0s autopkgtest [12:04:44]: starting date and time: 2025-11-17 12:04:44+0000 0s autopkgtest [12:04:44]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [12:04:44]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.59gzw9ew/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 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-arm64-10.secgroup --name adt-resolute-arm64-ncbi-acc-download-20251117-120444-juju-7f2275-prod-proposed-migration-environment-2-a8b9e3e2-f414-4f89-a7a5-e7bd89901dfc --image adt/ubuntu-resolute-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 4s Creating nova instance adt-resolute-arm64-ncbi-acc-download-20251117-120444-juju-7f2275-prod-proposed-migration-environment-2-a8b9e3e2-f414-4f89-a7a5-e7bd89901dfc from image adt/ubuntu-resolute-arm64-server-20251117.img (UUID 1cd33fbb-18df-4c5a-b8f0-2dcb25269485)... 61s autopkgtest [12:05:45]: testbed dpkg architecture: arm64 62s autopkgtest [12:05:46]: testbed apt version: 3.1.11 62s autopkgtest [12:05:46]: @@@@@@@@@@@@@@@@@@@@ test bed setup 62s autopkgtest [12:05:46]: testbed release detected to be: None 63s autopkgtest [12:05:47]: updating testbed package index (apt update) 64s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [87.8 kB] 64s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 64s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 64s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 64s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [868 kB] 64s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [9848 B] 64s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [81.1 kB] 64s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [22.9 kB] 64s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 Packages [149 kB] 64s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 c-n-f Metadata [3084 B] 64s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/restricted arm64 Packages [107 kB] 64s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/restricted arm64 c-n-f Metadata [324 B] 64s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 Packages [577 kB] 64s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 c-n-f Metadata [17.8 kB] 64s Get:15 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse arm64 Packages [12.5 kB] 64s Get:16 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse arm64 c-n-f Metadata [576 B] 65s Fetched 1938 kB in 1s (1798 kB/s) 67s Reading package lists... 68s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 68s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 68s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 68s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 69s Reading package lists... 69s Reading package lists... 70s Building dependency tree... 70s Reading state information... 70s Calculating upgrade... 71s The following packages will be upgraded: 71s libpython3-stdlib python3 python3-minimal python3-requests usbutils 72s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 72s Need to get 197 kB of archives. 72s After this operation, 1024 B of additional disk space will be used. 72s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 python3-minimal arm64 3.13.7-2 [27.8 kB] 72s Get:2 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 python3 arm64 3.13.7-2 [23.9 kB] 72s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 libpython3-stdlib arm64 3.13.7-2 [10.6 kB] 72s Get:4 http://ftpmaster.internal/ubuntu resolute/main arm64 usbutils arm64 1:019-1 [81.7 kB] 72s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 python3-requests all 2.32.5+dfsg-1ubuntu1 [53.1 kB] 72s dpkg-preconfigure: unable to re-open stdin: No such file or directory 73s Fetched 197 kB in 0s (462 kB/s) 73s (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 ... 88137 files and directories currently installed.) 73s Preparing to unpack .../python3-minimal_3.13.7-2_arm64.deb ... 73s Unpacking python3-minimal (3.13.7-2) over (3.13.7-1) ... 73s Setting up python3-minimal (3.13.7-2) ... 73s (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 ... 88137 files and directories currently installed.) 73s Preparing to unpack .../python3_3.13.7-2_arm64.deb ... 73s running python pre-rtupdate hooks for python3.13... 73s Unpacking python3 (3.13.7-2) over (3.13.7-1) ... 74s Preparing to unpack .../libpython3-stdlib_3.13.7-2_arm64.deb ... 74s Unpacking libpython3-stdlib:arm64 (3.13.7-2) over (3.13.7-1) ... 74s Preparing to unpack .../usbutils_1%3a019-1_arm64.deb ... 74s Unpacking usbutils (1:019-1) over (1:018-2) ... 74s Preparing to unpack .../python3-requests_2.32.5+dfsg-1ubuntu1_all.deb ... 74s Unpacking python3-requests (2.32.5+dfsg-1ubuntu1) over (2.32.3+dfsg-5ubuntu2) ... 74s Setting up usbutils (1:019-1) ... 74s Setting up libpython3-stdlib:arm64 (3.13.7-2) ... 74s Setting up python3 (3.13.7-2) ... 74s running python rtupdate hooks for python3.13... 74s running python post-rtupdate hooks for python3.13... 74s Setting up python3-requests (2.32.5+dfsg-1ubuntu1) ... 75s Processing triggers for man-db (2.13.1-1) ... 76s autopkgtest [12:06:00]: upgrading testbed (apt dist-upgrade and autopurge) 76s Reading package lists... 77s Building dependency tree... 77s Reading state information... 77s Calculating upgrade... 78s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 78s Reading package lists... 78s Building dependency tree... 78s Reading state information... 78s Solving dependencies... 79s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 82s autopkgtest [12:06:06]: testbed running kernel: Linux 6.17.0-5-generic #5-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 22 09:50:31 UTC 2025 82s autopkgtest [12:06:06]: @@@@@@@@@@@@@@@@@@@@ apt-source ncbi-acc-download 84s Get:1 http://ftpmaster.internal/ubuntu resolute/universe ncbi-acc-download 0.2.8-3 (dsc) [2434 B] 84s Get:2 http://ftpmaster.internal/ubuntu resolute/universe ncbi-acc-download 0.2.8-3 (tar) [20.9 kB] 84s Get:3 http://ftpmaster.internal/ubuntu resolute/universe ncbi-acc-download 0.2.8-3 (diff) [4420 B] 84s gpgv: Signature made Thu Aug 1 23:03:26 2024 UTC 84s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 84s gpgv: issuer "tille@debian.org" 84s gpgv: Can't check signature: No public key 84s dpkg-source: warning: cannot verify inline signature for ./ncbi-acc-download_0.2.8-3.dsc: no acceptable signature found 84s autopkgtest [12:06:08]: testing package ncbi-acc-download version 0.2.8-3 85s autopkgtest [12:06:09]: build not needed 85s autopkgtest [12:06:09]: test run-unit-test: preparing testbed 86s Reading package lists... 86s Building dependency tree... 86s Reading state information... 86s Solving dependencies... 87s The following NEW packages will be installed: 87s fontconfig-config fonts-urw-base35 libblas3 libcairo2 libdeflate0 87s libfontconfig1 libfontenc1 libgfortran5 libgomp1 libgraphite2-3 87s libharfbuzz0b libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 libjs-jquery 87s libjs-jquery-hotkeys libjs-jquery-isonscreen libjs-jquery-metadata 87s libjs-jquery-tablesorter libjs-jquery-throttle-debounce liblapack3 87s liblcms2-2 liblerc4 libopenjp2-7 libpixman-1-0 libpython3.14-minimal 87s libpython3.14-stdlib libraqm0 libsharpyuv0 libtiff6 libwebp7 libwebpdemux2 87s libwebpmux3 libxcb-render0 libxcb-shm0 libxrender1 ncbi-acc-download 87s python3-all python3-biopython python3-cairo python3-charset-normalizer 87s python3-coverage python3-freetype python3-iniconfig python3-numpy 87s python3-numpy-dev python3-pil python3-pluggy python3-pytest 87s python3-pytest-cov python3-pytest-mock python3-reportlab 87s python3-requests-mock python3-rlpycairo python3.14 python3.14-minimal 87s sgml-base w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core 87s 0 upgraded, 63 newly installed, 0 to remove and 0 not upgraded. 87s Need to get 33.5 MB of archives. 87s After this operation, 113 MB of additional disk space will be used. 87s Get:1 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-numpy-dev arm64 1:2.2.4+ds-1ubuntu1 [146 kB] 88s Get:2 http://ftpmaster.internal/ubuntu resolute/main arm64 libblas3 arm64 3.12.1-7 [181 kB] 88s Get:3 http://ftpmaster.internal/ubuntu resolute/main arm64 libgfortran5 arm64 15.2.0-7ubuntu1 [450 kB] 88s Get:4 http://ftpmaster.internal/ubuntu resolute/main arm64 liblapack3 arm64 3.12.1-7 [2300 kB] 88s Get:5 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-numpy arm64 1:2.2.4+ds-1ubuntu1 [3986 kB] 88s Get:6 http://ftpmaster.internal/ubuntu resolute/main arm64 libpython3.14-minimal arm64 3.14.0-4 [903 kB] 88s Get:7 http://ftpmaster.internal/ubuntu resolute/main arm64 python3.14-minimal arm64 3.14.0-4 [2543 kB] 88s Get:8 http://ftpmaster.internal/ubuntu resolute/main arm64 libfontenc1 arm64 1:1.1.8-1build1 [13.9 kB] 88s Get:9 http://ftpmaster.internal/ubuntu resolute/main arm64 x11-common all 1:7.7+24ubuntu1 [22.4 kB] 88s Get:10 http://ftpmaster.internal/ubuntu resolute/main arm64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 88s Get:11 http://ftpmaster.internal/ubuntu resolute/main arm64 xfonts-utils arm64 1:7.7+7 [95.6 kB] 88s Get:12 http://ftpmaster.internal/ubuntu resolute/main arm64 fonts-urw-base35 all 20200910-8 [11.0 MB] 89s Get:13 http://ftpmaster.internal/ubuntu resolute/main arm64 fontconfig-config arm64 2.15.0-2.3ubuntu1 [38.1 kB] 89s Get:14 http://ftpmaster.internal/ubuntu resolute/main arm64 libfontconfig1 arm64 2.15.0-2.3ubuntu1 [144 kB] 89s Get:15 http://ftpmaster.internal/ubuntu resolute/main arm64 libpixman-1-0 arm64 0.46.4-1 [204 kB] 89s Get:16 http://ftpmaster.internal/ubuntu resolute/main arm64 libxcb-render0 arm64 1.17.0-2build1 [18.1 kB] 89s Get:17 http://ftpmaster.internal/ubuntu resolute/main arm64 libxcb-shm0 arm64 1.17.0-2build1 [6234 B] 89s Get:18 http://ftpmaster.internal/ubuntu resolute/main arm64 libxrender1 arm64 1:0.9.12-1 [19.5 kB] 89s Get:19 http://ftpmaster.internal/ubuntu resolute/main arm64 libcairo2 arm64 1.18.4-1build1 [592 kB] 89s Get:20 http://ftpmaster.internal/ubuntu resolute/main arm64 libdeflate0 arm64 1.23-2 [46.4 kB] 89s Get:21 http://ftpmaster.internal/ubuntu resolute/main arm64 libgomp1 arm64 15.2.0-7ubuntu1 [147 kB] 89s Get:22 http://ftpmaster.internal/ubuntu resolute/main arm64 libgraphite2-3 arm64 1.3.14-2ubuntu1 [70.6 kB] 89s Get:23 http://ftpmaster.internal/ubuntu resolute/main arm64 libharfbuzz0b arm64 12.1.0-1 [523 kB] 89s Get:24 http://ftpmaster.internal/ubuntu resolute/main arm64 libimagequant0 arm64 2.18.0-1build1 [37.1 kB] 89s Get:25 http://ftpmaster.internal/ubuntu resolute/main arm64 libjpeg-turbo8 arm64 2.1.5-4ubuntu2 [165 kB] 89s Get:26 http://ftpmaster.internal/ubuntu resolute/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 89s Get:27 http://ftpmaster.internal/ubuntu resolute/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 89s Get:28 http://ftpmaster.internal/ubuntu resolute/universe arm64 libjs-jquery-metadata all 12-4 [6582 B] 89s Get:29 http://ftpmaster.internal/ubuntu resolute/universe arm64 libjs-jquery-tablesorter all 1:2.31.3+dfsg1-4 [192 kB] 89s Get:30 http://ftpmaster.internal/ubuntu resolute/universe arm64 libjs-jquery-throttle-debounce all 1.1+dfsg.1-2 [12.5 kB] 89s Get:31 http://ftpmaster.internal/ubuntu resolute/main arm64 liblcms2-2 arm64 2.17-1 [170 kB] 89s Get:32 http://ftpmaster.internal/ubuntu resolute/main arm64 liblerc4 arm64 4.0.0+ds-5ubuntu1 [167 kB] 89s Get:33 http://ftpmaster.internal/ubuntu resolute/main arm64 libpython3.14-stdlib arm64 3.14.0-4 [2349 kB] 89s Get:34 http://ftpmaster.internal/ubuntu resolute/main arm64 libraqm0 arm64 0.10.3-1 [15.0 kB] 89s Get:35 http://ftpmaster.internal/ubuntu resolute/main arm64 libsharpyuv0 arm64 1.5.0-0.1 [16.9 kB] 89s Get:36 http://ftpmaster.internal/ubuntu resolute/main arm64 libjbig0 arm64 2.1-6.1ubuntu2 [29.3 kB] 89s Get:37 http://ftpmaster.internal/ubuntu resolute/main arm64 libwebp7 arm64 1.5.0-0.1 [194 kB] 89s Get:38 http://ftpmaster.internal/ubuntu resolute/main arm64 libtiff6 arm64 4.7.0-3ubuntu3 [196 kB] 89s Get:39 http://ftpmaster.internal/ubuntu resolute/main arm64 libwebpdemux2 arm64 1.5.0-0.1 [12.5 kB] 89s Get:40 http://ftpmaster.internal/ubuntu resolute/main arm64 libwebpmux3 arm64 1.5.0-0.1 [25.4 kB] 89s Get:41 http://ftpmaster.internal/ubuntu resolute/universe arm64 ncbi-acc-download all 0.2.8-3 [13.3 kB] 89s Get:42 http://ftpmaster.internal/ubuntu resolute/main arm64 python3.14 arm64 3.14.0-4 [805 kB] 89s Get:43 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 python3-all arm64 3.13.7-2 [890 B] 89s Get:44 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-charset-normalizer arm64 3.4.3-1 [165 kB] 89s Get:45 http://ftpmaster.internal/ubuntu resolute/main arm64 libopenjp2-7 arm64 2.5.3-2.1 [179 kB] 89s Get:46 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-pil arm64 11.3.0-1ubuntu2 [492 kB] 89s Get:47 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-cairo arm64 1.27.0-2build1 [141 kB] 89s Get:48 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-freetype all 2.5.1-2 [92.2 kB] 89s Get:49 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-rlpycairo all 0.3.0-4 [9332 B] 89s Get:50 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-reportlab all 4.4.4-2 [1147 kB] 89s Get:51 http://ftpmaster.internal/ubuntu resolute/main arm64 sgml-base all 1.31+nmu1 [11.0 kB] 89s Get:52 http://ftpmaster.internal/ubuntu resolute/main arm64 xml-core all 0.19 [20.3 kB] 89s Get:53 http://ftpmaster.internal/ubuntu resolute/universe arm64 w3c-sgml-lib all 1.3-3 [280 kB] 89s Get:54 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-biopython arm64 1.85+dfsg-4 [1710 kB] 89s Get:55 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-coverage arm64 7.8.2+dfsg1-1 [157 kB] 89s Get:56 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-iniconfig all 2.1.0-1 [6840 B] 89s Get:57 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-pluggy all 1.6.0-1 [21.0 kB] 89s Get:58 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-pytest all 8.3.5-2 [252 kB] 89s Get:59 http://ftpmaster.internal/ubuntu resolute/universe arm64 libjs-jquery-hotkeys all 0.2.0-1 [13.3 kB] 89s Get:60 http://ftpmaster.internal/ubuntu resolute/universe arm64 libjs-jquery-isonscreen all 1.2.0-1.1 [3244 B] 89s Get:61 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-pytest-cov all 5.0.0-1 [21.3 kB] 89s Get:62 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-pytest-mock all 3.15.1-1 [11.9 kB] 89s Get:63 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-requests-mock all 1.12.1-3 [17.8 kB] 90s Fetched 33.5 MB in 2s (15.9 MB/s) 90s Selecting previously unselected package python3-numpy-dev:arm64. 90s (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 ... 88137 files and directories currently installed.) 90s Preparing to unpack .../00-python3-numpy-dev_1%3a2.2.4+ds-1ubuntu1_arm64.deb ... 90s Unpacking python3-numpy-dev:arm64 (1:2.2.4+ds-1ubuntu1) ... 90s Selecting previously unselected package libblas3:arm64. 90s Preparing to unpack .../01-libblas3_3.12.1-7_arm64.deb ... 90s Unpacking libblas3:arm64 (3.12.1-7) ... 90s Selecting previously unselected package libgfortran5:arm64. 90s Preparing to unpack .../02-libgfortran5_15.2.0-7ubuntu1_arm64.deb ... 90s Unpacking libgfortran5:arm64 (15.2.0-7ubuntu1) ... 90s Selecting previously unselected package liblapack3:arm64. 90s Preparing to unpack .../03-liblapack3_3.12.1-7_arm64.deb ... 90s Unpacking liblapack3:arm64 (3.12.1-7) ... 90s Selecting previously unselected package python3-numpy. 90s Preparing to unpack .../04-python3-numpy_1%3a2.2.4+ds-1ubuntu1_arm64.deb ... 90s Unpacking python3-numpy (1:2.2.4+ds-1ubuntu1) ... 91s Selecting previously unselected package libpython3.14-minimal:arm64. 91s Preparing to unpack .../05-libpython3.14-minimal_3.14.0-4_arm64.deb ... 91s Unpacking libpython3.14-minimal:arm64 (3.14.0-4) ... 91s Selecting previously unselected package python3.14-minimal. 91s Preparing to unpack .../06-python3.14-minimal_3.14.0-4_arm64.deb ... 91s Unpacking python3.14-minimal (3.14.0-4) ... 91s Selecting previously unselected package libfontenc1:arm64. 91s Preparing to unpack .../07-libfontenc1_1%3a1.1.8-1build1_arm64.deb ... 91s Unpacking libfontenc1:arm64 (1:1.1.8-1build1) ... 91s Selecting previously unselected package x11-common. 91s Preparing to unpack .../08-x11-common_1%3a7.7+24ubuntu1_all.deb ... 91s Unpacking x11-common (1:7.7+24ubuntu1) ... 91s Selecting previously unselected package xfonts-encodings. 91s Preparing to unpack .../09-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 91s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 91s Selecting previously unselected package xfonts-utils. 91s Preparing to unpack .../10-xfonts-utils_1%3a7.7+7_arm64.deb ... 91s Unpacking xfonts-utils (1:7.7+7) ... 91s Selecting previously unselected package fonts-urw-base35. 91s Preparing to unpack .../11-fonts-urw-base35_20200910-8_all.deb ... 91s Unpacking fonts-urw-base35 (20200910-8) ... 91s Selecting previously unselected package fontconfig-config. 91s Preparing to unpack .../12-fontconfig-config_2.15.0-2.3ubuntu1_arm64.deb ... 92s Unpacking fontconfig-config (2.15.0-2.3ubuntu1) ... 92s Selecting previously unselected package libfontconfig1:arm64. 92s Preparing to unpack .../13-libfontconfig1_2.15.0-2.3ubuntu1_arm64.deb ... 92s Unpacking libfontconfig1:arm64 (2.15.0-2.3ubuntu1) ... 92s Selecting previously unselected package libpixman-1-0:arm64. 92s Preparing to unpack .../14-libpixman-1-0_0.46.4-1_arm64.deb ... 92s Unpacking libpixman-1-0:arm64 (0.46.4-1) ... 92s Selecting previously unselected package libxcb-render0:arm64. 92s Preparing to unpack .../15-libxcb-render0_1.17.0-2build1_arm64.deb ... 92s Unpacking libxcb-render0:arm64 (1.17.0-2build1) ... 92s Selecting previously unselected package libxcb-shm0:arm64. 92s Preparing to unpack .../16-libxcb-shm0_1.17.0-2build1_arm64.deb ... 92s Unpacking libxcb-shm0:arm64 (1.17.0-2build1) ... 92s Selecting previously unselected package libxrender1:arm64. 92s Preparing to unpack .../17-libxrender1_1%3a0.9.12-1_arm64.deb ... 92s Unpacking libxrender1:arm64 (1:0.9.12-1) ... 92s Selecting previously unselected package libcairo2:arm64. 92s Preparing to unpack .../18-libcairo2_1.18.4-1build1_arm64.deb ... 92s Unpacking libcairo2:arm64 (1.18.4-1build1) ... 92s Selecting previously unselected package libdeflate0:arm64. 92s Preparing to unpack .../19-libdeflate0_1.23-2_arm64.deb ... 92s Unpacking libdeflate0:arm64 (1.23-2) ... 92s Selecting previously unselected package libgomp1:arm64. 92s Preparing to unpack .../20-libgomp1_15.2.0-7ubuntu1_arm64.deb ... 92s Unpacking libgomp1:arm64 (15.2.0-7ubuntu1) ... 92s Selecting previously unselected package libgraphite2-3:arm64. 92s Preparing to unpack .../21-libgraphite2-3_1.3.14-2ubuntu1_arm64.deb ... 92s Unpacking libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 92s Selecting previously unselected package libharfbuzz0b:arm64. 92s Preparing to unpack .../22-libharfbuzz0b_12.1.0-1_arm64.deb ... 92s Unpacking libharfbuzz0b:arm64 (12.1.0-1) ... 93s Selecting previously unselected package libimagequant0:arm64. 93s Preparing to unpack .../23-libimagequant0_2.18.0-1build1_arm64.deb ... 93s 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unselected package libsharpyuv0:arm64. 93s Preparing to unpack .../34-libsharpyuv0_1.5.0-0.1_arm64.deb ... 93s Unpacking libsharpyuv0:arm64 (1.5.0-0.1) ... 93s Selecting previously unselected package libjbig0:arm64. 93s Preparing to unpack .../35-libjbig0_2.1-6.1ubuntu2_arm64.deb ... 93s Unpacking libjbig0:arm64 (2.1-6.1ubuntu2) ... 93s Selecting previously unselected package libwebp7:arm64. 93s Preparing to unpack .../36-libwebp7_1.5.0-0.1_arm64.deb ... 93s Unpacking libwebp7:arm64 (1.5.0-0.1) ... 93s Selecting previously unselected package libtiff6:arm64. 93s Preparing to unpack .../37-libtiff6_4.7.0-3ubuntu3_arm64.deb ... 93s Unpacking libtiff6:arm64 (4.7.0-3ubuntu3) ... 93s Selecting previously unselected package libwebpdemux2:arm64. 93s Preparing to unpack .../38-libwebpdemux2_1.5.0-0.1_arm64.deb ... 93s Unpacking libwebpdemux2:arm64 (1.5.0-0.1) ... 94s Selecting previously unselected package libwebpmux3:arm64. 94s Preparing to unpack .../39-libwebpmux3_1.5.0-0.1_arm64.deb ... 94s 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python3-requests-mock. 95s Preparing to unpack .../62-python3-requests-mock_1.12.1-3_all.deb ... 95s Unpacking python3-requests-mock (1.12.1-3) ... 95s Setting up libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 95s Setting up liblcms2-2:arm64 (2.17-1) ... 95s Setting up python3-iniconfig (2.1.0-1) ... 96s Setting up libpixman-1-0:arm64 (0.46.4-1) ... 96s Setting up libsharpyuv0:arm64 (1.5.0-0.1) ... 96s Setting up liblerc4:arm64 (4.0.0+ds-5ubuntu1) ... 96s Setting up libxrender1:arm64 (1:0.9.12-1) ... 96s Setting up libxcb-render0:arm64 (1.17.0-2build1) ... 96s Setting up python3-charset-normalizer (3.4.3-1) ... 96s Setting up libpython3.14-minimal:arm64 (3.14.0-4) ... 96s Setting up x11-common (1:7.7+24ubuntu1) ... 97s Setting up libdeflate0:arm64 (1.23-2) ... 97s Setting up python3-coverage (7.8.2+dfsg1-1) ... 97s Setting up libxcb-shm0:arm64 (1.17.0-2build1) ... 97s Setting up libjs-jquery-throttle-debounce (1.1+dfsg.1-2) ... 97s Setting up libgomp1:arm64 (15.2.0-7ubuntu1) ... 97s Setting up python3-freetype (2.5.1-2) ... 98s Setting up libjbig0:arm64 (2.1-6.1ubuntu2) ... 98s Setting up libfontenc1:arm64 (1:1.1.8-1build1) ... 98s Setting up libblas3:arm64 (3.12.1-7) ... 98s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-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:arm64 (2.18.0-1build1) ... 98s Setting up python3-numpy-dev:arm64 (1:2.2.4+ds-1ubuntu1) ... 98s Setting up libjpeg-turbo8:arm64 (2.1.5-4ubuntu2) ... 98s Setting up libgfortran5:arm64 (15.2.0-7ubuntu1) ... 98s Setting up python3-pluggy (1.6.0-1) ... 98s Setting up libwebp7:arm64 (1.5.0-0.1) ... 98s Setting up libopenjp2-7:arm64 (2.5.3-2.1) ... 98s Setting up ncbi-acc-download (0.2.8-3) ... 99s Setting up libharfbuzz0b:arm64 (12.1.0-1) ... 99s Setting up sgml-base (1.31+nmu1) ... 99s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 99s Setting up libjs-jquery-hotkeys (0.2.0-1) ... 99s Setting up libwebpmux3:arm64 (1.5.0-0.1) ... 99s Setting up python3.14-minimal (3.14.0-4) ... 100s Setting up libjpeg8:arm64 (8c-2ubuntu11) ... 100s Setting up liblapack3:arm64 (3.12.1-7) ... 100s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode 100s Setting up libpython3.14-stdlib:arm64 (3.14.0-4) ... 100s Setting up python3-pytest (8.3.5-2) ... 101s Setting up libwebpdemux2:arm64 (1.5.0-0.1) ... 101s Setting up xfonts-utils (1:7.7+7) ... 101s Setting up libjs-jquery-metadata (12-4) ... 101s Setting up libraqm0:arm64 (0.10.3-1) ... 101s Setting up libjs-jquery-isonscreen (1.2.0-1.1) ... 101s Setting up python3-numpy (1:2.2.4+ds-1ubuntu1) ... 107s Setting up libjs-jquery-tablesorter (1:2.31.3+dfsg1-4) ... 107s Setting up python3-pytest-mock (3.15.1-1) ... 107s Setting up libtiff6:arm64 (4.7.0-3ubuntu3) ... 107s Setting up xml-core (0.19) ... 107s Setting up python3.14 (3.14.0-4) ... 109s Setting up python3-all (3.13.7-2) ... 109s Setting up python3-pytest-cov (5.0.0-1) ... 109s Setting up fonts-urw-base35 (20200910-8) ... 110s Setting up python3-pil:arm64 (11.3.0-1ubuntu2) ... 111s Setting up fontconfig-config (2.15.0-2.3ubuntu1) ... 111s Setting up libfontconfig1:arm64 (2.15.0-2.3ubuntu1) ... 111s Setting up libcairo2:arm64 (1.18.4-1build1) ... 111s Setting up python3-cairo (1.27.0-2build1) ... 111s Setting up python3-rlpycairo (0.3.0-4) ... 112s Setting up python3-reportlab (4.4.4-2) ... 114s Processing triggers for libc-bin (2.42-2ubuntu2) ... 114s Processing triggers for systemd (257.9-0ubuntu2) ... 114s Processing triggers for man-db (2.13.1-1) ... 115s Processing triggers for sgml-base (1.31+nmu1) ... 115s Setting up w3c-sgml-lib (1.3-3) ... 151s Setting up python3-biopython (1.85+dfsg-4) ... 154s autopkgtest [12:07:18]: test run-unit-test: [----------------------- 155s /tmp/autopkgtest.7lsnVF/build.wK0/src/tests /tmp/autopkgtest.7lsnVF/build.wK0/src 155s Testing with python3.14 in /tmp/autopkgtest.7lsnVF/build.wK0/src/tests: 156s ============================= test session starts ============================== 156s platform linux -- Python 3.14.0, pytest-8.3.5, pluggy-1.6.0 -- /usr/bin/python3.14 156s cachedir: .pytest_cache 156s rootdir: /tmp/autopkgtest.7lsnVF/build.wK0/src 156s plugins: cov-5.0.0, typeguard-4.4.2, requests_mock-1.12.1, mock-3.15.1 156s collecting ... collected 32 items 156s 156s test_core.py::test_config PASSED [ 3%] 156s test_core.py::test_config_no_biopython PASSED [ 6%] 156s test_core.py::test_config_have_biopython FAILED [ 9%] 156s test_core.py::test_download_to_file PASSED [ 12%] 156s test_core.py::test_download_to_file_append PASSED [ 15%] 156s test_core.py::test_download_to_file_retry PASSED [ 18%] 156s test_core.py::test_build_params PASSED [ 21%] 156s test_core.py::test_generate_filename PASSED [ 25%] 156s test_core.py::test_validate_and_write_error_pattern_raises PASSED [ 28%] 156s test_core.py::test_validate_and_write_emit PASSED [ 31%] 156s test_core.py::test_validate_and_write_extended_validation FAILED [ 34%] 156s test_core.py::test_get_stream_exception PASSED [ 37%] 156s test_core.py::test_get_stream_bad_status PASSED [ 40%] 156s test_core.py::test_get_stream_too_many_requests PASSED [ 43%] 156s test_core.py::test_generate_url PASSED [ 46%] 156s test_core.py::test_generate_url_with_api_key PASSED [ 50%] 156s test_correct.py::test_download_and_validate_partial_wgs FAILED [ 53%] 156s test_download.py::test_write_stream PASSED [ 56%] 156s test_validate.py::test_run_extended_validation_no_biopython PASSED [ 59%] 156s test_validate.py::test_run_extended_validation_raises FAILED [ 62%] 156s test_validate.py::test_run_extended_validation_loads FAILED [ 65%] 156s test_wgs.py::test_init PASSED [ 68%] 156s test_wgs.py::test_get_ids PASSED [ 71%] 156s test_wgs.py::test_from_string PASSED [ 75%] 156s test_wgs.py::test_download_wgs_parts_no_biopython PASSED [ 78%] 156s test_wgs.py::test_download_wgs_parts_wgs FAILED [ 81%] 156s test_wgs.py::test_download_wgs_parts_wgs_retry FAILED [ 84%] 156s test_wgs.py::test_download_wgs_parts_wgs_scafld FAILED [ 87%] 156s test_wgs.py::test_download_wgs_parts_supercontig FAILED [ 90%] 156s test_wgs.py::test_download_wgs_parts_supercontig_retry FAILED [ 93%] 156s test_wgs.py::test_download_wgs_no_parts FAILED [ 96%] 156s test_wgs.py::test_download_wgs_parts_tsa XFAIL [100%] 156s 156s =================================== FAILURES =================================== 156s __________________________ test_config_have_biopython __________________________ 156s 156s def test_config_have_biopython(): 156s """Test we detect Biopython.""" 156s > assert core.HAVE_BIOPYTHON 156s E assert False 156s E + where False = core.HAVE_BIOPYTHON 156s 156s test_core.py:46: AssertionError 156s _________________ test_validate_and_write_extended_validation __________________ 156s 156s req = 156s 156s def test_validate_and_write_extended_validation(req): 156s """Test extended validation before writing.""" 156s handle = StringIO() 156s req.get('http://fake/', text=u'>foo\nMAGIC') 156s r = requests.get('http://fake/') 156s > config = core.Config(extended_validation='loads', molecule='protein') 156s 156s test_core.py:226: 156s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 156s /usr/lib/python3/dist-packages/ncbi_acc_download/core.py:64: in __init__ 156s self.extended_validation = extended_validation 156s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 156s 156s self = , value = 'loads' 156s 156s @extended_validation.setter 156s def extended_validation(self, value): 156s if value != 'none' and not HAVE_BIOPYTHON: 156s > raise ValueError("Asked for extended validation, but Biopython not available") 156s E ValueError: Asked for extended validation, but Biopython not available 156s 156s /usr/lib/python3/dist-packages/ncbi_acc_download/core.py:96: ValueError 156s ____________________ test_download_and_validate_partial_wgs ____________________ 156s 156s req = 156s 156s def test_download_and_validate_partial_wgs(req): 156s handle = StringIO(open(full_path('partialcontig.gbk'), 'r').read()) 156s > assert validate.run_extended_validation(handle, 'genbank', 'loads') 156s E AssertionError: assert False 156s E + where False = (<_io.StringIO object at 0xe0c6fd1c2f80>, 'genbank', 'loads') 156s E + where = validate.run_extended_validation 156s 156s test_correct.py:15: AssertionError 156s _____________________ test_run_extended_validation_raises ______________________ 156s 156s monkeypatch = <_pytest.monkeypatch.MonkeyPatch object at 0xe0c6fd0444d0> 156s mocker = 156s 156s def test_run_extended_validation_raises(monkeypatch, mocker): 156s """Test the "seqence loads" validator catches exceptions in SeqIO.parse().""" 156s seqio_mock = mocker.MagicMock() 156s seqio_mock.parse = mocker.MagicMock(side_effect=ValueError) 156s > monkeypatch.setattr(validate, 'SeqIO', seqio_mock) 156s E AttributeError: has no attribute 'SeqIO' 156s 156s test_validate.py:19: AttributeError 156s ______________________ test_run_extended_validation_loads ______________________ 156s 156s def test_run_extended_validation_loads(): 156s """Test the "sequence loads" validator.""" 156s handle = StringIO(u'>foo\nATGC\n>bar\nATGTGA\n') 156s > assert validate.run_extended_validation(handle, 'fasta', 'loads') 156s E AssertionError: assert False 156s E + where False = (<_io.StringIO object at 0xe0c6fd1c2320>, 'fasta', 'loads') 156s E + where = validate.run_extended_validation 156s 156s test_validate.py:29: AssertionError 156s _________________________ test_download_wgs_parts_wgs __________________________ 156s 156s req = 156s 156s def test_download_wgs_parts_wgs(req): 156s cfg = Config(format="genbank") 156s wgs_contig = open(full_path('wgs.gbk'), 'rt') 156s req.get( 156s ENTREZ_URL, 156s body=open(full_path('wgs_full.gbk'), 'rb'), 156s headers={"Content-Type": "text/plain; charset=UTF-8"}, 156s ) 156s 156s outhandle = wgs.download_wgs_parts(wgs_contig, cfg) 156s wgs_full = open(full_path('wgs_full.gbk'), 'rt') 156s > assert outhandle.getvalue() == wgs_full.read() 156s E AttributeError: '_io.TextIOWrapper' object has no attribute 'getvalue' 156s 156s test_wgs.py:95: AttributeError 156s ______________________ test_download_wgs_parts_wgs_retry _______________________ 156s 156s req = 156s 156s def test_download_wgs_parts_wgs_retry(req): 156s cfg = Config(format="genbank") 156s wgs_contig = open(full_path('wgs.gbk'), 'rt') 156s req.get(ENTREZ_URL, response_list=[ 156s {"text": u'Whoa, slow down', "status_code": 429, "headers": {"Retry-After": "0"}}, 156s { 156s "body": open(full_path('wgs_full.gbk'), 'rb'), 156s "headers": {"Content-Type": "text/plain; charset=UTF-8"}, 156s }, 156s ]) 156s 156s outhandle = wgs.download_wgs_parts(wgs_contig, cfg) 156s wgs_full = open(full_path('wgs_full.gbk'), 'rt') 156s > assert outhandle.getvalue() == wgs_full.read() 156s E AttributeError: '_io.TextIOWrapper' object has no attribute 'getvalue' 156s 156s test_wgs.py:113: AttributeError 156s ______________________ test_download_wgs_parts_wgs_scafld ______________________ 156s 156s req = 156s 156s def test_download_wgs_parts_wgs_scafld(req): 156s cfg = Config(format="genbank") 156s wgs_contig = open(full_path('wgs_scafld.gbk'), 'rt') 156s with open(full_path('wgs_full.gbk'), 'rt') as handle: 156s full_file = handle.read() 156s req.get(ENTREZ_URL, text=full_file) 156s 156s outhandle = wgs.download_wgs_parts(wgs_contig, cfg) 156s > assert outhandle.getvalue() == full_file 156s E AttributeError: '_io.TextIOWrapper' object has no attribute 'getvalue' 156s 156s test_wgs.py:126: AttributeError 156s _____________________ test_download_wgs_parts_supercontig ______________________ 156s 156s req = 156s 156s def test_download_wgs_parts_supercontig(req): 156s cfg = Config(format="genbank") 156s supercontig = open(full_path('supercontig.gbk'), 'rt') 156s req.get( 156s ENTREZ_URL, 156s body=open(full_path('supercontig_full.gbk'), 'rb'), 156s headers={"Content-Type": "text/plain; charset=UTF-8"}, 156s ) 156s 156s outhandle = wgs.download_wgs_parts(supercontig, cfg) 156s supercontig_full = open(full_path('supercontig_full.gbk'), 'rt') 156s > assert outhandle.getvalue() == supercontig_full.read() 156s E AttributeError: '_io.TextIOWrapper' object has no attribute 'getvalue' 156s 156s test_wgs.py:141: AttributeError 156s __________________ test_download_wgs_parts_supercontig_retry ___________________ 156s 156s req = 156s 156s def test_download_wgs_parts_supercontig_retry(req): 156s cfg = Config(format="genbank") 156s supercontig = open(full_path('supercontig.gbk'), 'rt') 156s req.get(ENTREZ_URL, response_list=[ 156s {"text": u'Whoa, slow down', "status_code": 429, "headers": {"Retry-After": "0"}}, 156s { 156s "body": open(full_path('supercontig_full.gbk'), 'rb'), 156s "headers": {"Content-Type": "text/plain; charset=UTF-8"}, 156s }, 156s ]) 156s 156s outhandle = wgs.download_wgs_parts(supercontig, cfg) 156s supercontig_full = open(full_path('supercontig_full.gbk'), 'rt') 156s > assert outhandle.getvalue() == supercontig_full.read() 156s E AttributeError: '_io.TextIOWrapper' object has no attribute 'getvalue' 156s 156s test_wgs.py:159: AttributeError 156s __________________________ test_download_wgs_no_parts __________________________ 156s 156s req = 156s 156s def test_download_wgs_no_parts(req): 156s cfg = Config(format="genbank") 156s supercontig = open(full_path('supercontig_full.gbk'), 'rt') 156s req.get(ENTREZ_URL, status_code=404) 156s 156s outhandle = wgs.download_wgs_parts(supercontig, cfg) 156s supercontig_full = open(full_path('supercontig_full.gbk'), 'rt') 156s > assert outhandle.getvalue() == supercontig_full.read() 156s E AttributeError: '_io.TextIOWrapper' object has no attribute 'getvalue' 156s 156s test_wgs.py:171: AttributeError 156s =========================== short test summary info ============================ 156s FAILED test_core.py::test_config_have_biopython - assert False 156s FAILED test_core.py::test_validate_and_write_extended_validation - ValueError... 156s FAILED test_correct.py::test_download_and_validate_partial_wgs - AssertionErr... 156s FAILED test_validate.py::test_run_extended_validation_raises - AttributeError... 156s FAILED test_validate.py::test_run_extended_validation_loads - AssertionError:... 156s FAILED test_wgs.py::test_download_wgs_parts_wgs - AttributeError: '_io.TextIO... 156s FAILED test_wgs.py::test_download_wgs_parts_wgs_retry - AttributeError: '_io.... 156s FAILED test_wgs.py::test_download_wgs_parts_wgs_scafld - AttributeError: '_io... 156s FAILED test_wgs.py::test_download_wgs_parts_supercontig - AttributeError: '_i... 156s FAILED test_wgs.py::test_download_wgs_parts_supercontig_retry - AttributeErro... 156s FAILED test_wgs.py::test_download_wgs_no_parts - AttributeError: '_io.TextIOW... 156s =================== 11 failed, 20 passed, 1 xfailed in 0.32s =================== 156s autopkgtest [12:07:20]: test run-unit-test: -----------------------] 157s autopkgtest [12:07:21]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 157s run-unit-test FAIL non-zero exit status 1 157s autopkgtest [12:07:21]: @@@@@@@@@@@@@@@@@@@@ summary 157s run-unit-test FAIL non-zero exit status 1