0s autopkgtest [11:32:37]: starting date and time: 2025-11-17 11:32:37+0000 0s autopkgtest [11:32:37]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [11:32:37]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.7f90x_iv/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:requests,src:python3-defaults --apt-upgrade ncbi-acc-download --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=requests/2.32.5+dfsg-1ubuntu1 python3-defaults/3.13.7-2' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-ppc64el --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-ppc64el-5.secgroup --name adt-resolute-ppc64el-ncbi-acc-download-20251117-113236-juju-7f2275-prod-proposed-migration-environment-2-ddc4eac5-0d64-4f36-abe2-b5bfc4d5189d --image adt/ubuntu-resolute-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration-ppc64el -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 4s Creating nova instance adt-resolute-ppc64el-ncbi-acc-download-20251117-113236-juju-7f2275-prod-proposed-migration-environment-2-ddc4eac5-0d64-4f36-abe2-b5bfc4d5189d from image adt/ubuntu-resolute-ppc64el-server-20251117.img (UUID c6f5b741-c77a-45db-84cb-f00b40e77676)... 69s autopkgtest [11:33:46]: testbed dpkg architecture: ppc64el 69s autopkgtest [11:33:46]: testbed apt version: 3.1.11 69s autopkgtest [11:33:46]: @@@@@@@@@@@@@@@@@@@@ test bed setup 70s autopkgtest [11:33:47]: testbed release detected to be: None 70s autopkgtest [11:33:47]: updating testbed package index (apt update) 71s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [87.8 kB] 71s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 71s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 71s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 71s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [9848 B] 71s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [868 kB] 72s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [81.1 kB] 72s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [22.9 kB] 72s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main ppc64el Packages [140 kB] 72s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/restricted ppc64el Packages [940 B] 72s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/universe ppc64el Packages [562 kB] 72s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse ppc64el Packages [11.0 kB] 72s Fetched 1784 kB in 1s (1472 kB/s) 73s Reading package lists... 74s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 74s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 74s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 74s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 75s Reading package lists... 75s Reading package lists... 75s Building dependency tree... 75s Reading state information... 75s Calculating upgrade... 75s The following packages will be upgraded: 75s libpython3-stdlib python3 python3-minimal python3-requests usbutils 75s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 75s Need to get 207 kB of archives. 75s After this operation, 1024 B of additional disk space will be used. 75s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed/main ppc64el python3-minimal ppc64el 3.13.7-2 [27.8 kB] 76s Get:2 http://ftpmaster.internal/ubuntu resolute-proposed/main ppc64el python3 ppc64el 3.13.7-2 [23.9 kB] 76s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main ppc64el libpython3-stdlib ppc64el 3.13.7-2 [10.6 kB] 76s Get:4 http://ftpmaster.internal/ubuntu resolute/main ppc64el usbutils ppc64el 1:019-1 [91.5 kB] 76s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/main ppc64el python3-requests all 2.32.5+dfsg-1ubuntu1 [53.1 kB] 76s dpkg-preconfigure: unable to re-open stdin: No such file or directory 76s Fetched 207 kB in 0s (431 kB/s) 76s (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 ... 81022 files and directories currently installed.) 76s Preparing to unpack .../python3-minimal_3.13.7-2_ppc64el.deb ... 77s Unpacking python3-minimal (3.13.7-2) over (3.13.7-1) ... 77s Setting up python3-minimal (3.13.7-2) ... 77s (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 ... 81022 files and directories currently installed.) 77s Preparing to unpack .../python3_3.13.7-2_ppc64el.deb ... 77s running python pre-rtupdate hooks for python3.13... 77s Unpacking python3 (3.13.7-2) over (3.13.7-1) ... 77s Preparing to unpack .../libpython3-stdlib_3.13.7-2_ppc64el.deb ... 77s Unpacking libpython3-stdlib:ppc64el (3.13.7-2) over (3.13.7-1) ... 77s Preparing to unpack .../usbutils_1%3a019-1_ppc64el.deb ... 77s Unpacking usbutils (1:019-1) over (1:018-2) ... 77s Preparing to unpack .../python3-requests_2.32.5+dfsg-1ubuntu1_all.deb ... 77s Unpacking python3-requests (2.32.5+dfsg-1ubuntu1) over (2.32.3+dfsg-5ubuntu2) ... 77s Setting up usbutils (1:019-1) ... 77s Setting up libpython3-stdlib:ppc64el (3.13.7-2) ... 77s Setting up python3 (3.13.7-2) ... 78s running python rtupdate hooks for python3.13... 78s running python post-rtupdate hooks for python3.13... 78s Setting up python3-requests (2.32.5+dfsg-1ubuntu1) ... 78s Processing triggers for man-db (2.13.1-1) ... 80s autopkgtest [11:33:57]: upgrading testbed (apt dist-upgrade and autopurge) 81s Reading package lists... 81s Building dependency tree... 81s Reading state information... 81s Calculating upgrade... 81s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 81s Reading package lists... 82s Building dependency tree... 82s Reading state information... 82s Solving dependencies... 82s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 85s autopkgtest [11:34:02]: testbed running kernel: Linux 6.17.0-5-generic #5-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 22 10:02:41 UTC 2025 85s autopkgtest [11:34:02]: @@@@@@@@@@@@@@@@@@@@ apt-source ncbi-acc-download 87s Get:1 http://ftpmaster.internal/ubuntu resolute/universe ncbi-acc-download 0.2.8-3 (dsc) [2434 B] 87s Get:2 http://ftpmaster.internal/ubuntu resolute/universe ncbi-acc-download 0.2.8-3 (tar) [20.9 kB] 87s Get:3 http://ftpmaster.internal/ubuntu resolute/universe ncbi-acc-download 0.2.8-3 (diff) [4420 B] 87s gpgv: Signature made Thu Aug 1 23:03:26 2024 UTC 87s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 87s gpgv: issuer "tille@debian.org" 87s gpgv: Can't check signature: No public key 87s dpkg-source: warning: cannot verify inline signature for ./ncbi-acc-download_0.2.8-3.dsc: no acceptable signature found 87s autopkgtest [11:34:04]: testing package ncbi-acc-download version 0.2.8-3 88s autopkgtest [11:34:05]: build not needed 89s autopkgtest [11:34:06]: test run-unit-test: preparing testbed 89s Reading package lists... 89s Building dependency tree... 89s Reading state information... 89s Solving dependencies... 89s The following NEW packages will be installed: 89s fontconfig-config fonts-urw-base35 libblas3 libcairo2 libdeflate0 89s libfontconfig1 libfontenc1 libgfortran5 libgomp1 libgraphite2-3 89s libharfbuzz0b libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 libjs-jquery 89s libjs-jquery-hotkeys libjs-jquery-isonscreen libjs-jquery-metadata 89s libjs-jquery-tablesorter libjs-jquery-throttle-debounce liblapack3 89s liblcms2-2 liblerc4 libopenjp2-7 libpixman-1-0 libpython3.14-minimal 89s libpython3.14-stdlib libraqm0 libsharpyuv0 libtiff6 libwebp7 libwebpdemux2 89s libwebpmux3 libxcb-render0 libxcb-shm0 libxrender1 ncbi-acc-download 89s python3-all python3-biopython python3-cairo python3-charset-normalizer 89s python3-coverage python3-freetype python3-iniconfig python3-numpy 89s python3-numpy-dev python3-pil python3-pluggy python3-pytest 89s python3-pytest-cov python3-pytest-mock python3-reportlab 89s python3-requests-mock python3-rlpycairo python3.14 python3.14-minimal 89s sgml-base w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core 89s 0 upgraded, 63 newly installed, 0 to remove and 0 not upgraded. 89s Need to get 37.0 MB of archives. 89s After this operation, 128 MB of additional disk space will be used. 89s Get:1 http://ftpmaster.internal/ubuntu resolute/main ppc64el python3-numpy-dev ppc64el 1:2.2.4+ds-1ubuntu1 [153 kB] 90s Get:2 http://ftpmaster.internal/ubuntu resolute/main ppc64el libblas3 ppc64el 3.12.1-7 [291 kB] 90s Get:3 http://ftpmaster.internal/ubuntu resolute/main ppc64el libgfortran5 ppc64el 15.2.0-7ubuntu1 [620 kB] 90s Get:4 http://ftpmaster.internal/ubuntu resolute/main ppc64el liblapack3 ppc64el 3.12.1-7 [2960 kB] 90s Get:5 http://ftpmaster.internal/ubuntu resolute/main ppc64el python3-numpy ppc64el 1:2.2.4+ds-1ubuntu1 [4887 kB] 91s Get:6 http://ftpmaster.internal/ubuntu resolute/main ppc64el libpython3.14-minimal ppc64el 3.14.0-4 [908 kB] 91s Get:7 http://ftpmaster.internal/ubuntu resolute/main ppc64el python3.14-minimal ppc64el 3.14.0-4 [2705 kB] 91s Get:8 http://ftpmaster.internal/ubuntu resolute/main ppc64el libfontenc1 ppc64el 1:1.1.8-1build1 [15.8 kB] 91s Get:9 http://ftpmaster.internal/ubuntu resolute/main ppc64el x11-common all 1:7.7+24ubuntu1 [22.4 kB] 91s Get:10 http://ftpmaster.internal/ubuntu resolute/main ppc64el xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 91s Get:11 http://ftpmaster.internal/ubuntu resolute/main ppc64el xfonts-utils ppc64el 1:7.7+7 [114 kB] 91s Get:12 http://ftpmaster.internal/ubuntu resolute/main ppc64el fonts-urw-base35 all 20200910-8 [11.0 MB] 92s Get:13 http://ftpmaster.internal/ubuntu resolute/main ppc64el fontconfig-config ppc64el 2.15.0-2.3ubuntu1 [38.1 kB] 92s Get:14 http://ftpmaster.internal/ubuntu resolute/main ppc64el libfontconfig1 ppc64el 2.15.0-2.3ubuntu1 [188 kB] 92s Get:15 http://ftpmaster.internal/ubuntu resolute/main ppc64el libpixman-1-0 ppc64el 0.46.4-1 [347 kB] 92s Get:16 http://ftpmaster.internal/ubuntu resolute/main ppc64el libxcb-render0 ppc64el 1.17.0-2build1 [17.2 kB] 92s Get:17 http://ftpmaster.internal/ubuntu resolute/main ppc64el libxcb-shm0 ppc64el 1.17.0-2build1 [6078 B] 92s Get:18 http://ftpmaster.internal/ubuntu resolute/main ppc64el libxrender1 ppc64el 1:0.9.12-1 [23.0 kB] 92s Get:19 http://ftpmaster.internal/ubuntu resolute/main ppc64el libcairo2 ppc64el 1.18.4-1build1 [759 kB] 92s Get:20 http://ftpmaster.internal/ubuntu resolute/main ppc64el libdeflate0 ppc64el 1.23-2 [63.3 kB] 92s Get:21 http://ftpmaster.internal/ubuntu resolute/main ppc64el libgomp1 ppc64el 15.2.0-7ubuntu1 [169 kB] 92s Get:22 http://ftpmaster.internal/ubuntu resolute/main ppc64el libgraphite2-3 ppc64el 1.3.14-2ubuntu1 [84.6 kB] 92s Get:23 http://ftpmaster.internal/ubuntu resolute/main ppc64el libharfbuzz0b ppc64el 12.1.0-1 [679 kB] 92s Get:24 http://ftpmaster.internal/ubuntu resolute/main ppc64el libimagequant0 ppc64el 2.18.0-1build1 [43.2 kB] 92s Get:25 http://ftpmaster.internal/ubuntu resolute/main ppc64el libjpeg-turbo8 ppc64el 2.1.5-4ubuntu2 [215 kB] 92s Get:26 http://ftpmaster.internal/ubuntu resolute/main ppc64el libjpeg8 ppc64el 8c-2ubuntu11 [2148 B] 92s Get:27 http://ftpmaster.internal/ubuntu resolute/main ppc64el libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 92s Get:28 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libjs-jquery-metadata all 12-4 [6582 B] 92s Get:29 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libjs-jquery-tablesorter all 1:2.31.3+dfsg1-4 [192 kB] 92s Get:30 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libjs-jquery-throttle-debounce all 1.1+dfsg.1-2 [12.5 kB] 92s Get:31 http://ftpmaster.internal/ubuntu resolute/main ppc64el liblcms2-2 ppc64el 2.17-1 [246 kB] 92s Get:32 http://ftpmaster.internal/ubuntu resolute/main ppc64el liblerc4 ppc64el 4.0.0+ds-5ubuntu1 [298 kB] 92s Get:33 http://ftpmaster.internal/ubuntu resolute/main ppc64el libpython3.14-stdlib ppc64el 3.14.0-4 [2446 kB] 92s Get:34 http://ftpmaster.internal/ubuntu resolute/main ppc64el libraqm0 ppc64el 0.10.3-1 [19.6 kB] 92s Get:35 http://ftpmaster.internal/ubuntu resolute/main ppc64el libsharpyuv0 ppc64el 1.5.0-0.1 [22.3 kB] 92s Get:36 http://ftpmaster.internal/ubuntu resolute/main ppc64el libjbig0 ppc64el 2.1-6.1ubuntu2 [35.9 kB] 92s Get:37 http://ftpmaster.internal/ubuntu resolute/main ppc64el libwebp7 ppc64el 1.5.0-0.1 [315 kB] 92s Get:38 http://ftpmaster.internal/ubuntu resolute/main ppc64el libtiff6 ppc64el 4.7.0-3ubuntu3 [307 kB] 92s Get:39 http://ftpmaster.internal/ubuntu resolute/main ppc64el libwebpdemux2 ppc64el 1.5.0-0.1 [14.6 kB] 92s Get:40 http://ftpmaster.internal/ubuntu resolute/main ppc64el libwebpmux3 ppc64el 1.5.0-0.1 [31.1 kB] 92s Get:41 http://ftpmaster.internal/ubuntu resolute/universe ppc64el ncbi-acc-download all 0.2.8-3 [13.3 kB] 92s Get:42 http://ftpmaster.internal/ubuntu resolute/main ppc64el python3.14 ppc64el 3.14.0-4 [805 kB] 92s Get:43 http://ftpmaster.internal/ubuntu resolute-proposed/main ppc64el python3-all ppc64el 3.13.7-2 [892 B] 92s Get:44 http://ftpmaster.internal/ubuntu resolute/universe ppc64el python3-charset-normalizer ppc64el 3.4.3-1 [174 kB] 92s Get:45 http://ftpmaster.internal/ubuntu resolute/main ppc64el libopenjp2-7 ppc64el 2.5.3-2.1 [251 kB] 92s Get:46 http://ftpmaster.internal/ubuntu resolute/main ppc64el python3-pil ppc64el 11.3.0-1ubuntu2 [654 kB] 92s Get:47 http://ftpmaster.internal/ubuntu resolute/main ppc64el python3-cairo ppc64el 1.27.0-2build1 [150 kB] 92s Get:48 http://ftpmaster.internal/ubuntu resolute/universe ppc64el python3-freetype all 2.5.1-2 [92.2 kB] 92s Get:49 http://ftpmaster.internal/ubuntu resolute/universe ppc64el python3-rlpycairo all 0.3.0-4 [9332 B] 92s Get:50 http://ftpmaster.internal/ubuntu resolute/universe ppc64el python3-reportlab all 4.4.4-2 [1147 kB] 92s Get:51 http://ftpmaster.internal/ubuntu resolute/main ppc64el sgml-base all 1.31+nmu1 [11.0 kB] 92s Get:52 http://ftpmaster.internal/ubuntu resolute/main ppc64el xml-core all 0.19 [20.3 kB] 92s Get:53 http://ftpmaster.internal/ubuntu resolute/universe ppc64el w3c-sgml-lib all 1.3-3 [280 kB] 92s Get:54 http://ftpmaster.internal/ubuntu resolute/universe ppc64el python3-biopython ppc64el 1.85+dfsg-4 [1764 kB] 92s Get:55 http://ftpmaster.internal/ubuntu resolute/universe ppc64el python3-coverage ppc64el 7.8.2+dfsg1-1 [158 kB] 92s Get:56 http://ftpmaster.internal/ubuntu resolute/universe ppc64el python3-iniconfig all 2.1.0-1 [6840 B] 92s Get:57 http://ftpmaster.internal/ubuntu resolute/universe ppc64el python3-pluggy all 1.6.0-1 [21.0 kB] 92s Get:58 http://ftpmaster.internal/ubuntu resolute/universe ppc64el python3-pytest all 8.3.5-2 [252 kB] 92s Get:59 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libjs-jquery-hotkeys all 0.2.0-1 [13.3 kB] 92s Get:60 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libjs-jquery-isonscreen all 1.2.0-1.1 [3244 B] 92s Get:61 http://ftpmaster.internal/ubuntu resolute/universe ppc64el python3-pytest-cov all 5.0.0-1 [21.3 kB] 92s Get:62 http://ftpmaster.internal/ubuntu resolute/universe ppc64el python3-pytest-mock all 3.15.1-1 [11.9 kB] 93s Get:63 http://ftpmaster.internal/ubuntu resolute/universe ppc64el python3-requests-mock all 1.12.1-3 [17.8 kB] 93s Fetched 37.0 MB in 3s (11.3 MB/s) 93s Selecting previously unselected package python3-numpy-dev:ppc64el. 93s (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 ... 81022 files and directories currently installed.) 93s Preparing to unpack .../00-python3-numpy-dev_1%3a2.2.4+ds-1ubuntu1_ppc64el.deb ... 93s Unpacking python3-numpy-dev:ppc64el (1:2.2.4+ds-1ubuntu1) ... 93s Selecting previously unselected package libblas3:ppc64el. 93s Preparing to unpack .../01-libblas3_3.12.1-7_ppc64el.deb ... 93s Unpacking libblas3:ppc64el (3.12.1-7) ... 93s Selecting previously unselected package libgfortran5:ppc64el. 93s Preparing to unpack .../02-libgfortran5_15.2.0-7ubuntu1_ppc64el.deb ... 93s Unpacking libgfortran5:ppc64el (15.2.0-7ubuntu1) ... 93s Selecting previously unselected package liblapack3:ppc64el. 93s Preparing to unpack .../03-liblapack3_3.12.1-7_ppc64el.deb ... 93s Unpacking liblapack3:ppc64el (3.12.1-7) ... 93s Selecting previously unselected package python3-numpy. 93s Preparing to unpack .../04-python3-numpy_1%3a2.2.4+ds-1ubuntu1_ppc64el.deb ... 93s Unpacking python3-numpy (1:2.2.4+ds-1ubuntu1) ... 93s Selecting previously unselected package libpython3.14-minimal:ppc64el. 93s Preparing to unpack .../05-libpython3.14-minimal_3.14.0-4_ppc64el.deb ... 93s Unpacking libpython3.14-minimal:ppc64el (3.14.0-4) ... 93s Selecting previously unselected package python3.14-minimal. 93s Preparing to unpack .../06-python3.14-minimal_3.14.0-4_ppc64el.deb ... 93s Unpacking python3.14-minimal (3.14.0-4) ... 93s Selecting previously unselected package libfontenc1:ppc64el. 93s Preparing to unpack .../07-libfontenc1_1%3a1.1.8-1build1_ppc64el.deb ... 93s Unpacking libfontenc1:ppc64el (1:1.1.8-1build1) ... 93s Selecting previously unselected package x11-common. 94s Preparing to unpack .../08-x11-common_1%3a7.7+24ubuntu1_all.deb ... 94s Unpacking x11-common (1:7.7+24ubuntu1) ... 94s Selecting previously unselected package xfonts-encodings. 94s Preparing to unpack .../09-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 94s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 94s Selecting previously unselected package xfonts-utils. 94s Preparing to unpack .../10-xfonts-utils_1%3a7.7+7_ppc64el.deb ... 94s Unpacking xfonts-utils (1:7.7+7) ... 94s Selecting previously unselected package fonts-urw-base35. 94s Preparing to unpack .../11-fonts-urw-base35_20200910-8_all.deb ... 94s Unpacking fonts-urw-base35 (20200910-8) ... 94s Selecting previously unselected package fontconfig-config. 94s Preparing to unpack .../12-fontconfig-config_2.15.0-2.3ubuntu1_ppc64el.deb ... 94s Unpacking fontconfig-config (2.15.0-2.3ubuntu1) ... 94s Selecting previously unselected package libfontconfig1:ppc64el. 94s Preparing to unpack .../13-libfontconfig1_2.15.0-2.3ubuntu1_ppc64el.deb ... 94s Unpacking libfontconfig1:ppc64el (2.15.0-2.3ubuntu1) ... 94s Selecting previously unselected package libpixman-1-0:ppc64el. 94s Preparing to unpack .../14-libpixman-1-0_0.46.4-1_ppc64el.deb ... 94s Unpacking libpixman-1-0:ppc64el (0.46.4-1) ... 94s Selecting previously unselected package libxcb-render0:ppc64el. 94s Preparing to unpack .../15-libxcb-render0_1.17.0-2build1_ppc64el.deb ... 94s Unpacking libxcb-render0:ppc64el (1.17.0-2build1) ... 94s Selecting previously unselected package libxcb-shm0:ppc64el. 94s Preparing to unpack .../16-libxcb-shm0_1.17.0-2build1_ppc64el.deb ... 94s Unpacking libxcb-shm0:ppc64el (1.17.0-2build1) ... 94s Selecting previously unselected package libxrender1:ppc64el. 94s Preparing to unpack .../17-libxrender1_1%3a0.9.12-1_ppc64el.deb ... 94s Unpacking libxrender1:ppc64el (1:0.9.12-1) ... 94s Selecting previously unselected package libcairo2:ppc64el. 94s Preparing to unpack .../18-libcairo2_1.18.4-1build1_ppc64el.deb ... 94s Unpacking libcairo2:ppc64el (1.18.4-1build1) ... 94s Selecting previously unselected package libdeflate0:ppc64el. 94s Preparing to unpack .../19-libdeflate0_1.23-2_ppc64el.deb ... 94s Unpacking libdeflate0:ppc64el (1.23-2) ... 94s Selecting previously unselected package libgomp1:ppc64el. 94s Preparing to unpack .../20-libgomp1_15.2.0-7ubuntu1_ppc64el.deb ... 94s Unpacking libgomp1:ppc64el (15.2.0-7ubuntu1) ... 94s Selecting previously unselected package libgraphite2-3:ppc64el. 94s Preparing to unpack .../21-libgraphite2-3_1.3.14-2ubuntu1_ppc64el.deb ... 94s Unpacking libgraphite2-3:ppc64el (1.3.14-2ubuntu1) ... 94s Selecting previously unselected package libharfbuzz0b:ppc64el. 94s Preparing to unpack .../22-libharfbuzz0b_12.1.0-1_ppc64el.deb ... 94s Unpacking libharfbuzz0b:ppc64el (12.1.0-1) ... 94s Selecting previously unselected package libimagequant0:ppc64el. 94s Preparing to unpack .../23-libimagequant0_2.18.0-1build1_ppc64el.deb ... 94s Unpacking libimagequant0:ppc64el (2.18.0-1build1) ... 94s Selecting previously unselected package libjpeg-turbo8:ppc64el. 95s Preparing to unpack .../24-libjpeg-turbo8_2.1.5-4ubuntu2_ppc64el.deb ... 95s Unpacking libjpeg-turbo8:ppc64el (2.1.5-4ubuntu2) ... 95s Selecting previously unselected package libjpeg8:ppc64el. 95s Preparing to unpack .../25-libjpeg8_8c-2ubuntu11_ppc64el.deb ... 95s Unpacking libjpeg8:ppc64el (8c-2ubuntu11) ... 95s Selecting previously unselected package libjs-jquery. 95s Preparing to unpack .../26-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 95s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 95s Selecting previously unselected package libjs-jquery-metadata. 95s Preparing to unpack .../27-libjs-jquery-metadata_12-4_all.deb ... 95s Unpacking libjs-jquery-metadata (12-4) ... 95s Selecting previously unselected package libjs-jquery-tablesorter. 95s Preparing to unpack .../28-libjs-jquery-tablesorter_1%3a2.31.3+dfsg1-4_all.deb ... 95s Unpacking libjs-jquery-tablesorter (1:2.31.3+dfsg1-4) ... 95s Selecting previously unselected package libjs-jquery-throttle-debounce. 95s Preparing to unpack .../29-libjs-jquery-throttle-debounce_1.1+dfsg.1-2_all.deb ... 95s Unpacking libjs-jquery-throttle-debounce (1.1+dfsg.1-2) ... 95s Selecting previously unselected package liblcms2-2:ppc64el. 95s Preparing to unpack .../30-liblcms2-2_2.17-1_ppc64el.deb ... 95s Unpacking liblcms2-2:ppc64el (2.17-1) ... 95s Selecting previously unselected package liblerc4:ppc64el. 95s Preparing to unpack .../31-liblerc4_4.0.0+ds-5ubuntu1_ppc64el.deb ... 95s Unpacking liblerc4:ppc64el (4.0.0+ds-5ubuntu1) ... 95s Selecting previously unselected package libpython3.14-stdlib:ppc64el. 95s Preparing to unpack .../32-libpython3.14-stdlib_3.14.0-4_ppc64el.deb ... 95s Unpacking libpython3.14-stdlib:ppc64el (3.14.0-4) ... 95s Selecting previously unselected package libraqm0:ppc64el. 95s Preparing to unpack .../33-libraqm0_0.10.3-1_ppc64el.deb ... 95s Unpacking libraqm0:ppc64el (0.10.3-1) ... 95s Selecting previously unselected package libsharpyuv0:ppc64el. 95s Preparing to unpack .../34-libsharpyuv0_1.5.0-0.1_ppc64el.deb ... 95s Unpacking libsharpyuv0:ppc64el (1.5.0-0.1) ... 95s Selecting previously unselected package libjbig0:ppc64el. 95s Preparing to unpack .../35-libjbig0_2.1-6.1ubuntu2_ppc64el.deb ... 95s Unpacking libjbig0:ppc64el (2.1-6.1ubuntu2) ... 95s Selecting previously unselected package libwebp7:ppc64el. 95s Preparing to unpack .../36-libwebp7_1.5.0-0.1_ppc64el.deb ... 95s Unpacking libwebp7:ppc64el (1.5.0-0.1) ... 95s Selecting previously unselected package libtiff6:ppc64el. 95s Preparing to unpack .../37-libtiff6_4.7.0-3ubuntu3_ppc64el.deb ... 95s Unpacking libtiff6:ppc64el (4.7.0-3ubuntu3) ... 95s Selecting previously unselected package libwebpdemux2:ppc64el. 95s Preparing to unpack .../38-libwebpdemux2_1.5.0-0.1_ppc64el.deb ... 95s Unpacking libwebpdemux2:ppc64el (1.5.0-0.1) ... 95s Selecting previously unselected package libwebpmux3:ppc64el. 95s Preparing to unpack .../39-libwebpmux3_1.5.0-0.1_ppc64el.deb ... 95s Unpacking libwebpmux3:ppc64el (1.5.0-0.1) ... 95s Selecting previously unselected package ncbi-acc-download. 95s Preparing to unpack .../40-ncbi-acc-download_0.2.8-3_all.deb ... 95s Unpacking ncbi-acc-download (0.2.8-3) ... 95s Selecting previously unselected package python3.14. 95s Preparing to unpack .../41-python3.14_3.14.0-4_ppc64el.deb ... 95s Unpacking python3.14 (3.14.0-4) ... 95s Selecting previously unselected package python3-all. 95s Preparing to unpack .../42-python3-all_3.13.7-2_ppc64el.deb ... 95s Unpacking python3-all (3.13.7-2) ... 95s Selecting previously unselected package python3-charset-normalizer. 95s Preparing to unpack .../43-python3-charset-normalizer_3.4.3-1_ppc64el.deb ... 95s Unpacking python3-charset-normalizer (3.4.3-1) ... 95s Selecting previously unselected package libopenjp2-7:ppc64el. 95s Preparing to unpack .../44-libopenjp2-7_2.5.3-2.1_ppc64el.deb ... 95s Unpacking libopenjp2-7:ppc64el (2.5.3-2.1) ... 95s Selecting previously unselected package python3-pil:ppc64el. 95s Preparing to unpack .../45-python3-pil_11.3.0-1ubuntu2_ppc64el.deb ... 95s Unpacking python3-pil:ppc64el (11.3.0-1ubuntu2) ... 95s Selecting previously unselected package python3-cairo. 95s Preparing to unpack .../46-python3-cairo_1.27.0-2build1_ppc64el.deb ... 95s Unpacking python3-cairo (1.27.0-2build1) ... 95s Selecting previously unselected package python3-freetype. 95s Preparing to unpack .../47-python3-freetype_2.5.1-2_all.deb ... 95s Unpacking python3-freetype (2.5.1-2) ... 95s Selecting previously unselected package python3-rlpycairo. 95s Preparing to unpack .../48-python3-rlpycairo_0.3.0-4_all.deb ... 95s Unpacking python3-rlpycairo (0.3.0-4) ... 95s Selecting previously unselected package python3-reportlab. 95s Preparing to unpack .../49-python3-reportlab_4.4.4-2_all.deb ... 95s Unpacking python3-reportlab (4.4.4-2) ... 95s Selecting previously unselected package sgml-base. 95s Preparing to unpack .../50-sgml-base_1.31+nmu1_all.deb ... 95s Unpacking sgml-base (1.31+nmu1) ... 95s Selecting previously unselected package xml-core. 95s Preparing to unpack .../51-xml-core_0.19_all.deb ... 95s Unpacking xml-core (0.19) ... 95s Selecting previously unselected package w3c-sgml-lib. 95s Preparing to unpack .../52-w3c-sgml-lib_1.3-3_all.deb ... 95s Unpacking w3c-sgml-lib (1.3-3) ... 95s Selecting previously unselected package python3-biopython. 95s Preparing to unpack .../53-python3-biopython_1.85+dfsg-4_ppc64el.deb ... 95s Unpacking python3-biopython (1.85+dfsg-4) ... 96s Selecting previously unselected package python3-coverage. 96s Preparing to unpack .../54-python3-coverage_7.8.2+dfsg1-1_ppc64el.deb ... 96s Unpacking python3-coverage (7.8.2+dfsg1-1) ... 96s Selecting previously unselected package python3-iniconfig. 96s Preparing to unpack .../55-python3-iniconfig_2.1.0-1_all.deb ... 96s Unpacking python3-iniconfig (2.1.0-1) ... 96s Selecting previously unselected package python3-pluggy. 96s Preparing to unpack .../56-python3-pluggy_1.6.0-1_all.deb ... 96s Unpacking python3-pluggy (1.6.0-1) ... 96s Selecting previously unselected package python3-pytest. 96s Preparing to unpack .../57-python3-pytest_8.3.5-2_all.deb ... 96s Unpacking python3-pytest (8.3.5-2) ... 96s Selecting previously unselected package libjs-jquery-hotkeys. 96s Preparing to unpack .../58-libjs-jquery-hotkeys_0.2.0-1_all.deb ... 96s Unpacking libjs-jquery-hotkeys (0.2.0-1) ... 96s Selecting previously unselected package libjs-jquery-isonscreen. 96s Preparing to unpack .../59-libjs-jquery-isonscreen_1.2.0-1.1_all.deb ... 96s Unpacking libjs-jquery-isonscreen (1.2.0-1.1) ... 96s Selecting previously unselected package python3-pytest-cov. 96s Preparing to unpack .../60-python3-pytest-cov_5.0.0-1_all.deb ... 96s Unpacking python3-pytest-cov (5.0.0-1) ... 96s Selecting previously unselected package python3-pytest-mock. 96s Preparing to unpack .../61-python3-pytest-mock_3.15.1-1_all.deb ... 96s Unpacking python3-pytest-mock (3.15.1-1) ... 96s Selecting previously unselected package python3-requests-mock. 96s Preparing to unpack .../62-python3-requests-mock_1.12.1-3_all.deb ... 96s Unpacking python3-requests-mock (1.12.1-3) ... 96s Setting up libgraphite2-3:ppc64el (1.3.14-2ubuntu1) ... 96s Setting up liblcms2-2:ppc64el (2.17-1) ... 96s Setting up python3-iniconfig (2.1.0-1) ... 96s Setting up libpixman-1-0:ppc64el (0.46.4-1) ... 96s Setting up libsharpyuv0:ppc64el (1.5.0-0.1) ... 96s Setting up liblerc4:ppc64el (4.0.0+ds-5ubuntu1) ... 96s Setting up libxrender1:ppc64el (1:0.9.12-1) ... 96s Setting up libxcb-render0:ppc64el (1.17.0-2build1) ... 96s Setting up python3-charset-normalizer (3.4.3-1) ... 96s Setting up libpython3.14-minimal:ppc64el (3.14.0-4) ... 96s Setting up x11-common (1:7.7+24ubuntu1) ... 97s Setting up libdeflate0:ppc64el (1.23-2) ... 97s Setting up python3-coverage (7.8.2+dfsg1-1) ... 97s Setting up libxcb-shm0:ppc64el (1.17.0-2build1) ... 97s Setting up libjs-jquery-throttle-debounce (1.1+dfsg.1-2) ... 97s Setting up libgomp1:ppc64el (15.2.0-7ubuntu1) ... 97s Setting up python3-freetype (2.5.1-2) ... 98s Setting up libjbig0:ppc64el (2.1-6.1ubuntu2) ... 98s Setting up libfontenc1:ppc64el (1:1.1.8-1build1) ... 98s Setting up libblas3:ppc64el (3.12.1-7) ... 98s 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 98s Setting up python3-requests-mock (1.12.1-3) ... 98s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 98s Setting up libimagequant0:ppc64el (2.18.0-1build1) ... 98s Setting up python3-numpy-dev:ppc64el (1:2.2.4+ds-1ubuntu1) ... 98s Setting up libjpeg-turbo8:ppc64el (2.1.5-4ubuntu2) ... 98s Setting up libgfortran5:ppc64el (15.2.0-7ubuntu1) ... 98s Setting up python3-pluggy (1.6.0-1) ... 98s Setting up libwebp7:ppc64el (1.5.0-0.1) ... 98s Setting up libopenjp2-7:ppc64el (2.5.3-2.1) ... 98s Setting up ncbi-acc-download (0.2.8-3) ... 98s Setting up libharfbuzz0b:ppc64el (12.1.0-1) ... 98s Setting up sgml-base (1.31+nmu1) ... 98s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 98s Setting up libjs-jquery-hotkeys (0.2.0-1) ... 98s Setting up libwebpmux3:ppc64el (1.5.0-0.1) ... 98s Setting up python3.14-minimal (3.14.0-4) ... 99s Setting up libjpeg8:ppc64el (8c-2ubuntu11) ... 99s Setting up liblapack3:ppc64el (3.12.1-7) ... 99s 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 99s Setting up libpython3.14-stdlib:ppc64el (3.14.0-4) ... 99s Setting up python3-pytest (8.3.5-2) ... 100s Setting up libwebpdemux2:ppc64el (1.5.0-0.1) ... 100s Setting up xfonts-utils (1:7.7+7) ... 100s Setting up libjs-jquery-metadata (12-4) ... 100s Setting up libraqm0:ppc64el (0.10.3-1) ... 100s Setting up libjs-jquery-isonscreen (1.2.0-1.1) ... 100s Setting up python3-numpy (1:2.2.4+ds-1ubuntu1) ... 104s Setting up libjs-jquery-tablesorter (1:2.31.3+dfsg1-4) ... 104s Setting up python3-pytest-mock (3.15.1-1) ... 104s Setting up libtiff6:ppc64el (4.7.0-3ubuntu3) ... 104s Setting up xml-core (0.19) ... 105s Setting up python3.14 (3.14.0-4) ... 106s Setting up python3-all (3.13.7-2) ... 106s Setting up python3-pytest-cov (5.0.0-1) ... 106s Setting up fonts-urw-base35 (20200910-8) ... 106s Setting up python3-pil:ppc64el (11.3.0-1ubuntu2) ... 107s Setting up fontconfig-config (2.15.0-2.3ubuntu1) ... 107s Setting up libfontconfig1:ppc64el (2.15.0-2.3ubuntu1) ... 107s Setting up libcairo2:ppc64el (1.18.4-1build1) ... 107s Setting up python3-cairo (1.27.0-2build1) ... 107s Setting up python3-rlpycairo (0.3.0-4) ... 108s Setting up python3-reportlab (4.4.4-2) ... 109s Processing triggers for libc-bin (2.42-2ubuntu2) ... 109s Processing triggers for systemd (257.9-0ubuntu2) ... 109s Processing triggers for man-db (2.13.1-1) ... 110s Processing triggers for sgml-base (1.31+nmu1) ... 110s Setting up w3c-sgml-lib (1.3-3) ... 143s Setting up python3-biopython (1.85+dfsg-4) ... 146s autopkgtest [11:35:03]: test run-unit-test: [----------------------- 146s /tmp/autopkgtest.EhOKlQ/build.2Rz/src/tests /tmp/autopkgtest.EhOKlQ/build.2Rz/src 146s Testing with python3.14 in /tmp/autopkgtest.EhOKlQ/build.2Rz/src/tests: 147s ============================= test session starts ============================== 147s platform linux -- Python 3.14.0, pytest-8.3.5, pluggy-1.6.0 -- /usr/bin/python3.14 147s cachedir: .pytest_cache 147s rootdir: /tmp/autopkgtest.EhOKlQ/build.2Rz/src 147s plugins: mock-3.15.1, cov-5.0.0, requests_mock-1.12.1, typeguard-4.4.2 147s collecting ... collected 32 items 147s 147s test_core.py::test_config PASSED [ 3%] 147s test_core.py::test_config_no_biopython PASSED [ 6%] 147s test_core.py::test_config_have_biopython FAILED [ 9%] 147s test_core.py::test_download_to_file PASSED [ 12%] 147s test_core.py::test_download_to_file_append PASSED [ 15%] 147s test_core.py::test_download_to_file_retry PASSED [ 18%] 147s test_core.py::test_build_params PASSED [ 21%] 147s test_core.py::test_generate_filename PASSED [ 25%] 147s test_core.py::test_validate_and_write_error_pattern_raises PASSED [ 28%] 147s test_core.py::test_validate_and_write_emit PASSED [ 31%] 147s test_core.py::test_validate_and_write_extended_validation FAILED [ 34%] 147s test_core.py::test_get_stream_exception PASSED [ 37%] 147s test_core.py::test_get_stream_bad_status PASSED [ 40%] 147s test_core.py::test_get_stream_too_many_requests PASSED [ 43%] 147s test_core.py::test_generate_url PASSED [ 46%] 147s test_core.py::test_generate_url_with_api_key PASSED [ 50%] 147s test_correct.py::test_download_and_validate_partial_wgs FAILED [ 53%] 147s test_download.py::test_write_stream PASSED [ 56%] 147s test_validate.py::test_run_extended_validation_no_biopython PASSED [ 59%] 147s test_validate.py::test_run_extended_validation_raises FAILED [ 62%] 147s test_validate.py::test_run_extended_validation_loads FAILED [ 65%] 147s test_wgs.py::test_init PASSED [ 68%] 147s test_wgs.py::test_get_ids PASSED [ 71%] 147s test_wgs.py::test_from_string PASSED [ 75%] 147s test_wgs.py::test_download_wgs_parts_no_biopython PASSED [ 78%] 147s test_wgs.py::test_download_wgs_parts_wgs FAILED [ 81%] 147s test_wgs.py::test_download_wgs_parts_wgs_retry FAILED [ 84%] 147s test_wgs.py::test_download_wgs_parts_wgs_scafld FAILED [ 87%] 147s test_wgs.py::test_download_wgs_parts_supercontig FAILED [ 90%] 147s test_wgs.py::test_download_wgs_parts_supercontig_retry FAILED [ 93%] 147s test_wgs.py::test_download_wgs_no_parts FAILED [ 96%] 148s test_wgs.py::test_download_wgs_parts_tsa XFAIL [100%] 148s 148s =================================== FAILURES =================================== 148s __________________________ test_config_have_biopython __________________________ 148s 148s def test_config_have_biopython(): 148s """Test we detect Biopython.""" 148s > assert core.HAVE_BIOPYTHON 148s E assert False 148s E + where False = core.HAVE_BIOPYTHON 148s 148s test_core.py:46: AssertionError 148s _________________ test_validate_and_write_extended_validation __________________ 148s 148s req = 148s 148s def test_validate_and_write_extended_validation(req): 148s """Test extended validation before writing.""" 148s handle = StringIO() 148s req.get('http://fake/', text=u'>foo\nMAGIC') 148s r = requests.get('http://fake/') 148s > config = core.Config(extended_validation='loads', molecule='protein') 148s 148s test_core.py:226: 148s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 148s /usr/lib/python3/dist-packages/ncbi_acc_download/core.py:64: in __init__ 148s self.extended_validation = extended_validation 148s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 148s 148s self = , value = 'loads' 148s 148s @extended_validation.setter 148s def extended_validation(self, value): 148s if value != 'none' and not HAVE_BIOPYTHON: 148s > raise ValueError("Asked for extended validation, but Biopython not available") 148s E ValueError: Asked for extended validation, but Biopython not available 148s 148s /usr/lib/python3/dist-packages/ncbi_acc_download/core.py:96: ValueError 148s ____________________ test_download_and_validate_partial_wgs ____________________ 148s 148s req = 148s 148s def test_download_and_validate_partial_wgs(req): 148s handle = StringIO(open(full_path('partialcontig.gbk'), 'r').read()) 148s > assert validate.run_extended_validation(handle, 'genbank', 'loads') 148s E AssertionError: assert False 148s E + where False = (<_io.StringIO object at 0x66828382b2e0>, 'genbank', 'loads') 148s E + where = validate.run_extended_validation 148s 148s test_correct.py:15: AssertionError 148s _____________________ test_run_extended_validation_raises ______________________ 148s 148s monkeypatch = <_pytest.monkeypatch.MonkeyPatch object at 0x6682831ac950> 148s mocker = 148s 148s def test_run_extended_validation_raises(monkeypatch, mocker): 148s """Test the "seqence loads" validator catches exceptions in SeqIO.parse().""" 148s seqio_mock = mocker.MagicMock() 148s seqio_mock.parse = mocker.MagicMock(side_effect=ValueError) 148s > monkeypatch.setattr(validate, 'SeqIO', seqio_mock) 148s E AttributeError: has no attribute 'SeqIO' 148s 148s test_validate.py:19: AttributeError 148s ______________________ test_run_extended_validation_loads ______________________ 148s 148s def test_run_extended_validation_loads(): 148s """Test the "sequence loads" validator.""" 148s handle = StringIO(u'>foo\nATGC\n>bar\nATGTGA\n') 148s > assert validate.run_extended_validation(handle, 'fasta', 'loads') 148s E AssertionError: assert False 148s E + where False = (<_io.StringIO object at 0x66828382be20>, 'fasta', 'loads') 148s E + where = validate.run_extended_validation 148s 148s test_validate.py:29: AssertionError 148s _________________________ test_download_wgs_parts_wgs __________________________ 148s 148s req = 148s 148s def test_download_wgs_parts_wgs(req): 148s cfg = Config(format="genbank") 148s wgs_contig = open(full_path('wgs.gbk'), 'rt') 148s req.get( 148s ENTREZ_URL, 148s body=open(full_path('wgs_full.gbk'), 'rb'), 148s headers={"Content-Type": "text/plain; charset=UTF-8"}, 148s ) 148s 148s outhandle = wgs.download_wgs_parts(wgs_contig, cfg) 148s wgs_full = open(full_path('wgs_full.gbk'), 'rt') 148s > assert outhandle.getvalue() == wgs_full.read() 148s E AttributeError: '_io.TextIOWrapper' object has no attribute 'getvalue' 148s 148s test_wgs.py:95: AttributeError 148s ______________________ test_download_wgs_parts_wgs_retry _______________________ 148s 148s req = 148s 148s def test_download_wgs_parts_wgs_retry(req): 148s cfg = Config(format="genbank") 148s wgs_contig = open(full_path('wgs.gbk'), 'rt') 148s req.get(ENTREZ_URL, response_list=[ 148s {"text": u'Whoa, slow down', "status_code": 429, "headers": {"Retry-After": "0"}}, 148s { 148s "body": open(full_path('wgs_full.gbk'), 'rb'), 148s "headers": {"Content-Type": "text/plain; charset=UTF-8"}, 148s }, 148s ]) 148s 148s outhandle = wgs.download_wgs_parts(wgs_contig, cfg) 148s wgs_full = open(full_path('wgs_full.gbk'), 'rt') 148s > assert outhandle.getvalue() == wgs_full.read() 148s E AttributeError: '_io.TextIOWrapper' object has no attribute 'getvalue' 148s 148s test_wgs.py:113: AttributeError 148s ______________________ test_download_wgs_parts_wgs_scafld ______________________ 148s 148s req = 148s 148s def test_download_wgs_parts_wgs_scafld(req): 148s cfg = Config(format="genbank") 148s wgs_contig = open(full_path('wgs_scafld.gbk'), 'rt') 148s with open(full_path('wgs_full.gbk'), 'rt') as handle: 148s full_file = handle.read() 148s req.get(ENTREZ_URL, text=full_file) 148s 148s outhandle = wgs.download_wgs_parts(wgs_contig, cfg) 148s > assert outhandle.getvalue() == full_file 148s E AttributeError: '_io.TextIOWrapper' object has no attribute 'getvalue' 148s 148s test_wgs.py:126: AttributeError 148s _____________________ test_download_wgs_parts_supercontig ______________________ 148s 148s req = 148s 148s def test_download_wgs_parts_supercontig(req): 148s cfg = Config(format="genbank") 148s supercontig = open(full_path('supercontig.gbk'), 'rt') 148s req.get( 148s ENTREZ_URL, 148s body=open(full_path('supercontig_full.gbk'), 'rb'), 148s headers={"Content-Type": "text/plain; charset=UTF-8"}, 148s ) 148s 148s outhandle = wgs.download_wgs_parts(supercontig, cfg) 148s supercontig_full = open(full_path('supercontig_full.gbk'), 'rt') 148s > assert outhandle.getvalue() == supercontig_full.read() 148s E AttributeError: '_io.TextIOWrapper' object has no attribute 'getvalue' 148s 148s test_wgs.py:141: AttributeError 148s __________________ test_download_wgs_parts_supercontig_retry ___________________ 148s 148s req = 148s 148s def test_download_wgs_parts_supercontig_retry(req): 148s cfg = Config(format="genbank") 148s supercontig = open(full_path('supercontig.gbk'), 'rt') 148s req.get(ENTREZ_URL, response_list=[ 148s {"text": u'Whoa, slow down', "status_code": 429, "headers": {"Retry-After": "0"}}, 148s { 148s "body": open(full_path('supercontig_full.gbk'), 'rb'), 148s "headers": {"Content-Type": "text/plain; charset=UTF-8"}, 148s }, 148s ]) 148s 148s outhandle = wgs.download_wgs_parts(supercontig, cfg) 148s supercontig_full = open(full_path('supercontig_full.gbk'), 'rt') 148s > assert outhandle.getvalue() == supercontig_full.read() 148s E AttributeError: '_io.TextIOWrapper' object has no attribute 'getvalue' 148s 148s test_wgs.py:159: AttributeError 148s __________________________ test_download_wgs_no_parts __________________________ 148s 148s req = 148s 148s def test_download_wgs_no_parts(req): 148s cfg = Config(format="genbank") 148s supercontig = open(full_path('supercontig_full.gbk'), 'rt') 148s req.get(ENTREZ_URL, status_code=404) 148s 148s outhandle = wgs.download_wgs_parts(supercontig, cfg) 148s supercontig_full = open(full_path('supercontig_full.gbk'), 'rt') 148s > assert outhandle.getvalue() == supercontig_full.read() 148s E AttributeError: '_io.TextIOWrapper' object has no attribute 'getvalue' 148s 148s test_wgs.py:171: AttributeError 148s =========================== short test summary info ============================ 148s FAILED test_core.py::test_config_have_biopython - assert False 148s FAILED test_core.py::test_validate_and_write_extended_validation - ValueError... 148s FAILED test_correct.py::test_download_and_validate_partial_wgs - AssertionErr... 148s FAILED test_validate.py::test_run_extended_validation_raises - AttributeError... 148s FAILED test_validate.py::test_run_extended_validation_loads - AssertionError:... 148s FAILED test_wgs.py::test_download_wgs_parts_wgs - AttributeError: '_io.TextIO... 148s FAILED test_wgs.py::test_download_wgs_parts_wgs_retry - AttributeError: '_io.... 148s FAILED test_wgs.py::test_download_wgs_parts_wgs_scafld - AttributeError: '_io... 148s FAILED test_wgs.py::test_download_wgs_parts_supercontig - AttributeError: '_i... 148s FAILED test_wgs.py::test_download_wgs_parts_supercontig_retry - AttributeErro... 148s FAILED test_wgs.py::test_download_wgs_no_parts - AttributeError: '_io.TextIOW... 148s =================== 11 failed, 20 passed, 1 xfailed in 0.26s =================== 148s autopkgtest [11:35:05]: test run-unit-test: -----------------------] 148s autopkgtest [11:35:05]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 148s run-unit-test FAIL non-zero exit status 1 149s autopkgtest [11:35:06]: @@@@@@@@@@@@@@@@@@@@ summary 149s run-unit-test FAIL non-zero exit status 1