0s autopkgtest [17:52:51]: starting date and time: 2025-03-15 17:52:51+0000 0s autopkgtest [17:52:51]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [17:52:51]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.kdjpgwvz/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-s390x --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-s390x-10.secgroup --name adt-plucky-s390x-r-cran-bdsmatrix-20250315-175251-juju-7f2275-prod-proposed-migration-environment-2-72c2606b-4bc4-48d1-af6a-a6e57d4f4d4f --image adt/ubuntu-plucky-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration-s390x -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/ 90s autopkgtest [17:54:21]: testbed dpkg architecture: s390x 90s autopkgtest [17:54:21]: testbed apt version: 2.9.33 91s autopkgtest [17:54:22]: @@@@@@@@@@@@@@@@@@@@ test bed setup 91s autopkgtest [17:54:22]: testbed release detected to be: None 92s autopkgtest [17:54:23]: updating testbed package index (apt update) 92s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 92s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 92s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 93s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 93s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [99.7 kB] 93s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 93s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [379 kB] 93s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x Packages [113 kB] 93s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x c-n-f Metadata [1824 B] 93s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted s390x c-n-f Metadata [116 B] 93s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x Packages [320 kB] 94s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x c-n-f Metadata [13.4 kB] 94s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x Packages [3776 B] 94s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x c-n-f Metadata [240 B] 94s Fetched 1073 kB in 2s (605 kB/s) 94s Reading package lists... 95s Reading package lists... 95s Building dependency tree... 95s Reading state information... 95s Calculating upgrade... 95s Calculating upgrade... 95s The following packages were automatically installed and are no longer required: 95s libnsl2 libpython3.12-minimal libpython3.12-stdlib libpython3.12t64 95s linux-headers-6.11.0-8 linux-headers-6.11.0-8-generic 95s linux-modules-6.11.0-8-generic linux-tools-6.11.0-8 95s linux-tools-6.11.0-8-generic 95s Use 'sudo apt autoremove' to remove them. 95s The following packages will be upgraded: 95s pinentry-curses python3-jinja2 strace 96s 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 96s Need to get 652 kB of archives. 96s After this operation, 27.6 kB of additional disk space will be used. 96s Get:1 http://ftpmaster.internal/ubuntu plucky/main s390x strace s390x 6.13+ds-1ubuntu1 [500 kB] 96s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x pinentry-curses s390x 1.3.1-2ubuntu3 [42.9 kB] 96s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 97s Fetched 652 kB in 1s (593 kB/s) 97s (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 ... 81428 files and directories currently installed.) 97s Preparing to unpack .../strace_6.13+ds-1ubuntu1_s390x.deb ... 97s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 97s Preparing to unpack .../pinentry-curses_1.3.1-2ubuntu3_s390x.deb ... 97s Unpacking pinentry-curses (1.3.1-2ubuntu3) over (1.3.1-2ubuntu2) ... 97s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 97s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 97s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 97s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 97s Setting up strace (6.13+ds-1ubuntu1) ... 97s Processing triggers for man-db (2.13.0-1) ... 98s Reading package lists... 98s Building dependency tree... 98s Reading state information... 98s Solving dependencies... 98s The following packages will be REMOVED: 98s libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64* 98s linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 98s linux-modules-6.11.0-8-generic* linux-tools-6.11.0-8* 98s linux-tools-6.11.0-8-generic* 98s 0 upgraded, 0 newly installed, 9 to remove and 5 not upgraded. 98s After this operation, 167 MB disk space will be freed. 98s (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 ... 81428 files and directories currently installed.) 98s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 98s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 98s Removing libpython3.12t64:s390x (3.12.9-1) ... 98s Removing libpython3.12-stdlib:s390x (3.12.9-1) ... 98s Removing libnsl2:s390x (1.3.0-3build3) ... 98s Removing libpython3.12-minimal:s390x (3.12.9-1) ... 98s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 98s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 99s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 99s Processing triggers for libc-bin (2.41-1ubuntu1) ... 99s (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 ... 56328 files and directories currently installed.) 99s Purging configuration files for libpython3.12-minimal:s390x (3.12.9-1) ... 99s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 99s autopkgtest [17:54:30]: upgrading testbed (apt dist-upgrade and autopurge) 99s Reading package lists... 100s Building dependency tree... 100s Reading state information... 100s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 100s Starting 2 pkgProblemResolver with broken count: 0 100s Done 100s Entering ResolveByKeep 100s 100s Calculating upgrade... 100s The following packages will be upgraded: 100s libc-bin libc-dev-bin libc6 libc6-dev locales 100s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 100s Need to get 9512 kB of archives. 100s After this operation, 8192 B of additional disk space will be used. 100s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc6-dev s390x 2.41-1ubuntu2 [1678 kB] 103s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc-dev-bin s390x 2.41-1ubuntu2 [24.3 kB] 103s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc6 s390x 2.41-1ubuntu2 [2892 kB] 106s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc-bin s390x 2.41-1ubuntu2 [671 kB] 107s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x locales all 2.41-1ubuntu2 [4246 kB] 112s Preconfiguring packages ... 112s Fetched 9512 kB in 11s (847 kB/s) 112s (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 ... 56326 files and directories currently installed.) 112s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_s390x.deb ... 112s Unpacking libc6-dev:s390x (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 112s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_s390x.deb ... 112s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 112s Preparing to unpack .../libc6_2.41-1ubuntu2_s390x.deb ... 112s Unpacking libc6:s390x (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 112s Setting up libc6:s390x (2.41-1ubuntu2) ... 112s (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 ... 56326 files and directories currently installed.) 112s Preparing to unpack .../libc-bin_2.41-1ubuntu2_s390x.deb ... 112s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 112s Setting up libc-bin (2.41-1ubuntu2) ... 112s (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 ... 56326 files and directories currently installed.) 112s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 112s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 112s Setting up locales (2.41-1ubuntu2) ... 113s Generating locales (this might take a while)... 113s en_US.UTF-8... done 113s Generation complete. 113s Setting up libc-dev-bin (2.41-1ubuntu2) ... 113s Setting up libc6-dev:s390x (2.41-1ubuntu2) ... 113s Processing triggers for man-db (2.13.0-1) ... 114s Processing triggers for systemd (257.3-1ubuntu3) ... 115s Reading package lists... 115s Building dependency tree... 115s Reading state information... 115s Starting pkgProblemResolver with broken count: 0 115s Starting 2 pkgProblemResolver with broken count: 0 115s Done 115s Solving dependencies... 115s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 116s autopkgtest [17:54:47]: rebooting testbed after setup commands that affected boot 133s autopkgtest [17:55:04]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP Wed Mar 12 14:53:49 UTC 2025 135s autopkgtest [17:55:06]: @@@@@@@@@@@@@@@@@@@@ apt-source r-cran-bdsmatrix 137s Get:1 http://ftpmaster.internal/ubuntu plucky/universe r-cran-bdsmatrix 1.3-7-1 (dsc) [2072 B] 137s Get:2 http://ftpmaster.internal/ubuntu plucky/universe r-cran-bdsmatrix 1.3-7-1 (tar) [48.0 kB] 137s Get:3 http://ftpmaster.internal/ubuntu plucky/universe r-cran-bdsmatrix 1.3-7-1 (diff) [2520 B] 137s gpgv: Signature made Tue Mar 12 13:10:28 2024 UTC 137s gpgv: using RSA key 53951D95272E0C5B82BE8C4A2CECE9350ECEBE4A 137s gpgv: Can't check signature: No public key 137s dpkg-source: warning: cannot verify inline signature for ./r-cran-bdsmatrix_1.3-7-1.dsc: no acceptable signature found 137s autopkgtest [17:55:08]: testing package r-cran-bdsmatrix version 1.3-7-1 137s autopkgtest [17:55:08]: build not needed 139s autopkgtest [17:55:10]: test run-unit-test: preparing testbed 139s Reading package lists... 139s Building dependency tree... 139s Reading state information... 139s Starting pkgProblemResolver with broken count: 0 139s Starting 2 pkgProblemResolver with broken count: 0 139s Done 140s The following NEW packages will be installed: 140s fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono libblas3 140s libcairo2 libdatrie1 libdeflate0 libfontconfig1 libfreetype6 libgfortran5 140s libgomp1 libgraphite2-3 libharfbuzz0b libice6 libjbig0 libjpeg-turbo8 140s libjpeg8 liblapack3 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 140s libpaper-utils libpaper2 libpixman-1-0 libsharpyuv0 libsm6 libtcl8.6 140s libthai-data libthai0 libtiff6 libtk8.6 libwebp7 libxcb-render0 libxcb-shm0 140s libxft2 libxrender1 libxss1 libxt6t64 r-base-core r-cran-bdsmatrix unzip 140s x11-common xdg-utils zip 140s 0 upgraded, 45 newly installed, 0 to remove and 0 not upgraded. 140s Need to get 40.4 MB of archives. 140s After this operation, 81.5 MB of additional disk space will be used. 140s Get:1 http://ftpmaster.internal/ubuntu plucky/main s390x libfreetype6 s390x 2.13.3+dfsg-1 [431 kB] 140s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x fonts-dejavu-mono all 2.37-8 [502 kB] 141s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x fonts-dejavu-core all 2.37-8 [835 kB] 142s Get:4 http://ftpmaster.internal/ubuntu plucky/main s390x fontconfig-config s390x 2.15.0-2ubuntu1 [37.5 kB] 142s Get:5 http://ftpmaster.internal/ubuntu plucky/main s390x libfontconfig1 s390x 2.15.0-2ubuntu1 [150 kB] 142s Get:6 http://ftpmaster.internal/ubuntu plucky/main s390x fontconfig s390x 2.15.0-2ubuntu1 [191 kB] 142s Get:7 http://ftpmaster.internal/ubuntu plucky/main s390x libblas3 s390x 3.12.1-2 [252 kB] 142s Get:8 http://ftpmaster.internal/ubuntu plucky/main s390x libpixman-1-0 s390x 0.44.0-3 [201 kB] 143s Get:9 http://ftpmaster.internal/ubuntu plucky/main s390x libxcb-render0 s390x 1.17.0-2 [17.0 kB] 143s Get:10 http://ftpmaster.internal/ubuntu plucky/main s390x libxcb-shm0 s390x 1.17.0-2 [5862 B] 143s Get:11 http://ftpmaster.internal/ubuntu plucky/main s390x libxrender1 s390x 1:0.9.10-1.1build1 [20.4 kB] 143s Get:12 http://ftpmaster.internal/ubuntu plucky/main s390x libcairo2 s390x 1.18.2-2 [580 kB] 143s Get:13 http://ftpmaster.internal/ubuntu plucky/main s390x libdatrie1 s390x 0.2.13-3build1 [20.6 kB] 143s Get:14 http://ftpmaster.internal/ubuntu plucky/main s390x libdeflate0 s390x 1.23-1 [46.1 kB] 143s Get:15 http://ftpmaster.internal/ubuntu plucky/main s390x libgfortran5 s390x 15-20250222-0ubuntu1 [620 kB] 144s Get:16 http://ftpmaster.internal/ubuntu plucky/main s390x libgomp1 s390x 15-20250222-0ubuntu1 [152 kB] 144s Get:17 http://ftpmaster.internal/ubuntu plucky/main s390x libgraphite2-3 s390x 1.3.14-2ubuntu1 [79.8 kB] 144s Get:18 http://ftpmaster.internal/ubuntu plucky/main s390x libharfbuzz0b s390x 10.2.0-1 [538 kB] 144s Get:19 http://ftpmaster.internal/ubuntu plucky/main s390x x11-common all 1:7.7+23ubuntu3 [21.7 kB] 144s Get:20 http://ftpmaster.internal/ubuntu plucky/main s390x libice6 s390x 2:1.1.1-1 [45.4 kB] 144s Get:21 http://ftpmaster.internal/ubuntu plucky/main s390x libjpeg-turbo8 s390x 2.1.5-3ubuntu2 [147 kB] 145s Get:22 http://ftpmaster.internal/ubuntu plucky/main s390x libjpeg8 s390x 8c-2ubuntu11 [2146 B] 145s Get:23 http://ftpmaster.internal/ubuntu plucky/main s390x liblapack3 s390x 3.12.1-2 [2971 kB] 147s Get:24 http://ftpmaster.internal/ubuntu plucky/main s390x libthai-data all 0.1.29-2build1 [158 kB] 147s Get:25 http://ftpmaster.internal/ubuntu plucky/main s390x libthai0 s390x 0.1.29-2build1 [20.7 kB] 147s Get:26 http://ftpmaster.internal/ubuntu plucky/main s390x libpango-1.0-0 s390x 1.56.2-1 [253 kB] 148s Get:27 http://ftpmaster.internal/ubuntu plucky/main s390x libpangoft2-1.0-0 s390x 1.56.2-1 [50.2 kB] 148s Get:28 http://ftpmaster.internal/ubuntu plucky/main s390x libpangocairo-1.0-0 s390x 1.56.2-1 [28.2 kB] 148s Get:29 http://ftpmaster.internal/ubuntu plucky/main s390x libpaper2 s390x 2.2.5-0.3 [17.2 kB] 148s Get:30 http://ftpmaster.internal/ubuntu plucky/main s390x libpaper-utils s390x 2.2.5-0.3 [15.3 kB] 148s Get:31 http://ftpmaster.internal/ubuntu plucky/main s390x libsharpyuv0 s390x 1.5.0-0.1 [16.7 kB] 148s Get:32 http://ftpmaster.internal/ubuntu plucky/main s390x libsm6 s390x 2:1.2.4-1 [18.4 kB] 148s Get:33 http://ftpmaster.internal/ubuntu plucky/main s390x libtcl8.6 s390x 8.6.16+dfsg-1 [1034 kB] 149s Get:34 http://ftpmaster.internal/ubuntu plucky/main s390x libjbig0 s390x 2.1-6.1ubuntu2 [33.1 kB] 149s Get:35 http://ftpmaster.internal/ubuntu plucky/main s390x libwebp7 s390x 1.5.0-0.1 [210 kB] 149s Get:36 http://ftpmaster.internal/ubuntu plucky/main s390x libtiff6 s390x 4.5.1+git230720-4ubuntu4 [217 kB] 149s Get:37 http://ftpmaster.internal/ubuntu plucky/main s390x libxft2 s390x 2.3.6-1build1 [49.6 kB] 149s Get:38 http://ftpmaster.internal/ubuntu plucky/main s390x libxss1 s390x 1:1.2.3-1build3 [7396 B] 149s Get:39 http://ftpmaster.internal/ubuntu plucky/main s390x libtk8.6 s390x 8.6.16-1 [830 kB] 150s Get:40 http://ftpmaster.internal/ubuntu plucky/main s390x libxt6t64 s390x 1:1.2.1-1.2build1 [184 kB] 150s Get:41 http://ftpmaster.internal/ubuntu plucky/main s390x zip s390x 3.0-14ubuntu2 [187 kB] 151s Get:42 http://ftpmaster.internal/ubuntu plucky/main s390x unzip s390x 6.0-28ubuntu6 [186 kB] 151s Get:43 http://ftpmaster.internal/ubuntu plucky/main s390x xdg-utils all 1.2.1-2ubuntu1 [66.0 kB] 151s Get:44 http://ftpmaster.internal/ubuntu plucky/universe s390x r-base-core s390x 4.4.3-1 [28.6 MB] 177s Get:45 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-bdsmatrix s390x 1.3-7-1 [307 kB] 178s Preconfiguring packages ... 178s Fetched 40.4 MB in 38s (1071 kB/s) 178s Selecting previously unselected package libfreetype6:s390x. 178s (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 ... 56326 files and directories currently installed.) 178s Preparing to unpack .../00-libfreetype6_2.13.3+dfsg-1_s390x.deb ... 178s Unpacking libfreetype6:s390x (2.13.3+dfsg-1) ... 178s Selecting previously unselected package fonts-dejavu-mono. 178s Preparing to unpack .../01-fonts-dejavu-mono_2.37-8_all.deb ... 178s Unpacking fonts-dejavu-mono (2.37-8) ... 178s Selecting previously unselected package fonts-dejavu-core. 178s Preparing to unpack .../02-fonts-dejavu-core_2.37-8_all.deb ... 178s Unpacking fonts-dejavu-core (2.37-8) ... 178s Selecting previously unselected package fontconfig-config. 178s Preparing to unpack .../03-fontconfig-config_2.15.0-2ubuntu1_s390x.deb ... 178s Unpacking fontconfig-config (2.15.0-2ubuntu1) ... 178s Selecting previously unselected package libfontconfig1:s390x. 178s Preparing to unpack .../04-libfontconfig1_2.15.0-2ubuntu1_s390x.deb ... 178s Unpacking libfontconfig1:s390x (2.15.0-2ubuntu1) ... 178s Selecting previously unselected package fontconfig. 178s Preparing to unpack .../05-fontconfig_2.15.0-2ubuntu1_s390x.deb ... 178s Unpacking fontconfig (2.15.0-2ubuntu1) ... 178s Selecting previously unselected package libblas3:s390x. 178s Preparing to unpack .../06-libblas3_3.12.1-2_s390x.deb ... 178s Unpacking libblas3:s390x (3.12.1-2) ... 178s Selecting previously unselected package libpixman-1-0:s390x. 178s Preparing to unpack .../07-libpixman-1-0_0.44.0-3_s390x.deb ... 178s Unpacking libpixman-1-0:s390x (0.44.0-3) ... 178s Selecting previously unselected package libxcb-render0:s390x. 178s Preparing to unpack .../08-libxcb-render0_1.17.0-2_s390x.deb ... 178s Unpacking libxcb-render0:s390x (1.17.0-2) ... 178s Selecting previously unselected package libxcb-shm0:s390x. 178s Preparing to unpack .../09-libxcb-shm0_1.17.0-2_s390x.deb ... 178s Unpacking libxcb-shm0:s390x (1.17.0-2) ... 178s Selecting previously unselected package libxrender1:s390x. 178s Preparing to unpack .../10-libxrender1_1%3a0.9.10-1.1build1_s390x.deb ... 178s Unpacking libxrender1:s390x (1:0.9.10-1.1build1) ... 178s Selecting previously unselected package libcairo2:s390x. 178s Preparing to unpack .../11-libcairo2_1.18.2-2_s390x.deb ... 178s Unpacking libcairo2:s390x (1.18.2-2) ... 178s Selecting previously unselected package libdatrie1:s390x. 178s Preparing to unpack .../12-libdatrie1_0.2.13-3build1_s390x.deb ... 178s Unpacking libdatrie1:s390x (0.2.13-3build1) ... 178s Selecting previously unselected package libdeflate0:s390x. 178s Preparing to unpack .../13-libdeflate0_1.23-1_s390x.deb ... 178s Unpacking libdeflate0:s390x (1.23-1) ... 178s Selecting previously unselected package libgfortran5:s390x. 178s Preparing to unpack .../14-libgfortran5_15-20250222-0ubuntu1_s390x.deb ... 178s Unpacking libgfortran5:s390x (15-20250222-0ubuntu1) ... 178s Selecting previously unselected package libgomp1:s390x. 178s Preparing to unpack .../15-libgomp1_15-20250222-0ubuntu1_s390x.deb ... 178s Unpacking libgomp1:s390x (15-20250222-0ubuntu1) ... 178s Selecting previously unselected package libgraphite2-3:s390x. 178s Preparing to unpack .../16-libgraphite2-3_1.3.14-2ubuntu1_s390x.deb ... 178s Unpacking libgraphite2-3:s390x (1.3.14-2ubuntu1) ... 178s Selecting previously unselected package libharfbuzz0b:s390x. 178s Preparing to unpack .../17-libharfbuzz0b_10.2.0-1_s390x.deb ... 178s Unpacking libharfbuzz0b:s390x (10.2.0-1) ... 178s Selecting previously unselected package x11-common. 178s Preparing to unpack .../18-x11-common_1%3a7.7+23ubuntu3_all.deb ... 178s Unpacking x11-common (1:7.7+23ubuntu3) ... 178s Selecting previously unselected package libice6:s390x. 178s Preparing to unpack .../19-libice6_2%3a1.1.1-1_s390x.deb ... 178s Unpacking libice6:s390x (2:1.1.1-1) ... 178s Selecting previously unselected package libjpeg-turbo8:s390x. 178s Preparing to unpack .../20-libjpeg-turbo8_2.1.5-3ubuntu2_s390x.deb ... 178s Unpacking libjpeg-turbo8:s390x (2.1.5-3ubuntu2) ... 178s Selecting previously unselected package libjpeg8:s390x. 178s Preparing to unpack .../21-libjpeg8_8c-2ubuntu11_s390x.deb ... 178s Unpacking libjpeg8:s390x (8c-2ubuntu11) ... 178s Selecting previously unselected package liblapack3:s390x. 178s Preparing to unpack .../22-liblapack3_3.12.1-2_s390x.deb ... 178s Unpacking liblapack3:s390x (3.12.1-2) ... 178s Selecting previously unselected package libthai-data. 178s Preparing to unpack .../23-libthai-data_0.1.29-2build1_all.deb ... 178s Unpacking libthai-data (0.1.29-2build1) ... 178s Selecting previously unselected package libthai0:s390x. 178s Preparing to unpack .../24-libthai0_0.1.29-2build1_s390x.deb ... 178s Unpacking libthai0:s390x (0.1.29-2build1) ... 178s Selecting previously unselected package libpango-1.0-0:s390x. 178s Preparing to unpack .../25-libpango-1.0-0_1.56.2-1_s390x.deb ... 178s Unpacking libpango-1.0-0:s390x (1.56.2-1) ... 178s Selecting previously unselected package libpangoft2-1.0-0:s390x. 178s Preparing to unpack .../26-libpangoft2-1.0-0_1.56.2-1_s390x.deb ... 178s Unpacking libpangoft2-1.0-0:s390x (1.56.2-1) ... 178s Selecting previously unselected package libpangocairo-1.0-0:s390x. 178s Preparing to unpack .../27-libpangocairo-1.0-0_1.56.2-1_s390x.deb ... 178s Unpacking libpangocairo-1.0-0:s390x (1.56.2-1) ... 178s Selecting previously unselected package libpaper2:s390x. 178s Preparing to unpack .../28-libpaper2_2.2.5-0.3_s390x.deb ... 178s Unpacking libpaper2:s390x (2.2.5-0.3) ... 178s Selecting previously unselected package libpaper-utils. 178s Preparing to unpack .../29-libpaper-utils_2.2.5-0.3_s390x.deb ... 178s Unpacking libpaper-utils (2.2.5-0.3) ... 178s Selecting previously unselected package libsharpyuv0:s390x. 178s Preparing to unpack .../30-libsharpyuv0_1.5.0-0.1_s390x.deb ... 178s Unpacking libsharpyuv0:s390x (1.5.0-0.1) ... 178s Selecting previously unselected package libsm6:s390x. 178s Preparing to unpack .../31-libsm6_2%3a1.2.4-1_s390x.deb ... 178s Unpacking libsm6:s390x (2:1.2.4-1) ... 178s Selecting previously unselected package libtcl8.6:s390x. 178s Preparing to unpack .../32-libtcl8.6_8.6.16+dfsg-1_s390x.deb ... 178s Unpacking libtcl8.6:s390x (8.6.16+dfsg-1) ... 178s Selecting previously unselected package libjbig0:s390x. 178s Preparing to unpack .../33-libjbig0_2.1-6.1ubuntu2_s390x.deb ... 178s Unpacking libjbig0:s390x (2.1-6.1ubuntu2) ... 178s Selecting previously unselected package libwebp7:s390x. 178s Preparing to unpack .../34-libwebp7_1.5.0-0.1_s390x.deb ... 178s Unpacking libwebp7:s390x (1.5.0-0.1) ... 178s Selecting previously unselected package libtiff6:s390x. 178s Preparing to unpack .../35-libtiff6_4.5.1+git230720-4ubuntu4_s390x.deb ... 178s Unpacking libtiff6:s390x (4.5.1+git230720-4ubuntu4) ... 178s Selecting previously unselected package libxft2:s390x. 178s Preparing to unpack .../36-libxft2_2.3.6-1build1_s390x.deb ... 178s Unpacking libxft2:s390x (2.3.6-1build1) ... 178s Selecting previously unselected package libxss1:s390x. 178s Preparing to unpack .../37-libxss1_1%3a1.2.3-1build3_s390x.deb ... 178s Unpacking libxss1:s390x (1:1.2.3-1build3) ... 178s Selecting previously unselected package libtk8.6:s390x. 178s Preparing to unpack .../38-libtk8.6_8.6.16-1_s390x.deb ... 178s Unpacking libtk8.6:s390x (8.6.16-1) ... 178s Selecting previously unselected package libxt6t64:s390x. 178s Preparing to unpack .../39-libxt6t64_1%3a1.2.1-1.2build1_s390x.deb ... 178s Unpacking libxt6t64:s390x (1:1.2.1-1.2build1) ... 178s Selecting previously unselected package zip. 178s Preparing to unpack .../40-zip_3.0-14ubuntu2_s390x.deb ... 178s Unpacking zip (3.0-14ubuntu2) ... 178s Selecting previously unselected package unzip. 178s Preparing to unpack .../41-unzip_6.0-28ubuntu6_s390x.deb ... 178s Unpacking unzip (6.0-28ubuntu6) ... 178s Selecting previously unselected package xdg-utils. 178s Preparing to unpack .../42-xdg-utils_1.2.1-2ubuntu1_all.deb ... 178s Unpacking xdg-utils (1.2.1-2ubuntu1) ... 178s Selecting previously unselected package r-base-core. 178s Preparing to unpack .../43-r-base-core_4.4.3-1_s390x.deb ... 178s Unpacking r-base-core (4.4.3-1) ... 179s Selecting previously unselected package r-cran-bdsmatrix. 179s Preparing to unpack .../44-r-cran-bdsmatrix_1.3-7-1_s390x.deb ... 179s Unpacking r-cran-bdsmatrix (1.3-7-1) ... 179s Setting up libgraphite2-3:s390x (1.3.14-2ubuntu1) ... 179s Setting up libpixman-1-0:s390x (0.44.0-3) ... 179s Setting up libsharpyuv0:s390x (1.5.0-0.1) ... 179s Setting up libxrender1:s390x (1:0.9.10-1.1build1) ... 179s Setting up libdatrie1:s390x (0.2.13-3build1) ... 179s Setting up libxcb-render0:s390x (1.17.0-2) ... 179s Setting up unzip (6.0-28ubuntu6) ... 179s Setting up x11-common (1:7.7+23ubuntu3) ... 179s Setting up libdeflate0:s390x (1.23-1) ... 179s Setting up libxcb-shm0:s390x (1.17.0-2) ... 179s Setting up libgomp1:s390x (15-20250222-0ubuntu1) ... 179s Setting up libjbig0:s390x (2.1-6.1ubuntu2) ... 179s Setting up zip (3.0-14ubuntu2) ... 179s Setting up libblas3:s390x (3.12.1-2) ... 179s update-alternatives: using /usr/lib/s390x-linux-gnu/blas/libblas.so.3 to provide /usr/lib/s390x-linux-gnu/libblas.so.3 (libblas.so.3-s390x-linux-gnu) in auto mode 179s Setting up libfreetype6:s390x (2.13.3+dfsg-1) ... 179s Setting up fonts-dejavu-mono (2.37-8) ... 179s Setting up libtcl8.6:s390x (8.6.16+dfsg-1) ... 179s Setting up fonts-dejavu-core (2.37-8) ... 179s Setting up libjpeg-turbo8:s390x (2.1.5-3ubuntu2) ... 179s Setting up libgfortran5:s390x (15-20250222-0ubuntu1) ... 179s Setting up libwebp7:s390x (1.5.0-0.1) ... 179s Setting up libharfbuzz0b:s390x (10.2.0-1) ... 179s Setting up libthai-data (0.1.29-2build1) ... 179s Setting up libxss1:s390x (1:1.2.3-1build3) ... 179s Setting up libpaper2:s390x (2.2.5-0.3) ... 179s Setting up xdg-utils (1.2.1-2ubuntu1) ... 179s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode 179s Setting up libjpeg8:s390x (8c-2ubuntu11) ... 179s Setting up libice6:s390x (2:1.1.1-1) ... 179s Setting up liblapack3:s390x (3.12.1-2) ... 179s update-alternatives: using /usr/lib/s390x-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/s390x-linux-gnu/liblapack.so.3 (liblapack.so.3-s390x-linux-gnu) in auto mode 179s Setting up fontconfig-config (2.15.0-2ubuntu1) ... 179s Setting up libpaper-utils (2.2.5-0.3) ... 179s Setting up libthai0:s390x (0.1.29-2build1) ... 179s Setting up libtiff6:s390x (4.5.1+git230720-4ubuntu4) ... 179s Setting up libfontconfig1:s390x (2.15.0-2ubuntu1) ... 179s Setting up libsm6:s390x (2:1.2.4-1) ... 179s Setting up fontconfig (2.15.0-2ubuntu1) ... 181s Regenerating fonts cache... done. 181s Setting up libxft2:s390x (2.3.6-1build1) ... 181s Setting up libtk8.6:s390x (8.6.16-1) ... 181s Setting up libpango-1.0-0:s390x (1.56.2-1) ... 181s Setting up libcairo2:s390x (1.18.2-2) ... 181s Setting up libxt6t64:s390x (1:1.2.1-1.2build1) ... 181s Setting up libpangoft2-1.0-0:s390x (1.56.2-1) ... 181s Setting up libpangocairo-1.0-0:s390x (1.56.2-1) ... 181s Setting up r-base-core (4.4.3-1) ... 181s Creating config file /etc/R/Renviron with new version 181s Setting up r-cran-bdsmatrix (1.3-7-1) ... 181s Processing triggers for install-info (7.1.1-1) ... 181s Processing triggers for libc-bin (2.41-1ubuntu2) ... 181s Processing triggers for man-db (2.13.0-1) ... 183s autopkgtest [17:55:54]: test run-unit-test: [----------------------- 183s BEGIN TEST backsolvetest.R 183s 183s R version 4.4.3 (2025-02-28) -- "Trophy Case" 183s Copyright (C) 2025 The R Foundation for Statistical Computing 183s Platform: s390x-ibm-linux-gnu 183s 183s R is free software and comes with ABSOLUTELY NO WARRANTY. 183s You are welcome to redistribute it under certain conditions. 183s Type 'license()' or 'licence()' for distribution details. 183s 183s R is a collaborative project with many contributors. 183s Type 'contributors()' for more information and 183s 'citation()' on how to cite R or R packages in publications. 183s 183s Type 'demo()' for some demos, 'help()' for on-line help, or 183s 'help.start()' for an HTML browser interface to help. 183s Type 'q()' to quit R. 183s 183s > library(bdsmatrix) 184s > # 184s > # A test of the backsolve function 184s > # 184s > aeq <- function(x,y) all.equal(as.vector(x), as.vector(y)) 184s > 184s > tmat <- matrix(rep(1:5,5), 5, 5) 184s > tmat <- tmat + t(tmat) 184s > diag(tmat) <- diag(tmat) + 10 184s > 184s > gt <- gchol(tmat) 184s > g1 <- as.matrix(gt) 184s > gd <- diag(sqrt(diag(gt))) 184s > gc <- gd %*% t(g1) #usual cholesky form 184s > 184s > xmat <- cbind(1:5, 11:15) 184s > 184s > s1 <- backsolve(gt, xmat, upper=TRUE) #the default 184s > aeq(gd %*% t(g1) %*% s1, xmat) 184s [1] TRUE 184s > all.equal(s1, backsolve(gc, xmat)) 184s [1] TRUE 184s > 184s > s2 <- backsolve(gt, xmat, upper=FALSE) 184s > aeq(g1 %*% gd %*% s2, xmat) 184s 184s Attaching package: 'bdsmatrix' 184s 184s The following object is masked from 'package:base': 184s 184s backsolve 184s 184s [1] TRUE 184s > all.equal(backsolve(gt,xmat, upper=F), backsolve(t(gc),xmat, upper=F)) 184s [1] TRUE 184s > 184s > 184s > # Now for bdsmatrix objects 184s > tmat <- bdsmatrix(c(3,2,2,4), 184s + c(22,1,2,21,3,20,19,4,18,17,5,16,15,6,7, 8,14,9,10,13,11,12), 184s + matrix(c(1,0,1,1,0,0,1,1,0,1,0,10,0, 184s + 0,1,1,0,1,1,0,1,1,0,1,0,10), ncol=2)) 184s > dimnames(tmat) <- list(NULL, letters[1:13]) 184s > smat <- as.matrix(tmat) 184s > 184s > gt <- gchol(tmat) 184s > gs <- gchol(smat) 184s > 184s > xmat <- cbind(1:13, 1:13*2 + 3) 184s > 184s > s1 <- backsolve(gt, xmat) 184s > s2 <- backsolve(gs, xmat) 184s > s3 <- backsolve(gt, xmat, upper=FALSE) 184s > s4 <- backsolve(gs, xmat, upper=FALSE) 184s > 184s > aeq(s1, s2) 184s [1] TRUE 184s > aeq(s3, s4) 184s [1] TRUE 184s > 184s > g1 <- as.matrix(gt) 184s > gd <- diag(sqrt(diag(gt))) 184s > aeq(gd %*% t(g1) %*% s1, xmat) 184s [1] TRUE 184s > aeq(g1 %*% gd %*% s3, xmat) 184s [1] TRUE 184s > 184s BEGIN TEST bdstest.R 184s 184s R version 4.4.3 (2025-02-28) -- "Trophy Case" 184s Copyright (C) 2025 The R Foundation for Statistical Computing 184s Platform: s390x-ibm-linux-gnu 184s 184s R is free software and comes with ABSOLUTELY NO WARRANTY. 184s You are welcome to redistribute it under certain conditions. 184s Type 'license()' or 'licence()' for distribution details. 184s 184s R is a collaborative project with many contributors. 184s Type 'contributors()' for more information and 184s 'citation()' on how to cite R or R packages in publications. 184s 184s Type 'demo()' for some demos, 'help()' for on-line help, or 184s 'help.start()' for an HTML browser interface to help. 184s Type 'q()' to quit R. 184s 184s > # 184s > # Test out math aspects 184s > # 184s > library(bdsmatrix) 184s > aeq <- function(x,y) all.equal(as.vector(x), as.vector(y)) 184s 184s Attaching package: 'bdsmatrix' 184s 184s The following object is masked from 'package:base': 184s 184s backsolve 184s 184s > 184s > tmat <- bdsmatrix(c(3,2,2,4), 184s + c(22,1,2,21,3,20,19,4,18,17,5,16,15,6,7, 8,14,9,10,13,11,12), 184s + matrix(c(1,0,1,1,0,0,1,1,0,1,0,10,0, 184s + 0,1,1,0,1,1,0,1,1,0,1,0,10), ncol=2)) 184s > dimnames(tmat) <- list(NULL, letters[1:13]) 184s > 184s > smat <- as.matrix(tmat) 184s > 184s > aeq(smat+2.1, as.matrix(tmat+2.1)) 184s [1] TRUE 184s > aeq(smat/2.1, as.matrix(tmat/2.1)) 184s [1] TRUE 184s > aeq(smat-2.1, as.matrix(tmat-2.1)) 184s [1] TRUE 184s > aeq(smat*2.1, as.matrix(tmat*2.1)) 184s [1] TRUE 184s > aeq(round(smat,1), as.matrix(round(tmat,1))) 184s [1] TRUE 184s > aeq(exp(smat), as.matrix(exp(tmat))) 184s [1] TRUE 184s > 184s > aeq(sum(smat), sum(tmat)) 184s [1] TRUE 184s > aeq(prod(smat), prod(tmat)) 184s [1] TRUE 184s > aeq(sum(smat+3), sum(tmat+3)) 184s [1] TRUE 184s > aeq(prod(smat+2), prod(tmat+2)) 184s [1] TRUE 184s > aeq(range(smat), range(tmat)) 184s [1] TRUE 184s > aeq(max(smat), max(tmat)) 184s [1] TRUE 184s > aeq(min(smat), min(tmat)) 184s [1] TRUE 184s > 184s > aeq(smat+1:13, tmat+1:13) 184s [1] TRUE 184s > aeq(smat+1:13, 1:13 +tmat ) 184s [1] TRUE 184s > aeq(smat+tmat, 2*smat) 184s [1] TRUE 184s > all.equal(tmat+tmat, 2*tmat) 184s [1] TRUE 184s > 184s > aeq(sort(unique(c(smat))), sort(unique(tmat))) 184s [1] TRUE 184s > 184s > # 184s > # check out the alternate input style, with full blocks 184s > # 184s > rmat <- bdsmatrix(c(3,2,2,4), 184s + c(22,1,2,1,21,3,2,3,20, 19,4,4,18, 17,5,5,16, 184s + 15,6,7,8,6,14,9,10,7,9,13,11,8,10,11,12), 184s + matrix(c(1,0,1,1,0,0,1,1,0,1,0,10,0, 184s + 0,1,1,0,1,1,0,1,1,0,1,0,10), ncol=2), 184s + dimnames=list(NULL, letters[1:13])) 184s > all.equal(rmat, tmat) 184s [1] TRUE 184s > 184s > 184s > # Do some subscripting 184s > zz <- c(1,2,7,8,9,11) 184s > aeq(smat[zz,zz], as.matrix(tmat[zz,zz])) 184s [1] TRUE 184s > 184s > all.equal(smat[zz, 8:13], tmat[zz, 8:13]) # both are matrices 184s [1] TRUE 184s > 184s > # Diagonals 184s > aeq(diag(smat), diag(tmat)) 184s [1] TRUE 184s > zz <- diag(smat) 184s > diag(smat) <- zz*2 184s > diag(tmat) <- zz*2 184s > all.equal(smat, as.matrix(tmat)) 184s [1] TRUE 184s > 184s BEGIN TEST chtest.R 184s 184s R version 4.4.3 (2025-02-28) -- "Trophy Case" 184s Copyright (C) 2025 The R Foundation for Statistical Computing 184s Platform: s390x-ibm-linux-gnu 184s 184s R is free software and comes with ABSOLUTELY NO WARRANTY. 184s You are welcome to redistribute it under certain conditions. 184s Type 'license()' or 'licence()' for distribution details. 184s 184s R is a collaborative project with many contributors. 184s Type 'contributors()' for more information and 184s 'citation()' on how to cite R or R packages in publications. 184s 184s Type 'demo()' for some demos, 'help()' for on-line help, or 184s 'help.start()' for an HTML browser interface to help. 184s Type 'q()' to quit R. 184s 184s > # 184s > # Test out the Cholesky 184s > # 184s > library(bdsmatrix) 184s 184s Attaching package: 'bdsmatrix' 184s 184s The following object is masked from 'package:base': 184s 184s backsolve 184s 184s > aeq <- function(x,y) all.equal(as.vector(x), as.vector(y)) 184s > 184s > tmat <- bdsmatrix(c(3,2,2,4), 184s + c(22,1,2,21,3,20,19,4,18,17,5,16,15,6,7, 8,14,9,10,13,11,12), 184s + matrix(c(1,0,1,1,0,0,1,1,0,1,0,10,0, 184s + 0,1,1,0,1,1,0,1,1,0,1,0,10), ncol=2)) 184s > dimnames(tmat) <- list(NULL, letters[1:13]) 184s > smat <- as.matrix(tmat) 184s > yy <- c(30,35,42,56,34,45,32,37,78,56,40,52,39) 184s > 184s > aeq(diag(tmat), diag(smat)) 184s [1] TRUE 184s > zz <- seq(1,13,2) 184s > aeq(as.matrix(tmat[zz,zz]), smat[zz,zz]) 184s [1] TRUE 184s > 184s > ch0 <- chol(smat) 184s > ch1 <- gchol(smat) 184s > ch2 <- gchol(tmat) 184s > # The gchol routines use the composition LDL', where L is lower triangular 184s > # with a diagonal of 1's, and D is diagonal. chol() uses U'U where U is 184s > # upper trangular. 184s > # The as.matrix function returns L and the diag function returns D. 184s > # Convert and compare 184s > aeq(diag(ch1), diag(ch2)) 184s [1] TRUE 184s > temp <- as.matrix(ch2) 184s > aeq(temp, as.matrix(ch1)) 184s [1] TRUE 184s > temp3 <- temp %*% diag(sqrt(diag(ch2))) 184s > aeq(temp3, t(ch0)) 184s [1] TRUE 184s > 184s > zz0 <- solve(smat, yy) 184s > zz1 <- solve(ch1, yy) 184s > zz2 <- solve(tmat, yy) 184s > aeq(zz1, zz2) 184s [1] TRUE 184s > aeq(zz0, zz1) 184s [1] TRUE 184s > 184s > 184s BEGIN TEST chtest2.R 184s 184s R version 4.4.3 (2025-02-28) -- "Trophy Case" 184s Copyright (C) 2025 The R Foundation for Statistical Computing 184s Platform: s390x-ibm-linux-gnu 184s 184s R is free software and comes with ABSOLUTELY NO WARRANTY. 184s You are welcome to redistribute it under certain conditions. 184s Type 'license()' or 'licence()' for distribution details. 184s 184s R is a collaborative project with many contributors. 184s Type 'contributors()' for more information and 184s 'citation()' on how to cite R or R packages in publications. 184s 184s Type 'demo()' for some demos, 'help()' for on-line help, or 184s 'help.start()' for an HTML browser interface to help. 184s Type 'q()' to quit R. 184s 184s > # 184s > # Inverse of the matrix: 184s > # 184s > library(bdsmatrix) 185s > aeq <- function(x,y) all.equal(as.vector(x), as.vector(y)) 185s > 185s Attaching package: 'bdsmatrix' 185s 185s The following object is masked from 'package:base': 185s 185s backsolve 185s 185s 185s > tmat <- bdsmatrix(c(3,2,2,4), 185s + c(22,1,2,21,3,20,19,4,18,17,5,16,15,6,7, 8,14,9,10,13,11,12), 185s + matrix(c(1,0,1,1,0,0,1,1,0,1,0,10,0, 185s + 0,1,1,0,1,1,0,1,1,0,1,0,10), ncol=2)) 185s > dimnames(tmat) <- list(NULL, letters[1:13]) 185s > 185s > smat <- as.matrix(tmat) 185s > 185s > inv1 <- solve(smat) 185s > inv2 <- as.matrix(solve(tmat)) # the result is a full, non-sparse matrix 185s > aeq(inv1, inv2) 185s [1] TRUE 185s > 185s > inv3 <- solve(gchol(tmat)) #sparse version, not all parts will be there 185s > inherits(inv3, 'bdsmatrix') #This should be true 185s [1] TRUE 185s > aeq(inv3@blocksize, tmat@blocksize) # Should be the same shape at tmat 185s [1] TRUE 185s > inv3 <- as.matrix(inv3) # What is returned should be correct 185s > aeq(inv1[1:3,1:3], inv3[1:3, 1:3]) 185s [1] TRUE 185s > aeq(inv1[4:5,4:5], inv3[4:5, 4:5]) 185s [1] TRUE 185s > aeq(inv1[6:7,6:7], inv3[6:7, 6:7]) 185s [1] TRUE 185s > aeq(inv1[8:11,8:11], inv3[8:11, 8:11]) 185s [1] TRUE 185s > aeq(inv1[,12:13], inv3[, 12:13]) # and rmat the same too 185s [1] TRUE 185s > 185s BEGIN TEST corner.R 185s 185s R version 4.4.3 (2025-02-28) -- "Trophy Case" 185s Copyright (C) 2025 The R Foundation for Statistical Computing 185s Platform: s390x-ibm-linux-gnu 185s 185s R is free software and comes with ABSOLUTELY NO WARRANTY. 185s You are welcome to redistribute it under certain conditions. 185s Type 'license()' or 'licence()' for distribution details. 185s 185s R is a collaborative project with many contributors. 185s Type 'contributors()' for more information and 185s 'citation()' on how to cite R or R packages in publications. 185s 185s Type 'demo()' for some demos, 'help()' for on-line help, or 185s 'help.start()' for an HTML browser interface to help. 185s Type 'q()' to quit R. 185s 185s > # 185s > # Test out the behavior of a 1x1 bds corner. 185s > # Actually, the problem that motivated this occurred whenever the 185s > # rmat portion was larger than the block diagonal portion. 185s > # 185s > library(bdsmatrix) 185s > test1 <- bdsmatrix(blocksize=1, blocks=33, 185s + rmat=matrix(c(17,33,7,-1, -7,7,48,-7, 185s + 1, -1, -7,4),4)) 185s > 185s > test2 <- bdsmatrix(blocksize=2, blocks=c(33,17,33), 185s + rmat=matrix(c( -7,7,48,-7, 1, -1, -7,4),4)) 185s > all.equal(as.matrix(test1), as.matrix(test2)) 185s [1] TRUE 185s > 185s > g1 <- gchol(test1) 185s > g2 <- gchol(test2) 185s > all.equal(as.matrix(g1), as.matrix(g2)) 185s [1] TRUE 185s > 185s > s1 <- solve(g1, full=T) 185s > s2 <- solve(g2, full=T) 185s > all.equal(as.matrix(s1), as.matrix(s2)) 185s [1] TRUE 185s > 185s > all.equal(solve(test1), solve(test2)) 185s 185s Attaching package: 'bdsmatrix' 185s 185s The following object is masked from 'package:base': 185s 185s backsolve 185s 185s [1] TRUE 185s > 185s BEGIN TEST corner2.R 185s 185s R version 4.4.3 (2025-02-28) -- "Trophy Case" 185s Copyright (C) 2025 The R Foundation for Statistical Computing 185s Platform: s390x-ibm-linux-gnu 185s 185s R is free software and comes with ABSOLUTELY NO WARRANTY. 185s You are welcome to redistribute it under certain conditions. 185s Type 'license()' or 'licence()' for distribution details. 185s 185s R is a collaborative project with many contributors. 185s Type 'contributors()' for more information and 185s 'citation()' on how to cite R or R packages in publications. 185s 185s Type 'demo()' for some demos, 'help()' for on-line help, or 185s 'help.start()' for an HTML browser interface to help. 185s Type 'q()' to quit R. 185s 185s > # 185s > # Test out the Cholesky, special case of a null block corner 185s > # In this case there is no advantage to a bdsmatrix as it consists of only 185s > # the ordinary matrix part. This case arises in coxme with an (x1+x2 | 1) 185s > # term, however, so it is nice to have it work instead of coding lots of 185s > # if/else logic in that code base. 185s > # 185s > library(bdsmatrix) 185s 185s Attaching package: 'bdsmatrix' 185s 185s The following object is masked from 'package:base': 185s 185s backsolve 185s 185s > aeq <- function(x,y) all.equal(as.vector(x), as.vector(y)) 185s > 185s > tmat <- bdsmatrix(c(3,2,2,4), 185s + c(22,1,2,21,3,20,19,4,18,17,5,16,15,6,7, 8,14,9,10,13,11,12), 185s + matrix(c(1,0,1,1,0,0,1,1,0,1,0,10,0, 185s + 0,1,1,0,1,1,0,1,1,0,1,0,10), ncol=2)) 185s > dimnames(tmat) <- list(NULL, letters[1:13]) 185s > smat <- as.matrix(tmat) 185s > tmat <- bdsmatrix(integer(0), numeric(0), rmat=smat) 185s > yy <- c(30,35,42,56,34,45,32,37,78,56,40,52,39) 185s > 185s > aeq(diag(tmat), diag(smat)) 185s [1] TRUE 185s > zz <- seq(1,13,2) 185s > aeq(as.matrix(tmat[zz,zz]), smat[zz,zz]) 185s [1] TRUE 185s > 185s > ch0 <- chol(smat) 185s > ch1 <- gchol(smat) 185s > ch2 <- gchol(tmat) 185s > # The gchol routines use the composition LDL', where L is lower triangular 185s > # with a diagonal of 1's, and D is diagonal. chol() uses U'U where U is 185s > # upper trangular. 185s > # The as.matrix function returns L and the diag function returns D. 185s > # Convert and compare 185s > aeq(diag(ch1), diag(ch2)) 185s [1] TRUE 185s > temp <- as.matrix(ch2) 185s > aeq(temp, as.matrix(ch1)) 185s [1] TRUE 185s > temp3 <- temp %*% diag(sqrt(diag(ch2))) 185s > aeq(temp3, t(ch0)) 185s [1] TRUE 185s > 185s > zz0 <- solve(smat, yy) 185s > zz1 <- solve(ch1, yy) 185s > zz2 <- solve(tmat, yy) 185s > aeq(zz1, zz2) 185s [1] TRUE 185s > aeq(zz0, zz1) 185s [1] TRUE 185s > 185s > inv1 <- solve(smat) 185s > inv2 <- as.matrix(solve(tmat)) # the result is a full, non-sparse matrix 185s > aeq(inv1, inv2) 185s [1] TRUE 185s > 185s > inv3 <- solve(gchol(tmat)) 185s > aeq(inv1, as.matrix(inv3)) 185s [1] TRUE 185s > 185s > gmat <- gchol(tmat) 185s > g2 <- as.matrix(gmat) %*% diag(sqrt(diag(gmat))) 185s > aeq(1:13 %*% g2, 1:13 %*% gmat) #vectors first 185s [1] TRUE 185s > aeq(g2 %*% 1:13, gmat %*% 1:13) 185s [1] TRUE 185s > temp <- matrix(runif(39), nrow=3) 185s > aeq(temp %*% g2, temp %*% gmat) 185s [1] TRUE 185s > aeq(g2 %*% t(temp), gmat %*% t(temp)) 185s [1] TRUE 185s > 185s BEGIN TEST gtest.R 185s 185s R version 4.4.3 (2025-02-28) -- "Trophy Case" 185s Copyright (C) 2025 The R Foundation for Statistical Computing 185s Platform: s390x-ibm-linux-gnu 185s 185s R is free software and comes with ABSOLUTELY NO WARRANTY. 185s You are welcome to redistribute it under certain conditions. 185s Type 'license()' or 'licence()' for distribution details. 185s 185s R is a collaborative project with many contributors. 185s Type 'contributors()' for more information and 185s 'citation()' on how to cite R or R packages in publications. 185s 185s Type 'demo()' for some demos, 'help()' for on-line help, or 185s 'help.start()' for an HTML browser interface to help. 185s Type 'q()' to quit R. 185s 185s > library(bdsmatrix) 185s 185s Attaching package: 'bdsmatrix' 185s 185s The following object is masked from 'package:base': 185s 185s backsolve 185s 185s > aeq <- function(x,y) all.equal(as.vector(x), as.vector(y)) 185s > 185s > tmat <- bdsmatrix(c(3,2,2,4), 185s + c(22,1,2,21,3,20,19,4,18,17,5,16,15,6,7, 8,14,9,10,13,11,12), 185s + matrix(c(1,0,1,1,0,0,1,1,0,1,0,10,0, 185s + 0,1,1,0,1,1,0,1,1,0,1,0,10), ncol=2)) 185s > dimnames(tmat) <- list(NULL, letters[1:13]) 185s > 185s > smat <- as.matrix(tmat) 185s > 185s > # Create a matrix that is symmetric, but not positive definite 185s > # The first one, temp, has column 6 redundant with cols 1-5 185s > temp <- smat[c(1:5, 5:10), c(1:5, 5:10)] 185s > ch1 <- gchol(temp) 185s > aeq(diag(ch1)[6], 0) # Check that it has a zero in the proper place 185s [1] TRUE 185s > ginv <- solve(ch1) # see if I get a generalized inverse 185s > aeq(temp %*% ginv %*% temp, temp) 186s [1] TRUE 186s > aeq(ginv %*% temp %*% ginv, ginv) 186s [1] TRUE 186s > 186s > # Now create one that is negative definite 186s > ch2 <- gchol(smat) 186s > temp2 <- as.matrix(ch2) 186s > temp3 <- diag(ch2) * rep(c(1, -1), length=nrow(smat)) 186s > xmat <- temp2 %*% diag(temp3) %*% t(temp2) 186s > xmat <- (xmat + t(xmat))/2 #work out round-off errors 186s > ch3 <- gchol(xmat) 186s > 186s > aeq(diag(ch3), temp3) 186s [1] TRUE 186s > aeq(as.matrix(ch3), temp2) 186s [1] TRUE 186s > 186s BEGIN TEST gtest2.R 186s 186s R version 4.4.3 (2025-02-28) -- "Trophy Case" 186s Copyright (C) 2025 The R Foundation for Statistical Computing 186s Platform: s390x-ibm-linux-gnu 186s 186s R is free software and comes with ABSOLUTELY NO WARRANTY. 186s You are welcome to redistribute it under certain conditions. 186s Type 'license()' or 'licence()' for distribution details. 186s 186s R is a collaborative project with many contributors. 186s Type 'contributors()' for more information and 186s 'citation()' on how to cite R or R packages in publications. 186s 186s Type 'demo()' for some demos, 'help()' for on-line help, or 186s 'help.start()' for an HTML browser interface to help. 186s Type 'q()' to quit R. 186s 186s > library(bdsmatrix) 186s 186s Attaching package: 'bdsmatrix' 186s 186s The following object is masked from 'package:base': 186s 186s backsolve 186s 186s > aeq <- function(x,y) all.equal(as.vector(x), as.vector(y)) 186s > 186s > # 186s > # Test multiplication of a vector/matrix times a gchol 186s > # 186s > tmat <- bdsmatrix(c(3,2,2,4), 186s + c(22,1,2,21,3,20,19,4,18,17,5,16,15,6,7, 8,14,9,10,13,11,12), 186s + matrix(c(1,0,1,1,0,0,1,1,0,1,0,10,0, 186s + 0,1,1,0,1,1,0,1,1,0,1,0,10), ncol=2)) 186s > dimnames(tmat) <- list(NULL, letters[1:13]) 186s > 186s > gmat <- gchol(tmat) 186s > g2 <- as.matrix(gmat) %*% diag(sqrt(diag(gmat))) 186s > 186s > 186s > aeq(1:13 %*% g2, 1:13 %*% gmat) #vectors first 186s [1] TRUE 186s > aeq(g2 %*% 1:13, gmat %*% 1:13) 186s [1] TRUE 186s > 186s > temp <- matrix(runif(39), nrow=3) 186s > aeq(temp %*% g2, temp %*% gmat) 186s [1] TRUE 186s > aeq(g2 %*% t(temp), gmat %*% t(temp)) 186s [1] TRUE 186s > 186s BEGIN TEST matrix.R 186s 186s R version 4.4.3 (2025-02-28) -- "Trophy Case" 186s Copyright (C) 2025 The R Foundation for Statistical Computing 186s Platform: s390x-ibm-linux-gnu 186s 186s R is free software and comes with ABSOLUTELY NO WARRANTY. 186s You are welcome to redistribute it under certain conditions. 186s Type 'license()' or 'licence()' for distribution details. 186s 186s R is a collaborative project with many contributors. 186s Type 'contributors()' for more information and 186s 'citation()' on how to cite R or R packages in publications. 186s 186s Type 'demo()' for some demos, 'help()' for on-line help, or 186s 'help.start()' for an HTML browser interface to help. 186s Type 'q()' to quit R. 186s 186s > library(bdsmatrix) 186s > aeq <- function(x,y) all.equal(as.vector(x), as.vector(y)) 186s > 186s > tmat <- bdsmatrix(c(3,2,2,4), 186s + c(22,1,2,21,3,20,19,4,18,17,5,16,15,6,7, 8,14,9,10,13,11,12), 186s + matrix(c(1,0,1,1,0,0,1,1,0,1,0,10,0, 186s + 0,1,1,0,1,1,0,1,1,0,1,0,10), ncol=2)) 186s > dimnames(tmat) <- list(NULL, letters[1:13]) 186s > 186s > smat <- as.matrix(tmat) 186s > yy <- c(30,35,42,56,34,45,32,37,78,56,40,52,39) 186s > 186s > # matrix multiplication 186s > zz <- runif(13) 186s > aeq(zz%*% smat, zz%*% tmat) 186s [1] TRUE 186s > aeq(smat%*%zz, tmat%*% zz) 186s 186s Attaching package: 'bdsmatrix' 186s 186s The following object is masked from 'package:base': 186s 186s backsolve 186s 186s [1] TRUE 186s > 186s > xx <- matrix(1:39, ncol=3) 186s > aeq(smat %*% zz, tmat %*% zz) 186s [1] TRUE 186s > aeq(t(xx) %*% smat, t(xx) %*% tmat) 186s [1] TRUE 186s > 186s > 186s > amat <- tmat 186s > amat@offdiag <- pi 186s > bmat <- as.matrix(amat) 186s > 186s > aeq(zz%*% amat, zz%*% bmat) 186s [1] TRUE 186s > aeq(amat%*%zz, bmat%*% zz) 186s [1] TRUE 186s > 186s > 186s > # Solve the right-hand side wrt a matrix 186s > yy2 <- cbind(yy, -yy, yy+3) 186s > zz1 <- solve(smat, yy2) 186s > zz2 <- solve(tmat, yy2) 186s > aeq(zz1, zz2) 186s [1] TRUE 186s > aeq(zz2[,1], solve(tmat, yy)) 186s [1] TRUE 186s > 186s BEGIN TEST nullr.R 186s 186s R version 4.4.3 (2025-02-28) -- "Trophy Case" 186s Copyright (C) 2025 The R Foundation for Statistical Computing 186s Platform: s390x-ibm-linux-gnu 186s 186s R is free software and comes with ABSOLUTELY NO WARRANTY. 186s You are welcome to redistribute it under certain conditions. 186s Type 'license()' or 'licence()' for distribution details. 186s 186s R is a collaborative project with many contributors. 186s Type 'contributors()' for more information and 186s 'citation()' on how to cite R or R packages in publications. 186s 186s Type 'demo()' for some demos, 'help()' for on-line help, or 186s 'help.start()' for an HTML browser interface to help. 186s Type 'q()' to quit R. 186s 186s > # 186s > # Make sure things work in the simpler case of no rmat component 186s > # 186s > library(bdsmatrix) 186s 186s Attaching package: 'bdsmatrix' 186s 186s > aeq <- function(x,y) all.equal(as.vector(x), as.vector(y)) 186s > 186s > tmat <- bdsmatrix(blocksize= c(3,2,2,4), 186s + blocks= c(22,1,2,21,3,20,19,4,18,17,5,16,15,6,7, 186s + 8,14,9,10,13,11,12)) 186s > dimnames(tmat) <- list(NULL, letters[1:11]) 186s > smat <- as.matrix(tmat) 186s > yy <- c(30,35,42,56,34,45,32,37,78,56,40) 186s > 186s > aeq(diag(tmat), diag(smat)) 186s [1] TRUE 186s > zz <- seq(1,11,2) 186s > aeq(as.matrix(tmat[zz,zz]), smat[zz,zz]) 186s The following object is masked from 'package:base': 186s 186s backsolve 186s 186s [1] TRUE 186s > 186s > ch0 <- chol(smat) 186s > ch1 <- gchol(smat) 186s > ch2 <- gchol(tmat) 186s > 186s > aeq(diag(ch1), diag(ch2)) 186s [1] TRUE 186s > temp <- as.matrix(ch2) 186s > aeq(temp, as.matrix(ch1)) 186s [1] TRUE 186s > temp3 <- temp %*% diag(sqrt(diag(ch2))) 186s > aeq(temp3, t(ch0)) 186s [1] TRUE 186s > 186s > zz0 <- solve(smat, yy) 186s > zz1 <- solve(ch1, yy) 186s > zz2 <- solve(tmat, yy) 186s > aeq(zz1, zz2) 186s [1] TRUE 186s > aeq(zz0, zz1) 186s [1] TRUE 186s > 186s BEGIN TEST reconcile.R 186s 186s R version 4.4.3 (2025-02-28) -- "Trophy Case" 186s Copyright (C) 2025 The R Foundation for Statistical Computing 186s Platform: s390x-ibm-linux-gnu 186s 186s R is free software and comes with ABSOLUTELY NO WARRANTY. 186s You are welcome to redistribute it under certain conditions. 186s Type 'license()' or 'licence()' for distribution details. 186s 186s R is a collaborative project with many contributors. 186s Type 'contributors()' for more information and 186s 'citation()' on how to cite R or R packages in publications. 187s 187s Type 'demo()' for some demos, 'help()' for on-line help, or 187s 'help.start()' for an HTML browser interface to help. 187s Type 'q()' to quit R. 187s 187s > # 187s > # Test cases for bdsmatrix.reconcile 187s > # 187s > library(bdsmatrix) 187s > aeq <- function(x,y) all.equal(as.vector(x), as.vector(y)) 187s > 187s > tmat <- bdsmatrix(c(3,2,2,4), 187s + c(22,1,2,21,3,20,19,4,18,17,5,16,15,6,7, 8,14,9,10,13,11,12), 187s + matrix(c(1,0,1,1,0,0,1,1,0,1,0,10,0, 187s + 0,1,1,0,1,1,0,1,1,0,1,0,10), ncol=2)) 187s > id <- letters[1:13] 187s > dimnames(tmat) <- list(id, id) 187s > 187s > rmat <- matrix(1:169, 13,13) 187s > rmat <- (rmat + t(rmat))/2 187s > dimnames(rmat) <- list(rev(id), rev(id)) 187s > 187s > xmat <- bdsmatrix.reconcile(list(tmat, rmat), group=id) 187s > temp <- xmat[[1]] 187s 187s Attaching package: 'bdsmatrix' 187s 187s The following object is masked from 'package:base': 187s 187s backsolve 187s 187s > aeq(temp@blocksize, 13) 187s [1] TRUE 187s > aeq(as.matrix(temp), as.matrix(tmat)) 187s [1] TRUE 187s > 187s > temp <- xmat[[2]] 187s > aeq(temp@blocksize, 13) 187s [1] TRUE 187s > aeq(as.matrix(temp), rmat[13:1, 13:1]) 187s [1] TRUE 187s > 187s > xmat <- bdsmatrix.reconcile(list(rmat, bdsI, tmat), group= rev(id)) 187s > temp <- xmat[[1]] 187s > aeq(as.matrix(temp), rmat) 187s [1] TRUE 187s > 187s > temp <- xmat[[2]] 187s > aeq(as.matrix(temp), diag(13)) 187s [1] TRUE 187s > 187s > temp <- xmat[[3]] 187s > aeq(as.matrix(temp), (as.matrix(tmat))[13:1,13:1]) 187s [1] TRUE 187s > 187s > # 187s > # Simplest case 187s > # 187s > xmat <- bdsmatrix.reconcile(bdsI, id) 187s > all(xmat@blocksize==1) 187s [1] TRUE 187s > aeq(as.matrix(xmat), diag(13)) 187s [1] TRUE 187s > 187s > # 187s > # The case list(tmat, tmat) will fail - can't have 2 rmats 187s > # 187s > #xmat <- bdsmatrix.reconcile(list(tmat, tmat), id) 187s > 187s > xmat <- bdsmatrix.reconcile(list(tmat, bdsI), rev(id)) 187s > temp <- xmat[[1]] 187s > aeq(as.matrix(temp), as.matrix(tmat)) 187s [1] TRUE 187s > aeq(dimnames(temp)[[1]], id) 187s [1] TRUE 187s > 187s > aeq(as.matrix(xmat[[2]]), diag(13)) 187s [1] TRUE 187s > 187s > # 187s > # Now for the hard one: 2 bdsmatrices, different orders, different 187s > # blocksize, but one contains the other 187s > # 187s > tmat <- tmat[1:11, 1:11] 187s > tord <- c(11:8, 2,1,3, 6,7,5,4) 187s > rmat <- (as.matrix(tmat))[tord, tord] 187s > rmat <- bdsmatrix(blocksize=c(4,5,2), 187s + blocks=c(rmat[1:4,1:4], rmat[5:9,5:9], rmat[10:11, 10:11]), 187s + dimnames=list(id[tord], id[tord])) 187s > 187s > aeq(as.matrix(tmat)[tord,tord], as.matrix(rmat)) 187s [1] TRUE 187s > 187s > xmat <- bdsmatrix.reconcile(list(tmat/2, rmat), id[1:11]) 187s > all.equal(xmat[[2]], rmat) 187s [1] TRUE 187s > all.equal(xmat[[1]]*2, rmat) 187s [1] TRUE 187s > 187s > # Now toss out a row/col 187s > # Give it a different name, too 187s > xx <- id[tord] 187s > xx[1] <- 44 187s > dimnames(rmat) <- list(xx,xx) 187s > xmat <- bdsmatrix.reconcile(list(tmat/2, rmat), id[1:9]) 187s > all.equal(xmat[[1]]*2, xmat[[2]]) 187s [1] TRUE 187s > 187s BEGIN TEST tinv.R 187s 187s R version 4.4.3 (2025-02-28) -- "Trophy Case" 187s Copyright (C) 2025 The R Foundation for Statistical Computing 187s Platform: s390x-ibm-linux-gnu 187s 187s R is free software and comes with ABSOLUTELY NO WARRANTY. 187s You are welcome to redistribute it under certain conditions. 187s Type 'license()' or 'licence()' for distribution details. 187s 187s R is a collaborative project with many contributors. 187s Type 'contributors()' for more information and 187s 'citation()' on how to cite R or R packages in publications. 187s 187s Type 'demo()' for some demos, 'help()' for on-line help, or 187s 'help.start()' for an HTML browser interface to help. 187s Type 'q()' to quit R. 187s 187s > library(bdsmatrix) 187s > aeq <- function(x,y) all.equal(as.vector(x), as.vector(y)) 187s > 187s > tmat <- bdsmatrix(c(3,2,2,4), 187s + c(22,1,2,21,3,20,19,4,18,17,5,16,15,6,7, 8,14,9,10,13,11,12), 187s + matrix(c(1,0,1,1,0,0,1,1,0,1,0,10,0, 187s + 0,1,1,0,1,1,0,1,1,0,1,0,10), ncol=2)) 187s > dimnames(tmat) <- list(NULL, letters[1:13]) 187s > 187s > smat <- as.matrix(tmat) 187s > yy <- c(30,35,42,56,34,45,32,37,78,56,40,52,39) 187s > # look at inverses more closely 187s > # (I needed this when some of the other tests weren't being passed, 187s > # to figure out where in the decomposition/inversion/multiply process 187s > # the flaw was). 187s > 187s > ch1 <- gchol(smat) 187s > ch2 <- gchol(tmat) 187s > 187s > inv1 <- solve(as.matrix(ch1)) 187s > inv2 <- solve(ch2,full=F) #inverse of the cholesky, not of tmat 187s > aeq(inv1, as.matrix(inv2)) 187s [1] TRUE 187s > 187s > # Full matrix tests 187s > inv3 <- solve(smat) 187s > inv4 <- solve(tmat) 187s 187s Attaching package: 'bdsmatrix' 187s 187s The following object is masked from 'package:base': 187s 187s backsolve 187s 187s > inv5 <- solve(gchol(smat), full=T) 187s > aeq(inv3, inv4) 187s [1] TRUE 187s > aeq(inv3, inv5) 187s [1] TRUE 187s > 187s > # The following test is false by design: when called with a bdsmatrix 187s > # object that has an rmat portion, the true inverse is dense. But 187s > # coxme only needs the trace for one calcluation; solve(gchol(tmat)) 187s > # cheats and only returns the block diagonal portion of the inverse. 187s > #inv6 <- solve(gchol(tmat), full=T) 187s > #aeq(inv3, inv6) 187s > 187s > # 187s > # Now test the solution to a partial solve 187s > # We want to be able to transform a matrix to uncorrelated form 187s > # If tmat= LDL', and A is general, I want (D^{-1/2}) L^{-1} A 187s > # 187s > amat <- matrix(runif(5*nrow(tmat)), nrow=nrow(tmat)) 187s > xx1 <- diag(1/sqrt(diag(ch1))) %*% solve(as.matrix(ch1), amat) 187s > xx2 <- solve(ch2, amat, full=F) 187s > aeq(xx1, xx2) 187s [1] TRUE 187s > 187s > xx1 <- diag(1/sqrt(diag(ch1))) %*% solve(as.matrix(ch1), yy) 187s > xx2 <- solve(ch2, yy, full=F) 187s > aeq(xx1, xx2) 187s [1] TRUE 187s > 187s autopkgtest [17:55:58]: test run-unit-test: -----------------------] 188s autopkgtest [17:55:59]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 188s run-unit-test PASS 188s autopkgtest [17:55:59]: test pkg-r-autopkgtest: preparing testbed 189s Reading package lists... 189s Building dependency tree... 189s Reading state information... 189s Starting pkgProblemResolver with broken count: 0 189s Starting 2 pkgProblemResolver with broken count: 0 189s Done 189s The following NEW packages will be installed: 189s build-essential cpp cpp-14 cpp-14-s390x-linux-gnu cpp-s390x-linux-gnu 189s dctrl-tools g++ g++-14 g++-14-s390x-linux-gnu g++-s390x-linux-gnu gcc gcc-14 189s gcc-14-s390x-linux-gnu gcc-s390x-linux-gnu gfortran gfortran-14 189s gfortran-14-s390x-linux-gnu gfortran-s390x-linux-gnu icu-devtools libasan8 189s libblas-dev libbz2-dev libcc1-0 libdeflate-dev libgcc-14-dev 189s libgfortran-14-dev libicu-dev libisl23 libitm1 libjpeg-dev 189s libjpeg-turbo8-dev libjpeg8-dev liblapack-dev liblzma-dev libmpc3 189s libncurses-dev libpcre2-16-0 libpcre2-32-0 libpcre2-dev libpcre2-posix3 189s libpkgconf3 libpng-dev libreadline-dev libstdc++-14-dev libtirpc-dev 189s libubsan1 pkg-r-autopkgtest pkgconf pkgconf-bin r-base-dev zlib1g-dev 189s 0 upgraded, 51 newly installed, 0 to remove and 0 not upgraded. 189s Need to get 82.3 MB of archives. 189s After this operation, 279 MB of additional disk space will be used. 189s Get:1 http://ftpmaster.internal/ubuntu plucky/main s390x libisl23 s390x 0.27-1 [704 kB] 190s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x libmpc3 s390x 1.3.1-1build2 [57.8 kB] 190s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x cpp-14-s390x-linux-gnu s390x 14.2.0-17ubuntu3 [9572 kB] 198s Get:4 http://ftpmaster.internal/ubuntu plucky/main s390x cpp-14 s390x 14.2.0-17ubuntu3 [1028 B] 198s Get:5 http://ftpmaster.internal/ubuntu plucky/main s390x cpp-s390x-linux-gnu s390x 4:14.2.0-1ubuntu1 [5556 B] 198s Get:6 http://ftpmaster.internal/ubuntu plucky/main s390x cpp s390x 4:14.2.0-1ubuntu1 [22.4 kB] 199s Get:7 http://ftpmaster.internal/ubuntu plucky/main s390x libcc1-0 s390x 15-20250222-0ubuntu1 [49.2 kB] 199s Get:8 http://ftpmaster.internal/ubuntu plucky/main s390x libitm1 s390x 15-20250222-0ubuntu1 [31.2 kB] 199s Get:9 http://ftpmaster.internal/ubuntu plucky/main s390x libasan8 s390x 15-20250222-0ubuntu1 [2970 kB] 201s Get:10 http://ftpmaster.internal/ubuntu plucky/main s390x libubsan1 s390x 15-20250222-0ubuntu1 [1212 kB] 202s Get:11 http://ftpmaster.internal/ubuntu plucky/main s390x libgcc-14-dev s390x 14.2.0-17ubuntu3 [1037 kB] 203s Get:12 http://ftpmaster.internal/ubuntu plucky/main s390x gcc-14-s390x-linux-gnu s390x 14.2.0-17ubuntu3 [18.7 MB] 220s Get:13 http://ftpmaster.internal/ubuntu plucky/main s390x gcc-14 s390x 14.2.0-17ubuntu3 [526 kB] 221s Get:14 http://ftpmaster.internal/ubuntu plucky/main s390x gcc-s390x-linux-gnu s390x 4:14.2.0-1ubuntu1 [1204 B] 221s Get:15 http://ftpmaster.internal/ubuntu plucky/main s390x gcc s390x 4:14.2.0-1ubuntu1 [5004 B] 221s Get:16 http://ftpmaster.internal/ubuntu plucky/main s390x libstdc++-14-dev s390x 14.2.0-17ubuntu3 [2611 kB] 223s Get:17 http://ftpmaster.internal/ubuntu plucky/main s390x g++-14-s390x-linux-gnu s390x 14.2.0-17ubuntu3 [11.0 MB] 235s Get:18 http://ftpmaster.internal/ubuntu plucky/main s390x g++-14 s390x 14.2.0-17ubuntu3 [21.8 kB] 235s Get:19 http://ftpmaster.internal/ubuntu plucky/main s390x g++-s390x-linux-gnu s390x 4:14.2.0-1ubuntu1 [956 B] 235s Get:20 http://ftpmaster.internal/ubuntu plucky/main s390x g++ s390x 4:14.2.0-1ubuntu1 [1080 B] 235s Get:21 http://ftpmaster.internal/ubuntu plucky/main s390x build-essential s390x 12.10ubuntu1 [4930 B] 235s Get:22 http://ftpmaster.internal/ubuntu plucky/main s390x dctrl-tools s390x 2.24-3build3 [106 kB] 235s Get:23 http://ftpmaster.internal/ubuntu plucky/main s390x libgfortran-14-dev s390x 14.2.0-17ubuntu3 [654 kB] 236s Get:24 http://ftpmaster.internal/ubuntu plucky/main s390x gfortran-14-s390x-linux-gnu s390x 14.2.0-17ubuntu3 [10.3 MB] 246s Get:25 http://ftpmaster.internal/ubuntu plucky/main s390x gfortran-14 s390x 14.2.0-17ubuntu3 [13.6 kB] 246s Get:26 http://ftpmaster.internal/ubuntu plucky/main s390x gfortran-s390x-linux-gnu s390x 4:14.2.0-1ubuntu1 [1012 B] 246s Get:27 http://ftpmaster.internal/ubuntu plucky/main s390x gfortran s390x 4:14.2.0-1ubuntu1 [1160 B] 246s Get:28 http://ftpmaster.internal/ubuntu plucky/main s390x icu-devtools s390x 76.1-1ubuntu2 [225 kB] 246s Get:29 http://ftpmaster.internal/ubuntu plucky/main s390x libblas-dev s390x 3.12.1-2 [254 kB] 246s Get:30 http://ftpmaster.internal/ubuntu plucky/main s390x libbz2-dev s390x 1.0.8-6 [39.1 kB] 246s Get:31 http://ftpmaster.internal/ubuntu plucky/main s390x libdeflate-dev s390x 1.23-1 [52.2 kB] 246s Get:32 http://ftpmaster.internal/ubuntu plucky/main s390x libicu-dev s390x 76.1-1ubuntu2 [12.2 MB] 259s Get:33 http://ftpmaster.internal/ubuntu plucky/main s390x libjpeg-turbo8-dev s390x 2.1.5-3ubuntu2 [281 kB] 259s Get:34 http://ftpmaster.internal/ubuntu plucky/main s390x libjpeg8-dev s390x 8c-2ubuntu11 [1484 B] 259s Get:35 http://ftpmaster.internal/ubuntu plucky/main s390x libjpeg-dev s390x 8c-2ubuntu11 [1484 B] 259s Get:36 http://ftpmaster.internal/ubuntu plucky/main s390x liblapack-dev s390x 3.12.1-2 [5967 kB] 264s Get:37 http://ftpmaster.internal/ubuntu plucky/main s390x libncurses-dev s390x 6.5+20250216-2 [407 kB] 265s Get:38 http://ftpmaster.internal/ubuntu plucky/main s390x libpcre2-16-0 s390x 10.45-1 [259 kB] 265s Get:39 http://ftpmaster.internal/ubuntu plucky/main s390x libpcre2-32-0 s390x 10.45-1 [245 kB] 265s Get:40 http://ftpmaster.internal/ubuntu plucky/main s390x libpcre2-posix3 s390x 10.45-1 [7080 B] 265s Get:41 http://ftpmaster.internal/ubuntu plucky/main s390x libpcre2-dev s390x 10.45-1 [899 kB] 266s Get:42 http://ftpmaster.internal/ubuntu plucky/main s390x libpkgconf3 s390x 1.8.1-4 [31.2 kB] 266s Get:43 http://ftpmaster.internal/ubuntu plucky/main s390x zlib1g-dev s390x 1:1.3.dfsg+really1.3.1-1ubuntu1 [898 kB] 266s Get:44 http://ftpmaster.internal/ubuntu plucky/main s390x libpng-dev s390x 1.6.47-1 [278 kB] 267s Get:45 http://ftpmaster.internal/ubuntu plucky/main s390x libreadline-dev s390x 8.2-6 [187 kB] 267s Get:46 http://ftpmaster.internal/ubuntu plucky/main s390x liblzma-dev s390x 5.6.4-1 [183 kB] 267s Get:47 http://ftpmaster.internal/ubuntu plucky/main s390x pkgconf-bin s390x 1.8.1-4 [21.5 kB] 267s Get:48 http://ftpmaster.internal/ubuntu plucky/main s390x pkgconf s390x 1.8.1-4 [16.7 kB] 267s Get:49 http://ftpmaster.internal/ubuntu plucky/main s390x libtirpc-dev s390x 1.3.4+ds-1.3 [196 kB] 267s Get:50 http://ftpmaster.internal/ubuntu plucky/universe s390x r-base-dev all 4.4.3-1 [4176 B] 267s Get:51 http://ftpmaster.internal/ubuntu plucky/universe s390x pkg-r-autopkgtest all 20231212ubuntu1 [6448 B] 268s Fetched 82.3 MB in 1min 18s (1053 kB/s) 268s Selecting previously unselected package libisl23:s390x. 268s (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 ... 58550 files and directories currently installed.) 268s Preparing to unpack .../00-libisl23_0.27-1_s390x.deb ... 268s Unpacking libisl23:s390x (0.27-1) ... 268s Selecting previously unselected package libmpc3:s390x. 268s Preparing to unpack .../01-libmpc3_1.3.1-1build2_s390x.deb ... 268s Unpacking libmpc3:s390x (1.3.1-1build2) ... 268s Selecting previously unselected package cpp-14-s390x-linux-gnu. 268s Preparing to unpack .../02-cpp-14-s390x-linux-gnu_14.2.0-17ubuntu3_s390x.deb ... 268s Unpacking cpp-14-s390x-linux-gnu (14.2.0-17ubuntu3) ... 268s Selecting previously unselected package cpp-14. 268s Preparing to unpack .../03-cpp-14_14.2.0-17ubuntu3_s390x.deb ... 268s Unpacking cpp-14 (14.2.0-17ubuntu3) ... 268s Selecting previously unselected package cpp-s390x-linux-gnu. 268s Preparing to unpack .../04-cpp-s390x-linux-gnu_4%3a14.2.0-1ubuntu1_s390x.deb ... 268s Unpacking cpp-s390x-linux-gnu (4:14.2.0-1ubuntu1) ... 268s Selecting previously unselected package cpp. 268s Preparing to unpack .../05-cpp_4%3a14.2.0-1ubuntu1_s390x.deb ... 268s Unpacking cpp (4:14.2.0-1ubuntu1) ... 268s Selecting previously unselected package libcc1-0:s390x. 268s Preparing to unpack .../06-libcc1-0_15-20250222-0ubuntu1_s390x.deb ... 268s Unpacking libcc1-0:s390x (15-20250222-0ubuntu1) ... 268s Selecting previously unselected package libitm1:s390x. 268s Preparing to unpack .../07-libitm1_15-20250222-0ubuntu1_s390x.deb ... 268s Unpacking libitm1:s390x (15-20250222-0ubuntu1) ... 268s Selecting previously unselected package libasan8:s390x. 268s Preparing to unpack .../08-libasan8_15-20250222-0ubuntu1_s390x.deb ... 268s Unpacking libasan8:s390x (15-20250222-0ubuntu1) ... 268s Selecting previously unselected package libubsan1:s390x. 268s Preparing to unpack .../09-libubsan1_15-20250222-0ubuntu1_s390x.deb ... 268s Unpacking libubsan1:s390x (15-20250222-0ubuntu1) ... 268s Selecting previously unselected package libgcc-14-dev:s390x. 268s Preparing to unpack .../10-libgcc-14-dev_14.2.0-17ubuntu3_s390x.deb ... 268s Unpacking libgcc-14-dev:s390x (14.2.0-17ubuntu3) ... 268s Selecting previously unselected package gcc-14-s390x-linux-gnu. 268s Preparing to unpack .../11-gcc-14-s390x-linux-gnu_14.2.0-17ubuntu3_s390x.deb ... 268s Unpacking gcc-14-s390x-linux-gnu (14.2.0-17ubuntu3) ... 268s Selecting previously unselected package gcc-14. 268s Preparing to unpack .../12-gcc-14_14.2.0-17ubuntu3_s390x.deb ... 268s Unpacking gcc-14 (14.2.0-17ubuntu3) ... 268s Selecting previously unselected package gcc-s390x-linux-gnu. 268s Preparing to unpack .../13-gcc-s390x-linux-gnu_4%3a14.2.0-1ubuntu1_s390x.deb ... 268s Unpacking gcc-s390x-linux-gnu (4:14.2.0-1ubuntu1) ... 268s Selecting previously unselected package gcc. 268s Preparing to unpack .../14-gcc_4%3a14.2.0-1ubuntu1_s390x.deb ... 268s Unpacking gcc (4:14.2.0-1ubuntu1) ... 268s Selecting previously unselected package libstdc++-14-dev:s390x. 268s Preparing to unpack .../15-libstdc++-14-dev_14.2.0-17ubuntu3_s390x.deb ... 268s Unpacking libstdc++-14-dev:s390x (14.2.0-17ubuntu3) ... 268s Selecting previously unselected package g++-14-s390x-linux-gnu. 268s Preparing to unpack .../16-g++-14-s390x-linux-gnu_14.2.0-17ubuntu3_s390x.deb ... 268s Unpacking g++-14-s390x-linux-gnu (14.2.0-17ubuntu3) ... 268s Selecting previously unselected package g++-14. 268s Preparing to unpack .../17-g++-14_14.2.0-17ubuntu3_s390x.deb ... 268s Unpacking g++-14 (14.2.0-17ubuntu3) ... 268s Selecting previously unselected package g++-s390x-linux-gnu. 268s Preparing to unpack .../18-g++-s390x-linux-gnu_4%3a14.2.0-1ubuntu1_s390x.deb ... 268s Unpacking g++-s390x-linux-gnu (4:14.2.0-1ubuntu1) ... 268s Selecting previously unselected package g++. 268s Preparing to unpack .../19-g++_4%3a14.2.0-1ubuntu1_s390x.deb ... 268s Unpacking g++ (4:14.2.0-1ubuntu1) ... 268s Selecting previously unselected package build-essential. 268s Preparing to unpack .../20-build-essential_12.10ubuntu1_s390x.deb ... 268s Unpacking build-essential (12.10ubuntu1) ... 268s Selecting previously unselected package dctrl-tools. 268s Preparing to unpack .../21-dctrl-tools_2.24-3build3_s390x.deb ... 268s Unpacking dctrl-tools (2.24-3build3) ... 268s Selecting previously unselected package libgfortran-14-dev:s390x. 268s Preparing to unpack .../22-libgfortran-14-dev_14.2.0-17ubuntu3_s390x.deb ... 268s Unpacking libgfortran-14-dev:s390x (14.2.0-17ubuntu3) ... 268s Selecting previously unselected package gfortran-14-s390x-linux-gnu. 268s Preparing to unpack .../23-gfortran-14-s390x-linux-gnu_14.2.0-17ubuntu3_s390x.deb ... 268s Unpacking gfortran-14-s390x-linux-gnu (14.2.0-17ubuntu3) ... 269s Selecting previously unselected package gfortran-14. 269s Preparing to unpack .../24-gfortran-14_14.2.0-17ubuntu3_s390x.deb ... 269s Unpacking gfortran-14 (14.2.0-17ubuntu3) ... 269s Selecting previously unselected package gfortran-s390x-linux-gnu. 269s Preparing to unpack .../25-gfortran-s390x-linux-gnu_4%3a14.2.0-1ubuntu1_s390x.deb ... 269s Unpacking gfortran-s390x-linux-gnu (4:14.2.0-1ubuntu1) ... 269s Selecting previously unselected package gfortran. 269s Preparing to unpack .../26-gfortran_4%3a14.2.0-1ubuntu1_s390x.deb ... 269s Unpacking gfortran (4:14.2.0-1ubuntu1) ... 269s Selecting previously unselected package icu-devtools. 269s Preparing to unpack .../27-icu-devtools_76.1-1ubuntu2_s390x.deb ... 269s Unpacking icu-devtools (76.1-1ubuntu2) ... 269s Selecting previously unselected package libblas-dev:s390x. 269s Preparing to unpack .../28-libblas-dev_3.12.1-2_s390x.deb ... 269s Unpacking libblas-dev:s390x (3.12.1-2) ... 269s Selecting previously unselected package libbz2-dev:s390x. 269s Preparing to unpack .../29-libbz2-dev_1.0.8-6_s390x.deb ... 269s Unpacking libbz2-dev:s390x (1.0.8-6) ... 269s Selecting previously unselected package libdeflate-dev:s390x. 269s Preparing to unpack .../30-libdeflate-dev_1.23-1_s390x.deb ... 269s Unpacking libdeflate-dev:s390x (1.23-1) ... 269s Selecting previously unselected package libicu-dev:s390x. 269s Preparing to unpack .../31-libicu-dev_76.1-1ubuntu2_s390x.deb ... 269s Unpacking libicu-dev:s390x (76.1-1ubuntu2) ... 269s Selecting previously unselected package libjpeg-turbo8-dev:s390x. 269s Preparing to unpack .../32-libjpeg-turbo8-dev_2.1.5-3ubuntu2_s390x.deb ... 269s Unpacking libjpeg-turbo8-dev:s390x (2.1.5-3ubuntu2) ... 269s Selecting previously unselected package libjpeg8-dev:s390x. 269s Preparing to unpack .../33-libjpeg8-dev_8c-2ubuntu11_s390x.deb ... 269s Unpacking libjpeg8-dev:s390x (8c-2ubuntu11) ... 269s Selecting previously unselected package libjpeg-dev:s390x. 269s Preparing to unpack .../34-libjpeg-dev_8c-2ubuntu11_s390x.deb ... 269s Unpacking libjpeg-dev:s390x (8c-2ubuntu11) ... 269s Selecting previously unselected package liblapack-dev:s390x. 269s Preparing to unpack .../35-liblapack-dev_3.12.1-2_s390x.deb ... 269s Unpacking liblapack-dev:s390x (3.12.1-2) ... 269s Selecting previously unselected package libncurses-dev:s390x. 269s Preparing to unpack .../36-libncurses-dev_6.5+20250216-2_s390x.deb ... 269s Unpacking libncurses-dev:s390x (6.5+20250216-2) ... 269s Selecting previously unselected package libpcre2-16-0:s390x. 269s Preparing to unpack .../37-libpcre2-16-0_10.45-1_s390x.deb ... 269s Unpacking libpcre2-16-0:s390x (10.45-1) ... 269s Selecting previously unselected package libpcre2-32-0:s390x. 269s Preparing to unpack .../38-libpcre2-32-0_10.45-1_s390x.deb ... 269s Unpacking libpcre2-32-0:s390x (10.45-1) ... 269s Selecting previously unselected package libpcre2-posix3:s390x. 269s Preparing to unpack .../39-libpcre2-posix3_10.45-1_s390x.deb ... 269s Unpacking libpcre2-posix3:s390x (10.45-1) ... 269s Selecting previously unselected package libpcre2-dev:s390x. 269s Preparing to unpack .../40-libpcre2-dev_10.45-1_s390x.deb ... 269s Unpacking libpcre2-dev:s390x (10.45-1) ... 269s Selecting previously unselected package libpkgconf3:s390x. 269s Preparing to unpack .../41-libpkgconf3_1.8.1-4_s390x.deb ... 269s Unpacking libpkgconf3:s390x (1.8.1-4) ... 269s Selecting previously unselected package zlib1g-dev:s390x. 269s Preparing to unpack .../42-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1ubuntu1_s390x.deb ... 269s Unpacking zlib1g-dev:s390x (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 269s Selecting previously unselected package libpng-dev:s390x. 269s Preparing to unpack .../43-libpng-dev_1.6.47-1_s390x.deb ... 269s Unpacking libpng-dev:s390x (1.6.47-1) ... 269s Selecting previously unselected package libreadline-dev:s390x. 269s Preparing to unpack .../44-libreadline-dev_8.2-6_s390x.deb ... 269s Unpacking libreadline-dev:s390x (8.2-6) ... 269s Selecting previously unselected package liblzma-dev:s390x. 269s Preparing to unpack .../45-liblzma-dev_5.6.4-1_s390x.deb ... 269s Unpacking liblzma-dev:s390x (5.6.4-1) ... 269s Selecting previously unselected package pkgconf-bin. 269s Preparing to unpack .../46-pkgconf-bin_1.8.1-4_s390x.deb ... 269s Unpacking pkgconf-bin (1.8.1-4) ... 269s Selecting previously unselected package pkgconf:s390x. 269s Preparing to unpack .../47-pkgconf_1.8.1-4_s390x.deb ... 269s Unpacking pkgconf:s390x (1.8.1-4) ... 269s Selecting previously unselected package libtirpc-dev:s390x. 269s Preparing to unpack .../48-libtirpc-dev_1.3.4+ds-1.3_s390x.deb ... 269s Unpacking libtirpc-dev:s390x (1.3.4+ds-1.3) ... 269s Selecting previously unselected package r-base-dev. 269s Preparing to unpack .../49-r-base-dev_4.4.3-1_all.deb ... 269s Unpacking r-base-dev (4.4.3-1) ... 269s Selecting previously unselected package pkg-r-autopkgtest. 269s Preparing to unpack .../50-pkg-r-autopkgtest_20231212ubuntu1_all.deb ... 269s Unpacking pkg-r-autopkgtest (20231212ubuntu1) ... 269s Setting up libjpeg-turbo8-dev:s390x (2.1.5-3ubuntu2) ... 269s Setting up libncurses-dev:s390x (6.5+20250216-2) ... 269s Setting up libreadline-dev:s390x (8.2-6) ... 269s Setting up libpcre2-16-0:s390x (10.45-1) ... 269s Setting up libpcre2-32-0:s390x (10.45-1) ... 269s Setting up libtirpc-dev:s390x (1.3.4+ds-1.3) ... 269s Setting up libpkgconf3:s390x (1.8.1-4) ... 269s Setting up libmpc3:s390x (1.3.1-1build2) ... 269s Setting up icu-devtools (76.1-1ubuntu2) ... 269s Setting up pkgconf-bin (1.8.1-4) ... 269s Setting up liblzma-dev:s390x (5.6.4-1) ... 269s Setting up libubsan1:s390x (15-20250222-0ubuntu1) ... 269s Setting up zlib1g-dev:s390x (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 269s Setting up libpcre2-posix3:s390x (10.45-1) ... 269s Setting up libasan8:s390x (15-20250222-0ubuntu1) ... 269s Setting up libjpeg8-dev:s390x (8c-2ubuntu11) ... 269s Setting up libisl23:s390x (0.27-1) ... 269s Setting up libdeflate-dev:s390x (1.23-1) ... 269s Setting up libicu-dev:s390x (76.1-1ubuntu2) ... 269s Setting up libcc1-0:s390x (15-20250222-0ubuntu1) ... 269s Setting up libblas-dev:s390x (3.12.1-2) ... 269s update-alternatives: using /usr/lib/s390x-linux-gnu/blas/libblas.so to provide /usr/lib/s390x-linux-gnu/libblas.so (libblas.so-s390x-linux-gnu) in auto mode 269s Setting up dctrl-tools (2.24-3build3) ... 269s Setting up libitm1:s390x (15-20250222-0ubuntu1) ... 269s Setting up libbz2-dev:s390x (1.0.8-6) ... 269s Setting up libpcre2-dev:s390x (10.45-1) ... 269s Setting up libpng-dev:s390x (1.6.47-1) ... 269s Setting up libjpeg-dev:s390x (8c-2ubuntu11) ... 269s Setting up pkgconf:s390x (1.8.1-4) ... 269s Setting up liblapack-dev:s390x (3.12.1-2) ... 269s update-alternatives: using /usr/lib/s390x-linux-gnu/lapack/liblapack.so to provide /usr/lib/s390x-linux-gnu/liblapack.so (liblapack.so-s390x-linux-gnu) in auto mode 269s Setting up cpp-14-s390x-linux-gnu (14.2.0-17ubuntu3) ... 269s Setting up cpp-14 (14.2.0-17ubuntu3) ... 269s Setting up libgcc-14-dev:s390x (14.2.0-17ubuntu3) ... 269s Setting up libstdc++-14-dev:s390x (14.2.0-17ubuntu3) ... 269s Setting up libgfortran-14-dev:s390x (14.2.0-17ubuntu3) ... 269s Setting up cpp-s390x-linux-gnu (4:14.2.0-1ubuntu1) ... 269s Setting up gcc-14-s390x-linux-gnu (14.2.0-17ubuntu3) ... 269s Setting up gcc-s390x-linux-gnu (4:14.2.0-1ubuntu1) ... 269s Setting up g++-14-s390x-linux-gnu (14.2.0-17ubuntu3) ... 269s Setting up cpp (4:14.2.0-1ubuntu1) ... 269s Setting up gfortran-14-s390x-linux-gnu (14.2.0-17ubuntu3) ... 269s Setting up g++-s390x-linux-gnu (4:14.2.0-1ubuntu1) ... 269s Setting up gcc-14 (14.2.0-17ubuntu3) ... 269s Setting up g++-14 (14.2.0-17ubuntu3) ... 269s Setting up gfortran-14 (14.2.0-17ubuntu3) ... 269s Setting up gfortran-s390x-linux-gnu (4:14.2.0-1ubuntu1) ... 269s Setting up gcc (4:14.2.0-1ubuntu1) ... 269s Setting up g++ (4:14.2.0-1ubuntu1) ... 269s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 269s Setting up build-essential (12.10ubuntu1) ... 269s Setting up gfortran (4:14.2.0-1ubuntu1) ... 269s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode 269s 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 269s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode 269s 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 269s Setting up r-base-dev (4.4.3-1) ... 269s Setting up pkg-r-autopkgtest (20231212ubuntu1) ... 269s Processing triggers for libc-bin (2.41-1ubuntu2) ... 269s Processing triggers for man-db (2.13.0-1) ... 270s Processing triggers for install-info (7.1.1-1) ... 271s autopkgtest [17:57:22]: test pkg-r-autopkgtest: /usr/share/dh-r/pkg-r-autopkgtest 271s autopkgtest [17:57:22]: test pkg-r-autopkgtest: [----------------------- 271s Test: Try to load the R library bdsmatrix 271s 271s R version 4.4.3 (2025-02-28) -- "Trophy Case" 271s Copyright (C) 2025 The R Foundation for Statistical Computing 271s Platform: s390x-ibm-linux-gnu 271s 271s R is free software and comes with ABSOLUTELY NO WARRANTY. 271s You are welcome to redistribute it under certain conditions. 271s Type 'license()' or 'licence()' for distribution details. 271s 271s R is a collaborative project with many contributors. 271s Type 'contributors()' for more information and 271s 'citation()' on how to cite R or R packages in publications. 271s 271s Type 'demo()' for some demos, 'help()' for on-line help, or 271s 'help.start()' for an HTML browser interface to help. 271s Type 'q()' to quit R. 271s 271s > library('bdsmatrix') 272s 272s Attaching package: ‘bdsmatrix’ 272s 272s > 272s > 272s Other tests are currently unsupported! 272s They will be progressively added. 272s The following object is masked from ‘package:base’: 272s 272s backsolve 272s 272s autopkgtest [17:57:23]: test pkg-r-autopkgtest: -----------------------] 272s autopkgtest [17:57:23]: test pkg-r-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 272s pkg-r-autopkgtest PASS 273s autopkgtest [17:57:24]: @@@@@@@@@@@@@@@@@@@@ summary 273s run-unit-test PASS 273s pkg-r-autopkgtest PASS 278s nova [W] Using flock in prodstack6-s390x 278s Creating nova instance adt-plucky-s390x-r-cran-bdsmatrix-20250315-175251-juju-7f2275-prod-proposed-migration-environment-2-72c2606b-4bc4-48d1-af6a-a6e57d4f4d4f from image adt/ubuntu-plucky-s390x-server-20250315.img (UUID 3d3557fa-fd0f-4bba-9b89-8d5964e09f61)... 278s nova [W] Timed out waiting for 94ce58cd-558f-4d3a-a3d1-19301752133f to get deleted.