0s autopkgtest [22:21:15]: starting date and time: 2025-02-15 22:21:15+0000 0s autopkgtest [22:21:15]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [22:21:15]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.rt17vk05/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc,src:iproute2,src:php-twig,src:postgresql-17,src:postgresql-common,src:roundcube --apt-upgrade r-cran-fastcluster --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=glibc/2.41-1ubuntu1 iproute2/6.13.0-1ubuntu1 php-twig/3.19.0-1 postgresql-17/17.3-2 postgresql-common/273 roundcube/1.6.10+dfsg-1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor builder-cpu2-ram4-disk20 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@bos03-16.secgroup --name adt-plucky-amd64-r-cran-fastcluster-20250215-222114-juju-7f2275-prod-proposed-migration-environment-20-4b473b4d-b5ea-4b9c-8e9d-bf5dc2ef1578 --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --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,radosgw.ps5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 61s autopkgtest [22:22:16]: testbed dpkg architecture: amd64 61s autopkgtest [22:22:16]: testbed apt version: 2.9.28 62s autopkgtest [22:22:17]: @@@@@@@@@@@@@@@@@@@@ test bed setup 62s autopkgtest [22:22:17]: testbed release detected to be: None 63s autopkgtest [22:22:18]: updating testbed package index (apt update) 63s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [110 kB] 63s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 63s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 64s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 64s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [828 kB] 64s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [74.3 kB] 64s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [3120 B] 64s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [13.1 kB] 64s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [175 kB] 64s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [154 kB] 64s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [7984 B] 64s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/restricted i386 Packages [2412 B] 64s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [949 kB] 64s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [403 kB] 64s Get:15 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [10.3 kB] 64s Get:16 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [3520 B] 64s Fetched 2734 kB in 1s (2621 kB/s) 65s Reading package lists... 65s Reading package lists... 66s Building dependency tree... 66s Reading state information... 66s Calculating upgrade... 66s The following packages will be upgraded: 66s libtasn1-6 66s 1 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 66s Need to get 51.2 kB of archives. 66s After this operation, 22.5 kB of additional disk space will be used. 66s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 libtasn1-6 amd64 4.20.0-2 [51.2 kB] 67s Fetched 51.2 kB in 0s (153 kB/s) 67s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 108914 files and directories currently installed.) 67s Preparing to unpack .../libtasn1-6_4.20.0-2_amd64.deb ... 67s Unpacking libtasn1-6:amd64 (4.20.0-2) over (4.19.0-3build1) ... 67s Setting up libtasn1-6:amd64 (4.20.0-2) ... 67s Processing triggers for libc-bin (2.40-4ubuntu1) ... 67s Reading package lists... 67s Building dependency tree... 67s Reading state information... 68s 0 upgraded, 0 newly installed, 0 to remove and 6 not upgraded. 68s autopkgtest [22:22:23]: upgrading testbed (apt dist-upgrade and autopurge) 68s Reading package lists... 68s Building dependency tree... 68s Reading state information... 68s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 68s Starting 2 pkgProblemResolver with broken count: 0 68s Done 69s Entering ResolveByKeep 69s 69s The following packages will be upgraded: 69s iproute2 libc-bin libc-dev-bin libc6 libc6-dev locales 70s 6 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 70s Need to get 11.8 MB of archives. 70s After this operation, 746 kB of additional disk space will be used. 70s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc-dev-bin amd64 2.41-1ubuntu1 [24.7 kB] 70s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc6-dev amd64 2.41-1ubuntu1 [2182 kB] 71s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 locales all 2.41-1ubuntu1 [4246 kB] 72s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc6 amd64 2.41-1ubuntu1 [3327 kB] 72s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc-bin amd64 2.41-1ubuntu1 [701 kB] 72s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 iproute2 amd64 6.13.0-1ubuntu1 [1277 kB] 73s Preconfiguring packages ... 73s Fetched 11.8 MB in 3s (4193 kB/s) 73s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 108914 files and directories currently installed.) 73s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu1_amd64.deb ... 73s Unpacking libc-dev-bin (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 73s Preparing to unpack .../libc6-dev_2.41-1ubuntu1_amd64.deb ... 73s Unpacking libc6-dev:amd64 (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 73s Preparing to unpack .../locales_2.41-1ubuntu1_all.deb ... 73s Unpacking locales (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 73s Preparing to unpack .../libc6_2.41-1ubuntu1_amd64.deb ... 73s Checking for services that may need to be restarted... 73s Checking init scripts... 73s Checking for services that may need to be restarted... 73s Checking init scripts... 73s Stopping some services possibly affected by the upgrade (will be restarted later): 73s cron: stopping...done. 73s 73s Unpacking libc6:amd64 (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 74s Setting up libc6:amd64 (2.41-1ubuntu1) ... 74s Checking for services that may need to be restarted... 74s Checking init scripts... 74s Restarting services possibly affected by the upgrade: 74s cron: restarting...done. 74s 74s Services restarted successfully. 74s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 108915 files and directories currently installed.) 74s Preparing to unpack .../libc-bin_2.41-1ubuntu1_amd64.deb ... 74s Unpacking libc-bin (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 74s Setting up libc-bin (2.41-1ubuntu1) ... 74s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 108915 files and directories currently installed.) 74s Preparing to unpack .../iproute2_6.13.0-1ubuntu1_amd64.deb ... 74s Unpacking iproute2 (6.13.0-1ubuntu1) over (6.10.0-2ubuntu1) ... 74s Setting up iproute2 (6.13.0-1ubuntu1) ... 75s Setting up locales (2.41-1ubuntu1) ... 75s Installing new version of config file /etc/locale.alias ... 75s Generating locales (this might take a while)... 77s en_US.UTF-8... done 77s Generation complete. 77s Setting up libc-dev-bin (2.41-1ubuntu1) ... 77s Setting up libc6-dev:amd64 (2.41-1ubuntu1) ... 77s Processing triggers for man-db (2.13.0-1) ... 78s Processing triggers for systemd (257.2-3ubuntu1) ... 79s Reading package lists... 79s Building dependency tree... 79s Reading state information... 79s Starting pkgProblemResolver with broken count: 0 79s Starting 2 pkgProblemResolver with broken count: 0 79s Done 79s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 82s autopkgtest [22:22:37]: testbed running kernel: Linux 6.12.0-15-generic #15-Ubuntu SMP PREEMPT_DYNAMIC Tue Feb 4 16:02:16 UTC 2025 82s autopkgtest [22:22:37]: @@@@@@@@@@@@@@@@@@@@ apt-source r-cran-fastcluster 85s Get:1 http://ftpmaster.internal/ubuntu plucky/universe r-cran-fastcluster 1.2.6-1build2 (dsc) [2272 B] 85s Get:2 http://ftpmaster.internal/ubuntu plucky/universe r-cran-fastcluster 1.2.6-1build2 (tar) [208 kB] 85s Get:3 http://ftpmaster.internal/ubuntu plucky/universe r-cran-fastcluster 1.2.6-1build2 (diff) [4884 B] 85s gpgv: Signature made Thu Nov 14 18:29:06 2024 UTC 85s gpgv: using RSA key 568BF22A66337CBFC9A6B9B72C83DBC8E9BD0E37 85s gpgv: Can't check signature: No public key 85s dpkg-source: warning: cannot verify inline signature for ./r-cran-fastcluster_1.2.6-1build2.dsc: no acceptable signature found 85s autopkgtest [22:22:40]: testing package r-cran-fastcluster version 1.2.6-1build2 86s autopkgtest [22:22:41]: build not needed 87s autopkgtest [22:22:42]: test run-unit-test: preparing testbed 87s Reading package lists... 87s Building dependency tree... 87s Reading state information... 87s Starting pkgProblemResolver with broken count: 0 87s Starting 2 pkgProblemResolver with broken count: 0 87s Done 88s The following NEW packages will be installed: 88s fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono libblas3 88s libcairo2 libdatrie1 libdeflate0 libfontconfig1 libgfortran5 libgomp1 88s libgraphite2-3 libharfbuzz0b libice6 libjbig0 libjpeg-turbo8 libjpeg8 88s liblapack3 liblerc4 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 88s libpaper-utils libpaper2 libpixman-1-0 libsharpyuv0 libsm6 libtcl8.6 88s libthai-data libthai0 libtiff6 libtk8.6 libwebp7 libxcb-render0 libxcb-shm0 88s libxft2 libxrender1 libxss1 libxt6t64 python3-fastcluster python3-numpy 88s r-base-core r-cran-fastcluster unzip x11-common xdg-utils zip 88s 0 upgraded, 47 newly installed, 0 to remove and 0 not upgraded. 88s Need to get 46.8 MB of archives. 88s After this operation, 125 MB of additional disk space will be used. 88s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB] 89s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-core all 2.37-8 [835 kB] 89s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig-config amd64 2.15.0-1.1ubuntu2 [37.3 kB] 89s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontconfig1 amd64 2.15.0-1.1ubuntu2 [139 kB] 89s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig amd64 2.15.0-1.1ubuntu2 [180 kB] 89s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.1-2 [359 kB] 89s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 libpixman-1-0 amd64 0.44.0-3 [427 kB] 89s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-render0 amd64 1.17.0-2 [16.2 kB] 89s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-shm0 amd64 1.17.0-2 [5758 B] 89s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 libxrender1 amd64 1:0.9.10-1.1build1 [19.0 kB] 89s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 libcairo2 amd64 1.18.2-2 [569 kB] 89s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 libdatrie1 amd64 0.2.13-3build1 [19.0 kB] 89s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate0 amd64 1.23-1 [64.1 kB] 89s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 14.2.0-17ubuntu1 [910 kB] 89s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 libgomp1 amd64 14.2.0-17ubuntu1 [148 kB] 89s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB] 89s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 libharfbuzz0b amd64 10.2.0-1 [543 kB] 89s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 89s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 libice6 amd64 2:1.1.1-1 [44.1 kB] 89s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg-turbo8 amd64 2.1.5-3ubuntu2 [179 kB] 89s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 89s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.1-2 [3179 kB] 90s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 liblerc4 amd64 4.0.0+ds-5ubuntu1 [271 kB] 90s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 libthai-data all 0.1.29-2build1 [158 kB] 90s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 libthai0 amd64 0.1.29-2build1 [18.9 kB] 90s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 libpango-1.0-0 amd64 1.56.1-1 [255 kB] 90s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 libpangoft2-1.0-0 amd64 1.56.1-1 [52.6 kB] 90s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 libpangocairo-1.0-0 amd64 1.56.1-1 [29.1 kB] 90s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 libpaper2 amd64 2.2.5-0.3 [17.4 kB] 90s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 libpaper-utils amd64 2.2.5-0.3 [15.5 kB] 90s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [25.9 kB] 90s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 libsm6 amd64 2:1.2.4-1 [17.4 kB] 90s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 libtcl8.6 amd64 8.6.16+dfsg-1 [1086 kB] 90s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB] 90s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebp7 amd64 1.5.0-0.1 [378 kB] 90s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 libtiff6 amd64 4.5.1+git230720-4ubuntu4 [200 kB] 90s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 libxft2 amd64 2.3.6-1build1 [45.3 kB] 90s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 libxss1 amd64 1:1.2.3-1build3 [7204 B] 90s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 libtk8.6 amd64 8.6.16-1 [868 kB] 90s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 libxt6t64 amd64 1:1.2.1-1.2build1 [171 kB] 90s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-numpy amd64 1:1.26.4+ds-13 [5319 kB] 90s Get:42 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-fastcluster amd64 1.2.6-1build2 [47.6 kB] 90s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 zip amd64 3.0-14ubuntu2 [185 kB] 90s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 unzip amd64 6.0-28ubuntu6 [181 kB] 90s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 xdg-utils all 1.2.1-2ubuntu1 [66.0 kB] 90s Get:46 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-base-core amd64 4.4.2-1build1 [28.9 MB] 91s Get:47 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-fastcluster amd64 1.2.6-1build2 [197 kB] 92s Preconfiguring packages ... 92s Fetched 46.8 MB in 4s (12.5 MB/s) 92s Selecting previously unselected package fonts-dejavu-mono. 92s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 108916 files and directories currently installed.) 92s Preparing to unpack .../00-fonts-dejavu-mono_2.37-8_all.deb ... 92s Unpacking fonts-dejavu-mono (2.37-8) ... 92s Selecting previously unselected package fonts-dejavu-core. 92s Preparing to unpack .../01-fonts-dejavu-core_2.37-8_all.deb ... 92s Unpacking fonts-dejavu-core (2.37-8) ... 92s Selecting previously unselected package fontconfig-config. 92s Preparing to unpack .../02-fontconfig-config_2.15.0-1.1ubuntu2_amd64.deb ... 92s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ... 92s Selecting previously unselected package libfontconfig1:amd64. 92s Preparing to unpack .../03-libfontconfig1_2.15.0-1.1ubuntu2_amd64.deb ... 92s Unpacking libfontconfig1:amd64 (2.15.0-1.1ubuntu2) ... 92s Selecting previously unselected package fontconfig. 92s Preparing to unpack .../04-fontconfig_2.15.0-1.1ubuntu2_amd64.deb ... 92s Unpacking fontconfig (2.15.0-1.1ubuntu2) ... 92s Selecting previously unselected package libblas3:amd64. 92s Preparing to unpack .../05-libblas3_3.12.1-2_amd64.deb ... 92s Unpacking libblas3:amd64 (3.12.1-2) ... 92s Selecting previously unselected package libpixman-1-0:amd64. 92s Preparing to unpack .../06-libpixman-1-0_0.44.0-3_amd64.deb ... 92s Unpacking libpixman-1-0:amd64 (0.44.0-3) ... 92s Selecting previously unselected package libxcb-render0:amd64. 92s Preparing to unpack .../07-libxcb-render0_1.17.0-2_amd64.deb ... 92s Unpacking libxcb-render0:amd64 (1.17.0-2) ... 92s Selecting previously unselected package libxcb-shm0:amd64. 92s Preparing to unpack .../08-libxcb-shm0_1.17.0-2_amd64.deb ... 92s Unpacking libxcb-shm0:amd64 (1.17.0-2) ... 92s Selecting previously unselected package libxrender1:amd64. 92s Preparing to unpack .../09-libxrender1_1%3a0.9.10-1.1build1_amd64.deb ... 92s Unpacking libxrender1:amd64 (1:0.9.10-1.1build1) ... 92s Selecting previously unselected package libcairo2:amd64. 92s Preparing to unpack .../10-libcairo2_1.18.2-2_amd64.deb ... 92s Unpacking libcairo2:amd64 (1.18.2-2) ... 92s Selecting previously unselected package libdatrie1:amd64. 92s Preparing to unpack .../11-libdatrie1_0.2.13-3build1_amd64.deb ... 92s Unpacking libdatrie1:amd64 (0.2.13-3build1) ... 92s Selecting previously unselected package libdeflate0:amd64. 92s Preparing to unpack .../12-libdeflate0_1.23-1_amd64.deb ... 92s Unpacking libdeflate0:amd64 (1.23-1) ... 92s Selecting previously unselected package libgfortran5:amd64. 93s Preparing to unpack .../13-libgfortran5_14.2.0-17ubuntu1_amd64.deb ... 93s Unpacking libgfortran5:amd64 (14.2.0-17ubuntu1) ... 93s Selecting previously unselected package libgomp1:amd64. 93s Preparing to unpack .../14-libgomp1_14.2.0-17ubuntu1_amd64.deb ... 93s Unpacking libgomp1:amd64 (14.2.0-17ubuntu1) ... 93s Selecting previously unselected package libgraphite2-3:amd64. 93s Preparing to unpack .../15-libgraphite2-3_1.3.14-2ubuntu1_amd64.deb ... 93s Unpacking libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 93s Selecting previously unselected package libharfbuzz0b:amd64. 93s Preparing to unpack .../16-libharfbuzz0b_10.2.0-1_amd64.deb ... 93s Unpacking libharfbuzz0b:amd64 (10.2.0-1) ... 93s Selecting previously unselected package x11-common. 93s Preparing to unpack .../17-x11-common_1%3a7.7+23ubuntu3_all.deb ... 93s Unpacking x11-common (1:7.7+23ubuntu3) ... 93s Selecting previously unselected package libice6:amd64. 93s Preparing to unpack .../18-libice6_2%3a1.1.1-1_amd64.deb ... 93s Unpacking libice6:amd64 (2:1.1.1-1) ... 93s Selecting previously unselected package libjpeg-turbo8:amd64. 93s Preparing to unpack .../19-libjpeg-turbo8_2.1.5-3ubuntu2_amd64.deb ... 93s Unpacking libjpeg-turbo8:amd64 (2.1.5-3ubuntu2) ... 93s Selecting previously unselected package libjpeg8:amd64. 93s Preparing to unpack .../20-libjpeg8_8c-2ubuntu11_amd64.deb ... 93s Unpacking libjpeg8:amd64 (8c-2ubuntu11) ... 93s Selecting previously unselected package liblapack3:amd64. 93s Preparing to unpack .../21-liblapack3_3.12.1-2_amd64.deb ... 93s Unpacking liblapack3:amd64 (3.12.1-2) ... 93s Selecting previously unselected package liblerc4:amd64. 93s Preparing to unpack .../22-liblerc4_4.0.0+ds-5ubuntu1_amd64.deb ... 93s Unpacking liblerc4:amd64 (4.0.0+ds-5ubuntu1) ... 93s Selecting previously unselected package libthai-data. 93s Preparing to unpack .../23-libthai-data_0.1.29-2build1_all.deb ... 93s Unpacking libthai-data (0.1.29-2build1) ... 93s Selecting previously unselected package 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/etc/R/Renviron with new version 99s Setting up r-cran-fastcluster (1.2.6-1build2) ... 99s Processing triggers for man-db (2.13.0-1) ... 99s Processing triggers for install-info (7.1.1-1) ... 99s Processing triggers for libc-bin (2.41-1ubuntu1) ... 101s autopkgtest [22:22:56]: test run-unit-test: [----------------------- 101s 101s R version 4.4.2 (2024-10-31) -- "Pile of Leaves" 101s Copyright (C) 2024 The R Foundation for Statistical Computing 101s Platform: x86_64-pc-linux-gnu 101s 101s R is free software and comes with ABSOLUTELY NO WARRANTY. 101s You are welcome to redistribute it under certain conditions. 101s Type 'license()' or 'licence()' for distribution details. 101s 101s R is a collaborative project with many contributors. 101s Type 'contributors()' for more information and 101s 'citation()' on how to cite R or R packages in publications. 101s 101s Type 'demo()' for some demos, 'help()' for on-line help, or 101s 'help.start()' for an HTML browser interface to help. 101s Type 'q()' to quit R. 101s 101s > # fastcluster: Fast hierarchical clustering routines for R and Python 101s > # 101s > # Copyright: 101s > # * Until package version 1.1.23: © 2011 Daniel Müllner 101s > # * All changes from version 1.1.24 on: © Google Inc. 101s > # 101s > # Test script for the R interface 101s > 101s > seed = as.integer(runif(1, 0, 1e9)) 101s > set.seed(seed) 101s > cat(sprintf("Random seed: %d\n",seed)) 101s Random seed: 112050647 101s > 101s > print_seed <- function() { 101s + return(sprintf(' 101s + Please send a report to the author of the \'fastcluster\' package, Daniel Müllner. 101s + For contact details, see . To make the error 101s + reproducible, you must include the following number (the random seed value) in 101s + your error report: %d.\n\n', seed)) 101s + } 101s > 101s > hasWardD2 = getRversion() >= '3.1.0' 101s > 101s > # Compare two dendrograms and check whether they are equal, except that 101s > # ties may be resolved differently. 101s > compare <- function(dg1, dg2) { 101s + h1 <- dg1$height 101s + h2 <- dg2$height 101s + # "height" vectors may have small numerical errors. 101s + rdiffs <- abs(h1-h2)/pmax(abs(h1),abs(h2)) 101s + rdiffs = rdiffs[complete.cases(rdiffs)] 101s + rel_error <- max(rdiffs) 101s + # We allow a relative error of 1e-13. 101s + if (rel_error>1e-13) { 101s + print(h1) 101s + print(h2) 101s + cat(sprintf('Height vectors differ! The maximum relative error is %e.\n', rel_error)) 101s + return(FALSE) 101s + } 101s + # Filter the indices where consecutive merging distances are distinct. 101s + d = diff(dg1$height) 101s + b = (c(d,1)!=0 & c(1,d)!=0) 101s + #cat(sprintf("Percentage of indices where we can test: %g.\n",100.0*length(b[b])/length(b))) 101s + if (any(b)) { 101s + m1 = dg1$merge[b,] 101s + m2 = dg2$merge[b,] 101s + 101s + r = function(i) { 101s + if (i<0) { 101s + return(1) 101s + } 101s + else { 101s + return(b[i]) 101s + } 101s + } 101s + 101s + f = sapply(m1,r) 101s + fm1 = m1*f 101s + fm2 = m2*f 101s + # The "merge" matrices must be identical whereever indices are not ambiguous 101s + # due to ties. 101s + if (!identical(fm1,fm2)) { 101s + cat('Merge matrices differ!\n') 101s + return(FALSE) 101s + } 101s + # Compare the "order" vectors only if all merging distances were distinct. 101s + if (all(b) && !identical(dg1$order,dg2$order)) { 101s + cat('Order vectors differ!\n') 101s + return(FALSE) 101s + } 101s + } 101s + return(TRUE) 101s + } 101s > 101s > # Generate uniformly distributed random data 101s > generate.uniform <- function() { 101s + n = sample(10:1000,1) 101s + range_exp = runif(1,min=-10, max=10) 101s + cat(sprintf("Number of sample points: %d\n",n)) 101s + cat(sprintf("Dissimilarity range: [0,%g]\n",10^range_exp)) 101s + d = runif(n*(n-1)/2, min=0, max=10^range_exp) 101s + # Fake a compressed distance matrix 101s + attributes(d) <- NULL 101s + attr(d,"Size") <- n 101s + attr(d, "call") <- 'N/A' 101s + class(d) <- "dist" 101s + return(d) 101s + } 101s > 101s > # Generate normally distributed random data 101s > generate.normal <- function() { 101s + n = sample(10:1000,1) 101s + dim = sample(2:20,1) 101s + 101s + cat (sprintf("Number of sample points: %d\n",n)) 101s + cat (sprintf("Dimension: %d\n",dim)) 101s + 101s + pcd = matrix(rnorm(n*dim), c(n,dim)) 101s + d = dist(pcd) 101s + return(d) 101s + } 101s > 101s > # Test the clustering functions when a distance matrix is given. 101s > test.dm <- function(d) { 101s + d2 = d 101s + if (hasWardD2) { 101s + methods = c('single','complete','average','mcquitty','ward.D','ward.D2','centroid','median') 101s + } 101s + else { 101s + methods = c('single','complete','average','mcquitty','ward','centroid','median') 101s + } 101s + for (method in methods) { 101s + cat(paste('Method :', method, '\n')) 101s + dg_stats = stats::hclust(d, method=method) 101s + if (method == 'ward') { 101s + method = 'ward.D' 101s + } 101s + dg_fastcluster = fastcluster::hclust(d, method=method) 101s + if (!identical(d,d2)) { 101s + cat('Input array was corrupted!\n') 101s + stop(print_seed()) 101s + } 101s + if (!compare(dg_stats, dg_fastcluster)) { 101s + stop(print_seed()) 101s + } 101s + } 101s + cat('Passed.\n') 101s + } 101s > 101s > # Test the clustering functions for vector input in Euclidean space. 101s > test.vector <- function() { 101s + # generate test data 101s + n = sample(10:1000,1) 101s + dim = sample(2:20,1) 101s + cat (sprintf("Number of sample points: %d\n",n)) 101s + cat (sprintf("Dimension: %d\n",dim)) 101s + 101s + range_exp = runif(1,min=-10, max=10) 101s + pcd = matrix(rnorm(n*dim, sd=10^range_exp), c(n,dim)) 101s + pcd2 = pcd 101s + # test 101s + method='single' 101s + cat(paste('Method:', method, '\n')) 101s + for (metric in c('euclidean', 'maximum', 'manhattan', 'canberra', 'minkowski')) { 101s + cat(paste(' Metric:', metric, '\n')) 101s + if (metric=='minkowski') { 101s + p = runif(1, min=1.0, max=10.0) 101s + cat (sprintf(" p: %g\n",p)); 101s + dg_fastcluster = fastcluster::hclust.vector(pcd, method=method, metric=metric, p=p) 101s + d = dist(pcd, method=metric, p=p) 101s + } 101s + else { 101s + dg_fastcluster = fastcluster::hclust.vector(pcd, method=method, metric=metric) 101s + d = dist(pcd, method=metric) 101s + } 101s + d2 = d 101s + dg_fastcluster_dist = fastcluster::hclust(d, method=method) 101s + if (!identical(d,d2) || !identical(pcd,pcd2)) { 101s + cat('Input array was corrupted!\n') 101s + stop(print_seed()) 101s + } 101s + if (!compare(dg_fastcluster_dist, dg_fastcluster)) { 101s + stop(print_seed()) 101s + } 101s + } 101s + for (method in c('ward','centroid','median') ) { 101s + cat(paste('Method:', method, '\n')) 101s + dg_fastcluster = fastcluster::hclust.vector(pcd, method=method) 101s + if (!identical(pcd,pcd2)) { 101s + cat('Input array was corrupted!\n') 101s + stop(print_seed()) 101s + } 101s + d = dist(pcd) 101s + if(method == "ward" && hasWardD2) { 101s + method = "ward.D2" 101s + } 101s + else 101s + { 101s + # Workaround: fastcluster::hclust expects _squared_ euclidean distances. 101s + d = d^2 101s + } 101s + d2 = d 101s + dg_fastcluster_dist = fastcluster::hclust(d, method=method) 101s + if (!identical(d,d2)) { 101s + cat('Input array was corrupted!\n') 101s + stop(print_seed()) 101s + } 101s + if(method != "ward.D2") { 101s + dg_fastcluster_dist$height = sqrt(dg_fastcluster_dist$height) 101s + } 101s + # The Euclidean methods may have small numerical errors due to squaring/ 101s + # taking the root in the Euclidean distances. 101s + if (!compare(dg_fastcluster_dist, dg_fastcluster)) { 101s + stop(print_seed()) 101s + } 101s + } 101s + cat('Passed.\n') 101s + } 101s > 101s > # Test the single linkage function with the "binary" metric 101s > test.vector.binary <- function() { 101s + # generate test data 101s + cat (sprintf("Uniform sampling for the 'binary' metric:\n")) 101s + n = sample(10:400,1) 101s + dim = sample(n:(2*n),1) 101s + cat (sprintf("Number of sample points: %d\n",n)) 101s + cat (sprintf("Dimension: %d\n",dim)) 101s + pcd = matrix(sample(-1:2, n*dim, replace=T), c(n,dim)) 101s + pcd2 = pcd 101s + # test 101s + method='single' 101s + metric='binary' 101s + cat(paste('Method:', method, '\n')) 101s + cat(paste(' Metric:', metric, '\n')) 101s + dg_fastcluster = fastcluster::hclust.vector(pcd, method=method, metric=metric) 101s + d = dist(pcd, method=metric) 101s + d2 = d 101s + dg_fastcluster_dist = fastcluster::hclust(d, method=method) 101s + if (!identical(d,d2) || !identical(d,d2)) { 101s + cat('Input array was corrupted!\n') 101s + stop(print_seed()) 101s + } 101s + if (!compare(dg_fastcluster_dist, dg_fastcluster)) { 101s + stop(print_seed()) 101s + } 101s + cat('Passed.\n') 101s + } 101s > 101s > 101s > N = 15 101s > for (i in (1:N)) { 101s + if (i%%2==1) { 101s + cat(sprintf('Random test %d of %d (uniform distribution of distances):\n',i,2*N)) 101s + d = generate.uniform() 101s + } 101s + else { 101s + cat(sprintf('Random test %d of %d (Gaussian density):\n',i,2*N)) 101s + d = generate.normal() 101s + } 101s + test.dm(d) 101s + } 101s Random test 1 of 30 (uniform distribution of distances): 101s Number of sample points: 430 101s Dissimilarity range: [0,58734.9] 101s Method : single 101s Method : complete 101s Method : average 101s Method : mcquitty 101s Method : ward.D 101s Method : ward.D2 101s Method : centroid 101s Method : median 101s Passed. 101s Random test 2 of 30 (Gaussian density): 101s Number of sample points: 703 101s Dimension: 15 101s Method : single 101s Method : complete 101s Method : average 101s Method : mcquitty 101s Method : ward.D 101s Method : ward.D2 101s Method : centroid 101s Method : median 101s Passed. 101s Random test 3 of 30 (uniform distribution of distances): 101s Number of sample points: 697 101s Dissimilarity range: [0,0.132077] 101s Method : single 101s Method : complete 101s Method : average 101s Method : mcquitty 101s Method : ward.D 101s Method : ward.D2 101s Method : centroid 101s Method : median 101s Passed. 101s Random test 4 of 30 (Gaussian density): 101s Number of sample points: 341 101s Dimension: 13 101s Method : single 101s Method : complete 101s Method : average 101s Method : mcquitty 101s Method : ward.D 101s Method : ward.D2 101s Method : centroid 101s Method : median 101s Passed. 101s Random test 5 of 30 (uniform distribution of distances): 101s Number of sample points: 480 101s Dissimilarity range: [0,3.22045e-09] 101s Method : single 101s Method : complete 101s Method : average 101s Method : mcquitty 101s Method : ward.D 101s Method : ward.D2 101s Method : centroid 101s Method : median 101s Passed. 101s Random test 6 of 30 (Gaussian density): 101s Number of sample points: 821 101s Dimension: 14 101s Method : single 101s Method : complete 101s Method : average 101s Method : mcquitty 101s Method : ward.D 101s Method : ward.D2 101s Method : centroid 101s Method : median 102s Passed. 102s Random test 7 of 30 (uniform distribution of distances): 102s Number of sample points: 74 102s Dissimilarity range: [0,8.36269e+09] 102s Method : single 102s Method : complete 102s Method : average 102s Method : mcquitty 102s Method : ward.D 102s Method : ward.D2 102s Method : centroid 102s Method : median 102s Passed. 102s Random test 8 of 30 (Gaussian density): 102s Number of sample points: 332 102s Dimension: 15 102s Method : single 102s Method : complete 102s Method : average 102s Method : mcquitty 102s Method : ward.D 102s Method : ward.D2 102s Method : centroid 102s Method : median 102s Passed. 102s Random test 9 of 30 (uniform distribution of distances): 102s Number of sample points: 731 102s Dissimilarity range: [0,1.73045e-06] 102s Method : single 102s Method : complete 102s Method : average 102s Method : mcquitty 102s Method : ward.D 102s Method : ward.D2 102s Method : centroid 102s Method : median 102s Passed. 102s Random test 10 of 30 (Gaussian density): 102s Number of sample points: 279 102s Dimension: 10 102s Method : single 102s Method : complete 102s Method : average 102s Method : mcquitty 102s Method : ward.D 102s Method : ward.D2 102s Method : centroid 102s Method : median 102s Passed. 102s Random test 11 of 30 (uniform distribution of distances): 102s Number of sample points: 624 102s Dissimilarity range: [0,6.76617e+09] 102s Method : single 102s Method : complete 102s Method : average 102s Method : mcquitty 102s Method : ward.D 102s Method : ward.D2 102s Method : centroid 102s Method : median 102s Passed. 102s Random test 12 of 30 (Gaussian density): 102s Number of sample points: 745 102s Dimension: 2 102s Method : single 102s Method : complete 102s Method : average 102s Method : mcquitty 102s Method : ward.D 102s Method : ward.D2 102s Method : centroid 102s Method : median 102s Passed. 102s Random test 13 of 30 (uniform distribution of distances): 102s Number of sample points: 504 102s Dissimilarity range: [0,8.03477e+07] 102s Method : single 102s Method : complete 102s Method : average 102s Method : mcquitty 102s Method : ward.D 102s Method : ward.D2 102s Method : centroid 102s Method : median 102s Passed. 102s Random test 14 of 30 (Gaussian density): 102s Number of sample points: 806 102s Dimension: 8 102s Method : single 102s Method : complete 102s Method : average 102s Method : mcquitty 102s Method : ward.D 102s Method : ward.D2 102s Method : centroid 102s Method : median 102s Passed. 102s Random test 15 of 30 (uniform distribution of distances): 102s Number of sample points: 400 102s Dissimilarity range: [0,5.65914e+08] 102s Method : single 102s Method : complete 102s Method : average 102s Method : mcquitty 102s Method : ward.D 102s Method : ward.D2 102s Method : centroid 102s Method : median 102s Passed. 102s > for (i in (N+1:N)) { 102s + cat(sprintf('Random test %d of %d (Gaussian density):\n',i,2*N)) 102s + test.vector() 102s + test.vector.binary() 102s + } 102s Random test 16 of 30 (Gaussian density): 102s Number of sample points: 233 102s Dimension: 12 102s Method: single 102s Metric: euclidean 102s Metric: maximum 102s Metric: manhattan 102s Metric: canberra 102s Metric: minkowski 102s p: 9.32176 102s Method: ward 102s Method: centroid 102s Method: median 102s Passed. 102s Uniform sampling for the 'binary' metric: 102s Number of sample points: 394 102s Dimension: 404 102s Method: single 102s Metric: binary 103s Passed. 103s Random test 17 of 30 (Gaussian density): 103s Number of sample points: 936 103s Dimension: 4 103s Method: single 103s Metric: euclidean 103s Metric: maximum 103s Metric: manhattan 103s Metric: canberra 103s Metric: minkowski 103s p: 1.16109 103s Method: ward 103s Method: centroid 103s Method: median 103s Passed. 103s Uniform sampling for the 'binary' metric: 103s Number of sample points: 98 103s Dimension: 179 103s Method: single 103s Metric: binary 103s Passed. 103s Random test 18 of 30 (Gaussian density): 103s Number of sample points: 307 103s Dimension: 3 103s Method: single 103s Metric: euclidean 103s Metric: maximum 103s Metric: manhattan 103s Metric: canberra 103s Metric: minkowski 103s p: 3.29986 103s Method: ward 103s Method: centroid 103s Method: median 103s Passed. 103s Uniform sampling for the 'binary' metric: 103s Number of sample points: 166 103s Dimension: 228 103s Method: single 103s Metric: binary 103s Passed. 103s Random test 19 of 30 (Gaussian density): 103s Number of sample points: 603 103s Dimension: 20 103s Method: single 103s Metric: euclidean 103s Metric: maximum 103s Metric: manhattan 103s Metric: canberra 103s Metric: minkowski 103s p: 2.56959 103s Method: ward 103s Method: centroid 104s Method: median 104s Passed. 104s Uniform sampling for the 'binary' metric: 104s Number of sample points: 300 104s Dimension: 470 104s Method: single 104s Metric: binary 104s Passed. 104s Random test 20 of 30 (Gaussian density): 104s Number of sample points: 775 104s Dimension: 17 104s Method: single 104s Metric: euclidean 104s Metric: maximum 104s Metric: manhattan 104s Metric: canberra 104s Metric: minkowski 104s p: 8.21103 104s Method: ward 105s Method: centroid 105s Method: median 105s Passed. 105s Uniform sampling for the 'binary' metric: 105s Number of sample points: 18 105s Dimension: 30 105s Method: single 105s Metric: binary 105s Passed. 105s Random test 21 of 30 (Gaussian density): 105s Number of sample points: 810 105s Dimension: 17 105s Method: single 105s Metric: euclidean 105s Metric: maximum 105s Metric: manhattan 105s Metric: canberra 105s Metric: minkowski 105s p: 2.56478 105s Method: ward 105s Method: centroid 105s Method: median 105s Passed. 105s Uniform sampling for the 'binary' metric: 105s Number of sample points: 379 105s Dimension: 657 105s Method: single 105s Metric: binary 106s Passed. 106s Random test 22 of 30 (Gaussian density): 106s Number of sample points: 892 106s Dimension: 8 106s Method: single 106s Metric: euclidean 106s Metric: maximum 106s Metric: manhattan 106s Metric: canberra 106s Metric: minkowski 106s p: 8.02878 107s Method: ward 107s Method: centroid 107s Method: median 107s Passed. 107s Uniform sampling for the 'binary' metric: 107s Number of sample points: 164 107s Dimension: 271 107s Method: single 107s Metric: binary 107s Passed. 107s Random test 23 of 30 (Gaussian density): 107s Number of sample points: 731 107s Dimension: 6 107s Method: single 107s Metric: euclidean 107s Metric: maximum 107s Metric: manhattan 107s Metric: canberra 107s Metric: minkowski 107s p: 9.22641 107s Method: ward 107s Method: centroid 107s Method: median 107s Passed. 107s Uniform sampling for the 'binary' metric: 107s Number of sample points: 321 107s Dimension: 609 107s Method: single 107s Metric: binary 108s Passed. 108s Random test 24 of 30 (Gaussian density): 108s Number of sample points: 306 108s Dimension: 11 108s Method: single 108s Metric: euclidean 108s Metric: maximum 108s Metric: manhattan 108s Metric: canberra 108s Metric: minkowski 108s p: 1.4828 108s Method: ward 108s Method: centroid 108s Method: median 108s Passed. 108s Uniform sampling for the 'binary' metric: 108s Number of sample points: 362 108s Dimension: 697 108s Method: single 108s Metric: binary 109s Passed. 109s Random test 25 of 30 (Gaussian density): 109s Number of sample points: 497 109s Dimension: 7 109s Method: single 109s Metric: euclidean 109s Metric: maximum 109s Metric: manhattan 109s Metric: canberra 109s Metric: minkowski 109s p: 1.40787 109s Method: ward 109s Method: centroid 109s Method: median 109s Passed. 109s Uniform sampling for the 'binary' metric: 109s Number of sample points: 235 109s Dimension: 357 109s Method: single 109s Metric: binary 109s Passed. 109s Random test 26 of 30 (Gaussian density): 109s Number of sample points: 337 109s Dimension: 18 109s Method: single 109s Metric: euclidean 109s Metric: maximum 109s Metric: manhattan 109s Metric: canberra 109s Metric: minkowski 109s p: 5.33181 109s Method: ward 109s Method: centroid 109s Method: median 109s Passed. 109s Uniform sampling for the 'binary' metric: 109s Number of sample points: 300 109s Dimension: 431 109s Method: single 109s Metric: binary 109s Passed. 109s Random test 27 of 30 (Gaussian density): 109s Number of sample points: 926 109s Dimension: 13 109s Method: single 109s Metric: euclidean 109s Metric: maximum 109s Metric: manhattan 109s Metric: canberra 110s Metric: minkowski 110s p: 5.31119 111s Method: ward 111s Method: centroid 111s Method: median 111s Passed. 111s Uniform sampling for the 'binary' metric: 111s Number of sample points: 318 111s Dimension: 565 111s Method: single 111s Metric: binary 111s Passed. 111s Random test 28 of 30 (Gaussian density): 111s Number of sample points: 387 111s Dimension: 5 111s Method: single 111s Metric: euclidean 111s Metric: maximum 111s Metric: manhattan 111s Metric: canberra 111s Metric: minkowski 111s p: 2.13148 111s Method: ward 111s Method: centroid 111s Method: median 111s Passed. 111s Uniform sampling for the 'binary' metric: 111s Number of sample points: 104 111s Dimension: 118 111s Method: single 111s Metric: binary 111s Passed. 111s Random test 29 of 30 (Gaussian density): 111s Number of sample points: 727 111s Dimension: 12 111s Method: single 111s Metric: euclidean 111s Metric: maximum 111s Metric: manhattan 111s Metric: canberra 111s Metric: minkowski 111s p: 7.64943 111s Method: ward 111s Method: centroid 111s Method: median 111s Passed. 111s Uniform sampling for the 'binary' metric: 111s Number of sample points: 170 111s Dimension: 284 111s Method: single 111s Metric: binary 111s Passed. 111s Random test 30 of 30 (Gaussian density): 111s Number of sample points: 79 111s Dimension: 18 111s Method: single 111s Metric: euclidean 111s Metric: maximum 111s Metric: manhattan 111s Metric: canberra 111s Metric: minkowski 111s p: 5.0876 111s Method: ward 111s Method: centroid 111s Method: median 111s Passed. 111s Uniform sampling for the 'binary' metric: 111s Number of sample points: 254 111s Dimension: 419 111s Method: single 111s Metric: binary 111s Passed. 111s > 111s > cat('Done.\n') 111s Done. 111s > 112s autopkgtest [22:23:07]: test run-unit-test: -----------------------] 113s run-unit-test PASS 113s autopkgtest [22:23:08]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 113s autopkgtest [22:23:08]: test autodep8-python3: preparing testbed 183s autopkgtest [22:24:18]: testbed dpkg architecture: amd64 183s autopkgtest [22:24:18]: testbed apt version: 2.9.28 184s autopkgtest [22:24:19]: @@@@@@@@@@@@@@@@@@@@ test bed setup 184s autopkgtest [22:24:19]: testbed release detected to be: plucky 185s autopkgtest [22:24:20]: updating testbed package index (apt update) 186s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [110 kB] 186s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 186s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 186s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 186s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [13.1 kB] 186s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [828 kB] 186s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [3120 B] 186s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [74.3 kB] 186s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [175 kB] 186s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [154 kB] 186s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/restricted i386 Packages [2412 B] 186s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [7984 B] 186s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [403 kB] 186s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [949 kB] 186s Get:15 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [10.3 kB] 186s Get:16 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [3520 B] 186s Fetched 2734 kB in 1s (2599 kB/s) 187s Reading package lists... 187s Reading package lists... 187s Building dependency tree... 187s Reading state information... 188s Calculating upgrade... 188s The following packages will be upgraded: 188s libtasn1-6 188s 1 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 188s Need to get 51.2 kB of archives. 188s After this operation, 22.5 kB of additional disk space will be used. 188s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 libtasn1-6 amd64 4.20.0-2 [51.2 kB] 189s Fetched 51.2 kB in 0s (176 kB/s) 189s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 108914 files and directories currently installed.) 189s Preparing to unpack .../libtasn1-6_4.20.0-2_amd64.deb ... 189s Unpacking libtasn1-6:amd64 (4.20.0-2) over (4.19.0-3build1) ... 189s Setting up libtasn1-6:amd64 (4.20.0-2) ... 189s Processing triggers for libc-bin (2.40-4ubuntu1) ... 189s Reading package lists... 189s Building dependency tree... 189s Reading state information... 190s 0 upgraded, 0 newly installed, 0 to remove and 6 not upgraded. 190s autopkgtest [22:24:25]: upgrading testbed (apt dist-upgrade and autopurge) 190s Reading package lists... 190s Building dependency tree... 190s Reading state information... 191s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 191s Starting 2 pkgProblemResolver with broken count: 0 191s Done 191s Entering ResolveByKeep 191s 192s The following packages will be upgraded: 192s iproute2 libc-bin libc-dev-bin libc6 libc6-dev locales 192s 6 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 192s Need to get 11.8 MB of archives. 192s After this operation, 746 kB of additional disk space will be used. 192s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc-dev-bin amd64 2.41-1ubuntu1 [24.7 kB] 192s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc6-dev amd64 2.41-1ubuntu1 [2182 kB] 192s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 locales all 2.41-1ubuntu1 [4246 kB] 193s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc6 amd64 2.41-1ubuntu1 [3327 kB] 193s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc-bin amd64 2.41-1ubuntu1 [701 kB] 193s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 iproute2 amd64 6.13.0-1ubuntu1 [1277 kB] 193s Preconfiguring packages ... 193s Fetched 11.8 MB in 1s (10.6 MB/s) 193s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 108914 files and directories currently installed.) 193s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu1_amd64.deb ... 193s Unpacking libc-dev-bin (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 193s Preparing to unpack .../libc6-dev_2.41-1ubuntu1_amd64.deb ... 193s Unpacking libc6-dev:amd64 (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 194s Preparing to unpack .../locales_2.41-1ubuntu1_all.deb ... 194s Unpacking locales (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 194s Preparing to unpack .../libc6_2.41-1ubuntu1_amd64.deb ... 194s Checking for services that may need to be restarted... 194s Checking init scripts... 194s Checking for services that may need to be restarted... 194s Checking init scripts... 194s Stopping some services possibly affected by the upgrade (will be restarted later): 194s cron: stopping...done. 194s 194s Unpacking libc6:amd64 (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 194s Setting up libc6:amd64 (2.41-1ubuntu1) ... 194s Checking for services that may need to be restarted... 194s Checking init scripts... 194s Restarting services possibly affected by the upgrade: 195s cron: restarting...done. 195s 195s Services restarted successfully. 195s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 108915 files and directories currently installed.) 195s Preparing to unpack .../libc-bin_2.41-1ubuntu1_amd64.deb ... 195s Unpacking libc-bin (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 195s Setting up libc-bin (2.41-1ubuntu1) ... 195s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 108915 files and directories currently installed.) 195s Preparing to unpack .../iproute2_6.13.0-1ubuntu1_amd64.deb ... 195s Unpacking iproute2 (6.13.0-1ubuntu1) over (6.10.0-2ubuntu1) ... 195s Setting up iproute2 (6.13.0-1ubuntu1) ... 195s Setting up locales (2.41-1ubuntu1) ... 195s Installing new version of config file /etc/locale.alias ... 196s Generating locales (this might take a while)... 197s en_US.UTF-8... done 197s Generation complete. 197s Setting up libc-dev-bin (2.41-1ubuntu1) ... 197s Setting up libc6-dev:amd64 (2.41-1ubuntu1) ... 197s Processing triggers for man-db (2.13.0-1) ... 199s Processing triggers for systemd (257.2-3ubuntu1) ... 200s Reading package lists... 200s Building dependency tree... 200s Reading state information... 200s Starting pkgProblemResolver with broken count: 0 200s Starting 2 pkgProblemResolver with broken count: 0 200s Done 200s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 204s Reading package lists... 205s Building dependency tree... 205s Reading state information... 205s Starting pkgProblemResolver with broken count: 0 205s Starting 2 pkgProblemResolver with broken count: 0 205s Done 205s The following NEW packages will be installed: 205s libblas3 libgfortran5 liblapack3 python3-all python3-fastcluster 205s python3-numpy python3.12 python3.12-minimal 205s 0 upgraded, 8 newly installed, 0 to remove and 0 not upgraded. 205s Need to get 12.8 MB of archives. 205s After this operation, 60.9 MB of additional disk space will be used. 205s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.12-minimal amd64 3.12.9-1 [2348 kB] 206s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.12 amd64 3.12.9-1 [671 kB] 206s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.1-2 [359 kB] 206s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 14.2.0-17ubuntu1 [910 kB] 206s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.1-2 [3179 kB] 206s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-all amd64 3.13.1-1~exp2 [894 B] 206s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-numpy amd64 1:1.26.4+ds-13 [5319 kB] 207s Get:8 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-fastcluster amd64 1.2.6-1build2 [47.6 kB] 207s Fetched 12.8 MB in 1s (8843 kB/s) 207s Selecting previously unselected package python3.12-minimal. 207s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 108916 files and directories currently installed.) 207s Preparing to unpack .../0-python3.12-minimal_3.12.9-1_amd64.deb ... 207s Unpacking python3.12-minimal (3.12.9-1) ... 207s Selecting previously unselected package python3.12. 207s Preparing to unpack .../1-python3.12_3.12.9-1_amd64.deb ... 207s Unpacking python3.12 (3.12.9-1) ... 207s Selecting previously unselected package libblas3:amd64. 207s Preparing to unpack .../2-libblas3_3.12.1-2_amd64.deb ... 207s Unpacking libblas3:amd64 (3.12.1-2) ... 207s Selecting previously unselected package libgfortran5:amd64. 207s Preparing to unpack .../3-libgfortran5_14.2.0-17ubuntu1_amd64.deb ... 207s Unpacking libgfortran5:amd64 (14.2.0-17ubuntu1) ... 207s Selecting previously unselected package liblapack3:amd64. 207s Preparing to unpack .../4-liblapack3_3.12.1-2_amd64.deb ... 207s Unpacking liblapack3:amd64 (3.12.1-2) ... 207s Selecting previously unselected package python3-all. 207s Preparing to unpack .../5-python3-all_3.13.1-1~exp2_amd64.deb ... 207s Unpacking python3-all (3.13.1-1~exp2) ... 207s Selecting previously unselected package python3-numpy. 207s Preparing to unpack .../6-python3-numpy_1%3a1.26.4+ds-13_amd64.deb ... 207s Unpacking python3-numpy (1:1.26.4+ds-13) ... 208s Selecting previously unselected package python3-fastcluster. 208s Preparing to unpack .../7-python3-fastcluster_1.2.6-1build2_amd64.deb ... 208s Unpacking python3-fastcluster (1.2.6-1build2) ... 208s Setting up python3.12-minimal (3.12.9-1) ... 209s Setting up python3.12 (3.12.9-1) ... 210s Setting up python3-all (3.13.1-1~exp2) ... 210s Setting up libblas3:amd64 (3.12.1-2) ... 210s 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 210s Setting up libgfortran5:amd64 (14.2.0-17ubuntu1) ... 210s Setting up liblapack3:amd64 (3.12.1-2) ... 210s 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 210s Setting up python3-numpy (1:1.26.4+ds-13) ... 213s Setting up python3-fastcluster (1.2.6-1build2) ... 213s Processing triggers for systemd (257.2-3ubuntu1) ... 213s Processing triggers for man-db (2.13.0-1) ... 214s Processing triggers for libc-bin (2.41-1ubuntu1) ... 216s autopkgtest [22:24:51]: 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 216s autopkgtest [22:24:51]: test autodep8-python3: [----------------------- 216s Testing with python3.12: 216s 216s Testing with python3.13: 216s 216s autopkgtest [22:24:51]: test autodep8-python3: -----------------------] 217s autodep8-python3 PASS (superficial) 217s autopkgtest [22:24:52]: test autodep8-python3: - - - - - - - - - - results - - - - - - - - - - 217s autopkgtest [22:24:52]: @@@@@@@@@@@@@@@@@@@@ summary 217s run-unit-test PASS 217s autodep8-python3 PASS (superficial) 234s nova [W] Skipping flock for amd64 234s Creating nova instance adt-plucky-amd64-r-cran-fastcluster-20250215-222114-juju-7f2275-prod-proposed-migration-environment-20-4b473b4d-b5ea-4b9c-8e9d-bf5dc2ef1578 from image adt/ubuntu-plucky-amd64-server-20250215.img (UUID d1f7bb98-7df8-4026-816e-9f6798166d8b)... 234s nova [W] Timed out waiting for 72a84d5d-6c20-4b7a-8b79-01b0fe14b9a3 to get deleted. 234s nova [W] Skipping flock for amd64 234s Creating nova instance adt-plucky-amd64-r-cran-fastcluster-20250215-222114-juju-7f2275-prod-proposed-migration-environment-20-4b473b4d-b5ea-4b9c-8e9d-bf5dc2ef1578 from image adt/ubuntu-plucky-amd64-server-20250215.img (UUID d1f7bb98-7df8-4026-816e-9f6798166d8b)... 234s nova [W] Timed out waiting for 9b19caca-ce01-4576-80aa-64b006b6b53c to get deleted.