0s autopkgtest [10:41:24]: starting date and time: 2025-02-16 10:41:24+0000 0s autopkgtest [10:41:24]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [10:41:24]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.9jhn7v0h/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 autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-arm64-32.secgroup --name adt-plucky-arm64-r-cran-fastcluster-20250216-104123-juju-7f2275-prod-proposed-migration-environment-15-5114b67d-24aa-490a-92b0-759c321c2bb7 --image adt/ubuntu-plucky-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --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,radosgw.ps5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 180s autopkgtest [10:44:24]: testbed dpkg architecture: arm64 180s autopkgtest [10:44:24]: testbed apt version: 2.9.28 180s autopkgtest [10:44:24]: @@@@@@@@@@@@@@@@@@@@ test bed setup 181s autopkgtest [10:44:25]: testbed release detected to be: None 181s autopkgtest [10:44:25]: updating testbed package index (apt update) 182s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [110 kB] 182s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 182s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 182s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 182s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [3120 B] 182s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [807 kB] 182s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [13.1 kB] 182s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [74.8 kB] 182s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [154 kB] 182s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 Packages [7960 B] 182s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [929 kB] 182s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [10.0 kB] 183s Fetched 2110 kB in 1s (2205 kB/s) 183s Reading package lists... 184s + lsb_release --codename --short 184s + RELEASE=plucky 184s + cat 184s + [ plucky != trusty ] 184s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y --allow-downgrades -o Dpkg::Options::=--force-confnew dist-upgrade 184s Reading package lists... 184s Building dependency tree... 184s Reading state information... 185s Calculating upgrade... 185s The following packages will be upgraded: 185s pci.ids 186s 1 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 186s Need to get 284 kB of archives. 186s After this operation, 1024 B of additional disk space will be used. 186s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 pci.ids all 0.0~2025.02.12-1 [284 kB] 186s Fetched 284 kB in 0s (640 kB/s) 187s (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 ... 116609 files and directories currently installed.) 187s Preparing to unpack .../pci.ids_0.0~2025.02.12-1_all.deb ... 187s Unpacking pci.ids (0.0~2025.02.12-1) over (0.0~2025.02.05-1) ... 187s Setting up pci.ids (0.0~2025.02.12-1) ... 187s + rm /etc/apt/preferences.d/force-downgrade-to-release.pref 187s + /usr/lib/apt/apt-helper analyze-pattern ?true 187s + + uname -r 187s sed s/\./\\./g 187s + running_kernel_pattern=^linux-.*6\.12\.0-15-generic.* 187s + apt list ?obsolete 187s + tail -n+2 187s + cut -d/ -f1 187s + grep -v ^linux-.*6\.12\.0-15-generic.* 187s + true 187s + obsolete_pkgs= 187s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y purge --autoremove 187s Reading package lists... 188s Building dependency tree... 188s Reading state information... 188s + grep -q trusty /etc/lsb-release 188s 0 upgraded, 0 newly installed, 0 to remove and 6 not upgraded. 188s + [ ! -d /usr/share/doc/unattended-upgrades ] 188s + [ ! -d /usr/share/doc/lxd ] 188s + [ ! -d /usr/share/doc/lxd-client ] 188s + [ ! -d /usr/share/doc/snapd ] 188s + type iptables 188s + cat 188s + chmod 755 /etc/rc.local 188s + . /etc/rc.local 188s + iptables -w -t mangle -A FORWARD -p tcp --tcp-flags SYN,RST SYN -j TCPMSS --clamp-mss-to-pmtu 188s + iptables -A OUTPUT -d 10.255.255.1/32 -p tcp -j DROP 188s + iptables -A OUTPUT -d 10.255.255.2/32 -p tcp -j DROP 188s + uname -m 188s + [ aarch64 = ppc64le ] 188s + [ -d /run/systemd/system ] 188s + systemd-detect-virt --quiet --vm 188s + mkdir -p /etc/systemd/system/systemd-random-seed.service.d/ 188s + cat 188s + grep -q lz4 /etc/initramfs-tools/initramfs.conf 188s + echo COMPRESS=lz4 188s autopkgtest [10:44:32]: upgrading testbed (apt dist-upgrade and autopurge) 188s Reading package lists... 189s Building dependency tree... 189s Reading state information... 189s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 189s Starting 2 pkgProblemResolver with broken count: 0 189s Done 190s Entering ResolveByKeep 191s 191s The following packages will be upgraded: 191s iproute2 libc-bin libc-dev-bin libc6 libc6-dev locales 191s 6 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 191s Need to get 10.7 MB of archives. 191s After this operation, 358 kB of additional disk space will be used. 191s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-dev-bin arm64 2.41-1ubuntu1 [24.0 kB] 191s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6-dev arm64 2.41-1ubuntu1 [1750 kB] 192s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 locales all 2.41-1ubuntu1 [4246 kB] 193s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6 arm64 2.41-1ubuntu1 [2910 kB] 193s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-bin arm64 2.41-1ubuntu1 [600 kB] 193s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 iproute2 arm64 6.13.0-1ubuntu1 [1158 kB] 194s Preconfiguring packages ... 194s Fetched 10.7 MB in 2s (4287 kB/s) 194s (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 ... 116609 files and directories currently installed.) 194s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu1_arm64.deb ... 194s Unpacking libc-dev-bin (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 194s Preparing to unpack .../libc6-dev_2.41-1ubuntu1_arm64.deb ... 194s Unpacking libc6-dev:arm64 (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) ... 195s Preparing to unpack .../libc6_2.41-1ubuntu1_arm64.deb ... 195s Checking for services that may need to be restarted... 195s Checking init scripts... 195s Checking for services that may need to be restarted... 195s Checking init scripts... 195s Stopping some services possibly affected by the upgrade (will be restarted later): 195s cron: stopping...done. 195s 195s Unpacking libc6:arm64 (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 195s Setting up libc6:arm64 (2.41-1ubuntu1) ... 195s Checking for services that may need to be restarted... 195s Checking init scripts... 195s 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 ... 116610 files and directories currently installed.) 195s Preparing to unpack .../libc-bin_2.41-1ubuntu1_arm64.deb ... 195s Unpacking libc-bin (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 195s Setting up libc-bin (2.41-1ubuntu1) ... 196s (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 ... 116610 files and directories currently installed.) 196s Preparing to unpack .../iproute2_6.13.0-1ubuntu1_arm64.deb ... 196s Unpacking iproute2 (6.13.0-1ubuntu1) over (6.10.0-2ubuntu1) ... 196s Setting up iproute2 (6.13.0-1ubuntu1) ... 196s Setting up locales (2.41-1ubuntu1) ... 196s Installing new version of config file /etc/locale.alias ... 197s Generating locales (this might take a while)... 199s en_US.UTF-8... done 199s Generation complete. 199s Setting up libc-dev-bin (2.41-1ubuntu1) ... 199s Setting up libc6-dev:arm64 (2.41-1ubuntu1) ... 199s Processing triggers for man-db (2.13.0-1) ... 200s Processing triggers for systemd (257.2-3ubuntu1) ... 201s Reading package lists... 202s Building dependency tree... 202s Reading state information... 202s Starting pkgProblemResolver with broken count: 0 202s Starting 2 pkgProblemResolver with broken count: 0 202s Done 203s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 205s autopkgtest [10:44:49]: testbed running kernel: Linux 6.12.0-15-generic #15-Ubuntu SMP PREEMPT_DYNAMIC Tue Feb 4 15:49:33 UTC 2025 205s autopkgtest [10:44:49]: @@@@@@@@@@@@@@@@@@@@ apt-source r-cran-fastcluster 207s Get:1 http://ftpmaster.internal/ubuntu plucky/universe r-cran-fastcluster 1.2.6-1build2 (dsc) [2272 B] 207s Get:2 http://ftpmaster.internal/ubuntu plucky/universe r-cran-fastcluster 1.2.6-1build2 (tar) [208 kB] 207s Get:3 http://ftpmaster.internal/ubuntu plucky/universe r-cran-fastcluster 1.2.6-1build2 (diff) [4884 B] 208s gpgv: Signature made Thu Nov 14 18:29:06 2024 UTC 208s gpgv: using RSA key 568BF22A66337CBFC9A6B9B72C83DBC8E9BD0E37 208s gpgv: Can't check signature: No public key 208s dpkg-source: warning: cannot verify inline signature for ./r-cran-fastcluster_1.2.6-1build2.dsc: no acceptable signature found 208s autopkgtest [10:44:52]: testing package r-cran-fastcluster version 1.2.6-1build2 208s autopkgtest [10:44:52]: build not needed 209s autopkgtest [10:44:53]: test run-unit-test: preparing testbed 209s Reading package lists... 210s Building dependency tree... 210s Reading state information... 210s Starting pkgProblemResolver with broken count: 0 210s Starting 2 pkgProblemResolver with broken count: 0 210s Done 211s The following NEW packages will be installed: 211s fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono libblas3 211s libcairo2 libdatrie1 libdeflate0 libfontconfig1 libgfortran5 libgomp1 211s libgraphite2-3 libharfbuzz0b libice6 libjbig0 libjpeg-turbo8 libjpeg8 211s liblapack3 liblerc4 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 211s libpaper-utils libpaper2 libpixman-1-0 libsharpyuv0 libsm6 libtcl8.6 211s libthai-data libthai0 libtiff6 libtk8.6 libwebp7 libxcb-render0 libxcb-shm0 211s libxft2 libxrender1 libxss1 libxt6t64 python3-fastcluster python3-numpy 211s r-base-core r-cran-fastcluster unzip x11-common xdg-utils zip 211s 0 upgraded, 47 newly installed, 0 to remove and 0 not upgraded. 211s Need to get 42.7 MB of archives. 211s After this operation, 107 MB of additional disk space will be used. 211s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 211s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 211s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig-config arm64 2.15.0-1.1ubuntu2 [37.4 kB] 211s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 libfontconfig1 arm64 2.15.0-1.1ubuntu2 [142 kB] 211s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig arm64 2.15.0-1.1ubuntu2 [190 kB] 211s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.1-2 [161 kB] 211s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 libpixman-1-0 arm64 0.44.0-3 [197 kB] 212s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-render0 arm64 1.17.0-2 [16.6 kB] 212s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-shm0 arm64 1.17.0-2 [5884 B] 212s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 libxrender1 arm64 1:0.9.10-1.1build1 [18.8 kB] 212s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 libcairo2 arm64 1.18.2-2 [560 kB] 212s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 libdatrie1 arm64 0.2.13-3build1 [19.2 kB] 212s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate0 arm64 1.23-1 [46.2 kB] 212s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 14.2.0-17ubuntu1 [437 kB] 212s Get:15 http://ftpmaster.internal/ubuntu plucky/main arm64 libgomp1 arm64 14.2.0-17ubuntu1 [145 kB] 212s Get:16 http://ftpmaster.internal/ubuntu plucky/main arm64 libgraphite2-3 arm64 1.3.14-2ubuntu1 [70.6 kB] 212s Get:17 http://ftpmaster.internal/ubuntu plucky/main arm64 libharfbuzz0b arm64 10.2.0-1 [490 kB] 212s Get:18 http://ftpmaster.internal/ubuntu plucky/main arm64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 212s Get:19 http://ftpmaster.internal/ubuntu plucky/main arm64 libice6 arm64 2:1.1.1-1 [42.3 kB] 212s Get:20 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg-turbo8 arm64 2.1.5-3ubuntu2 [165 kB] 212s Get:21 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 212s Get:22 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.1-2 [2307 kB] 212s Get:23 http://ftpmaster.internal/ubuntu plucky/main arm64 liblerc4 arm64 4.0.0+ds-5ubuntu1 [167 kB] 212s Get:24 http://ftpmaster.internal/ubuntu plucky/main arm64 libthai-data all 0.1.29-2build1 [158 kB] 212s Get:25 http://ftpmaster.internal/ubuntu plucky/main arm64 libthai0 arm64 0.1.29-2build1 [18.2 kB] 212s Get:26 http://ftpmaster.internal/ubuntu plucky/main arm64 libpango-1.0-0 arm64 1.56.1-1 [238 kB] 212s Get:27 http://ftpmaster.internal/ubuntu plucky/main arm64 libpangoft2-1.0-0 arm64 1.56.1-1 [49.6 kB] 212s Get:28 http://ftpmaster.internal/ubuntu plucky/main arm64 libpangocairo-1.0-0 arm64 1.56.1-1 [27.6 kB] 212s Get:29 http://ftpmaster.internal/ubuntu plucky/main arm64 libpaper2 arm64 2.2.5-0.3 [17.3 kB] 212s Get:30 http://ftpmaster.internal/ubuntu plucky/main arm64 libpaper-utils arm64 2.2.5-0.3 [15.4 kB] 212s Get:31 http://ftpmaster.internal/ubuntu plucky/main arm64 libsharpyuv0 arm64 1.5.0-0.1 [16.9 kB] 212s Get:32 http://ftpmaster.internal/ubuntu plucky/main arm64 libsm6 arm64 2:1.2.4-1 [16.4 kB] 212s Get:33 http://ftpmaster.internal/ubuntu plucky/main arm64 libtcl8.6 arm64 8.6.16+dfsg-1 [987 kB] 212s Get:34 http://ftpmaster.internal/ubuntu plucky/main arm64 libjbig0 arm64 2.1-6.1ubuntu2 [29.3 kB] 212s Get:35 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebp7 arm64 1.5.0-0.1 [194 kB] 212s Get:36 http://ftpmaster.internal/ubuntu plucky/main arm64 libtiff6 arm64 4.5.1+git230720-4ubuntu4 [193 kB] 212s Get:37 http://ftpmaster.internal/ubuntu plucky/main arm64 libxft2 arm64 2.3.6-1build1 [44.1 kB] 212s Get:38 http://ftpmaster.internal/ubuntu plucky/main arm64 libxss1 arm64 1:1.2.3-1build3 [7244 B] 212s Get:39 http://ftpmaster.internal/ubuntu plucky/main arm64 libtk8.6 arm64 8.6.16-1 [776 kB] 212s Get:40 http://ftpmaster.internal/ubuntu plucky/main arm64 libxt6t64 arm64 1:1.2.1-1.2build1 [168 kB] 212s Get:41 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy arm64 1:1.26.4+ds-13 [4148 kB] 213s Get:42 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-fastcluster arm64 1.2.6-1build2 [42.0 kB] 213s Get:43 http://ftpmaster.internal/ubuntu plucky/main arm64 zip arm64 3.0-14ubuntu2 [173 kB] 213s Get:44 http://ftpmaster.internal/ubuntu plucky/main arm64 unzip arm64 6.0-28ubuntu6 [178 kB] 213s Get:45 http://ftpmaster.internal/ubuntu plucky/main arm64 xdg-utils all 1.2.1-2ubuntu1 [66.0 kB] 213s Get:46 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-base-core arm64 4.4.2-1build1 [28.4 MB] 214s Get:47 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-fastcluster arm64 1.2.6-1build2 [192 kB] 214s Preconfiguring packages ... 214s Fetched 42.7 MB in 3s (13.2 MB/s) 214s Selecting previously unselected package fonts-dejavu-mono. 214s (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 ... 116611 files and directories currently installed.) 214s Preparing to unpack .../00-fonts-dejavu-mono_2.37-8_all.deb ... 214s Unpacking fonts-dejavu-mono (2.37-8) ... 214s Selecting previously unselected package fonts-dejavu-core. 214s Preparing to unpack .../01-fonts-dejavu-core_2.37-8_all.deb ... 214s Unpacking fonts-dejavu-core (2.37-8) ... 214s Selecting previously unselected package fontconfig-config. 215s Preparing to unpack .../02-fontconfig-config_2.15.0-1.1ubuntu2_arm64.deb ... 215s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ... 215s Selecting previously unselected package libfontconfig1:arm64. 215s Preparing to unpack .../03-libfontconfig1_2.15.0-1.1ubuntu2_arm64.deb ... 215s Unpacking libfontconfig1:arm64 (2.15.0-1.1ubuntu2) ... 215s Selecting previously unselected package fontconfig. 215s Preparing to unpack .../04-fontconfig_2.15.0-1.1ubuntu2_arm64.deb ... 215s Unpacking fontconfig (2.15.0-1.1ubuntu2) ... 215s Selecting previously unselected package libblas3:arm64. 215s Preparing to unpack .../05-libblas3_3.12.1-2_arm64.deb ... 215s Unpacking libblas3:arm64 (3.12.1-2) ... 215s Selecting previously unselected package libpixman-1-0:arm64. 215s Preparing to unpack .../06-libpixman-1-0_0.44.0-3_arm64.deb ... 215s Unpacking libpixman-1-0:arm64 (0.44.0-3) ... 215s Selecting previously unselected package libxcb-render0:arm64. 215s Preparing to unpack .../07-libxcb-render0_1.17.0-2_arm64.deb ... 215s Unpacking libxcb-render0:arm64 (1.17.0-2) ... 215s Selecting previously unselected package libxcb-shm0:arm64. 215s Preparing to unpack .../08-libxcb-shm0_1.17.0-2_arm64.deb ... 215s Unpacking libxcb-shm0:arm64 (1.17.0-2) ... 215s Selecting previously unselected package libxrender1:arm64. 215s Preparing to unpack .../09-libxrender1_1%3a0.9.10-1.1build1_arm64.deb ... 215s Unpacking libxrender1:arm64 (1:0.9.10-1.1build1) ... 215s Selecting previously unselected package libcairo2:arm64. 215s Preparing to unpack .../10-libcairo2_1.18.2-2_arm64.deb ... 215s Unpacking libcairo2:arm64 (1.18.2-2) ... 215s Selecting previously unselected package libdatrie1:arm64. 215s Preparing to unpack .../11-libdatrie1_0.2.13-3build1_arm64.deb ... 215s Unpacking libdatrie1:arm64 (0.2.13-3build1) ... 215s Selecting previously unselected package libdeflate0:arm64. 215s Preparing to unpack .../12-libdeflate0_1.23-1_arm64.deb ... 215s Unpacking libdeflate0:arm64 (1.23-1) ... 215s Selecting previously unselected package libgfortran5:arm64. 215s Preparing to unpack .../13-libgfortran5_14.2.0-17ubuntu1_arm64.deb ... 215s Unpacking libgfortran5:arm64 (14.2.0-17ubuntu1) ... 215s Selecting previously unselected package libgomp1:arm64. 215s Preparing to unpack .../14-libgomp1_14.2.0-17ubuntu1_arm64.deb ... 215s Unpacking libgomp1:arm64 (14.2.0-17ubuntu1) ... 215s Selecting previously unselected package libgraphite2-3:arm64. 215s Preparing to unpack .../15-libgraphite2-3_1.3.14-2ubuntu1_arm64.deb ... 215s Unpacking libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 215s Selecting previously unselected package libharfbuzz0b:arm64. 215s Preparing to unpack .../16-libharfbuzz0b_10.2.0-1_arm64.deb ... 215s Unpacking libharfbuzz0b:arm64 (10.2.0-1) ... 215s Selecting previously unselected package x11-common. 215s Preparing to unpack .../17-x11-common_1%3a7.7+23ubuntu3_all.deb ... 215s Unpacking x11-common (1:7.7+23ubuntu3) ... 215s Selecting previously unselected package libice6:arm64. 215s Preparing to unpack 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Type 'demo()' for some demos, 'help()' for on-line help, or 224s 'help.start()' for an HTML browser interface to help. 224s Type 'q()' to quit R. 224s 224s > # fastcluster: Fast hierarchical clustering routines for R and Python 224s > # 224s > # Copyright: 224s > # * Until package version 1.1.23: © 2011 Daniel Müllner 224s > # * All changes from version 1.1.24 on: © Google Inc. 224s > # 224s > # Test script for the R interface 224s > 224s > seed = as.integer(runif(1, 0, 1e9)) 224s > set.seed(seed) 224s > cat(sprintf("Random seed: %d\n",seed)) 224s Random seed: 95437060 224s > 224s > print_seed <- function() { 224s + return(sprintf(' 224s + Please send a report to the author of the \'fastcluster\' package, Daniel Müllner. 224s + For contact details, see . To make the error 224s + reproducible, you must include the following number (the random seed value) in 224s + your error report: %d.\n\n', seed)) 224s + } 224s > 224s > hasWardD2 = getRversion() >= '3.1.0' 224s > 224s > # Compare two dendrograms and check whether they are equal, except that 224s > # ties may be resolved differently. 224s > compare <- function(dg1, dg2) { 224s + h1 <- dg1$height 224s + h2 <- dg2$height 224s + # "height" vectors may have small numerical errors. 224s + rdiffs <- abs(h1-h2)/pmax(abs(h1),abs(h2)) 224s + rdiffs = rdiffs[complete.cases(rdiffs)] 224s + rel_error <- max(rdiffs) 224s + # We allow a relative error of 1e-13. 224s + if (rel_error>1e-13) { 224s + print(h1) 224s + print(h2) 224s + cat(sprintf('Height vectors differ! The maximum relative error is %e.\n', rel_error)) 224s + return(FALSE) 224s + } 224s + # Filter the indices where consecutive merging distances are distinct. 224s + d = diff(dg1$height) 224s + b = (c(d,1)!=0 & c(1,d)!=0) 224s + #cat(sprintf("Percentage of indices where we can test: %g.\n",100.0*length(b[b])/length(b))) 224s + if (any(b)) { 224s + m1 = dg1$merge[b,] 224s + m2 = dg2$merge[b,] 224s + 224s + r = function(i) { 224s + if (i<0) { 224s + return(1) 224s + } 224s + else { 224s + return(b[i]) 224s + } 224s + } 224s + 224s + f = sapply(m1,r) 224s + fm1 = m1*f 224s + fm2 = m2*f 224s + # The "merge" matrices must be identical whereever indices are not ambiguous 224s + # due to ties. 224s + if (!identical(fm1,fm2)) { 224s + cat('Merge matrices differ!\n') 224s + return(FALSE) 224s + } 224s + # Compare the "order" vectors only if all merging distances were distinct. 224s + if (all(b) && !identical(dg1$order,dg2$order)) { 224s + cat('Order vectors differ!\n') 224s + return(FALSE) 224s + } 224s + } 224s + return(TRUE) 224s + } 224s > 224s > # Generate uniformly distributed random data 224s > generate.uniform <- function() { 224s + n = sample(10:1000,1) 224s + range_exp = runif(1,min=-10, max=10) 224s + cat(sprintf("Number of sample points: %d\n",n)) 224s + cat(sprintf("Dissimilarity range: [0,%g]\n",10^range_exp)) 224s + d = runif(n*(n-1)/2, min=0, max=10^range_exp) 224s + # Fake a compressed distance matrix 224s + attributes(d) <- NULL 224s + attr(d,"Size") <- n 224s + attr(d, "call") <- 'N/A' 224s + class(d) <- "dist" 224s + return(d) 224s + } 224s > 224s > # Generate normally distributed random data 224s > generate.normal <- function() { 224s + n = sample(10:1000,1) 224s + dim = sample(2:20,1) 224s + 224s + cat (sprintf("Number of sample points: %d\n",n)) 224s + cat (sprintf("Dimension: %d\n",dim)) 224s + 224s + pcd = matrix(rnorm(n*dim), c(n,dim)) 224s + d = dist(pcd) 224s + return(d) 224s + } 224s > 224s > # Test the clustering functions when a distance matrix is given. 224s > test.dm <- function(d) { 224s + d2 = d 224s + if (hasWardD2) { 224s + methods = c('single','complete','average','mcquitty','ward.D','ward.D2','centroid','median') 224s + } 224s + else { 224s + methods = c('single','complete','average','mcquitty','ward','centroid','median') 224s + } 224s + for (method in methods) { 224s + cat(paste('Method :', method, '\n')) 224s + dg_stats = stats::hclust(d, method=method) 224s + if (method == 'ward') { 224s + method = 'ward.D' 224s + } 224s + dg_fastcluster = fastcluster::hclust(d, method=method) 224s + if (!identical(d,d2)) { 224s + cat('Input array was corrupted!\n') 224s + stop(print_seed()) 224s + } 224s + if (!compare(dg_stats, dg_fastcluster)) { 224s + stop(print_seed()) 224s + } 224s + } 224s + cat('Passed.\n') 224s + } 224s > 224s > # Test the clustering functions for vector input in Euclidean space. 224s > test.vector <- function() { 224s + # generate test data 224s + n = sample(10:1000,1) 224s + dim = sample(2:20,1) 224s + cat (sprintf("Number of sample points: %d\n",n)) 224s + cat (sprintf("Dimension: %d\n",dim)) 224s + 224s + range_exp = runif(1,min=-10, max=10) 224s + pcd = matrix(rnorm(n*dim, sd=10^range_exp), c(n,dim)) 224s + pcd2 = pcd 224s + # test 224s + method='single' 224s + cat(paste('Method:', method, '\n')) 224s + for (metric in c('euclidean', 'maximum', 'manhattan', 'canberra', 'minkowski')) { 224s + cat(paste(' Metric:', metric, '\n')) 224s + if (metric=='minkowski') { 224s + p = runif(1, min=1.0, max=10.0) 224s + cat (sprintf(" p: %g\n",p)); 224s + dg_fastcluster = fastcluster::hclust.vector(pcd, method=method, metric=metric, p=p) 224s + d = dist(pcd, method=metric, p=p) 224s + } 224s + else { 224s + dg_fastcluster = fastcluster::hclust.vector(pcd, method=method, metric=metric) 224s + d = dist(pcd, method=metric) 224s + } 224s + d2 = d 224s + dg_fastcluster_dist = fastcluster::hclust(d, method=method) 224s + if (!identical(d,d2) || !identical(pcd,pcd2)) { 224s + cat('Input array was corrupted!\n') 224s + stop(print_seed()) 224s + } 224s + if (!compare(dg_fastcluster_dist, dg_fastcluster)) { 224s + stop(print_seed()) 224s + } 224s + } 224s + for (method in c('ward','centroid','median') ) { 224s + cat(paste('Method:', method, '\n')) 224s + dg_fastcluster = fastcluster::hclust.vector(pcd, method=method) 224s + if (!identical(pcd,pcd2)) { 224s + cat('Input array was corrupted!\n') 224s + stop(print_seed()) 224s + } 224s + d = dist(pcd) 224s + if(method == "ward" && hasWardD2) { 224s + method = "ward.D2" 224s + } 224s + else 224s + { 224s + # Workaround: fastcluster::hclust expects _squared_ euclidean distances. 224s + d = d^2 224s + } 224s + d2 = d 224s + dg_fastcluster_dist = fastcluster::hclust(d, method=method) 224s + if (!identical(d,d2)) { 224s + cat('Input array was corrupted!\n') 224s + stop(print_seed()) 224s + } 224s + if(method != "ward.D2") { 224s + dg_fastcluster_dist$height = sqrt(dg_fastcluster_dist$height) 224s + } 224s + # The Euclidean methods may have small numerical errors due to squaring/ 224s + # taking the root in the Euclidean distances. 224s + if (!compare(dg_fastcluster_dist, dg_fastcluster)) { 224s + stop(print_seed()) 224s + } 224s + } 224s + cat('Passed.\n') 224s + } 224s > 224s > # Test the single linkage function with the "binary" metric 224s > test.vector.binary <- function() { 224s + # generate test data 224s + cat (sprintf("Uniform sampling for the 'binary' metric:\n")) 224s + n = sample(10:400,1) 224s + dim = sample(n:(2*n),1) 224s + cat (sprintf("Number of sample points: %d\n",n)) 224s + cat (sprintf("Dimension: %d\n",dim)) 224s + pcd = matrix(sample(-1:2, n*dim, replace=T), c(n,dim)) 224s + pcd2 = pcd 224s + # test 224s + method='single' 224s + metric='binary' 224s + cat(paste('Method:', method, '\n')) 224s + cat(paste(' Metric:', metric, '\n')) 224s + dg_fastcluster = fastcluster::hclust.vector(pcd, method=method, metric=metric) 224s + d = dist(pcd, method=metric) 224s + d2 = d 224s + dg_fastcluster_dist = fastcluster::hclust(d, method=method) 224s + if (!identical(d,d2) || !identical(d,d2)) { 224s + cat('Input array was corrupted!\n') 224s + stop(print_seed()) 224s + } 224s + if (!compare(dg_fastcluster_dist, dg_fastcluster)) { 224s + stop(print_seed()) 224s + } 224s + cat('Passed.\n') 224s + } 224s > 224s > 224s > N = 15 224s > for (i in (1:N)) { 224s + if (i%%2==1) { 224s + cat(sprintf('Random test %d of %d (uniform distribution of distances):\n',i,2*N)) 224s + d = generate.uniform() 224s + } 224s + else { 224s + cat(sprintf('Random test %d of %d (Gaussian density):\n',i,2*N)) 224s + d = generate.normal() 224s + } 224s + test.dm(d) 224s + } 224s Random test 1 of 30 (uniform distribution of distances): 224s Number of sample points: 350 224s Dissimilarity range: [0,5.47353e-07] 224s Method : single 224s Method : complete 224s Method : average 224s Method : mcquitty 224s Method : ward.D 224s Method : ward.D2 224s Method : centroid 224s Method : median 224s Passed. 224s Random test 2 of 30 (Gaussian density): 224s Number of sample points: 172 224s Dimension: 20 224s Method : single 224s Method : complete 224s Method : average 224s Method : mcquitty 224s Method : ward.D 224s Method : ward.D2 224s Method : centroid 224s Method : median 224s Passed. 224s Random test 3 of 30 (uniform distribution of distances): 224s Number of sample points: 741 224s Dissimilarity range: [0,4.00372e+08] 224s Method : single 224s Method : complete 224s Method : average 224s Method : mcquitty 224s Method : ward.D 224s Method : ward.D2 224s Method : centroid 224s Method : median 224s Passed. 224s Random test 4 of 30 (Gaussian density): 224s Number of sample points: 611 224s Dimension: 14 224s Method : single 224s Method : complete 224s Method : average 224s Method : mcquitty 224s Method : ward.D 224s Method : ward.D2 224s Method : centroid 224s Method : median 224s Passed. 224s Random test 5 of 30 (uniform distribution of distances): 224s Number of sample points: 600 224s Dissimilarity range: [0,1.25734e-06] 224s Method : single 224s Method : complete 224s Method : average 224s Method : mcquitty 224s Method : ward.D 224s Method : ward.D2 224s Method : centroid 224s Method : median 225s Passed. 225s Random test 6 of 30 (Gaussian density): 225s Number of sample points: 41 225s Dimension: 7 225s Method : single 225s Method : complete 225s Method : average 225s Method : mcquitty 225s Method : ward.D 225s Method : ward.D2 225s Method : centroid 225s Method : median 225s Passed. 225s Random test 7 of 30 (uniform distribution of distances): 225s Number of sample points: 265 225s Dissimilarity range: [0,4.46478e+06] 225s Method : single 225s Method : complete 225s Method : average 225s Method : mcquitty 225s Method : ward.D 225s Method : ward.D2 225s Method : centroid 225s Method : median 225s Passed. 225s Random test 8 of 30 (Gaussian density): 225s Number of sample points: 920 225s Dimension: 4 225s Method : single 225s Method : complete 225s Method : average 225s Method : mcquitty 225s Method : ward.D 225s Method : ward.D2 225s Method : centroid 225s Method : median 225s Passed. 225s Random test 9 of 30 (uniform distribution of distances): 225s Number of sample points: 224 225s Dissimilarity range: [0,2.45648e-06] 225s Method : single 225s Method : complete 225s Method : average 225s Method : mcquitty 225s Method : ward.D 225s Method : ward.D2 225s Method : centroid 225s Method : median 225s Passed. 225s Random test 10 of 30 (Gaussian density): 225s Number of sample points: 766 225s Dimension: 20 225s Method : single 225s Method : complete 225s Method : average 225s Method : mcquitty 225s Method : ward.D 225s Method : ward.D2 225s Method : centroid 225s Method : median 225s Passed. 225s Random test 11 of 30 (uniform distribution of distances): 225s Number of sample points: 378 225s Dissimilarity range: [0,2.38296e-10] 225s Method : single 225s Method : complete 225s Method : average 225s Method : mcquitty 225s Method : ward.D 225s Method : ward.D2 225s Method : centroid 225s Method : median 225s Passed. 225s Random test 12 of 30 (Gaussian density): 225s Number of sample points: 815 225s Dimension: 10 225s Method : single 225s Method : complete 225s Method : average 225s Method : mcquitty 225s Method : ward.D 225s Method : ward.D2 225s Method : centroid 225s Method : median 225s Passed. 225s Random test 13 of 30 (uniform distribution of distances): 225s Number of sample points: 412 225s Dissimilarity range: [0,9.22985e+06] 225s Method : single 225s Method : complete 225s Method : average 225s Method : mcquitty 225s Method : ward.D 225s Method : ward.D2 225s Method : centroid 225s Method : median 225s Passed. 225s Random test 14 of 30 (Gaussian density): 225s Number of sample points: 824 225s Dimension: 9 225s Method : single 225s Method : complete 225s Method : average 225s Method : mcquitty 225s Method : ward.D 225s Method : ward.D2 225s Method : centroid 225s Method : median 225s Passed. 225s Random test 15 of 30 (uniform distribution of distances): 225s Number of sample points: 839 225s Dissimilarity range: [0,1.00753e-08] 225s Method : single 225s Method : complete 225s Method : average 226s Method : mcquitty 226s Method : ward.D 226s Method : ward.D2 226s Method : centroid 226s Method : median 226s Passed. 226s > for (i in (N+1:N)) { 226s + cat(sprintf('Random test %d of %d (Gaussian density):\n',i,2*N)) 226s + test.vector() 226s + test.vector.binary() 226s + } 226s Random test 16 of 30 (Gaussian density): 226s Number of sample points: 576 226s Dimension: 15 226s Method: single 226s Metric: euclidean 226s Metric: maximum 226s Metric: manhattan 226s Metric: canberra 226s Metric: minkowski 226s p: 7.95315 226s Method: ward 226s Method: centroid 226s Method: median 226s Passed. 226s Uniform sampling for the 'binary' metric: 226s Number of sample points: 253 226s Dimension: 456 226s Method: single 226s Metric: binary 227s Passed. 227s Random test 17 of 30 (Gaussian density): 227s Number of sample points: 689 227s Dimension: 2 227s Method: single 227s Metric: euclidean 227s Metric: maximum 227s Metric: manhattan 227s Metric: canberra 227s Metric: minkowski 227s p: 7.53611 227s Method: ward 227s Method: centroid 227s Method: median 227s Passed. 227s Uniform sampling for the 'binary' metric: 227s Number of sample points: 71 227s Dimension: 79 227s Method: single 227s Metric: binary 227s Passed. 227s Random test 18 of 30 (Gaussian density): 227s Number of sample points: 520 227s Dimension: 18 227s Method: single 227s Metric: euclidean 227s Metric: maximum 227s Metric: manhattan 227s Metric: canberra 227s Metric: minkowski 227s p: 2.76918 227s Method: ward 227s Method: centroid 227s Method: median 227s Passed. 227s Uniform sampling for the 'binary' metric: 227s Number of sample points: 372 227s Dimension: 426 227s Method: single 227s Metric: binary 228s Passed. 228s Random test 19 of 30 (Gaussian density): 228s Number of sample points: 488 228s Dimension: 15 228s Method: single 228s Metric: euclidean 228s Metric: maximum 228s Metric: manhattan 228s Metric: canberra 228s Metric: minkowski 228s p: 2.90576 228s Method: ward 228s Method: centroid 228s Method: median 228s Passed. 228s Uniform sampling for the 'binary' metric: 228s Number of sample points: 102 228s Dimension: 139 228s Method: single 228s Metric: binary 228s Passed. 228s Random test 20 of 30 (Gaussian density): 228s Number of sample points: 537 228s Dimension: 3 228s Method: single 228s Metric: euclidean 228s Metric: maximum 228s Metric: manhattan 228s Metric: canberra 228s Metric: minkowski 228s p: 2.04903 228s Method: ward 228s Method: centroid 228s Method: median 228s Passed. 228s Uniform sampling for the 'binary' metric: 228s Number of sample points: 298 228s Dimension: 535 228s Method: single 228s Metric: binary 229s Passed. 229s Random test 21 of 30 (Gaussian density): 229s Number of sample points: 386 229s Dimension: 10 229s Method: single 229s Metric: euclidean 229s Metric: maximum 229s Metric: manhattan 229s Metric: canberra 229s Metric: minkowski 229s p: 8.03033 229s Method: ward 229s Method: centroid 229s Method: median 229s Passed. 229s Uniform sampling for the 'binary' metric: 229s Number of sample points: 272 229s Dimension: 302 229s Method: single 229s Metric: binary 229s Passed. 229s Random test 22 of 30 (Gaussian density): 229s Number of sample points: 428 229s Dimension: 3 229s Method: single 229s Metric: euclidean 229s Metric: maximum 229s Metric: manhattan 229s Metric: canberra 229s Metric: minkowski 229s p: 6.38075 229s Method: ward 229s Method: centroid 229s Method: median 229s Passed. 229s Uniform sampling for the 'binary' metric: 229s Number of sample points: 335 229s Dimension: 622 229s Method: single 229s Metric: binary 230s Passed. 230s Random test 23 of 30 (Gaussian density): 230s Number of sample points: 500 230s Dimension: 7 230s Method: single 230s Metric: euclidean 230s Metric: maximum 230s Metric: manhattan 230s Metric: canberra 230s Metric: minkowski 230s p: 1.0394 230s Method: ward 230s Method: centroid 230s Method: median 230s Passed. 230s Uniform sampling for the 'binary' metric: 230s Number of sample points: 142 230s Dimension: 207 230s Method: single 230s Metric: binary 230s Passed. 230s Random test 24 of 30 (Gaussian density): 230s Number of sample points: 824 230s Dimension: 8 230s Method: single 230s Metric: euclidean 231s Metric: maximum 231s Metric: manhattan 231s Metric: canberra 231s Metric: minkowski 231s p: 2.94511 231s Method: ward 231s Method: centroid 231s Method: median 231s Passed. 231s Uniform sampling for the 'binary' metric: 231s Number of sample points: 247 231s Dimension: 421 231s Method: single 231s Metric: binary 231s Passed. 231s Random test 25 of 30 (Gaussian density): 231s Number of sample points: 84 231s Dimension: 13 231s Method: single 231s Metric: euclidean 231s Metric: maximum 231s Metric: manhattan 231s Metric: canberra 231s Metric: minkowski 231s p: 8.40924 231s Method: ward 231s Method: centroid 231s Method: median 231s Passed. 231s Uniform sampling for the 'binary' metric: 231s Number of sample points: 271 231s Dimension: 318 231s Method: single 231s Metric: binary 232s Passed. 232s Random test 26 of 30 (Gaussian density): 232s Number of sample points: 630 232s Dimension: 6 232s Method: single 232s Metric: euclidean 232s Metric: maximum 232s Metric: manhattan 232s Metric: canberra 232s Metric: minkowski 232s p: 6.7156 232s Method: ward 232s Method: centroid 232s Method: median 232s Passed. 232s Uniform sampling for the 'binary' metric: 232s Number of sample points: 349 232s Dimension: 467 232s Method: single 232s Metric: binary 233s Passed. 233s Random test 27 of 30 (Gaussian density): 233s Number of sample points: 963 233s Dimension: 12 233s Method: single 233s Metric: euclidean 233s Metric: maximum 233s Metric: manhattan 233s Metric: canberra 233s Metric: minkowski 233s p: 9.25767 233s Method: ward 233s Method: centroid 234s Method: median 234s Passed. 234s Uniform sampling for the 'binary' metric: 234s Number of sample points: 273 234s Dimension: 428 234s Method: single 234s Metric: binary 234s Passed. 234s Random test 28 of 30 (Gaussian density): 234s Number of sample points: 171 234s Dimension: 7 234s Method: single 234s Metric: euclidean 234s Metric: maximum 234s Metric: manhattan 234s Metric: canberra 234s Metric: minkowski 234s p: 5.49751 234s Method: ward 234s Method: centroid 234s Method: median 234s Passed. 234s Uniform sampling for the 'binary' metric: 234s Number of sample points: 190 234s Dimension: 285 234s Method: single 234s Metric: binary 234s Passed. 234s Random test 29 of 30 (Gaussian density): 234s Number of sample points: 395 234s Dimension: 7 234s Method: single 234s Metric: euclidean 234s Metric: maximum 234s Metric: manhattan 234s Metric: canberra 234s Metric: minkowski 234s p: 1.62424 234s Method: ward 234s Method: centroid 234s Method: median 234s Passed. 234s Uniform sampling for the 'binary' metric: 234s Number of sample points: 235 234s Dimension: 425 234s Method: single 234s Metric: binary 235s Passed. 235s Random test 30 of 30 (Gaussian density): 235s Number of sample points: 817 235s Dimension: 13 235s Method: single 235s Metric: euclidean 235s Metric: maximum 235s Metric: manhattan 235s Metric: canberra 235s Metric: minkowski 235s p: 7.9519 235s Method: ward 235s Method: centroid 235s Method: median 235s Passed. 235s Uniform sampling for the 'binary' metric: 235s Number of sample points: 269 235s Dimension: 364 235s Method: single 235s Metric: binary 236s Passed. 236s > 236s > cat('Done.\n') 236s Done. 236s > 236s autopkgtest [10:45:20]: test run-unit-test: -----------------------] 237s run-unit-test PASS 237s autopkgtest [10:45:21]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 237s autopkgtest [10:45:21]: test autodep8-python3: preparing testbed 485s autopkgtest [10:49:29]: testbed dpkg architecture: arm64 485s autopkgtest [10:49:29]: testbed apt version: 2.9.28 485s autopkgtest [10:49:29]: @@@@@@@@@@@@@@@@@@@@ test bed setup 486s autopkgtest [10:49:30]: testbed release detected to be: plucky 486s autopkgtest [10:49:30]: updating testbed package index (apt update) 487s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [110 kB] 487s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 487s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 487s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 487s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [13.1 kB] 487s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [807 kB] 487s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [3120 B] 487s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [74.8 kB] 487s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [154 kB] 487s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 Packages [7960 B] 487s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [929 kB] 487s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [10.0 kB] 488s Fetched 2110 kB in 1s (2064 kB/s) 488s Reading package lists... 489s + lsb_release --codename --short 489s + RELEASE=plucky 489s + cat 489s + [ plucky != trusty ] 489s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y --allow-downgrades -o Dpkg::Options::=--force-confnew dist-upgrade 489s Reading package lists... 489s Building dependency tree... 489s Reading state information... 490s Calculating upgrade... 490s The following packages will be upgraded: 490s pci.ids 490s 1 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 490s Need to get 284 kB of archives. 490s After this operation, 1024 B of additional disk space will be used. 490s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 pci.ids all 0.0~2025.02.12-1 [284 kB] 491s Fetched 284 kB in 0s (653 kB/s) 491s (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 ... 116609 files and directories currently installed.) 491s Preparing to unpack .../pci.ids_0.0~2025.02.12-1_all.deb ... 491s Unpacking pci.ids (0.0~2025.02.12-1) over (0.0~2025.02.05-1) ... 491s Setting up pci.ids (0.0~2025.02.12-1) ... 491s + rm /etc/apt/preferences.d/force-downgrade-to-release.pref 491s + /usr/lib/apt/apt-helper analyze-pattern ?true 491s + uname -r 491s + sed s/\./\\./g 491s + running_kernel_pattern=^linux-.*6\.12\.0-15-generic.* 491s + apt list ?obsolete 491s + tail -n+2 491s + grep -v ^linux-.*6\.12\.0-15-generic.* 491s + cut -d/ -f1 492s + true 492s + obsolete_pkgs= 492s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y purge --autoremove 492s Reading package lists... 492s Building dependency tree... 492s Reading state information... 493s 0 upgraded, 0 newly installed, 0 to remove and 6 not upgraded. 493s + grep -q trusty /etc/lsb-release 493s + [ ! -d /usr/share/doc/unattended-upgrades ] 493s + [ ! -d /usr/share/doc/lxd ] 493s + [ ! -d /usr/share/doc/lxd-client ] 493s + [ ! -d /usr/share/doc/snapd ] 493s + type iptables 493s + cat 493s + chmod 755 /etc/rc.local 493s + . /etc/rc.local 493s + iptables -w -t mangle -A FORWARD -p tcp --tcp-flags SYN,RST SYN -j TCPMSS --clamp-mss-to-pmtu 493s + iptables -A OUTPUT -d 10.255.255.1/32 -p tcp -j DROP 493s + iptables -A OUTPUT -d 10.255.255.2/32 -p tcp -j DROP 493s + uname -m 493s + [ aarch64 = ppc64le ] 493s + [ -d /run/systemd/system ] 493s + systemd-detect-virt --quiet --vm 493s + mkdir -p /etc/systemd/system/systemd-random-seed.service.d/ 493s + cat 493s + grep -q lz4 /etc/initramfs-tools/initramfs.conf 493s + echo COMPRESS=lz4 493s autopkgtest [10:49:37]: upgrading testbed (apt dist-upgrade and autopurge) 493s Reading package lists... 493s Building dependency tree... 493s Reading state information... 494s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 494s Starting 2 pkgProblemResolver with broken count: 0 494s Done 494s Entering ResolveByKeep 495s 495s The following packages will be upgraded: 495s iproute2 libc-bin libc-dev-bin libc6 libc6-dev locales 495s 6 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 495s Need to get 10.7 MB of archives. 495s After this operation, 358 kB of additional disk space will be used. 495s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-dev-bin arm64 2.41-1ubuntu1 [24.0 kB] 495s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6-dev arm64 2.41-1ubuntu1 [1750 kB] 496s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 locales all 2.41-1ubuntu1 [4246 kB] 496s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6 arm64 2.41-1ubuntu1 [2910 kB] 496s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-bin arm64 2.41-1ubuntu1 [600 kB] 496s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 iproute2 arm64 6.13.0-1ubuntu1 [1158 kB] 496s Preconfiguring packages ... 496s Fetched 10.7 MB in 1s (12.3 MB/s) 496s (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 ... 116609 files and directories currently installed.) 496s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu1_arm64.deb ... 496s Unpacking libc-dev-bin (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 496s Preparing to unpack .../libc6-dev_2.41-1ubuntu1_arm64.deb ... 496s Unpacking libc6-dev:arm64 (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 497s Preparing to unpack .../locales_2.41-1ubuntu1_all.deb ... 497s Unpacking locales (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 497s Preparing to unpack .../libc6_2.41-1ubuntu1_arm64.deb ... 497s Checking for services that may need to be restarted... 497s Checking init scripts... 497s Checking for services that may need to be restarted... 497s Checking init scripts... 497s Stopping some services possibly affected by the upgrade (will be restarted later): 497s cron: stopping...done. 497s 497s Unpacking libc6:arm64 (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 497s Setting up libc6:arm64 (2.41-1ubuntu1) ... 497s Checking for services that may need to be restarted... 497s Checking init scripts... 497s Restarting services possibly affected by the upgrade: 497s cron: restarting...done. 497s 497s Services restarted successfully. 498s (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 ... 116610 files and directories currently installed.) 498s Preparing to unpack .../libc-bin_2.41-1ubuntu1_arm64.deb ... 498s Unpacking libc-bin (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 498s Setting up libc-bin (2.41-1ubuntu1) ... 498s (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 ... 116610 files and directories currently installed.) 498s Preparing to unpack .../iproute2_6.13.0-1ubuntu1_arm64.deb ... 498s Unpacking iproute2 (6.13.0-1ubuntu1) over (6.10.0-2ubuntu1) ... 498s Setting up iproute2 (6.13.0-1ubuntu1) ... 499s Setting up locales (2.41-1ubuntu1) ... 499s Installing new version of config file /etc/locale.alias ... 499s Generating locales (this might take a while)... 501s en_US.UTF-8... done 501s Generation complete. 501s Setting up libc-dev-bin (2.41-1ubuntu1) ... 501s Setting up libc6-dev:arm64 (2.41-1ubuntu1) ... 501s Processing triggers for man-db (2.13.0-1) ... 503s Processing triggers for systemd (257.2-3ubuntu1) ... 503s Reading package lists... 504s Building dependency tree... 504s Reading state information... 504s Starting pkgProblemResolver with broken count: 0 504s Starting 2 pkgProblemResolver with broken count: 0 504s Done 505s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 508s Reading package lists... 508s Building dependency tree... 508s Reading state information... 508s Starting pkgProblemResolver with broken count: 0 508s Starting 2 pkgProblemResolver with broken count: 0 508s Done 509s The following NEW packages will be installed: 509s libblas3 libgfortran5 liblapack3 python3-all python3-fastcluster 509s python3-numpy python3.12 python3.12-minimal 509s 0 upgraded, 8 newly installed, 0 to remove and 0 not upgraded. 509s Need to get 10.0 MB of archives. 509s After this operation, 44.3 MB of additional disk space will be used. 509s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.12-minimal arm64 3.12.9-1 [2236 kB] 510s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.12 arm64 3.12.9-1 [671 kB] 510s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.1-2 [161 kB] 510s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 14.2.0-17ubuntu1 [437 kB] 510s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.1-2 [2307 kB] 510s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-all arm64 3.13.1-1~exp2 [894 B] 510s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy arm64 1:1.26.4+ds-13 [4148 kB] 510s Get:8 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-fastcluster arm64 1.2.6-1build2 [42.0 kB] 510s Fetched 10.0 MB in 1s (11.0 MB/s) 510s Selecting previously unselected package python3.12-minimal. 510s (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 ... 116611 files and directories currently installed.) 510s Preparing to unpack .../0-python3.12-minimal_3.12.9-1_arm64.deb ... 510s Unpacking python3.12-minimal (3.12.9-1) ... 510s Selecting previously unselected package python3.12. 510s Preparing to unpack .../1-python3.12_3.12.9-1_arm64.deb ... 510s Unpacking python3.12 (3.12.9-1) ... 510s Selecting previously unselected package libblas3:arm64. 510s Preparing to unpack .../2-libblas3_3.12.1-2_arm64.deb ... 510s Unpacking libblas3:arm64 (3.12.1-2) ... 511s Selecting previously unselected package libgfortran5:arm64. 511s Preparing to unpack .../3-libgfortran5_14.2.0-17ubuntu1_arm64.deb ... 511s Unpacking libgfortran5:arm64 (14.2.0-17ubuntu1) ... 511s Selecting previously unselected package liblapack3:arm64. 511s Preparing to unpack .../4-liblapack3_3.12.1-2_arm64.deb ... 511s Unpacking liblapack3:arm64 (3.12.1-2) ... 511s Selecting previously unselected package python3-all. 511s Preparing to unpack .../5-python3-all_3.13.1-1~exp2_arm64.deb ... 511s Unpacking python3-all (3.13.1-1~exp2) ... 511s Selecting previously unselected package python3-numpy. 511s Preparing to unpack .../6-python3-numpy_1%3a1.26.4+ds-13_arm64.deb ... 511s Unpacking python3-numpy (1:1.26.4+ds-13) ... 511s Selecting previously unselected package python3-fastcluster. 511s Preparing to unpack .../7-python3-fastcluster_1.2.6-1build2_arm64.deb ... 511s Unpacking python3-fastcluster (1.2.6-1build2) ... 511s Setting up python3.12-minimal (3.12.9-1) ... 512s Setting up python3.12 (3.12.9-1) ... 513s Setting up python3-all (3.13.1-1~exp2) ... 513s Setting up libblas3:arm64 (3.12.1-2) ... 513s 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 513s Setting up libgfortran5:arm64 (14.2.0-17ubuntu1) ... 513s Setting up liblapack3:arm64 (3.12.1-2) ... 513s 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 513s Setting up python3-numpy (1:1.26.4+ds-13) ... 517s Setting up python3-fastcluster (1.2.6-1build2) ... 517s Processing triggers for systemd (257.2-3ubuntu1) ... 517s Processing triggers for man-db (2.13.0-1) ... 518s Processing triggers for libc-bin (2.41-1ubuntu1) ... 520s autopkgtest [10:50:04]: 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 520s autopkgtest [10:50:04]: test autodep8-python3: [----------------------- 520s Testing with python3.12: 520s 520s Testing with python3.13: 520s 521s autopkgtest [10:50:05]: test autodep8-python3: -----------------------] 521s autopkgtest [10:50:05]: test autodep8-python3: - - - - - - - - - - results - - - - - - - - - - 521s autodep8-python3 PASS (superficial) 521s autopkgtest [10:50:05]: @@@@@@@@@@@@@@@@@@@@ summary 521s run-unit-test PASS 521s autodep8-python3 PASS (superficial) 587s nova [W] Using flock in prodstack6-arm64 587s Creating nova instance adt-plucky-arm64-r-cran-fastcluster-20250216-104123-juju-7f2275-prod-proposed-migration-environment-15-5114b67d-24aa-490a-92b0-759c321c2bb7 from image adt/ubuntu-plucky-arm64-server-20250216.img (UUID a098a761-c895-418e-827f-00d410a1ece9)... 587s nova [W] Timed out waiting for 0d466761-cea5-4462-8e54-edbe8c321535 to get deleted. 587s nova [W] Using flock in prodstack6-arm64 587s Creating nova instance adt-plucky-arm64-r-cran-fastcluster-20250216-104123-juju-7f2275-prod-proposed-migration-environment-15-5114b67d-24aa-490a-92b0-759c321c2bb7 from image adt/ubuntu-plucky-arm64-server-20250216.img (UUID a098a761-c895-418e-827f-00d410a1ece9)... 587s nova [W] Timed out waiting for 442f6aa3-a2f1-4005-9be9-cfe21e1feaca to get deleted.