0s autopkgtest [15:35:25]: starting date and time: 2025-03-15 15:35:25+0000 0s autopkgtest [15:35:25]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [15:35:25]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.4hfmtv0d/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc --apt-upgrade r-cran-fastcluster --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glibc/2.41-1ubuntu2 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-arm64-25.secgroup --name adt-plucky-arm64-r-cran-fastcluster-20250315-152609-juju-7f2275-prod-proposed-migration-environment-2-d63a6a08-4ec3-418b-a073-eeb55b37515b --image adt/ubuntu-plucky-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 117s autopkgtest [15:37:22]: testbed dpkg architecture: arm64 117s autopkgtest [15:37:22]: testbed apt version: 2.9.33 118s autopkgtest [15:37:23]: @@@@@@@@@@@@@@@@@@@@ test bed setup 118s autopkgtest [15:37:23]: testbed release detected to be: None 119s autopkgtest [15:37:24]: updating testbed package index (apt update) 119s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 120s Get:2 http://ftpmaster.internal/ubuntu plucky InRelease [257 kB] 120s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 120s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 120s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [379 kB] 120s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 120s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [99.7 kB] 121s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [111 kB] 121s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 c-n-f Metadata [1856 B] 121s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 c-n-f Metadata [116 B] 121s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [324 kB] 121s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 c-n-f Metadata [14.7 kB] 121s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [4948 B] 121s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 c-n-f Metadata [268 B] 121s Get:15 http://ftpmaster.internal/ubuntu plucky/universe Sources [21.0 MB] 152s Get:16 http://ftpmaster.internal/ubuntu plucky/main Sources [1394 kB] 155s Get:17 http://ftpmaster.internal/ubuntu plucky/main arm64 Packages [1452 kB] 157s Get:18 http://ftpmaster.internal/ubuntu plucky/universe arm64 Packages [15.8 MB] 185s Fetched 41.1 MB in 1min 6s (621 kB/s) 186s Reading package lists... 187s Reading package lists... 187s Building dependency tree... 187s Reading state information... 188s Calculating upgrade... 188s Calculating upgrade... 188s The following packages will be upgraded: 188s pinentry-curses python3-jinja2 strace 189s 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 189s Need to get 647 kB of archives. 189s After this operation, 11.3 kB of additional disk space will be used. 189s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 strace arm64 6.13+ds-1ubuntu1 [499 kB] 189s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 pinentry-curses arm64 1.3.1-2ubuntu3 [39.2 kB] 189s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 190s Fetched 647 kB in 1s (580 kB/s) 190s (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 ... 117701 files and directories currently installed.) 190s Preparing to unpack .../strace_6.13+ds-1ubuntu1_arm64.deb ... 190s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 190s Preparing to unpack .../pinentry-curses_1.3.1-2ubuntu3_arm64.deb ... 190s Unpacking pinentry-curses (1.3.1-2ubuntu3) over (1.3.1-2ubuntu2) ... 190s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 190s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 190s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 190s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 191s Setting up strace (6.13+ds-1ubuntu1) ... 191s Processing triggers for man-db (2.13.0-1) ... 192s Reading package lists... 192s Building dependency tree... 192s Reading state information... 192s Solving dependencies... 193s The following packages will be REMOVED: 193s libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64* 193s libunwind8* linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 193s linux-image-6.11.0-8-generic* linux-modules-6.11.0-8-generic* 193s linux-tools-6.11.0-8* linux-tools-6.11.0-8-generic* 193s 0 upgraded, 0 newly installed, 11 to remove and 5 not upgraded. 193s After this operation, 267 MB disk space will be freed. 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 ... 117701 files and directories currently installed.) 193s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 193s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 193s Removing libpython3.12t64:arm64 (3.12.9-1) ... 193s Removing libpython3.12-stdlib:arm64 (3.12.9-1) ... 193s Removing libnsl2:arm64 (1.3.0-3build3) ... 193s Removing libpython3.12-minimal:arm64 (3.12.9-1) ... 193s Removing libunwind8:arm64 (1.6.2-3.1) ... 193s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 194s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 196s Removing linux-image-6.11.0-8-generic (6.11.0-8.8) ... 196s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.14.0-10-generic 196s I: /boot/initrd.img.old is now a symlink to initrd.img-6.14.0-10-generic 196s /etc/kernel/postrm.d/initramfs-tools: 196s update-initramfs: Deleting /boot/initrd.img-6.11.0-8-generic 196s /etc/kernel/postrm.d/zz-flash-kernel: 196s flash-kernel: Kernel 6.11.0-8-generic has been removed. 196s flash-kernel: A higher version (6.14.0-10-generic) is still installed, no reflashing required. 196s /etc/kernel/postrm.d/zz-update-grub: 196s Sourcing file `/etc/default/grub' 196s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 196s Generating grub configuration file ... 196s Found linux image: /boot/vmlinuz-6.14.0-10-generic 196s Found initrd image: /boot/initrd.img-6.14.0-10-generic 197s Warning: os-prober will not be executed to detect other bootable partitions. 197s Systems on them will not be added to the GRUB boot configuration. 197s Check GRUB_DISABLE_OS_PROBER documentation entry. 197s Adding boot menu entry for UEFI Firmware Settings ... 197s done 197s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 197s Processing triggers for libc-bin (2.41-1ubuntu1) ... 197s (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 ... 81650 files and directories currently installed.) 197s Purging configuration files for linux-image-6.11.0-8-generic (6.11.0-8.8) ... 197s Purging configuration files for libpython3.12-minimal:arm64 (3.12.9-1) ... 197s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 198s autopkgtest [15:38:43]: upgrading testbed (apt dist-upgrade and autopurge) 198s Reading package lists... 198s Building dependency tree... 198s Reading state information... 199s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 199s Starting 2 pkgProblemResolver with broken count: 0 199s Done 200s Entering ResolveByKeep 200s 200s Calculating upgrade... 201s The following packages will be upgraded: 201s libc-bin libc-dev-bin libc6 libc6-dev locales 201s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 201s Need to get 9530 kB of archives. 201s After this operation, 0 B of additional disk space will be used. 201s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6-dev arm64 2.41-1ubuntu2 [1750 kB] 203s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-dev-bin arm64 2.41-1ubuntu2 [24.0 kB] 203s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6 arm64 2.41-1ubuntu2 [2910 kB] 206s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-bin arm64 2.41-1ubuntu2 [600 kB] 207s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 locales all 2.41-1ubuntu2 [4246 kB] 212s Preconfiguring packages ... 212s Fetched 9530 kB in 11s (839 kB/s) 213s (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 ... 81647 files and directories currently installed.) 213s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_arm64.deb ... 213s Unpacking libc6-dev:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 213s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_arm64.deb ... 213s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 213s Preparing to unpack .../libc6_2.41-1ubuntu2_arm64.deb ... 213s Unpacking libc6:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 213s Setting up libc6:arm64 (2.41-1ubuntu2) ... 213s (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 ... 81647 files and directories currently installed.) 213s Preparing to unpack .../libc-bin_2.41-1ubuntu2_arm64.deb ... 213s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 213s Setting up libc-bin (2.41-1ubuntu2) ... 213s (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 ... 81647 files and directories currently installed.) 213s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 213s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 214s Setting up locales (2.41-1ubuntu2) ... 214s Generating locales (this might take a while)... 217s en_US.UTF-8... done 217s Generation complete. 217s Setting up libc-dev-bin (2.41-1ubuntu2) ... 217s Setting up libc6-dev:arm64 (2.41-1ubuntu2) ... 217s Processing triggers for man-db (2.13.0-1) ... 218s Processing triggers for systemd (257.3-1ubuntu3) ... 219s Reading package lists... 219s Building dependency tree... 219s Reading state information... 219s Starting pkgProblemResolver with broken count: 0 220s Starting 2 pkgProblemResolver with broken count: 0 220s Done 220s Solving dependencies... 220s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 221s autopkgtest [15:39:06]: rebooting testbed after setup commands that affected boot 244s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 250s autopkgtest [15:39:35]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP PREEMPT_DYNAMIC Wed Mar 12 15:45:31 UTC 2025 253s autopkgtest [15:39:38]: @@@@@@@@@@@@@@@@@@@@ apt-source r-cran-fastcluster 256s Get:1 http://ftpmaster.internal/ubuntu plucky/universe r-cran-fastcluster 1.2.6-2 (dsc) [2239 B] 256s Get:2 http://ftpmaster.internal/ubuntu plucky/universe r-cran-fastcluster 1.2.6-2 (tar) [208 kB] 256s Get:3 http://ftpmaster.internal/ubuntu plucky/universe r-cran-fastcluster 1.2.6-2 (diff) [5752 B] 256s gpgv: Signature made Mon Feb 24 10:14:54 2025 UTC 256s gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 256s gpgv: Can't check signature: No public key 256s dpkg-source: warning: cannot verify inline signature for ./r-cran-fastcluster_1.2.6-2.dsc: no acceptable signature found 256s autopkgtest [15:39:41]: testing package r-cran-fastcluster version 1.2.6-2 257s autopkgtest [15:39:42]: build not needed 258s autopkgtest [15:39:43]: test run-unit-test: preparing testbed 258s Reading package lists... 258s Building dependency tree... 258s Reading state information... 259s Starting pkgProblemResolver with broken count: 0 259s Starting 2 pkgProblemResolver with broken count: 0 259s Done 260s The following NEW packages will be installed: 260s fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono libblas3 260s libcairo2 libdatrie1 libdeflate0 libfontconfig1 libgfortran5 libgomp1 260s libgraphite2-3 libharfbuzz0b libice6 libjbig0 libjpeg-turbo8 libjpeg8 260s liblapack3 liblerc4 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 260s libpaper-utils libpaper2 libpixman-1-0 libsharpyuv0 libsm6 libtcl8.6 260s libthai-data libthai0 libtiff6 libtk8.6 libwebp7 libxcb-render0 libxcb-shm0 260s libxft2 libxrender1 libxss1 libxt6t64 python3-fastcluster python3-numpy 260s python3-numpy-dev r-base-core r-cran-fastcluster unzip x11-common xdg-utils 260s zip 260s 0 upgraded, 48 newly installed, 0 to remove and 0 not upgraded. 260s Need to get 42.7 MB of archives. 260s After this operation, 101 MB of additional disk space will be used. 260s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy-dev arm64 1:2.2.3+ds-5 [146 kB] 260s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.1-2 [161 kB] 260s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 15-20250222-0ubuntu1 [444 kB] 261s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.1-2 [2307 kB] 264s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy arm64 1:2.2.3+ds-5 [3981 kB] 269s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 270s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 270s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig-config arm64 2.15.0-2ubuntu1 [37.5 kB] 271s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 libfontconfig1 arm64 2.15.0-2ubuntu1 [144 kB] 271s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig arm64 2.15.0-2ubuntu1 [191 kB] 271s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 libpixman-1-0 arm64 0.44.0-3 [197 kB] 271s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-render0 arm64 1.17.0-2 [16.6 kB] 271s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-shm0 arm64 1.17.0-2 [5884 B] 271s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 libxrender1 arm64 1:0.9.10-1.1build1 [18.8 kB] 271s Get:15 http://ftpmaster.internal/ubuntu plucky/main arm64 libcairo2 arm64 1.18.2-2 [560 kB] 272s Get:16 http://ftpmaster.internal/ubuntu plucky/main arm64 libdatrie1 arm64 0.2.13-3build1 [19.2 kB] 272s Get:17 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate0 arm64 1.23-1 [46.2 kB] 272s Get:18 http://ftpmaster.internal/ubuntu plucky/main arm64 libgomp1 arm64 15-20250222-0ubuntu1 [146 kB] 272s Get:19 http://ftpmaster.internal/ubuntu plucky/main arm64 libgraphite2-3 arm64 1.3.14-2ubuntu1 [70.6 kB] 272s Get:20 http://ftpmaster.internal/ubuntu plucky/main arm64 libharfbuzz0b arm64 10.2.0-1 [490 kB] 273s Get:21 http://ftpmaster.internal/ubuntu plucky/main arm64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 273s Get:22 http://ftpmaster.internal/ubuntu plucky/main arm64 libice6 arm64 2:1.1.1-1 [42.3 kB] 273s Get:23 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg-turbo8 arm64 2.1.5-3ubuntu2 [165 kB] 273s Get:24 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 273s Get:25 http://ftpmaster.internal/ubuntu plucky/main arm64 liblerc4 arm64 4.0.0+ds-5ubuntu1 [167 kB] 273s Get:26 http://ftpmaster.internal/ubuntu plucky/main arm64 libthai-data all 0.1.29-2build1 [158 kB] 273s Get:27 http://ftpmaster.internal/ubuntu plucky/main arm64 libthai0 arm64 0.1.29-2build1 [18.2 kB] 273s Get:28 http://ftpmaster.internal/ubuntu plucky/main arm64 libpango-1.0-0 arm64 1.56.2-1 [237 kB] 274s Get:29 http://ftpmaster.internal/ubuntu plucky/main arm64 libpangoft2-1.0-0 arm64 1.56.2-1 [49.5 kB] 274s Get:30 http://ftpmaster.internal/ubuntu plucky/main arm64 libpangocairo-1.0-0 arm64 1.56.2-1 [27.6 kB] 274s Get:31 http://ftpmaster.internal/ubuntu plucky/main arm64 libpaper2 arm64 2.2.5-0.3 [17.3 kB] 274s Get:32 http://ftpmaster.internal/ubuntu plucky/main arm64 libpaper-utils arm64 2.2.5-0.3 [15.4 kB] 274s Get:33 http://ftpmaster.internal/ubuntu plucky/main arm64 libsharpyuv0 arm64 1.5.0-0.1 [16.9 kB] 274s Get:34 http://ftpmaster.internal/ubuntu plucky/main arm64 libsm6 arm64 2:1.2.4-1 [16.4 kB] 274s Get:35 http://ftpmaster.internal/ubuntu plucky/main arm64 libtcl8.6 arm64 8.6.16+dfsg-1 [987 kB] 275s Get:36 http://ftpmaster.internal/ubuntu plucky/main arm64 libjbig0 arm64 2.1-6.1ubuntu2 [29.3 kB] 275s Get:37 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebp7 arm64 1.5.0-0.1 [194 kB] 275s Get:38 http://ftpmaster.internal/ubuntu plucky/main arm64 libtiff6 arm64 4.5.1+git230720-4ubuntu4 [193 kB] 275s Get:39 http://ftpmaster.internal/ubuntu plucky/main arm64 libxft2 arm64 2.3.6-1build1 [44.1 kB] 276s Get:40 http://ftpmaster.internal/ubuntu plucky/main arm64 libxss1 arm64 1:1.2.3-1build3 [7244 B] 276s Get:41 http://ftpmaster.internal/ubuntu plucky/main arm64 libtk8.6 arm64 8.6.16-1 [776 kB] 277s Get:42 http://ftpmaster.internal/ubuntu plucky/main arm64 libxt6t64 arm64 1:1.2.1-1.2build1 [168 kB] 277s Get:43 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-fastcluster arm64 1.2.6-2 [42.1 kB] 277s Get:44 http://ftpmaster.internal/ubuntu plucky/main arm64 zip arm64 3.0-14ubuntu2 [173 kB] 277s Get:45 http://ftpmaster.internal/ubuntu plucky/main arm64 unzip arm64 6.0-28ubuntu6 [178 kB] 277s Get:46 http://ftpmaster.internal/ubuntu plucky/main arm64 xdg-utils all 1.2.1-2ubuntu1 [66.0 kB] 278s Get:47 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-base-core arm64 4.4.3-1 [28.4 MB] 312s Get:48 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-fastcluster arm64 1.2.6-2 [193 kB] 313s Preconfiguring packages ... 313s Fetched 42.7 MB in 53s (806 kB/s) 313s Selecting previously unselected package python3-numpy-dev:arm64. 313s (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 ... 81647 files and directories currently installed.) 313s Preparing to unpack .../00-python3-numpy-dev_1%3a2.2.3+ds-5_arm64.deb ... 313s Unpacking python3-numpy-dev:arm64 (1:2.2.3+ds-5) ... 314s Selecting previously unselected package libblas3:arm64. 314s Preparing to unpack .../01-libblas3_3.12.1-2_arm64.deb ... 314s Unpacking libblas3:arm64 (3.12.1-2) ... 314s Selecting previously unselected package libgfortran5:arm64. 314s Preparing to unpack .../02-libgfortran5_15-20250222-0ubuntu1_arm64.deb ... 314s Unpacking libgfortran5:arm64 (15-20250222-0ubuntu1) ... 314s Selecting previously unselected package liblapack3:arm64. 314s Preparing to unpack .../03-liblapack3_3.12.1-2_arm64.deb ... 314s Unpacking liblapack3:arm64 (3.12.1-2) ... 314s Selecting previously unselected package python3-numpy. 314s Preparing to unpack .../04-python3-numpy_1%3a2.2.3+ds-5_arm64.deb ... 314s Unpacking python3-numpy (1:2.2.3+ds-5) ... 314s Selecting previously unselected package fonts-dejavu-mono. 314s Preparing to unpack .../05-fonts-dejavu-mono_2.37-8_all.deb ... 314s Unpacking fonts-dejavu-mono (2.37-8) ... 314s Selecting previously unselected package fonts-dejavu-core. 314s Preparing to unpack .../06-fonts-dejavu-core_2.37-8_all.deb ... 314s Unpacking fonts-dejavu-core (2.37-8) ... 314s Selecting previously unselected package fontconfig-config. 314s Preparing to unpack .../07-fontconfig-config_2.15.0-2ubuntu1_arm64.deb ... 314s Unpacking 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'license()' or 'licence()' for distribution details. 325s 325s R is a collaborative project with many contributors. 325s Type 'contributors()' for more information and 325s 'citation()' on how to cite R or R packages in publications. 325s 325s Type 'demo()' for some demos, 'help()' for on-line help, or 325s 'help.start()' for an HTML browser interface to help. 325s Type 'q()' to quit R. 325s 325s > # fastcluster: Fast hierarchical clustering routines for R and Python 325s > # 325s > # Copyright: 325s > # * Until package version 1.1.23: © 2011 Daniel Müllner 325s > # * All changes from version 1.1.24 on: © Google Inc. 325s > # 325s > # Test script for the R interface 325s > 325s > seed = as.integer(runif(1, 0, 1e9)) 325s > set.seed(seed) 325s > cat(sprintf("Random seed: %d\n",seed)) 325s Random seed: 18774973 325s > 325s > print_seed <- function() { 325s + return(sprintf(' 325s + Please send a report to the author of the \'fastcluster\' package, Daniel Müllner. 325s + For contact details, see . To make the error 325s + reproducible, you must include the following number (the random seed value) in 325s + your error report: %d.\n\n', seed)) 325s + } 325s > 325s > hasWardD2 = getRversion() >= '3.1.0' 325s > 325s > # Compare two dendrograms and check whether they are equal, except that 325s > # ties may be resolved differently. 325s > compare <- function(dg1, dg2) { 325s + h1 <- dg1$height 325s + h2 <- dg2$height 325s + # "height" vectors may have small numerical errors. 325s + rdiffs <- abs(h1-h2)/pmax(abs(h1),abs(h2)) 325s + rdiffs = rdiffs[complete.cases(rdiffs)] 325s + rel_error <- max(rdiffs) 325s + # We allow a relative error of 1e-13. 325s + if (rel_error>1e-13) { 325s + print(h1) 325s + print(h2) 325s + cat(sprintf('Height vectors differ! The maximum relative error is %e.\n', rel_error)) 325s + return(FALSE) 325s + } 325s + # Filter the indices where consecutive merging distances are distinct. 325s + d = diff(dg1$height) 325s + b = (c(d,1)!=0 & c(1,d)!=0) 325s + #cat(sprintf("Percentage of indices where we can test: %g.\n",100.0*length(b[b])/length(b))) 325s + if (any(b)) { 325s + m1 = dg1$merge[b,] 325s + m2 = dg2$merge[b,] 325s + 325s + r = function(i) { 325s + if (i<0) { 325s + return(1) 325s + } 325s + else { 325s + return(b[i]) 325s + } 325s + } 325s + 325s + f = sapply(m1,r) 325s + fm1 = m1*f 325s + fm2 = m2*f 325s + # The "merge" matrices must be identical whereever indices are not ambiguous 325s + # due to ties. 325s + if (!identical(fm1,fm2)) { 325s + cat('Merge matrices differ!\n') 325s + return(FALSE) 325s + } 325s + # Compare the "order" vectors only if all merging distances were distinct. 325s + if (all(b) && !identical(dg1$order,dg2$order)) { 325s + cat('Order vectors differ!\n') 325s + return(FALSE) 325s + } 325s + } 325s + return(TRUE) 325s + } 325s > 325s > # Generate uniformly distributed random data 325s > generate.uniform <- function() { 325s + n = sample(10:1000,1) 325s + range_exp = runif(1,min=-10, max=10) 325s + cat(sprintf("Number of sample points: %d\n",n)) 325s + cat(sprintf("Dissimilarity range: [0,%g]\n",10^range_exp)) 325s + d = runif(n*(n-1)/2, min=0, max=10^range_exp) 325s + # Fake a compressed distance matrix 325s + attributes(d) <- NULL 325s + attr(d,"Size") <- n 325s + attr(d, "call") <- 'N/A' 325s + class(d) <- "dist" 325s + return(d) 325s + } 325s > 325s > # Generate normally distributed random data 325s > generate.normal <- function() { 325s + n = sample(10:1000,1) 325s + dim = sample(2:20,1) 325s + 325s + cat (sprintf("Number of sample points: %d\n",n)) 325s + cat (sprintf("Dimension: %d\n",dim)) 325s + 325s + pcd = matrix(rnorm(n*dim), c(n,dim)) 325s + d = dist(pcd) 325s + return(d) 325s + } 325s > 325s > # Test the clustering functions when a distance matrix is given. 325s > test.dm <- function(d) { 325s + d2 = d 325s + if (hasWardD2) { 325s + methods = c('single','complete','average','mcquitty','ward.D','ward.D2','centroid','median') 325s + } 325s + else { 325s + methods = c('single','complete','average','mcquitty','ward','centroid','median') 325s + } 325s + for (method in methods) { 325s + cat(paste('Method :', method, '\n')) 325s + dg_stats = stats::hclust(d, method=method) 325s + if (method == 'ward') { 325s + method = 'ward.D' 325s + } 325s + dg_fastcluster = fastcluster::hclust(d, method=method) 325s + if (!identical(d,d2)) { 325s + cat('Input array was corrupted!\n') 325s + stop(print_seed()) 325s + } 325s + if (!compare(dg_stats, dg_fastcluster)) { 325s + stop(print_seed()) 325s + } 325s + } 325s + cat('Passed.\n') 325s + } 325s > 325s > # Test the clustering functions for vector input in Euclidean space. 325s > test.vector <- function() { 325s + # generate test data 325s + n = sample(10:1000,1) 325s + dim = sample(2:20,1) 325s + cat (sprintf("Number of sample points: %d\n",n)) 325s + cat (sprintf("Dimension: %d\n",dim)) 325s + 325s + range_exp = runif(1,min=-10, max=10) 325s + pcd = matrix(rnorm(n*dim, sd=10^range_exp), c(n,dim)) 325s + pcd2 = pcd 325s + # test 325s + method='single' 325s + cat(paste('Method:', method, '\n')) 325s + for (metric in c('euclidean', 'maximum', 'manhattan', 'canberra', 'minkowski')) { 325s + cat(paste(' Metric:', metric, '\n')) 325s + if (metric=='minkowski') { 325s + p = runif(1, min=1.0, max=10.0) 325s + cat (sprintf(" p: %g\n",p)); 325s + dg_fastcluster = fastcluster::hclust.vector(pcd, method=method, metric=metric, p=p) 325s + d = dist(pcd, method=metric, p=p) 325s + } 325s + else { 325s + dg_fastcluster = fastcluster::hclust.vector(pcd, method=method, metric=metric) 325s + d = dist(pcd, method=metric) 325s + } 325s + d2 = d 325s + dg_fastcluster_dist = fastcluster::hclust(d, method=method) 325s + if (!identical(d,d2) || !identical(pcd,pcd2)) { 325s + cat('Input array was corrupted!\n') 325s + stop(print_seed()) 325s + } 325s + if (!compare(dg_fastcluster_dist, dg_fastcluster)) { 325s + stop(print_seed()) 325s + } 325s + } 325s + for (method in c('ward','centroid','median') ) { 325s + cat(paste('Method:', method, '\n')) 325s + dg_fastcluster = fastcluster::hclust.vector(pcd, method=method) 325s + if (!identical(pcd,pcd2)) { 325s + cat('Input array was corrupted!\n') 325s + stop(print_seed()) 325s + } 325s + d = dist(pcd) 325s + if(method == "ward" && hasWardD2) { 325s + method = "ward.D2" 325s + } 325s + else 325s + { 325s + # Workaround: fastcluster::hclust expects _squared_ euclidean distances. 325s + d = d^2 325s + } 325s + d2 = d 325s + dg_fastcluster_dist = fastcluster::hclust(d, method=method) 325s + if (!identical(d,d2)) { 325s + cat('Input array was corrupted!\n') 325s + stop(print_seed()) 325s + } 325s + if(method != "ward.D2") { 325s + dg_fastcluster_dist$height = sqrt(dg_fastcluster_dist$height) 325s + } 325s + # The Euclidean methods may have small numerical errors due to squaring/ 325s + # taking the root in the Euclidean distances. 325s + if (!compare(dg_fastcluster_dist, dg_fastcluster)) { 325s + stop(print_seed()) 325s + } 325s + } 325s + cat('Passed.\n') 325s + } 325s > 325s > # Test the single linkage function with the "binary" metric 325s > test.vector.binary <- function() { 325s + # generate test data 325s + cat (sprintf("Uniform sampling for the 'binary' metric:\n")) 325s + n = sample(10:400,1) 325s + dim = sample(n:(2*n),1) 325s + cat (sprintf("Number of sample points: %d\n",n)) 325s + cat (sprintf("Dimension: %d\n",dim)) 325s + pcd = matrix(sample(-1:2, n*dim, replace=T), c(n,dim)) 325s + pcd2 = pcd 325s + # test 325s + method='single' 325s + metric='binary' 325s + cat(paste('Method:', method, '\n')) 325s + cat(paste(' Metric:', metric, '\n')) 325s + dg_fastcluster = fastcluster::hclust.vector(pcd, method=method, metric=metric) 325s + d = dist(pcd, method=metric) 325s + d2 = d 325s + dg_fastcluster_dist = fastcluster::hclust(d, method=method) 325s + if (!identical(d,d2) || !identical(d,d2)) { 325s + cat('Input array was corrupted!\n') 325s + stop(print_seed()) 325s + } 325s + if (!compare(dg_fastcluster_dist, dg_fastcluster)) { 325s + stop(print_seed()) 325s + } 325s + cat('Passed.\n') 325s + } 325s > 325s > 325s > N = 15 325s > for (i in (1:N)) { 325s + if (i%%2==1) { 325s + cat(sprintf('Random test %d of %d (uniform distribution of distances):\n',i,2*N)) 325s + d = generate.uniform() 325s + } 325s + else { 325s + cat(sprintf('Random test %d of %d (Gaussian density):\n',i,2*N)) 325s + d = generate.normal() 325s + } 325s + test.dm(d) 325s + } 325s Random test 1 of 30 (uniform distribution of distances): 325s Number of sample points: 662 325s Dissimilarity range: [0,0.000113872] 325s Method : single 325s Method : complete 326s Method : average 326s Method : mcquitty 326s Method : ward.D 326s Method : ward.D2 326s Method : centroid 326s Method : median 326s Passed. 326s Random test 2 of 30 (Gaussian density): 326s Number of sample points: 672 326s Dimension: 3 326s Method : single 326s Method : complete 326s Method : average 326s Method : mcquitty 326s Method : ward.D 326s Method : ward.D2 326s Method : centroid 326s Method : median 326s Passed. 326s Random test 3 of 30 (uniform distribution of distances): 326s Number of sample points: 927 326s Dissimilarity range: [0,6.32371e-10] 326s Method : single 326s Method : complete 326s Method : average 326s Method : mcquitty 326s Method : ward.D 326s Method : ward.D2 326s Method : centroid 326s Method : median 326s Passed. 326s Random test 4 of 30 (Gaussian density): 326s Number of sample points: 394 326s Dimension: 3 326s Method : single 326s Method : complete 326s Method : average 326s Method : mcquitty 326s Method : ward.D 326s Method : ward.D2 326s Method : centroid 326s Method : median 326s Passed. 326s Random test 5 of 30 (uniform distribution of distances): 326s Number of sample points: 534 326s Dissimilarity range: [0,3.49403e+09] 326s Method : single 326s Method : complete 326s Method : average 326s Method : mcquitty 326s Method : ward.D 326s Method : ward.D2 326s Method : centroid 326s Method : median 326s Passed. 326s Random test 6 of 30 (Gaussian density): 326s Number of sample points: 98 326s Dimension: 6 326s Method : single 326s Method : complete 326s Method : average 326s Method : mcquitty 326s Method : ward.D 326s Method : ward.D2 326s Method : centroid 326s Method : median 326s Passed. 326s Random test 7 of 30 (uniform distribution of distances): 326s Number of sample points: 404 326s Dissimilarity range: [0,1.92051e+08] 326s Method : single 326s Method : complete 326s Method : average 326s Method : mcquitty 326s Method : ward.D 326s Method : ward.D2 326s Method : centroid 326s Method : median 326s Passed. 326s Random test 8 of 30 (Gaussian density): 326s Number of sample points: 840 326s Dimension: 5 326s Method : single 326s Method : complete 326s Method : average 326s Method : mcquitty 326s Method : ward.D 326s Method : ward.D2 326s Method : centroid 326s Method : median 327s Passed. 327s Random test 9 of 30 (uniform distribution of distances): 327s Number of sample points: 799 327s Dissimilarity range: [0,0.00087935] 327s Method : single 327s Method : complete 327s Method : average 327s Method : mcquitty 327s Method : ward.D 327s Method : ward.D2 327s Method : centroid 327s Method : median 327s Passed. 327s Random test 10 of 30 (Gaussian density): 327s Number of sample points: 491 327s Dimension: 16 327s Method : single 327s Method : complete 327s Method : average 327s Method : mcquitty 327s Method : ward.D 327s Method : ward.D2 327s Method : centroid 327s Method : median 327s Passed. 327s Random test 11 of 30 (uniform distribution of distances): 327s Number of sample points: 975 327s Dissimilarity range: [0,7.30223e+07] 327s Method : single 327s Method : complete 327s Method : average 327s Method : mcquitty 327s Method : ward.D 327s Method : ward.D2 327s Method : centroid 327s Method : median 327s Passed. 327s Random test 12 of 30 (Gaussian density): 327s Number of sample points: 338 327s Dimension: 16 327s Method : single 327s Method : complete 327s Method : average 327s Method : mcquitty 327s Method : ward.D 327s Method : ward.D2 327s Method : centroid 327s Method : median 327s Passed. 327s Random test 13 of 30 (uniform distribution of distances): 327s Number of sample points: 510 327s Dissimilarity range: [0,0.000319891] 327s Method : single 327s Method : complete 327s Method : average 327s Method : mcquitty 327s Method : ward.D 327s Method : ward.D2 327s Method : centroid 327s Method : median 327s Passed. 327s Random test 14 of 30 (Gaussian density): 327s Number of sample points: 759 327s Dimension: 19 327s Method : single 327s Method : complete 327s Method : average 327s Method : mcquitty 327s Method : ward.D 327s Method : ward.D2 328s Method : centroid 328s Method : median 328s Passed. 328s Random test 15 of 30 (uniform distribution of distances): 328s Number of sample points: 137 328s Dissimilarity range: [0,1.53049e-10] 328s Method : single 328s Method : complete 328s Method : average 328s Method : mcquitty 328s Method : ward.D 328s Method : ward.D2 328s Method : centroid 328s Method : median 328s Passed. 328s > for (i in (N+1:N)) { 328s + cat(sprintf('Random test %d of %d (Gaussian density):\n',i,2*N)) 328s + test.vector() 328s + test.vector.binary() 328s + } 328s Random test 16 of 30 (Gaussian density): 328s Number of sample points: 591 328s Dimension: 19 328s Method: single 328s Metric: euclidean 328s Metric: maximum 328s Metric: manhattan 328s Metric: canberra 328s Metric: minkowski 328s p: 8.44491 328s Method: ward 328s Method: centroid 328s Method: median 328s Passed. 328s Uniform sampling for the 'binary' metric: 328s Number of sample points: 175 328s Dimension: 228 328s Method: single 328s Metric: binary 328s Passed. 328s Random test 17 of 30 (Gaussian density): 328s Number of sample points: 680 328s Dimension: 12 328s Method: single 328s Metric: euclidean 328s Metric: maximum 328s Metric: manhattan 329s Metric: canberra 329s Metric: minkowski 329s p: 7.59786 329s Method: ward 329s Method: centroid 329s Method: median 329s Passed. 329s Uniform sampling for the 'binary' metric: 329s Number of sample points: 257 329s Dimension: 340 329s Method: single 329s Metric: binary 329s Passed. 329s Random test 18 of 30 (Gaussian density): 329s Number of sample points: 593 329s Dimension: 12 329s Method: single 329s Metric: euclidean 329s Metric: maximum 329s Metric: manhattan 329s Metric: canberra 329s Metric: minkowski 329s p: 6.26934 330s Method: ward 330s Method: centroid 330s Method: median 330s Passed. 330s Uniform sampling for the 'binary' metric: 330s Number of sample points: 68 330s Dimension: 79 330s Method: single 330s Metric: binary 330s Passed. 330s Random test 19 of 30 (Gaussian density): 330s Number of sample points: 274 330s Dimension: 13 330s Method: single 330s Metric: euclidean 330s Metric: maximum 330s Metric: manhattan 330s Metric: canberra 330s Metric: minkowski 330s p: 5.20114 330s Method: ward 330s Method: centroid 330s Method: median 330s Passed. 330s Uniform sampling for the 'binary' metric: 330s Number of sample points: 46 330s Dimension: 48 330s Method: single 330s Metric: binary 330s Passed. 330s Random test 20 of 30 (Gaussian density): 330s Number of sample points: 918 330s Dimension: 12 330s Method: single 330s Metric: euclidean 330s Metric: maximum 330s Metric: manhattan 330s Metric: canberra 330s Metric: minkowski 330s p: 4.08113 330s Method: ward 331s Method: centroid 331s Method: median 331s Passed. 331s Uniform sampling for the 'binary' metric: 331s Number of sample points: 37 331s Dimension: 43 331s Method: single 331s Metric: binary 331s Passed. 331s Random test 21 of 30 (Gaussian density): 331s Number of sample points: 568 331s Dimension: 10 331s Method: single 331s Metric: euclidean 331s Metric: maximum 331s Metric: manhattan 331s Metric: canberra 331s Metric: minkowski 331s p: 4.31805 331s Method: ward 331s Method: centroid 331s Method: median 331s Passed. 331s Uniform sampling for the 'binary' metric: 331s Number of sample points: 317 331s Dimension: 567 331s Method: single 331s Metric: binary 332s Passed. 332s Random test 22 of 30 (Gaussian density): 332s Number of sample points: 331 332s Dimension: 19 332s Method: single 332s Metric: euclidean 332s Metric: maximum 332s Metric: manhattan 332s Metric: canberra 332s Metric: minkowski 332s p: 9.2668 332s Method: ward 332s Method: centroid 332s Method: median 332s Passed. 332s Uniform sampling for the 'binary' metric: 332s Number of sample points: 263 332s Dimension: 506 332s Method: single 332s Metric: binary 332s Passed. 332s Random test 23 of 30 (Gaussian density): 332s Number of sample points: 296 332s Dimension: 18 332s Method: single 332s Metric: euclidean 332s Metric: maximum 333s Metric: manhattan 333s Metric: canberra 333s Metric: minkowski 333s p: 7.42316 333s Method: ward 333s Method: centroid 333s Method: median 333s Passed. 333s Uniform sampling for the 'binary' metric: 333s Number of sample points: 107 333s Dimension: 160 333s Method: single 333s Metric: binary 333s Passed. 333s Random test 24 of 30 (Gaussian density): 333s Number of sample points: 609 333s Dimension: 4 333s Method: single 333s Metric: euclidean 333s Metric: maximum 333s Metric: manhattan 333s Metric: canberra 333s Metric: minkowski 333s p: 9.64776 333s Method: ward 333s Method: centroid 333s Method: median 333s Passed. 333s Uniform sampling for the 'binary' metric: 333s Number of sample points: 130 333s Dimension: 207 333s Method: single 333s Metric: binary 333s Passed. 333s Random test 25 of 30 (Gaussian density): 333s Number of sample points: 253 333s Dimension: 15 333s Method: single 333s Metric: euclidean 333s Metric: maximum 333s Metric: manhattan 333s Metric: canberra 333s Metric: minkowski 333s p: 9.49058 333s Method: ward 333s Method: centroid 333s Method: median 333s Passed. 333s Uniform sampling for the 'binary' metric: 333s Number of sample points: 223 333s Dimension: 283 333s Method: single 333s Metric: binary 333s Passed. 333s Random test 26 of 30 (Gaussian density): 333s Number of sample points: 637 333s Dimension: 15 333s Method: single 333s Metric: euclidean 333s Metric: maximum 333s Metric: manhattan 333s Metric: canberra 333s Metric: minkowski 333s p: 4.44616 333s Method: ward 334s Method: centroid 334s Method: median 334s Passed. 334s Uniform sampling for the 'binary' metric: 334s Number of sample points: 314 334s Dimension: 325 334s Method: single 334s Metric: binary 334s Passed. 334s Random test 27 of 30 (Gaussian density): 334s Number of sample points: 866 334s Dimension: 15 334s Method: single 334s Metric: euclidean 334s Metric: maximum 334s Metric: manhattan 334s Metric: canberra 334s Metric: minkowski 334s p: 9.68849 335s Method: ward 335s Method: centroid 335s Method: median 335s Passed. 335s Uniform sampling for the 'binary' metric: 335s Number of sample points: 187 335s Dimension: 374 335s Method: single 335s Metric: binary 335s Passed. 335s Random test 28 of 30 (Gaussian density): 335s Number of sample points: 932 335s Dimension: 19 335s Method: single 335s Metric: euclidean 335s Metric: maximum 336s Metric: manhattan 336s Metric: canberra 336s Metric: minkowski 336s p: 2.36161 336s Method: ward 337s Method: centroid 337s Method: median 337s Passed. 337s Uniform sampling for the 'binary' metric: 337s Number of sample points: 189 337s Dimension: 312 337s Method: single 337s Metric: binary 337s Passed. 337s Random test 29 of 30 (Gaussian density): 337s Number of sample points: 452 337s Dimension: 10 337s Method: single 337s Metric: euclidean 337s Metric: maximum 337s Metric: manhattan 337s Metric: canberra 337s Metric: minkowski 337s p: 2.21355 337s Method: ward 337s Method: centroid 337s Method: median 337s Passed. 337s Uniform sampling for the 'binary' metric: 337s Number of sample points: 153 337s Dimension: 165 337s Method: single 337s Metric: binary 337s Passed. 337s Random test 30 of 30 (Gaussian density): 337s Number of sample points: 788 337s Dimension: 6 337s Method: single 337s Metric: euclidean 337s Metric: maximum 337s Metric: manhattan 337s Metric: canberra 337s Metric: minkowski 337s p: 9.21606 338s Method: ward 338s Method: centroid 338s Method: median 338s Passed. 338s Uniform sampling for the 'binary' metric: 338s Number of sample points: 191 338s Dimension: 198 338s Method: single 338s Metric: binary 338s Passed. 338s > 338s > cat('Done.\n') 338s Done. 338s > 338s autopkgtest [15:41:03]: test run-unit-test: -----------------------] 339s autopkgtest [15:41:04]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 339s run-unit-test PASS 339s autopkgtest [15:41:04]: test autodep8-python3: preparing testbed 504s autopkgtest [15:43:49]: testbed dpkg architecture: arm64 505s autopkgtest [15:43:50]: testbed apt version: 2.9.33 505s autopkgtest [15:43:50]: @@@@@@@@@@@@@@@@@@@@ test bed setup 505s autopkgtest [15:43:50]: testbed release detected to be: plucky 506s autopkgtest [15:43:51]: updating testbed package index (apt update) 506s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 507s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 507s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 507s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 507s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [379 kB] 508s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [99.7 kB] 508s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 508s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [111 kB] 508s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 c-n-f Metadata [1856 B] 508s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 c-n-f Metadata [116 B] 508s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [324 kB] 508s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 c-n-f Metadata [14.7 kB] 508s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [4948 B] 508s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 c-n-f Metadata [268 B] 509s Fetched 1078 kB in 2s (544 kB/s) 510s Reading package lists... 511s Reading package lists... 511s Building dependency tree... 511s Reading state information... 512s Calculating upgrade... 512s Calculating upgrade... 512s The following packages will be upgraded: 512s pinentry-curses python3-jinja2 strace 513s 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 513s Need to get 647 kB of archives. 513s After this operation, 11.3 kB of additional disk space will be used. 513s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 strace arm64 6.13+ds-1ubuntu1 [499 kB] 513s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 pinentry-curses arm64 1.3.1-2ubuntu3 [39.2 kB] 513s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 514s Fetched 647 kB in 1s (625 kB/s) 514s (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 ... 117701 files and directories currently installed.) 514s Preparing to unpack .../strace_6.13+ds-1ubuntu1_arm64.deb ... 514s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 514s Preparing to unpack .../pinentry-curses_1.3.1-2ubuntu3_arm64.deb ... 514s Unpacking pinentry-curses (1.3.1-2ubuntu3) over (1.3.1-2ubuntu2) ... 514s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 515s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 515s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 515s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 515s Setting up strace (6.13+ds-1ubuntu1) ... 515s Processing triggers for man-db (2.13.0-1) ... 516s Reading package lists... 516s Building dependency tree... 516s Reading state information... 516s Solving dependencies... 517s The following packages will be REMOVED: 517s libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64* 517s libunwind8* linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 517s linux-image-6.11.0-8-generic* linux-modules-6.11.0-8-generic* 517s linux-tools-6.11.0-8* linux-tools-6.11.0-8-generic* 517s 0 upgraded, 0 newly installed, 11 to remove and 5 not upgraded. 517s After this operation, 267 MB disk space will be freed. 517s (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 ... 117701 files and directories currently installed.) 517s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 517s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 517s Removing libpython3.12t64:arm64 (3.12.9-1) ... 517s Removing libpython3.12-stdlib:arm64 (3.12.9-1) ... 517s Removing libnsl2:arm64 (1.3.0-3build3) ... 517s Removing libpython3.12-minimal:arm64 (3.12.9-1) ... 518s Removing libunwind8:arm64 (1.6.2-3.1) ... 518s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 518s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 520s Removing linux-image-6.11.0-8-generic (6.11.0-8.8) ... 520s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.14.0-10-generic 520s I: /boot/initrd.img.old is now a symlink to initrd.img-6.14.0-10-generic 520s /etc/kernel/postrm.d/initramfs-tools: 520s update-initramfs: Deleting /boot/initrd.img-6.11.0-8-generic 520s /etc/kernel/postrm.d/zz-flash-kernel: 520s flash-kernel: Kernel 6.11.0-8-generic has been removed. 520s flash-kernel: A higher version (6.14.0-10-generic) is still installed, no reflashing required. 521s /etc/kernel/postrm.d/zz-update-grub: 521s Sourcing file `/etc/default/grub' 521s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 521s Generating grub configuration file ... 521s Found linux image: /boot/vmlinuz-6.14.0-10-generic 521s Found initrd image: /boot/initrd.img-6.14.0-10-generic 521s Warning: os-prober will not be executed to detect other bootable partitions. 521s Systems on them will not be added to the GRUB boot configuration. 521s Check GRUB_DISABLE_OS_PROBER documentation entry. 521s Adding boot menu entry for UEFI Firmware Settings ... 521s done 521s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 521s Processing triggers for libc-bin (2.41-1ubuntu1) ... 522s (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 ... 81650 files and directories currently installed.) 522s Purging configuration files for linux-image-6.11.0-8-generic (6.11.0-8.8) ... 522s Purging configuration files for libpython3.12-minimal:arm64 (3.12.9-1) ... 522s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 522s autopkgtest [15:44:07]: upgrading testbed (apt dist-upgrade and autopurge) 522s Reading package lists... 522s Building dependency tree... 522s Reading state information... 523s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 523s Starting 2 pkgProblemResolver with broken count: 0 523s Done 524s Entering ResolveByKeep 524s 524s Calculating upgrade... 525s The following packages will be upgraded: 525s libc-bin libc-dev-bin libc6 libc6-dev locales 526s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 526s Need to get 9530 kB of archives. 526s After this operation, 0 B of additional disk space will be used. 526s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6-dev arm64 2.41-1ubuntu2 [1750 kB] 528s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-dev-bin arm64 2.41-1ubuntu2 [24.0 kB] 528s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6 arm64 2.41-1ubuntu2 [2910 kB] 532s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-bin arm64 2.41-1ubuntu2 [600 kB] 532s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 locales all 2.41-1ubuntu2 [4246 kB] 537s Preconfiguring packages ... 538s Fetched 9530 kB in 12s (776 kB/s) 538s (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 ... 81647 files and directories currently installed.) 538s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_arm64.deb ... 538s Unpacking libc6-dev:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 538s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_arm64.deb ... 538s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 538s Preparing to unpack .../libc6_2.41-1ubuntu2_arm64.deb ... 538s Unpacking libc6:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 539s Setting up libc6:arm64 (2.41-1ubuntu2) ... 539s (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 ... 81647 files and directories currently installed.) 539s Preparing to unpack .../libc-bin_2.41-1ubuntu2_arm64.deb ... 539s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 539s Setting up libc-bin (2.41-1ubuntu2) ... 539s (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 ... 81647 files and directories currently installed.) 539s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 539s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 539s Setting up locales (2.41-1ubuntu2) ... 540s Generating locales (this might take a while)... 542s en_US.UTF-8... done 542s Generation complete. 542s Setting up libc-dev-bin (2.41-1ubuntu2) ... 542s Setting up libc6-dev:arm64 (2.41-1ubuntu2) ... 542s Processing triggers for man-db (2.13.0-1) ... 543s Processing triggers for systemd (257.3-1ubuntu3) ... 544s Reading package lists... 544s Building dependency tree... 544s Reading state information... 544s Starting pkgProblemResolver with broken count: 0 545s Starting 2 pkgProblemResolver with broken count: 0 545s Done 545s Solving dependencies... 545s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 546s autopkgtest [15:44:31]: rebooting testbed after setup commands that affected boot 574s Reading package lists... 574s Building dependency tree... 574s Reading state information... 574s Starting pkgProblemResolver with broken count: 0 574s Starting 2 pkgProblemResolver with broken count: 0 574s Done 575s The following NEW packages will be installed: 575s libblas3 libgfortran5 liblapack3 python3-all python3-fastcluster 575s python3-numpy python3-numpy-dev 575s 0 upgraded, 7 newly installed, 0 to remove and 0 not upgraded. 575s Need to get 7081 kB of archives. 575s After this operation, 29.8 MB of additional disk space will be used. 575s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy-dev arm64 1:2.2.3+ds-5 [146 kB] 576s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.1-2 [161 kB] 576s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 15-20250222-0ubuntu1 [444 kB] 577s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.1-2 [2307 kB] 580s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy arm64 1:2.2.3+ds-5 [3981 kB] 584s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-all arm64 3.13.2-2 [886 B] 584s Get:7 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-fastcluster arm64 1.2.6-2 [42.1 kB] 585s Fetched 7081 kB in 9s (778 kB/s) 585s Selecting previously unselected package python3-numpy-dev:arm64. 585s (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 ... 81647 files and directories currently installed.) 585s Preparing to unpack .../0-python3-numpy-dev_1%3a2.2.3+ds-5_arm64.deb ... 585s Unpacking python3-numpy-dev:arm64 (1:2.2.3+ds-5) ... 585s Selecting previously unselected package libblas3:arm64. 585s Preparing to unpack .../1-libblas3_3.12.1-2_arm64.deb ... 585s Unpacking libblas3:arm64 (3.12.1-2) ... 585s Selecting previously unselected package libgfortran5:arm64. 585s Preparing to unpack .../2-libgfortran5_15-20250222-0ubuntu1_arm64.deb ... 585s Unpacking libgfortran5:arm64 (15-20250222-0ubuntu1) ... 585s Selecting previously unselected package liblapack3:arm64. 585s Preparing to unpack .../3-liblapack3_3.12.1-2_arm64.deb ... 585s Unpacking liblapack3:arm64 (3.12.1-2) ... 585s Selecting previously unselected package python3-numpy. 585s Preparing to unpack .../4-python3-numpy_1%3a2.2.3+ds-5_arm64.deb ... 585s Unpacking python3-numpy (1:2.2.3+ds-5) ... 585s Selecting previously unselected package python3-all. 585s Preparing to unpack .../5-python3-all_3.13.2-2_arm64.deb ... 585s Unpacking python3-all (3.13.2-2) ... 585s Selecting previously unselected package python3-fastcluster. 586s Preparing to unpack .../6-python3-fastcluster_1.2.6-2_arm64.deb ... 586s Unpacking python3-fastcluster (1.2.6-2) ... 586s Setting up python3-all (3.13.2-2) ... 586s Setting up libblas3:arm64 (3.12.1-2) ... 586s 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 586s Setting up python3-numpy-dev:arm64 (1:2.2.3+ds-5) ... 586s Setting up libgfortran5:arm64 (15-20250222-0ubuntu1) ... 586s Setting up liblapack3:arm64 (3.12.1-2) ... 586s 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 586s Setting up python3-numpy (1:2.2.3+ds-5) ... 587s Setting up python3-fastcluster (1.2.6-2) ... 588s Processing triggers for man-db (2.13.0-1) ... 588s Processing triggers for libc-bin (2.41-1ubuntu2) ... 591s autopkgtest [15:45:16]: 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 591s autopkgtest [15:45:16]: test autodep8-python3: [----------------------- 591s Testing with python3.13: 591s 592s autopkgtest [15:45:17]: test autodep8-python3: -----------------------] 592s autopkgtest [15:45:17]: test autodep8-python3: - - - - - - - - - - results - - - - - - - - - - 592s autodep8-python3 PASS (superficial) 593s autopkgtest [15:45:18]: @@@@@@@@@@@@@@@@@@@@ summary 593s run-unit-test PASS 593s autodep8-python3 PASS (superficial) 598s nova [W] Using flock in prodstack6-arm64 598s Creating nova instance adt-plucky-arm64-r-cran-fastcluster-20250315-152609-juju-7f2275-prod-proposed-migration-environment-2-d63a6a08-4ec3-418b-a073-eeb55b37515b from image adt/ubuntu-plucky-arm64-server-20250315.img (UUID bd6e766c-b51f-4b53-86d6-23aa4d18f524)... 598s nova [W] Timed out waiting for c50d96be-73bf-4ba0-82ea-3acd290bd0c0 to get deleted. 598s nova [W] Using flock in prodstack6-arm64 598s Creating nova instance adt-plucky-arm64-r-cran-fastcluster-20250315-152609-juju-7f2275-prod-proposed-migration-environment-2-d63a6a08-4ec3-418b-a073-eeb55b37515b from image adt/ubuntu-plucky-arm64-server-20250315.img (UUID bd6e766c-b51f-4b53-86d6-23aa4d18f524)... 598s nova [W] Timed out waiting for 7a68d689-5fe8-4465-a9d1-53aa7797bd70 to get deleted.