0s autopkgtest [14:33:25]: starting date and time: 2024-11-13 14:33:25+0000 0s autopkgtest [14:33:25]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [14:33:25]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.f_xtgih3/out --timeout-copy=6000 --setup-commands 'ln -s /dev/null /etc/systemd/system/bluetooth.service; printf "http_proxy=http://squid.internal:3128\nhttps_proxy=http://squid.internal:3128\nno_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\n" >> /etc/environment' --apt-pocket=proposed=src:python3-defaults,src:python3-stdlib-extensions --apt-upgrade r-cran-fastcluster --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=python3-defaults/3.12.7-1 python3-stdlib-extensions/3.12.7-1' -- lxd -r lxd-armhf-10.145.243.85 lxd-armhf-10.145.243.85:autopkgtest/ubuntu/plucky/armhf 55s autopkgtest [14:34:20]: testbed dpkg architecture: armhf 57s autopkgtest [14:34:22]: testbed apt version: 2.9.8 57s autopkgtest [14:34:22]: @@@@@@@@@@@@@@@@@@@@ test bed setup 65s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 65s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [105 kB] 65s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [962 kB] 65s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 65s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [16.5 kB] 65s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf Packages [104 kB] 65s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf Packages [645 kB] 65s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf Packages [16.9 kB] 65s Fetched 1931 kB in 1s (2169 kB/s) 66s Reading package lists... 84s tee: /proc/self/fd/2: Permission denied 105s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 105s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 105s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 105s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 106s Reading package lists... 106s Reading package lists... 106s Building dependency tree... 106s Reading state information... 107s Calculating upgrade... 107s The following NEW packages will be installed: 107s python3.13-gdbm 107s The following packages will be upgraded: 107s libgnutls30t64 libjson-glib-1.0-0 libjson-glib-1.0-common libpython3-stdlib 107s libutempter0 python3 python3-gdbm python3-minimal 108s 8 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 108s Need to get 1131 kB of archives. 108s After this operation, 95.2 kB of additional disk space will be used. 108s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf python3-minimal armhf 3.12.7-1 [27.4 kB] 108s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf python3 armhf 3.12.7-1 [24.0 kB] 108s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libpython3-stdlib armhf 3.12.7-1 [10.0 kB] 108s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf libgnutls30t64 armhf 3.8.8-2ubuntu1 [955 kB] 108s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf python3.13-gdbm armhf 3.13.0-2 [29.5 kB] 108s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf python3-gdbm armhf 3.12.7-1 [8642 B] 108s Get:7 http://ftpmaster.internal/ubuntu plucky/main armhf libjson-glib-1.0-common all 1.10.0+ds-3 [5586 B] 108s Get:8 http://ftpmaster.internal/ubuntu plucky/main armhf libjson-glib-1.0-0 armhf 1.10.0+ds-3 [61.7 kB] 108s Get:9 http://ftpmaster.internal/ubuntu plucky/main armhf libutempter0 armhf 1.2.1-4 [9062 B] 108s Fetched 1131 kB in 1s (2006 kB/s) 109s (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 ... 59559 files and directories currently installed.) 109s Preparing to unpack .../python3-minimal_3.12.7-1_armhf.deb ... 109s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ... 109s Setting up python3-minimal (3.12.7-1) ... 109s (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 ... 59559 files and directories currently installed.) 109s Preparing to unpack .../python3_3.12.7-1_armhf.deb ... 109s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ... 109s Preparing to unpack .../libpython3-stdlib_3.12.7-1_armhf.deb ... 109s Unpacking libpython3-stdlib:armhf (3.12.7-1) over (3.12.6-0ubuntu1) ... 109s Preparing to unpack .../libgnutls30t64_3.8.8-2ubuntu1_armhf.deb ... 109s Unpacking libgnutls30t64:armhf (3.8.8-2ubuntu1) over (3.8.6-2ubuntu1) ... 109s Setting up libgnutls30t64:armhf (3.8.8-2ubuntu1) ... 109s Selecting previously unselected package python3.13-gdbm. 109s (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 ... 59559 files and directories currently installed.) 109s Preparing to unpack .../python3.13-gdbm_3.13.0-2_armhf.deb ... 109s Unpacking python3.13-gdbm (3.13.0-2) ... 109s Preparing to unpack .../python3-gdbm_3.12.7-1_armhf.deb ... 109s Unpacking python3-gdbm:armhf (3.12.7-1) over (3.12.6-1ubuntu1) ... 109s Preparing to unpack .../libjson-glib-1.0-common_1.10.0+ds-3_all.deb ... 109s Unpacking libjson-glib-1.0-common (1.10.0+ds-3) over (1.10.0+ds-2) ... 109s Preparing to unpack .../libjson-glib-1.0-0_1.10.0+ds-3_armhf.deb ... 109s Unpacking libjson-glib-1.0-0:armhf (1.10.0+ds-3) over (1.10.0+ds-2) ... 109s Preparing to unpack .../libutempter0_1.2.1-4_armhf.deb ... 109s Unpacking libutempter0:armhf (1.2.1-4) over (1.2.1-3build1) ... 109s Setting up libutempter0:armhf (1.2.1-4) ... 109s Setting up libjson-glib-1.0-common (1.10.0+ds-3) ... 109s Setting up python3.13-gdbm (3.13.0-2) ... 109s Setting up libpython3-stdlib:armhf (3.12.7-1) ... 109s Setting up python3 (3.12.7-1) ... 110s Setting up libjson-glib-1.0-0:armhf (1.10.0+ds-3) ... 110s Setting up python3-gdbm:armhf (3.12.7-1) ... 110s Processing triggers for man-db (2.12.1-3) ... 110s Processing triggers for libc-bin (2.40-1ubuntu3) ... 111s Reading package lists... 111s Building dependency tree... 111s Reading state information... 112s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 114s autopkgtest [14:35:19]: rebooting testbed after setup commands that affected boot 183s autopkgtest [14:36:28]: testbed running kernel: Linux 6.8.0-48-generic #48~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Mon Oct 7 11:49:53 UTC 2 210s autopkgtest [14:36:55]: @@@@@@@@@@@@@@@@@@@@ apt-source r-cran-fastcluster 225s Get:1 http://ftpmaster.internal/ubuntu plucky/universe r-cran-fastcluster 1.2.6-1build1 (dsc) [2272 B] 225s Get:2 http://ftpmaster.internal/ubuntu plucky/universe r-cran-fastcluster 1.2.6-1build1 (tar) [208 kB] 225s Get:3 http://ftpmaster.internal/ubuntu plucky/universe r-cran-fastcluster 1.2.6-1build1 (diff) [4828 B] 225s gpgv: Signature made Wed Apr 10 18:03:18 2024 UTC 225s gpgv: using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2 225s gpgv: Can't check signature: No public key 225s dpkg-source: warning: cannot verify inline signature for ./r-cran-fastcluster_1.2.6-1build1.dsc: no acceptable signature found 225s autopkgtest [14:37:10]: testing package r-cran-fastcluster version 1.2.6-1build1 227s autopkgtest [14:37:12]: build not needed 230s autopkgtest [14:37:15]: test run-unit-test: preparing testbed 240s Reading package lists... 240s Building dependency tree... 240s Reading state information... 240s Starting pkgProblemResolver with broken count: 0 240s Starting 2 pkgProblemResolver with broken count: 0 240s Done 241s The following additional packages will be installed: 241s fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono libblas3 241s libcairo2 libdatrie1 libdeflate0 libfontconfig1 libfreetype6 libgfortran5 241s libgomp1 libgraphite2-3 libharfbuzz0b libice6 libjbig0 libjpeg-turbo8 241s libjpeg8 liblapack3 liblerc4 libpango-1.0-0 libpangocairo-1.0-0 241s libpangoft2-1.0-0 libpaper-utils libpaper1 libpixman-1-0 libsharpyuv0 libsm6 241s libtcl8.6 libthai-data libthai0 libtiff6 libtk8.6 libwebp7 libxcb-render0 241s libxcb-shm0 libxft2 libxrender1 libxss1 libxt6t64 python3-fastcluster 241s python3-numpy r-base-core r-cran-fastcluster unzip x11-common xdg-utils zip 241s Suggested packages: 241s tcl8.6 tk8.6 gcc gfortran python-numpy-doc python3-dev python3-pytest 241s elpa-ess r-doc-info | r-doc-pdf r-mathlib r-base-html 241s Recommended packages: 241s python3-scipy r-recommended r-base-dev r-doc-html libfile-mimeinfo-perl 241s libnet-dbus-perl libx11-protocol-perl x11-utils x11-xserver-utils 241s The following NEW packages will be installed: 241s autopkgtest-satdep fontconfig fontconfig-config fonts-dejavu-core 241s fonts-dejavu-mono libblas3 libcairo2 libdatrie1 libdeflate0 libfontconfig1 241s libfreetype6 libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libice6 241s libjbig0 libjpeg-turbo8 libjpeg8 liblapack3 liblerc4 libpango-1.0-0 241s libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpixman-1-0 241s libsharpyuv0 libsm6 libtcl8.6 libthai-data libthai0 libtiff6 libtk8.6 241s libwebp7 libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxss1 libxt6t64 241s python3-fastcluster python3-numpy r-base-core r-cran-fastcluster unzip 241s x11-common xdg-utils zip 241s 0 upgraded, 49 newly installed, 0 to remove and 0 not upgraded. 241s Need to get 41.3 MB/41.3 MB of archives. 241s After this operation, 85.3 MB of additional disk space will be used. 241s Get:1 /tmp/autopkgtest.rzuJUT/1-autopkgtest-satdep.deb autopkgtest-satdep armhf 0 [720 B] 241s Get:2 http://ftpmaster.internal/ubuntu plucky/main armhf libfreetype6 armhf 2.13.3+dfsg-1 [330 kB] 242s Get:3 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-dejavu-mono all 2.37-8 [502 kB] 242s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-dejavu-core all 2.37-8 [835 kB] 242s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf fontconfig-config armhf 2.15.0-1.1ubuntu2 [37.4 kB] 242s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf libfontconfig1 armhf 2.15.0-1.1ubuntu2 [113 kB] 242s Get:7 http://ftpmaster.internal/ubuntu plucky/main armhf fontconfig armhf 2.15.0-1.1ubuntu2 [189 kB] 242s Get:8 http://ftpmaster.internal/ubuntu plucky/main armhf libblas3 armhf 3.12.0-3build2 [126 kB] 242s Get:9 http://ftpmaster.internal/ubuntu plucky/main armhf libpixman-1-0 armhf 0.44.0-3 [183 kB] 242s Get:10 http://ftpmaster.internal/ubuntu plucky/main armhf libxcb-render0 armhf 1.17.0-2 [15.3 kB] 242s Get:11 http://ftpmaster.internal/ubuntu plucky/main armhf libxcb-shm0 armhf 1.17.0-2 [5774 B] 242s Get:12 http://ftpmaster.internal/ubuntu plucky/main armhf libxrender1 armhf 1:0.9.10-1.1build1 [16.0 kB] 242s Get:13 http://ftpmaster.internal/ubuntu plucky/main armhf libcairo2 armhf 1.18.2-2 [484 kB] 242s Get:14 http://ftpmaster.internal/ubuntu plucky/main armhf libdatrie1 armhf 0.2.13-3build1 [15.7 kB] 242s Get:15 http://ftpmaster.internal/ubuntu plucky/main armhf libdeflate0 armhf 1.22-1 [38.9 kB] 242s Get:16 http://ftpmaster.internal/ubuntu plucky/main armhf libgfortran5 armhf 14.2.0-8ubuntu1 [311 kB] 242s Get:17 http://ftpmaster.internal/ubuntu plucky/main armhf libgomp1 armhf 14.2.0-8ubuntu1 [125 kB] 242s Get:18 http://ftpmaster.internal/ubuntu plucky/main armhf libgraphite2-3 armhf 1.3.14-2ubuntu1 [64.8 kB] 242s Get:19 http://ftpmaster.internal/ubuntu plucky/main armhf libharfbuzz0b armhf 10.0.1-1 [463 kB] 242s Get:20 http://ftpmaster.internal/ubuntu plucky/main armhf x11-common all 1:7.7+23ubuntu3 [21.7 kB] 242s Get:21 http://ftpmaster.internal/ubuntu plucky/main armhf libice6 armhf 2:1.1.1-1 [36.5 kB] 242s Get:22 http://ftpmaster.internal/ubuntu plucky/main armhf libjpeg-turbo8 armhf 2.1.5-2ubuntu2 [125 kB] 242s Get:23 http://ftpmaster.internal/ubuntu plucky/main armhf libjpeg8 armhf 8c-2ubuntu11 [2148 B] 242s Get:24 http://ftpmaster.internal/ubuntu plucky/main armhf liblapack3 armhf 3.12.0-3build2 [2086 kB] 242s Get:25 http://ftpmaster.internal/ubuntu plucky/main armhf liblerc4 armhf 4.0.0+ds-4ubuntu2 [151 kB] 242s Get:26 http://ftpmaster.internal/ubuntu plucky/main armhf libthai-data all 0.1.29-2build1 [158 kB] 242s Get:27 http://ftpmaster.internal/ubuntu plucky/main armhf libthai0 armhf 0.1.29-2build1 [15.2 kB] 242s Get:28 http://ftpmaster.internal/ubuntu plucky/main armhf libpango-1.0-0 armhf 1.54.0+ds-3 [212 kB] 242s Get:29 http://ftpmaster.internal/ubuntu plucky/main armhf libpangoft2-1.0-0 armhf 1.54.0+ds-3 [42.9 kB] 242s Get:30 http://ftpmaster.internal/ubuntu plucky/main armhf libpangocairo-1.0-0 armhf 1.54.0+ds-3 [24.8 kB] 242s Get:31 http://ftpmaster.internal/ubuntu plucky/main armhf libpaper1 armhf 1.1.29build1 [12.6 kB] 242s Get:32 http://ftpmaster.internal/ubuntu plucky/main armhf libpaper-utils armhf 1.1.29build1 [8184 B] 242s Get:33 http://ftpmaster.internal/ubuntu plucky/main armhf libsharpyuv0 armhf 1.4.0-0.1 [16.3 kB] 242s Get:34 http://ftpmaster.internal/ubuntu plucky/main armhf libsm6 armhf 2:1.2.4-1 [15.1 kB] 242s Get:35 http://ftpmaster.internal/ubuntu plucky/main armhf libtcl8.6 armhf 8.6.15+dfsg-2 [909 kB] 242s Get:36 http://ftpmaster.internal/ubuntu plucky/main armhf libjbig0 armhf 2.1-6.1ubuntu2 [24.9 kB] 242s Get:37 http://ftpmaster.internal/ubuntu plucky/main armhf libwebp7 armhf 1.4.0-0.1 [184 kB] 242s Get:38 http://ftpmaster.internal/ubuntu plucky/main armhf libtiff6 armhf 4.5.1+git230720-4ubuntu4 [179 kB] 242s Get:39 http://ftpmaster.internal/ubuntu plucky/main armhf libxft2 armhf 2.3.6-1build1 [37.4 kB] 242s Get:40 http://ftpmaster.internal/ubuntu plucky/main armhf libxss1 armhf 1:1.2.3-1build3 [6500 B] 242s Get:41 http://ftpmaster.internal/ubuntu plucky/main armhf libtk8.6 armhf 8.6.15-1 [685 kB] 242s Get:42 http://ftpmaster.internal/ubuntu plucky/main armhf libxt6t64 armhf 1:1.2.1-1.2build1 [145 kB] 242s Get:43 http://ftpmaster.internal/ubuntu plucky/main armhf python3-numpy armhf 1:1.26.4+ds-11build1 [3570 kB] 242s Get:44 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-fastcluster armhf 1.2.6-1build1 [39.2 kB] 242s Get:45 http://ftpmaster.internal/ubuntu plucky/main armhf zip armhf 3.0-14ubuntu1 [164 kB] 242s Get:46 http://ftpmaster.internal/ubuntu plucky/main armhf unzip armhf 6.0-28ubuntu6 [167 kB] 242s Get:47 http://ftpmaster.internal/ubuntu plucky/main armhf xdg-utils all 1.2.1-0ubuntu1 [67.5 kB] 242s Get:48 http://ftpmaster.internal/ubuntu plucky/universe armhf r-base-core armhf 4.4.2-1 [28.1 MB] 243s Get:49 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-fastcluster armhf 1.2.6-1build1 [189 kB] 244s Preconfiguring packages ... 244s Fetched 41.3 MB in 2s (20.3 MB/s) 244s Selecting previously unselected package libfreetype6:armhf. 244s (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 ... 59566 files and directories currently installed.) 244s Preparing to unpack .../00-libfreetype6_2.13.3+dfsg-1_armhf.deb ... 244s Unpacking libfreetype6:armhf (2.13.3+dfsg-1) ... 244s Selecting previously unselected package fonts-dejavu-mono. 244s Preparing to unpack .../01-fonts-dejavu-mono_2.37-8_all.deb ... 244s Unpacking fonts-dejavu-mono (2.37-8) ... 244s Selecting previously unselected package fonts-dejavu-core. 244s Preparing to unpack .../02-fonts-dejavu-core_2.37-8_all.deb ... 244s Unpacking fonts-dejavu-core (2.37-8) ... 244s Selecting previously unselected package fontconfig-config. 244s Preparing to unpack .../03-fontconfig-config_2.15.0-1.1ubuntu2_armhf.deb ... 245s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ... 245s Selecting previously unselected package libfontconfig1:armhf. 245s Preparing to unpack .../04-libfontconfig1_2.15.0-1.1ubuntu2_armhf.deb ... 245s Unpacking libfontconfig1:armhf (2.15.0-1.1ubuntu2) ... 245s Selecting previously unselected package fontconfig. 245s Preparing to unpack .../05-fontconfig_2.15.0-1.1ubuntu2_armhf.deb ... 245s Unpacking fontconfig (2.15.0-1.1ubuntu2) ... 245s Selecting previously unselected package libblas3:armhf. 245s Preparing to unpack .../06-libblas3_3.12.0-3build2_armhf.deb ... 245s Unpacking libblas3:armhf (3.12.0-3build2) ... 245s Selecting previously unselected package libpixman-1-0:armhf. 245s Preparing to unpack .../07-libpixman-1-0_0.44.0-3_armhf.deb ... 245s Unpacking libpixman-1-0:armhf (0.44.0-3) ... 245s Selecting previously unselected package libxcb-render0:armhf. 245s Preparing to unpack .../08-libxcb-render0_1.17.0-2_armhf.deb ... 245s Unpacking libxcb-render0:armhf (1.17.0-2) ... 245s Selecting previously unselected package libxcb-shm0:armhf. 245s Preparing to unpack .../09-libxcb-shm0_1.17.0-2_armhf.deb ... 245s Unpacking libxcb-shm0:armhf (1.17.0-2) ... 245s Selecting previously unselected package libxrender1:armhf. 245s Preparing to unpack .../10-libxrender1_1%3a0.9.10-1.1build1_armhf.deb ... 245s Unpacking libxrender1:armhf (1:0.9.10-1.1build1) ... 245s Selecting previously unselected package libcairo2:armhf. 245s Preparing to unpack .../11-libcairo2_1.18.2-2_armhf.deb ... 245s Unpacking libcairo2:armhf (1.18.2-2) ... 245s Selecting previously unselected package libdatrie1:armhf. 245s Preparing to unpack .../12-libdatrie1_0.2.13-3build1_armhf.deb ... 245s Unpacking libdatrie1:armhf (0.2.13-3build1) ... 245s Selecting previously unselected package libdeflate0:armhf. 245s Preparing to unpack .../13-libdeflate0_1.22-1_armhf.deb ... 245s Unpacking libdeflate0:armhf (1.22-1) ... 245s Selecting previously unselected package libgfortran5:armhf. 245s Preparing to unpack .../14-libgfortran5_14.2.0-8ubuntu1_armhf.deb ... 245s Unpacking libgfortran5:armhf (14.2.0-8ubuntu1) ... 245s Selecting previously unselected package libgomp1:armhf. 245s Preparing to unpack .../15-libgomp1_14.2.0-8ubuntu1_armhf.deb ... 245s Unpacking libgomp1:armhf (14.2.0-8ubuntu1) ... 245s Selecting previously unselected package libgraphite2-3:armhf. 245s Preparing to unpack .../16-libgraphite2-3_1.3.14-2ubuntu1_armhf.deb ... 245s Unpacking libgraphite2-3:armhf (1.3.14-2ubuntu1) ... 245s Selecting previously unselected package libharfbuzz0b:armhf. 245s Preparing to unpack .../17-libharfbuzz0b_10.0.1-1_armhf.deb ... 245s Unpacking libharfbuzz0b:armhf (10.0.1-1) ... 245s Selecting previously unselected package x11-common. 245s Preparing to unpack .../18-x11-common_1%3a7.7+23ubuntu3_all.deb ... 245s Unpacking x11-common (1:7.7+23ubuntu3) ... 245s Selecting previously unselected package libice6:armhf. 245s Preparing to unpack .../19-libice6_2%3a1.1.1-1_armhf.deb ... 245s Unpacking libice6:armhf (2:1.1.1-1) ... 245s Selecting previously unselected package libjpeg-turbo8:armhf. 245s Preparing to unpack .../20-libjpeg-turbo8_2.1.5-2ubuntu2_armhf.deb ... 245s Unpacking libjpeg-turbo8:armhf (2.1.5-2ubuntu2) ... 245s Selecting previously unselected package libjpeg8:armhf. 245s Preparing to unpack .../21-libjpeg8_8c-2ubuntu11_armhf.deb ... 245s Unpacking libjpeg8:armhf (8c-2ubuntu11) ... 245s Selecting previously unselected package liblapack3:armhf. 245s Preparing to unpack .../22-liblapack3_3.12.0-3build2_armhf.deb ... 245s Unpacking liblapack3:armhf (3.12.0-3build2) ... 245s Selecting previously unselected package liblerc4:armhf. 245s Preparing to unpack .../23-liblerc4_4.0.0+ds-4ubuntu2_armhf.deb ... 245s Unpacking 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... 62675 files and directories currently installed.) 271s Removing autopkgtest-satdep (0) ... 277s autopkgtest [14:38:02]: test run-unit-test: [----------------------- 279s 279s R version 4.4.2 (2024-10-31) -- "Pile of Leaves" 279s Copyright (C) 2024 The R Foundation for Statistical Computing 279s Platform: arm-unknown-linux-gnueabihf (32-bit) 279s 279s R is free software and comes with ABSOLUTELY NO WARRANTY. 279s You are welcome to redistribute it under certain conditions. 279s Type 'license()' or 'licence()' for distribution details. 279s 279s R is a collaborative project with many contributors. 279s Type 'contributors()' for more information and 279s 'citation()' on how to cite R or R packages in publications. 279s 279s Type 'demo()' for some demos, 'help()' for on-line help, or 279s 'help.start()' for an HTML browser interface to help. 279s Type 'q()' to quit R. 279s 280s > # fastcluster: Fast hierarchical clustering routines for R and Python 280s > # 280s > # Copyright: 280s > # * Until package version 1.1.23: © 2011 Daniel Müllner 280s > # * All changes from version 1.1.24 on: © Google Inc. 280s > # 280s > # Test script for the R interface 280s > 280s > seed = as.integer(runif(1, 0, 1e9)) 280s > set.seed(seed) 280s > cat(sprintf("Random seed: %d\n",seed)) 280s Random seed: 807851067 280s > 280s > print_seed <- function() { 280s + return(sprintf(' 280s + Please send a report to the author of the \'fastcluster\' package, Daniel Müllner. 280s + For contact details, see . To make the error 280s + reproducible, you must include the following number (the random seed value) in 280s + your error report: %d.\n\n', seed)) 280s + } 280s > 280s > hasWardD2 = getRversion() >= '3.1.0' 280s > 280s > # Compare two dendrograms and check whether they are equal, except that 280s > # ties may be resolved differently. 280s > compare <- function(dg1, dg2) { 280s + h1 <- dg1$height 280s + h2 <- dg2$height 280s + # "height" vectors may have small numerical errors. 280s + rdiffs <- abs(h1-h2)/pmax(abs(h1),abs(h2)) 280s + rdiffs = rdiffs[complete.cases(rdiffs)] 280s + rel_error <- max(rdiffs) 280s + # We allow a relative error of 1e-13. 280s + if (rel_error>1e-13) { 280s + print(h1) 280s + print(h2) 280s + cat(sprintf('Height vectors differ! The maximum relative error is %e.\n', rel_error)) 280s + return(FALSE) 280s + } 280s + # Filter the indices where consecutive merging distances are distinct. 280s + d = diff(dg1$height) 280s + b = (c(d,1)!=0 & c(1,d)!=0) 280s + #cat(sprintf("Percentage of indices where we can test: %g.\n",100.0*length(b[b])/length(b))) 280s + if (any(b)) { 280s + m1 = dg1$merge[b,] 280s + m2 = dg2$merge[b,] 280s + 280s + r = function(i) { 280s + if (i<0) { 280s + return(1) 280s + } 280s + else { 280s + return(b[i]) 280s + } 280s + } 280s + 280s + f = sapply(m1,r) 280s + fm1 = m1*f 280s + fm2 = m2*f 280s + # The "merge" matrices must be identical whereever indices are not ambiguous 280s + # due to ties. 280s + if (!identical(fm1,fm2)) { 280s + cat('Merge matrices differ!\n') 280s + return(FALSE) 280s + } 280s + # Compare the "order" vectors only if all merging distances were distinct. 280s + if (all(b) && !identical(dg1$order,dg2$order)) { 280s + cat('Order vectors differ!\n') 280s + return(FALSE) 280s + } 280s + } 280s + return(TRUE) 280s + } 280s > 280s > # Generate uniformly distributed random data 280s > generate.uniform <- function() { 280s + n = sample(10:1000,1) 280s + range_exp = runif(1,min=-10, max=10) 280s + cat(sprintf("Number of sample points: %d\n",n)) 280s + cat(sprintf("Dissimilarity range: [0,%g]\n",10^range_exp)) 280s + d = runif(n*(n-1)/2, min=0, max=10^range_exp) 280s + # Fake a compressed distance matrix 280s + attributes(d) <- NULL 280s + attr(d,"Size") <- n 280s + attr(d, "call") <- 'N/A' 280s + class(d) <- "dist" 280s + return(d) 280s + } 280s > 280s > # Generate normally distributed random data 280s > generate.normal <- function() { 280s + n = sample(10:1000,1) 280s + dim = sample(2:20,1) 280s + 280s + cat (sprintf("Number of sample points: %d\n",n)) 280s + cat (sprintf("Dimension: %d\n",dim)) 280s + 280s + pcd = matrix(rnorm(n*dim), c(n,dim)) 280s + d = dist(pcd) 280s + return(d) 280s + } 280s > 280s > # Test the clustering functions when a distance matrix is given. 280s > test.dm <- function(d) { 280s + d2 = d 280s + if (hasWardD2) { 280s + methods = c('single','complete','average','mcquitty','ward.D','ward.D2','centroid','median') 280s + } 280s + else { 280s + methods = c('single','complete','average','mcquitty','ward','centroid','median') 280s + } 280s + for (method in methods) { 280s + cat(paste('Method :', method, '\n')) 280s + dg_stats = stats::hclust(d, method=method) 280s + if (method == 'ward') { 280s + method = 'ward.D' 280s + } 280s + dg_fastcluster = fastcluster::hclust(d, method=method) 280s + if (!identical(d,d2)) { 280s + cat('Input array was corrupted!\n') 280s + stop(print_seed()) 280s + } 280s + if (!compare(dg_stats, dg_fastcluster)) { 280s + stop(print_seed()) 280s + } 280s + } 280s + cat('Passed.\n') 280s + } 280s > 280s > # Test the clustering functions for vector input in Euclidean space. 280s > test.vector <- function() { 280s + # generate test data 280s + n = sample(10:1000,1) 280s + dim = sample(2:20,1) 280s + cat (sprintf("Number of sample points: %d\n",n)) 280s + cat (sprintf("Dimension: %d\n",dim)) 280s + 280s + range_exp = runif(1,min=-10, max=10) 280s + pcd = matrix(rnorm(n*dim, sd=10^range_exp), c(n,dim)) 280s + pcd2 = pcd 280s + # test 280s + method='single' 280s + cat(paste('Method:', method, '\n')) 280s + for (metric in c('euclidean', 'maximum', 'manhattan', 'canberra', 'minkowski')) { 280s + cat(paste(' Metric:', metric, '\n')) 280s + if (metric=='minkowski') { 280s + p = runif(1, min=1.0, max=10.0) 280s + cat (sprintf(" p: %g\n",p)); 280s + dg_fastcluster = fastcluster::hclust.vector(pcd, method=method, metric=metric, p=p) 280s + d = dist(pcd, method=metric, p=p) 280s + } 280s + else { 280s + dg_fastcluster = fastcluster::hclust.vector(pcd, method=method, metric=metric) 280s + d = dist(pcd, method=metric) 280s + } 280s + d2 = d 280s + dg_fastcluster_dist = fastcluster::hclust(d, method=method) 280s + if (!identical(d,d2) || !identical(pcd,pcd2)) { 280s + cat('Input array was corrupted!\n') 280s + stop(print_seed()) 280s + } 280s + if (!compare(dg_fastcluster_dist, dg_fastcluster)) { 280s + stop(print_seed()) 280s + } 280s + } 280s + for (method in c('ward','centroid','median') ) { 280s + cat(paste('Method:', method, '\n')) 280s + dg_fastcluster = fastcluster::hclust.vector(pcd, method=method) 280s + if (!identical(pcd,pcd2)) { 280s + cat('Input array was corrupted!\n') 280s + stop(print_seed()) 280s + } 280s + d = dist(pcd) 280s + if(method == "ward" && hasWardD2) { 280s + method = "ward.D2" 280s + } 280s + else 280s + { 280s + # Workaround: fastcluster::hclust expects _squared_ euclidean distances. 280s + d = d^2 280s + } 280s + d2 = d 280s + dg_fastcluster_dist = fastcluster::hclust(d, method=method) 280s + if (!identical(d,d2)) { 280s + cat('Input array was corrupted!\n') 280s + stop(print_seed()) 280s + } 280s + if(method != "ward.D2") { 280s + dg_fastcluster_dist$height = sqrt(dg_fastcluster_dist$height) 280s + } 280s + # The Euclidean methods may have small numerical errors due to squaring/ 280s + # taking the root in the Euclidean distances. 280s + if (!compare(dg_fastcluster_dist, dg_fastcluster)) { 280s + stop(print_seed()) 280s + } 280s + } 280s + cat('Passed.\n') 280s + } 280s > 280s > # Test the single linkage function with the "binary" metric 280s > test.vector.binary <- function() { 280s + # generate test data 280s + cat (sprintf("Uniform sampling for the 'binary' metric:\n")) 280s + n = sample(10:400,1) 280s + dim = sample(n:(2*n),1) 280s + cat (sprintf("Number of sample points: %d\n",n)) 280s + cat (sprintf("Dimension: %d\n",dim)) 280s + pcd = matrix(sample(-1:2, n*dim, replace=T), c(n,dim)) 280s + pcd2 = pcd 280s + # test 280s + method='single' 280s + metric='binary' 280s + cat(paste('Method:', method, '\n')) 280s + cat(paste(' Metric:', metric, '\n')) 280s + dg_fastcluster = fastcluster::hclust.vector(pcd, method=method, metric=metric) 280s + d = dist(pcd, method=metric) 280s + d2 = d 280s + dg_fastcluster_dist = fastcluster::hclust(d, method=method) 280s + if (!identical(d,d2) || !identical(d,d2)) { 280s + cat('Input array was corrupted!\n') 280s + stop(print_seed()) 280s + } 280s + if (!compare(dg_fastcluster_dist, dg_fastcluster)) { 280s + stop(print_seed()) 280s + } 280s + cat('Passed.\n') 280s + } 280s > 280s > 280s > N = 15 280s > for (i in (1:N)) { 280s + if (i%%2==1) { 280s + cat(sprintf('Random test %d of %d (uniform distribution of distances):\n',i,2*N)) 280s + d = generate.uniform() 280s + } 280s + else { 280s + cat(sprintf('Random test %d of %d (Gaussian density):\n',i,2*N)) 280s + d = generate.normal() 280s + } 280s + test.dm(d) 280s + } 280s Random test 1 of 30 (uniform distribution of distances): 280s Number of sample points: 642 280s Dissimilarity range: [0,1.25657e-09] 280s Method : single 280s Method : complete 280s Method : average 280s Method : mcquitty 280s Method : ward.D 280s Method : ward.D2 280s Method : centroid 280s Method : median 280s Passed. 280s Random test 2 of 30 (Gaussian density): 280s Number of sample points: 549 280s Dimension: 20 280s Method : single 280s Method : complete 280s Method : average 280s Method : mcquitty 280s Method : ward.D 280s Method : ward.D2 280s Method : centroid 280s Method : median 280s Passed. 280s Random test 3 of 30 (uniform distribution of distances): 280s Number of sample points: 481 280s Dissimilarity range: [0,8.1574e-10] 280s Method : single 280s Method : complete 280s Method : average 280s Method : mcquitty 280s Method : ward.D 280s Method : ward.D2 280s Method : centroid 280s Method : median 280s Passed. 280s Random test 4 of 30 (Gaussian density): 280s Number of sample points: 555 280s Dimension: 7 280s Method : single 280s Method : complete 280s Method : average 280s Method : mcquitty 280s Method : ward.D 280s Method : ward.D2 280s Method : centroid 280s Method : median 280s Passed. 280s Random test 5 of 30 (uniform distribution of distances): 280s Number of sample points: 957 280s Dissimilarity range: [0,8.32169e+08] 280s Method : single 280s Method : complete 280s Method : average 280s Method : mcquitty 280s Method : ward.D 280s Method : ward.D2 281s Method : centroid 281s Method : median 281s Passed. 281s Random test 6 of 30 (Gaussian density): 281s Number of sample points: 853 281s Dimension: 17 281s Method : single 281s Method : complete 281s Method : average 281s Method : mcquitty 281s Method : ward.D 281s Method : ward.D2 281s Method : centroid 281s Method : median 281s Passed. 281s Random test 7 of 30 (uniform distribution of distances): 281s Number of sample points: 463 281s Dissimilarity range: [0,2.03428] 281s Method : single 281s Method : complete 281s Method : average 281s Method : mcquitty 281s Method : ward.D 281s Method : ward.D2 281s Method : centroid 281s Method : median 281s Passed. 281s Random test 8 of 30 (Gaussian density): 281s Number of sample points: 585 281s Dimension: 2 281s Method : single 281s Method : complete 281s Method : average 281s Method : mcquitty 281s Method : ward.D 281s Method : ward.D2 281s Method : centroid 281s Method : median 281s Passed. 281s Random test 9 of 30 (uniform distribution of distances): 281s Number of sample points: 674 281s Dissimilarity range: [0,6.39122e-08] 281s Method : single 281s Method : complete 281s Method : average 281s Method : mcquitty 281s Method : ward.D 281s Method : ward.D2 281s Method : centroid 281s Method : median 281s Passed. 281s Random test 10 of 30 (Gaussian density): 281s Number of sample points: 200 281s Dimension: 5 281s Method : single 281s Method : complete 281s Method : average 281s Method : mcquitty 281s Method : ward.D 281s Method : ward.D2 281s Method : centroid 281s Method : median 281s Passed. 281s Random test 11 of 30 (uniform distribution of distances): 281s Number of sample points: 61 281s Dissimilarity range: [0,8.46525e-05] 281s Method : single 281s Method : complete 281s Method : average 281s Method : mcquitty 281s Method : ward.D 281s Method : ward.D2 281s Method : centroid 281s Method : median 281s Passed. 281s Random test 12 of 30 (Gaussian density): 281s Number of sample points: 773 281s Dimension: 16 281s Method : single 281s Method : complete 281s Method : average 281s Method : mcquitty 282s Method : ward.D 282s Method : ward.D2 282s Method : centroid 282s Method : median 282s Passed. 282s Random test 13 of 30 (uniform distribution of distances): 282s Number of sample points: 234 282s Dissimilarity range: [0,0.0126312] 282s Method : single 282s Method : complete 282s Method : average 282s Method : mcquitty 282s Method : ward.D 282s Method : ward.D2 282s Method : centroid 282s Method : median 282s Passed. 282s Random test 14 of 30 (Gaussian density): 282s Number of sample points: 34 282s Dimension: 19 282s Method : single 282s Method : complete 282s Method : average 282s Method : mcquitty 282s Method : ward.D 282s Method : ward.D2 282s Method : centroid 282s Method : median 282s Passed. 282s Random test 15 of 30 (uniform distribution of distances): 282s Number of sample points: 255 282s Dissimilarity range: [0,2.00415e-06] 282s Method : single 282s Method : complete 282s Method : average 282s Method : mcquitty 282s Method : ward.D 282s Method : ward.D2 282s Method : centroid 282s Method : median 282s Passed. 282s > for (i in (N+1:N)) { 282s + cat(sprintf('Random test %d of %d (Gaussian density):\n',i,2*N)) 282s + test.vector() 282s + test.vector.binary() 282s + } 282s Random test 16 of 30 (Gaussian density): 282s Number of sample points: 683 282s Dimension: 13 282s Method: single 282s Metric: euclidean 282s Metric: maximum 282s Metric: manhattan 282s Metric: canberra 282s Metric: minkowski 282s p: 5.94066 282s Method: ward 282s Method: centroid 282s Method: median 283s Passed. 283s Uniform sampling for the 'binary' metric: 283s Number of sample points: 372 283s Dimension: 706 283s Method: single 283s Metric: binary 284s Passed. 284s Random test 17 of 30 (Gaussian density): 284s Number of sample points: 333 284s Dimension: 4 284s Method: single 284s Metric: euclidean 284s Metric: maximum 284s Metric: manhattan 284s Metric: canberra 284s Metric: minkowski 284s p: 4.28178 284s Method: ward 284s Method: centroid 284s Method: median 284s Passed. 284s Uniform sampling for the 'binary' metric: 284s Number of sample points: 56 284s Dimension: 64 284s Method: single 284s Metric: binary 284s Passed. 284s Random test 18 of 30 (Gaussian density): 284s Number of sample points: 826 284s Dimension: 5 284s Method: single 284s Metric: euclidean 284s Metric: maximum 284s Metric: manhattan 284s Metric: canberra 284s Metric: minkowski 284s p: 9.65386 284s Method: ward 284s Method: centroid 284s Method: median 284s Passed. 284s Uniform sampling for the 'binary' metric: 284s Number of sample points: 227 284s Dimension: 293 284s Method: single 284s Metric: binary 285s Passed. 285s Random test 19 of 30 (Gaussian density): 285s Number of sample points: 677 285s Dimension: 19 285s Method: single 285s Metric: euclidean 285s Metric: maximum 285s Metric: manhattan 285s Metric: canberra 285s Metric: minkowski 285s p: 3.45938 285s Method: ward 285s Method: centroid 286s Method: median 286s Passed. 286s Uniform sampling for the 'binary' metric: 286s Number of sample points: 341 286s Dimension: 435 286s Method: single 286s Metric: binary 286s Passed. 286s Random test 20 of 30 (Gaussian density): 286s Number of sample points: 475 286s Dimension: 8 286s Method: single 286s Metric: euclidean 286s Metric: maximum 286s Metric: manhattan 286s Metric: canberra 286s Metric: minkowski 286s p: 2.91962 287s Method: ward 287s Method: centroid 287s Method: median 287s Passed. 287s Uniform sampling for the 'binary' metric: 287s Number of sample points: 379 287s Dimension: 636 287s Method: single 287s Metric: binary 288s Passed. 288s Random test 21 of 30 (Gaussian density): 288s Number of sample points: 418 288s Dimension: 11 288s Method: single 288s Metric: euclidean 288s Metric: maximum 288s Metric: manhattan 288s Metric: canberra 288s Metric: minkowski 288s p: 5.27478 288s Method: ward 288s Method: centroid 288s Method: median 288s Passed. 288s Uniform sampling for the 'binary' metric: 288s Number of sample points: 94 288s Dimension: 135 288s Method: single 288s Metric: binary 288s Passed. 288s Random test 22 of 30 (Gaussian density): 288s Number of sample points: 481 288s Dimension: 12 288s Method: single 288s Metric: euclidean 288s Metric: maximum 288s Metric: manhattan 288s Metric: canberra 288s Metric: minkowski 288s p: 5.67748 288s Method: ward 288s Method: centroid 288s Method: median 289s Passed. 289s Uniform sampling for the 'binary' metric: 289s Number of sample points: 53 289s Dimension: 75 289s Method: single 289s Metric: binary 289s Passed. 289s Random test 23 of 30 (Gaussian density): 289s Number of sample points: 340 289s Dimension: 17 289s Method: single 289s Metric: euclidean 289s Metric: maximum 289s Metric: manhattan 289s Metric: canberra 289s Metric: minkowski 289s p: 4.40971 289s Method: ward 289s Method: centroid 289s Method: median 289s Passed. 289s Uniform sampling for the 'binary' metric: 289s Number of sample points: 393 289s Dimension: 694 289s Method: single 289s Metric: binary 290s Passed. 290s Random test 24 of 30 (Gaussian density): 290s Number of sample points: 524 290s Dimension: 9 290s Method: single 290s Metric: euclidean 290s Metric: maximum 290s Metric: manhattan 290s Metric: canberra 290s Metric: minkowski 290s p: 8.07965 290s Method: ward 291s Method: centroid 291s Method: median 291s Passed. 291s Uniform sampling for the 'binary' metric: 291s Number of sample points: 394 291s Dimension: 733 291s Method: single 291s Metric: binary 292s Passed. 292s Random test 25 of 30 (Gaussian density): 292s Number of sample points: 436 292s Dimension: 19 292s Method: single 292s Metric: euclidean 292s Metric: maximum 292s Metric: manhattan 292s Metric: canberra 292s Metric: minkowski 292s p: 5.69415 293s Method: ward 293s Method: centroid 293s Method: median 293s Passed. 293s Uniform sampling for the 'binary' metric: 293s Number of sample points: 51 293s Dimension: 70 293s Method: single 293s Metric: binary 293s Passed. 293s Random test 26 of 30 (Gaussian density): 293s Number of sample points: 200 293s Dimension: 17 293s Method: single 293s Metric: euclidean 293s Metric: maximum 293s Metric: manhattan 293s Metric: canberra 293s Metric: minkowski 293s p: 2.54395 293s Method: ward 293s Method: centroid 293s Method: median 293s Passed. 293s Uniform sampling for the 'binary' metric: 293s Number of sample points: 289 293s Dimension: 567 293s Method: single 293s Metric: binary 293s Passed. 293s Random test 27 of 30 (Gaussian density): 293s Number of sample points: 402 293s Dimension: 14 293s Method: single 293s Metric: euclidean 293s Metric: maximum 293s Metric: manhattan 293s Metric: canberra 293s Metric: minkowski 293s p: 2.17657 294s Method: ward 294s Method: centroid 294s Method: median 294s Passed. 294s Uniform sampling for the 'binary' metric: 294s Number of sample points: 98 294s Dimension: 162 294s Method: single 294s Metric: binary 294s Passed. 294s Random test 28 of 30 (Gaussian density): 294s Number of sample points: 489 294s Dimension: 10 294s Method: single 294s Metric: euclidean 294s Metric: maximum 294s Metric: manhattan 294s Metric: canberra 294s Metric: minkowski 294s p: 9.69986 294s Method: ward 294s Method: centroid 294s Method: median 294s Passed. 294s Uniform sampling for the 'binary' metric: 294s Number of sample points: 68 294s Dimension: 113 294s Method: single 294s Metric: binary 294s Passed. 294s Random test 29 of 30 (Gaussian density): 294s Number of sample points: 283 294s Dimension: 16 294s Method: single 294s Metric: euclidean 294s Metric: maximum 294s Metric: manhattan 294s Metric: canberra 294s Metric: minkowski 294s p: 8.12715 294s Method: ward 294s Method: centroid 294s Method: median 294s Passed. 294s Uniform sampling for the 'binary' metric: 294s Number of sample points: 144 294s Dimension: 189 294s Method: single 294s Metric: binary 294s Passed. 294s Random test 30 of 30 (Gaussian density): 294s Number of sample points: 26 294s Dimension: 16 294s Method: single 294s Metric: euclidean 294s Metric: maximum 294s Metric: manhattan 294s Metric: canberra 294s Metric: minkowski 294s p: 7.2718 294s Method: ward 294s Method: centroid 294s Method: median 294s Passed. 294s Uniform sampling for the 'binary' metric: 294s Number of sample points: 62 294s Dimension: 84 294s Method: single 294s Metric: binary 294s Passed. 294s > 294s > cat('Done.\n') 294s Done. 294s > 295s autopkgtest [14:38:20]: test run-unit-test: -----------------------] 299s autopkgtest [14:38:24]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 299s run-unit-test PASS 307s autopkgtest [14:38:32]: test autodep8-python3: preparing testbed 361s autopkgtest [14:39:26]: testbed dpkg architecture: armhf 363s autopkgtest [14:39:28]: testbed apt version: 2.9.8 363s autopkgtest [14:39:28]: @@@@@@@@@@@@@@@@@@@@ test bed setup 371s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 371s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 371s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [16.5 kB] 371s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [962 kB] 372s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [105 kB] 372s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf Packages [104 kB] 372s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf Packages [645 kB] 372s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf Packages [16.9 kB] 372s Fetched 1931 kB in 1s (1498 kB/s) 372s Reading package lists... 387s tee: /proc/self/fd/2: Permission denied 411s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 411s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 411s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 411s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 412s Reading package lists... 412s Reading package lists... 412s Building dependency tree... 412s Reading state information... 413s Calculating upgrade... 413s The following NEW packages will be installed: 413s python3.13-gdbm 413s The following packages will be upgraded: 413s libgnutls30t64 libjson-glib-1.0-0 libjson-glib-1.0-common libpython3-stdlib 413s libutempter0 python3 python3-gdbm python3-minimal 413s 8 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 413s Need to get 1131 kB of archives. 413s After this operation, 95.2 kB of additional disk space will be used. 413s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf python3-minimal armhf 3.12.7-1 [27.4 kB] 414s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf python3 armhf 3.12.7-1 [24.0 kB] 414s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libpython3-stdlib armhf 3.12.7-1 [10.0 kB] 414s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf libgnutls30t64 armhf 3.8.8-2ubuntu1 [955 kB] 414s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf python3.13-gdbm armhf 3.13.0-2 [29.5 kB] 414s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf python3-gdbm armhf 3.12.7-1 [8642 B] 414s Get:7 http://ftpmaster.internal/ubuntu plucky/main armhf libjson-glib-1.0-common all 1.10.0+ds-3 [5586 B] 414s Get:8 http://ftpmaster.internal/ubuntu plucky/main armhf libjson-glib-1.0-0 armhf 1.10.0+ds-3 [61.7 kB] 414s Get:9 http://ftpmaster.internal/ubuntu plucky/main armhf libutempter0 armhf 1.2.1-4 [9062 B] 414s Fetched 1131 kB in 1s (1994 kB/s) 414s (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 ... 59559 files and directories currently installed.) 414s Preparing to unpack .../python3-minimal_3.12.7-1_armhf.deb ... 414s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ... 414s Setting up python3-minimal (3.12.7-1) ... 415s (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 ... 59559 files and directories currently installed.) 415s Preparing to unpack .../python3_3.12.7-1_armhf.deb ... 415s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ... 415s Preparing to unpack .../libpython3-stdlib_3.12.7-1_armhf.deb ... 415s Unpacking libpython3-stdlib:armhf (3.12.7-1) over (3.12.6-0ubuntu1) ... 415s Preparing to unpack .../libgnutls30t64_3.8.8-2ubuntu1_armhf.deb ... 415s Unpacking libgnutls30t64:armhf (3.8.8-2ubuntu1) over (3.8.6-2ubuntu1) ... 415s Setting up libgnutls30t64:armhf (3.8.8-2ubuntu1) ... 415s Selecting previously unselected package python3.13-gdbm. 415s (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 ... 59559 files and directories currently installed.) 415s Preparing to unpack .../python3.13-gdbm_3.13.0-2_armhf.deb ... 415s Unpacking python3.13-gdbm (3.13.0-2) ... 415s Preparing to unpack .../python3-gdbm_3.12.7-1_armhf.deb ... 415s Unpacking python3-gdbm:armhf (3.12.7-1) over (3.12.6-1ubuntu1) ... 415s Preparing to unpack .../libjson-glib-1.0-common_1.10.0+ds-3_all.deb ... 415s Unpacking libjson-glib-1.0-common (1.10.0+ds-3) over (1.10.0+ds-2) ... 415s Preparing to unpack .../libjson-glib-1.0-0_1.10.0+ds-3_armhf.deb ... 415s Unpacking libjson-glib-1.0-0:armhf (1.10.0+ds-3) over (1.10.0+ds-2) ... 415s Preparing to unpack .../libutempter0_1.2.1-4_armhf.deb ... 415s Unpacking libutempter0:armhf (1.2.1-4) over (1.2.1-3build1) ... 415s Setting up libutempter0:armhf (1.2.1-4) ... 415s Setting up libjson-glib-1.0-common (1.10.0+ds-3) ... 415s Setting up python3.13-gdbm (3.13.0-2) ... 415s Setting up libpython3-stdlib:armhf (3.12.7-1) ... 415s Setting up python3 (3.12.7-1) ... 415s Setting up libjson-glib-1.0-0:armhf (1.10.0+ds-3) ... 415s Setting up python3-gdbm:armhf (3.12.7-1) ... 415s Processing triggers for man-db (2.12.1-3) ... 416s Processing triggers for libc-bin (2.40-1ubuntu3) ... 416s Reading package lists... 416s Building dependency tree... 416s Reading state information... 417s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 419s autopkgtest [14:40:24]: rebooting testbed after setup commands that affected boot 526s Reading package lists... 526s Building dependency tree... 526s Reading state information... 526s Starting pkgProblemResolver with broken count: 0 526s Starting 2 pkgProblemResolver with broken count: 0 526s Done 527s The following additional packages will be installed: 527s libblas3 libgfortran5 liblapack3 libpython3.13-minimal libpython3.13-stdlib 527s python3-all python3-fastcluster python3-numpy python3.13 python3.13-minimal 527s Suggested packages: 527s gcc gfortran python-numpy-doc python3-dev python3-pytest python3.13-venv 527s python3.13-doc binfmt-support 527s Recommended packages: 527s python3-scipy 527s The following NEW packages will be installed: 527s autopkgtest-satdep libblas3 libgfortran5 liblapack3 libpython3.13-minimal 527s libpython3.13-stdlib python3-all python3-fastcluster python3-numpy 527s python3.13 python3.13-minimal 527s 0 upgraded, 11 newly installed, 0 to remove and 0 not upgraded. 527s Need to get 11.5 MB/11.5 MB of archives. 527s After this operation, 41.1 MB of additional disk space will be used. 527s Get:1 /tmp/autopkgtest.rzuJUT/2-autopkgtest-satdep.deb autopkgtest-satdep armhf 0 [720 B] 527s Get:2 http://ftpmaster.internal/ubuntu plucky/main armhf libpython3.13-minimal armhf 3.13.0-2 [866 kB] 528s Get:3 http://ftpmaster.internal/ubuntu plucky/main armhf python3.13-minimal armhf 3.13.0-2 [1854 kB] 529s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf libblas3 armhf 3.12.0-3build2 [126 kB] 529s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf libgfortran5 armhf 14.2.0-8ubuntu1 [311 kB] 529s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf liblapack3 armhf 3.12.0-3build2 [2086 kB] 530s Get:7 http://ftpmaster.internal/ubuntu plucky/main armhf libpython3.13-stdlib armhf 3.13.0-2 [1972 kB] 530s Get:8 http://ftpmaster.internal/ubuntu plucky/main armhf python3.13 armhf 3.13.0-2 [719 kB] 530s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf python3-all armhf 3.12.7-1 [890 B] 530s Get:10 http://ftpmaster.internal/ubuntu plucky/main armhf python3-numpy armhf 1:1.26.4+ds-11build1 [3570 kB] 530s Get:11 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-fastcluster armhf 1.2.6-1build1 [39.2 kB] 531s Fetched 11.5 MB in 3s (3480 kB/s) 531s Selecting previously unselected package libpython3.13-minimal:armhf. 531s (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 ... 59566 files and directories currently installed.) 531s Preparing to unpack .../00-libpython3.13-minimal_3.13.0-2_armhf.deb ... 531s Unpacking libpython3.13-minimal:armhf (3.13.0-2) ... 531s Selecting previously unselected package python3.13-minimal. 531s Preparing to unpack .../01-python3.13-minimal_3.13.0-2_armhf.deb ... 531s Unpacking python3.13-minimal (3.13.0-2) ... 531s Selecting previously unselected package libblas3:armhf. 531s Preparing to unpack .../02-libblas3_3.12.0-3build2_armhf.deb ... 531s Unpacking libblas3:armhf (3.12.0-3build2) ... 531s Selecting previously unselected package libgfortran5:armhf. 531s Preparing to unpack .../03-libgfortran5_14.2.0-8ubuntu1_armhf.deb ... 531s Unpacking libgfortran5:armhf (14.2.0-8ubuntu1) ... 531s Selecting previously unselected package liblapack3:armhf. 531s Preparing to unpack .../04-liblapack3_3.12.0-3build2_armhf.deb ... 531s Unpacking liblapack3:armhf (3.12.0-3build2) ... 531s Selecting previously unselected package libpython3.13-stdlib:armhf. 531s Preparing to unpack .../05-libpython3.13-stdlib_3.13.0-2_armhf.deb ... 531s Unpacking libpython3.13-stdlib:armhf (3.13.0-2) ... 531s Selecting previously unselected package python3.13. 531s Preparing to unpack .../06-python3.13_3.13.0-2_armhf.deb ... 531s Unpacking python3.13 (3.13.0-2) ... 531s Selecting previously unselected package python3-all. 531s Preparing to unpack .../07-python3-all_3.12.7-1_armhf.deb ... 531s Unpacking python3-all (3.12.7-1) ... 531s Selecting previously unselected package python3-numpy. 531s Preparing to unpack .../08-python3-numpy_1%3a1.26.4+ds-11build1_armhf.deb ... 531s Unpacking python3-numpy (1:1.26.4+ds-11build1) ... 532s Selecting previously unselected package python3-fastcluster. 532s Preparing to unpack .../09-python3-fastcluster_1.2.6-1build1_armhf.deb ... 532s Unpacking python3-fastcluster (1.2.6-1build1) ... 532s Selecting previously unselected package autopkgtest-satdep. 532s Preparing to unpack .../10-2-autopkgtest-satdep.deb ... 532s Unpacking autopkgtest-satdep (0) ... 532s Setting up libpython3.13-minimal:armhf (3.13.0-2) ... 532s Setting up libblas3:armhf (3.12.0-3build2) ... 532s update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode 532s Setting up libgfortran5:armhf (14.2.0-8ubuntu1) ... 532s Setting up python3.13-minimal (3.13.0-2) ... 533s Setting up libpython3.13-stdlib:armhf (3.13.0-2) ... 533s Setting up liblapack3:armhf (3.12.0-3build2) ... 533s update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode 533s Setting up python3.13 (3.13.0-2) ... 534s Setting up python3-all (3.12.7-1) ... 534s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 538s Setting up python3-fastcluster (1.2.6-1build1) ... 538s Setting up autopkgtest-satdep (0) ... 538s Processing triggers for systemd (256.5-2ubuntu4) ... 538s Processing triggers for man-db (2.12.1-3) ... 538s Processing triggers for libc-bin (2.40-1ubuntu3) ... 556s (Reading database ... 61215 files and directories currently installed.) 556s Removing autopkgtest-satdep (0) ... 571s autopkgtest [14:42:56]: 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 571s autopkgtest [14:42:56]: test autodep8-python3: [----------------------- 573s Testing with python3.13: 573s Traceback (most recent call last): 573s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 573s from . import multiarray 573s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 573s from . import overrides 573s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 573s from numpy.core._multiarray_umath import ( 573s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 573s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 573s 573s During handling of the above exception, another exception occurred: 573s 573s Traceback (most recent call last): 573s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 573s from numpy.__config__ import show as show_config 573s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 573s from numpy.core._multiarray_umath import ( 573s ...<3 lines>... 573s ) 573s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 573s raise ImportError(msg) 573s ImportError: 573s 573s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 573s 573s Importing the numpy C-extensions failed. This error can happen for 573s many reasons, often due to issues with your setup or how NumPy was 573s installed. 573s 573s We have compiled some common reasons and troubleshooting tips at: 573s 573s https://numpy.org/devdocs/user/troubleshooting-importerror.html 573s 573s Please note and check the following: 573s 573s * The Python version is: Python3.13 from "/usr/bin/python3.13" 573s * The NumPy version is: "1.26.4" 573s 573s and make sure that they are the versions you expect. 573s Please carefully study the documentation linked above for further help. 573s 573s Original error was: No module named 'numpy.core._multiarray_umath' 573s 573s 573s The above exception was the direct cause of the following exception: 573s 573s Traceback (most recent call last): 573s File "", line 1, in 573s import fastcluster; print(fastcluster) 573s ^^^^^^^^^^^^^^^^^^ 573s File "/usr/lib/python3/dist-packages/fastcluster.py", line 26, in 573s from numpy import double, empty, array, ndarray, var, cov, dot, expand_dims, \ 573s ceil, sqrt 573s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 573s raise ImportError(msg) from e 573s ImportError: Error importing numpy: you should not try to import numpy from 573s its source directory; please exit the numpy source tree, and relaunch 573s your python interpreter from there. 573s autopkgtest [14:42:58]: test autodep8-python3: -----------------------] 578s autopkgtest [14:43:03]: test autodep8-python3: - - - - - - - - - - results - - - - - - - - - - 578s autodep8-python3 FAIL non-zero exit status 1 582s autopkgtest [14:43:07]: @@@@@@@@@@@@@@@@@@@@ summary 582s run-unit-test PASS 582s autodep8-python3 FAIL non-zero exit status 1