0s autopkgtest [22:22:37]: starting date and time: 2024-11-14 22:22:37+0000
  0s autopkgtest [22:22:37]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky
  0s autopkgtest [22:22:37]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.ownj2d5c/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 builder-cpu2-ram4-disk20 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-30.secgroup --name adt-plucky-amd64-r-cran-fastcluster-20241114-222237-juju-7f2275-prod-proposed-migration-environment-15-903047cd-3df4-47f8-af07-2f8d3adec5fc --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration-amd64 -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/
 40s autopkgtest [22:23:17]: testbed dpkg architecture: amd64
 40s autopkgtest [22:23:17]: testbed apt version: 2.9.8
 40s autopkgtest [22:23:17]: @@@@@@@@@@@@@@@@@@@@ test bed setup
 41s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB]
 41s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [106 kB]
 41s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B]
 41s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [16.1 kB]
 41s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [1037 kB]
 41s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [144 kB]
 41s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [79.0 kB]
 41s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [32.6 kB]
 41s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [296 kB]
 41s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [807 kB]
 41s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [9388 B]
 41s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [740 B]
 41s Fetched 2609 kB in 1s (2975 kB/s)
 42s Reading package lists...
 44s Reading package lists...
 44s Building dependency tree...
 44s Reading state information...
 44s Calculating upgrade...
 45s The following NEW packages will be installed:
 45s   python3.13-gdbm
 45s The following packages will be upgraded:
 45s   libcap-ng0 libpython3-stdlib pastebinit python3 python3-gdbm python3-minimal
 45s   python3-systemd
 45s 7 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
 45s Need to get 178 kB of archives.
 45s After this operation, 256 kB of additional disk space will be used.
 45s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-minimal amd64 3.12.7-1 [27.4 kB]
 45s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3 amd64 3.12.7-1 [24.0 kB]
 45s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libpython3-stdlib amd64 3.12.7-1 [10.0 kB]
 45s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 libcap-ng0 amd64 0.8.5-3build1 [15.6 kB]
 45s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-gdbm amd64 3.13.0-2 [31.3 kB]
 45s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-gdbm amd64 3.12.7-1 [8642 B]
 45s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 pastebinit all 1.7.1-1 [14.9 kB]
 45s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-systemd amd64 235-1build5 [45.7 kB]
 45s Fetched 178 kB in 0s (426 kB/s)
 46s (Reading database ... 
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(Reading database ... 95%
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(Reading database ... 75542 files and directories currently installed.)
 46s Preparing to unpack .../python3-minimal_3.12.7-1_amd64.deb ...
 46s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ...
 46s Setting up python3-minimal (3.12.7-1) ...
 46s (Reading database ... 
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(Reading database ... 100%
(Reading database ... 75542 files and directories currently installed.)
 46s Preparing to unpack .../python3_3.12.7-1_amd64.deb ...
 46s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ...
 46s Preparing to unpack .../libpython3-stdlib_3.12.7-1_amd64.deb ...
 46s Unpacking libpython3-stdlib:amd64 (3.12.7-1) over (3.12.6-0ubuntu1) ...
 46s Preparing to unpack .../libcap-ng0_0.8.5-3build1_amd64.deb ...
 46s Unpacking libcap-ng0:amd64 (0.8.5-3build1) over (0.8.5-1) ...
 46s Setting up libcap-ng0:amd64 (0.8.5-3build1) ...
 46s Selecting previously unselected package python3.13-gdbm.
 46s (Reading database ... 
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(Reading database ... 75542 files and directories currently installed.)
 46s Preparing to unpack .../python3.13-gdbm_3.13.0-2_amd64.deb ...
 46s Unpacking python3.13-gdbm (3.13.0-2) ...
 46s Preparing to unpack .../python3-gdbm_3.12.7-1_amd64.deb ...
 46s Unpacking python3-gdbm:amd64 (3.12.7-1) over (3.12.6-1ubuntu1) ...
 46s Preparing to unpack .../pastebinit_1.7.1-1_all.deb ...
 46s Unpacking pastebinit (1.7.1-1) over (1.7.0-1) ...
 46s Preparing to unpack .../python3-systemd_235-1build5_amd64.deb ...
 46s Unpacking python3-systemd (235-1build5) over (235-1build4) ...
 46s Setting up python3.13-gdbm (3.13.0-2) ...
 46s Setting up libpython3-stdlib:amd64 (3.12.7-1) ...
 46s Setting up python3 (3.12.7-1) ...
 46s Setting up python3-systemd (235-1build5) ...
 46s Setting up python3-gdbm:amd64 (3.12.7-1) ...
 46s Setting up pastebinit (1.7.1-1) ...
 46s Processing triggers for libc-bin (2.40-1ubuntu3) ...
 46s Processing triggers for man-db (2.12.1-3) ...
 47s Reading package lists...
 47s Building dependency tree...
 47s Reading state information...
 47s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 48s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease
 48s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease
 48s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease
 48s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease
 49s Reading package lists...
 49s Reading package lists...
 49s Building dependency tree...
 49s Reading state information...
 49s Calculating upgrade...
 49s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 49s Reading package lists...
 49s Building dependency tree...
 49s Reading state information...
 50s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 52s autopkgtest [22:23:29]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 13:41:20 UTC 2024
 52s autopkgtest [22:23:29]: @@@@@@@@@@@@@@@@@@@@ apt-source r-cran-fastcluster
 54s Get:1 http://ftpmaster.internal/ubuntu plucky/universe r-cran-fastcluster 1.2.6-1build1 (dsc) [2272 B]
 54s Get:2 http://ftpmaster.internal/ubuntu plucky/universe r-cran-fastcluster 1.2.6-1build1 (tar) [208 kB]
 54s Get:3 http://ftpmaster.internal/ubuntu plucky/universe r-cran-fastcluster 1.2.6-1build1 (diff) [4828 B]
 54s gpgv: Signature made Wed Apr 10 18:03:18 2024 UTC
 54s gpgv:                using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2
 54s gpgv: Can't check signature: No public key
 54s dpkg-source: warning: cannot verify inline signature for ./r-cran-fastcluster_1.2.6-1build1.dsc: no acceptable signature found
 55s autopkgtest [22:23:32]: testing package r-cran-fastcluster version 1.2.6-1build1
 55s autopkgtest [22:23:32]: build not needed
 55s autopkgtest [22:23:32]: test run-unit-test: preparing testbed
 56s Reading package lists...
 57s Building dependency tree...
 57s Reading state information...
 57s Starting pkgProblemResolver with broken count: 0
 57s Starting 2 pkgProblemResolver with broken count: 0
 57s Done
 57s The following additional packages will be installed:
 57s   fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono libblas3
 57s   libcairo2 libdatrie1 libdeflate0 libfontconfig1 libgfortran5 libgomp1
 57s   libgraphite2-3 libharfbuzz0b libice6 libjbig0 libjpeg-turbo8 libjpeg8
 57s   liblapack3 liblerc4 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0
 57s   libpaper-utils libpaper1 libpixman-1-0 libsharpyuv0 libsm6 libtcl8.6
 57s   libthai-data libthai0 libtiff6 libtk8.6 libwebp7 libxcb-render0 libxcb-shm0
 57s   libxft2 libxrender1 libxss1 libxt6t64 python3-fastcluster python3-numpy
 57s   r-base-core r-cran-fastcluster unzip x11-common xdg-utils zip
 57s Suggested packages:
 57s   tcl8.6 tk8.6 gcc gfortran python-numpy-doc python3-dev python3-pytest
 57s   elpa-ess r-doc-info | r-doc-pdf r-mathlib r-base-html
 57s Recommended packages:
 57s   python3-scipy r-recommended r-base-dev r-doc-html libfile-mimeinfo-perl
 57s   libnet-dbus-perl libx11-protocol-perl x11-utils x11-xserver-utils
 57s The following NEW packages will be installed:
 57s   autopkgtest-satdep fontconfig fontconfig-config fonts-dejavu-core
 57s   fonts-dejavu-mono libblas3 libcairo2 libdatrie1 libdeflate0 libfontconfig1
 57s   libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libice6 libjbig0
 57s   libjpeg-turbo8 libjpeg8 liblapack3 liblerc4 libpango-1.0-0
 57s   libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpixman-1-0
 57s   libsharpyuv0 libsm6 libtcl8.6 libthai-data libthai0 libtiff6 libtk8.6
 57s   libwebp7 libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxss1 libxt6t64
 57s   python3-fastcluster python3-numpy r-base-core r-cran-fastcluster unzip
 57s   x11-common xdg-utils zip
 57s 0 upgraded, 48 newly installed, 0 to remove and 0 not upgraded.
 57s Need to get 45.0 MB/45.0 MB of archives.
 57s After this operation, 107 MB of additional disk space will be used.
 57s Get:1 /tmp/autopkgtest.wOlcOF/1-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [720 B]
 57s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB]
 58s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-core all 2.37-8 [835 kB]
 58s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig-config amd64 2.15.0-1.1ubuntu2 [37.3 kB]
 58s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontconfig1 amd64 2.15.0-1.1ubuntu2 [139 kB]
 58s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig amd64 2.15.0-1.1ubuntu2 [180 kB]
 58s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.0-3build2 [247 kB]
 58s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 libpixman-1-0 amd64 0.44.0-3 [427 kB]
 58s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-render0 amd64 1.17.0-2 [16.2 kB]
 58s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-shm0 amd64 1.17.0-2 [5758 B]
 58s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 libxrender1 amd64 1:0.9.10-1.1build1 [19.0 kB]
 58s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 libcairo2 amd64 1.18.2-2 [569 kB]
 58s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 libdatrie1 amd64 0.2.13-3build1 [19.0 kB]
 58s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate0 amd64 1.22-1 [64.5 kB]
 58s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 14.2.0-8ubuntu1 [909 kB]
 58s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 libgomp1 amd64 14.2.0-8ubuntu1 [148 kB]
 58s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB]
 58s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 libharfbuzz0b amd64 10.0.1-1 [540 kB]
 58s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 x11-common all 1:7.7+23ubuntu3 [21.7 kB]
 58s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 libice6 amd64 2:1.1.1-1 [44.1 kB]
 58s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg-turbo8 amd64 2.1.5-2ubuntu2 [150 kB]
 58s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B]
 58s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.0-3build2 [2668 kB]
 58s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 liblerc4 amd64 4.0.0+ds-4ubuntu2 [179 kB]
 58s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 libthai-data all 0.1.29-2build1 [158 kB]
 58s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 libthai0 amd64 0.1.29-2build1 [18.9 kB]
 58s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 libpango-1.0-0 amd64 1.54.0+ds-3 [252 kB]
 58s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 libpangoft2-1.0-0 amd64 1.54.0+ds-3 [51.6 kB]
 58s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 libpangocairo-1.0-0 amd64 1.54.0+ds-3 [29.1 kB]
 58s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 libpaper1 amd64 1.1.29build1 [13.4 kB]
 58s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 libpaper-utils amd64 1.1.29build1 [8650 B]
 58s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 libsharpyuv0 amd64 1.4.0-0.1 [17.5 kB]
 58s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 libsm6 amd64 2:1.2.4-1 [17.4 kB]
 58s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 libtcl8.6 amd64 8.6.15+dfsg-2 [1085 kB]
 58s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB]
 58s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebp7 amd64 1.4.0-0.1 [231 kB]
 58s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 libtiff6 amd64 4.5.1+git230720-4ubuntu4 [200 kB]
 58s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 libxft2 amd64 2.3.6-1build1 [45.3 kB]
 58s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 libxss1 amd64 1:1.2.3-1build3 [7204 B]
 58s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 libtk8.6 amd64 8.6.15-1 [862 kB]
 58s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 libxt6t64 amd64 1:1.2.1-1.2build1 [171 kB]
 58s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-numpy amd64 1:1.26.4+ds-11build1 [4479 kB]
 58s Get:43 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-fastcluster amd64 1.2.6-1build1 [42.7 kB]
 58s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 zip amd64 3.0-14ubuntu1 [185 kB]
 58s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 unzip amd64 6.0-28ubuntu6 [181 kB]
 58s Get:46 http://ftpmaster.internal/ubuntu plucky/main amd64 xdg-utils all 1.2.1-0ubuntu1 [67.5 kB]
 58s Get:47 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-base-core amd64 4.4.2-1 [28.9 MB]
 59s Get:48 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-fastcluster amd64 1.2.6-1build1 [192 kB]
 60s Preconfiguring packages ...
 60s Fetched 45.0 MB in 2s (20.0 MB/s)
 60s Selecting previously unselected package fonts-dejavu-mono.
 60s (Reading database ... 
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(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 ... 75554 files and directories currently installed.)
 60s Preparing to unpack .../00-fonts-dejavu-mono_2.37-8_all.deb ...
 60s Unpacking fonts-dejavu-mono (2.37-8) ...
 60s Selecting previously unselected package fonts-dejavu-core.
 60s Preparing to unpack .../01-fonts-dejavu-core_2.37-8_all.deb ...
 60s Unpacking fonts-dejavu-core (2.37-8) ...
 60s Selecting previously unselected package fontconfig-config.
 60s Preparing to unpack .../02-fontconfig-config_2.15.0-1.1ubuntu2_amd64.deb ...
 60s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ...
 60s Selecting previously unselected package libfontconfig1:amd64.
 60s Preparing to unpack .../03-libfontconfig1_2.15.0-1.1ubuntu2_amd64.deb ...
 60s Unpacking libfontconfig1:amd64 (2.15.0-1.1ubuntu2) ...
 60s Selecting previously unselected package fontconfig.
 60s Preparing to unpack .../04-fontconfig_2.15.0-1.1ubuntu2_amd64.deb ...
 60s Unpacking fontconfig (2.15.0-1.1ubuntu2) ...
 60s Selecting previously unselected package libblas3:amd64.
 60s Preparing to unpack .../05-libblas3_3.12.0-3build2_amd64.deb ...
 60s Unpacking libblas3:amd64 (3.12.0-3build2) ...
 60s Selecting previously unselected package libpixman-1-0:amd64.
 60s Preparing to unpack .../06-libpixman-1-0_0.44.0-3_amd64.deb ...
 60s Unpacking libpixman-1-0:amd64 (0.44.0-3) ...
 60s Selecting previously unselected package libxcb-render0:amd64.
 60s Preparing to unpack .../07-libxcb-render0_1.17.0-2_amd64.deb ...
 60s Unpacking libxcb-render0:amd64 (1.17.0-2) ...
 60s Selecting previously unselected package libxcb-shm0:amd64.
 60s Preparing to unpack .../08-libxcb-shm0_1.17.0-2_amd64.deb ...
 60s Unpacking libxcb-shm0:amd64 (1.17.0-2) ...
 60s Selecting previously unselected package libxrender1:amd64.
 60s Preparing to unpack .../09-libxrender1_1%3a0.9.10-1.1build1_amd64.deb ...
 60s Unpacking libxrender1:amd64 (1:0.9.10-1.1build1) ...
 60s Selecting previously unselected package libcairo2:amd64.
 60s Preparing to unpack .../10-libcairo2_1.18.2-2_amd64.deb ...
 60s Unpacking libcairo2:amd64 (1.18.2-2) ...
 60s Selecting previously unselected package libdatrie1:amd64.
 60s Preparing to unpack .../11-libdatrie1_0.2.13-3build1_amd64.deb ...
 60s Unpacking libdatrie1:amd64 (0.2.13-3build1) ...
 60s Selecting previously unselected package libdeflate0:amd64.
 60s Preparing to unpack .../12-libdeflate0_1.22-1_amd64.deb ...
 60s Unpacking libdeflate0:amd64 (1.22-1) ...
 60s Selecting previously unselected package libgfortran5:amd64.
 60s Preparing to unpack .../13-libgfortran5_14.2.0-8ubuntu1_amd64.deb ...
 60s Unpacking libgfortran5:amd64 (14.2.0-8ubuntu1) ...
 60s Selecting previously unselected package libgomp1:amd64.
 60s Preparing to unpack .../14-libgomp1_14.2.0-8ubuntu1_amd64.deb ...
 60s Unpacking libgomp1:amd64 (14.2.0-8ubuntu1) ...
 60s Selecting previously unselected package libgraphite2-3:amd64.
 60s Preparing to unpack .../15-libgraphite2-3_1.3.14-2ubuntu1_amd64.deb ...
 60s Unpacking libgraphite2-3:amd64 (1.3.14-2ubuntu1) ...
 60s Selecting previously unselected package libharfbuzz0b:amd64.
 60s Preparing to unpack .../16-libharfbuzz0b_10.0.1-1_amd64.deb ...
 60s Unpacking libharfbuzz0b:amd64 (10.0.1-1) ...
 60s Selecting previously unselected package x11-common.
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 71s 
 71s R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
 71s Copyright (C) 2024 The R Foundation for Statistical Computing
 71s Platform: x86_64-pc-linux-gnu
 71s 
 71s R is free software and comes with ABSOLUTELY NO WARRANTY.
 71s You are welcome to redistribute it under certain conditions.
 71s Type 'license()' or 'licence()' for distribution details.
 71s 
 71s R is a collaborative project with many contributors.
 71s Type 'contributors()' for more information and
 71s 'citation()' on how to cite R or R packages in publications.
 71s 
 71s Type 'demo()' for some demos, 'help()' for on-line help, or
 71s 'help.start()' for an HTML browser interface to help.
 71s Type 'q()' to quit R.
 71s 
 71s > #  fastcluster: Fast hierarchical clustering routines for R and Python
 71s > #
 71s > #  Copyright:
 71s > #    * Until package version 1.1.23: © 2011 Daniel Müllner <https://danifold.net>
 71s > #    * All changes from version 1.1.24 on: © Google Inc. <https://www.google.com>
 71s > #
 71s > # Test script for the R interface
 71s > 
 71s > seed = as.integer(runif(1, 0, 1e9))
 71s > set.seed(seed)
 71s > cat(sprintf("Random seed: %d\n",seed))
 71s Random seed: 566905721
 71s > 
 71s > print_seed <- function() {
 71s +   return(sprintf('
 71s + Please send a report to the author of the \'fastcluster\' package, Daniel Müllner.
 71s + For contact details, see <https://danifold.net>. To make the error
 71s + reproducible, you must include the following number (the random seed value) in
 71s + your error report: %d.\n\n', seed))
 71s + }
 71s > 
 71s > hasWardD2 = getRversion() >= '3.1.0'
 71s > 
 71s > # Compare two dendrograms and check whether they are equal, except that
 71s > # ties may be resolved differently.
 71s > compare <- function(dg1, dg2) {
 71s +   h1 <- dg1$height
 71s +   h2 <- dg2$height
 71s +   # "height" vectors may have small numerical errors.
 71s +   rdiffs <- abs(h1-h2)/pmax(abs(h1),abs(h2))
 71s +   rdiffs = rdiffs[complete.cases(rdiffs)]
 71s +   rel_error <-  max(rdiffs)
 71s +   # We allow a relative error of 1e-13.
 71s +   if (rel_error>1e-13) {
 71s +     print(h1)
 71s +     print(h2)
 71s +     cat(sprintf('Height vectors differ! The maximum relative error is %e.\n', rel_error))
 71s +     return(FALSE)
 71s +   }
 71s +   # Filter the indices where consecutive merging distances are distinct.
 71s +   d = diff(dg1$height)
 71s +   b = (c(d,1)!=0 & c(1,d)!=0)
 71s +   #cat(sprintf("Percentage of indices where we can test: %g.\n",100.0*length(b[b])/length(b)))
 71s +   if (any(b)) {
 71s +     m1 = dg1$merge[b,]
 71s +     m2 = dg2$merge[b,]
 71s + 
 71s +     r = function(i) {
 71s +       if (i<0) {
 71s +         return(1)
 71s +       }
 71s +       else {
 71s +         return(b[i])
 71s +       }
 71s +     }
 71s + 
 71s +     f = sapply(m1,r)
 71s +     fm1 = m1*f
 71s +     fm2 = m2*f
 71s +     # The "merge" matrices must be identical whereever indices are not ambiguous
 71s +     # due to ties.
 71s +     if (!identical(fm1,fm2)) {
 71s +       cat('Merge matrices differ!\n')
 71s +       return(FALSE)
 71s +     }
 71s +     # Compare the "order" vectors only if all merging distances were distinct.
 71s +     if (all(b) && !identical(dg1$order,dg2$order)) {
 71s +       cat('Order vectors differ!\n')
 71s +       return(FALSE)
 71s +     }
 71s +   }
 71s +   return(TRUE)
 71s + }
 71s > 
 71s > # Generate uniformly distributed random data
 71s > generate.uniform <- function() {
 71s +   n = sample(10:1000,1)
 71s +   range_exp = runif(1,min=-10, max=10)
 71s +   cat(sprintf("Number of sample points: %d\n",n))
 71s +   cat(sprintf("Dissimilarity range: [0,%g]\n",10^range_exp))
 71s +   d = runif(n*(n-1)/2, min=0, max=10^range_exp)
 71s +   # Fake a compressed distance matrix
 71s +   attributes(d) <- NULL
 71s +   attr(d,"Size") <- n
 71s +   attr(d, "call") <- 'N/A'
 71s +   class(d) <- "dist"
 71s +   return(d)
 71s + }
 71s > 
 71s > # Generate normally distributed random data
 71s > generate.normal <- function() {
 71s +   n = sample(10:1000,1)
 71s +   dim = sample(2:20,1)
 71s + 
 71s +   cat (sprintf("Number of sample points: %d\n",n))
 71s +   cat (sprintf("Dimension: %d\n",dim))
 71s + 
 71s +   pcd = matrix(rnorm(n*dim), c(n,dim))
 71s +   d = dist(pcd)
 71s +   return(d)
 71s + }
 71s > 
 71s > # Test the clustering functions when a distance matrix is given.
 71s > test.dm <-  function(d) {
 71s +   d2 = d
 71s +   if (hasWardD2) {
 71s +     methods = c('single','complete','average','mcquitty','ward.D','ward.D2','centroid','median')
 71s +   }
 71s +   else {
 71s +     methods = c('single','complete','average','mcquitty','ward','centroid','median')
 71s +   }
 71s +   for (method in methods) {
 71s +     cat(paste('Method :', method, '\n'))
 71s +     dg_stats       = stats::hclust(d, method=method)
 71s +     if (method == 'ward') {
 71s +       method = 'ward.D'
 71s +     }
 71s +     dg_fastcluster = fastcluster::hclust(d, method=method)
 71s +     if (!identical(d,d2)) {
 71s +       cat('Input array was corrupted!\n')
 71s +       stop(print_seed())
 71s +     }
 71s +     if (!compare(dg_stats, dg_fastcluster)) {
 71s +       stop(print_seed())
 71s +     }
 71s +   }
 71s +   cat('Passed.\n')
 71s + }
 71s > 
 71s > # Test the clustering functions for vector input in Euclidean space.
 71s > test.vector <-  function() {
 71s +   # generate test data
 71s +   n = sample(10:1000,1)
 71s +   dim = sample(2:20,1)
 71s +   cat (sprintf("Number of sample points: %d\n",n))
 71s +   cat (sprintf("Dimension: %d\n",dim))
 71s + 
 71s +   range_exp = runif(1,min=-10, max=10)
 71s +   pcd = matrix(rnorm(n*dim, sd=10^range_exp), c(n,dim))
 71s +   pcd2 = pcd
 71s +   # test
 71s +   method='single'
 71s +   cat(paste('Method:', method, '\n'))
 71s +   for (metric in c('euclidean', 'maximum', 'manhattan', 'canberra', 'minkowski')) {
 71s +     cat(paste('    Metric:', metric, '\n'))
 71s +     if (metric=='minkowski') {
 71s +       p = runif(1, min=1.0, max=10.0)
 71s +       cat (sprintf("    p: %g\n",p));
 71s +       dg_fastcluster = fastcluster::hclust.vector(pcd, method=method, metric=metric, p=p)
 71s +       d = dist(pcd, method=metric, p=p)
 71s +     }
 71s +     else {
 71s +       dg_fastcluster = fastcluster::hclust.vector(pcd, method=method, metric=metric)
 71s +       d = dist(pcd, method=metric)
 71s +     }
 71s +     d2 = d
 71s +     dg_fastcluster_dist = fastcluster::hclust(d, method=method)
 71s +     if (!identical(d,d2) || !identical(pcd,pcd2)) {
 71s +       cat('Input array was corrupted!\n')
 71s +       stop(print_seed())
 71s +     }
 71s +     if (!compare(dg_fastcluster_dist, dg_fastcluster)) {
 71s +       stop(print_seed())
 71s +     }
 71s +   }
 71s +   for (method in c('ward','centroid','median') ) {
 71s +     cat(paste('Method:', method, '\n'))
 71s +     dg_fastcluster = fastcluster::hclust.vector(pcd, method=method)
 71s +     if (!identical(pcd,pcd2)) {
 71s +       cat('Input array was corrupted!\n')
 71s +       stop(print_seed())
 71s +     }
 71s +     d = dist(pcd)
 71s +     if(method == "ward" && hasWardD2) {
 71s +       method = "ward.D2"
 71s +     }
 71s +     else
 71s +     {
 71s +       # Workaround: fastcluster::hclust expects _squared_ euclidean distances.
 71s +       d = d^2
 71s +     }
 71s +     d2 = d
 71s +     dg_fastcluster_dist = fastcluster::hclust(d, method=method)
 71s +     if (!identical(d,d2)) {
 71s +       cat('Input array was corrupted!\n')
 71s +       stop(print_seed())
 71s +     }
 71s +     if(method != "ward.D2") {
 71s +       dg_fastcluster_dist$height = sqrt(dg_fastcluster_dist$height)
 71s +     }
 71s +     # The Euclidean methods may have small numerical errors due to squaring/
 71s +     # taking the root in the Euclidean distances.
 71s +     if (!compare(dg_fastcluster_dist, dg_fastcluster)) {
 71s +       stop(print_seed())
 71s +     }
 71s +   }
 71s +   cat('Passed.\n')
 71s + }
 71s > 
 71s > # Test the single linkage function with the "binary" metric
 71s > test.vector.binary <- function() {
 71s +   # generate test data
 71s +   cat (sprintf("Uniform sampling for the 'binary' metric:\n"))
 71s +   n = sample(10:400,1)
 71s +   dim = sample(n:(2*n),1)
 71s +   cat (sprintf("Number of sample points: %d\n",n))
 71s +   cat (sprintf("Dimension: %d\n",dim))
 71s +   pcd = matrix(sample(-1:2, n*dim, replace=T), c(n,dim))
 71s +   pcd2 = pcd
 71s +   # test
 71s +   method='single'
 71s +   metric='binary'
 71s +   cat(paste('Method:', method, '\n'))
 71s +   cat(paste('    Metric:', metric, '\n'))
 71s +   dg_fastcluster = fastcluster::hclust.vector(pcd, method=method, metric=metric)
 71s +   d = dist(pcd, method=metric)
 71s +   d2 = d
 71s +   dg_fastcluster_dist       = fastcluster::hclust(d, method=method)
 71s +   if (!identical(d,d2) || !identical(d,d2)) {
 71s +     cat('Input array was corrupted!\n')
 71s +     stop(print_seed())
 71s +   }
 71s +   if (!compare(dg_fastcluster_dist, dg_fastcluster)) {
 71s +     stop(print_seed())
 71s +   }
 71s +   cat('Passed.\n')
 71s + }
 71s > 
 71s > 
 71s > N = 15
 71s > for (i in (1:N)) {
 71s +   if (i%%2==1) {
 71s +     cat(sprintf('Random test %d of %d (uniform distribution of distances):\n',i,2*N))
 71s +     d = generate.uniform()
 71s +   }
 71s +   else {
 71s +     cat(sprintf('Random test %d of %d (Gaussian density):\n',i,2*N))
 71s +     d = generate.normal()
 71s +   }
 71s +   test.dm(d)
 71s + }
 71s Random test 1 of 30 (uniform distribution of distances):
 71s Number of sample points: 561
 71s Dissimilarity range: [0,8.01321e-09]
 71s Method : single 
 71s Method : complete 
 71s Method : average 
 71s Method : mcquitty 
 71s Method : ward.D 
 71s Method : ward.D2 
 71s Method : centroid 
 71s Method : median 
 71s Passed.
 71s Random test 2 of 30 (Gaussian density):
 71s Number of sample points: 31
 71s Dimension: 13
 71s Method : single 
 71s Method : complete 
 71s Method : average 
 71s Method : mcquitty 
 71s Method : ward.D 
 71s Method : ward.D2 
 71s Method : centroid 
 71s Method : median 
 71s Passed.
 71s Random test 3 of 30 (uniform distribution of distances):
 71s Number of sample points: 732
 71s Dissimilarity range: [0,7.1002e-09]
 71s Method : single 
 71s Method : complete 
 71s Method : average 
 71s Method : mcquitty 
 71s Method : ward.D 
 71s Method : ward.D2 
 71s Method : centroid 
 71s Method : median 
 71s Passed.
 71s Random test 4 of 30 (Gaussian density):
 71s Number of sample points: 319
 71s Dimension: 14
 71s Method : single 
 71s Method : complete 
 71s Method : average 
 71s Method : mcquitty 
 71s Method : ward.D 
 71s Method : ward.D2 
 71s Method : centroid 
 71s Method : median 
 71s Passed.
 71s Random test 5 of 30 (uniform distribution of distances):
 71s Number of sample points: 173
 71s Dissimilarity range: [0,5.45937e-08]
 71s Method : single 
 71s Method : complete 
 71s Method : average 
 71s Method : mcquitty 
 71s Method : ward.D 
 71s Method : ward.D2 
 71s Method : centroid 
 71s Method : median 
 71s Passed.
 71s Random test 6 of 30 (Gaussian density):
 71s Number of sample points: 400
 71s Dimension: 3
 71s Method : single 
 71s Method : complete 
 71s Method : average 
 71s Method : mcquitty 
 71s Method : ward.D 
 71s Method : ward.D2 
 71s Method : centroid 
 71s Method : median 
 71s Passed.
 71s Random test 7 of 30 (uniform distribution of distances):
 71s Number of sample points: 217
 71s Dissimilarity range: [0,1177.08]
 71s Method : single 
 71s Method : complete 
 71s Method : average 
 71s Method : mcquitty 
 71s Method : ward.D 
 71s Method : ward.D2 
 71s Method : centroid 
 71s Method : median 
 71s Passed.
 71s Random test 8 of 30 (Gaussian density):
 71s Number of sample points: 146
 71s Dimension: 20
 71s Method : single 
 71s Method : complete 
 71s Method : average 
 71s Method : mcquitty 
 71s Method : ward.D 
 71s Method : ward.D2 
 71s Method : centroid 
 71s Method : median 
 71s Passed.
 71s Random test 9 of 30 (uniform distribution of distances):
 71s Number of sample points: 444
 71s Dissimilarity range: [0,0.000162817]
 71s Method : single 
 71s Method : complete 
 71s Method : average 
 71s Method : mcquitty 
 71s Method : ward.D 
 71s Method : ward.D2 
 71s Method : centroid 
 71s Method : median 
 71s Passed.
 71s Random test 10 of 30 (Gaussian density):
 71s Number of sample points: 244
 71s Dimension: 5
 71s Method : single 
 71s Method : complete 
 71s Method : average 
 71s Method : mcquitty 
 71s Method : ward.D 
 71s Method : ward.D2 
 71s Method : centroid 
 71s Method : median 
 71s Passed.
 71s Random test 11 of 30 (uniform distribution of distances):
 71s Number of sample points: 953
 71s Dissimilarity range: [0,0.0019966]
 71s Method : single 
 71s Method : complete 
 71s Method : average 
 71s Method : mcquitty 
 71s Method : ward.D 
 71s Method : ward.D2 
 71s Method : centroid 
 71s Method : median 
 71s Passed.
 71s Random test 12 of 30 (Gaussian density):
 71s Number of sample points: 525
 71s Dimension: 8
 71s Method : single 
 71s Method : complete 
 71s Method : average 
 71s Method : mcquitty 
 71s Method : ward.D 
 71s Method : ward.D2 
 71s Method : centroid 
 71s Method : median 
 71s Passed.
 71s Random test 13 of 30 (uniform distribution of distances):
 71s Number of sample points: 487
 71s Dissimilarity range: [0,1228.03]
 71s Method : single 
 71s Method : complete 
 71s Method : average 
 71s Method : mcquitty 
 71s Method : ward.D 
 71s Method : ward.D2 
 71s Method : centroid 
 71s Method : median 
 71s Passed.
 71s Random test 14 of 30 (Gaussian density):
 71s Number of sample points: 176
 71s Dimension: 18
 71s Method : single 
 71s Method : complete 
 71s Method : average 
 71s Method : mcquitty 
 71s Method : ward.D 
 71s Method : ward.D2 
 71s Method : centroid 
 71s Method : median 
 71s Passed.
 71s Random test 15 of 30 (uniform distribution of distances):
 71s Number of sample points: 305
 71s Dissimilarity range: [0,19956.1]
 71s Method : single 
 71s Method : complete 
 71s Method : average 
 72s Method : mcquitty 
 72s Method : ward.D 
 72s Method : ward.D2 
 72s Method : centroid 
 72s Method : median 
 72s Passed.
 72s > for (i in (N+1:N)) {
 72s +   cat(sprintf('Random test %d of %d (Gaussian density):\n',i,2*N))
 72s +   test.vector()
 72s +   test.vector.binary()
 72s + }
 72s Random test 16 of 30 (Gaussian density):
 72s Number of sample points: 569
 72s Dimension: 5
 72s Method: single 
 72s     Metric: euclidean 
 72s     Metric: maximum 
 72s     Metric: manhattan 
 72s     Metric: canberra 
 72s     Metric: minkowski 
 72s     p: 7.97347
 72s Method: ward 
 72s Method: centroid 
 72s Method: median 
 72s Passed.
 72s Uniform sampling for the 'binary' metric:
 72s Number of sample points: 315
 72s Dimension: 486
 72s Method: single 
 72s     Metric: binary 
 72s Passed.
 72s Random test 17 of 30 (Gaussian density):
 72s Number of sample points: 911
 72s Dimension: 3
 72s Method: single 
 72s     Metric: euclidean 
 72s     Metric: maximum 
 72s     Metric: manhattan 
 72s     Metric: canberra 
 72s     Metric: minkowski 
 72s     p: 8.60682
 72s Method: ward 
 72s Method: centroid 
 72s Method: median 
 72s Passed.
 72s Uniform sampling for the 'binary' metric:
 72s Number of sample points: 349
 72s Dimension: 582
 72s Method: single 
 72s     Metric: binary 
 73s Passed.
 73s Random test 18 of 30 (Gaussian density):
 73s Number of sample points: 919
 73s Dimension: 12
 73s Method: single 
 73s     Metric: euclidean 
 73s     Metric: maximum 
 73s     Metric: manhattan 
 73s     Metric: canberra 
 73s     Metric: minkowski 
 73s     p: 6.88842
 73s Method: ward 
 73s Method: centroid 
 74s Method: median 
 74s Passed.
 74s Uniform sampling for the 'binary' metric:
 74s Number of sample points: 304
 74s Dimension: 559
 74s Method: single 
 74s     Metric: binary 
 74s Passed.
 74s Random test 19 of 30 (Gaussian density):
 74s Number of sample points: 627
 74s Dimension: 19
 74s Method: single 
 74s     Metric: euclidean 
 74s     Metric: maximum 
 74s     Metric: manhattan 
 74s     Metric: canberra 
 74s     Metric: minkowski 
 74s     p: 4.47277
 74s Method: ward 
 74s Method: centroid 
 74s Method: median 
 75s Passed.
 75s Uniform sampling for the 'binary' metric:
 75s Number of sample points: 82
 75s Dimension: 124
 75s Method: single 
 75s     Metric: binary 
 75s Passed.
 75s Random test 20 of 30 (Gaussian density):
 75s Number of sample points: 782
 75s Dimension: 12
 75s Method: single 
 75s     Metric: euclidean 
 75s     Metric: maximum 
 75s     Metric: manhattan 
 75s     Metric: canberra 
 75s     Metric: minkowski 
 75s     p: 9.00556
 75s Method: ward 
 75s Method: centroid 
 75s Method: median 
 75s Passed.
 75s Uniform sampling for the 'binary' metric:
 75s Number of sample points: 230
 75s Dimension: 251
 75s Method: single 
 75s     Metric: binary 
 75s Passed.
 75s Random test 21 of 30 (Gaussian density):
 75s Number of sample points: 372
 75s Dimension: 9
 75s Method: single 
 75s     Metric: euclidean 
 75s     Metric: maximum 
 75s     Metric: manhattan 
 75s     Metric: canberra 
 75s     Metric: minkowski 
 75s     p: 5.33924
 75s Method: ward 
 75s Method: centroid 
 75s Method: median 
 75s Passed.
 75s Uniform sampling for the 'binary' metric:
 75s Number of sample points: 217
 75s Dimension: 305
 75s Method: single 
 75s     Metric: binary 
 75s Passed.
 75s Random test 22 of 30 (Gaussian density):
 75s Number of sample points: 209
 75s Dimension: 2
 75s Method: single 
 75s     Metric: euclidean 
 75s     Metric: maximum 
 75s     Metric: manhattan 
 75s     Metric: canberra 
 75s     Metric: minkowski 
 75s     p: 6.8808
 75s Method: ward 
 75s Method: centroid 
 75s Method: median 
 75s Passed.
 75s Uniform sampling for the 'binary' metric:
 75s Number of sample points: 10
 75s Dimension: 14
 75s Method: single 
 75s     Metric: binary 
 75s Passed.
 75s Random test 23 of 30 (Gaussian density):
 75s Number of sample points: 997
 75s Dimension: 6
 75s Method: single 
 75s     Metric: euclidean 
 75s     Metric: maximum 
 75s     Metric: manhattan 
 75s     Metric: canberra 
 75s     Metric: minkowski 
 75s     p: 9.09452
 76s Method: ward 
 76s Method: centroid 
 76s Method: median 
 76s Passed.
 76s Uniform sampling for the 'binary' metric:
 76s Number of sample points: 86
 76s Dimension: 106
 76s Method: single 
 76s     Metric: binary 
 76s Passed.
 76s Random test 24 of 30 (Gaussian density):
 76s Number of sample points: 748
 76s Dimension: 13
 76s Method: single 
 76s     Metric: euclidean 
 76s     Metric: maximum 
 76s     Metric: manhattan 
 76s     Metric: canberra 
 76s     Metric: minkowski 
 76s     p: 1.13438
 76s Method: ward 
 76s Method: centroid 
 76s Method: median 
 76s Passed.
 76s Uniform sampling for the 'binary' metric:
 76s Number of sample points: 152
 76s Dimension: 209
 76s Method: single 
 76s     Metric: binary 
 76s Passed.
 76s Random test 25 of 30 (Gaussian density):
 76s Number of sample points: 799
 76s Dimension: 5
 76s Method: single 
 76s     Metric: euclidean 
 76s     Metric: maximum 
 76s     Metric: manhattan 
 76s     Metric: canberra 
 76s     Metric: minkowski 
 76s     p: 2.08287
 76s Method: ward 
 76s Method: centroid 
 76s Method: median 
 76s Passed.
 76s Uniform sampling for the 'binary' metric:
 76s Number of sample points: 99
 76s Dimension: 103
 76s Method: single 
 76s     Metric: binary 
 76s Passed.
 76s Random test 26 of 30 (Gaussian density):
 76s Number of sample points: 157
 76s Dimension: 10
 76s Method: single 
 76s     Metric: euclidean 
 76s     Metric: maximum 
 76s     Metric: manhattan 
 76s     Metric: canberra 
 76s     Metric: minkowski 
 76s     p: 4.95775
 76s Method: ward 
 76s Method: centroid 
 76s Method: median 
 76s Passed.
 76s Uniform sampling for the 'binary' metric:
 76s Number of sample points: 236
 76s Dimension: 362
 76s Method: single 
 76s     Metric: binary 
 77s Passed.
 77s Random test 27 of 30 (Gaussian density):
 77s Number of sample points: 173
 77s Dimension: 14
 77s Method: single 
 77s     Metric: euclidean 
 77s     Metric: maximum 
 77s     Metric: manhattan 
 77s     Metric: canberra 
 77s     Metric: minkowski 
 77s     p: 2.70894
 77s Method: ward 
 77s Method: centroid 
 77s Method: median 
 77s Passed.
 77s Uniform sampling for the 'binary' metric:
 77s Number of sample points: 350
 77s Dimension: 596
 77s Method: single 
 77s     Metric: binary 
 77s Passed.
 77s Random test 28 of 30 (Gaussian density):
 77s Number of sample points: 863
 77s Dimension: 8
 77s Method: single 
 77s     Metric: euclidean 
 77s     Metric: maximum 
 77s     Metric: manhattan 
 77s     Metric: canberra 
 77s     Metric: minkowski 
 77s     p: 9.61957
 78s Method: ward 
 78s Method: centroid 
 78s Method: median 
 78s Passed.
 78s Uniform sampling for the 'binary' metric:
 78s Number of sample points: 105
 78s Dimension: 193
 78s Method: single 
 78s     Metric: binary 
 78s Passed.
 78s Random test 29 of 30 (Gaussian density):
 78s Number of sample points: 272
 78s Dimension: 3
 78s Method: single 
 78s     Metric: euclidean 
 78s     Metric: maximum 
 78s     Metric: manhattan 
 78s     Metric: canberra 
 78s     Metric: minkowski 
 78s     p: 5.10094
 78s Method: ward 
 78s Method: centroid 
 78s Method: median 
 78s Passed.
 78s Uniform sampling for the 'binary' metric:
 78s Number of sample points: 243
 78s Dimension: 305
 78s Method: single 
 78s     Metric: binary 
 78s Passed.
 78s Random test 30 of 30 (Gaussian density):
 78s Number of sample points: 774
 78s Dimension: 11
 78s Method: single 
 78s     Metric: euclidean 
 78s     Metric: maximum 
 78s     Metric: manhattan 
 78s     Metric: canberra 
 78s     Metric: minkowski 
 78s     p: 3.18249
 78s Method: ward 
 78s Method: centroid 
 78s Method: median 
 78s Passed.
 78s Uniform sampling for the 'binary' metric:
 78s Number of sample points: 147
 78s Dimension: 170
 78s Method: single 
 78s     Metric: binary 
 78s Passed.
 78s > 
 78s > cat('Done.\n')
 78s Done.
 78s > 
 79s autopkgtest [22:23:56]: test run-unit-test: -----------------------]
 79s autopkgtest [22:23:56]: test run-unit-test:  - - - - - - - - - - results - - - - - - - - - -
 79s run-unit-test        PASS
 80s autopkgtest [22:23:57]: test autodep8-python3: preparing testbed
131s autopkgtest [22:24:48]: testbed dpkg architecture: amd64
131s autopkgtest [22:24:48]: testbed apt version: 2.9.8
131s autopkgtest [22:24:48]: @@@@@@@@@@@@@@@@@@@@ test bed setup
132s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB]
132s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [1025 kB]
133s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B]
133s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.5 kB]
133s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [102 kB]
133s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [144 kB]
133s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [77.0 kB]
133s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [32.6 kB]
133s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [293 kB]
133s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [803 kB]
133s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [740 B]
133s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [9128 B]
133s Fetched 2583 kB in 1s (3144 kB/s)
133s Reading package lists...
136s Reading package lists...
136s Building dependency tree...
136s Reading state information...
136s Calculating upgrade...
136s The following NEW packages will be installed:
136s   python3.13-gdbm
136s The following packages will be upgraded:
136s   libcap-ng0 libpython3-stdlib pastebinit python3 python3-gdbm python3-minimal
136s   python3-systemd
136s 7 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
136s Need to get 178 kB of archives.
136s After this operation, 256 kB of additional disk space will be used.
136s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-minimal amd64 3.12.7-1 [27.4 kB]
137s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3 amd64 3.12.7-1 [24.0 kB]
137s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libpython3-stdlib amd64 3.12.7-1 [10.0 kB]
137s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 libcap-ng0 amd64 0.8.5-3build1 [15.6 kB]
137s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-gdbm amd64 3.13.0-2 [31.3 kB]
137s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-gdbm amd64 3.12.7-1 [8642 B]
137s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 pastebinit all 1.7.1-1 [14.9 kB]
137s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-systemd amd64 235-1build5 [45.7 kB]
137s Fetched 178 kB in 0s (438 kB/s)
137s (Reading database ... 
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137s Preparing to unpack .../python3-minimal_3.12.7-1_amd64.deb ...
137s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ...
137s Setting up python3-minimal (3.12.7-1) ...
137s (Reading database ... 
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137s Preparing to unpack .../python3_3.12.7-1_amd64.deb ...
137s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ...
137s Preparing to unpack .../libpython3-stdlib_3.12.7-1_amd64.deb ...
137s Unpacking libpython3-stdlib:amd64 (3.12.7-1) over (3.12.6-0ubuntu1) ...
137s Preparing to unpack .../libcap-ng0_0.8.5-3build1_amd64.deb ...
137s Unpacking libcap-ng0:amd64 (0.8.5-3build1) over (0.8.5-1) ...
138s Setting up libcap-ng0:amd64 (0.8.5-3build1) ...
138s Selecting previously unselected package python3.13-gdbm.
138s (Reading database ... 
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138s Preparing to unpack .../python3.13-gdbm_3.13.0-2_amd64.deb ...
138s Unpacking python3.13-gdbm (3.13.0-2) ...
138s Preparing to unpack .../python3-gdbm_3.12.7-1_amd64.deb ...
138s Unpacking python3-gdbm:amd64 (3.12.7-1) over (3.12.6-1ubuntu1) ...
138s Preparing to unpack .../pastebinit_1.7.1-1_all.deb ...
138s Unpacking pastebinit (1.7.1-1) over (1.7.0-1) ...
138s Preparing to unpack .../python3-systemd_235-1build5_amd64.deb ...
138s Unpacking python3-systemd (235-1build5) over (235-1build4) ...
138s Setting up python3.13-gdbm (3.13.0-2) ...
138s Setting up libpython3-stdlib:amd64 (3.12.7-1) ...
138s Setting up python3 (3.12.7-1) ...
138s Setting up python3-systemd (235-1build5) ...
138s Setting up python3-gdbm:amd64 (3.12.7-1) ...
138s Setting up pastebinit (1.7.1-1) ...
138s Processing triggers for libc-bin (2.40-1ubuntu3) ...
138s Processing triggers for man-db (2.12.1-3) ...
139s Reading package lists...
139s Building dependency tree...
139s Reading state information...
139s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
140s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease
140s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease
140s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease
140s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease
141s Reading package lists...
141s Reading package lists...
141s Building dependency tree...
141s Reading state information...
141s Calculating upgrade...
141s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
141s Reading package lists...
141s Building dependency tree...
141s Reading state information...
141s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
145s Reading package lists...
145s Building dependency tree...
145s Reading state information...
145s Starting pkgProblemResolver with broken count: 0
145s Starting 2 pkgProblemResolver with broken count: 0
145s Done
146s The following additional packages will be installed:
146s   libblas3 libgfortran5 liblapack3 libpython3.13-minimal libpython3.13-stdlib
146s   python3-all python3-fastcluster python3-numpy python3.13 python3.13-minimal
146s Suggested packages:
146s   gcc gfortran python-numpy-doc python3-dev python3-pytest python3.13-venv
146s   python3.13-doc binfmt-support
146s Recommended packages:
146s   python3-scipy
146s The following NEW packages will be installed:
146s   autopkgtest-satdep libblas3 libgfortran5 liblapack3 libpython3.13-minimal
146s   libpython3.13-stdlib python3-all python3-fastcluster python3-numpy
146s   python3.13 python3.13-minimal
146s 0 upgraded, 11 newly installed, 0 to remove and 0 not upgraded.
146s Need to get 14.2 MB/14.2 MB of archives.
146s After this operation, 58.1 MB of additional disk space will be used.
146s Get:1 /tmp/autopkgtest.wOlcOF/2-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [716 B]
146s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-minimal amd64 3.13.0-2 [879 kB]
146s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-minimal amd64 3.13.0-2 [2188 kB]
146s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.0-3build2 [247 kB]
146s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 14.2.0-8ubuntu1 [909 kB]
146s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.0-3build2 [2668 kB]
147s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-stdlib amd64 3.13.0-2 [2107 kB]
147s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13 amd64 3.13.0-2 [719 kB]
147s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-all amd64 3.12.7-1 [890 B]
147s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-numpy amd64 1:1.26.4+ds-11build1 [4479 kB]
147s Get:11 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-fastcluster amd64 1.2.6-1build1 [42.7 kB]
147s Fetched 14.2 MB in 1s (14.6 MB/s)
147s Selecting previously unselected package libpython3.13-minimal:amd64.
147s (Reading database ... 
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147s Preparing to unpack .../00-libpython3.13-minimal_3.13.0-2_amd64.deb ...
147s Unpacking libpython3.13-minimal:amd64 (3.13.0-2) ...
147s Selecting previously unselected package python3.13-minimal.
147s Preparing to unpack .../01-python3.13-minimal_3.13.0-2_amd64.deb ...
147s Unpacking python3.13-minimal (3.13.0-2) ...
147s Selecting previously unselected package libblas3:amd64.
147s Preparing to unpack .../02-libblas3_3.12.0-3build2_amd64.deb ...
147s Unpacking libblas3:amd64 (3.12.0-3build2) ...
147s Selecting previously unselected package libgfortran5:amd64.
147s Preparing to unpack .../03-libgfortran5_14.2.0-8ubuntu1_amd64.deb ...
147s Unpacking libgfortran5:amd64 (14.2.0-8ubuntu1) ...
147s Selecting previously unselected package liblapack3:amd64.
147s Preparing to unpack .../04-liblapack3_3.12.0-3build2_amd64.deb ...
147s Unpacking liblapack3:amd64 (3.12.0-3build2) ...
147s Selecting previously unselected package libpython3.13-stdlib:amd64.
147s Preparing to unpack .../05-libpython3.13-stdlib_3.13.0-2_amd64.deb ...
147s Unpacking libpython3.13-stdlib:amd64 (3.13.0-2) ...
147s Selecting previously unselected package python3.13.
147s Preparing to unpack .../06-python3.13_3.13.0-2_amd64.deb ...
147s Unpacking python3.13 (3.13.0-2) ...
147s Selecting previously unselected package python3-all.
147s Preparing to unpack .../07-python3-all_3.12.7-1_amd64.deb ...
147s Unpacking python3-all (3.12.7-1) ...
147s Selecting previously unselected package python3-numpy.
147s Preparing to unpack .../08-python3-numpy_1%3a1.26.4+ds-11build1_amd64.deb ...
147s Unpacking python3-numpy (1:1.26.4+ds-11build1) ...
148s Selecting previously unselected package python3-fastcluster.
148s Preparing to unpack .../09-python3-fastcluster_1.2.6-1build1_amd64.deb ...
148s Unpacking python3-fastcluster (1.2.6-1build1) ...
148s Selecting previously unselected package autopkgtest-satdep.
148s Preparing to unpack .../10-2-autopkgtest-satdep.deb ...
148s Unpacking autopkgtest-satdep (0) ...
148s Setting up libpython3.13-minimal:amd64 (3.13.0-2) ...
148s Setting up libblas3:amd64 (3.12.0-3build2) ...
148s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode
148s Setting up libgfortran5:amd64 (14.2.0-8ubuntu1) ...
148s Setting up python3.13-minimal (3.13.0-2) ...
148s Setting up libpython3.13-stdlib:amd64 (3.13.0-2) ...
148s Setting up liblapack3:amd64 (3.12.0-3build2) ...
148s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode
148s Setting up python3.13 (3.13.0-2) ...
149s Setting up python3-all (3.12.7-1) ...
149s Setting up python3-numpy (1:1.26.4+ds-11build1) ...
152s Setting up python3-fastcluster (1.2.6-1build1) ...
152s Setting up autopkgtest-satdep (0) ...
152s Processing triggers for systemd (256.5-2ubuntu4) ...
152s Processing triggers for man-db (2.12.1-3) ...
152s Processing triggers for libc-bin (2.40-1ubuntu3) ...
154s (Reading database ... 77202 files and directories currently installed.)
154s Removing autopkgtest-satdep (0) ...
156s autopkgtest [22:25:13]: 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
156s autopkgtest [22:25:13]: test autodep8-python3: [-----------------------
156s Testing with python3.13:
156s Traceback (most recent call last):
156s   File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in <module>
156s     from . import multiarray
156s   File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in <module>
156s     from . import overrides
156s   File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in <module>
156s     from numpy.core._multiarray_umath import (
156s         add_docstring,  _get_implementing_args, _ArrayFunctionDispatcher)
156s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath'
156s 
156s During handling of the above exception, another exception occurred:
156s 
156s Traceback (most recent call last):
156s   File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in <module>
156s     from numpy.__config__ import show as show_config
156s   File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in <module>
156s     from numpy.core._multiarray_umath import (
156s     ...<3 lines>...
156s     )
156s   File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in <module>
156s     raise ImportError(msg)
156s ImportError: 
156s 
156s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE!
156s 
156s Importing the numpy C-extensions failed. This error can happen for
156s many reasons, often due to issues with your setup or how NumPy was
156s installed.
156s 
156s We have compiled some common reasons and troubleshooting tips at:
156s 
156s     https://numpy.org/devdocs/user/troubleshooting-importerror.html
156s 
156s Please note and check the following:
156s 
156s   * The Python version is: Python3.13 from "/usr/bin/python3.13"
156s   * The NumPy version is: "1.26.4"
156s 
156s and make sure that they are the versions you expect.
156s Please carefully study the documentation linked above for further help.
156s 
156s Original error was: No module named 'numpy.core._multiarray_umath'
156s 
156s 
156s The above exception was the direct cause of the following exception:
156s 
156s Traceback (most recent call last):
156s   File "<string>", line 1, in <module>
156s     import fastcluster; print(fastcluster)
156s     ^^^^^^^^^^^^^^^^^^
156s   File "/usr/lib/python3/dist-packages/fastcluster.py", line 26, in <module>
156s     from numpy import double, empty, array, ndarray, var, cov, dot, expand_dims, \
156s         ceil, sqrt
156s   File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in <module>
156s     raise ImportError(msg) from e
156s ImportError: Error importing numpy: you should not try to import numpy from
156s         its source directory; please exit the numpy source tree, and relaunch
156s         your python interpreter from there.
156s autopkgtest [22:25:13]: test autodep8-python3: -----------------------]
157s autodep8-python3     FAIL non-zero exit status 1
157s autopkgtest [22:25:14]: test autodep8-python3:  - - - - - - - - - - results - - - - - - - - - -
157s autopkgtest [22:25:14]: @@@@@@@@@@@@@@@@@@@@ summary
157s run-unit-test        PASS
157s autodep8-python3     FAIL non-zero exit status 1
169s nova [W] Skipping flock for amd64
169s Creating nova instance adt-plucky-amd64-r-cran-fastcluster-20241114-222237-juju-7f2275-prod-proposed-migration-environment-15-903047cd-3df4-47f8-af07-2f8d3adec5fc from image adt/ubuntu-plucky-amd64-server-20241114.img (UUID 79d80331-8736-463c-82c6-8c9e13c0a4ca)...
169s nova [W] Skipping flock for amd64
169s Creating nova instance adt-plucky-amd64-r-cran-fastcluster-20241114-222237-juju-7f2275-prod-proposed-migration-environment-15-903047cd-3df4-47f8-af07-2f8d3adec5fc from image adt/ubuntu-plucky-amd64-server-20241114.img (UUID 79d80331-8736-463c-82c6-8c9e13c0a4ca)...