0s autopkgtest [11:18:35]: starting date and time: 2024-11-13 11:18:35+0000 1s autopkgtest [11:18:36]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 1s autopkgtest [11:18:36]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.c0on6ie4/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@lcy02-14.secgroup --name adt-plucky-amd64-python-csb-20241113-111834-juju-7f2275-prod-proposed-migration-environment-20-c993f37d-7713-43dd-9b89-e5837bf25e28 --image adt/ubuntu-plucky-amd64-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/ 83s autopkgtest [11:19:58]: testbed dpkg architecture: amd64 83s autopkgtest [11:19:58]: testbed apt version: 2.9.8 83s autopkgtest [11:19:58]: @@@@@@@@@@@@@@@@@@@@ test bed setup 84s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 84s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 84s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [849 kB] 84s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [76.4 kB] 84s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.3 kB] 84s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [111 kB] 84s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [65.2 kB] 84s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [32.6 kB] 84s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [255 kB] 84s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [639 kB] 84s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [13.0 kB] 84s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [37.7 kB] 84s Fetched 2175 kB in 0s (6962 kB/s) 84s Reading package lists... 85s Reading package lists... 86s Building dependency tree... 86s Reading state information... 86s Calculating upgrade... 87s The following NEW packages will be installed: 87s python3.13-gdbm 87s The following packages will be upgraded: 87s libgpgme11t64 libpython3-stdlib python3 python3-gdbm python3-minimal 87s 5 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 87s Need to get 253 kB of archives. 87s After this operation, 147 kB of additional disk space will be used. 87s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-minimal amd64 3.12.7-1 [27.4 kB] 87s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3 amd64 3.12.7-1 [24.0 kB] 87s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libpython3-stdlib amd64 3.12.7-1 [10.0 kB] 87s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-gdbm amd64 3.13.0-2 [31.3 kB] 87s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-gdbm amd64 3.12.7-1 [8642 B] 87s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 libgpgme11t64 amd64 1.23.2-5ubuntu4 [152 kB] 87s Fetched 253 kB in 0s (6741 kB/s) 87s (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 ... 75541 files and directories currently installed.) 87s Preparing to unpack .../python3-minimal_3.12.7-1_amd64.deb ... 87s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ... 87s Setting up python3-minimal (3.12.7-1) ... 87s (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 ... 75541 files and directories currently installed.) 87s Preparing to unpack .../python3_3.12.7-1_amd64.deb ... 87s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ... 88s Preparing to unpack .../libpython3-stdlib_3.12.7-1_amd64.deb ... 88s Unpacking libpython3-stdlib:amd64 (3.12.7-1) over (3.12.6-0ubuntu1) ... 88s Selecting previously unselected package python3.13-gdbm. 88s Preparing to unpack .../python3.13-gdbm_3.13.0-2_amd64.deb ... 88s Unpacking python3.13-gdbm (3.13.0-2) ... 88s Preparing to unpack .../python3-gdbm_3.12.7-1_amd64.deb ... 88s Unpacking python3-gdbm:amd64 (3.12.7-1) over (3.12.6-1ubuntu1) ... 88s Preparing to unpack .../libgpgme11t64_1.23.2-5ubuntu4_amd64.deb ... 88s Unpacking libgpgme11t64:amd64 (1.23.2-5ubuntu4) over (1.18.0-4.1ubuntu4) ... 88s Setting up libgpgme11t64:amd64 (1.23.2-5ubuntu4) ... 88s Setting up python3.13-gdbm (3.13.0-2) ... 88s Setting up libpython3-stdlib:amd64 (3.12.7-1) ... 88s Setting up python3 (3.12.7-1) ... 88s Setting up python3-gdbm:amd64 (3.12.7-1) ... 88s Processing triggers for man-db (2.12.1-3) ... 88s Processing triggers for libc-bin (2.40-1ubuntu3) ... 89s Reading package lists... 89s Building dependency tree... 89s Reading state information... 90s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 90s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 90s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 90s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 90s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 91s Reading package lists... 91s Reading package lists... 91s Building dependency tree... 91s Reading state information... 92s 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. 93s autopkgtest [11:20:08]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 13:41:20 UTC 2024 93s autopkgtest [11:20:08]: @@@@@@@@@@@@@@@@@@@@ apt-source python-csb 94s Get:1 http://ftpmaster.internal/ubuntu plucky/universe python-csb 1.2.5+dfsg-10 (dsc) [1627 B] 94s Get:2 http://ftpmaster.internal/ubuntu plucky/universe python-csb 1.2.5+dfsg-10 (tar) [3000 kB] 94s Get:3 http://ftpmaster.internal/ubuntu plucky/universe python-csb 1.2.5+dfsg-10 (diff) [11.5 kB] 94s gpgv: Signature made Sat Dec 9 16:03:46 2023 UTC 94s gpgv: using EDDSA key A095B66EE09024BEE6A2F0722A27904BD7243EDA 94s gpgv: Can't check signature: No public key 94s dpkg-source: warning: cannot verify inline signature for ./python-csb_1.2.5+dfsg-10.dsc: no acceptable signature found 95s autopkgtest [11:20:10]: testing package python-csb version 1.2.5+dfsg-10 95s autopkgtest [11:20:10]: build not needed 95s autopkgtest [11:20:10]: test build: preparing testbed 96s Reading package lists... 96s Building dependency tree... 96s Reading state information... 96s Starting pkgProblemResolver with broken count: 0 96s Starting 2 pkgProblemResolver with broken count: 0 96s Done 97s The following additional packages will be installed: 97s blt fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-lyx libblas3 97s libdeflate0 libfontconfig1 libgfortran5 libgomp1 libgraphite2-3 97s libharfbuzz0b libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 libjs-jquery 97s libjs-jquery-ui liblapack3 liblbfgsb0 liblcms2-2 liblerc4 libopenjp2-7 97s libpython3.13-minimal libpython3.13-stdlib libqhull-r8.0 libraqm0 97s libsharpyuv0 libtcl8.6 libtiff6 libtk8.6 libwebp7 libwebpdemux2 libwebpmux3 97s libxft2 libxrender1 libxslt1.1 libxss1 python-matplotlib-data python3-all 97s python3-appdirs python3-brotli python3-contourpy python3-csb python3-cycler 97s python3-dateutil python3-decorator python3-fonttools python3-fs 97s python3-kiwisolver python3-lxml python3-lz4 python3-matplotlib 97s python3-mpmath python3-numpy python3-packaging python3-pil 97s python3-pil.imagetk python3-scipy python3-six python3-sympy python3-tk 97s python3-tz python3-ufolib2 python3-unicodedata2 python3.12-tk python3.13 97s python3.13-minimal python3.13-tk tk8.6-blt2.5 unicode-data x11-common 97s Suggested packages: 97s blt-demo libjs-jquery-ui-docs liblcms2-utils tcl8.6 tk8.6 python-cycler-doc 97s python-lxml-doc cm-super-minimal dvipng ffmpeg fonts-staypuft ghostscript 97s gir1.2-gtk-3.0 inkscape ipython3 librsvg2-common python-matplotlib-doc 97s python3-cairocffi python3-gi-cairo python3-gobject python3-pyqt5 python3-sip 97s python3-tornado texlive-extra-utils texlive-latex-extra python-mpmath-doc 97s python3-gmpy2 gcc gfortran python-numpy-doc python3-dev python3-pytest 97s python-pil-doc python-scipy-doc texlive-fonts-extra python-sympy-doc tix 97s python3-tk-dbg python3.13-venv python3.13-doc binfmt-support 97s Recommended packages: 97s javascript-common python3-bs4 python3-cssselect python3-html5lib 97s python3-olefile g++ | c++-compiler isympy-common 97s The following NEW packages will be installed: 97s autopkgtest-satdep blt fontconfig-config fonts-dejavu-core fonts-dejavu-mono 97s fonts-lyx libblas3 libdeflate0 libfontconfig1 libgfortran5 libgomp1 97s libgraphite2-3 libharfbuzz0b libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 97s libjs-jquery libjs-jquery-ui liblapack3 liblbfgsb0 liblcms2-2 liblerc4 97s libopenjp2-7 libpython3.13-minimal libpython3.13-stdlib libqhull-r8.0 97s libraqm0 libsharpyuv0 libtcl8.6 libtiff6 libtk8.6 libwebp7 libwebpdemux2 97s libwebpmux3 libxft2 libxrender1 libxslt1.1 libxss1 python-matplotlib-data 97s python3-all python3-appdirs python3-brotli python3-contourpy python3-csb 97s python3-cycler python3-dateutil python3-decorator python3-fonttools 97s python3-fs python3-kiwisolver python3-lxml python3-lz4 python3-matplotlib 97s python3-mpmath python3-numpy python3-packaging python3-pil 97s python3-pil.imagetk python3-scipy python3-six python3-sympy python3-tk 97s python3-tz python3-ufolib2 python3-unicodedata2 python3.12-tk python3.13 97s python3.13-minimal python3.13-tk tk8.6-blt2.5 unicode-data x11-common 97s 0 upgraded, 73 newly installed, 0 to remove and 0 not upgraded. 97s Need to get 68.0 MB/68.0 MB of archives. 97s After this operation, 280 MB of additional disk space will be used. 97s Get:1 /tmp/autopkgtest.dFvL7d/1-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [712 B] 97s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-minimal amd64 3.13.0-2 [879 kB] 97s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-minimal amd64 3.13.0-2 [2188 kB] 97s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 libtcl8.6 amd64 8.6.15+dfsg-2 [1085 kB] 97s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB] 97s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-core all 2.37-8 [835 kB] 97s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig-config amd64 2.15.0-1.1ubuntu2 [37.3 kB] 97s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontconfig1 amd64 2.15.0-1.1ubuntu2 [139 kB] 97s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 libxrender1 amd64 1:0.9.10-1.1build1 [19.0 kB] 97s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 libxft2 amd64 2.3.6-1build1 [45.3 kB] 97s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 97s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 libxss1 amd64 1:1.2.3-1build3 [7204 B] 97s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 libtk8.6 amd64 8.6.15-1 [862 kB] 97s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-7build1 [630 kB] 97s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 blt amd64 2.5.3+dfsg-7build1 [4840 B] 97s Get:16 http://ftpmaster.internal/ubuntu plucky/universe amd64 fonts-lyx all 2.4.2.1-1 [171 kB] 97s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.0-3build2 [247 kB] 97s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate0 amd64 1.22-1 [64.5 kB] 97s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 14.2.0-8ubuntu1 [909 kB] 97s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 libgomp1 amd64 14.2.0-8ubuntu1 [148 kB] 97s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB] 97s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 libharfbuzz0b amd64 10.0.1-1 [540 kB] 97s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 libimagequant0 amd64 2.18.0-1build1 [36.3 kB] 97s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg-turbo8 amd64 2.1.5-2ubuntu2 [150 kB] 97s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 97s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 97s Get:27 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 97s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.0-3build2 [2668 kB] 97s Get:29 http://ftpmaster.internal/ubuntu plucky/universe amd64 liblbfgsb0 amd64 3.0+dfsg.4-1build1 [29.9 kB] 97s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 liblcms2-2 amd64 2.16-2 [212 kB] 97s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 liblerc4 amd64 4.0.0+ds-4ubuntu2 [179 kB] 97s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-stdlib amd64 3.13.0-2 [2107 kB] 97s Get:33 http://ftpmaster.internal/ubuntu plucky/universe amd64 libqhull-r8.0 amd64 2020.2-6build1 [193 kB] 97s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 libraqm0 amd64 0.10.1-1build1 [15.0 kB] 97s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 libsharpyuv0 amd64 1.4.0-0.1 [17.5 kB] 97s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB] 97s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebp7 amd64 1.4.0-0.1 [231 kB] 97s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 libtiff6 amd64 4.5.1+git230720-4ubuntu4 [200 kB] 97s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpdemux2 amd64 1.4.0-0.1 [12.4 kB] 97s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpmux3 amd64 1.4.0-0.1 [25.8 kB] 97s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 libxslt1.1 amd64 1.1.39-0exp1ubuntu1 [169 kB] 97s Get:42 http://ftpmaster.internal/ubuntu plucky/universe amd64 python-matplotlib-data all 3.8.3-3 [2928 kB] 97s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13 amd64 3.13.0-2 [719 kB] 97s Get:44 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-all amd64 3.12.7-1 [890 B] 97s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-appdirs all 1.4.4-4 [10.9 kB] 97s Get:46 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-brotli amd64 1.1.0-2build2 [332 kB] 97s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-numpy amd64 1:1.26.4+ds-11build1 [4479 kB] 97s Get:48 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-contourpy amd64 1.3.0-2 [217 kB] 97s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-six all 1.16.0-7 [13.1 kB] 97s Get:50 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-dateutil all 2.9.0-2 [80.3 kB] 97s Get:51 http://ftpmaster.internal/ubuntu plucky/main amd64 libopenjp2-7 amd64 2.5.0-2ubuntu1 [184 kB] 97s Get:52 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-pil amd64 10.4.0-1ubuntu1 [463 kB] 97s Get:53 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.12-tk amd64 3.12.7-3 [116 kB] 97s Get:54 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-tk amd64 3.13.0-2 [106 kB] 97s Get:55 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-tk amd64 3.12.7-1 [9752 B] 97s Get:56 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pil.imagetk amd64 10.4.0-1ubuntu1 [9394 B] 97s Get:57 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-cycler all 0.12.1-1 [9716 B] 97s Get:58 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-decorator all 5.1.1-5 [10.1 kB] 97s Get:59 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-scipy amd64 1.13.1-5 [18.2 MB] 98s Get:60 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-ufolib2 all 0.16.1+dfsg1-1 [33.4 kB] 98s Get:61 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-mpmath all 1.3.0-1 [425 kB] 98s Get:62 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-sympy all 1.13.3-1 [4228 kB] 98s Get:63 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-tz all 2024.1-2 [31.4 kB] 98s Get:64 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-fs all 2.4.16-4 [91.3 kB] 98s Get:65 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-lxml amd64 5.3.0-1 [1282 kB] 98s Get:66 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-lz4 amd64 4.0.2+dfsg-1build4 [26.2 kB] 98s Get:67 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-unicodedata2 amd64 15.1.0+ds-1build1 [362 kB] 98s Get:68 http://ftpmaster.internal/ubuntu plucky/universe amd64 unicode-data all 15.1.0-1 [8878 kB] 98s Get:69 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-fonttools amd64 4.46.0-1build2 [1436 kB] 98s Get:70 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-kiwisolver amd64 1.4.7-2 [55.1 kB] 98s Get:71 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-packaging all 24.1-1 [41.4 kB] 98s Get:72 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-matplotlib amd64 3.8.3-3 [4545 kB] 98s Get:73 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-csb all 1.2.5+dfsg-10 [2392 kB] 98s Fetched 68.0 MB in 1s (90.5 MB/s) 98s Selecting previously unselected package libpython3.13-minimal:amd64. 98s (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 ... 75548 files and directories currently installed.) 98s Preparing to unpack .../00-libpython3.13-minimal_3.13.0-2_amd64.deb ... 98s Unpacking libpython3.13-minimal:amd64 (3.13.0-2) ... 98s Selecting previously unselected package python3.13-minimal. 98s Preparing to unpack .../01-python3.13-minimal_3.13.0-2_amd64.deb ... 98s Unpacking python3.13-minimal (3.13.0-2) ... 98s Selecting previously unselected package libtcl8.6:amd64. 98s Preparing to unpack .../02-libtcl8.6_8.6.15+dfsg-2_amd64.deb ... 98s Unpacking libtcl8.6:amd64 (8.6.15+dfsg-2) ... 98s Selecting previously unselected package fonts-dejavu-mono. 98s Preparing to unpack .../03-fonts-dejavu-mono_2.37-8_all.deb ... 98s Unpacking fonts-dejavu-mono (2.37-8) ... 99s Selecting previously unselected package fonts-dejavu-core. 99s Preparing to unpack .../04-fonts-dejavu-core_2.37-8_all.deb ... 99s Unpacking fonts-dejavu-core (2.37-8) ... 99s Selecting previously unselected package fontconfig-config. 99s Preparing to unpack .../05-fontconfig-config_2.15.0-1.1ubuntu2_amd64.deb ... 99s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ... 99s Selecting previously unselected package libfontconfig1:amd64. 99s Preparing to unpack .../06-libfontconfig1_2.15.0-1.1ubuntu2_amd64.deb ... 99s Unpacking libfontconfig1:amd64 (2.15.0-1.1ubuntu2) ... 99s Selecting previously unselected package libxrender1:amd64. 99s Preparing to unpack .../07-libxrender1_1%3a0.9.10-1.1build1_amd64.deb ... 99s 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to unpack .../13-blt_2.5.3+dfsg-7build1_amd64.deb ... 99s Unpacking blt (2.5.3+dfsg-7build1) ... 99s Selecting previously unselected package fonts-lyx. 99s Preparing to unpack .../14-fonts-lyx_2.4.2.1-1_all.deb ... 99s Unpacking fonts-lyx (2.4.2.1-1) ... 99s Selecting previously unselected package libblas3:amd64. 99s Preparing to unpack .../15-libblas3_3.12.0-3build2_amd64.deb ... 99s Unpacking libblas3:amd64 (3.12.0-3build2) ... 99s Selecting previously unselected package libdeflate0:amd64. 99s Preparing to unpack .../16-libdeflate0_1.22-1_amd64.deb ... 99s Unpacking libdeflate0:amd64 (1.22-1) ... 99s Selecting previously unselected package libgfortran5:amd64. 99s Preparing to unpack .../17-libgfortran5_14.2.0-8ubuntu1_amd64.deb ... 99s Unpacking libgfortran5:amd64 (14.2.0-8ubuntu1) ... 99s Selecting previously unselected package libgomp1:amd64. 99s Preparing to unpack .../18-libgomp1_14.2.0-8ubuntu1_amd64.deb ... 99s Unpacking libgomp1:amd64 (14.2.0-8ubuntu1) ... 99s Selecting previously unselected package libgraphite2-3:amd64. 99s Preparing to unpack .../19-libgraphite2-3_1.3.14-2ubuntu1_amd64.deb ... 99s Unpacking libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 99s Selecting previously unselected package libharfbuzz0b:amd64. 99s Preparing to unpack .../20-libharfbuzz0b_10.0.1-1_amd64.deb ... 99s Unpacking libharfbuzz0b:amd64 (10.0.1-1) ... 99s Selecting previously unselected package libimagequant0:amd64. 99s Preparing to unpack .../21-libimagequant0_2.18.0-1build1_amd64.deb ... 99s Unpacking libimagequant0:amd64 (2.18.0-1build1) ... 99s Selecting previously unselected package libjpeg-turbo8:amd64. 99s Preparing to unpack .../22-libjpeg-turbo8_2.1.5-2ubuntu2_amd64.deb ... 99s Unpacking libjpeg-turbo8:amd64 (2.1.5-2ubuntu2) ... 99s Selecting previously unselected package libjpeg8:amd64. 99s Preparing to unpack .../23-libjpeg8_8c-2ubuntu11_amd64.deb ... 99s Unpacking libjpeg8:amd64 (8c-2ubuntu11) ... 99s Selecting previously unselected package libjs-jquery. 99s 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... 100s Selecting previously unselected package libwebp7:amd64. 100s Preparing to unpack .../35-libwebp7_1.4.0-0.1_amd64.deb ... 100s Unpacking libwebp7:amd64 (1.4.0-0.1) ... 100s Selecting previously unselected package libtiff6:amd64. 100s Preparing to unpack .../36-libtiff6_4.5.1+git230720-4ubuntu4_amd64.deb ... 100s Unpacking libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ... 100s Selecting previously unselected package libwebpdemux2:amd64. 100s Preparing to unpack .../37-libwebpdemux2_1.4.0-0.1_amd64.deb ... 100s Unpacking libwebpdemux2:amd64 (1.4.0-0.1) ... 100s Selecting previously unselected package libwebpmux3:amd64. 100s Preparing to unpack .../38-libwebpmux3_1.4.0-0.1_amd64.deb ... 100s Unpacking libwebpmux3:amd64 (1.4.0-0.1) ... 100s Selecting previously unselected package libxslt1.1:amd64. 100s Preparing to unpack .../39-libxslt1.1_1.1.39-0exp1ubuntu1_amd64.deb ... 100s Unpacking libxslt1.1:amd64 (1.1.39-0exp1ubuntu1) ... 100s Selecting previously unselected package python-matplotlib-data. 100s Preparing to unpack .../40-python-matplotlib-data_3.8.3-3_all.deb ... 100s Unpacking python-matplotlib-data (3.8.3-3) ... 100s Selecting previously unselected package python3.13. 100s Preparing to unpack .../41-python3.13_3.13.0-2_amd64.deb ... 100s Unpacking python3.13 (3.13.0-2) ... 100s Selecting previously unselected package python3-all. 100s Preparing to unpack .../42-python3-all_3.12.7-1_amd64.deb ... 100s Unpacking python3-all (3.12.7-1) ... 100s Selecting previously unselected package python3-appdirs. 100s Preparing to unpack .../43-python3-appdirs_1.4.4-4_all.deb ... 100s Unpacking python3-appdirs (1.4.4-4) ... 100s Selecting previously unselected package python3-brotli. 100s Preparing to unpack .../44-python3-brotli_1.1.0-2build2_amd64.deb ... 100s Unpacking python3-brotli (1.1.0-2build2) ... 100s Selecting previously unselected package python3-numpy. 100s Preparing to unpack .../45-python3-numpy_1%3a1.26.4+ds-11build1_amd64.deb ... 100s Unpacking python3-numpy (1:1.26.4+ds-11build1) ... 100s Selecting previously unselected package python3-contourpy. 100s Preparing to unpack .../46-python3-contourpy_1.3.0-2_amd64.deb ... 100s Unpacking python3-contourpy (1.3.0-2) ... 100s Selecting previously unselected package python3-six. 100s Preparing to unpack .../47-python3-six_1.16.0-7_all.deb ... 100s Unpacking python3-six (1.16.0-7) ... 100s Selecting previously unselected package python3-dateutil. 100s Preparing to unpack .../48-python3-dateutil_2.9.0-2_all.deb ... 100s Unpacking python3-dateutil (2.9.0-2) ... 100s Selecting previously unselected package libopenjp2-7:amd64. 100s Preparing to unpack .../49-libopenjp2-7_2.5.0-2ubuntu1_amd64.deb ... 100s Unpacking libopenjp2-7:amd64 (2.5.0-2ubuntu1) ... 101s Selecting previously unselected package python3-pil:amd64. 101s Preparing to unpack .../50-python3-pil_10.4.0-1ubuntu1_amd64.deb ... 101s Unpacking python3-pil:amd64 (10.4.0-1ubuntu1) ... 101s Selecting previously unselected package python3.12-tk. 101s Preparing to unpack .../51-python3.12-tk_3.12.7-3_amd64.deb ... 101s Unpacking python3.12-tk (3.12.7-3) ... 101s Selecting previously unselected package python3.13-tk. 101s Preparing to unpack .../52-python3.13-tk_3.13.0-2_amd64.deb ... 101s Unpacking python3.13-tk (3.13.0-2) ... 101s Selecting previously unselected package python3-tk:amd64. 101s Preparing to unpack .../53-python3-tk_3.12.7-1_amd64.deb ... 101s Unpacking python3-tk:amd64 (3.12.7-1) ... 101s Selecting previously unselected package python3-pil.imagetk:amd64. 101s Preparing to unpack .../54-python3-pil.imagetk_10.4.0-1ubuntu1_amd64.deb ... 101s Unpacking python3-pil.imagetk:amd64 (10.4.0-1ubuntu1) ... 101s Selecting previously unselected package python3-cycler. 101s Preparing to unpack .../55-python3-cycler_0.12.1-1_all.deb ... 101s Unpacking python3-cycler (0.12.1-1) ... 101s Selecting previously unselected package python3-decorator. 101s Preparing to unpack .../56-python3-decorator_5.1.1-5_all.deb 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.../62-python3-fs_2.4.16-4_all.deb ... 102s Unpacking python3-fs (2.4.16-4) ... 102s Selecting previously unselected package python3-lxml:amd64. 102s Preparing to unpack .../63-python3-lxml_5.3.0-1_amd64.deb ... 102s Unpacking python3-lxml:amd64 (5.3.0-1) ... 102s Selecting previously unselected package python3-lz4. 102s Preparing to unpack .../64-python3-lz4_4.0.2+dfsg-1build4_amd64.deb ... 102s Unpacking python3-lz4 (4.0.2+dfsg-1build4) ... 102s Selecting previously unselected package python3-unicodedata2. 102s Preparing to unpack .../65-python3-unicodedata2_15.1.0+ds-1build1_amd64.deb ... 102s Unpacking python3-unicodedata2 (15.1.0+ds-1build1) ... 102s Selecting previously unselected package unicode-data. 102s Preparing to unpack .../66-unicode-data_15.1.0-1_all.deb ... 102s Unpacking unicode-data (15.1.0-1) ... 102s Selecting previously unselected package python3-fonttools. 102s Preparing to unpack .../67-python3-fonttools_4.46.0-1build2_amd64.deb ... 102s Unpacking python3-fonttools (4.46.0-1build2) ... 102s Selecting previously unselected package python3-kiwisolver. 102s Preparing to unpack .../68-python3-kiwisolver_1.4.7-2_amd64.deb ... 102s Unpacking python3-kiwisolver (1.4.7-2) ... 102s Selecting previously unselected package python3-packaging. 102s Preparing to unpack .../69-python3-packaging_24.1-1_all.deb ... 102s Unpacking python3-packaging (24.1-1) ... 102s Selecting previously unselected package python3-matplotlib. 102s Preparing to unpack .../70-python3-matplotlib_3.8.3-3_amd64.deb ... 102s Unpacking python3-matplotlib (3.8.3-3) ... 102s Selecting previously unselected package python3-csb. 102s Preparing to unpack .../71-python3-csb_1.2.5+dfsg-10_all.deb ... 102s Unpacking python3-csb (1.2.5+dfsg-10) ... 102s Selecting previously unselected package autopkgtest-satdep. 102s Preparing to unpack .../72-1-autopkgtest-satdep.deb ... 102s Unpacking autopkgtest-satdep (0) ... 102s Setting up libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 102s Setting up liblcms2-2:amd64 (2.16-2) ... 102s Setting up libsharpyuv0:amd64 (1.4.0-0.1) ... 102s Setting up liblerc4:amd64 (4.0.0+ds-4ubuntu2) ... 102s Setting up libxrender1:amd64 (1:0.9.10-1.1build1) ... 102s Setting up python3-lz4 (4.0.2+dfsg-1build4) ... 103s Setting up python3-unicodedata2 (15.1.0+ds-1build1) ... 103s Setting up fonts-lyx (2.4.2.1-1) ... 103s Setting up x11-common (1:7.7+23ubuntu3) ... 103s Setting up libdeflate0:amd64 (1.22-1) ... 103s Setting up libqhull-r8.0:amd64 (2020.2-6build1) ... 103s Setting up libgomp1:amd64 (14.2.0-8ubuntu1) ... 103s Setting up libjbig0:amd64 (2.1-6.1ubuntu2) ... 103s Setting up python3-tz (2024.1-2) ... 103s Setting up unicode-data (15.1.0-1) ... 103s Setting up python3-six (1.16.0-7) ... 103s Setting up libpython3.13-minimal:amd64 (3.13.0-2) ... 103s Setting up python3-decorator (5.1.1-5) ... 103s Setting up libblas3:amd64 (3.12.0-3build2) ... 103s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode 103s Setting up python3-packaging (24.1-1) ... 104s Setting up python3-brotli (1.1.0-2build2) ... 104s Setting up python3-cycler (0.12.1-1) ... 104s Setting up libimagequant0:amd64 (2.18.0-1build1) ... 104s Setting up fonts-dejavu-mono (2.37-8) ... 104s Setting up python3-kiwisolver (1.4.7-2) ... 104s Setting up libtcl8.6:amd64 (8.6.15+dfsg-2) ... 104s Setting up fonts-dejavu-core (2.37-8) ... 104s Setting up libjpeg-turbo8:amd64 (2.1.5-2ubuntu2) ... 104s Setting up libgfortran5:amd64 (14.2.0-8ubuntu1) ... 104s Setting up libwebp7:amd64 (1.4.0-0.1) ... 104s Setting up libxslt1.1:amd64 (1.1.39-0exp1ubuntu1) ... 104s Setting up libopenjp2-7:amd64 (2.5.0-2ubuntu1) ... 104s Setting up python3.13-minimal (3.13.0-2) ... 105s Setting up libharfbuzz0b:amd64 (10.0.1-1) ... 105s Setting up python3-dateutil (2.9.0-2) ... 105s Setting up libxss1:amd64 (1:1.2.3-1build3) ... 105s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 105s Setting up python3-mpmath (1.3.0-1) ... 106s Setting up python-matplotlib-data (3.8.3-3) ... 106s Setting up libwebpmux3:amd64 (1.4.0-0.1) ... 106s Setting up python3-appdirs (1.4.4-4) ... 106s Setting up libpython3.13-stdlib:amd64 (3.13.0-2) ... 106s Setting up libjpeg8:amd64 (8c-2ubuntu11) ... 106s Setting up python3-sympy (1.13.3-1) ... 118s Setting up liblapack3:amd64 (3.12.0-3build2) ... 118s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode 118s Setting up python3.13 (3.13.0-2) ... 119s Setting up fontconfig-config (2.15.0-1.1ubuntu2) ... 119s Setting up libwebpdemux2:amd64 (1.4.0-0.1) ... 119s Setting up python3-all (3.12.7-1) ... 119s Setting up python3-fs (2.4.16-4) ... 120s Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... 120s Setting up libraqm0:amd64 (0.10.1-1build1) ... 120s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 123s Setting up python3-lxml:amd64 (5.3.0-1) ... 124s Setting up libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ... 124s Setting up python3-contourpy (1.3.0-2) ... 124s Setting up libfontconfig1:amd64 (2.15.0-1.1ubuntu2) ... 124s Setting up liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ... 124s Setting up libxft2:amd64 (2.3.6-1build1) ... 124s Setting up python3-scipy (1.13.1-5) ... 130s Setting up libtk8.6:amd64 (8.6.15-1) ... 130s Setting up python3.12-tk (3.12.7-3) ... 130s Setting up python3.13-tk (3.13.0-2) ... 130s Setting up python3-pil:amd64 (10.4.0-1ubuntu1) ... 130s Setting up tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 130s Setting up blt (2.5.3+dfsg-7build1) ... 130s Setting up python3-tk:amd64 (3.12.7-1) ... 131s Setting up python3-pil.imagetk:amd64 (10.4.0-1ubuntu1) ... 131s Setting up python3-fonttools (4.46.0-1build2) ... 132s Setting up python3-ufolib2 (0.16.1+dfsg1-1) ... 132s Setting up python3-matplotlib (3.8.3-3) ... 135s Setting up python3-csb (1.2.5+dfsg-10) ... 136s /usr/lib/python3/dist-packages/csb/bio/io/hhpred.py:210: SyntaxWarning: invalid escape sequence '\d' 136s m = re.search('(\d+)\D+(\d+)', line).groups() 136s /usr/lib/python3/dist-packages/csb/bio/io/hhpred.py:260: SyntaxWarning: invalid escape sequence '\s' 136s seq = re.sub('\s+', '', ''.join(lines[1:])) 136s /usr/lib/python3/dist-packages/csb/bio/io/hhpred.py:307: SyntaxWarning: invalid escape sequence '\-' 136s pattern = re.compile('^[A-Z\-]\s[0-9]+\s+') 136s /usr/lib/python3/dist-packages/csb/bio/io/procheck.py:31: SyntaxWarning: invalid escape sequence '\s' 136s input_file_name = re.compile('>>>-----.*?\n.*?\n\s*\|\s*(\S+)\s+') 136s /usr/lib/python3/dist-packages/csb/bio/io/procheck.py:32: SyntaxWarning: invalid escape sequence '\d' 136s residues = re.compile('(\d+)\s*residues\s\|') 136s /usr/lib/python3/dist-packages/csb/bio/io/procheck.py:33: SyntaxWarning: invalid escape sequence '\s' 136s ramachandran_plot = re.compile('Ramachandran\splot:\s*(\d+\.\d+)' + 136s /usr/lib/python3/dist-packages/csb/bio/io/procheck.py:34: SyntaxWarning: invalid escape sequence '\s' 136s '%\s*core\s*(\d+\.\d+)%\s*allow\s*(\d+\.\d+)' + 136s /usr/lib/python3/dist-packages/csb/bio/io/procheck.py:35: SyntaxWarning: invalid escape sequence '\s' 136s '%\s*gener\s*(\d+\.\d+)%\s*disall') 136s /usr/lib/python3/dist-packages/csb/bio/io/procheck.py:36: SyntaxWarning: invalid escape sequence '\s' 136s labelled_all = re.compile('Ramachandrans:\s*(\d+)\s*.*?out\sof\s*(\d+)') 136s /usr/lib/python3/dist-packages/csb/bio/io/procheck.py:37: SyntaxWarning: invalid escape sequence '\s' 136s labelled_chi = re.compile('Chi1-chi2\splots:\s*(\d+)\s*.*?out\sof\s*(\d+)') 136s /usr/lib/python3/dist-packages/csb/bio/io/procheck.py:38: SyntaxWarning: invalid escape sequence '\s' 136s bad_contacts = re.compile('Bad\scontacts:\s*(\d+)') 136s /usr/lib/python3/dist-packages/csb/bio/io/procheck.py:39: SyntaxWarning: invalid escape sequence '\s' 136s g_factors = re.compile('G-factors\s*Dihedrals:\s*([0-9-+.]+)' + 136s /usr/lib/python3/dist-packages/csb/bio/io/procheck.py:40: SyntaxWarning: invalid escape sequence '\s' 136s '\s*Covalent:\s*([0-9-+.]+)\s*Overall:\s*([0-9-+.]+)') 136s /usr/lib/python3/dist-packages/csb/bio/io/whatif.py:32: SyntaxWarning: invalid escape sequence '\s' 136s re_ramachandran = re.compile('Ramachandran\s*Z-score\s*:\s*([0-9.Ee-]+)') 136s /usr/lib/python3/dist-packages/csb/bio/io/whatif.py:33: SyntaxWarning: invalid escape sequence '\s' 136s re_1st = re.compile('1st\s*generation\s*packing\s*quality\s*:\s*([0-9.Ee-]+)') 136s /usr/lib/python3/dist-packages/csb/bio/io/whatif.py:34: SyntaxWarning: invalid escape sequence '\s' 136s re_2nd = re.compile('2nd\s*generation\s*packing\s*quality\s*:\s*([0-9.Ee-]+)') 136s /usr/lib/python3/dist-packages/csb/bio/io/whatif.py:35: SyntaxWarning: invalid escape sequence '\s' 136s re_backbone = re.compile('Backbone\s*conformation\s*Z-score\s*:\s*([0-9.Ee-]+)') 136s /usr/lib/python3/dist-packages/csb/bio/io/whatif.py:36: SyntaxWarning: invalid escape sequence '\S' 136s re_rotamer = re.compile('chi-1\S*chi-2\s*rotamer\s*normality\s*:\s*([0-9.Ee-]+)') 136s /usr/lib/python3/dist-packages/csb/bio/io/wwpdb.py:1222: SyntaxWarning: invalid escape sequence '\d' 136s res = re.search("(\d+(?:\.\d+)?)\s+ANGSTROM", line) 136s /usr/lib/python3/dist-packages/csb/bio/sequence/__init__.py:566: SyntaxWarning: invalid escape sequence '\w' 136s self._residues += re.sub('([^\w\-\.])+', '', string) 136s /usr/lib/python3/dist-packages/csb/bio/structure/__init__.py:2129: SyntaxWarning: invalid escape sequence '\s' 136s string = ''.join(re.split('\s+', string)) 136s /usr/lib/python3/dist-packages/csb/bio/structure/__init__.py:2131: SyntaxWarning: invalid escape sequence '\s' 136s conf_string = ''.join(re.split('\s+', conf_string)) 136s /usr/lib/python3/dist-packages/csb/statistics/__init__.py:341: SyntaxWarning: invalid escape sequence '\s' 136s """ 136s /usr/lib/python3/dist-packages/csb/test/cases/io/__init__.py:482: SyntaxWarning: invalid escape sequence '\w' 136s "([0-9a-zA-Z]([-.\w]*[0-9a-zA-Z])"] 136s /usr/lib/python3/dist-packages/csb/bio/io/hhpred.py:210: SyntaxWarning: invalid escape sequence '\d' 136s m = re.search('(\d+)\D+(\d+)', line).groups() 136s /usr/lib/python3/dist-packages/csb/bio/io/hhpred.py:260: SyntaxWarning: invalid escape sequence '\s' 136s seq = re.sub('\s+', '', ''.join(lines[1:])) 136s /usr/lib/python3/dist-packages/csb/bio/io/hhpred.py:307: SyntaxWarning: invalid escape sequence '\-' 136s pattern = re.compile('^[A-Z\-]\s[0-9]+\s+') 136s /usr/lib/python3/dist-packages/csb/bio/io/procheck.py:31: SyntaxWarning: invalid escape sequence '\s' 136s input_file_name = re.compile('>>>-----.*?\n.*?\n\s*\|\s*(\S+)\s+') 136s /usr/lib/python3/dist-packages/csb/bio/io/procheck.py:32: SyntaxWarning: invalid escape sequence '\d' 136s residues = re.compile('(\d+)\s*residues\s\|') 136s /usr/lib/python3/dist-packages/csb/bio/io/procheck.py:33: SyntaxWarning: invalid escape sequence '\s' 136s ramachandran_plot = re.compile('Ramachandran\splot:\s*(\d+\.\d+)' + 136s /usr/lib/python3/dist-packages/csb/bio/io/procheck.py:34: SyntaxWarning: invalid escape sequence '\s' 136s '%\s*core\s*(\d+\.\d+)%\s*allow\s*(\d+\.\d+)' + 136s /usr/lib/python3/dist-packages/csb/bio/io/procheck.py:35: SyntaxWarning: invalid escape sequence '\s' 136s '%\s*gener\s*(\d+\.\d+)%\s*disall') 136s /usr/lib/python3/dist-packages/csb/bio/io/procheck.py:36: SyntaxWarning: invalid escape sequence '\s' 136s labelled_all = re.compile('Ramachandrans:\s*(\d+)\s*.*?out\sof\s*(\d+)') 136s /usr/lib/python3/dist-packages/csb/bio/io/procheck.py:37: SyntaxWarning: invalid escape sequence '\s' 136s labelled_chi = re.compile('Chi1-chi2\splots:\s*(\d+)\s*.*?out\sof\s*(\d+)') 136s /usr/lib/python3/dist-packages/csb/bio/io/procheck.py:38: SyntaxWarning: invalid escape sequence '\s' 136s bad_contacts = re.compile('Bad\scontacts:\s*(\d+)') 136s /usr/lib/python3/dist-packages/csb/bio/io/procheck.py:39: SyntaxWarning: invalid escape sequence '\s' 136s g_factors = re.compile('G-factors\s*Dihedrals:\s*([0-9-+.]+)' + 136s /usr/lib/python3/dist-packages/csb/bio/io/procheck.py:40: SyntaxWarning: invalid escape sequence '\s' 136s '\s*Covalent:\s*([0-9-+.]+)\s*Overall:\s*([0-9-+.]+)') 136s /usr/lib/python3/dist-packages/csb/bio/io/whatif.py:32: SyntaxWarning: invalid escape sequence '\s' 136s re_ramachandran = re.compile('Ramachandran\s*Z-score\s*:\s*([0-9.Ee-]+)') 136s /usr/lib/python3/dist-packages/csb/bio/io/whatif.py:33: SyntaxWarning: invalid escape sequence '\s' 136s re_1st = re.compile('1st\s*generation\s*packing\s*quality\s*:\s*([0-9.Ee-]+)') 136s /usr/lib/python3/dist-packages/csb/bio/io/whatif.py:34: SyntaxWarning: invalid escape sequence '\s' 136s re_2nd = re.compile('2nd\s*generation\s*packing\s*quality\s*:\s*([0-9.Ee-]+)') 136s /usr/lib/python3/dist-packages/csb/bio/io/whatif.py:35: SyntaxWarning: invalid escape sequence '\s' 136s re_backbone = re.compile('Backbone\s*conformation\s*Z-score\s*:\s*([0-9.Ee-]+)') 136s /usr/lib/python3/dist-packages/csb/bio/io/whatif.py:36: SyntaxWarning: invalid escape sequence '\S' 136s re_rotamer = re.compile('chi-1\S*chi-2\s*rotamer\s*normality\s*:\s*([0-9.Ee-]+)') 136s /usr/lib/python3/dist-packages/csb/bio/io/wwpdb.py:1222: SyntaxWarning: invalid escape sequence '\d' 136s res = re.search("(\d+(?:\.\d+)?)\s+ANGSTROM", line) 136s /usr/lib/python3/dist-packages/csb/bio/sequence/__init__.py:566: SyntaxWarning: invalid escape sequence '\w' 136s self._residues += re.sub('([^\w\-\.])+', '', string) 136s /usr/lib/python3/dist-packages/csb/bio/structure/__init__.py:2129: SyntaxWarning: invalid escape sequence '\s' 136s string = ''.join(re.split('\s+', string)) 136s /usr/lib/python3/dist-packages/csb/bio/structure/__init__.py:2131: SyntaxWarning: invalid escape sequence '\s' 136s conf_string = ''.join(re.split('\s+', conf_string)) 136s /usr/lib/python3/dist-packages/csb/statistics/__init__.py:341: SyntaxWarning: invalid escape sequence '\s' 136s """ 136s /usr/lib/python3/dist-packages/csb/test/cases/io/__init__.py:482: SyntaxWarning: invalid escape sequence '\w' 136s "([0-9a-zA-Z]([-.\w]*[0-9a-zA-Z])"] 136s Setting up autopkgtest-satdep (0) ... 136s Processing triggers for libc-bin (2.40-1ubuntu3) ... 136s Processing triggers for systemd (256.5-2ubuntu4) ... 136s Processing triggers for man-db (2.12.1-3) ... 141s (Reading database ... 83470 files and directories currently installed.) 141s Removing autopkgtest-satdep (0) ... 142s autopkgtest [11:20:57]: test build: [----------------------- 143s Traceback (most recent call last): 143s File "/usr/lib/python3/dist-packages/csb/test/__init__.py", line 335, in ensureDataConsistency 143s self.getPickle('1nz9.model1.pickle') 143s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 143s File "/usr/lib/python3/dist-packages/csb/test/__init__.py", line 296, in getPickle 143s file = self.getTestFile(fileName, subDir) 143s File "/usr/lib/python3/dist-packages/csb/test/__init__.py", line 281, in getTestFile 143s raise IOError('Test file not found: {0}'.format(fileName)) 143s OSError: Test file not found: 1nz9.model1.pickle 143s 143s During handling of the above exception, another exception occurred: 143s 143s Traceback (most recent call last): 143s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 143s from . import multiarray 143s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 143s from . import overrides 143s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 143s from numpy.core._multiarray_umath import ( 143s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 143s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 143s 143s During handling of the above exception, another exception occurred: 143s 143s Traceback (most recent call last): 143s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 143s from numpy.__config__ import show as show_config 143s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 143s from numpy.core._multiarray_umath import ( 143s ...<3 lines>... 143s ) 143s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 143s raise ImportError(msg) 143s ImportError: 143s 143s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 143s 143s Importing the numpy C-extensions failed. This error can happen for 143s many reasons, often due to issues with your setup or how NumPy was 143s installed. 143s 143s We have compiled some common reasons and troubleshooting tips at: 143s 143s https://numpy.org/devdocs/user/troubleshooting-importerror.html 143s 143s Please note and check the following: 143s 143s * The Python version is: Python3.13 from "/usr/bin/python3.13" 143s * The NumPy version is: "1.26.4" 143s 143s and make sure that they are the versions you expect. 143s Please carefully study the documentation linked above for further help. 143s 143s Original error was: No module named 'numpy.core._multiarray_umath' 143s 143s 143s The above exception was the direct cause of the following exception: 143s 143s Traceback (most recent call last): 143s File "/tmp/autopkgtest.dFvL7d/autopkgtest_tmp/test/app.py", line 13, in 143s main() 143s ~~~~^^ 143s File "/tmp/autopkgtest.dFvL7d/autopkgtest_tmp/test/app.py", line 9, in main 143s return Console('csb.test.cases.*') 143s File "/usr/lib/python3/dist-packages/csb/test/__init__.py", line 806, in __init__ 143s self.run() 143s ~~~~~~~~^^ 143s File "/usr/lib/python3/dist-packages/csb/test/__init__.py", line 861, in run 143s Config().ensureDataConsistency() 143s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 143s File "/usr/lib/python3/dist-packages/csb/test/__init__.py", line 337, in ensureDataConsistency 143s self.updateDataFiles() 143s ~~~~~~~~~~~~~~~~~~~~^^ 143s File "/usr/lib/python3/dist-packages/csb/test/__init__.py", line 345, in updateDataFiles 143s from csb.bio.io.wwpdb import RegularStructureParser 143s File "/usr/lib/python3/dist-packages/csb/bio/io/__init__.py", line 5, in 143s from csb.bio.io.hhpred import HHOutputParser, HHProfileParser 143s File "/usr/lib/python3/dist-packages/csb/bio/io/hhpred.py", line 25, in 143s import csb.bio.structure as structure 143s File "/usr/lib/python3/dist-packages/csb/bio/structure/__init__.py", line 67, in 143s import numpy 143s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 143s raise ImportError(msg) from e 143s ImportError: Error importing numpy: you should not try to import numpy from 143s its source directory; please exit the numpy source tree, and relaunch 143s your python interpreter from there. 143s autopkgtest [11:20:58]: test build: -----------------------] 145s autopkgtest [11:21:00]: test build: - - - - - - - - - - results - - - - - - - - - - 145s build FAIL non-zero exit status 1 147s autopkgtest [11:21:02]: test autodep8-python3: preparing testbed 160s Reading package lists... 160s Building dependency tree... 160s Reading state information... 160s Starting pkgProblemResolver with broken count: 0 160s Starting 2 pkgProblemResolver with broken count: 0 160s Done 161s The following NEW packages will be installed: 161s autopkgtest-satdep 161s 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 161s Need to get 0 B/712 B of archives. 161s After this operation, 0 B of additional disk space will be used. 161s Get:1 /tmp/autopkgtest.dFvL7d/2-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [712 B] 161s Selecting previously unselected package autopkgtest-satdep. 161s (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 ... 83470 files and directories currently installed.) 161s Preparing to unpack .../2-autopkgtest-satdep.deb ... 161s Unpacking autopkgtest-satdep (0) ... 161s Setting up autopkgtest-satdep (0) ... 165s (Reading database ... 83470 files and directories currently installed.) 165s Removing autopkgtest-satdep (0) ... 166s autopkgtest [11:21:21]: 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 166s autopkgtest [11:21:21]: test autodep8-python3: [----------------------- 166s Testing with python3.13: 166s 166s Testing with python3.12: 166s 167s autopkgtest [11:21:22]: test autodep8-python3: -----------------------] 167s autodep8-python3 PASS (superficial) 167s autopkgtest [11:21:22]: test autodep8-python3: - - - - - - - - - - results - - - - - - - - - - 168s autopkgtest [11:21:23]: @@@@@@@@@@@@@@@@@@@@ summary 168s build FAIL non-zero exit status 1 168s autodep8-python3 PASS (superficial) 192s nova [W] Skipping flock for amd64 192s Creating nova instance adt-plucky-amd64-python-csb-20241113-111834-juju-7f2275-prod-proposed-migration-environment-20-c993f37d-7713-43dd-9b89-e5837bf25e28 from image adt/ubuntu-plucky-amd64-server-20241113.img (UUID 76b850f9-98f4-4b79-af06-fa11000b95b2)...