0s autopkgtest [15:19:29]: starting date and time: 2025-03-15 15:19:29+0000 0s autopkgtest [15:19:29]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [15:19:29]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.dmabngzb/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc --apt-upgrade r-cran-bdsmatrix --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glibc/2.41-1ubuntu2 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-arm64-4.secgroup --name adt-plucky-arm64-r-cran-bdsmatrix-20250315-151929-juju-7f2275-prod-proposed-migration-environment-2-c633927b-766d-4acb-a8c0-8f2da5f4b153 --image adt/ubuntu-plucky-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 153s autopkgtest [15:22:02]: testbed dpkg architecture: arm64 153s autopkgtest [15:22:02]: testbed apt version: 2.9.33 153s autopkgtest [15:22:02]: @@@@@@@@@@@@@@@@@@@@ test bed setup 154s autopkgtest [15:22:03]: testbed release detected to be: None 155s autopkgtest [15:22:04]: updating testbed package index (apt update) 155s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 156s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 156s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 156s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 156s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 156s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [404 kB] 156s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [101 kB] 156s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [78.2 kB] 156s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 c-n-f Metadata [1976 B] 156s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 c-n-f Metadata [116 B] 156s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [346 kB] 156s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 c-n-f Metadata [15.8 kB] 156s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [4948 B] 156s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 c-n-f Metadata [572 B] 157s Fetched 1094 kB in 1s (866 kB/s) 158s Reading package lists... 158s Reading package lists... 159s Building dependency tree... 159s Reading state information... 160s Calculating upgrade... 160s Calculating upgrade... 160s The following packages will be upgraded: 160s python3-jinja2 strace 160s 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 160s Need to get 608 kB of archives. 160s After this operation, 11.3 kB of additional disk space will be used. 160s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 strace arm64 6.13+ds-1ubuntu1 [499 kB] 161s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 162s Fetched 608 kB in 1s (769 kB/s) 162s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 117701 files and directories currently installed.) 162s Preparing to unpack .../strace_6.13+ds-1ubuntu1_arm64.deb ... 162s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 162s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 162s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 162s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 163s Setting up strace (6.13+ds-1ubuntu1) ... 163s Processing triggers for man-db (2.13.0-1) ... 164s Reading package lists... 165s Building dependency tree... 165s Reading state information... 165s Solving dependencies... 166s The following packages will be REMOVED: 166s libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64* 166s libunwind8* linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 166s linux-image-6.11.0-8-generic* linux-modules-6.11.0-8-generic* 166s linux-tools-6.11.0-8* linux-tools-6.11.0-8-generic* 167s 0 upgraded, 0 newly installed, 11 to remove and 5 not upgraded. 167s After this operation, 267 MB disk space will be freed. 167s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 117701 files and directories currently installed.) 167s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 167s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 167s Removing libpython3.12t64:arm64 (3.12.9-1) ... 167s Removing libpython3.12-stdlib:arm64 (3.12.9-1) ... 167s Removing libnsl2:arm64 (1.3.0-3build3) ... 167s Removing libpython3.12-minimal:arm64 (3.12.9-1) ... 167s Removing libunwind8:arm64 (1.6.2-3.1) ... 167s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 168s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 169s Removing linux-image-6.11.0-8-generic (6.11.0-8.8) ... 170s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.14.0-10-generic 170s I: /boot/initrd.img.old is now a symlink to initrd.img-6.14.0-10-generic 170s /etc/kernel/postrm.d/initramfs-tools: 170s update-initramfs: Deleting /boot/initrd.img-6.11.0-8-generic 170s /etc/kernel/postrm.d/zz-flash-kernel: 170s flash-kernel: Kernel 6.11.0-8-generic has been removed. 170s flash-kernel: A higher version (6.14.0-10-generic) is still installed, no reflashing required. 170s /etc/kernel/postrm.d/zz-update-grub: 170s Sourcing file `/etc/default/grub' 170s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 170s Generating grub configuration file ... 171s Found linux image: /boot/vmlinuz-6.14.0-10-generic 171s Found initrd image: /boot/initrd.img-6.14.0-10-generic 171s Warning: os-prober will not be executed to detect other bootable partitions. 171s Systems on them will not be added to the GRUB boot configuration. 171s Check GRUB_DISABLE_OS_PROBER documentation entry. 171s Adding boot menu entry for UEFI Firmware Settings ... 171s done 171s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 171s Processing triggers for libc-bin (2.41-1ubuntu1) ... 171s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 81650 files and directories currently installed.) 171s Purging configuration files for linux-image-6.11.0-8-generic (6.11.0-8.8) ... 172s Purging configuration files for libpython3.12-minimal:arm64 (3.12.9-1) ... 172s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 172s autopkgtest [15:22:21]: upgrading testbed (apt dist-upgrade and autopurge) 172s Reading package lists... 172s Building dependency tree... 172s Reading state information... 173s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 173s Starting 2 pkgProblemResolver with broken count: 0 173s Done 174s Entering ResolveByKeep 174s 174s Calculating upgrade... 175s The following packages will be upgraded: 175s libc-bin libc-dev-bin libc6 libc6-dev locales 175s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 175s Need to get 9530 kB of archives. 175s After this operation, 0 B of additional disk space will be used. 175s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6-dev arm64 2.41-1ubuntu2 [1750 kB] 176s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-dev-bin arm64 2.41-1ubuntu2 [24.0 kB] 176s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6 arm64 2.41-1ubuntu2 [2910 kB] 178s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-bin arm64 2.41-1ubuntu2 [600 kB] 178s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 locales all 2.41-1ubuntu2 [4246 kB] 181s Preconfiguring packages ... 181s Fetched 9530 kB in 6s (1666 kB/s) 181s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 81647 files and directories currently installed.) 181s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_arm64.deb ... 181s Unpacking libc6-dev:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 181s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_arm64.deb ... 181s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 181s Preparing to unpack .../libc6_2.41-1ubuntu2_arm64.deb ... 181s Unpacking libc6:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 182s Setting up libc6:arm64 (2.41-1ubuntu2) ... 182s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 81647 files and directories currently installed.) 182s Preparing to unpack .../libc-bin_2.41-1ubuntu2_arm64.deb ... 182s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 182s Setting up libc-bin (2.41-1ubuntu2) ... 182s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 81647 files and directories currently installed.) 182s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 182s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 182s Setting up locales (2.41-1ubuntu2) ... 183s Generating locales (this might take a while)... 185s en_US.UTF-8... done 185s Generation complete. 185s Setting up libc-dev-bin (2.41-1ubuntu2) ... 185s Setting up libc6-dev:arm64 (2.41-1ubuntu2) ... 185s Processing triggers for man-db (2.13.0-1) ... 186s Processing triggers for systemd (257.3-1ubuntu3) ... 187s Reading package lists... 187s Building dependency tree... 187s Reading state information... 187s Starting pkgProblemResolver with broken count: 0 187s Starting 2 pkgProblemResolver with broken count: 0 187s Done 188s Solving dependencies... 188s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 189s autopkgtest [15:22:38]: rebooting testbed after setup commands that affected boot 212s autopkgtest [15:23:01]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP PREEMPT_DYNAMIC Wed Mar 12 15:45:31 UTC 2025 215s autopkgtest [15:23:04]: @@@@@@@@@@@@@@@@@@@@ apt-source r-cran-bdsmatrix 218s Get:1 http://ftpmaster.internal/ubuntu plucky/universe r-cran-bdsmatrix 1.3-7-1 (dsc) [2072 B] 218s Get:2 http://ftpmaster.internal/ubuntu plucky/universe r-cran-bdsmatrix 1.3-7-1 (tar) [48.0 kB] 218s Get:3 http://ftpmaster.internal/ubuntu plucky/universe r-cran-bdsmatrix 1.3-7-1 (diff) [2520 B] 218s gpgv: Signature made Tue Mar 12 13:10:28 2024 UTC 218s gpgv: using RSA key 53951D95272E0C5B82BE8C4A2CECE9350ECEBE4A 218s gpgv: Can't check signature: No public key 218s dpkg-source: warning: cannot verify inline signature for ./r-cran-bdsmatrix_1.3-7-1.dsc: no acceptable signature found 218s autopkgtest [15:23:07]: testing package r-cran-bdsmatrix version 1.3-7-1 219s autopkgtest [15:23:08]: build not needed 221s autopkgtest [15:23:10]: test run-unit-test: preparing testbed 221s Reading package lists... 221s Building dependency tree... 221s Reading state information... 222s Starting pkgProblemResolver with broken count: 0 222s Starting 2 pkgProblemResolver with broken count: 0 222s Done 222s The following NEW packages will be installed: 222s fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono libblas3 222s libcairo2 libdatrie1 libdeflate0 libfontconfig1 libgfortran5 libgomp1 222s libgraphite2-3 libharfbuzz0b libice6 libjbig0 libjpeg-turbo8 libjpeg8 222s liblapack3 liblerc4 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 222s libpaper-utils libpaper2 libpixman-1-0 libsharpyuv0 libsm6 libtcl8.6 222s libthai-data libthai0 libtiff6 libtk8.6 libwebp7 libxcb-render0 libxcb-shm0 222s libxft2 libxrender1 libxss1 libxt6t64 r-base-core r-cran-bdsmatrix unzip 222s x11-common xdg-utils zip 223s 0 upgraded, 45 newly installed, 0 to remove and 0 not upgraded. 223s Need to get 38.7 MB of archives. 223s After this operation, 79.9 MB of additional disk space will be used. 223s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 223s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 223s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig-config arm64 2.15.0-2ubuntu1 [37.5 kB] 223s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 libfontconfig1 arm64 2.15.0-2ubuntu1 [144 kB] 224s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig arm64 2.15.0-2ubuntu1 [191 kB] 224s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.1-2 [161 kB] 224s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 libpixman-1-0 arm64 0.44.0-3 [197 kB] 224s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-render0 arm64 1.17.0-2 [16.6 kB] 224s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-shm0 arm64 1.17.0-2 [5884 B] 224s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 libxrender1 arm64 1:0.9.10-1.1build1 [18.8 kB] 224s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 libcairo2 arm64 1.18.2-2 [560 kB] 224s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 libdatrie1 arm64 0.2.13-3build1 [19.2 kB] 224s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate0 arm64 1.23-1 [46.2 kB] 224s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 15-20250222-0ubuntu1 [444 kB] 224s Get:15 http://ftpmaster.internal/ubuntu plucky/main arm64 libgomp1 arm64 15-20250222-0ubuntu1 [146 kB] 224s Get:16 http://ftpmaster.internal/ubuntu plucky/main arm64 libgraphite2-3 arm64 1.3.14-2ubuntu1 [70.6 kB] 224s Get:17 http://ftpmaster.internal/ubuntu plucky/main arm64 libharfbuzz0b arm64 10.2.0-1 [490 kB] 224s Get:18 http://ftpmaster.internal/ubuntu plucky/main arm64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 224s Get:19 http://ftpmaster.internal/ubuntu plucky/main arm64 libice6 arm64 2:1.1.1-1 [42.3 kB] 224s Get:20 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg-turbo8 arm64 2.1.5-3ubuntu2 [165 kB] 224s Get:21 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 224s Get:22 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.1-2 [2307 kB] 225s Get:23 http://ftpmaster.internal/ubuntu plucky/main arm64 liblerc4 arm64 4.0.0+ds-5ubuntu1 [167 kB] 225s Get:24 http://ftpmaster.internal/ubuntu plucky/main arm64 libthai-data all 0.1.29-2build1 [158 kB] 225s Get:25 http://ftpmaster.internal/ubuntu plucky/main arm64 libthai0 arm64 0.1.29-2build1 [18.2 kB] 225s Get:26 http://ftpmaster.internal/ubuntu plucky/main arm64 libpango-1.0-0 arm64 1.56.2-1 [237 kB] 225s Get:27 http://ftpmaster.internal/ubuntu plucky/main arm64 libpangoft2-1.0-0 arm64 1.56.2-1 [49.5 kB] 225s Get:28 http://ftpmaster.internal/ubuntu plucky/main arm64 libpangocairo-1.0-0 arm64 1.56.2-1 [27.6 kB] 225s Get:29 http://ftpmaster.internal/ubuntu plucky/main arm64 libpaper2 arm64 2.2.5-0.3 [17.3 kB] 225s Get:30 http://ftpmaster.internal/ubuntu plucky/main arm64 libpaper-utils arm64 2.2.5-0.3 [15.4 kB] 225s Get:31 http://ftpmaster.internal/ubuntu plucky/main arm64 libsharpyuv0 arm64 1.5.0-0.1 [16.9 kB] 225s Get:32 http://ftpmaster.internal/ubuntu plucky/main arm64 libsm6 arm64 2:1.2.4-1 [16.4 kB] 225s Get:33 http://ftpmaster.internal/ubuntu plucky/main arm64 libtcl8.6 arm64 8.6.16+dfsg-1 [987 kB] 225s Get:34 http://ftpmaster.internal/ubuntu plucky/main arm64 libjbig0 arm64 2.1-6.1ubuntu2 [29.3 kB] 225s Get:35 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebp7 arm64 1.5.0-0.1 [194 kB] 225s Get:36 http://ftpmaster.internal/ubuntu plucky/main arm64 libtiff6 arm64 4.5.1+git230720-4ubuntu4 [193 kB] 225s Get:37 http://ftpmaster.internal/ubuntu plucky/main arm64 libxft2 arm64 2.3.6-1build1 [44.1 kB] 225s Get:38 http://ftpmaster.internal/ubuntu plucky/main arm64 libxss1 arm64 1:1.2.3-1build3 [7244 B] 225s Get:39 http://ftpmaster.internal/ubuntu plucky/main arm64 libtk8.6 arm64 8.6.16-1 [776 kB] 225s Get:40 http://ftpmaster.internal/ubuntu plucky/main arm64 libxt6t64 arm64 1:1.2.1-1.2build1 [168 kB] 225s Get:41 http://ftpmaster.internal/ubuntu plucky/main arm64 zip arm64 3.0-14ubuntu2 [173 kB] 226s Get:42 http://ftpmaster.internal/ubuntu plucky/main arm64 unzip arm64 6.0-28ubuntu6 [178 kB] 226s Get:43 http://ftpmaster.internal/ubuntu plucky/main arm64 xdg-utils all 1.2.1-2ubuntu1 [66.0 kB] 226s Get:44 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-base-core arm64 4.4.3-1 [28.4 MB] 228s Get:45 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-bdsmatrix arm64 1.3-7-1 [300 kB] 228s Preconfiguring packages ... 228s Fetched 38.7 MB in 5s (7492 kB/s) 228s Selecting previously unselected package fonts-dejavu-mono. 228s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 81647 files and directories currently installed.) 228s Preparing to unpack .../00-fonts-dejavu-mono_2.37-8_all.deb ... 228s Unpacking fonts-dejavu-mono (2.37-8) ... 228s Selecting previously unselected package fonts-dejavu-core. 228s Preparing to unpack .../01-fonts-dejavu-core_2.37-8_all.deb ... 228s Unpacking fonts-dejavu-core (2.37-8) ... 228s Selecting previously unselected package fontconfig-config. 228s Preparing to unpack .../02-fontconfig-config_2.15.0-2ubuntu1_arm64.deb ... 229s Unpacking fontconfig-config (2.15.0-2ubuntu1) ... 229s Selecting previously unselected package libfontconfig1:arm64. 229s Preparing to unpack .../03-libfontconfig1_2.15.0-2ubuntu1_arm64.deb ... 229s Unpacking libfontconfig1:arm64 (2.15.0-2ubuntu1) ... 229s Selecting previously unselected package fontconfig. 229s Preparing to unpack .../04-fontconfig_2.15.0-2ubuntu1_arm64.deb ... 229s Unpacking fontconfig (2.15.0-2ubuntu1) ... 229s Selecting previously unselected package libblas3:arm64. 229s Preparing to unpack .../05-libblas3_3.12.1-2_arm64.deb ... 229s Unpacking libblas3:arm64 (3.12.1-2) ... 229s Selecting previously unselected package libpixman-1-0:arm64. 229s Preparing to unpack .../06-libpixman-1-0_0.44.0-3_arm64.deb ... 229s Unpacking libpixman-1-0:arm64 (0.44.0-3) ... 229s Selecting previously unselected package libxcb-render0:arm64. 229s Preparing to unpack .../07-libxcb-render0_1.17.0-2_arm64.deb ... 229s Unpacking libxcb-render0:arm64 (1.17.0-2) ... 229s Selecting previously unselected package libxcb-shm0:arm64. 229s Preparing to unpack .../08-libxcb-shm0_1.17.0-2_arm64.deb ... 229s Unpacking libxcb-shm0:arm64 (1.17.0-2) ... 229s Selecting previously unselected package libxrender1:arm64. 229s Preparing to unpack .../09-libxrender1_1%3a0.9.10-1.1build1_arm64.deb ... 229s Unpacking libxrender1:arm64 (1:0.9.10-1.1build1) ... 229s Selecting previously unselected package libcairo2:arm64. 229s Preparing to unpack .../10-libcairo2_1.18.2-2_arm64.deb ... 229s Unpacking libcairo2:arm64 (1.18.2-2) ... 229s Selecting previously unselected package libdatrie1:arm64. 229s Preparing to unpack .../11-libdatrie1_0.2.13-3build1_arm64.deb ... 229s Unpacking libdatrie1:arm64 (0.2.13-3build1) ... 229s Selecting previously unselected package libdeflate0:arm64. 229s Preparing to unpack .../12-libdeflate0_1.23-1_arm64.deb ... 229s Unpacking libdeflate0:arm64 (1.23-1) ... 229s Selecting previously unselected package 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Copyright (C) 2025 The R Foundation for Statistical Computing 237s Platform: aarch64-unknown-linux-gnu 237s 237s R is free software and comes with ABSOLUTELY NO WARRANTY. 237s You are welcome to redistribute it under certain conditions. 237s Type 'license()' or 'licence()' for distribution details. 237s 237s R is a collaborative project with many contributors. 237s Type 'contributors()' for more information and 237s 'citation()' on how to cite R or R packages in publications. 237s 237s Type 'demo()' for some demos, 'help()' for on-line help, or 237s 'help.start()' for an HTML browser interface to help. 237s Type 'q()' to quit R. 237s 237s > library(bdsmatrix) 237s > # 237s > # A test of the backsolve function 237s > # 237s > aeq <- function(x,y) all.equal(as.vector(x), as.vector(y)) 237s > 237s > tmat <- matrix(rep(1:5,5), 5, 5) 237s > tmat <- tmat + t(tmat) 237s > diag(tmat) <- diag(tmat) + 10 237s > 237s > gt <- gchol(tmat) 237s > g1 <- as.matrix(gt) 237s > gd <- diag(sqrt(diag(gt))) 237s > gc <- gd %*% t(g1) #usual cholesky form 237s > 237s > xmat <- cbind(1:5, 11:15) 237s > 237s > s1 <- backsolve(gt, xmat, upper=TRUE) #the default 237s > aeq(gd %*% t(g1) %*% s1, xmat) 237s [1] TRUE 237s > all.equal(s1, backsolve(gc, xmat)) 237s [1] TRUE 237s > 237s > s2 <- backsolve(gt, xmat, upper=FALSE) 237s > aeq(g1 %*% gd %*% s2, xmat) 237s 237s Attaching package: 'bdsmatrix' 237s 237s The following object is masked from 'package:base': 237s 237s backsolve 237s 237s [1] TRUE 237s > all.equal(backsolve(gt,xmat, upper=F), backsolve(t(gc),xmat, upper=F)) 237s [1] TRUE 237s > 237s > 237s > # Now for bdsmatrix objects 237s > tmat <- bdsmatrix(c(3,2,2,4), 237s + c(22,1,2,21,3,20,19,4,18,17,5,16,15,6,7, 8,14,9,10,13,11,12), 237s + matrix(c(1,0,1,1,0,0,1,1,0,1,0,10,0, 237s + 0,1,1,0,1,1,0,1,1,0,1,0,10), ncol=2)) 237s > dimnames(tmat) <- list(NULL, letters[1:13]) 237s > smat <- as.matrix(tmat) 237s > 237s > gt <- gchol(tmat) 237s > gs <- gchol(smat) 237s > 237s > xmat <- cbind(1:13, 1:13*2 + 3) 237s > 237s > s1 <- backsolve(gt, xmat) 237s > s2 <- backsolve(gs, xmat) 237s > s3 <- backsolve(gt, xmat, upper=FALSE) 237s > s4 <- backsolve(gs, xmat, upper=FALSE) 237s > 237s > aeq(s1, s2) 237s [1] TRUE 237s > aeq(s3, s4) 237s [1] TRUE 237s > 237s > g1 <- as.matrix(gt) 237s > gd <- diag(sqrt(diag(gt))) 237s > aeq(gd %*% t(g1) %*% s1, xmat) 237s [1] TRUE 237s > aeq(g1 %*% gd %*% s3, xmat) 237s [1] TRUE 237s > 237s BEGIN TEST bdstest.R 237s 237s R version 4.4.3 (2025-02-28) -- "Trophy Case" 237s Copyright (C) 2025 The R Foundation for Statistical Computing 237s Platform: aarch64-unknown-linux-gnu 237s 237s R is free software and comes with ABSOLUTELY NO WARRANTY. 237s You are welcome to redistribute it under certain conditions. 237s Type 'license()' or 'licence()' for distribution details. 237s 237s R is a collaborative project with many contributors. 237s Type 'contributors()' for more information and 237s 'citation()' on how to cite R or R packages in publications. 237s 237s Type 'demo()' for some demos, 'help()' for on-line help, or 237s 'help.start()' for an HTML browser interface to help. 237s Type 'q()' to quit R. 237s 237s > # 237s > # Test out math aspects 237s > # 237s > library(bdsmatrix) 237s 237s Attaching package: 'bdsmatrix' 237s 237s The following object is masked from 'package:base': 237s 237s backsolve 237s 237s > aeq <- function(x,y) all.equal(as.vector(x), as.vector(y)) 237s > 237s > tmat <- bdsmatrix(c(3,2,2,4), 237s + c(22,1,2,21,3,20,19,4,18,17,5,16,15,6,7, 8,14,9,10,13,11,12), 237s + matrix(c(1,0,1,1,0,0,1,1,0,1,0,10,0, 237s + 0,1,1,0,1,1,0,1,1,0,1,0,10), ncol=2)) 237s > dimnames(tmat) <- list(NULL, letters[1:13]) 237s > 237s > smat <- as.matrix(tmat) 237s > 237s > aeq(smat+2.1, as.matrix(tmat+2.1)) 237s [1] TRUE 237s > aeq(smat/2.1, as.matrix(tmat/2.1)) 237s [1] TRUE 237s > aeq(smat-2.1, as.matrix(tmat-2.1)) 237s [1] TRUE 237s > aeq(smat*2.1, as.matrix(tmat*2.1)) 237s [1] TRUE 237s > aeq(round(smat,1), as.matrix(round(tmat,1))) 237s [1] TRUE 237s > aeq(exp(smat), as.matrix(exp(tmat))) 237s [1] TRUE 237s > 237s > aeq(sum(smat), sum(tmat)) 237s [1] TRUE 237s > aeq(prod(smat), prod(tmat)) 237s [1] TRUE 237s > aeq(sum(smat+3), sum(tmat+3)) 237s [1] TRUE 237s > aeq(prod(smat+2), prod(tmat+2)) 237s [1] TRUE 237s > aeq(range(smat), range(tmat)) 237s [1] TRUE 237s > aeq(max(smat), max(tmat)) 237s [1] TRUE 237s > aeq(min(smat), min(tmat)) 237s [1] TRUE 237s > 237s > aeq(smat+1:13, tmat+1:13) 237s [1] TRUE 237s > aeq(smat+1:13, 1:13 +tmat ) 237s [1] TRUE 237s > aeq(smat+tmat, 2*smat) 237s [1] TRUE 237s > all.equal(tmat+tmat, 2*tmat) 237s [1] TRUE 237s > 237s > aeq(sort(unique(c(smat))), sort(unique(tmat))) 237s [1] TRUE 237s > 237s > # 237s > # check out the alternate input style, with full blocks 237s > # 237s > rmat <- bdsmatrix(c(3,2,2,4), 237s + c(22,1,2,1,21,3,2,3,20, 19,4,4,18, 17,5,5,16, 237s + 15,6,7,8,6,14,9,10,7,9,13,11,8,10,11,12), 237s + matrix(c(1,0,1,1,0,0,1,1,0,1,0,10,0, 237s + 0,1,1,0,1,1,0,1,1,0,1,0,10), ncol=2), 237s + dimnames=list(NULL, letters[1:13])) 237s > all.equal(rmat, tmat) 237s [1] TRUE 237s > 237s > 237s > # Do some subscripting 237s > zz <- c(1,2,7,8,9,11) 237s > aeq(smat[zz,zz], as.matrix(tmat[zz,zz])) 237s [1] TRUE 237s > 237s > all.equal(smat[zz, 8:13], tmat[zz, 8:13]) # both are matrices 237s [1] TRUE 237s > 237s > # Diagonals 237s > aeq(diag(smat), diag(tmat)) 237s [1] TRUE 237s > zz <- diag(smat) 237s > diag(smat) <- zz*2 237s > diag(tmat) <- zz*2 237s > all.equal(smat, as.matrix(tmat)) 237s [1] TRUE 237s > 237s BEGIN TEST chtest.R 237s 237s R version 4.4.3 (2025-02-28) -- "Trophy Case" 237s Copyright (C) 2025 The R Foundation for Statistical Computing 237s Platform: aarch64-unknown-linux-gnu 237s 237s R is free software and comes with ABSOLUTELY NO WARRANTY. 237s You are welcome to redistribute it under certain conditions. 237s Type 'license()' or 'licence()' for distribution details. 237s 237s R is a collaborative project with many contributors. 237s Type 'contributors()' for more information and 237s 'citation()' on how to cite R or R packages in publications. 237s 237s Type 'demo()' for some demos, 'help()' for on-line help, or 237s 'help.start()' for an HTML browser interface to help. 237s Type 'q()' to quit R. 237s 238s > # 238s > # Test out the Cholesky 238s > # 238s > library(bdsmatrix) 238s 238s Attaching package: 'bdsmatrix' 238s 238s > aeq <- function(x,y) all.equal(as.vector(x), as.vector(y)) 238s > 238s > tmat <- bdsmatrix(c(3,2,2,4), 238s + c(22,1,2,21,3,20,19,4,18,17,5,16,15,6,7, 8,14,9,10,13,11,12), 238s + matrix(c(1,0,1,1,0,0,1,1,0,1,0,10,0, 238s + 0,1,1,0,1,1,0,1,1,0,1,0,10), ncol=2)) 238s > dimnames(tmat) <- list(NULL, letters[1:13]) 238s > smat <- as.matrix(tmat) 238s > yy <- c(30,35,42,56,34,45,32,37,78,56,40,52,39) 238s > 238s > aeq(diag(tmat), diag(smat)) 238s The following object is masked from 'package:base': 238s 238s backsolve 238s 238s [1] TRUE 238s > zz <- seq(1,13,2) 238s > aeq(as.matrix(tmat[zz,zz]), smat[zz,zz]) 238s [1] TRUE 238s > 238s > ch0 <- chol(smat) 238s > ch1 <- gchol(smat) 238s > ch2 <- gchol(tmat) 238s > # The gchol routines use the composition LDL', where L is lower triangular 238s > # with a diagonal of 1's, and D is diagonal. chol() uses U'U where U is 238s > # upper trangular. 238s > # The as.matrix function returns L and the diag function returns D. 238s > # Convert and compare 238s > aeq(diag(ch1), diag(ch2)) 238s [1] TRUE 238s > temp <- as.matrix(ch2) 238s > aeq(temp, as.matrix(ch1)) 238s [1] TRUE 238s > temp3 <- temp %*% diag(sqrt(diag(ch2))) 238s > aeq(temp3, t(ch0)) 238s [1] TRUE 238s > 238s > zz0 <- solve(smat, yy) 238s > zz1 <- solve(ch1, yy) 238s > zz2 <- solve(tmat, yy) 238s > aeq(zz1, zz2) 238s [1] TRUE 238s > aeq(zz0, zz1) 238s [1] TRUE 238s > 238s > 238s BEGIN TEST chtest2.R 238s 238s R version 4.4.3 (2025-02-28) -- "Trophy Case" 238s Copyright (C) 2025 The R Foundation for Statistical Computing 238s Platform: aarch64-unknown-linux-gnu 238s 238s R is free software and comes with ABSOLUTELY NO WARRANTY. 238s You are welcome to redistribute it under certain conditions. 238s Type 'license()' or 'licence()' for distribution details. 238s 238s R is a collaborative project with many contributors. 238s Type 'contributors()' for more information and 238s 'citation()' on how to cite R or R packages in publications. 238s 238s Type 'demo()' for some demos, 'help()' for on-line help, or 238s 'help.start()' for an HTML browser interface to help. 238s Type 'q()' to quit R. 238s 238s > # 238s > # Inverse of the matrix: 238s > # 238s > library(bdsmatrix) 238s > aeq <- function(x,y) all.equal(as.vector(x), as.vector(y)) 238s > 238s > tmat <- bdsmatrix(c(3,2,2,4), 238s + c(22,1,2,21,3,20,19,4,18,17,5,16,15,6,7, 8,14,9,10,13,11,12), 238s + matrix(c(1,0,1,1,0,0,1,1,0,1,0,10,0, 238s + 0,1,1,0,1,1,0,1,1,0,1,0,10), ncol=2)) 238s > dimnames(tmat) <- list(NULL, letters[1:13]) 238s > 238s > smat <- as.matrix(tmat) 238s > 238s > inv1 <- solve(smat) 238s > inv2 <- as.matrix(solve(tmat)) # the result is a full, non-sparse matrix 238s 238s Attaching package: 'bdsmatrix' 238s 238s The following object is masked from 'package:base': 238s 238s backsolve 238s 238s > aeq(inv1, inv2) 238s [1] TRUE 238s > 238s > inv3 <- solve(gchol(tmat)) #sparse version, not all parts will be there 238s > inherits(inv3, 'bdsmatrix') #This should be true 238s [1] TRUE 238s > aeq(inv3@blocksize, tmat@blocksize) # Should be the same shape at tmat 238s [1] TRUE 238s > inv3 <- as.matrix(inv3) # What is returned should be correct 238s > aeq(inv1[1:3,1:3], inv3[1:3, 1:3]) 238s [1] TRUE 238s > aeq(inv1[4:5,4:5], inv3[4:5, 4:5]) 238s [1] TRUE 238s > aeq(inv1[6:7,6:7], inv3[6:7, 6:7]) 238s [1] TRUE 238s > aeq(inv1[8:11,8:11], inv3[8:11, 8:11]) 238s [1] TRUE 238s > aeq(inv1[,12:13], inv3[, 12:13]) # and rmat the same too 238s [1] TRUE 238s > 238s BEGIN TEST corner.R 238s 238s R version 4.4.3 (2025-02-28) -- "Trophy Case" 238s Copyright (C) 2025 The R Foundation for Statistical Computing 238s Platform: aarch64-unknown-linux-gnu 238s 238s R is free software and comes with ABSOLUTELY NO WARRANTY. 238s You are welcome to redistribute it under certain conditions. 238s Type 'license()' or 'licence()' for distribution details. 238s 238s R is a collaborative project with many contributors. 238s Type 'contributors()' for more information and 238s 'citation()' on how to cite R or R packages in publications. 238s 238s Type 'demo()' for some demos, 'help()' for on-line help, or 238s 'help.start()' for an HTML browser interface to help. 238s Type 'q()' to quit R. 238s 238s > # 238s > # Test out the behavior of a 1x1 bds corner. 238s > # Actually, the problem that motivated this occurred whenever the 238s > # rmat portion was larger than the block diagonal portion. 238s > # 238s > library(bdsmatrix) 239s > test1 <- bdsmatrix(blocksize=1, blocks=33, 239s + rmat=matrix(c(17,33,7,-1, -7,7,48,-7, 239s + 1, -1, -7,4),4)) 239s > 239s > test2 <- bdsmatrix(blocksize=2, blocks=c(33,17,33), 239s + rmat=matrix(c( -7,7,48,-7, 1, -1, -7,4),4)) 239s > all.equal(as.matrix(test1), as.matrix(test2)) 239s 239s Attaching package: 'bdsmatrix' 239s 239s The following object is masked from 'package:base': 239s 239s backsolve 239s 239s [1] TRUE 239s > 239s > g1 <- gchol(test1) 239s > g2 <- gchol(test2) 239s > all.equal(as.matrix(g1), as.matrix(g2)) 239s [1] TRUE 239s > 239s > s1 <- solve(g1, full=T) 239s > s2 <- solve(g2, full=T) 239s > all.equal(as.matrix(s1), as.matrix(s2)) 239s [1] TRUE 239s > 239s > all.equal(solve(test1), solve(test2)) 239s [1] TRUE 239s > 239s BEGIN TEST corner2.R 239s 239s R version 4.4.3 (2025-02-28) -- "Trophy Case" 239s Copyright (C) 2025 The R Foundation for Statistical Computing 239s Platform: aarch64-unknown-linux-gnu 239s 239s R is free software and comes with ABSOLUTELY NO WARRANTY. 239s You are welcome to redistribute it under certain conditions. 239s Type 'license()' or 'licence()' for distribution details. 239s 239s R is a collaborative project with many contributors. 239s Type 'contributors()' for more information and 239s 'citation()' on how to cite R or R packages in publications. 239s 239s Type 'demo()' for some demos, 'help()' for on-line help, or 239s 'help.start()' for an HTML browser interface to help. 239s Type 'q()' to quit R. 239s 239s > # 239s > # Test out the Cholesky, special case of a null block corner 239s > # In this case there is no advantage to a bdsmatrix as it consists of only 239s > # the ordinary matrix part. This case arises in coxme with an (x1+x2 | 1) 239s > # term, however, so it is nice to have it work instead of coding lots of 239s > # if/else logic in that code base. 239s > # 239s > library(bdsmatrix) 239s > aeq <- function(x,y) all.equal(as.vector(x), as.vector(y)) 239s > 239s > tmat <- bdsmatrix(c(3,2,2,4), 239s + c(22,1,2,21,3,20,19,4,18,17,5,16,15,6,7, 8,14,9,10,13,11,12), 239s + matrix(c(1,0,1,1,0,0,1,1,0,1,0,10,0, 239s + 0,1,1,0,1,1,0,1,1,0,1,0,10), ncol=2)) 239s > dimnames(tmat) <- list(NULL, letters[1:13]) 239s > smat <- as.matrix(tmat) 239s > tmat <- bdsmatrix(integer(0), numeric(0), rmat=smat) 239s > yy <- c(30,35,42,56,34,45,32,37,78,56,40,52,39) 239s > 239s > aeq(diag(tmat), diag(smat)) 239s [1] TRUE 239s > zz <- seq(1,13,2) 239s > aeq(as.matrix(tmat[zz,zz]), smat[zz,zz]) 239s 239s Attaching package: 'bdsmatrix' 239s 239s The following object is masked from 'package:base': 239s 239s backsolve 239s 239s [1] TRUE 239s > 239s > ch0 <- chol(smat) 239s > ch1 <- gchol(smat) 239s > ch2 <- gchol(tmat) 239s > # The gchol routines use the composition LDL', where L is lower triangular 239s > # with a diagonal of 1's, and D is diagonal. chol() uses U'U where U is 239s > # upper trangular. 239s > # The as.matrix function returns L and the diag function returns D. 239s > # Convert and compare 239s > aeq(diag(ch1), diag(ch2)) 239s [1] TRUE 239s > temp <- as.matrix(ch2) 239s > aeq(temp, as.matrix(ch1)) 239s [1] TRUE 239s > temp3 <- temp %*% diag(sqrt(diag(ch2))) 239s > aeq(temp3, t(ch0)) 239s [1] TRUE 239s > 239s > zz0 <- solve(smat, yy) 239s > zz1 <- solve(ch1, yy) 239s > zz2 <- solve(tmat, yy) 239s > aeq(zz1, zz2) 239s [1] TRUE 239s > aeq(zz0, zz1) 239s [1] TRUE 239s > 239s > inv1 <- solve(smat) 239s > inv2 <- as.matrix(solve(tmat)) # the result is a full, non-sparse matrix 239s > aeq(inv1, inv2) 239s [1] TRUE 239s > 239s > inv3 <- solve(gchol(tmat)) 239s > aeq(inv1, as.matrix(inv3)) 239s [1] TRUE 239s > 239s > gmat <- gchol(tmat) 239s > g2 <- as.matrix(gmat) %*% diag(sqrt(diag(gmat))) 239s > aeq(1:13 %*% g2, 1:13 %*% gmat) #vectors first 239s [1] TRUE 239s > aeq(g2 %*% 1:13, gmat %*% 1:13) 239s [1] TRUE 239s > temp <- matrix(runif(39), nrow=3) 239s > aeq(temp %*% g2, temp %*% gmat) 239s [1] TRUE 239s > aeq(g2 %*% t(temp), gmat %*% t(temp)) 239s [1] TRUE 239s > 239s BEGIN TEST gtest.R 239s 239s R version 4.4.3 (2025-02-28) -- "Trophy Case" 239s Copyright (C) 2025 The R Foundation for Statistical Computing 239s Platform: aarch64-unknown-linux-gnu 239s 239s R is free software and comes with ABSOLUTELY NO WARRANTY. 239s You are welcome to redistribute it under certain conditions. 239s Type 'license()' or 'licence()' for distribution details. 239s 239s R is a collaborative project with many contributors. 239s Type 'contributors()' for more information and 239s 'citation()' on how to cite R or R packages in publications. 239s 239s Type 'demo()' for some demos, 'help()' for on-line help, or 239s 'help.start()' for an HTML browser interface to help. 239s Type 'q()' to quit R. 239s 239s > library(bdsmatrix) 239s > aeq <- function(x,y) all.equal(as.vector(x), as.vector(y)) 239s > 239s > tmat <- bdsmatrix(c(3,2,2,4), 239s + c(22,1,2,21,3,20,19,4,18,17,5,16,15,6,7, 8,14,9,10,13,11,12), 239s + matrix(c(1,0,1,1,0,0,1,1,0,1,0,10,0, 239s + 0,1,1,0,1,1,0,1,1,0,1,0,10), ncol=2)) 239s > dimnames(tmat) <- list(NULL, letters[1:13]) 239s > 239s > smat <- as.matrix(tmat) 239s > 239s > # Create a matrix that is symmetric, but not positive definite 239s > # The first one, temp, has column 6 redundant with cols 1-5 239s > temp <- smat[c(1:5, 5:10), c(1:5, 5:10)] 239s > ch1 <- gchol(temp) 239s > aeq(diag(ch1)[6], 0) # Check that it has a zero in the proper place 239s [1] TRUE 239s > ginv <- solve(ch1) # see if I get a generalized inverse 239s > aeq(temp %*% ginv %*% temp, temp) 239s 239s Attaching package: 'bdsmatrix' 239s 239s The following object is masked from 'package:base': 239s 239s backsolve 239s 239s [1] TRUE 239s > aeq(ginv %*% temp %*% ginv, ginv) 239s [1] TRUE 239s > 239s > # Now create one that is negative definite 239s > ch2 <- gchol(smat) 239s > temp2 <- as.matrix(ch2) 239s > temp3 <- diag(ch2) * rep(c(1, -1), length=nrow(smat)) 239s > xmat <- temp2 %*% diag(temp3) %*% t(temp2) 239s > xmat <- (xmat + t(xmat))/2 #work out round-off errors 239s > ch3 <- gchol(xmat) 239s > 239s > aeq(diag(ch3), temp3) 239s [1] TRUE 239s > aeq(as.matrix(ch3), temp2) 239s [1] TRUE 239s > 239s BEGIN TEST gtest2.R 239s 239s R version 4.4.3 (2025-02-28) -- "Trophy Case" 239s Copyright (C) 2025 The R Foundation for Statistical Computing 239s Platform: aarch64-unknown-linux-gnu 239s 239s R is free software and comes with ABSOLUTELY NO WARRANTY. 239s You are welcome to redistribute it under certain conditions. 239s Type 'license()' or 'licence()' for distribution details. 239s 239s R is a collaborative project with many contributors. 239s Type 'contributors()' for more information and 239s 'citation()' on how to cite R or R packages in publications. 239s 239s Type 'demo()' for some demos, 'help()' for on-line help, or 239s 'help.start()' for an HTML browser interface to help. 239s Type 'q()' to quit R. 239s 239s > library(bdsmatrix) 240s > aeq <- function(x,y) all.equal(as.vector(x), as.vector(y)) 240s > 240s > # 240s > # Test multiplication of a vector/matrix times a gchol 240s > # 240s > tmat <- bdsmatrix(c(3,2,2,4), 240s + c(22,1,2,21,3,20,19,4,18,17,5,16,15,6,7, 8,14,9,10,13,11,12), 240s + matrix(c(1,0,1,1,0,0,1,1,0,1,0,10,0, 240s + 0,1,1,0,1,1,0,1,1,0,1,0,10), ncol=2)) 240s > dimnames(tmat) <- list(NULL, letters[1:13]) 240s > 240s > gmat <- gchol(tmat) 240s > g2 <- as.matrix(gmat) %*% diag(sqrt(diag(gmat))) 240s > 240s > 240s > aeq(1:13 %*% g2, 1:13 %*% gmat) #vectors first 240s 240s Attaching package: 'bdsmatrix' 240s 240s The following object is masked from 'package:base': 240s 240s backsolve 240s 240s [1] TRUE 240s > aeq(g2 %*% 1:13, gmat %*% 1:13) 240s [1] TRUE 240s > 240s > temp <- matrix(runif(39), nrow=3) 240s > aeq(temp %*% g2, temp %*% gmat) 240s [1] TRUE 240s > aeq(g2 %*% t(temp), gmat %*% t(temp)) 240s [1] TRUE 240s > 240s BEGIN TEST matrix.R 240s 240s R version 4.4.3 (2025-02-28) -- "Trophy Case" 240s Copyright (C) 2025 The R Foundation for Statistical Computing 240s Platform: aarch64-unknown-linux-gnu 240s 240s R is free software and comes with ABSOLUTELY NO WARRANTY. 240s You are welcome to redistribute it under certain conditions. 240s Type 'license()' or 'licence()' for distribution details. 240s 240s R is a collaborative project with many contributors. 240s Type 'contributors()' for more information and 240s 'citation()' on how to cite R or R packages in publications. 240s 240s Type 'demo()' for some demos, 'help()' for on-line help, or 240s 'help.start()' for an HTML browser interface to help. 240s Type 'q()' to quit R. 240s 240s > library(bdsmatrix) 240s > aeq <- function(x,y) all.equal(as.vector(x), as.vector(y)) 240s > 240s > tmat <- bdsmatrix(c(3,2,2,4), 240s + c(22,1,2,21,3,20,19,4,18,17,5,16,15,6,7, 8,14,9,10,13,11,12), 240s + matrix(c(1,0,1,1,0,0,1,1,0,1,0,10,0, 240s + 0,1,1,0,1,1,0,1,1,0,1,0,10), ncol=2)) 240s 240s Attaching package: 'bdsmatrix' 240s 240s The following object is masked from 'package:base': 240s 240s backsolve 240s 240s > dimnames(tmat) <- list(NULL, letters[1:13]) 240s > 240s > smat <- as.matrix(tmat) 240s > yy <- c(30,35,42,56,34,45,32,37,78,56,40,52,39) 240s > 240s > # matrix multiplication 240s > zz <- runif(13) 240s > aeq(zz%*% smat, zz%*% tmat) 240s [1] TRUE 240s > aeq(smat%*%zz, tmat%*% zz) 240s [1] TRUE 240s > 240s > xx <- matrix(1:39, ncol=3) 240s > aeq(smat %*% zz, tmat %*% zz) 240s [1] TRUE 240s > aeq(t(xx) %*% smat, t(xx) %*% tmat) 240s [1] TRUE 240s > 240s > 240s > amat <- tmat 240s > amat@offdiag <- pi 240s > bmat <- as.matrix(amat) 240s > 240s > aeq(zz%*% amat, zz%*% bmat) 240s [1] TRUE 240s > aeq(amat%*%zz, bmat%*% zz) 240s [1] TRUE 240s > 240s > 240s > # Solve the right-hand side wrt a matrix 240s > yy2 <- cbind(yy, -yy, yy+3) 240s > zz1 <- solve(smat, yy2) 240s > zz2 <- solve(tmat, yy2) 240s > aeq(zz1, zz2) 240s [1] TRUE 240s > aeq(zz2[,1], solve(tmat, yy)) 240s [1] TRUE 240s > 240s BEGIN TEST nullr.R 240s 240s R version 4.4.3 (2025-02-28) -- "Trophy Case" 240s Copyright (C) 2025 The R Foundation for Statistical Computing 240s Platform: aarch64-unknown-linux-gnu 240s 240s R is free software and comes with ABSOLUTELY NO WARRANTY. 240s You are welcome to redistribute it under certain conditions. 240s Type 'license()' or 'licence()' for distribution details. 240s 240s R is a collaborative project with many contributors. 240s Type 'contributors()' for more information and 240s 'citation()' on how to cite R or R packages in publications. 240s 240s Type 'demo()' for some demos, 'help()' for on-line help, or 240s 'help.start()' for an HTML browser interface to help. 240s Type 'q()' to quit R. 240s 240s > # 240s > # Make sure things work in the simpler case of no rmat component 240s > # 240s > library(bdsmatrix) 240s > aeq <- function(x,y) all.equal(as.vector(x), as.vector(y)) 240s > 240s > tmat <- bdsmatrix(blocksize= c(3,2,2,4), 240s + blocks= c(22,1,2,21,3,20,19,4,18,17,5,16,15,6,7, 240s + 8,14,9,10,13,11,12)) 240s 240s Attaching package: 'bdsmatrix' 240s 240s The following object is masked from 'package:base': 240s 240s backsolve 240s 240s > dimnames(tmat) <- list(NULL, letters[1:11]) 240s > smat <- as.matrix(tmat) 240s > yy <- c(30,35,42,56,34,45,32,37,78,56,40) 240s > 240s > aeq(diag(tmat), diag(smat)) 240s [1] TRUE 240s > zz <- seq(1,11,2) 240s > aeq(as.matrix(tmat[zz,zz]), smat[zz,zz]) 240s [1] TRUE 240s > 240s > ch0 <- chol(smat) 240s > ch1 <- gchol(smat) 240s > ch2 <- gchol(tmat) 240s > 240s > aeq(diag(ch1), diag(ch2)) 240s [1] TRUE 240s > temp <- as.matrix(ch2) 240s > aeq(temp, as.matrix(ch1)) 240s [1] TRUE 240s > temp3 <- temp %*% diag(sqrt(diag(ch2))) 241s > aeq(temp3, t(ch0)) 241s [1] TRUE 241s > 241s > zz0 <- solve(smat, yy) 241s > zz1 <- solve(ch1, yy) 241s > zz2 <- solve(tmat, yy) 241s > aeq(zz1, zz2) 241s [1] TRUE 241s > aeq(zz0, zz1) 241s [1] TRUE 241s > 241s BEGIN TEST reconcile.R 241s 241s R version 4.4.3 (2025-02-28) -- "Trophy Case" 241s Copyright (C) 2025 The R Foundation for Statistical Computing 241s Platform: aarch64-unknown-linux-gnu 241s 241s R is free software and comes with ABSOLUTELY NO WARRANTY. 241s You are welcome to redistribute it under certain conditions. 241s Type 'license()' or 'licence()' for distribution details. 241s 241s R is a collaborative project with many contributors. 241s Type 'contributors()' for more information and 241s 'citation()' on how to cite R or R packages in publications. 241s 241s Type 'demo()' for some demos, 'help()' for on-line help, or 241s 'help.start()' for an HTML browser interface to help. 241s Type 'q()' to quit R. 241s 241s > # 241s > # Test cases for bdsmatrix.reconcile 241s > # 241s > library(bdsmatrix) 241s 241s Attaching package: 'bdsmatrix' 241s 241s The following object is masked from 'package:base': 241s 241s backsolve 241s 241s > aeq <- function(x,y) all.equal(as.vector(x), as.vector(y)) 241s > 241s > tmat <- bdsmatrix(c(3,2,2,4), 241s + c(22,1,2,21,3,20,19,4,18,17,5,16,15,6,7, 8,14,9,10,13,11,12), 241s + matrix(c(1,0,1,1,0,0,1,1,0,1,0,10,0, 241s + 0,1,1,0,1,1,0,1,1,0,1,0,10), ncol=2)) 241s > id <- letters[1:13] 241s > dimnames(tmat) <- list(id, id) 241s > 241s > rmat <- matrix(1:169, 13,13) 241s > rmat <- (rmat + t(rmat))/2 241s > dimnames(rmat) <- list(rev(id), rev(id)) 241s > 241s > xmat <- bdsmatrix.reconcile(list(tmat, rmat), group=id) 241s > temp <- xmat[[1]] 241s > aeq(temp@blocksize, 13) 241s [1] TRUE 241s > aeq(as.matrix(temp), as.matrix(tmat)) 241s [1] TRUE 241s > 241s > temp <- xmat[[2]] 241s > aeq(temp@blocksize, 13) 241s [1] TRUE 241s > aeq(as.matrix(temp), rmat[13:1, 13:1]) 241s [1] TRUE 241s > 241s > xmat <- bdsmatrix.reconcile(list(rmat, bdsI, tmat), group= rev(id)) 241s > temp <- xmat[[1]] 241s > aeq(as.matrix(temp), rmat) 241s [1] TRUE 241s > 241s > temp <- xmat[[2]] 241s > aeq(as.matrix(temp), diag(13)) 241s [1] TRUE 241s > 241s > temp <- xmat[[3]] 241s > aeq(as.matrix(temp), (as.matrix(tmat))[13:1,13:1]) 241s [1] TRUE 241s > 241s > # 241s > # Simplest case 241s > # 241s > xmat <- bdsmatrix.reconcile(bdsI, id) 241s > all(xmat@blocksize==1) 241s [1] TRUE 241s > aeq(as.matrix(xmat), diag(13)) 241s [1] TRUE 241s > 241s > # 241s > # The case list(tmat, tmat) will fail - can't have 2 rmats 241s > # 241s > #xmat <- bdsmatrix.reconcile(list(tmat, tmat), id) 241s > 241s > xmat <- bdsmatrix.reconcile(list(tmat, bdsI), rev(id)) 241s > temp <- xmat[[1]] 241s > aeq(as.matrix(temp), as.matrix(tmat)) 241s [1] TRUE 241s > aeq(dimnames(temp)[[1]], id) 241s [1] TRUE 241s > 241s > aeq(as.matrix(xmat[[2]]), diag(13)) 241s [1] TRUE 241s > 241s > # 241s > # Now for the hard one: 2 bdsmatrices, different orders, different 241s > # blocksize, but one contains the other 241s > # 241s > tmat <- tmat[1:11, 1:11] 241s > tord <- c(11:8, 2,1,3, 6,7,5,4) 241s > rmat <- (as.matrix(tmat))[tord, tord] 241s > rmat <- bdsmatrix(blocksize=c(4,5,2), 241s + blocks=c(rmat[1:4,1:4], rmat[5:9,5:9], rmat[10:11, 10:11]), 241s + dimnames=list(id[tord], id[tord])) 241s > 241s > aeq(as.matrix(tmat)[tord,tord], as.matrix(rmat)) 241s [1] TRUE 241s > 241s > xmat <- bdsmatrix.reconcile(list(tmat/2, rmat), id[1:11]) 241s > all.equal(xmat[[2]], rmat) 241s [1] TRUE 241s > all.equal(xmat[[1]]*2, rmat) 241s [1] TRUE 241s > 241s > # Now toss out a row/col 241s > # Give it a different name, too 241s > xx <- id[tord] 241s > xx[1] <- 44 241s > dimnames(rmat) <- list(xx,xx) 241s > xmat <- bdsmatrix.reconcile(list(tmat/2, rmat), id[1:9]) 241s > all.equal(xmat[[1]]*2, xmat[[2]]) 241s [1] TRUE 241s > 241s BEGIN TEST tinv.R 241s 241s R version 4.4.3 (2025-02-28) -- "Trophy Case" 241s Copyright (C) 2025 The R Foundation for Statistical Computing 241s Platform: aarch64-unknown-linux-gnu 241s 241s R is free software and comes with ABSOLUTELY NO WARRANTY. 241s You are welcome to redistribute it under certain conditions. 241s Type 'license()' or 'licence()' for distribution details. 241s 241s R is a collaborative project with many contributors. 241s Type 'contributors()' for more information and 241s 'citation()' on how to cite R or R packages in publications. 241s 241s Type 'demo()' for some demos, 'help()' for on-line help, or 241s 'help.start()' for an HTML browser interface to help. 241s Type 'q()' to quit R. 241s 241s > library(bdsmatrix) 241s 241s Attaching package: 'bdsmatrix' 241s 241s The following object is masked from 'package:base': 241s 241s backsolve 241s 241s > aeq <- function(x,y) all.equal(as.vector(x), as.vector(y)) 241s > 241s > tmat <- bdsmatrix(c(3,2,2,4), 241s + c(22,1,2,21,3,20,19,4,18,17,5,16,15,6,7, 8,14,9,10,13,11,12), 241s + matrix(c(1,0,1,1,0,0,1,1,0,1,0,10,0, 241s + 0,1,1,0,1,1,0,1,1,0,1,0,10), ncol=2)) 241s > dimnames(tmat) <- list(NULL, letters[1:13]) 241s > 241s > smat <- as.matrix(tmat) 241s > yy <- c(30,35,42,56,34,45,32,37,78,56,40,52,39) 241s > # look at inverses more closely 241s > # (I needed this when some of the other tests weren't being passed, 241s > # to figure out where in the decomposition/inversion/multiply process 241s > # the flaw was). 241s > 241s > ch1 <- gchol(smat) 241s > ch2 <- gchol(tmat) 241s > 241s > inv1 <- solve(as.matrix(ch1)) 241s > inv2 <- solve(ch2,full=F) #inverse of the cholesky, not of tmat 241s > aeq(inv1, as.matrix(inv2)) 241s [1] TRUE 241s > 241s > # Full matrix tests 241s > inv3 <- solve(smat) 241s > inv4 <- solve(tmat) 241s > inv5 <- solve(gchol(smat), full=T) 241s > aeq(inv3, inv4) 241s [1] TRUE 241s > aeq(inv3, inv5) 241s [1] TRUE 241s > 241s > # The following test is false by design: when called with a bdsmatrix 241s > # object that has an rmat portion, the true inverse is dense. But 241s > # coxme only needs the trace for one calcluation; solve(gchol(tmat)) 241s > # cheats and only returns the block diagonal portion of the inverse. 241s > #inv6 <- solve(gchol(tmat), full=T) 241s > #aeq(inv3, inv6) 241s > 241s > # 241s > # Now test the solution to a partial solve 241s > # We want to be able to transform a matrix to uncorrelated form 241s > # If tmat= LDL', and A is general, I want (D^{-1/2}) L^{-1} A 241s > # 241s > amat <- matrix(runif(5*nrow(tmat)), nrow=nrow(tmat)) 241s > xx1 <- diag(1/sqrt(diag(ch1))) %*% solve(as.matrix(ch1), amat) 241s > xx2 <- solve(ch2, amat, full=F) 241s > aeq(xx1, xx2) 241s [1] TRUE 241s > 241s > xx1 <- diag(1/sqrt(diag(ch1))) %*% solve(as.matrix(ch1), yy) 241s > xx2 <- solve(ch2, yy, full=F) 241s > aeq(xx1, xx2) 241s [1] TRUE 241s > 242s autopkgtest [15:23:31]: test run-unit-test: -----------------------] 242s autopkgtest [15:23:31]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 242s run-unit-test PASS 243s autopkgtest [15:23:32]: test pkg-r-autopkgtest: preparing testbed 243s Reading package lists... 243s Building dependency tree... 243s Reading state information... 244s Starting pkgProblemResolver with broken count: 0 244s Starting 2 pkgProblemResolver with broken count: 0 244s Done 244s The following NEW packages will be installed: 244s build-essential cpp cpp-14 cpp-14-aarch64-linux-gnu cpp-aarch64-linux-gnu 244s dctrl-tools g++ g++-14 g++-14-aarch64-linux-gnu g++-aarch64-linux-gnu gcc 244s gcc-14 gcc-14-aarch64-linux-gnu gcc-aarch64-linux-gnu gfortran gfortran-14 244s gfortran-14-aarch64-linux-gnu gfortran-aarch64-linux-gnu icu-devtools 244s libasan8 libblas-dev libbz2-dev libcc1-0 libdeflate-dev libgcc-14-dev 244s libgfortran-14-dev libhwasan0 libicu-dev libisl23 libitm1 libjpeg-dev 244s libjpeg-turbo8-dev libjpeg8-dev liblapack-dev liblsan0 liblzma-dev libmpc3 244s libncurses-dev libpcre2-16-0 libpcre2-32-0 libpcre2-dev libpcre2-posix3 244s libpkgconf3 libpng-dev libreadline-dev libstdc++-14-dev libtirpc-dev 244s libtsan2 libubsan1 pkg-r-autopkgtest pkgconf pkgconf-bin r-base-dev 244s zlib1g-dev 245s 0 upgraded, 54 newly installed, 0 to remove and 0 not upgraded. 245s Need to get 92.7 MB of archives. 245s After this operation, 334 MB of additional disk space will be used. 245s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 libisl23 arm64 0.27-1 [676 kB] 245s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 libmpc3 arm64 1.3.1-1build2 [56.8 kB] 245s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp-14-aarch64-linux-gnu arm64 14.2.0-17ubuntu3 [10.6 MB] 246s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp-14 arm64 14.2.0-17ubuntu3 [1028 B] 246s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp-aarch64-linux-gnu arm64 4:14.2.0-1ubuntu1 [5558 B] 246s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp arm64 4:14.2.0-1ubuntu1 [22.4 kB] 246s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 libcc1-0 arm64 15-20250222-0ubuntu1 [44.2 kB] 246s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 libitm1 arm64 15-20250222-0ubuntu1 [28.0 kB] 246s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 libasan8 arm64 15-20250222-0ubuntu1 [2924 kB] 247s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 liblsan0 arm64 15-20250222-0ubuntu1 [1319 kB] 247s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 libtsan2 arm64 15-20250222-0ubuntu1 [2694 kB] 247s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 libubsan1 arm64 15-20250222-0ubuntu1 [1178 kB] 247s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 libhwasan0 arm64 15-20250222-0ubuntu1 [1642 kB] 247s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 libgcc-14-dev arm64 14.2.0-17ubuntu3 [2593 kB] 247s Get:15 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc-14-aarch64-linux-gnu arm64 14.2.0-17ubuntu3 [20.9 MB] 249s Get:16 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc-14 arm64 14.2.0-17ubuntu3 [526 kB] 249s Get:17 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc-aarch64-linux-gnu arm64 4:14.2.0-1ubuntu1 [1200 B] 249s Get:18 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc arm64 4:14.2.0-1ubuntu1 [4998 B] 249s Get:19 http://ftpmaster.internal/ubuntu plucky/main arm64 libstdc++-14-dev arm64 14.2.0-17ubuntu3 [2499 kB] 250s Get:20 http://ftpmaster.internal/ubuntu plucky/main arm64 g++-14-aarch64-linux-gnu arm64 14.2.0-17ubuntu3 [12.1 MB] 251s Get:21 http://ftpmaster.internal/ubuntu plucky/main arm64 g++-14 arm64 14.2.0-17ubuntu3 [21.8 kB] 251s Get:22 http://ftpmaster.internal/ubuntu plucky/main arm64 g++-aarch64-linux-gnu arm64 4:14.2.0-1ubuntu1 [956 B] 251s Get:23 http://ftpmaster.internal/ubuntu plucky/main arm64 g++ arm64 4:14.2.0-1ubuntu1 [1080 B] 251s Get:24 http://ftpmaster.internal/ubuntu plucky/main arm64 build-essential arm64 12.10ubuntu1 [4932 B] 251s Get:25 http://ftpmaster.internal/ubuntu plucky/main arm64 dctrl-tools arm64 2.24-3build3 [103 kB] 251s Get:26 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran-14-dev arm64 14.2.0-17ubuntu3 [498 kB] 251s Get:27 http://ftpmaster.internal/ubuntu plucky/main arm64 gfortran-14-aarch64-linux-gnu arm64 14.2.0-17ubuntu3 [11.4 MB] 252s Get:28 http://ftpmaster.internal/ubuntu plucky/main arm64 gfortran-14 arm64 14.2.0-17ubuntu3 [13.6 kB] 252s Get:29 http://ftpmaster.internal/ubuntu plucky/main arm64 gfortran-aarch64-linux-gnu arm64 4:14.2.0-1ubuntu1 [1022 B] 252s Get:30 http://ftpmaster.internal/ubuntu plucky/main arm64 gfortran arm64 4:14.2.0-1ubuntu1 [1166 B] 252s Get:31 http://ftpmaster.internal/ubuntu plucky/main arm64 icu-devtools arm64 76.1-1ubuntu2 [213 kB] 252s Get:32 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas-dev arm64 3.12.1-2 [126 kB] 252s Get:33 http://ftpmaster.internal/ubuntu plucky/main arm64 libbz2-dev arm64 1.0.8-6 [36.1 kB] 252s Get:34 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate-dev arm64 1.23-1 [53.7 kB] 252s Get:35 http://ftpmaster.internal/ubuntu plucky/main arm64 libicu-dev arm64 76.1-1ubuntu2 [12.2 MB] 253s Get:36 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg-turbo8-dev arm64 2.1.5-3ubuntu2 [306 kB] 253s Get:37 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg8-dev arm64 8c-2ubuntu11 [1484 B] 253s Get:38 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg-dev arm64 8c-2ubuntu11 [1482 B] 253s Get:39 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack-dev arm64 3.12.1-2 [4439 kB] 253s Get:40 http://ftpmaster.internal/ubuntu plucky/main arm64 libncurses-dev arm64 6.5+20250216-2 [389 kB] 253s Get:41 http://ftpmaster.internal/ubuntu plucky/main arm64 libpcre2-16-0 arm64 10.45-1 [222 kB] 253s Get:42 http://ftpmaster.internal/ubuntu plucky/main arm64 libpcre2-32-0 arm64 10.45-1 [210 kB] 253s Get:43 http://ftpmaster.internal/ubuntu plucky/main arm64 libpcre2-posix3 arm64 10.45-1 [7084 B] 253s Get:44 http://ftpmaster.internal/ubuntu plucky/main arm64 libpcre2-dev arm64 10.45-1 [768 kB] 253s Get:45 http://ftpmaster.internal/ubuntu plucky/main arm64 libpkgconf3 arm64 1.8.1-4 [31.4 kB] 253s Get:46 http://ftpmaster.internal/ubuntu plucky/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1ubuntu1 [894 kB] 253s Get:47 http://ftpmaster.internal/ubuntu plucky/main arm64 libpng-dev arm64 1.6.47-1 [269 kB] 253s Get:48 http://ftpmaster.internal/ubuntu plucky/main arm64 libreadline-dev arm64 8.2-6 [179 kB] 253s Get:49 http://ftpmaster.internal/ubuntu plucky/main arm64 liblzma-dev arm64 5.6.4-1 [180 kB] 253s Get:50 http://ftpmaster.internal/ubuntu plucky/main arm64 pkgconf-bin arm64 1.8.1-4 [20.9 kB] 253s Get:51 http://ftpmaster.internal/ubuntu plucky/main arm64 pkgconf arm64 1.8.1-4 [16.7 kB] 253s Get:52 http://ftpmaster.internal/ubuntu plucky/main arm64 libtirpc-dev arm64 1.3.4+ds-1.3 [201 kB] 253s Get:53 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-base-dev all 4.4.3-1 [4176 B] 253s Get:54 http://ftpmaster.internal/ubuntu plucky/universe arm64 pkg-r-autopkgtest all 20231212ubuntu1 [6448 B] 254s Fetched 92.7 MB in 9s (10.4 MB/s) 254s Selecting previously unselected package libisl23:arm64. 254s (Reading database ... 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libcc1-0:arm64 (15-20250222-0ubuntu1) ... 258s Setting up liblsan0:arm64 (15-20250222-0ubuntu1) ... 258s Setting up libblas-dev:arm64 (3.12.1-2) ... 258s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so to provide /usr/lib/aarch64-linux-gnu/libblas.so (libblas.so-aarch64-linux-gnu) in auto mode 258s Setting up dctrl-tools (2.24-3build3) ... 258s Setting up libitm1:arm64 (15-20250222-0ubuntu1) ... 258s Setting up libbz2-dev:arm64 (1.0.8-6) ... 258s Setting up libpcre2-dev:arm64 (10.45-1) ... 258s Setting up libpng-dev:arm64 (1.6.47-1) ... 258s Setting up libjpeg-dev:arm64 (8c-2ubuntu11) ... 258s Setting up pkgconf:arm64 (1.8.1-4) ... 258s Setting up liblapack-dev:arm64 (3.12.1-2) ... 258s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so to provide /usr/lib/aarch64-linux-gnu/liblapack.so (liblapack.so-aarch64-linux-gnu) in auto mode 258s Setting up cpp-14-aarch64-linux-gnu (14.2.0-17ubuntu3) ... 258s Setting up libgcc-14-dev:arm64 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auto mode 258s Setting up build-essential (12.10ubuntu1) ... 258s Setting up gfortran (4:14.2.0-1ubuntu1) ... 258s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode 258s 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 258s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode 258s 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 258s Setting up r-base-dev (4.4.3-1) ... 258s Setting up pkg-r-autopkgtest (20231212ubuntu1) ... 258s Processing triggers for libc-bin (2.41-1ubuntu2) ... 258s Processing triggers for man-db (2.13.0-1) ... 259s Processing triggers for install-info (7.1.1-1) ... 260s autopkgtest [15:23:49]: test pkg-r-autopkgtest: /usr/share/dh-r/pkg-r-autopkgtest 260s autopkgtest [15:23:49]: test pkg-r-autopkgtest: [----------------------- 260s Test: Try to load the R library bdsmatrix 260s 260s R version 4.4.3 (2025-02-28) -- "Trophy Case" 260s Copyright (C) 2025 The R Foundation for Statistical Computing 260s Platform: aarch64-unknown-linux-gnu 260s 260s R is free software and comes with ABSOLUTELY NO WARRANTY. 260s You are welcome to redistribute it under certain conditions. 260s Type 'license()' or 'licence()' for distribution details. 260s 260s R is a collaborative project with many contributors. 260s Type 'contributors()' for more information and 260s 'citation()' on how to cite R or R packages in publications. 260s 260s Type 'demo()' for some demos, 'help()' for on-line help, or 260s 'help.start()' for an HTML browser interface to help. 260s Type 'q()' to quit R. 260s 261s > library('bdsmatrix') 261s 261s Attaching package: ‘bdsmatrix’ 261s 261s The following object is masked from ‘package:base’: 261s 261s backsolve 261s 261s > 261s > 261s Other tests are currently unsupported! 261s They will be progressively added. 261s autopkgtest [15:23:50]: test pkg-r-autopkgtest: -----------------------] 262s autopkgtest [15:23:51]: test pkg-r-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 262s pkg-r-autopkgtest PASS 262s autopkgtest [15:23:51]: @@@@@@@@@@@@@@@@@@@@ summary 262s run-unit-test PASS 262s pkg-r-autopkgtest PASS 283s nova [W] Using flock in prodstack6-arm64 283s flock: timeout while waiting to get lock 283s Creating nova instance adt-plucky-arm64-r-cran-bdsmatrix-20250315-151929-juju-7f2275-prod-proposed-migration-environment-2-c633927b-766d-4acb-a8c0-8f2da5f4b153 from image adt/ubuntu-plucky-arm64-server-20250315.img (UUID bd6e766c-b51f-4b53-86d6-23aa4d18f524)... 283s nova [W] Timed out waiting for 1716da8c-4268-4d3a-9760-9a253123b8d0 to get deleted.