0s autopkgtest [16:25:52]: starting date and time: 2025-03-15 16:25:52+0000 0s autopkgtest [16:25:52]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [16:25:52]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.lnqnjvzi/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-irlba --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-20@bos03-s390x-7.secgroup --name adt-plucky-s390x-r-cran-irlba-20250315-160931-juju-7f2275-prod-proposed-migration-environment-20-1c8b10f2-74f7-47f2-beb7-2b0bb6bef5c6 --image adt/ubuntu-plucky-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --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/ 101s autopkgtest [16:27:33]: testbed dpkg architecture: s390x 101s autopkgtest [16:27:33]: testbed apt version: 2.9.33 102s autopkgtest [16:27:34]: @@@@@@@@@@@@@@@@@@@@ test bed setup 102s autopkgtest [16:27:34]: testbed release detected to be: None 102s autopkgtest [16:27:34]: updating testbed package index (apt update) 103s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 103s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 103s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 103s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 103s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [99.7 kB] 103s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 103s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [379 kB] 104s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x Packages [113 kB] 104s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x c-n-f Metadata [1824 B] 104s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted s390x c-n-f Metadata [116 B] 104s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x Packages [320 kB] 104s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x c-n-f Metadata [13.4 kB] 104s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x Packages [3776 B] 104s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x c-n-f Metadata [240 B] 105s Fetched 1073 kB in 2s (598 kB/s) 105s Reading package lists... 106s Reading package lists... 106s Building dependency tree... 106s Reading state information... 106s Calculating upgrade... 106s Calculating upgrade... 106s The following packages were automatically installed and are no longer required: 106s libnsl2 libpython3.12-minimal libpython3.12-stdlib libpython3.12t64 106s linux-headers-6.11.0-8 linux-headers-6.11.0-8-generic 106s linux-modules-6.11.0-8-generic linux-tools-6.11.0-8 106s linux-tools-6.11.0-8-generic 106s Use 'sudo apt autoremove' to remove them. 106s The following packages will be upgraded: 106s pinentry-curses python3-jinja2 strace 107s 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 107s Need to get 652 kB of archives. 107s After this operation, 27.6 kB of additional disk space will be used. 107s Get:1 http://ftpmaster.internal/ubuntu plucky/main s390x strace s390x 6.13+ds-1ubuntu1 [500 kB] 107s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x pinentry-curses s390x 1.3.1-2ubuntu3 [42.9 kB] 107s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 108s Fetched 652 kB in 1s (629 kB/s) 108s (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.) 108s Preparing to unpack .../strace_6.13+ds-1ubuntu1_s390x.deb ... 108s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 108s Preparing to unpack .../pinentry-curses_1.3.1-2ubuntu3_s390x.deb ... 108s Unpacking pinentry-curses (1.3.1-2ubuntu3) over (1.3.1-2ubuntu2) ... 108s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 108s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 108s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 108s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 108s Setting up strace (6.13+ds-1ubuntu1) ... 108s Processing triggers for man-db (2.13.0-1) ... 109s Reading package lists... 109s Building dependency tree... 109s Reading state information... 109s Solving dependencies... 109s The following packages will be REMOVED: 109s libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64* 109s linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 109s linux-modules-6.11.0-8-generic* linux-tools-6.11.0-8* 109s linux-tools-6.11.0-8-generic* 109s 0 upgraded, 0 newly installed, 9 to remove and 5 not upgraded. 109s After this operation, 167 MB disk space will be freed. 109s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 81428 files and directories currently installed.) 109s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 109s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 109s Removing libpython3.12t64:s390x (3.12.9-1) ... 109s Removing libpython3.12-stdlib:s390x (3.12.9-1) ... 109s Removing libnsl2:s390x (1.3.0-3build3) ... 109s Removing libpython3.12-minimal:s390x (3.12.9-1) ... 109s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 109s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 110s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 110s Processing triggers for libc-bin (2.41-1ubuntu1) ... 110s (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.) 110s Purging configuration files for libpython3.12-minimal:s390x (3.12.9-1) ... 110s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 110s autopkgtest [16:27:42]: upgrading testbed (apt dist-upgrade and autopurge) 111s Reading package lists... 111s Building dependency tree... 111s Reading state information... 111s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 111s Starting 2 pkgProblemResolver with broken count: 0 111s Done 111s Entering ResolveByKeep 111s 111s Calculating upgrade... 111s The following packages will be upgraded: 111s libc-bin libc-dev-bin libc6 libc6-dev locales 112s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 112s Need to get 9512 kB of archives. 112s After this operation, 8192 B of additional disk space will be used. 112s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc6-dev s390x 2.41-1ubuntu2 [1678 kB] 114s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc-dev-bin s390x 2.41-1ubuntu2 [24.3 kB] 114s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc6 s390x 2.41-1ubuntu2 [2892 kB] 117s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc-bin s390x 2.41-1ubuntu2 [671 kB] 118s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x locales all 2.41-1ubuntu2 [4246 kB] 123s Preconfiguring packages ... 123s Fetched 9512 kB in 12s (826 kB/s) 123s (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.) 123s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_s390x.deb ... 123s Unpacking libc6-dev:s390x (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 123s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_s390x.deb ... 123s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 123s Preparing to unpack .../libc6_2.41-1ubuntu2_s390x.deb ... 123s Unpacking libc6:s390x (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 123s Setting up libc6:s390x (2.41-1ubuntu2) ... 124s (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.) 124s Preparing to unpack .../libc-bin_2.41-1ubuntu2_s390x.deb ... 124s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 124s Setting up libc-bin (2.41-1ubuntu2) ... 124s (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.) 124s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 124s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 124s Setting up locales (2.41-1ubuntu2) ... 124s Generating locales (this might take a while)... 125s en_US.UTF-8... done 125s Generation complete. 125s Setting up libc-dev-bin (2.41-1ubuntu2) ... 125s Setting up libc6-dev:s390x (2.41-1ubuntu2) ... 125s Processing triggers for man-db (2.13.0-1) ... 126s Processing triggers for systemd (257.3-1ubuntu3) ... 126s Reading package lists... 126s Building dependency tree... 126s Reading state information... 127s Starting pkgProblemResolver with broken count: 0 127s Starting 2 pkgProblemResolver with broken count: 0 127s Done 127s Solving dependencies... 127s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 127s autopkgtest [16:27:59]: rebooting testbed after setup commands that affected boot 145s autopkgtest [16:28:17]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP Wed Mar 12 14:53:49 UTC 2025 148s autopkgtest [16:28:20]: @@@@@@@@@@@@@@@@@@@@ apt-source r-cran-irlba 150s Get:1 http://ftpmaster.internal/ubuntu plucky/universe r-cran-irlba 2.3.5.1-4 (dsc) [2071 B] 150s Get:2 http://ftpmaster.internal/ubuntu plucky/universe r-cran-irlba 2.3.5.1-4 (tar) [234 kB] 150s Get:3 http://ftpmaster.internal/ubuntu plucky/universe r-cran-irlba 2.3.5.1-4 (diff) [3672 B] 150s gpgv: Signature made Tue May 7 00:07:23 2024 UTC 150s gpgv: using RSA key 73471499CC60ED9EEE805946C5BD6C8F2295D502 150s gpgv: issuer "plessy@debian.org" 150s gpgv: Can't check signature: No public key 150s dpkg-source: warning: cannot verify inline signature for ./r-cran-irlba_2.3.5.1-4.dsc: no acceptable signature found 150s autopkgtest [16:28:22]: testing package r-cran-irlba version 2.3.5.1-4 150s autopkgtest [16:28:22]: build not needed 153s autopkgtest [16:28:25]: test run-unit-test: preparing testbed 153s Reading package lists... 153s Building dependency tree... 153s Reading state information... 153s Starting pkgProblemResolver with broken count: 0 153s Starting 2 pkgProblemResolver with broken count: 0 153s Done 154s The following NEW packages will be installed: 154s fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono libblas3 154s libcairo2 libdatrie1 libdeflate0 libfontconfig1 libfreetype6 libgfortran5 154s libgomp1 libgraphite2-3 libharfbuzz0b libice6 libjbig0 libjpeg-turbo8 154s libjpeg8 liblapack3 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 154s libpaper-utils libpaper2 libpixman-1-0 libsharpyuv0 libsm6 libtcl8.6 154s libthai-data libthai0 libtiff6 libtk8.6 libwebp7 libxcb-render0 libxcb-shm0 154s libxft2 libxrender1 libxss1 libxt6t64 r-base-core r-cran-irlba 154s r-cran-lattice r-cran-matrix unzip x11-common xdg-utils zip 154s 0 upgraded, 47 newly installed, 0 to remove and 0 not upgraded. 154s Need to get 46.2 MB of archives. 154s After this operation, 91.5 MB of additional disk space will be used. 154s Get:1 http://ftpmaster.internal/ubuntu plucky/main s390x libfreetype6 s390x 2.13.3+dfsg-1 [431 kB] 154s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x fonts-dejavu-mono all 2.37-8 [502 kB] 155s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x fonts-dejavu-core all 2.37-8 [835 kB] 156s Get:4 http://ftpmaster.internal/ubuntu plucky/main s390x fontconfig-config s390x 2.15.0-2ubuntu1 [37.5 kB] 156s Get:5 http://ftpmaster.internal/ubuntu plucky/main s390x libfontconfig1 s390x 2.15.0-2ubuntu1 [150 kB] 156s Get:6 http://ftpmaster.internal/ubuntu plucky/main s390x fontconfig s390x 2.15.0-2ubuntu1 [191 kB] 156s Get:7 http://ftpmaster.internal/ubuntu plucky/main s390x libblas3 s390x 3.12.1-2 [252 kB] 156s Get:8 http://ftpmaster.internal/ubuntu plucky/main s390x libpixman-1-0 s390x 0.44.0-3 [201 kB] 157s Get:9 http://ftpmaster.internal/ubuntu plucky/main s390x libxcb-render0 s390x 1.17.0-2 [17.0 kB] 157s Get:10 http://ftpmaster.internal/ubuntu plucky/main s390x libxcb-shm0 s390x 1.17.0-2 [5862 B] 157s Get:11 http://ftpmaster.internal/ubuntu plucky/main s390x libxrender1 s390x 1:0.9.10-1.1build1 [20.4 kB] 157s Get:12 http://ftpmaster.internal/ubuntu plucky/main s390x libcairo2 s390x 1.18.2-2 [580 kB] 157s Get:13 http://ftpmaster.internal/ubuntu plucky/main s390x libdatrie1 s390x 0.2.13-3build1 [20.6 kB] 157s Get:14 http://ftpmaster.internal/ubuntu plucky/main s390x libdeflate0 s390x 1.23-1 [46.1 kB] 157s Get:15 http://ftpmaster.internal/ubuntu plucky/main s390x libgfortran5 s390x 15-20250222-0ubuntu1 [620 kB] 158s Get:16 http://ftpmaster.internal/ubuntu plucky/main s390x libgomp1 s390x 15-20250222-0ubuntu1 [152 kB] 158s Get:17 http://ftpmaster.internal/ubuntu plucky/main s390x libgraphite2-3 s390x 1.3.14-2ubuntu1 [79.8 kB] 158s Get:18 http://ftpmaster.internal/ubuntu plucky/main s390x libharfbuzz0b s390x 10.2.0-1 [538 kB] 159s Get:19 http://ftpmaster.internal/ubuntu plucky/main s390x x11-common all 1:7.7+23ubuntu3 [21.7 kB] 159s Get:20 http://ftpmaster.internal/ubuntu plucky/main s390x libice6 s390x 2:1.1.1-1 [45.4 kB] 159s Get:21 http://ftpmaster.internal/ubuntu plucky/main s390x libjpeg-turbo8 s390x 2.1.5-3ubuntu2 [147 kB] 159s Get:22 http://ftpmaster.internal/ubuntu plucky/main s390x libjpeg8 s390x 8c-2ubuntu11 [2146 B] 159s Get:23 http://ftpmaster.internal/ubuntu plucky/main s390x liblapack3 s390x 3.12.1-2 [2971 kB] 163s Get:24 http://ftpmaster.internal/ubuntu plucky/main s390x libthai-data all 0.1.29-2build1 [158 kB] 163s Get:25 http://ftpmaster.internal/ubuntu plucky/main s390x libthai0 s390x 0.1.29-2build1 [20.7 kB] 163s Get:26 http://ftpmaster.internal/ubuntu plucky/main s390x libpango-1.0-0 s390x 1.56.2-1 [253 kB] 163s Get:27 http://ftpmaster.internal/ubuntu plucky/main s390x libpangoft2-1.0-0 s390x 1.56.2-1 [50.2 kB] 163s Get:28 http://ftpmaster.internal/ubuntu plucky/main s390x libpangocairo-1.0-0 s390x 1.56.2-1 [28.2 kB] 163s Get:29 http://ftpmaster.internal/ubuntu plucky/main s390x libpaper2 s390x 2.2.5-0.3 [17.2 kB] 163s Get:30 http://ftpmaster.internal/ubuntu plucky/main s390x libpaper-utils s390x 2.2.5-0.3 [15.3 kB] 163s Get:31 http://ftpmaster.internal/ubuntu plucky/main s390x libsharpyuv0 s390x 1.5.0-0.1 [16.7 kB] 163s Get:32 http://ftpmaster.internal/ubuntu plucky/main s390x libsm6 s390x 2:1.2.4-1 [18.4 kB] 163s Get:33 http://ftpmaster.internal/ubuntu plucky/main s390x libtcl8.6 s390x 8.6.16+dfsg-1 [1034 kB] 164s Get:34 http://ftpmaster.internal/ubuntu plucky/main s390x libjbig0 s390x 2.1-6.1ubuntu2 [33.1 kB] 165s Get:35 http://ftpmaster.internal/ubuntu plucky/main s390x libwebp7 s390x 1.5.0-0.1 [210 kB] 165s Get:36 http://ftpmaster.internal/ubuntu plucky/main s390x libtiff6 s390x 4.5.1+git230720-4ubuntu4 [217 kB] 165s Get:37 http://ftpmaster.internal/ubuntu plucky/main s390x libxft2 s390x 2.3.6-1build1 [49.6 kB] 165s Get:38 http://ftpmaster.internal/ubuntu plucky/main s390x libxss1 s390x 1:1.2.3-1build3 [7396 B] 165s Get:39 http://ftpmaster.internal/ubuntu plucky/main s390x libtk8.6 s390x 8.6.16-1 [830 kB] 166s Get:40 http://ftpmaster.internal/ubuntu plucky/main s390x libxt6t64 s390x 1:1.2.1-1.2build1 [184 kB] 166s Get:41 http://ftpmaster.internal/ubuntu plucky/main s390x zip s390x 3.0-14ubuntu2 [187 kB] 166s Get:42 http://ftpmaster.internal/ubuntu plucky/main s390x unzip s390x 6.0-28ubuntu6 [186 kB] 166s Get:43 http://ftpmaster.internal/ubuntu plucky/main s390x xdg-utils all 1.2.1-2ubuntu1 [66.0 kB] 167s Get:44 http://ftpmaster.internal/ubuntu plucky/universe s390x r-base-core s390x 4.4.3-1 [28.6 MB] 198s Get:45 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-lattice s390x 0.22-6-1 [1340 kB] 199s Get:46 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-matrix s390x 1.7-3-1 [4449 kB] 204s Get:47 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-irlba s390x 2.3.5.1-4 [296 kB] 205s Preconfiguring packages ... 205s Fetched 46.2 MB in 51s (903 kB/s) 205s Selecting previously unselected package libfreetype6:s390x. 205s (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.) 205s Preparing to unpack .../00-libfreetype6_2.13.3+dfsg-1_s390x.deb ... 205s Unpacking libfreetype6:s390x (2.13.3+dfsg-1) ... 205s Selecting previously unselected package fonts-dejavu-mono. 205s Preparing to unpack .../01-fonts-dejavu-mono_2.37-8_all.deb ... 205s Unpacking fonts-dejavu-mono (2.37-8) ... 205s Selecting previously unselected package fonts-dejavu-core. 205s Preparing to unpack .../02-fonts-dejavu-core_2.37-8_all.deb ... 205s Unpacking fonts-dejavu-core (2.37-8) ... 205s Selecting previously unselected package fontconfig-config. 205s Preparing to unpack .../03-fontconfig-config_2.15.0-2ubuntu1_s390x.deb ... 205s Unpacking fontconfig-config (2.15.0-2ubuntu1) ... 205s Selecting previously unselected package libfontconfig1:s390x. 205s Preparing to unpack .../04-libfontconfig1_2.15.0-2ubuntu1_s390x.deb ... 205s Unpacking libfontconfig1:s390x (2.15.0-2ubuntu1) ... 205s Selecting previously unselected package fontconfig. 205s Preparing to unpack .../05-fontconfig_2.15.0-2ubuntu1_s390x.deb ... 205s Unpacking fontconfig (2.15.0-2ubuntu1) ... 205s Selecting previously unselected package libblas3:s390x. 205s Preparing to unpack .../06-libblas3_3.12.1-2_s390x.deb ... 205s Unpacking libblas3:s390x (3.12.1-2) ... 205s Selecting previously unselected package libpixman-1-0:s390x. 205s Preparing to unpack .../07-libpixman-1-0_0.44.0-3_s390x.deb ... 205s Unpacking libpixman-1-0:s390x (0.44.0-3) ... 205s Selecting previously unselected package libxcb-render0:s390x. 205s Preparing to unpack .../08-libxcb-render0_1.17.0-2_s390x.deb ... 205s Unpacking libxcb-render0:s390x (1.17.0-2) ... 205s Selecting previously unselected package libxcb-shm0:s390x. 205s Preparing to unpack .../09-libxcb-shm0_1.17.0-2_s390x.deb ... 205s Unpacking libxcb-shm0:s390x (1.17.0-2) ... 205s Selecting previously unselected package libxrender1:s390x. 205s Preparing to unpack .../10-libxrender1_1%3a0.9.10-1.1build1_s390x.deb ... 205s Unpacking libxrender1:s390x (1:0.9.10-1.1build1) ... 205s Selecting previously unselected package libcairo2:s390x. 205s Preparing to unpack .../11-libcairo2_1.18.2-2_s390x.deb ... 205s Unpacking libcairo2:s390x (1.18.2-2) ... 205s Selecting previously unselected package libdatrie1:s390x. 205s Preparing to unpack .../12-libdatrie1_0.2.13-3build1_s390x.deb ... 205s Unpacking libdatrie1:s390x (0.2.13-3build1) ... 205s Selecting previously unselected package libdeflate0:s390x. 205s Preparing to unpack .../13-libdeflate0_1.23-1_s390x.deb ... 205s Unpacking libdeflate0:s390x (1.23-1) ... 205s Selecting previously unselected package libgfortran5:s390x. 205s Preparing to unpack .../14-libgfortran5_15-20250222-0ubuntu1_s390x.deb ... 205s Unpacking libgfortran5:s390x (15-20250222-0ubuntu1) ... 205s Selecting previously unselected package libgomp1:s390x. 205s Preparing to unpack .../15-libgomp1_15-20250222-0ubuntu1_s390x.deb ... 205s Unpacking libgomp1:s390x (15-20250222-0ubuntu1) ... 205s Selecting previously unselected package libgraphite2-3:s390x. 205s Preparing to unpack .../16-libgraphite2-3_1.3.14-2ubuntu1_s390x.deb ... 205s Unpacking libgraphite2-3:s390x (1.3.14-2ubuntu1) ... 205s Selecting previously unselected package libharfbuzz0b:s390x. 205s Preparing to unpack .../17-libharfbuzz0b_10.2.0-1_s390x.deb ... 205s Unpacking libharfbuzz0b:s390x (10.2.0-1) ... 205s Selecting previously unselected package x11-common. 205s Preparing to unpack .../18-x11-common_1%3a7.7+23ubuntu3_all.deb ... 205s Unpacking x11-common (1:7.7+23ubuntu3) ... 205s Selecting previously unselected package libice6:s390x. 205s Preparing to unpack .../19-libice6_2%3a1.1.1-1_s390x.deb ... 205s Unpacking libice6:s390x (2:1.1.1-1) ... 205s Selecting previously unselected package libjpeg-turbo8:s390x. 205s Preparing to unpack .../20-libjpeg-turbo8_2.1.5-3ubuntu2_s390x.deb ... 205s Unpacking libjpeg-turbo8:s390x (2.1.5-3ubuntu2) ... 205s Selecting previously unselected package libjpeg8:s390x. 205s Preparing to unpack .../21-libjpeg8_8c-2ubuntu11_s390x.deb ... 205s Unpacking libjpeg8:s390x (8c-2ubuntu11) ... 205s Selecting previously unselected package liblapack3:s390x. 205s Preparing to unpack .../22-liblapack3_3.12.1-2_s390x.deb ... 205s Unpacking liblapack3:s390x (3.12.1-2) ... 205s Selecting previously unselected package libthai-data. 205s Preparing to unpack .../23-libthai-data_0.1.29-2build1_all.deb ... 205s Unpacking libthai-data (0.1.29-2build1) ... 205s Selecting previously unselected package libthai0:s390x. 205s Preparing to unpack .../24-libthai0_0.1.29-2build1_s390x.deb ... 205s Unpacking libthai0:s390x (0.1.29-2build1) ... 205s Selecting previously unselected package libpango-1.0-0:s390x. 205s Preparing to unpack .../25-libpango-1.0-0_1.56.2-1_s390x.deb ... 205s Unpacking libpango-1.0-0:s390x (1.56.2-1) ... 205s Selecting previously unselected package libpangoft2-1.0-0:s390x. 205s Preparing to unpack .../26-libpangoft2-1.0-0_1.56.2-1_s390x.deb ... 205s Unpacking libpangoft2-1.0-0:s390x (1.56.2-1) ... 205s Selecting previously unselected package libpangocairo-1.0-0:s390x. 205s Preparing to unpack .../27-libpangocairo-1.0-0_1.56.2-1_s390x.deb ... 205s Unpacking libpangocairo-1.0-0:s390x (1.56.2-1) ... 205s Selecting previously unselected package libpaper2:s390x. 205s Preparing to unpack .../28-libpaper2_2.2.5-0.3_s390x.deb ... 205s Unpacking libpaper2:s390x (2.2.5-0.3) ... 205s Selecting previously unselected package libpaper-utils. 205s Preparing to unpack .../29-libpaper-utils_2.2.5-0.3_s390x.deb ... 205s Unpacking libpaper-utils (2.2.5-0.3) ... 205s Selecting previously unselected package libsharpyuv0:s390x. 205s Preparing to unpack .../30-libsharpyuv0_1.5.0-0.1_s390x.deb ... 205s Unpacking libsharpyuv0:s390x (1.5.0-0.1) ... 206s Selecting previously unselected package libsm6:s390x. 206s Preparing to unpack .../31-libsm6_2%3a1.2.4-1_s390x.deb ... 206s Unpacking libsm6:s390x (2:1.2.4-1) ... 206s Selecting previously unselected package libtcl8.6:s390x. 206s Preparing to unpack .../32-libtcl8.6_8.6.16+dfsg-1_s390x.deb ... 206s Unpacking libtcl8.6:s390x (8.6.16+dfsg-1) ... 206s Selecting previously unselected package libjbig0:s390x. 206s Preparing to unpack .../33-libjbig0_2.1-6.1ubuntu2_s390x.deb ... 206s Unpacking libjbig0:s390x (2.1-6.1ubuntu2) ... 206s Selecting previously unselected package libwebp7:s390x. 206s Preparing to unpack .../34-libwebp7_1.5.0-0.1_s390x.deb ... 206s Unpacking libwebp7:s390x (1.5.0-0.1) ... 206s Selecting previously unselected package libtiff6:s390x. 206s Preparing to unpack .../35-libtiff6_4.5.1+git230720-4ubuntu4_s390x.deb ... 206s Unpacking libtiff6:s390x (4.5.1+git230720-4ubuntu4) ... 206s Selecting previously unselected package libxft2:s390x. 206s Preparing to unpack .../36-libxft2_2.3.6-1build1_s390x.deb ... 206s Unpacking libxft2:s390x (2.3.6-1build1) ... 206s Selecting previously unselected package libxss1:s390x. 206s Preparing to unpack .../37-libxss1_1%3a1.2.3-1build3_s390x.deb ... 206s Unpacking libxss1:s390x (1:1.2.3-1build3) ... 206s Selecting previously unselected package libtk8.6:s390x. 206s Preparing to unpack .../38-libtk8.6_8.6.16-1_s390x.deb ... 206s Unpacking libtk8.6:s390x (8.6.16-1) ... 206s Selecting previously unselected package libxt6t64:s390x. 206s Preparing to unpack .../39-libxt6t64_1%3a1.2.1-1.2build1_s390x.deb ... 206s Unpacking libxt6t64:s390x (1:1.2.1-1.2build1) ... 206s Selecting previously unselected package zip. 206s Preparing to unpack .../40-zip_3.0-14ubuntu2_s390x.deb ... 206s Unpacking zip (3.0-14ubuntu2) ... 206s Selecting previously unselected package unzip. 206s Preparing to unpack .../41-unzip_6.0-28ubuntu6_s390x.deb ... 206s Unpacking unzip (6.0-28ubuntu6) ... 206s Selecting previously unselected package xdg-utils. 206s Preparing to unpack .../42-xdg-utils_1.2.1-2ubuntu1_all.deb ... 206s Unpacking xdg-utils (1.2.1-2ubuntu1) ... 206s Selecting previously unselected package r-base-core. 206s Preparing to unpack .../43-r-base-core_4.4.3-1_s390x.deb ... 206s Unpacking r-base-core (4.4.3-1) ... 206s Selecting previously unselected package r-cran-lattice. 206s Preparing to unpack .../44-r-cran-lattice_0.22-6-1_s390x.deb ... 206s Unpacking r-cran-lattice (0.22-6-1) ... 206s Selecting previously unselected package r-cran-matrix. 206s Preparing to unpack .../45-r-cran-matrix_1.7-3-1_s390x.deb ... 206s Unpacking r-cran-matrix (1.7-3-1) ... 206s Selecting previously unselected package r-cran-irlba. 206s Preparing to unpack .../46-r-cran-irlba_2.3.5.1-4_s390x.deb ... 206s Unpacking r-cran-irlba (2.3.5.1-4) ... 206s Setting up libgraphite2-3:s390x (1.3.14-2ubuntu1) ... 206s Setting up libpixman-1-0:s390x (0.44.0-3) ... 206s Setting up libsharpyuv0:s390x (1.5.0-0.1) ... 206s Setting up libxrender1:s390x (1:0.9.10-1.1build1) ... 206s Setting up libdatrie1:s390x (0.2.13-3build1) ... 206s Setting up libxcb-render0:s390x (1.17.0-2) ... 206s Setting up unzip (6.0-28ubuntu6) ... 206s Setting up x11-common (1:7.7+23ubuntu3) ... 206s Setting up libdeflate0:s390x (1.23-1) ... 206s Setting up libxcb-shm0:s390x (1.17.0-2) ... 206s Setting up libgomp1:s390x (15-20250222-0ubuntu1) ... 206s Setting up libjbig0:s390x (2.1-6.1ubuntu2) ... 206s Setting up zip (3.0-14ubuntu2) ... 206s Setting up libblas3:s390x (3.12.1-2) ... 206s 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 206s Setting up libfreetype6:s390x (2.13.3+dfsg-1) ... 206s Setting up fonts-dejavu-mono (2.37-8) ... 206s Setting up libtcl8.6:s390x (8.6.16+dfsg-1) ... 206s Setting up fonts-dejavu-core (2.37-8) ... 206s Setting up libjpeg-turbo8:s390x (2.1.5-3ubuntu2) ... 206s Setting up libgfortran5:s390x (15-20250222-0ubuntu1) ... 206s Setting up libwebp7:s390x (1.5.0-0.1) ... 206s Setting up libharfbuzz0b:s390x (10.2.0-1) ... 206s Setting up libthai-data (0.1.29-2build1) ... 206s Setting up libxss1:s390x (1:1.2.3-1build3) ... 206s Setting up libpaper2:s390x (2.2.5-0.3) ... 206s Setting up xdg-utils (1.2.1-2ubuntu1) ... 206s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode 206s Setting up libjpeg8:s390x (8c-2ubuntu11) ... 206s Setting up libice6:s390x (2:1.1.1-1) ... 206s Setting up liblapack3:s390x (3.12.1-2) ... 206s 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 206s Setting up fontconfig-config (2.15.0-2ubuntu1) ... 206s Setting up libpaper-utils (2.2.5-0.3) ... 206s Setting up libthai0:s390x (0.1.29-2build1) ... 206s Setting up libtiff6:s390x (4.5.1+git230720-4ubuntu4) ... 206s Setting up libfontconfig1:s390x (2.15.0-2ubuntu1) ... 206s Setting up libsm6:s390x (2:1.2.4-1) ... 206s Setting up fontconfig (2.15.0-2ubuntu1) ... 208s Regenerating fonts cache... done. 208s Setting up libxft2:s390x (2.3.6-1build1) ... 208s Setting up libtk8.6:s390x (8.6.16-1) ... 208s Setting up libpango-1.0-0:s390x (1.56.2-1) ... 208s Setting up libcairo2:s390x (1.18.2-2) ... 208s Setting up libxt6t64:s390x (1:1.2.1-1.2build1) ... 208s Setting up libpangoft2-1.0-0:s390x (1.56.2-1) ... 208s Setting up libpangocairo-1.0-0:s390x (1.56.2-1) ... 208s Setting up r-base-core (4.4.3-1) ... 208s Creating config file /etc/R/Renviron with new version 209s Setting up r-cran-lattice (0.22-6-1) ... 209s Setting up r-cran-matrix (1.7-3-1) ... 209s Setting up r-cran-irlba (2.3.5.1-4) ... 209s Processing triggers for libc-bin (2.41-1ubuntu2) ... 209s Processing triggers for man-db (2.13.0-1) ... 209s Processing triggers for install-info (7.1.1-1) ... 210s autopkgtest [16:29:22]: test run-unit-test: [----------------------- 211s 211s R version 4.4.3 (2025-02-28) -- "Trophy Case" 211s Copyright (C) 2025 The R Foundation for Statistical Computing 211s Platform: s390x-ibm-linux-gnu 211s 211s R is free software and comes with ABSOLUTELY NO WARRANTY. 211s You are welcome to redistribute it under certain conditions. 211s Type 'license()' or 'licence()' for distribution details. 211s 211s R is a collaborative project with many contributors. 211s Type 'contributors()' for more information and 211s 'citation()' on how to cite R or R packages in publications. 211s 211s Type 'demo()' for some demos, 'help()' for on-line help, or 211s 'help.start()' for an HTML browser interface to help. 211s Type 'q()' to quit R. 211s 211s > Stangle("irlba.Rnw") 211s Writing to file irlba.R 211s > source("irlba.R", echo=TRUE) 211s > 211s irlba.Rnw passed 211s 211s R version 4.4.3 (2025-02-28) -- "Trophy Case" 211s Copyright (C) 2025 The R Foundation for Statistical Computing 211s Platform: s390x-ibm-linux-gnu 211s 211s R is free software and comes with ABSOLUTELY NO WARRANTY. 211s You are welcome to redistribute it under certain conditions. 211s Type 'license()' or 'licence()' for distribution details. 211s 211s R is a collaborative project with many contributors. 211s Type 'contributors()' for more information and 211s 'citation()' on how to cite R or R packages in publications. 211s 211s Type 'demo()' for some demos, 'help()' for on-line help, or 211s 'help.start()' for an HTML browser interface to help. 211s Type 'q()' to quit R. 211s 211s Loading required package: irlba 211s > require("irlba") 211s Loading required package: Matrix 211s > 211s > for (FAST in c(FALSE, TRUE)) 211s + { 211s + # Dense matrix 211s + set.seed(1) 212s + A <- matrix(rnorm(400), 20) 212s + L <- irlba(A, nu=2, nv=2, tol=1e-9, fastpath=FAST) 212s + S <- svd(A, nu=2, nv=2) 212s + if (!isTRUE(all.equal(L$d, S$d[1:2]))) 212s + { 212s + stop("Failed simple dense singular value test", " fastpath=", FAST) 212s + } 212s + 212s + # restart 212s + L1 <- irlba(A, nv=3, v=L, fastpath=FAST) 212s + if (!isTRUE(all.equal(L1$d, S$d[1:3]))) 212s + { 212s + stop("Failed restart", " fastpath=", FAST) 212s + } 212s + 212s + # unequal nu, nv 212s + L <- irlba(A, nv=2, nu=3, fastpath=FAST) 212s + if (!isTRUE(ncol(L$v) == 2 && ncol(L$u) == 3)) 212s + { 212s + stop("Failed unequal nu,nv", " fastpath=", FAST) 212s + } 212s + 212s + # Scaling and centering, dense 212s + s <- sqrt(apply(A, 2, crossprod)) 212s + m <- colMeans(A) 212s + L <- irlba(A, 3, tol=1e-9, center=m, scale=s, fastpath=FAST) 212s + S <- svd(scale(A, center=TRUE, scale=s)) 212s + if (!isTRUE(all.equal(L$d, S$d[1:3]))) 212s + { 212s + stop("Failed scaling/centering test", " fastpath=", FAST) 212s + } 212s + # Scale only, non-square, dense 212s + A <- matrix(rnorm(200), 10) 212s + s <- seq(1, ncol(A)) 212s + m <- colMeans(A) 212s + L <- irlba(A, 3, tol=1e-9, scale=s, fastpath=FAST) 212s + S <- svd(scale(A, center=FALSE, scale=s)) 212s + if (!isTRUE(all.equal(L$d, S$d[1:3]))) 212s + { 212s + stop("Failed dense scaling test", " fastpath=", FAST) 212s + } 212s + # Center only, non-square, dense 212s + L <- irlba(A, 3, tol=1e-9, center=m, fastpath=FAST) 212s + S <- svd(scale(A, center=TRUE, scale=FALSE)) 212s + if (!isTRUE(all.equal(L$d, S$d[1:3]))) 212s + { 212s + stop("Failed dense centering test", " fastpath=", FAST) 212s + } 212s + # Sparse matrix 212s + require("Matrix") 212s + K <- 400 212s + N <- 2000 212s + i <- sample(K, size=N, replace=TRUE) 212s + j <- sample(K, size=N, replace=TRUE) 212s + A <- sparseMatrix(i, j, x=rnorm(N)) 212s + L <- irlba(A, nu=2, nv=2, tol=1e-9, fastpath=FAST) 212s + S <- svd(A, nu=2, nv=2) 212s + if (!isTRUE(all.equal(L$d, S$d[1:2]))) 212s + { 212s + stop("Failed simple sparse singular value test", " fastpath=", FAST) 212s + } 212s + # Center only, sparse 212s + m <- colMeans(A) 212s + L <- irlba(A, 3, tol=1e-9, center=m, fastpath=FAST) 212s + S <- svd(scale(A, center=TRUE, scale=FALSE)) 212s + if (!isTRUE(all.equal(L$d, S$d[1:3]))) 212s + { 212s + stop("Failed sparse centering test", " fastpath=", FAST) 212s + } 212s + # scale only, spase 212s + s <- seq(1, ncol(A)) 212s + L <- irlba(A, 3, tol=1e-9, scale=s, fastpath=FAST) 212s + S <- svd(scale(A, center=FALSE, scale=s)) 212s + if (!isTRUE(all.equal(L$d, S$d[1:3]))) 212s + { 212s + stop("Failed sparse scaling test", " fastpath=", FAST) 212s + } 212s + 212s + # Symmetric partial eigendecomposition 212s + set.seed(1) 212s + V <- qr.Q(qr(matrix(runif(100), nrow=10))) 212s + x <- V %*% diag(c(10, -9, 8, -7, 6, -5, 4, -3, 2, -1)) %*% t(V) 212s + if (!isTRUE(all.equal(partial_eigen(x, 3, fastpath=FAST)$values, c(10, 8, 6)))) 212s + { 212s + stop("Failed partial_eigen test", " fastpath=", FAST) 212s + } 212s + 212s + # Test right-only option 212s + L <- irlba(A, 2, tol=1e-3, right_only=TRUE, fastpath=FAST, work=20) 212s + S <- svd(A, nu=2, nv=2) 212s + if (isTRUE(max(L$d - S$d[1:2]) > 1e-3)) 212s + { 212s + stop("Failed right_only test", " fastpath=", FAST) 212s + } 212s + 212s + # Dense complex-valued matrix 212s + A <- matrix(rnorm(400), 20) + 1i * matrix(rnorm(400), 20) 212s + L <- irlba(A, nu=2, nv=2, tol=1e-9, fastpath=FAST) 212s + S <- svd(A, nu=2, nv=2) 212s + if (!isTRUE(all.equal(L$d, S$d[1:2]))) 212s + { 212s + stop("Failed complex-valued dense singular value test", " fastpath=", FAST) 212s + } 212s + 212s + # test extra reorthogonalization 212s + L <- irlba(A, nu=2, nv=2, tol=1e-9, reorth=TRUE, fastpath=FAST) 212s + if (!isTRUE(all.equal(L$d, S$d[1:2]))) 212s + { 212s + stop("Failed reorthogonalization test", " fastpath=", FAST) 212s + } 212s + 212s + # very non-square dense matrices 212s + set.seed(1) 212s + A <- matrix(rnorm(2000), 20) 212s + L1 <- irlba(A, nu=2, nv=2, tol=1e-9, fastpath=FAST) 212s + L2 <- irlba(t(A), nu=2, nv=2, tol=1e-9, fastpath=FAST) 212s + if (!isTRUE(all.equal(L1$d, L2$d))) 212s + { 212s + stop("Failed nonsquare test", " fastpath=", FAST) 212s + } 212s + 212s + # This pathological example was provided by Giuseppe Rodriguez, http://bugs.unica.it/~gppe/ 212s + # The singular values cluster at 1 and 0, making it hard to converge to a truncated 212s + # subspace containing the largest few singular values (they are all very close). 212s + # Or, for that matter, the smallest. 212s + # 212s + # Reference: 212s + # J. M. Varah. The Prolate matrix. Linear Algebra and Appl., 212s + # 187:269-278, 1993. 212s + # Michela Redivo-Zaglia, University of Padova, Italy 212s + # Email: Michela.RedivoZaglia@unipd.it 212s + # Giuseppe Rodriguez, University of Cagliari, Italy 212s + # Email: rodriguez@unica.it 212s + tprolate <- function(n, w=0.25) 212s + { 212s + a <- rep(0, n) 212s + a[1] <- 2 * w 212s + a[2:n] <- sin(2 * pi * w * (1:(n-1))) / (pi * (1:(n-1))) 212s + toeplitz(a) 212s + } 212s + 212s + x <- tprolate(512) 212s + set.seed(1) 212s + l <- irlba(x, nv=20, fastpath=FAST) 212s + if (isTRUE(max(abs(l$d - 1)) > 1e-2)) 212s + { 212s + stop("Failed tprolate test fastpath=", FAST) 212s + } 212s + 212s + # test for issue #7 and issue #14 212s + mx <- matrix(sample(1:100, 100 * 100, replace=TRUE), nrow=100) 212s + set.seed(1) 212s + l <- irlba(mx, nv=30, center=colMeans(mx), fastpath=FAST) 212s + s <- svd(scale(mx, center=TRUE, scale=FALSE)) 212s + if (isTRUE(max(abs(l$d - s$d[1:30])) > 1e-3)) 212s + { 212s + stop("Failed integer matrix test fastpath=", FAST) 212s + } 212s + 212s + # test for https://github.com/bwlewis/irlba/issues/22 212s + set.seed(1000) 212s + ncells <- 50 212s + ngenes <- 1000 212s + counts <- matrix(as.double(rpois(ncells*ngenes, lambda=100)), nrow=ncells) 212s + centers <- colMeans(counts) 212s + set.seed(1) 212s + out <- irlba(scale(counts, scale=FALSE, center=centers), nu=10, nv=10) 212s + set.seed(1) 212s + l <- irlba(counts, center=centers, nu=10, nv=10, fastpath=FAST) 212s + if (isTRUE(max(abs(out$d - l$d)) > 1e-3)) 212s + { 212s + stop("Failed centering test (n > m) fastpath=", FAST) 212s + } 212s + 212s + # test for https://github.com/bwlewis/irlba/issues/42 212s + set.seed(1234) 212s + a <- matrix(rnorm(10000), ncol=20) 212s + center <- runif(ncol(a)) 212s + scale <- runif(ncol(a)) 212s + L <- irlba(a, 5, scale=scale, center=center, fastpath=FAST) 212s + S <- svd(scale(a, center=center, scale=scale)) 212s + if (isTRUE(max(abs(S$d[1:5] - L$d)) > 1e-3)) 212s + { 212s + stop("Failed scale + center test fastpath=", FAST) 212s + } 212s + } 214s > 214s > # smallest=TRUE, m > n (fastpath always FALSE in this case) 214s > x <- matrix(rnorm(5000), 100) 214s > set.seed(1) 214s > L <- irlba(x, nv=5, smallest=TRUE) 214s > if (!isTRUE(all.equal(L$d, tail(svd(x)$d, 5)))) 214s + { 214s + stop("Failed smallest svd test") 214s + } 214s > 214s > # smallest=TRUE, n > m 214s > x <- matrix(rnorm(5000), 50) 214s > set.seed(1) 214s > L <- irlba(x, nv=5, smallest=TRUE) 214s > if (!isTRUE(all.equal(L$d, tail(svd(x)$d, 5)))) 214s + { 214s + stop("Failed smallest svd test") 214s + } 214s > 214s > # test for https://github.com/bwlewis/irlba/issues/47 (again, fastpath always FALSE) 214s > set.seed(2345) 214s > a <- spMatrix(50, 40, x=runif(200), i=sample(50, 200, replace=TRUE), j=sample(40, 200, replace=TRUE)) 214s > center <- runif(ncol(a)) 214s > scale <- runif(ncol(a)) 214s > L <- irlba(a, 5, scale=scale, center=center) 214s > S <- svd(scale(a, center=center, scale=scale)) 214s > if (isTRUE(max(abs(S$d[1:5] - L$d)) > 1e-3)) 214s + { 214s + stop("Failed scale + center test for non-fastpath'able matrices") 214s + } 214s > 214s autopkgtest [16:29:26]: test run-unit-test: -----------------------] 214s run-unit-test PASS 214s autopkgtest [16:29:26]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 215s autopkgtest [16:29:27]: test pkg-r-autopkgtest: preparing testbed 215s Reading package lists... 215s Building dependency tree... 215s Reading state information... 215s Starting pkgProblemResolver with broken count: 0 215s Starting 2 pkgProblemResolver with broken count: 0 215s Done 215s The following NEW packages will be installed: 215s build-essential cpp cpp-14 cpp-14-s390x-linux-gnu cpp-s390x-linux-gnu 215s dctrl-tools g++ g++-14 g++-14-s390x-linux-gnu g++-s390x-linux-gnu gcc gcc-14 215s gcc-14-s390x-linux-gnu gcc-s390x-linux-gnu gfortran gfortran-14 215s gfortran-14-s390x-linux-gnu gfortran-s390x-linux-gnu icu-devtools libasan8 215s libblas-dev libbz2-dev libcc1-0 libdeflate-dev libgcc-14-dev 215s libgfortran-14-dev libicu-dev libisl23 libitm1 libjpeg-dev 215s libjpeg-turbo8-dev libjpeg8-dev liblapack-dev liblzma-dev libmpc3 215s libncurses-dev libpcre2-16-0 libpcre2-32-0 libpcre2-dev libpcre2-posix3 215s libpkgconf3 libpng-dev libreadline-dev libstdc++-14-dev libtirpc-dev 215s libubsan1 pkg-r-autopkgtest pkgconf pkgconf-bin r-base-dev zlib1g-dev 216s 0 upgraded, 51 newly installed, 0 to remove and 0 not upgraded. 216s Need to get 82.3 MB of archives. 216s After this operation, 279 MB of additional disk space will be used. 216s Get:1 http://ftpmaster.internal/ubuntu plucky/main s390x libisl23 s390x 0.27-1 [704 kB] 217s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x libmpc3 s390x 1.3.1-1build2 [57.8 kB] 217s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x cpp-14-s390x-linux-gnu s390x 14.2.0-17ubuntu3 [9572 kB] 228s Get:4 http://ftpmaster.internal/ubuntu plucky/main s390x cpp-14 s390x 14.2.0-17ubuntu3 [1028 B] 228s Get:5 http://ftpmaster.internal/ubuntu plucky/main s390x cpp-s390x-linux-gnu s390x 4:14.2.0-1ubuntu1 [5556 B] 228s Get:6 http://ftpmaster.internal/ubuntu plucky/main s390x cpp s390x 4:14.2.0-1ubuntu1 [22.4 kB] 228s Get:7 http://ftpmaster.internal/ubuntu plucky/main s390x libcc1-0 s390x 15-20250222-0ubuntu1 [49.2 kB] 228s Get:8 http://ftpmaster.internal/ubuntu plucky/main s390x libitm1 s390x 15-20250222-0ubuntu1 [31.2 kB] 228s Get:9 http://ftpmaster.internal/ubuntu plucky/main s390x libasan8 s390x 15-20250222-0ubuntu1 [2970 kB] 232s Get:10 http://ftpmaster.internal/ubuntu plucky/main s390x libubsan1 s390x 15-20250222-0ubuntu1 [1212 kB] 233s Get:11 http://ftpmaster.internal/ubuntu plucky/main s390x libgcc-14-dev s390x 14.2.0-17ubuntu3 [1037 kB] 234s Get:12 http://ftpmaster.internal/ubuntu plucky/main s390x gcc-14-s390x-linux-gnu s390x 14.2.0-17ubuntu3 [18.7 MB] 257s Get:13 http://ftpmaster.internal/ubuntu plucky/main s390x gcc-14 s390x 14.2.0-17ubuntu3 [526 kB] 258s Get:14 http://ftpmaster.internal/ubuntu plucky/main s390x gcc-s390x-linux-gnu s390x 4:14.2.0-1ubuntu1 [1204 B] 258s Get:15 http://ftpmaster.internal/ubuntu plucky/main s390x gcc s390x 4:14.2.0-1ubuntu1 [5004 B] 258s Get:16 http://ftpmaster.internal/ubuntu plucky/main s390x libstdc++-14-dev s390x 14.2.0-17ubuntu3 [2611 kB] 261s Get:17 http://ftpmaster.internal/ubuntu plucky/main s390x g++-14-s390x-linux-gnu s390x 14.2.0-17ubuntu3 [11.0 MB] 273s Get:18 http://ftpmaster.internal/ubuntu plucky/main s390x g++-14 s390x 14.2.0-17ubuntu3 [21.8 kB] 273s Get:19 http://ftpmaster.internal/ubuntu plucky/main s390x g++-s390x-linux-gnu s390x 4:14.2.0-1ubuntu1 [956 B] 273s Get:20 http://ftpmaster.internal/ubuntu plucky/main s390x g++ s390x 4:14.2.0-1ubuntu1 [1080 B] 273s Get:21 http://ftpmaster.internal/ubuntu plucky/main s390x build-essential s390x 12.10ubuntu1 [4930 B] 273s Get:22 http://ftpmaster.internal/ubuntu plucky/main s390x dctrl-tools s390x 2.24-3build3 [106 kB] 273s Get:23 http://ftpmaster.internal/ubuntu plucky/main s390x libgfortran-14-dev s390x 14.2.0-17ubuntu3 [654 kB] 274s Get:24 http://ftpmaster.internal/ubuntu plucky/main s390x gfortran-14-s390x-linux-gnu s390x 14.2.0-17ubuntu3 [10.3 MB] 285s Get:25 http://ftpmaster.internal/ubuntu plucky/main s390x gfortran-14 s390x 14.2.0-17ubuntu3 [13.6 kB] 285s Get:26 http://ftpmaster.internal/ubuntu plucky/main s390x gfortran-s390x-linux-gnu s390x 4:14.2.0-1ubuntu1 [1012 B] 285s Get:27 http://ftpmaster.internal/ubuntu plucky/main s390x gfortran s390x 4:14.2.0-1ubuntu1 [1160 B] 285s Get:28 http://ftpmaster.internal/ubuntu plucky/main s390x icu-devtools s390x 76.1-1ubuntu2 [225 kB] 285s Get:29 http://ftpmaster.internal/ubuntu plucky/main s390x libblas-dev s390x 3.12.1-2 [254 kB] 285s Get:30 http://ftpmaster.internal/ubuntu plucky/main s390x libbz2-dev s390x 1.0.8-6 [39.1 kB] 285s Get:31 http://ftpmaster.internal/ubuntu plucky/main s390x libdeflate-dev s390x 1.23-1 [52.2 kB] 285s Get:32 http://ftpmaster.internal/ubuntu plucky/main s390x libicu-dev s390x 76.1-1ubuntu2 [12.2 MB] 298s Get:33 http://ftpmaster.internal/ubuntu plucky/main s390x libjpeg-turbo8-dev s390x 2.1.5-3ubuntu2 [281 kB] 299s Get:34 http://ftpmaster.internal/ubuntu plucky/main s390x libjpeg8-dev s390x 8c-2ubuntu11 [1484 B] 299s Get:35 http://ftpmaster.internal/ubuntu plucky/main s390x libjpeg-dev s390x 8c-2ubuntu11 [1484 B] 299s Get:36 http://ftpmaster.internal/ubuntu plucky/main s390x liblapack-dev s390x 3.12.1-2 [5967 kB] 305s Get:37 http://ftpmaster.internal/ubuntu plucky/main s390x libncurses-dev s390x 6.5+20250216-2 [407 kB] 305s Get:38 http://ftpmaster.internal/ubuntu plucky/main s390x libpcre2-16-0 s390x 10.45-1 [259 kB] 305s Get:39 http://ftpmaster.internal/ubuntu plucky/main s390x libpcre2-32-0 s390x 10.45-1 [245 kB] 306s Get:40 http://ftpmaster.internal/ubuntu plucky/main s390x libpcre2-posix3 s390x 10.45-1 [7080 B] 306s Get:41 http://ftpmaster.internal/ubuntu plucky/main s390x libpcre2-dev s390x 10.45-1 [899 kB] 307s Get:42 http://ftpmaster.internal/ubuntu plucky/main s390x libpkgconf3 s390x 1.8.1-4 [31.2 kB] 307s Get:43 http://ftpmaster.internal/ubuntu plucky/main s390x zlib1g-dev s390x 1:1.3.dfsg+really1.3.1-1ubuntu1 [898 kB] 308s Get:44 http://ftpmaster.internal/ubuntu plucky/main s390x libpng-dev s390x 1.6.47-1 [278 kB] 308s Get:45 http://ftpmaster.internal/ubuntu plucky/main s390x libreadline-dev s390x 8.2-6 [187 kB] 308s Get:46 http://ftpmaster.internal/ubuntu plucky/main s390x liblzma-dev s390x 5.6.4-1 [183 kB] 308s Get:47 http://ftpmaster.internal/ubuntu plucky/main s390x pkgconf-bin s390x 1.8.1-4 [21.5 kB] 308s Get:48 http://ftpmaster.internal/ubuntu plucky/main s390x pkgconf s390x 1.8.1-4 [16.7 kB] 308s Get:49 http://ftpmaster.internal/ubuntu plucky/main s390x libtirpc-dev s390x 1.3.4+ds-1.3 [196 kB] 309s Get:50 http://ftpmaster.internal/ubuntu plucky/universe s390x r-base-dev all 4.4.3-1 [4176 B] 309s Get:51 http://ftpmaster.internal/ubuntu plucky/universe s390x pkg-r-autopkgtest all 20231212ubuntu1 [6448 B] 309s Fetched 82.3 MB in 1min 33s (884 kB/s) 309s Selecting previously unselected package libisl23:s390x. 309s (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 ... 58769 files and directories currently installed.) 309s Preparing to unpack .../00-libisl23_0.27-1_s390x.deb ... 309s Unpacking libisl23:s390x (0.27-1) ... 309s Selecting previously unselected package libmpc3:s390x. 309s Preparing to unpack .../01-libmpc3_1.3.1-1build2_s390x.deb ... 309s Unpacking libmpc3:s390x (1.3.1-1build2) ... 309s Selecting previously unselected package cpp-14-s390x-linux-gnu. 309s Preparing to unpack .../02-cpp-14-s390x-linux-gnu_14.2.0-17ubuntu3_s390x.deb ... 309s Unpacking cpp-14-s390x-linux-gnu (14.2.0-17ubuntu3) ... 309s Selecting previously unselected package cpp-14. 309s Preparing to unpack .../03-cpp-14_14.2.0-17ubuntu3_s390x.deb ... 309s Unpacking cpp-14 (14.2.0-17ubuntu3) ... 309s Selecting previously unselected package cpp-s390x-linux-gnu. 309s Preparing to unpack .../04-cpp-s390x-linux-gnu_4%3a14.2.0-1ubuntu1_s390x.deb ... 309s Unpacking cpp-s390x-linux-gnu (4:14.2.0-1ubuntu1) ... 309s Selecting previously unselected package cpp. 309s Preparing to unpack .../05-cpp_4%3a14.2.0-1ubuntu1_s390x.deb ... 309s Unpacking cpp (4:14.2.0-1ubuntu1) ... 309s Selecting previously unselected package libcc1-0:s390x. 309s Preparing to unpack .../06-libcc1-0_15-20250222-0ubuntu1_s390x.deb ... 309s Unpacking libcc1-0:s390x (15-20250222-0ubuntu1) ... 309s Selecting previously unselected package libitm1:s390x. 309s Preparing to unpack .../07-libitm1_15-20250222-0ubuntu1_s390x.deb ... 309s Unpacking libitm1:s390x (15-20250222-0ubuntu1) ... 309s Selecting previously unselected package libasan8:s390x. 309s Preparing to unpack .../08-libasan8_15-20250222-0ubuntu1_s390x.deb ... 309s Unpacking libasan8:s390x (15-20250222-0ubuntu1) ... 309s Selecting previously unselected package libubsan1:s390x. 309s Preparing to unpack .../09-libubsan1_15-20250222-0ubuntu1_s390x.deb ... 309s Unpacking libubsan1:s390x (15-20250222-0ubuntu1) ... 309s Selecting previously unselected package libgcc-14-dev:s390x. 309s Preparing to unpack .../10-libgcc-14-dev_14.2.0-17ubuntu3_s390x.deb ... 309s Unpacking libgcc-14-dev:s390x (14.2.0-17ubuntu3) ... 309s Selecting previously unselected package gcc-14-s390x-linux-gnu. 309s Preparing to unpack .../11-gcc-14-s390x-linux-gnu_14.2.0-17ubuntu3_s390x.deb ... 309s Unpacking gcc-14-s390x-linux-gnu (14.2.0-17ubuntu3) ... 309s Selecting previously unselected package gcc-14. 309s Preparing to unpack .../12-gcc-14_14.2.0-17ubuntu3_s390x.deb ... 309s Unpacking gcc-14 (14.2.0-17ubuntu3) ... 309s Selecting previously unselected package gcc-s390x-linux-gnu. 309s Preparing to unpack .../13-gcc-s390x-linux-gnu_4%3a14.2.0-1ubuntu1_s390x.deb ... 309s Unpacking gcc-s390x-linux-gnu (4:14.2.0-1ubuntu1) ... 309s Selecting previously unselected package gcc. 309s Preparing to unpack .../14-gcc_4%3a14.2.0-1ubuntu1_s390x.deb ... 309s Unpacking gcc (4:14.2.0-1ubuntu1) ... 309s Selecting previously unselected package libstdc++-14-dev:s390x. 309s Preparing to unpack .../15-libstdc++-14-dev_14.2.0-17ubuntu3_s390x.deb ... 309s Unpacking libstdc++-14-dev:s390x (14.2.0-17ubuntu3) ... 310s Selecting previously unselected package g++-14-s390x-linux-gnu. 310s Preparing to unpack .../16-g++-14-s390x-linux-gnu_14.2.0-17ubuntu3_s390x.deb ... 310s Unpacking g++-14-s390x-linux-gnu (14.2.0-17ubuntu3) ... 310s Selecting previously unselected package g++-14. 310s Preparing to unpack .../17-g++-14_14.2.0-17ubuntu3_s390x.deb ... 310s Unpacking g++-14 (14.2.0-17ubuntu3) ... 310s Selecting previously unselected package g++-s390x-linux-gnu. 310s Preparing to unpack .../18-g++-s390x-linux-gnu_4%3a14.2.0-1ubuntu1_s390x.deb ... 310s Unpacking g++-s390x-linux-gnu (4:14.2.0-1ubuntu1) ... 310s Selecting previously unselected package g++. 310s Preparing to unpack .../19-g++_4%3a14.2.0-1ubuntu1_s390x.deb ... 310s Unpacking g++ (4:14.2.0-1ubuntu1) ... 310s Selecting previously unselected package build-essential. 310s Preparing to unpack .../20-build-essential_12.10ubuntu1_s390x.deb ... 310s Unpacking build-essential (12.10ubuntu1) ... 310s Selecting previously unselected package dctrl-tools. 310s Preparing to unpack .../21-dctrl-tools_2.24-3build3_s390x.deb ... 310s Unpacking dctrl-tools (2.24-3build3) ... 310s Selecting previously unselected package libgfortran-14-dev:s390x. 310s Preparing to unpack .../22-libgfortran-14-dev_14.2.0-17ubuntu3_s390x.deb ... 310s Unpacking libgfortran-14-dev:s390x (14.2.0-17ubuntu3) ... 310s Selecting previously unselected package gfortran-14-s390x-linux-gnu. 310s Preparing to unpack .../23-gfortran-14-s390x-linux-gnu_14.2.0-17ubuntu3_s390x.deb ... 310s Unpacking gfortran-14-s390x-linux-gnu (14.2.0-17ubuntu3) ... 310s Selecting previously unselected package gfortran-14. 310s Preparing to unpack .../24-gfortran-14_14.2.0-17ubuntu3_s390x.deb ... 310s Unpacking gfortran-14 (14.2.0-17ubuntu3) ... 310s Selecting previously unselected package gfortran-s390x-linux-gnu. 310s Preparing to unpack .../25-gfortran-s390x-linux-gnu_4%3a14.2.0-1ubuntu1_s390x.deb ... 310s Unpacking gfortran-s390x-linux-gnu (4:14.2.0-1ubuntu1) ... 310s Selecting previously unselected package gfortran. 310s Preparing to unpack .../26-gfortran_4%3a14.2.0-1ubuntu1_s390x.deb ... 310s Unpacking gfortran (4:14.2.0-1ubuntu1) ... 310s Selecting previously unselected package icu-devtools. 310s Preparing to unpack .../27-icu-devtools_76.1-1ubuntu2_s390x.deb ... 310s Unpacking icu-devtools (76.1-1ubuntu2) ... 310s Selecting previously unselected package libblas-dev:s390x. 310s Preparing to unpack .../28-libblas-dev_3.12.1-2_s390x.deb ... 310s Unpacking libblas-dev:s390x (3.12.1-2) ... 310s Selecting previously unselected package libbz2-dev:s390x. 310s Preparing to unpack .../29-libbz2-dev_1.0.8-6_s390x.deb ... 310s Unpacking libbz2-dev:s390x (1.0.8-6) ... 310s Selecting previously unselected package libdeflate-dev:s390x. 310s Preparing to unpack .../30-libdeflate-dev_1.23-1_s390x.deb ... 310s Unpacking libdeflate-dev:s390x (1.23-1) ... 310s Selecting previously unselected package libicu-dev:s390x. 310s Preparing to unpack .../31-libicu-dev_76.1-1ubuntu2_s390x.deb ... 310s Unpacking libicu-dev:s390x (76.1-1ubuntu2) ... 310s Selecting previously unselected package libjpeg-turbo8-dev:s390x. 310s Preparing to unpack .../32-libjpeg-turbo8-dev_2.1.5-3ubuntu2_s390x.deb ... 310s Unpacking libjpeg-turbo8-dev:s390x (2.1.5-3ubuntu2) ... 310s Selecting previously unselected package libjpeg8-dev:s390x. 310s Preparing to unpack .../33-libjpeg8-dev_8c-2ubuntu11_s390x.deb ... 310s Unpacking libjpeg8-dev:s390x (8c-2ubuntu11) ... 310s Selecting previously unselected package libjpeg-dev:s390x. 310s Preparing to unpack .../34-libjpeg-dev_8c-2ubuntu11_s390x.deb ... 310s Unpacking libjpeg-dev:s390x (8c-2ubuntu11) ... 310s Selecting previously unselected package liblapack-dev:s390x. 310s Preparing to unpack .../35-liblapack-dev_3.12.1-2_s390x.deb ... 310s Unpacking liblapack-dev:s390x (3.12.1-2) ... 310s Selecting previously unselected package libncurses-dev:s390x. 310s Preparing to unpack .../36-libncurses-dev_6.5+20250216-2_s390x.deb ... 310s Unpacking libncurses-dev:s390x (6.5+20250216-2) ... 310s Selecting previously unselected package libpcre2-16-0:s390x. 310s Preparing to unpack .../37-libpcre2-16-0_10.45-1_s390x.deb ... 310s Unpacking libpcre2-16-0:s390x (10.45-1) ... 310s Selecting previously unselected package libpcre2-32-0:s390x. 310s Preparing to unpack .../38-libpcre2-32-0_10.45-1_s390x.deb ... 310s Unpacking libpcre2-32-0:s390x (10.45-1) ... 310s Selecting previously unselected package libpcre2-posix3:s390x. 310s Preparing to unpack .../39-libpcre2-posix3_10.45-1_s390x.deb ... 310s Unpacking libpcre2-posix3:s390x (10.45-1) ... 310s Selecting previously unselected package libpcre2-dev:s390x. 310s Preparing to unpack .../40-libpcre2-dev_10.45-1_s390x.deb ... 310s Unpacking libpcre2-dev:s390x (10.45-1) ... 310s Selecting previously unselected package libpkgconf3:s390x. 310s Preparing to unpack .../41-libpkgconf3_1.8.1-4_s390x.deb ... 310s Unpacking libpkgconf3:s390x (1.8.1-4) ... 310s Selecting previously unselected package zlib1g-dev:s390x. 310s Preparing to unpack .../42-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1ubuntu1_s390x.deb ... 310s Unpacking zlib1g-dev:s390x (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 310s Selecting previously unselected package libpng-dev:s390x. 310s Preparing to unpack .../43-libpng-dev_1.6.47-1_s390x.deb ... 310s Unpacking libpng-dev:s390x (1.6.47-1) ... 310s Selecting previously unselected package libreadline-dev:s390x. 310s Preparing to unpack .../44-libreadline-dev_8.2-6_s390x.deb ... 310s Unpacking libreadline-dev:s390x (8.2-6) ... 310s Selecting previously unselected package liblzma-dev:s390x. 310s Preparing to unpack .../45-liblzma-dev_5.6.4-1_s390x.deb ... 310s Unpacking liblzma-dev:s390x (5.6.4-1) ... 310s Selecting previously unselected package pkgconf-bin. 310s Preparing to unpack .../46-pkgconf-bin_1.8.1-4_s390x.deb ... 310s Unpacking pkgconf-bin (1.8.1-4) ... 310s Selecting previously unselected package pkgconf:s390x. 310s Preparing to unpack .../47-pkgconf_1.8.1-4_s390x.deb ... 310s Unpacking pkgconf:s390x (1.8.1-4) ... 311s Selecting previously unselected package libtirpc-dev:s390x. 311s Preparing to unpack .../48-libtirpc-dev_1.3.4+ds-1.3_s390x.deb ... 311s Unpacking libtirpc-dev:s390x (1.3.4+ds-1.3) ... 311s Selecting previously unselected package r-base-dev. 311s Preparing to unpack .../49-r-base-dev_4.4.3-1_all.deb ... 311s Unpacking r-base-dev (4.4.3-1) ... 311s Selecting previously unselected package pkg-r-autopkgtest. 311s Preparing to unpack .../50-pkg-r-autopkgtest_20231212ubuntu1_all.deb ... 311s Unpacking pkg-r-autopkgtest (20231212ubuntu1) ... 311s Setting up libjpeg-turbo8-dev:s390x (2.1.5-3ubuntu2) ... 311s Setting up libncurses-dev:s390x (6.5+20250216-2) ... 311s Setting up libreadline-dev:s390x (8.2-6) ... 311s Setting up libpcre2-16-0:s390x (10.45-1) ... 311s Setting up libpcre2-32-0:s390x (10.45-1) ... 311s Setting up libtirpc-dev:s390x (1.3.4+ds-1.3) ... 311s Setting up libpkgconf3:s390x (1.8.1-4) ... 311s Setting up libmpc3:s390x (1.3.1-1build2) ... 311s Setting up icu-devtools (76.1-1ubuntu2) ... 311s Setting up pkgconf-bin (1.8.1-4) ... 311s Setting up liblzma-dev:s390x (5.6.4-1) ... 311s Setting up libubsan1:s390x (15-20250222-0ubuntu1) ... 311s Setting up zlib1g-dev:s390x (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 311s Setting up libpcre2-posix3:s390x (10.45-1) ... 311s Setting up libasan8:s390x (15-20250222-0ubuntu1) ... 311s Setting up libjpeg8-dev:s390x (8c-2ubuntu11) ... 311s Setting up libisl23:s390x (0.27-1) ... 311s Setting up libdeflate-dev:s390x (1.23-1) ... 311s Setting up libicu-dev:s390x (76.1-1ubuntu2) ... 311s Setting up libcc1-0:s390x (15-20250222-0ubuntu1) ... 311s Setting up libblas-dev:s390x (3.12.1-2) ... 311s 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 311s Setting up dctrl-tools (2.24-3build3) ... 311s Setting up libitm1:s390x (15-20250222-0ubuntu1) ... 311s Setting up libbz2-dev:s390x (1.0.8-6) ... 311s Setting up libpcre2-dev:s390x (10.45-1) ... 311s Setting up libpng-dev:s390x (1.6.47-1) ... 311s Setting up libjpeg-dev:s390x (8c-2ubuntu11) ... 311s Setting up pkgconf:s390x (1.8.1-4) ... 311s Setting up liblapack-dev:s390x (3.12.1-2) ... 311s 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 311s Setting up cpp-14-s390x-linux-gnu (14.2.0-17ubuntu3) ... 311s Setting up cpp-14 (14.2.0-17ubuntu3) ... 311s Setting up libgcc-14-dev:s390x (14.2.0-17ubuntu3) ... 311s Setting up libstdc++-14-dev:s390x (14.2.0-17ubuntu3) ... 311s Setting up libgfortran-14-dev:s390x (14.2.0-17ubuntu3) ... 311s Setting up cpp-s390x-linux-gnu (4:14.2.0-1ubuntu1) ... 311s Setting up gcc-14-s390x-linux-gnu (14.2.0-17ubuntu3) ... 311s Setting up gcc-s390x-linux-gnu (4:14.2.0-1ubuntu1) ... 311s Setting up g++-14-s390x-linux-gnu (14.2.0-17ubuntu3) ... 311s Setting up cpp (4:14.2.0-1ubuntu1) ... 311s Setting up gfortran-14-s390x-linux-gnu (14.2.0-17ubuntu3) ... 311s Setting up g++-s390x-linux-gnu (4:14.2.0-1ubuntu1) ... 311s Setting up gcc-14 (14.2.0-17ubuntu3) ... 311s Setting up g++-14 (14.2.0-17ubuntu3) ... 311s Setting up gfortran-14 (14.2.0-17ubuntu3) ... 311s Setting up gfortran-s390x-linux-gnu (4:14.2.0-1ubuntu1) ... 311s Setting up gcc (4:14.2.0-1ubuntu1) ... 311s Setting up g++ (4:14.2.0-1ubuntu1) ... 311s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 311s Setting up build-essential (12.10ubuntu1) ... 311s Setting up gfortran (4:14.2.0-1ubuntu1) ... 311s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode 311s 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 311s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode 311s 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 311s Setting up r-base-dev (4.4.3-1) ... 311s Setting up pkg-r-autopkgtest (20231212ubuntu1) ... 311s Processing triggers for libc-bin (2.41-1ubuntu2) ... 311s Processing triggers for man-db (2.13.0-1) ... 311s Processing triggers for install-info (7.1.1-1) ... 312s autopkgtest [16:31:04]: test pkg-r-autopkgtest: /usr/share/dh-r/pkg-r-autopkgtest 312s autopkgtest [16:31:04]: test pkg-r-autopkgtest: [----------------------- 312s Test: Try to load the R library irlba 313s 313s R version 4.4.3 (2025-02-28) -- "Trophy Case" 313s Copyright (C) 2025 The R Foundation for Statistical Computing 313s Platform: s390x-ibm-linux-gnu 313s 313s R is free software and comes with ABSOLUTELY NO WARRANTY. 313s You are welcome to redistribute it under certain conditions. 313s Type 'license()' or 'licence()' for distribution details. 313s 313s R is a collaborative project with many contributors. 313s Type 'contributors()' for more information and 313s 'citation()' on how to cite R or R packages in publications. 313s 313s Type 'demo()' for some demos, 'help()' for on-line help, or 313s 'help.start()' for an HTML browser interface to help. 313s Type 'q()' to quit R. 313s 313s > library('irlba') 313s Loading required package: Matrix 313s > 313s > 313s Other tests are currently unsupported! 313s They will be progressively added. 314s autopkgtest [16:31:06]: test pkg-r-autopkgtest: -----------------------] 314s pkg-r-autopkgtest PASS 314s autopkgtest [16:31:06]: test pkg-r-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 314s autopkgtest [16:31:06]: @@@@@@@@@@@@@@@@@@@@ summary 314s run-unit-test PASS 314s pkg-r-autopkgtest PASS 331s nova [W] Using flock in prodstack6-s390x 331s Creating nova instance adt-plucky-s390x-r-cran-irlba-20250315-160931-juju-7f2275-prod-proposed-migration-environment-20-1c8b10f2-74f7-47f2-beb7-2b0bb6bef5c6 from image adt/ubuntu-plucky-s390x-server-20250315.img (UUID 3d3557fa-fd0f-4bba-9b89-8d5964e09f61)... 331s nova [W] Timed out waiting for f6676d1c-793b-4709-8554-88a9a8730515 to get deleted.