0s autopkgtest [06:00:38]: starting date and time: 2025-10-24 06:00:38+0000 0s autopkgtest [06:00:38]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [06:00:38]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.c65cog5m/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-cpu2-ram4-disk20-amd64 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@sto01-9.secgroup --name adt-resolute-amd64-pairtools-20251024-060038-juju-7f2275-prod-proposed-migration-environment-2-c85f862d-b48d-44b1-9eec-2729e9c8e66f --image adt/ubuntu-resolute-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-autopkgtest-workers-amd64 -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 4s Creating nova instance adt-resolute-amd64-pairtools-20251024-060038-juju-7f2275-prod-proposed-migration-environment-2-c85f862d-b48d-44b1-9eec-2729e9c8e66f from image adt/ubuntu-resolute-amd64-server-20251024.img (UUID 310022dd-8dd9-48c7-a816-c2d8419ef402)... 36s autopkgtest [06:01:14]: testbed dpkg architecture: amd64 36s autopkgtest [06:01:14]: testbed apt version: 3.1.8ubuntu1 36s autopkgtest [06:01:14]: @@@@@@@@@@@@@@@@@@@@ test bed setup 37s autopkgtest [06:01:15]: testbed release detected to be: None 37s autopkgtest [06:01:15]: updating testbed package index (apt update) 37s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [87.8 kB] 37s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 37s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 38s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 38s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [533 kB] 38s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [15.0 kB] 38s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [61.6 kB] 38s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [5028 B] 38s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 Packages [147 kB] 38s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/main i386 Packages [97.2 kB] 38s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 c-n-f Metadata [3040 B] 38s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/restricted i386 Packages [3208 B] 38s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/restricted amd64 Packages [28.0 kB] 38s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/restricted amd64 c-n-f Metadata [336 B] 38s Get:15 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 Packages [385 kB] 38s Get:16 http://ftpmaster.internal/ubuntu resolute-proposed/universe i386 Packages [145 kB] 38s Get:17 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 c-n-f Metadata [10.8 kB] 38s Get:18 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 Packages [6744 B] 38s Get:19 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse i386 Packages [3156 B] 38s Get:20 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 c-n-f Metadata [492 B] 39s Fetched 1532 kB in 1s (1873 kB/s) 39s Reading package lists... 40s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 40s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 40s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 40s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 40s Reading package lists... 40s Reading package lists... 40s Building dependency tree... 40s Reading state information... 41s Calculating upgrade... 41s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 41s autopkgtest [06:01:19]: upgrading testbed (apt dist-upgrade and autopurge) 41s Reading package lists... 41s Building dependency tree... 41s Reading state information... 41s Calculating upgrade... 41s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 41s Reading package lists... 41s Building dependency tree... 41s Reading state information... 41s Solving dependencies... 41s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 43s autopkgtest [06:01:21]: testbed running kernel: Linux 6.17.0-5-generic #5-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 22 10:00:33 UTC 2025 44s autopkgtest [06:01:22]: @@@@@@@@@@@@@@@@@@@@ apt-source pairtools 45s Get:1 http://ftpmaster.internal/ubuntu resolute/universe pairtools 1.1.3-1build2 (dsc) [2493 B] 45s Get:2 http://ftpmaster.internal/ubuntu resolute/universe pairtools 1.1.3-1build2 (tar) [1420 kB] 45s Get:3 http://ftpmaster.internal/ubuntu resolute/universe pairtools 1.1.3-1build2 (diff) [7752 B] 46s gpgv: Signature made Tue Oct 21 10:20:57 2025 UTC 46s gpgv: using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2 46s gpgv: Can't check signature: No public key 46s dpkg-source: warning: cannot verify inline signature for ./pairtools_1.1.3-1build2.dsc: no acceptable signature found 46s autopkgtest [06:01:24]: testing package pairtools version 1.1.3-1build2 46s autopkgtest [06:01:24]: build not needed 47s autopkgtest [06:01:25]: test upstream-tests: preparing testbed 47s Reading package lists... 47s Building dependency tree... 47s Reading state information... 47s Solving dependencies... 47s The following NEW packages will be installed: 47s blt fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-lyx libblas3 47s libdeflate0 libfontconfig1 libgfortran5 libgomp1 libgraphite2-3 47s libharfbuzz0b libhts3t64 libhtscodecs2 libimagequant0 libjbig0 47s libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui liblapack3 liblcms2-2 47s liblerc4 libopenjp2-7 libqhull-r8.0 libraqm0 libsharpyuv0 libtcl8.6 libtiff6 47s libtk8.6 libwebp7 libwebpdemux2 libwebpmux3 libxft2 libxrender1 libxslt1.1 47s libxss1 libzopfli1 python-is-python3 python-matplotlib-data python3-bioframe 47s python3-brotli python3-click python3-contourpy python3-cycler 47s python3-dateutil python3-decorator python3-fonttools python3-fs 47s python3-iniconfig python3-kiwisolver python3-lxml python3-lz4 47s python3-matplotlib python3-mpmath python3-numpy python3-numpy-dev 47s python3-packaging python3-pairtools python3-pandas python3-pandas-lib 47s python3-pil python3-pil.imagetk python3-platformdirs python3-pluggy 47s python3-pysam python3-pytest python3-pytz python3-scipy 47s python3-standard-pipes python3-sympy python3-tk python3-ufolib2 47s python3-unicodedata2 python3-zopfli python3.13-tk tk8.6-blt2.5 unicode-data 47s x11-common 47s 0 upgraded, 79 newly installed, 0 to remove and 0 not upgraded. 47s Need to get 94.7 MB of archives. 47s After this operation, 462 MB of additional disk space will be used. 47s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-numpy-dev amd64 1:2.2.4+ds-1ubuntu1 [147 kB] 47s Get:2 http://ftpmaster.internal/ubuntu resolute/main amd64 libblas3 amd64 3.12.1-6build1 [263 kB] 47s Get:3 http://ftpmaster.internal/ubuntu resolute/main amd64 libgfortran5 amd64 15.2.0-5ubuntu1 [939 kB] 48s Get:4 http://ftpmaster.internal/ubuntu resolute/main amd64 liblapack3 amd64 3.12.1-6build1 [2762 kB] 48s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-numpy amd64 1:2.2.4+ds-1ubuntu1 [5377 kB] 49s Get:6 http://ftpmaster.internal/ubuntu resolute/main amd64 libtcl8.6 amd64 8.6.17+dfsg-1 [1036 kB] 49s Get:7 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB] 49s Get:8 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-dejavu-core all 2.37-8 [835 kB] 49s Get:9 http://ftpmaster.internal/ubuntu resolute/main amd64 fontconfig-config amd64 2.15.0-2.3ubuntu1 [38.0 kB] 49s Get:10 http://ftpmaster.internal/ubuntu resolute/main amd64 libfontconfig1 amd64 2.15.0-2.3ubuntu1 [141 kB] 49s Get:11 http://ftpmaster.internal/ubuntu resolute/main amd64 libxrender1 amd64 1:0.9.12-1 [19.8 kB] 49s Get:12 http://ftpmaster.internal/ubuntu resolute/main amd64 libxft2 amd64 2.3.6-1build1 [45.3 kB] 49s Get:13 http://ftpmaster.internal/ubuntu resolute/main amd64 x11-common all 1:7.7+24ubuntu1 [22.4 kB] 49s Get:14 http://ftpmaster.internal/ubuntu resolute/main amd64 libxss1 amd64 1:1.2.3-1build3 [7204 B] 49s Get:15 http://ftpmaster.internal/ubuntu resolute/main amd64 libtk8.6 amd64 8.6.17-1 [823 kB] 49s Get:16 http://ftpmaster.internal/ubuntu resolute/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-8 [694 kB] 49s Get:17 http://ftpmaster.internal/ubuntu resolute/main amd64 blt amd64 2.5.3+dfsg-8 [4824 B] 49s Get:18 http://ftpmaster.internal/ubuntu resolute/universe amd64 fonts-lyx all 2.4.4-1 [171 kB] 49s Get:19 http://ftpmaster.internal/ubuntu resolute/main amd64 libdeflate0 amd64 1.23-2 [49.9 kB] 49s Get:20 http://ftpmaster.internal/ubuntu resolute/main amd64 libgomp1 amd64 15.2.0-5ubuntu1 [151 kB] 49s Get:21 http://ftpmaster.internal/ubuntu resolute/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB] 49s Get:22 http://ftpmaster.internal/ubuntu resolute/main amd64 libharfbuzz0b amd64 12.1.0-1 [535 kB] 49s Get:23 http://ftpmaster.internal/ubuntu resolute/universe amd64 libhtscodecs2 amd64 1.6.1-2 [132 kB] 49s Get:24 http://ftpmaster.internal/ubuntu resolute/universe amd64 libhts3t64 amd64 1.21+ds-1 [514 kB] 49s Get:25 http://ftpmaster.internal/ubuntu resolute/main amd64 libimagequant0 amd64 2.18.0-1build1 [36.3 kB] 49s Get:26 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg-turbo8 amd64 2.1.5-4ubuntu2 [152 kB] 49s Get:27 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 49s Get:28 http://ftpmaster.internal/ubuntu resolute/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 49s Get:29 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 49s Get:30 http://ftpmaster.internal/ubuntu resolute/main amd64 liblcms2-2 amd64 2.16-2 [212 kB] 49s Get:31 http://ftpmaster.internal/ubuntu resolute/main amd64 liblerc4 amd64 4.0.0+ds-5ubuntu1 [271 kB] 49s Get:32 http://ftpmaster.internal/ubuntu resolute/universe amd64 libqhull-r8.0 amd64 2020.2-6build1 [193 kB] 49s Get:33 http://ftpmaster.internal/ubuntu resolute/main amd64 libraqm0 amd64 0.10.3-1 [15.4 kB] 49s Get:34 http://ftpmaster.internal/ubuntu resolute/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [25.9 kB] 49s Get:35 http://ftpmaster.internal/ubuntu resolute/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB] 49s Get:36 http://ftpmaster.internal/ubuntu resolute/main amd64 libwebp7 amd64 1.5.0-0.1 [378 kB] 49s Get:37 http://ftpmaster.internal/ubuntu resolute/main amd64 libtiff6 amd64 4.7.0-3ubuntu3 [209 kB] 49s Get:38 http://ftpmaster.internal/ubuntu resolute/main amd64 libwebpdemux2 amd64 1.5.0-0.1 [13.0 kB] 49s Get:39 http://ftpmaster.internal/ubuntu resolute/main amd64 libwebpmux3 amd64 1.5.0-0.1 [27.6 kB] 49s Get:40 http://ftpmaster.internal/ubuntu resolute/main amd64 libxslt1.1 amd64 1.1.43-0.1 [172 kB] 49s Get:41 http://ftpmaster.internal/ubuntu resolute/universe amd64 libzopfli1 amd64 1.0.3-3 [141 kB] 49s Get:42 http://ftpmaster.internal/ubuntu resolute/main amd64 python-is-python3 all 3.13.3-1 [2768 B] 49s Get:43 http://ftpmaster.internal/ubuntu resolute/universe amd64 python-matplotlib-data all 3.10.1+dfsg1-4 [2930 kB] 50s Get:44 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-dateutil all 2.9.0-4 [80.3 kB] 50s Get:45 http://ftpmaster.internal/ubuntu resolute/main amd64 libopenjp2-7 amd64 2.5.3-2.1 [188 kB] 50s Get:46 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-pil amd64 11.3.0-1ubuntu2 [504 kB] 50s Get:47 http://ftpmaster.internal/ubuntu resolute/main amd64 python3.13-tk amd64 3.13.9-1 [108 kB] 50s Get:48 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-tk amd64 3.13.5-1 [9916 B] 50s Get:49 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pil.imagetk amd64 11.3.0-1ubuntu2 [9804 B] 50s Get:50 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-contourpy amd64 1.3.1-1build1 [218 kB] 50s Get:51 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-cycler all 0.12.1-2 [9850 B] 50s Get:52 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-brotli amd64 1.1.0-2build6 [340 kB] 50s Get:53 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-platformdirs all 4.3.7-1 [16.9 kB] 50s Get:54 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-fs all 2.4.16-7 [90.8 kB] 50s Get:55 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-lxml amd64 6.0.1-1build1 [2336 kB] 50s Get:56 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-lz4 amd64 4.4.4+dfsg-3 [27.5 kB] 50s Get:57 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-decorator all 5.2.1-2 [28.1 kB] 50s Get:58 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-scipy amd64 1.15.3-1ubuntu1 [20.3 MB] 52s Get:59 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-mpmath all 1.3.0-1 [425 kB] 52s Get:60 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-sympy all 1.13.3-5 [4229 kB] 52s Get:61 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-ufolib2 all 0.17.1+dfsg1-1 [33.5 kB] 52s Get:62 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-unicodedata2 amd64 16.0.0+ds-1build1 [400 kB] 52s Get:63 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-zopfli amd64 0.2.3.post1-1 [10.8 kB] 52s Get:64 http://ftpmaster.internal/ubuntu resolute/universe amd64 unicode-data all 16.0.0-1 [9513 kB] 52s Get:65 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-fonttools amd64 4.57.0-2build1 [1731 kB] 52s Get:66 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-kiwisolver amd64 1.4.7-3build2 [63.0 kB] 52s Get:67 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-packaging all 25.0-1 [52.8 kB] 52s Get:68 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-matplotlib amd64 3.10.1+dfsg1-4 [18.0 MB] 53s Get:69 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-pytz all 2025.2-4 [32.3 kB] 53s Get:70 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pandas-lib amd64 2.3.3+dfsg-1ubuntu1 [7668 kB] 53s Get:71 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pandas all 2.3.3+dfsg-1ubuntu1 [2948 kB] 53s Get:72 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-bioframe all 0.4.1-2 [76.3 kB] 53s Get:73 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-click all 8.2.0+0.really.8.1.8-1 [80.0 kB] 53s Get:74 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-iniconfig all 1.1.1-2 [6024 B] 53s Get:75 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-standard-pipes all 3.13.0-5 [7414 B] 53s Get:76 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pysam amd64 0.23.0+ds-1build1 [3966 kB] 53s Get:77 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pairtools amd64 1.1.3-1build2 [279 kB] 53s Get:78 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pluggy all 1.6.0-1 [21.0 kB] 53s Get:79 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 python3-pytest all 8.4.2-1 [268 kB] 54s Fetched 94.7 MB in 6s (15.0 MB/s) 54s Selecting previously unselected package python3-numpy-dev:amd64. 54s (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 ... 78459 files and directories currently installed.) 54s Preparing to unpack .../00-python3-numpy-dev_1%3a2.2.4+ds-1ubuntu1_amd64.deb ... 54s Unpacking python3-numpy-dev:amd64 (1:2.2.4+ds-1ubuntu1) ... 54s Selecting previously unselected package libblas3:amd64. 54s Preparing to unpack .../01-libblas3_3.12.1-6build1_amd64.deb ... 54s Unpacking libblas3:amd64 (3.12.1-6build1) ... 54s Selecting previously unselected package libgfortran5:amd64. 54s Preparing to unpack .../02-libgfortran5_15.2.0-5ubuntu1_amd64.deb ... 54s Unpacking libgfortran5:amd64 (15.2.0-5ubuntu1) ... 54s Selecting previously unselected package liblapack3:amd64. 54s Preparing to unpack .../03-liblapack3_3.12.1-6build1_amd64.deb ... 54s Unpacking liblapack3:amd64 (3.12.1-6build1) ... 54s Selecting previously unselected package python3-numpy. 54s Preparing to unpack .../04-python3-numpy_1%3a2.2.4+ds-1ubuntu1_amd64.deb ... 54s Unpacking python3-numpy (1:2.2.4+ds-1ubuntu1) ... 54s Selecting previously unselected package libtcl8.6:amd64. 54s Preparing to unpack .../05-libtcl8.6_8.6.17+dfsg-1_amd64.deb ... 54s Unpacking libtcl8.6:amd64 (8.6.17+dfsg-1) ... 54s Selecting previously unselected package fonts-dejavu-mono. 54s Preparing to unpack .../06-fonts-dejavu-mono_2.37-8_all.deb ... 54s Unpacking fonts-dejavu-mono (2.37-8) ... 54s Selecting previously unselected package fonts-dejavu-core. 54s Preparing to unpack .../07-fonts-dejavu-core_2.37-8_all.deb ... 54s Unpacking fonts-dejavu-core (2.37-8) ... 54s Selecting previously unselected package fontconfig-config. 54s Preparing to unpack .../08-fontconfig-config_2.15.0-2.3ubuntu1_amd64.deb ... 54s Unpacking fontconfig-config (2.15.0-2.3ubuntu1) ... 54s Selecting previously unselected package libfontconfig1:amd64. 54s Preparing to unpack .../09-libfontconfig1_2.15.0-2.3ubuntu1_amd64.deb ... 54s Unpacking libfontconfig1:amd64 (2.15.0-2.3ubuntu1) ... 54s Selecting previously unselected package libxrender1:amd64. 54s Preparing to unpack .../10-libxrender1_1%3a0.9.12-1_amd64.deb ... 54s Unpacking libxrender1:amd64 (1:0.9.12-1) ... 54s Selecting previously unselected package libxft2:amd64. 54s Preparing to unpack .../11-libxft2_2.3.6-1build1_amd64.deb ... 54s Unpacking libxft2:amd64 (2.3.6-1build1) ... 54s Selecting previously unselected package x11-common. 54s Preparing to unpack .../12-x11-common_1%3a7.7+24ubuntu1_all.deb ... 54s Unpacking x11-common (1:7.7+24ubuntu1) ... 54s Selecting previously unselected package libxss1:amd64. 54s Preparing to unpack .../13-libxss1_1%3a1.2.3-1build3_amd64.deb ... 54s Unpacking libxss1:amd64 (1:1.2.3-1build3) ... 54s Selecting previously unselected package libtk8.6:amd64. 54s Preparing to unpack .../14-libtk8.6_8.6.17-1_amd64.deb ... 54s Unpacking libtk8.6:amd64 (8.6.17-1) ... 54s Selecting previously unselected package tk8.6-blt2.5. 54s Preparing to unpack .../15-tk8.6-blt2.5_2.5.3+dfsg-8_amd64.deb ... 54s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-8) ... 54s Selecting previously unselected package blt. 54s Preparing to unpack .../16-blt_2.5.3+dfsg-8_amd64.deb ... 54s Unpacking blt (2.5.3+dfsg-8) ... 54s Selecting previously unselected package fonts-lyx. 54s Preparing to unpack .../17-fonts-lyx_2.4.4-1_all.deb ... 54s Unpacking fonts-lyx (2.4.4-1) ... 54s Selecting previously unselected package libdeflate0:amd64. 54s Preparing to unpack .../18-libdeflate0_1.23-2_amd64.deb ... 54s Unpacking libdeflate0:amd64 (1.23-2) ... 54s Selecting previously unselected package libgomp1:amd64. 54s Preparing to unpack .../19-libgomp1_15.2.0-5ubuntu1_amd64.deb ... 54s Unpacking libgomp1:amd64 (15.2.0-5ubuntu1) ... 54s Selecting previously unselected package libgraphite2-3:amd64. 54s Preparing to unpack .../20-libgraphite2-3_1.3.14-2ubuntu1_amd64.deb ... 54s Unpacking libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 54s Selecting previously unselected package libharfbuzz0b:amd64. 54s Preparing to unpack .../21-libharfbuzz0b_12.1.0-1_amd64.deb ... 54s Unpacking libharfbuzz0b:amd64 (12.1.0-1) ... 54s Selecting previously unselected package libhtscodecs2:amd64. 54s Preparing to unpack .../22-libhtscodecs2_1.6.1-2_amd64.deb ... 54s Unpacking libhtscodecs2:amd64 (1.6.1-2) ... 54s Selecting previously unselected package libhts3t64:amd64. 54s Preparing to unpack .../23-libhts3t64_1.21+ds-1_amd64.deb ... 54s Unpacking libhts3t64:amd64 (1.21+ds-1) ... 54s Selecting previously unselected package libimagequant0:amd64. 54s Preparing to unpack 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57s Setting up unicode-data (16.0.0-1) ... 57s Setting up python3-decorator (5.2.1-2) ... 57s Setting up libblas3:amd64 (3.12.1-6build1) ... 57s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode 57s Setting up python3-packaging (25.0-1) ... 57s Setting up libzopfli1 (1.0.3-3) ... 57s Setting up python3-brotli (1.1.0-2build6) ... 57s Setting up python3-cycler (0.12.1-2) ... 57s Setting up libimagequant0:amd64 (2.18.0-1build1) ... 57s Setting up fonts-dejavu-mono (2.37-8) ... 57s Setting up python3-kiwisolver (1.4.7-3build2) ... 57s Setting up python3-numpy-dev:amd64 (1:2.2.4+ds-1ubuntu1) ... 57s Setting up libtcl8.6:amd64 (8.6.17+dfsg-1) ... 57s Setting up fonts-dejavu-core (2.37-8) ... 57s Setting up libjpeg-turbo8:amd64 (2.1.5-4ubuntu2) ... 57s Setting up libgfortran5:amd64 (15.2.0-5ubuntu1) ... 57s Setting up python3-pluggy (1.6.0-1) ... 57s Setting up libwebp7:amd64 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61s Setting up python3-pytest (8.4.2-1) ... 61s Setting up libwebpdemux2:amd64 (1.5.0-0.1) ... 61s Setting up python3-zopfli (0.2.3.post1-1) ... 61s Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... 61s Setting up libraqm0:amd64 (0.10.3-1) ... 61s Setting up python3-numpy (1:2.2.4+ds-1ubuntu1) ... 62s Setting up python3-lxml:amd64 (6.0.1-1build1) ... 62s Setting up libtiff6:amd64 (4.7.0-3ubuntu3) ... 62s Setting up python3-contourpy (1.3.1-1build1) ... 62s Setting up libfontconfig1:amd64 (2.15.0-2.3ubuntu1) ... 62s Setting up libxft2:amd64 (2.3.6-1build1) ... 62s Setting up python3-scipy (1.15.3-1ubuntu1) ... 64s Setting up libtk8.6:amd64 (8.6.17-1) ... 64s Setting up python3-pandas-lib:amd64 (2.3.3+dfsg-1ubuntu1) ... 64s Setting up python3.13-tk (3.13.9-1) ... 64s Setting up python3-pil:amd64 (11.3.0-1ubuntu2) ... 65s Setting up python3-pandas (2.3.3+dfsg-1ubuntu1) ... 67s Setting up tk8.6-blt2.5 (2.5.3+dfsg-8) ... 67s Setting up blt (2.5.3+dfsg-8) ... 67s Setting up python3-tk:amd64 (3.13.5-1) ... 67s Setting up python3-pil.imagetk:amd64 (11.3.0-1ubuntu2) ... 67s Setting up python3-fonttools (4.57.0-2build1) ... 68s Setting up python3-ufolib2 (0.17.1+dfsg1-1) ... 68s Setting up python3-matplotlib (3.10.1+dfsg1-4) ... 69s Setting up python3-bioframe (0.4.1-2) ... 69s Setting up python3-pairtools (1.1.3-1build2) ... 69s Processing triggers for libc-bin (2.42-0ubuntu3) ... 69s Processing triggers for man-db (2.13.1-1) ... 70s autopkgtest [06:01:48]: test upstream-tests: [----------------------- 70s 70s rm -rf pairtools 70s 70s pytest-3 --ignore=.pc 71s ============================= test session starts ============================== 71s platform linux -- Python 3.13.9, pytest-8.4.2, pluggy-1.6.0 71s rootdir: /tmp/autopkgtest.PUpHIi/build.8Ng/src 71s configfile: pytest.ini 71s testpaths: tests 71s plugins: typeguard-4.4.2 71s collected 34 items 71s 74s tests/test_dedup.py . [ 2%] 76s tests/test_filterbycov.py . [ 5%] 77s tests/test_flip.py . [ 8%] 77s tests/test_header.py . [ 11%] 77s tests/test_headerops.py ....... [ 32%] 78s tests/test_markasdup.py . [ 35%] 80s tests/test_merge.py . [ 38%] 82s tests/test_parse.py ... [ 47%] 84s tests/test_parse2.py .... [ 58%] 85s tests/test_restrict.py . [ 61%] 85s tests/test_scaling.py . [ 64%] 90s tests/test_select.py ....... [ 85%] 90s tests/test_sort.py . [ 88%] 91s tests/test_split.py . [ 91%] 95s tests/test_stats.py ... [100%] 95s 95s =============================== warnings summary =============================== 95s ../../../../usr/lib/python3/dist-packages/pairtools/lib/fileio.py:2 95s /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'. 95s import pipes 95s 95s tests/test_stats.py::test_find_dist_freq_convergence_distance 95s /usr/lib/python3/dist-packages/pairtools/lib/stats.py:466: RuntimeWarning: divide by zero encountered in scalar divide 95s strands: n_cis_pairs / norm_factor 95s 95s tests/test_stats.py::test_find_dist_freq_convergence_distance 95s /usr/lib/python3/dist-packages/pairtools/lib/stats.py:474: RuntimeWarning: divide by zero encountered in scalar divide 95s sum(list(n_cis_pairs_above_convergence_dist.values())) / norm_factor ) 95s 95s tests/test_stats.py::test_find_dist_freq_convergence_distance 95s /usr/lib/python3/dist-packages/pairtools/lib/stats.py:410: RuntimeWarning: invalid value encountered in divide 95s np.abs(dist_freqs_by_strands[strands] - avg_freq_all_strands) 95s 95s tests/test_stats.py::test_find_dist_freq_convergence_distance 95s /usr/lib/python3/dist-packages/pairtools/lib/stats.py:466: RuntimeWarning: invalid value encountered in scalar divide 95s strands: n_cis_pairs / norm_factor 95s 95s tests/test_stats.py::test_find_dist_freq_convergence_distance 95s /usr/lib/python3/dist-packages/pairtools/lib/stats.py:474: RuntimeWarning: invalid value encountered in scalar divide 95s sum(list(n_cis_pairs_above_convergence_dist.values())) / norm_factor ) 95s 95s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 95s ======================= 34 passed, 6 warnings in 24.19s ======================== 95s 95s echo ALL PASS 95s ALL PASS 95s autopkgtest [06:02:13]: test upstream-tests: -----------------------] 95s upstream-tests PASS 95s autopkgtest [06:02:13]: test upstream-tests: - - - - - - - - - - results - - - - - - - - - - 96s autopkgtest [06:02:14]: @@@@@@@@@@@@@@@@@@@@ summary 96s upstream-tests PASS