0s autopkgtest [00:52:11]: starting date and time: 2024-11-14 00:52:11+0000
  0s autopkgtest [00:52:11]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky
  0s autopkgtest [00:52:11]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.xhxrsdr6/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-ppc64el --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-ppc64el-29.secgroup --name adt-plucky-ppc64el-r-cran-fastcluster-20241114-005211-juju-7f2275-prod-proposed-migration-environment-15-2550a304-55f2-40b0-8ed8-f2fbb9083607 --image adt/ubuntu-plucky-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration-ppc64el -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/
 85s autopkgtest [00:53:36]: testbed dpkg architecture: ppc64el
 85s autopkgtest [00:53:36]: testbed apt version: 2.9.8
 85s autopkgtest [00:53:36]: @@@@@@@@@@@@@@@@@@@@ test bed setup
 86s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB]
 86s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B]
 86s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [17.2 kB]
 86s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [971 kB]
 86s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [101 kB]
 86s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el Packages [110 kB]
 86s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe ppc64el Packages [692 kB]
 86s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse ppc64el Packages [20.8 kB]
 87s Fetched 1993 kB in 1s (2174 kB/s)
 87s Reading package lists...
 89s Reading package lists...
 89s Building dependency tree...
 89s Reading state information...
 89s Calculating upgrade...
 90s The following NEW packages will be installed:
 90s   python3.13-gdbm
 90s The following packages will be upgraded:
 90s   bpfcc-tools bpftrace libbpfcc libgnutls30t64 libjson-glib-1.0-0
 90s   libjson-glib-1.0-common libnewt0.52 libpython3-stdlib libutempter0 python3
 90s   python3-bpfcc python3-gdbm python3-minimal python3-newt whiptail
 90s 15 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
 90s Need to get 4700 kB of archives.
 90s After this operation, 215 kB of additional disk space will be used.
 90s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el python3-minimal ppc64el 3.12.7-1 [27.4 kB]
 90s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el python3 ppc64el 3.12.7-1 [24.0 kB]
 90s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el libpython3-stdlib ppc64el 3.12.7-1 [10.0 kB]
 90s Get:4 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgnutls30t64 ppc64el 3.8.8-2ubuntu1 [1072 kB]
 90s Get:5 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-newt ppc64el 0.52.24-2ubuntu4 [21.8 kB]
 90s Get:6 http://ftpmaster.internal/ubuntu plucky/main ppc64el libnewt0.52 ppc64el 0.52.24-2ubuntu4 [62.1 kB]
 90s Get:7 http://ftpmaster.internal/ubuntu plucky/main ppc64el whiptail ppc64el 0.52.24-2ubuntu4 [19.5 kB]
 90s Get:8 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3.13-gdbm ppc64el 3.13.0-2 [31.5 kB]
 90s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el python3-gdbm ppc64el 3.12.7-1 [8640 B]
 90s Get:10 http://ftpmaster.internal/ubuntu plucky/main ppc64el libbpfcc ppc64el 0.30.0+ds-1ubuntu5 [696 kB]
 90s Get:11 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-bpfcc all 0.30.0+ds-1ubuntu5 [40.4 kB]
 90s Get:12 http://ftpmaster.internal/ubuntu plucky/main ppc64el bpfcc-tools all 0.30.0+ds-1ubuntu5 [697 kB]
 90s Get:13 http://ftpmaster.internal/ubuntu plucky/main ppc64el bpftrace ppc64el 0.21.2-2ubuntu2 [1898 kB]
 90s Get:14 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjson-glib-1.0-common all 1.10.0+ds-3 [5586 B]
 90s Get:15 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjson-glib-1.0-0 ppc64el 1.10.0+ds-3 [76.0 kB]
 90s Get:16 http://ftpmaster.internal/ubuntu plucky/main ppc64el libutempter0 ppc64el 1.2.1-4 [9850 B]
 91s Fetched 4700 kB in 1s (6170 kB/s)
 91s (Reading database ... 
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(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 73767 files and directories currently installed.)
 91s Preparing to unpack .../python3-minimal_3.12.7-1_ppc64el.deb ...
 91s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ...
 91s Setting up python3-minimal (3.12.7-1) ...
 91s (Reading database ... 
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(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 73767 files and directories currently installed.)
 91s Preparing to unpack .../python3_3.12.7-1_ppc64el.deb ...
 91s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ...
 91s Preparing to unpack .../libpython3-stdlib_3.12.7-1_ppc64el.deb ...
 91s Unpacking libpython3-stdlib:ppc64el (3.12.7-1) over (3.12.6-0ubuntu1) ...
 91s Preparing to unpack .../libgnutls30t64_3.8.8-2ubuntu1_ppc64el.deb ...
 91s Unpacking libgnutls30t64:ppc64el (3.8.8-2ubuntu1) over (3.8.6-2ubuntu1) ...
 91s Setting up libgnutls30t64:ppc64el (3.8.8-2ubuntu1) ...
 91s (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 ... 73767 files and directories currently installed.)
 91s Preparing to unpack .../00-python3-newt_0.52.24-2ubuntu4_ppc64el.deb ...
 91s Unpacking python3-newt:ppc64el (0.52.24-2ubuntu4) over (0.52.24-2ubuntu3) ...
 91s Preparing to unpack .../01-libnewt0.52_0.52.24-2ubuntu4_ppc64el.deb ...
 91s Unpacking libnewt0.52:ppc64el (0.52.24-2ubuntu4) over (0.52.24-2ubuntu3) ...
 91s Preparing to unpack .../02-whiptail_0.52.24-2ubuntu4_ppc64el.deb ...
 91s Unpacking whiptail (0.52.24-2ubuntu4) over (0.52.24-2ubuntu3) ...
 91s Selecting previously unselected package python3.13-gdbm.
 91s Preparing to unpack .../03-python3.13-gdbm_3.13.0-2_ppc64el.deb ...
 91s Unpacking python3.13-gdbm (3.13.0-2) ...
 91s Preparing to unpack .../04-python3-gdbm_3.12.7-1_ppc64el.deb ...
 91s Unpacking python3-gdbm:ppc64el (3.12.7-1) over (3.12.6-1ubuntu1) ...
 91s Preparing to unpack .../05-libbpfcc_0.30.0+ds-1ubuntu5_ppc64el.deb ...
 91s Unpacking libbpfcc:ppc64el (0.30.0+ds-1ubuntu5) over (0.30.0+ds-1ubuntu4) ...
 91s Preparing to unpack .../06-python3-bpfcc_0.30.0+ds-1ubuntu5_all.deb ...
 91s Unpacking python3-bpfcc (0.30.0+ds-1ubuntu5) over (0.30.0+ds-1ubuntu4) ...
 91s Preparing to unpack .../07-bpfcc-tools_0.30.0+ds-1ubuntu5_all.deb ...
 91s Unpacking bpfcc-tools (0.30.0+ds-1ubuntu5) over (0.30.0+ds-1ubuntu4) ...
 92s Preparing to unpack .../08-bpftrace_0.21.2-2ubuntu2_ppc64el.deb ...
 92s Unpacking bpftrace (0.21.2-2ubuntu2) over (0.21.2-2) ...
 92s Preparing to unpack .../09-libjson-glib-1.0-common_1.10.0+ds-3_all.deb ...
 92s Unpacking libjson-glib-1.0-common (1.10.0+ds-3) over (1.10.0+ds-2) ...
 92s Preparing to unpack .../10-libjson-glib-1.0-0_1.10.0+ds-3_ppc64el.deb ...
 92s Unpacking libjson-glib-1.0-0:ppc64el (1.10.0+ds-3) over (1.10.0+ds-2) ...
 92s Preparing to unpack .../11-libutempter0_1.2.1-4_ppc64el.deb ...
 92s Unpacking libutempter0:ppc64el (1.2.1-4) over (1.2.1-3build1) ...
 92s Setting up libnewt0.52:ppc64el (0.52.24-2ubuntu4) ...
 92s Setting up libutempter0:ppc64el (1.2.1-4) ...
 92s Setting up whiptail (0.52.24-2ubuntu4) ...
 92s Setting up libjson-glib-1.0-common (1.10.0+ds-3) ...
 92s Setting up libbpfcc:ppc64el (0.30.0+ds-1ubuntu5) ...
 92s Setting up python3.13-gdbm (3.13.0-2) ...
 92s Setting up libpython3-stdlib:ppc64el (3.12.7-1) ...
 92s Setting up bpftrace (0.21.2-2ubuntu2) ...
 92s Setting up python3 (3.12.7-1) ...
 92s Setting up python3-newt:ppc64el (0.52.24-2ubuntu4) ...
 92s Setting up libjson-glib-1.0-0:ppc64el (1.10.0+ds-3) ...
 92s Setting up python3-bpfcc (0.30.0+ds-1ubuntu5) ...
 92s Setting up python3-gdbm:ppc64el (3.12.7-1) ...
 92s Setting up bpfcc-tools (0.30.0+ds-1ubuntu5) ...
 92s Processing triggers for man-db (2.12.1-3) ...
 93s Processing triggers for libc-bin (2.40-1ubuntu3) ...
 93s Reading package lists...
 94s Building dependency tree...
 94s Reading state information...
 94s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 94s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease
 94s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease
 94s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease
 94s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease
 95s Reading package lists...
 95s Reading package lists...
 95s Building dependency tree...
 95s Reading state information...
 96s Calculating upgrade...
 96s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 96s Reading package lists...
 96s Building dependency tree...
 96s Reading state information...
 96s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 99s autopkgtest [00:53:50]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP Mon Sep 16 13:49:23 UTC 2024
 99s autopkgtest [00:53:50]: @@@@@@@@@@@@@@@@@@@@ apt-source r-cran-fastcluster
101s Get:1 http://ftpmaster.internal/ubuntu plucky/universe r-cran-fastcluster 1.2.6-1build1 (dsc) [2272 B]
101s Get:2 http://ftpmaster.internal/ubuntu plucky/universe r-cran-fastcluster 1.2.6-1build1 (tar) [208 kB]
101s Get:3 http://ftpmaster.internal/ubuntu plucky/universe r-cran-fastcluster 1.2.6-1build1 (diff) [4828 B]
101s gpgv: Signature made Wed Apr 10 18:03:18 2024 UTC
101s gpgv:                using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2
101s gpgv: Can't check signature: No public key
101s dpkg-source: warning: cannot verify inline signature for ./r-cran-fastcluster_1.2.6-1build1.dsc: no acceptable signature found
101s autopkgtest [00:53:52]: testing package r-cran-fastcluster version 1.2.6-1build1
101s autopkgtest [00:53:52]: build not needed
102s autopkgtest [00:53:53]: test run-unit-test: preparing testbed
103s Reading package lists...
104s Building dependency tree...
104s Reading state information...
104s Starting pkgProblemResolver with broken count: 0
104s Starting 2 pkgProblemResolver with broken count: 0
104s Done
104s The following additional packages will be installed:
104s   fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono libblas3
104s   libcairo2 libdatrie1 libdeflate0 libfontconfig1 libgfortran5 libgomp1
104s   libgraphite2-3 libharfbuzz0b libice6 libjbig0 libjpeg-turbo8 libjpeg8
104s   liblapack3 liblerc4 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0
104s   libpaper-utils libpaper1 libpixman-1-0 libsharpyuv0 libsm6 libtcl8.6
104s   libthai-data libthai0 libtiff6 libtk8.6 libwebp7 libxcb-render0 libxcb-shm0
104s   libxft2 libxrender1 libxss1 libxt6t64 python3-fastcluster python3-numpy
104s   r-base-core r-cran-fastcluster unzip x11-common xdg-utils zip
104s Suggested packages:
104s   tcl8.6 tk8.6 gcc gfortran python-numpy-doc python3-dev python3-pytest
104s   elpa-ess r-doc-info | r-doc-pdf r-mathlib r-base-html
104s Recommended packages:
104s   python3-scipy r-recommended r-base-dev r-doc-html libfile-mimeinfo-perl
104s   libnet-dbus-perl libx11-protocol-perl x11-utils x11-xserver-utils
104s The following NEW packages will be installed:
104s   autopkgtest-satdep fontconfig fontconfig-config fonts-dejavu-core
104s   fonts-dejavu-mono libblas3 libcairo2 libdatrie1 libdeflate0 libfontconfig1
104s   libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libice6 libjbig0
104s   libjpeg-turbo8 libjpeg8 liblapack3 liblerc4 libpango-1.0-0
104s   libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpixman-1-0
104s   libsharpyuv0 libsm6 libtcl8.6 libthai-data libthai0 libtiff6 libtk8.6
104s   libwebp7 libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxss1 libxt6t64
104s   python3-fastcluster python3-numpy r-base-core r-cran-fastcluster unzip
104s   x11-common xdg-utils zip
104s 0 upgraded, 48 newly installed, 0 to remove and 0 not upgraded.
104s Need to get 45.7 MB/45.7 MB of archives.
104s After this operation, 113 MB of additional disk space will be used.
104s Get:1 /tmp/autopkgtest.5uHIBP/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [724 B]
104s Get:2 http://ftpmaster.internal/ubuntu plucky/main ppc64el fonts-dejavu-mono all 2.37-8 [502 kB]
105s Get:3 http://ftpmaster.internal/ubuntu plucky/main ppc64el fonts-dejavu-core all 2.37-8 [835 kB]
105s Get:4 http://ftpmaster.internal/ubuntu plucky/main ppc64el fontconfig-config ppc64el 2.15.0-1.1ubuntu2 [37.4 kB]
105s Get:5 http://ftpmaster.internal/ubuntu plucky/main ppc64el libfontconfig1 ppc64el 2.15.0-1.1ubuntu2 [190 kB]
105s Get:6 http://ftpmaster.internal/ubuntu plucky/main ppc64el fontconfig ppc64el 2.15.0-1.1ubuntu2 [192 kB]
105s Get:7 http://ftpmaster.internal/ubuntu plucky/main ppc64el libblas3 ppc64el 3.12.0-3build2 [222 kB]
105s Get:8 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpixman-1-0 ppc64el 0.44.0-3 [334 kB]
105s Get:9 http://ftpmaster.internal/ubuntu plucky/main ppc64el libxcb-render0 ppc64el 1.17.0-2 [17.2 kB]
105s Get:10 http://ftpmaster.internal/ubuntu plucky/main ppc64el libxcb-shm0 ppc64el 1.17.0-2 [5980 B]
105s Get:11 http://ftpmaster.internal/ubuntu plucky/main ppc64el libxrender1 ppc64el 1:0.9.10-1.1build1 [23.1 kB]
105s Get:12 http://ftpmaster.internal/ubuntu plucky/main ppc64el libcairo2 ppc64el 1.18.2-2 [747 kB]
105s Get:13 http://ftpmaster.internal/ubuntu plucky/main ppc64el libdatrie1 ppc64el 0.2.13-3build1 [22.7 kB]
105s Get:14 http://ftpmaster.internal/ubuntu plucky/main ppc64el libdeflate0 ppc64el 1.22-1 [63.3 kB]
105s Get:15 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgfortran5 ppc64el 14.2.0-8ubuntu1 [571 kB]
105s Get:16 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgomp1 ppc64el 14.2.0-8ubuntu1 [161 kB]
105s Get:17 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgraphite2-3 ppc64el 1.3.14-2ubuntu1 [84.6 kB]
105s Get:18 http://ftpmaster.internal/ubuntu plucky/main ppc64el libharfbuzz0b ppc64el 10.0.1-1 [596 kB]
105s Get:19 http://ftpmaster.internal/ubuntu plucky/main ppc64el x11-common all 1:7.7+23ubuntu3 [21.7 kB]
105s Get:20 http://ftpmaster.internal/ubuntu plucky/main ppc64el libice6 ppc64el 2:1.1.1-1 [49.9 kB]
105s Get:21 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjpeg-turbo8 ppc64el 2.1.5-2ubuntu2 [219 kB]
105s Get:22 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjpeg8 ppc64el 8c-2ubuntu11 [2148 B]
105s Get:23 http://ftpmaster.internal/ubuntu plucky/main ppc64el liblapack3 ppc64el 3.12.0-3build2 [2806 kB]
105s Get:24 http://ftpmaster.internal/ubuntu plucky/main ppc64el liblerc4 ppc64el 4.0.0+ds-4ubuntu2 [270 kB]
105s Get:25 http://ftpmaster.internal/ubuntu plucky/main ppc64el libthai-data all 0.1.29-2build1 [158 kB]
105s Get:26 http://ftpmaster.internal/ubuntu plucky/main ppc64el libthai0 ppc64el 0.1.29-2build1 [21.8 kB]
105s Get:27 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpango-1.0-0 ppc64el 1.54.0+ds-3 [272 kB]
105s Get:28 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpangoft2-1.0-0 ppc64el 1.54.0+ds-3 [57.5 kB]
105s Get:29 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpangocairo-1.0-0 ppc64el 1.54.0+ds-3 [30.6 kB]
105s Get:30 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpaper1 ppc64el 1.1.29build1 [13.7 kB]
105s Get:31 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpaper-utils ppc64el 1.1.29build1 [8742 B]
105s Get:32 http://ftpmaster.internal/ubuntu plucky/main ppc64el libsharpyuv0 ppc64el 1.4.0-0.1 [22.0 kB]
105s Get:33 http://ftpmaster.internal/ubuntu plucky/main ppc64el libsm6 ppc64el 2:1.2.4-1 [18.4 kB]
105s Get:34 http://ftpmaster.internal/ubuntu plucky/main ppc64el libtcl8.6 ppc64el 8.6.15+dfsg-2 [1201 kB]
105s Get:35 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjbig0 ppc64el 2.1-6.1ubuntu2 [35.9 kB]
105s Get:36 http://ftpmaster.internal/ubuntu plucky/main ppc64el libwebp7 ppc64el 1.4.0-0.1 [309 kB]
105s Get:37 http://ftpmaster.internal/ubuntu plucky/main ppc64el libtiff6 ppc64el 4.5.1+git230720-4ubuntu4 [272 kB]
105s Get:38 http://ftpmaster.internal/ubuntu plucky/main ppc64el libxft2 ppc64el 2.3.6-1build1 [61.5 kB]
105s Get:39 http://ftpmaster.internal/ubuntu plucky/main ppc64el libxss1 ppc64el 1:1.2.3-1build3 [7980 B]
105s Get:40 http://ftpmaster.internal/ubuntu plucky/main ppc64el libtk8.6 ppc64el 8.6.15-1 [942 kB]
105s Get:41 http://ftpmaster.internal/ubuntu plucky/main ppc64el libxt6t64 ppc64el 1:1.2.1-1.2build1 [202 kB]
105s Get:42 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-numpy ppc64el 1:1.26.4+ds-11build1 [4434 kB]
105s Get:43 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-fastcluster ppc64el 1.2.6-1build1 [52.0 kB]
105s Get:44 http://ftpmaster.internal/ubuntu plucky/main ppc64el zip ppc64el 3.0-14ubuntu1 [196 kB]
105s Get:45 http://ftpmaster.internal/ubuntu plucky/main ppc64el unzip ppc64el 6.0-28ubuntu6 [200 kB]
105s Get:46 http://ftpmaster.internal/ubuntu plucky/main ppc64el xdg-utils all 1.2.1-0ubuntu1 [67.5 kB]
105s Get:47 http://ftpmaster.internal/ubuntu plucky/universe ppc64el r-base-core ppc64el 4.4.2-1 [28.9 MB]
106s Get:48 http://ftpmaster.internal/ubuntu plucky/universe ppc64el r-cran-fastcluster ppc64el 1.2.6-1build1 [198 kB]
106s Preconfiguring packages ...
106s Fetched 45.7 MB in 2s (24.3 MB/s)
106s Selecting previously unselected package fonts-dejavu-mono.
106s (Reading database ... 
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(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%
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117s autopkgtest [00:54:08]: test run-unit-test: [-----------------------
118s 
118s R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
118s Copyright (C) 2024 The R Foundation for Statistical Computing
118s Platform: powerpc64le-unknown-linux-gnu
118s 
118s R is free software and comes with ABSOLUTELY NO WARRANTY.
118s You are welcome to redistribute it under certain conditions.
118s Type 'license()' or 'licence()' for distribution details.
118s 
118s R is a collaborative project with many contributors.
118s Type 'contributors()' for more information and
118s 'citation()' on how to cite R or R packages in publications.
118s 
118s Type 'demo()' for some demos, 'help()' for on-line help, or
118s 'help.start()' for an HTML browser interface to help.
118s Type 'q()' to quit R.
118s 
118s > #  fastcluster: Fast hierarchical clustering routines for R and Python
118s > #
118s > #  Copyright:
118s > #    * Until package version 1.1.23: © 2011 Daniel Müllner <https://danifold.net>
118s > #    * All changes from version 1.1.24 on: © Google Inc. <https://www.google.com>
118s > #
118s > # Test script for the R interface
118s > 
118s > seed = as.integer(runif(1, 0, 1e9))
118s > set.seed(seed)
118s > cat(sprintf("Random seed: %d\n",seed))
118s Random seed: 613517218
118s > 
118s > print_seed <- function() {
118s +   return(sprintf('
118s + Please send a report to the author of the \'fastcluster\' package, Daniel Müllner.
118s + For contact details, see <https://danifold.net>. To make the error
118s + reproducible, you must include the following number (the random seed value) in
118s + your error report: %d.\n\n', seed))
118s + }
118s > 
118s > hasWardD2 = getRversion() >= '3.1.0'
118s > 
118s > # Compare two dendrograms and check whether they are equal, except that
118s > # ties may be resolved differently.
118s > compare <- function(dg1, dg2) {
118s +   h1 <- dg1$height
118s +   h2 <- dg2$height
118s +   # "height" vectors may have small numerical errors.
118s +   rdiffs <- abs(h1-h2)/pmax(abs(h1),abs(h2))
118s +   rdiffs = rdiffs[complete.cases(rdiffs)]
118s +   rel_error <-  max(rdiffs)
118s +   # We allow a relative error of 1e-13.
118s +   if (rel_error>1e-13) {
118s +     print(h1)
118s +     print(h2)
118s +     cat(sprintf('Height vectors differ! The maximum relative error is %e.\n', rel_error))
118s +     return(FALSE)
118s +   }
118s +   # Filter the indices where consecutive merging distances are distinct.
118s +   d = diff(dg1$height)
118s +   b = (c(d,1)!=0 & c(1,d)!=0)
118s +   #cat(sprintf("Percentage of indices where we can test: %g.\n",100.0*length(b[b])/length(b)))
118s +   if (any(b)) {
118s +     m1 = dg1$merge[b,]
118s +     m2 = dg2$merge[b,]
118s + 
118s +     r = function(i) {
118s +       if (i<0) {
118s +         return(1)
118s +       }
118s +       else {
118s +         return(b[i])
118s +       }
118s +     }
118s + 
118s +     f = sapply(m1,r)
118s +     fm1 = m1*f
118s +     fm2 = m2*f
118s +     # The "merge" matrices must be identical whereever indices are not ambiguous
118s +     # due to ties.
118s +     if (!identical(fm1,fm2)) {
118s +       cat('Merge matrices differ!\n')
118s +       return(FALSE)
118s +     }
118s +     # Compare the "order" vectors only if all merging distances were distinct.
118s +     if (all(b) && !identical(dg1$order,dg2$order)) {
118s +       cat('Order vectors differ!\n')
118s +       return(FALSE)
118s +     }
118s +   }
118s +   return(TRUE)
118s + }
118s > 
118s > # Generate uniformly distributed random data
118s > generate.uniform <- function() {
118s +   n = sample(10:1000,1)
118s +   range_exp = runif(1,min=-10, max=10)
118s +   cat(sprintf("Number of sample points: %d\n",n))
118s +   cat(sprintf("Dissimilarity range: [0,%g]\n",10^range_exp))
118s +   d = runif(n*(n-1)/2, min=0, max=10^range_exp)
118s +   # Fake a compressed distance matrix
118s +   attributes(d) <- NULL
118s +   attr(d,"Size") <- n
118s +   attr(d, "call") <- 'N/A'
118s +   class(d) <- "dist"
118s +   return(d)
118s + }
118s > 
118s > # Generate normally distributed random data
118s > generate.normal <- function() {
118s +   n = sample(10:1000,1)
118s +   dim = sample(2:20,1)
118s + 
118s +   cat (sprintf("Number of sample points: %d\n",n))
118s +   cat (sprintf("Dimension: %d\n",dim))
118s + 
118s +   pcd = matrix(rnorm(n*dim), c(n,dim))
118s +   d = dist(pcd)
118s +   return(d)
118s + }
118s > 
118s > # Test the clustering functions when a distance matrix is given.
118s > test.dm <-  function(d) {
118s +   d2 = d
118s +   if (hasWardD2) {
118s +     methods = c('single','complete','average','mcquitty','ward.D','ward.D2','centroid','median')
118s +   }
118s +   else {
118s +     methods = c('single','complete','average','mcquitty','ward','centroid','median')
118s +   }
118s +   for (method in methods) {
118s +     cat(paste('Method :', method, '\n'))
118s +     dg_stats       = stats::hclust(d, method=method)
118s +     if (method == 'ward') {
118s +       method = 'ward.D'
118s +     }
118s +     dg_fastcluster = fastcluster::hclust(d, method=method)
118s +     if (!identical(d,d2)) {
118s +       cat('Input array was corrupted!\n')
118s +       stop(print_seed())
118s +     }
118s +     if (!compare(dg_stats, dg_fastcluster)) {
118s +       stop(print_seed())
118s +     }
118s +   }
118s +   cat('Passed.\n')
118s + }
118s > 
118s > # Test the clustering functions for vector input in Euclidean space.
118s > test.vector <-  function() {
118s +   # generate test data
118s +   n = sample(10:1000,1)
118s +   dim = sample(2:20,1)
118s +   cat (sprintf("Number of sample points: %d\n",n))
118s +   cat (sprintf("Dimension: %d\n",dim))
118s + 
118s +   range_exp = runif(1,min=-10, max=10)
118s +   pcd = matrix(rnorm(n*dim, sd=10^range_exp), c(n,dim))
118s +   pcd2 = pcd
118s +   # test
118s +   method='single'
118s +   cat(paste('Method:', method, '\n'))
118s +   for (metric in c('euclidean', 'maximum', 'manhattan', 'canberra', 'minkowski')) {
118s +     cat(paste('    Metric:', metric, '\n'))
118s +     if (metric=='minkowski') {
118s +       p = runif(1, min=1.0, max=10.0)
118s +       cat (sprintf("    p: %g\n",p));
118s +       dg_fastcluster = fastcluster::hclust.vector(pcd, method=method, metric=metric, p=p)
118s +       d = dist(pcd, method=metric, p=p)
118s +     }
118s +     else {
118s +       dg_fastcluster = fastcluster::hclust.vector(pcd, method=method, metric=metric)
118s +       d = dist(pcd, method=metric)
118s +     }
118s +     d2 = d
118s +     dg_fastcluster_dist = fastcluster::hclust(d, method=method)
118s +     if (!identical(d,d2) || !identical(pcd,pcd2)) {
118s +       cat('Input array was corrupted!\n')
118s +       stop(print_seed())
118s +     }
118s +     if (!compare(dg_fastcluster_dist, dg_fastcluster)) {
118s +       stop(print_seed())
118s +     }
118s +   }
118s +   for (method in c('ward','centroid','median') ) {
118s +     cat(paste('Method:', method, '\n'))
118s +     dg_fastcluster = fastcluster::hclust.vector(pcd, method=method)
118s +     if (!identical(pcd,pcd2)) {
118s +       cat('Input array was corrupted!\n')
118s +       stop(print_seed())
118s +     }
118s +     d = dist(pcd)
118s +     if(method == "ward" && hasWardD2) {
118s +       method = "ward.D2"
118s +     }
118s +     else
118s +     {
118s +       # Workaround: fastcluster::hclust expects _squared_ euclidean distances.
118s +       d = d^2
118s +     }
118s +     d2 = d
118s +     dg_fastcluster_dist = fastcluster::hclust(d, method=method)
118s +     if (!identical(d,d2)) {
118s +       cat('Input array was corrupted!\n')
118s +       stop(print_seed())
118s +     }
118s +     if(method != "ward.D2") {
118s +       dg_fastcluster_dist$height = sqrt(dg_fastcluster_dist$height)
118s +     }
118s +     # The Euclidean methods may have small numerical errors due to squaring/
118s +     # taking the root in the Euclidean distances.
118s +     if (!compare(dg_fastcluster_dist, dg_fastcluster)) {
118s +       stop(print_seed())
118s +     }
118s +   }
118s +   cat('Passed.\n')
118s + }
118s > 
118s > # Test the single linkage function with the "binary" metric
118s > test.vector.binary <- function() {
118s +   # generate test data
118s +   cat (sprintf("Uniform sampling for the 'binary' metric:\n"))
118s +   n = sample(10:400,1)
118s +   dim = sample(n:(2*n),1)
118s +   cat (sprintf("Number of sample points: %d\n",n))
118s +   cat (sprintf("Dimension: %d\n",dim))
118s +   pcd = matrix(sample(-1:2, n*dim, replace=T), c(n,dim))
118s +   pcd2 = pcd
118s +   # test
118s +   method='single'
118s +   metric='binary'
118s +   cat(paste('Method:', method, '\n'))
118s +   cat(paste('    Metric:', metric, '\n'))
118s +   dg_fastcluster = fastcluster::hclust.vector(pcd, method=method, metric=metric)
118s +   d = dist(pcd, method=metric)
118s +   d2 = d
118s +   dg_fastcluster_dist       = fastcluster::hclust(d, method=method)
118s +   if (!identical(d,d2) || !identical(d,d2)) {
118s +     cat('Input array was corrupted!\n')
118s +     stop(print_seed())
118s +   }
118s +   if (!compare(dg_fastcluster_dist, dg_fastcluster)) {
118s +     stop(print_seed())
118s +   }
118s +   cat('Passed.\n')
118s + }
118s > 
118s > 
118s > N = 15
118s > for (i in (1:N)) {
118s +   if (i%%2==1) {
118s +     cat(sprintf('Random test %d of %d (uniform distribution of distances):\n',i,2*N))
118s +     d = generate.uniform()
118s +   }
118s +   else {
118s +     cat(sprintf('Random test %d of %d (Gaussian density):\n',i,2*N))
118s +     d = generate.normal()
118s +   }
118s +   test.dm(d)
118s + }
118s Random test 1 of 30 (uniform distribution of distances):
118s Number of sample points: 995
118s Dissimilarity range: [0,5.77322]
118s Method : single 
118s Method : complete 
118s Method : average 
118s Method : mcquitty 
118s Method : ward.D 
118s Method : ward.D2 
118s Method : centroid 
118s Method : median 
118s Passed.
118s Random test 2 of 30 (Gaussian density):
118s Number of sample points: 100
118s Dimension: 15
118s Method : single 
118s Method : complete 
118s Method : average 
118s Method : mcquitty 
118s Method : ward.D 
118s Method : ward.D2 
118s Method : centroid 
118s Method : median 
118s Passed.
118s Random test 3 of 30 (uniform distribution of distances):
118s Number of sample points: 365
118s Dissimilarity range: [0,5.73914e-09]
118s Method : single 
118s Method : complete 
118s Method : average 
118s Method : mcquitty 
118s Method : ward.D 
118s Method : ward.D2 
118s Method : centroid 
118s Method : median 
118s Passed.
118s Random test 4 of 30 (Gaussian density):
118s Number of sample points: 50
118s Dimension: 4
118s Method : single 
118s Method : complete 
118s Method : average 
118s Method : mcquitty 
118s Method : ward.D 
118s Method : ward.D2 
118s Method : centroid 
118s Method : median 
118s Passed.
118s Random test 5 of 30 (uniform distribution of distances):
118s Number of sample points: 682
118s Dissimilarity range: [0,1.31508e+06]
118s Method : single 
118s Method : complete 
118s Method : average 
118s Method : mcquitty 
118s Method : ward.D 
118s Method : ward.D2 
118s Method : centroid 
118s Method : median 
118s Passed.
118s Random test 6 of 30 (Gaussian density):
118s Number of sample points: 167
118s Dimension: 15
118s Method : single 
118s Method : complete 
118s Method : average 
118s Method : mcquitty 
118s Method : ward.D 
118s Method : ward.D2 
118s Method : centroid 
118s Method : median 
118s Passed.
118s Random test 7 of 30 (uniform distribution of distances):
118s Number of sample points: 785
118s Dissimilarity range: [0,3.39364e+06]
118s Method : single 
118s Method : complete 
118s Method : average 
118s Method : mcquitty 
119s Method : ward.D 
119s Method : ward.D2 
119s Method : centroid 
119s Method : median 
119s Passed.
119s Random test 8 of 30 (Gaussian density):
119s Number of sample points: 711
119s Dimension: 10
119s Method : single 
119s Method : complete 
119s Method : average 
119s Method : mcquitty 
119s Method : ward.D 
119s Method : ward.D2 
119s Method : centroid 
119s Method : median 
119s Passed.
119s Random test 9 of 30 (uniform distribution of distances):
119s Number of sample points: 503
119s Dissimilarity range: [0,0.473428]
119s Method : single 
119s Method : complete 
119s Method : average 
119s Method : mcquitty 
119s Method : ward.D 
119s Method : ward.D2 
119s Method : centroid 
119s Method : median 
119s Passed.
119s Random test 10 of 30 (Gaussian density):
119s Number of sample points: 237
119s Dimension: 6
119s Method : single 
119s Method : complete 
119s Method : average 
119s Method : mcquitty 
119s Method : ward.D 
119s Method : ward.D2 
119s Method : centroid 
119s Method : median 
119s Passed.
119s Random test 11 of 30 (uniform distribution of distances):
119s Number of sample points: 765
119s Dissimilarity range: [0,5.35491e+09]
119s Method : single 
119s Method : complete 
119s Method : average 
119s Method : mcquitty 
119s Method : ward.D 
119s Method : ward.D2 
119s Method : centroid 
119s Method : median 
119s Passed.
119s Random test 12 of 30 (Gaussian density):
119s Number of sample points: 454
119s Dimension: 13
119s Method : single 
119s Method : complete 
119s Method : average 
119s Method : mcquitty 
119s Method : ward.D 
119s Method : ward.D2 
119s Method : centroid 
119s Method : median 
119s Passed.
119s Random test 13 of 30 (uniform distribution of distances):
119s Number of sample points: 71
119s Dissimilarity range: [0,0.00920483]
119s Method : single 
119s Method : complete 
119s Method : average 
119s Method : mcquitty 
119s Method : ward.D 
119s Method : ward.D2 
119s Method : centroid 
119s Method : median 
119s Passed.
119s Random test 14 of 30 (Gaussian density):
119s Number of sample points: 504
119s Dimension: 11
119s Method : single 
119s Method : complete 
119s Method : average 
119s Method : mcquitty 
119s Method : ward.D 
119s Method : ward.D2 
119s Method : centroid 
119s Method : median 
119s Passed.
119s Random test 15 of 30 (uniform distribution of distances):
119s Number of sample points: 242
119s Dissimilarity range: [0,2.02663]
119s Method : single 
119s Method : complete 
119s Method : average 
119s Method : mcquitty 
119s Method : ward.D 
119s Method : ward.D2 
119s Method : centroid 
119s Method : median 
119s Passed.
119s > for (i in (N+1:N)) {
119s +   cat(sprintf('Random test %d of %d (Gaussian density):\n',i,2*N))
119s +   test.vector()
119s +   test.vector.binary()
119s + }
119s Random test 16 of 30 (Gaussian density):
119s Number of sample points: 38
119s Dimension: 4
119s Method: single 
119s     Metric: euclidean 
119s     Metric: maximum 
119s     Metric: manhattan 
119s     Metric: canberra 
119s     Metric: minkowski 
119s     p: 9.52289
119s Method: ward 
119s Method: centroid 
119s Method: median 
119s Passed.
119s Uniform sampling for the 'binary' metric:
119s Number of sample points: 354
119s Dimension: 412
119s Method: single 
119s     Metric: binary 
120s Passed.
120s Random test 17 of 30 (Gaussian density):
120s Number of sample points: 726
120s Dimension: 6
120s Method: single 
120s     Metric: euclidean 
120s     Metric: maximum 
120s     Metric: manhattan 
120s     Metric: canberra 
120s     Metric: minkowski 
120s     p: 4.83779
120s Method: ward 
120s Method: centroid 
120s Method: median 
121s Passed.
121s Uniform sampling for the 'binary' metric:
121s Number of sample points: 273
121s Dimension: 304
121s Method: single 
121s     Metric: binary 
121s Passed.
121s Random test 18 of 30 (Gaussian density):
121s Number of sample points: 879
121s Dimension: 6
121s Method: single 
121s     Metric: euclidean 
121s     Metric: maximum 
121s     Metric: manhattan 
121s     Metric: canberra 
121s     Metric: minkowski 
121s     p: 5.36413
121s Method: ward 
121s Method: centroid 
121s Method: median 
121s Passed.
121s Uniform sampling for the 'binary' metric:
121s Number of sample points: 75
121s Dimension: 95
121s Method: single 
121s     Metric: binary 
121s Passed.
121s Random test 19 of 30 (Gaussian density):
121s Number of sample points: 939
121s Dimension: 8
121s Method: single 
121s     Metric: euclidean 
121s     Metric: maximum 
122s     Metric: manhattan 
122s     Metric: canberra 
122s     Metric: minkowski 
122s     p: 8.62573
122s Method: ward 
122s Method: centroid 
122s Method: median 
122s Passed.
122s Uniform sampling for the 'binary' metric:
122s Number of sample points: 325
122s Dimension: 505
122s Method: single 
122s     Metric: binary 
123s Passed.
123s Random test 20 of 30 (Gaussian density):
123s Number of sample points: 484
123s Dimension: 19
123s Method: single 
123s     Metric: euclidean 
123s     Metric: maximum 
123s     Metric: manhattan 
123s     Metric: canberra 
123s     Metric: minkowski 
123s     p: 6.54992
123s Method: ward 
123s Method: centroid 
124s Method: median 
124s Passed.
124s Uniform sampling for the 'binary' metric:
124s Number of sample points: 108
124s Dimension: 130
124s Method: single 
124s     Metric: binary 
124s Passed.
124s Random test 21 of 30 (Gaussian density):
124s Number of sample points: 366
124s Dimension: 17
124s Method: single 
124s     Metric: euclidean 
124s     Metric: maximum 
124s     Metric: manhattan 
124s     Metric: canberra 
124s     Metric: minkowski 
124s     p: 8.85403
124s Method: ward 
124s Method: centroid 
124s Method: median 
124s Passed.
124s Uniform sampling for the 'binary' metric:
124s Number of sample points: 216
124s Dimension: 365
124s Method: single 
124s     Metric: binary 
124s Passed.
124s Random test 22 of 30 (Gaussian density):
124s Number of sample points: 518
124s Dimension: 20
124s Method: single 
124s     Metric: euclidean 
124s     Metric: maximum 
124s     Metric: manhattan 
124s     Metric: canberra 
124s     Metric: minkowski 
124s     p: 1.91488
125s Method: ward 
125s Method: centroid 
125s Method: median 
125s Passed.
125s Uniform sampling for the 'binary' metric:
125s Number of sample points: 382
125s Dimension: 386
125s Method: single 
125s     Metric: binary 
126s Passed.
126s Random test 23 of 30 (Gaussian density):
126s Number of sample points: 498
126s Dimension: 7
126s Method: single 
126s     Metric: euclidean 
126s     Metric: maximum 
126s     Metric: manhattan 
126s     Metric: canberra 
126s     Metric: minkowski 
126s     p: 4.6998
126s Method: ward 
126s Method: centroid 
126s Method: median 
126s Passed.
126s Uniform sampling for the 'binary' metric:
126s Number of sample points: 139
126s Dimension: 146
126s Method: single 
126s     Metric: binary 
126s Passed.
126s Random test 24 of 30 (Gaussian density):
126s Number of sample points: 989
126s Dimension: 17
126s Method: single 
126s     Metric: euclidean 
126s     Metric: maximum 
126s     Metric: manhattan 
126s     Metric: canberra 
126s     Metric: minkowski 
126s     p: 5.85137
127s Method: ward 
127s Method: centroid 
128s Method: median 
128s Passed.
128s Uniform sampling for the 'binary' metric:
128s Number of sample points: 361
128s Dimension: 378
128s Method: single 
128s     Metric: binary 
129s Passed.
129s Random test 25 of 30 (Gaussian density):
129s Number of sample points: 603
129s Dimension: 11
129s Method: single 
129s     Metric: euclidean 
129s     Metric: maximum 
129s     Metric: manhattan 
129s     Metric: canberra 
129s     Metric: minkowski 
129s     p: 7.40878
129s Method: ward 
129s Method: centroid 
129s Method: median 
129s Passed.
129s Uniform sampling for the 'binary' metric:
129s Number of sample points: 44
129s Dimension: 46
129s Method: single 
129s     Metric: binary 
129s Passed.
129s Random test 26 of 30 (Gaussian density):
129s Number of sample points: 138
129s Dimension: 18
129s Method: single 
129s     Metric: euclidean 
129s     Metric: maximum 
129s     Metric: manhattan 
129s     Metric: canberra 
129s     Metric: minkowski 
129s     p: 3.98162
129s Method: ward 
129s Method: centroid 
129s Method: median 
129s Passed.
129s Uniform sampling for the 'binary' metric:
129s Number of sample points: 351
129s Dimension: 558
129s Method: single 
129s     Metric: binary 
130s Passed.
130s Random test 27 of 30 (Gaussian density):
130s Number of sample points: 913
130s Dimension: 18
130s Method: single 
130s     Metric: euclidean 
130s     Metric: maximum 
130s     Metric: manhattan 
130s     Metric: canberra 
131s     Metric: minkowski 
131s     p: 3.52544
131s Method: ward 
131s Method: centroid 
132s Method: median 
132s Passed.
132s Uniform sampling for the 'binary' metric:
132s Number of sample points: 82
132s Dimension: 101
132s Method: single 
132s     Metric: binary 
132s Passed.
132s Random test 28 of 30 (Gaussian density):
132s Number of sample points: 947
132s Dimension: 16
132s Method: single 
132s     Metric: euclidean 
132s     Metric: maximum 
132s     Metric: manhattan 
132s     Metric: canberra 
132s     Metric: minkowski 
132s     p: 5.73213
133s Method: ward 
133s Method: centroid 
133s Method: median 
133s Passed.
133s Uniform sampling for the 'binary' metric:
133s Number of sample points: 212
133s Dimension: 325
133s Method: single 
133s     Metric: binary 
134s Passed.
134s Random test 29 of 30 (Gaussian density):
134s Number of sample points: 961
134s Dimension: 10
134s Method: single 
134s     Metric: euclidean 
134s     Metric: maximum 
134s     Metric: manhattan 
134s     Metric: canberra 
134s     Metric: minkowski 
134s     p: 5.30392
134s Method: ward 
134s Method: centroid 
135s Method: median 
135s Passed.
135s Uniform sampling for the 'binary' metric:
135s Number of sample points: 110
135s Dimension: 175
135s Method: single 
135s     Metric: binary 
135s Passed.
135s Random test 30 of 30 (Gaussian density):
135s Number of sample points: 898
135s Dimension: 11
135s Method: single 
135s     Metric: euclidean 
135s     Metric: maximum 
135s     Metric: manhattan 
135s     Metric: canberra 
135s     Metric: minkowski 
135s     p: 1.37411
135s Method: ward 
136s Method: centroid 
136s Method: median 
136s Passed.
136s Uniform sampling for the 'binary' metric:
136s Number of sample points: 369
136s Dimension: 583
136s Method: single 
136s     Metric: binary 
137s Passed.
137s > 
137s > cat('Done.\n')
137s Done.
137s > 
137s autopkgtest [00:54:28]: test run-unit-test: -----------------------]
138s autopkgtest [00:54:29]: test run-unit-test:  - - - - - - - - - - results - - - - - - - - - -
138s run-unit-test        PASS
138s autopkgtest [00:54:29]: test autodep8-python3: preparing testbed
257s autopkgtest [00:56:28]: testbed dpkg architecture: ppc64el
257s autopkgtest [00:56:28]: testbed apt version: 2.9.8
257s autopkgtest [00:56:28]: @@@@@@@@@@@@@@@@@@@@ test bed setup
258s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB]
258s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B]
258s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [101 kB]
258s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [17.2 kB]
258s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [971 kB]
258s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el Packages [110 kB]
258s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe ppc64el Packages [692 kB]
258s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse ppc64el Packages [20.8 kB]
259s Fetched 1993 kB in 1s (2131 kB/s)
259s Reading package lists...
261s Reading package lists...
261s Building dependency tree...
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261s Calculating upgrade...
261s The following NEW packages will be installed:
261s   python3.13-gdbm
261s The following packages will be upgraded:
261s   bpfcc-tools bpftrace libbpfcc libgnutls30t64 libjson-glib-1.0-0
261s   libjson-glib-1.0-common libnewt0.52 libpython3-stdlib libutempter0 python3
261s   python3-bpfcc python3-gdbm python3-minimal python3-newt whiptail
261s 15 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
261s Need to get 4700 kB of archives.
261s After this operation, 215 kB of additional disk space will be used.
261s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el python3-minimal ppc64el 3.12.7-1 [27.4 kB]
262s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el python3 ppc64el 3.12.7-1 [24.0 kB]
262s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el libpython3-stdlib ppc64el 3.12.7-1 [10.0 kB]
262s Get:4 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgnutls30t64 ppc64el 3.8.8-2ubuntu1 [1072 kB]
262s Get:5 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-newt ppc64el 0.52.24-2ubuntu4 [21.8 kB]
262s Get:6 http://ftpmaster.internal/ubuntu plucky/main ppc64el libnewt0.52 ppc64el 0.52.24-2ubuntu4 [62.1 kB]
262s Get:7 http://ftpmaster.internal/ubuntu plucky/main ppc64el whiptail ppc64el 0.52.24-2ubuntu4 [19.5 kB]
262s Get:8 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3.13-gdbm ppc64el 3.13.0-2 [31.5 kB]
262s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el python3-gdbm ppc64el 3.12.7-1 [8640 B]
262s Get:10 http://ftpmaster.internal/ubuntu plucky/main ppc64el libbpfcc ppc64el 0.30.0+ds-1ubuntu5 [696 kB]
262s Get:11 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-bpfcc all 0.30.0+ds-1ubuntu5 [40.4 kB]
262s Get:12 http://ftpmaster.internal/ubuntu plucky/main ppc64el bpfcc-tools all 0.30.0+ds-1ubuntu5 [697 kB]
262s Get:13 http://ftpmaster.internal/ubuntu plucky/main ppc64el bpftrace ppc64el 0.21.2-2ubuntu2 [1898 kB]
262s Get:14 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjson-glib-1.0-common all 1.10.0+ds-3 [5586 B]
262s Get:15 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjson-glib-1.0-0 ppc64el 1.10.0+ds-3 [76.0 kB]
262s Get:16 http://ftpmaster.internal/ubuntu plucky/main ppc64el libutempter0 ppc64el 1.2.1-4 [9850 B]
262s Fetched 4700 kB in 1s (6539 kB/s)
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263s Unpacking libnewt0.52:ppc64el (0.52.24-2ubuntu4) over (0.52.24-2ubuntu3) ...
263s Preparing to unpack .../02-whiptail_0.52.24-2ubuntu4_ppc64el.deb ...
263s Unpacking whiptail (0.52.24-2ubuntu4) over (0.52.24-2ubuntu3) ...
263s Selecting previously unselected package python3.13-gdbm.
263s Preparing to unpack .../03-python3.13-gdbm_3.13.0-2_ppc64el.deb ...
263s Unpacking python3.13-gdbm (3.13.0-2) ...
263s Preparing to unpack .../04-python3-gdbm_3.12.7-1_ppc64el.deb ...
263s Unpacking python3-gdbm:ppc64el (3.12.7-1) over (3.12.6-1ubuntu1) ...
263s Preparing to unpack .../05-libbpfcc_0.30.0+ds-1ubuntu5_ppc64el.deb ...
263s Unpacking libbpfcc:ppc64el (0.30.0+ds-1ubuntu5) over (0.30.0+ds-1ubuntu4) ...
263s Preparing to unpack .../06-python3-bpfcc_0.30.0+ds-1ubuntu5_all.deb ...
263s Unpacking python3-bpfcc (0.30.0+ds-1ubuntu5) over (0.30.0+ds-1ubuntu4) ...
263s Preparing to unpack .../07-bpfcc-tools_0.30.0+ds-1ubuntu5_all.deb ...
263s Unpacking bpfcc-tools (0.30.0+ds-1ubuntu5) over (0.30.0+ds-1ubuntu4) ...
263s Preparing to unpack .../08-bpftrace_0.21.2-2ubuntu2_ppc64el.deb ...
263s Unpacking bpftrace (0.21.2-2ubuntu2) over (0.21.2-2) ...
263s Preparing to unpack .../09-libjson-glib-1.0-common_1.10.0+ds-3_all.deb ...
263s Unpacking libjson-glib-1.0-common (1.10.0+ds-3) over (1.10.0+ds-2) ...
263s Preparing to unpack .../10-libjson-glib-1.0-0_1.10.0+ds-3_ppc64el.deb ...
263s Unpacking libjson-glib-1.0-0:ppc64el (1.10.0+ds-3) over (1.10.0+ds-2) ...
263s Preparing to unpack .../11-libutempter0_1.2.1-4_ppc64el.deb ...
263s Unpacking libutempter0:ppc64el (1.2.1-4) over (1.2.1-3build1) ...
263s Setting up libnewt0.52:ppc64el (0.52.24-2ubuntu4) ...
263s Setting up libutempter0:ppc64el (1.2.1-4) ...
263s Setting up whiptail (0.52.24-2ubuntu4) ...
263s Setting up libjson-glib-1.0-common (1.10.0+ds-3) ...
263s Setting up libbpfcc:ppc64el (0.30.0+ds-1ubuntu5) ...
263s Setting up python3.13-gdbm (3.13.0-2) ...
263s Setting up libpython3-stdlib:ppc64el (3.12.7-1) ...
263s Setting up bpftrace (0.21.2-2ubuntu2) ...
263s Setting up python3 (3.12.7-1) ...
264s Setting up python3-newt:ppc64el (0.52.24-2ubuntu4) ...
264s Setting up libjson-glib-1.0-0:ppc64el (1.10.0+ds-3) ...
264s Setting up python3-bpfcc (0.30.0+ds-1ubuntu5) ...
264s Setting up python3-gdbm:ppc64el (3.12.7-1) ...
264s Setting up bpfcc-tools (0.30.0+ds-1ubuntu5) ...
264s Processing triggers for man-db (2.12.1-3) ...
265s Processing triggers for libc-bin (2.40-1ubuntu3) ...
265s Reading package lists...
265s Building dependency tree...
265s Reading state information...
265s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
266s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease
266s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease
266s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease
266s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease
267s Reading package lists...
267s Reading package lists...
267s Building dependency tree...
267s Reading state information...
267s Calculating upgrade...
267s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
267s Reading package lists...
268s Building dependency tree...
268s Reading state information...
268s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
275s Reading package lists...
275s Building dependency tree...
275s Reading state information...
276s Starting pkgProblemResolver with broken count: 0
276s Starting 2 pkgProblemResolver with broken count: 0
276s Done
276s The following additional packages will be installed:
276s   libblas3 libgfortran5 liblapack3 libpython3.13-minimal libpython3.13-stdlib
276s   python3-all python3-fastcluster python3-numpy python3.13 python3.13-minimal
276s Suggested packages:
276s   gcc gfortran python-numpy-doc python3-dev python3-pytest python3.13-venv
276s   python3.13-doc binfmt-support
276s Recommended packages:
276s   python3-scipy
276s The following NEW packages will be installed:
276s   autopkgtest-satdep libblas3 libgfortran5 liblapack3 libpython3.13-minimal
276s   libpython3.13-stdlib python3-all python3-fastcluster python3-numpy
276s   python3.13 python3.13-minimal
276s 0 upgraded, 11 newly installed, 0 to remove and 0 not upgraded.
276s Need to get 14.1 MB/14.1 MB of archives.
276s After this operation, 60.6 MB of additional disk space will be used.
276s Get:1 /tmp/autopkgtest.5uHIBP/2-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [720 B]
276s Get:2 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpython3.13-minimal ppc64el 3.13.0-2 [881 kB]
277s Get:3 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3.13-minimal ppc64el 3.13.0-2 [2302 kB]
277s Get:4 http://ftpmaster.internal/ubuntu plucky/main ppc64el libblas3 ppc64el 3.12.0-3build2 [222 kB]
277s Get:5 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgfortran5 ppc64el 14.2.0-8ubuntu1 [571 kB]
277s Get:6 http://ftpmaster.internal/ubuntu plucky/main ppc64el liblapack3 ppc64el 3.12.0-3build2 [2806 kB]
277s Get:7 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpython3.13-stdlib ppc64el 3.13.0-2 [2148 kB]
277s Get:8 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3.13 ppc64el 3.13.0-2 [719 kB]
277s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el python3-all ppc64el 3.12.7-1 [888 B]
277s Get:10 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-numpy ppc64el 1:1.26.4+ds-11build1 [4434 kB]
278s Get:11 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-fastcluster ppc64el 1.2.6-1build1 [52.0 kB]
278s Fetched 14.1 MB in 2s (8022 kB/s)
278s Selecting previously unselected package libpython3.13-minimal:ppc64el.
278s (Reading database ... 
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278s Preparing to unpack .../00-libpython3.13-minimal_3.13.0-2_ppc64el.deb ...
278s Unpacking libpython3.13-minimal:ppc64el (3.13.0-2) ...
278s Selecting previously unselected package python3.13-minimal.
278s Preparing to unpack .../01-python3.13-minimal_3.13.0-2_ppc64el.deb ...
278s Unpacking python3.13-minimal (3.13.0-2) ...
278s Selecting previously unselected package libblas3:ppc64el.
278s Preparing to unpack .../02-libblas3_3.12.0-3build2_ppc64el.deb ...
278s Unpacking libblas3:ppc64el (3.12.0-3build2) ...
278s Selecting previously unselected package libgfortran5:ppc64el.
278s Preparing to unpack .../03-libgfortran5_14.2.0-8ubuntu1_ppc64el.deb ...
278s Unpacking libgfortran5:ppc64el (14.2.0-8ubuntu1) ...
278s Selecting previously unselected package liblapack3:ppc64el.
278s Preparing to unpack .../04-liblapack3_3.12.0-3build2_ppc64el.deb ...
278s Unpacking liblapack3:ppc64el (3.12.0-3build2) ...
278s Selecting previously unselected package libpython3.13-stdlib:ppc64el.
278s Preparing to unpack .../05-libpython3.13-stdlib_3.13.0-2_ppc64el.deb ...
278s Unpacking libpython3.13-stdlib:ppc64el (3.13.0-2) ...
278s Selecting previously unselected package python3.13.
278s Preparing to unpack .../06-python3.13_3.13.0-2_ppc64el.deb ...
278s Unpacking python3.13 (3.13.0-2) ...
278s Selecting previously unselected package python3-all.
278s Preparing to unpack .../07-python3-all_3.12.7-1_ppc64el.deb ...
278s Unpacking python3-all (3.12.7-1) ...
278s Selecting previously unselected package python3-numpy.
278s Preparing to unpack .../08-python3-numpy_1%3a1.26.4+ds-11build1_ppc64el.deb ...
278s Unpacking python3-numpy (1:1.26.4+ds-11build1) ...
279s Selecting previously unselected package python3-fastcluster.
279s Preparing to unpack .../09-python3-fastcluster_1.2.6-1build1_ppc64el.deb ...
279s Unpacking python3-fastcluster (1.2.6-1build1) ...
279s Selecting previously unselected package autopkgtest-satdep.
279s Preparing to unpack .../10-2-autopkgtest-satdep.deb ...
279s Unpacking autopkgtest-satdep (0) ...
279s Setting up libpython3.13-minimal:ppc64el (3.13.0-2) ...
279s Setting up libblas3:ppc64el (3.12.0-3build2) ...
279s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/blas/libblas.so.3 to provide /usr/lib/powerpc64le-linux-gnu/libblas.so.3 (libblas.so.3-powerpc64le-linux-gnu) in auto mode
279s Setting up libgfortran5:ppc64el (14.2.0-8ubuntu1) ...
279s Setting up python3.13-minimal (3.13.0-2) ...
280s Setting up libpython3.13-stdlib:ppc64el (3.13.0-2) ...
280s Setting up liblapack3:ppc64el (3.12.0-3build2) ...
280s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/powerpc64le-linux-gnu/liblapack.so.3 (liblapack.so.3-powerpc64le-linux-gnu) in auto mode
280s Setting up python3.13 (3.13.0-2) ...
281s Setting up python3-all (3.12.7-1) ...
281s Setting up python3-numpy (1:1.26.4+ds-11build1) ...
285s Setting up python3-fastcluster (1.2.6-1build1) ...
285s Setting up autopkgtest-satdep (0) ...
285s Processing triggers for systemd (256.5-2ubuntu4) ...
286s Processing triggers for man-db (2.12.1-3) ...
286s Processing triggers for libc-bin (2.40-1ubuntu3) ...
288s (Reading database ... 75423 files and directories currently installed.)
288s Removing autopkgtest-satdep (0) ...
290s autopkgtest [00:57:01]: 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
290s autopkgtest [00:57:01]: test autodep8-python3: [-----------------------
290s Testing with python3.13:
290s Traceback (most recent call last):
290s   File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in <module>
290s     from . import multiarray
290s   File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in <module>
290s     from . import overrides
290s   File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in <module>
290s     from numpy.core._multiarray_umath import (
290s         add_docstring,  _get_implementing_args, _ArrayFunctionDispatcher)
290s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath'
290s 
290s During handling of the above exception, another exception occurred:
290s 
290s Traceback (most recent call last):
290s   File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in <module>
290s     from numpy.__config__ import show as show_config
290s   File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in <module>
290s     from numpy.core._multiarray_umath import (
290s     ...<3 lines>...
290s     )
290s   File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in <module>
290s     raise ImportError(msg)
290s ImportError: 
290s 
290s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE!
290s 
290s Importing the numpy C-extensions failed. This error can happen for
290s many reasons, often due to issues with your setup or how NumPy was
290s installed.
290s 
290s We have compiled some common reasons and troubleshooting tips at:
290s 
290s     https://numpy.org/devdocs/user/troubleshooting-importerror.html
290s 
290s Please note and check the following:
290s 
290s   * The Python version is: Python3.13 from "/usr/bin/python3.13"
290s   * The NumPy version is: "1.26.4"
290s 
290s and make sure that they are the versions you expect.
290s Please carefully study the documentation linked above for further help.
290s 
290s Original error was: No module named 'numpy.core._multiarray_umath'
290s 
290s 
290s The above exception was the direct cause of the following exception:
290s 
290s Traceback (most recent call last):
290s   File "<string>", line 1, in <module>
290s     import fastcluster; print(fastcluster)
290s     ^^^^^^^^^^^^^^^^^^
290s   File "/usr/lib/python3/dist-packages/fastcluster.py", line 26, in <module>
290s     from numpy import double, empty, array, ndarray, var, cov, dot, expand_dims, \
290s         ceil, sqrt
290s   File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in <module>
290s     raise ImportError(msg) from e
290s ImportError: Error importing numpy: you should not try to import numpy from
290s         its source directory; please exit the numpy source tree, and relaunch
290s         your python interpreter from there.
290s autopkgtest [00:57:01]: test autodep8-python3: -----------------------]
291s autodep8-python3     FAIL non-zero exit status 1
291s autopkgtest [00:57:02]: test autodep8-python3:  - - - - - - - - - - results - - - - - - - - - -
291s autopkgtest [00:57:02]: @@@@@@@@@@@@@@@@@@@@ summary
291s run-unit-test        PASS
291s autodep8-python3     FAIL non-zero exit status 1
297s nova [W] Using flock in prodstack6-ppc64el
297s Creating nova instance adt-plucky-ppc64el-r-cran-fastcluster-20241114-005211-juju-7f2275-prod-proposed-migration-environment-15-2550a304-55f2-40b0-8ed8-f2fbb9083607 from image adt/ubuntu-plucky-ppc64el-server-20241113.img (UUID 0c5715b6-5cca-4485-b8bf-b85dfd917a5f)...
297s nova [W] Using flock in prodstack6-ppc64el
297s flock: timeout while waiting to get lock
297s Creating nova instance adt-plucky-ppc64el-r-cran-fastcluster-20241114-005211-juju-7f2275-prod-proposed-migration-environment-15-2550a304-55f2-40b0-8ed8-f2fbb9083607 from image adt/ubuntu-plucky-ppc64el-server-20241113.img (UUID 0c5715b6-5cca-4485-b8bf-b85dfd917a5f)...