0s autopkgtest [12:17:54]: starting date and time: 2025-11-01 12:17:54+0000 0s autopkgtest [12:17:54]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [12:17:54]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.tf412j2j/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:scipy --apt-upgrade pairtools --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-2@bos03-arm64-1.secgroup --name adt-resolute-arm64-pairtools-20251101-121753-juju-7f2275-prod-proposed-migration-environment-2-b2220cb5-e99c-49a4-894c-e597ee79d23c --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/ 3s Creating nova instance adt-resolute-arm64-pairtools-20251101-121753-juju-7f2275-prod-proposed-migration-environment-2-b2220cb5-e99c-49a4-894c-e597ee79d23c from image adt/ubuntu-resolute-arm64-server-20251101.img (UUID 895f8d05-65a0-4cf8-81a2-1a04d79b538c)... 61s autopkgtest [12:18:55]: testbed dpkg architecture: arm64 61s autopkgtest [12:18:55]: testbed apt version: 3.1.11 62s autopkgtest [12:18:56]: @@@@@@@@@@@@@@@@@@@@ test bed setup 62s autopkgtest [12:18:56]: testbed release detected to be: None 63s autopkgtest [12:18:57]: updating testbed package index (apt update) 63s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [87.8 kB] 63s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 63s 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/main Sources [138 kB] 64s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [2242 kB] 64s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [49.4 kB] 64s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [9848 B] 64s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 Packages [206 kB] 64s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 c-n-f Metadata [4948 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 [1619 kB] 64s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 c-n-f Metadata [48.3 kB] 64s Get:15 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse arm64 Packages [34.8 kB] 64s Get:16 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse arm64 c-n-f Metadata [1700 B] 66s Fetched 4550 kB in 1s (3145 kB/s) 66s Reading package lists... 67s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 67s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 67s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 67s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 68s Reading package lists... 68s Reading package lists... 69s Building dependency tree... 69s Reading state information... 69s Calculating upgrade... 69s The following packages will be upgraded: 69s gcc-15-base libatomic1 libgcc-s1 libstdc++6 publicsuffix 70s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 70s Need to get 1027 kB of archives. 70s After this operation, 14.3 kB of additional disk space will be used. 70s Get:1 http://ftpmaster.internal/ubuntu resolute/main arm64 libatomic1 arm64 15.2.0-7ubuntu1 [11.2 kB] 70s Get:2 http://ftpmaster.internal/ubuntu resolute/main arm64 libstdc++6 arm64 15.2.0-7ubuntu1 [760 kB] 70s Get:3 http://ftpmaster.internal/ubuntu resolute/main arm64 gcc-15-base arm64 15.2.0-7ubuntu1 [58.4 kB] 70s Get:4 http://ftpmaster.internal/ubuntu resolute/main arm64 libgcc-s1 arm64 15.2.0-7ubuntu1 [61.1 kB] 70s Get:5 http://ftpmaster.internal/ubuntu resolute/main arm64 publicsuffix all 20251016.1743-0.1 [136 kB] 71s dpkg-preconfigure: unable to re-open stdin: No such file or directory 71s Fetched 1027 kB in 1s (1028 kB/s) 71s (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.) 71s Preparing to unpack .../libatomic1_15.2.0-7ubuntu1_arm64.deb ... 71s Unpacking libatomic1:arm64 (15.2.0-7ubuntu1) over (15.2.0-5ubuntu1) ... 71s Preparing to unpack .../libstdc++6_15.2.0-7ubuntu1_arm64.deb ... 72s Unpacking libstdc++6:arm64 (15.2.0-7ubuntu1) over (15.2.0-5ubuntu1) ... 72s Preparing to unpack .../gcc-15-base_15.2.0-7ubuntu1_arm64.deb ... 72s Unpacking gcc-15-base:arm64 (15.2.0-7ubuntu1) over (15.2.0-5ubuntu1) ... 72s Setting up gcc-15-base:arm64 (15.2.0-7ubuntu1) ... 72s (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.) 72s Preparing to unpack .../libgcc-s1_15.2.0-7ubuntu1_arm64.deb ... 72s Unpacking libgcc-s1:arm64 (15.2.0-7ubuntu1) over (15.2.0-5ubuntu1) ... 72s Setting up libgcc-s1:arm64 (15.2.0-7ubuntu1) ... 72s (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.) 72s Preparing to unpack .../publicsuffix_20251016.1743-0.1_all.deb ... 72s Unpacking publicsuffix (20251016.1743-0.1) over (20250328.1952-0.1) ... 72s Setting up libatomic1:arm64 (15.2.0-7ubuntu1) ... 72s Setting up publicsuffix (20251016.1743-0.1) ... 72s Setting up libstdc++6:arm64 (15.2.0-7ubuntu1) ... 72s Processing triggers for libc-bin (2.42-0ubuntu3) ... 73s autopkgtest [12:19:07]: upgrading testbed (apt dist-upgrade and autopurge) 73s Reading package lists... 73s Building dependency tree... 73s Reading state information... 73s Calculating upgrade... 74s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 74s Reading package lists... 74s Building dependency tree... 74s Reading state information... 74s Solving dependencies... 75s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 78s autopkgtest [12:19:12]: testbed running kernel: Linux 6.17.0-5-generic #5-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 22 09:50:31 UTC 2025 78s autopkgtest [12:19:12]: @@@@@@@@@@@@@@@@@@@@ apt-source pairtools 81s Get:1 http://ftpmaster.internal/ubuntu resolute/universe pairtools 1.1.3-1build2 (dsc) [2493 B] 81s Get:2 http://ftpmaster.internal/ubuntu resolute/universe pairtools 1.1.3-1build2 (tar) [1420 kB] 81s Get:3 http://ftpmaster.internal/ubuntu resolute/universe pairtools 1.1.3-1build2 (diff) [7752 B] 81s gpgv: Signature made Tue Oct 21 10:20:57 2025 UTC 81s gpgv: using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2 81s gpgv: Can't check signature: No public key 81s dpkg-source: warning: cannot verify inline signature for ./pairtools_1.1.3-1build2.dsc: no acceptable signature found 81s autopkgtest [12:19:15]: testing package pairtools version 1.1.3-1build2 82s autopkgtest [12:19:16]: build not needed 83s autopkgtest [12:19:17]: test upstream-tests: preparing testbed 83s Reading package lists... 84s Building dependency tree... 84s Reading state information... 84s Solving dependencies... 84s The following NEW packages will be installed: 84s blt fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-lyx libblas3 84s libdeflate0 libfontconfig1 libgfortran5 libgomp1 libgraphite2-3 84s libharfbuzz0b libhts3t64 libhtscodecs2 libimagequant0 libjbig0 84s libjpeg-turbo8 libjpeg8 liblapack3 liblcms2-2 liblerc4 libopenjp2-7 84s libqhull-r8.0 libraqm0 libsharpyuv0 libtcl8.6 libtiff6 libtk8.6 libwebp7 84s libwebpdemux2 libwebpmux3 libxft2 libxrender1 libxslt1.1 libxss1 libzopfli1 84s python-is-python3 python-matplotlib-data python3-bioframe python3-brotli 84s python3-click python3-contourpy python3-cycler python3-dateutil 84s python3-decorator python3-fonttools python3-fs python3-iniconfig 84s python3-kiwisolver python3-lxml python3-lz4 python3-matplotlib 84s python3-mpmath python3-numpy python3-numpy-dev python3-packaging 84s python3-pairtools python3-pandas python3-pandas-lib python3-pil 84s python3-pil.imagetk python3-platformdirs python3-pluggy python3-pysam 84s python3-pytest python3-pytz python3-scipy python3-standard-pipes 84s python3-sympy python3-tk python3-ufolib2 python3-unicodedata2 python3-zopfli 84s python3.13-tk python3.14-tk tk8.6-blt2.5 unicode-data x11-common 84s 0 upgraded, 78 newly installed, 0 to remove and 0 not upgraded. 84s Need to get 86.9 MB of archives. 84s After this operation, 432 MB of additional disk space will be used. 84s Get:1 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-numpy-dev arm64 1:2.2.4+ds-1ubuntu1 [146 kB] 85s Get:2 http://ftpmaster.internal/ubuntu resolute/main arm64 libblas3 arm64 3.12.1-6build1 [186 kB] 85s Get:3 http://ftpmaster.internal/ubuntu resolute/main arm64 libgfortran5 arm64 15.2.0-7ubuntu1 [450 kB] 85s Get:4 http://ftpmaster.internal/ubuntu resolute/main arm64 liblapack3 arm64 3.12.1-6build1 [2340 kB] 85s Get:5 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-numpy arm64 1:2.2.4+ds-1ubuntu1 [3986 kB] 86s Get:6 http://ftpmaster.internal/ubuntu resolute/main arm64 libtcl8.6 arm64 8.6.17+dfsg-1 [1024 kB] 86s Get:7 http://ftpmaster.internal/ubuntu resolute/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 86s Get:8 http://ftpmaster.internal/ubuntu resolute/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 86s Get:9 http://ftpmaster.internal/ubuntu resolute/main arm64 fontconfig-config arm64 2.15.0-2.3ubuntu1 [38.1 kB] 86s Get:10 http://ftpmaster.internal/ubuntu resolute/main arm64 libfontconfig1 arm64 2.15.0-2.3ubuntu1 [144 kB] 86s Get:11 http://ftpmaster.internal/ubuntu resolute/main arm64 libxrender1 arm64 1:0.9.12-1 [19.5 kB] 86s Get:12 http://ftpmaster.internal/ubuntu resolute/main arm64 libxft2 arm64 2.3.6-1build1 [44.1 kB] 86s Get:13 http://ftpmaster.internal/ubuntu resolute/main arm64 x11-common all 1:7.7+24ubuntu1 [22.4 kB] 86s Get:14 http://ftpmaster.internal/ubuntu resolute/main arm64 libxss1 arm64 1:1.2.3-1build3 [7244 B] 86s Get:15 http://ftpmaster.internal/ubuntu resolute/main arm64 libtk8.6 arm64 8.6.17-1 [811 kB] 86s Get:16 http://ftpmaster.internal/ubuntu resolute/main arm64 tk8.6-blt2.5 arm64 2.5.3+dfsg-8 [624 kB] 86s Get:17 http://ftpmaster.internal/ubuntu resolute/main arm64 blt arm64 2.5.3+dfsg-8 [4824 B] 86s Get:18 http://ftpmaster.internal/ubuntu resolute/universe arm64 fonts-lyx all 2.4.4-1 [171 kB] 86s Get:19 http://ftpmaster.internal/ubuntu resolute/main arm64 libdeflate0 arm64 1.23-2 [46.4 kB] 86s Get:20 http://ftpmaster.internal/ubuntu resolute/main arm64 libgomp1 arm64 15.2.0-7ubuntu1 [147 kB] 86s Get:21 http://ftpmaster.internal/ubuntu resolute/main arm64 libgraphite2-3 arm64 1.3.14-2ubuntu1 [70.6 kB] 86s Get:22 http://ftpmaster.internal/ubuntu resolute/main arm64 libharfbuzz0b arm64 12.1.0-1 [523 kB] 86s Get:23 http://ftpmaster.internal/ubuntu resolute/universe arm64 libhtscodecs2 arm64 1.6.1-2 [82.7 kB] 86s Get:24 http://ftpmaster.internal/ubuntu resolute/universe arm64 libhts3t64 arm64 1.21+ds-1 [441 kB] 86s Get:25 http://ftpmaster.internal/ubuntu resolute/main arm64 libimagequant0 arm64 2.18.0-1build1 [37.1 kB] 86s Get:26 http://ftpmaster.internal/ubuntu resolute/main arm64 libjpeg-turbo8 arm64 2.1.5-4ubuntu2 [165 kB] 86s Get:27 http://ftpmaster.internal/ubuntu resolute/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 86s Get:28 http://ftpmaster.internal/ubuntu resolute/main arm64 liblcms2-2 arm64 2.16-2 [170 kB] 86s Get:29 http://ftpmaster.internal/ubuntu resolute/main arm64 liblerc4 arm64 4.0.0+ds-5ubuntu1 [167 kB] 86s Get:30 http://ftpmaster.internal/ubuntu resolute/universe arm64 libqhull-r8.0 arm64 2020.2-6build1 [189 kB] 86s Get:31 http://ftpmaster.internal/ubuntu resolute/main arm64 libraqm0 arm64 0.10.3-1 [15.0 kB] 86s Get:32 http://ftpmaster.internal/ubuntu resolute/main arm64 libsharpyuv0 arm64 1.5.0-0.1 [16.9 kB] 86s Get:33 http://ftpmaster.internal/ubuntu resolute/main arm64 libjbig0 arm64 2.1-6.1ubuntu2 [29.3 kB] 86s Get:34 http://ftpmaster.internal/ubuntu resolute/main arm64 libwebp7 arm64 1.5.0-0.1 [194 kB] 86s Get:35 http://ftpmaster.internal/ubuntu resolute/main arm64 libtiff6 arm64 4.7.0-3ubuntu3 [196 kB] 86s Get:36 http://ftpmaster.internal/ubuntu resolute/main arm64 libwebpdemux2 arm64 1.5.0-0.1 [12.5 kB] 86s Get:37 http://ftpmaster.internal/ubuntu resolute/main arm64 libwebpmux3 arm64 1.5.0-0.1 [25.4 kB] 86s Get:38 http://ftpmaster.internal/ubuntu resolute/main arm64 libxslt1.1 arm64 1.1.43-0.3 [172 kB] 86s Get:39 http://ftpmaster.internal/ubuntu resolute/universe arm64 libzopfli1 arm64 1.0.3-3 [108 kB] 86s Get:40 http://ftpmaster.internal/ubuntu resolute/main arm64 python-is-python3 all 3.13.3-1 [2768 B] 86s Get:41 http://ftpmaster.internal/ubuntu resolute/universe arm64 python-matplotlib-data all 3.10.7+dfsg1-1 [2930 kB] 86s Get:42 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-dateutil all 2.9.0-4 [80.3 kB] 86s Get:43 http://ftpmaster.internal/ubuntu resolute/main arm64 libopenjp2-7 arm64 2.5.3-2.1 [179 kB] 86s Get:44 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-pil arm64 11.3.0-1ubuntu2 [492 kB] 86s Get:45 http://ftpmaster.internal/ubuntu resolute/main arm64 python3.14-tk arm64 3.14.0-4 [107 kB] 86s Get:46 http://ftpmaster.internal/ubuntu resolute/main arm64 python3.13-tk arm64 3.13.9-1 [106 kB] 86s Get:47 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-tk arm64 3.13.9-1 [8946 B] 86s Get:48 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-pil.imagetk arm64 11.3.0-1ubuntu2 [9582 B] 86s Get:49 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-contourpy arm64 1.3.1-1build2 [253 kB] 86s Get:50 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-cycler all 0.12.1-2 [9850 B] 86s Get:51 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-brotli arm64 1.1.0-2build6 [343 kB] 86s Get:52 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-platformdirs all 4.3.7-1 [16.9 kB] 86s Get:53 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-fs all 2.4.16-7 [90.8 kB] 86s Get:54 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-lxml arm64 6.0.1-1build1 [2149 kB] 87s Get:55 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-lz4 arm64 4.4.4+dfsg-3 [27.6 kB] 87s Get:56 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-decorator all 5.2.1-2 [28.1 kB] 87s Get:57 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 python3-scipy arm64 1.16.3-1 [17.4 MB] 87s Get:58 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-mpmath all 1.3.0-1 [425 kB] 87s Get:59 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-sympy all 1.13.3-5 [4229 kB] 87s Get:60 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-ufolib2 all 0.17.1+dfsg1-1 [33.5 kB] 87s Get:61 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-unicodedata2 arm64 16.0.0+ds-1build1 [398 kB] 87s Get:62 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-zopfli arm64 0.2.3.post1-1 [10.7 kB] 87s Get:63 http://ftpmaster.internal/ubuntu resolute/universe arm64 unicode-data all 16.0.0-1 [9513 kB] 88s Get:64 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-fonttools arm64 4.57.0-2build1 [1648 kB] 88s Get:65 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-kiwisolver arm64 1.4.10~rc0-1 [60.1 kB] 88s Get:66 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-packaging all 25.0-1 [52.8 kB] 88s Get:67 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-matplotlib arm64 3.10.7+dfsg1-1 [17.1 MB] 88s Get:68 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-pytz all 2025.2-4 [32.3 kB] 88s Get:69 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-pandas-lib arm64 2.3.3+dfsg-1ubuntu1 [6979 kB] 88s Get:70 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-pandas all 2.3.3+dfsg-1ubuntu1 [2948 kB] 89s Get:71 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-bioframe all 0.4.1-2 [76.3 kB] 89s Get:72 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-click all 8.2.0+0.really.8.1.8-1 [80.0 kB] 89s Get:73 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-iniconfig all 1.1.1-2 [6024 B] 89s Get:74 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-standard-pipes all 3.13.0-5 [7414 B] 89s Get:75 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-pysam arm64 0.23.0+ds-1build2 [4334 kB] 89s Get:76 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-pairtools arm64 1.1.3-1build2 [261 kB] 89s Get:77 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-pluggy all 1.6.0-1 [21.0 kB] 89s Get:78 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-pytest all 8.3.5-2 [252 kB] 89s Fetched 86.9 MB in 4s (20.0 MB/s) 89s Selecting previously unselected package python3-numpy-dev:arm64. 89s (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.) 89s Preparing to unpack .../00-python3-numpy-dev_1%3a2.2.4+ds-1ubuntu1_arm64.deb ... 89s Unpacking python3-numpy-dev:arm64 (1:2.2.4+ds-1ubuntu1) ... 89s Selecting previously unselected package libblas3:arm64. 89s Preparing to unpack .../01-libblas3_3.12.1-6build1_arm64.deb ... 89s Unpacking libblas3:arm64 (3.12.1-6build1) ... 89s Selecting previously unselected package libgfortran5:arm64. 89s Preparing to unpack .../02-libgfortran5_15.2.0-7ubuntu1_arm64.deb ... 89s Unpacking libgfortran5:arm64 (15.2.0-7ubuntu1) ... 89s Selecting previously unselected package liblapack3:arm64. 89s Preparing to unpack .../03-liblapack3_3.12.1-6build1_arm64.deb ... 89s Unpacking liblapack3:arm64 (3.12.1-6build1) ... 89s Selecting previously unselected package python3-numpy. 89s Preparing to unpack .../04-python3-numpy_1%3a2.2.4+ds-1ubuntu1_arm64.deb ... 89s Unpacking python3-numpy (1:2.2.4+ds-1ubuntu1) ... 90s Selecting previously unselected package libtcl8.6:arm64. 90s Preparing to unpack .../05-libtcl8.6_8.6.17+dfsg-1_arm64.deb ... 90s Unpacking libtcl8.6:arm64 (8.6.17+dfsg-1) ... 90s Selecting previously unselected package fonts-dejavu-mono. 90s Preparing to unpack .../06-fonts-dejavu-mono_2.37-8_all.deb ... 90s Unpacking fonts-dejavu-mono (2.37-8) ... 90s Selecting previously unselected package fonts-dejavu-core. 90s Preparing to unpack .../07-fonts-dejavu-core_2.37-8_all.deb ... 90s Unpacking fonts-dejavu-core (2.37-8) ... 90s Selecting previously unselected package fontconfig-config. 90s Preparing to unpack .../08-fontconfig-config_2.15.0-2.3ubuntu1_arm64.deb ... 90s Unpacking fontconfig-config (2.15.0-2.3ubuntu1) ... 90s Selecting previously unselected package libfontconfig1:arm64. 90s Preparing to unpack .../09-libfontconfig1_2.15.0-2.3ubuntu1_arm64.deb ... 90s Unpacking libfontconfig1:arm64 (2.15.0-2.3ubuntu1) ... 90s Selecting previously unselected package libxrender1:arm64. 90s Preparing to unpack .../10-libxrender1_1%3a0.9.12-1_arm64.deb ... 90s Unpacking libxrender1:arm64 (1:0.9.12-1) ... 90s Selecting previously unselected package libxft2:arm64. 90s Preparing to unpack .../11-libxft2_2.3.6-1build1_arm64.deb ... 90s Unpacking libxft2:arm64 (2.3.6-1build1) ... 90s Selecting previously unselected package x11-common. 90s Preparing to unpack .../12-x11-common_1%3a7.7+24ubuntu1_all.deb ... 90s Unpacking x11-common (1:7.7+24ubuntu1) ... 90s Selecting previously unselected package libxss1:arm64. 90s Preparing to unpack .../13-libxss1_1%3a1.2.3-1build3_arm64.deb ... 90s Unpacking libxss1:arm64 (1:1.2.3-1build3) ... 90s Selecting previously unselected package libtk8.6:arm64. 90s Preparing to unpack .../14-libtk8.6_8.6.17-1_arm64.deb ... 90s Unpacking libtk8.6:arm64 (8.6.17-1) ... 90s Selecting previously unselected package tk8.6-blt2.5. 90s Preparing to unpack .../15-tk8.6-blt2.5_2.5.3+dfsg-8_arm64.deb ... 90s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-8) ... 90s Selecting previously unselected package blt. 90s Preparing to unpack .../16-blt_2.5.3+dfsg-8_arm64.deb ... 90s Unpacking blt (2.5.3+dfsg-8) ... 91s Selecting previously unselected package fonts-lyx. 91s Preparing to unpack .../17-fonts-lyx_2.4.4-1_all.deb ... 91s Unpacking fonts-lyx (2.4.4-1) ... 91s Selecting previously unselected package libdeflate0:arm64. 91s Preparing to unpack .../18-libdeflate0_1.23-2_arm64.deb ... 91s Unpacking libdeflate0:arm64 (1.23-2) ... 91s Selecting previously unselected package libgomp1:arm64. 91s Preparing to unpack .../19-libgomp1_15.2.0-7ubuntu1_arm64.deb ... 91s Unpacking libgomp1:arm64 (15.2.0-7ubuntu1) ... 91s Selecting previously unselected package libgraphite2-3:arm64. 91s Preparing to unpack .../20-libgraphite2-3_1.3.14-2ubuntu1_arm64.deb ... 91s Unpacking libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 91s Selecting previously unselected package libharfbuzz0b:arm64. 91s Preparing to unpack .../21-libharfbuzz0b_12.1.0-1_arm64.deb ... 91s Unpacking libharfbuzz0b:arm64 (12.1.0-1) ... 91s Selecting previously unselected package libhtscodecs2:arm64. 91s Preparing to unpack .../22-libhtscodecs2_1.6.1-2_arm64.deb ... 91s Unpacking libhtscodecs2:arm64 (1.6.1-2) ... 91s Selecting previously unselected package libhts3t64:arm64. 91s Preparing to unpack .../23-libhts3t64_1.21+ds-1_arm64.deb ... 91s Unpacking libhts3t64:arm64 (1.21+ds-1) ... 91s Selecting previously unselected package libimagequant0:arm64. 91s Preparing to unpack .../24-libimagequant0_2.18.0-1build1_arm64.deb ... 91s Unpacking libimagequant0:arm64 (2.18.0-1build1) ... 91s Selecting previously unselected package libjpeg-turbo8:arm64. 91s Preparing to unpack .../25-libjpeg-turbo8_2.1.5-4ubuntu2_arm64.deb ... 91s Unpacking libjpeg-turbo8:arm64 (2.1.5-4ubuntu2) ... 91s Selecting previously unselected package libjpeg8:arm64. 91s Preparing to unpack .../26-libjpeg8_8c-2ubuntu11_arm64.deb ... 91s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 91s Selecting previously unselected package liblcms2-2:arm64. 91s Preparing to unpack .../27-liblcms2-2_2.16-2_arm64.deb ... 91s Unpacking liblcms2-2:arm64 (2.16-2) ... 91s Selecting previously unselected package liblerc4:arm64. 91s Preparing to unpack .../28-liblerc4_4.0.0+ds-5ubuntu1_arm64.deb ... 91s Unpacking liblerc4:arm64 (4.0.0+ds-5ubuntu1) ... 91s Selecting previously unselected package libqhull-r8.0:arm64. 91s Preparing to unpack .../29-libqhull-r8.0_2020.2-6build1_arm64.deb ... 91s Unpacking libqhull-r8.0:arm64 (2020.2-6build1) ... 91s Selecting previously unselected package libraqm0:arm64. 91s Preparing to unpack .../30-libraqm0_0.10.3-1_arm64.deb ... 91s Unpacking libraqm0:arm64 (0.10.3-1) ... 91s Selecting previously unselected package libsharpyuv0:arm64. 91s Preparing to unpack .../31-libsharpyuv0_1.5.0-0.1_arm64.deb ... 91s Unpacking libsharpyuv0:arm64 (1.5.0-0.1) ... 91s Selecting previously unselected package libjbig0:arm64. 91s Preparing to unpack .../32-libjbig0_2.1-6.1ubuntu2_arm64.deb ... 91s Unpacking libjbig0:arm64 (2.1-6.1ubuntu2) ... 91s Selecting previously unselected package libwebp7:arm64. 91s Preparing to unpack .../33-libwebp7_1.5.0-0.1_arm64.deb ... 91s Unpacking libwebp7:arm64 (1.5.0-0.1) ... 91s Selecting previously unselected package libtiff6:arm64. 91s Preparing to unpack .../34-libtiff6_4.7.0-3ubuntu3_arm64.deb ... 91s Unpacking libtiff6:arm64 (4.7.0-3ubuntu3) ... 91s Selecting previously unselected package libwebpdemux2:arm64. 91s Preparing to 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.../46-python3-tk_3.13.9-1_arm64.deb ... 92s Unpacking python3-tk:arm64 (3.13.9-1) ... 92s Selecting previously unselected package python3-pil.imagetk:arm64. 92s Preparing to unpack .../47-python3-pil.imagetk_11.3.0-1ubuntu2_arm64.deb ... 92s Unpacking python3-pil.imagetk:arm64 (11.3.0-1ubuntu2) ... 92s Selecting previously unselected package python3-contourpy. 92s Preparing to unpack .../48-python3-contourpy_1.3.1-1build2_arm64.deb ... 92s Unpacking python3-contourpy (1.3.1-1build2) ... 92s Selecting previously unselected package python3-cycler. 92s Preparing to unpack .../49-python3-cycler_0.12.1-2_all.deb ... 92s Unpacking python3-cycler (0.12.1-2) ... 92s Selecting previously unselected package python3-brotli. 92s Preparing to unpack .../50-python3-brotli_1.1.0-2build6_arm64.deb ... 92s Unpacking python3-brotli (1.1.0-2build6) ... 92s Selecting previously unselected package python3-platformdirs. 92s Preparing to unpack .../51-python3-platformdirs_4.3.7-1_all.deb ... 92s Unpacking 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python3-iniconfig (1.1.1-2) ... 97s Setting up libsharpyuv0:arm64 (1.5.0-0.1) ... 97s Setting up liblerc4:arm64 (4.0.0+ds-5ubuntu1) ... 97s Setting up libxrender1:arm64 (1:0.9.12-1) ... 97s Setting up python3-standard-pipes (3.13.0-5) ... 97s Setting up python3-lz4 (4.4.4+dfsg-3) ... 97s Setting up python3-unicodedata2 (16.0.0+ds-1build1) ... 97s Setting up fonts-lyx (2.4.4-1) ... 97s Setting up x11-common (1:7.7+24ubuntu1) ... 97s Setting up libdeflate0:arm64 (1.23-2) ... 97s Setting up libqhull-r8.0:arm64 (2020.2-6build1) ... 97s Setting up python3-pytz (2025.2-4) ... 97s Setting up libgomp1:arm64 (15.2.0-7ubuntu1) ... 97s Setting up python3-click (8.2.0+0.really.8.1.8-1) ... 98s Setting up libjbig0:arm64 (2.1-6.1ubuntu2) ... 98s Setting up python3-platformdirs (4.3.7-1) ... 98s Setting up python3-fs (2.4.16-7) ... 98s Setting up unicode-data (16.0.0-1) ... 98s Setting up python3-decorator (5.2.1-2) ... 98s Setting up libblas3:arm64 (3.12.1-6build1) ... 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-packaging (25.0-1) ... 98s Setting up libzopfli1 (1.0.3-3) ... 98s Setting up python3-brotli (1.1.0-2build6) ... 98s Setting up python3-cycler (0.12.1-2) ... 99s Setting up libimagequant0:arm64 (2.18.0-1build1) ... 99s Setting up fonts-dejavu-mono (2.37-8) ... 99s Setting up python3-kiwisolver (1.4.10~rc0-1) ... 99s Setting up python3-numpy-dev:arm64 (1:2.2.4+ds-1ubuntu1) ... 99s Setting up libtcl8.6:arm64 (8.6.17+dfsg-1) ... 99s Setting up fonts-dejavu-core (2.37-8) ... 99s Setting up libjpeg-turbo8:arm64 (2.1.5-4ubuntu2) ... 99s Setting up libgfortran5:arm64 (15.2.0-7ubuntu1) ... 99s Setting up python3-pluggy (1.6.0-1) ... 99s Setting up libwebp7:arm64 (1.5.0-0.1) ... 99s Setting up libxslt1.1:arm64 (1.1.43-0.3) ... 99s Setting up libhts3t64:arm64 (1.21+ds-1) ... 99s Setting up libopenjp2-7:arm64 (2.5.3-2.1) ... 99s Setting up libharfbuzz0b:arm64 (12.1.0-1) ... 99s Setting up python3-dateutil (2.9.0-4) ... 99s Setting up libxss1:arm64 (1:1.2.3-1build3) ... 99s Setting up python3-mpmath (1.3.0-1) ... 99s Setting up python-matplotlib-data (3.10.7+dfsg1-1) ... 99s Setting up libwebpmux3:arm64 (1.5.0-0.1) ... 99s Setting up python-is-python3 (3.13.3-1) ... 99s Setting up libjpeg8:arm64 (8c-2ubuntu11) ... 99s Setting up python3-sympy (1.13.3-5) ... 106s Setting up liblapack3:arm64 (3.12.1-6build1) ... 106s 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 106s Setting up python3-pysam (0.23.0+ds-1build2) ... 106s Setting up fontconfig-config (2.15.0-2.3ubuntu1) ... 106s Setting up python3-pytest (8.3.5-2) ... 107s Setting up libwebpdemux2:arm64 (1.5.0-0.1) ... 107s Setting up python3-zopfli (0.2.3.post1-1) ... 107s Setting up libraqm0:arm64 (0.10.3-1) ... 107s Setting up python3-numpy (1:2.2.4+ds-1ubuntu1) ... 109s Setting up python3-lxml:arm64 (6.0.1-1build1) ... 109s Setting up libtiff6:arm64 (4.7.0-3ubuntu3) ... 109s Setting up python3-contourpy (1.3.1-1build2) ... 109s Setting up libfontconfig1:arm64 (2.15.0-2.3ubuntu1) ... 109s Setting up libxft2:arm64 (2.3.6-1build1) ... 109s Setting up python3-scipy (1.16.3-1) ... 113s Setting up libtk8.6:arm64 (8.6.17-1) ... 113s Setting up python3-pandas-lib:arm64 (2.3.3+dfsg-1ubuntu1) ... 113s Setting up python3.13-tk (3.13.9-1) ... 113s Setting up python3-pil:arm64 (11.3.0-1ubuntu2) ... 113s Setting up python3-pandas (2.3.3+dfsg-1ubuntu1) ... 118s Setting up tk8.6-blt2.5 (2.5.3+dfsg-8) ... 118s Setting up python3.14-tk (3.14.0-4) ... 118s Setting up blt (2.5.3+dfsg-8) ... 118s Setting up python3-tk:arm64 (3.13.9-1) ... 118s Setting up python3-pil.imagetk:arm64 (11.3.0-1ubuntu2) ... 118s Setting up python3-fonttools (4.57.0-2build1) ... 119s Setting up python3-ufolib2 (0.17.1+dfsg1-1) ... 119s Setting up python3-matplotlib (3.10.7+dfsg1-1) ... 121s Setting up python3-bioframe (0.4.1-2) ... 121s Setting up python3-pairtools (1.1.3-1build2) ... 121s Processing triggers for libc-bin (2.42-0ubuntu3) ... 121s Processing triggers for man-db (2.13.1-1) ... 124s autopkgtest [12:19:58]: test upstream-tests: [----------------------- 124s 124s rm -rf pairtools 124s 124s pytest-3 --ignore=.pc 125s ============================= test session starts ============================== 125s platform linux -- Python 3.13.9, pytest-8.3.5, pluggy-1.6.0 125s rootdir: /tmp/autopkgtest.YC2EyY/build.HZq/src 125s configfile: pytest.ini 125s testpaths: tests 125s plugins: typeguard-4.4.2 125s collected 34 items 125s 133s tests/test_dedup.py . [ 2%] 137s tests/test_filterbycov.py . [ 5%] 138s tests/test_flip.py . [ 8%] 139s tests/test_header.py . [ 11%] 139s tests/test_headerops.py ....... [ 32%] 140s tests/test_markasdup.py . [ 35%] 146s tests/test_merge.py . [ 38%] 148s tests/test_parse.py ... [ 47%] 153s tests/test_parse2.py .... [ 58%] 155s tests/test_restrict.py . [ 61%] 156s tests/test_scaling.py . [ 64%] 165s tests/test_select.py ....... [ 85%] 167s tests/test_sort.py . [ 88%] 168s tests/test_split.py . [ 91%] 176s tests/test_stats.py ... [100%] 176s 176s =============================== warnings summary =============================== 176s ../../../../usr/lib/python3/dist-packages/pairtools/lib/fileio.py:2 176s /usr/lib/python3/dist-packages/pairtools/lib/fileio.py:2: DeprecationWarning: pipes was removed in Python 3.13. Please be aware that you are currently NOT using standard 'pipes', but instead a separately installed 'standard-pipes'. 176s import pipes 176s 176s tests/test_stats.py::test_find_dist_freq_convergence_distance 176s /usr/lib/python3/dist-packages/pairtools/lib/stats.py:466: RuntimeWarning: divide by zero encountered in scalar divide 176s strands: n_cis_pairs / norm_factor 176s 176s tests/test_stats.py::test_find_dist_freq_convergence_distance 176s /usr/lib/python3/dist-packages/pairtools/lib/stats.py:474: RuntimeWarning: divide by zero encountered in scalar divide 176s sum(list(n_cis_pairs_above_convergence_dist.values())) / norm_factor ) 176s 176s tests/test_stats.py::test_find_dist_freq_convergence_distance 176s /usr/lib/python3/dist-packages/pairtools/lib/stats.py:410: RuntimeWarning: invalid value encountered in divide 176s np.abs(dist_freqs_by_strands[strands] - avg_freq_all_strands) 176s 176s tests/test_stats.py::test_find_dist_freq_convergence_distance 176s /usr/lib/python3/dist-packages/pairtools/lib/stats.py:466: RuntimeWarning: invalid value encountered in scalar divide 176s strands: n_cis_pairs / norm_factor 176s 176s tests/test_stats.py::test_find_dist_freq_convergence_distance 176s /usr/lib/python3/dist-packages/pairtools/lib/stats.py:474: RuntimeWarning: invalid value encountered in scalar divide 176s sum(list(n_cis_pairs_above_convergence_dist.values())) / norm_factor ) 176s 176s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 176s ======================= 34 passed, 6 warnings in 51.97s ======================== 176s ALL PASS 176s 176s echo ALL PASS 177s autopkgtest [12:20:51]: test upstream-tests: -----------------------] 177s upstream-tests PASS 177s autopkgtest [12:20:51]: test upstream-tests: - - - - - - - - - - results - - - - - - - - - - 178s autopkgtest [12:20:52]: @@@@@@@@@@@@@@@@@@@@ summary 178s upstream-tests PASS