0s autopkgtest [16:05:19]: starting date and time: 2024-11-13 16:05:19+0000
  0s autopkgtest [16:05:19]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky
  0s autopkgtest [16:05:19]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.k8s6a0kq/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 r-cran-fastcluster --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-15@bos03-s390x-3.secgroup --name adt-plucky-s390x-r-cran-fastcluster-20241113-160519-juju-7f2275-prod-proposed-migration-environment-15-736b3ea0-8aed-4a5d-9bd2-7e7914b96258 --image adt/ubuntu-plucky-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --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/
105s autopkgtest [16:07:04]: testbed dpkg architecture: s390x
106s autopkgtest [16:07:05]: testbed apt version: 2.9.8
106s autopkgtest [16:07:05]: @@@@@@@@@@@@@@@@@@@@ test bed setup
106s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB]
107s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [104 kB]
107s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [17.2 kB]
107s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B]
107s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [950 kB]
107s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x Packages [110 kB]
107s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x Packages [636 kB]
108s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x Packages [17.8 kB]
108s Fetched 1916 kB in 1s (1326 kB/s)
108s Reading package lists...
110s Reading package lists...
110s Building dependency tree...
110s Reading state information...
110s Calculating upgrade...
110s The following NEW packages will be installed:
110s   python3.13-gdbm
110s The following packages will be upgraded:
110s   libgnutls30t64 libgpgme11t64 libjson-glib-1.0-0 libjson-glib-1.0-common
110s   libpython3-stdlib libutempter0 python3 python3-gdbm python3-minimal
110s 9 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
110s Need to get 1285 kB of archives.
110s After this operation, 103 kB of additional disk space will be used.
110s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x python3-minimal s390x 3.12.7-1 [27.4 kB]
110s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x python3 s390x 3.12.7-1 [24.0 kB]
110s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libpython3-stdlib s390x 3.12.7-1 [10.0 kB]
110s Get:4 http://ftpmaster.internal/ubuntu plucky/main s390x libgnutls30t64 s390x 3.8.8-2ubuntu1 [950 kB]
111s Get:5 http://ftpmaster.internal/ubuntu plucky/main s390x python3.13-gdbm s390x 3.13.0-2 [31.0 kB]
111s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x python3-gdbm s390x 3.12.7-1 [8642 B]
111s Get:7 http://ftpmaster.internal/ubuntu plucky/main s390x libgpgme11t64 s390x 1.23.2-5ubuntu4 [151 kB]
111s Get:8 http://ftpmaster.internal/ubuntu plucky/main s390x libjson-glib-1.0-common all 1.10.0+ds-3 [5586 B]
111s Get:9 http://ftpmaster.internal/ubuntu plucky/main s390x libjson-glib-1.0-0 s390x 1.10.0+ds-3 [67.5 kB]
111s Get:10 http://ftpmaster.internal/ubuntu plucky/main s390x libutempter0 s390x 1.2.1-4 [9708 B]
111s Fetched 1285 kB in 1s (1351 kB/s)
111s (Reading database ... 
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(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 55510 files and directories currently installed.)
111s Preparing to unpack .../python3-minimal_3.12.7-1_s390x.deb ...
111s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ...
111s Setting up python3-minimal (3.12.7-1) ...
111s (Reading database ... 
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(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.)
111s Preparing to unpack .../python3_3.12.7-1_s390x.deb ...
112s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ...
112s Preparing to unpack .../libpython3-stdlib_3.12.7-1_s390x.deb ...
112s Unpacking libpython3-stdlib:s390x (3.12.7-1) over (3.12.6-0ubuntu1) ...
112s Preparing to unpack .../libgnutls30t64_3.8.8-2ubuntu1_s390x.deb ...
112s Unpacking libgnutls30t64:s390x (3.8.8-2ubuntu1) over (3.8.6-2ubuntu1) ...
112s Setting up libgnutls30t64:s390x (3.8.8-2ubuntu1) ...
112s Selecting previously unselected package python3.13-gdbm.
112s (Reading database ... 
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(Reading database ... 60%
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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 ... 55510 files and directories currently installed.)
112s Preparing to unpack .../0-python3.13-gdbm_3.13.0-2_s390x.deb ...
112s Unpacking python3.13-gdbm (3.13.0-2) ...
112s Preparing to unpack .../1-python3-gdbm_3.12.7-1_s390x.deb ...
112s Unpacking python3-gdbm:s390x (3.12.7-1) over (3.12.6-1ubuntu1) ...
112s Preparing to unpack .../2-libgpgme11t64_1.23.2-5ubuntu4_s390x.deb ...
112s Unpacking libgpgme11t64:s390x (1.23.2-5ubuntu4) over (1.18.0-4.1ubuntu4) ...
112s Preparing to unpack .../3-libjson-glib-1.0-common_1.10.0+ds-3_all.deb ...
112s Unpacking libjson-glib-1.0-common (1.10.0+ds-3) over (1.10.0+ds-2) ...
112s Preparing to unpack .../4-libjson-glib-1.0-0_1.10.0+ds-3_s390x.deb ...
112s Unpacking libjson-glib-1.0-0:s390x (1.10.0+ds-3) over (1.10.0+ds-2) ...
112s Preparing to unpack .../5-libutempter0_1.2.1-4_s390x.deb ...
112s Unpacking libutempter0:s390x (1.2.1-4) over (1.2.1-3build1) ...
112s Setting up libutempter0:s390x (1.2.1-4) ...
112s Setting up libjson-glib-1.0-common (1.10.0+ds-3) ...
112s Setting up libgpgme11t64:s390x (1.23.2-5ubuntu4) ...
112s Setting up python3.13-gdbm (3.13.0-2) ...
112s Setting up libpython3-stdlib:s390x (3.12.7-1) ...
112s Setting up python3 (3.12.7-1) ...
112s Setting up libjson-glib-1.0-0:s390x (1.10.0+ds-3) ...
112s Setting up python3-gdbm:s390x (3.12.7-1) ...
112s Processing triggers for man-db (2.12.1-3) ...
112s Processing triggers for libc-bin (2.40-1ubuntu3) ...
112s Reading package lists...
112s Building dependency tree...
112s Reading state information...
113s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
113s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease
113s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease
114s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease
114s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease
115s Reading package lists...
115s Reading package lists...
116s Building dependency tree...
116s Reading state information...
116s Calculating upgrade...
116s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
116s Reading package lists...
116s Building dependency tree...
116s Reading state information...
116s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
118s autopkgtest [16:07:17]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP Mon Sep 16 12:49:35 UTC 2024
118s autopkgtest [16:07:17]: @@@@@@@@@@@@@@@@@@@@ apt-source r-cran-fastcluster
120s Get:1 http://ftpmaster.internal/ubuntu plucky/universe r-cran-fastcluster 1.2.6-1build1 (dsc) [2272 B]
120s Get:2 http://ftpmaster.internal/ubuntu plucky/universe r-cran-fastcluster 1.2.6-1build1 (tar) [208 kB]
120s Get:3 http://ftpmaster.internal/ubuntu plucky/universe r-cran-fastcluster 1.2.6-1build1 (diff) [4828 B]
120s gpgv: Signature made Wed Apr 10 18:03:18 2024 UTC
120s gpgv:                using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2
120s gpgv: Can't check signature: No public key
120s dpkg-source: warning: cannot verify inline signature for ./r-cran-fastcluster_1.2.6-1build1.dsc: no acceptable signature found
120s autopkgtest [16:07:19]: testing package r-cran-fastcluster version 1.2.6-1build1
120s autopkgtest [16:07:19]: build not needed
121s autopkgtest [16:07:20]: test run-unit-test: preparing testbed
122s Reading package lists...
122s Building dependency tree...
122s Reading state information...
122s Starting pkgProblemResolver with broken count: 0
122s Starting 2 pkgProblemResolver with broken count: 0
122s Done
122s The following additional packages will be installed:
122s   fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono libblas3
122s   libcairo2 libdatrie1 libdeflate0 libfontconfig1 libfreetype6 libgfortran5
122s   libgomp1 libgraphite2-3 libharfbuzz0b libice6 libjbig0 libjpeg-turbo8
122s   libjpeg8 liblapack3 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0
122s   libpaper-utils libpaper1 libpixman-1-0 libsharpyuv0 libsm6 libtcl8.6
122s   libthai-data libthai0 libtiff6 libtk8.6 libwebp7 libxcb-render0 libxcb-shm0
122s   libxft2 libxrender1 libxss1 libxt6t64 python3-fastcluster python3-numpy
122s   r-base-core r-cran-fastcluster unzip x11-common xdg-utils zip
122s Suggested packages:
122s   tcl8.6 tk8.6 gcc gfortran python-numpy-doc python3-dev python3-pytest
122s   elpa-ess r-doc-info | r-doc-pdf r-mathlib r-base-html
122s Recommended packages:
122s   python3-scipy r-recommended r-base-dev r-doc-html libfile-mimeinfo-perl
122s   libnet-dbus-perl libx11-protocol-perl x11-utils x11-xserver-utils
123s The following NEW packages will be installed:
123s   autopkgtest-satdep fontconfig fontconfig-config fonts-dejavu-core
123s   fonts-dejavu-mono libblas3 libcairo2 libdatrie1 libdeflate0 libfontconfig1
123s   libfreetype6 libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libice6
123s   libjbig0 libjpeg-turbo8 libjpeg8 liblapack3 libpango-1.0-0
123s   libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpixman-1-0
123s   libsharpyuv0 libsm6 libtcl8.6 libthai-data libthai0 libtiff6 libtk8.6
123s   libwebp7 libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxss1 libxt6t64
123s   python3-fastcluster python3-numpy r-base-core r-cran-fastcluster unzip
123s   x11-common xdg-utils zip
123s 0 upgraded, 48 newly installed, 0 to remove and 0 not upgraded.
123s Need to get 44.3 MB/44.3 MB of archives.
123s After this operation, 103 MB of additional disk space will be used.
123s Get:1 /tmp/autopkgtest.utMhOa/1-autopkgtest-satdep.deb autopkgtest-satdep s390x 0 [720 B]
123s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x libfreetype6 s390x 2.13.3+dfsg-1 [431 kB]
123s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x fonts-dejavu-mono all 2.37-8 [502 kB]
123s Get:4 http://ftpmaster.internal/ubuntu plucky/main s390x fonts-dejavu-core all 2.37-8 [835 kB]
124s Get:5 http://ftpmaster.internal/ubuntu plucky/main s390x fontconfig-config s390x 2.15.0-1.1ubuntu2 [37.4 kB]
124s Get:6 http://ftpmaster.internal/ubuntu plucky/main s390x libfontconfig1 s390x 2.15.0-1.1ubuntu2 [150 kB]
124s Get:7 http://ftpmaster.internal/ubuntu plucky/main s390x fontconfig s390x 2.15.0-1.1ubuntu2 [191 kB]
124s Get:8 http://ftpmaster.internal/ubuntu plucky/main s390x libblas3 s390x 3.12.0-3build2 [238 kB]
124s Get:9 http://ftpmaster.internal/ubuntu plucky/main s390x libpixman-1-0 s390x 0.44.0-3 [201 kB]
124s Get:10 http://ftpmaster.internal/ubuntu plucky/main s390x libxcb-render0 s390x 1.17.0-2 [17.0 kB]
124s Get:11 http://ftpmaster.internal/ubuntu plucky/main s390x libxcb-shm0 s390x 1.17.0-2 [5862 B]
124s Get:12 http://ftpmaster.internal/ubuntu plucky/main s390x libxrender1 s390x 1:0.9.10-1.1build1 [20.4 kB]
124s Get:13 http://ftpmaster.internal/ubuntu plucky/main s390x libcairo2 s390x 1.18.2-2 [580 kB]
124s Get:14 http://ftpmaster.internal/ubuntu plucky/main s390x libdatrie1 s390x 0.2.13-3build1 [20.6 kB]
124s Get:15 http://ftpmaster.internal/ubuntu plucky/main s390x libdeflate0 s390x 1.22-1 [46.1 kB]
124s Get:16 http://ftpmaster.internal/ubuntu plucky/main s390x libgfortran5 s390x 14.2.0-8ubuntu1 [587 kB]
124s Get:17 http://ftpmaster.internal/ubuntu plucky/main s390x libgomp1 s390x 14.2.0-8ubuntu1 [151 kB]
124s Get:18 http://ftpmaster.internal/ubuntu plucky/main s390x libgraphite2-3 s390x 1.3.14-2ubuntu1 [79.8 kB]
124s Get:19 http://ftpmaster.internal/ubuntu plucky/main s390x libharfbuzz0b s390x 10.0.1-1 [536 kB]
124s Get:20 http://ftpmaster.internal/ubuntu plucky/main s390x x11-common all 1:7.7+23ubuntu3 [21.7 kB]
125s Get:21 http://ftpmaster.internal/ubuntu plucky/main s390x libice6 s390x 2:1.1.1-1 [45.4 kB]
125s Get:22 http://ftpmaster.internal/ubuntu plucky/main s390x libjpeg-turbo8 s390x 2.1.5-2ubuntu2 [150 kB]
125s Get:23 http://ftpmaster.internal/ubuntu plucky/main s390x libjpeg8 s390x 8c-2ubuntu11 [2146 B]
125s Get:24 http://ftpmaster.internal/ubuntu plucky/main s390x liblapack3 s390x 3.12.0-3build2 [2953 kB]
125s Get:25 http://ftpmaster.internal/ubuntu plucky/main s390x libthai-data all 0.1.29-2build1 [158 kB]
125s Get:26 http://ftpmaster.internal/ubuntu plucky/main s390x libthai0 s390x 0.1.29-2build1 [20.7 kB]
125s Get:27 http://ftpmaster.internal/ubuntu plucky/main s390x libpango-1.0-0 s390x 1.54.0+ds-3 [249 kB]
125s Get:28 http://ftpmaster.internal/ubuntu plucky/main s390x libpangoft2-1.0-0 s390x 1.54.0+ds-3 [49.5 kB]
125s Get:29 http://ftpmaster.internal/ubuntu plucky/main s390x libpangocairo-1.0-0 s390x 1.54.0+ds-3 [28.0 kB]
125s Get:30 http://ftpmaster.internal/ubuntu plucky/main s390x libpaper1 s390x 1.1.29build1 [13.4 kB]
125s Get:31 http://ftpmaster.internal/ubuntu plucky/main s390x libpaper-utils s390x 1.1.29build1 [8442 B]
125s Get:32 http://ftpmaster.internal/ubuntu plucky/main s390x libsharpyuv0 s390x 1.4.0-0.1 [16.2 kB]
125s Get:33 http://ftpmaster.internal/ubuntu plucky/main s390x libsm6 s390x 2:1.2.4-1 [18.4 kB]
125s Get:34 http://ftpmaster.internal/ubuntu plucky/main s390x libtcl8.6 s390x 8.6.15+dfsg-2 [1034 kB]
125s Get:35 http://ftpmaster.internal/ubuntu plucky/main s390x libjbig0 s390x 2.1-6.1ubuntu2 [33.1 kB]
125s Get:36 http://ftpmaster.internal/ubuntu plucky/main s390x libwebp7 s390x 1.4.0-0.1 [204 kB]
125s Get:37 http://ftpmaster.internal/ubuntu plucky/main s390x libtiff6 s390x 4.5.1+git230720-4ubuntu4 [217 kB]
125s Get:38 http://ftpmaster.internal/ubuntu plucky/main s390x libxft2 s390x 2.3.6-1build1 [49.6 kB]
125s Get:39 http://ftpmaster.internal/ubuntu plucky/main s390x libxss1 s390x 1:1.2.3-1build3 [7396 B]
125s Get:40 http://ftpmaster.internal/ubuntu plucky/main s390x libtk8.6 s390x 8.6.15-1 [828 kB]
125s Get:41 http://ftpmaster.internal/ubuntu plucky/main s390x libxt6t64 s390x 1:1.2.1-1.2build1 [184 kB]
125s Get:42 http://ftpmaster.internal/ubuntu plucky/main s390x python3-numpy s390x 1:1.26.4+ds-11build1 [4113 kB]
126s Get:43 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-fastcluster s390x 1.2.6-1build1 [49.7 kB]
126s Get:44 http://ftpmaster.internal/ubuntu plucky/main s390x zip s390x 3.0-14ubuntu1 [187 kB]
126s Get:45 http://ftpmaster.internal/ubuntu plucky/main s390x unzip s390x 6.0-28ubuntu6 [186 kB]
126s Get:46 http://ftpmaster.internal/ubuntu plucky/main s390x xdg-utils all 1.2.1-0ubuntu1 [67.5 kB]
126s Get:47 http://ftpmaster.internal/ubuntu plucky/universe s390x r-base-core s390x 4.4.2-1 [28.6 MB]
127s Get:48 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-fastcluster s390x 1.2.6-1build1 [197 kB]
127s Preconfiguring packages ...
128s Fetched 44.3 MB in 5s (9378 kB/s)
128s Selecting previously unselected package libfreetype6:s390x.
128s (Reading database ... 
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(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.)
128s Preparing to unpack .../00-libfreetype6_2.13.3+dfsg-1_s390x.deb ...
128s Unpacking libfreetype6:s390x (2.13.3+dfsg-1) ...
128s Selecting previously unselected package fonts-dejavu-mono.
128s Preparing to unpack .../01-fonts-dejavu-mono_2.37-8_all.deb ...
128s Unpacking fonts-dejavu-mono (2.37-8) ...
128s Selecting previously unselected package fonts-dejavu-core.
128s Preparing to unpack .../02-fonts-dejavu-core_2.37-8_all.deb ...
128s Unpacking fonts-dejavu-core (2.37-8) ...
128s Selecting previously unselected package fontconfig-config.
128s Preparing to unpack .../03-fontconfig-config_2.15.0-1.1ubuntu2_s390x.deb ...
128s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ...
128s Selecting previously unselected package libfontconfig1:s390x.
128s Preparing to unpack .../04-libfontconfig1_2.15.0-1.1ubuntu2_s390x.deb ...
128s Unpacking libfontconfig1:s390x (2.15.0-1.1ubuntu2) ...
128s Selecting previously unselected package fontconfig.
128s Preparing to unpack .../05-fontconfig_2.15.0-1.1ubuntu2_s390x.deb ...
128s Unpacking fontconfig (2.15.0-1.1ubuntu2) ...
128s Selecting previously unselected package libblas3:s390x.
128s Preparing to unpack .../06-libblas3_3.12.0-3build2_s390x.deb ...
128s Unpacking libblas3:s390x (3.12.0-3build2) ...
128s Selecting previously unselected package libpixman-1-0:s390x.
128s Preparing to unpack .../07-libpixman-1-0_0.44.0-3_s390x.deb ...
128s Unpacking libpixman-1-0:s390x (0.44.0-3) ...
128s Selecting previously unselected package libxcb-render0:s390x.
128s Preparing to unpack .../08-libxcb-render0_1.17.0-2_s390x.deb ...
128s Unpacking libxcb-render0:s390x (1.17.0-2) ...
128s Selecting previously unselected package libxcb-shm0:s390x.
128s Preparing to unpack .../09-libxcb-shm0_1.17.0-2_s390x.deb ...
128s Unpacking libxcb-shm0:s390x (1.17.0-2) ...
128s Selecting previously unselected package libxrender1:s390x.
128s Preparing to unpack .../10-libxrender1_1%3a0.9.10-1.1build1_s390x.deb ...
128s Unpacking libxrender1:s390x (1:0.9.10-1.1build1) ...
128s Selecting previously unselected package libcairo2:s390x.
128s Preparing to unpack .../11-libcairo2_1.18.2-2_s390x.deb ...
128s Unpacking libcairo2:s390x (1.18.2-2) ...
128s Selecting previously unselected package libdatrie1:s390x.
128s Preparing to unpack .../12-libdatrie1_0.2.13-3build1_s390x.deb ...
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136s (Reading database ... 58620 files and directories currently installed.)
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136s autopkgtest [16:07:35]: test run-unit-test: [-----------------------
136s 
136s R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
136s Copyright (C) 2024 The R Foundation for Statistical Computing
136s Platform: s390x-ibm-linux-gnu
136s 
136s R is free software and comes with ABSOLUTELY NO WARRANTY.
136s You are welcome to redistribute it under certain conditions.
136s Type 'license()' or 'licence()' for distribution details.
136s 
136s R is a collaborative project with many contributors.
136s Type 'contributors()' for more information and
136s 'citation()' on how to cite R or R packages in publications.
136s 
136s Type 'demo()' for some demos, 'help()' for on-line help, or
136s 'help.start()' for an HTML browser interface to help.
136s Type 'q()' to quit R.
136s 
136s > #  fastcluster: Fast hierarchical clustering routines for R and Python
136s > #
136s > #  Copyright:
136s > #    * Until package version 1.1.23: © 2011 Daniel Müllner <https://danifold.net>
136s > #    * All changes from version 1.1.24 on: © Google Inc. <https://www.google.com>
136s > #
136s > # Test script for the R interface
136s > 
136s > seed = as.integer(runif(1, 0, 1e9))
136s > set.seed(seed)
136s > cat(sprintf("Random seed: %d\n",seed))
136s Random seed: 123614499
136s > 
136s > print_seed <- function() {
136s +   return(sprintf('
136s + Please send a report to the author of the \'fastcluster\' package, Daniel Müllner.
136s + For contact details, see <https://danifold.net>. To make the error
136s + reproducible, you must include the following number (the random seed value) in
136s + your error report: %d.\n\n', seed))
136s + }
136s > 
136s > hasWardD2 = getRversion() >= '3.1.0'
136s > 
136s > # Compare two dendrograms and check whether they are equal, except that
136s > # ties may be resolved differently.
136s > compare <- function(dg1, dg2) {
136s +   h1 <- dg1$height
136s +   h2 <- dg2$height
136s +   # "height" vectors may have small numerical errors.
136s +   rdiffs <- abs(h1-h2)/pmax(abs(h1),abs(h2))
136s +   rdiffs = rdiffs[complete.cases(rdiffs)]
136s +   rel_error <-  max(rdiffs)
136s +   # We allow a relative error of 1e-13.
136s +   if (rel_error>1e-13) {
136s +     print(h1)
136s +     print(h2)
136s +     cat(sprintf('Height vectors differ! The maximum relative error is %e.\n', rel_error))
136s +     return(FALSE)
136s +   }
136s +   # Filter the indices where consecutive merging distances are distinct.
136s +   d = diff(dg1$height)
136s +   b = (c(d,1)!=0 & c(1,d)!=0)
136s +   #cat(sprintf("Percentage of indices where we can test: %g.\n",100.0*length(b[b])/length(b)))
136s +   if (any(b)) {
136s +     m1 = dg1$merge[b,]
136s +     m2 = dg2$merge[b,]
136s + 
136s +     r = function(i) {
136s +       if (i<0) {
136s +         return(1)
136s +       }
136s +       else {
136s +         return(b[i])
136s +       }
136s +     }
136s + 
136s +     f = sapply(m1,r)
136s +     fm1 = m1*f
136s +     fm2 = m2*f
136s +     # The "merge" matrices must be identical whereever indices are not ambiguous
136s +     # due to ties.
136s +     if (!identical(fm1,fm2)) {
136s +       cat('Merge matrices differ!\n')
136s +       return(FALSE)
136s +     }
136s +     # Compare the "order" vectors only if all merging distances were distinct.
136s +     if (all(b) && !identical(dg1$order,dg2$order)) {
136s +       cat('Order vectors differ!\n')
136s +       return(FALSE)
136s +     }
136s +   }
136s +   return(TRUE)
136s + }
136s > 
136s > # Generate uniformly distributed random data
136s > generate.uniform <- function() {
136s +   n = sample(10:1000,1)
136s +   range_exp = runif(1,min=-10, max=10)
136s +   cat(sprintf("Number of sample points: %d\n",n))
136s +   cat(sprintf("Dissimilarity range: [0,%g]\n",10^range_exp))
136s +   d = runif(n*(n-1)/2, min=0, max=10^range_exp)
136s +   # Fake a compressed distance matrix
136s +   attributes(d) <- NULL
136s +   attr(d,"Size") <- n
136s +   attr(d, "call") <- 'N/A'
136s +   class(d) <- "dist"
136s +   return(d)
136s + }
136s > 
136s > # Generate normally distributed random data
136s > generate.normal <- function() {
136s +   n = sample(10:1000,1)
136s +   dim = sample(2:20,1)
136s + 
136s +   cat (sprintf("Number of sample points: %d\n",n))
136s +   cat (sprintf("Dimension: %d\n",dim))
136s + 
136s +   pcd = matrix(rnorm(n*dim), c(n,dim))
136s +   d = dist(pcd)
136s +   return(d)
136s + }
136s > 
136s > # Test the clustering functions when a distance matrix is given.
136s > test.dm <-  function(d) {
136s +   d2 = d
136s +   if (hasWardD2) {
136s +     methods = c('single','complete','average','mcquitty','ward.D','ward.D2','centroid','median')
136s +   }
136s +   else {
136s +     methods = c('single','complete','average','mcquitty','ward','centroid','median')
136s +   }
136s +   for (method in methods) {
136s +     cat(paste('Method :', method, '\n'))
136s +     dg_stats       = stats::hclust(d, method=method)
136s +     if (method == 'ward') {
136s +       method = 'ward.D'
136s +     }
136s +     dg_fastcluster = fastcluster::hclust(d, method=method)
136s +     if (!identical(d,d2)) {
136s +       cat('Input array was corrupted!\n')
136s +       stop(print_seed())
136s +     }
136s +     if (!compare(dg_stats, dg_fastcluster)) {
136s +       stop(print_seed())
136s +     }
136s +   }
136s +   cat('Passed.\n')
136s + }
136s > 
136s > # Test the clustering functions for vector input in Euclidean space.
136s > test.vector <-  function() {
136s +   # generate test data
136s +   n = sample(10:1000,1)
136s +   dim = sample(2:20,1)
136s +   cat (sprintf("Number of sample points: %d\n",n))
136s +   cat (sprintf("Dimension: %d\n",dim))
136s + 
136s +   range_exp = runif(1,min=-10, max=10)
136s +   pcd = matrix(rnorm(n*dim, sd=10^range_exp), c(n,dim))
136s +   pcd2 = pcd
136s +   # test
136s +   method='single'
136s +   cat(paste('Method:', method, '\n'))
136s +   for (metric in c('euclidean', 'maximum', 'manhattan', 'canberra', 'minkowski')) {
136s +     cat(paste('    Metric:', metric, '\n'))
136s +     if (metric=='minkowski') {
136s +       p = runif(1, min=1.0, max=10.0)
136s +       cat (sprintf("    p: %g\n",p));
136s +       dg_fastcluster = fastcluster::hclust.vector(pcd, method=method, metric=metric, p=p)
136s +       d = dist(pcd, method=metric, p=p)
136s +     }
136s +     else {
136s +       dg_fastcluster = fastcluster::hclust.vector(pcd, method=method, metric=metric)
136s +       d = dist(pcd, method=metric)
136s +     }
136s +     d2 = d
136s +     dg_fastcluster_dist = fastcluster::hclust(d, method=method)
136s +     if (!identical(d,d2) || !identical(pcd,pcd2)) {
136s +       cat('Input array was corrupted!\n')
136s +       stop(print_seed())
136s +     }
136s +     if (!compare(dg_fastcluster_dist, dg_fastcluster)) {
136s +       stop(print_seed())
136s +     }
136s +   }
136s +   for (method in c('ward','centroid','median') ) {
136s +     cat(paste('Method:', method, '\n'))
136s +     dg_fastcluster = fastcluster::hclust.vector(pcd, method=method)
136s +     if (!identical(pcd,pcd2)) {
136s +       cat('Input array was corrupted!\n')
136s +       stop(print_seed())
136s +     }
136s +     d = dist(pcd)
136s +     if(method == "ward" && hasWardD2) {
136s +       method = "ward.D2"
136s +     }
136s +     else
136s +     {
136s +       # Workaround: fastcluster::hclust expects _squared_ euclidean distances.
136s +       d = d^2
136s +     }
136s +     d2 = d
136s +     dg_fastcluster_dist = fastcluster::hclust(d, method=method)
136s +     if (!identical(d,d2)) {
136s +       cat('Input array was corrupted!\n')
136s +       stop(print_seed())
136s +     }
136s +     if(method != "ward.D2") {
136s +       dg_fastcluster_dist$height = sqrt(dg_fastcluster_dist$height)
136s +     }
136s +     # The Euclidean methods may have small numerical errors due to squaring/
136s +     # taking the root in the Euclidean distances.
136s +     if (!compare(dg_fastcluster_dist, dg_fastcluster)) {
136s +       stop(print_seed())
136s +     }
136s +   }
136s +   cat('Passed.\n')
136s + }
136s > 
136s > # Test the single linkage function with the "binary" metric
136s > test.vector.binary <- function() {
136s +   # generate test data
136s +   cat (sprintf("Uniform sampling for the 'binary' metric:\n"))
136s +   n = sample(10:400,1)
136s +   dim = sample(n:(2*n),1)
136s +   cat (sprintf("Number of sample points: %d\n",n))
136s +   cat (sprintf("Dimension: %d\n",dim))
136s +   pcd = matrix(sample(-1:2, n*dim, replace=T), c(n,dim))
136s +   pcd2 = pcd
136s +   # test
136s +   method='single'
136s +   metric='binary'
136s +   cat(paste('Method:', method, '\n'))
136s +   cat(paste('    Metric:', metric, '\n'))
136s +   dg_fastcluster = fastcluster::hclust.vector(pcd, method=method, metric=metric)
136s +   d = dist(pcd, method=metric)
136s +   d2 = d
136s +   dg_fastcluster_dist       = fastcluster::hclust(d, method=method)
136s +   if (!identical(d,d2) || !identical(d,d2)) {
136s +     cat('Input array was corrupted!\n')
136s +     stop(print_seed())
136s +   }
136s +   if (!compare(dg_fastcluster_dist, dg_fastcluster)) {
136s +     stop(print_seed())
136s +   }
136s +   cat('Passed.\n')
136s + }
136s > 
136s > 
136s > N = 15
136s > for (i in (1:N)) {
136s +   if (i%%2==1) {
136s +     cat(sprintf('Random test %d of %d (uniform distribution of distances):\n',i,2*N))
136s +     d = generate.uniform()
136s +   }
136s +   else {
136s +     cat(sprintf('Random test %d of %d (Gaussian density):\n',i,2*N))
136s +     d = generate.normal()
136s +   }
136s +   test.dm(d)
136s + }
136s Random test 1 of 30 (uniform distribution of distances):
136s Number of sample points: 521
136s Dissimilarity range: [0,5332.48]
136s Method : single 
136s Method : complete 
137s Method : average 
137s Method : mcquitty 
137s Method : ward.D 
137s Method : ward.D2 
137s Method : centroid 
137s Method : median 
137s Passed.
137s Random test 2 of 30 (Gaussian density):
137s Number of sample points: 251
137s Dimension: 6
137s Method : single 
137s Method : complete 
137s Method : average 
137s Method : mcquitty 
137s Method : ward.D 
137s Method : ward.D2 
137s Method : centroid 
137s Method : median 
137s Passed.
137s Random test 3 of 30 (uniform distribution of distances):
137s Number of sample points: 689
137s Dissimilarity range: [0,0.000735662]
137s Method : single 
137s Method : complete 
137s Method : average 
137s Method : mcquitty 
137s Method : ward.D 
137s Method : ward.D2 
137s Method : centroid 
137s Method : median 
137s Passed.
137s Random test 4 of 30 (Gaussian density):
137s Number of sample points: 997
137s Dimension: 2
137s Method : single 
137s Method : complete 
137s Method : average 
137s Method : mcquitty 
137s Method : ward.D 
137s Method : ward.D2 
137s Method : centroid 
137s Method : median 
137s Passed.
137s Random test 5 of 30 (uniform distribution of distances):
137s Number of sample points: 30
137s Dissimilarity range: [0,2.58814e-10]
137s Method : single 
137s Method : complete 
137s Method : average 
137s Method : mcquitty 
137s Method : ward.D 
137s Method : ward.D2 
137s Method : centroid 
137s Method : median 
137s Passed.
137s Random test 6 of 30 (Gaussian density):
137s Number of sample points: 721
137s Dimension: 18
137s Method : single 
137s Method : complete 
137s Method : average 
137s Method : mcquitty 
137s Method : ward.D 
137s Method : ward.D2 
137s Method : centroid 
137s Method : median 
137s Passed.
137s Random test 7 of 30 (uniform distribution of distances):
137s Number of sample points: 204
137s Dissimilarity range: [0,1.05452e-07]
137s Method : single 
137s Method : complete 
137s Method : average 
137s Method : mcquitty 
137s Method : ward.D 
137s Method : ward.D2 
137s Method : centroid 
137s Method : median 
137s Passed.
137s Random test 8 of 30 (Gaussian density):
137s Number of sample points: 648
137s Dimension: 7
137s Method : single 
137s Method : complete 
137s Method : average 
137s Method : mcquitty 
137s Method : ward.D 
137s Method : ward.D2 
137s Method : centroid 
137s Method : median 
137s Passed.
137s Random test 9 of 30 (uniform distribution of distances):
137s Number of sample points: 317
137s Dissimilarity range: [0,2.56636e-09]
137s Method : single 
137s Method : complete 
137s Method : average 
137s Method : mcquitty 
137s Method : ward.D 
137s Method : ward.D2 
137s Method : centroid 
137s Method : median 
137s Passed.
137s Random test 10 of 30 (Gaussian density):
137s Number of sample points: 562
137s Dimension: 16
137s Method : single 
137s Method : complete 
137s Method : average 
137s Method : mcquitty 
137s Method : ward.D 
137s Method : ward.D2 
137s Method : centroid 
137s Method : median 
137s Passed.
137s Random test 11 of 30 (uniform distribution of distances):
137s Number of sample points: 432
137s Dissimilarity range: [0,0.00300667]
137s Method : single 
137s Method : complete 
137s Method : average 
137s Method : mcquitty 
137s Method : ward.D 
137s Method : ward.D2 
137s Method : centroid 
137s Method : median 
137s Passed.
137s Random test 12 of 30 (Gaussian density):
137s Number of sample points: 610
137s Dimension: 13
137s Method : single 
137s Method : complete 
137s Method : average 
137s Method : mcquitty 
138s Method : ward.D 
138s Method : ward.D2 
138s Method : centroid 
138s Method : median 
138s Passed.
138s Random test 13 of 30 (uniform distribution of distances):
138s Number of sample points: 808
138s Dissimilarity range: [0,9.00526e+07]
138s Method : single 
138s Method : complete 
138s Method : average 
138s Method : mcquitty 
138s Method : ward.D 
138s Method : ward.D2 
138s Method : centroid 
138s Method : median 
138s Passed.
138s Random test 14 of 30 (Gaussian density):
138s Number of sample points: 164
138s Dimension: 8
138s Method : single 
138s Method : complete 
138s Method : average 
138s Method : mcquitty 
138s Method : ward.D 
138s Method : ward.D2 
138s Method : centroid 
138s Method : median 
138s Passed.
138s Random test 15 of 30 (uniform distribution of distances):
138s Number of sample points: 264
138s Dissimilarity range: [0,2.08004e-06]
138s Method : single 
138s Method : complete 
138s Method : average 
138s Method : mcquitty 
138s Method : ward.D 
138s Method : ward.D2 
138s Method : centroid 
138s Method : median 
138s Passed.
138s > for (i in (N+1:N)) {
138s +   cat(sprintf('Random test %d of %d (Gaussian density):\n',i,2*N))
138s +   test.vector()
138s +   test.vector.binary()
138s + }
138s Random test 16 of 30 (Gaussian density):
138s Number of sample points: 827
138s Dimension: 20
138s Method: single 
138s     Metric: euclidean 
138s     Metric: maximum 
138s     Metric: manhattan 
138s     Metric: canberra 
138s     Metric: minkowski 
138s     p: 7.10407
139s Method: ward 
139s Method: centroid 
140s Method: median 
140s Passed.
140s Uniform sampling for the 'binary' metric:
140s Number of sample points: 29
140s Dimension: 54
140s Method: single 
140s     Metric: binary 
140s Passed.
140s Random test 17 of 30 (Gaussian density):
140s Number of sample points: 391
140s Dimension: 17
140s Method: single 
140s     Metric: euclidean 
140s     Metric: maximum 
140s     Metric: manhattan 
140s     Metric: canberra 
140s     Metric: minkowski 
140s     p: 7.3192
140s Method: ward 
140s Method: centroid 
140s Method: median 
140s Passed.
140s Uniform sampling for the 'binary' metric:
140s Number of sample points: 162
140s Dimension: 300
140s Method: single 
140s     Metric: binary 
140s Passed.
140s Random test 18 of 30 (Gaussian density):
140s Number of sample points: 980
140s Dimension: 16
140s Method: single 
140s     Metric: euclidean 
140s     Metric: maximum 
140s     Metric: manhattan 
140s     Metric: canberra 
140s     Metric: minkowski 
140s     p: 7.94928
140s Method: ward 
140s Method: centroid 
140s Method: median 
140s Passed.
140s Uniform sampling for the 'binary' metric:
140s Number of sample points: 348
140s Dimension: 417
140s Method: single 
140s     Metric: binary 
141s Passed.
141s Random test 19 of 30 (Gaussian density):
141s Number of sample points: 259
141s Dimension: 4
141s Method: single 
141s     Metric: euclidean 
141s     Metric: maximum 
141s     Metric: manhattan 
141s     Metric: canberra 
141s     Metric: minkowski 
141s     p: 4.35403
141s Method: ward 
141s Method: centroid 
141s Method: median 
141s Passed.
141s Uniform sampling for the 'binary' metric:
141s Number of sample points: 143
141s Dimension: 228
141s Method: single 
141s     Metric: binary 
141s Passed.
141s Random test 20 of 30 (Gaussian density):
141s Number of sample points: 636
141s Dimension: 15
141s Method: single 
141s     Metric: euclidean 
141s     Metric: maximum 
141s     Metric: manhattan 
141s     Metric: canberra 
141s     Metric: minkowski 
141s     p: 1.96714
141s Method: ward 
142s Method: centroid 
142s Method: median 
142s Passed.
142s Uniform sampling for the 'binary' metric:
142s Number of sample points: 358
142s Dimension: 504
142s Method: single 
142s     Metric: binary 
142s Passed.
142s Random test 21 of 30 (Gaussian density):
142s Number of sample points: 102
142s Dimension: 16
142s Method: single 
142s     Metric: euclidean 
142s     Metric: maximum 
142s     Metric: manhattan 
142s     Metric: canberra 
142s     Metric: minkowski 
142s     p: 3.27809
142s Method: ward 
142s Method: centroid 
142s Method: median 
142s Passed.
142s Uniform sampling for the 'binary' metric:
142s Number of sample points: 18
142s Dimension: 27
142s Method: single 
142s     Metric: binary 
142s Passed.
142s Random test 22 of 30 (Gaussian density):
142s Number of sample points: 694
142s Dimension: 5
142s Method: single 
142s     Metric: euclidean 
142s     Metric: maximum 
142s     Metric: manhattan 
142s     Metric: canberra 
142s     Metric: minkowski 
142s     p: 3.50758
142s Method: ward 
142s Method: centroid 
142s Method: median 
142s Passed.
142s Uniform sampling for the 'binary' metric:
142s Number of sample points: 188
142s Dimension: 250
142s Method: single 
142s     Metric: binary 
142s Passed.
142s Random test 23 of 30 (Gaussian density):
142s Number of sample points: 782
142s Dimension: 13
142s Method: single 
142s     Metric: euclidean 
142s     Metric: maximum 
143s     Metric: manhattan 
143s     Metric: canberra 
143s     Metric: minkowski 
143s     p: 2.97698
143s Method: ward 
143s Method: centroid 
143s Method: median 
143s Passed.
143s Uniform sampling for the 'binary' metric:
143s Number of sample points: 281
143s Dimension: 383
143s Method: single 
143s     Metric: binary 
143s Passed.
143s Random test 24 of 30 (Gaussian density):
143s Number of sample points: 702
143s Dimension: 8
143s Method: single 
143s     Metric: euclidean 
143s     Metric: maximum 
143s     Metric: manhattan 
143s     Metric: canberra 
143s     Metric: minkowski 
143s     p: 6.37216
144s Method: ward 
144s Method: centroid 
144s Method: median 
144s Passed.
144s Uniform sampling for the 'binary' metric:
144s Number of sample points: 267
144s Dimension: 444
144s Method: single 
144s     Metric: binary 
144s Passed.
144s Random test 25 of 30 (Gaussian density):
144s Number of sample points: 15
144s Dimension: 9
144s Method: single 
144s     Metric: euclidean 
144s     Metric: maximum 
144s     Metric: manhattan 
144s     Metric: canberra 
144s     Metric: minkowski 
144s     p: 1.93963
144s Method: ward 
144s Method: centroid 
144s Method: median 
144s Passed.
144s Uniform sampling for the 'binary' metric:
144s Number of sample points: 375
144s Dimension: 627
144s Method: single 
144s     Metric: binary 
145s Passed.
145s Random test 26 of 30 (Gaussian density):
145s Number of sample points: 51
145s Dimension: 3
145s Method: single 
145s     Metric: euclidean 
145s     Metric: maximum 
145s     Metric: manhattan 
145s     Metric: canberra 
145s     Metric: minkowski 
145s     p: 2.67754
145s Method: ward 
145s Method: centroid 
145s Method: median 
145s Passed.
145s Uniform sampling for the 'binary' metric:
145s Number of sample points: 102
145s Dimension: 147
145s Method: single 
145s     Metric: binary 
145s Passed.
145s Random test 27 of 30 (Gaussian density):
145s Number of sample points: 933
145s Dimension: 3
145s Method: single 
145s     Metric: euclidean 
145s     Metric: maximum 
145s     Metric: manhattan 
145s     Metric: canberra 
145s     Metric: minkowski 
145s     p: 8.02559
145s Method: ward 
145s Method: centroid 
145s Method: median 
145s Passed.
145s Uniform sampling for the 'binary' metric:
145s Number of sample points: 172
145s Dimension: 251
145s Method: single 
145s     Metric: binary 
145s Passed.
145s Random test 28 of 30 (Gaussian density):
145s Number of sample points: 257
145s Dimension: 7
145s Method: single 
145s     Metric: euclidean 
145s     Metric: maximum 
145s     Metric: manhattan 
145s     Metric: canberra 
145s     Metric: minkowski 
145s     p: 6.45081
145s Method: ward 
145s Method: centroid 
145s Method: median 
145s Passed.
145s Uniform sampling for the 'binary' metric:
145s Number of sample points: 235
145s Dimension: 242
145s Method: single 
145s     Metric: binary 
145s Passed.
145s Random test 29 of 30 (Gaussian density):
145s Number of sample points: 278
145s Dimension: 4
145s Method: single 
145s     Metric: euclidean 
145s     Metric: maximum 
145s     Metric: manhattan 
145s     Metric: canberra 
145s     Metric: minkowski 
145s     p: 6.40431
145s Method: ward 
145s Method: centroid 
145s Method: median 
145s Passed.
145s Uniform sampling for the 'binary' metric:
145s Number of sample points: 110
145s Dimension: 114
145s Method: single 
145s     Metric: binary 
145s Passed.
145s Random test 30 of 30 (Gaussian density):
145s Number of sample points: 702
145s Dimension: 11
145s Method: single 
145s     Metric: euclidean 
145s     Metric: maximum 
146s     Metric: manhattan 
146s     Metric: canberra 
146s     Metric: minkowski 
146s     p: 8.68013
146s Method: ward 
146s Method: centroid 
146s Method: median 
146s Passed.
146s Uniform sampling for the 'binary' metric:
146s Number of sample points: 160
146s Dimension: 302
146s Method: single 
146s     Metric: binary 
146s Passed.
146s > 
146s > cat('Done.\n')
146s Done.
146s > 
146s autopkgtest [16:07:45]: test run-unit-test: -----------------------]
147s autopkgtest [16:07:46]: test run-unit-test:  - - - - - - - - - - results - - - - - - - - - -
147s run-unit-test        PASS
147s autopkgtest [16:07:46]: test autodep8-python3: preparing testbed
274s autopkgtest [16:09:53]: testbed dpkg architecture: s390x
274s autopkgtest [16:09:53]: testbed apt version: 2.9.8
274s autopkgtest [16:09:53]: @@@@@@@@@@@@@@@@@@@@ test bed setup
275s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB]
275s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B]
275s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [950 kB]
276s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [104 kB]
276s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [17.2 kB]
276s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x Packages [110 kB]
276s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x Packages [636 kB]
276s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x Packages [17.8 kB]
276s Fetched 1916 kB in 1s (2290 kB/s)
276s Reading package lists...
278s Reading package lists...
278s Building dependency tree...
278s Reading state information...
278s Calculating upgrade...
278s The following NEW packages will be installed:
278s   python3.13-gdbm
278s The following packages will be upgraded:
278s   libgnutls30t64 libgpgme11t64 libjson-glib-1.0-0 libjson-glib-1.0-common
278s   libpython3-stdlib libutempter0 python3 python3-gdbm python3-minimal
278s 9 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
278s Need to get 1285 kB of archives.
278s After this operation, 103 kB of additional disk space will be used.
278s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x python3-minimal s390x 3.12.7-1 [27.4 kB]
278s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x python3 s390x 3.12.7-1 [24.0 kB]
278s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libpython3-stdlib s390x 3.12.7-1 [10.0 kB]
278s Get:4 http://ftpmaster.internal/ubuntu plucky/main s390x libgnutls30t64 s390x 3.8.8-2ubuntu1 [950 kB]
279s Get:5 http://ftpmaster.internal/ubuntu plucky/main s390x python3.13-gdbm s390x 3.13.0-2 [31.0 kB]
279s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x python3-gdbm s390x 3.12.7-1 [8642 B]
279s Get:7 http://ftpmaster.internal/ubuntu plucky/main s390x libgpgme11t64 s390x 1.23.2-5ubuntu4 [151 kB]
279s Get:8 http://ftpmaster.internal/ubuntu plucky/main s390x libjson-glib-1.0-common all 1.10.0+ds-3 [5586 B]
279s Get:9 http://ftpmaster.internal/ubuntu plucky/main s390x libjson-glib-1.0-0 s390x 1.10.0+ds-3 [67.5 kB]
279s Get:10 http://ftpmaster.internal/ubuntu plucky/main s390x libutempter0 s390x 1.2.1-4 [9708 B]
279s Fetched 1285 kB in 1s (1917 kB/s)
279s (Reading database ... 
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279s Preparing to unpack .../python3-minimal_3.12.7-1_s390x.deb ...
279s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ...
279s Setting up python3-minimal (3.12.7-1) ...
279s (Reading database ... 
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279s Preparing to unpack .../python3_3.12.7-1_s390x.deb ...
279s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ...
279s Preparing to unpack .../libpython3-stdlib_3.12.7-1_s390x.deb ...
279s Unpacking libpython3-stdlib:s390x (3.12.7-1) over (3.12.6-0ubuntu1) ...
279s Preparing to unpack .../libgnutls30t64_3.8.8-2ubuntu1_s390x.deb ...
279s Unpacking libgnutls30t64:s390x (3.8.8-2ubuntu1) over (3.8.6-2ubuntu1) ...
279s Setting up libgnutls30t64:s390x (3.8.8-2ubuntu1) ...
279s Selecting previously unselected package python3.13-gdbm.
279s (Reading database ... 
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279s Preparing to unpack .../0-python3.13-gdbm_3.13.0-2_s390x.deb ...
279s Unpacking python3.13-gdbm (3.13.0-2) ...
279s Preparing to unpack .../1-python3-gdbm_3.12.7-1_s390x.deb ...
279s Unpacking python3-gdbm:s390x (3.12.7-1) over (3.12.6-1ubuntu1) ...
279s Preparing to unpack .../2-libgpgme11t64_1.23.2-5ubuntu4_s390x.deb ...
279s Unpacking libgpgme11t64:s390x (1.23.2-5ubuntu4) over (1.18.0-4.1ubuntu4) ...
279s Preparing to unpack .../3-libjson-glib-1.0-common_1.10.0+ds-3_all.deb ...
279s Unpacking libjson-glib-1.0-common (1.10.0+ds-3) over (1.10.0+ds-2) ...
279s Preparing to unpack .../4-libjson-glib-1.0-0_1.10.0+ds-3_s390x.deb ...
279s Unpacking libjson-glib-1.0-0:s390x (1.10.0+ds-3) over (1.10.0+ds-2) ...
279s Preparing to unpack .../5-libutempter0_1.2.1-4_s390x.deb ...
279s Unpacking libutempter0:s390x (1.2.1-4) over (1.2.1-3build1) ...
279s Setting up libutempter0:s390x (1.2.1-4) ...
279s Setting up libjson-glib-1.0-common (1.10.0+ds-3) ...
279s Setting up libgpgme11t64:s390x (1.23.2-5ubuntu4) ...
279s Setting up python3.13-gdbm (3.13.0-2) ...
279s Setting up libpython3-stdlib:s390x (3.12.7-1) ...
279s Setting up python3 (3.12.7-1) ...
279s Setting up libjson-glib-1.0-0:s390x (1.10.0+ds-3) ...
279s Setting up python3-gdbm:s390x (3.12.7-1) ...
279s Processing triggers for man-db (2.12.1-3) ...
280s Processing triggers for libc-bin (2.40-1ubuntu3) ...
280s Reading package lists...
280s Building dependency tree...
280s Reading state information...
280s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
281s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease
281s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease
281s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease
281s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease
281s Reading package lists...
281s Reading package lists...
282s Building dependency tree...
282s Reading state information...
282s Calculating upgrade...
282s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
282s Reading package lists...
282s Building dependency tree...
282s Reading state information...
282s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
286s Reading package lists...
286s Building dependency tree...
286s Reading state information...
286s Starting pkgProblemResolver with broken count: 0
286s Starting 2 pkgProblemResolver with broken count: 0
286s Done
286s The following additional packages will be installed:
286s   libblas3 libgfortran5 liblapack3 libpython3.13-minimal libpython3.13-stdlib
286s   python3-all python3-fastcluster python3-numpy python3.13 python3.13-minimal
286s Suggested packages:
286s   gcc gfortran python-numpy-doc python3-dev python3-pytest python3.13-venv
286s   python3.13-doc binfmt-support
286s Recommended packages:
286s   python3-scipy
286s The following NEW packages will be installed:
286s   autopkgtest-satdep libblas3 libgfortran5 liblapack3 libpython3.13-minimal
286s   libpython3.13-stdlib python3-all python3-fastcluster python3-numpy
286s   python3.13 python3.13-minimal
286s 0 upgraded, 11 newly installed, 0 to remove and 0 not upgraded.
286s Need to get 13.8 MB/13.8 MB of archives.
286s After this operation, 54.7 MB of additional disk space will be used.
286s Get:1 /tmp/autopkgtest.utMhOa/2-autopkgtest-satdep.deb autopkgtest-satdep s390x 0 [720 B]
286s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x libpython3.13-minimal s390x 3.13.0-2 [877 kB]
287s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x python3.13-minimal s390x 3.13.0-2 [2172 kB]
287s Get:4 http://ftpmaster.internal/ubuntu plucky/main s390x libblas3 s390x 3.12.0-3build2 [238 kB]
287s Get:5 http://ftpmaster.internal/ubuntu plucky/main s390x libgfortran5 s390x 14.2.0-8ubuntu1 [587 kB]
287s Get:6 http://ftpmaster.internal/ubuntu plucky/main s390x liblapack3 s390x 3.12.0-3build2 [2953 kB]
287s Get:7 http://ftpmaster.internal/ubuntu plucky/main s390x libpython3.13-stdlib s390x 3.13.0-2 [2086 kB]
287s Get:8 http://ftpmaster.internal/ubuntu plucky/main s390x python3.13 s390x 3.13.0-2 [719 kB]
287s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x python3-all s390x 3.12.7-1 [890 B]
287s Get:10 http://ftpmaster.internal/ubuntu plucky/main s390x python3-numpy s390x 1:1.26.4+ds-11build1 [4113 kB]
287s Get:11 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-fastcluster s390x 1.2.6-1build1 [49.7 kB]
287s Fetched 13.8 MB in 1s (11.5 MB/s)
287s Selecting previously unselected package libpython3.13-minimal:s390x.
287s (Reading database ... 
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287s Preparing to unpack .../00-libpython3.13-minimal_3.13.0-2_s390x.deb ...
287s Unpacking libpython3.13-minimal:s390x (3.13.0-2) ...
287s Selecting previously unselected package python3.13-minimal.
287s Preparing to unpack .../01-python3.13-minimal_3.13.0-2_s390x.deb ...
287s Unpacking python3.13-minimal (3.13.0-2) ...
287s Selecting previously unselected package libblas3:s390x.
287s Preparing to unpack .../02-libblas3_3.12.0-3build2_s390x.deb ...
287s Unpacking libblas3:s390x (3.12.0-3build2) ...
287s Selecting previously unselected package libgfortran5:s390x.
288s Preparing to unpack .../03-libgfortran5_14.2.0-8ubuntu1_s390x.deb ...
288s Unpacking libgfortran5:s390x (14.2.0-8ubuntu1) ...
288s Selecting previously unselected package liblapack3:s390x.
288s Preparing to unpack .../04-liblapack3_3.12.0-3build2_s390x.deb ...
288s Unpacking liblapack3:s390x (3.12.0-3build2) ...
288s Selecting previously unselected package libpython3.13-stdlib:s390x.
288s Preparing to unpack .../05-libpython3.13-stdlib_3.13.0-2_s390x.deb ...
288s Unpacking libpython3.13-stdlib:s390x (3.13.0-2) ...
288s Selecting previously unselected package python3.13.
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288s Unpacking python3.13 (3.13.0-2) ...
288s Selecting previously unselected package python3-all.
288s Preparing to unpack .../07-python3-all_3.12.7-1_s390x.deb ...
288s Unpacking python3-all (3.12.7-1) ...
288s Selecting previously unselected package python3-numpy.
288s Preparing to unpack .../08-python3-numpy_1%3a1.26.4+ds-11build1_s390x.deb ...
288s Unpacking python3-numpy (1:1.26.4+ds-11build1) ...
288s Selecting previously unselected package python3-fastcluster.
288s Preparing to unpack .../09-python3-fastcluster_1.2.6-1build1_s390x.deb ...
288s Unpacking python3-fastcluster (1.2.6-1build1) ...
288s Selecting previously unselected package autopkgtest-satdep.
288s Preparing to unpack .../10-2-autopkgtest-satdep.deb ...
288s Unpacking autopkgtest-satdep (0) ...
288s Setting up libpython3.13-minimal:s390x (3.13.0-2) ...
288s Setting up libblas3:s390x (3.12.0-3build2) ...
288s 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
288s Setting up libgfortran5:s390x (14.2.0-8ubuntu1) ...
288s Setting up python3.13-minimal (3.13.0-2) ...
289s Setting up libpython3.13-stdlib:s390x (3.13.0-2) ...
289s Setting up liblapack3:s390x (3.12.0-3build2) ...
289s 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
289s Setting up python3.13 (3.13.0-2) ...
290s Setting up python3-all (3.12.7-1) ...
290s Setting up python3-numpy (1:1.26.4+ds-11build1) ...
293s Setting up python3-fastcluster (1.2.6-1build1) ...
293s Setting up autopkgtest-satdep (0) ...
293s Processing triggers for systemd (256.5-2ubuntu4) ...
293s Processing triggers for man-db (2.12.1-3) ...
294s Processing triggers for libc-bin (2.40-1ubuntu3) ...
295s (Reading database ... 57165 files and directories currently installed.)
295s Removing autopkgtest-satdep (0) ...
297s autopkgtest [16:10:16]: test autodep8-python3: set -e ; for py in $(py3versions -r 2>/dev/null) ; do cd "$AUTOPKGTEST_TMP" ; echo "Testing with $py:" ; $py -c "import fastcluster; print(fastcluster)" ; done
297s autopkgtest [16:10:16]: test autodep8-python3: [-----------------------
297s Testing with python3.13:
297s Traceback (most recent call last):
297s   File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in <module>
297s     from . import multiarray
297s   File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in <module>
297s     from . import overrides
297s   File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in <module>
297s     from numpy.core._multiarray_umath import (
297s         add_docstring,  _get_implementing_args, _ArrayFunctionDispatcher)
297s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath'
297s 
297s During handling of the above exception, another exception occurred:
297s 
297s Traceback (most recent call last):
297s   File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in <module>
297s     from numpy.__config__ import show as show_config
297s   File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in <module>
297s     from numpy.core._multiarray_umath import (
297s     ...<3 lines>...
297s     )
297s   File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in <module>
297s     raise ImportError(msg)
297s ImportError: 
297s 
297s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE!
297s 
297s Importing the numpy C-extensions failed. This error can happen for
297s many reasons, often due to issues with your setup or how NumPy was
297s installed.
297s 
297s We have compiled some common reasons and troubleshooting tips at:
297s 
297s     https://numpy.org/devdocs/user/troubleshooting-importerror.html
297s 
297s Please note and check the following:
297s 
297s   * The Python version is: Python3.13 from "/usr/bin/python3.13"
297s   * The NumPy version is: "1.26.4"
297s 
297s and make sure that they are the versions you expect.
297s Please carefully study the documentation linked above for further help.
297s 
297s Original error was: No module named 'numpy.core._multiarray_umath'
297s 
297s 
297s The above exception was the direct cause of the following exception:
297s 
297s Traceback (most recent call last):
297s   File "<string>", line 1, in <module>
297s     import fastcluster; print(fastcluster)
297s     ^^^^^^^^^^^^^^^^^^
297s   File "/usr/lib/python3/dist-packages/fastcluster.py", line 26, in <module>
297s     from numpy import double, empty, array, ndarray, var, cov, dot, expand_dims, \
297s         ceil, sqrt
297s   File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in <module>
297s     raise ImportError(msg) from e
297s ImportError: Error importing numpy: you should not try to import numpy from
297s         its source directory; please exit the numpy source tree, and relaunch
297s         your python interpreter from there.
297s autopkgtest [16:10:16]: test autodep8-python3: -----------------------]
298s autopkgtest [16:10:17]: test autodep8-python3:  - - - - - - - - - - results - - - - - - - - - -
298s autodep8-python3     FAIL non-zero exit status 1
298s autopkgtest [16:10:17]: @@@@@@@@@@@@@@@@@@@@ summary
298s run-unit-test        PASS
298s autodep8-python3     FAIL non-zero exit status 1
310s nova [W] Using flock in prodstack6-s390x
310s flock: timeout while waiting to get lock
310s Creating nova instance adt-plucky-s390x-r-cran-fastcluster-20241113-160519-juju-7f2275-prod-proposed-migration-environment-15-736b3ea0-8aed-4a5d-9bd2-7e7914b96258 from image adt/ubuntu-plucky-s390x-server-20241113.img (UUID e740277e-1f72-40ae-bfbe-46030537c71c)...
310s nova [W] Using flock in prodstack6-s390x
310s Creating nova instance adt-plucky-s390x-r-cran-fastcluster-20241113-160519-juju-7f2275-prod-proposed-migration-environment-15-736b3ea0-8aed-4a5d-9bd2-7e7914b96258 from image adt/ubuntu-plucky-s390x-server-20241113.img (UUID e740277e-1f72-40ae-bfbe-46030537c71c)...