0s autopkgtest [00:33:32]: starting date and time: 2025-11-16 00:33:32+0000 0s autopkgtest [00:33:32]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [00:33:32]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.e9bg_p7c/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-s390x --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-s390x-11.secgroup --name adt-resolute-s390x-python-bioframe-20251116-003332-juju-7f2275-prod-proposed-migration-environment-2-d097c9b6-7c17-4b38-b139-8b65ac1a48dc --image adt/ubuntu-resolute-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration-s390x -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 4s Creating nova instance adt-resolute-s390x-python-bioframe-20251116-003332-juju-7f2275-prod-proposed-migration-environment-2-d097c9b6-7c17-4b38-b139-8b65ac1a48dc from image adt/ubuntu-resolute-s390x-server-20251115.img (UUID 06234799-3082-4560-bce8-5266014337ad)... 186s autopkgtest [00:36:38]: testbed dpkg architecture: s390x 186s autopkgtest [00:36:38]: testbed apt version: 3.1.11 187s autopkgtest [00:36:39]: @@@@@@@@@@@@@@@@@@@@ test bed setup 187s autopkgtest [00:36:39]: testbed release detected to be: None 188s autopkgtest [00:36:40]: updating testbed package index (apt update) 188s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [87.8 kB] 188s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 189s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 189s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 189s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [9848 B] 189s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [80.8 kB] 189s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [817 kB] 189s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [22.9 kB] 189s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main s390x Packages [138 kB] 189s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/restricted s390x Packages [940 B] 189s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/universe s390x Packages [523 kB] 189s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse s390x Packages [10.6 kB] 189s Fetched 1690 kB in 1s (1409 kB/s) 190s Reading package lists... 191s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 191s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 191s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 191s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 191s Reading package lists... 191s Reading package lists... 191s Building dependency tree... 191s Reading state information... 192s Calculating upgrade... 192s The following packages will be upgraded: 192s python3-requests python3-rpds-py 192s 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 192s Need to get 418 kB of archives. 192s After this operation, 796 kB of additional disk space will be used. 192s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed/main s390x python3-requests all 2.32.5+dfsg-1ubuntu1 [53.1 kB] 192s Get:2 http://ftpmaster.internal/ubuntu resolute/main s390x python3-rpds-py s390x 0.27.1-2ubuntu1 [364 kB] 192s dpkg-preconfigure: unable to re-open stdin: No such file or directory 192s Fetched 418 kB in 1s (715 kB/s) 192s (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 ... 61308 files and directories currently installed.) 192s Preparing to unpack .../python3-requests_2.32.5+dfsg-1ubuntu1_all.deb ... 193s Unpacking python3-requests (2.32.5+dfsg-1ubuntu1) over (2.32.3+dfsg-5ubuntu2) ... 193s Preparing to unpack .../python3-rpds-py_0.27.1-2ubuntu1_s390x.deb ... 193s Unpacking python3-rpds-py (0.27.1-2ubuntu1) over (0.21.0-2ubuntu2) ... 193s Setting up python3-requests (2.32.5+dfsg-1ubuntu1) ... 193s Setting up python3-rpds-py (0.27.1-2ubuntu1) ... 193s autopkgtest [00:36:45]: upgrading testbed (apt dist-upgrade and autopurge) 193s Reading package lists... 193s Building dependency tree... 193s Reading state information... 193s Calculating upgrade... 193s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 194s Reading package lists... 194s Building dependency tree... 194s Reading state information... 194s Solving dependencies... 194s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 196s autopkgtest [00:36:48]: testbed running kernel: Linux 6.17.0-5-generic #5-Ubuntu SMP Mon Sep 22 08:56:47 UTC 2025 196s autopkgtest [00:36:48]: @@@@@@@@@@@@@@@@@@@@ apt-source python-bioframe 198s Get:1 http://ftpmaster.internal/ubuntu resolute/universe python-bioframe 0.4.1-2 (dsc) [2253 B] 198s Get:2 http://ftpmaster.internal/ubuntu resolute/universe python-bioframe 0.4.1-2 (tar) [816 kB] 198s Get:3 http://ftpmaster.internal/ubuntu resolute/universe python-bioframe 0.4.1-2 (diff) [3576 B] 198s gpgv: Signature made Sat Feb 15 19:14:39 2025 UTC 198s gpgv: using RSA key 8F6DE104377F3B11E741748731F3144544A1741A 198s gpgv: issuer "tchet@debian.org" 198s gpgv: Can't check signature: No public key 198s dpkg-source: warning: cannot verify inline signature for ./python-bioframe_0.4.1-2.dsc: no acceptable signature found 198s autopkgtest [00:36:50]: testing package python-bioframe version 0.4.1-2 198s autopkgtest [00:36:50]: build not needed 199s autopkgtest [00:36:51]: test run-unit-test: preparing testbed 199s Reading package lists... 199s Building dependency tree... 199s Reading state information... 199s Solving dependencies... 199s The following NEW packages will be installed: 199s blt fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-lyx libblas3 199s libdeflate0 libfontconfig1 libfreetype6 libgfortran5 libgomp1 libgraphite2-3 199s libharfbuzz0b libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 liblapack3 199s liblcms2-2 libopenjp2-7 libqhull-r8.0 libraqm0 libsharpyuv0 libtcl8.6 199s libtiff6 libtk8.6 libwebp7 libwebpdemux2 libwebpmux3 libxft2 libxrender1 199s libxslt1.1 libxss1 libzopfli1 python-matplotlib-data python3-all 199s python3-bioframe python3-brotli python3-contourpy python3-cycler 199s python3-decorator python3-fonttools python3-fs python3-iniconfig 199s python3-kiwisolver python3-lxml python3-lz4 python3-matplotlib 199s python3-mpmath python3-numpy python3-numpy-dev python3-pandas 199s python3-pandas-lib python3-pil python3-pil.imagetk python3-platformdirs 199s python3-pluggy python3-pytest python3-pytz python3-scipy python3-sympy 199s python3-tk python3-ufolib2 python3-zopfli python3.13-tk python3.14-tk 199s tk8.6-blt2.5 unicode-data x11-common 199s 0 upgraded, 69 newly installed, 0 to remove and 0 not upgraded. 199s Need to get 89.2 MB of archives. 199s After this operation, 404 MB of additional disk space will be used. 199s Get:1 http://ftpmaster.internal/ubuntu resolute/main s390x python3-numpy-dev s390x 1:2.2.4+ds-1ubuntu1 [147 kB] 200s Get:2 http://ftpmaster.internal/ubuntu resolute/main s390x libblas3 s390x 3.12.1-7 [254 kB] 200s Get:3 http://ftpmaster.internal/ubuntu resolute/main s390x libgfortran5 s390x 15.2.0-7ubuntu1 [629 kB] 200s Get:4 http://ftpmaster.internal/ubuntu resolute/main s390x liblapack3 s390x 3.12.1-7 [2983 kB] 201s Get:5 http://ftpmaster.internal/ubuntu resolute/main s390x python3-numpy s390x 1:2.2.4+ds-1ubuntu1 [4399 kB] 201s Get:6 http://ftpmaster.internal/ubuntu resolute/main s390x libtcl8.6 s390x 8.6.17+dfsg-1 [1034 kB] 202s Get:7 http://ftpmaster.internal/ubuntu resolute/main s390x libfreetype6 s390x 2.13.3+dfsg-1build1 [430 kB] 202s Get:8 http://ftpmaster.internal/ubuntu resolute/main s390x fonts-dejavu-mono all 2.37-8 [502 kB] 202s Get:9 http://ftpmaster.internal/ubuntu resolute/main s390x fonts-dejavu-core all 2.37-8 [835 kB] 202s Get:10 http://ftpmaster.internal/ubuntu resolute/main s390x fontconfig-config s390x 2.15.0-2.3ubuntu1 [38.1 kB] 202s Get:11 http://ftpmaster.internal/ubuntu resolute/main s390x libfontconfig1 s390x 2.15.0-2.3ubuntu1 [149 kB] 202s Get:12 http://ftpmaster.internal/ubuntu resolute/main s390x libxrender1 s390x 1:0.9.12-1 [20.9 kB] 202s Get:13 http://ftpmaster.internal/ubuntu resolute/main s390x libxft2 s390x 2.3.6-1build1 [49.6 kB] 202s Get:14 http://ftpmaster.internal/ubuntu resolute/main s390x x11-common all 1:7.7+24ubuntu1 [22.4 kB] 202s Get:15 http://ftpmaster.internal/ubuntu resolute/main s390x libxss1 s390x 1:1.2.3-1build3 [7396 B] 202s Get:16 http://ftpmaster.internal/ubuntu resolute/main s390x libtk8.6 s390x 8.6.17-1 [828 kB] 202s Get:17 http://ftpmaster.internal/ubuntu resolute/main s390x tk8.6-blt2.5 s390x 2.5.3+dfsg-8 [657 kB] 202s Get:18 http://ftpmaster.internal/ubuntu resolute/main s390x blt s390x 2.5.3+dfsg-8 [4826 B] 202s Get:19 http://ftpmaster.internal/ubuntu resolute/universe s390x fonts-lyx all 2.4.4-2 [171 kB] 202s Get:20 http://ftpmaster.internal/ubuntu resolute/main s390x libdeflate0 s390x 1.23-2 [46.0 kB] 202s Get:21 http://ftpmaster.internal/ubuntu resolute/main s390x libgomp1 s390x 15.2.0-7ubuntu1 [154 kB] 202s Get:22 http://ftpmaster.internal/ubuntu resolute/main s390x libgraphite2-3 s390x 1.3.14-2ubuntu1 [79.8 kB] 202s Get:23 http://ftpmaster.internal/ubuntu resolute/main s390x libharfbuzz0b s390x 12.1.0-1 [576 kB] 202s Get:24 http://ftpmaster.internal/ubuntu resolute/main s390x libimagequant0 s390x 2.18.0-1build1 [43.3 kB] 202s Get:25 http://ftpmaster.internal/ubuntu resolute/main s390x libjpeg-turbo8 s390x 2.1.5-4ubuntu2 [147 kB] 202s Get:26 http://ftpmaster.internal/ubuntu resolute/main s390x libjpeg8 s390x 8c-2ubuntu11 [2146 B] 202s Get:27 http://ftpmaster.internal/ubuntu resolute/main s390x liblcms2-2 s390x 2.17-1 [176 kB] 202s Get:28 http://ftpmaster.internal/ubuntu resolute/universe s390x libqhull-r8.0 s390x 2020.2-7 [199 kB] 202s Get:29 http://ftpmaster.internal/ubuntu resolute/main s390x libraqm0 s390x 0.10.3-1 [15.6 kB] 202s Get:30 http://ftpmaster.internal/ubuntu resolute/main s390x libsharpyuv0 s390x 1.5.0-0.1 [16.7 kB] 202s Get:31 http://ftpmaster.internal/ubuntu resolute/main s390x libjbig0 s390x 2.1-6.1ubuntu2 [33.1 kB] 202s Get:32 http://ftpmaster.internal/ubuntu resolute/main s390x libwebp7 s390x 1.5.0-0.1 [210 kB] 202s Get:33 http://ftpmaster.internal/ubuntu resolute/main s390x libtiff6 s390x 4.7.0-3ubuntu3 [222 kB] 202s Get:34 http://ftpmaster.internal/ubuntu resolute/main s390x libwebpdemux2 s390x 1.5.0-0.1 [12.6 kB] 202s Get:35 http://ftpmaster.internal/ubuntu resolute/main s390x libwebpmux3 s390x 1.5.0-0.1 [25.8 kB] 202s Get:36 http://ftpmaster.internal/ubuntu resolute/main s390x libxslt1.1 s390x 1.1.43-0.3 [163 kB] 202s Get:37 http://ftpmaster.internal/ubuntu resolute/universe s390x libzopfli1 s390x 1.0.3-3 [124 kB] 202s Get:38 http://ftpmaster.internal/ubuntu resolute/universe s390x python-matplotlib-data all 3.10.7+dfsg1-1 [2930 kB] 202s Get:39 http://ftpmaster.internal/ubuntu resolute/main s390x python3-all s390x 3.13.7-1 [886 B] 202s Get:40 http://ftpmaster.internal/ubuntu resolute/main s390x libopenjp2-7 s390x 2.5.3-2.1 [207 kB] 202s Get:41 http://ftpmaster.internal/ubuntu resolute/main s390x python3-pil s390x 11.3.0-1ubuntu2 [542 kB] 202s Get:42 http://ftpmaster.internal/ubuntu resolute/main s390x python3.14-tk s390x 3.14.0-4 [109 kB] 202s Get:43 http://ftpmaster.internal/ubuntu resolute/main s390x python3.13-tk s390x 3.13.9-1 [109 kB] 202s Get:44 http://ftpmaster.internal/ubuntu resolute/main s390x python3-tk s390x 3.13.9-1 [8948 B] 202s Get:45 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-pil.imagetk s390x 11.3.0-1ubuntu2 [9922 B] 202s Get:46 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-contourpy s390x 1.3.1-2 [266 kB] 202s Get:47 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-cycler all 0.12.1-2 [9850 B] 202s Get:48 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-brotli s390x 1.1.0-2build6 [386 kB] 203s Get:49 http://ftpmaster.internal/ubuntu resolute/main s390x python3-platformdirs all 4.3.7-1 [16.9 kB] 203s Get:50 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-fs all 2.4.16-9ubuntu1 [91.5 kB] 203s Get:51 http://ftpmaster.internal/ubuntu resolute/main s390x python3-lxml s390x 6.0.2-1 [2478 kB] 203s Get:52 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-lz4 s390x 4.4.4+dfsg-3 [27.4 kB] 203s Get:53 http://ftpmaster.internal/ubuntu resolute/main s390x python3-decorator all 5.2.1-2 [28.1 kB] 203s Get:54 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-scipy s390x 1.15.3-1ubuntu1 [21.3 MB] 204s Get:55 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-mpmath all 1.3.0-2 [423 kB] 204s Get:56 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-sympy all 1.14.0-2 [4306 kB] 204s Get:57 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-ufolib2 all 0.17.1+dfsg1-1 [33.5 kB] 204s Get:58 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-zopfli s390x 0.4.0-1 [11.2 kB] 204s Get:59 http://ftpmaster.internal/ubuntu resolute/universe s390x unicode-data all 16.0.0-1 [9513 kB] 204s Get:60 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-fonttools s390x 4.57.0-2build1 [1773 kB] 204s Get:61 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-kiwisolver s390x 1.4.10~rc0-1 [65.0 kB] 204s Get:62 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-matplotlib s390x 3.10.7+dfsg1-1 [17.2 MB] 204s Get:63 http://ftpmaster.internal/ubuntu resolute/main s390x python3-pytz all 2025.2-4 [32.3 kB] 204s Get:64 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-pandas-lib s390x 2.3.3+dfsg-1ubuntu1 [8668 kB] 205s Get:65 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-pandas all 2.3.3+dfsg-1ubuntu1 [2948 kB] 205s Get:66 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-bioframe all 0.4.1-2 [76.3 kB] 205s Get:67 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-iniconfig all 2.1.0-1 [6840 B] 205s Get:68 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-pluggy all 1.6.0-1 [21.0 kB] 205s Get:69 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-pytest all 8.3.5-2 [252 kB] 205s Fetched 89.2 MB in 5s (16.8 MB/s) 205s Selecting previously unselected package python3-numpy-dev:s390x. 205s (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 ... 61309 files and directories currently installed.) 205s Preparing to unpack .../00-python3-numpy-dev_1%3a2.2.4+ds-1ubuntu1_s390x.deb ... 205s Unpacking python3-numpy-dev:s390x (1:2.2.4+ds-1ubuntu1) ... 205s Selecting previously unselected package libblas3:s390x. 205s Preparing to unpack .../01-libblas3_3.12.1-7_s390x.deb ... 205s Unpacking libblas3:s390x (3.12.1-7) ... 205s Selecting previously unselected package libgfortran5:s390x. 205s Preparing to unpack .../02-libgfortran5_15.2.0-7ubuntu1_s390x.deb ... 205s Unpacking libgfortran5:s390x (15.2.0-7ubuntu1) ... 205s Selecting previously unselected package liblapack3:s390x. 205s Preparing to unpack .../03-liblapack3_3.12.1-7_s390x.deb ... 205s Unpacking liblapack3:s390x (3.12.1-7) ... 205s Selecting previously unselected package python3-numpy. 205s Preparing to unpack .../04-python3-numpy_1%3a2.2.4+ds-1ubuntu1_s390x.deb ... 205s Unpacking python3-numpy (1:2.2.4+ds-1ubuntu1) ... 205s Selecting previously unselected package libtcl8.6:s390x. 205s Preparing to unpack .../05-libtcl8.6_8.6.17+dfsg-1_s390x.deb ... 205s Unpacking libtcl8.6:s390x (8.6.17+dfsg-1) ... 205s Selecting previously unselected package libfreetype6:s390x. 205s Preparing to unpack .../06-libfreetype6_2.13.3+dfsg-1build1_s390x.deb ... 205s Unpacking libfreetype6:s390x (2.13.3+dfsg-1build1) ... 205s Selecting previously unselected package fonts-dejavu-mono. 205s Preparing to unpack .../07-fonts-dejavu-mono_2.37-8_all.deb ... 205s Unpacking fonts-dejavu-mono (2.37-8) ... 205s Selecting previously unselected package fonts-dejavu-core. 205s Preparing to unpack .../08-fonts-dejavu-core_2.37-8_all.deb ... 205s Unpacking fonts-dejavu-core (2.37-8) ... 205s Selecting previously unselected package fontconfig-config. 205s Preparing to unpack .../09-fontconfig-config_2.15.0-2.3ubuntu1_s390x.deb ... 205s Unpacking fontconfig-config (2.15.0-2.3ubuntu1) ... 205s Selecting previously unselected package libfontconfig1:s390x. 205s Preparing to unpack .../10-libfontconfig1_2.15.0-2.3ubuntu1_s390x.deb ... 205s Unpacking libfontconfig1:s390x (2.15.0-2.3ubuntu1) ... 205s Selecting previously unselected package libxrender1:s390x. 205s Preparing to unpack .../11-libxrender1_1%3a0.9.12-1_s390x.deb ... 205s Unpacking libxrender1:s390x (1:0.9.12-1) ... 205s Selecting previously unselected package libxft2:s390x. 205s Preparing to unpack .../12-libxft2_2.3.6-1build1_s390x.deb ... 205s Unpacking libxft2:s390x (2.3.6-1build1) ... 205s Selecting previously unselected package x11-common. 205s Preparing to unpack .../13-x11-common_1%3a7.7+24ubuntu1_all.deb ... 205s Unpacking x11-common (1:7.7+24ubuntu1) ... 205s Selecting previously unselected package libxss1:s390x. 205s Preparing to unpack .../14-libxss1_1%3a1.2.3-1build3_s390x.deb ... 205s Unpacking libxss1:s390x (1:1.2.3-1build3) ... 205s Selecting previously unselected package libtk8.6:s390x. 205s Preparing to unpack .../15-libtk8.6_8.6.17-1_s390x.deb ... 205s Unpacking libtk8.6:s390x (8.6.17-1) ... 205s Selecting previously unselected package tk8.6-blt2.5. 205s Preparing to unpack .../16-tk8.6-blt2.5_2.5.3+dfsg-8_s390x.deb ... 205s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-8) ... 206s Selecting previously unselected package blt. 206s Preparing to unpack .../17-blt_2.5.3+dfsg-8_s390x.deb ... 206s Unpacking blt (2.5.3+dfsg-8) ... 206s Selecting previously unselected package fonts-lyx. 206s Preparing to unpack .../18-fonts-lyx_2.4.4-2_all.deb ... 206s Unpacking fonts-lyx (2.4.4-2) ... 206s Selecting previously unselected package libdeflate0:s390x. 206s Preparing to unpack .../19-libdeflate0_1.23-2_s390x.deb ... 206s Unpacking libdeflate0:s390x (1.23-2) ... 206s Selecting previously unselected package libgomp1:s390x. 206s Preparing to unpack .../20-libgomp1_15.2.0-7ubuntu1_s390x.deb ... 206s Unpacking libgomp1:s390x (15.2.0-7ubuntu1) ... 206s Selecting previously unselected package libgraphite2-3:s390x. 206s Preparing to unpack .../21-libgraphite2-3_1.3.14-2ubuntu1_s390x.deb ... 206s Unpacking libgraphite2-3:s390x (1.3.14-2ubuntu1) ... 206s Selecting previously unselected package libharfbuzz0b:s390x. 206s Preparing to unpack .../22-libharfbuzz0b_12.1.0-1_s390x.deb ... 206s Unpacking libharfbuzz0b:s390x (12.1.0-1) ... 206s Selecting previously unselected package libimagequant0:s390x. 206s Preparing to unpack .../23-libimagequant0_2.18.0-1build1_s390x.deb ... 206s Unpacking libimagequant0:s390x (2.18.0-1build1) ... 206s Selecting previously unselected package libjpeg-turbo8:s390x. 206s Preparing to unpack .../24-libjpeg-turbo8_2.1.5-4ubuntu2_s390x.deb ... 206s Unpacking libjpeg-turbo8:s390x (2.1.5-4ubuntu2) ... 206s Selecting previously unselected package libjpeg8:s390x. 206s Preparing to unpack .../25-libjpeg8_8c-2ubuntu11_s390x.deb ... 206s Unpacking libjpeg8:s390x (8c-2ubuntu11) ... 206s Selecting previously unselected package liblcms2-2:s390x. 206s Preparing to unpack .../26-liblcms2-2_2.17-1_s390x.deb ... 206s Unpacking liblcms2-2:s390x (2.17-1) ... 206s Selecting previously unselected package libqhull-r8.0:s390x. 206s Preparing to unpack .../27-libqhull-r8.0_2020.2-7_s390x.deb ... 206s Unpacking libqhull-r8.0:s390x (2020.2-7) ... 206s Selecting previously unselected package libraqm0:s390x. 206s Preparing to unpack .../28-libraqm0_0.10.3-1_s390x.deb ... 206s Unpacking libraqm0:s390x (0.10.3-1) ... 206s Selecting previously unselected package libsharpyuv0:s390x. 206s Preparing to unpack .../29-libsharpyuv0_1.5.0-0.1_s390x.deb ... 206s Unpacking libsharpyuv0:s390x (1.5.0-0.1) ... 206s Selecting previously unselected package libjbig0:s390x. 206s Preparing to unpack .../30-libjbig0_2.1-6.1ubuntu2_s390x.deb ... 206s Unpacking libjbig0:s390x (2.1-6.1ubuntu2) ... 206s Selecting previously unselected package libwebp7:s390x. 206s Preparing to unpack .../31-libwebp7_1.5.0-0.1_s390x.deb ... 206s Unpacking libwebp7:s390x (1.5.0-0.1) ... 206s Selecting previously unselected package libtiff6:s390x. 206s Preparing to unpack .../32-libtiff6_4.7.0-3ubuntu3_s390x.deb ... 206s Unpacking libtiff6:s390x (4.7.0-3ubuntu3) ... 206s Selecting previously unselected package libwebpdemux2:s390x. 206s Preparing to unpack .../33-libwebpdemux2_1.5.0-0.1_s390x.deb ... 206s Unpacking libwebpdemux2:s390x (1.5.0-0.1) ... 206s Selecting previously unselected package libwebpmux3:s390x. 206s Preparing to unpack .../34-libwebpmux3_1.5.0-0.1_s390x.deb ... 206s Unpacking libwebpmux3:s390x (1.5.0-0.1) ... 206s Selecting previously unselected package libxslt1.1:s390x. 206s Preparing to unpack .../35-libxslt1.1_1.1.43-0.3_s390x.deb ... 206s Unpacking libxslt1.1:s390x (1.1.43-0.3) ... 206s Selecting previously unselected package libzopfli1. 206s Preparing to unpack .../36-libzopfli1_1.0.3-3_s390x.deb ... 206s Unpacking libzopfli1 (1.0.3-3) ... 206s Selecting previously unselected package python-matplotlib-data. 206s Preparing to unpack .../37-python-matplotlib-data_3.10.7+dfsg1-1_all.deb ... 206s Unpacking python-matplotlib-data (3.10.7+dfsg1-1) ... 206s Selecting previously unselected package python3-all. 206s Preparing to unpack .../38-python3-all_3.13.7-1_s390x.deb ... 206s Unpacking python3-all (3.13.7-1) ... 206s Selecting previously unselected package libopenjp2-7:s390x. 206s Preparing to unpack .../39-libopenjp2-7_2.5.3-2.1_s390x.deb ... 206s Unpacking libopenjp2-7:s390x (2.5.3-2.1) ... 206s Selecting previously unselected package python3-pil:s390x. 206s Preparing to unpack .../40-python3-pil_11.3.0-1ubuntu2_s390x.deb ... 206s Unpacking python3-pil:s390x (11.3.0-1ubuntu2) ... 206s Selecting previously unselected package python3.14-tk. 206s Preparing to unpack .../41-python3.14-tk_3.14.0-4_s390x.deb ... 206s Unpacking python3.14-tk (3.14.0-4) ... 206s Selecting previously unselected package python3.13-tk. 206s Preparing to unpack .../42-python3.13-tk_3.13.9-1_s390x.deb ... 206s Unpacking python3.13-tk (3.13.9-1) ... 206s Selecting previously unselected package python3-tk:s390x. 206s Preparing to unpack .../43-python3-tk_3.13.9-1_s390x.deb ... 206s Unpacking python3-tk:s390x (3.13.9-1) ... 206s Selecting previously unselected package python3-pil.imagetk:s390x. 206s Preparing to unpack .../44-python3-pil.imagetk_11.3.0-1ubuntu2_s390x.deb ... 206s Unpacking python3-pil.imagetk:s390x (11.3.0-1ubuntu2) ... 206s Selecting previously unselected package python3-contourpy. 206s Preparing to unpack .../45-python3-contourpy_1.3.1-2_s390x.deb ... 206s Unpacking python3-contourpy (1.3.1-2) ... 206s Selecting previously unselected package python3-cycler. 206s Preparing to unpack .../46-python3-cycler_0.12.1-2_all.deb ... 206s Unpacking python3-cycler (0.12.1-2) ... 206s Selecting previously unselected package python3-brotli. 206s Preparing to unpack .../47-python3-brotli_1.1.0-2build6_s390x.deb ... 206s Unpacking python3-brotli (1.1.0-2build6) ... 206s Selecting previously unselected package python3-platformdirs. 206s Preparing to unpack .../48-python3-platformdirs_4.3.7-1_all.deb ... 206s Unpacking python3-platformdirs (4.3.7-1) ... 206s Selecting previously unselected package python3-fs. 206s Preparing to unpack .../49-python3-fs_2.4.16-9ubuntu1_all.deb ... 206s Unpacking python3-fs (2.4.16-9ubuntu1) ... 206s Selecting previously unselected package python3-lxml:s390x. 206s Preparing to unpack .../50-python3-lxml_6.0.2-1_s390x.deb ... 206s Unpacking python3-lxml:s390x (6.0.2-1) ... 206s Selecting previously unselected package python3-lz4. 206s Preparing to unpack .../51-python3-lz4_4.4.4+dfsg-3_s390x.deb ... 206s Unpacking python3-lz4 (4.4.4+dfsg-3) ... 206s Selecting previously unselected package python3-decorator. 206s Preparing to unpack .../52-python3-decorator_5.2.1-2_all.deb ... 206s Unpacking python3-decorator (5.2.1-2) ... 206s Selecting previously unselected package python3-scipy. 206s Preparing to unpack .../53-python3-scipy_1.15.3-1ubuntu1_s390x.deb ... 206s Unpacking python3-scipy (1.15.3-1ubuntu1) ... 206s Selecting previously unselected package python3-mpmath. 206s Preparing to unpack .../54-python3-mpmath_1.3.0-2_all.deb ... 206s Unpacking python3-mpmath (1.3.0-2) ... 206s Selecting previously unselected package python3-sympy. 206s Preparing to unpack .../55-python3-sympy_1.14.0-2_all.deb ... 206s Unpacking python3-sympy (1.14.0-2) ... 207s Selecting previously unselected package python3-ufolib2. 207s Preparing to unpack .../56-python3-ufolib2_0.17.1+dfsg1-1_all.deb ... 207s Unpacking python3-ufolib2 (0.17.1+dfsg1-1) ... 207s Selecting previously unselected package python3-zopfli. 207s Preparing to unpack .../57-python3-zopfli_0.4.0-1_s390x.deb ... 207s Unpacking python3-zopfli (0.4.0-1) ... 207s Selecting previously unselected package unicode-data. 207s Preparing to unpack .../58-unicode-data_16.0.0-1_all.deb ... 207s Unpacking unicode-data (16.0.0-1) ... 207s Selecting previously unselected package python3-fonttools. 207s Preparing to unpack .../59-python3-fonttools_4.57.0-2build1_s390x.deb ... 207s Unpacking python3-fonttools (4.57.0-2build1) ... 207s Selecting previously unselected package python3-kiwisolver. 207s Preparing to unpack .../60-python3-kiwisolver_1.4.10~rc0-1_s390x.deb ... 207s Unpacking python3-kiwisolver (1.4.10~rc0-1) ... 207s Selecting previously unselected package python3-matplotlib. 207s Preparing to unpack .../61-python3-matplotlib_3.10.7+dfsg1-1_s390x.deb ... 207s Unpacking python3-matplotlib (3.10.7+dfsg1-1) ... 207s Selecting previously unselected package python3-pytz. 207s Preparing to unpack .../62-python3-pytz_2025.2-4_all.deb ... 207s Unpacking python3-pytz (2025.2-4) ... 207s Selecting previously unselected package python3-pandas-lib:s390x. 207s Preparing to unpack .../63-python3-pandas-lib_2.3.3+dfsg-1ubuntu1_s390x.deb ... 207s Unpacking python3-pandas-lib:s390x (2.3.3+dfsg-1ubuntu1) ... 207s Selecting previously unselected package python3-pandas. 207s Preparing to unpack .../64-python3-pandas_2.3.3+dfsg-1ubuntu1_all.deb ... 207s Unpacking python3-pandas (2.3.3+dfsg-1ubuntu1) ... 207s Selecting previously unselected package python3-bioframe. 207s Preparing to unpack .../65-python3-bioframe_0.4.1-2_all.deb ... 207s Unpacking python3-bioframe (0.4.1-2) ... 207s Selecting previously unselected package python3-iniconfig. 207s Preparing to unpack .../66-python3-iniconfig_2.1.0-1_all.deb ... 207s Unpacking python3-iniconfig (2.1.0-1) ... 207s Selecting previously unselected package python3-pluggy. 207s Preparing to unpack .../67-python3-pluggy_1.6.0-1_all.deb ... 207s Unpacking python3-pluggy (1.6.0-1) ... 207s Selecting previously unselected package python3-pytest. 207s Preparing to unpack .../68-python3-pytest_8.3.5-2_all.deb ... 207s Unpacking python3-pytest (8.3.5-2) ... 207s Setting up libgraphite2-3:s390x (1.3.14-2ubuntu1) ... 207s Setting up liblcms2-2:s390x (2.17-1) ... 207s Setting up python3-iniconfig (2.1.0-1) ... 207s Setting up libsharpyuv0:s390x (1.5.0-0.1) ... 207s Setting up libxrender1:s390x (1:0.9.12-1) ... 207s Setting up python3-lz4 (4.4.4+dfsg-3) ... 208s Setting up fonts-lyx (2.4.4-2) ... 208s Setting up x11-common (1:7.7+24ubuntu1) ... 208s Setting up libdeflate0:s390x (1.23-2) ... 208s Setting up libqhull-r8.0:s390x (2020.2-7) ... 208s Setting up python3-all (3.13.7-1) ... 208s Setting up python3-pytz (2025.2-4) ... 208s Setting up libgomp1:s390x (15.2.0-7ubuntu1) ... 208s Setting up libjbig0:s390x (2.1-6.1ubuntu2) ... 208s Setting up python3-platformdirs (4.3.7-1) ... 208s Setting up python3-fs (2.4.16-9ubuntu1) ... 208s Setting up unicode-data (16.0.0-1) ... 208s Setting up python3-decorator (5.2.1-2) ... 208s Setting up libblas3:s390x (3.12.1-7) ... 208s update-alternatives: using /usr/lib/s390x-linux-gnu/blas/libblas.so.3 to provide /usr/lib/s390x-linux-gnu/libblas.so.3 (libblas.so.3-s390x-linux-gnu) in auto mode 208s Setting up libzopfli1 (1.0.3-3) ... 208s Setting up libfreetype6:s390x (2.13.3+dfsg-1build1) ... 208s Setting up python3-brotli (1.1.0-2build6) ... 208s Setting up python3-cycler (0.12.1-2) ... 208s Setting up libimagequant0:s390x (2.18.0-1build1) ... 208s Setting up fonts-dejavu-mono (2.37-8) ... 208s Setting up python3-kiwisolver (1.4.10~rc0-1) ... 208s Setting up python3-numpy-dev:s390x (1:2.2.4+ds-1ubuntu1) ... 208s Setting up libtcl8.6:s390x (8.6.17+dfsg-1) ... 208s Setting up fonts-dejavu-core (2.37-8) ... 208s Setting up libjpeg-turbo8:s390x (2.1.5-4ubuntu2) ... 208s Setting up libgfortran5:s390x (15.2.0-7ubuntu1) ... 208s Setting up python3-pluggy (1.6.0-1) ... 208s Setting up libwebp7:s390x (1.5.0-0.1) ... 208s Setting up libxslt1.1:s390x (1.1.43-0.3) ... 208s Setting up libopenjp2-7:s390x (2.5.3-2.1) ... 208s Setting up libharfbuzz0b:s390x (12.1.0-1) ... 208s Setting up libxss1:s390x (1:1.2.3-1build3) ... 208s Setting up python3-mpmath (1.3.0-2) ... 209s Setting up python-matplotlib-data (3.10.7+dfsg1-1) ... 209s Setting up libwebpmux3:s390x (1.5.0-0.1) ... 209s Setting up libjpeg8:s390x (8c-2ubuntu11) ... 209s Setting up python3-sympy (1.14.0-2) ... 213s Setting up liblapack3:s390x (3.12.1-7) ... 213s update-alternatives: using /usr/lib/s390x-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/s390x-linux-gnu/liblapack.so.3 (liblapack.so.3-s390x-linux-gnu) in auto mode 213s Setting up fontconfig-config (2.15.0-2.3ubuntu1) ... 213s Setting up python3-pytest (8.3.5-2) ... 213s Setting up libwebpdemux2:s390x (1.5.0-0.1) ... 213s Setting up python3-zopfli (0.4.0-1) ... 213s Setting up libraqm0:s390x (0.10.3-1) ... 213s Setting up python3-numpy (1:2.2.4+ds-1ubuntu1) ... 215s Setting up python3-lxml:s390x (6.0.2-1) ... 215s Setting up libtiff6:s390x (4.7.0-3ubuntu3) ... 215s Setting up python3-contourpy (1.3.1-2) ... 215s Setting up libfontconfig1:s390x (2.15.0-2.3ubuntu1) ... 215s Setting up libxft2:s390x (2.3.6-1build1) ... 215s Setting up python3-scipy (1.15.3-1ubuntu1) ... 217s Setting up libtk8.6:s390x (8.6.17-1) ... 217s Setting up python3-pandas-lib:s390x (2.3.3+dfsg-1ubuntu1) ... 217s Setting up python3.13-tk (3.13.9-1) ... 217s Setting up python3-pil:s390x (11.3.0-1ubuntu2) ... 218s Setting up python3-pandas (2.3.3+dfsg-1ubuntu1) ... 221s Setting up tk8.6-blt2.5 (2.5.3+dfsg-8) ... 221s Setting up python3.14-tk (3.14.0-4) ... 221s Setting up blt (2.5.3+dfsg-8) ... 221s Setting up python3-tk:s390x (3.13.9-1) ... 221s Setting up python3-pil.imagetk:s390x (11.3.0-1ubuntu2) ... 221s Setting up python3-fonttools (4.57.0-2build1) ... 222s Setting up python3-ufolib2 (0.17.1+dfsg1-1) ... 222s Setting up python3-matplotlib (3.10.7+dfsg1-1) ... 223s Setting up python3-bioframe (0.4.1-2) ... 223s Processing triggers for libc-bin (2.42-2ubuntu2) ... 223s Processing triggers for man-db (2.13.1-1) ... 224s autopkgtest [00:37:16]: test run-unit-test: [----------------------- 225s ============================= test session starts ============================== 225s platform linux -- Python 3.13.9, pytest-8.3.5, pluggy-1.6.0 -- /usr/bin/python3.13 225s cachedir: .pytest_cache 225s rootdir: /tmp/autopkgtest.I2ohUb/autopkgtest_tmp 225s plugins: typeguard-4.4.2 226s collecting ... collected 50 items 226s 226s tests/test_core_checks.py::test_is_cataloged PASSED [ 2%] 226s tests/test_core_checks.py::test_is_contained PASSED [ 4%] 226s tests/test_core_checks.py::test_is_overlapping PASSED [ 6%] 226s tests/test_core_checks.py::test_is_covering PASSED [ 8%] 226s tests/test_core_checks.py::test_is_tiling PASSED [ 10%] 226s tests/test_core_checks.py::test_is_bedframe PASSED [ 12%] 226s tests/test_core_checks.py::test_is_viewframe PASSED [ 14%] 226s tests/test_core_checks.py::test_is_sorted PASSED [ 16%] 226s tests/test_core_construction.py::test_add_ucsc_name_column PASSED [ 18%] 226s tests/test_core_construction.py::test_any PASSED [ 20%] 226s tests/test_core_construction.py::test_sanitize_bedframe PASSED [ 22%] 226s tests/test_core_construction.py::test_make_viewframe PASSED [ 24%] 226s tests/test_core_specs.py::test_get_default_colnames PASSED [ 26%] 226s tests/test_core_specs.py::test_update_default_colnames PASSED [ 28%] 226s tests/test_core_specs.py::test_verify_columns PASSED [ 30%] 226s tests/test_core_specs.py::test_verify_column_dtypes PASSED [ 32%] 226s tests/test_core_specs.py::test_is_chrom_dtype PASSED [ 34%] 226s tests/test_core_stringops.py::test_to_ucsc_string PASSED [ 36%] 226s tests/test_core_stringops.py::test_parse_region PASSED [ 38%] 226s tests/test_core_stringops.py::test_parse_region_string PASSED [ 40%] 226s tests/test_core_stringops.py::test_is_complete_ucsc_string PASSED [ 42%] 226s tests/test_extras.py::test_make_chromarms PASSED [ 44%] 226s tests/test_extras.py::test_binnify PASSED [ 46%] 226s tests/test_extras.py::test_digest SKIPPED (could not import 'Bio': N...) [ 48%] 226s tests/test_extras.py::test_frac_mapped SKIPPED (could not import 'py...) [ 50%] 226s tests/test_extras.py::test_frac_gc SKIPPED (could not import 'pysam'...) [ 52%] 226s tests/test_extras.py::test_seq_gc PASSED [ 54%] 226s tests/test_extras.py::test_pair_by_distance PASSED [ 56%] 226s tests/test_io.py::test_read_table PASSED [ 58%] 226s tests/test_io.py::test_read_chromsizes PASSED [ 60%] 226s tests/test_ops.py::test_trim PASSED [ 62%] 226s tests/test_ops.py::test_expand PASSED [ 64%] 226s tests/test_ops.py::test_overlap PASSED [ 66%] 226s tests/test_ops.py::test_cluster PASSED [ 68%] 226s tests/test_ops.py::test_merge PASSED [ 70%] 226s tests/test_ops.py::test_complement PASSED [ 72%] 226s tests/test_ops.py::test_closest PASSED [ 74%] 226s tests/test_ops.py::test_coverage PASSED [ 76%] 227s tests/test_ops.py::test_subtract PASSED [ 78%] 227s tests/test_ops.py::test_setdiff PASSED [ 80%] 227s tests/test_ops.py::test_count_overlaps PASSED [ 82%] 227s tests/test_ops.py::test_assign_view PASSED [ 84%] 227s tests/test_ops.py::test_sort_bedframe PASSED [ 86%] 227s tests/test_ops_select.py::test_select PASSED [ 88%] 227s tests/test_ops_select.py::test_select__with_colnames PASSED [ 90%] 227s tests/test_ops_select.py::test_select__with_nulls PASSED [ 92%] 227s tests/test_ops_select.py::test_select__mask_indices_labels PASSED [ 94%] 227s tests/test_ops_select.py::test_select__query_intervals_are_half_open PASSED [ 96%] 227s tests/test_ops_select.py::test_select__with_point_intervals PASSED [ 98%] 227s tests/test_ops_select.py::test_select__with_points PASSED [100%] 227s 227s =============================== warnings summary =============================== 227s ../../../usr/lib/python3/dist-packages/bioframe/io/resources.py:13 227s /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 227s import pkg_resources 227s 227s tests/test_io.py:23 227s /tmp/autopkgtest.I2ohUb/autopkgtest_tmp/tests/test_io.py:23: SyntaxWarning: invalid escape sequence '\s' 227s assert bioframe.read_table(StringIO(d), schema="bed3", sep="\s+").shape == (3, 3) 227s 227s tests/test_io.py:24 227s /tmp/autopkgtest.I2ohUb/autopkgtest_tmp/tests/test_io.py:24: SyntaxWarning: invalid escape sequence '\s' 227s assert bioframe.read_table(StringIO(d), schema="bed6", sep="\s+").shape == (3, 6) 227s 227s tests/test_io.py:25 227s /tmp/autopkgtest.I2ohUb/autopkgtest_tmp/tests/test_io.py:25: SyntaxWarning: invalid escape sequence '\s' 227s assert bioframe.read_table(StringIO(d), schema="bed12", sep="\s+").shape == (3, 12) 227s 227s tests/test_io.py:33 227s /tmp/autopkgtest.I2ohUb/autopkgtest_tmp/tests/test_io.py:33: SyntaxWarning: invalid escape sequence '\s' 227s StringIO(d), schema="bedpe", sep="\s+", schema_is_strict=True 227s 227s tests/test_core_checks.py: 84 warnings 227s tests/test_core_construction.py: 28 warnings 227s tests/test_core_specs.py: 12 warnings 227s tests/test_extras.py: 24 warnings 227s tests/test_ops.py: 326 warnings 227s /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 227s pd.api.types.is_categorical_dtype(chrom_dtype), 227s 227s tests/test_core_checks.py: 4 warnings 227s tests/test_ops.py: 6 warnings 227s /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. 227s 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. 227s 227s 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. 227s 227s 227s df_trimmed[sk].clip(lower=lower_vector, upper=upper_vector, inplace=True) 227s 227s tests/test_core_checks.py: 4 warnings 227s tests/test_ops.py: 6 warnings 227s /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. 227s 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. 227s 227s 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. 227s 227s 227s df_trimmed[ek].clip(lower=lower_vector, upper=upper_vector, inplace=True) 227s 227s tests/test_core_construction.py::test_any 227s /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. 227s 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. 227s 227s 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. 227s 227s 227s out_df[sk1].fillna(0, inplace=True) 227s 227s tests/test_core_construction.py::test_any 227s /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)` 227s out_df[sk1].fillna(0, inplace=True) 227s 227s tests/test_ops.py::test_trim 227s /tmp/autopkgtest.I2ohUb/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. 227s pd.testing.assert_frame_equal( 227s 227s tests/test_ops.py::test_overlap 227s /tmp/autopkgtest.I2ohUb/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. 227s assert ~df1.equals( 227s 227s tests/test_ops.py::test_assign_view 227s /tmp/autopkgtest.I2ohUb/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. 227s pd.testing.assert_frame_equal( 227s 227s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 227s ================= 47 passed, 3 skipped, 504 warnings in 2.04s ================== 227s autopkgtest [00:37:19]: test run-unit-test: -----------------------] 228s autopkgtest [00:37:20]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 228s run-unit-test PASS 228s autopkgtest [00:37:20]: @@@@@@@@@@@@@@@@@@@@ summary 228s run-unit-test PASS