0s autopkgtest [15:58:49]: starting date and time: 2025-03-15 15:58:49+0000 0s autopkgtest [15:58:49]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [15:58:49]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.hzsmt2re/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,radosgw.ps5.canonical.com\n" >> /etc/environment' --apt-pocket=proposed=src:glibc --apt-upgrade r-cran-bdsmatrix --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glibc/2.41-1ubuntu2 -- lxd -r lxd-armhf-10.145.243.160 lxd-armhf-10.145.243.160:autopkgtest/ubuntu/plucky/armhf 23s autopkgtest [15:59:12]: testbed dpkg architecture: armhf 25s autopkgtest [15:59:14]: testbed apt version: 2.9.33 29s autopkgtest [15:59:18]: @@@@@@@@@@@@@@@@@@@@ test bed setup 31s autopkgtest [15:59:20]: testbed release detected to be: None 39s autopkgtest [15:59:28]: updating testbed package index (apt update) 41s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 42s Get:2 http://ftpmaster.internal/ubuntu plucky InRelease [257 kB] 42s Get:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease [126 kB] 42s Get:4 http://ftpmaster.internal/ubuntu plucky-security InRelease [126 kB] 42s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 42s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [379 kB] 43s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [99.7 kB] 43s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf Packages [114 kB] 43s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf c-n-f Metadata [1832 B] 43s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted armhf c-n-f Metadata [116 B] 43s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf Packages [312 kB] 44s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf c-n-f Metadata [11.1 kB] 44s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf Packages [3472 B] 44s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf c-n-f Metadata [240 B] 44s Get:15 http://ftpmaster.internal/ubuntu plucky/main Sources [1394 kB] 45s Get:16 http://ftpmaster.internal/ubuntu plucky/multiverse Sources [299 kB] 45s Get:17 http://ftpmaster.internal/ubuntu plucky/universe Sources [21.0 MB] 68s Get:18 http://ftpmaster.internal/ubuntu plucky/main armhf Packages [1378 kB] 70s Get:19 http://ftpmaster.internal/ubuntu plucky/main armhf c-n-f Metadata [29.4 kB] 70s Get:20 http://ftpmaster.internal/ubuntu plucky/restricted armhf c-n-f Metadata [108 B] 70s Get:21 http://ftpmaster.internal/ubuntu plucky/universe armhf Packages [15.1 MB] 89s Get:22 http://ftpmaster.internal/ubuntu plucky/multiverse armhf Packages [172 kB] 90s Fetched 41.0 MB in 49s (839 kB/s) 91s Reading package lists... 97s autopkgtest [16:00:26]: upgrading testbed (apt dist-upgrade and autopurge) 99s Reading package lists... 99s Building dependency tree... 99s Reading state information... 100s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 100s Starting 2 pkgProblemResolver with broken count: 0 100s Done 101s Entering ResolveByKeep 101s 101s Calculating upgrade... 102s The following packages will be upgraded: 102s libc-bin libc6 locales pinentry-curses python3-jinja2 sos strace 102s 7 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 102s Need to get 8683 kB of archives. 102s After this operation, 23.6 kB of additional disk space will be used. 102s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libc6 armhf 2.41-1ubuntu2 [2932 kB] 106s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libc-bin armhf 2.41-1ubuntu2 [545 kB] 107s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf locales all 2.41-1ubuntu2 [4246 kB] 111s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf strace armhf 6.13+ds-1ubuntu1 [445 kB] 112s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf pinentry-curses armhf 1.3.1-2ubuntu3 [40.6 kB] 112s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 112s Get:7 http://ftpmaster.internal/ubuntu plucky/main armhf sos all 4.9.0-5 [365 kB] 113s Preconfiguring packages ... 114s Fetched 8683 kB in 11s (808 kB/s) 114s (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 ... 64655 files and directories currently installed.) 114s Preparing to unpack .../libc6_2.41-1ubuntu2_armhf.deb ... 114s Unpacking libc6:armhf (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 114s Setting up libc6:armhf (2.41-1ubuntu2) ... 114s (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 ... 64655 files and directories currently installed.) 114s Preparing to unpack .../libc-bin_2.41-1ubuntu2_armhf.deb ... 114s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 114s Setting up libc-bin (2.41-1ubuntu2) ... 115s (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 ... 64655 files and directories currently installed.) 115s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 115s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 115s Preparing to unpack .../strace_6.13+ds-1ubuntu1_armhf.deb ... 115s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 115s Preparing to unpack .../pinentry-curses_1.3.1-2ubuntu3_armhf.deb ... 115s Unpacking pinentry-curses (1.3.1-2ubuntu3) over (1.3.1-2ubuntu2) ... 115s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 115s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 115s Preparing to unpack .../archives/sos_4.9.0-5_all.deb ... 115s Unpacking sos (4.9.0-5) over (4.9.0-4) ... 116s Setting up sos (4.9.0-5) ... 117s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 117s Setting up locales (2.41-1ubuntu2) ... 117s Generating locales (this might take a while)... 119s en_US.UTF-8... done 119s Generation complete. 119s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 120s Setting up strace (6.13+ds-1ubuntu1) ... 120s Processing triggers for man-db (2.13.0-1) ... 121s Processing triggers for systemd (257.3-1ubuntu3) ... 123s Reading package lists... 124s Building dependency tree... 124s Reading state information... 124s Starting pkgProblemResolver with broken count: 0 124s Starting 2 pkgProblemResolver with broken count: 0 124s Done 125s Solving dependencies... 125s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 127s autopkgtest [16:00:56]: rebooting testbed after setup commands that affected boot 167s autopkgtest [16:01:36]: testbed running kernel: Linux 6.8.0-52-generic #53~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Wed Jan 15 18:10:51 UTC 2 199s autopkgtest [16:02:08]: @@@@@@@@@@@@@@@@@@@@ apt-source r-cran-bdsmatrix 209s Get:1 http://ftpmaster.internal/ubuntu plucky/universe r-cran-bdsmatrix 1.3-7-1 (dsc) [2072 B] 209s Get:2 http://ftpmaster.internal/ubuntu plucky/universe r-cran-bdsmatrix 1.3-7-1 (tar) [48.0 kB] 209s Get:3 http://ftpmaster.internal/ubuntu plucky/universe r-cran-bdsmatrix 1.3-7-1 (diff) [2520 B] 209s gpgv: Signature made Tue Mar 12 13:10:28 2024 UTC 209s gpgv: using RSA key 53951D95272E0C5B82BE8C4A2CECE9350ECEBE4A 209s gpgv: Can't check signature: No public key 209s dpkg-source: warning: cannot verify inline signature for ./r-cran-bdsmatrix_1.3-7-1.dsc: no acceptable signature found 209s autopkgtest [16:02:18]: testing package r-cran-bdsmatrix version 1.3-7-1 212s autopkgtest [16:02:21]: build not needed 215s autopkgtest [16:02:24]: test run-unit-test: preparing testbed 217s Reading package lists... 217s Building dependency tree... 217s Reading state information... 217s Starting pkgProblemResolver with broken count: 0 218s Starting 2 pkgProblemResolver with broken count: 0 218s Done 218s The following NEW packages will be installed: 218s fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono libblas3 218s libcairo2 libdatrie1 libdeflate0 libfontconfig1 libfreetype6 libgfortran5 218s libgomp1 libgraphite2-3 libharfbuzz0b libice6 libjbig0 libjpeg-turbo8 218s libjpeg8 liblapack3 liblerc4 libpango-1.0-0 libpangocairo-1.0-0 218s libpangoft2-1.0-0 libpaper-utils libpaper2 libpixman-1-0 libsharpyuv0 libsm6 218s libtcl8.6 libthai-data libthai0 libtiff6 libtk8.6 libwebp7 libxcb-render0 218s libxcb-shm0 libxft2 libxrender1 libxss1 libxt6t64 r-base-core 218s r-cran-bdsmatrix unzip x11-common xdg-utils zip 219s 0 upgraded, 46 newly installed, 0 to remove and 0 not upgraded. 219s Need to get 37.9 MB of archives. 219s After this operation, 70.9 MB of additional disk space will be used. 219s Get:1 http://ftpmaster.internal/ubuntu plucky/main armhf libfreetype6 armhf 2.13.3+dfsg-1 [330 kB] 219s Get:2 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-dejavu-mono all 2.37-8 [502 kB] 220s Get:3 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-dejavu-core all 2.37-8 [835 kB] 221s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf fontconfig-config armhf 2.15.0-2ubuntu1 [37.5 kB] 221s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf libfontconfig1 armhf 2.15.0-2ubuntu1 [114 kB] 222s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf fontconfig armhf 2.15.0-2ubuntu1 [190 kB] 222s Get:7 http://ftpmaster.internal/ubuntu plucky/main armhf libblas3 armhf 3.12.1-2 [132 kB] 222s Get:8 http://ftpmaster.internal/ubuntu plucky/main armhf libpixman-1-0 armhf 0.44.0-3 [183 kB] 222s Get:9 http://ftpmaster.internal/ubuntu plucky/main armhf libxcb-render0 armhf 1.17.0-2 [15.3 kB] 222s Get:10 http://ftpmaster.internal/ubuntu plucky/main armhf libxcb-shm0 armhf 1.17.0-2 [5774 B] 222s Get:11 http://ftpmaster.internal/ubuntu plucky/main armhf libxrender1 armhf 1:0.9.10-1.1build1 [16.0 kB] 223s Get:12 http://ftpmaster.internal/ubuntu plucky/main armhf libcairo2 armhf 1.18.2-2 [484 kB] 223s Get:13 http://ftpmaster.internal/ubuntu plucky/main armhf libdatrie1 armhf 0.2.13-3build1 [15.7 kB] 223s Get:14 http://ftpmaster.internal/ubuntu plucky/main armhf libdeflate0 armhf 1.23-1 [38.5 kB] 223s Get:15 http://ftpmaster.internal/ubuntu plucky/main armhf libgfortran5 armhf 15-20250222-0ubuntu1 [330 kB] 224s Get:16 http://ftpmaster.internal/ubuntu plucky/main armhf libgomp1 armhf 15-20250222-0ubuntu1 [128 kB] 224s Get:17 http://ftpmaster.internal/ubuntu plucky/main armhf libgraphite2-3 armhf 1.3.14-2ubuntu1 [64.8 kB] 224s Get:18 http://ftpmaster.internal/ubuntu plucky/main armhf libharfbuzz0b armhf 10.2.0-1 [464 kB] 225s Get:19 http://ftpmaster.internal/ubuntu plucky/main armhf x11-common all 1:7.7+23ubuntu3 [21.7 kB] 225s Get:20 http://ftpmaster.internal/ubuntu plucky/main armhf libice6 armhf 2:1.1.1-1 [36.5 kB] 225s Get:21 http://ftpmaster.internal/ubuntu plucky/main armhf libjpeg-turbo8 armhf 2.1.5-3ubuntu2 [127 kB] 226s Get:22 http://ftpmaster.internal/ubuntu plucky/main armhf libjpeg8 armhf 8c-2ubuntu11 [2148 B] 226s Get:23 http://ftpmaster.internal/ubuntu plucky/main armhf liblapack3 armhf 3.12.1-2 [2091 kB] 229s Get:24 http://ftpmaster.internal/ubuntu plucky/main armhf liblerc4 armhf 4.0.0+ds-5ubuntu1 [160 kB] 229s Get:25 http://ftpmaster.internal/ubuntu plucky/main armhf libthai-data all 0.1.29-2build1 [158 kB] 230s Get:26 http://ftpmaster.internal/ubuntu plucky/main armhf libthai0 armhf 0.1.29-2build1 [15.2 kB] 230s Get:27 http://ftpmaster.internal/ubuntu plucky/main armhf libpango-1.0-0 armhf 1.56.2-1 [216 kB] 230s Get:28 http://ftpmaster.internal/ubuntu plucky/main armhf libpangoft2-1.0-0 armhf 1.56.2-1 [43.6 kB] 230s Get:29 http://ftpmaster.internal/ubuntu plucky/main armhf libpangocairo-1.0-0 armhf 1.56.2-1 [25.1 kB] 230s Get:30 http://ftpmaster.internal/ubuntu plucky/main armhf libpaper2 armhf 2.2.5-0.3 [16.3 kB] 230s Get:31 http://ftpmaster.internal/ubuntu plucky/main armhf libpaper-utils armhf 2.2.5-0.3 [14.2 kB] 230s Get:32 http://ftpmaster.internal/ubuntu plucky/main armhf libsharpyuv0 armhf 1.5.0-0.1 [16.4 kB] 230s Get:33 http://ftpmaster.internal/ubuntu plucky/main armhf libsm6 armhf 2:1.2.4-1 [15.1 kB] 230s Get:34 http://ftpmaster.internal/ubuntu plucky/main armhf libtcl8.6 armhf 8.6.16+dfsg-1 [909 kB] 232s Get:35 http://ftpmaster.internal/ubuntu plucky/main armhf libjbig0 armhf 2.1-6.1ubuntu2 [24.9 kB] 232s Get:36 http://ftpmaster.internal/ubuntu plucky/main armhf libwebp7 armhf 1.5.0-0.1 [188 kB] 232s Get:37 http://ftpmaster.internal/ubuntu plucky/main armhf libtiff6 armhf 4.5.1+git230720-4ubuntu4 [179 kB] 232s Get:38 http://ftpmaster.internal/ubuntu plucky/main armhf libxft2 armhf 2.3.6-1build1 [37.4 kB] 232s Get:39 http://ftpmaster.internal/ubuntu plucky/main armhf libxss1 armhf 1:1.2.3-1build3 [6500 B] 232s Get:40 http://ftpmaster.internal/ubuntu plucky/main armhf libtk8.6 armhf 8.6.16-1 [686 kB] 234s Get:41 http://ftpmaster.internal/ubuntu plucky/main armhf libxt6t64 armhf 1:1.2.1-1.2build1 [145 kB] 234s Get:42 http://ftpmaster.internal/ubuntu plucky/main armhf zip armhf 3.0-14ubuntu2 [164 kB] 234s Get:43 http://ftpmaster.internal/ubuntu plucky/main armhf unzip armhf 6.0-28ubuntu6 [167 kB] 234s Get:44 http://ftpmaster.internal/ubuntu plucky/main armhf xdg-utils all 1.2.1-2ubuntu1 [66.0 kB] 235s Get:45 http://ftpmaster.internal/ubuntu plucky/universe armhf r-base-core armhf 4.4.3-1 [28.2 MB] 280s Get:46 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-bdsmatrix armhf 1.3-7-1 [298 kB] 281s Preconfiguring packages ... 281s Fetched 37.9 MB in 1min 2s (608 kB/s) 281s Selecting previously unselected package libfreetype6:armhf. 281s (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 ... 64655 files and directories currently installed.) 281s Preparing to unpack .../00-libfreetype6_2.13.3+dfsg-1_armhf.deb ... 281s Unpacking libfreetype6:armhf (2.13.3+dfsg-1) ... 281s Selecting previously unselected package fonts-dejavu-mono. 281s Preparing to unpack .../01-fonts-dejavu-mono_2.37-8_all.deb ... 281s Unpacking fonts-dejavu-mono (2.37-8) ... 281s Selecting previously unselected package fonts-dejavu-core. 281s Preparing to unpack .../02-fonts-dejavu-core_2.37-8_all.deb ... 281s Unpacking fonts-dejavu-core (2.37-8) ... 281s Selecting previously unselected package fontconfig-config. 281s Preparing to unpack .../03-fontconfig-config_2.15.0-2ubuntu1_armhf.deb ... 282s Unpacking fontconfig-config (2.15.0-2ubuntu1) ... 282s Selecting previously unselected package libfontconfig1:armhf. 282s Preparing to unpack .../04-libfontconfig1_2.15.0-2ubuntu1_armhf.deb ... 282s Unpacking libfontconfig1:armhf (2.15.0-2ubuntu1) ... 282s Selecting previously unselected package fontconfig. 282s Preparing to unpack .../05-fontconfig_2.15.0-2ubuntu1_armhf.deb ... 282s Unpacking fontconfig (2.15.0-2ubuntu1) ... 282s Selecting previously unselected package libblas3:armhf. 282s Preparing to unpack .../06-libblas3_3.12.1-2_armhf.deb ... 282s Unpacking libblas3:armhf (3.12.1-2) ... 282s Selecting previously unselected package libpixman-1-0:armhf. 282s Preparing to unpack .../07-libpixman-1-0_0.44.0-3_armhf.deb ... 282s Unpacking libpixman-1-0:armhf (0.44.0-3) ... 282s Selecting previously unselected package libxcb-render0:armhf. 282s Preparing to unpack .../08-libxcb-render0_1.17.0-2_armhf.deb ... 282s Unpacking libxcb-render0:armhf (1.17.0-2) ... 282s Selecting previously unselected package libxcb-shm0:armhf. 282s Preparing to unpack .../09-libxcb-shm0_1.17.0-2_armhf.deb ... 282s Unpacking libxcb-shm0:armhf (1.17.0-2) ... 282s Selecting previously unselected package libxrender1:armhf. 282s Preparing to unpack .../10-libxrender1_1%3a0.9.10-1.1build1_armhf.deb ... 282s Unpacking libxrender1:armhf (1:0.9.10-1.1build1) ... 282s Selecting previously unselected package libcairo2:armhf. 282s Preparing to unpack .../11-libcairo2_1.18.2-2_armhf.deb ... 282s Unpacking libcairo2:armhf (1.18.2-2) ... 282s Selecting previously unselected package libdatrie1:armhf. 282s Preparing to unpack .../12-libdatrie1_0.2.13-3build1_armhf.deb ... 282s Unpacking libdatrie1:armhf (0.2.13-3build1) ... 282s Selecting previously unselected package libdeflate0:armhf. 282s Preparing to unpack .../13-libdeflate0_1.23-1_armhf.deb ... 282s Unpacking libdeflate0:armhf (1.23-1) ... 282s Selecting previously unselected package libgfortran5:armhf. 282s Preparing to unpack .../14-libgfortran5_15-20250222-0ubuntu1_armhf.deb ... 282s Unpacking libgfortran5:armhf (15-20250222-0ubuntu1) ... 282s Selecting previously unselected package libgomp1:armhf. 282s Preparing to unpack .../15-libgomp1_15-20250222-0ubuntu1_armhf.deb ... 282s Unpacking libgomp1:armhf (15-20250222-0ubuntu1) ... 282s Selecting previously unselected package libgraphite2-3:armhf. 282s Preparing to unpack .../16-libgraphite2-3_1.3.14-2ubuntu1_armhf.deb ... 282s Unpacking libgraphite2-3:armhf (1.3.14-2ubuntu1) ... 282s Selecting previously unselected package libharfbuzz0b:armhf. 282s Preparing to unpack .../17-libharfbuzz0b_10.2.0-1_armhf.deb ... 282s Unpacking libharfbuzz0b:armhf (10.2.0-1) ... 282s Selecting previously unselected package x11-common. 282s Preparing to unpack .../18-x11-common_1%3a7.7+23ubuntu3_all.deb ... 282s Unpacking x11-common (1:7.7+23ubuntu3) ... 282s Selecting previously unselected package libice6:armhf. 282s Preparing to unpack .../19-libice6_2%3a1.1.1-1_armhf.deb ... 282s Unpacking libice6:armhf (2:1.1.1-1) ... 282s Selecting previously unselected package libjpeg-turbo8:armhf. 282s Preparing to unpack .../20-libjpeg-turbo8_2.1.5-3ubuntu2_armhf.deb ... 282s Unpacking libjpeg-turbo8:armhf (2.1.5-3ubuntu2) ... 282s Selecting previously unselected package libjpeg8:armhf. 282s Preparing to unpack .../21-libjpeg8_8c-2ubuntu11_armhf.deb ... 282s Unpacking libjpeg8:armhf (8c-2ubuntu11) ... 282s Selecting previously unselected package liblapack3:armhf. 282s Preparing to unpack .../22-liblapack3_3.12.1-2_armhf.deb ... 282s Unpacking liblapack3:armhf (3.12.1-2) ... 282s Selecting previously unselected package liblerc4:armhf. 282s Preparing to unpack .../23-liblerc4_4.0.0+ds-5ubuntu1_armhf.deb ... 282s Unpacking liblerc4:armhf (4.0.0+ds-5ubuntu1) ... 282s Selecting previously unselected package libthai-data. 282s Preparing to unpack .../24-libthai-data_0.1.29-2build1_all.deb ... 282s Unpacking libthai-data (0.1.29-2build1) ... 282s Selecting previously unselected package libthai0:armhf. 282s Preparing to unpack .../25-libthai0_0.1.29-2build1_armhf.deb ... 282s Unpacking libthai0:armhf (0.1.29-2build1) ... 282s Selecting previously unselected package libpango-1.0-0:armhf. 282s Preparing to unpack .../26-libpango-1.0-0_1.56.2-1_armhf.deb ... 282s Unpacking libpango-1.0-0:armhf (1.56.2-1) ... 282s Selecting previously unselected package libpangoft2-1.0-0:armhf. 282s Preparing to unpack .../27-libpangoft2-1.0-0_1.56.2-1_armhf.deb ... 282s Unpacking libpangoft2-1.0-0:armhf (1.56.2-1) ... 282s Selecting previously unselected package libpangocairo-1.0-0:armhf. 283s Preparing to unpack .../28-libpangocairo-1.0-0_1.56.2-1_armhf.deb ... 283s Unpacking libpangocairo-1.0-0:armhf (1.56.2-1) ... 283s Selecting previously unselected package libpaper2:armhf. 283s Preparing to unpack .../29-libpaper2_2.2.5-0.3_armhf.deb ... 283s Unpacking libpaper2:armhf (2.2.5-0.3) ... 283s Selecting previously unselected package libpaper-utils. 283s Preparing to unpack .../30-libpaper-utils_2.2.5-0.3_armhf.deb ... 283s Unpacking libpaper-utils (2.2.5-0.3) ... 283s Selecting previously unselected package libsharpyuv0:armhf. 283s Preparing to unpack .../31-libsharpyuv0_1.5.0-0.1_armhf.deb ... 283s Unpacking libsharpyuv0:armhf (1.5.0-0.1) ... 283s Selecting previously unselected package libsm6:armhf. 283s Preparing to unpack .../32-libsm6_2%3a1.2.4-1_armhf.deb ... 283s Unpacking libsm6:armhf (2:1.2.4-1) ... 283s Selecting previously unselected package libtcl8.6:armhf. 283s Preparing to unpack .../33-libtcl8.6_8.6.16+dfsg-1_armhf.deb ... 283s Unpacking libtcl8.6:armhf (8.6.16+dfsg-1) ... 283s Selecting previously unselected package libjbig0:armhf. 283s Preparing to unpack .../34-libjbig0_2.1-6.1ubuntu2_armhf.deb ... 283s 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(2.41-1ubuntu2) ... 287s Processing triggers for man-db (2.13.0-1) ... 295s autopkgtest [16:03:44]: test run-unit-test: [----------------------- 297s BEGIN TEST backsolvetest.R 297s 297s R version 4.4.3 (2025-02-28) -- "Trophy Case" 297s Copyright (C) 2025 The R Foundation for Statistical Computing 297s Platform: arm-unknown-linux-gnueabihf (32-bit) 297s 297s R is free software and comes with ABSOLUTELY NO WARRANTY. 297s You are welcome to redistribute it under certain conditions. 297s Type 'license()' or 'licence()' for distribution details. 297s 297s R is a collaborative project with many contributors. 297s Type 'contributors()' for more information and 297s 'citation()' on how to cite R or R packages in publications. 297s 297s Type 'demo()' for some demos, 'help()' for on-line help, or 297s 'help.start()' for an HTML browser interface to help. 297s Type 'q()' to quit R. 297s 297s > library(bdsmatrix) 297s 297s Attaching package: 'bdsmatrix' 297s 297s The following object is masked from 'package:base': 297s 297s backsolve 297s 297s > # 297s > # A test of the backsolve function 297s > # 297s > aeq <- function(x,y) all.equal(as.vector(x), as.vector(y)) 297s > 297s > tmat <- matrix(rep(1:5,5), 5, 5) 297s > tmat <- tmat + t(tmat) 297s > diag(tmat) <- diag(tmat) + 10 297s > 297s > gt <- gchol(tmat) 297s > g1 <- as.matrix(gt) 297s > gd <- diag(sqrt(diag(gt))) 297s > gc <- gd %*% t(g1) #usual cholesky form 297s > 297s > xmat <- cbind(1:5, 11:15) 297s > 297s > s1 <- backsolve(gt, xmat, upper=TRUE) #the default 297s > aeq(gd %*% t(g1) %*% s1, xmat) 297s [1] TRUE 297s > all.equal(s1, backsolve(gc, xmat)) 297s [1] TRUE 297s > 297s > s2 <- backsolve(gt, xmat, upper=FALSE) 297s > aeq(g1 %*% gd %*% s2, xmat) 297s [1] TRUE 297s > all.equal(backsolve(gt,xmat, upper=F), backsolve(t(gc),xmat, upper=F)) 297s [1] TRUE 297s > 297s > 297s > # Now for bdsmatrix objects 297s > tmat <- bdsmatrix(c(3,2,2,4), 297s + c(22,1,2,21,3,20,19,4,18,17,5,16,15,6,7, 8,14,9,10,13,11,12), 297s + matrix(c(1,0,1,1,0,0,1,1,0,1,0,10,0, 297s + 0,1,1,0,1,1,0,1,1,0,1,0,10), ncol=2)) 297s > dimnames(tmat) <- list(NULL, letters[1:13]) 297s > smat <- as.matrix(tmat) 297s > 297s > gt <- gchol(tmat) 297s > gs <- gchol(smat) 297s > 297s > xmat <- cbind(1:13, 1:13*2 + 3) 297s > 297s > s1 <- backsolve(gt, xmat) 297s > s2 <- backsolve(gs, xmat) 297s > s3 <- backsolve(gt, xmat, upper=FALSE) 297s > s4 <- backsolve(gs, xmat, upper=FALSE) 297s > 297s > aeq(s1, s2) 297s [1] TRUE 297s > aeq(s3, s4) 297s [1] TRUE 297s > 297s > g1 <- as.matrix(gt) 297s > gd <- diag(sqrt(diag(gt))) 297s > aeq(gd %*% t(g1) %*% s1, xmat) 297s [1] TRUE 297s > aeq(g1 %*% gd %*% s3, xmat) 297s [1] TRUE 297s > 297s BEGIN TEST bdstest.R 297s 297s R version 4.4.3 (2025-02-28) -- "Trophy Case" 297s Copyright (C) 2025 The R Foundation for Statistical Computing 297s Platform: arm-unknown-linux-gnueabihf (32-bit) 297s 297s R is free software and comes with ABSOLUTELY NO WARRANTY. 297s You are welcome to redistribute it under certain conditions. 297s Type 'license()' or 'licence()' for distribution details. 297s 297s R is a collaborative project with many contributors. 297s Type 'contributors()' for more information and 297s 'citation()' on how to cite R or R packages in publications. 297s 297s Type 'demo()' for some demos, 'help()' for on-line help, or 297s 'help.start()' for an HTML browser interface to help. 297s Type 'q()' to quit R. 297s 298s > # 298s > # Test out math aspects 298s > # 298s > library(bdsmatrix) 298s 298s Attaching package: 'bdsmatrix' 298s 298s The following object is masked from 'package:base': 298s 298s backsolve 298s 298s > aeq <- function(x,y) all.equal(as.vector(x), as.vector(y)) 298s > 298s > tmat <- bdsmatrix(c(3,2,2,4), 298s + c(22,1,2,21,3,20,19,4,18,17,5,16,15,6,7, 8,14,9,10,13,11,12), 298s + matrix(c(1,0,1,1,0,0,1,1,0,1,0,10,0, 298s + 0,1,1,0,1,1,0,1,1,0,1,0,10), ncol=2)) 298s > dimnames(tmat) <- list(NULL, letters[1:13]) 298s > 298s > smat <- as.matrix(tmat) 298s > 298s > aeq(smat+2.1, as.matrix(tmat+2.1)) 298s [1] TRUE 298s > aeq(smat/2.1, as.matrix(tmat/2.1)) 298s [1] TRUE 298s > aeq(smat-2.1, as.matrix(tmat-2.1)) 298s [1] TRUE 298s > aeq(smat*2.1, as.matrix(tmat*2.1)) 298s [1] TRUE 298s > aeq(round(smat,1), as.matrix(round(tmat,1))) 298s [1] TRUE 298s > aeq(exp(smat), as.matrix(exp(tmat))) 298s [1] TRUE 298s > 298s > aeq(sum(smat), sum(tmat)) 298s [1] TRUE 298s > aeq(prod(smat), prod(tmat)) 298s [1] TRUE 298s > aeq(sum(smat+3), sum(tmat+3)) 298s [1] TRUE 298s > aeq(prod(smat+2), prod(tmat+2)) 298s [1] TRUE 298s > aeq(range(smat), range(tmat)) 298s [1] TRUE 298s > aeq(max(smat), max(tmat)) 298s [1] TRUE 298s > aeq(min(smat), min(tmat)) 298s [1] TRUE 298s > 298s > aeq(smat+1:13, tmat+1:13) 298s [1] TRUE 298s > aeq(smat+1:13, 1:13 +tmat ) 298s [1] TRUE 298s > aeq(smat+tmat, 2*smat) 298s [1] TRUE 298s > all.equal(tmat+tmat, 2*tmat) 298s [1] TRUE 298s > 298s > aeq(sort(unique(c(smat))), sort(unique(tmat))) 298s [1] TRUE 298s > 298s > # 298s > # check out the alternate input style, with full blocks 298s > # 298s > rmat <- bdsmatrix(c(3,2,2,4), 298s + c(22,1,2,1,21,3,2,3,20, 19,4,4,18, 17,5,5,16, 298s + 15,6,7,8,6,14,9,10,7,9,13,11,8,10,11,12), 298s + matrix(c(1,0,1,1,0,0,1,1,0,1,0,10,0, 298s + 0,1,1,0,1,1,0,1,1,0,1,0,10), ncol=2), 298s + dimnames=list(NULL, letters[1:13])) 298s > all.equal(rmat, tmat) 298s [1] TRUE 298s > 298s > 298s > # Do some subscripting 298s > zz <- c(1,2,7,8,9,11) 298s > aeq(smat[zz,zz], as.matrix(tmat[zz,zz])) 298s [1] TRUE 298s > 298s > all.equal(smat[zz, 8:13], tmat[zz, 8:13]) # both are matrices 298s [1] TRUE 298s > 298s > # Diagonals 298s > aeq(diag(smat), diag(tmat)) 298s [1] TRUE 298s > zz <- diag(smat) 298s > diag(smat) <- zz*2 298s > diag(tmat) <- zz*2 298s > all.equal(smat, as.matrix(tmat)) 298s [1] TRUE 298s > 298s BEGIN TEST chtest.R 298s 298s R version 4.4.3 (2025-02-28) -- "Trophy Case" 298s Copyright (C) 2025 The R Foundation for Statistical Computing 298s Platform: arm-unknown-linux-gnueabihf (32-bit) 298s 298s R is free software and comes with ABSOLUTELY NO WARRANTY. 298s You are welcome to redistribute it under certain conditions. 298s Type 'license()' or 'licence()' for distribution details. 298s 298s R is a collaborative project with many contributors. 298s Type 'contributors()' for more information and 298s 'citation()' on how to cite R or R packages in publications. 298s 298s Type 'demo()' for some demos, 'help()' for on-line help, or 298s 'help.start()' for an HTML browser interface to help. 298s Type 'q()' to quit R. 298s 298s > # 298s > # Test out the Cholesky 298s > # 298s > library(bdsmatrix) 298s 298s Attaching package: 'bdsmatrix' 298s 298s The following object is masked from 'package:base': 298s 298s backsolve 298s 298s > aeq <- function(x,y) all.equal(as.vector(x), as.vector(y)) 298s > 298s > tmat <- bdsmatrix(c(3,2,2,4), 298s + c(22,1,2,21,3,20,19,4,18,17,5,16,15,6,7, 8,14,9,10,13,11,12), 298s + matrix(c(1,0,1,1,0,0,1,1,0,1,0,10,0, 298s + 0,1,1,0,1,1,0,1,1,0,1,0,10), ncol=2)) 298s > dimnames(tmat) <- list(NULL, letters[1:13]) 298s > smat <- as.matrix(tmat) 298s > yy <- c(30,35,42,56,34,45,32,37,78,56,40,52,39) 298s > 298s > aeq(diag(tmat), diag(smat)) 298s [1] TRUE 298s > zz <- seq(1,13,2) 298s > aeq(as.matrix(tmat[zz,zz]), smat[zz,zz]) 298s [1] TRUE 298s > 298s > ch0 <- chol(smat) 298s > ch1 <- gchol(smat) 298s > ch2 <- gchol(tmat) 298s > # The gchol routines use the composition LDL', where L is lower triangular 298s > # with a diagonal of 1's, and D is diagonal. chol() uses U'U where U is 298s > # upper trangular. 298s > # The as.matrix function returns L and the diag function returns D. 298s > # Convert and compare 298s > aeq(diag(ch1), diag(ch2)) 298s [1] TRUE 298s > temp <- as.matrix(ch2) 298s > aeq(temp, as.matrix(ch1)) 298s [1] TRUE 298s > temp3 <- temp %*% diag(sqrt(diag(ch2))) 298s > aeq(temp3, t(ch0)) 298s [1] TRUE 298s > 298s > zz0 <- solve(smat, yy) 298s > zz1 <- solve(ch1, yy) 298s > zz2 <- solve(tmat, yy) 298s > aeq(zz1, zz2) 298s [1] TRUE 298s > aeq(zz0, zz1) 298s [1] TRUE 298s > 298s > 298s BEGIN TEST chtest2.R 298s 298s R version 4.4.3 (2025-02-28) -- "Trophy Case" 298s Copyright (C) 2025 The R Foundation for Statistical Computing 298s Platform: arm-unknown-linux-gnueabihf (32-bit) 298s 298s R is free software and comes with ABSOLUTELY NO WARRANTY. 298s You are welcome to redistribute it under certain conditions. 298s Type 'license()' or 'licence()' for distribution details. 298s 298s R is a collaborative project with many contributors. 298s Type 'contributors()' for more information and 298s 'citation()' on how to cite R or R packages in publications. 298s 298s Type 'demo()' for some demos, 'help()' for on-line help, or 298s 'help.start()' for an HTML browser interface to help. 298s Type 'q()' to quit R. 298s 298s > # 298s > # Inverse of the matrix: 298s > # 298s > library(bdsmatrix) 299s 299s Attaching package: 'bdsmatrix' 299s 299s The following object is masked from 'package:base': 299s 299s backsolve 299s 299s > aeq <- function(x,y) all.equal(as.vector(x), as.vector(y)) 299s > 299s > tmat <- bdsmatrix(c(3,2,2,4), 299s + c(22,1,2,21,3,20,19,4,18,17,5,16,15,6,7, 8,14,9,10,13,11,12), 299s + matrix(c(1,0,1,1,0,0,1,1,0,1,0,10,0, 299s + 0,1,1,0,1,1,0,1,1,0,1,0,10), ncol=2)) 299s > dimnames(tmat) <- list(NULL, letters[1:13]) 299s > 299s > smat <- as.matrix(tmat) 299s > 299s > inv1 <- solve(smat) 299s > inv2 <- as.matrix(solve(tmat)) # the result is a full, non-sparse matrix 299s > aeq(inv1, inv2) 299s [1] TRUE 299s > 299s > inv3 <- solve(gchol(tmat)) #sparse version, not all parts will be there 299s > inherits(inv3, 'bdsmatrix') #This should be true 299s [1] TRUE 299s > aeq(inv3@blocksize, tmat@blocksize) # Should be the same shape at tmat 299s [1] TRUE 299s > inv3 <- as.matrix(inv3) # What is returned should be correct 299s > aeq(inv1[1:3,1:3], inv3[1:3, 1:3]) 299s [1] TRUE 299s > aeq(inv1[4:5,4:5], inv3[4:5, 4:5]) 299s [1] TRUE 299s > aeq(inv1[6:7,6:7], inv3[6:7, 6:7]) 299s [1] TRUE 299s > aeq(inv1[8:11,8:11], inv3[8:11, 8:11]) 299s [1] TRUE 299s > aeq(inv1[,12:13], inv3[, 12:13]) # and rmat the same too 299s [1] TRUE 299s > 299s BEGIN TEST corner.R 299s 299s R version 4.4.3 (2025-02-28) -- "Trophy Case" 299s Copyright (C) 2025 The R Foundation for Statistical Computing 299s Platform: arm-unknown-linux-gnueabihf (32-bit) 299s 299s R is free software and comes with ABSOLUTELY NO WARRANTY. 299s You are welcome to redistribute it under certain conditions. 299s Type 'license()' or 'licence()' for distribution details. 299s 299s R is a collaborative project with many contributors. 299s Type 'contributors()' for more information and 299s 'citation()' on how to cite R or R packages in publications. 299s 299s Type 'demo()' for some demos, 'help()' for on-line help, or 299s 'help.start()' for an HTML browser interface to help. 299s Type 'q()' to quit R. 299s 299s > # 299s > # Test out the behavior of a 1x1 bds corner. 299s > # Actually, the problem that motivated this occurred whenever the 299s > # rmat portion was larger than the block diagonal portion. 299s > # 299s > library(bdsmatrix) 299s 299s Attaching package: 'bdsmatrix' 299s 299s The following object is masked from 'package:base': 299s 299s backsolve 299s 299s > test1 <- bdsmatrix(blocksize=1, blocks=33, 299s + rmat=matrix(c(17,33,7,-1, -7,7,48,-7, 299s + 1, -1, -7,4),4)) 299s > 299s > test2 <- bdsmatrix(blocksize=2, blocks=c(33,17,33), 299s + rmat=matrix(c( -7,7,48,-7, 1, -1, -7,4),4)) 299s > all.equal(as.matrix(test1), as.matrix(test2)) 299s [1] TRUE 299s > 299s > g1 <- gchol(test1) 299s > g2 <- gchol(test2) 299s > all.equal(as.matrix(g1), as.matrix(g2)) 299s [1] TRUE 299s > 299s > s1 <- solve(g1, full=T) 299s > s2 <- solve(g2, full=T) 299s > all.equal(as.matrix(s1), as.matrix(s2)) 299s [1] TRUE 299s > 299s > all.equal(solve(test1), solve(test2)) 299s [1] TRUE 299s > 299s BEGIN TEST corner2.R 299s 299s R version 4.4.3 (2025-02-28) -- "Trophy Case" 299s Copyright (C) 2025 The R Foundation for Statistical Computing 299s Platform: arm-unknown-linux-gnueabihf (32-bit) 299s 299s R is free software and comes with ABSOLUTELY NO WARRANTY. 299s You are welcome to redistribute it under certain conditions. 299s Type 'license()' or 'licence()' for distribution details. 299s 299s R is a collaborative project with many contributors. 299s Type 'contributors()' for more information and 299s 'citation()' on how to cite R or R packages in publications. 299s 299s Type 'demo()' for some demos, 'help()' for on-line help, or 299s 'help.start()' for an HTML browser interface to help. 299s Type 'q()' to quit R. 299s 299s > # 299s > # Test out the Cholesky, special case of a null block corner 299s > # In this case there is no advantage to a bdsmatrix as it consists of only 299s > # the ordinary matrix part. This case arises in coxme with an (x1+x2 | 1) 299s > # term, however, so it is nice to have it work instead of coding lots of 299s > # if/else logic in that code base. 299s > # 299s > library(bdsmatrix) 300s 300s Attaching package: 'bdsmatrix' 300s 300s > aeq <- function(x,y) all.equal(as.vector(x), as.vector(y)) 300s > 300s > tmat <- bdsmatrix(c(3,2,2,4), 300s + c(22,1,2,21,3,20,19,4,18,17,5,16,15,6,7, 8,14,9,10,13,11,12), 300s + matrix(c(1,0,1,1,0,0,1,1,0,1,0,10,0, 300s + 0,1,1,0,1,1,0,1,1,0,1,0,10), ncol=2)) 300s The following object is masked from 'package:base': 300s 300s backsolve 300s 300s > dimnames(tmat) <- list(NULL, letters[1:13]) 300s > smat <- as.matrix(tmat) 300s > tmat <- bdsmatrix(integer(0), numeric(0), rmat=smat) 300s > yy <- c(30,35,42,56,34,45,32,37,78,56,40,52,39) 300s > 300s > aeq(diag(tmat), diag(smat)) 300s [1] TRUE 300s > zz <- seq(1,13,2) 300s > aeq(as.matrix(tmat[zz,zz]), smat[zz,zz]) 300s [1] TRUE 300s > 300s > ch0 <- chol(smat) 300s > ch1 <- gchol(smat) 300s > ch2 <- gchol(tmat) 300s > # The gchol routines use the composition LDL', where L is lower triangular 300s > # with a diagonal of 1's, and D is diagonal. chol() uses U'U where U is 300s > # upper trangular. 300s > # The as.matrix function returns L and the diag function returns D. 300s > # Convert and compare 300s > aeq(diag(ch1), diag(ch2)) 300s [1] TRUE 300s > temp <- as.matrix(ch2) 300s > aeq(temp, as.matrix(ch1)) 300s [1] TRUE 300s > temp3 <- temp %*% diag(sqrt(diag(ch2))) 300s > aeq(temp3, t(ch0)) 300s [1] TRUE 300s > 300s > zz0 <- solve(smat, yy) 300s > zz1 <- solve(ch1, yy) 300s > zz2 <- solve(tmat, yy) 300s > aeq(zz1, zz2) 300s [1] TRUE 300s > aeq(zz0, zz1) 300s [1] TRUE 300s > 300s > inv1 <- solve(smat) 300s > inv2 <- as.matrix(solve(tmat)) # the result is a full, non-sparse matrix 300s > aeq(inv1, inv2) 300s [1] TRUE 300s > 300s > inv3 <- solve(gchol(tmat)) 300s > aeq(inv1, as.matrix(inv3)) 300s [1] TRUE 300s > 300s > gmat <- gchol(tmat) 300s > g2 <- as.matrix(gmat) %*% diag(sqrt(diag(gmat))) 300s > aeq(1:13 %*% g2, 1:13 %*% gmat) #vectors first 300s [1] TRUE 300s > aeq(g2 %*% 1:13, gmat %*% 1:13) 300s [1] TRUE 300s > temp <- matrix(runif(39), nrow=3) 300s > aeq(temp %*% g2, temp %*% gmat) 300s [1] TRUE 300s > aeq(g2 %*% t(temp), gmat %*% t(temp)) 300s [1] TRUE 300s > 300s BEGIN TEST gtest.R 300s 300s R version 4.4.3 (2025-02-28) -- "Trophy Case" 300s Copyright (C) 2025 The R Foundation for Statistical Computing 300s Platform: arm-unknown-linux-gnueabihf (32-bit) 300s 300s R is free software and comes with ABSOLUTELY NO WARRANTY. 300s You are welcome to redistribute it under certain conditions. 300s Type 'license()' or 'licence()' for distribution details. 300s 300s R is a collaborative project with many contributors. 300s Type 'contributors()' for more information and 300s 'citation()' on how to cite R or R packages in publications. 300s 300s Type 'demo()' for some demos, 'help()' for on-line help, or 300s 'help.start()' for an HTML browser interface to help. 300s Type 'q()' to quit R. 300s 300s > library(bdsmatrix) 300s 300s Attaching package: 'bdsmatrix' 300s 300s The following object is masked from 'package:base': 300s 300s backsolve 300s 300s > aeq <- function(x,y) all.equal(as.vector(x), as.vector(y)) 300s > 300s > tmat <- bdsmatrix(c(3,2,2,4), 300s + c(22,1,2,21,3,20,19,4,18,17,5,16,15,6,7, 8,14,9,10,13,11,12), 300s + matrix(c(1,0,1,1,0,0,1,1,0,1,0,10,0, 300s + 0,1,1,0,1,1,0,1,1,0,1,0,10), ncol=2)) 300s > dimnames(tmat) <- list(NULL, letters[1:13]) 300s > 300s > smat <- as.matrix(tmat) 300s > 300s > # Create a matrix that is symmetric, but not positive definite 300s > # The first one, temp, has column 6 redundant with cols 1-5 300s > temp <- smat[c(1:5, 5:10), c(1:5, 5:10)] 300s > ch1 <- gchol(temp) 300s > aeq(diag(ch1)[6], 0) # Check that it has a zero in the proper place 300s [1] TRUE 300s > ginv <- solve(ch1) # see if I get a generalized inverse 300s > aeq(temp %*% ginv %*% temp, temp) 300s [1] TRUE 300s > aeq(ginv %*% temp %*% ginv, ginv) 300s [1] TRUE 300s > 300s > # Now create one that is negative definite 300s > ch2 <- gchol(smat) 300s > temp2 <- as.matrix(ch2) 300s > temp3 <- diag(ch2) * rep(c(1, -1), length=nrow(smat)) 300s > xmat <- temp2 %*% diag(temp3) %*% t(temp2) 300s > xmat <- (xmat + t(xmat))/2 #work out round-off errors 300s > ch3 <- gchol(xmat) 300s > 300s > aeq(diag(ch3), temp3) 300s [1] TRUE 300s > aeq(as.matrix(ch3), temp2) 300s [1] TRUE 300s > 300s BEGIN TEST gtest2.R 300s 300s R version 4.4.3 (2025-02-28) -- "Trophy Case" 300s Copyright (C) 2025 The R Foundation for Statistical Computing 300s Platform: arm-unknown-linux-gnueabihf (32-bit) 300s 300s R is free software and comes with ABSOLUTELY NO WARRANTY. 300s You are welcome to redistribute it under certain conditions. 300s Type 'license()' or 'licence()' for distribution details. 300s 300s R is a collaborative project with many contributors. 300s Type 'contributors()' for more information and 300s 'citation()' on how to cite R or R packages in publications. 300s 300s Type 'demo()' for some demos, 'help()' for on-line help, or 300s 'help.start()' for an HTML browser interface to help. 300s Type 'q()' to quit R. 300s 300s > library(bdsmatrix) 300s 300s Attaching package: 'bdsmatrix' 300s 300s The following object is masked from 'package:base': 300s 300s backsolve 300s 300s > aeq <- function(x,y) all.equal(as.vector(x), as.vector(y)) 300s > 300s > # 300s > # Test multiplication of a vector/matrix times a gchol 300s > # 300s > tmat <- bdsmatrix(c(3,2,2,4), 300s + c(22,1,2,21,3,20,19,4,18,17,5,16,15,6,7, 8,14,9,10,13,11,12), 300s + matrix(c(1,0,1,1,0,0,1,1,0,1,0,10,0, 300s + 0,1,1,0,1,1,0,1,1,0,1,0,10), ncol=2)) 300s > dimnames(tmat) <- list(NULL, letters[1:13]) 300s > 300s > gmat <- gchol(tmat) 300s > g2 <- as.matrix(gmat) %*% diag(sqrt(diag(gmat))) 300s > 300s > 300s > aeq(1:13 %*% g2, 1:13 %*% gmat) #vectors first 300s [1] TRUE 300s > aeq(g2 %*% 1:13, gmat %*% 1:13) 300s [1] TRUE 300s > 300s > temp <- matrix(runif(39), nrow=3) 300s > aeq(temp %*% g2, temp %*% gmat) 300s [1] TRUE 300s > aeq(g2 %*% t(temp), gmat %*% t(temp)) 300s [1] TRUE 300s > 300s BEGIN TEST matrix.R 300s 300s R version 4.4.3 (2025-02-28) -- "Trophy Case" 300s Copyright (C) 2025 The R Foundation for Statistical Computing 300s Platform: arm-unknown-linux-gnueabihf (32-bit) 300s 300s R is free software and comes with ABSOLUTELY NO WARRANTY. 300s You are welcome to redistribute it under certain conditions. 300s Type 'license()' or 'licence()' for distribution details. 300s 300s R is a collaborative project with many contributors. 300s Type 'contributors()' for more information and 300s 'citation()' on how to cite R or R packages in publications. 300s 300s Type 'demo()' for some demos, 'help()' for on-line help, or 300s 'help.start()' for an HTML browser interface to help. 300s Type 'q()' to quit R. 300s 301s > library(bdsmatrix) 301s 301s Attaching package: 'bdsmatrix' 301s 301s The following object is masked from 'package:base': 301s 301s backsolve 301s 301s > aeq <- function(x,y) all.equal(as.vector(x), as.vector(y)) 301s > 301s > tmat <- bdsmatrix(c(3,2,2,4), 301s + c(22,1,2,21,3,20,19,4,18,17,5,16,15,6,7, 8,14,9,10,13,11,12), 301s + matrix(c(1,0,1,1,0,0,1,1,0,1,0,10,0, 301s + 0,1,1,0,1,1,0,1,1,0,1,0,10), ncol=2)) 301s > dimnames(tmat) <- list(NULL, letters[1:13]) 301s > 301s > smat <- as.matrix(tmat) 301s > yy <- c(30,35,42,56,34,45,32,37,78,56,40,52,39) 301s > 301s > # matrix multiplication 301s > zz <- runif(13) 301s > aeq(zz%*% smat, zz%*% tmat) 301s [1] TRUE 301s > aeq(smat%*%zz, tmat%*% zz) 301s [1] TRUE 301s > 301s > xx <- matrix(1:39, ncol=3) 301s > aeq(smat %*% zz, tmat %*% zz) 301s [1] TRUE 301s > aeq(t(xx) %*% smat, t(xx) %*% tmat) 301s [1] TRUE 301s > 301s > 301s > amat <- tmat 301s > amat@offdiag <- pi 301s > bmat <- as.matrix(amat) 301s > 301s > aeq(zz%*% amat, zz%*% bmat) 301s [1] TRUE 301s > aeq(amat%*%zz, bmat%*% zz) 301s [1] TRUE 301s > 301s > 301s > # Solve the right-hand side wrt a matrix 301s > yy2 <- cbind(yy, -yy, yy+3) 301s > zz1 <- solve(smat, yy2) 301s > zz2 <- solve(tmat, yy2) 301s > aeq(zz1, zz2) 301s [1] TRUE 301s > aeq(zz2[,1], solve(tmat, yy)) 301s [1] TRUE 301s > 301s BEGIN TEST nullr.R 301s 301s R version 4.4.3 (2025-02-28) -- "Trophy Case" 301s Copyright (C) 2025 The R Foundation for Statistical Computing 301s Platform: arm-unknown-linux-gnueabihf (32-bit) 301s 301s R is free software and comes with ABSOLUTELY NO WARRANTY. 301s You are welcome to redistribute it under certain conditions. 301s Type 'license()' or 'licence()' for distribution details. 301s 301s R is a collaborative project with many contributors. 301s Type 'contributors()' for more information and 301s 'citation()' on how to cite R or R packages in publications. 301s 301s Type 'demo()' for some demos, 'help()' for on-line help, or 301s 'help.start()' for an HTML browser interface to help. 301s Type 'q()' to quit R. 301s 301s > # 301s > # Make sure things work in the simpler case of no rmat component 301s > # 301s > library(bdsmatrix) 301s 301s Attaching package: 'bdsmatrix' 301s 301s > aeq <- function(x,y) all.equal(as.vector(x), as.vector(y)) 301s > 301s > tmat <- bdsmatrix(blocksize= c(3,2,2,4), 301s + blocks= c(22,1,2,21,3,20,19,4,18,17,5,16,15,6,7, 301s + 8,14,9,10,13,11,12)) 301s > dimnames(tmat) <- list(NULL, letters[1:11]) 301s > smat <- as.matrix(tmat) 301s > yy <- c(30,35,42,56,34,45,32,37,78,56,40) 301s > 301s > aeq(diag(tmat), diag(smat)) 301s The following object is masked from 'package:base': 301s 301s backsolve 301s 301s [1] TRUE 301s > zz <- seq(1,11,2) 301s > aeq(as.matrix(tmat[zz,zz]), smat[zz,zz]) 301s [1] TRUE 301s > 301s > ch0 <- chol(smat) 301s > ch1 <- gchol(smat) 301s > ch2 <- gchol(tmat) 301s > 301s > aeq(diag(ch1), diag(ch2)) 301s [1] TRUE 301s > temp <- as.matrix(ch2) 301s > aeq(temp, as.matrix(ch1)) 301s [1] TRUE 301s > temp3 <- temp %*% diag(sqrt(diag(ch2))) 301s > aeq(temp3, t(ch0)) 301s [1] TRUE 301s > 301s > zz0 <- solve(smat, yy) 301s > zz1 <- solve(ch1, yy) 301s > zz2 <- solve(tmat, yy) 301s > aeq(zz1, zz2) 301s [1] TRUE 301s > aeq(zz0, zz1) 301s [1] TRUE 301s > 301s BEGIN TEST reconcile.R 301s 301s R version 4.4.3 (2025-02-28) -- "Trophy Case" 301s Copyright (C) 2025 The R Foundation for Statistical Computing 301s Platform: arm-unknown-linux-gnueabihf (32-bit) 301s 301s R is free software and comes with ABSOLUTELY NO WARRANTY. 301s You are welcome to redistribute it under certain conditions. 301s Type 'license()' or 'licence()' for distribution details. 301s 301s R is a collaborative project with many contributors. 301s Type 'contributors()' for more information and 301s 'citation()' on how to cite R or R packages in publications. 301s 301s Type 'demo()' for some demos, 'help()' for on-line help, or 301s 'help.start()' for an HTML browser interface to help. 301s Type 'q()' to quit R. 301s 301s > # 301s > # Test cases for bdsmatrix.reconcile 301s > # 301s > library(bdsmatrix) 302s > aeq <- function(x,y) all.equal(as.vector(x), as.vector(y)) 302s > 302s > tmat <- bdsmatrix(c(3,2,2,4), 302s + c(22,1,2,21,3,20,19,4,18,17,5,16,15,6,7, 8,14,9,10,13,11,12), 302s + matrix(c(1,0,1,1,0,0,1,1,0,1,0,10,0, 302s + 0,1,1,0,1,1,0,1,1,0,1,0,10), ncol=2)) 302s > id <- letters[1:13] 302s > dimnames(tmat) <- list(id, id) 302s > 302s > rmat <- matrix(1:169, 13,13) 302s > rmat <- (rmat + t(rmat))/2 302s > dimnames(rmat) <- list(rev(id), rev(id)) 302s > 302s > xmat <- bdsmatrix.reconcile(list(tmat, rmat), group=id) 302s 302s Attaching package: 'bdsmatrix' 302s 302s The following object is masked from 'package:base': 302s 302s backsolve 302s 302s > temp <- xmat[[1]] 302s > aeq(temp@blocksize, 13) 302s [1] TRUE 302s > aeq(as.matrix(temp), as.matrix(tmat)) 302s [1] TRUE 302s > 302s > temp <- xmat[[2]] 302s > aeq(temp@blocksize, 13) 302s [1] TRUE 302s > aeq(as.matrix(temp), rmat[13:1, 13:1]) 302s [1] TRUE 302s > 302s > xmat <- bdsmatrix.reconcile(list(rmat, bdsI, tmat), group= rev(id)) 302s > temp <- xmat[[1]] 302s > aeq(as.matrix(temp), rmat) 302s [1] TRUE 302s > 302s > temp <- xmat[[2]] 302s > aeq(as.matrix(temp), diag(13)) 302s [1] TRUE 302s > 302s > temp <- xmat[[3]] 302s > aeq(as.matrix(temp), (as.matrix(tmat))[13:1,13:1]) 302s [1] TRUE 302s > 302s > # 302s > # Simplest case 302s > # 302s > xmat <- bdsmatrix.reconcile(bdsI, id) 302s > all(xmat@blocksize==1) 302s [1] TRUE 302s > aeq(as.matrix(xmat), diag(13)) 302s [1] TRUE 302s > 302s > # 302s > # The case list(tmat, tmat) will fail - can't have 2 rmats 302s > # 302s > #xmat <- bdsmatrix.reconcile(list(tmat, tmat), id) 302s > 302s > xmat <- bdsmatrix.reconcile(list(tmat, bdsI), rev(id)) 302s > temp <- xmat[[1]] 302s > aeq(as.matrix(temp), as.matrix(tmat)) 302s [1] TRUE 302s > aeq(dimnames(temp)[[1]], id) 302s [1] TRUE 302s > 302s > aeq(as.matrix(xmat[[2]]), diag(13)) 302s [1] TRUE 302s > 302s > # 302s > # Now for the hard one: 2 bdsmatrices, different orders, different 302s > # blocksize, but one contains the other 302s > # 302s > tmat <- tmat[1:11, 1:11] 302s > tord <- c(11:8, 2,1,3, 6,7,5,4) 302s > rmat <- (as.matrix(tmat))[tord, tord] 302s > rmat <- bdsmatrix(blocksize=c(4,5,2), 302s + blocks=c(rmat[1:4,1:4], rmat[5:9,5:9], rmat[10:11, 10:11]), 302s + dimnames=list(id[tord], id[tord])) 302s > 302s > aeq(as.matrix(tmat)[tord,tord], as.matrix(rmat)) 302s [1] TRUE 302s > 302s > xmat <- bdsmatrix.reconcile(list(tmat/2, rmat), id[1:11]) 302s > all.equal(xmat[[2]], rmat) 302s [1] TRUE 302s > all.equal(xmat[[1]]*2, rmat) 302s [1] TRUE 302s > 302s > # Now toss out a row/col 302s > # Give it a different name, too 302s > xx <- id[tord] 302s > xx[1] <- 44 302s > dimnames(rmat) <- list(xx,xx) 302s > xmat <- bdsmatrix.reconcile(list(tmat/2, rmat), id[1:9]) 302s > all.equal(xmat[[1]]*2, xmat[[2]]) 302s [1] TRUE 302s > 302s BEGIN TEST tinv.R 302s 302s R version 4.4.3 (2025-02-28) -- "Trophy Case" 302s Copyright (C) 2025 The R Foundation for Statistical Computing 302s Platform: arm-unknown-linux-gnueabihf (32-bit) 302s 302s R is free software and comes with ABSOLUTELY NO WARRANTY. 302s You are welcome to redistribute it under certain conditions. 302s Type 'license()' or 'licence()' for distribution details. 302s 302s R is a collaborative project with many contributors. 302s Type 'contributors()' for more information and 302s 'citation()' on how to cite R or R packages in publications. 302s 302s Type 'demo()' for some demos, 'help()' for on-line help, or 302s 'help.start()' for an HTML browser interface to help. 302s Type 'q()' to quit R. 302s 302s > library(bdsmatrix) 302s 302s Attaching package: 'bdsmatrix' 302s 302s > aeq <- function(x,y) all.equal(as.vector(x), as.vector(y)) 302s > 302s > tmat <- bdsmatrix(c(3,2,2,4), 302s + c(22,1,2,21,3,20,19,4,18,17,5,16,15,6,7, 8,14,9,10,13,11,12), 302s + matrix(c(1,0,1,1,0,0,1,1,0,1,0,10,0, 302s + 0,1,1,0,1,1,0,1,1,0,1,0,10), ncol=2)) 302s The following object is masked from 'package:base': 302s 302s backsolve 302s 302s > dimnames(tmat) <- list(NULL, letters[1:13]) 302s > 302s > smat <- as.matrix(tmat) 302s > yy <- c(30,35,42,56,34,45,32,37,78,56,40,52,39) 302s > # look at inverses more closely 302s > # (I needed this when some of the other tests weren't being passed, 302s > # to figure out where in the decomposition/inversion/multiply process 302s > # the flaw was). 302s > 302s > ch1 <- gchol(smat) 302s > ch2 <- gchol(tmat) 302s > 302s > inv1 <- solve(as.matrix(ch1)) 302s > inv2 <- solve(ch2,full=F) #inverse of the cholesky, not of tmat 302s > aeq(inv1, as.matrix(inv2)) 302s [1] TRUE 302s > 302s > # Full matrix tests 302s > inv3 <- solve(smat) 302s > inv4 <- solve(tmat) 302s > inv5 <- solve(gchol(smat), full=T) 302s > aeq(inv3, inv4) 302s [1] TRUE 302s > aeq(inv3, inv5) 302s [1] TRUE 302s > 302s > # The following test is false by design: when called with a bdsmatrix 302s > # object that has an rmat portion, the true inverse is dense. But 302s > # coxme only needs the trace for one calcluation; solve(gchol(tmat)) 302s > # cheats and only returns the block diagonal portion of the inverse. 302s > #inv6 <- solve(gchol(tmat), full=T) 302s > #aeq(inv3, inv6) 302s > 302s > # 302s > # Now test the solution to a partial solve 302s > # We want to be able to transform a matrix to uncorrelated form 302s > # If tmat= LDL', and A is general, I want (D^{-1/2}) L^{-1} A 302s > # 302s > amat <- matrix(runif(5*nrow(tmat)), nrow=nrow(tmat)) 302s > xx1 <- diag(1/sqrt(diag(ch1))) %*% solve(as.matrix(ch1), amat) 302s > xx2 <- solve(ch2, amat, full=F) 302s > aeq(xx1, xx2) 302s [1] TRUE 302s > 302s > xx1 <- diag(1/sqrt(diag(ch1))) %*% solve(as.matrix(ch1), yy) 302s > xx2 <- solve(ch2, yy, full=F) 302s > aeq(xx1, xx2) 302s [1] TRUE 302s > 303s autopkgtest [16:03:52]: test run-unit-test: -----------------------] 306s autopkgtest [16:03:55]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 306s run-unit-test PASS 310s autopkgtest [16:03:59]: test pkg-r-autopkgtest: preparing testbed 312s Reading package lists... 312s Building dependency tree... 312s Reading state information... 312s Starting pkgProblemResolver with broken count: 0 312s Starting 2 pkgProblemResolver with broken count: 0 313s Done 313s The following NEW packages will be installed: 313s build-essential cpp cpp-14 cpp-14-arm-linux-gnueabihf 313s cpp-arm-linux-gnueabihf dctrl-tools g++ g++-14 g++-14-arm-linux-gnueabihf 313s g++-arm-linux-gnueabihf gcc gcc-14 gcc-14-arm-linux-gnueabihf 313s gcc-arm-linux-gnueabihf gfortran gfortran-14 gfortran-14-arm-linux-gnueabihf 313s gfortran-arm-linux-gnueabihf icu-devtools libasan8 libblas-dev libbz2-dev 313s libc-dev-bin libc6-dev libcc1-0 libcrypt-dev libdeflate-dev libgcc-14-dev 313s libgfortran-14-dev libicu-dev libisl23 libjpeg-dev libjpeg-turbo8-dev 313s libjpeg8-dev liblapack-dev liblzma-dev libmpc3 libncurses-dev libpcre2-16-0 313s libpcre2-32-0 libpcre2-dev libpcre2-posix3 libpkgconf3 libpng-dev 313s libreadline-dev libstdc++-14-dev libtirpc-dev libubsan1 linux-libc-dev 313s pkg-r-autopkgtest pkgconf pkgconf-bin r-base-dev rpcsvc-proto zlib1g-dev 314s 0 upgraded, 55 newly installed, 0 to remove and 0 not upgraded. 314s Need to get 78.1 MB of archives. 314s After this operation, 243 MB of additional disk space will be used. 314s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libc-dev-bin armhf 2.41-1ubuntu2 [23.0 kB] 314s Get:2 http://ftpmaster.internal/ubuntu plucky/main armhf linux-libc-dev armhf 6.14.0-10.10 [1683 kB] 316s Get:3 http://ftpmaster.internal/ubuntu plucky/main armhf libcrypt-dev armhf 1:4.4.38-1 [120 kB] 316s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf rpcsvc-proto armhf 1.4.2-0ubuntu7 [62.2 kB] 316s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libc6-dev armhf 2.41-1ubuntu2 [1396 kB] 318s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf libisl23 armhf 0.27-1 [546 kB] 319s Get:7 http://ftpmaster.internal/ubuntu plucky/main armhf libmpc3 armhf 1.3.1-1build2 [47.1 kB] 319s Get:8 http://ftpmaster.internal/ubuntu plucky/main armhf cpp-14-arm-linux-gnueabihf armhf 14.2.0-17ubuntu3 [9220 kB] 330s Get:9 http://ftpmaster.internal/ubuntu plucky/main armhf cpp-14 armhf 14.2.0-17ubuntu3 [1030 B] 330s Get:10 http://ftpmaster.internal/ubuntu plucky/main armhf cpp-arm-linux-gnueabihf armhf 4:14.2.0-1ubuntu1 [5578 B] 330s Get:11 http://ftpmaster.internal/ubuntu plucky/main armhf cpp armhf 4:14.2.0-1ubuntu1 [22.4 kB] 330s Get:12 http://ftpmaster.internal/ubuntu plucky/main armhf libcc1-0 armhf 15-20250222-0ubuntu1 [38.9 kB] 330s Get:13 http://ftpmaster.internal/ubuntu plucky/main armhf libasan8 armhf 15-20250222-0ubuntu1 [2955 kB] 334s Get:14 http://ftpmaster.internal/ubuntu plucky/main armhf libubsan1 armhf 15-20250222-0ubuntu1 [1191 kB] 336s Get:15 http://ftpmaster.internal/ubuntu plucky/main armhf libgcc-14-dev armhf 14.2.0-17ubuntu3 [897 kB] 337s Get:16 http://ftpmaster.internal/ubuntu plucky/main armhf gcc-14-arm-linux-gnueabihf armhf 14.2.0-17ubuntu3 [18.0 MB] 359s Get:17 http://ftpmaster.internal/ubuntu plucky/main armhf gcc-14 armhf 14.2.0-17ubuntu3 [506 kB] 360s Get:18 http://ftpmaster.internal/ubuntu plucky/main armhf gcc-arm-linux-gnueabihf armhf 4:14.2.0-1ubuntu1 [1218 B] 360s Get:19 http://ftpmaster.internal/ubuntu plucky/main armhf gcc armhf 4:14.2.0-1ubuntu1 [5004 B] 360s Get:20 http://ftpmaster.internal/ubuntu plucky/main armhf libstdc++-14-dev armhf 14.2.0-17ubuntu3 [2573 kB] 363s Get:21 http://ftpmaster.internal/ubuntu plucky/main armhf g++-14-arm-linux-gnueabihf armhf 14.2.0-17ubuntu3 [10.5 MB] 377s Get:22 http://ftpmaster.internal/ubuntu plucky/main armhf g++-14 armhf 14.2.0-17ubuntu3 [21.8 kB] 377s Get:23 http://ftpmaster.internal/ubuntu plucky/main armhf g++-arm-linux-gnueabihf armhf 4:14.2.0-1ubuntu1 [966 B] 377s Get:24 http://ftpmaster.internal/ubuntu plucky/main armhf g++ armhf 4:14.2.0-1ubuntu1 [1084 B] 377s Get:25 http://ftpmaster.internal/ubuntu plucky/main armhf build-essential armhf 12.10ubuntu1 [4928 B] 377s Get:26 http://ftpmaster.internal/ubuntu plucky/main armhf dctrl-tools armhf 2.24-3build3 [94.7 kB] 377s Get:27 http://ftpmaster.internal/ubuntu plucky/main armhf libgfortran-14-dev armhf 14.2.0-17ubuntu3 [370 kB] 377s Get:28 http://ftpmaster.internal/ubuntu plucky/main armhf gfortran-14-arm-linux-gnueabihf armhf 14.2.0-17ubuntu3 [9763 kB] 389s Get:29 http://ftpmaster.internal/ubuntu plucky/main armhf gfortran-14 armhf 14.2.0-17ubuntu3 [13.6 kB] 389s Get:30 http://ftpmaster.internal/ubuntu plucky/main armhf gfortran-arm-linux-gnueabihf armhf 4:14.2.0-1ubuntu1 [1026 B] 389s Get:31 http://ftpmaster.internal/ubuntu plucky/main armhf gfortran armhf 4:14.2.0-1ubuntu1 [1166 B] 389s Get:32 http://ftpmaster.internal/ubuntu plucky/main armhf icu-devtools armhf 76.1-1ubuntu2 [206 kB] 390s Get:33 http://ftpmaster.internal/ubuntu plucky/main armhf libblas-dev armhf 3.12.1-2 [141 kB] 390s Get:34 http://ftpmaster.internal/ubuntu plucky/main armhf libbz2-dev armhf 1.0.8-6 [30.9 kB] 390s Get:35 http://ftpmaster.internal/ubuntu plucky/main armhf libdeflate-dev armhf 1.23-1 [45.0 kB] 390s Get:36 http://ftpmaster.internal/ubuntu plucky/main armhf libicu-dev armhf 76.1-1ubuntu2 [12.0 MB] 405s Get:37 http://ftpmaster.internal/ubuntu plucky/main armhf libjpeg-turbo8-dev armhf 2.1.5-3ubuntu2 [265 kB] 405s Get:38 http://ftpmaster.internal/ubuntu plucky/main armhf libjpeg8-dev armhf 8c-2ubuntu11 [1484 B] 405s Get:39 http://ftpmaster.internal/ubuntu plucky/main armhf libjpeg-dev armhf 8c-2ubuntu11 [1482 B] 405s Get:40 http://ftpmaster.internal/ubuntu plucky/main armhf liblapack-dev armhf 3.12.1-2 [2207 kB] 408s Get:41 http://ftpmaster.internal/ubuntu plucky/main armhf libncurses-dev armhf 6.5+20250216-2 [345 kB] 408s Get:42 http://ftpmaster.internal/ubuntu plucky/main armhf libpcre2-16-0 armhf 10.45-1 [207 kB] 408s Get:43 http://ftpmaster.internal/ubuntu plucky/main armhf libpcre2-32-0 armhf 10.45-1 [197 kB] 409s Get:44 http://ftpmaster.internal/ubuntu plucky/main armhf libpcre2-posix3 armhf 10.45-1 [6300 B] 409s Get:45 http://ftpmaster.internal/ubuntu plucky/main armhf libpcre2-dev armhf 10.45-1 [752 kB] 410s Get:46 http://ftpmaster.internal/ubuntu plucky/main armhf libpkgconf3 armhf 1.8.1-4 [26.6 kB] 410s Get:47 http://ftpmaster.internal/ubuntu plucky/main armhf zlib1g-dev armhf 1:1.3.dfsg+really1.3.1-1ubuntu1 [880 kB] 411s Get:48 http://ftpmaster.internal/ubuntu plucky/main armhf libpng-dev armhf 1.6.47-1 [251 kB] 411s Get:49 http://ftpmaster.internal/ubuntu plucky/main armhf libreadline-dev armhf 8.2-6 [153 kB] 411s Get:50 http://ftpmaster.internal/ubuntu plucky/main armhf liblzma-dev armhf 5.6.4-1 [166 kB] 411s Get:51 http://ftpmaster.internal/ubuntu plucky/main armhf pkgconf-bin armhf 1.8.1-4 [21.2 kB] 411s Get:52 http://ftpmaster.internal/ubuntu plucky/main armhf pkgconf armhf 1.8.1-4 [16.8 kB] 411s Get:53 http://ftpmaster.internal/ubuntu plucky/main armhf libtirpc-dev armhf 1.3.4+ds-1.3 [184 kB] 412s Get:54 http://ftpmaster.internal/ubuntu plucky/universe armhf r-base-dev all 4.4.3-1 [4176 B] 412s Get:55 http://ftpmaster.internal/ubuntu plucky/universe armhf pkg-r-autopkgtest all 20231212ubuntu1 [6448 B] 412s Fetched 78.1 MB in 1min 38s (795 kB/s) 412s Selecting previously unselected package libc-dev-bin. 412s (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 ... 66884 files and directories currently installed.) 412s Preparing to unpack .../00-libc-dev-bin_2.41-1ubuntu2_armhf.deb ... 412s Unpacking libc-dev-bin (2.41-1ubuntu2) ... 412s Selecting previously unselected package linux-libc-dev:armhf. 412s Preparing to unpack .../01-linux-libc-dev_6.14.0-10.10_armhf.deb ... 412s Unpacking linux-libc-dev:armhf (6.14.0-10.10) ... 412s Selecting previously unselected package libcrypt-dev:armhf. 412s Preparing to unpack .../02-libcrypt-dev_1%3a4.4.38-1_armhf.deb ... 412s Unpacking libcrypt-dev:armhf (1:4.4.38-1) ... 412s Selecting previously unselected package rpcsvc-proto. 412s Preparing to unpack .../03-rpcsvc-proto_1.4.2-0ubuntu7_armhf.deb ... 412s Unpacking rpcsvc-proto (1.4.2-0ubuntu7) ... 412s Selecting previously unselected package libc6-dev:armhf. 413s Preparing to unpack .../04-libc6-dev_2.41-1ubuntu2_armhf.deb ... 413s Unpacking libc6-dev:armhf (2.41-1ubuntu2) ... 413s Selecting previously unselected package libisl23:armhf. 413s Preparing to unpack .../05-libisl23_0.27-1_armhf.deb ... 413s Unpacking libisl23:armhf (0.27-1) ... 413s Selecting previously unselected package libmpc3:armhf. 413s Preparing to unpack .../06-libmpc3_1.3.1-1build2_armhf.deb ... 413s Unpacking libmpc3:armhf (1.3.1-1build2) ... 413s Selecting previously unselected package cpp-14-arm-linux-gnueabihf. 413s Preparing to unpack .../07-cpp-14-arm-linux-gnueabihf_14.2.0-17ubuntu3_armhf.deb ... 413s Unpacking cpp-14-arm-linux-gnueabihf (14.2.0-17ubuntu3) ... 413s Selecting previously unselected package cpp-14. 413s Preparing to unpack .../08-cpp-14_14.2.0-17ubuntu3_armhf.deb ... 413s Unpacking cpp-14 (14.2.0-17ubuntu3) ... 413s Selecting previously unselected package cpp-arm-linux-gnueabihf. 413s Preparing to unpack .../09-cpp-arm-linux-gnueabihf_4%3a14.2.0-1ubuntu1_armhf.deb ... 413s Unpacking cpp-arm-linux-gnueabihf (4:14.2.0-1ubuntu1) ... 413s Selecting previously unselected package cpp. 413s Preparing to unpack .../10-cpp_4%3a14.2.0-1ubuntu1_armhf.deb ... 413s Unpacking cpp (4:14.2.0-1ubuntu1) ... 413s Selecting previously unselected package libcc1-0:armhf. 413s Preparing to unpack .../11-libcc1-0_15-20250222-0ubuntu1_armhf.deb ... 413s Unpacking libcc1-0:armhf (15-20250222-0ubuntu1) ... 413s Selecting previously unselected package libasan8:armhf. 413s Preparing to unpack .../12-libasan8_15-20250222-0ubuntu1_armhf.deb ... 413s Unpacking libasan8:armhf (15-20250222-0ubuntu1) ... 413s Selecting previously unselected package libubsan1:armhf. 413s Preparing to unpack .../13-libubsan1_15-20250222-0ubuntu1_armhf.deb ... 413s Unpacking libubsan1:armhf (15-20250222-0ubuntu1) ... 413s Selecting previously unselected package libgcc-14-dev:armhf. 413s Preparing to unpack .../14-libgcc-14-dev_14.2.0-17ubuntu3_armhf.deb ... 413s Unpacking libgcc-14-dev:armhf (14.2.0-17ubuntu3) ... 413s Selecting previously unselected package gcc-14-arm-linux-gnueabihf. 413s Preparing to unpack .../15-gcc-14-arm-linux-gnueabihf_14.2.0-17ubuntu3_armhf.deb ... 413s Unpacking gcc-14-arm-linux-gnueabihf (14.2.0-17ubuntu3) ... 414s Selecting previously unselected package gcc-14. 414s Preparing to unpack .../16-gcc-14_14.2.0-17ubuntu3_armhf.deb ... 414s Unpacking gcc-14 (14.2.0-17ubuntu3) ... 414s Selecting previously unselected package gcc-arm-linux-gnueabihf. 414s Preparing to unpack .../17-gcc-arm-linux-gnueabihf_4%3a14.2.0-1ubuntu1_armhf.deb ... 414s Unpacking gcc-arm-linux-gnueabihf (4:14.2.0-1ubuntu1) ... 414s Selecting previously unselected package gcc. 414s Preparing to unpack .../18-gcc_4%3a14.2.0-1ubuntu1_armhf.deb ... 414s Unpacking gcc (4:14.2.0-1ubuntu1) ... 414s Selecting previously unselected package libstdc++-14-dev:armhf. 414s Preparing to unpack .../19-libstdc++-14-dev_14.2.0-17ubuntu3_armhf.deb ... 414s Unpacking libstdc++-14-dev:armhf (14.2.0-17ubuntu3) ... 414s Selecting previously unselected package g++-14-arm-linux-gnueabihf. 414s Preparing to unpack .../20-g++-14-arm-linux-gnueabihf_14.2.0-17ubuntu3_armhf.deb ... 414s Unpacking g++-14-arm-linux-gnueabihf (14.2.0-17ubuntu3) ... 415s Selecting previously unselected package g++-14. 415s Preparing to unpack .../21-g++-14_14.2.0-17ubuntu3_armhf.deb ... 415s Unpacking g++-14 (14.2.0-17ubuntu3) ... 415s Selecting previously unselected package g++-arm-linux-gnueabihf. 415s Preparing to unpack .../22-g++-arm-linux-gnueabihf_4%3a14.2.0-1ubuntu1_armhf.deb ... 415s Unpacking g++-arm-linux-gnueabihf (4:14.2.0-1ubuntu1) ... 415s Selecting previously unselected package g++. 415s Preparing to unpack .../23-g++_4%3a14.2.0-1ubuntu1_armhf.deb ... 415s Unpacking g++ (4:14.2.0-1ubuntu1) ... 415s Selecting previously unselected package build-essential. 415s Preparing to unpack .../24-build-essential_12.10ubuntu1_armhf.deb ... 415s Unpacking build-essential (12.10ubuntu1) ... 415s Selecting previously unselected package dctrl-tools. 415s Preparing to unpack .../25-dctrl-tools_2.24-3build3_armhf.deb ... 415s Unpacking dctrl-tools (2.24-3build3) ... 415s Selecting previously unselected package libgfortran-14-dev:armhf. 415s Preparing to unpack .../26-libgfortran-14-dev_14.2.0-17ubuntu3_armhf.deb ... 415s Unpacking libgfortran-14-dev:armhf (14.2.0-17ubuntu3) ... 415s Selecting previously unselected package gfortran-14-arm-linux-gnueabihf. 415s Preparing to unpack .../27-gfortran-14-arm-linux-gnueabihf_14.2.0-17ubuntu3_armhf.deb ... 415s Unpacking gfortran-14-arm-linux-gnueabihf (14.2.0-17ubuntu3) ... 415s Selecting previously unselected package gfortran-14. 415s Preparing to unpack .../28-gfortran-14_14.2.0-17ubuntu3_armhf.deb ... 415s Unpacking gfortran-14 (14.2.0-17ubuntu3) ... 415s Selecting previously unselected package gfortran-arm-linux-gnueabihf. 415s Preparing to unpack .../29-gfortran-arm-linux-gnueabihf_4%3a14.2.0-1ubuntu1_armhf.deb ... 415s Unpacking gfortran-arm-linux-gnueabihf (4:14.2.0-1ubuntu1) ... 415s Selecting previously unselected package gfortran. 415s Preparing to unpack .../30-gfortran_4%3a14.2.0-1ubuntu1_armhf.deb ... 415s Unpacking gfortran (4:14.2.0-1ubuntu1) ... 415s Selecting previously unselected package icu-devtools. 415s Preparing to unpack .../31-icu-devtools_76.1-1ubuntu2_armhf.deb ... 415s Unpacking icu-devtools (76.1-1ubuntu2) ... 415s Selecting previously unselected package libblas-dev:armhf. 415s Preparing to unpack .../32-libblas-dev_3.12.1-2_armhf.deb ... 415s Unpacking libblas-dev:armhf (3.12.1-2) ... 415s Selecting previously unselected package libbz2-dev:armhf. 415s Preparing to unpack .../33-libbz2-dev_1.0.8-6_armhf.deb ... 415s Unpacking libbz2-dev:armhf (1.0.8-6) ... 415s Selecting previously unselected package libdeflate-dev:armhf. 415s Preparing to unpack .../34-libdeflate-dev_1.23-1_armhf.deb ... 415s Unpacking libdeflate-dev:armhf (1.23-1) ... 415s Selecting previously unselected package libicu-dev:armhf. 415s Preparing to unpack .../35-libicu-dev_76.1-1ubuntu2_armhf.deb ... 415s Unpacking libicu-dev:armhf (76.1-1ubuntu2) ... 416s Selecting previously unselected package libjpeg-turbo8-dev:armhf. 416s Preparing to unpack .../36-libjpeg-turbo8-dev_2.1.5-3ubuntu2_armhf.deb ... 416s Unpacking libjpeg-turbo8-dev:armhf (2.1.5-3ubuntu2) ... 416s Selecting previously unselected package libjpeg8-dev:armhf. 416s Preparing to unpack .../37-libjpeg8-dev_8c-2ubuntu11_armhf.deb ... 416s Unpacking libjpeg8-dev:armhf (8c-2ubuntu11) ... 416s Selecting previously unselected package libjpeg-dev:armhf. 416s Preparing to unpack .../38-libjpeg-dev_8c-2ubuntu11_armhf.deb ... 416s Unpacking libjpeg-dev:armhf (8c-2ubuntu11) ... 416s Selecting previously unselected package liblapack-dev:armhf. 416s Preparing to unpack .../39-liblapack-dev_3.12.1-2_armhf.deb ... 416s Unpacking liblapack-dev:armhf (3.12.1-2) ... 416s Selecting previously unselected package libncurses-dev:armhf. 416s Preparing to unpack .../40-libncurses-dev_6.5+20250216-2_armhf.deb ... 416s Unpacking libncurses-dev:armhf (6.5+20250216-2) ... 416s Selecting previously unselected package libpcre2-16-0:armhf. 416s Preparing to unpack .../41-libpcre2-16-0_10.45-1_armhf.deb ... 416s Unpacking libpcre2-16-0:armhf (10.45-1) ... 416s Selecting previously unselected package libpcre2-32-0:armhf. 416s Preparing to unpack .../42-libpcre2-32-0_10.45-1_armhf.deb ... 416s Unpacking libpcre2-32-0:armhf (10.45-1) ... 416s Selecting previously unselected package libpcre2-posix3:armhf. 416s Preparing to unpack .../43-libpcre2-posix3_10.45-1_armhf.deb ... 416s Unpacking libpcre2-posix3:armhf (10.45-1) ... 416s Selecting previously unselected package libpcre2-dev:armhf. 416s Preparing to unpack .../44-libpcre2-dev_10.45-1_armhf.deb ... 416s Unpacking libpcre2-dev:armhf (10.45-1) ... 416s Selecting previously unselected package libpkgconf3:armhf. 416s Preparing to unpack .../45-libpkgconf3_1.8.1-4_armhf.deb ... 416s Unpacking libpkgconf3:armhf (1.8.1-4) ... 416s Selecting previously unselected package zlib1g-dev:armhf. 416s Preparing to unpack .../46-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1ubuntu1_armhf.deb ... 416s Unpacking zlib1g-dev:armhf (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 416s Selecting previously unselected package libpng-dev:armhf. 416s Preparing to unpack .../47-libpng-dev_1.6.47-1_armhf.deb ... 416s Unpacking libpng-dev:armhf (1.6.47-1) ... 416s Selecting previously unselected package libreadline-dev:armhf. 416s Preparing to unpack .../48-libreadline-dev_8.2-6_armhf.deb ... 416s Unpacking libreadline-dev:armhf (8.2-6) ... 416s Selecting previously unselected package liblzma-dev:armhf. 416s Preparing to unpack .../49-liblzma-dev_5.6.4-1_armhf.deb ... 416s Unpacking liblzma-dev:armhf (5.6.4-1) ... 416s Selecting previously unselected package pkgconf-bin. 416s Preparing to unpack .../50-pkgconf-bin_1.8.1-4_armhf.deb ... 416s Unpacking pkgconf-bin (1.8.1-4) ... 416s Selecting previously unselected package pkgconf:armhf. 416s Preparing to unpack .../51-pkgconf_1.8.1-4_armhf.deb ... 416s Unpacking pkgconf:armhf (1.8.1-4) ... 416s Selecting previously unselected package libtirpc-dev:armhf. 416s Preparing to unpack .../52-libtirpc-dev_1.3.4+ds-1.3_armhf.deb ... 416s Unpacking libtirpc-dev:armhf (1.3.4+ds-1.3) ... 417s Selecting previously unselected package r-base-dev. 417s Preparing to unpack .../53-r-base-dev_4.4.3-1_all.deb ... 417s Unpacking r-base-dev (4.4.3-1) ... 417s Selecting previously unselected package pkg-r-autopkgtest. 417s Preparing to unpack .../54-pkg-r-autopkgtest_20231212ubuntu1_all.deb ... 417s Unpacking pkg-r-autopkgtest (20231212ubuntu1) ... 417s Setting up linux-libc-dev:armhf (6.14.0-10.10) ... 417s Setting up libpcre2-16-0:armhf (10.45-1) ... 417s Setting up libpcre2-32-0:armhf (10.45-1) ... 417s Setting up libtirpc-dev:armhf (1.3.4+ds-1.3) ... 417s Setting up libpkgconf3:armhf (1.8.1-4) ... 417s Setting up rpcsvc-proto (1.4.2-0ubuntu7) ... 417s Setting up libmpc3:armhf (1.3.1-1build2) ... 417s Setting up icu-devtools (76.1-1ubuntu2) ... 417s Setting up pkgconf-bin (1.8.1-4) ... 417s Setting up liblzma-dev:armhf (5.6.4-1) ... 417s Setting up libubsan1:armhf (15-20250222-0ubuntu1) ... 417s Setting up libpcre2-posix3:armhf (10.45-1) ... 417s Setting up libcrypt-dev:armhf (1:4.4.38-1) ... 417s Setting up libasan8:armhf (15-20250222-0ubuntu1) ... 417s Setting up libgcc-14-dev:armhf (14.2.0-17ubuntu3) ... 417s Setting up libisl23:armhf (0.27-1) ... 417s Setting up libc-dev-bin (2.41-1ubuntu2) ... 417s Setting up libdeflate-dev:armhf (1.23-1) ... 417s Setting up libcc1-0:armhf (15-20250222-0ubuntu1) ... 417s Setting up libblas-dev:armhf (3.12.1-2) ... 417s update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so to provide /usr/lib/arm-linux-gnueabihf/libblas.so (libblas.so-arm-linux-gnueabihf) in auto mode 417s Setting up dctrl-tools (2.24-3build3) ... 417s Setting up cpp-14-arm-linux-gnueabihf (14.2.0-17ubuntu3) ... 417s Setting up libgfortran-14-dev:armhf (14.2.0-17ubuntu3) ... 417s Setting up gcc-14-arm-linux-gnueabihf (14.2.0-17ubuntu3) ... 417s Setting up pkgconf:armhf (1.8.1-4) ... 417s Setting up liblapack-dev:armhf (3.12.1-2) ... 417s update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so to provide /usr/lib/arm-linux-gnueabihf/liblapack.so (liblapack.so-arm-linux-gnueabihf) in auto mode 417s Setting up cpp-14 (14.2.0-17ubuntu3) ... 417s Setting up libc6-dev:armhf (2.41-1ubuntu2) ... 417s Setting up libstdc++-14-dev:armhf (14.2.0-17ubuntu3) ... 417s 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(4:14.2.0-1ubuntu1) ... 417s Setting up libpng-dev:armhf (1.6.47-1) ... 417s Setting up libjpeg-dev:armhf (8c-2ubuntu11) ... 417s Setting up gcc (4:14.2.0-1ubuntu1) ... 417s Setting up g++ (4:14.2.0-1ubuntu1) ... 417s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 417s Setting up build-essential (12.10ubuntu1) ... 417s Setting up gfortran (4:14.2.0-1ubuntu1) ... 417s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode 417s update-alternatives: warning: skip creation of /usr/share/man/man1/f95.1.gz because associated file /usr/share/man/man1/gfortran.1.gz (of link group f95) doesn't exist 417s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode 417s update-alternatives: warning: skip creation of /usr/share/man/man1/f77.1.gz because associated file /usr/share/man/man1/gfortran.1.gz (of link group f77) doesn't exist 417s Setting up r-base-dev (4.4.3-1) ... 417s Setting up pkg-r-autopkgtest (20231212ubuntu1) ... 417s Processing triggers for libc-bin (2.41-1ubuntu2) ... 417s Processing triggers for man-db (2.13.0-1) ... 418s Processing triggers for install-info (7.1.1-1) ... 426s autopkgtest [16:05:55]: test pkg-r-autopkgtest: /usr/share/dh-r/pkg-r-autopkgtest 426s autopkgtest [16:05:55]: test pkg-r-autopkgtest: [----------------------- 428s Test: Try to load the R library bdsmatrix 428s 428s R version 4.4.3 (2025-02-28) -- "Trophy Case" 428s Copyright (C) 2025 The R Foundation for Statistical Computing 428s Platform: arm-unknown-linux-gnueabihf (32-bit) 428s 428s R is free software and comes with ABSOLUTELY NO WARRANTY. 428s You are welcome to redistribute it under certain conditions. 428s Type 'license()' or 'licence()' for distribution details. 428s 428s R is a collaborative project with many contributors. 428s Type 'contributors()' for more information and 428s 'citation()' on how to cite R or R packages in publications. 428s 428s Type 'demo()' for some demos, 'help()' for on-line help, or 428s 'help.start()' for an HTML browser interface to help. 428s Type 'q()' to quit R. 428s 428s > library('bdsmatrix') 428s 428s Attaching package: ‘bdsmatrix’ 428s 428s The following object is masked from ‘package:base’: 428s 428s backsolve 428s 428s > 428s > 428s Other tests are currently unsupported! 428s They will be progressively added. 428s autopkgtest [16:05:57]: test pkg-r-autopkgtest: -----------------------] 432s pkg-r-autopkgtest PASS 432s autopkgtest [16:06:01]: test pkg-r-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 436s autopkgtest [16:06:05]: @@@@@@@@@@@@@@@@@@@@ summary 436s run-unit-test PASS 436s pkg-r-autopkgtest PASS