ 205s FAILED test_core.py::test_config_have_biopython - assert False 205s FAILED test_core.py::test_validate_and_write_extended_validation - ValueError... 205s FAILED test_correct.py::test_download_and_validate_partial_wgs - AssertionErr... 205s FAILED test_validate.py::test_run_extended_validation_raises - AttributeError... 205s FAILED test_validate.py::test_run_extended_validation_loads - AssertionError:... 205s FAILED test_wgs.py::test_download_wgs_parts_wgs - AttributeError: '_io.TextIO... 205s FAILED test_wgs.py::test_download_wgs_parts_wgs_retry - AttributeError: '_io.... 205s FAILED test_wgs.py::test_download_wgs_parts_wgs_scafld - AttributeError: '_io... 205s FAILED test_wgs.py::test_download_wgs_parts_supercontig - AttributeError: '_i... 205s FAILED test_wgs.py::test_download_wgs_parts_supercontig_retry - AttributeErro... 205s FAILED test_wgs.py::test_download_wgs_no_parts - AttributeError: '_io.TextIOW... 205s =================== 11 failed, 20 passed, 1 xfailed in 0.29s =================== 205s autopkgtest [18:50:15]: test run-unit-test: -----------------------] 206s run-unit-test FAIL non-zero exit status 1 206s autopkgtest [18:50:16]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 206s autopkgtest [18:50:16]: @@@@@@@@@@@@@@@@@@@@ summary 206s run-unit-test FAIL non-zero exit status 1 217s nova [W] Using flock in prodstack6-ppc64el 217s Creating nova instance adt-plucky-ppc64el-ncbi-acc-download-20241113-184649-juju-7f2275-prod-proposed-migration-environment-20-35f6eeed-cbc2-4946-83d5-481856f3696a from image adt/ubuntu-plucky-ppc64el-server-20241113.img (UUID 0c5715b6-5cca-4485-b8bf-b85dfd917a5f)...