0s autopkgtest [13:36:10]: starting date and time: 2024-11-13 13:36:10+0000 0s autopkgtest [13:36:10]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [13:36:10]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.cj_l0v8u/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-s390x --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@bos03-s390x-30.secgroup --name adt-plucky-s390x-python-csb-20241113-133610-juju-7f2275-prod-proposed-migration-environment-20-8035e2bc-04dc-4042-b3cb-c8c035bba264 --image adt/ubuntu-plucky-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-proposed-migration-s390x -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/ 133s autopkgtest [13:38:23]: testbed dpkg architecture: s390x 133s autopkgtest [13:38:23]: testbed apt version: 2.9.8 133s autopkgtest [13:38:23]: @@@@@@@@@@@@@@@@@@@@ test bed setup 134s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 135s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 135s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [16.5 kB] 135s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [104 kB] 135s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [967 kB] 135s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x Packages [107 kB] 135s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x Packages [641 kB] 135s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x Packages [17.4 kB] 135s Fetched 1934 kB in 1s (1707 kB/s) 135s Reading package lists... 137s Reading package lists... 137s Building dependency tree... 137s Reading state information... 137s Calculating upgrade... 137s The following NEW packages will be installed: 137s python3.13-gdbm 137s The following packages will be upgraded: 137s libgpgme11t64 libpython3-stdlib python3 python3-gdbm python3-minimal 138s 5 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 138s Need to get 252 kB of archives. 138s After this operation, 98.3 kB of additional disk space will be used. 138s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x python3-minimal s390x 3.12.7-1 [27.4 kB] 138s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x python3 s390x 3.12.7-1 [24.0 kB] 138s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libpython3-stdlib s390x 3.12.7-1 [10.0 kB] 138s Get:4 http://ftpmaster.internal/ubuntu plucky/main s390x python3.13-gdbm s390x 3.13.0-2 [31.0 kB] 138s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x python3-gdbm s390x 3.12.7-1 [8642 B] 138s Get:6 http://ftpmaster.internal/ubuntu plucky/main s390x libgpgme11t64 s390x 1.23.2-5ubuntu4 [151 kB] 138s Fetched 252 kB in 0s (563 kB/s) 138s (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 ... 55510 files and directories currently installed.) 138s Preparing to unpack .../python3-minimal_3.12.7-1_s390x.deb ... 138s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ... 138s Setting up python3-minimal (3.12.7-1) ... 138s (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 ... 55510 files and directories currently installed.) 138s Preparing to unpack .../python3_3.12.7-1_s390x.deb ... 138s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ... 138s Preparing to unpack .../libpython3-stdlib_3.12.7-1_s390x.deb ... 138s Unpacking libpython3-stdlib:s390x (3.12.7-1) over (3.12.6-0ubuntu1) ... 138s Selecting previously unselected package python3.13-gdbm. 138s Preparing to unpack .../python3.13-gdbm_3.13.0-2_s390x.deb ... 138s Unpacking python3.13-gdbm (3.13.0-2) ... 138s Preparing to unpack .../python3-gdbm_3.12.7-1_s390x.deb ... 138s Unpacking python3-gdbm:s390x (3.12.7-1) over (3.12.6-1ubuntu1) ... 138s Preparing to unpack .../libgpgme11t64_1.23.2-5ubuntu4_s390x.deb ... 138s Unpacking libgpgme11t64:s390x (1.23.2-5ubuntu4) over (1.18.0-4.1ubuntu4) ... 138s Setting up libgpgme11t64:s390x (1.23.2-5ubuntu4) ... 138s Setting up python3.13-gdbm (3.13.0-2) ... 138s Setting up libpython3-stdlib:s390x (3.12.7-1) ... 138s Setting up python3 (3.12.7-1) ... 139s Setting up python3-gdbm:s390x (3.12.7-1) ... 139s Processing triggers for man-db (2.12.1-3) ... 139s Processing triggers for libc-bin (2.40-1ubuntu3) ... 139s Reading package lists... 139s Building dependency tree... 139s Reading state information... 139s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 140s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 140s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 140s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 140s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 141s Reading package lists... 141s Reading package lists... 141s Building dependency tree... 141s Reading state information... 141s Calculating upgrade... 141s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 141s Reading package lists... 141s Building dependency tree... 141s Reading state information... 141s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 144s autopkgtest [13:38:34]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP Mon Sep 16 12:49:35 UTC 2024 144s autopkgtest [13:38:34]: @@@@@@@@@@@@@@@@@@@@ apt-source python-csb 146s Get:1 http://ftpmaster.internal/ubuntu plucky/universe python-csb 1.2.5+dfsg-10 (dsc) [1627 B] 146s Get:2 http://ftpmaster.internal/ubuntu plucky/universe python-csb 1.2.5+dfsg-10 (tar) [3000 kB] 146s Get:3 http://ftpmaster.internal/ubuntu plucky/universe python-csb 1.2.5+dfsg-10 (diff) [11.5 kB] 146s gpgv: Signature made Sat Dec 9 16:03:46 2023 UTC 146s gpgv: using EDDSA key A095B66EE09024BEE6A2F0722A27904BD7243EDA 146s gpgv: Can't check signature: No public key 146s dpkg-source: warning: cannot verify inline signature for ./python-csb_1.2.5+dfsg-10.dsc: no acceptable signature found 146s autopkgtest [13:38:36]: testing package python-csb version 1.2.5+dfsg-10 147s autopkgtest [13:38:37]: build not needed 148s autopkgtest [13:38:38]: test build: preparing testbed 152s Reading package lists... 152s Building dependency tree... 152s Reading state information... 152s Starting pkgProblemResolver with broken count: 0 152s Starting 2 pkgProblemResolver with broken count: 0 152s Done 152s The following additional packages will be installed: 152s blt fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-lyx libblas3 152s libdeflate0 libfontconfig1 libfreetype6 libgfortran5 libgomp1 libgraphite2-3 152s libharfbuzz0b libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 libjs-jquery 152s libjs-jquery-ui liblapack3 liblbfgsb0 liblcms2-2 libopenjp2-7 152s libpython3.13-minimal libpython3.13-stdlib libqhull-r8.0 libraqm0 152s libsharpyuv0 libtcl8.6 libtiff6 libtk8.6 libwebp7 libwebpdemux2 libwebpmux3 152s libxft2 libxrender1 libxslt1.1 libxss1 python-matplotlib-data python3-all 152s python3-appdirs python3-brotli python3-contourpy python3-csb python3-cycler 152s python3-dateutil python3-decorator python3-fonttools python3-fs 152s python3-kiwisolver python3-lxml python3-lz4 python3-matplotlib 152s python3-mpmath python3-numpy python3-packaging python3-pil 152s python3-pil.imagetk python3-scipy python3-six python3-sympy python3-tk 152s python3-tz python3-ufolib2 python3-unicodedata2 python3.12-tk python3.13 153s python3.13-minimal python3.13-tk tk8.6-blt2.5 unicode-data x11-common 153s Suggested packages: 153s blt-demo libjs-jquery-ui-docs liblcms2-utils tcl8.6 tk8.6 python-cycler-doc 153s python-lxml-doc cm-super-minimal dvipng ffmpeg fonts-staypuft ghostscript 153s gir1.2-gtk-3.0 inkscape ipython3 librsvg2-common python-matplotlib-doc 153s python3-cairocffi python3-gi-cairo python3-gobject python3-pyqt5 python3-sip 153s python3-tornado texlive-extra-utils texlive-latex-extra python-mpmath-doc 153s python3-gmpy2 gcc gfortran python-numpy-doc python3-dev python3-pytest 153s python-pil-doc python-scipy-doc texlive-fonts-extra python-sympy-doc tix 153s python3-tk-dbg python3.13-venv python3.13-doc binfmt-support 153s Recommended packages: 153s javascript-common python3-bs4 python3-cssselect python3-html5lib 153s python3-olefile g++ | c++-compiler isympy-common 153s The following NEW packages will be installed: 153s autopkgtest-satdep blt fontconfig-config fonts-dejavu-core fonts-dejavu-mono 153s fonts-lyx libblas3 libdeflate0 libfontconfig1 libfreetype6 libgfortran5 153s libgomp1 libgraphite2-3 libharfbuzz0b libimagequant0 libjbig0 libjpeg-turbo8 153s libjpeg8 libjs-jquery libjs-jquery-ui liblapack3 liblbfgsb0 liblcms2-2 153s libopenjp2-7 libpython3.13-minimal libpython3.13-stdlib libqhull-r8.0 153s libraqm0 libsharpyuv0 libtcl8.6 libtiff6 libtk8.6 libwebp7 libwebpdemux2 153s libwebpmux3 libxft2 libxrender1 libxslt1.1 libxss1 python-matplotlib-data 153s python3-all python3-appdirs python3-brotli python3-contourpy python3-csb 153s python3-cycler python3-dateutil python3-decorator python3-fonttools 153s python3-fs python3-kiwisolver python3-lxml python3-lz4 python3-matplotlib 153s python3-mpmath python3-numpy python3-packaging python3-pil 153s python3-pil.imagetk python3-scipy python3-six python3-sympy python3-tk 153s python3-tz python3-ufolib2 python3-unicodedata2 python3.12-tk python3.13 153s python3.13-minimal python3.13-tk tk8.6-blt2.5 unicode-data x11-common 153s 0 upgraded, 73 newly installed, 0 to remove and 0 not upgraded. 153s Need to get 67.2 MB/67.2 MB of archives. 153s After this operation, 273 MB of additional disk space will be used. 153s Get:1 /tmp/autopkgtest.ZP1Moh/1-autopkgtest-satdep.deb autopkgtest-satdep s390x 0 [712 B] 153s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x libpython3.13-minimal s390x 3.13.0-2 [877 kB] 153s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x python3.13-minimal s390x 3.13.0-2 [2172 kB] 153s Get:4 http://ftpmaster.internal/ubuntu plucky/main s390x libtcl8.6 s390x 8.6.15+dfsg-2 [1034 kB] 153s Get:5 http://ftpmaster.internal/ubuntu plucky/main s390x libfreetype6 s390x 2.13.3+dfsg-1 [431 kB] 153s Get:6 http://ftpmaster.internal/ubuntu plucky/main s390x fonts-dejavu-mono all 2.37-8 [502 kB] 153s Get:7 http://ftpmaster.internal/ubuntu plucky/main s390x fonts-dejavu-core all 2.37-8 [835 kB] 153s Get:8 http://ftpmaster.internal/ubuntu plucky/main s390x fontconfig-config s390x 2.15.0-1.1ubuntu2 [37.4 kB] 153s Get:9 http://ftpmaster.internal/ubuntu plucky/main s390x libfontconfig1 s390x 2.15.0-1.1ubuntu2 [150 kB] 153s Get:10 http://ftpmaster.internal/ubuntu plucky/main s390x libxrender1 s390x 1:0.9.10-1.1build1 [20.4 kB] 153s Get:11 http://ftpmaster.internal/ubuntu plucky/main s390x libxft2 s390x 2.3.6-1build1 [49.6 kB] 153s Get:12 http://ftpmaster.internal/ubuntu plucky/main s390x x11-common all 1:7.7+23ubuntu3 [21.7 kB] 153s Get:13 http://ftpmaster.internal/ubuntu plucky/main s390x libxss1 s390x 1:1.2.3-1build3 [7396 B] 153s Get:14 http://ftpmaster.internal/ubuntu plucky/main s390x libtk8.6 s390x 8.6.15-1 [828 kB] 153s Get:15 http://ftpmaster.internal/ubuntu plucky/main s390x tk8.6-blt2.5 s390x 2.5.3+dfsg-7build1 [662 kB] 153s Get:16 http://ftpmaster.internal/ubuntu plucky/main s390x blt s390x 2.5.3+dfsg-7build1 [4840 B] 153s Get:17 http://ftpmaster.internal/ubuntu plucky/universe s390x fonts-lyx all 2.4.2.1-1 [171 kB] 153s Get:18 http://ftpmaster.internal/ubuntu plucky/main s390x libblas3 s390x 3.12.0-3build2 [238 kB] 153s Get:19 http://ftpmaster.internal/ubuntu plucky/main s390x libdeflate0 s390x 1.22-1 [46.1 kB] 153s Get:20 http://ftpmaster.internal/ubuntu plucky/main s390x libgfortran5 s390x 14.2.0-8ubuntu1 [587 kB] 153s Get:21 http://ftpmaster.internal/ubuntu plucky/main s390x libgomp1 s390x 14.2.0-8ubuntu1 [151 kB] 153s Get:22 http://ftpmaster.internal/ubuntu plucky/main s390x libgraphite2-3 s390x 1.3.14-2ubuntu1 [79.8 kB] 153s Get:23 http://ftpmaster.internal/ubuntu plucky/main s390x libharfbuzz0b s390x 10.0.1-1 [536 kB] 153s Get:24 http://ftpmaster.internal/ubuntu plucky/main s390x libimagequant0 s390x 2.18.0-1build1 [43.3 kB] 153s Get:25 http://ftpmaster.internal/ubuntu plucky/main s390x libjpeg-turbo8 s390x 2.1.5-2ubuntu2 [150 kB] 153s Get:26 http://ftpmaster.internal/ubuntu plucky/main s390x libjpeg8 s390x 8c-2ubuntu11 [2146 B] 153s Get:27 http://ftpmaster.internal/ubuntu plucky/main s390x libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 154s Get:28 http://ftpmaster.internal/ubuntu plucky/universe s390x libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 154s Get:29 http://ftpmaster.internal/ubuntu plucky/main s390x liblapack3 s390x 3.12.0-3build2 [2953 kB] 154s Get:30 http://ftpmaster.internal/ubuntu plucky/universe s390x liblbfgsb0 s390x 3.0+dfsg.4-1build1 [32.4 kB] 154s Get:31 http://ftpmaster.internal/ubuntu plucky/main s390x liblcms2-2 s390x 2.16-2 [175 kB] 154s Get:32 http://ftpmaster.internal/ubuntu plucky/main s390x libpython3.13-stdlib s390x 3.13.0-2 [2086 kB] 154s Get:33 http://ftpmaster.internal/ubuntu plucky/universe s390x libqhull-r8.0 s390x 2020.2-6build1 [199 kB] 154s Get:34 http://ftpmaster.internal/ubuntu plucky/main s390x libraqm0 s390x 0.10.1-1build1 [16.2 kB] 154s Get:35 http://ftpmaster.internal/ubuntu plucky/main s390x libsharpyuv0 s390x 1.4.0-0.1 [16.2 kB] 154s Get:36 http://ftpmaster.internal/ubuntu plucky/main s390x libjbig0 s390x 2.1-6.1ubuntu2 [33.1 kB] 154s Get:37 http://ftpmaster.internal/ubuntu plucky/main s390x libwebp7 s390x 1.4.0-0.1 [204 kB] 154s Get:38 http://ftpmaster.internal/ubuntu plucky/main s390x libtiff6 s390x 4.5.1+git230720-4ubuntu4 [217 kB] 154s Get:39 http://ftpmaster.internal/ubuntu plucky/main s390x libwebpdemux2 s390x 1.4.0-0.1 [12.2 kB] 154s Get:40 http://ftpmaster.internal/ubuntu plucky/main s390x libwebpmux3 s390x 1.4.0-0.1 [25.3 kB] 154s Get:41 http://ftpmaster.internal/ubuntu plucky/main s390x libxslt1.1 s390x 1.1.39-0exp1ubuntu1 [169 kB] 154s Get:42 http://ftpmaster.internal/ubuntu plucky/universe s390x python-matplotlib-data all 3.8.3-3 [2928 kB] 154s Get:43 http://ftpmaster.internal/ubuntu plucky/main s390x python3.13 s390x 3.13.0-2 [719 kB] 154s Get:44 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x python3-all s390x 3.12.7-1 [890 B] 154s Get:45 http://ftpmaster.internal/ubuntu plucky/main s390x python3-appdirs all 1.4.4-4 [10.9 kB] 154s Get:46 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-brotli s390x 1.1.0-2build2 [376 kB] 154s Get:47 http://ftpmaster.internal/ubuntu plucky/main s390x python3-numpy s390x 1:1.26.4+ds-11build1 [4113 kB] 154s Get:48 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-contourpy s390x 1.3.0-2 [195 kB] 154s Get:49 http://ftpmaster.internal/ubuntu plucky/main s390x python3-six all 1.16.0-7 [13.1 kB] 154s Get:50 http://ftpmaster.internal/ubuntu plucky/main s390x python3-dateutil all 2.9.0-2 [80.3 kB] 154s Get:51 http://ftpmaster.internal/ubuntu plucky/main s390x libopenjp2-7 s390x 2.5.0-2ubuntu1 [208 kB] 154s Get:52 http://ftpmaster.internal/ubuntu plucky/main s390x python3-pil s390x 10.4.0-1ubuntu1 [492 kB] 154s Get:53 http://ftpmaster.internal/ubuntu plucky/main s390x python3.12-tk s390x 3.12.7-3 [117 kB] 154s Get:54 http://ftpmaster.internal/ubuntu plucky/main s390x python3.13-tk s390x 3.13.0-2 [107 kB] 154s Get:55 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x python3-tk s390x 3.12.7-1 [9750 B] 154s Get:56 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-pil.imagetk s390x 10.4.0-1ubuntu1 [9314 B] 154s Get:57 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-cycler all 0.12.1-1 [9716 B] 154s Get:58 http://ftpmaster.internal/ubuntu plucky/main s390x python3-decorator all 5.1.1-5 [10.1 kB] 154s Get:59 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-scipy s390x 1.13.1-5 [17.5 MB] 155s Get:60 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-ufolib2 all 0.16.1+dfsg1-1 [33.4 kB] 155s Get:61 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-mpmath all 1.3.0-1 [425 kB] 155s Get:62 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-sympy all 1.13.3-1 [4228 kB] 155s Get:63 http://ftpmaster.internal/ubuntu plucky/main s390x python3-tz all 2024.1-2 [31.4 kB] 155s Get:64 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-fs all 2.4.16-4 [91.3 kB] 155s Get:65 http://ftpmaster.internal/ubuntu plucky/main s390x python3-lxml s390x 5.3.0-1 [1314 kB] 155s Get:66 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-lz4 s390x 4.0.2+dfsg-1build4 [26.4 kB] 155s Get:67 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-unicodedata2 s390x 15.1.0+ds-1build1 [367 kB] 155s Get:68 http://ftpmaster.internal/ubuntu plucky/universe s390x unicode-data all 15.1.0-1 [8878 kB] 156s Get:69 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-fonttools s390x 4.46.0-1build2 [1453 kB] 156s Get:70 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-kiwisolver s390x 1.4.7-2 [54.9 kB] 156s Get:71 http://ftpmaster.internal/ubuntu plucky/main s390x python3-packaging all 24.1-1 [41.4 kB] 156s Get:72 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-matplotlib s390x 3.8.3-3 [4554 kB] 156s Get:73 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-csb all 1.2.5+dfsg-10 [2392 kB] 156s Fetched 67.2 MB in 3s (19.7 MB/s) 156s Selecting previously unselected package libpython3.13-minimal:s390x. 156s (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 ... 55517 files and directories currently installed.) 156s Preparing to unpack .../00-libpython3.13-minimal_3.13.0-2_s390x.deb ... 156s Unpacking libpython3.13-minimal:s390x (3.13.0-2) ... 156s Selecting previously unselected package python3.13-minimal. 156s Preparing to unpack .../01-python3.13-minimal_3.13.0-2_s390x.deb ... 156s Unpacking python3.13-minimal (3.13.0-2) ... 156s Selecting previously unselected package libtcl8.6:s390x. 156s Preparing to unpack .../02-libtcl8.6_8.6.15+dfsg-2_s390x.deb ... 156s Unpacking libtcl8.6:s390x (8.6.15+dfsg-2) ... 156s Selecting previously unselected package libfreetype6:s390x. 156s Preparing to unpack .../03-libfreetype6_2.13.3+dfsg-1_s390x.deb ... 156s Unpacking libfreetype6:s390x (2.13.3+dfsg-1) ... 156s Selecting previously unselected package fonts-dejavu-mono. 156s Preparing to unpack .../04-fonts-dejavu-mono_2.37-8_all.deb ... 156s Unpacking fonts-dejavu-mono (2.37-8) ... 156s Selecting previously unselected package fonts-dejavu-core. 156s Preparing to unpack .../05-fonts-dejavu-core_2.37-8_all.deb ... 156s Unpacking fonts-dejavu-core (2.37-8) ... 156s Selecting previously unselected package fontconfig-config. 156s Preparing to unpack .../06-fontconfig-config_2.15.0-1.1ubuntu2_s390x.deb ... 157s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ... 157s Selecting previously unselected package libfontconfig1:s390x. 157s Preparing to unpack .../07-libfontconfig1_2.15.0-1.1ubuntu2_s390x.deb ... 157s Unpacking libfontconfig1:s390x (2.15.0-1.1ubuntu2) ... 157s Selecting previously unselected package libxrender1:s390x. 157s Preparing to unpack .../08-libxrender1_1%3a0.9.10-1.1build1_s390x.deb ... 157s Unpacking libxrender1:s390x (1:0.9.10-1.1build1) ... 157s Selecting previously unselected package libxft2:s390x. 157s Preparing to unpack .../09-libxft2_2.3.6-1build1_s390x.deb ... 157s Unpacking libxft2:s390x (2.3.6-1build1) ... 157s Selecting previously unselected package x11-common. 157s Preparing to unpack .../10-x11-common_1%3a7.7+23ubuntu3_all.deb ... 157s Unpacking x11-common (1:7.7+23ubuntu3) ... 157s Selecting previously unselected package libxss1:s390x. 157s Preparing to unpack .../11-libxss1_1%3a1.2.3-1build3_s390x.deb ... 157s Unpacking libxss1:s390x (1:1.2.3-1build3) ... 157s Selecting previously unselected package libtk8.6:s390x. 157s Preparing to unpack .../12-libtk8.6_8.6.15-1_s390x.deb ... 157s Unpacking libtk8.6:s390x (8.6.15-1) ... 157s Selecting previously unselected package tk8.6-blt2.5. 157s Preparing to unpack .../13-tk8.6-blt2.5_2.5.3+dfsg-7build1_s390x.deb ... 157s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 157s Selecting previously unselected package blt. 157s Preparing to unpack .../14-blt_2.5.3+dfsg-7build1_s390x.deb ... 157s Unpacking blt (2.5.3+dfsg-7build1) ... 157s Selecting previously unselected package fonts-lyx. 157s Preparing to unpack .../15-fonts-lyx_2.4.2.1-1_all.deb ... 157s Unpacking fonts-lyx (2.4.2.1-1) ... 157s Selecting previously unselected package libblas3:s390x. 157s Preparing to unpack .../16-libblas3_3.12.0-3build2_s390x.deb ... 157s Unpacking libblas3:s390x (3.12.0-3build2) ... 157s Selecting previously unselected package libdeflate0:s390x. 157s Preparing to unpack .../17-libdeflate0_1.22-1_s390x.deb ... 157s Unpacking libdeflate0:s390x (1.22-1) ... 157s Selecting previously unselected package libgfortran5:s390x. 157s Preparing to unpack .../18-libgfortran5_14.2.0-8ubuntu1_s390x.deb ... 157s Unpacking libgfortran5:s390x (14.2.0-8ubuntu1) ... 157s Selecting previously unselected package libgomp1:s390x. 157s Preparing to unpack .../19-libgomp1_14.2.0-8ubuntu1_s390x.deb ... 157s Unpacking libgomp1:s390x (14.2.0-8ubuntu1) ... 157s Selecting previously unselected package libgraphite2-3:s390x. 157s Preparing to unpack .../20-libgraphite2-3_1.3.14-2ubuntu1_s390x.deb ... 157s Unpacking libgraphite2-3:s390x (1.3.14-2ubuntu1) ... 157s Selecting previously unselected package libharfbuzz0b:s390x. 157s Preparing to unpack .../21-libharfbuzz0b_10.0.1-1_s390x.deb ... 157s Unpacking libharfbuzz0b:s390x (10.0.1-1) ... 157s Selecting previously unselected package libimagequant0:s390x. 157s Preparing to unpack .../22-libimagequant0_2.18.0-1build1_s390x.deb ... 157s Unpacking libimagequant0:s390x (2.18.0-1build1) ... 157s Selecting previously unselected package libjpeg-turbo8:s390x. 157s Preparing to unpack .../23-libjpeg-turbo8_2.1.5-2ubuntu2_s390x.deb ... 157s Unpacking libjpeg-turbo8:s390x (2.1.5-2ubuntu2) ... 157s Selecting previously unselected package libjpeg8:s390x. 157s Preparing to unpack .../24-libjpeg8_8c-2ubuntu11_s390x.deb ... 157s Unpacking libjpeg8:s390x (8c-2ubuntu11) ... 157s Selecting previously unselected package libjs-jquery. 157s Preparing to unpack .../25-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 157s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 157s Selecting previously unselected package libjs-jquery-ui. 157s Preparing to unpack .../26-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... 157s Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... 157s Selecting previously unselected package liblapack3:s390x. 157s Preparing to unpack .../27-liblapack3_3.12.0-3build2_s390x.deb ... 157s Unpacking liblapack3:s390x (3.12.0-3build2) ... 157s Selecting previously unselected package liblbfgsb0:s390x. 157s Preparing to unpack .../28-liblbfgsb0_3.0+dfsg.4-1build1_s390x.deb ... 157s Unpacking liblbfgsb0:s390x (3.0+dfsg.4-1build1) ... 157s Selecting previously unselected package liblcms2-2:s390x. 157s Preparing to unpack .../29-liblcms2-2_2.16-2_s390x.deb ... 157s Unpacking liblcms2-2:s390x (2.16-2) ... 157s Selecting previously unselected package libpython3.13-stdlib:s390x. 157s Preparing to unpack .../30-libpython3.13-stdlib_3.13.0-2_s390x.deb ... 157s Unpacking libpython3.13-stdlib:s390x (3.13.0-2) ... 157s Selecting previously unselected package libqhull-r8.0:s390x. 157s Preparing to unpack .../31-libqhull-r8.0_2020.2-6build1_s390x.deb ... 157s Unpacking libqhull-r8.0:s390x (2020.2-6build1) ... 157s Selecting previously unselected package libraqm0:s390x. 157s Preparing to unpack .../32-libraqm0_0.10.1-1build1_s390x.deb ... 157s Unpacking libraqm0:s390x (0.10.1-1build1) ... 157s Selecting previously unselected package libsharpyuv0:s390x. 157s Preparing to unpack .../33-libsharpyuv0_1.4.0-0.1_s390x.deb ... 157s Unpacking libsharpyuv0:s390x (1.4.0-0.1) ... 157s Selecting previously unselected package libjbig0:s390x. 157s Preparing to unpack .../34-libjbig0_2.1-6.1ubuntu2_s390x.deb ... 157s Unpacking libjbig0:s390x (2.1-6.1ubuntu2) ... 157s Selecting previously unselected package libwebp7:s390x. 157s Preparing to unpack .../35-libwebp7_1.4.0-0.1_s390x.deb ... 157s Unpacking libwebp7:s390x (1.4.0-0.1) ... 157s Selecting previously unselected package libtiff6:s390x. 157s Preparing to unpack .../36-libtiff6_4.5.1+git230720-4ubuntu4_s390x.deb ... 157s Unpacking libtiff6:s390x (4.5.1+git230720-4ubuntu4) ... 157s Selecting previously unselected package libwebpdemux2:s390x. 157s Preparing to unpack .../37-libwebpdemux2_1.4.0-0.1_s390x.deb ... 157s Unpacking libwebpdemux2:s390x (1.4.0-0.1) ... 157s Selecting previously unselected package libwebpmux3:s390x. 157s Preparing to unpack .../38-libwebpmux3_1.4.0-0.1_s390x.deb ... 157s Unpacking libwebpmux3:s390x (1.4.0-0.1) ... 157s Selecting previously unselected package libxslt1.1:s390x. 157s Preparing to unpack .../39-libxslt1.1_1.1.39-0exp1ubuntu1_s390x.deb ... 157s Unpacking libxslt1.1:s390x (1.1.39-0exp1ubuntu1) ... 157s Selecting previously unselected package python-matplotlib-data. 157s Preparing to unpack .../40-python-matplotlib-data_3.8.3-3_all.deb ... 157s Unpacking python-matplotlib-data (3.8.3-3) ... 157s Selecting previously unselected package python3.13. 157s Preparing to unpack .../41-python3.13_3.13.0-2_s390x.deb ... 157s Unpacking python3.13 (3.13.0-2) ... 157s Selecting previously unselected package python3-all. 157s Preparing to unpack .../42-python3-all_3.12.7-1_s390x.deb ... 157s Unpacking python3-all (3.12.7-1) ... 157s Selecting previously unselected package python3-appdirs. 157s Preparing to unpack .../43-python3-appdirs_1.4.4-4_all.deb ... 157s Unpacking python3-appdirs (1.4.4-4) ... 157s Selecting previously unselected package python3-brotli. 157s Preparing to unpack .../44-python3-brotli_1.1.0-2build2_s390x.deb ... 157s Unpacking python3-brotli (1.1.0-2build2) ... 157s Selecting previously unselected package python3-numpy. 157s Preparing to unpack .../45-python3-numpy_1%3a1.26.4+ds-11build1_s390x.deb ... 157s Unpacking python3-numpy (1:1.26.4+ds-11build1) ... 157s Selecting previously unselected package python3-contourpy. 157s Preparing to unpack .../46-python3-contourpy_1.3.0-2_s390x.deb ... 157s Unpacking python3-contourpy (1.3.0-2) ... 157s Selecting previously unselected package python3-six. 157s Preparing to unpack .../47-python3-six_1.16.0-7_all.deb ... 157s Unpacking python3-six (1.16.0-7) ... 157s Selecting previously unselected package python3-dateutil. 157s Preparing to unpack .../48-python3-dateutil_2.9.0-2_all.deb ... 157s Unpacking python3-dateutil (2.9.0-2) ... 157s Selecting previously unselected package libopenjp2-7:s390x. 157s Preparing to unpack .../49-libopenjp2-7_2.5.0-2ubuntu1_s390x.deb ... 157s Unpacking libopenjp2-7:s390x (2.5.0-2ubuntu1) ... 157s Selecting previously unselected package python3-pil:s390x. 157s Preparing to unpack .../50-python3-pil_10.4.0-1ubuntu1_s390x.deb ... 157s Unpacking python3-pil:s390x (10.4.0-1ubuntu1) ... 157s Selecting previously unselected package python3.12-tk. 157s Preparing to unpack .../51-python3.12-tk_3.12.7-3_s390x.deb ... 157s Unpacking python3.12-tk (3.12.7-3) ... 157s Selecting previously unselected package python3.13-tk. 157s Preparing to unpack .../52-python3.13-tk_3.13.0-2_s390x.deb ... 157s Unpacking python3.13-tk (3.13.0-2) ... 157s Selecting previously unselected package python3-tk:s390x. 157s Preparing to unpack .../53-python3-tk_3.12.7-1_s390x.deb ... 157s Unpacking python3-tk:s390x (3.12.7-1) ... 157s Selecting previously unselected package python3-pil.imagetk:s390x. 157s Preparing to unpack .../54-python3-pil.imagetk_10.4.0-1ubuntu1_s390x.deb ... 157s Unpacking python3-pil.imagetk:s390x (10.4.0-1ubuntu1) ... 157s Selecting previously unselected package python3-cycler. 157s Preparing to unpack .../55-python3-cycler_0.12.1-1_all.deb ... 157s Unpacking python3-cycler (0.12.1-1) ... 157s Selecting previously unselected package python3-decorator. 157s Preparing to unpack .../56-python3-decorator_5.1.1-5_all.deb ... 157s Unpacking python3-decorator (5.1.1-5) ... 157s Selecting previously unselected package python3-scipy. 157s Preparing to unpack .../57-python3-scipy_1.13.1-5_s390x.deb ... 157s Unpacking python3-scipy (1.13.1-5) ... 158s Selecting previously unselected package python3-ufolib2. 158s Preparing to unpack .../58-python3-ufolib2_0.16.1+dfsg1-1_all.deb ... 158s Unpacking python3-ufolib2 (0.16.1+dfsg1-1) ... 158s Selecting previously unselected package python3-mpmath. 158s Preparing to unpack .../59-python3-mpmath_1.3.0-1_all.deb ... 158s Unpacking python3-mpmath (1.3.0-1) ... 158s Selecting previously unselected package python3-sympy. 158s Preparing to unpack .../60-python3-sympy_1.13.3-1_all.deb ... 158s Unpacking python3-sympy (1.13.3-1) ... 158s Selecting previously unselected package python3-tz. 158s Preparing to unpack .../61-python3-tz_2024.1-2_all.deb ... 158s Unpacking python3-tz (2024.1-2) ... 158s Selecting previously unselected package python3-fs. 158s Preparing to unpack .../62-python3-fs_2.4.16-4_all.deb ... 158s Unpacking python3-fs (2.4.16-4) ... 158s Selecting previously unselected package python3-lxml:s390x. 158s Preparing to unpack .../63-python3-lxml_5.3.0-1_s390x.deb ... 158s Unpacking python3-lxml:s390x (5.3.0-1) ... 158s Selecting previously unselected package python3-lz4. 158s Preparing to unpack .../64-python3-lz4_4.0.2+dfsg-1build4_s390x.deb ... 158s Unpacking python3-lz4 (4.0.2+dfsg-1build4) ... 158s Selecting previously unselected package python3-unicodedata2. 158s Preparing to unpack .../65-python3-unicodedata2_15.1.0+ds-1build1_s390x.deb ... 158s Unpacking python3-unicodedata2 (15.1.0+ds-1build1) ... 158s Selecting previously unselected package unicode-data. 158s Preparing to unpack .../66-unicode-data_15.1.0-1_all.deb ... 158s Unpacking unicode-data (15.1.0-1) ... 158s Selecting previously unselected package python3-fonttools. 158s Preparing to unpack .../67-python3-fonttools_4.46.0-1build2_s390x.deb ... 158s Unpacking python3-fonttools (4.46.0-1build2) ... 158s Selecting previously unselected package python3-kiwisolver. 158s Preparing to unpack .../68-python3-kiwisolver_1.4.7-2_s390x.deb ... 158s Unpacking python3-kiwisolver (1.4.7-2) ... 158s Selecting previously unselected package python3-packaging. 158s Preparing to unpack .../69-python3-packaging_24.1-1_all.deb ... 158s Unpacking python3-packaging (24.1-1) ... 158s Selecting previously unselected package python3-matplotlib. 158s Preparing to unpack .../70-python3-matplotlib_3.8.3-3_s390x.deb ... 158s Unpacking python3-matplotlib (3.8.3-3) ... 158s Selecting previously unselected package python3-csb. 158s Preparing to unpack .../71-python3-csb_1.2.5+dfsg-10_all.deb ... 158s Unpacking python3-csb (1.2.5+dfsg-10) ... 158s Selecting previously unselected package autopkgtest-satdep. 158s Preparing to unpack .../72-1-autopkgtest-satdep.deb ... 158s Unpacking autopkgtest-satdep (0) ... 158s Setting up libgraphite2-3:s390x (1.3.14-2ubuntu1) ... 158s Setting up liblcms2-2:s390x (2.16-2) ... 158s Setting up libsharpyuv0:s390x (1.4.0-0.1) ... 158s Setting up libxrender1:s390x (1:0.9.10-1.1build1) ... 158s Setting up python3-lz4 (4.0.2+dfsg-1build4) ... 159s Setting up python3-unicodedata2 (15.1.0+ds-1build1) ... 159s Setting up fonts-lyx (2.4.2.1-1) ... 159s Setting up x11-common (1:7.7+23ubuntu3) ... 159s Setting up libdeflate0:s390x (1.22-1) ... 159s Setting up libqhull-r8.0:s390x (2020.2-6build1) ... 159s Setting up libgomp1:s390x (14.2.0-8ubuntu1) ... 159s Setting up libjbig0:s390x (2.1-6.1ubuntu2) ... 159s Setting up python3-tz (2024.1-2) ... 159s Setting up unicode-data (15.1.0-1) ... 159s Setting up python3-six (1.16.0-7) ... 159s Setting up libpython3.13-minimal:s390x (3.13.0-2) ... 159s Setting up python3-decorator (5.1.1-5) ... 159s Setting up libblas3:s390x (3.12.0-3build2) ... 159s 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 159s Setting up python3-packaging (24.1-1) ... 159s Setting up libfreetype6:s390x (2.13.3+dfsg-1) ... 159s Setting up python3-brotli (1.1.0-2build2) ... 159s Setting up python3-cycler (0.12.1-1) ... 160s Setting up libimagequant0:s390x (2.18.0-1build1) ... 160s Setting up fonts-dejavu-mono (2.37-8) ... 160s Setting up python3-kiwisolver (1.4.7-2) ... 160s Setting up libtcl8.6:s390x (8.6.15+dfsg-2) ... 160s Setting up fonts-dejavu-core (2.37-8) ... 160s Setting up libjpeg-turbo8:s390x (2.1.5-2ubuntu2) ... 160s Setting up libgfortran5:s390x (14.2.0-8ubuntu1) ... 160s Setting up libwebp7:s390x (1.4.0-0.1) ... 160s Setting up libxslt1.1:s390x (1.1.39-0exp1ubuntu1) ... 160s Setting up libopenjp2-7:s390x (2.5.0-2ubuntu1) ... 160s Setting up python3.13-minimal (3.13.0-2) ... 160s Setting up libharfbuzz0b:s390x (10.0.1-1) ... 160s Setting up python3-dateutil (2.9.0-2) ... 161s Setting up libxss1:s390x (1:1.2.3-1build3) ... 161s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 161s Setting up python3-mpmath (1.3.0-1) ... 162s Setting up python-matplotlib-data (3.8.3-3) ... 162s Setting up libwebpmux3:s390x (1.4.0-0.1) ... 162s Setting up python3-appdirs (1.4.4-4) ... 162s Setting up libpython3.13-stdlib:s390x (3.13.0-2) ... 162s Setting up libjpeg8:s390x (8c-2ubuntu11) ... 162s Setting up python3-sympy (1.13.3-1) ... 174s Setting up liblapack3:s390x (3.12.0-3build2) ... 174s 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 174s Setting up python3.13 (3.13.0-2) ... 175s Setting up fontconfig-config (2.15.0-1.1ubuntu2) ... 175s Setting up libwebpdemux2:s390x (1.4.0-0.1) ... 175s Setting up python3-all (3.12.7-1) ... 175s Setting up python3-fs (2.4.16-4) ... 176s Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... 176s Setting up libraqm0:s390x (0.10.1-1build1) ... 176s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 179s Setting up python3-lxml:s390x (5.3.0-1) ... 179s Setting up libtiff6:s390x (4.5.1+git230720-4ubuntu4) ... 179s Setting up python3-contourpy (1.3.0-2) ... 180s Setting up libfontconfig1:s390x (2.15.0-1.1ubuntu2) ... 180s Setting up liblbfgsb0:s390x (3.0+dfsg.4-1build1) ... 180s Setting up libxft2:s390x (2.3.6-1build1) ... 180s Setting up python3-scipy (1.13.1-5) ... 186s Setting up libtk8.6:s390x (8.6.15-1) ... 186s Setting up python3.12-tk (3.12.7-3) ... 186s Setting up python3.13-tk (3.13.0-2) ... 186s Setting up python3-pil:s390x (10.4.0-1ubuntu1) ... 187s Setting up tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 187s Setting up blt (2.5.3+dfsg-7build1) ... 187s Setting up python3-tk:s390x (3.12.7-1) ... 187s Setting up python3-pil.imagetk:s390x (10.4.0-1ubuntu1) ... 187s Setting up python3-fonttools (4.46.0-1build2) ... 189s Setting up python3-ufolib2 (0.16.1+dfsg1-1) ... 189s Setting up python3-matplotlib (3.8.3-3) ... 192s Setting up python3-csb (1.2.5+dfsg-10) ... 192s /usr/lib/python3/dist-packages/csb/bio/io/hhpred.py:210: SyntaxWarning: invalid escape sequence '\d' 192s m = re.search('(\d+)\D+(\d+)', line).groups() 192s /usr/lib/python3/dist-packages/csb/bio/io/hhpred.py:260: SyntaxWarning: invalid escape sequence '\s' 192s seq = re.sub('\s+', '', ''.join(lines[1:])) 192s /usr/lib/python3/dist-packages/csb/bio/io/hhpred.py:307: SyntaxWarning: invalid escape sequence '\-' 192s pattern = re.compile('^[A-Z\-]\s[0-9]+\s+') 192s /usr/lib/python3/dist-packages/csb/bio/io/procheck.py:31: SyntaxWarning: invalid escape sequence '\s' 192s input_file_name = re.compile('>>>-----.*?\n.*?\n\s*\|\s*(\S+)\s+') 192s /usr/lib/python3/dist-packages/csb/bio/io/procheck.py:32: SyntaxWarning: invalid escape sequence '\d' 192s residues = re.compile('(\d+)\s*residues\s\|') 192s /usr/lib/python3/dist-packages/csb/bio/io/procheck.py:33: SyntaxWarning: invalid escape sequence '\s' 192s ramachandran_plot = re.compile('Ramachandran\splot:\s*(\d+\.\d+)' + 192s /usr/lib/python3/dist-packages/csb/bio/io/procheck.py:34: SyntaxWarning: invalid escape sequence '\s' 192s '%\s*core\s*(\d+\.\d+)%\s*allow\s*(\d+\.\d+)' + 192s /usr/lib/python3/dist-packages/csb/bio/io/procheck.py:35: SyntaxWarning: invalid escape sequence '\s' 192s '%\s*gener\s*(\d+\.\d+)%\s*disall') 192s /usr/lib/python3/dist-packages/csb/bio/io/procheck.py:36: SyntaxWarning: invalid escape sequence '\s' 192s labelled_all = re.compile('Ramachandrans:\s*(\d+)\s*.*?out\sof\s*(\d+)') 192s /usr/lib/python3/dist-packages/csb/bio/io/procheck.py:37: SyntaxWarning: invalid escape sequence '\s' 192s labelled_chi = re.compile('Chi1-chi2\splots:\s*(\d+)\s*.*?out\sof\s*(\d+)') 192s /usr/lib/python3/dist-packages/csb/bio/io/procheck.py:38: SyntaxWarning: invalid escape sequence '\s' 192s bad_contacts = re.compile('Bad\scontacts:\s*(\d+)') 192s /usr/lib/python3/dist-packages/csb/bio/io/procheck.py:39: SyntaxWarning: invalid escape sequence '\s' 192s g_factors = re.compile('G-factors\s*Dihedrals:\s*([0-9-+.]+)' + 192s /usr/lib/python3/dist-packages/csb/bio/io/procheck.py:40: SyntaxWarning: invalid escape sequence '\s' 192s '\s*Covalent:\s*([0-9-+.]+)\s*Overall:\s*([0-9-+.]+)') 192s /usr/lib/python3/dist-packages/csb/bio/io/whatif.py:32: SyntaxWarning: invalid escape sequence '\s' 192s re_ramachandran = re.compile('Ramachandran\s*Z-score\s*:\s*([0-9.Ee-]+)') 192s /usr/lib/python3/dist-packages/csb/bio/io/whatif.py:33: SyntaxWarning: invalid escape sequence '\s' 192s re_1st = re.compile('1st\s*generation\s*packing\s*quality\s*:\s*([0-9.Ee-]+)') 192s /usr/lib/python3/dist-packages/csb/bio/io/whatif.py:34: SyntaxWarning: invalid escape sequence '\s' 192s re_2nd = re.compile('2nd\s*generation\s*packing\s*quality\s*:\s*([0-9.Ee-]+)') 192s /usr/lib/python3/dist-packages/csb/bio/io/whatif.py:35: SyntaxWarning: invalid escape sequence '\s' 192s re_backbone = re.compile('Backbone\s*conformation\s*Z-score\s*:\s*([0-9.Ee-]+)') 192s /usr/lib/python3/dist-packages/csb/bio/io/whatif.py:36: SyntaxWarning: invalid escape sequence '\S' 192s re_rotamer = re.compile('chi-1\S*chi-2\s*rotamer\s*normality\s*:\s*([0-9.Ee-]+)') 192s /usr/lib/python3/dist-packages/csb/bio/io/wwpdb.py:1222: SyntaxWarning: invalid escape sequence '\d' 192s res = re.search("(\d+(?:\.\d+)?)\s+ANGSTROM", line) 192s /usr/lib/python3/dist-packages/csb/bio/sequence/__init__.py:566: SyntaxWarning: invalid escape sequence '\w' 192s self._residues += re.sub('([^\w\-\.])+', '', string) 192s /usr/lib/python3/dist-packages/csb/bio/structure/__init__.py:2129: SyntaxWarning: invalid escape sequence '\s' 192s string = ''.join(re.split('\s+', string)) 192s /usr/lib/python3/dist-packages/csb/bio/structure/__init__.py:2131: SyntaxWarning: invalid escape sequence '\s' 192s conf_string = ''.join(re.split('\s+', conf_string)) 192s /usr/lib/python3/dist-packages/csb/statistics/__init__.py:341: SyntaxWarning: invalid escape sequence '\s' 192s """ 192s /usr/lib/python3/dist-packages/csb/test/cases/io/__init__.py:482: SyntaxWarning: invalid escape sequence '\w' 192s "([0-9a-zA-Z]([-.\w]*[0-9a-zA-Z])"] 192s /usr/lib/python3/dist-packages/csb/bio/io/hhpred.py:210: SyntaxWarning: invalid escape sequence '\d' 192s m = re.search('(\d+)\D+(\d+)', line).groups() 192s /usr/lib/python3/dist-packages/csb/bio/io/hhpred.py:260: SyntaxWarning: invalid escape sequence '\s' 192s seq = re.sub('\s+', '', ''.join(lines[1:])) 192s /usr/lib/python3/dist-packages/csb/bio/io/hhpred.py:307: SyntaxWarning: invalid escape sequence '\-' 192s pattern = re.compile('^[A-Z\-]\s[0-9]+\s+') 192s /usr/lib/python3/dist-packages/csb/bio/io/procheck.py:31: SyntaxWarning: invalid escape sequence '\s' 192s input_file_name = re.compile('>>>-----.*?\n.*?\n\s*\|\s*(\S+)\s+') 192s /usr/lib/python3/dist-packages/csb/bio/io/procheck.py:32: SyntaxWarning: invalid escape sequence '\d' 192s residues = re.compile('(\d+)\s*residues\s\|') 192s /usr/lib/python3/dist-packages/csb/bio/io/procheck.py:33: SyntaxWarning: invalid escape sequence '\s' 192s ramachandran_plot = re.compile('Ramachandran\splot:\s*(\d+\.\d+)' + 192s /usr/lib/python3/dist-packages/csb/bio/io/procheck.py:34: SyntaxWarning: invalid escape sequence '\s' 192s '%\s*core\s*(\d+\.\d+)%\s*allow\s*(\d+\.\d+)' + 192s /usr/lib/python3/dist-packages/csb/bio/io/procheck.py:35: SyntaxWarning: invalid escape sequence '\s' 192s '%\s*gener\s*(\d+\.\d+)%\s*disall') 192s /usr/lib/python3/dist-packages/csb/bio/io/procheck.py:36: SyntaxWarning: invalid escape sequence '\s' 192s labelled_all = re.compile('Ramachandrans:\s*(\d+)\s*.*?out\sof\s*(\d+)') 192s /usr/lib/python3/dist-packages/csb/bio/io/procheck.py:37: SyntaxWarning: invalid escape sequence '\s' 192s labelled_chi = re.compile('Chi1-chi2\splots:\s*(\d+)\s*.*?out\sof\s*(\d+)') 192s /usr/lib/python3/dist-packages/csb/bio/io/procheck.py:38: SyntaxWarning: invalid escape sequence '\s' 192s bad_contacts = re.compile('Bad\scontacts:\s*(\d+)') 192s /usr/lib/python3/dist-packages/csb/bio/io/procheck.py:39: SyntaxWarning: invalid escape sequence '\s' 192s g_factors = re.compile('G-factors\s*Dihedrals:\s*([0-9-+.]+)' + 192s /usr/lib/python3/dist-packages/csb/bio/io/procheck.py:40: SyntaxWarning: invalid escape sequence '\s' 192s '\s*Covalent:\s*([0-9-+.]+)\s*Overall:\s*([0-9-+.]+)') 192s /usr/lib/python3/dist-packages/csb/bio/io/whatif.py:32: SyntaxWarning: invalid escape sequence '\s' 192s re_ramachandran = re.compile('Ramachandran\s*Z-score\s*:\s*([0-9.Ee-]+)') 192s /usr/lib/python3/dist-packages/csb/bio/io/whatif.py:33: SyntaxWarning: invalid escape sequence '\s' 192s re_1st = re.compile('1st\s*generation\s*packing\s*quality\s*:\s*([0-9.Ee-]+)') 192s /usr/lib/python3/dist-packages/csb/bio/io/whatif.py:34: SyntaxWarning: invalid escape sequence '\s' 192s re_2nd = re.compile('2nd\s*generation\s*packing\s*quality\s*:\s*([0-9.Ee-]+)') 192s /usr/lib/python3/dist-packages/csb/bio/io/whatif.py:35: SyntaxWarning: invalid escape sequence '\s' 192s re_backbone = re.compile('Backbone\s*conformation\s*Z-score\s*:\s*([0-9.Ee-]+)') 192s /usr/lib/python3/dist-packages/csb/bio/io/whatif.py:36: SyntaxWarning: invalid escape sequence '\S' 192s re_rotamer = re.compile('chi-1\S*chi-2\s*rotamer\s*normality\s*:\s*([0-9.Ee-]+)') 192s /usr/lib/python3/dist-packages/csb/bio/io/wwpdb.py:1222: SyntaxWarning: invalid escape sequence '\d' 192s res = re.search("(\d+(?:\.\d+)?)\s+ANGSTROM", line) 192s /usr/lib/python3/dist-packages/csb/bio/sequence/__init__.py:566: SyntaxWarning: invalid escape sequence '\w' 192s self._residues += re.sub('([^\w\-\.])+', '', string) 192s /usr/lib/python3/dist-packages/csb/bio/structure/__init__.py:2129: SyntaxWarning: invalid escape sequence '\s' 192s string = ''.join(re.split('\s+', string)) 192s /usr/lib/python3/dist-packages/csb/bio/structure/__init__.py:2131: SyntaxWarning: invalid escape sequence '\s' 192s conf_string = ''.join(re.split('\s+', conf_string)) 192s /usr/lib/python3/dist-packages/csb/statistics/__init__.py:341: SyntaxWarning: invalid escape sequence '\s' 192s """ 192s /usr/lib/python3/dist-packages/csb/test/cases/io/__init__.py:482: SyntaxWarning: invalid escape sequence '\w' 192s "([0-9a-zA-Z]([-.\w]*[0-9a-zA-Z])"] 193s Setting up autopkgtest-satdep (0) ... 193s Processing triggers for libc-bin (2.40-1ubuntu3) ... 193s Processing triggers for systemd (256.5-2ubuntu4) ... 193s Processing triggers for man-db (2.12.1-3) ... 195s (Reading database ... 63440 files and directories currently installed.) 195s Removing autopkgtest-satdep (0) ... 196s autopkgtest [13:39:26]: test build: [----------------------- 196s Traceback (most recent call last): 196s File "/usr/lib/python3/dist-packages/csb/test/__init__.py", line 335, in ensureDataConsistency 196s self.getPickle('1nz9.model1.pickle') 196s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 196s File "/usr/lib/python3/dist-packages/csb/test/__init__.py", line 296, in getPickle 196s file = self.getTestFile(fileName, subDir) 196s File "/usr/lib/python3/dist-packages/csb/test/__init__.py", line 281, in getTestFile 196s raise IOError('Test file not found: {0}'.format(fileName)) 196s OSError: Test file not found: 1nz9.model1.pickle 196s 196s During handling of the above exception, another exception occurred: 196s 196s Traceback (most recent call last): 196s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 196s from . import multiarray 196s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 196s from . import overrides 196s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 196s from numpy.core._multiarray_umath import ( 196s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 196s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 196s 196s During handling of the above exception, another exception occurred: 196s 196s Traceback (most recent call last): 196s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 196s from numpy.__config__ import show as show_config 196s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 196s from numpy.core._multiarray_umath import ( 196s ...<3 lines>... 196s ) 196s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 196s raise ImportError(msg) 196s ImportError: 196s 196s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 196s 196s Importing the numpy C-extensions failed. This error can happen for 196s many reasons, often due to issues with your setup or how NumPy was 196s installed. 196s 196s We have compiled some common reasons and troubleshooting tips at: 196s 196s https://numpy.org/devdocs/user/troubleshooting-importerror.html 196s 196s Please note and check the following: 196s 196s * The Python version is: Python3.13 from "/usr/bin/python3.13" 196s * The NumPy version is: "1.26.4" 196s 196s and make sure that they are the versions you expect. 196s Please carefully study the documentation linked above for further help. 196s 196s Original error was: No module named 'numpy.core._multiarray_umath' 196s 196s 196s The above exception was the direct cause of the following exception: 196s 196s Traceback (most recent call last): 196s File "/tmp/autopkgtest.ZP1Moh/autopkgtest_tmp/test/app.py", line 13, in 196s main() 196s ~~~~^^ 196s File "/tmp/autopkgtest.ZP1Moh/autopkgtest_tmp/test/app.py", line 9, in main 196s return Console('csb.test.cases.*') 196s File "/usr/lib/python3/dist-packages/csb/test/__init__.py", line 806, in __init__ 196s self.run() 196s ~~~~~~~~^^ 196s File "/usr/lib/python3/dist-packages/csb/test/__init__.py", line 861, in run 196s Config().ensureDataConsistency() 196s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 196s File "/usr/lib/python3/dist-packages/csb/test/__init__.py", line 337, in ensureDataConsistency 196s self.updateDataFiles() 196s ~~~~~~~~~~~~~~~~~~~~^^ 196s File "/usr/lib/python3/dist-packages/csb/test/__init__.py", line 345, in updateDataFiles 196s from csb.bio.io.wwpdb import RegularStructureParser 196s File "/usr/lib/python3/dist-packages/csb/bio/io/__init__.py", line 5, in 196s from csb.bio.io.hhpred import HHOutputParser, HHProfileParser 196s File "/usr/lib/python3/dist-packages/csb/bio/io/hhpred.py", line 25, in 196s import csb.bio.structure as structure 196s File "/usr/lib/python3/dist-packages/csb/bio/structure/__init__.py", line 67, in 196s import numpy 196s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 196s raise ImportError(msg) from e 196s ImportError: Error importing numpy: you should not try to import numpy from 196s its source directory; please exit the numpy source tree, and relaunch 196s your python interpreter from there. 196s autopkgtest [13:39:26]: test build: -----------------------] 197s autopkgtest [13:39:27]: test build: - - - - - - - - - - results - - - - - - - - - - 197s build FAIL non-zero exit status 1 197s autopkgtest [13:39:27]: test autodep8-python3: preparing testbed 200s Reading package lists... 200s Building dependency tree... 200s Reading state information... 200s Starting pkgProblemResolver with broken count: 0 200s Starting 2 pkgProblemResolver with broken count: 0 200s Done 200s The following NEW packages will be installed: 200s autopkgtest-satdep 200s 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 200s Need to get 0 B/716 B of archives. 200s After this operation, 0 B of additional disk space will be used. 200s Get:1 /tmp/autopkgtest.ZP1Moh/2-autopkgtest-satdep.deb autopkgtest-satdep s390x 0 [716 B] 201s Selecting previously unselected package autopkgtest-satdep. 201s (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 ... 63440 files and directories currently installed.) 201s Preparing to unpack .../2-autopkgtest-satdep.deb ... 201s Unpacking autopkgtest-satdep (0) ... 201s Setting up autopkgtest-satdep (0) ... 202s (Reading database ... 63440 files and directories currently installed.) 202s Removing autopkgtest-satdep (0) ... 203s autopkgtest [13:39:33]: 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 [13:39:33]: test autodep8-python3: [----------------------- 203s Testing with python3.13: 203s 203s Testing with python3.12: 203s 203s autopkgtest [13:39:33]: test autodep8-python3: -----------------------] 204s autopkgtest [13:39:34]: test autodep8-python3: - - - - - - - - - - results - - - - - - - - - - 204s autodep8-python3 PASS (superficial) 204s autopkgtest [13:39:34]: @@@@@@@@@@@@@@@@@@@@ summary 204s build FAIL non-zero exit status 1 204s autodep8-python3 PASS (superficial) 218s nova [W] Using flock in prodstack6-s390x 218s Creating nova instance adt-plucky-s390x-python-csb-20241113-133610-juju-7f2275-prod-proposed-migration-environment-20-8035e2bc-04dc-4042-b3cb-c8c035bba264 from image adt/ubuntu-plucky-s390x-server-20241113.img (UUID e740277e-1f72-40ae-bfbe-46030537c71c)...