0s autopkgtest [19:48:05]: starting date and time: 2025-11-15 19:48:05+0000 0s autopkgtest [19:48:05]: git checkout: 508d4a25 a-v-ssh wait_for_ssh: demote "ssh connection failed" to a debug message 0s autopkgtest [19:48:05]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.mr0t9_a9/out --timeout-copy=6000 --setup-commands 'ln -s /dev/null /etc/systemd/system/bluetooth.service; printf "http_proxy=http://squid.internal:3128\nhttps_proxy=http://squid.internal:3128\nno_proxy=127.0.0.1,127.0.1.1,localhost,localdomain,internal,login.ubuntu.com,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com\n" >> /etc/environment' --apt-pocket=proposed=src:requests --apt-upgrade python-bioframe --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=requests/2.32.5+dfsg-1ubuntu1 -- lxd -r lxd-armhf-10.145.243.85 lxd-armhf-10.145.243.85:autopkgtest/ubuntu/resolute/armhf 21s autopkgtest [19:48:26]: testbed dpkg architecture: armhf 23s autopkgtest [19:48:28]: testbed apt version: 3.1.11 26s autopkgtest [19:48:31]: @@@@@@@@@@@@@@@@@@@@ test bed setup 28s autopkgtest [19:48:33]: testbed release detected to be: None 36s autopkgtest [19:48:41]: updating testbed package index (apt update) 38s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [87.8 kB] 38s Get:2 http://ftpmaster.internal/ubuntu resolute InRelease [87.8 kB] 38s 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/main Sources [78.5 kB] 38s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [821 kB] 38s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [9848 B] 38s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [22.9 kB] 38s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf Packages [136 kB] 38s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/restricted armhf Packages [940 B] 38s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/universe armhf Packages [506 kB] 38s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse armhf Packages [9140 B] 38s Get:13 http://ftpmaster.internal/ubuntu resolute/main Sources [1404 kB] 38s Get:14 http://ftpmaster.internal/ubuntu resolute/universe Sources [21.3 MB] 40s Get:15 http://ftpmaster.internal/ubuntu resolute/main armhf Packages [1369 kB] 40s Get:16 http://ftpmaster.internal/ubuntu resolute/universe armhf Packages [15.2 MB] 40s Get:17 http://ftpmaster.internal/ubuntu resolute/multiverse armhf Packages [184 kB] 44s Fetched 41.2 MB in 6s (6770 kB/s) 45s Reading package lists... 51s autopkgtest [19:48:56]: upgrading testbed (apt dist-upgrade and autopurge) 52s Reading package lists... 53s Building dependency tree... 53s Reading state information... 54s Calculating upgrade... 55s The following packages will be upgraded: 55s python3-requests python3-rpds-py 55s 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 55s Need to get 396 kB of archives. 55s After this operation, 727 kB of additional disk space will be used. 55s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf python3-requests all 2.32.5+dfsg-1ubuntu1 [53.1 kB] 55s Get:2 http://ftpmaster.internal/ubuntu resolute/main armhf python3-rpds-py armhf 0.27.1-2ubuntu1 [343 kB] 56s Fetched 396 kB in 0s (815 kB/s) 56s (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 ... 65903 files and directories currently installed.) 56s Preparing to unpack .../python3-requests_2.32.5+dfsg-1ubuntu1_all.deb ... 56s Unpacking python3-requests (2.32.5+dfsg-1ubuntu1) over (2.32.3+dfsg-5ubuntu2) ... 56s Preparing to unpack .../python3-rpds-py_0.27.1-2ubuntu1_armhf.deb ... 56s Unpacking python3-rpds-py (0.27.1-2ubuntu1) over (0.21.0-2ubuntu2) ... 56s Setting up python3-requests (2.32.5+dfsg-1ubuntu1) ... 57s Setting up python3-rpds-py (0.27.1-2ubuntu1) ... 59s Reading package lists... 59s Building dependency tree... 59s Reading state information... 60s Solving dependencies... 61s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 63s autopkgtest [19:49:08]: rebooting testbed after setup commands that affected boot 105s autopkgtest [19:49:49]: testbed running kernel: Linux 6.8.0-86-generic #87~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 29 09:26:46 UTC 2 129s autopkgtest [19:50:14]: @@@@@@@@@@@@@@@@@@@@ apt-source python-bioframe 140s Get:1 http://ftpmaster.internal/ubuntu resolute/universe python-bioframe 0.4.1-2 (dsc) [2253 B] 140s Get:2 http://ftpmaster.internal/ubuntu resolute/universe python-bioframe 0.4.1-2 (tar) [816 kB] 140s Get:3 http://ftpmaster.internal/ubuntu resolute/universe python-bioframe 0.4.1-2 (diff) [3576 B] 140s gpgv: Signature made Sat Feb 15 19:14:39 2025 UTC 140s gpgv: using RSA key 8F6DE104377F3B11E741748731F3144544A1741A 140s gpgv: issuer "tchet@debian.org" 140s gpgv: Can't check signature: No public key 140s dpkg-source: warning: cannot verify inline signature for ./python-bioframe_0.4.1-2.dsc: no acceptable signature found 140s autopkgtest [19:50:25]: testing package python-bioframe version 0.4.1-2 142s autopkgtest [19:50:27]: build not needed 145s autopkgtest [19:50:30]: test run-unit-test: preparing testbed 146s Reading package lists... 147s Building dependency tree... 147s Reading state information... 147s Solving dependencies... 148s The following NEW packages will be installed: 148s blt fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-lyx libblas3 148s libdeflate0 libfontconfig1 libfreetype6 libgfortran5 libgomp1 libgraphite2-3 148s libharfbuzz0b libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 liblapack3 148s liblcms2-2 liblerc4 libopenjp2-7 libqhull-r8.0 libraqm0 libsharpyuv0 148s libtcl8.6 libtiff6 libtk8.6 libwebp7 libwebpdemux2 libwebpmux3 libxft2 148s libxrender1 libxslt1.1 libxss1 libzopfli1 python-matplotlib-data python3-all 148s python3-bioframe python3-brotli python3-contourpy python3-cycler 148s python3-decorator python3-fonttools python3-fs python3-iniconfig 148s python3-kiwisolver python3-lxml python3-lz4 python3-matplotlib 148s python3-mpmath python3-numpy python3-numpy-dev python3-pandas 148s python3-pandas-lib python3-pil python3-pil.imagetk python3-platformdirs 148s python3-pluggy python3-pytest python3-pytz python3-scipy python3-sympy 148s python3-tk python3-ufolib2 python3-zopfli python3.13-tk python3.14-tk 148s tk8.6-blt2.5 unicode-data x11-common 148s 0 upgraded, 70 newly installed, 0 to remove and 0 not upgraded. 148s Need to get 83.8 MB of archives. 148s After this operation, 352 MB of additional disk space will be used. 148s Get:1 http://ftpmaster.internal/ubuntu resolute/main armhf python3-numpy-dev armhf 1:2.2.4+ds-1ubuntu1 [141 kB] 149s Get:2 http://ftpmaster.internal/ubuntu resolute/main armhf libblas3 armhf 3.12.1-7 [133 kB] 149s Get:3 http://ftpmaster.internal/ubuntu resolute/main armhf libgfortran5 armhf 15.2.0-7ubuntu1 [334 kB] 149s Get:4 http://ftpmaster.internal/ubuntu resolute/main armhf liblapack3 armhf 3.12.1-7 [2091 kB] 149s Get:5 http://ftpmaster.internal/ubuntu resolute/main armhf python3-numpy armhf 1:2.2.4+ds-1ubuntu1 [3724 kB] 149s Get:6 http://ftpmaster.internal/ubuntu resolute/main armhf libtcl8.6 armhf 8.6.17+dfsg-1 [918 kB] 149s Get:7 http://ftpmaster.internal/ubuntu resolute/main armhf libfreetype6 armhf 2.13.3+dfsg-1build1 [334 kB] 149s Get:8 http://ftpmaster.internal/ubuntu resolute/main armhf fonts-dejavu-mono all 2.37-8 [502 kB] 149s Get:9 http://ftpmaster.internal/ubuntu resolute/main armhf fonts-dejavu-core all 2.37-8 [835 kB] 149s Get:10 http://ftpmaster.internal/ubuntu resolute/main armhf fontconfig-config armhf 2.15.0-2.3ubuntu1 [38.1 kB] 149s Get:11 http://ftpmaster.internal/ubuntu resolute/main armhf libfontconfig1 armhf 2.15.0-2.3ubuntu1 [114 kB] 149s Get:12 http://ftpmaster.internal/ubuntu resolute/main armhf libxrender1 armhf 1:0.9.12-1 [16.6 kB] 149s Get:13 http://ftpmaster.internal/ubuntu resolute/main armhf libxft2 armhf 2.3.6-1build1 [37.4 kB] 149s Get:14 http://ftpmaster.internal/ubuntu resolute/main armhf x11-common all 1:7.7+24ubuntu1 [22.4 kB] 149s Get:15 http://ftpmaster.internal/ubuntu resolute/main armhf libxss1 armhf 1:1.2.3-1build3 [6500 B] 149s Get:16 http://ftpmaster.internal/ubuntu resolute/main armhf libtk8.6 armhf 8.6.17-1 [694 kB] 149s Get:17 http://ftpmaster.internal/ubuntu resolute/main armhf tk8.6-blt2.5 armhf 2.5.3+dfsg-8 [527 kB] 149s Get:18 http://ftpmaster.internal/ubuntu resolute/main armhf blt armhf 2.5.3+dfsg-8 [4824 B] 149s Get:19 http://ftpmaster.internal/ubuntu resolute/universe armhf fonts-lyx all 2.4.4-2 [171 kB] 149s Get:20 http://ftpmaster.internal/ubuntu resolute/main armhf libdeflate0 armhf 1.23-2 [38.7 kB] 149s Get:21 http://ftpmaster.internal/ubuntu resolute/main armhf libgomp1 armhf 15.2.0-7ubuntu1 [129 kB] 149s Get:22 http://ftpmaster.internal/ubuntu resolute/main armhf libgraphite2-3 armhf 1.3.14-2ubuntu1 [64.8 kB] 149s Get:23 http://ftpmaster.internal/ubuntu resolute/main armhf libharfbuzz0b armhf 12.1.0-1 [512 kB] 149s Get:24 http://ftpmaster.internal/ubuntu resolute/main armhf libimagequant0 armhf 2.18.0-1build1 [31.1 kB] 149s Get:25 http://ftpmaster.internal/ubuntu resolute/main armhf libjpeg-turbo8 armhf 2.1.5-4ubuntu2 [127 kB] 149s Get:26 http://ftpmaster.internal/ubuntu resolute/main armhf libjpeg8 armhf 8c-2ubuntu11 [2148 B] 149s Get:27 http://ftpmaster.internal/ubuntu resolute/main armhf liblcms2-2 armhf 2.16-2 [137 kB] 149s Get:28 http://ftpmaster.internal/ubuntu resolute/main armhf liblerc4 armhf 4.0.0+ds-5ubuntu1 [160 kB] 149s Get:29 http://ftpmaster.internal/ubuntu resolute/universe armhf libqhull-r8.0 armhf 2020.2-7 [174 kB] 149s Get:30 http://ftpmaster.internal/ubuntu resolute/main armhf libraqm0 armhf 0.10.3-1 [12.7 kB] 149s Get:31 http://ftpmaster.internal/ubuntu resolute/main armhf libsharpyuv0 armhf 1.5.0-0.1 [16.4 kB] 149s Get:32 http://ftpmaster.internal/ubuntu resolute/main armhf libjbig0 armhf 2.1-6.1ubuntu2 [24.9 kB] 149s Get:33 http://ftpmaster.internal/ubuntu resolute/main armhf libwebp7 armhf 1.5.0-0.1 [188 kB] 149s Get:34 http://ftpmaster.internal/ubuntu resolute/main armhf libtiff6 armhf 4.7.0-3ubuntu3 [188 kB] 149s Get:35 http://ftpmaster.internal/ubuntu resolute/main armhf libwebpdemux2 armhf 1.5.0-0.1 [11.5 kB] 149s Get:36 http://ftpmaster.internal/ubuntu resolute/main armhf libwebpmux3 armhf 1.5.0-0.1 [22.4 kB] 149s Get:37 http://ftpmaster.internal/ubuntu resolute/main armhf libxslt1.1 armhf 1.1.43-0.3 [146 kB] 150s Get:38 http://ftpmaster.internal/ubuntu resolute/universe armhf libzopfli1 armhf 1.0.3-3 [91.7 kB] 150s Get:39 http://ftpmaster.internal/ubuntu resolute/universe armhf python-matplotlib-data all 3.10.7+dfsg1-1 [2930 kB] 150s Get:40 http://ftpmaster.internal/ubuntu resolute/main armhf python3-all armhf 3.13.7-1 [884 B] 150s Get:41 http://ftpmaster.internal/ubuntu resolute/main armhf libopenjp2-7 armhf 2.5.3-2.1 [174 kB] 150s Get:42 http://ftpmaster.internal/ubuntu resolute/main armhf python3-pil armhf 11.3.0-1ubuntu2 [465 kB] 150s Get:43 http://ftpmaster.internal/ubuntu resolute/main armhf python3.14-tk armhf 3.14.0-4 [105 kB] 150s Get:44 http://ftpmaster.internal/ubuntu resolute/main armhf python3.13-tk armhf 3.13.9-1 [104 kB] 150s Get:45 http://ftpmaster.internal/ubuntu resolute/main armhf python3-tk armhf 3.13.9-1 [8944 B] 150s Get:46 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-pil.imagetk armhf 11.3.0-1ubuntu2 [9236 B] 150s Get:47 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-contourpy armhf 1.3.1-2 [267 kB] 150s Get:48 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-cycler all 0.12.1-2 [9850 B] 150s Get:49 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-brotli armhf 1.1.0-2build6 [327 kB] 150s Get:50 http://ftpmaster.internal/ubuntu resolute/main armhf python3-platformdirs all 4.3.7-1 [16.9 kB] 150s Get:51 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-fs all 2.4.16-9ubuntu1 [91.5 kB] 150s Get:52 http://ftpmaster.internal/ubuntu resolute/main armhf python3-lxml armhf 6.0.2-1 [2260 kB] 150s Get:53 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-lz4 armhf 4.4.4+dfsg-3 [25.9 kB] 150s Get:54 http://ftpmaster.internal/ubuntu resolute/main armhf python3-decorator all 5.2.1-2 [28.1 kB] 150s Get:55 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-scipy armhf 1.15.3-1ubuntu1 [19.7 MB] 150s Get:56 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-mpmath all 1.3.0-2 [423 kB] 150s Get:57 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-sympy all 1.14.0-2 [4306 kB] 150s Get:58 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-ufolib2 all 0.17.1+dfsg1-1 [33.5 kB] 150s Get:59 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-zopfli armhf 0.4.0-1 [10.5 kB] 150s Get:60 http://ftpmaster.internal/ubuntu resolute/universe armhf unicode-data all 16.0.0-1 [9513 kB] 151s Get:61 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-fonttools armhf 4.57.0-2build1 [1688 kB] 151s Get:62 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-kiwisolver armhf 1.4.10~rc0-1 [77.8 kB] 151s Get:63 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-matplotlib armhf 3.10.7+dfsg1-1 [17.2 MB] 151s Get:64 http://ftpmaster.internal/ubuntu resolute/main armhf python3-pytz all 2025.2-4 [32.3 kB] 151s Get:65 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-pandas-lib armhf 2.3.3+dfsg-1ubuntu1 [8020 kB] 151s Get:66 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-pandas all 2.3.3+dfsg-1ubuntu1 [2948 kB] 151s Get:67 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-bioframe all 0.4.1-2 [76.3 kB] 151s Get:68 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-iniconfig all 2.1.0-1 [6840 B] 151s Get:69 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-pluggy all 1.6.0-1 [21.0 kB] 151s Get:70 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-pytest all 8.3.5-2 [252 kB] 152s Fetched 83.8 MB in 3s (26.2 MB/s) 152s Selecting previously unselected package python3-numpy-dev:armhf. 152s (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 ... 65904 files and directories currently installed.) 152s Preparing to unpack .../00-python3-numpy-dev_1%3a2.2.4+ds-1ubuntu1_armhf.deb ... 152s Unpacking python3-numpy-dev:armhf (1:2.2.4+ds-1ubuntu1) ... 152s Selecting previously unselected package libblas3:armhf. 152s Preparing to unpack .../01-libblas3_3.12.1-7_armhf.deb ... 152s Unpacking libblas3:armhf (3.12.1-7) ... 152s Selecting previously unselected package libgfortran5:armhf. 152s Preparing to unpack .../02-libgfortran5_15.2.0-7ubuntu1_armhf.deb ... 152s Unpacking libgfortran5:armhf (15.2.0-7ubuntu1) ... 152s Selecting previously unselected package liblapack3:armhf. 152s Preparing to unpack .../03-liblapack3_3.12.1-7_armhf.deb ... 152s Unpacking liblapack3:armhf (3.12.1-7) ... 153s Selecting previously unselected package python3-numpy. 153s Preparing to unpack .../04-python3-numpy_1%3a2.2.4+ds-1ubuntu1_armhf.deb ... 153s Unpacking python3-numpy (1:2.2.4+ds-1ubuntu1) ... 153s Selecting previously unselected package libtcl8.6:armhf. 153s Preparing to unpack .../05-libtcl8.6_8.6.17+dfsg-1_armhf.deb ... 153s Unpacking libtcl8.6:armhf (8.6.17+dfsg-1) ... 153s Selecting previously unselected package libfreetype6:armhf. 153s Preparing to unpack .../06-libfreetype6_2.13.3+dfsg-1build1_armhf.deb ... 153s Unpacking libfreetype6:armhf (2.13.3+dfsg-1build1) ... 153s Selecting previously unselected package fonts-dejavu-mono. 153s Preparing to unpack .../07-fonts-dejavu-mono_2.37-8_all.deb ... 153s Unpacking fonts-dejavu-mono (2.37-8) ... 153s Selecting previously unselected package fonts-dejavu-core. 153s Preparing to unpack .../08-fonts-dejavu-core_2.37-8_all.deb ... 153s Unpacking fonts-dejavu-core (2.37-8) ... 153s Selecting previously unselected package fontconfig-config. 153s Preparing to unpack .../09-fontconfig-config_2.15.0-2.3ubuntu1_armhf.deb ... 154s Unpacking fontconfig-config (2.15.0-2.3ubuntu1) ... 154s Selecting previously unselected package libfontconfig1:armhf. 154s Preparing to unpack .../10-libfontconfig1_2.15.0-2.3ubuntu1_armhf.deb ... 154s Unpacking libfontconfig1:armhf (2.15.0-2.3ubuntu1) ... 154s Selecting previously unselected package libxrender1:armhf. 154s Preparing to unpack .../11-libxrender1_1%3a0.9.12-1_armhf.deb ... 154s Unpacking libxrender1:armhf (1:0.9.12-1) ... 154s Selecting previously unselected package libxft2:armhf. 154s Preparing to unpack .../12-libxft2_2.3.6-1build1_armhf.deb ... 154s Unpacking libxft2:armhf (2.3.6-1build1) ... 154s Selecting previously unselected package x11-common. 154s Preparing to unpack .../13-x11-common_1%3a7.7+24ubuntu1_all.deb ... 154s Unpacking x11-common (1:7.7+24ubuntu1) ... 154s Selecting previously unselected package libxss1:armhf. 154s Preparing to unpack .../14-libxss1_1%3a1.2.3-1build3_armhf.deb ... 154s Unpacking libxss1:armhf (1:1.2.3-1build3) ... 154s Selecting previously unselected package libtk8.6:armhf. 154s Preparing to unpack .../15-libtk8.6_8.6.17-1_armhf.deb ... 154s Unpacking libtk8.6:armhf (8.6.17-1) ... 154s Selecting previously unselected package tk8.6-blt2.5. 154s Preparing to unpack .../16-tk8.6-blt2.5_2.5.3+dfsg-8_armhf.deb ... 154s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-8) ... 154s Selecting previously unselected package blt. 154s Preparing to unpack .../17-blt_2.5.3+dfsg-8_armhf.deb ... 154s Unpacking blt (2.5.3+dfsg-8) ... 154s Selecting previously unselected package fonts-lyx. 154s Preparing to unpack .../18-fonts-lyx_2.4.4-2_all.deb ... 154s Unpacking fonts-lyx (2.4.4-2) ... 154s Selecting previously unselected package libdeflate0:armhf. 154s Preparing to unpack .../19-libdeflate0_1.23-2_armhf.deb ... 154s Unpacking libdeflate0:armhf (1.23-2) ... 154s Selecting previously unselected package libgomp1:armhf. 154s Preparing to unpack .../20-libgomp1_15.2.0-7ubuntu1_armhf.deb ... 154s Unpacking libgomp1:armhf (15.2.0-7ubuntu1) ... 154s Selecting previously unselected package libgraphite2-3:armhf. 154s Preparing to unpack .../21-libgraphite2-3_1.3.14-2ubuntu1_armhf.deb ... 154s Unpacking libgraphite2-3:armhf (1.3.14-2ubuntu1) ... 154s Selecting previously unselected package libharfbuzz0b:armhf. 154s Preparing to unpack .../22-libharfbuzz0b_12.1.0-1_armhf.deb ... 154s Unpacking libharfbuzz0b:armhf (12.1.0-1) ... 154s Selecting previously unselected package libimagequant0:armhf. 154s Preparing to unpack .../23-libimagequant0_2.18.0-1build1_armhf.deb ... 154s Unpacking libimagequant0:armhf (2.18.0-1build1) ... 154s Selecting previously unselected package libjpeg-turbo8:armhf. 154s Preparing to unpack .../24-libjpeg-turbo8_2.1.5-4ubuntu2_armhf.deb ... 154s Unpacking libjpeg-turbo8:armhf (2.1.5-4ubuntu2) ... 154s Selecting previously unselected package libjpeg8:armhf. 154s Preparing to unpack .../25-libjpeg8_8c-2ubuntu11_armhf.deb ... 154s Unpacking libjpeg8:armhf (8c-2ubuntu11) ... 155s Selecting previously unselected package liblcms2-2:armhf. 155s Preparing to unpack .../26-liblcms2-2_2.16-2_armhf.deb ... 155s Unpacking liblcms2-2:armhf (2.16-2) ... 155s Selecting previously unselected package liblerc4:armhf. 155s Preparing to unpack .../27-liblerc4_4.0.0+ds-5ubuntu1_armhf.deb ... 155s Unpacking liblerc4:armhf (4.0.0+ds-5ubuntu1) ... 155s Selecting previously unselected package libqhull-r8.0:armhf. 155s Preparing to unpack .../28-libqhull-r8.0_2020.2-7_armhf.deb ... 155s Unpacking libqhull-r8.0:armhf (2020.2-7) ... 155s Selecting previously unselected package libraqm0:armhf. 155s Preparing to unpack .../29-libraqm0_0.10.3-1_armhf.deb ... 155s Unpacking libraqm0:armhf (0.10.3-1) ... 155s Selecting previously unselected package libsharpyuv0:armhf. 155s Preparing to unpack .../30-libsharpyuv0_1.5.0-0.1_armhf.deb ... 155s Unpacking libsharpyuv0:armhf (1.5.0-0.1) ... 155s Selecting previously unselected package libjbig0:armhf. 155s Preparing to unpack .../31-libjbig0_2.1-6.1ubuntu2_armhf.deb ... 155s Unpacking libjbig0:armhf (2.1-6.1ubuntu2) ... 155s Selecting previously unselected package libwebp7:armhf. 156s Preparing to unpack .../32-libwebp7_1.5.0-0.1_armhf.deb ... 156s Unpacking libwebp7:armhf (1.5.0-0.1) ... 156s Selecting previously unselected package libtiff6:armhf. 156s Preparing to unpack .../33-libtiff6_4.7.0-3ubuntu3_armhf.deb ... 156s Unpacking libtiff6:armhf (4.7.0-3ubuntu3) ... 156s Selecting previously unselected package libwebpdemux2:armhf. 156s Preparing to unpack .../34-libwebpdemux2_1.5.0-0.1_armhf.deb ... 156s Unpacking 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161s Setting up python3-all (3.13.7-1) ... 161s Setting up python3-pytz (2025.2-4) ... 162s Setting up libgomp1:armhf (15.2.0-7ubuntu1) ... 162s Setting up libjbig0:armhf (2.1-6.1ubuntu2) ... 162s Setting up python3-platformdirs (4.3.7-1) ... 162s Setting up python3-fs (2.4.16-9ubuntu1) ... 162s Setting up unicode-data (16.0.0-1) ... 162s Setting up python3-decorator (5.2.1-2) ... 162s Setting up libblas3:armhf (3.12.1-7) ... 162s update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode 162s Setting up libzopfli1 (1.0.3-3) ... 162s Setting up libfreetype6:armhf (2.13.3+dfsg-1build1) ... 162s Setting up python3-brotli (1.1.0-2build6) ... 163s Setting up python3-cycler (0.12.1-2) ... 163s Setting up libimagequant0:armhf (2.18.0-1build1) ... 163s Setting up fonts-dejavu-mono (2.37-8) ... 163s Setting up python3-kiwisolver (1.4.10~rc0-1) ... 163s Setting up python3-numpy-dev:armhf (1:2.2.4+ds-1ubuntu1) ... 163s Setting up libtcl8.6:armhf (8.6.17+dfsg-1) ... 163s Setting up fonts-dejavu-core (2.37-8) ... 163s Setting up libjpeg-turbo8:armhf (2.1.5-4ubuntu2) ... 163s Setting up libgfortran5:armhf (15.2.0-7ubuntu1) ... 163s Setting up python3-pluggy (1.6.0-1) ... 163s Setting up libwebp7:armhf (1.5.0-0.1) ... 163s Setting up libxslt1.1:armhf (1.1.43-0.3) ... 163s Setting up libopenjp2-7:armhf (2.5.3-2.1) ... 163s Setting up libharfbuzz0b:armhf (12.1.0-1) ... 163s Setting up libxss1:armhf (1:1.2.3-1build3) ... 163s Setting up python3-mpmath (1.3.0-2) ... 164s Setting up python-matplotlib-data (3.10.7+dfsg1-1) ... 164s Setting up libwebpmux3:armhf (1.5.0-0.1) ... 164s Setting up libjpeg8:armhf (8c-2ubuntu11) ... 164s Setting up python3-sympy (1.14.0-2) ... 173s Setting up liblapack3:armhf (3.12.1-7) ... 173s update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode 173s Setting up fontconfig-config (2.15.0-2.3ubuntu1) ... 174s Setting up python3-pytest (8.3.5-2) ... 174s Setting up libwebpdemux2:armhf (1.5.0-0.1) ... 174s Setting up python3-zopfli (0.4.0-1) ... 174s Setting up libraqm0:armhf (0.10.3-1) ... 174s Setting up python3-numpy (1:2.2.4+ds-1ubuntu1) ... 177s Setting up python3-lxml:armhf (6.0.2-1) ... 177s Setting up libtiff6:armhf (4.7.0-3ubuntu3) ... 177s Setting up python3-contourpy (1.3.1-2) ... 177s Setting up libfontconfig1:armhf (2.15.0-2.3ubuntu1) ... 177s Setting up libxft2:armhf (2.3.6-1build1) ... 177s Setting up python3-scipy (1.15.3-1ubuntu1) ... 183s Setting up libtk8.6:armhf (8.6.17-1) ... 183s Setting up python3-pandas-lib:armhf (2.3.3+dfsg-1ubuntu1) ... 183s Setting up python3.13-tk (3.13.9-1) ... 183s Setting up python3-pil:armhf (11.3.0-1ubuntu2) ... 184s Setting up python3-pandas (2.3.3+dfsg-1ubuntu1) ... 191s Setting up tk8.6-blt2.5 (2.5.3+dfsg-8) ... 191s Setting up python3.14-tk (3.14.0-4) ... 191s Setting up blt (2.5.3+dfsg-8) ... 191s Setting up python3-tk:armhf (3.13.9-1) ... 191s Setting up python3-pil.imagetk:armhf (11.3.0-1ubuntu2) ... 191s Setting up python3-fonttools (4.57.0-2build1) ... 193s Setting up python3-ufolib2 (0.17.1+dfsg1-1) ... 193s Setting up python3-matplotlib (3.10.7+dfsg1-1) ... 195s Setting up python3-bioframe (0.4.1-2) ... 196s Processing triggers for libc-bin (2.42-2ubuntu2) ... 196s Processing triggers for man-db (2.13.1-1) ... 205s autopkgtest [19:51:30]: test run-unit-test: [----------------------- 207s ============================= test session starts ============================== 207s platform linux -- Python 3.13.9, pytest-8.3.5, pluggy-1.6.0 -- /usr/bin/python3.13 207s cachedir: .pytest_cache 207s rootdir: /tmp/autopkgtest.zSk1h9/autopkgtest_tmp 207s plugins: typeguard-4.4.2 209s collecting ... collected 50 items 209s 209s tests/test_core_checks.py::test_is_cataloged PASSED [ 2%] 209s tests/test_core_checks.py::test_is_contained PASSED [ 4%] 209s tests/test_core_checks.py::test_is_overlapping PASSED [ 6%] 209s tests/test_core_checks.py::test_is_covering PASSED [ 8%] 209s tests/test_core_checks.py::test_is_tiling PASSED [ 10%] 209s tests/test_core_checks.py::test_is_bedframe PASSED [ 12%] 209s tests/test_core_checks.py::test_is_viewframe PASSED [ 14%] 209s tests/test_core_checks.py::test_is_sorted PASSED [ 16%] 209s tests/test_core_construction.py::test_add_ucsc_name_column PASSED [ 18%] 209s tests/test_core_construction.py::test_any PASSED [ 20%] 209s tests/test_core_construction.py::test_sanitize_bedframe PASSED [ 22%] 209s tests/test_core_construction.py::test_make_viewframe PASSED [ 24%] 209s tests/test_core_specs.py::test_get_default_colnames PASSED [ 26%] 209s tests/test_core_specs.py::test_update_default_colnames PASSED [ 28%] 209s tests/test_core_specs.py::test_verify_columns PASSED [ 30%] 209s tests/test_core_specs.py::test_verify_column_dtypes PASSED [ 32%] 209s tests/test_core_specs.py::test_is_chrom_dtype PASSED [ 34%] 210s tests/test_core_stringops.py::test_to_ucsc_string PASSED [ 36%] 210s tests/test_core_stringops.py::test_parse_region PASSED [ 38%] 210s tests/test_core_stringops.py::test_parse_region_string PASSED [ 40%] 210s tests/test_core_stringops.py::test_is_complete_ucsc_string PASSED [ 42%] 210s tests/test_extras.py::test_make_chromarms PASSED [ 44%] 210s tests/test_extras.py::test_binnify PASSED [ 46%] 210s tests/test_extras.py::test_digest SKIPPED (could not import 'Bio': N...) [ 48%] 210s tests/test_extras.py::test_frac_mapped SKIPPED (could not import 'py...) [ 50%] 210s tests/test_extras.py::test_frac_gc SKIPPED (could not import 'pysam'...) [ 52%] 210s tests/test_extras.py::test_seq_gc PASSED [ 54%] 210s tests/test_extras.py::test_pair_by_distance PASSED [ 56%] 210s tests/test_io.py::test_read_table PASSED [ 58%] 210s tests/test_io.py::test_read_chromsizes PASSED [ 60%] 210s tests/test_ops.py::test_trim PASSED [ 62%] 210s tests/test_ops.py::test_expand PASSED [ 64%] 210s tests/test_ops.py::test_overlap PASSED [ 66%] 210s tests/test_ops.py::test_cluster PASSED [ 68%] 210s tests/test_ops.py::test_merge PASSED [ 70%] 211s tests/test_ops.py::test_complement PASSED [ 72%] 211s tests/test_ops.py::test_closest PASSED [ 74%] 211s tests/test_ops.py::test_coverage PASSED [ 76%] 211s tests/test_ops.py::test_subtract PASSED [ 78%] 211s tests/test_ops.py::test_setdiff PASSED [ 80%] 212s tests/test_ops.py::test_count_overlaps PASSED [ 82%] 212s tests/test_ops.py::test_assign_view PASSED [ 84%] 212s tests/test_ops.py::test_sort_bedframe PASSED [ 86%] 212s tests/test_ops_select.py::test_select PASSED [ 88%] 212s tests/test_ops_select.py::test_select__with_colnames PASSED [ 90%] 212s tests/test_ops_select.py::test_select__with_nulls PASSED [ 92%] 212s tests/test_ops_select.py::test_select__mask_indices_labels PASSED [ 94%] 212s tests/test_ops_select.py::test_select__query_intervals_are_half_open PASSED [ 96%] 212s tests/test_ops_select.py::test_select__with_point_intervals PASSED [ 98%] 212s tests/test_ops_select.py::test_select__with_points PASSED [100%] 212s 212s =============================== warnings summary =============================== 212s ../../../usr/lib/python3/dist-packages/bioframe/io/resources.py:13 212s /usr/lib/python3/dist-packages/bioframe/io/resources.py:13: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html 212s import pkg_resources 212s 212s tests/test_io.py:23 212s /tmp/autopkgtest.zSk1h9/autopkgtest_tmp/tests/test_io.py:23: SyntaxWarning: invalid escape sequence '\s' 212s assert bioframe.read_table(StringIO(d), schema="bed3", sep="\s+").shape == (3, 3) 212s 212s tests/test_io.py:24 212s /tmp/autopkgtest.zSk1h9/autopkgtest_tmp/tests/test_io.py:24: SyntaxWarning: invalid escape sequence '\s' 212s assert bioframe.read_table(StringIO(d), schema="bed6", sep="\s+").shape == (3, 6) 212s 212s tests/test_io.py:25 212s /tmp/autopkgtest.zSk1h9/autopkgtest_tmp/tests/test_io.py:25: SyntaxWarning: invalid escape sequence '\s' 212s assert bioframe.read_table(StringIO(d), schema="bed12", sep="\s+").shape == (3, 12) 212s 212s tests/test_io.py:33 212s /tmp/autopkgtest.zSk1h9/autopkgtest_tmp/tests/test_io.py:33: SyntaxWarning: invalid escape sequence '\s' 212s StringIO(d), schema="bedpe", sep="\s+", schema_is_strict=True 212s 212s tests/test_core_checks.py: 84 warnings 212s tests/test_core_construction.py: 28 warnings 212s tests/test_core_specs.py: 12 warnings 212s tests/test_extras.py: 24 warnings 212s tests/test_ops.py: 326 warnings 212s /usr/lib/python3/dist-packages/bioframe/core/specs.py:150: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead 212s pd.api.types.is_categorical_dtype(chrom_dtype), 212s 212s tests/test_core_checks.py: 4 warnings 212s tests/test_ops.py: 6 warnings 212s /usr/lib/python3/dist-packages/bioframe/ops.py:1550: FutureWarning: A value is trying to be set on a copy of a DataFrame or Series through chained assignment using an inplace method. 212s The behavior will change in pandas 3.0. This inplace method will never work because the intermediate object on which we are setting values always behaves as a copy. 212s 212s For example, when doing 'df[col].method(value, inplace=True)', try using 'df.method({col: value}, inplace=True)' or df[col] = df[col].method(value) instead, to perform the operation inplace on the original object. 212s 212s 212s df_trimmed[sk].clip(lower=lower_vector, upper=upper_vector, inplace=True) 212s 212s tests/test_core_checks.py: 4 warnings 212s tests/test_ops.py: 6 warnings 212s /usr/lib/python3/dist-packages/bioframe/ops.py:1551: FutureWarning: A value is trying to be set on a copy of a DataFrame or Series through chained assignment using an inplace method. 212s The behavior will change in pandas 3.0. This inplace method will never work because the intermediate object on which we are setting values always behaves as a copy. 212s 212s For example, when doing 'df[col].method(value, inplace=True)', try using 'df.method({col: value}, inplace=True)' or df[col] = df[col].method(value) instead, to perform the operation inplace on the original object. 212s 212s 212s df_trimmed[ek].clip(lower=lower_vector, upper=upper_vector, inplace=True) 212s 212s tests/test_core_construction.py::test_any 212s /usr/lib/python3/dist-packages/bioframe/core/construction.py:154: FutureWarning: A value is trying to be set on a copy of a DataFrame or Series through chained assignment using an inplace method. 212s The behavior will change in pandas 3.0. This inplace method will never work because the intermediate object on which we are setting values always behaves as a copy. 212s 212s For example, when doing 'df[col].method(value, inplace=True)', try using 'df.method({col: value}, inplace=True)' or df[col] = df[col].method(value) instead, to perform the operation inplace on the original object. 212s 212s 212s out_df[sk1].fillna(0, inplace=True) 212s 212s tests/test_core_construction.py::test_any 212s /usr/lib/python3/dist-packages/bioframe/core/construction.py:154: FutureWarning: Downcasting object dtype arrays on .fillna, .ffill, .bfill is deprecated and will change in a future version. Call result.infer_objects(copy=False) instead. To opt-in to the future behavior, set `pd.set_option('future.no_silent_downcasting', True)` 212s out_df[sk1].fillna(0, inplace=True) 212s 212s tests/test_ops.py::test_trim 212s /tmp/autopkgtest.zSk1h9/autopkgtest_tmp/tests/test_ops.py:210: FutureWarning: Mismatched null-like values and None found. In a future version, pandas equality-testing functions (e.g. assert_frame_equal) will consider these not-matching and raise. 212s pd.testing.assert_frame_equal( 212s 212s tests/test_ops.py::test_overlap 212s /tmp/autopkgtest.zSk1h9/autopkgtest_tmp/tests/test_ops.py:442: DeprecationWarning: Bitwise inversion '~' on bool is deprecated and will be removed in Python 3.16. This returns the bitwise inversion of the underlying int object and is usually not what you expect from negating a bool. Use the 'not' operator for boolean negation or ~int(x) if you really want the bitwise inversion of the underlying int. 212s assert ~df1.equals( 212s 212s tests/test_ops.py::test_assign_view 212s /tmp/autopkgtest.zSk1h9/autopkgtest_tmp/tests/test_ops.py:1632: FutureWarning: Mismatched null-like values and None found. In a future version, pandas equality-testing functions (e.g. assert_frame_equal) will consider these not-matching and raise. 212s pd.testing.assert_frame_equal( 212s 212s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 212s ================= 47 passed, 3 skipped, 504 warnings in 5.04s ================== 213s autopkgtest [19:51:38]: test run-unit-test: -----------------------] 217s autopkgtest [19:51:42]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 217s run-unit-test PASS 221s autopkgtest [19:51:46]: @@@@@@@@@@@@@@@@@@@@ summary 221s run-unit-test PASS