0s autopkgtest [12:38:54]: starting date and time: 2025-11-01 12:38:54+0000 0s autopkgtest [12:38:54]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [12:38:54]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.datiodey/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:scipy --apt-upgrade svim --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=scipy/1.16.3-1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-arm64-12.secgroup --name adt-resolute-arm64-svim-20251101-123854-juju-7f2275-prod-proposed-migration-environment-15-fae8e5d7-0427-4db3-8194-82a1e7c8108e --image adt/ubuntu-resolute-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 3s Creating nova instance adt-resolute-arm64-svim-20251101-123854-juju-7f2275-prod-proposed-migration-environment-15-fae8e5d7-0427-4db3-8194-82a1e7c8108e from image adt/ubuntu-resolute-arm64-server-20251101.img (UUID 895f8d05-65a0-4cf8-81a2-1a04d79b538c)... 55s autopkgtest [12:39:49]: testbed dpkg architecture: arm64 56s autopkgtest [12:39:50]: testbed apt version: 3.1.11 56s autopkgtest [12:39:50]: @@@@@@@@@@@@@@@@@@@@ test bed setup 56s autopkgtest [12:39:50]: testbed release detected to be: None 57s autopkgtest [12:39:51]: updating testbed package index (apt update) 57s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [87.8 kB] 58s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 58s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 58s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 58s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [2242 kB] 58s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [49.4 kB] 58s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [138 kB] 58s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [9848 B] 58s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 Packages [206 kB] 58s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 c-n-f Metadata [4948 B] 58s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/restricted arm64 Packages [107 kB] 58s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/restricted arm64 c-n-f Metadata [324 B] 58s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 Packages [1619 kB] 59s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 c-n-f Metadata [48.3 kB] 59s Get:15 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse arm64 Packages [34.8 kB] 59s Get:16 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse arm64 c-n-f Metadata [1700 B] 60s Fetched 4550 kB in 2s (2899 kB/s) 61s Reading package lists... 61s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 61s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 62s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 62s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 62s Reading package lists... 62s Reading package lists... 63s Building dependency tree... 63s Reading state information... 63s Calculating upgrade... 63s The following packages will be upgraded: 63s gcc-15-base libatomic1 libgcc-s1 libstdc++6 publicsuffix 64s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 64s Need to get 1027 kB of archives. 64s After this operation, 14.3 kB of additional disk space will be used. 64s Get:1 http://ftpmaster.internal/ubuntu resolute/main arm64 libatomic1 arm64 15.2.0-7ubuntu1 [11.2 kB] 64s Get:2 http://ftpmaster.internal/ubuntu resolute/main arm64 libstdc++6 arm64 15.2.0-7ubuntu1 [760 kB] 64s Get:3 http://ftpmaster.internal/ubuntu resolute/main arm64 gcc-15-base arm64 15.2.0-7ubuntu1 [58.4 kB] 64s Get:4 http://ftpmaster.internal/ubuntu resolute/main arm64 libgcc-s1 arm64 15.2.0-7ubuntu1 [61.1 kB] 64s Get:5 http://ftpmaster.internal/ubuntu resolute/main arm64 publicsuffix all 20251016.1743-0.1 [136 kB] 65s dpkg-preconfigure: unable to re-open stdin: No such file or directory 65s Fetched 1027 kB in 1s (1480 kB/s) 65s (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 ... 83460 files and directories currently installed.) 65s Preparing to unpack .../libatomic1_15.2.0-7ubuntu1_arm64.deb ... 65s Unpacking libatomic1:arm64 (15.2.0-7ubuntu1) over (15.2.0-5ubuntu1) ... 65s Preparing to unpack .../libstdc++6_15.2.0-7ubuntu1_arm64.deb ... 65s Unpacking libstdc++6:arm64 (15.2.0-7ubuntu1) over (15.2.0-5ubuntu1) ... 65s Preparing to unpack .../gcc-15-base_15.2.0-7ubuntu1_arm64.deb ... 65s Unpacking gcc-15-base:arm64 (15.2.0-7ubuntu1) over (15.2.0-5ubuntu1) ... 66s Setting up gcc-15-base:arm64 (15.2.0-7ubuntu1) ... 66s (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 ... 83460 files and directories currently installed.) 66s Preparing to unpack .../libgcc-s1_15.2.0-7ubuntu1_arm64.deb ... 66s Unpacking libgcc-s1:arm64 (15.2.0-7ubuntu1) over (15.2.0-5ubuntu1) ... 66s Setting up libgcc-s1:arm64 (15.2.0-7ubuntu1) ... 66s (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 ... 83460 files and directories currently installed.) 66s Preparing to unpack .../publicsuffix_20251016.1743-0.1_all.deb ... 66s Unpacking publicsuffix (20251016.1743-0.1) over (20250328.1952-0.1) ... 66s Setting up libatomic1:arm64 (15.2.0-7ubuntu1) ... 66s Setting up publicsuffix (20251016.1743-0.1) ... 66s Setting up libstdc++6:arm64 (15.2.0-7ubuntu1) ... 66s Processing triggers for libc-bin (2.42-0ubuntu3) ... 66s autopkgtest [12:40:00]: upgrading testbed (apt dist-upgrade and autopurge) 66s Reading package lists... 67s Building dependency tree... 67s Reading state information... 67s Calculating upgrade... 67s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 67s Reading package lists... 68s Building dependency tree... 68s Reading state information... 68s Solving dependencies... 68s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 71s autopkgtest [12:40:05]: testbed running kernel: Linux 6.17.0-5-generic #5-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 22 09:50:31 UTC 2025 71s autopkgtest [12:40:05]: @@@@@@@@@@@@@@@@@@@@ apt-source svim 73s Get:1 http://ftpmaster.internal/ubuntu resolute/universe svim 2.0.0-3 (dsc) [1467 B] 73s Get:2 http://ftpmaster.internal/ubuntu resolute/universe svim 2.0.0-3 (tar) [190 kB] 73s Get:3 http://ftpmaster.internal/ubuntu resolute/universe svim 2.0.0-3 (diff) [4216 B] 73s gpgv: Signature made Tue Dec 20 21:12:47 2022 UTC 73s gpgv: using EDDSA key A095B66EE09024BEE6A2F0722A27904BD7243EDA 73s gpgv: Can't check signature: No public key 73s dpkg-source: warning: cannot verify inline signature for ./svim_2.0.0-3.dsc: no acceptable signature found 73s autopkgtest [12:40:07]: testing package svim version 2.0.0-3 73s autopkgtest [12:40:07]: build not needed 74s autopkgtest [12:40:08]: test run-unit-test: preparing testbed 74s Reading package lists... 74s Building dependency tree... 74s Reading state information... 74s Solving dependencies... 75s The following NEW packages will be installed: 75s blt fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-lyx libblas3 75s libdeflate0 libfontconfig1 libgfortran5 libgomp1 libgraphite2-3 75s libharfbuzz0b libhts3t64 libhtscodecs2 libimagequant0 libjbig0 75s libjpeg-turbo8 libjpeg8 liblapack3 liblcms2-2 liblerc4 libopenjp2-7 75s libqhull-r8.0 libraqm0 libsharpyuv0 libspoa7.0.0 libtcl8.6 libtiff6 libtk8.6 75s libwebp7 libwebpdemux2 libwebpmux3 libxft2 libxrender1 libxslt1.1 libxss1 75s libzopfli1 python-matplotlib-data python3-brotli python3-contourpy 75s python3-cpuinfo python3-cycler python3-dateutil python3-decorator 75s python3-edlib python3-fonttools python3-fs python3-kiwisolver python3-lxml 75s python3-lz4 python3-matplotlib python3-mpmath python3-numpy 75s python3-numpy-dev python3-packaging python3-pil python3-pil.imagetk 75s python3-platformdirs python3-pysam python3-pyspoa python3-scipy 75s python3-sympy python3-tk python3-ufolib2 python3-unicodedata2 python3-zopfli 75s python3.13-tk python3.14-tk svim tk8.6-blt2.5 unicode-data x11-common 75s 0 upgraded, 72 newly installed, 0 to remove and 0 not upgraded. 75s Need to get 76.5 MB of archives. 75s After this operation, 367 MB of additional disk space will be used. 75s Get:1 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-numpy-dev arm64 1:2.2.4+ds-1ubuntu1 [146 kB] 75s Get:2 http://ftpmaster.internal/ubuntu resolute/main arm64 libblas3 arm64 3.12.1-6build1 [186 kB] 75s Get:3 http://ftpmaster.internal/ubuntu resolute/main arm64 libgfortran5 arm64 15.2.0-7ubuntu1 [450 kB] 76s Get:4 http://ftpmaster.internal/ubuntu resolute/main arm64 liblapack3 arm64 3.12.1-6build1 [2340 kB] 76s Get:5 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-numpy arm64 1:2.2.4+ds-1ubuntu1 [3986 kB] 77s Get:6 http://ftpmaster.internal/ubuntu resolute/main arm64 libtcl8.6 arm64 8.6.17+dfsg-1 [1024 kB] 77s Get:7 http://ftpmaster.internal/ubuntu resolute/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 77s Get:8 http://ftpmaster.internal/ubuntu resolute/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 77s Get:9 http://ftpmaster.internal/ubuntu resolute/main arm64 fontconfig-config arm64 2.15.0-2.3ubuntu1 [38.1 kB] 77s Get:10 http://ftpmaster.internal/ubuntu resolute/main arm64 libfontconfig1 arm64 2.15.0-2.3ubuntu1 [144 kB] 77s Get:11 http://ftpmaster.internal/ubuntu resolute/main arm64 libxrender1 arm64 1:0.9.12-1 [19.5 kB] 77s Get:12 http://ftpmaster.internal/ubuntu resolute/main arm64 libxft2 arm64 2.3.6-1build1 [44.1 kB] 77s Get:13 http://ftpmaster.internal/ubuntu resolute/main arm64 x11-common all 1:7.7+24ubuntu1 [22.4 kB] 77s Get:14 http://ftpmaster.internal/ubuntu resolute/main arm64 libxss1 arm64 1:1.2.3-1build3 [7244 B] 77s Get:15 http://ftpmaster.internal/ubuntu resolute/main arm64 libtk8.6 arm64 8.6.17-1 [811 kB] 77s Get:16 http://ftpmaster.internal/ubuntu resolute/main arm64 tk8.6-blt2.5 arm64 2.5.3+dfsg-8 [624 kB] 77s Get:17 http://ftpmaster.internal/ubuntu resolute/main arm64 blt arm64 2.5.3+dfsg-8 [4824 B] 77s Get:18 http://ftpmaster.internal/ubuntu resolute/universe arm64 fonts-lyx all 2.4.4-1 [171 kB] 77s Get:19 http://ftpmaster.internal/ubuntu resolute/main arm64 libdeflate0 arm64 1.23-2 [46.4 kB] 77s Get:20 http://ftpmaster.internal/ubuntu resolute/main arm64 libgomp1 arm64 15.2.0-7ubuntu1 [147 kB] 77s Get:21 http://ftpmaster.internal/ubuntu resolute/main arm64 libgraphite2-3 arm64 1.3.14-2ubuntu1 [70.6 kB] 77s Get:22 http://ftpmaster.internal/ubuntu resolute/main arm64 libharfbuzz0b arm64 12.1.0-1 [523 kB] 77s Get:23 http://ftpmaster.internal/ubuntu resolute/universe arm64 libhtscodecs2 arm64 1.6.1-2 [82.7 kB] 77s Get:24 http://ftpmaster.internal/ubuntu resolute/universe arm64 libhts3t64 arm64 1.21+ds-1 [441 kB] 77s Get:25 http://ftpmaster.internal/ubuntu resolute/main arm64 libimagequant0 arm64 2.18.0-1build1 [37.1 kB] 77s Get:26 http://ftpmaster.internal/ubuntu resolute/main arm64 libjpeg-turbo8 arm64 2.1.5-4ubuntu2 [165 kB] 77s Get:27 http://ftpmaster.internal/ubuntu resolute/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 77s Get:28 http://ftpmaster.internal/ubuntu resolute/main arm64 liblcms2-2 arm64 2.16-2 [170 kB] 77s Get:29 http://ftpmaster.internal/ubuntu resolute/main arm64 liblerc4 arm64 4.0.0+ds-5ubuntu1 [167 kB] 77s Get:30 http://ftpmaster.internal/ubuntu resolute/universe arm64 libqhull-r8.0 arm64 2020.2-6build1 [189 kB] 77s Get:31 http://ftpmaster.internal/ubuntu resolute/main arm64 libraqm0 arm64 0.10.3-1 [15.0 kB] 77s Get:32 http://ftpmaster.internal/ubuntu resolute/main arm64 libsharpyuv0 arm64 1.5.0-0.1 [16.9 kB] 77s Get:33 http://ftpmaster.internal/ubuntu resolute/universe arm64 libspoa7.0.0 arm64 4.1.4-2 [60.1 kB] 77s Get:34 http://ftpmaster.internal/ubuntu resolute/main arm64 libjbig0 arm64 2.1-6.1ubuntu2 [29.3 kB] 77s Get:35 http://ftpmaster.internal/ubuntu resolute/main arm64 libwebp7 arm64 1.5.0-0.1 [194 kB] 77s Get:36 http://ftpmaster.internal/ubuntu resolute/main arm64 libtiff6 arm64 4.7.0-3ubuntu3 [196 kB] 77s Get:37 http://ftpmaster.internal/ubuntu resolute/main arm64 libwebpdemux2 arm64 1.5.0-0.1 [12.5 kB] 77s Get:38 http://ftpmaster.internal/ubuntu resolute/main arm64 libwebpmux3 arm64 1.5.0-0.1 [25.4 kB] 78s Get:39 http://ftpmaster.internal/ubuntu resolute/main arm64 libxslt1.1 arm64 1.1.43-0.3 [172 kB] 78s Get:40 http://ftpmaster.internal/ubuntu resolute/universe arm64 libzopfli1 arm64 1.0.3-3 [108 kB] 78s Get:41 http://ftpmaster.internal/ubuntu resolute/universe arm64 python-matplotlib-data all 3.10.7+dfsg1-1 [2930 kB] 78s Get:42 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-brotli arm64 1.1.0-2build6 [343 kB] 78s Get:43 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-contourpy arm64 1.3.1-1build2 [253 kB] 78s Get:44 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-cpuinfo all 9.0.0+git20221119-3 [21.7 kB] 78s Get:45 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-cycler all 0.12.1-2 [9850 B] 78s Get:46 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-dateutil all 2.9.0-4 [80.3 kB] 78s Get:47 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-decorator all 5.2.1-2 [28.1 kB] 78s Get:48 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-edlib arm64 1.2.7-7 [97.8 kB] 78s Get:49 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-platformdirs all 4.3.7-1 [16.9 kB] 78s Get:50 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-fs all 2.4.16-7 [90.8 kB] 78s Get:51 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-lxml arm64 6.0.1-1build1 [2149 kB] 78s Get:52 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-lz4 arm64 4.4.4+dfsg-3 [27.6 kB] 78s Get:53 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 python3-scipy arm64 1.16.3-1 [17.4 MB] 79s Get:54 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-mpmath all 1.3.0-1 [425 kB] 79s Get:55 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-sympy all 1.13.3-5 [4229 kB] 79s Get:56 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-ufolib2 all 0.17.1+dfsg1-1 [33.5 kB] 79s Get:57 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-unicodedata2 arm64 16.0.0+ds-1build1 [398 kB] 79s Get:58 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-zopfli arm64 0.2.3.post1-1 [10.7 kB] 79s Get:59 http://ftpmaster.internal/ubuntu resolute/universe arm64 unicode-data all 16.0.0-1 [9513 kB] 80s Get:60 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-fonttools arm64 4.57.0-2build1 [1648 kB] 80s Get:61 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-kiwisolver arm64 1.4.10~rc0-1 [60.1 kB] 80s Get:62 http://ftpmaster.internal/ubuntu resolute/main arm64 libopenjp2-7 arm64 2.5.3-2.1 [179 kB] 80s Get:63 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-pil arm64 11.3.0-1ubuntu2 [492 kB] 80s Get:64 http://ftpmaster.internal/ubuntu resolute/main arm64 python3.14-tk arm64 3.14.0-4 [107 kB] 80s Get:65 http://ftpmaster.internal/ubuntu resolute/main arm64 python3.13-tk arm64 3.13.9-1 [106 kB] 80s Get:66 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-tk arm64 3.13.9-1 [8946 B] 80s Get:67 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-pil.imagetk arm64 11.3.0-1ubuntu2 [9582 B] 80s Get:68 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-packaging all 25.0-1 [52.8 kB] 80s Get:69 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-matplotlib arm64 3.10.7+dfsg1-1 [17.1 MB] 80s Get:70 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-pysam arm64 0.23.0+ds-1build2 [4334 kB] 80s Get:71 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-pyspoa arm64 0.2.1-2build2 [69.8 kB] 80s Get:72 http://ftpmaster.internal/ubuntu resolute/universe arm64 svim all 2.0.0-3 [34.9 kB] 81s Fetched 76.5 MB in 6s (13.8 MB/s) 81s Selecting previously unselected package python3-numpy-dev:arm64. 81s (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 ... 83460 files and directories currently installed.) 81s Preparing to unpack .../00-python3-numpy-dev_1%3a2.2.4+ds-1ubuntu1_arm64.deb ... 81s Unpacking python3-numpy-dev:arm64 (1:2.2.4+ds-1ubuntu1) ... 81s Selecting previously unselected package libblas3:arm64. 81s Preparing to unpack .../01-libblas3_3.12.1-6build1_arm64.deb ... 81s Unpacking libblas3:arm64 (3.12.1-6build1) ... 81s Selecting previously unselected package libgfortran5:arm64. 81s Preparing to unpack .../02-libgfortran5_15.2.0-7ubuntu1_arm64.deb ... 81s Unpacking libgfortran5:arm64 (15.2.0-7ubuntu1) ... 81s Selecting previously unselected package liblapack3:arm64. 81s Preparing to unpack .../03-liblapack3_3.12.1-6build1_arm64.deb ... 81s Unpacking liblapack3:arm64 (3.12.1-6build1) ... 81s Selecting previously unselected package python3-numpy. 81s Preparing to unpack .../04-python3-numpy_1%3a2.2.4+ds-1ubuntu1_arm64.deb ... 81s Unpacking python3-numpy (1:2.2.4+ds-1ubuntu1) ... 81s Selecting previously unselected package libtcl8.6:arm64. 81s Preparing to unpack .../05-libtcl8.6_8.6.17+dfsg-1_arm64.deb ... 81s Unpacking libtcl8.6:arm64 (8.6.17+dfsg-1) ... 81s Selecting previously unselected package fonts-dejavu-mono. 81s Preparing to unpack .../06-fonts-dejavu-mono_2.37-8_all.deb ... 81s Unpacking fonts-dejavu-mono (2.37-8) ... 81s Selecting previously unselected package fonts-dejavu-core. 81s Preparing to unpack .../07-fonts-dejavu-core_2.37-8_all.deb ... 81s Unpacking fonts-dejavu-core (2.37-8) ... 81s Selecting previously unselected package fontconfig-config. 81s Preparing to unpack .../08-fontconfig-config_2.15.0-2.3ubuntu1_arm64.deb ... 82s Unpacking fontconfig-config (2.15.0-2.3ubuntu1) ... 82s Selecting previously unselected package libfontconfig1:arm64. 82s Preparing to unpack .../09-libfontconfig1_2.15.0-2.3ubuntu1_arm64.deb ... 82s Unpacking libfontconfig1:arm64 (2.15.0-2.3ubuntu1) ... 82s Selecting previously unselected package libxrender1:arm64. 82s Preparing to unpack .../10-libxrender1_1%3a0.9.12-1_arm64.deb ... 82s Unpacking libxrender1:arm64 (1:0.9.12-1) ... 82s Selecting previously unselected package libxft2:arm64. 82s Preparing to unpack .../11-libxft2_2.3.6-1build1_arm64.deb ... 82s Unpacking libxft2:arm64 (2.3.6-1build1) ... 82s Selecting previously unselected package x11-common. 82s Preparing to unpack .../12-x11-common_1%3a7.7+24ubuntu1_all.deb ... 82s Unpacking x11-common (1:7.7+24ubuntu1) ... 82s Selecting previously unselected package libxss1:arm64. 82s Preparing to unpack .../13-libxss1_1%3a1.2.3-1build3_arm64.deb ... 82s Unpacking libxss1:arm64 (1:1.2.3-1build3) ... 82s Selecting previously unselected package libtk8.6:arm64. 82s Preparing to unpack .../14-libtk8.6_8.6.17-1_arm64.deb ... 82s Unpacking libtk8.6:arm64 (8.6.17-1) ... 82s Selecting previously unselected package tk8.6-blt2.5. 82s Preparing to unpack .../15-tk8.6-blt2.5_2.5.3+dfsg-8_arm64.deb ... 82s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-8) ... 82s Selecting previously unselected package blt. 82s Preparing to unpack .../16-blt_2.5.3+dfsg-8_arm64.deb ... 82s Unpacking blt (2.5.3+dfsg-8) ... 82s Selecting previously unselected package fonts-lyx. 82s Preparing to unpack .../17-fonts-lyx_2.4.4-1_all.deb ... 82s Unpacking fonts-lyx (2.4.4-1) ... 82s Selecting previously unselected package libdeflate0:arm64. 82s Preparing to unpack .../18-libdeflate0_1.23-2_arm64.deb ... 82s Unpacking libdeflate0:arm64 (1.23-2) ... 82s Selecting previously unselected package libgomp1:arm64. 82s Preparing to unpack .../19-libgomp1_15.2.0-7ubuntu1_arm64.deb ... 82s Unpacking libgomp1:arm64 (15.2.0-7ubuntu1) ... 82s Selecting previously unselected package libgraphite2-3:arm64. 82s Preparing to unpack .../20-libgraphite2-3_1.3.14-2ubuntu1_arm64.deb ... 82s Unpacking libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 82s Selecting previously unselected package libharfbuzz0b:arm64. 82s Preparing to unpack .../21-libharfbuzz0b_12.1.0-1_arm64.deb ... 82s Unpacking libharfbuzz0b:arm64 (12.1.0-1) ... 82s Selecting previously unselected package libhtscodecs2:arm64. 82s Preparing to unpack .../22-libhtscodecs2_1.6.1-2_arm64.deb ... 82s Unpacking libhtscodecs2:arm64 (1.6.1-2) ... 82s Selecting previously unselected package libhts3t64:arm64. 82s Preparing to unpack .../23-libhts3t64_1.21+ds-1_arm64.deb ... 82s Unpacking libhts3t64:arm64 (1.21+ds-1) ... 82s Selecting previously unselected package libimagequant0:arm64. 82s Preparing to unpack .../24-libimagequant0_2.18.0-1build1_arm64.deb ... 82s Unpacking libimagequant0:arm64 (2.18.0-1build1) ... 82s Selecting previously unselected package libjpeg-turbo8:arm64. 82s Preparing to unpack .../25-libjpeg-turbo8_2.1.5-4ubuntu2_arm64.deb ... 82s Unpacking libjpeg-turbo8:arm64 (2.1.5-4ubuntu2) ... 82s Selecting previously unselected package libjpeg8:arm64. 82s Preparing to unpack .../26-libjpeg8_8c-2ubuntu11_arm64.deb ... 82s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 82s Selecting previously unselected package liblcms2-2:arm64. 82s Preparing to unpack .../27-liblcms2-2_2.16-2_arm64.deb ... 82s Unpacking liblcms2-2:arm64 (2.16-2) ... 82s Selecting previously unselected package liblerc4:arm64. 82s Preparing to unpack .../28-liblerc4_4.0.0+ds-5ubuntu1_arm64.deb ... 82s Unpacking liblerc4:arm64 (4.0.0+ds-5ubuntu1) ... 82s Selecting previously unselected package libqhull-r8.0:arm64. 82s Preparing to unpack .../29-libqhull-r8.0_2020.2-6build1_arm64.deb ... 82s Unpacking libqhull-r8.0:arm64 (2020.2-6build1) ... 82s Selecting previously unselected package libraqm0:arm64. 82s Preparing to unpack .../30-libraqm0_0.10.3-1_arm64.deb ... 82s Unpacking libraqm0:arm64 (0.10.3-1) ... 83s Selecting previously unselected package libsharpyuv0:arm64. 83s Preparing to unpack .../31-libsharpyuv0_1.5.0-0.1_arm64.deb ... 83s Unpacking libsharpyuv0:arm64 (1.5.0-0.1) ... 83s Selecting previously unselected package libspoa7.0.0:arm64. 83s Preparing to unpack .../32-libspoa7.0.0_4.1.4-2_arm64.deb ... 83s Unpacking libspoa7.0.0:arm64 (4.1.4-2) ... 83s Selecting previously unselected package libjbig0:arm64. 83s Preparing to unpack .../33-libjbig0_2.1-6.1ubuntu2_arm64.deb ... 83s Unpacking libjbig0:arm64 (2.1-6.1ubuntu2) ... 83s Selecting previously unselected package libwebp7:arm64. 83s Preparing to unpack .../34-libwebp7_1.5.0-0.1_arm64.deb ... 83s Unpacking libwebp7:arm64 (1.5.0-0.1) ... 83s Selecting previously unselected package libtiff6:arm64. 83s Preparing to unpack .../35-libtiff6_4.7.0-3ubuntu3_arm64.deb ... 83s Unpacking libtiff6:arm64 (4.7.0-3ubuntu3) ... 83s Selecting previously unselected package libwebpdemux2:arm64. 83s Preparing to unpack .../36-libwebpdemux2_1.5.0-0.1_arm64.deb ... 83s Unpacking libwebpdemux2:arm64 (1.5.0-0.1) ... 83s Selecting previously unselected package libwebpmux3:arm64. 83s Preparing to unpack .../37-libwebpmux3_1.5.0-0.1_arm64.deb ... 83s Unpacking libwebpmux3:arm64 (1.5.0-0.1) ... 83s Selecting previously unselected package libxslt1.1:arm64. 83s Preparing to unpack .../38-libxslt1.1_1.1.43-0.3_arm64.deb ... 83s Unpacking libxslt1.1:arm64 (1.1.43-0.3) ... 83s Selecting previously unselected package libzopfli1. 83s Preparing to unpack .../39-libzopfli1_1.0.3-3_arm64.deb ... 83s Unpacking libzopfli1 (1.0.3-3) ... 83s Selecting previously unselected package python-matplotlib-data. 83s Preparing to unpack .../40-python-matplotlib-data_3.10.7+dfsg1-1_all.deb ... 83s Unpacking python-matplotlib-data (3.10.7+dfsg1-1) ... 83s Selecting previously unselected package python3-brotli. 83s Preparing to unpack .../41-python3-brotli_1.1.0-2build6_arm64.deb ... 83s Unpacking python3-brotli (1.1.0-2build6) ... 83s Selecting previously unselected package python3-contourpy. 83s Preparing to unpack .../42-python3-contourpy_1.3.1-1build2_arm64.deb ... 83s Unpacking python3-contourpy (1.3.1-1build2) ... 83s Selecting previously unselected package python3-cpuinfo. 83s Preparing to unpack .../43-python3-cpuinfo_9.0.0+git20221119-3_all.deb ... 83s Unpacking python3-cpuinfo (9.0.0+git20221119-3) ... 83s Selecting previously unselected package python3-cycler. 83s Preparing to unpack .../44-python3-cycler_0.12.1-2_all.deb ... 83s Unpacking python3-cycler (0.12.1-2) ... 83s Selecting previously unselected package python3-dateutil. 83s Preparing to unpack .../45-python3-dateutil_2.9.0-4_all.deb ... 83s Unpacking python3-dateutil (2.9.0-4) ... 83s Selecting previously unselected package python3-decorator. 83s Preparing to unpack .../46-python3-decorator_5.2.1-2_all.deb ... 83s Unpacking python3-decorator (5.2.1-2) ... 83s Selecting previously unselected package python3-edlib:arm64. 83s Preparing to unpack .../47-python3-edlib_1.2.7-7_arm64.deb ... 83s Unpacking python3-edlib:arm64 (1.2.7-7) ... 83s Selecting previously unselected package python3-platformdirs. 83s Preparing to unpack .../48-python3-platformdirs_4.3.7-1_all.deb ... 83s Unpacking python3-platformdirs (4.3.7-1) ... 83s Selecting previously unselected package python3-fs. 83s Preparing to unpack .../49-python3-fs_2.4.16-7_all.deb ... 83s Unpacking python3-fs (2.4.16-7) ... 83s Selecting previously unselected package python3-lxml:arm64. 83s Preparing to unpack .../50-python3-lxml_6.0.1-1build1_arm64.deb ... 83s Unpacking python3-lxml:arm64 (6.0.1-1build1) ... 83s Selecting previously unselected package python3-lz4. 83s Preparing to unpack .../51-python3-lz4_4.4.4+dfsg-3_arm64.deb ... 83s Unpacking python3-lz4 (4.4.4+dfsg-3) ... 83s Selecting previously unselected package python3-scipy. 83s Preparing to unpack .../52-python3-scipy_1.16.3-1_arm64.deb ... 83s Unpacking python3-scipy (1.16.3-1) ... 84s Selecting previously unselected package python3-mpmath. 84s Preparing to unpack .../53-python3-mpmath_1.3.0-1_all.deb ... 84s Unpacking python3-mpmath (1.3.0-1) ... 84s Selecting previously unselected package python3-sympy. 84s Preparing to unpack .../54-python3-sympy_1.13.3-5_all.deb ... 84s Unpacking python3-sympy (1.13.3-5) ... 84s Selecting previously unselected package python3-ufolib2. 84s Preparing to unpack .../55-python3-ufolib2_0.17.1+dfsg1-1_all.deb ... 84s Unpacking python3-ufolib2 (0.17.1+dfsg1-1) ... 84s Selecting previously unselected package python3-unicodedata2. 84s Preparing to unpack .../56-python3-unicodedata2_16.0.0+ds-1build1_arm64.deb ... 84s Unpacking python3-unicodedata2 (16.0.0+ds-1build1) ... 84s Selecting previously unselected package python3-zopfli. 84s Preparing to unpack .../57-python3-zopfli_0.2.3.post1-1_arm64.deb ... 84s Unpacking python3-zopfli (0.2.3.post1-1) ... 84s Selecting previously unselected package unicode-data. 84s Preparing to unpack .../58-unicode-data_16.0.0-1_all.deb ... 84s Unpacking unicode-data (16.0.0-1) ... 84s Selecting previously unselected package python3-fonttools. 84s Preparing to unpack .../59-python3-fonttools_4.57.0-2build1_arm64.deb ... 84s Unpacking python3-fonttools (4.57.0-2build1) ... 85s Selecting previously unselected package python3-kiwisolver. 85s Preparing to unpack .../60-python3-kiwisolver_1.4.10~rc0-1_arm64.deb ... 85s Unpacking python3-kiwisolver (1.4.10~rc0-1) ... 85s Selecting previously unselected package libopenjp2-7:arm64. 85s Preparing to unpack .../61-libopenjp2-7_2.5.3-2.1_arm64.deb ... 85s Unpacking libopenjp2-7:arm64 (2.5.3-2.1) ... 85s Selecting previously unselected package python3-pil:arm64. 85s Preparing to unpack .../62-python3-pil_11.3.0-1ubuntu2_arm64.deb ... 85s Unpacking python3-pil:arm64 (11.3.0-1ubuntu2) ... 85s Selecting previously unselected package python3.14-tk. 85s Preparing to unpack .../63-python3.14-tk_3.14.0-4_arm64.deb ... 85s Unpacking python3.14-tk (3.14.0-4) ... 85s Selecting previously unselected package python3.13-tk. 85s Preparing to unpack .../64-python3.13-tk_3.13.9-1_arm64.deb ... 85s Unpacking python3.13-tk (3.13.9-1) ... 85s Selecting previously unselected package python3-tk:arm64. 85s Preparing to unpack .../65-python3-tk_3.13.9-1_arm64.deb ... 85s Unpacking python3-tk:arm64 (3.13.9-1) ... 85s Selecting previously unselected package python3-pil.imagetk:arm64. 85s Preparing to unpack .../66-python3-pil.imagetk_11.3.0-1ubuntu2_arm64.deb ... 85s Unpacking python3-pil.imagetk:arm64 (11.3.0-1ubuntu2) ... 85s Selecting previously unselected package python3-packaging. 85s Preparing to unpack .../67-python3-packaging_25.0-1_all.deb ... 85s Unpacking python3-packaging (25.0-1) ... 85s Selecting previously unselected package python3-matplotlib. 85s Preparing to unpack .../68-python3-matplotlib_3.10.7+dfsg1-1_arm64.deb ... 85s Unpacking python3-matplotlib (3.10.7+dfsg1-1) ... 85s Selecting previously unselected package python3-pysam. 85s Preparing to unpack .../69-python3-pysam_0.23.0+ds-1build2_arm64.deb ... 85s Unpacking python3-pysam (0.23.0+ds-1build2) ... 85s Selecting previously unselected package python3-pyspoa. 85s Preparing to unpack .../70-python3-pyspoa_0.2.1-2build2_arm64.deb ... 85s Unpacking python3-pyspoa (0.2.1-2build2) ... 86s Selecting previously unselected package svim. 86s Preparing to unpack .../71-svim_2.0.0-3_all.deb ... 86s Unpacking svim (2.0.0-3) ... 86s Setting up libhtscodecs2:arm64 (1.6.1-2) ... 86s Setting up libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 86s Setting up liblcms2-2:arm64 (2.16-2) ... 86s Setting up libsharpyuv0:arm64 (1.5.0-0.1) ... 86s Setting up liblerc4:arm64 (4.0.0+ds-5ubuntu1) ... 86s Setting up libxrender1:arm64 (1:0.9.12-1) ... 86s Setting up python3-lz4 (4.4.4+dfsg-3) ... 86s Setting up python3-unicodedata2 (16.0.0+ds-1build1) ... 86s Setting up fonts-lyx (2.4.4-1) ... 86s Setting up x11-common (1:7.7+24ubuntu1) ... 86s Setting up libdeflate0:arm64 (1.23-2) ... 86s Setting up libqhull-r8.0:arm64 (2020.2-6build1) ... 86s Setting up libgomp1:arm64 (15.2.0-7ubuntu1) ... 86s Setting up libjbig0:arm64 (2.1-6.1ubuntu2) ... 86s Setting up python3-platformdirs (4.3.7-1) ... 86s Setting up python3-fs (2.4.16-7) ... 86s Setting up unicode-data (16.0.0-1) ... 86s Setting up python3-decorator (5.2.1-2) ... 86s Setting up libblas3:arm64 (3.12.1-6build1) ... 87s 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 87s Setting up python3-packaging (25.0-1) ... 87s Setting up libzopfli1 (1.0.3-3) ... 87s Setting up python3-brotli (1.1.0-2build6) ... 87s Setting up python3-cycler (0.12.1-2) ... 87s Setting up libimagequant0:arm64 (2.18.0-1build1) ... 87s Setting up fonts-dejavu-mono (2.37-8) ... 87s Setting up python3-kiwisolver (1.4.10~rc0-1) ... 87s Setting up libspoa7.0.0:arm64 (4.1.4-2) ... 87s Setting up python3-numpy-dev:arm64 (1:2.2.4+ds-1ubuntu1) ... 87s Setting up libtcl8.6:arm64 (8.6.17+dfsg-1) ... 87s Setting up fonts-dejavu-core (2.37-8) ... 87s Setting up libjpeg-turbo8:arm64 (2.1.5-4ubuntu2) ... 87s Setting up python3-cpuinfo (9.0.0+git20221119-3) ... 87s Setting up libgfortran5:arm64 (15.2.0-7ubuntu1) ... 87s Setting up libwebp7:arm64 (1.5.0-0.1) ... 87s Setting up libxslt1.1:arm64 (1.1.43-0.3) ... 87s Setting up libhts3t64:arm64 (1.21+ds-1) ... 87s Setting up libopenjp2-7:arm64 (2.5.3-2.1) ... 87s Setting up libharfbuzz0b:arm64 (12.1.0-1) ... 87s Setting up python3-dateutil (2.9.0-4) ... 87s Setting up libxss1:arm64 (1:1.2.3-1build3) ... 87s Setting up python3-mpmath (1.3.0-1) ... 88s Setting up python-matplotlib-data (3.10.7+dfsg1-1) ... 88s Setting up libwebpmux3:arm64 (1.5.0-0.1) ... 88s Setting up python3-edlib:arm64 (1.2.7-7) ... 88s Setting up libjpeg8:arm64 (8c-2ubuntu11) ... 88s Setting up python3-sympy (1.13.3-5) ... 94s Setting up python3-pyspoa (0.2.1-2build2) ... 94s Setting up liblapack3:arm64 (3.12.1-6build1) ... 94s 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 94s Setting up python3-pysam (0.23.0+ds-1build2) ... 94s Setting up fontconfig-config (2.15.0-2.3ubuntu1) ... 94s Setting up libwebpdemux2:arm64 (1.5.0-0.1) ... 94s Setting up python3-zopfli (0.2.3.post1-1) ... 94s Setting up libraqm0:arm64 (0.10.3-1) ... 94s Setting up python3-numpy (1:2.2.4+ds-1ubuntu1) ... 96s Setting up python3-lxml:arm64 (6.0.1-1build1) ... 96s Setting up libtiff6:arm64 (4.7.0-3ubuntu3) ... 96s Setting up python3-contourpy (1.3.1-1build2) ... 96s Setting up libfontconfig1:arm64 (2.15.0-2.3ubuntu1) ... 96s Setting up libxft2:arm64 (2.3.6-1build1) ... 96s Setting up python3-scipy (1.16.3-1) ... 100s Setting up libtk8.6:arm64 (8.6.17-1) ... 100s Setting up python3.13-tk (3.13.9-1) ... 100s Setting up python3-pil:arm64 (11.3.0-1ubuntu2) ... 101s Setting up tk8.6-blt2.5 (2.5.3+dfsg-8) ... 101s Setting up python3.14-tk (3.14.0-4) ... 101s Setting up blt (2.5.3+dfsg-8) ... 101s Setting up python3-tk:arm64 (3.13.9-1) ... 101s Setting up python3-pil.imagetk:arm64 (11.3.0-1ubuntu2) ... 101s Setting up python3-fonttools (4.57.0-2build1) ... 102s Setting up python3-ufolib2 (0.17.1+dfsg1-1) ... 102s Setting up python3-matplotlib (3.10.7+dfsg1-1) ... 103s Setting up svim (2.0.0-3) ... 104s Processing triggers for libc-bin (2.42-0ubuntu3) ... 104s Processing triggers for man-db (2.13.1-1) ... 105s autopkgtest [12:40:39]: test run-unit-test: [----------------------- 106s test_analyze_alignment_file_querysorted (tests.test_Collect.TestCollect.test_analyze_alignment_file_querysorted) ... ok 106s test_bam_iterator (tests.test_Collect.TestCollect.test_bam_iterator) ... ok 106s test_retrieve_primary_alignment_from_supplementary (tests.test_Collect.TestCollect.test_retrieve_primary_alignment_from_supplementary) ... ok 106s test_retrieve_supplementary_alignment_from_primary (tests.test_Collect.TestCollect.test_retrieve_supplementary_alignment_from_primary) ... ok 106s test_downstream_distance_to (tests.test_SVCandidate.DeletionCandidateTestCase.test_downstream_distance_to) ... ok 106s test_get_key (tests.test_SVCandidate.DeletionCandidateTestCase.test_get_key) ... ok 106s test_get_source (tests.test_SVCandidate.DeletionCandidateTestCase.test_get_source) ... ok 106s test_get_std_pos (tests.test_SVCandidate.DeletionCandidateTestCase.test_get_std_pos) ... ok 106s test_get_std_span (tests.test_SVCandidate.DeletionCandidateTestCase.test_get_std_span) ... ok 106s test_get_vcf_entry (tests.test_SVCandidate.DeletionCandidateTestCase.test_get_vcf_entry) ... ok 106s test_accessors (tests.test_Signature.TestSVSignature.test_accessors) ... ok 106s test_as_string (tests.test_Signature.TestSVSignature.test_as_string) ... ok 106s test_downstream_distance_to (tests.test_Signature.TestSVSignature.test_downstream_distance_to) ... ok 107s test_clustering (tests.test_clustering.TestSVIMClustering.test_clustering) ... ok 107s test_partitioning (tests.test_clustering.TestSVIMClustering.test_partitioning) ... ok 107s test_partitioning_large_distance (tests.test_clustering.TestSVIMClustering.test_partitioning_large_distance) ... ok 107s test_scores (tests.test_clustering.TestSVIMClustering.test_scores) ... ok 107s test_simple (tests.test_consensus.TestSVIMConsensus.test_simple) ... ok 107s test_skipping (tests.test_consensus.TestSVIMConsensus.test_skipping) ... ok 107s test_guess_file_type (tests.test_input_parsing.TestInputParsing.test_guess_file_type) ... ok 107s test_is_similar (tests.test_inter.TestSVIMInter.test_is_similar) ... ok 107s test_analyze_cigar_indel (tests.test_intra.TestSVIMIntra.test_analyze_cigar_indel) ... ok 107s test_fetch (tests.test_satag.TestSAExtraction.test_fetch) ... ok 107s test_satag_extraction_complete (tests.test_satag.TestSAExtraction.test_satag_extraction_complete) ... ok 107s test_satag_length (tests.test_satag.TestSAExtraction.test_satag_length) ... ok 107s 107s ---------------------------------------------------------------------- 107s Ran 25 tests in 0.541s 107s 107s OK 107s autopkgtest [12:40:41]: test run-unit-test: -----------------------] 108s autopkgtest [12:40:42]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 108s run-unit-test PASS 108s autopkgtest [12:40:42]: @@@@@@@@@@@@@@@@@@@@ summary 108s run-unit-test PASS