0s autopkgtest [20:02:06]: starting date and time: 2025-11-15 20:02:06+0000 0s autopkgtest [20:02:06]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [20:02:06]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.9ubxqzur/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --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 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-cpu2-ram4-disk20-amd64 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@sto01-2.secgroup --name adt-resolute-amd64-python-bioframe-20251115-200206-juju-7f2275-prod-proposed-migration-environment-20-f3eab520-dea8-4575-8444-b44a21c3daa9 --image adt/ubuntu-resolute-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-autopkgtest-workers-amd64 -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 3s Creating nova instance adt-resolute-amd64-python-bioframe-20251115-200206-juju-7f2275-prod-proposed-migration-environment-20-f3eab520-dea8-4575-8444-b44a21c3daa9 from image adt/ubuntu-resolute-amd64-server-20251115.img (UUID defe59a7-3f6c-4c3e-b6a5-c1b00ec74db3)... 44s autopkgtest [20:02:50]: testbed dpkg architecture: amd64 44s autopkgtest [20:02:50]: testbed apt version: 3.1.11 44s autopkgtest [20:02:50]: @@@@@@@@@@@@@@@@@@@@ test bed setup 45s autopkgtest [20:02:51]: testbed release detected to be: None 45s autopkgtest [20:02:51]: updating testbed package index (apt update) 45s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [87.8 kB] 45s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 45s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 46s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 46s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [22.9 kB] 46s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [9848 B] 46s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [78.5 kB] 46s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [821 kB] 46s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 Packages [154 kB] 46s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/main i386 Packages [115 kB] 46s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 c-n-f Metadata [3108 B] 46s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/restricted amd64 Packages [64.6 kB] 46s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/restricted i386 Packages [3744 B] 46s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/restricted amd64 c-n-f Metadata [336 B] 46s Get:15 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 Packages [581 kB] 46s Get:16 http://ftpmaster.internal/ubuntu resolute-proposed/universe i386 Packages [272 kB] 46s Get:17 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 c-n-f Metadata [17.0 kB] 46s Get:18 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse i386 Packages [5984 B] 46s Get:19 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 Packages [12.9 kB] 46s Get:20 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 c-n-f Metadata [628 B] 47s Fetched 2251 kB in 1s (2994 kB/s) 48s Reading package lists... 48s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 48s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 48s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 48s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 49s Reading package lists... 49s Reading package lists... 49s Building dependency tree... 49s Reading state information... 49s Calculating upgrade... 49s The following packages will be upgraded: 49s python3-requests python3-rpds-py 49s 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 49s Need to get 420 kB of archives. 49s After this operation, 843 kB of additional disk space will be used. 49s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3-requests all 2.32.5+dfsg-1ubuntu1 [53.1 kB] 49s Get:2 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-rpds-py amd64 0.27.1-2ubuntu1 [366 kB] 49s dpkg-preconfigure: unable to re-open stdin: No such file or directory 49s Fetched 420 kB in 0s (0 B/s) 50s (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 ... 83371 files and directories currently installed.) 50s Preparing to unpack .../python3-requests_2.32.5+dfsg-1ubuntu1_all.deb ... 50s Unpacking python3-requests (2.32.5+dfsg-1ubuntu1) over (2.32.3+dfsg-5ubuntu2) ... 50s Preparing to unpack .../python3-rpds-py_0.27.1-2ubuntu1_amd64.deb ... 50s Unpacking python3-rpds-py (0.27.1-2ubuntu1) over (0.21.0-2ubuntu2) ... 50s Setting up python3-requests (2.32.5+dfsg-1ubuntu1) ... 50s Setting up python3-rpds-py (0.27.1-2ubuntu1) ... 50s autopkgtest [20:02:56]: upgrading testbed (apt dist-upgrade and autopurge) 50s Reading package lists... 50s Building dependency tree... 50s Reading state information... 50s Calculating upgrade... 50s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 50s Reading package lists... 51s Building dependency tree... 51s Reading state information... 51s Solving dependencies... 51s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 53s autopkgtest [20:02:59]: testbed running kernel: Linux 6.17.0-5-generic #5-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 22 10:00:33 UTC 2025 53s autopkgtest [20:02:59]: @@@@@@@@@@@@@@@@@@@@ apt-source python-bioframe 54s Get:1 http://ftpmaster.internal/ubuntu resolute/universe python-bioframe 0.4.1-2 (dsc) [2253 B] 54s Get:2 http://ftpmaster.internal/ubuntu resolute/universe python-bioframe 0.4.1-2 (tar) [816 kB] 54s Get:3 http://ftpmaster.internal/ubuntu resolute/universe python-bioframe 0.4.1-2 (diff) [3576 B] 54s gpgv: Signature made Sat Feb 15 19:14:39 2025 UTC 54s gpgv: using RSA key 8F6DE104377F3B11E741748731F3144544A1741A 54s gpgv: issuer "tchet@debian.org" 54s gpgv: Can't check signature: No public key 54s dpkg-source: warning: cannot verify inline signature for ./python-bioframe_0.4.1-2.dsc: no acceptable signature found 54s autopkgtest [20:03:00]: testing package python-bioframe version 0.4.1-2 55s autopkgtest [20:03:01]: build not needed 55s autopkgtest [20:03:01]: test run-unit-test: preparing testbed 56s Reading package lists... 56s Building dependency tree... 56s Reading state information... 56s Solving dependencies... 56s The following NEW packages will be installed: 56s blt fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-lyx libblas3 56s libdeflate0 libfontconfig1 libgfortran5 libgomp1 libgraphite2-3 56s libharfbuzz0b libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 liblapack3 56s liblcms2-2 liblerc4 libopenjp2-7 libqhull-r8.0 libraqm0 libsharpyuv0 56s libtcl8.6 libtiff6 libtk8.6 libwebp7 libwebpdemux2 libwebpmux3 libxft2 56s libxrender1 libxslt1.1 libxss1 libzopfli1 python-matplotlib-data python3-all 56s python3-bioframe python3-brotli python3-contourpy python3-cycler 56s python3-decorator python3-fonttools python3-fs python3-iniconfig 56s python3-kiwisolver python3-lxml python3-lz4 python3-matplotlib 56s python3-mpmath python3-numpy python3-numpy-dev python3-pandas 56s python3-pandas-lib python3-pil python3-pil.imagetk python3-platformdirs 56s python3-pluggy python3-pytest python3-pytz python3-scipy python3-sympy 56s python3-tk python3-ufolib2 python3-zopfli python3.13-tk python3.14-tk 56s tk8.6-blt2.5 unicode-data x11-common 56s 0 upgraded, 69 newly installed, 0 to remove and 0 not upgraded. 56s Need to get 88.0 MB of archives. 56s After this operation, 414 MB of additional disk space will be used. 56s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-numpy-dev amd64 1:2.2.4+ds-1ubuntu1 [147 kB] 56s Get:2 http://ftpmaster.internal/ubuntu resolute/main amd64 libblas3 amd64 3.12.1-7 [259 kB] 56s Get:3 http://ftpmaster.internal/ubuntu resolute/main amd64 libgfortran5 amd64 15.2.0-7ubuntu1 [939 kB] 56s Get:4 http://ftpmaster.internal/ubuntu resolute/main amd64 liblapack3 amd64 3.12.1-7 [2739 kB] 56s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-numpy amd64 1:2.2.4+ds-1ubuntu1 [5377 kB] 56s Get:6 http://ftpmaster.internal/ubuntu resolute/main amd64 libtcl8.6 amd64 8.6.17+dfsg-1 [1036 kB] 56s Get:7 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB] 56s Get:8 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-dejavu-core all 2.37-8 [835 kB] 56s Get:9 http://ftpmaster.internal/ubuntu resolute/main amd64 fontconfig-config amd64 2.15.0-2.3ubuntu1 [38.0 kB] 56s Get:10 http://ftpmaster.internal/ubuntu resolute/main amd64 libfontconfig1 amd64 2.15.0-2.3ubuntu1 [141 kB] 56s Get:11 http://ftpmaster.internal/ubuntu resolute/main amd64 libxrender1 amd64 1:0.9.12-1 [19.8 kB] 56s Get:12 http://ftpmaster.internal/ubuntu resolute/main amd64 libxft2 amd64 2.3.6-1build1 [45.3 kB] 56s Get:13 http://ftpmaster.internal/ubuntu resolute/main amd64 x11-common all 1:7.7+24ubuntu1 [22.4 kB] 56s Get:14 http://ftpmaster.internal/ubuntu resolute/main amd64 libxss1 amd64 1:1.2.3-1build3 [7204 B] 56s Get:15 http://ftpmaster.internal/ubuntu resolute/main amd64 libtk8.6 amd64 8.6.17-1 [823 kB] 57s Get:16 http://ftpmaster.internal/ubuntu resolute/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-8 [694 kB] 57s Get:17 http://ftpmaster.internal/ubuntu resolute/main amd64 blt amd64 2.5.3+dfsg-8 [4824 B] 57s Get:18 http://ftpmaster.internal/ubuntu resolute/universe amd64 fonts-lyx all 2.4.4-2 [171 kB] 57s Get:19 http://ftpmaster.internal/ubuntu resolute/main amd64 libdeflate0 amd64 1.23-2 [49.9 kB] 57s Get:20 http://ftpmaster.internal/ubuntu resolute/main amd64 libgomp1 amd64 15.2.0-7ubuntu1 [151 kB] 57s Get:21 http://ftpmaster.internal/ubuntu resolute/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB] 57s Get:22 http://ftpmaster.internal/ubuntu resolute/main amd64 libharfbuzz0b amd64 12.1.0-1 [535 kB] 57s Get:23 http://ftpmaster.internal/ubuntu resolute/main amd64 libimagequant0 amd64 2.18.0-1build1 [36.3 kB] 57s Get:24 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg-turbo8 amd64 2.1.5-4ubuntu2 [152 kB] 57s Get:25 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 57s Get:26 http://ftpmaster.internal/ubuntu resolute/main amd64 liblcms2-2 amd64 2.16-2 [212 kB] 57s Get:27 http://ftpmaster.internal/ubuntu resolute/main amd64 liblerc4 amd64 4.0.0+ds-5ubuntu1 [271 kB] 57s Get:28 http://ftpmaster.internal/ubuntu resolute/universe amd64 libqhull-r8.0 amd64 2020.2-7 [197 kB] 57s Get:29 http://ftpmaster.internal/ubuntu resolute/main amd64 libraqm0 amd64 0.10.3-1 [15.4 kB] 57s Get:30 http://ftpmaster.internal/ubuntu resolute/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [25.9 kB] 57s Get:31 http://ftpmaster.internal/ubuntu resolute/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB] 57s Get:32 http://ftpmaster.internal/ubuntu resolute/main amd64 libwebp7 amd64 1.5.0-0.1 [378 kB] 57s Get:33 http://ftpmaster.internal/ubuntu resolute/main amd64 libtiff6 amd64 4.7.0-3ubuntu3 [209 kB] 57s Get:34 http://ftpmaster.internal/ubuntu resolute/main amd64 libwebpdemux2 amd64 1.5.0-0.1 [13.0 kB] 57s Get:35 http://ftpmaster.internal/ubuntu resolute/main amd64 libwebpmux3 amd64 1.5.0-0.1 [27.6 kB] 57s Get:36 http://ftpmaster.internal/ubuntu resolute/main amd64 libxslt1.1 amd64 1.1.43-0.3 [172 kB] 57s Get:37 http://ftpmaster.internal/ubuntu resolute/universe amd64 libzopfli1 amd64 1.0.3-3 [141 kB] 57s Get:38 http://ftpmaster.internal/ubuntu resolute/universe amd64 python-matplotlib-data all 3.10.7+dfsg1-1 [2930 kB] 57s Get:39 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-all amd64 3.13.7-1 [884 B] 57s Get:40 http://ftpmaster.internal/ubuntu resolute/main amd64 libopenjp2-7 amd64 2.5.3-2.1 [188 kB] 57s Get:41 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-pil amd64 11.3.0-1ubuntu2 [504 kB] 57s Get:42 http://ftpmaster.internal/ubuntu resolute/main amd64 python3.14-tk amd64 3.14.0-4 [108 kB] 57s Get:43 http://ftpmaster.internal/ubuntu resolute/main amd64 python3.13-tk amd64 3.13.9-1 [108 kB] 57s Get:44 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-tk amd64 3.13.9-1 [8946 B] 57s Get:45 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pil.imagetk amd64 11.3.0-1ubuntu2 [9804 B] 57s Get:46 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-contourpy amd64 1.3.1-2 [255 kB] 57s Get:47 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-cycler all 0.12.1-2 [9850 B] 57s Get:48 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-brotli amd64 1.1.0-2build6 [340 kB] 57s Get:49 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-platformdirs all 4.3.7-1 [16.9 kB] 57s Get:50 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-fs all 2.4.16-9ubuntu1 [91.5 kB] 57s Get:51 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-lxml amd64 6.0.2-1 [2333 kB] 57s Get:52 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-lz4 amd64 4.4.4+dfsg-3 [27.5 kB] 57s Get:53 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-decorator all 5.2.1-2 [28.1 kB] 57s Get:54 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-scipy amd64 1.15.3-1ubuntu1 [20.3 MB] 57s Get:55 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-mpmath all 1.3.0-2 [423 kB] 57s Get:56 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-sympy all 1.14.0-2 [4306 kB] 57s Get:57 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-ufolib2 all 0.17.1+dfsg1-1 [33.5 kB] 57s Get:58 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-zopfli amd64 0.4.0-1 [11.1 kB] 57s Get:59 http://ftpmaster.internal/ubuntu resolute/universe amd64 unicode-data all 16.0.0-1 [9513 kB] 58s Get:60 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-fonttools amd64 4.57.0-2build1 [1731 kB] 58s Get:61 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-kiwisolver amd64 1.4.10~rc0-1 [65.5 kB] 58s Get:62 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-matplotlib amd64 3.10.7+dfsg1-1 [17.2 MB] 58s Get:63 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-pytz all 2025.2-4 [32.3 kB] 58s Get:64 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pandas-lib amd64 2.3.3+dfsg-1ubuntu1 [7668 kB] 58s Get:65 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pandas all 2.3.3+dfsg-1ubuntu1 [2948 kB] 59s Get:66 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-bioframe all 0.4.1-2 [76.3 kB] 59s Get:67 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-iniconfig all 2.1.0-1 [6840 B] 59s Get:68 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pluggy all 1.6.0-1 [21.0 kB] 59s Get:69 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pytest all 8.3.5-2 [252 kB] 59s Fetched 88.0 MB in 3s (32.8 MB/s) 59s Selecting previously unselected package python3-numpy-dev:amd64. 59s (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 ... 83372 files and directories currently installed.) 59s Preparing to unpack .../00-python3-numpy-dev_1%3a2.2.4+ds-1ubuntu1_amd64.deb ... 59s Unpacking python3-numpy-dev:amd64 (1:2.2.4+ds-1ubuntu1) ... 59s Selecting previously unselected package libblas3:amd64. 59s Preparing to unpack .../01-libblas3_3.12.1-7_amd64.deb ... 59s Unpacking libblas3:amd64 (3.12.1-7) ... 59s Selecting previously unselected package libgfortran5:amd64. 59s Preparing to unpack .../02-libgfortran5_15.2.0-7ubuntu1_amd64.deb ... 59s Unpacking libgfortran5:amd64 (15.2.0-7ubuntu1) ... 59s Selecting previously unselected package liblapack3:amd64. 59s Preparing to unpack .../03-liblapack3_3.12.1-7_amd64.deb ... 59s Unpacking liblapack3:amd64 (3.12.1-7) ... 59s Selecting previously unselected package python3-numpy. 59s Preparing to unpack .../04-python3-numpy_1%3a2.2.4+ds-1ubuntu1_amd64.deb ... 59s Unpacking python3-numpy (1:2.2.4+ds-1ubuntu1) ... 59s Selecting previously unselected package libtcl8.6:amd64. 59s Preparing to unpack .../05-libtcl8.6_8.6.17+dfsg-1_amd64.deb ... 59s Unpacking libtcl8.6:amd64 (8.6.17+dfsg-1) ... 59s Selecting previously unselected package fonts-dejavu-mono. 59s Preparing to unpack .../06-fonts-dejavu-mono_2.37-8_all.deb ... 59s Unpacking fonts-dejavu-mono (2.37-8) ... 59s Selecting previously unselected package fonts-dejavu-core. 59s Preparing to unpack .../07-fonts-dejavu-core_2.37-8_all.deb ... 59s Unpacking fonts-dejavu-core (2.37-8) ... 59s Selecting previously unselected package fontconfig-config. 59s Preparing to unpack .../08-fontconfig-config_2.15.0-2.3ubuntu1_amd64.deb ... 59s Unpacking fontconfig-config (2.15.0-2.3ubuntu1) ... 59s Selecting previously unselected package libfontconfig1:amd64. 59s Preparing to unpack .../09-libfontconfig1_2.15.0-2.3ubuntu1_amd64.deb ... 59s Unpacking libfontconfig1:amd64 (2.15.0-2.3ubuntu1) ... 59s Selecting previously unselected package libxrender1:amd64. 59s Preparing to unpack .../10-libxrender1_1%3a0.9.12-1_amd64.deb ... 59s Unpacking libxrender1:amd64 (1:0.9.12-1) ... 59s Selecting previously unselected package libxft2:amd64. 59s Preparing to unpack .../11-libxft2_2.3.6-1build1_amd64.deb ... 59s Unpacking libxft2:amd64 (2.3.6-1build1) ... 59s Selecting previously unselected package x11-common. 59s Preparing to unpack .../12-x11-common_1%3a7.7+24ubuntu1_all.deb ... 59s Unpacking x11-common (1:7.7+24ubuntu1) ... 59s Selecting previously unselected package libxss1:amd64. 59s Preparing to unpack .../13-libxss1_1%3a1.2.3-1build3_amd64.deb ... 59s Unpacking libxss1:amd64 (1:1.2.3-1build3) ... 59s Selecting previously unselected package libtk8.6:amd64. 59s Preparing to unpack .../14-libtk8.6_8.6.17-1_amd64.deb ... 59s Unpacking libtk8.6:amd64 (8.6.17-1) ... 59s Selecting previously unselected package tk8.6-blt2.5. 59s Preparing to unpack .../15-tk8.6-blt2.5_2.5.3+dfsg-8_amd64.deb ... 59s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-8) ... 59s Selecting previously unselected package blt. 59s Preparing to unpack .../16-blt_2.5.3+dfsg-8_amd64.deb ... 59s Unpacking blt (2.5.3+dfsg-8) ... 59s Selecting previously unselected package fonts-lyx. 59s Preparing to unpack .../17-fonts-lyx_2.4.4-2_all.deb ... 59s Unpacking fonts-lyx (2.4.4-2) ... 59s Selecting previously unselected package libdeflate0:amd64. 59s Preparing to unpack .../18-libdeflate0_1.23-2_amd64.deb ... 59s Unpacking libdeflate0:amd64 (1.23-2) ... 59s Selecting previously unselected package libgomp1:amd64. 59s Preparing to unpack .../19-libgomp1_15.2.0-7ubuntu1_amd64.deb ... 59s Unpacking libgomp1:amd64 (15.2.0-7ubuntu1) ... 59s Selecting previously unselected package libgraphite2-3:amd64. 59s Preparing to unpack .../20-libgraphite2-3_1.3.14-2ubuntu1_amd64.deb ... 59s Unpacking libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 59s Selecting previously unselected package libharfbuzz0b:amd64. 59s Preparing to unpack .../21-libharfbuzz0b_12.1.0-1_amd64.deb ... 59s Unpacking libharfbuzz0b:amd64 (12.1.0-1) ... 59s Selecting previously unselected package libimagequant0:amd64. 59s Preparing to unpack .../22-libimagequant0_2.18.0-1build1_amd64.deb ... 59s Unpacking libimagequant0:amd64 (2.18.0-1build1) ... 59s Selecting previously unselected package libjpeg-turbo8:amd64. 59s Preparing to unpack .../23-libjpeg-turbo8_2.1.5-4ubuntu2_amd64.deb ... 59s Unpacking libjpeg-turbo8:amd64 (2.1.5-4ubuntu2) ... 59s Selecting previously unselected package libjpeg8:amd64. 59s Preparing to unpack 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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 61s Setting up libzopfli1 (1.0.3-3) ... 61s Setting up python3-brotli (1.1.0-2build6) ... 61s Setting up python3-cycler (0.12.1-2) ... 62s Setting up libimagequant0:amd64 (2.18.0-1build1) ... 62s Setting up fonts-dejavu-mono (2.37-8) ... 62s Setting up python3-kiwisolver (1.4.10~rc0-1) ... 62s Setting up python3-numpy-dev:amd64 (1:2.2.4+ds-1ubuntu1) ... 62s Setting up libtcl8.6:amd64 (8.6.17+dfsg-1) ... 62s Setting up fonts-dejavu-core (2.37-8) ... 62s Setting up libjpeg-turbo8:amd64 (2.1.5-4ubuntu2) ... 62s Setting up libgfortran5:amd64 (15.2.0-7ubuntu1) ... 62s Setting up python3-pluggy (1.6.0-1) ... 62s Setting up libwebp7:amd64 (1.5.0-0.1) ... 62s Setting up libxslt1.1:amd64 (1.1.43-0.3) ... 62s Setting up libopenjp2-7:amd64 (2.5.3-2.1) ... 62s Setting up libharfbuzz0b:amd64 (12.1.0-1) ... 62s Setting up libxss1:amd64 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Setting up libxft2:amd64 (2.3.6-1build1) ... 67s Setting up python3-scipy (1.15.3-1ubuntu1) ... 69s Setting up libtk8.6:amd64 (8.6.17-1) ... 69s Setting up python3-pandas-lib:amd64 (2.3.3+dfsg-1ubuntu1) ... 69s Setting up python3.13-tk (3.13.9-1) ... 69s Setting up python3-pil:amd64 (11.3.0-1ubuntu2) ... 69s Setting up python3-pandas (2.3.3+dfsg-1ubuntu1) ... 72s Setting up tk8.6-blt2.5 (2.5.3+dfsg-8) ... 72s Setting up python3.14-tk (3.14.0-4) ... 72s Setting up blt (2.5.3+dfsg-8) ... 72s Setting up python3-tk:amd64 (3.13.9-1) ... 72s Setting up python3-pil.imagetk:amd64 (11.3.0-1ubuntu2) ... 72s Setting up python3-fonttools (4.57.0-2build1) ... 72s Setting up python3-ufolib2 (0.17.1+dfsg1-1) ... 72s Setting up python3-matplotlib (3.10.7+dfsg1-1) ... 73s Setting up python3-bioframe (0.4.1-2) ... 73s Processing triggers for libc-bin (2.42-2ubuntu2) ... 73s Processing triggers for man-db (2.13.1-1) ... 74s autopkgtest [20:03:20]: test run-unit-test: [----------------------- 75s ============================= test session starts ============================== 75s platform linux -- Python 3.13.9, pytest-8.3.5, pluggy-1.6.0 -- /usr/bin/python3.13 75s cachedir: .pytest_cache 75s rootdir: /tmp/autopkgtest.FVy1i1/autopkgtest_tmp 75s plugins: typeguard-4.4.2 76s collecting ... collected 50 items 76s 76s tests/test_core_checks.py::test_is_cataloged PASSED [ 2%] 76s tests/test_core_checks.py::test_is_contained PASSED [ 4%] 76s tests/test_core_checks.py::test_is_overlapping PASSED [ 6%] 76s tests/test_core_checks.py::test_is_covering PASSED [ 8%] 76s tests/test_core_checks.py::test_is_tiling PASSED [ 10%] 76s tests/test_core_checks.py::test_is_bedframe PASSED [ 12%] 76s tests/test_core_checks.py::test_is_viewframe PASSED [ 14%] 76s tests/test_core_checks.py::test_is_sorted PASSED [ 16%] 76s tests/test_core_construction.py::test_add_ucsc_name_column PASSED [ 18%] 76s tests/test_core_construction.py::test_any PASSED [ 20%] 76s tests/test_core_construction.py::test_sanitize_bedframe PASSED [ 22%] 76s tests/test_core_construction.py::test_make_viewframe PASSED [ 24%] 76s tests/test_core_specs.py::test_get_default_colnames PASSED [ 26%] 76s tests/test_core_specs.py::test_update_default_colnames PASSED [ 28%] 76s tests/test_core_specs.py::test_verify_columns PASSED [ 30%] 76s tests/test_core_specs.py::test_verify_column_dtypes PASSED [ 32%] 76s tests/test_core_specs.py::test_is_chrom_dtype PASSED [ 34%] 76s tests/test_core_stringops.py::test_to_ucsc_string PASSED [ 36%] 76s tests/test_core_stringops.py::test_parse_region PASSED [ 38%] 76s tests/test_core_stringops.py::test_parse_region_string PASSED [ 40%] 76s tests/test_core_stringops.py::test_is_complete_ucsc_string PASSED [ 42%] 76s tests/test_extras.py::test_make_chromarms PASSED [ 44%] 76s tests/test_extras.py::test_binnify PASSED [ 46%] 76s tests/test_extras.py::test_digest SKIPPED (could not import 'Bio': N...) [ 48%] 76s tests/test_extras.py::test_frac_mapped SKIPPED (could not import 'py...) [ 50%] 76s tests/test_extras.py::test_frac_gc SKIPPED (could not import 'pysam'...) [ 52%] 76s tests/test_extras.py::test_seq_gc PASSED [ 54%] 76s tests/test_extras.py::test_pair_by_distance PASSED [ 56%] 76s tests/test_io.py::test_read_table PASSED [ 58%] 76s tests/test_io.py::test_read_chromsizes PASSED [ 60%] 76s tests/test_ops.py::test_trim PASSED [ 62%] 76s tests/test_ops.py::test_expand PASSED [ 64%] 76s tests/test_ops.py::test_overlap PASSED [ 66%] 76s tests/test_ops.py::test_cluster PASSED [ 68%] 76s tests/test_ops.py::test_merge PASSED [ 70%] 76s tests/test_ops.py::test_complement PASSED [ 72%] 76s tests/test_ops.py::test_closest PASSED [ 74%] 76s tests/test_ops.py::test_coverage PASSED [ 76%] 76s tests/test_ops.py::test_subtract PASSED [ 78%] 76s tests/test_ops.py::test_setdiff PASSED [ 80%] 76s tests/test_ops.py::test_count_overlaps PASSED [ 82%] 77s tests/test_ops.py::test_assign_view PASSED [ 84%] 77s tests/test_ops.py::test_sort_bedframe PASSED [ 86%] 77s tests/test_ops_select.py::test_select PASSED [ 88%] 77s tests/test_ops_select.py::test_select__with_colnames PASSED [ 90%] 77s tests/test_ops_select.py::test_select__with_nulls PASSED [ 92%] 77s tests/test_ops_select.py::test_select__mask_indices_labels PASSED [ 94%] 77s tests/test_ops_select.py::test_select__query_intervals_are_half_open PASSED [ 96%] 77s tests/test_ops_select.py::test_select__with_point_intervals PASSED [ 98%] 77s tests/test_ops_select.py::test_select__with_points PASSED [100%] 77s 77s =============================== warnings summary =============================== 77s ../../../usr/lib/python3/dist-packages/bioframe/io/resources.py:13 77s /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 77s import pkg_resources 77s 77s tests/test_io.py:23 77s /tmp/autopkgtest.FVy1i1/autopkgtest_tmp/tests/test_io.py:23: SyntaxWarning: invalid escape sequence '\s' 77s assert bioframe.read_table(StringIO(d), schema="bed3", sep="\s+").shape == (3, 3) 77s 77s tests/test_io.py:24 77s /tmp/autopkgtest.FVy1i1/autopkgtest_tmp/tests/test_io.py:24: SyntaxWarning: invalid escape sequence '\s' 77s assert bioframe.read_table(StringIO(d), schema="bed6", sep="\s+").shape == (3, 6) 77s 77s tests/test_io.py:25 77s /tmp/autopkgtest.FVy1i1/autopkgtest_tmp/tests/test_io.py:25: SyntaxWarning: invalid escape sequence '\s' 77s assert bioframe.read_table(StringIO(d), schema="bed12", sep="\s+").shape == (3, 12) 77s 77s tests/test_io.py:33 77s /tmp/autopkgtest.FVy1i1/autopkgtest_tmp/tests/test_io.py:33: SyntaxWarning: invalid escape sequence '\s' 77s StringIO(d), schema="bedpe", sep="\s+", schema_is_strict=True 77s 77s tests/test_core_checks.py: 84 warnings 77s tests/test_core_construction.py: 28 warnings 77s tests/test_core_specs.py: 12 warnings 77s tests/test_extras.py: 24 warnings 77s tests/test_ops.py: 326 warnings 77s /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 77s pd.api.types.is_categorical_dtype(chrom_dtype), 77s 77s tests/test_core_checks.py: 4 warnings 77s tests/test_ops.py: 6 warnings 77s /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. 77s 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. 77s 77s 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. 77s 77s 77s df_trimmed[sk].clip(lower=lower_vector, upper=upper_vector, inplace=True) 77s 77s tests/test_core_checks.py: 4 warnings 77s tests/test_ops.py: 6 warnings 77s /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. 77s 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. 77s 77s 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. 77s 77s 77s df_trimmed[ek].clip(lower=lower_vector, upper=upper_vector, inplace=True) 77s 77s tests/test_core_construction.py::test_any 77s /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. 77s 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. 77s 77s 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. 77s 77s 77s out_df[sk1].fillna(0, inplace=True) 77s 77s tests/test_core_construction.py::test_any 77s /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)` 77s out_df[sk1].fillna(0, inplace=True) 77s 77s tests/test_ops.py::test_trim 77s /tmp/autopkgtest.FVy1i1/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. 77s pd.testing.assert_frame_equal( 77s 77s tests/test_ops.py::test_overlap 77s /tmp/autopkgtest.FVy1i1/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. 77s assert ~df1.equals( 77s 77s tests/test_ops.py::test_assign_view 77s /tmp/autopkgtest.FVy1i1/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. 77s pd.testing.assert_frame_equal( 77s 77s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 77s ================= 47 passed, 3 skipped, 504 warnings in 1.86s ================== 77s autopkgtest [20:03:23]: test run-unit-test: -----------------------] 77s run-unit-test PASS 77s autopkgtest [20:03:23]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 78s autopkgtest [20:03:24]: @@@@@@@@@@@@@@@@@@@@ summary 78s run-unit-test PASS