0s autopkgtest [10:20:08]: starting date and time: 2024-11-13 10:20:08+0000 0s autopkgtest [10:20:08]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [10:20:08]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.fdhl5qvi/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:python3-defaults,src:python3-stdlib-extensions --apt-upgrade python-csb --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=python3-defaults/3.12.7-1 python3-stdlib-extensions/3.12.7-1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@bos03-arm64-11.secgroup --name adt-plucky-arm64-python-csb-20241113-102007-juju-7f2275-prod-proposed-migration-environment-20-7bdae569-3891-4b73-a4ab-4b21bf4282a3 --image adt/ubuntu-plucky-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 74s autopkgtest [10:21:22]: testbed dpkg architecture: arm64 75s autopkgtest [10:21:23]: testbed apt version: 2.9.8 75s autopkgtest [10:21:23]: @@@@@@@@@@@@@@@@@@@@ test bed setup 76s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 76s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [849 kB] 76s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [76.4 kB] 76s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.3 kB] 76s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 76s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [104 kB] 76s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 Packages [50.3 kB] 76s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [601 kB] 76s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [17.1 kB] 76s Fetched 1794 kB in 1s (1970 kB/s) 77s Reading package lists... 80s Reading package lists... 80s Building dependency tree... 80s Reading state information... 81s Calculating upgrade... 82s The following NEW packages will be installed: 82s python3.13-gdbm 82s The following packages will be upgraded: 82s libpython3-stdlib python3 python3-gdbm python3-minimal 82s 4 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 82s Need to get 101 kB of archives. 82s After this operation, 141 kB of additional disk space will be used. 82s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-minimal arm64 3.12.7-1 [27.4 kB] 82s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3 arm64 3.12.7-1 [24.0 kB] 82s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libpython3-stdlib arm64 3.12.7-1 [10.0 kB] 82s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-gdbm arm64 3.13.0-2 [30.7 kB] 82s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-gdbm arm64 3.12.7-1 [8642 B] 82s Fetched 101 kB in 0s (278 kB/s) 83s (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 ... 79924 files and directories currently installed.) 83s Preparing to unpack .../python3-minimal_3.12.7-1_arm64.deb ... 83s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ... 83s Setting up python3-minimal (3.12.7-1) ... 83s (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 ... 79924 files and directories currently installed.) 83s Preparing to unpack .../python3_3.12.7-1_arm64.deb ... 83s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ... 84s Preparing to unpack .../libpython3-stdlib_3.12.7-1_arm64.deb ... 84s Unpacking libpython3-stdlib:arm64 (3.12.7-1) over (3.12.6-0ubuntu1) ... 84s Selecting previously unselected package python3.13-gdbm. 84s Preparing to unpack .../python3.13-gdbm_3.13.0-2_arm64.deb ... 84s Unpacking python3.13-gdbm (3.13.0-2) ... 84s Preparing to unpack .../python3-gdbm_3.12.7-1_arm64.deb ... 84s Unpacking python3-gdbm:arm64 (3.12.7-1) over (3.12.6-1ubuntu1) ... 84s Setting up python3.13-gdbm (3.13.0-2) ... 84s Setting up libpython3-stdlib:arm64 (3.12.7-1) ... 84s Setting up python3 (3.12.7-1) ... 84s Setting up python3-gdbm:arm64 (3.12.7-1) ... 84s Processing triggers for man-db (2.12.1-3) ... 85s Reading package lists... 86s Building dependency tree... 86s Reading state information... 88s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 88s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 88s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 88s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 89s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 90s Reading package lists... 90s Reading package lists... 90s Building dependency tree... 90s Reading state information... 91s Calculating upgrade... 92s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 92s Reading package lists... 92s Building dependency tree... 92s Reading state information... 93s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 96s autopkgtest [10:21:44]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 14:19:41 UTC 2024 96s autopkgtest [10:21:44]: @@@@@@@@@@@@@@@@@@@@ apt-source python-csb 99s Get:1 http://ftpmaster.internal/ubuntu plucky/universe python-csb 1.2.5+dfsg-10 (dsc) [1627 B] 99s Get:2 http://ftpmaster.internal/ubuntu plucky/universe python-csb 1.2.5+dfsg-10 (tar) [3000 kB] 99s Get:3 http://ftpmaster.internal/ubuntu plucky/universe python-csb 1.2.5+dfsg-10 (diff) [11.5 kB] 99s gpgv: Signature made Sat Dec 9 16:03:46 2023 UTC 99s gpgv: using EDDSA key A095B66EE09024BEE6A2F0722A27904BD7243EDA 99s gpgv: Can't check signature: No public key 99s dpkg-source: warning: cannot verify inline signature for ./python-csb_1.2.5+dfsg-10.dsc: no acceptable signature found 99s autopkgtest [10:21:47]: testing package python-csb version 1.2.5+dfsg-10 100s autopkgtest [10:21:48]: build not needed 108s autopkgtest [10:21:56]: test build: preparing testbed 111s Reading package lists... 112s Building dependency tree... 112s Reading state information... 112s Starting pkgProblemResolver with broken count: 0 112s Starting 2 pkgProblemResolver with broken count: 0 112s Done 113s The following additional packages will be installed: 113s blt fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-lyx libblas3 113s libdeflate0 libfontconfig1 libgfortran5 libgomp1 libgraphite2-3 113s libharfbuzz0b libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 libjs-jquery 113s libjs-jquery-ui liblapack3 liblbfgsb0 liblcms2-2 liblerc4 libopenjp2-7 113s libpython3.13-minimal libpython3.13-stdlib libqhull-r8.0 libraqm0 113s libsharpyuv0 libtcl8.6 libtiff6 libtk8.6 libwebp7 libwebpdemux2 libwebpmux3 113s libxft2 libxrender1 libxslt1.1 libxss1 python-matplotlib-data python3-all 113s python3-appdirs python3-brotli python3-contourpy python3-csb python3-cycler 113s python3-dateutil python3-decorator python3-fonttools python3-fs 113s python3-kiwisolver python3-lxml python3-lz4 python3-matplotlib 113s python3-mpmath python3-numpy python3-packaging python3-pil 113s python3-pil.imagetk python3-scipy python3-six python3-sympy python3-tk 113s python3-tz python3-ufolib2 python3-unicodedata2 python3.12-tk python3.13 113s python3.13-minimal python3.13-tk tk8.6-blt2.5 unicode-data x11-common 113s Suggested packages: 113s blt-demo libjs-jquery-ui-docs liblcms2-utils tcl8.6 tk8.6 python-cycler-doc 113s python-lxml-doc cm-super-minimal dvipng ffmpeg fonts-staypuft ghostscript 113s gir1.2-gtk-3.0 inkscape ipython3 librsvg2-common python-matplotlib-doc 113s python3-cairocffi python3-gi-cairo python3-gobject python3-pyqt5 python3-sip 113s python3-tornado texlive-extra-utils texlive-latex-extra python-mpmath-doc 113s python3-gmpy2 gcc gfortran python-numpy-doc python3-dev python3-pytest 113s python-pil-doc python-scipy-doc texlive-fonts-extra python-sympy-doc tix 113s python3-tk-dbg python3.13-venv python3.13-doc binfmt-support 113s Recommended packages: 113s javascript-common python3-bs4 python3-cssselect python3-html5lib 113s python3-olefile g++ | c++-compiler isympy-common 113s The following NEW packages will be installed: 113s autopkgtest-satdep blt fontconfig-config fonts-dejavu-core fonts-dejavu-mono 113s fonts-lyx libblas3 libdeflate0 libfontconfig1 libgfortran5 libgomp1 113s libgraphite2-3 libharfbuzz0b libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 113s libjs-jquery libjs-jquery-ui liblapack3 liblbfgsb0 liblcms2-2 liblerc4 113s libopenjp2-7 libpython3.13-minimal libpython3.13-stdlib libqhull-r8.0 113s libraqm0 libsharpyuv0 libtcl8.6 libtiff6 libtk8.6 libwebp7 libwebpdemux2 113s libwebpmux3 libxft2 libxrender1 libxslt1.1 libxss1 python-matplotlib-data 113s python3-all python3-appdirs python3-brotli python3-contourpy python3-csb 113s python3-cycler python3-dateutil python3-decorator python3-fonttools 113s python3-fs python3-kiwisolver python3-lxml python3-lz4 python3-matplotlib 113s python3-mpmath python3-numpy python3-packaging python3-pil 113s python3-pil.imagetk python3-scipy python3-six python3-sympy python3-tk 113s python3-tz python3-ufolib2 python3-unicodedata2 python3.12-tk python3.13 113s python3.13-minimal python3.13-tk tk8.6-blt2.5 unicode-data x11-common 114s 0 upgraded, 73 newly installed, 0 to remove and 0 not upgraded. 114s Need to get 63.6 MB/63.6 MB of archives. 114s After this operation, 267 MB of additional disk space will be used. 114s Get:1 /tmp/autopkgtest.GgJI0a/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [712 B] 114s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3.13-minimal arm64 3.13.0-2 [877 kB] 114s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-minimal arm64 3.13.0-2 [2100 kB] 114s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 libtcl8.6 arm64 8.6.15+dfsg-2 [987 kB] 114s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 114s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 114s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig-config arm64 2.15.0-1.1ubuntu2 [37.4 kB] 114s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 libfontconfig1 arm64 2.15.0-1.1ubuntu2 [142 kB] 114s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 libxrender1 arm64 1:0.9.10-1.1build1 [18.8 kB] 114s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 libxft2 arm64 2.3.6-1build1 [44.1 kB] 114s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 114s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 libxss1 arm64 1:1.2.3-1build3 [7244 B] 114s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 libtk8.6 arm64 8.6.15-1 [774 kB] 114s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 tk8.6-blt2.5 arm64 2.5.3+dfsg-7build1 [618 kB] 114s Get:15 http://ftpmaster.internal/ubuntu plucky/main arm64 blt arm64 2.5.3+dfsg-7build1 [4840 B] 114s Get:16 http://ftpmaster.internal/ubuntu plucky/universe arm64 fonts-lyx all 2.4.2.1-1 [171 kB] 114s Get:17 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.0-3build2 [152 kB] 114s Get:18 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate0 arm64 1.22-1 [46.2 kB] 114s Get:19 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 14.2.0-8ubuntu1 [438 kB] 114s Get:20 http://ftpmaster.internal/ubuntu plucky/main arm64 libgomp1 arm64 14.2.0-8ubuntu1 [145 kB] 114s Get:21 http://ftpmaster.internal/ubuntu plucky/main arm64 libgraphite2-3 arm64 1.3.14-2ubuntu1 [70.6 kB] 114s Get:22 http://ftpmaster.internal/ubuntu plucky/main arm64 libharfbuzz0b arm64 10.0.1-1 [487 kB] 115s Get:23 http://ftpmaster.internal/ubuntu plucky/main arm64 libimagequant0 arm64 2.18.0-1build1 [37.1 kB] 115s Get:24 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg-turbo8 arm64 2.1.5-2ubuntu2 [163 kB] 115s Get:25 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 115s Get:26 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 115s Get:27 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 115s Get:28 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.0-3build2 [2293 kB] 115s Get:29 http://ftpmaster.internal/ubuntu plucky/universe arm64 liblbfgsb0 arm64 3.0+dfsg.4-1build1 [27.7 kB] 115s Get:30 http://ftpmaster.internal/ubuntu plucky/main arm64 liblcms2-2 arm64 2.16-2 [170 kB] 115s Get:31 http://ftpmaster.internal/ubuntu plucky/main arm64 liblerc4 arm64 4.0.0+ds-4ubuntu2 [154 kB] 115s Get:32 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3.13-stdlib arm64 3.13.0-2 [2073 kB] 115s Get:33 http://ftpmaster.internal/ubuntu plucky/universe arm64 libqhull-r8.0 arm64 2020.2-6build1 [189 kB] 115s Get:34 http://ftpmaster.internal/ubuntu plucky/main arm64 libraqm0 arm64 0.10.1-1build1 [14.7 kB] 115s Get:35 http://ftpmaster.internal/ubuntu plucky/main arm64 libsharpyuv0 arm64 1.4.0-0.1 [16.3 kB] 115s Get:36 http://ftpmaster.internal/ubuntu plucky/main arm64 libjbig0 arm64 2.1-6.1ubuntu2 [29.3 kB] 115s Get:37 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebp7 arm64 1.4.0-0.1 [192 kB] 115s Get:38 http://ftpmaster.internal/ubuntu plucky/main arm64 libtiff6 arm64 4.5.1+git230720-4ubuntu4 [193 kB] 115s Get:39 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebpdemux2 arm64 1.4.0-0.1 [12.3 kB] 115s Get:40 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebpmux3 arm64 1.4.0-0.1 [25.1 kB] 115s Get:41 http://ftpmaster.internal/ubuntu plucky/main arm64 libxslt1.1 arm64 1.1.39-0exp1ubuntu1 [167 kB] 115s Get:42 http://ftpmaster.internal/ubuntu plucky/universe arm64 python-matplotlib-data all 3.8.3-3 [2928 kB] 115s Get:43 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13 arm64 3.13.0-2 [719 kB] 115s Get:44 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-all arm64 3.12.7-1 [890 B] 115s Get:45 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-appdirs all 1.4.4-4 [10.9 kB] 115s Get:46 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-brotli arm64 1.1.0-2build2 [340 kB] 115s Get:47 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy arm64 1:1.26.4+ds-11build1 [3654 kB] 115s Get:48 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-contourpy arm64 1.3.0-2 [179 kB] 115s Get:49 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-six all 1.16.0-7 [13.1 kB] 115s Get:50 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-dateutil all 2.9.0-2 [80.3 kB] 115s Get:51 http://ftpmaster.internal/ubuntu plucky/main arm64 libopenjp2-7 arm64 2.5.0-2ubuntu1 [182 kB] 115s Get:52 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-pil arm64 10.4.0-1ubuntu1 [456 kB] 115s Get:53 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.12-tk arm64 3.12.7-3 [115 kB] 115s Get:54 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-tk arm64 3.13.0-2 [105 kB] 115s Get:55 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-tk arm64 3.12.7-1 [9752 B] 115s Get:56 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pil.imagetk arm64 10.4.0-1ubuntu1 [9504 B] 115s Get:57 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-cycler all 0.12.1-1 [9716 B] 115s Get:58 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-decorator all 5.1.1-5 [10.1 kB] 115s Get:59 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-scipy arm64 1.13.1-5 [16.3 MB] 116s Get:60 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-ufolib2 all 0.16.1+dfsg1-1 [33.4 kB] 116s Get:61 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-mpmath all 1.3.0-1 [425 kB] 116s Get:62 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-sympy all 1.13.3-1 [4228 kB] 116s Get:63 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-tz all 2024.1-2 [31.4 kB] 116s Get:64 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-fs all 2.4.16-4 [91.3 kB] 116s Get:65 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-lxml arm64 5.3.0-1 [1205 kB] 116s Get:66 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-lz4 arm64 4.0.2+dfsg-1build4 [26.7 kB] 116s Get:67 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-unicodedata2 arm64 15.1.0+ds-1build1 [362 kB] 116s Get:68 http://ftpmaster.internal/ubuntu plucky/universe arm64 unicode-data all 15.1.0-1 [8878 kB] 116s Get:69 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-fonttools arm64 4.46.0-1build2 [1398 kB] 116s Get:70 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-kiwisolver arm64 1.4.7-2 [50.4 kB] 116s Get:71 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-packaging all 24.1-1 [41.4 kB] 116s Get:72 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-matplotlib arm64 3.8.3-3 [4515 kB] 116s Get:73 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-csb all 1.2.5+dfsg-10 [2392 kB] 117s Fetched 63.6 MB in 3s (22.3 MB/s) 117s Selecting previously unselected package libpython3.13-minimal:arm64. 117s (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 ... 79931 files and directories currently installed.) 117s Preparing to unpack .../00-libpython3.13-minimal_3.13.0-2_arm64.deb ... 117s Unpacking libpython3.13-minimal:arm64 (3.13.0-2) ... 117s Selecting previously unselected package python3.13-minimal. 117s Preparing to unpack .../01-python3.13-minimal_3.13.0-2_arm64.deb ... 117s Unpacking python3.13-minimal (3.13.0-2) ... 117s Selecting previously unselected package libtcl8.6:arm64. 117s Preparing to unpack .../02-libtcl8.6_8.6.15+dfsg-2_arm64.deb ... 117s Unpacking libtcl8.6:arm64 (8.6.15+dfsg-2) ... 118s Selecting previously unselected package fonts-dejavu-mono. 118s Preparing to unpack .../03-fonts-dejavu-mono_2.37-8_all.deb ... 118s Unpacking fonts-dejavu-mono (2.37-8) ... 118s Selecting previously unselected package fonts-dejavu-core. 118s Preparing to unpack .../04-fonts-dejavu-core_2.37-8_all.deb ... 118s Unpacking fonts-dejavu-core (2.37-8) ... 118s Selecting previously unselected package fontconfig-config. 118s Preparing to unpack .../05-fontconfig-config_2.15.0-1.1ubuntu2_arm64.deb ... 118s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ... 118s Selecting previously unselected package libfontconfig1:arm64. 118s Preparing to unpack .../06-libfontconfig1_2.15.0-1.1ubuntu2_arm64.deb ... 118s Unpacking libfontconfig1:arm64 (2.15.0-1.1ubuntu2) ... 118s Selecting previously unselected package libxrender1:arm64. 118s Preparing to unpack .../07-libxrender1_1%3a0.9.10-1.1build1_arm64.deb ... 118s Unpacking libxrender1:arm64 (1:0.9.10-1.1build1) ... 118s Selecting previously unselected package libxft2:arm64. 118s Preparing to unpack .../08-libxft2_2.3.6-1build1_arm64.deb ... 118s Unpacking libxft2:arm64 (2.3.6-1build1) ... 118s Selecting previously unselected package x11-common. 118s Preparing to unpack .../09-x11-common_1%3a7.7+23ubuntu3_all.deb ... 118s Unpacking x11-common (1:7.7+23ubuntu3) ... 119s Selecting previously unselected package libxss1:arm64. 119s Preparing to unpack .../10-libxss1_1%3a1.2.3-1build3_arm64.deb ... 119s Unpacking libxss1:arm64 (1:1.2.3-1build3) ... 119s Selecting previously unselected package libtk8.6:arm64. 119s Preparing to unpack .../11-libtk8.6_8.6.15-1_arm64.deb ... 119s Unpacking libtk8.6:arm64 (8.6.15-1) ... 119s Selecting previously unselected package tk8.6-blt2.5. 119s Preparing to unpack .../12-tk8.6-blt2.5_2.5.3+dfsg-7build1_arm64.deb ... 119s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 119s Selecting previously unselected package blt. 119s Preparing to unpack .../13-blt_2.5.3+dfsg-7build1_arm64.deb ... 119s Unpacking blt (2.5.3+dfsg-7build1) ... 119s Selecting previously unselected package fonts-lyx. 119s Preparing to unpack .../14-fonts-lyx_2.4.2.1-1_all.deb ... 119s Unpacking fonts-lyx (2.4.2.1-1) ... 119s Selecting previously unselected package libblas3:arm64. 119s Preparing to unpack .../15-libblas3_3.12.0-3build2_arm64.deb ... 119s Unpacking libblas3:arm64 (3.12.0-3build2) ... 119s Selecting previously unselected package libdeflate0:arm64. 119s Preparing to unpack .../16-libdeflate0_1.22-1_arm64.deb ... 119s Unpacking libdeflate0:arm64 (1.22-1) ... 119s Selecting previously unselected package libgfortran5:arm64. 119s Preparing to unpack .../17-libgfortran5_14.2.0-8ubuntu1_arm64.deb ... 119s Unpacking libgfortran5:arm64 (14.2.0-8ubuntu1) ... 119s Selecting previously unselected package libgomp1:arm64. 119s Preparing to unpack .../18-libgomp1_14.2.0-8ubuntu1_arm64.deb ... 119s Unpacking libgomp1:arm64 (14.2.0-8ubuntu1) ... 119s Selecting previously unselected package libgraphite2-3:arm64. 119s Preparing to unpack .../19-libgraphite2-3_1.3.14-2ubuntu1_arm64.deb ... 119s Unpacking libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 119s Selecting previously unselected package libharfbuzz0b:arm64. 119s Preparing to unpack .../20-libharfbuzz0b_10.0.1-1_arm64.deb ... 119s Unpacking libharfbuzz0b:arm64 (10.0.1-1) ... 119s Selecting previously unselected package libimagequant0:arm64. 119s Preparing to unpack .../21-libimagequant0_2.18.0-1build1_arm64.deb ... 119s Unpacking libimagequant0:arm64 (2.18.0-1build1) ... 119s Selecting previously unselected package libjpeg-turbo8:arm64. 119s Preparing to unpack .../22-libjpeg-turbo8_2.1.5-2ubuntu2_arm64.deb ... 119s Unpacking libjpeg-turbo8:arm64 (2.1.5-2ubuntu2) ... 119s Selecting previously unselected package libjpeg8:arm64. 119s Preparing to unpack .../23-libjpeg8_8c-2ubuntu11_arm64.deb ... 119s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 119s Selecting previously unselected package libjs-jquery. 119s Preparing to unpack .../24-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 119s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 119s Selecting previously unselected package libjs-jquery-ui. 119s Preparing to unpack .../25-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... 119s Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... 120s Selecting previously unselected package liblapack3:arm64. 120s Preparing to unpack .../26-liblapack3_3.12.0-3build2_arm64.deb ... 120s Unpacking liblapack3:arm64 (3.12.0-3build2) ... 120s Selecting previously unselected package liblbfgsb0:arm64. 120s Preparing to unpack .../27-liblbfgsb0_3.0+dfsg.4-1build1_arm64.deb ... 120s Unpacking liblbfgsb0:arm64 (3.0+dfsg.4-1build1) ... 120s Selecting previously unselected package liblcms2-2:arm64. 120s Preparing to unpack .../28-liblcms2-2_2.16-2_arm64.deb ... 120s Unpacking liblcms2-2:arm64 (2.16-2) ... 120s Selecting previously unselected package liblerc4:arm64. 120s Preparing to unpack .../29-liblerc4_4.0.0+ds-4ubuntu2_arm64.deb ... 120s Unpacking liblerc4:arm64 (4.0.0+ds-4ubuntu2) ... 120s Selecting previously unselected package libpython3.13-stdlib:arm64. 120s Preparing to unpack .../30-libpython3.13-stdlib_3.13.0-2_arm64.deb ... 120s Unpacking libpython3.13-stdlib:arm64 (3.13.0-2) ... 120s Selecting previously unselected package libqhull-r8.0:arm64. 120s Preparing to unpack .../31-libqhull-r8.0_2020.2-6build1_arm64.deb ... 120s Unpacking libqhull-r8.0:arm64 (2020.2-6build1) ... 120s Selecting previously unselected package libraqm0:arm64. 120s Preparing to unpack .../32-libraqm0_0.10.1-1build1_arm64.deb ... 120s Unpacking libraqm0:arm64 (0.10.1-1build1) ... 120s Selecting previously unselected package libsharpyuv0:arm64. 120s Preparing to unpack .../33-libsharpyuv0_1.4.0-0.1_arm64.deb ... 120s Unpacking libsharpyuv0:arm64 (1.4.0-0.1) ... 120s Selecting previously unselected package libjbig0:arm64. 120s Preparing to unpack .../34-libjbig0_2.1-6.1ubuntu2_arm64.deb ... 120s Unpacking libjbig0:arm64 (2.1-6.1ubuntu2) ... 120s Selecting previously unselected package libwebp7:arm64. 120s Preparing to unpack .../35-libwebp7_1.4.0-0.1_arm64.deb ... 120s Unpacking libwebp7:arm64 (1.4.0-0.1) ... 120s Selecting previously unselected package libtiff6:arm64. 120s Preparing to unpack .../36-libtiff6_4.5.1+git230720-4ubuntu4_arm64.deb ... 120s Unpacking libtiff6:arm64 (4.5.1+git230720-4ubuntu4) ... 120s Selecting previously unselected package libwebpdemux2:arm64. 120s Preparing to unpack .../37-libwebpdemux2_1.4.0-0.1_arm64.deb ... 120s Unpacking libwebpdemux2:arm64 (1.4.0-0.1) ... 120s Selecting previously unselected package libwebpmux3:arm64. 120s Preparing to unpack .../38-libwebpmux3_1.4.0-0.1_arm64.deb ... 120s Unpacking libwebpmux3:arm64 (1.4.0-0.1) ... 121s Selecting previously unselected package libxslt1.1:arm64. 121s Preparing to unpack .../39-libxslt1.1_1.1.39-0exp1ubuntu1_arm64.deb ... 121s Unpacking libxslt1.1:arm64 (1.1.39-0exp1ubuntu1) ... 121s Selecting previously unselected package python-matplotlib-data. 121s Preparing to unpack .../40-python-matplotlib-data_3.8.3-3_all.deb ... 121s Unpacking python-matplotlib-data (3.8.3-3) ... 121s Selecting previously unselected package python3.13. 121s Preparing to unpack .../41-python3.13_3.13.0-2_arm64.deb ... 121s Unpacking python3.13 (3.13.0-2) ... 121s Selecting previously unselected package python3-all. 121s Preparing to unpack .../42-python3-all_3.12.7-1_arm64.deb ... 121s Unpacking python3-all (3.12.7-1) ... 121s Selecting previously unselected package python3-appdirs. 121s Preparing to unpack .../43-python3-appdirs_1.4.4-4_all.deb ... 121s Unpacking python3-appdirs (1.4.4-4) ... 121s Selecting previously unselected package python3-brotli. 121s Preparing to unpack .../44-python3-brotli_1.1.0-2build2_arm64.deb ... 121s Unpacking python3-brotli (1.1.0-2build2) ... 121s Selecting previously unselected package python3-numpy. 121s Preparing to unpack .../45-python3-numpy_1%3a1.26.4+ds-11build1_arm64.deb ... 121s Unpacking python3-numpy (1:1.26.4+ds-11build1) ... 121s Selecting previously unselected package python3-contourpy. 121s Preparing to unpack .../46-python3-contourpy_1.3.0-2_arm64.deb ... 121s Unpacking python3-contourpy (1.3.0-2) ... 121s Selecting previously unselected package python3-six. 121s Preparing to unpack .../47-python3-six_1.16.0-7_all.deb ... 121s Unpacking python3-six (1.16.0-7) ... 121s Selecting previously unselected package python3-dateutil. 121s Preparing to unpack .../48-python3-dateutil_2.9.0-2_all.deb ... 121s Unpacking python3-dateutil (2.9.0-2) ... 121s Selecting previously unselected package libopenjp2-7:arm64. 121s Preparing to unpack .../49-libopenjp2-7_2.5.0-2ubuntu1_arm64.deb ... 121s Unpacking libopenjp2-7:arm64 (2.5.0-2ubuntu1) ... 121s Selecting previously unselected package python3-pil:arm64. 122s Preparing to unpack .../50-python3-pil_10.4.0-1ubuntu1_arm64.deb ... 122s Unpacking python3-pil:arm64 (10.4.0-1ubuntu1) ... 122s Selecting previously unselected package python3.12-tk. 122s Preparing to unpack .../51-python3.12-tk_3.12.7-3_arm64.deb ... 122s Unpacking python3.12-tk (3.12.7-3) ... 122s Selecting previously unselected package python3.13-tk. 122s Preparing to unpack .../52-python3.13-tk_3.13.0-2_arm64.deb ... 122s Unpacking python3.13-tk (3.13.0-2) ... 122s Selecting previously unselected package python3-tk:arm64. 122s Preparing to unpack .../53-python3-tk_3.12.7-1_arm64.deb ... 122s Unpacking python3-tk:arm64 (3.12.7-1) ... 122s Selecting previously unselected package python3-pil.imagetk:arm64. 122s Preparing to unpack .../54-python3-pil.imagetk_10.4.0-1ubuntu1_arm64.deb ... 122s Unpacking python3-pil.imagetk:arm64 (10.4.0-1ubuntu1) ... 122s Selecting previously unselected package python3-cycler. 122s Preparing to unpack .../55-python3-cycler_0.12.1-1_all.deb ... 122s Unpacking python3-cycler (0.12.1-1) ... 122s Selecting previously unselected package python3-decorator. 122s Preparing to unpack .../56-python3-decorator_5.1.1-5_all.deb ... 122s Unpacking python3-decorator (5.1.1-5) ... 122s Selecting previously unselected package python3-scipy. 122s Preparing to unpack .../57-python3-scipy_1.13.1-5_arm64.deb ... 122s Unpacking python3-scipy (1.13.1-5) ... 123s Selecting previously unselected package python3-ufolib2. 123s Preparing to unpack .../58-python3-ufolib2_0.16.1+dfsg1-1_all.deb ... 123s Unpacking python3-ufolib2 (0.16.1+dfsg1-1) ... 123s Selecting previously unselected package python3-mpmath. 123s Preparing to unpack .../59-python3-mpmath_1.3.0-1_all.deb ... 123s Unpacking python3-mpmath (1.3.0-1) ... 123s Selecting previously unselected package python3-sympy. 123s Preparing to unpack .../60-python3-sympy_1.13.3-1_all.deb ... 123s Unpacking python3-sympy (1.13.3-1) ... 123s Selecting previously unselected package python3-tz. 123s Preparing to unpack .../61-python3-tz_2024.1-2_all.deb ... 123s Unpacking python3-tz (2024.1-2) ... 123s Selecting previously unselected package python3-fs. 123s Preparing to unpack .../62-python3-fs_2.4.16-4_all.deb ... 123s Unpacking python3-fs (2.4.16-4) ... 123s Selecting previously unselected package python3-lxml:arm64. 123s Preparing to unpack .../63-python3-lxml_5.3.0-1_arm64.deb ... 123s Unpacking python3-lxml:arm64 (5.3.0-1) ... 123s Selecting previously unselected package python3-lz4. 123s Preparing to unpack .../64-python3-lz4_4.0.2+dfsg-1build4_arm64.deb ... 123s Unpacking python3-lz4 (4.0.2+dfsg-1build4) ... 124s Selecting previously unselected package python3-unicodedata2. 124s Preparing to unpack .../65-python3-unicodedata2_15.1.0+ds-1build1_arm64.deb ... 124s Unpacking python3-unicodedata2 (15.1.0+ds-1build1) ... 124s Selecting previously unselected package unicode-data. 124s Preparing to unpack .../66-unicode-data_15.1.0-1_all.deb ... 124s Unpacking unicode-data (15.1.0-1) ... 124s Selecting previously unselected package python3-fonttools. 124s Preparing to unpack .../67-python3-fonttools_4.46.0-1build2_arm64.deb ... 124s Unpacking python3-fonttools (4.46.0-1build2) ... 124s Selecting previously unselected package python3-kiwisolver. 124s Preparing to unpack .../68-python3-kiwisolver_1.4.7-2_arm64.deb ... 124s Unpacking python3-kiwisolver (1.4.7-2) ... 124s Selecting previously unselected package python3-packaging. 124s Preparing to unpack .../69-python3-packaging_24.1-1_all.deb ... 124s Unpacking python3-packaging (24.1-1) ... 124s Selecting previously unselected package python3-matplotlib. 124s Preparing to unpack .../70-python3-matplotlib_3.8.3-3_arm64.deb ... 124s Unpacking python3-matplotlib (3.8.3-3) ... 124s Selecting previously unselected package python3-csb. 124s Preparing to unpack .../71-python3-csb_1.2.5+dfsg-10_all.deb ... 124s Unpacking python3-csb (1.2.5+dfsg-10) ... 125s Selecting previously unselected package autopkgtest-satdep. 125s Preparing to unpack .../72-1-autopkgtest-satdep.deb ... 125s Unpacking autopkgtest-satdep (0) ... 125s Setting up libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 125s Setting up liblcms2-2:arm64 (2.16-2) ... 125s Setting up libsharpyuv0:arm64 (1.4.0-0.1) ... 125s Setting up liblerc4:arm64 (4.0.0+ds-4ubuntu2) ... 125s Setting up libxrender1:arm64 (1:0.9.10-1.1build1) ... 125s Setting up python3-lz4 (4.0.2+dfsg-1build4) ... 125s Setting up python3-unicodedata2 (15.1.0+ds-1build1) ... 125s Setting up fonts-lyx (2.4.2.1-1) ... 125s Setting up x11-common (1:7.7+23ubuntu3) ... 126s Setting up libdeflate0:arm64 (1.22-1) ... 126s Setting up libqhull-r8.0:arm64 (2020.2-6build1) ... 126s Setting up libgomp1:arm64 (14.2.0-8ubuntu1) ... 126s Setting up libjbig0:arm64 (2.1-6.1ubuntu2) ... 126s Setting up python3-tz (2024.1-2) ... 126s Setting up unicode-data (15.1.0-1) ... 126s Setting up python3-six (1.16.0-7) ... 126s Setting up libpython3.13-minimal:arm64 (3.13.0-2) ... 126s Setting up python3-decorator (5.1.1-5) ... 127s Setting up libblas3:arm64 (3.12.0-3build2) ... 127s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode 127s Setting up python3-packaging (24.1-1) ... 127s Setting up python3-brotli (1.1.0-2build2) ... 128s Setting up python3-cycler (0.12.1-1) ... 128s Setting up libimagequant0:arm64 (2.18.0-1build1) ... 128s Setting up fonts-dejavu-mono (2.37-8) ... 128s Setting up python3-kiwisolver (1.4.7-2) ... 128s Setting up libtcl8.6:arm64 (8.6.15+dfsg-2) ... 128s Setting up fonts-dejavu-core (2.37-8) ... 128s Setting up libjpeg-turbo8:arm64 (2.1.5-2ubuntu2) ... 128s Setting up libgfortran5:arm64 (14.2.0-8ubuntu1) ... 128s Setting up libwebp7:arm64 (1.4.0-0.1) ... 128s Setting up libxslt1.1:arm64 (1.1.39-0exp1ubuntu1) ... 128s Setting up libopenjp2-7:arm64 (2.5.0-2ubuntu1) ... 128s Setting up python3.13-minimal (3.13.0-2) ... 130s Setting up libharfbuzz0b:arm64 (10.0.1-1) ... 130s Setting up python3-dateutil (2.9.0-2) ... 130s Setting up libxss1:arm64 (1:1.2.3-1build3) ... 130s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 130s Setting up python3-mpmath (1.3.0-1) ... 132s Setting up python-matplotlib-data (3.8.3-3) ... 132s Setting up libwebpmux3:arm64 (1.4.0-0.1) ... 132s Setting up python3-appdirs (1.4.4-4) ... 132s Setting up libpython3.13-stdlib:arm64 (3.13.0-2) ... 132s Setting up libjpeg8:arm64 (8c-2ubuntu11) ... 132s Setting up python3-sympy (1.13.3-1) ... 154s Setting up liblapack3:arm64 (3.12.0-3build2) ... 154s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode 154s Setting up python3.13 (3.13.0-2) ... 157s Setting up fontconfig-config (2.15.0-1.1ubuntu2) ... 157s Setting up libwebpdemux2:arm64 (1.4.0-0.1) ... 157s Setting up python3-all (3.12.7-1) ... 157s Setting up python3-fs (2.4.16-4) ... 158s Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... 158s Setting up libraqm0:arm64 (0.10.1-1build1) ... 158s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 162s Setting up python3-lxml:arm64 (5.3.0-1) ... 163s Setting up libtiff6:arm64 (4.5.1+git230720-4ubuntu4) ... 163s Setting up python3-contourpy (1.3.0-2) ... 163s Setting up libfontconfig1:arm64 (2.15.0-1.1ubuntu2) ... 163s Setting up liblbfgsb0:arm64 (3.0+dfsg.4-1build1) ... 163s Setting up libxft2:arm64 (2.3.6-1build1) ... 163s Setting up python3-scipy (1.13.1-5) ... 173s Setting up libtk8.6:arm64 (8.6.15-1) ... 173s Setting up python3.12-tk (3.12.7-3) ... 173s Setting up python3.13-tk (3.13.0-2) ... 174s Setting up python3-pil:arm64 (10.4.0-1ubuntu1) ... 175s Setting up tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 175s Setting up blt (2.5.3+dfsg-7build1) ... 175s Setting up python3-tk:arm64 (3.12.7-1) ... 175s Setting up python3-pil.imagetk:arm64 (10.4.0-1ubuntu1) ... 175s Setting up python3-fonttools (4.46.0-1build2) ... 178s Setting up python3-ufolib2 (0.16.1+dfsg1-1) ... 178s Setting up python3-matplotlib (3.8.3-3) ... 183s Setting up python3-csb (1.2.5+dfsg-10) ... 183s /usr/lib/python3/dist-packages/csb/bio/io/hhpred.py:210: SyntaxWarning: invalid escape sequence '\d' 183s m = re.search('(\d+)\D+(\d+)', line).groups() 183s /usr/lib/python3/dist-packages/csb/bio/io/hhpred.py:260: SyntaxWarning: invalid escape sequence '\s' 183s seq = re.sub('\s+', '', ''.join(lines[1:])) 183s /usr/lib/python3/dist-packages/csb/bio/io/hhpred.py:307: SyntaxWarning: invalid escape sequence '\-' 183s pattern = re.compile('^[A-Z\-]\s[0-9]+\s+') 183s /usr/lib/python3/dist-packages/csb/bio/io/procheck.py:31: SyntaxWarning: invalid escape sequence '\s' 183s input_file_name = re.compile('>>>-----.*?\n.*?\n\s*\|\s*(\S+)\s+') 183s /usr/lib/python3/dist-packages/csb/bio/io/procheck.py:32: SyntaxWarning: invalid escape sequence '\d' 183s residues = re.compile('(\d+)\s*residues\s\|') 183s /usr/lib/python3/dist-packages/csb/bio/io/procheck.py:33: SyntaxWarning: invalid escape sequence '\s' 183s ramachandran_plot = re.compile('Ramachandran\splot:\s*(\d+\.\d+)' + 183s /usr/lib/python3/dist-packages/csb/bio/io/procheck.py:34: SyntaxWarning: invalid escape sequence '\s' 183s '%\s*core\s*(\d+\.\d+)%\s*allow\s*(\d+\.\d+)' + 183s /usr/lib/python3/dist-packages/csb/bio/io/procheck.py:35: SyntaxWarning: invalid escape sequence '\s' 183s '%\s*gener\s*(\d+\.\d+)%\s*disall') 183s /usr/lib/python3/dist-packages/csb/bio/io/procheck.py:36: SyntaxWarning: invalid escape sequence '\s' 183s labelled_all = re.compile('Ramachandrans:\s*(\d+)\s*.*?out\sof\s*(\d+)') 183s /usr/lib/python3/dist-packages/csb/bio/io/procheck.py:37: SyntaxWarning: invalid escape sequence '\s' 183s labelled_chi = re.compile('Chi1-chi2\splots:\s*(\d+)\s*.*?out\sof\s*(\d+)') 183s /usr/lib/python3/dist-packages/csb/bio/io/procheck.py:38: SyntaxWarning: invalid escape sequence '\s' 183s bad_contacts = re.compile('Bad\scontacts:\s*(\d+)') 183s /usr/lib/python3/dist-packages/csb/bio/io/procheck.py:39: SyntaxWarning: invalid escape sequence '\s' 183s g_factors = re.compile('G-factors\s*Dihedrals:\s*([0-9-+.]+)' + 183s /usr/lib/python3/dist-packages/csb/bio/io/procheck.py:40: SyntaxWarning: invalid escape sequence '\s' 183s '\s*Covalent:\s*([0-9-+.]+)\s*Overall:\s*([0-9-+.]+)') 183s /usr/lib/python3/dist-packages/csb/bio/io/whatif.py:32: SyntaxWarning: invalid escape sequence '\s' 183s re_ramachandran = re.compile('Ramachandran\s*Z-score\s*:\s*([0-9.Ee-]+)') 183s /usr/lib/python3/dist-packages/csb/bio/io/whatif.py:33: SyntaxWarning: invalid escape sequence '\s' 183s re_1st = re.compile('1st\s*generation\s*packing\s*quality\s*:\s*([0-9.Ee-]+)') 183s /usr/lib/python3/dist-packages/csb/bio/io/whatif.py:34: SyntaxWarning: invalid escape sequence '\s' 183s re_2nd = re.compile('2nd\s*generation\s*packing\s*quality\s*:\s*([0-9.Ee-]+)') 183s /usr/lib/python3/dist-packages/csb/bio/io/whatif.py:35: SyntaxWarning: invalid escape sequence '\s' 183s re_backbone = re.compile('Backbone\s*conformation\s*Z-score\s*:\s*([0-9.Ee-]+)') 183s /usr/lib/python3/dist-packages/csb/bio/io/whatif.py:36: SyntaxWarning: invalid escape sequence '\S' 183s re_rotamer = re.compile('chi-1\S*chi-2\s*rotamer\s*normality\s*:\s*([0-9.Ee-]+)') 183s /usr/lib/python3/dist-packages/csb/bio/io/wwpdb.py:1222: SyntaxWarning: invalid escape sequence '\d' 183s res = re.search("(\d+(?:\.\d+)?)\s+ANGSTROM", line) 184s /usr/lib/python3/dist-packages/csb/bio/sequence/__init__.py:566: SyntaxWarning: invalid escape sequence '\w' 184s self._residues += re.sub('([^\w\-\.])+', '', string) 184s /usr/lib/python3/dist-packages/csb/bio/structure/__init__.py:2129: SyntaxWarning: invalid escape sequence '\s' 184s string = ''.join(re.split('\s+', string)) 184s /usr/lib/python3/dist-packages/csb/bio/structure/__init__.py:2131: SyntaxWarning: invalid escape sequence '\s' 184s conf_string = ''.join(re.split('\s+', conf_string)) 184s /usr/lib/python3/dist-packages/csb/statistics/__init__.py:341: SyntaxWarning: invalid escape sequence '\s' 184s """ 184s /usr/lib/python3/dist-packages/csb/test/cases/io/__init__.py:482: SyntaxWarning: invalid escape sequence '\w' 184s "([0-9a-zA-Z]([-.\w]*[0-9a-zA-Z])"] 184s /usr/lib/python3/dist-packages/csb/bio/io/hhpred.py:210: SyntaxWarning: invalid escape sequence '\d' 184s m = re.search('(\d+)\D+(\d+)', line).groups() 184s /usr/lib/python3/dist-packages/csb/bio/io/hhpred.py:260: SyntaxWarning: invalid escape sequence '\s' 184s seq = re.sub('\s+', '', ''.join(lines[1:])) 184s /usr/lib/python3/dist-packages/csb/bio/io/hhpred.py:307: SyntaxWarning: invalid escape sequence '\-' 184s pattern = re.compile('^[A-Z\-]\s[0-9]+\s+') 184s /usr/lib/python3/dist-packages/csb/bio/io/procheck.py:31: SyntaxWarning: invalid escape sequence '\s' 184s input_file_name = re.compile('>>>-----.*?\n.*?\n\s*\|\s*(\S+)\s+') 184s /usr/lib/python3/dist-packages/csb/bio/io/procheck.py:32: SyntaxWarning: invalid escape sequence '\d' 184s residues = re.compile('(\d+)\s*residues\s\|') 184s /usr/lib/python3/dist-packages/csb/bio/io/procheck.py:33: SyntaxWarning: invalid escape sequence '\s' 184s ramachandran_plot = re.compile('Ramachandran\splot:\s*(\d+\.\d+)' + 184s /usr/lib/python3/dist-packages/csb/bio/io/procheck.py:34: SyntaxWarning: invalid escape sequence '\s' 184s '%\s*core\s*(\d+\.\d+)%\s*allow\s*(\d+\.\d+)' + 184s /usr/lib/python3/dist-packages/csb/bio/io/procheck.py:35: SyntaxWarning: invalid escape sequence '\s' 184s '%\s*gener\s*(\d+\.\d+)%\s*disall') 184s /usr/lib/python3/dist-packages/csb/bio/io/procheck.py:36: SyntaxWarning: invalid escape sequence '\s' 184s labelled_all = re.compile('Ramachandrans:\s*(\d+)\s*.*?out\sof\s*(\d+)') 184s /usr/lib/python3/dist-packages/csb/bio/io/procheck.py:37: SyntaxWarning: invalid escape sequence '\s' 184s labelled_chi = re.compile('Chi1-chi2\splots:\s*(\d+)\s*.*?out\sof\s*(\d+)') 184s /usr/lib/python3/dist-packages/csb/bio/io/procheck.py:38: SyntaxWarning: invalid escape sequence '\s' 184s bad_contacts = re.compile('Bad\scontacts:\s*(\d+)') 184s /usr/lib/python3/dist-packages/csb/bio/io/procheck.py:39: SyntaxWarning: invalid escape sequence '\s' 184s g_factors = re.compile('G-factors\s*Dihedrals:\s*([0-9-+.]+)' + 184s /usr/lib/python3/dist-packages/csb/bio/io/procheck.py:40: SyntaxWarning: invalid escape sequence '\s' 184s '\s*Covalent:\s*([0-9-+.]+)\s*Overall:\s*([0-9-+.]+)') 184s /usr/lib/python3/dist-packages/csb/bio/io/whatif.py:32: SyntaxWarning: invalid escape sequence '\s' 184s re_ramachandran = re.compile('Ramachandran\s*Z-score\s*:\s*([0-9.Ee-]+)') 184s /usr/lib/python3/dist-packages/csb/bio/io/whatif.py:33: SyntaxWarning: invalid escape sequence '\s' 184s re_1st = re.compile('1st\s*generation\s*packing\s*quality\s*:\s*([0-9.Ee-]+)') 184s /usr/lib/python3/dist-packages/csb/bio/io/whatif.py:34: SyntaxWarning: invalid escape sequence '\s' 184s re_2nd = re.compile('2nd\s*generation\s*packing\s*quality\s*:\s*([0-9.Ee-]+)') 184s /usr/lib/python3/dist-packages/csb/bio/io/whatif.py:35: SyntaxWarning: invalid escape sequence '\s' 184s re_backbone = re.compile('Backbone\s*conformation\s*Z-score\s*:\s*([0-9.Ee-]+)') 184s /usr/lib/python3/dist-packages/csb/bio/io/whatif.py:36: SyntaxWarning: invalid escape sequence '\S' 184s re_rotamer = re.compile('chi-1\S*chi-2\s*rotamer\s*normality\s*:\s*([0-9.Ee-]+)') 184s /usr/lib/python3/dist-packages/csb/bio/io/wwpdb.py:1222: SyntaxWarning: invalid escape sequence '\d' 184s res = re.search("(\d+(?:\.\d+)?)\s+ANGSTROM", line) 184s /usr/lib/python3/dist-packages/csb/bio/sequence/__init__.py:566: SyntaxWarning: invalid escape sequence '\w' 184s self._residues += re.sub('([^\w\-\.])+', '', string) 184s /usr/lib/python3/dist-packages/csb/bio/structure/__init__.py:2129: SyntaxWarning: invalid escape sequence '\s' 184s string = ''.join(re.split('\s+', string)) 184s /usr/lib/python3/dist-packages/csb/bio/structure/__init__.py:2131: SyntaxWarning: invalid escape sequence '\s' 184s conf_string = ''.join(re.split('\s+', conf_string)) 184s /usr/lib/python3/dist-packages/csb/statistics/__init__.py:341: SyntaxWarning: invalid escape sequence '\s' 184s """ 184s /usr/lib/python3/dist-packages/csb/test/cases/io/__init__.py:482: SyntaxWarning: invalid escape sequence '\w' 184s "([0-9a-zA-Z]([-.\w]*[0-9a-zA-Z])"] 184s Setting up autopkgtest-satdep (0) ... 184s Processing triggers for libc-bin (2.40-1ubuntu3) ... 184s Processing triggers for systemd (256.5-2ubuntu4) ... 184s Processing triggers for man-db (2.12.1-3) ... 190s (Reading database ... 87853 files and directories currently installed.) 190s Removing autopkgtest-satdep (0) ... 192s autopkgtest [10:23:20]: test build: [----------------------- 192s Traceback (most recent call last): 192s File "/usr/lib/python3/dist-packages/csb/test/__init__.py", line 335, in ensureDataConsistency 192s self.getPickle('1nz9.model1.pickle') 192s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 192s File "/usr/lib/python3/dist-packages/csb/test/__init__.py", line 296, in getPickle 192s file = self.getTestFile(fileName, subDir) 192s File "/usr/lib/python3/dist-packages/csb/test/__init__.py", line 281, in getTestFile 192s raise IOError('Test file not found: {0}'.format(fileName)) 192s OSError: Test file not found: 1nz9.model1.pickle 192s 192s During handling of the above exception, another exception occurred: 192s 192s Traceback (most recent call last): 192s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 192s from . import multiarray 192s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 192s from . import overrides 192s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 192s from numpy.core._multiarray_umath import ( 192s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 192s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 192s 192s During handling of the above exception, another exception occurred: 192s 192s Traceback (most recent call last): 192s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 192s from numpy.__config__ import show as show_config 192s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 192s from numpy.core._multiarray_umath import ( 192s ...<3 lines>... 192s ) 192s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 192s raise ImportError(msg) 192s ImportError: 192s 192s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 192s 192s Importing the numpy C-extensions failed. This error can happen for 192s many reasons, often due to issues with your setup or how NumPy was 192s installed. 192s 192s We have compiled some common reasons and troubleshooting tips at: 192s 192s https://numpy.org/devdocs/user/troubleshooting-importerror.html 192s 192s Please note and check the following: 192s 192s * The Python version is: Python3.13 from "/usr/bin/python3.13" 192s * The NumPy version is: "1.26.4" 192s 192s and make sure that they are the versions you expect. 192s Please carefully study the documentation linked above for further help. 192s 192s Original error was: No module named 'numpy.core._multiarray_umath' 192s 192s 192s The above exception was the direct cause of the following exception: 192s 192s Traceback (most recent call last): 192s File "/tmp/autopkgtest.GgJI0a/autopkgtest_tmp/test/app.py", line 13, in 192s main() 192s ~~~~^^ 192s File "/tmp/autopkgtest.GgJI0a/autopkgtest_tmp/test/app.py", line 9, in main 192s return Console('csb.test.cases.*') 192s File "/usr/lib/python3/dist-packages/csb/test/__init__.py", line 806, in __init__ 192s self.run() 192s ~~~~~~~~^^ 192s File "/usr/lib/python3/dist-packages/csb/test/__init__.py", line 861, in run 192s Config().ensureDataConsistency() 192s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 192s File "/usr/lib/python3/dist-packages/csb/test/__init__.py", line 337, in ensureDataConsistency 192s self.updateDataFiles() 192s ~~~~~~~~~~~~~~~~~~~~^^ 192s File "/usr/lib/python3/dist-packages/csb/test/__init__.py", line 345, in updateDataFiles 192s from csb.bio.io.wwpdb import RegularStructureParser 192s File "/usr/lib/python3/dist-packages/csb/bio/io/__init__.py", line 5, in 192s from csb.bio.io.hhpred import HHOutputParser, HHProfileParser 192s File "/usr/lib/python3/dist-packages/csb/bio/io/hhpred.py", line 25, in 192s import csb.bio.structure as structure 192s File "/usr/lib/python3/dist-packages/csb/bio/structure/__init__.py", line 67, in 192s import numpy 192s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 192s raise ImportError(msg) from e 192s ImportError: Error importing numpy: you should not try to import numpy from 192s its source directory; please exit the numpy source tree, and relaunch 192s your python interpreter from there. 192s autopkgtest [10:23:20]: test build: -----------------------] 193s build FAIL non-zero exit status 1 193s autopkgtest [10:23:21]: test build: - - - - - - - - - - results - - - - - - - - - - 194s autopkgtest [10:23:22]: test autodep8-python3: preparing testbed 197s Reading package lists... 197s Building dependency tree... 197s Reading state information... 197s Starting pkgProblemResolver with broken count: 0 198s Starting 2 pkgProblemResolver with broken count: 0 198s Done 199s The following NEW packages will be installed: 199s autopkgtest-satdep 199s 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 199s Need to get 0 B/716 B of archives. 199s After this operation, 0 B of additional disk space will be used. 199s Get:1 /tmp/autopkgtest.GgJI0a/2-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [716 B] 199s Selecting previously unselected package autopkgtest-satdep. 199s (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 ... 87853 files and directories currently installed.) 199s Preparing to unpack .../2-autopkgtest-satdep.deb ... 199s Unpacking autopkgtest-satdep (0) ... 199s Setting up autopkgtest-satdep (0) ... 202s (Reading database ... 87853 files and directories currently installed.) 202s Removing autopkgtest-satdep (0) ... 203s autopkgtest [10:23:31]: test autodep8-python3: set -e ; for py in $(py3versions -r 2>/dev/null) ; do cd "$AUTOPKGTEST_TMP" ; echo "Testing with $py:" ; $py -c "import csb; print(csb)" ; done 203s autopkgtest [10:23:31]: test autodep8-python3: [----------------------- 203s Testing with python3.13: 203s 203s Testing with python3.12: 203s 203s autopkgtest [10:23:31]: test autodep8-python3: -----------------------] 204s autopkgtest [10:23:32]: test autodep8-python3: - - - - - - - - - - results - - - - - - - - - - 204s autodep8-python3 PASS (superficial) 204s autopkgtest [10:23:32]: @@@@@@@@@@@@@@@@@@@@ summary 204s build FAIL non-zero exit status 1 204s autodep8-python3 PASS (superficial) 217s nova [W] Skipping flock in bos03-arm64 217s Creating nova instance adt-plucky-arm64-python-csb-20241113-102007-juju-7f2275-prod-proposed-migration-environment-20-7bdae569-3891-4b73-a4ab-4b21bf4282a3 from image adt/ubuntu-plucky-arm64-server-20241113.img (UUID 2d7760e6-2439-4200-89d6-5ed33e5c6330)...