0s autopkgtest [20:25:24]: starting date and time: 2025-10-20 20:25:24+0000 1s autopkgtest [20:25:25]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 1s autopkgtest [20:25:25]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.umxcid4q/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:pytest,src:python-pluggy --apt-upgrade pairtools --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=pytest/8.4.2-1 python-pluggy/1.6.0-1' -- 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-pairtools-20251020-202524-juju-7f2275-prod-proposed-migration-environment-15-9d87c996-54c4-40c4-8705-51cf4165284b --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/ 4s Creating nova instance adt-resolute-arm64-pairtools-20251020-202524-juju-7f2275-prod-proposed-migration-environment-15-9d87c996-54c4-40c4-8705-51cf4165284b from image adt/ubuntu-resolute-arm64-server-20251020.img (UUID 53f7e888-0b33-40b7-be7f-09b2db152d64)... 60s autopkgtest [20:26:24]: testbed dpkg architecture: arm64 60s autopkgtest [20:26:24]: testbed apt version: 3.1.8ubuntu1 60s autopkgtest [20:26:24]: @@@@@@@@@@@@@@@@@@@@ test bed setup 60s autopkgtest [20:26:24]: testbed release detected to be: None 61s autopkgtest [20:26:25]: updating testbed package index (apt update) 62s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [83.3 kB] 62s 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 Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [646 kB] 62s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [14.3 kB] 62s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [59.3 kB] 62s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [5028 B] 62s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 Packages [115 kB] 62s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/restricted arm64 Packages [43.8 kB] 62s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 Packages [409 kB] 63s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse arm64 Packages [5672 B] 63s Fetched 1382 kB in 1s (1339 kB/s) 64s Reading package lists... 64s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 64s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 65s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 65s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 66s Reading package lists... 66s Reading package lists... 66s Building dependency tree... 66s Reading state information... 66s Calculating upgrade... 67s The following packages will be upgraded: 67s libbrotli1 libjson-c5 python3-inflect python3-oauthlib python3-zipp 67s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 67s Need to get 512 kB of archives. 67s After this operation, 31.7 kB of additional disk space will be used. 67s Get:1 http://ftpmaster.internal/ubuntu resolute/main arm64 libjson-c5 arm64 0.18+ds-1.1 [37.5 kB] 67s Get:2 http://ftpmaster.internal/ubuntu resolute/main arm64 libbrotli1 arm64 1.1.0-2build6 [336 kB] 67s Get:3 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-inflect all 7.5.0-1 [33.9 kB] 67s Get:4 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-oauthlib all 3.3.1-1 [93.5 kB] 67s Get:5 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-zipp all 3.23.0-1 [10.4 kB] 68s dpkg-preconfigure: unable to re-open stdin: No such file or directory 68s Fetched 512 kB in 1s (926 kB/s) 68s (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 ... 83364 files and directories currently installed.) 68s Preparing to unpack .../libjson-c5_0.18+ds-1.1_arm64.deb ... 68s Unpacking libjson-c5:arm64 (0.18+ds-1.1) over (0.18+ds-1) ... 68s Preparing to unpack .../libbrotli1_1.1.0-2build6_arm64.deb ... 68s Unpacking libbrotli1:arm64 (1.1.0-2build6) over (1.1.0-2build5) ... 68s Preparing to unpack .../python3-inflect_7.5.0-1_all.deb ... 68s Unpacking python3-inflect (7.5.0-1) over (7.3.1-2) ... 68s Preparing to unpack .../python3-oauthlib_3.3.1-1_all.deb ... 69s Unpacking python3-oauthlib (3.3.1-1) over (3.2.2-3) ... 69s Preparing to unpack .../python3-zipp_3.23.0-1_all.deb ... 69s Unpacking python3-zipp (3.23.0-1) over (3.21.0-1) ... 69s Setting up libbrotli1:arm64 (1.1.0-2build6) ... 69s Setting up python3-zipp (3.23.0-1) ... 69s Setting up python3-inflect (7.5.0-1) ... 69s Setting up python3-oauthlib (3.3.1-1) ... 70s Setting up libjson-c5:arm64 (0.18+ds-1.1) ... 70s Processing triggers for libc-bin (2.42-0ubuntu3) ... 70s autopkgtest [20:26:34]: upgrading testbed (apt dist-upgrade and autopurge) 70s Reading package lists... 70s Building dependency tree... 70s Reading state information... 71s Calculating upgrade... 71s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 71s Reading package lists... 71s Building dependency tree... 71s Reading state information... 72s Solving dependencies... 73s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 75s autopkgtest [20:26:39]: testbed running kernel: Linux 6.17.0-5-generic #5-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 22 09:50:31 UTC 2025 75s autopkgtest [20:26:39]: @@@@@@@@@@@@@@@@@@@@ apt-source pairtools 78s Get:1 http://ftpmaster.internal/ubuntu resolute/universe pairtools 1.1.3-1build1 (dsc) [2493 B] 78s Get:2 http://ftpmaster.internal/ubuntu resolute/universe pairtools 1.1.3-1build1 (tar) [1420 kB] 78s Get:3 http://ftpmaster.internal/ubuntu resolute/universe pairtools 1.1.3-1build1 (diff) [7720 B] 78s gpgv: Signature made Tue Mar 4 15:54:00 2025 UTC 78s gpgv: using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2 78s gpgv: Can't check signature: No public key 78s dpkg-source: warning: cannot verify inline signature for ./pairtools_1.1.3-1build1.dsc: no acceptable signature found 79s autopkgtest [20:26:43]: testing package pairtools version 1.1.3-1build1 79s autopkgtest [20:26:43]: build not needed 80s autopkgtest [20:26:44]: test upstream-tests: preparing testbed 80s Reading package lists... 80s Building dependency tree... 80s Reading state information... 81s Solving dependencies... 81s The following NEW packages will be installed: 81s blt fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-lyx libblas3 81s libdeflate0 libfontconfig1 libgfortran5 libgomp1 libgraphite2-3 81s libharfbuzz0b libhts3t64 libhtscodecs2 libimagequant0 libjbig0 81s libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui liblapack3 liblcms2-2 81s liblerc4 libopenjp2-7 libqhull-r8.0 libraqm0 libsharpyuv0 libtcl8.6 libtiff6 81s libtk8.6 libwebp7 libwebpdemux2 libwebpmux3 libxft2 libxrender1 libxslt1.1 81s libxss1 libzopfli1 python-is-python3 python-matplotlib-data python3-bioframe 81s python3-brotli python3-click python3-contourpy python3-cycler 81s python3-dateutil python3-decorator python3-fonttools python3-fs 81s python3-iniconfig python3-kiwisolver python3-lxml python3-lz4 81s python3-matplotlib python3-mpmath python3-numpy python3-numpy-dev 81s python3-packaging python3-pairtools python3-pandas python3-pandas-lib 81s python3-pil python3-pil.imagetk python3-platformdirs python3-pluggy 81s python3-pysam python3-pytest python3-pytz python3-scipy 81s python3-standard-pipes python3-sympy python3-tk python3-ufolib2 81s python3-unicodedata2 python3-zopfli python3.13-tk tk8.6-blt2.5 unicode-data 81s x11-common 81s 0 upgraded, 79 newly installed, 0 to remove and 0 not upgraded. 81s Need to get 82.8 MB of archives. 81s After this operation, 374 MB of additional disk space will be used. 81s Get:1 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-numpy-dev arm64 1:2.2.4+ds-1ubuntu1 [146 kB] 82s Get:2 http://ftpmaster.internal/ubuntu resolute/main arm64 libblas3 arm64 3.12.1-6build1 [186 kB] 82s Get:3 http://ftpmaster.internal/ubuntu resolute/main arm64 libgfortran5 arm64 15.2.0-5ubuntu1 [450 kB] 82s Get:4 http://ftpmaster.internal/ubuntu resolute/main arm64 liblapack3 arm64 3.12.1-6build1 [2340 kB] 82s Get:5 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-numpy arm64 1:2.2.4+ds-1ubuntu1 [3986 kB] 82s Get:6 http://ftpmaster.internal/ubuntu resolute/main arm64 libtcl8.6 arm64 8.6.17+dfsg-1 [1024 kB] 83s Get:7 http://ftpmaster.internal/ubuntu resolute/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 83s Get:8 http://ftpmaster.internal/ubuntu resolute/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 83s Get:9 http://ftpmaster.internal/ubuntu resolute/main arm64 fontconfig-config arm64 2.15.0-2.3ubuntu1 [38.1 kB] 83s Get:10 http://ftpmaster.internal/ubuntu resolute/main arm64 libfontconfig1 arm64 2.15.0-2.3ubuntu1 [144 kB] 83s Get:11 http://ftpmaster.internal/ubuntu resolute/main arm64 libxrender1 arm64 1:0.9.12-1 [19.5 kB] 83s Get:12 http://ftpmaster.internal/ubuntu resolute/main arm64 libxft2 arm64 2.3.6-1build1 [44.1 kB] 83s Get:13 http://ftpmaster.internal/ubuntu resolute/main arm64 x11-common all 1:7.7+24ubuntu1 [22.4 kB] 83s Get:14 http://ftpmaster.internal/ubuntu resolute/main arm64 libxss1 arm64 1:1.2.3-1build3 [7244 B] 83s Get:15 http://ftpmaster.internal/ubuntu resolute/main arm64 libtk8.6 arm64 8.6.17-1 [811 kB] 83s Get:16 http://ftpmaster.internal/ubuntu resolute/main arm64 tk8.6-blt2.5 arm64 2.5.3+dfsg-8 [624 kB] 83s Get:17 http://ftpmaster.internal/ubuntu resolute/main arm64 blt arm64 2.5.3+dfsg-8 [4824 B] 83s Get:18 http://ftpmaster.internal/ubuntu resolute/universe arm64 fonts-lyx all 2.4.4-1 [171 kB] 83s Get:19 http://ftpmaster.internal/ubuntu resolute/main arm64 libdeflate0 arm64 1.23-2 [46.4 kB] 83s Get:20 http://ftpmaster.internal/ubuntu resolute/main arm64 libgomp1 arm64 15.2.0-5ubuntu1 [148 kB] 83s Get:21 http://ftpmaster.internal/ubuntu resolute/main arm64 libgraphite2-3 arm64 1.3.14-2ubuntu1 [70.6 kB] 83s Get:22 http://ftpmaster.internal/ubuntu resolute/main arm64 libharfbuzz0b arm64 12.1.0-1 [523 kB] 83s Get:23 http://ftpmaster.internal/ubuntu resolute/universe arm64 libhtscodecs2 arm64 1.6.1-2 [82.7 kB] 83s Get:24 http://ftpmaster.internal/ubuntu resolute/universe arm64 libhts3t64 arm64 1.21+ds-1 [441 kB] 83s Get:25 http://ftpmaster.internal/ubuntu resolute/main arm64 libimagequant0 arm64 2.18.0-1build1 [37.1 kB] 83s Get:26 http://ftpmaster.internal/ubuntu resolute/main arm64 libjpeg-turbo8 arm64 2.1.5-4ubuntu2 [165 kB] 83s Get:27 http://ftpmaster.internal/ubuntu resolute/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 83s Get:28 http://ftpmaster.internal/ubuntu resolute/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 83s Get:29 http://ftpmaster.internal/ubuntu resolute/universe arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 83s Get:30 http://ftpmaster.internal/ubuntu resolute/main arm64 liblcms2-2 arm64 2.16-2 [170 kB] 83s Get:31 http://ftpmaster.internal/ubuntu resolute/main arm64 liblerc4 arm64 4.0.0+ds-5ubuntu1 [167 kB] 83s Get:32 http://ftpmaster.internal/ubuntu resolute/universe arm64 libqhull-r8.0 arm64 2020.2-6build1 [189 kB] 83s Get:33 http://ftpmaster.internal/ubuntu resolute/main arm64 libraqm0 arm64 0.10.3-1 [15.0 kB] 83s Get:34 http://ftpmaster.internal/ubuntu resolute/main arm64 libsharpyuv0 arm64 1.5.0-0.1 [16.9 kB] 83s Get:35 http://ftpmaster.internal/ubuntu resolute/main arm64 libjbig0 arm64 2.1-6.1ubuntu2 [29.3 kB] 83s Get:36 http://ftpmaster.internal/ubuntu resolute/main arm64 libwebp7 arm64 1.5.0-0.1 [194 kB] 83s Get:37 http://ftpmaster.internal/ubuntu resolute/main arm64 libtiff6 arm64 4.7.0-3ubuntu3 [196 kB] 83s Get:38 http://ftpmaster.internal/ubuntu resolute/main arm64 libwebpdemux2 arm64 1.5.0-0.1 [12.5 kB] 83s Get:39 http://ftpmaster.internal/ubuntu resolute/main arm64 libwebpmux3 arm64 1.5.0-0.1 [25.4 kB] 83s Get:40 http://ftpmaster.internal/ubuntu resolute/main arm64 libxslt1.1 arm64 1.1.43-0.1 [171 kB] 83s Get:41 http://ftpmaster.internal/ubuntu resolute/universe arm64 libzopfli1 arm64 1.0.3-3 [108 kB] 83s Get:42 http://ftpmaster.internal/ubuntu resolute/main arm64 python-is-python3 all 3.13.3-1 [2768 B] 83s Get:43 http://ftpmaster.internal/ubuntu resolute/universe arm64 python-matplotlib-data all 3.10.1+dfsg1-4 [2930 kB] 83s Get:44 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-dateutil all 2.9.0-4 [80.3 kB] 83s Get:45 http://ftpmaster.internal/ubuntu resolute/main arm64 libopenjp2-7 arm64 2.5.3-2.1 [179 kB] 83s Get:46 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-pil arm64 11.3.0-1ubuntu1 [483 kB] 83s Get:47 http://ftpmaster.internal/ubuntu resolute/main arm64 python3.13-tk arm64 3.13.7-1 [108 kB] 83s Get:48 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-tk arm64 3.13.5-1 [9916 B] 83s Get:49 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-pil.imagetk arm64 11.3.0-1ubuntu1 [9878 B] 83s Get:50 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-contourpy arm64 1.3.1-1build1 [182 kB] 83s Get:51 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-cycler all 0.12.1-1 [9716 B] 83s Get:52 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-brotli arm64 1.1.0-2build6 [343 kB] 83s Get:53 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-platformdirs all 4.3.7-1 [16.9 kB] 83s Get:54 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-fs all 2.4.16-7 [90.8 kB] 83s Get:55 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-lxml arm64 6.0.1-1 [1428 kB] 83s Get:56 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-lz4 arm64 4.4.0+dfsg-2 [27.1 kB] 83s Get:57 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-decorator all 5.2.1-2 [28.1 kB] 83s Get:58 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-scipy arm64 1.15.3-1 [15.8 MB] 84s Get:59 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-mpmath all 1.3.0-1 [425 kB] 84s Get:60 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-sympy all 1.13.3-5 [4229 kB] 84s Get:61 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-ufolib2 all 0.17.1+dfsg1-1 [33.5 kB] 84s Get:62 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-unicodedata2 arm64 16.0.0+ds-1build1 [398 kB] 84s Get:63 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-zopfli arm64 0.2.3.post1-1 [10.7 kB] 84s Get:64 http://ftpmaster.internal/ubuntu resolute/universe arm64 unicode-data all 16.0.0-1 [9513 kB] 84s Get:65 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-fonttools arm64 4.57.0-1 [1453 kB] 84s Get:66 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-kiwisolver arm64 1.4.7-3build2 [60.7 kB] 84s Get:67 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-packaging all 25.0-1 [52.8 kB] 84s Get:68 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-matplotlib arm64 3.10.1+dfsg1-4 [18.0 MB] 85s Get:69 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-pytz all 2025.2-3 [163 kB] 85s Get:70 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-pandas-lib arm64 2.2.3+dfsg-9 [4579 kB] 85s Get:71 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-pandas all 2.2.3+dfsg-9 [3112 kB] 85s Get:72 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-bioframe all 0.4.1-2 [76.3 kB] 85s Get:73 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-click all 8.2.0+0.really.8.1.8-1 [80.0 kB] 85s Get:74 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-iniconfig all 1.1.1-2 [6024 B] 85s Get:75 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-standard-pipes all 3.13.0-5 [7414 B] 85s Get:76 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-pysam arm64 0.23.0+ds-1build1 [3621 kB] 85s Get:77 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-pairtools arm64 1.1.3-1build1 [208 kB] 85s Get:78 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 python3-pluggy all 1.6.0-1 [21.0 kB] 85s Get:79 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 python3-pytest all 8.4.2-1 [268 kB] 86s Fetched 82.8 MB in 4s (20.5 MB/s) 86s Selecting previously unselected package python3-numpy-dev:arm64. 86s (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 ... 83374 files and directories currently installed.) 86s Preparing to unpack .../00-python3-numpy-dev_1%3a2.2.4+ds-1ubuntu1_arm64.deb ... 86s Unpacking python3-numpy-dev:arm64 (1:2.2.4+ds-1ubuntu1) ... 86s Selecting previously unselected package libblas3:arm64. 86s Preparing to unpack .../01-libblas3_3.12.1-6build1_arm64.deb ... 86s Unpacking libblas3:arm64 (3.12.1-6build1) ... 86s Selecting previously unselected package libgfortran5:arm64. 86s Preparing to unpack .../02-libgfortran5_15.2.0-5ubuntu1_arm64.deb ... 86s Unpacking libgfortran5:arm64 (15.2.0-5ubuntu1) ... 86s Selecting previously unselected package liblapack3:arm64. 86s Preparing to unpack .../03-liblapack3_3.12.1-6build1_arm64.deb ... 86s Unpacking liblapack3:arm64 (3.12.1-6build1) ... 86s Selecting previously unselected package python3-numpy. 86s Preparing to unpack .../04-python3-numpy_1%3a2.2.4+ds-1ubuntu1_arm64.deb ... 86s Unpacking python3-numpy (1:2.2.4+ds-1ubuntu1) ... 86s Selecting previously unselected package libtcl8.6:arm64. 86s Preparing to unpack .../05-libtcl8.6_8.6.17+dfsg-1_arm64.deb ... 86s Unpacking libtcl8.6:arm64 (8.6.17+dfsg-1) ... 86s Selecting previously unselected package fonts-dejavu-mono. 86s Preparing to unpack .../06-fonts-dejavu-mono_2.37-8_all.deb ... 86s Unpacking fonts-dejavu-mono (2.37-8) ... 86s Selecting previously unselected package fonts-dejavu-core. 86s Preparing to unpack .../07-fonts-dejavu-core_2.37-8_all.deb ... 86s Unpacking fonts-dejavu-core (2.37-8) ... 86s Selecting previously unselected package fontconfig-config. 86s Preparing to unpack .../08-fontconfig-config_2.15.0-2.3ubuntu1_arm64.deb ... 87s Unpacking fontconfig-config (2.15.0-2.3ubuntu1) ... 87s Selecting previously unselected package libfontconfig1:arm64. 87s Preparing to unpack .../09-libfontconfig1_2.15.0-2.3ubuntu1_arm64.deb ... 87s Unpacking libfontconfig1:arm64 (2.15.0-2.3ubuntu1) ... 87s Selecting previously unselected package libxrender1:arm64. 87s Preparing to unpack .../10-libxrender1_1%3a0.9.12-1_arm64.deb ... 87s Unpacking libxrender1:arm64 (1:0.9.12-1) ... 87s Selecting previously unselected package libxft2:arm64. 87s Preparing to unpack .../11-libxft2_2.3.6-1build1_arm64.deb ... 87s Unpacking libxft2:arm64 (2.3.6-1build1) ... 87s Selecting previously unselected package x11-common. 87s Preparing to unpack .../12-x11-common_1%3a7.7+24ubuntu1_all.deb ... 87s Unpacking x11-common (1:7.7+24ubuntu1) ... 87s Selecting previously unselected package libxss1:arm64. 87s Preparing to unpack .../13-libxss1_1%3a1.2.3-1build3_arm64.deb ... 87s Unpacking libxss1:arm64 (1:1.2.3-1build3) ... 87s Selecting previously unselected package libtk8.6:arm64. 87s Preparing to unpack .../14-libtk8.6_8.6.17-1_arm64.deb ... 87s Unpacking libtk8.6:arm64 (8.6.17-1) ... 87s Selecting previously unselected package tk8.6-blt2.5. 87s Preparing to unpack .../15-tk8.6-blt2.5_2.5.3+dfsg-8_arm64.deb ... 87s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-8) ... 87s Selecting previously unselected package blt. 87s Preparing to unpack .../16-blt_2.5.3+dfsg-8_arm64.deb ... 87s Unpacking blt (2.5.3+dfsg-8) ... 87s Selecting previously unselected package fonts-lyx. 87s Preparing to unpack .../17-fonts-lyx_2.4.4-1_all.deb ... 87s Unpacking fonts-lyx (2.4.4-1) ... 87s Selecting previously unselected package libdeflate0:arm64. 87s Preparing to unpack .../18-libdeflate0_1.23-2_arm64.deb ... 87s Unpacking libdeflate0:arm64 (1.23-2) ... 87s Selecting previously unselected package libgomp1:arm64. 88s Preparing to unpack .../19-libgomp1_15.2.0-5ubuntu1_arm64.deb ... 88s Unpacking libgomp1:arm64 (15.2.0-5ubuntu1) ... 88s Selecting previously unselected package libgraphite2-3:arm64. 88s Preparing to unpack .../20-libgraphite2-3_1.3.14-2ubuntu1_arm64.deb ... 88s Unpacking libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 88s Selecting previously unselected package libharfbuzz0b:arm64. 88s Preparing to unpack .../21-libharfbuzz0b_12.1.0-1_arm64.deb ... 88s Unpacking libharfbuzz0b:arm64 (12.1.0-1) ... 88s Selecting previously unselected package libhtscodecs2:arm64. 88s Preparing to unpack .../22-libhtscodecs2_1.6.1-2_arm64.deb ... 88s Unpacking libhtscodecs2:arm64 (1.6.1-2) ... 88s Selecting previously unselected package libhts3t64:arm64. 88s Preparing to unpack .../23-libhts3t64_1.21+ds-1_arm64.deb ... 88s Unpacking libhts3t64:arm64 (1.21+ds-1) ... 88s Selecting previously unselected package libimagequant0:arm64. 88s Preparing to unpack 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python3-decorator (5.2.1-2) ... 95s Setting up libblas3:arm64 (3.12.1-6build1) ... 95s 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 95s Setting up python3-packaging (25.0-1) ... 95s Setting up libzopfli1 (1.0.3-3) ... 95s Setting up python3-brotli (1.1.0-2build6) ... 95s Setting up python3-cycler (0.12.1-1) ... 95s Setting up libimagequant0:arm64 (2.18.0-1build1) ... 95s Setting up fonts-dejavu-mono (2.37-8) ... 95s Setting up python3-kiwisolver (1.4.7-3build2) ... 96s Setting up python3-numpy-dev:arm64 (1:2.2.4+ds-1ubuntu1) ... 96s Setting up libtcl8.6:arm64 (8.6.17+dfsg-1) ... 96s Setting up fonts-dejavu-core (2.37-8) ... 96s Setting up libjpeg-turbo8:arm64 (2.1.5-4ubuntu2) ... 96s Setting up libgfortran5:arm64 (15.2.0-5ubuntu1) ... 96s Setting up python3-pluggy (1.6.0-1) ... 96s Setting up libwebp7:arm64 (1.5.0-0.1) ... 96s Setting up libxslt1.1:arm64 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python3-pil.imagetk:arm64 (11.3.0-1ubuntu1) ... 116s Setting up python3-fonttools (4.57.0-1) ... 117s Setting up python3-ufolib2 (0.17.1+dfsg1-1) ... 117s Setting up python3-matplotlib (3.10.1+dfsg1-4) ... 119s Setting up python3-bioframe (0.4.1-2) ... 119s Setting up python3-pairtools (1.1.3-1build1) ... 119s Processing triggers for libc-bin (2.42-0ubuntu3) ... 119s Processing triggers for man-db (2.13.1-1) ... 121s autopkgtest [20:27:25]: test upstream-tests: [----------------------- 121s 121s rm -rf pairtools 121s 121s pytest-3 --ignore=.pc 123s ============================= test session starts ============================== 123s platform linux -- Python 3.13.7, pytest-8.4.2, pluggy-1.6.0 123s rootdir: /tmp/autopkgtest.fZJPfd/build.nJd/src 123s configfile: pytest.ini 123s testpaths: tests 123s plugins: typeguard-4.4.2 123s collected 34 items 123s 130s tests/test_dedup.py . [ 2%] 134s tests/test_filterbycov.py . [ 5%] 135s tests/test_flip.py . [ 8%] 136s tests/test_header.py . [ 11%] 136s tests/test_headerops.py ....... [ 32%] 138s tests/test_markasdup.py . [ 35%] 143s tests/test_merge.py . [ 38%] 146s tests/test_parse.py ... [ 47%] 151s tests/test_parse2.py .... [ 58%] 153s tests/test_restrict.py . [ 61%] 154s tests/test_scaling.py . [ 64%] 164s tests/test_select.py ....... [ 85%] 165s tests/test_sort.py . [ 88%] 167s tests/test_split.py . [ 91%] 175s tests/test_stats.py ... [100%] 175s 175s =============================== warnings summary =============================== 175s ../../../../usr/lib/python3/dist-packages/pairtools/lib/fileio.py:2 175s /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'. 175s import pipes 175s 175s tests/test_stats.py::test_find_dist_freq_convergence_distance 175s /usr/lib/python3/dist-packages/pairtools/lib/stats.py:466: RuntimeWarning: divide by zero encountered in scalar divide 175s strands: n_cis_pairs / norm_factor 175s 175s tests/test_stats.py::test_find_dist_freq_convergence_distance 175s /usr/lib/python3/dist-packages/pairtools/lib/stats.py:474: RuntimeWarning: divide by zero encountered in scalar divide 175s sum(list(n_cis_pairs_above_convergence_dist.values())) / norm_factor ) 175s 175s tests/test_stats.py::test_find_dist_freq_convergence_distance 175s /usr/lib/python3/dist-packages/pairtools/lib/stats.py:410: RuntimeWarning: invalid value encountered in divide 175s np.abs(dist_freqs_by_strands[strands] - avg_freq_all_strands) 175s 175s tests/test_stats.py::test_find_dist_freq_convergence_distance 175s /usr/lib/python3/dist-packages/pairtools/lib/stats.py:466: RuntimeWarning: invalid value encountered in scalar divide 175s strands: n_cis_pairs / norm_factor 175s 175s tests/test_stats.py::test_find_dist_freq_convergence_distance 175s /usr/lib/python3/dist-packages/pairtools/lib/stats.py:474: RuntimeWarning: invalid value encountered in scalar divide 175s sum(list(n_cis_pairs_above_convergence_dist.values())) / norm_factor ) 175s 175s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 175s ======================= 34 passed, 6 warnings in 53.28s ======================== 175s ALL PASS 175s 175s echo ALL PASS 176s autopkgtest [20:28:20]: test upstream-tests: -----------------------] 176s autopkgtest [20:28:20]: test upstream-tests: - - - - - - - - - - results - - - - - - - - - - 176s upstream-tests PASS 177s autopkgtest [20:28:21]: @@@@@@@@@@@@@@@@@@@@ summary 177s upstream-tests PASS