0s autopkgtest [11:05:11]: starting date and time: 2024-11-13 11:05:11+0000
  0s autopkgtest [11:05:11]: git checkout: 0acbae0a WIP show VirtSubproc stderr in real-time
  0s autopkgtest [11:05:11]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.9zjhyw2o/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 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-arm64-52.secgroup --name adt-plucky-arm64-r-cran-fastcluster-20241113-110511-juju-7f2275-prod-proposed-migration-environment-2-13c924d8-4c2a-43f0-a291-375d1624dd0a --image adt/ubuntu-plucky-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/
 80s autopkgtest [11:06:31]: testbed dpkg architecture: arm64
 80s autopkgtest [11:06:31]: testbed apt version: 2.9.8
 80s autopkgtest [11:06:31]: @@@@@@@@@@@@@@@@@@@@ test bed setup
 82s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB]
 82s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [849 kB]
 82s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B]
 82s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [76.4 kB]
 82s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.3 kB]
 82s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [104 kB]
 82s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 Packages [50.3 kB]
 82s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [601 kB]
 82s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [17.1 kB]
 82s Fetched 1794 kB in 1s (2158 kB/s)
 83s Reading package lists...
 85s Reading package lists...
 86s Building dependency tree...
 86s Reading state information...
 86s Calculating upgrade...
 87s The following NEW packages will be installed:
 87s   python3.13-gdbm
 87s The following packages will be upgraded:
 87s   libpython3-stdlib python3 python3-gdbm python3-minimal
 87s 4 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
 87s Need to get 101 kB of archives.
 87s After this operation, 141 kB of additional disk space will be used.
 87s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-minimal arm64 3.12.7-1 [27.4 kB]
 87s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3 arm64 3.12.7-1 [24.0 kB]
 87s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libpython3-stdlib arm64 3.12.7-1 [10.0 kB]
 87s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-gdbm arm64 3.13.0-2 [30.7 kB]
 87s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-gdbm arm64 3.12.7-1 [8642 B]
 88s Fetched 101 kB in 0s (296 kB/s)
 88s (Reading database ... 
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(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 79924 files and directories currently installed.)
 88s Preparing to unpack .../python3-minimal_3.12.7-1_arm64.deb ...
 88s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ...
 88s Setting up python3-minimal (3.12.7-1) ...
 88s (Reading database ... 
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(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 ... 79924 files and directories currently installed.)
 88s Preparing to unpack .../python3_3.12.7-1_arm64.deb ...
 88s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ...
 88s Preparing to unpack .../libpython3-stdlib_3.12.7-1_arm64.deb ...
 88s Unpacking libpython3-stdlib:arm64 (3.12.7-1) over (3.12.6-0ubuntu1) ...
 88s Selecting previously unselected package python3.13-gdbm.
 88s Preparing to unpack .../python3.13-gdbm_3.13.0-2_arm64.deb ...
 88s Unpacking python3.13-gdbm (3.13.0-2) ...
 88s Preparing to unpack .../python3-gdbm_3.12.7-1_arm64.deb ...
 88s Unpacking python3-gdbm:arm64 (3.12.7-1) over (3.12.6-1ubuntu1) ...
 88s Setting up python3.13-gdbm (3.13.0-2) ...
 88s Setting up libpython3-stdlib:arm64 (3.12.7-1) ...
 88s Setting up python3 (3.12.7-1) ...
 89s Setting up python3-gdbm:arm64 (3.12.7-1) ...
 89s Processing triggers for man-db (2.12.1-3) ...
 90s Reading package lists...
 90s Building dependency tree...
 90s Reading state information...
 91s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 91s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease
 91s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease
 91s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease
 91s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease
 92s Reading package lists...
 92s Reading package lists...
 93s Building dependency tree...
 93s Reading state information...
 93s Calculating upgrade...
 94s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 94s Reading package lists...
 94s Building dependency tree...
 94s Reading state information...
 95s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 98s autopkgtest [11:06:49]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 14:19:41 UTC 2024
 99s autopkgtest [11:06:50]: @@@@@@@@@@@@@@@@@@@@ apt-source r-cran-fastcluster
102s Get:1 http://ftpmaster.internal/ubuntu plucky/universe r-cran-fastcluster 1.2.6-1build1 (dsc) [2272 B]
102s Get:2 http://ftpmaster.internal/ubuntu plucky/universe r-cran-fastcluster 1.2.6-1build1 (tar) [208 kB]
102s Get:3 http://ftpmaster.internal/ubuntu plucky/universe r-cran-fastcluster 1.2.6-1build1 (diff) [4828 B]
102s gpgv: Signature made Wed Apr 10 18:03:18 2024 UTC
102s gpgv:                using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2
102s gpgv: Can't check signature: No public key
102s dpkg-source: warning: cannot verify inline signature for ./r-cran-fastcluster_1.2.6-1build1.dsc: no acceptable signature found
102s autopkgtest [11:06:53]: testing package r-cran-fastcluster version 1.2.6-1build1
103s autopkgtest [11:06:54]: build not needed
104s autopkgtest [11:06:55]: test run-unit-test: preparing testbed
105s Reading package lists...
106s Building dependency tree...
106s Reading state information...
106s Starting pkgProblemResolver with broken count: 0
106s Starting 2 pkgProblemResolver with broken count: 0
106s Done
107s The following additional packages will be installed:
107s   fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono libblas3
107s   libcairo2 libdatrie1 libdeflate0 libfontconfig1 libgfortran5 libgomp1
107s   libgraphite2-3 libharfbuzz0b libice6 libjbig0 libjpeg-turbo8 libjpeg8
107s   liblapack3 liblerc4 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0
107s   libpaper-utils libpaper1 libpixman-1-0 libsharpyuv0 libsm6 libtcl8.6
107s   libthai-data libthai0 libtiff6 libtk8.6 libwebp7 libxcb-render0 libxcb-shm0
107s   libxft2 libxrender1 libxss1 libxt6t64 python3-fastcluster python3-numpy
107s   r-base-core r-cran-fastcluster unzip x11-common xdg-utils zip
107s Suggested packages:
107s   tcl8.6 tk8.6 gcc gfortran python-numpy-doc python3-dev python3-pytest
107s   elpa-ess r-doc-info | r-doc-pdf r-mathlib r-base-html
107s Recommended packages:
107s   python3-scipy r-recommended r-base-dev r-doc-html libfile-mimeinfo-perl
107s   libnet-dbus-perl libx11-protocol-perl x11-utils x11-xserver-utils
107s The following NEW packages will be installed:
107s   autopkgtest-satdep fontconfig fontconfig-config fonts-dejavu-core
107s   fonts-dejavu-mono libblas3 libcairo2 libdatrie1 libdeflate0 libfontconfig1
107s   libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libice6 libjbig0
107s   libjpeg-turbo8 libjpeg8 liblapack3 liblerc4 libpango-1.0-0
107s   libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpixman-1-0
107s   libsharpyuv0 libsm6 libtcl8.6 libthai-data libthai0 libtiff6 libtk8.6
107s   libwebp7 libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxss1 libxt6t64
107s   python3-fastcluster python3-numpy r-base-core r-cran-fastcluster unzip
107s   x11-common xdg-utils zip
107s 0 upgraded, 48 newly installed, 0 to remove and 0 not upgraded.
107s Need to get 42.1 MB/42.1 MB of archives.
107s After this operation, 98.6 MB of additional disk space will be used.
107s Get:1 /tmp/autopkgtest.xHBNsl/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [720 B]
107s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB]
108s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-core all 2.37-8 [835 kB]
108s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig-config arm64 2.15.0-1.1ubuntu2 [37.4 kB]
108s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 libfontconfig1 arm64 2.15.0-1.1ubuntu2 [142 kB]
108s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig arm64 2.15.0-1.1ubuntu2 [190 kB]
108s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.0-3build2 [152 kB]
108s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 libpixman-1-0 arm64 0.44.0-3 [197 kB]
108s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-render0 arm64 1.17.0-2 [16.6 kB]
108s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-shm0 arm64 1.17.0-2 [5884 B]
108s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 libxrender1 arm64 1:0.9.10-1.1build1 [18.8 kB]
108s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 libcairo2 arm64 1.18.2-2 [560 kB]
108s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 libdatrie1 arm64 0.2.13-3build1 [19.2 kB]
108s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate0 arm64 1.22-1 [46.2 kB]
108s Get:15 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 14.2.0-8ubuntu1 [438 kB]
108s Get:16 http://ftpmaster.internal/ubuntu plucky/main arm64 libgomp1 arm64 14.2.0-8ubuntu1 [145 kB]
108s Get:17 http://ftpmaster.internal/ubuntu plucky/main arm64 libgraphite2-3 arm64 1.3.14-2ubuntu1 [70.6 kB]
108s Get:18 http://ftpmaster.internal/ubuntu plucky/main arm64 libharfbuzz0b arm64 10.0.1-1 [487 kB]
108s Get:19 http://ftpmaster.internal/ubuntu plucky/main arm64 x11-common all 1:7.7+23ubuntu3 [21.7 kB]
108s Get:20 http://ftpmaster.internal/ubuntu plucky/main arm64 libice6 arm64 2:1.1.1-1 [42.3 kB]
108s Get:21 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg-turbo8 arm64 2.1.5-2ubuntu2 [163 kB]
108s Get:22 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B]
108s Get:23 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.0-3build2 [2293 kB]
108s Get:24 http://ftpmaster.internal/ubuntu plucky/main arm64 liblerc4 arm64 4.0.0+ds-4ubuntu2 [154 kB]
108s Get:25 http://ftpmaster.internal/ubuntu plucky/main arm64 libthai-data all 0.1.29-2build1 [158 kB]
108s Get:26 http://ftpmaster.internal/ubuntu plucky/main arm64 libthai0 arm64 0.1.29-2build1 [18.2 kB]
108s Get:27 http://ftpmaster.internal/ubuntu plucky/main arm64 libpango-1.0-0 arm64 1.54.0+ds-3 [234 kB]
108s Get:28 http://ftpmaster.internal/ubuntu plucky/main arm64 libpangoft2-1.0-0 arm64 1.54.0+ds-3 [48.9 kB]
108s Get:29 http://ftpmaster.internal/ubuntu plucky/main arm64 libpangocairo-1.0-0 arm64 1.54.0+ds-3 [27.5 kB]
108s Get:30 http://ftpmaster.internal/ubuntu plucky/main arm64 libpaper1 arm64 1.1.29build1 [13.4 kB]
108s Get:31 http://ftpmaster.internal/ubuntu plucky/main arm64 libpaper-utils arm64 1.1.29build1 [8490 B]
108s Get:32 http://ftpmaster.internal/ubuntu plucky/main arm64 libsharpyuv0 arm64 1.4.0-0.1 [16.3 kB]
108s Get:33 http://ftpmaster.internal/ubuntu plucky/main arm64 libsm6 arm64 2:1.2.4-1 [16.4 kB]
108s Get:34 http://ftpmaster.internal/ubuntu plucky/main arm64 libtcl8.6 arm64 8.6.15+dfsg-2 [987 kB]
108s Get:35 http://ftpmaster.internal/ubuntu plucky/main arm64 libjbig0 arm64 2.1-6.1ubuntu2 [29.3 kB]
108s Get:36 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebp7 arm64 1.4.0-0.1 [192 kB]
108s Get:37 http://ftpmaster.internal/ubuntu plucky/main arm64 libtiff6 arm64 4.5.1+git230720-4ubuntu4 [193 kB]
108s Get:38 http://ftpmaster.internal/ubuntu plucky/main arm64 libxft2 arm64 2.3.6-1build1 [44.1 kB]
108s Get:39 http://ftpmaster.internal/ubuntu plucky/main arm64 libxss1 arm64 1:1.2.3-1build3 [7244 B]
108s Get:40 http://ftpmaster.internal/ubuntu plucky/main arm64 libtk8.6 arm64 8.6.15-1 [774 kB]
108s Get:41 http://ftpmaster.internal/ubuntu plucky/main arm64 libxt6t64 arm64 1:1.2.1-1.2build1 [168 kB]
108s Get:42 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy arm64 1:1.26.4+ds-11build1 [3654 kB]
109s Get:43 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-fastcluster arm64 1.2.6-1build1 [40.9 kB]
109s Get:44 http://ftpmaster.internal/ubuntu plucky/main arm64 zip arm64 3.0-14ubuntu1 [172 kB]
109s Get:45 http://ftpmaster.internal/ubuntu plucky/main arm64 unzip arm64 6.0-28ubuntu6 [178 kB]
109s Get:46 http://ftpmaster.internal/ubuntu plucky/main arm64 xdg-utils all 1.2.1-0ubuntu1 [67.5 kB]
109s Get:47 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-base-core arm64 4.4.2-1 [28.4 MB]
110s Get:48 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-fastcluster arm64 1.2.6-1build1 [190 kB]
110s Preconfiguring packages ...
110s Fetched 42.1 MB in 3s (15.1 MB/s)
110s Selecting previously unselected package fonts-dejavu-mono.
110s (Reading database ... 
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(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 ... 79931 files and directories currently installed.)
110s Preparing to unpack .../00-fonts-dejavu-mono_2.37-8_all.deb ...
110s Unpacking fonts-dejavu-mono (2.37-8) ...
110s Selecting previously unselected package fonts-dejavu-core.
110s Preparing to unpack .../01-fonts-dejavu-core_2.37-8_all.deb ...
110s Unpacking fonts-dejavu-core (2.37-8) ...
111s Selecting previously unselected package fontconfig-config.
111s Preparing to unpack .../02-fontconfig-config_2.15.0-1.1ubuntu2_arm64.deb ...
111s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ...
111s Selecting previously unselected package libfontconfig1:arm64.
111s Preparing to unpack .../03-libfontconfig1_2.15.0-1.1ubuntu2_arm64.deb ...
111s Unpacking libfontconfig1:arm64 (2.15.0-1.1ubuntu2) ...
111s Selecting previously unselected package fontconfig.
111s Preparing to unpack .../04-fontconfig_2.15.0-1.1ubuntu2_arm64.deb ...
111s Unpacking fontconfig (2.15.0-1.1ubuntu2) ...
111s Selecting previously unselected package libblas3:arm64.
111s Preparing to unpack .../05-libblas3_3.12.0-3build2_arm64.deb ...
111s Unpacking libblas3:arm64 (3.12.0-3build2) ...
111s Selecting previously unselected package libpixman-1-0:arm64.
111s Preparing to unpack .../06-libpixman-1-0_0.44.0-3_arm64.deb ...
111s Unpacking libpixman-1-0:arm64 (0.44.0-3) ...
111s Selecting previously unselected package libxcb-render0:arm64.
111s Preparing to unpack .../07-libxcb-render0_1.17.0-2_arm64.deb ...
111s Unpacking libxcb-render0:arm64 (1.17.0-2) ...
111s Selecting previously unselected package libxcb-shm0:arm64.
111s Preparing to unpack .../08-libxcb-shm0_1.17.0-2_arm64.deb ...
111s Unpacking libxcb-shm0:arm64 (1.17.0-2) ...
111s Selecting previously unselected package libxrender1:arm64.
111s Preparing to unpack .../09-libxrender1_1%3a0.9.10-1.1build1_arm64.deb ...
111s Unpacking libxrender1:arm64 (1:0.9.10-1.1build1) ...
111s Selecting previously unselected package libcairo2:arm64.
111s Preparing to unpack .../10-libcairo2_1.18.2-2_arm64.deb ...
111s Unpacking libcairo2:arm64 (1.18.2-2) ...
111s Selecting previously unselected package libdatrie1:arm64.
111s Preparing to unpack .../11-libdatrie1_0.2.13-3build1_arm64.deb ...
111s Unpacking libdatrie1:arm64 (0.2.13-3build1) ...
111s Selecting previously unselected package libdeflate0:arm64.
111s Preparing to unpack .../12-libdeflate0_1.22-1_arm64.deb ...
111s Unpacking libdeflate0:arm64 (1.22-1) ...
111s Selecting previously unselected package libgfortran5:arm64.
111s Preparing to unpack .../13-libgfortran5_14.2.0-8ubuntu1_arm64.deb ...
111s Unpacking libgfortran5:arm64 (14.2.0-8ubuntu1) ...
111s Selecting previously unselected package libgomp1:arm64.
111s Preparing to unpack .../14-libgomp1_14.2.0-8ubuntu1_arm64.deb ...
111s Unpacking libgomp1:arm64 (14.2.0-8ubuntu1) ...
111s Selecting previously unselected package libgraphite2-3:arm64.
111s Preparing to unpack .../15-libgraphite2-3_1.3.14-2ubuntu1_arm64.deb ...
111s Unpacking libgraphite2-3:arm64 (1.3.14-2ubuntu1) ...
111s Selecting previously unselected package libharfbuzz0b:arm64.
111s Preparing to unpack .../16-libharfbuzz0b_10.0.1-1_arm64.deb ...
111s Unpacking libharfbuzz0b:arm64 (10.0.1-1) ...
111s Selecting previously unselected package x11-common.
111s Preparing to unpack .../17-x11-common_1%3a7.7+23ubuntu3_all.deb ...
111s Unpacking x11-common (1:7.7+23ubuntu3) ...
111s Selecting previously unselected package libice6:arm64.
111s Preparing to unpack .../18-libice6_2%3a1.1.1-1_arm64.deb ...
111s Unpacking libice6:arm64 (2:1.1.1-1) ...
111s Selecting previously unselected package libjpeg-turbo8:arm64.
111s Preparing to unpack .../19-libjpeg-turbo8_2.1.5-2ubuntu2_arm64.deb ...
111s Unpacking libjpeg-turbo8:arm64 (2.1.5-2ubuntu2) ...
111s Selecting previously unselected package libjpeg8:arm64.
111s Preparing to unpack .../20-libjpeg8_8c-2ubuntu11_arm64.deb ...
111s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ...
111s Selecting previously unselected package liblapack3:arm64.
111s Preparing to unpack .../21-liblapack3_3.12.0-3build2_arm64.deb ...
111s Unpacking liblapack3:arm64 (3.12.0-3build2) ...
112s Selecting previously unselected package liblerc4:arm64.
112s Preparing to unpack .../22-liblerc4_4.0.0+ds-4ubuntu2_arm64.deb ...
112s Unpacking liblerc4:arm64 (4.0.0+ds-4ubuntu2) ...
112s Selecting previously unselected package libthai-data.
112s Preparing to unpack .../23-libthai-data_0.1.29-2build1_all.deb ...
112s Unpacking libthai-data (0.1.29-2build1) ...
112s Selecting previously unselected package libthai0:arm64.
112s Preparing to unpack .../24-libthai0_0.1.29-2build1_arm64.deb ...
112s Unpacking libthai0:arm64 (0.1.29-2build1) ...
112s Selecting previously unselected package libpango-1.0-0:arm64.
112s Preparing to unpack .../25-libpango-1.0-0_1.54.0+ds-3_arm64.deb ...
112s Unpacking libpango-1.0-0:arm64 (1.54.0+ds-3) ...
112s Selecting previously unselected package libpangoft2-1.0-0:arm64.
112s Preparing to unpack .../26-libpangoft2-1.0-0_1.54.0+ds-3_arm64.deb ...
112s Unpacking libpangoft2-1.0-0:arm64 (1.54.0+ds-3) ...
112s Selecting previously unselected package libpangocairo-1.0-0:arm64.
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125s autopkgtest [11:07:16]: test run-unit-test: [-----------------------
126s 
126s R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
126s Copyright (C) 2024 The R Foundation for Statistical Computing
126s Platform: aarch64-unknown-linux-gnu
126s 
126s R is free software and comes with ABSOLUTELY NO WARRANTY.
126s You are welcome to redistribute it under certain conditions.
126s Type 'license()' or 'licence()' for distribution details.
126s 
126s R is a collaborative project with many contributors.
126s Type 'contributors()' for more information and
126s 'citation()' on how to cite R or R packages in publications.
126s 
126s Type 'demo()' for some demos, 'help()' for on-line help, or
126s 'help.start()' for an HTML browser interface to help.
126s Type 'q()' to quit R.
126s 
126s > #  fastcluster: Fast hierarchical clustering routines for R and Python
126s > #
126s > #  Copyright:
126s > #    * Until package version 1.1.23: © 2011 Daniel Müllner <https://danifold.net>
126s > #    * All changes from version 1.1.24 on: © Google Inc. <https://www.google.com>
126s > #
126s > # Test script for the R interface
126s > 
126s > seed = as.integer(runif(1, 0, 1e9))
126s > set.seed(seed)
126s > cat(sprintf("Random seed: %d\n",seed))
126s Random seed: 694594148
126s > 
126s > print_seed <- function() {
126s +   return(sprintf('
126s + Please send a report to the author of the \'fastcluster\' package, Daniel Müllner.
126s + For contact details, see <https://danifold.net>. To make the error
126s + reproducible, you must include the following number (the random seed value) in
126s + your error report: %d.\n\n', seed))
126s + }
126s > 
126s > hasWardD2 = getRversion() >= '3.1.0'
126s > 
126s > # Compare two dendrograms and check whether they are equal, except that
126s > # ties may be resolved differently.
126s > compare <- function(dg1, dg2) {
126s +   h1 <- dg1$height
126s +   h2 <- dg2$height
126s +   # "height" vectors may have small numerical errors.
126s +   rdiffs <- abs(h1-h2)/pmax(abs(h1),abs(h2))
126s +   rdiffs = rdiffs[complete.cases(rdiffs)]
126s +   rel_error <-  max(rdiffs)
126s +   # We allow a relative error of 1e-13.
126s +   if (rel_error>1e-13) {
126s +     print(h1)
126s +     print(h2)
126s +     cat(sprintf('Height vectors differ! The maximum relative error is %e.\n', rel_error))
126s +     return(FALSE)
126s +   }
126s +   # Filter the indices where consecutive merging distances are distinct.
126s +   d = diff(dg1$height)
126s +   b = (c(d,1)!=0 & c(1,d)!=0)
126s +   #cat(sprintf("Percentage of indices where we can test: %g.\n",100.0*length(b[b])/length(b)))
126s +   if (any(b)) {
126s +     m1 = dg1$merge[b,]
126s +     m2 = dg2$merge[b,]
126s + 
126s +     r = function(i) {
126s +       if (i<0) {
126s +         return(1)
126s +       }
126s +       else {
126s +         return(b[i])
126s +       }
126s +     }
126s + 
126s +     f = sapply(m1,r)
126s +     fm1 = m1*f
126s +     fm2 = m2*f
126s +     # The "merge" matrices must be identical whereever indices are not ambiguous
126s +     # due to ties.
126s +     if (!identical(fm1,fm2)) {
126s +       cat('Merge matrices differ!\n')
126s +       return(FALSE)
126s +     }
126s +     # Compare the "order" vectors only if all merging distances were distinct.
126s +     if (all(b) && !identical(dg1$order,dg2$order)) {
126s +       cat('Order vectors differ!\n')
126s +       return(FALSE)
126s +     }
126s +   }
126s +   return(TRUE)
126s + }
126s > 
126s > # Generate uniformly distributed random data
126s > generate.uniform <- function() {
126s +   n = sample(10:1000,1)
126s +   range_exp = runif(1,min=-10, max=10)
126s +   cat(sprintf("Number of sample points: %d\n",n))
126s +   cat(sprintf("Dissimilarity range: [0,%g]\n",10^range_exp))
126s +   d = runif(n*(n-1)/2, min=0, max=10^range_exp)
126s +   # Fake a compressed distance matrix
126s +   attributes(d) <- NULL
126s +   attr(d,"Size") <- n
126s +   attr(d, "call") <- 'N/A'
126s +   class(d) <- "dist"
126s +   return(d)
126s + }
126s > 
126s > # Generate normally distributed random data
126s > generate.normal <- function() {
126s +   n = sample(10:1000,1)
126s +   dim = sample(2:20,1)
126s + 
126s +   cat (sprintf("Number of sample points: %d\n",n))
126s +   cat (sprintf("Dimension: %d\n",dim))
126s + 
126s +   pcd = matrix(rnorm(n*dim), c(n,dim))
126s +   d = dist(pcd)
126s +   return(d)
126s + }
126s > 
126s > # Test the clustering functions when a distance matrix is given.
126s > test.dm <-  function(d) {
126s +   d2 = d
126s +   if (hasWardD2) {
126s +     methods = c('single','complete','average','mcquitty','ward.D','ward.D2','centroid','median')
126s +   }
126s +   else {
126s +     methods = c('single','complete','average','mcquitty','ward','centroid','median')
126s +   }
126s +   for (method in methods) {
126s +     cat(paste('Method :', method, '\n'))
126s +     dg_stats       = stats::hclust(d, method=method)
126s +     if (method == 'ward') {
126s +       method = 'ward.D'
126s +     }
126s +     dg_fastcluster = fastcluster::hclust(d, method=method)
126s +     if (!identical(d,d2)) {
126s +       cat('Input array was corrupted!\n')
126s +       stop(print_seed())
126s +     }
126s +     if (!compare(dg_stats, dg_fastcluster)) {
126s +       stop(print_seed())
126s +     }
126s +   }
126s +   cat('Passed.\n')
126s + }
126s > 
126s > # Test the clustering functions for vector input in Euclidean space.
126s > test.vector <-  function() {
126s +   # generate test data
126s +   n = sample(10:1000,1)
126s +   dim = sample(2:20,1)
126s +   cat (sprintf("Number of sample points: %d\n",n))
126s +   cat (sprintf("Dimension: %d\n",dim))
126s + 
126s +   range_exp = runif(1,min=-10, max=10)
126s +   pcd = matrix(rnorm(n*dim, sd=10^range_exp), c(n,dim))
126s +   pcd2 = pcd
126s +   # test
126s +   method='single'
126s +   cat(paste('Method:', method, '\n'))
126s +   for (metric in c('euclidean', 'maximum', 'manhattan', 'canberra', 'minkowski')) {
126s +     cat(paste('    Metric:', metric, '\n'))
126s +     if (metric=='minkowski') {
126s +       p = runif(1, min=1.0, max=10.0)
126s +       cat (sprintf("    p: %g\n",p));
126s +       dg_fastcluster = fastcluster::hclust.vector(pcd, method=method, metric=metric, p=p)
126s +       d = dist(pcd, method=metric, p=p)
126s +     }
126s +     else {
126s +       dg_fastcluster = fastcluster::hclust.vector(pcd, method=method, metric=metric)
126s +       d = dist(pcd, method=metric)
126s +     }
126s +     d2 = d
126s +     dg_fastcluster_dist = fastcluster::hclust(d, method=method)
126s +     if (!identical(d,d2) || !identical(pcd,pcd2)) {
126s +       cat('Input array was corrupted!\n')
126s +       stop(print_seed())
126s +     }
126s +     if (!compare(dg_fastcluster_dist, dg_fastcluster)) {
126s +       stop(print_seed())
126s +     }
126s +   }
126s +   for (method in c('ward','centroid','median') ) {
126s +     cat(paste('Method:', method, '\n'))
126s +     dg_fastcluster = fastcluster::hclust.vector(pcd, method=method)
126s +     if (!identical(pcd,pcd2)) {
126s +       cat('Input array was corrupted!\n')
126s +       stop(print_seed())
126s +     }
126s +     d = dist(pcd)
126s +     if(method == "ward" && hasWardD2) {
126s +       method = "ward.D2"
126s +     }
126s +     else
126s +     {
126s +       # Workaround: fastcluster::hclust expects _squared_ euclidean distances.
126s +       d = d^2
126s +     }
126s +     d2 = d
126s +     dg_fastcluster_dist = fastcluster::hclust(d, method=method)
126s +     if (!identical(d,d2)) {
126s +       cat('Input array was corrupted!\n')
126s +       stop(print_seed())
126s +     }
126s +     if(method != "ward.D2") {
126s +       dg_fastcluster_dist$height = sqrt(dg_fastcluster_dist$height)
126s +     }
126s +     # The Euclidean methods may have small numerical errors due to squaring/
126s +     # taking the root in the Euclidean distances.
126s +     if (!compare(dg_fastcluster_dist, dg_fastcluster)) {
126s +       stop(print_seed())
126s +     }
126s +   }
126s +   cat('Passed.\n')
126s + }
126s > 
126s > # Test the single linkage function with the "binary" metric
126s > test.vector.binary <- function() {
126s +   # generate test data
126s +   cat (sprintf("Uniform sampling for the 'binary' metric:\n"))
126s +   n = sample(10:400,1)
126s +   dim = sample(n:(2*n),1)
126s +   cat (sprintf("Number of sample points: %d\n",n))
126s +   cat (sprintf("Dimension: %d\n",dim))
126s +   pcd = matrix(sample(-1:2, n*dim, replace=T), c(n,dim))
126s +   pcd2 = pcd
126s +   # test
126s +   method='single'
126s +   metric='binary'
126s +   cat(paste('Method:', method, '\n'))
126s +   cat(paste('    Metric:', metric, '\n'))
126s +   dg_fastcluster = fastcluster::hclust.vector(pcd, method=method, metric=metric)
126s +   d = dist(pcd, method=metric)
126s +   d2 = d
126s +   dg_fastcluster_dist       = fastcluster::hclust(d, method=method)
126s +   if (!identical(d,d2) || !identical(d,d2)) {
126s +     cat('Input array was corrupted!\n')
126s +     stop(print_seed())
126s +   }
126s +   if (!compare(dg_fastcluster_dist, dg_fastcluster)) {
126s +     stop(print_seed())
126s +   }
126s +   cat('Passed.\n')
126s + }
126s > 
126s > 
126s > N = 15
126s > for (i in (1:N)) {
126s +   if (i%%2==1) {
126s +     cat(sprintf('Random test %d of %d (uniform distribution of distances):\n',i,2*N))
126s +     d = generate.uniform()
126s +   }
126s +   else {
126s +     cat(sprintf('Random test %d of %d (Gaussian density):\n',i,2*N))
126s +     d = generate.normal()
126s +   }
126s +   test.dm(d)
126s + }
126s Random test 1 of 30 (uniform distribution of distances):
126s Number of sample points: 964
126s Dissimilarity range: [0,4.08115e+09]
126s Method : single 
126s Method : complete 
126s Method : average 
126s Method : mcquitty 
126s Method : ward.D 
126s Method : ward.D2 
126s Method : centroid 
126s Method : median 
126s Passed.
126s Random test 2 of 30 (Gaussian density):
126s Number of sample points: 311
126s Dimension: 11
126s Method : single 
126s Method : complete 
126s Method : average 
126s Method : mcquitty 
126s Method : ward.D 
126s Method : ward.D2 
126s Method : centroid 
126s Method : median 
126s Passed.
126s Random test 3 of 30 (uniform distribution of distances):
126s Number of sample points: 215
126s Dissimilarity range: [0,3.69021]
126s Method : single 
126s Method : complete 
126s Method : average 
126s Method : mcquitty 
126s Method : ward.D 
126s Method : ward.D2 
126s Method : centroid 
126s Method : median 
126s Passed.
126s Random test 4 of 30 (Gaussian density):
126s Number of sample points: 624
126s Dimension: 8
126s Method : single 
126s Method : complete 
126s Method : average 
126s Method : mcquitty 
126s Method : ward.D 
126s Method : ward.D2 
126s Method : centroid 
126s Method : median 
126s Passed.
126s Random test 5 of 30 (uniform distribution of distances):
126s Number of sample points: 825
126s Dissimilarity range: [0,4.89165e-06]
126s Method : single 
126s Method : complete 
127s Method : average 
127s Method : mcquitty 
127s Method : ward.D 
127s Method : ward.D2 
127s Method : centroid 
127s Method : median 
127s Passed.
127s Random test 6 of 30 (Gaussian density):
127s Number of sample points: 965
127s Dimension: 4
127s Method : single 
127s Method : complete 
127s Method : average 
127s Method : mcquitty 
127s Method : ward.D 
127s Method : ward.D2 
127s Method : centroid 
127s Method : median 
127s Passed.
127s Random test 7 of 30 (uniform distribution of distances):
127s Number of sample points: 750
127s Dissimilarity range: [0,6702.51]
127s Method : single 
127s Method : complete 
127s Method : average 
127s Method : mcquitty 
127s Method : ward.D 
127s Method : ward.D2 
127s Method : centroid 
127s Method : median 
127s Passed.
127s Random test 8 of 30 (Gaussian density):
127s Number of sample points: 213
127s Dimension: 6
127s Method : single 
127s Method : complete 
127s Method : average 
127s Method : mcquitty 
127s Method : ward.D 
127s Method : ward.D2 
127s Method : centroid 
127s Method : median 
127s Passed.
127s Random test 9 of 30 (uniform distribution of distances):
127s Number of sample points: 489
127s Dissimilarity range: [0,2.40362e-09]
127s Method : single 
127s Method : complete 
127s Method : average 
127s Method : mcquitty 
127s Method : ward.D 
127s Method : ward.D2 
127s Method : centroid 
127s Method : median 
127s Passed.
127s Random test 10 of 30 (Gaussian density):
127s Number of sample points: 556
127s Dimension: 7
127s Method : single 
127s Method : complete 
127s Method : average 
127s Method : mcquitty 
127s Method : ward.D 
127s Method : ward.D2 
127s Method : centroid 
127s Method : median 
127s Passed.
127s Random test 11 of 30 (uniform distribution of distances):
127s Number of sample points: 80
127s Dissimilarity range: [0,2.08906e+08]
127s Method : single 
127s Method : complete 
127s Method : average 
127s Method : mcquitty 
127s Method : ward.D 
127s Method : ward.D2 
127s Method : centroid 
127s Method : median 
127s Passed.
127s Random test 12 of 30 (Gaussian density):
127s Number of sample points: 52
127s Dimension: 2
127s Method : single 
127s Method : complete 
127s Method : average 
127s Method : mcquitty 
127s Method : ward.D 
127s Method : ward.D2 
127s Method : centroid 
127s Method : median 
127s Passed.
127s Random test 13 of 30 (uniform distribution of distances):
127s Number of sample points: 974
127s Dissimilarity range: [0,1.33641e-08]
127s Method : single 
128s Method : complete 
128s Method : average 
128s Method : mcquitty 
128s Method : ward.D 
128s Method : ward.D2 
128s Method : centroid 
128s Method : median 
128s Passed.
128s Random test 14 of 30 (Gaussian density):
128s Number of sample points: 383
128s Dimension: 13
128s Method : single 
128s Method : complete 
128s Method : average 
128s Method : mcquitty 
128s Method : ward.D 
128s Method : ward.D2 
128s Method : centroid 
128s Method : median 
128s Passed.
128s Random test 15 of 30 (uniform distribution of distances):
128s Number of sample points: 496
128s Dissimilarity range: [0,86915.6]
128s Method : single 
128s Method : complete 
128s Method : average 
128s Method : mcquitty 
128s Method : ward.D 
128s Method : ward.D2 
128s Method : centroid 
128s Method : median 
128s Passed.
128s > for (i in (N+1:N)) {
128s +   cat(sprintf('Random test %d of %d (Gaussian density):\n',i,2*N))
128s +   test.vector()
128s +   test.vector.binary()
128s + }
128s Random test 16 of 30 (Gaussian density):
128s Number of sample points: 419
128s Dimension: 5
128s Method: single 
128s     Metric: euclidean 
128s     Metric: maximum 
128s     Metric: manhattan 
128s     Metric: canberra 
128s     Metric: minkowski 
128s     p: 2.15931
128s Method: ward 
128s Method: centroid 
128s Method: median 
128s Passed.
128s Uniform sampling for the 'binary' metric:
128s Number of sample points: 93
128s Dimension: 170
128s Method: single 
128s     Metric: binary 
128s Passed.
128s Random test 17 of 30 (Gaussian density):
128s Number of sample points: 70
128s Dimension: 15
128s Method: single 
128s     Metric: euclidean 
128s     Metric: maximum 
128s     Metric: manhattan 
128s     Metric: canberra 
128s     Metric: minkowski 
128s     p: 7.90301
128s Method: ward 
128s Method: centroid 
128s Method: median 
128s Passed.
128s Uniform sampling for the 'binary' metric:
128s Number of sample points: 23
128s Dimension: 32
128s Method: single 
128s     Metric: binary 
128s Passed.
128s Random test 18 of 30 (Gaussian density):
128s Number of sample points: 289
128s Dimension: 8
128s Method: single 
128s     Metric: euclidean 
128s     Metric: maximum 
128s     Metric: manhattan 
128s     Metric: canberra 
128s     Metric: minkowski 
128s     p: 4.57163
128s Method: ward 
128s Method: centroid 
128s Method: median 
128s Passed.
128s Uniform sampling for the 'binary' metric:
128s Number of sample points: 127
128s Dimension: 170
128s Method: single 
128s     Metric: binary 
128s Passed.
128s Random test 19 of 30 (Gaussian density):
128s Number of sample points: 417
128s Dimension: 12
128s Method: single 
128s     Metric: euclidean 
128s     Metric: maximum 
128s     Metric: manhattan 
128s     Metric: canberra 
128s     Metric: minkowski 
128s     p: 2.41888
128s Method: ward 
128s Method: centroid 
128s Method: median 
129s Passed.
129s Uniform sampling for the 'binary' metric:
129s Number of sample points: 184
129s Dimension: 190
129s Method: single 
129s     Metric: binary 
129s Passed.
129s Random test 20 of 30 (Gaussian density):
129s Number of sample points: 242
129s Dimension: 4
129s Method: single 
129s     Metric: euclidean 
129s     Metric: maximum 
129s     Metric: manhattan 
129s     Metric: canberra 
129s     Metric: minkowski 
129s     p: 2.01013
129s Method: ward 
129s Method: centroid 
129s Method: median 
129s Passed.
129s Uniform sampling for the 'binary' metric:
129s Number of sample points: 196
129s Dimension: 209
129s Method: single 
129s     Metric: binary 
129s Passed.
129s Random test 21 of 30 (Gaussian density):
129s Number of sample points: 748
129s Dimension: 12
129s Method: single 
129s     Metric: euclidean 
129s     Metric: maximum 
129s     Metric: manhattan 
129s     Metric: canberra 
129s     Metric: minkowski 
129s     p: 1.75208
129s Method: ward 
129s Method: centroid 
129s Method: median 
129s Passed.
129s Uniform sampling for the 'binary' metric:
129s Number of sample points: 235
129s Dimension: 270
129s Method: single 
129s     Metric: binary 
130s Passed.
130s Random test 22 of 30 (Gaussian density):
130s Number of sample points: 931
130s Dimension: 5
130s Method: single 
130s     Metric: euclidean 
130s     Metric: maximum 
130s     Metric: manhattan 
130s     Metric: canberra 
130s     Metric: minkowski 
130s     p: 4.31948
130s Method: ward 
130s Method: centroid 
130s Method: median 
130s Passed.
130s Uniform sampling for the 'binary' metric:
130s Number of sample points: 399
130s Dimension: 425
130s Method: single 
130s     Metric: binary 
131s Passed.
131s Random test 23 of 30 (Gaussian density):
131s Number of sample points: 71
131s Dimension: 5
131s Method: single 
131s     Metric: euclidean 
131s     Metric: maximum 
131s     Metric: manhattan 
131s     Metric: canberra 
131s     Metric: minkowski 
131s     p: 5.78128
131s Method: ward 
131s Method: centroid 
131s Method: median 
131s Passed.
131s Uniform sampling for the 'binary' metric:
131s Number of sample points: 357
131s Dimension: 661
131s Method: single 
131s     Metric: binary 
132s Passed.
132s Random test 24 of 30 (Gaussian density):
132s Number of sample points: 286
132s Dimension: 9
132s Method: single 
132s     Metric: euclidean 
132s     Metric: maximum 
132s     Metric: manhattan 
132s     Metric: canberra 
132s     Metric: minkowski 
132s     p: 3.67639
132s Method: ward 
132s Method: centroid 
132s Method: median 
132s Passed.
132s Uniform sampling for the 'binary' metric:
132s Number of sample points: 47
132s Dimension: 87
132s Method: single 
132s     Metric: binary 
132s Passed.
132s Random test 25 of 30 (Gaussian density):
132s Number of sample points: 543
132s Dimension: 20
132s Method: single 
132s     Metric: euclidean 
132s     Metric: maximum 
132s     Metric: manhattan 
132s     Metric: canberra 
132s     Metric: minkowski 
132s     p: 1.69591
132s Method: ward 
133s Method: centroid 
133s Method: median 
133s Passed.
133s Uniform sampling for the 'binary' metric:
133s Number of sample points: 225
133s Dimension: 317
133s Method: single 
133s     Metric: binary 
133s Passed.
133s Random test 26 of 30 (Gaussian density):
133s Number of sample points: 735
133s Dimension: 16
133s Method: single 
133s     Metric: euclidean 
133s     Metric: maximum 
133s     Metric: manhattan 
133s     Metric: canberra 
133s     Metric: minkowski 
133s     p: 7.24438
133s Method: ward 
134s Method: centroid 
134s Method: median 
134s Passed.
134s Uniform sampling for the 'binary' metric:
134s Number of sample points: 258
134s Dimension: 311
134s Method: single 
134s     Metric: binary 
134s Passed.
134s Random test 27 of 30 (Gaussian density):
134s Number of sample points: 791
134s Dimension: 9
134s Method: single 
134s     Metric: euclidean 
134s     Metric: maximum 
134s     Metric: manhattan 
134s     Metric: canberra 
134s     Metric: minkowski 
134s     p: 3.12688
134s Method: ward 
134s Method: centroid 
135s Method: median 
135s Passed.
135s Uniform sampling for the 'binary' metric:
135s Number of sample points: 274
135s Dimension: 367
135s Method: single 
135s     Metric: binary 
135s Passed.
135s Random test 28 of 30 (Gaussian density):
135s Number of sample points: 548
135s Dimension: 15
135s Method: single 
135s     Metric: euclidean 
135s     Metric: maximum 
135s     Metric: manhattan 
135s     Metric: canberra 
135s     Metric: minkowski 
135s     p: 3.29194
135s Method: ward 
135s Method: centroid 
135s Method: median 
135s Passed.
135s Uniform sampling for the 'binary' metric:
135s Number of sample points: 92
135s Dimension: 141
135s Method: single 
135s     Metric: binary 
135s Passed.
135s Random test 29 of 30 (Gaussian density):
135s Number of sample points: 402
135s Dimension: 5
135s Method: single 
135s     Metric: euclidean 
135s     Metric: maximum 
135s     Metric: manhattan 
135s     Metric: canberra 
135s     Metric: minkowski 
135s     p: 3.9671
135s Method: ward 
135s Method: centroid 
135s Method: median 
135s Passed.
135s Uniform sampling for the 'binary' metric:
135s Number of sample points: 269
135s Dimension: 475
135s Method: single 
135s     Metric: binary 
136s Passed.
136s Random test 30 of 30 (Gaussian density):
136s Number of sample points: 870
136s Dimension: 14
136s Method: single 
136s     Metric: euclidean 
136s     Metric: maximum 
136s     Metric: manhattan 
136s     Metric: canberra 
136s     Metric: minkowski 
136s     p: 7.8692
136s Method: ward 
137s Method: centroid 
137s Method: median 
137s Passed.
137s Uniform sampling for the 'binary' metric:
137s Number of sample points: 103
137s Dimension: 115
137s Method: single 
137s     Metric: binary 
137s Passed.
137s > 
137s > cat('Done.\n')
137s Done.
137s > 
137s autopkgtest [11:07:28]: test run-unit-test: -----------------------]
138s autopkgtest [11:07:29]: test run-unit-test:  - - - - - - - - - - results - - - - - - - - - -
138s run-unit-test        PASS
138s autopkgtest [11:07:29]: test autodep8-python3: preparing testbed
221s autopkgtest [11:08:52]: testbed dpkg architecture: arm64
221s autopkgtest [11:08:52]: testbed apt version: 2.9.8
221s autopkgtest [11:08:52]: @@@@@@@@@@@@@@@@@@@@ test bed setup
222s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB]
222s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B]
222s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [849 kB]
223s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.3 kB]
223s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [76.4 kB]
223s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [104 kB]
223s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 Packages [50.3 kB]
223s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [601 kB]
223s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [17.1 kB]
223s Fetched 1794 kB in 1s (2034 kB/s)
223s Reading package lists...
225s Reading package lists...
226s Building dependency tree...
226s Reading state information...
226s Calculating upgrade...
227s The following NEW packages will be installed:
227s   python3.13-gdbm
227s The following packages will be upgraded:
227s   libpython3-stdlib python3 python3-gdbm python3-minimal
227s 4 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
227s Need to get 101 kB of archives.
227s After this operation, 141 kB of additional disk space will be used.
227s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-minimal arm64 3.12.7-1 [27.4 kB]
227s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3 arm64 3.12.7-1 [24.0 kB]
227s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libpython3-stdlib arm64 3.12.7-1 [10.0 kB]
227s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-gdbm arm64 3.13.0-2 [30.7 kB]
227s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-gdbm arm64 3.12.7-1 [8642 B]
228s Fetched 101 kB in 0s (286 kB/s)
228s (Reading database ... 
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228s Preparing to unpack .../python3-minimal_3.12.7-1_arm64.deb ...
228s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ...
228s Setting up python3-minimal (3.12.7-1) ...
228s (Reading database ... 
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228s Preparing to unpack .../python3_3.12.7-1_arm64.deb ...
228s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ...
228s Preparing to unpack .../libpython3-stdlib_3.12.7-1_arm64.deb ...
228s Unpacking libpython3-stdlib:arm64 (3.12.7-1) over (3.12.6-0ubuntu1) ...
228s Selecting previously unselected package python3.13-gdbm.
228s Preparing to unpack .../python3.13-gdbm_3.13.0-2_arm64.deb ...
228s Unpacking python3.13-gdbm (3.13.0-2) ...
228s Preparing to unpack .../python3-gdbm_3.12.7-1_arm64.deb ...
228s Unpacking python3-gdbm:arm64 (3.12.7-1) over (3.12.6-1ubuntu1) ...
228s Setting up python3.13-gdbm (3.13.0-2) ...
228s Setting up libpython3-stdlib:arm64 (3.12.7-1) ...
228s Setting up python3 (3.12.7-1) ...
229s Setting up python3-gdbm:arm64 (3.12.7-1) ...
229s Processing triggers for man-db (2.12.1-3) ...
230s Reading package lists...
230s Building dependency tree...
230s Reading state information...
231s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
231s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease
231s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease
231s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease
231s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease
232s Reading package lists...
232s Reading package lists...
232s Building dependency tree...
232s Reading state information...
233s Calculating upgrade...
234s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
234s Reading package lists...
234s Building dependency tree...
234s Reading state information...
235s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
239s Reading package lists...
239s Building dependency tree...
239s Reading state information...
240s Starting pkgProblemResolver with broken count: 0
240s Starting 2 pkgProblemResolver with broken count: 0
240s Done
241s The following additional packages will be installed:
241s   libblas3 libgfortran5 liblapack3 libpython3.13-minimal libpython3.13-stdlib
241s   python3-all python3-fastcluster python3-numpy python3.13 python3.13-minimal
241s Suggested packages:
241s   gcc gfortran python-numpy-doc python3-dev python3-pytest python3.13-venv
241s   python3.13-doc binfmt-support
241s Recommended packages:
241s   python3-scipy
241s The following NEW packages will be installed:
241s   autopkgtest-satdep libblas3 libgfortran5 liblapack3 libpython3.13-minimal
241s   libpython3.13-stdlib python3-all python3-fastcluster python3-numpy
241s   python3.13 python3.13-minimal
241s 0 upgraded, 11 newly installed, 0 to remove and 0 not upgraded.
241s Need to get 12.3 MB/12.3 MB of archives.
241s After this operation, 51.7 MB of additional disk space will be used.
241s Get:1 /tmp/autopkgtest.xHBNsl/2-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [720 B]
241s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3.13-minimal arm64 3.13.0-2 [877 kB]
241s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-minimal arm64 3.13.0-2 [2100 kB]
241s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.0-3build2 [152 kB]
241s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 14.2.0-8ubuntu1 [438 kB]
242s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.0-3build2 [2293 kB]
242s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3.13-stdlib arm64 3.13.0-2 [2073 kB]
242s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13 arm64 3.13.0-2 [719 kB]
242s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-all arm64 3.12.7-1 [890 B]
242s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy arm64 1:1.26.4+ds-11build1 [3654 kB]
242s Get:11 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-fastcluster arm64 1.2.6-1build1 [40.9 kB]
242s Fetched 12.3 MB in 1s (11.2 MB/s)
242s Selecting previously unselected package libpython3.13-minimal:arm64.
242s (Reading database ... 
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242s Preparing to unpack .../00-libpython3.13-minimal_3.13.0-2_arm64.deb ...
242s Unpacking libpython3.13-minimal:arm64 (3.13.0-2) ...
242s Selecting previously unselected package python3.13-minimal.
242s Preparing to unpack .../01-python3.13-minimal_3.13.0-2_arm64.deb ...
242s Unpacking python3.13-minimal (3.13.0-2) ...
242s Selecting previously unselected package libblas3:arm64.
242s Preparing to unpack .../02-libblas3_3.12.0-3build2_arm64.deb ...
242s Unpacking libblas3:arm64 (3.12.0-3build2) ...
243s Selecting previously unselected package libgfortran5:arm64.
243s Preparing to unpack .../03-libgfortran5_14.2.0-8ubuntu1_arm64.deb ...
243s Unpacking libgfortran5:arm64 (14.2.0-8ubuntu1) ...
243s Selecting previously unselected package liblapack3:arm64.
243s Preparing to unpack .../04-liblapack3_3.12.0-3build2_arm64.deb ...
243s Unpacking liblapack3:arm64 (3.12.0-3build2) ...
243s Selecting previously unselected package libpython3.13-stdlib:arm64.
243s Preparing to unpack .../05-libpython3.13-stdlib_3.13.0-2_arm64.deb ...
243s Unpacking libpython3.13-stdlib:arm64 (3.13.0-2) ...
243s Selecting previously unselected package python3.13.
243s Preparing to unpack .../06-python3.13_3.13.0-2_arm64.deb ...
243s Unpacking python3.13 (3.13.0-2) ...
243s Selecting previously unselected package python3-all.
243s Preparing to unpack .../07-python3-all_3.12.7-1_arm64.deb ...
243s Unpacking python3-all (3.12.7-1) ...
243s Selecting previously unselected package python3-numpy.
243s Preparing to unpack .../08-python3-numpy_1%3a1.26.4+ds-11build1_arm64.deb ...
243s Unpacking python3-numpy (1:1.26.4+ds-11build1) ...
243s Selecting previously unselected package python3-fastcluster.
243s Preparing to unpack .../09-python3-fastcluster_1.2.6-1build1_arm64.deb ...
243s Unpacking python3-fastcluster (1.2.6-1build1) ...
243s Selecting previously unselected package autopkgtest-satdep.
243s Preparing to unpack .../10-2-autopkgtest-satdep.deb ...
243s Unpacking autopkgtest-satdep (0) ...
243s Setting up libpython3.13-minimal:arm64 (3.13.0-2) ...
243s Setting up libblas3:arm64 (3.12.0-3build2) ...
243s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode
243s Setting up libgfortran5:arm64 (14.2.0-8ubuntu1) ...
243s Setting up python3.13-minimal (3.13.0-2) ...
244s Setting up libpython3.13-stdlib:arm64 (3.13.0-2) ...
244s Setting up liblapack3:arm64 (3.12.0-3build2) ...
244s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode
244s Setting up python3.13 (3.13.0-2) ...
246s Setting up python3-all (3.12.7-1) ...
246s Setting up python3-numpy (1:1.26.4+ds-11build1) ...
250s Setting up python3-fastcluster (1.2.6-1build1) ...
250s Setting up autopkgtest-satdep (0) ...
250s Processing triggers for systemd (256.5-2ubuntu4) ...
250s Processing triggers for man-db (2.12.1-3) ...
250s Processing triggers for libc-bin (2.40-1ubuntu3) ...
254s (Reading database ... 81579 files and directories currently installed.)
254s Removing autopkgtest-satdep (0) ...
256s autopkgtest [11:09:27]: 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
256s autopkgtest [11:09:27]: test autodep8-python3: [-----------------------
256s Testing with python3.13:
256s Traceback (most recent call last):
256s   File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in <module>
256s     from . import multiarray
256s   File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in <module>
256s     from . import overrides
256s   File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in <module>
256s     from numpy.core._multiarray_umath import (
256s         add_docstring,  _get_implementing_args, _ArrayFunctionDispatcher)
256s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath'
256s 
256s During handling of the above exception, another exception occurred:
256s 
256s Traceback (most recent call last):
256s   File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in <module>
256s     from numpy.__config__ import show as show_config
256s   File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in <module>
256s     from numpy.core._multiarray_umath import (
256s     ...<3 lines>...
256s     )
256s   File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in <module>
256s     raise ImportError(msg)
256s ImportError: 
256s 
256s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE!
256s 
256s Importing the numpy C-extensions failed. This error can happen for
256s many reasons, often due to issues with your setup or how NumPy was
256s installed.
256s 
256s We have compiled some common reasons and troubleshooting tips at:
256s 
256s     https://numpy.org/devdocs/user/troubleshooting-importerror.html
256s 
256s Please note and check the following:
256s 
256s   * The Python version is: Python3.13 from "/usr/bin/python3.13"
256s   * The NumPy version is: "1.26.4"
256s 
256s and make sure that they are the versions you expect.
256s Please carefully study the documentation linked above for further help.
256s 
256s Original error was: No module named 'numpy.core._multiarray_umath'
256s 
256s 
256s The above exception was the direct cause of the following exception:
256s 
256s Traceback (most recent call last):
256s   File "<string>", line 1, in <module>
256s     import fastcluster; print(fastcluster)
256s     ^^^^^^^^^^^^^^^^^^
256s   File "/usr/lib/python3/dist-packages/fastcluster.py", line 26, in <module>
256s     from numpy import double, empty, array, ndarray, var, cov, dot, expand_dims, \
256s         ceil, sqrt
256s   File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in <module>
256s     raise ImportError(msg) from e
256s ImportError: Error importing numpy: you should not try to import numpy from
256s         its source directory; please exit the numpy source tree, and relaunch
256s         your python interpreter from there.
256s autopkgtest [11:09:27]: test autodep8-python3: -----------------------]
257s autodep8-python3     FAIL non-zero exit status 1
257s autopkgtest [11:09:28]: test autodep8-python3:  - - - - - - - - - - results - - - - - - - - - -
257s autopkgtest [11:09:28]: @@@@@@@@@@@@@@@@@@@@ summary
257s run-unit-test        PASS
257s autodep8-python3     FAIL non-zero exit status 1
273s virt: nova [W] Skipping flock in bos03-arm64
273s virt: Creating nova instance adt-plucky-arm64-r-cran-fastcluster-20241113-110511-juju-7f2275-prod-proposed-migration-environment-2-13c924d8-4c2a-43f0-a291-375d1624dd0a from image adt/ubuntu-plucky-arm64-server-20241113.img (UUID 2d7760e6-2439-4200-89d6-5ed33e5c6330)...
273s virt: nova [W] Skipping flock in bos03-arm64
273s virt: Creating nova instance adt-plucky-arm64-r-cran-fastcluster-20241113-110511-juju-7f2275-prod-proposed-migration-environment-2-13c924d8-4c2a-43f0-a291-375d1624dd0a from image adt/ubuntu-plucky-arm64-server-20241113.img (UUID 2d7760e6-2439-4200-89d6-5ed33e5c6330)...