0s autopkgtest [22:20:15]: starting date and time: 2024-11-14 22:20:15+0000
  0s autopkgtest [22:20:15]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky
  0s autopkgtest [22:20:15]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.b7yq7mj6/out --timeout-copy=6000 -a i386 --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 builder-cpu2-ram4-disk20 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-23.secgroup --name adt-plucky-i386-python-csb-20241114-222015-juju-7f2275-prod-proposed-migration-environment-15-7e0c658d-4dd3-4acc-b4df-db0887aef25e --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration-amd64 -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/
 38s autopkgtest [22:20:53]: testbed dpkg architecture: amd64
 38s autopkgtest [22:20:53]: testbed apt version: 2.9.8
 38s autopkgtest [22:20:53]: test architecture: i386
 38s autopkgtest [22:20:53]: @@@@@@@@@@@@@@@@@@@@ test bed setup
 39s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB]
 40s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [16.1 kB]
 40s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [1037 kB]
 40s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [106 kB]
 40s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B]
 40s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [79.0 kB]
 40s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [144 kB]
 40s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [32.6 kB]
 40s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [296 kB]
 40s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [807 kB]
 40s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [740 B]
 40s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [9388 B]
 40s Fetched 2609 kB in 1s (3112 kB/s)
 40s Reading package lists...
 42s Reading package lists...
 43s Building dependency tree...
 43s Reading state information...
 43s Calculating upgrade...
 43s The following NEW packages will be installed:
 43s   python3.13-gdbm
 43s The following packages will be upgraded:
 43s   libcap-ng0 libpython3-stdlib pastebinit python3 python3-gdbm python3-minimal
 43s   python3-systemd
 43s 7 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
 43s Need to get 178 kB of archives.
 43s After this operation, 256 kB of additional disk space will be used.
 43s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-minimal amd64 3.12.7-1 [27.4 kB]
 43s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3 amd64 3.12.7-1 [24.0 kB]
 43s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libpython3-stdlib amd64 3.12.7-1 [10.0 kB]
 43s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 libcap-ng0 amd64 0.8.5-3build1 [15.6 kB]
 43s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-gdbm amd64 3.13.0-2 [31.3 kB]
 43s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-gdbm amd64 3.12.7-1 [8642 B]
 43s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 pastebinit all 1.7.1-1 [14.9 kB]
 43s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-systemd amd64 235-1build5 [45.7 kB]
 44s Fetched 178 kB in 0s (442 kB/s)
 44s (Reading database ... 
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(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 75542 files and directories currently installed.)
 44s Preparing to unpack .../python3-minimal_3.12.7-1_amd64.deb ...
 44s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ...
 44s Setting up python3-minimal (3.12.7-1) ...
 44s (Reading database ... 
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(Reading database ... 75542 files and directories currently installed.)
 44s Preparing to unpack .../python3_3.12.7-1_amd64.deb ...
 44s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ...
 44s Preparing to unpack .../libpython3-stdlib_3.12.7-1_amd64.deb ...
 44s Unpacking libpython3-stdlib:amd64 (3.12.7-1) over (3.12.6-0ubuntu1) ...
 44s Preparing to unpack .../libcap-ng0_0.8.5-3build1_amd64.deb ...
 44s Unpacking libcap-ng0:amd64 (0.8.5-3build1) over (0.8.5-1) ...
 44s Setting up libcap-ng0:amd64 (0.8.5-3build1) ...
 44s Selecting previously unselected package python3.13-gdbm.
 44s (Reading database ... 
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(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 75542 files and directories currently installed.)
 44s Preparing to unpack .../python3.13-gdbm_3.13.0-2_amd64.deb ...
 44s Unpacking python3.13-gdbm (3.13.0-2) ...
 44s Preparing to unpack .../python3-gdbm_3.12.7-1_amd64.deb ...
 44s Unpacking python3-gdbm:amd64 (3.12.7-1) over (3.12.6-1ubuntu1) ...
 44s Preparing to unpack .../pastebinit_1.7.1-1_all.deb ...
 44s Unpacking pastebinit (1.7.1-1) over (1.7.0-1) ...
 45s Preparing to unpack .../python3-systemd_235-1build5_amd64.deb ...
 45s Unpacking python3-systemd (235-1build5) over (235-1build4) ...
 45s Setting up python3.13-gdbm (3.13.0-2) ...
 45s Setting up libpython3-stdlib:amd64 (3.12.7-1) ...
 45s Setting up python3 (3.12.7-1) ...
 45s Setting up python3-systemd (235-1build5) ...
 45s Setting up python3-gdbm:amd64 (3.12.7-1) ...
 45s Setting up pastebinit (1.7.1-1) ...
 45s Processing triggers for libc-bin (2.40-1ubuntu3) ...
 45s Processing triggers for man-db (2.12.1-3) ...
 46s Reading package lists...
 46s Building dependency tree...
 46s Reading state information...
 46s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 47s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease
 47s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease
 47s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease
 47s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease
 48s Reading package lists...
 48s Reading package lists...
 48s Building dependency tree...
 48s Reading state information...
 48s Calculating upgrade...
 48s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 48s Reading package lists...
 49s Building dependency tree...
 49s Reading state information...
 49s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 51s autopkgtest [22:21:06]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 13:41:20 UTC 2024
 51s autopkgtest [22:21:06]: @@@@@@@@@@@@@@@@@@@@ apt-source python-csb
 54s Get:1 http://ftpmaster.internal/ubuntu plucky/universe python-csb 1.2.5+dfsg-10 (dsc) [1627 B]
 54s Get:2 http://ftpmaster.internal/ubuntu plucky/universe python-csb 1.2.5+dfsg-10 (tar) [3000 kB]
 54s Get:3 http://ftpmaster.internal/ubuntu plucky/universe python-csb 1.2.5+dfsg-10 (diff) [11.5 kB]
 54s gpgv: Signature made Sat Dec  9 16:03:46 2023 UTC
 54s gpgv:                using EDDSA key A095B66EE09024BEE6A2F0722A27904BD7243EDA
 54s gpgv: Can't check signature: No public key
 54s dpkg-source: warning: cannot verify inline signature for ./python-csb_1.2.5+dfsg-10.dsc: no acceptable signature found
 54s autopkgtest [22:21:09]: testing package python-csb version 1.2.5+dfsg-10
 54s autopkgtest [22:21:09]: build not needed
 55s autopkgtest [22:21:10]: test build: preparing testbed
 57s Note, using file '/tmp/autopkgtest.EvsUud/1-autopkgtest-satdep.dsc' to get the build dependencies
 58s Reading package lists...
 58s Building dependency tree...
 58s Reading state information...
 58s Starting pkgProblemResolver with broken count: 0
 58s Starting 2 pkgProblemResolver with broken count: 0
 58s Done
 58s The following NEW packages will be installed:
 58s   blt build-essential cpp cpp-14 cpp-14-x86-64-linux-gnu cpp-x86-64-linux-gnu
 58s   fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-lyx g++ g++-14
 58s   g++-14-x86-64-linux-gnu g++-x86-64-linux-gnu gcc gcc-14
 58s   gcc-14-x86-64-linux-gnu gcc-x86-64-linux-gnu libasan8 libblas3 libcc1-0
 58s   libdeflate0 libfontconfig1 libgcc-14-dev libgfortran5 libgomp1
 58s   libgraphite2-3 libharfbuzz0b libhwasan0 libimagequant0 libisl23 libitm1
 58s   libjbig0 libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui liblapack3
 58s   liblbfgsb0 liblcms2-2 liblerc4 liblsan0 libmpc3 libopenjp2-7
 58s   libpython3.13-minimal libpython3.13-stdlib libqhull-r8.0 libquadmath0
 58s   libraqm0 libsharpyuv0 libstdc++-14-dev libtcl8.6 libtiff6 libtk8.6 libtsan2
 58s   libubsan1 libwebp7 libwebpdemux2 libwebpmux3 libxft2 libxrender1 libxslt1.1
 58s   libxss1 python-matplotlib-data python3-all python3-appdirs python3-brotli
 58s   python3-contourpy python3-csb python3-cycler python3-dateutil
 58s   python3-decorator python3-fonttools python3-fs python3-kiwisolver
 58s   python3-lxml python3-lz4 python3-matplotlib python3-mpmath python3-numpy
 58s   python3-packaging python3-pil python3-pil.imagetk python3-scipy python3-six
 58s   python3-sympy python3-tk python3-tz python3-ufolib2 python3-unicodedata2
 58s   python3.12-tk python3.13 python3.13-minimal python3.13-tk tk8.6-blt2.5
 58s   unicode-data x11-common
 58s 0 upgraded, 97 newly installed, 0 to remove and 0 not upgraded.
 58s Need to get 133 MB of archives.
 58s After this operation, 503 MB of additional disk space will be used.
 58s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-minimal amd64 3.13.0-2 [879 kB]
 59s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-minimal amd64 3.13.0-2 [2188 kB]
 59s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 libtcl8.6 amd64 8.6.15+dfsg-2 [1085 kB]
 59s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB]
 59s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-core all 2.37-8 [835 kB]
 59s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig-config amd64 2.15.0-1.1ubuntu2 [37.3 kB]
 59s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontconfig1 amd64 2.15.0-1.1ubuntu2 [139 kB]
 59s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 libxrender1 amd64 1:0.9.10-1.1build1 [19.0 kB]
 59s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 libxft2 amd64 2.3.6-1build1 [45.3 kB]
 59s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 x11-common all 1:7.7+23ubuntu3 [21.7 kB]
 59s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 libxss1 amd64 1:1.2.3-1build3 [7204 B]
 59s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 libtk8.6 amd64 8.6.15-1 [862 kB]
 59s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-7build1 [630 kB]
 59s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 blt amd64 2.5.3+dfsg-7build1 [4840 B]
 59s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 libisl23 amd64 0.27-1 [685 kB]
 59s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 libmpc3 amd64 1.3.1-1build2 [55.3 kB]
 59s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-14-x86-64-linux-gnu amd64 14.2.0-8ubuntu1 [11.9 MB]
 60s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-14 amd64 14.2.0-8ubuntu1 [1030 B]
 60s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-x86-64-linux-gnu amd64 4:14.1.0-2ubuntu1 [5452 B]
 60s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp amd64 4:14.1.0-2ubuntu1 [22.4 kB]
 60s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 libcc1-0 amd64 14.2.0-8ubuntu1 [47.6 kB]
 60s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 libgomp1 amd64 14.2.0-8ubuntu1 [148 kB]
 60s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 libitm1 amd64 14.2.0-8ubuntu1 [29.1 kB]
 60s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 libasan8 amd64 14.2.0-8ubuntu1 [2998 kB]
 60s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 liblsan0 amd64 14.2.0-8ubuntu1 [1317 kB]
 60s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 libtsan2 amd64 14.2.0-8ubuntu1 [2732 kB]
 60s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 libubsan1 amd64 14.2.0-8ubuntu1 [1177 kB]
 60s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 libhwasan0 amd64 14.2.0-8ubuntu1 [1634 kB]
 60s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 libquadmath0 amd64 14.2.0-8ubuntu1 [153 kB]
 60s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 libgcc-14-dev amd64 14.2.0-8ubuntu1 [2814 kB]
 60s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-14-x86-64-linux-gnu amd64 14.2.0-8ubuntu1 [23.3 MB]
 60s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-14 amd64 14.2.0-8ubuntu1 [528 kB]
 60s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-x86-64-linux-gnu amd64 4:14.1.0-2ubuntu1 [1214 B]
 60s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc amd64 4:14.1.0-2ubuntu1 [5000 B]
 60s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 libstdc++-14-dev amd64 14.2.0-8ubuntu1 [2504 kB]
 60s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-14-x86-64-linux-gnu amd64 14.2.0-8ubuntu1 [13.3 MB]
 61s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-14 amd64 14.2.0-8ubuntu1 [19.9 kB]
 61s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-x86-64-linux-gnu amd64 4:14.1.0-2ubuntu1 [966 B]
 61s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 g++ amd64 4:14.1.0-2ubuntu1 [1100 B]
 61s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 build-essential amd64 12.10ubuntu1 [4928 B]
 61s Get:41 http://ftpmaster.internal/ubuntu plucky/universe amd64 fonts-lyx all 2.4.2.1-1 [171 kB]
 61s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.0-3build2 [247 kB]
 61s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate0 amd64 1.22-1 [64.5 kB]
 61s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 14.2.0-8ubuntu1 [909 kB]
 61s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB]
 61s Get:46 http://ftpmaster.internal/ubuntu plucky/main amd64 libharfbuzz0b amd64 10.0.1-1 [540 kB]
 61s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 libimagequant0 amd64 2.18.0-1build1 [36.3 kB]
 61s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg-turbo8 amd64 2.1.5-2ubuntu2 [150 kB]
 61s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B]
 61s Get:50 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB]
 61s Get:51 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB]
 61s Get:52 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.0-3build2 [2668 kB]
 61s Get:53 http://ftpmaster.internal/ubuntu plucky/universe amd64 liblbfgsb0 amd64 3.0+dfsg.4-1build1 [29.9 kB]
 61s Get:54 http://ftpmaster.internal/ubuntu plucky/main amd64 liblcms2-2 amd64 2.16-2 [212 kB]
 61s Get:55 http://ftpmaster.internal/ubuntu plucky/main amd64 liblerc4 amd64 4.0.0+ds-4ubuntu2 [179 kB]
 61s Get:56 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-stdlib amd64 3.13.0-2 [2107 kB]
 61s Get:57 http://ftpmaster.internal/ubuntu plucky/universe amd64 libqhull-r8.0 amd64 2020.2-6build1 [193 kB]
 61s Get:58 http://ftpmaster.internal/ubuntu plucky/main amd64 libraqm0 amd64 0.10.1-1build1 [15.0 kB]
 61s Get:59 http://ftpmaster.internal/ubuntu plucky/main amd64 libsharpyuv0 amd64 1.4.0-0.1 [17.5 kB]
 61s Get:60 http://ftpmaster.internal/ubuntu plucky/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB]
 61s Get:61 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebp7 amd64 1.4.0-0.1 [231 kB]
 61s Get:62 http://ftpmaster.internal/ubuntu plucky/main amd64 libtiff6 amd64 4.5.1+git230720-4ubuntu4 [200 kB]
 61s Get:63 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpdemux2 amd64 1.4.0-0.1 [12.4 kB]
 61s Get:64 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpmux3 amd64 1.4.0-0.1 [25.8 kB]
 61s Get:65 http://ftpmaster.internal/ubuntu plucky/main amd64 libxslt1.1 amd64 1.1.39-0exp1ubuntu1 [169 kB]
 61s Get:66 http://ftpmaster.internal/ubuntu plucky/universe amd64 python-matplotlib-data all 3.8.3-3 [2928 kB]
 61s Get:67 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13 amd64 3.13.0-2 [719 kB]
 61s Get:68 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-all amd64 3.12.7-1 [890 B]
 61s Get:69 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-appdirs all 1.4.4-4 [10.9 kB]
 61s Get:70 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-brotli amd64 1.1.0-2build2 [332 kB]
 61s Get:71 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-numpy amd64 1:1.26.4+ds-11build1 [4479 kB]
 61s Get:72 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-contourpy amd64 1.3.0-2 [217 kB]
 61s Get:73 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-six all 1.16.0-7 [13.1 kB]
 61s Get:74 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-dateutil all 2.9.0-2 [80.3 kB]
 61s Get:75 http://ftpmaster.internal/ubuntu plucky/main amd64 libopenjp2-7 amd64 2.5.0-2ubuntu1 [184 kB]
 61s Get:76 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-pil amd64 10.4.0-1ubuntu1 [463 kB]
 61s Get:77 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.12-tk amd64 3.12.7-3 [116 kB]
 61s Get:78 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-tk amd64 3.13.0-2 [106 kB]
 61s Get:79 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-tk amd64 3.12.7-1 [9752 B]
 61s Get:80 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pil.imagetk amd64 10.4.0-1ubuntu1 [9394 B]
 61s Get:81 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-cycler all 0.12.1-1 [9716 B]
 61s Get:82 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-decorator all 5.1.1-5 [10.1 kB]
 61s Get:83 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-scipy amd64 1.13.1-5 [18.2 MB]
 62s Get:84 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-ufolib2 all 0.16.1+dfsg1-1 [33.4 kB]
 62s Get:85 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-mpmath all 1.3.0-1 [425 kB]
 62s Get:86 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-sympy all 1.13.3-1 [4228 kB]
 62s Get:87 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-tz all 2024.1-2 [31.4 kB]
 62s Get:88 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-fs all 2.4.16-4 [91.3 kB]
 62s Get:89 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-lxml amd64 5.3.0-1 [1282 kB]
 62s Get:90 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-lz4 amd64 4.0.2+dfsg-1build4 [26.2 kB]
 62s Get:91 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-unicodedata2 amd64 15.1.0+ds-1build2 [360 kB]
 63s Get:92 http://ftpmaster.internal/ubuntu plucky/universe amd64 unicode-data all 15.1.0-1 [8878 kB]
 63s Get:93 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-fonttools amd64 4.46.0-1build2 [1436 kB]
 63s Get:94 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-kiwisolver amd64 1.4.7-2build1 [70.3 kB]
 63s Get:95 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-packaging all 24.1-1 [41.4 kB]
 63s Get:96 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-matplotlib amd64 3.8.3-3 [4545 kB]
 63s Get:97 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-csb all 1.2.5+dfsg-10 [2392 kB]
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 94s Setting up python3-csb (1.2.5+dfsg-10) ...
 94s /usr/lib/python3/dist-packages/csb/bio/io/hhpred.py:210: SyntaxWarning: invalid escape sequence '\d'
 94s   m = re.search('(\d+)\D+(\d+)', line).groups()
 94s /usr/lib/python3/dist-packages/csb/bio/io/hhpred.py:260: SyntaxWarning: invalid escape sequence '\s'
 94s   seq = re.sub('\s+', '', ''.join(lines[1:]))
 94s /usr/lib/python3/dist-packages/csb/bio/io/hhpred.py:307: SyntaxWarning: invalid escape sequence '\-'
 94s   pattern = re.compile('^[A-Z\-]\s[0-9]+\s+')
 94s /usr/lib/python3/dist-packages/csb/bio/io/procheck.py:31: SyntaxWarning: invalid escape sequence '\s'
 94s   input_file_name = re.compile('>>>-----.*?\n.*?\n\s*\|\s*(\S+)\s+')
 94s /usr/lib/python3/dist-packages/csb/bio/io/procheck.py:32: SyntaxWarning: invalid escape sequence '\d'
 94s   residues = re.compile('(\d+)\s*residues\s\|')
 94s /usr/lib/python3/dist-packages/csb/bio/io/procheck.py:33: SyntaxWarning: invalid escape sequence '\s'
 94s   ramachandran_plot = re.compile('Ramachandran\splot:\s*(\d+\.\d+)' +
 94s /usr/lib/python3/dist-packages/csb/bio/io/procheck.py:34: SyntaxWarning: invalid escape sequence '\s'
 94s   '%\s*core\s*(\d+\.\d+)%\s*allow\s*(\d+\.\d+)' +
 94s /usr/lib/python3/dist-packages/csb/bio/io/procheck.py:35: SyntaxWarning: invalid escape sequence '\s'
 94s   '%\s*gener\s*(\d+\.\d+)%\s*disall')
 94s /usr/lib/python3/dist-packages/csb/bio/io/procheck.py:36: SyntaxWarning: invalid escape sequence '\s'
 94s   labelled_all = re.compile('Ramachandrans:\s*(\d+)\s*.*?out\sof\s*(\d+)')
 94s /usr/lib/python3/dist-packages/csb/bio/io/procheck.py:37: SyntaxWarning: invalid escape sequence '\s'
 94s   labelled_chi = re.compile('Chi1-chi2\splots:\s*(\d+)\s*.*?out\sof\s*(\d+)')
 94s /usr/lib/python3/dist-packages/csb/bio/io/procheck.py:38: SyntaxWarning: invalid escape sequence '\s'
 94s   bad_contacts = re.compile('Bad\scontacts:\s*(\d+)')
 94s /usr/lib/python3/dist-packages/csb/bio/io/procheck.py:39: SyntaxWarning: invalid escape sequence '\s'
 94s   g_factors = re.compile('G-factors\s*Dihedrals:\s*([0-9-+.]+)' +
 94s /usr/lib/python3/dist-packages/csb/bio/io/procheck.py:40: SyntaxWarning: invalid escape sequence '\s'
 94s   '\s*Covalent:\s*([0-9-+.]+)\s*Overall:\s*([0-9-+.]+)')
 94s /usr/lib/python3/dist-packages/csb/bio/io/whatif.py:32: SyntaxWarning: invalid escape sequence '\s'
 94s   re_ramachandran = re.compile('Ramachandran\s*Z-score\s*:\s*([0-9.Ee-]+)')
 94s /usr/lib/python3/dist-packages/csb/bio/io/whatif.py:33: SyntaxWarning: invalid escape sequence '\s'
 94s   re_1st = re.compile('1st\s*generation\s*packing\s*quality\s*:\s*([0-9.Ee-]+)')
 94s /usr/lib/python3/dist-packages/csb/bio/io/whatif.py:34: SyntaxWarning: invalid escape sequence '\s'
 94s   re_2nd = re.compile('2nd\s*generation\s*packing\s*quality\s*:\s*([0-9.Ee-]+)')
 94s /usr/lib/python3/dist-packages/csb/bio/io/whatif.py:35: SyntaxWarning: invalid escape sequence '\s'
 94s   re_backbone = re.compile('Backbone\s*conformation\s*Z-score\s*:\s*([0-9.Ee-]+)')
 94s /usr/lib/python3/dist-packages/csb/bio/io/whatif.py:36: SyntaxWarning: invalid escape sequence '\S'
 94s   re_rotamer = re.compile('chi-1\S*chi-2\s*rotamer\s*normality\s*:\s*([0-9.Ee-]+)')
 94s /usr/lib/python3/dist-packages/csb/bio/io/wwpdb.py:1222: SyntaxWarning: invalid escape sequence '\d'
 94s   res = re.search("(\d+(?:\.\d+)?)\s+ANGSTROM", line)
 94s /usr/lib/python3/dist-packages/csb/bio/sequence/__init__.py:566: SyntaxWarning: invalid escape sequence '\w'
 94s   self._residues += re.sub('([^\w\-\.])+', '', string)
 94s /usr/lib/python3/dist-packages/csb/bio/structure/__init__.py:2129: SyntaxWarning: invalid escape sequence '\s'
 94s   string = ''.join(re.split('\s+', string))
 94s /usr/lib/python3/dist-packages/csb/bio/structure/__init__.py:2131: SyntaxWarning: invalid escape sequence '\s'
 94s   conf_string = ''.join(re.split('\s+', conf_string))
 94s /usr/lib/python3/dist-packages/csb/statistics/__init__.py:341: SyntaxWarning: invalid escape sequence '\s'
 94s   """
 95s /usr/lib/python3/dist-packages/csb/test/cases/io/__init__.py:482: SyntaxWarning: invalid escape sequence '\w'
 95s   "([0-9a-zA-Z]([-.\w]*[0-9a-zA-Z])"]
 95s /usr/lib/python3/dist-packages/csb/bio/io/hhpred.py:210: SyntaxWarning: invalid escape sequence '\d'
 95s   m = re.search('(\d+)\D+(\d+)', line).groups()
 95s /usr/lib/python3/dist-packages/csb/bio/io/hhpred.py:260: SyntaxWarning: invalid escape sequence '\s'
 95s   seq = re.sub('\s+', '', ''.join(lines[1:]))
 95s /usr/lib/python3/dist-packages/csb/bio/io/hhpred.py:307: SyntaxWarning: invalid escape sequence '\-'
 95s   pattern = re.compile('^[A-Z\-]\s[0-9]+\s+')
 95s /usr/lib/python3/dist-packages/csb/bio/io/procheck.py:31: SyntaxWarning: invalid escape sequence '\s'
 95s   input_file_name = re.compile('>>>-----.*?\n.*?\n\s*\|\s*(\S+)\s+')
 95s /usr/lib/python3/dist-packages/csb/bio/io/procheck.py:32: SyntaxWarning: invalid escape sequence '\d'
 95s   residues = re.compile('(\d+)\s*residues\s\|')
 95s /usr/lib/python3/dist-packages/csb/bio/io/procheck.py:33: SyntaxWarning: invalid escape sequence '\s'
 95s   ramachandran_plot = re.compile('Ramachandran\splot:\s*(\d+\.\d+)' +
 95s /usr/lib/python3/dist-packages/csb/bio/io/procheck.py:34: SyntaxWarning: invalid escape sequence '\s'
 95s   '%\s*core\s*(\d+\.\d+)%\s*allow\s*(\d+\.\d+)' +
 95s /usr/lib/python3/dist-packages/csb/bio/io/procheck.py:35: SyntaxWarning: invalid escape sequence '\s'
 95s   '%\s*gener\s*(\d+\.\d+)%\s*disall')
 95s /usr/lib/python3/dist-packages/csb/bio/io/procheck.py:36: SyntaxWarning: invalid escape sequence '\s'
 95s   labelled_all = re.compile('Ramachandrans:\s*(\d+)\s*.*?out\sof\s*(\d+)')
 95s /usr/lib/python3/dist-packages/csb/bio/io/procheck.py:37: SyntaxWarning: invalid escape sequence '\s'
 95s   labelled_chi = re.compile('Chi1-chi2\splots:\s*(\d+)\s*.*?out\sof\s*(\d+)')
 95s /usr/lib/python3/dist-packages/csb/bio/io/procheck.py:38: SyntaxWarning: invalid escape sequence '\s'
 95s   bad_contacts = re.compile('Bad\scontacts:\s*(\d+)')
 95s /usr/lib/python3/dist-packages/csb/bio/io/procheck.py:39: SyntaxWarning: invalid escape sequence '\s'
 95s   g_factors = re.compile('G-factors\s*Dihedrals:\s*([0-9-+.]+)' +
 95s /usr/lib/python3/dist-packages/csb/bio/io/procheck.py:40: SyntaxWarning: invalid escape sequence '\s'
 95s   '\s*Covalent:\s*([0-9-+.]+)\s*Overall:\s*([0-9-+.]+)')
 95s /usr/lib/python3/dist-packages/csb/bio/io/whatif.py:32: SyntaxWarning: invalid escape sequence '\s'
 95s   re_ramachandran = re.compile('Ramachandran\s*Z-score\s*:\s*([0-9.Ee-]+)')
 95s /usr/lib/python3/dist-packages/csb/bio/io/whatif.py:33: SyntaxWarning: invalid escape sequence '\s'
 95s   re_1st = re.compile('1st\s*generation\s*packing\s*quality\s*:\s*([0-9.Ee-]+)')
 95s /usr/lib/python3/dist-packages/csb/bio/io/whatif.py:34: SyntaxWarning: invalid escape sequence '\s'
 95s   re_2nd = re.compile('2nd\s*generation\s*packing\s*quality\s*:\s*([0-9.Ee-]+)')
 95s /usr/lib/python3/dist-packages/csb/bio/io/whatif.py:35: SyntaxWarning: invalid escape sequence '\s'
 95s   re_backbone = re.compile('Backbone\s*conformation\s*Z-score\s*:\s*([0-9.Ee-]+)')
 95s /usr/lib/python3/dist-packages/csb/bio/io/whatif.py:36: SyntaxWarning: invalid escape sequence '\S'
 95s   re_rotamer = re.compile('chi-1\S*chi-2\s*rotamer\s*normality\s*:\s*([0-9.Ee-]+)')
 95s /usr/lib/python3/dist-packages/csb/bio/io/wwpdb.py:1222: SyntaxWarning: invalid escape sequence '\d'
 95s   res = re.search("(\d+(?:\.\d+)?)\s+ANGSTROM", line)
 95s /usr/lib/python3/dist-packages/csb/bio/sequence/__init__.py:566: SyntaxWarning: invalid escape sequence '\w'
 95s   self._residues += re.sub('([^\w\-\.])+', '', string)
 95s /usr/lib/python3/dist-packages/csb/bio/structure/__init__.py:2129: SyntaxWarning: invalid escape sequence '\s'
 95s   string = ''.join(re.split('\s+', string))
 95s /usr/lib/python3/dist-packages/csb/bio/structure/__init__.py:2131: SyntaxWarning: invalid escape sequence '\s'
 95s   conf_string = ''.join(re.split('\s+', conf_string))
 95s /usr/lib/python3/dist-packages/csb/statistics/__init__.py:341: SyntaxWarning: invalid escape sequence '\s'
 95s   """
 95s /usr/lib/python3/dist-packages/csb/test/cases/io/__init__.py:482: SyntaxWarning: invalid escape sequence '\w'
 95s   "([0-9a-zA-Z]([-.\w]*[0-9a-zA-Z])"]
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 98s Selecting previously unselected package autopkgtest-satdep.
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 98s Setting up autopkgtest-satdep (0) ...
 99s autopkgtest: WARNING: package python3-csb:i386 is not installed though it should be
100s (Reading database ... 84735 files and directories currently installed.)
100s Removing autopkgtest-satdep (0) ...
101s autopkgtest [22:21:56]: test build: [-----------------------
101s Traceback (most recent call last):
101s   File "/usr/lib/python3/dist-packages/csb/test/__init__.py", line 335, in ensureDataConsistency
101s     self.getPickle('1nz9.model1.pickle')
101s     ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^
101s   File "/usr/lib/python3/dist-packages/csb/test/__init__.py", line 296, in getPickle
101s     file = self.getTestFile(fileName, subDir)
101s   File "/usr/lib/python3/dist-packages/csb/test/__init__.py", line 281, in getTestFile
101s     raise IOError('Test file not found: {0}'.format(fileName))
101s OSError: Test file not found: 1nz9.model1.pickle
101s 
101s During handling of the above exception, another exception occurred:
101s 
101s Traceback (most recent call last):
101s   File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in <module>
101s     from . import multiarray
101s   File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in <module>
101s     from . import overrides
101s   File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in <module>
101s     from numpy.core._multiarray_umath import (
101s         add_docstring,  _get_implementing_args, _ArrayFunctionDispatcher)
101s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath'
101s 
101s During handling of the above exception, another exception occurred:
101s 
101s Traceback (most recent call last):
101s   File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in <module>
101s     from numpy.__config__ import show as show_config
101s   File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in <module>
101s     from numpy.core._multiarray_umath import (
101s     ...<3 lines>...
101s     )
101s   File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in <module>
101s     raise ImportError(msg)
101s ImportError: 
101s 
101s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE!
101s 
101s Importing the numpy C-extensions failed. This error can happen for
101s many reasons, often due to issues with your setup or how NumPy was
101s installed.
101s 
101s We have compiled some common reasons and troubleshooting tips at:
101s 
101s     https://numpy.org/devdocs/user/troubleshooting-importerror.html
101s 
101s Please note and check the following:
101s 
101s   * The Python version is: Python3.13 from "/usr/bin/python3.13"
101s   * The NumPy version is: "1.26.4"
101s 
101s and make sure that they are the versions you expect.
101s Please carefully study the documentation linked above for further help.
101s 
101s Original error was: No module named 'numpy.core._multiarray_umath'
101s 
101s 
101s The above exception was the direct cause of the following exception:
101s 
101s Traceback (most recent call last):
101s   File "/tmp/autopkgtest.EvsUud/autopkgtest_tmp/test/app.py", line 13, in <module>
101s     main()
101s     ~~~~^^
101s   File "/tmp/autopkgtest.EvsUud/autopkgtest_tmp/test/app.py", line 9, in main
101s     return Console('csb.test.cases.*')
101s   File "/usr/lib/python3/dist-packages/csb/test/__init__.py", line 806, in __init__
101s     self.run()
101s     ~~~~~~~~^^
101s   File "/usr/lib/python3/dist-packages/csb/test/__init__.py", line 861, in run
101s     Config().ensureDataConsistency()
101s     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^
101s   File "/usr/lib/python3/dist-packages/csb/test/__init__.py", line 337, in ensureDataConsistency
101s     self.updateDataFiles()
101s     ~~~~~~~~~~~~~~~~~~~~^^
101s   File "/usr/lib/python3/dist-packages/csb/test/__init__.py", line 345, in updateDataFiles
101s     from csb.bio.io.wwpdb import RegularStructureParser
101s   File "/usr/lib/python3/dist-packages/csb/bio/io/__init__.py", line 5, in <module>
101s     from csb.bio.io.hhpred import HHOutputParser, HHProfileParser
101s   File "/usr/lib/python3/dist-packages/csb/bio/io/hhpred.py", line 25, in <module>
101s     import csb.bio.structure as structure
101s   File "/usr/lib/python3/dist-packages/csb/bio/structure/__init__.py", line 67, in <module>
101s     import numpy
101s   File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in <module>
101s     raise ImportError(msg) from e
101s ImportError: Error importing numpy: you should not try to import numpy from
101s         its source directory; please exit the numpy source tree, and relaunch
101s         your python interpreter from there.
102s autopkgtest [22:21:57]: test build: -----------------------]
102s build                FAIL non-zero exit status 1
102s autopkgtest [22:21:57]: test build:  - - - - - - - - - - results - - - - - - - - - -
102s autopkgtest [22:21:57]: test autodep8-python3: preparing testbed
105s Reading package lists...
105s Building dependency tree...
105s Reading state information...
105s Starting pkgProblemResolver with broken count: 0
106s Starting 2 pkgProblemResolver with broken count: 0
106s Done
106s The following NEW packages will be installed:
106s   autopkgtest-satdep
106s 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
106s Need to get 0 B/696 B of archives.
106s After this operation, 0 B of additional disk space will be used.
106s Get:1 /tmp/autopkgtest.EvsUud/4-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [696 B]
106s Selecting previously unselected package autopkgtest-satdep.
106s (Reading database ... 
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106s Preparing to unpack .../4-autopkgtest-satdep.deb ...
106s Unpacking autopkgtest-satdep (0) ...
106s Setting up autopkgtest-satdep (0) ...
107s autopkgtest: WARNING: package python3-csb:i386 is not installed though it should be
108s (Reading database ... 84735 files and directories currently installed.)
108s Removing autopkgtest-satdep (0) ...
109s autopkgtest [22:22:04]: 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
109s autopkgtest [22:22:04]: test autodep8-python3: [-----------------------
109s Testing with python3.13:
109s <module 'csb' from '/usr/lib/python3/dist-packages/csb/__init__.py'>
109s Testing with python3.12:
109s <module 'csb' from '/usr/lib/python3/dist-packages/csb/__init__.py'>
109s autopkgtest [22:22:04]: test autodep8-python3: -----------------------]
110s autodep8-python3     PASS (superficial)
110s autopkgtest [22:22:05]: test autodep8-python3:  - - - - - - - - - - results - - - - - - - - - -
110s autopkgtest [22:22:05]: @@@@@@@@@@@@@@@@@@@@ summary
110s build                FAIL non-zero exit status 1
110s autodep8-python3     PASS (superficial)
115s nova [W] Skipping flock for amd64
115s Creating nova instance adt-plucky-i386-python-csb-20241114-222015-juju-7f2275-prod-proposed-migration-environment-15-7e0c658d-4dd3-4acc-b4df-db0887aef25e from image adt/ubuntu-plucky-amd64-server-20241114.img (UUID 79d80331-8736-463c-82c6-8c9e13c0a4ca)...