0s autopkgtest [17:51:36]: starting date and time: 2025-03-15 17:51:36+0000 0s autopkgtest [17:51:36]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [17:51:36]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.biku5uql/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-ape --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-16.secgroup --name adt-plucky-s390x-r-cran-ape-20250315-175136-juju-7f2275-prod-proposed-migration-environment-20-a2005986-0c56-43b8-b641-ca9867251466 --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/ 140s autopkgtest [17:53:56]: testbed dpkg architecture: s390x 140s autopkgtest [17:53:56]: testbed apt version: 2.9.33 140s autopkgtest [17:53:56]: @@@@@@@@@@@@@@@@@@@@ test bed setup 140s autopkgtest [17:53:56]: testbed release detected to be: None 141s autopkgtest [17:53:57]: updating testbed package index (apt update) 141s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 142s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 142s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 142s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 142s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 142s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [99.7 kB] 142s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [379 kB] 142s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x Packages [113 kB] 142s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x c-n-f Metadata [1824 B] 142s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted s390x c-n-f Metadata [116 B] 142s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x Packages [320 kB] 143s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x c-n-f Metadata [13.4 kB] 143s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x Packages [3776 B] 143s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x c-n-f Metadata [240 B] 143s Fetched 1073 kB in 2s (657 kB/s) 144s Reading package lists... 144s Reading package lists... 144s Building dependency tree... 144s Reading state information... 144s Calculating upgrade... 145s Calculating upgrade... 145s The following packages were automatically installed and are no longer required: 145s libnsl2 libpython3.12-minimal libpython3.12-stdlib libpython3.12t64 145s linux-headers-6.11.0-8 linux-headers-6.11.0-8-generic 145s linux-modules-6.11.0-8-generic linux-tools-6.11.0-8 145s linux-tools-6.11.0-8-generic 145s Use 'sudo apt autoremove' to remove them. 145s The following packages will be upgraded: 145s pinentry-curses python3-jinja2 strace 145s 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 145s Need to get 652 kB of archives. 145s After this operation, 27.6 kB of additional disk space will be used. 145s Get:1 http://ftpmaster.internal/ubuntu plucky/main s390x strace s390x 6.13+ds-1ubuntu1 [500 kB] 146s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x pinentry-curses s390x 1.3.1-2ubuntu3 [42.9 kB] 146s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 146s Fetched 652 kB in 1s (606 kB/s) 146s (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.) 146s Preparing to unpack .../strace_6.13+ds-1ubuntu1_s390x.deb ... 146s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 146s Preparing to unpack .../pinentry-curses_1.3.1-2ubuntu3_s390x.deb ... 146s Unpacking pinentry-curses (1.3.1-2ubuntu3) over (1.3.1-2ubuntu2) ... 146s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 146s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 146s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 146s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 146s Setting up strace (6.13+ds-1ubuntu1) ... 146s Processing triggers for man-db (2.13.0-1) ... 147s Reading package lists... 147s Building dependency tree... 147s Reading state information... 147s Solving dependencies... 147s The following packages will be REMOVED: 147s libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64* 147s linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 147s linux-modules-6.11.0-8-generic* linux-tools-6.11.0-8* 147s linux-tools-6.11.0-8-generic* 148s 0 upgraded, 0 newly installed, 9 to remove and 5 not upgraded. 148s After this operation, 167 MB disk space will be freed. 148s (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.) 148s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 148s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 148s Removing libpython3.12t64:s390x (3.12.9-1) ... 148s Removing libpython3.12-stdlib:s390x (3.12.9-1) ... 148s Removing libnsl2:s390x (1.3.0-3build3) ... 148s Removing libpython3.12-minimal:s390x (3.12.9-1) ... 148s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 148s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 149s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 149s Processing triggers for libc-bin (2.41-1ubuntu1) ... 149s (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.) 149s Purging configuration files for libpython3.12-minimal:s390x (3.12.9-1) ... 149s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 149s autopkgtest [17:54:05]: upgrading testbed (apt dist-upgrade and autopurge) 149s Reading package lists... 149s Building dependency tree... 149s Reading state information... 149s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 149s Starting 2 pkgProblemResolver with broken count: 0 149s Done 150s Entering ResolveByKeep 150s 150s Calculating upgrade... 150s The following packages will be upgraded: 150s libc-bin libc-dev-bin libc6 libc6-dev locales 150s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 150s Need to get 9512 kB of archives. 150s After this operation, 8192 B of additional disk space will be used. 150s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc6-dev s390x 2.41-1ubuntu2 [1678 kB] 152s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc-dev-bin s390x 2.41-1ubuntu2 [24.3 kB] 152s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc6 s390x 2.41-1ubuntu2 [2892 kB] 155s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc-bin s390x 2.41-1ubuntu2 [671 kB] 156s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x locales all 2.41-1ubuntu2 [4246 kB] 161s Preconfiguring packages ... 161s Fetched 9512 kB in 11s (858 kB/s) 161s (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.) 161s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_s390x.deb ... 161s Unpacking libc6-dev:s390x (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 162s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_s390x.deb ... 162s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 162s Preparing to unpack .../libc6_2.41-1ubuntu2_s390x.deb ... 162s Unpacking libc6:s390x (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 162s Setting up libc6:s390x (2.41-1ubuntu2) ... 162s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 56326 files and directories currently installed.) 162s Preparing to unpack .../libc-bin_2.41-1ubuntu2_s390x.deb ... 162s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 162s Setting up libc-bin (2.41-1ubuntu2) ... 162s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 56326 files and directories currently installed.) 162s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 162s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 162s Setting up locales (2.41-1ubuntu2) ... 162s Generating locales (this might take a while)... 163s en_US.UTF-8... done 163s Generation complete. 163s Setting up libc-dev-bin (2.41-1ubuntu2) ... 163s Setting up libc6-dev:s390x (2.41-1ubuntu2) ... 163s Processing triggers for man-db (2.13.0-1) ... 164s Processing triggers for systemd (257.3-1ubuntu3) ... 165s Reading package lists... 165s Building dependency tree... 165s Reading state information... 165s Starting pkgProblemResolver with broken count: 0 165s Starting 2 pkgProblemResolver with broken count: 0 165s Done 166s Solving dependencies... 166s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 166s autopkgtest [17:54:22]: rebooting testbed after setup commands that affected boot 179s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 186s autopkgtest [17:54:42]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP Wed Mar 12 14:53:49 UTC 2025 188s autopkgtest [17:54:44]: @@@@@@@@@@@@@@@@@@@@ apt-source r-cran-ape 191s Get:1 http://ftpmaster.internal/ubuntu plucky/universe r-cran-ape 5.8-1-1 (dsc) [2114 B] 191s Get:2 http://ftpmaster.internal/ubuntu plucky/universe r-cran-ape 5.8-1-1 (tar) [1425 kB] 191s Get:3 http://ftpmaster.internal/ubuntu plucky/universe r-cran-ape 5.8-1-1 (diff) [5600 B] 192s gpgv: Signature made Wed Jan 22 08:35:21 2025 UTC 192s gpgv: using RSA key 73471499CC60ED9EEE805946C5BD6C8F2295D502 192s gpgv: issuer "plessy@debian.org" 192s gpgv: Can't check signature: No public key 192s dpkg-source: warning: cannot verify inline signature for ./r-cran-ape_5.8-1-1.dsc: no acceptable signature found 192s autopkgtest [17:54:48]: testing package r-cran-ape version 5.8-1-1 192s autopkgtest [17:54:48]: build not needed 194s autopkgtest [17:54:50]: test run-unit-test: preparing testbed 194s Reading package lists... 195s Building dependency tree... 195s Reading state information... 195s Starting pkgProblemResolver with broken count: 0 195s Starting 2 pkgProblemResolver with broken count: 0 195s Done 195s The following NEW packages will be installed: 195s fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono libamd3 195s libblas3 libcairo2 libcolamd3 libdatrie1 libdeflate0 libfontconfig1 195s libfreetype6 libgfortran5 libglpk40 libgomp1 libgraphite2-3 libharfbuzz0b 195s libice6 libjbig0 libjpeg-turbo8 libjpeg8 liblapack3 libltdl7 libpango-1.0-0 195s libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper2 libpixman-1-0 195s libsharpyuv0 libsm6 libsuitesparseconfig7 libtcl8.6 libthai-data libthai0 195s libtiff6 libtk8.6 libwebp7 libxcb-render0 libxcb-shm0 libxft2 libxrender1 195s libxss1 libxt6t64 littler r-base-core r-cran-ape r-cran-cli r-cran-cpp11 195s r-cran-digest r-cran-fastmatch r-cran-generics r-cran-glue r-cran-igraph 195s r-cran-lattice r-cran-lifecycle r-cran-littler r-cran-magrittr r-cran-matrix 195s r-cran-nlme r-cran-phangorn r-cran-pkgconfig r-cran-pkgkitten 195s r-cran-quadprog r-cran-rcpp r-cran-rlang r-cran-vctrs unzip x11-common 195s xdg-utils zip 195s 0 upgraded, 71 newly installed, 0 to remove and 0 not upgraded. 195s Need to get 66.5 MB of archives. 195s After this operation, 131 MB of additional disk space will be used. 195s Get:1 http://ftpmaster.internal/ubuntu plucky/main s390x libfreetype6 s390x 2.13.3+dfsg-1 [431 kB] 196s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x fonts-dejavu-mono all 2.37-8 [502 kB] 196s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x fonts-dejavu-core all 2.37-8 [835 kB] 197s Get:4 http://ftpmaster.internal/ubuntu plucky/main s390x fontconfig-config s390x 2.15.0-2ubuntu1 [37.5 kB] 197s Get:5 http://ftpmaster.internal/ubuntu plucky/main s390x libfontconfig1 s390x 2.15.0-2ubuntu1 [150 kB] 197s Get:6 http://ftpmaster.internal/ubuntu plucky/main s390x fontconfig s390x 2.15.0-2ubuntu1 [191 kB] 198s Get:7 http://ftpmaster.internal/ubuntu plucky/main s390x libgomp1 s390x 15-20250222-0ubuntu1 [152 kB] 198s Get:8 http://ftpmaster.internal/ubuntu plucky/main s390x libsuitesparseconfig7 s390x 1:7.8.3+dfsg-3 [13.2 kB] 198s Get:9 http://ftpmaster.internal/ubuntu plucky/universe s390x libamd3 s390x 1:7.8.3+dfsg-3 [35.1 kB] 198s Get:10 http://ftpmaster.internal/ubuntu plucky/main s390x libblas3 s390x 3.12.1-2 [252 kB] 198s Get:11 http://ftpmaster.internal/ubuntu plucky/main s390x libpixman-1-0 s390x 0.44.0-3 [201 kB] 198s Get:12 http://ftpmaster.internal/ubuntu plucky/main s390x libxcb-render0 s390x 1.17.0-2 [17.0 kB] 198s Get:13 http://ftpmaster.internal/ubuntu plucky/main s390x libxcb-shm0 s390x 1.17.0-2 [5862 B] 198s Get:14 http://ftpmaster.internal/ubuntu plucky/main s390x libxrender1 s390x 1:0.9.10-1.1build1 [20.4 kB] 198s Get:15 http://ftpmaster.internal/ubuntu plucky/main s390x libcairo2 s390x 1.18.2-2 [580 kB] 199s Get:16 http://ftpmaster.internal/ubuntu plucky/main s390x libcolamd3 s390x 1:7.8.3+dfsg-3 [23.4 kB] 199s Get:17 http://ftpmaster.internal/ubuntu plucky/main s390x libdatrie1 s390x 0.2.13-3build1 [20.6 kB] 199s Get:18 http://ftpmaster.internal/ubuntu plucky/main s390x libdeflate0 s390x 1.23-1 [46.1 kB] 199s Get:19 http://ftpmaster.internal/ubuntu plucky/main s390x libgfortran5 s390x 15-20250222-0ubuntu1 [620 kB] 199s Get:20 http://ftpmaster.internal/ubuntu plucky/main s390x libltdl7 s390x 2.5.4-4 [43.8 kB] 199s Get:21 http://ftpmaster.internal/ubuntu plucky/universe s390x libglpk40 s390x 5.0-1build2 [406 kB] 200s Get:22 http://ftpmaster.internal/ubuntu plucky/main s390x libgraphite2-3 s390x 1.3.14-2ubuntu1 [79.8 kB] 200s Get:23 http://ftpmaster.internal/ubuntu plucky/main s390x libharfbuzz0b s390x 10.2.0-1 [538 kB] 200s Get:24 http://ftpmaster.internal/ubuntu plucky/main s390x x11-common all 1:7.7+23ubuntu3 [21.7 kB] 200s Get:25 http://ftpmaster.internal/ubuntu plucky/main s390x libice6 s390x 2:1.1.1-1 [45.4 kB] 200s Get:26 http://ftpmaster.internal/ubuntu plucky/main s390x libjpeg-turbo8 s390x 2.1.5-3ubuntu2 [147 kB] 201s Get:27 http://ftpmaster.internal/ubuntu plucky/main s390x libjpeg8 s390x 8c-2ubuntu11 [2146 B] 201s Get:28 http://ftpmaster.internal/ubuntu plucky/main s390x liblapack3 s390x 3.12.1-2 [2971 kB] 203s Get:29 http://ftpmaster.internal/ubuntu plucky/main s390x libthai-data all 0.1.29-2build1 [158 kB] 203s Get:30 http://ftpmaster.internal/ubuntu plucky/main s390x libthai0 s390x 0.1.29-2build1 [20.7 kB] 203s Get:31 http://ftpmaster.internal/ubuntu plucky/main s390x libpango-1.0-0 s390x 1.56.2-1 [253 kB] 204s Get:32 http://ftpmaster.internal/ubuntu plucky/main s390x libpangoft2-1.0-0 s390x 1.56.2-1 [50.2 kB] 204s Get:33 http://ftpmaster.internal/ubuntu plucky/main s390x libpangocairo-1.0-0 s390x 1.56.2-1 [28.2 kB] 204s Get:34 http://ftpmaster.internal/ubuntu plucky/main s390x libpaper2 s390x 2.2.5-0.3 [17.2 kB] 204s Get:35 http://ftpmaster.internal/ubuntu plucky/main s390x libpaper-utils s390x 2.2.5-0.3 [15.3 kB] 204s Get:36 http://ftpmaster.internal/ubuntu plucky/main s390x libsharpyuv0 s390x 1.5.0-0.1 [16.7 kB] 204s Get:37 http://ftpmaster.internal/ubuntu plucky/main s390x libsm6 s390x 2:1.2.4-1 [18.4 kB] 204s Get:38 http://ftpmaster.internal/ubuntu plucky/main s390x libtcl8.6 s390x 8.6.16+dfsg-1 [1034 kB] 205s Get:39 http://ftpmaster.internal/ubuntu plucky/main s390x libjbig0 s390x 2.1-6.1ubuntu2 [33.1 kB] 205s Get:40 http://ftpmaster.internal/ubuntu plucky/main s390x libwebp7 s390x 1.5.0-0.1 [210 kB] 205s Get:41 http://ftpmaster.internal/ubuntu plucky/main s390x libtiff6 s390x 4.5.1+git230720-4ubuntu4 [217 kB] 205s Get:42 http://ftpmaster.internal/ubuntu plucky/main s390x libxft2 s390x 2.3.6-1build1 [49.6 kB] 205s Get:43 http://ftpmaster.internal/ubuntu plucky/main s390x libxss1 s390x 1:1.2.3-1build3 [7396 B] 205s Get:44 http://ftpmaster.internal/ubuntu plucky/main s390x libtk8.6 s390x 8.6.16-1 [830 kB] 206s Get:45 http://ftpmaster.internal/ubuntu plucky/main s390x libxt6t64 s390x 1:1.2.1-1.2build1 [184 kB] 206s Get:46 http://ftpmaster.internal/ubuntu plucky/main s390x zip s390x 3.0-14ubuntu2 [187 kB] 206s Get:47 http://ftpmaster.internal/ubuntu plucky/main s390x unzip s390x 6.0-28ubuntu6 [186 kB] 207s Get:48 http://ftpmaster.internal/ubuntu plucky/main s390x xdg-utils all 1.2.1-2ubuntu1 [66.0 kB] 207s Get:49 http://ftpmaster.internal/ubuntu plucky/universe s390x r-base-core s390x 4.4.3-1 [28.6 MB] 232s Get:50 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-littler s390x 0.3.20-2 [95.0 kB] 232s Get:51 http://ftpmaster.internal/ubuntu plucky/universe s390x littler all 0.3.20-2 [2554 B] 232s Get:52 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-lattice s390x 0.22-6-1 [1340 kB] 233s Get:53 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-nlme s390x 3.1.167-1 [2323 kB] 235s Get:54 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-pkgkitten all 0.2.4-1 [27.2 kB] 235s Get:55 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-rcpp s390x 1.0.14-1 [2003 kB] 237s Get:56 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-digest s390x 0.6.37-1 [205 kB] 237s Get:57 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-ape s390x 5.8-1-1 [2921 kB] 240s Get:58 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-cli s390x 3.6.4-1 [1379 kB] 241s Get:59 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-cpp11 all 0.5.2-1 [233 kB] 241s Get:60 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-fastmatch s390x 1.1-6-1 [37.1 kB] 241s Get:61 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-generics all 0.1.3-1 [81.3 kB] 241s Get:62 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-glue s390x 1.8.0-1 [164 kB] 241s Get:63 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-rlang s390x 1.1.5-1 [1713 kB] 243s Get:64 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB] 243s Get:65 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-magrittr s390x 2.0.3-1 [154 kB] 243s Get:66 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-matrix s390x 1.7-3-1 [4449 kB] 248s Get:67 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-pkgconfig all 2.0.3-2build1 [19.7 kB] 248s Get:68 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-vctrs s390x 0.6.5-1 [1448 kB] 249s Get:69 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-igraph s390x 2.1.4-1 [5311 kB] 255s Get:70 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-quadprog s390x 1.5-8-1build1 [30.8 kB] 255s Get:71 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-phangorn s390x 2.12.1+dfsg-1 [1832 kB] 257s Preconfiguring packages ... 257s Fetched 66.5 MB in 1min 1s (1084 kB/s) 257s Selecting previously unselected package libfreetype6:s390x. 257s (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.) 257s Preparing to unpack .../00-libfreetype6_2.13.3+dfsg-1_s390x.deb ... 257s Unpacking libfreetype6:s390x (2.13.3+dfsg-1) ... 257s Selecting previously unselected package fonts-dejavu-mono. 257s Preparing to unpack .../01-fonts-dejavu-mono_2.37-8_all.deb ... 257s Unpacking fonts-dejavu-mono (2.37-8) ... 257s Selecting previously unselected package fonts-dejavu-core. 257s Preparing to unpack .../02-fonts-dejavu-core_2.37-8_all.deb ... 257s Unpacking fonts-dejavu-core (2.37-8) ... 257s Selecting previously unselected package fontconfig-config. 257s Preparing to unpack .../03-fontconfig-config_2.15.0-2ubuntu1_s390x.deb ... 257s Unpacking fontconfig-config (2.15.0-2ubuntu1) ... 257s Selecting previously unselected package libfontconfig1:s390x. 257s Preparing to unpack .../04-libfontconfig1_2.15.0-2ubuntu1_s390x.deb ... 257s Unpacking libfontconfig1:s390x (2.15.0-2ubuntu1) ... 257s Selecting previously unselected package fontconfig. 257s Preparing to unpack .../05-fontconfig_2.15.0-2ubuntu1_s390x.deb ... 257s Unpacking fontconfig (2.15.0-2ubuntu1) ... 257s Selecting previously unselected package libgomp1:s390x. 257s Preparing to unpack .../06-libgomp1_15-20250222-0ubuntu1_s390x.deb ... 257s Unpacking libgomp1:s390x (15-20250222-0ubuntu1) ... 257s Selecting previously unselected package libsuitesparseconfig7:s390x. 257s Preparing to unpack .../07-libsuitesparseconfig7_1%3a7.8.3+dfsg-3_s390x.deb ... 257s Unpacking libsuitesparseconfig7:s390x (1:7.8.3+dfsg-3) ... 257s Selecting previously unselected package libamd3:s390x. 257s Preparing to unpack .../08-libamd3_1%3a7.8.3+dfsg-3_s390x.deb ... 257s Unpacking libamd3:s390x (1:7.8.3+dfsg-3) ... 257s Selecting previously unselected package libblas3:s390x. 257s Preparing to unpack .../09-libblas3_3.12.1-2_s390x.deb ... 257s Unpacking libblas3:s390x (3.12.1-2) ... 257s Selecting previously unselected package libpixman-1-0:s390x. 257s Preparing to unpack .../10-libpixman-1-0_0.44.0-3_s390x.deb ... 257s Unpacking libpixman-1-0:s390x (0.44.0-3) ... 257s Selecting previously unselected package libxcb-render0:s390x. 257s Preparing to unpack .../11-libxcb-render0_1.17.0-2_s390x.deb ... 257s Unpacking libxcb-render0:s390x (1.17.0-2) ... 257s Selecting previously unselected package libxcb-shm0:s390x. 257s Preparing to unpack .../12-libxcb-shm0_1.17.0-2_s390x.deb ... 257s Unpacking libxcb-shm0:s390x (1.17.0-2) ... 257s Selecting previously unselected package libxrender1:s390x. 257s Preparing to unpack .../13-libxrender1_1%3a0.9.10-1.1build1_s390x.deb ... 257s Unpacking libxrender1:s390x (1:0.9.10-1.1build1) ... 257s Selecting previously unselected package libcairo2:s390x. 257s Preparing to unpack .../14-libcairo2_1.18.2-2_s390x.deb ... 257s Unpacking libcairo2:s390x (1.18.2-2) ... 257s Selecting previously unselected package libcolamd3:s390x. 257s Preparing to unpack .../15-libcolamd3_1%3a7.8.3+dfsg-3_s390x.deb ... 257s Unpacking libcolamd3:s390x (1:7.8.3+dfsg-3) ... 257s Selecting previously unselected package libdatrie1:s390x. 257s Preparing to unpack .../16-libdatrie1_0.2.13-3build1_s390x.deb ... 257s Unpacking libdatrie1:s390x (0.2.13-3build1) ... 257s Selecting previously unselected package libdeflate0:s390x. 257s Preparing to unpack .../17-libdeflate0_1.23-1_s390x.deb ... 257s Unpacking libdeflate0:s390x (1.23-1) ... 257s Selecting previously unselected package libgfortran5:s390x. 257s Preparing to unpack .../18-libgfortran5_15-20250222-0ubuntu1_s390x.deb ... 257s Unpacking libgfortran5:s390x (15-20250222-0ubuntu1) ... 257s Selecting previously unselected package libltdl7:s390x. 257s Preparing to unpack .../19-libltdl7_2.5.4-4_s390x.deb ... 257s Unpacking libltdl7:s390x (2.5.4-4) ... 257s Selecting previously unselected package libglpk40:s390x. 257s Preparing to unpack .../20-libglpk40_5.0-1build2_s390x.deb ... 257s Unpacking libglpk40:s390x (5.0-1build2) ... 257s Selecting previously unselected package libgraphite2-3:s390x. 257s Preparing to unpack .../21-libgraphite2-3_1.3.14-2ubuntu1_s390x.deb ... 257s Unpacking libgraphite2-3:s390x (1.3.14-2ubuntu1) ... 257s Selecting previously unselected package libharfbuzz0b:s390x. 257s Preparing to unpack .../22-libharfbuzz0b_10.2.0-1_s390x.deb ... 257s Unpacking libharfbuzz0b:s390x (10.2.0-1) ... 257s Selecting previously unselected package x11-common. 257s Preparing to unpack .../23-x11-common_1%3a7.7+23ubuntu3_all.deb ... 257s Unpacking x11-common (1:7.7+23ubuntu3) ... 257s Selecting previously unselected package libice6:s390x. 257s Preparing to unpack .../24-libice6_2%3a1.1.1-1_s390x.deb ... 257s Unpacking libice6:s390x (2:1.1.1-1) ... 257s Selecting previously unselected package libjpeg-turbo8:s390x. 257s Preparing to unpack .../25-libjpeg-turbo8_2.1.5-3ubuntu2_s390x.deb ... 257s Unpacking libjpeg-turbo8:s390x (2.1.5-3ubuntu2) ... 257s Selecting previously unselected package libjpeg8:s390x. 257s Preparing to unpack .../26-libjpeg8_8c-2ubuntu11_s390x.deb ... 257s Unpacking libjpeg8:s390x (8c-2ubuntu11) ... 257s Selecting previously unselected package liblapack3:s390x. 257s Preparing to unpack .../27-liblapack3_3.12.1-2_s390x.deb ... 257s Unpacking liblapack3:s390x (3.12.1-2) ... 257s Selecting previously unselected package libthai-data. 257s Preparing to unpack .../28-libthai-data_0.1.29-2build1_all.deb ... 257s Unpacking libthai-data (0.1.29-2build1) ... 257s Selecting previously unselected package libthai0:s390x. 257s Preparing to unpack .../29-libthai0_0.1.29-2build1_s390x.deb ... 257s Unpacking libthai0:s390x (0.1.29-2build1) ... 257s Selecting previously unselected package libpango-1.0-0:s390x. 257s Preparing to unpack .../30-libpango-1.0-0_1.56.2-1_s390x.deb ... 257s Unpacking libpango-1.0-0:s390x (1.56.2-1) ... 257s Selecting previously unselected package libpangoft2-1.0-0:s390x. 257s Preparing to unpack .../31-libpangoft2-1.0-0_1.56.2-1_s390x.deb ... 257s Unpacking libpangoft2-1.0-0:s390x (1.56.2-1) ... 257s Selecting previously unselected package libpangocairo-1.0-0:s390x. 257s Preparing to unpack .../32-libpangocairo-1.0-0_1.56.2-1_s390x.deb ... 257s Unpacking libpangocairo-1.0-0:s390x (1.56.2-1) ... 257s Selecting previously unselected package libpaper2:s390x. 257s Preparing to unpack .../33-libpaper2_2.2.5-0.3_s390x.deb ... 257s Unpacking libpaper2:s390x (2.2.5-0.3) ... 257s Selecting previously unselected package libpaper-utils. 257s Preparing to unpack .../34-libpaper-utils_2.2.5-0.3_s390x.deb ... 257s Unpacking libpaper-utils (2.2.5-0.3) ... 257s Selecting previously unselected package libsharpyuv0:s390x. 257s Preparing to unpack .../35-libsharpyuv0_1.5.0-0.1_s390x.deb ... 257s Unpacking libsharpyuv0:s390x (1.5.0-0.1) ... 258s Selecting previously unselected package libsm6:s390x. 258s Preparing to unpack .../36-libsm6_2%3a1.2.4-1_s390x.deb ... 258s Unpacking libsm6:s390x (2:1.2.4-1) ... 258s Selecting previously unselected package libtcl8.6:s390x. 258s Preparing to unpack .../37-libtcl8.6_8.6.16+dfsg-1_s390x.deb ... 258s Unpacking libtcl8.6:s390x (8.6.16+dfsg-1) ... 258s Selecting previously unselected package libjbig0:s390x. 258s Preparing to unpack .../38-libjbig0_2.1-6.1ubuntu2_s390x.deb ... 258s Unpacking libjbig0:s390x (2.1-6.1ubuntu2) ... 258s Selecting previously unselected package libwebp7:s390x. 258s Preparing to unpack .../39-libwebp7_1.5.0-0.1_s390x.deb ... 258s Unpacking libwebp7:s390x (1.5.0-0.1) ... 258s Selecting previously unselected package libtiff6:s390x. 258s Preparing to unpack .../40-libtiff6_4.5.1+git230720-4ubuntu4_s390x.deb ... 258s Unpacking libtiff6:s390x (4.5.1+git230720-4ubuntu4) ... 258s Selecting previously unselected package libxft2:s390x. 258s Preparing to unpack .../41-libxft2_2.3.6-1build1_s390x.deb ... 258s Unpacking libxft2:s390x (2.3.6-1build1) ... 258s Selecting previously unselected package libxss1:s390x. 258s Preparing to unpack .../42-libxss1_1%3a1.2.3-1build3_s390x.deb ... 258s Unpacking libxss1:s390x (1:1.2.3-1build3) ... 258s Selecting previously unselected package libtk8.6:s390x. 258s Preparing to unpack .../43-libtk8.6_8.6.16-1_s390x.deb ... 258s Unpacking libtk8.6:s390x (8.6.16-1) ... 258s Selecting previously unselected package libxt6t64:s390x. 258s Preparing to unpack .../44-libxt6t64_1%3a1.2.1-1.2build1_s390x.deb ... 258s Unpacking libxt6t64:s390x (1:1.2.1-1.2build1) ... 258s Selecting previously unselected package zip. 258s Preparing to unpack .../45-zip_3.0-14ubuntu2_s390x.deb ... 258s Unpacking zip (3.0-14ubuntu2) ... 258s Selecting previously unselected package unzip. 258s Preparing to unpack .../46-unzip_6.0-28ubuntu6_s390x.deb ... 258s Unpacking unzip (6.0-28ubuntu6) ... 258s Selecting previously unselected package xdg-utils. 258s Preparing to unpack .../47-xdg-utils_1.2.1-2ubuntu1_all.deb ... 258s Unpacking xdg-utils (1.2.1-2ubuntu1) ... 258s Selecting previously unselected package r-base-core. 258s Preparing to unpack .../48-r-base-core_4.4.3-1_s390x.deb ... 258s Unpacking r-base-core (4.4.3-1) ... 258s Selecting previously unselected package r-cran-littler. 258s Preparing to unpack .../49-r-cran-littler_0.3.20-2_s390x.deb ... 258s Unpacking r-cran-littler (0.3.20-2) ... 258s Selecting previously unselected package littler. 258s Preparing to unpack .../50-littler_0.3.20-2_all.deb ... 258s Unpacking littler (0.3.20-2) ... 258s Selecting previously unselected package r-cran-lattice. 258s Preparing to unpack .../51-r-cran-lattice_0.22-6-1_s390x.deb ... 258s Unpacking r-cran-lattice (0.22-6-1) ... 258s Selecting previously unselected package r-cran-nlme. 258s Preparing to unpack .../52-r-cran-nlme_3.1.167-1_s390x.deb ... 258s Unpacking r-cran-nlme (3.1.167-1) ... 258s Selecting previously unselected package r-cran-pkgkitten. 258s Preparing to unpack .../53-r-cran-pkgkitten_0.2.4-1_all.deb ... 258s Unpacking r-cran-pkgkitten (0.2.4-1) ... 258s Selecting previously unselected package r-cran-rcpp. 258s Preparing to unpack .../54-r-cran-rcpp_1.0.14-1_s390x.deb ... 258s Unpacking r-cran-rcpp (1.0.14-1) ... 258s Selecting previously unselected package r-cran-digest. 258s Preparing to unpack .../55-r-cran-digest_0.6.37-1_s390x.deb ... 258s Unpacking r-cran-digest (0.6.37-1) ... 258s Selecting previously unselected package r-cran-ape. 258s Preparing to unpack .../56-r-cran-ape_5.8-1-1_s390x.deb ... 258s Unpacking r-cran-ape (5.8-1-1) ... 258s Selecting previously unselected package r-cran-cli. 258s Preparing to unpack .../57-r-cran-cli_3.6.4-1_s390x.deb ... 258s Unpacking r-cran-cli (3.6.4-1) ... 258s Selecting previously unselected package r-cran-cpp11. 258s Preparing to unpack .../58-r-cran-cpp11_0.5.2-1_all.deb ... 258s Unpacking r-cran-cpp11 (0.5.2-1) ... 258s Selecting previously unselected package r-cran-fastmatch. 258s Preparing to unpack .../59-r-cran-fastmatch_1.1-6-1_s390x.deb ... 258s Unpacking r-cran-fastmatch (1.1-6-1) ... 258s Selecting previously unselected package r-cran-generics. 258s Preparing to unpack .../60-r-cran-generics_0.1.3-1_all.deb ... 258s Unpacking r-cran-generics (0.1.3-1) ... 258s Selecting previously unselected package r-cran-glue. 258s Preparing to unpack .../61-r-cran-glue_1.8.0-1_s390x.deb ... 258s Unpacking r-cran-glue (1.8.0-1) ... 258s Selecting previously unselected package r-cran-rlang. 258s Preparing to unpack .../62-r-cran-rlang_1.1.5-1_s390x.deb ... 258s Unpacking r-cran-rlang (1.1.5-1) ... 258s Selecting previously unselected package r-cran-lifecycle. 258s Preparing to unpack .../63-r-cran-lifecycle_1.0.4+dfsg-1_all.deb ... 258s Unpacking r-cran-lifecycle (1.0.4+dfsg-1) ... 258s Selecting previously unselected package r-cran-magrittr. 258s Preparing to unpack .../64-r-cran-magrittr_2.0.3-1_s390x.deb ... 258s Unpacking r-cran-magrittr (2.0.3-1) ... 258s Selecting previously unselected package r-cran-matrix. 258s Preparing to unpack .../65-r-cran-matrix_1.7-3-1_s390x.deb ... 258s Unpacking r-cran-matrix (1.7-3-1) ... 258s Selecting previously unselected package r-cran-pkgconfig. 258s Preparing to unpack .../66-r-cran-pkgconfig_2.0.3-2build1_all.deb ... 258s Unpacking r-cran-pkgconfig (2.0.3-2build1) ... 258s Selecting previously unselected package r-cran-vctrs. 258s Preparing to unpack .../67-r-cran-vctrs_0.6.5-1_s390x.deb ... 258s Unpacking r-cran-vctrs (0.6.5-1) ... 258s Selecting previously unselected package r-cran-igraph. 258s Preparing to unpack .../68-r-cran-igraph_2.1.4-1_s390x.deb ... 258s Unpacking r-cran-igraph (2.1.4-1) ... 258s Selecting previously unselected package r-cran-quadprog. 258s Preparing to unpack .../69-r-cran-quadprog_1.5-8-1build1_s390x.deb ... 258s Unpacking r-cran-quadprog (1.5-8-1build1) ... 258s Selecting previously unselected package r-cran-phangorn. 258s Preparing to unpack .../70-r-cran-phangorn_2.12.1+dfsg-1_s390x.deb ... 258s Unpacking r-cran-phangorn (2.12.1+dfsg-1) ... 258s Setting up libgraphite2-3:s390x (1.3.14-2ubuntu1) ... 258s Setting up libpixman-1-0:s390x (0.44.0-3) ... 258s Setting up libsharpyuv0:s390x (1.5.0-0.1) ... 258s Setting up libxrender1:s390x (1:0.9.10-1.1build1) ... 258s Setting up libdatrie1:s390x (0.2.13-3build1) ... 258s Setting up libxcb-render0:s390x (1.17.0-2) ... 258s Setting up unzip (6.0-28ubuntu6) ... 258s Setting up x11-common (1:7.7+23ubuntu3) ... 259s Setting up libdeflate0:s390x (1.23-1) ... 259s Setting up libxcb-shm0:s390x (1.17.0-2) ... 259s Setting up libgomp1:s390x (15-20250222-0ubuntu1) ... 259s Setting up libjbig0:s390x (2.1-6.1ubuntu2) ... 259s Setting up zip (3.0-14ubuntu2) ... 259s Setting up libblas3:s390x (3.12.1-2) ... 259s 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 259s Setting up libfreetype6:s390x (2.13.3+dfsg-1) ... 259s Setting up fonts-dejavu-mono (2.37-8) ... 259s Setting up libtcl8.6:s390x (8.6.16+dfsg-1) ... 259s Setting up fonts-dejavu-core (2.37-8) ... 259s Setting up libjpeg-turbo8:s390x (2.1.5-3ubuntu2) ... 259s Setting up libltdl7:s390x (2.5.4-4) ... 259s Setting up libgfortran5:s390x (15-20250222-0ubuntu1) ... 259s Setting up libwebp7:s390x (1.5.0-0.1) ... 259s Setting up libsuitesparseconfig7:s390x (1:7.8.3+dfsg-3) ... 259s Setting up libharfbuzz0b:s390x (10.2.0-1) ... 259s Setting up libthai-data (0.1.29-2build1) ... 259s Setting up libxss1:s390x (1:1.2.3-1build3) ... 259s Setting up libpaper2:s390x (2.2.5-0.3) ... 259s Setting up xdg-utils (1.2.1-2ubuntu1) ... 259s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode 259s Setting up libjpeg8:s390x (8c-2ubuntu11) ... 259s Setting up libice6:s390x (2:1.1.1-1) ... 259s Setting up liblapack3:s390x (3.12.1-2) ... 259s 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 259s Setting up libamd3:s390x (1:7.8.3+dfsg-3) ... 259s Setting up libcolamd3:s390x (1:7.8.3+dfsg-3) ... 259s Setting up fontconfig-config (2.15.0-2ubuntu1) ... 259s Setting up libpaper-utils (2.2.5-0.3) ... 259s Setting up libthai0:s390x (0.1.29-2build1) ... 259s Setting up libglpk40:s390x (5.0-1build2) ... 259s Setting up libtiff6:s390x (4.5.1+git230720-4ubuntu4) ... 259s Setting up libfontconfig1:s390x (2.15.0-2ubuntu1) ... 259s Setting up libsm6:s390x (2:1.2.4-1) ... 259s Setting up fontconfig (2.15.0-2ubuntu1) ... 261s Regenerating fonts cache... done. 261s Setting up libxft2:s390x (2.3.6-1build1) ... 261s Setting up libtk8.6:s390x (8.6.16-1) ... 261s Setting up libpango-1.0-0:s390x (1.56.2-1) ... 261s Setting up libcairo2:s390x (1.18.2-2) ... 261s Setting up libxt6t64:s390x (1:1.2.1-1.2build1) ... 261s Setting up libpangoft2-1.0-0:s390x (1.56.2-1) ... 261s Setting up libpangocairo-1.0-0:s390x (1.56.2-1) ... 261s Setting up r-base-core (4.4.3-1) ... 261s Creating config file /etc/R/Renviron with new version 261s Setting up r-cran-fastmatch (1.1-6-1) ... 261s Setting up r-cran-lattice (0.22-6-1) ... 261s Setting up r-cran-nlme (3.1.167-1) ... 261s Setting up r-cran-pkgkitten (0.2.4-1) ... 261s Setting up r-cran-magrittr (2.0.3-1) ... 261s Setting up r-cran-quadprog (1.5-8-1build1) ... 261s Setting up r-cran-littler (0.3.20-2) ... 261s Setting up r-cran-rcpp (1.0.14-1) ... 261s Setting up r-cran-rlang (1.1.5-1) ... 261s Setting up littler (0.3.20-2) ... 261s Setting up r-cran-generics (0.1.3-1) ... 261s Setting up r-cran-digest (0.6.37-1) ... 261s Setting up r-cran-ape (5.8-1-1) ... 261s Setting up r-cran-glue (1.8.0-1) ... 261s Setting up r-cran-cli (3.6.4-1) ... 261s Setting up r-cran-lifecycle (1.0.4+dfsg-1) ... 261s Setting up r-cran-pkgconfig (2.0.3-2build1) ... 261s Setting up r-cran-cpp11 (0.5.2-1) ... 261s Setting up r-cran-matrix (1.7-3-1) ... 261s Setting up r-cran-vctrs (0.6.5-1) ... 261s Setting up r-cran-igraph (2.1.4-1) ... 261s Setting up r-cran-phangorn (2.12.1+dfsg-1) ... 261s Processing triggers for libc-bin (2.41-1ubuntu2) ... 261s Processing triggers for man-db (2.13.0-1) ... 262s Processing triggers for install-info (7.1.1-1) ... 263s autopkgtest [17:55:59]: test run-unit-test: [----------------------- 263s 263s R version 4.4.3 (2025-02-28) -- "Trophy Case" 263s Copyright (C) 2025 The R Foundation for Statistical Computing 263s Platform: s390x-ibm-linux-gnu 263s 263s R is free software and comes with ABSOLUTELY NO WARRANTY. 263s You are welcome to redistribute it under certain conditions. 263s Type 'license()' or 'licence()' for distribution details. 263s 263s R is a collaborative project with many contributors. 263s Type 'contributors()' for more information and 263s 'citation()' on how to cite R or R packages in publications. 263s 263s Type 'demo()' for some demos, 'help()' for on-line help, or 263s 'help.start()' for an HTML browser interface to help. 263s Type 'q()' to quit R. 263s 263s > Stangle("DrawingPhylogenies.Rnw") 263s Writing to file DrawingPhylogenies.R 263s > source("DrawingPhylogenies.R", echo=TRUE) 263s 263s > options(width = 80, prompt = "> ") 263s 263s > library(ape) 263s 263s > mytr <- read.tree(text = "((Pan:5,Homo:5):2,Gorilla:7);") 263s 263s > foo <- function() { 263s + col <- "green" 263s + for (i in 1:2) axis(i, col = col, col.ticks = col, col.axis = col, 263s + las = 1) 263s + box(lty .... [TRUNCATED] 263s 263s > layout(matrix(1:4, 2, 2, byrow = TRUE)) 264s 264s > plot(mytr) 264s 264s > foo() 264s 264s > plot(mytr, "c", FALSE) 264s 264s > foo() 264s 264s > plot(mytr, "u") 264s 264s > foo() 264s 264s > par(xpd = TRUE) 264s 264s > plot(mytr, "f") 264s 264s > foo() 264s 264s > box("outer") 264s 264s > tr <- compute.brlen(stree(8, "l"), 0.1) 264s 264s > tr$tip.label[] <- "" 264s 264s > foo <- function() { 264s + col <- "green" 264s + axis(1, col = col, col.ticks = col, col.axis = col) 264s + axis(2, col = col, col.ticks = col, col.axi .... [TRUNCATED] 264s 264s > layout(matrix(1:12, 6, 2)) 264s 264s > par(mar = c(2, 2, 0.3, 0)) 264s 264s > for (type in c("p", "c")) { 264s + plot(tr, type) 264s + foo() 264s + plot(tr, type, node.pos = 2) 264s + foo() 264s + plot(tr, type, FALSE) 264s + foo() 264s .... [TRUNCATED] 264s 264s > foo <- function() { 264s + col <- "green" 264s + for (i in 1:2) axis(i, col = col, col.ticks = col, col.axis = col, 264s + las = 1) 264s + box(lty .... [TRUNCATED] 264s 264s > layout(matrix(1:4, 2, 2)) 264s 264s > par(las = 1) 264s 264s > plot(tr, "u") 264s 264s > foo() 264s 264s > plot(tr, "u", FALSE) 264s 264s > foo() 264s 264s > plot(tr, "f") 264s 264s > foo() 264s 264s > plot(tr, "f", FALSE) 264s 264s > foo() 264s 264s > args(node.depth.edgelength) 264s function (phy) 264s NULL 264s 264s > args(node.depth) 264s function (phy, method = 1) 264s NULL 264s 264s > args(node.height) 264s function (phy, clado.style = FALSE) 264s NULL 264s 264s > args(unrooted.xy) 264s function (Ntip, Nnode, edge, edge.length, nb.sp, rotate.tree) 264s NULL 264s 264s > args(phylogram.plot) 264s function (edge, Ntip, Nnode, xx, yy, horizontal, edge.color = NULL, 264s edge.width = NULL, edge.lty = NULL, node.color = NULL, node.width = NULL, 264s node.lty = NULL) 264s NULL 264s 264s > args(cladogram.plot) 264s function (edge, xx, yy, edge.color, edge.width, edge.lty) 264s NULL 264s 264s > args(circular.plot) 264s function (edge, Ntip, Nnode, xx, yy, theta, r, edge.color, edge.width, 264s edge.lty) 264s NULL 264s 264s > args(plot.phylo) 264s function (x, type = "phylogram", use.edge.length = TRUE, node.pos = NULL, 264s show.tip.label = TRUE, show.node.label = FALSE, edge.color = NULL, 264s edge.width = NULL, edge.lty = NULL, node.color = NULL, node.width = NULL, 264s node.lty = NULL, font = 3, cex = par("cex"), adj = NULL, 264s srt = 0, no.margin = FALSE, root.edge = FALSE, label.offset = 0, 264s underscore = FALSE, x.lim = NULL, y.lim = NULL, direction = "rightwards", 264s lab4ut = NULL, tip.color = par("col"), plot = TRUE, rotate.tree = 0, 264s open.angle = 0, node.depth = 1, align.tip.label = FALSE, 264s ...) 264s NULL 264s 264s > geo <- factor(c("Africa", "World", "Africa")) 264s 264s > (mycol <- c("blue", "red")[geo]) 264s [1] "blue" "red" "blue" 264s 264s > plot(mytr, tip.color = mycol) 264s 264s > par(xpd = TRUE) 264s 264s > plot(mytr, tip.color = mycol, cex = c(1, 1, 1.5)) 264s 264s > args(def) 264s function (x, ..., default = NULL, regexp = FALSE) 264s NULL 264s 264s > mycol2 <- def(mytr$tip.label, Homo = "red", default = "blue") 264s 264s > identical(mycol, mycol2) 264s [1] TRUE 264s 264s > (i <- which.edge(mytr, c("Homo", "Pan"))) 264s [1] 2 3 264s 264s > co <- rep("black", Nedge(mytr)) 264s 264s > co[i] <- "blue" 264s 264s > par(xpd = TRUE) 264s 264s > plot(mytr, edge.col = co) 264s 264s > edgelabels() 264s 264s > args(axisPhylo) 264s function (side = NULL, root.time = NULL, backward = TRUE, ...) 264s NULL 264s 264s > args(add.scale.bar) 264s function (x, y, length = NULL, ask = FALSE, lwd = 1, lcol = "black", 264s ...) 264s NULL 264s 264s > plot(mytr) 264s 264s > add.scale.bar() 264s 264s > axisPhylo() 264s 264s > axis(3) 264s 264s > args(nodelabels) 264s function (text, node, adj = c(0.5, 0.5), frame = "rect", pch = NULL, 264s thermo = NULL, pie = NULL, piecol = NULL, col = "black", 264s bg = "lightblue", horiz = FALSE, width = NULL, height = NULL, 264s ...) 264s NULL 264s 264s > args(tiplabels) 264s function (text, tip, adj = c(0.5, 0.5), frame = "rect", pch = NULL, 264s thermo = NULL, pie = NULL, piecol = NULL, col = "black", 264s bg = "yellow", horiz = FALSE, width = NULL, height = NULL, 264s offset = 0, ...) 264s NULL 264s 264s > args(edgelabels) 264s function (text, edge, adj = c(0.5, 0.5), frame = "rect", pch = NULL, 264s thermo = NULL, pie = NULL, piecol = NULL, col = "black", 264s bg = "lightgreen", horiz = FALSE, width = NULL, height = NULL, 264s date = NULL, ...) 264s NULL 264s 264s > par(xpd = TRUE) 264s 264s > plot(mytr) 264s 264s > nodelabels() 264s 264s > tiplabels() 264s 264s > edgelabels() 264s 264s > plot(rep(1:5, 5), rep(1:5, each = 5), pch = 1:25, 264s + xlim = c(1, 5.2), col = "blue", bg = "yellow", cex = 2) 264s 264s > text(rep(1:5, 5) + 0.2, rep(1:5, each = 5), 1:25) 264s 264s > v <- c(0, 0.5, 1) 264s 264s > layout(matrix(1:9, 3, 3)) 264s 264s > par(mar = c(3, 3, 3, 0), las = 1) 264s 264s > for (i in v) { 264s + for (j in v) { 264s + plot(0, 0, "n", main = paste0("adj = c(", i, ", ", j, 264s + ")")) 264s + abline(v = 0, h = .... [TRUNCATED] 264s 264s > plot(rep(0, 3), 0:2, "n", las = 1) 264s 264s > abline(v = 0, h = 0:2, lty = 3) 264s 264s > text(0, 0:2, mytr$tip.label, adj = -1) 264s 264s > text(0, 0:2, mytr$tip.label, adj = 2, font = 2) 264s 264s > args(phydataplot) 264s function (x, phy, style = "bars", offset = 1, scaling = 1, continuous = FALSE, 264s width = NULL, legend = "below", funcol = rainbow, ...) 264s NULL 264s 264s > args(ring) 264s function (x, phy, style = "ring", offset = 1, ...) 264s NULL 264s 264s > x <- matrix(1:6, 3, 10) 264s 264s > dimnames(x) <- list(c("Homo", "Gorilla", "Pan"), LETTERS[1:ncol(x)]) 264s 264s > x 264s A B C D E F G H I J 264s Homo 1 4 1 4 1 4 1 4 1 4 264s Gorilla 2 5 2 5 2 5 2 5 2 5 264s Pan 3 6 3 6 3 6 3 6 3 6 264s 264s > mytr$tip.label 264s [1] "Pan" "Homo" "Gorilla" 264s 264s > par(mar = c(10, 2, 5, 5)) 264s 264s > plot(mytr, x.lim = 30) 264s 264s > phydataplot(x, mytr, "m", border = "white", offset = 2, 264s + width = 1) 264s 264s > phydataplot(x, mytr, "m", border = "white", offset = 15, 264s + width = 1, continuous = 2) 264s 264s > n <- 100 264s 264s > p <- 3 264s 264s > set.seed(3) 264s 264s > tr <- rcoal(n) 264s 264s > x <- matrix(runif(p * n), n, p) 264s 264s > rownames(x) <- tr$tip.label 264s 264s > COL <- c("red", "green", "blue") 264s 264s > par(xpd = TRUE) 264s 264s > plot(tr, "f", x.lim = c(-5, 5), show.tip.label = FALSE, 264s + no.margin = TRUE) 264s 264s > for (j in 1:p) ring(x[, j], tr, offset = j - 1 + 0.1, 264s + col = COL[j]) 264s 264s > tree <- rtree(10) 264s 264s > tree$edge.length[1] <- 1000 264s 264s > layout(matrix(1:2, 1)) 264s 264s > plot(tree) 264s 264s > axisPhylo() 264s 264s > plotBreakLongEdges(tree) 264s 264s > axisPhylo() 264s 264s > el <- tree$edge.length 264s 264s > sum(el > mean(el) + 2 * sd(el)) 264s [1] 1 264s 264s > tree$edge.length[8] <- 1000 264s 264s > el <- tree$edge.length 264s 264s > sum(el > mean(el) + 2 * sd(el)) 264s [1] 2 264s 264s > layout(matrix(1:2, 1)) 264s 264s > plotBreakLongEdges(tree) 264s 264s > plotBreakLongEdges(tree, n = 2) 264s 264s > TR <- replicate(10, rcoal(sample(11:20, size = 1)), 264s + simplify = FALSE) 264s 264s > kronoviz(TR, type = "c", show.tip.label = FALSE) 264s 264s > dates <- as.Date(.leap.seconds) 264s 264s > tr <- rcoal(length(dates)) 264s 264s > plotTreeTime(tr, dates) 264s 264s > par(oma = rep(2, 4)) 264s 264s > plot(mytr) 264s 264s > box(lty = 3) 264s 264s > box("figure", col = "blue") 264s 264s > for (i in 1:4) mtext("Outer margin", i, 0.5, outer = TRUE, 264s + font = 2, col = "blue") 264s 264s > box("outer") 264s 264s > layout(matrix(1:4, 2, 2)) 264s 264s > par(oma = rep(2, 4)) 264s 264s > for (i in 1:4) { 264s + par(mar = rep(i, 4)) 264s + plot(mytr) 264s + box(lty = 3) 264s + box("figure", col = "blue") 264s + } 264s 264s > for (i in 1:4) mtext("Outer margin", i, 0.5, outer = TRUE, 264s + font = 2, col = "blue") 264s 264s > box("outer") 264s 264s > layout(matrix(c(1, 2, 1, 3), 2, 2)) 264s 264s > for (i in 1:3) plot(rtree(5)) 264s 264s > (pp <- get("last_plot.phylo", envir = .PlotPhyloEnv)) 264s $type 264s [1] "phylogram" 264s 264s $use.edge.length 264s [1] TRUE 264s 264s $node.pos 264s [1] 1 264s 264s $node.depth 264s [1] 1 264s 264s $show.tip.label 264s [1] TRUE 264s 264s $show.node.label 264s [1] FALSE 264s 264s $font 264s [1] 3 264s 264s $cex 264s [1] 0.83 264s 264s $adj 264s [1] 0 264s 264s $srt 264s [1] 0 264s 264s $no.margin 264s [1] FALSE 264s 264s $label.offset 264s [1] 0 264s 264s $x.lim 264s [1] 0.00000 3.13046 264s 264s $y.lim 264s [1] 1 5 264s 264s $direction 264s [1] "rightwards" 264s 264s $tip.color 264s [1] "black" 264s 264s $Ntip 264s [1] 5 264s 264s $Nnode 264s [1] 4 264s 264s $root.time 264s NULL 264s 264s $align.tip.label 264s [1] FALSE 264s 264s $edge 264s [,1] [,2] 264s [1,] 6 1 264s [2,] 6 7 264s [3,] 7 2 264s [4,] 7 8 264s [5,] 8 3 264s [6,] 8 9 264s [7,] 9 4 264s [8,] 9 5 264s 264s $xx 264s [1] 0.3967457 1.7260289 2.2158455 2.9728029 2.8310192 0.0000000 0.8134181 264s [8] 1.3631198 1.9857132 264s 264s $yy 264s [1] 1.0000 2.0000 3.0000 4.0000 5.0000 1.9375 2.8750 3.7500 4.5000 264s 264s 264s > layout(matrix(1:2, 2)) 264s 264s > plot(rtree(4)) 264s 264s > pp <- get("last_plot.phylo", envir = .PlotPhyloEnv) 264s 264s > x <- pp$xx[1] 264s 264s > y <- pp$yy[1] 264s 264s > (pu <- par("usr")) 264s [1] -0.06364557 1.65478492 0.88000000 4.12000000 264s 264s > (x - pu[1])/(pu[2] - pu[1]) 264s [1] 0.9349839 264s 264s > (y - pu[3])/(pu[4] - pu[3]) 264s [1] 0.03703704 264s 264s > pi <- par("pin") 264s 264s > mi <- par("mai") 264s 264s > xi1 <- (x - pu[1])/(pu[2] - pu[1]) * pi[1] + mi[2] 264s 264s > yi1 <- (y - pu[3])/(pu[4] - pu[3]) * pi[2] + mi[1] 264s 264s > plot(rtree(4)) 264s 264s > pp <- get("last_plot.phylo", envir = .PlotPhyloEnv) 264s 264s > x <- pp$xx[5] 264s 264s > y <- pp$yy[5] 264s 264s > pu <- par("usr") 264s 264s > pi <- par("pin") 264s 264s > mi <- par("mai") 264s 264s > xi2 <- (x - pu[1])/(pu[2] - pu[1]) * pi[1] + mi[2] 264s 264s > yi2 <- (y - pu[3])/(pu[4] - pu[3]) * pi[2] + mi[1] 264s 264s > yi1 <- yi1 + par("fin")[2] 264s 264s > di <- par("din") 264s 264s > layout(1) 264s 264s > par(new = TRUE, mai = rep(0, 4)) 264s 264s > plot(NA, type = "n", ann = FALSE, axes = FALSE, xlim = 0:1, 264s + ylim = 0:1, xaxs = "i", yaxs = "i") 264s 264s > fancyarrows(xi1/di[1], yi1/di[2], xi2/di[1], yi2/di[2], 264s + 1, lwd = 10, col = rgb(1, 0.5, 0, 0.5), type = "h") 264s 264s > foo <- function(phy1, phy2, from) { 264s + layout(matrix(1:2, 2)) 264s + plot(phy1, font = 1) 264s + pp <- get("last_plot.phylo", envir = .PlotPhyloEnv .... [TRUNCATED] 264s 264s > trb <- read.tree(text = "((Primates,Carnivora),Monotremata);") 264s 264s > par(xpd = TRUE) 264s 264s > foo(trb, mytr, "Primates") 264s 264s > plot(mytr, plot = FALSE) 264s 264s > pp <- get("last_plot.phylo", envir = .PlotPhyloEnv) 264s 264s > rect(pp$xx[5] - 0.1, pp$yy[1] - 0.1, pp$xx[1] + 2, 264s + pp$yy[2] + 0.1, col = "yellow", border = NA) 264s 264s > par(new = TRUE) 264s 264s > plot(mytr) 264s > 264s 264s R version 4.4.3 (2025-02-28) -- "Trophy Case" 264s Copyright (C) 2025 The R Foundation for Statistical Computing 264s Platform: s390x-ibm-linux-gnu 264s 264s R is free software and comes with ABSOLUTELY NO WARRANTY. 264s You are welcome to redistribute it under certain conditions. 264s Type 'license()' or 'licence()' for distribution details. 264s 264s R is a collaborative project with many contributors. 264s Type 'contributors()' for more information and 264s 'citation()' on how to cite R or R packages in publications. 264s 264s Type 'demo()' for some demos, 'help()' for on-line help, or 264s 'help.start()' for an HTML browser interface to help. 264s Type 'q()' to quit R. 264s 264s > Stangle("MoranI.Rnw") 264s Writing to file MoranI.R 264s > source("MoranI.R", echo=TRUE) 264s 264s > options(width = 80, prompt = "> ") 264s 264s > body <- c(4.09434, 3.61092, 2.37024, 2.02815, -1.46968) 264s 264s > longevity <- c(4.74493, 3.3322, 3.3673, 2.89037, 2.30259) 264s 264s > names(body) <- names(longevity) <- c("Homo", "Pongo", 264s + "Macaca", "Ateles", "Galago") 264s 264s > library(ape) 264s 264s > trnwk <- "((((Homo:0.21,Pongo:0.21):0.28,Macaca:0.49):0.13,Ateles:0.62)" 264s 264s > trnwk[2] <- ":0.38,Galago:1.00);" 264s 264s > tr <- read.tree(text = trnwk) 264s 264s > plot(tr) 264s 264s > axisPhylo() 264s 264s > w <- 1/cophenetic(tr) 264s 264s > w 264s Homo Pongo Macaca Ateles Galago 264s Homo Inf 2.3809524 1.0204082 0.8064516 0.5 264s Pongo 2.3809524 Inf 1.0204082 0.8064516 0.5 264s Macaca 1.0204082 1.0204082 Inf 0.8064516 0.5 264s Ateles 0.8064516 0.8064516 0.8064516 Inf 0.5 264s Galago 0.5000000 0.5000000 0.5000000 0.5000000 Inf 264s 264s > diag(w) <- 0 264s 264s > Moran.I(body, w) 264s $observed 264s [1] -0.07312179 264s 264s $expected 264s [1] -0.25 264s 264s $sd 264s [1] 0.08910814 264s 264s $p.value 264s [1] 0.04714628 264s 264s 264s > Moran.I(body, w, alt = "greater") 264s $observed 264s [1] -0.07312179 264s 264s $expected 264s [1] -0.25 264s 264s $sd 264s [1] 0.08910814 264s 264s $p.value 264s [1] 0.02357314 264s 264s 264s > Moran.I(longevity, w) 264s $observed 264s [1] -0.1837739 264s 264s $expected 264s [1] -0.25 264s 264s $sd 264s [1] 0.09114549 264s 264s $p.value 264s [1] 0.4674727 264s 264s 264s > data(carnivora) 264s 264s > carnivora$log10SW <- log10(carnivora$SW) 264s 264s > carnivora$log10FW <- log10(carnivora$FW) 264s 264s > fm1.carn <- log10SW ~ Order/SuperFamily/Family/Genus 264s 264s > co1 <- correlogram.formula(fm1.carn, data = carnivora) 264s 264s > plot(co1) 264s 264s > fm2.carn <- log10SW + log10FW ~ Order/SuperFamily/Family/Genus 264s 264s > co2 <- correlogram.formula(fm2.carn, data = carnivora) 264s 264s > print(plot(co2)) 264s 264s > plot(co2, FALSE) 264s > 264s 264s R version 4.4.3 (2025-02-28) -- "Trophy Case" 264s Copyright (C) 2025 The R Foundation for Statistical Computing 264s Platform: s390x-ibm-linux-gnu 264s 264s R is free software and comes with ABSOLUTELY NO WARRANTY. 264s You are welcome to redistribute it under certain conditions. 264s Type 'license()' or 'licence()' for distribution details. 264s 264s R is a collaborative project with many contributors. 264s Type 'contributors()' for more information and 264s 'citation()' on how to cite R or R packages in publications. 264s 264s Type 'demo()' for some demos, 'help()' for on-line help, or 264s 'help.start()' for an HTML browser interface to help. 264s Type 'q()' to quit R. 264s 265s > Stangle("RandomTopologies.Rnw") 265s Writing to file RandomTopologies.R 265s > source("RandomTopologies.R", echo=TRUE) 265s 265s > options(width = 80, prompt = "> ") 265s 265s > library(ape) 265s 265s > n <- 1:10 265s 265s > data.frame(N.topo = sapply(n, howmanytrees)) 265s N.topo 265s 1 1 265s 2 1 265s 3 3 265s 4 15 265s 5 105 265s 6 945 265s 7 10395 265s 8 135135 265s 9 2027025 265s 10 34459425 265s 265s > howmanytrees(25) 265s [1] 1.192568e+30 265s 265s > howmanytrees(25) * 0.21 265s [1] 2.504393e+29 265s 265s > data.frame(N.topo = sapply(n, howmanytrees, labeled = FALSE)) 265s N.topo 265s 1 1 265s 2 1 265s 3 1 265s 4 2 265s 5 3 265s 6 6 265s 7 11 265s 8 23 265s 9 46 265s 10 98 265s 265s > n2 <- c(50, 100, 200) 265s 265s > data.frame(N.topo = sapply(n2, howmanytrees, labeled = FALSE), 265s + row.names = n2) 265s N.topo 265s 50 5.150149e+16 265s 100 1.019560e+36 265s 200 1.141703e+75 265s 265s > 1/howmanytrees(50) 265s [1] 3.632505e-77 265s 265s > 1/sapply(n, howmanytrees) 265s [1] 1.000000e+00 1.000000e+00 3.333333e-01 6.666667e-02 9.523810e-03 265s [6] 1.058201e-03 9.620010e-05 7.400007e-06 4.933338e-07 2.901964e-08 265s 265s > 1/sapply(n, howmanytrees, labeled = FALSE) 265s [1] 1.00000000 1.00000000 1.00000000 0.50000000 0.33333333 0.16666667 265s [7] 0.09090909 0.04347826 0.02173913 0.01020408 265s 265s > library(phangorn) 266s code for methods in class "Rcpp_Fitch" was not checked for suspicious field assignments (recommended package 'codetools' not available?) 266s code for methods in class "Rcpp_Fitch" was not checked for suspicious field assignments (recommended package 'codetools' not available?) 266s 266s > TR <- allTrees(4, rooted = TRUE) 266s 266s > TR 266s 15 phylogenetic trees 266s 266s > layout(matrix(1:15, 3, 5)) 266s 266s > par(mar = rep(1.5, 4), xpd = TRUE) 266s 266s > for (i in 1:15) plot(TR[[i]], "c", cex = 1.2, font = 1) 266s 266s > K <- 100 266s 266s > n <- 50 266s 266s > N <- howmanytrees(n, labeled = FALSE) 266s 266s > p <- 1/N 266s 266s > 1 - (dbinom(0, K, p) + dbinom(1, K, p)) 266s [1] 0 266s 266s > 1 - dbinom(0, K, p) - dbinom(1, K, p) 266s [1] -5.431212e-17 266s 266s > f <- function(n, K) { 266s + N <- howmanytrees(n, labeled = FALSE) 266s + p <- 1/N 266s + 1 - (dbinom(0, K, p) + dbinom(1, K, p)) 266s + } 266s 266s > DF <- expand.grid(n = 4:20, K = c(2, 5, 10, 100, 1000, 266s + 10000)) 266s 266s > DF$P <- mapply(f, n = DF$n, K = DF$K) 266s 266s > library(lattice) 266s 266s > xyplot(P ~ n, DF, groups = K, panel = panel.superpose, 266s + type = "b", auto.key = list(x = 0.8, y = 0.9, title = "K")) 266s 266s > subset(DF, n == 20) 266s n K P 266s 17 20 2 1.160494e-11 266s 34 20 5 1.160491e-10 266s 51 20 10 5.222149e-10 266s 68 20 100 5.743191e-08 266s 85 20 1000 5.783570e-06 266s 102 20 10000 5.671842e-04 266s 266s > f(20, 1e+05) 266s [1] 0.04638755 266s 266s > f(30, 1e+06) 266s [1] 2.525152e-07 266s 266s > txt <- c("((,),((,),));", "(((,),(,)),);", "((((,),),),);") 266s 266s > TR5 <- read.tree(text = txt) 266s 266s > layout(matrix(1:3, 1)) 266s 266s > for (i in 1:3) plot(TR5[[i]], "c", cex = 1.2, main = LETTERS[i]) 266s 266s > howmanytrees(1, labeled = FALSE) * howmanytrees(4, 266s + labeled = FALSE) 266s [1] 2 266s 266s > howmanytrees(2, labeled = FALSE) * howmanytrees(3, 266s + labeled = FALSE) 266s [1] 1 266s 266s > howmanytrees(400, labeled = FALSE) * howmanytrees(403, 266s + labeled = FALSE) 266s [1] Inf 266s 266s > TR <- list(rmtopology(1000, 4, TRUE, br = NULL), rmtree(1000, 266s + 4, TRUE, br = NULL), rmtree(1000, 4, TRUE, br = NULL, equiprob = TRUE)) 267s 267s > foo.test <- function(x, labeled = TRUE) { 267s + uTR <- unique(x, use.tip.label = labeled) 267s + f <- integer(length(uTR)) 267s + for (j in seq_along( .... [TRUNCATED] 267s 267s > lapply(TR, foo.test) 271s [1] 69 71 60 65 74 64 56 78 61 60 71 61 78 58 74 274s [1] 110 106 50 48 52 54 64 52 73 67 70 50 49 103 52 277s [1] 163 42 168 173 42 52 42 37 41 46 42 44 38 31 39 277s [[1]] 277s 277s Chi-squared test for given probabilities 277s 277s data: f 277s X-squared = 11.39, df = 14, p-value = 0.6552 277s 277s 277s [[2]] 277s 277s Chi-squared test for given probabilities 277s 277s data: f 277s X-squared = 102.38, df = 14, p-value = 1.656e-15 277s 277s 277s [[3]] 277s 277s Chi-squared test for given probabilities 277s 277s data: f 277s X-squared = 582.65, df = 14, p-value < 2.2e-16 277s 277s 277s 277s > lapply(TR, foo.test, labeled = FALSE) 278s [1] 809 191 278s [1] 319 681 279s [1] 504 496 279s [[1]] 279s 279s Chi-squared test for given probabilities 279s 279s data: f 279s X-squared = 381.92, df = 1, p-value < 2.2e-16 279s 279s 279s [[2]] 279s 279s Chi-squared test for given probabilities 279s 279s data: f 279s X-squared = 131.04, df = 1, p-value < 2.2e-16 279s 279s 279s [[3]] 279s 279s Chi-squared test for given probabilities 279s 279s data: f 279s X-squared = 0.064, df = 1, p-value = 0.8003 279s 279s 279s 279s > .Machine$double.xmax 279s [1] 1.797693e+308 279s 279s > howmanytrees(151) 279s [1] 3.753274e+306 279s 279s > howmanytrees(792, labeled = FALSE) 279s [1] 1.029038e+308 279s 279s > (N <- howmanytrees(2e+06)) 279s approximately 3.692364 * 10^12335524 279s 279s > N[2] + 1 279s n 279s 12335525 279s 279s > ceiling((N[2] + 1)/3000) 279s n 279s 4112 279s 279s > n <- 1:792 279s 279s > N <- howmanytrees(792, labeled = FALSE, detail = TRUE) 279s 279s > lN <- log10(N) 279s 279s > summary(lm(lN ~ n)) 279s 279s Call: 279s lm(formula = lN ~ n) 279s 279s Residuals: 279s Min 1Q Median 3Q Max 279s -0.25968 -0.21424 -0.08311 0.12406 2.82605 279s 279s Coefficients: 279s Estimate Std. Error t value Pr(>|t|) 279s (Intercept) -3.219e+00 2.258e-02 -142.5 <2e-16 *** 279s n 3.926e-01 4.934e-05 7956.3 <2e-16 *** 279s --- 279s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 279s 279s Residual standard error: 0.3175 on 790 degrees of freedom 279s Multiple R-squared: 1, Adjusted R-squared: 1 279s F-statistic: 6.33e+07 on 1 and 790 DF, p-value: < 2.2e-16 279s 279s 279s > s <- n > 700 279s 279s > summary(lm(lN[s] ~ n[s])) 279s 279s Call: 279s lm(formula = lN[s] ~ n[s]) 279s 279s Residuals: 279s Min 1Q Median 3Q Max 279s -0.0004133 -0.0003323 -0.0001032 0.0002834 0.0008197 279s 279s Coefficients: 279s Estimate Std. Error t value Pr(>|t|) 279s (Intercept) -4.153e+00 1.096e-03 -3788 <2e-16 *** 279s n[s] 3.941e-01 1.468e-06 268567 <2e-16 *** 279s --- 279s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 279s 279s Residual standard error: 0.0003738 on 90 degrees of freedom 279s Multiple R-squared: 1, Adjusted R-squared: 1 279s F-statistic: 7.213e+10 on 1 and 90 DF, p-value: < 2.2e-16 279s 279s 279s > n <- 788:792 279s 279s > log10(sapply(n, howmanytrees, labeled = FALSE)) 279s [1] 306.4356 306.8298 307.2240 307.6182 308.0124 279s 279s > 0.3941 * n - 4.153 279s [1] 306.3978 306.7919 307.1860 307.5801 307.9742 279s 279s > xi <- 2.477993 279s 279s > lxi <- log10(xi) 279s 279s > n <- 1000 279s 279s > (n - 1) * lxi 279s [1] 393.706 279s 279s > for (k in 2:11) print((n - k) * lxi + log10(sum(xi^(0:(k - 279s + 1))))) 279s [1] 393.8532 279s [1] 393.9009 279s [1] 393.9187 279s [1] 393.9257 279s [1] 393.9285 279s [1] 393.9296 279s [1] 393.9301 279s [1] 393.9303 279s [1] 393.9304 279s [1] 393.9304 279s > 279s autopkgtest [17:56:15]: test run-unit-test: -----------------------] 280s autopkgtest [17:56:16]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 280s run-unit-test PASS 280s autopkgtest [17:56:16]: test pkg-r-autopkgtest: preparing testbed 280s Reading package lists... 281s Building dependency tree... 281s Reading state information... 281s Starting pkgProblemResolver with broken count: 0 281s Starting 2 pkgProblemResolver with broken count: 0 281s Done 281s The following NEW packages will be installed: 281s build-essential cpp cpp-14 cpp-14-s390x-linux-gnu cpp-s390x-linux-gnu 281s dctrl-tools g++ g++-14 g++-14-s390x-linux-gnu g++-s390x-linux-gnu gcc gcc-14 281s gcc-14-s390x-linux-gnu gcc-s390x-linux-gnu gfortran gfortran-14 281s gfortran-14-s390x-linux-gnu gfortran-s390x-linux-gnu icu-devtools libasan8 281s libblas-dev libbz2-dev libcc1-0 libdeflate-dev libgcc-14-dev 281s libgfortran-14-dev libicu-dev libisl23 libitm1 libjpeg-dev 281s libjpeg-turbo8-dev libjpeg8-dev libjs-jquery liblapack-dev liblzma-dev 281s libmpc3 libncurses-dev libpcre2-16-0 libpcre2-32-0 libpcre2-dev 281s libpcre2-posix3 libpkgconf3 libpng-dev libreadline-dev libstdc++-14-dev 281s libtirpc-dev libubsan1 node-html5shiv pkg-r-autopkgtest pkgconf pkgconf-bin 281s r-base-dev r-cran-expm r-cran-gee r-cran-xml2 zlib1g-dev 281s 0 upgraded, 56 newly installed, 0 to remove and 0 not upgraded. 281s Need to get 83.3 MB of archives. 281s After this operation, 281 MB of additional disk space will be used. 281s Get:1 http://ftpmaster.internal/ubuntu plucky/main s390x libisl23 s390x 0.27-1 [704 kB] 282s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x libmpc3 s390x 1.3.1-1build2 [57.8 kB] 282s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x cpp-14-s390x-linux-gnu s390x 14.2.0-17ubuntu3 [9572 kB] 291s Get:4 http://ftpmaster.internal/ubuntu plucky/main s390x cpp-14 s390x 14.2.0-17ubuntu3 [1028 B] 291s Get:5 http://ftpmaster.internal/ubuntu plucky/main s390x cpp-s390x-linux-gnu s390x 4:14.2.0-1ubuntu1 [5556 B] 291s Get:6 http://ftpmaster.internal/ubuntu plucky/main s390x cpp s390x 4:14.2.0-1ubuntu1 [22.4 kB] 291s Get:7 http://ftpmaster.internal/ubuntu plucky/main s390x libcc1-0 s390x 15-20250222-0ubuntu1 [49.2 kB] 291s Get:8 http://ftpmaster.internal/ubuntu plucky/main s390x libitm1 s390x 15-20250222-0ubuntu1 [31.2 kB] 291s Get:9 http://ftpmaster.internal/ubuntu plucky/main s390x libasan8 s390x 15-20250222-0ubuntu1 [2970 kB] 294s Get:10 http://ftpmaster.internal/ubuntu plucky/main s390x libubsan1 s390x 15-20250222-0ubuntu1 [1212 kB] 296s Get:11 http://ftpmaster.internal/ubuntu plucky/main s390x libgcc-14-dev s390x 14.2.0-17ubuntu3 [1037 kB] 297s Get:12 http://ftpmaster.internal/ubuntu plucky/main s390x gcc-14-s390x-linux-gnu s390x 14.2.0-17ubuntu3 [18.7 MB] 316s Get:13 http://ftpmaster.internal/ubuntu plucky/main s390x gcc-14 s390x 14.2.0-17ubuntu3 [526 kB] 316s Get:14 http://ftpmaster.internal/ubuntu plucky/main s390x gcc-s390x-linux-gnu s390x 4:14.2.0-1ubuntu1 [1204 B] 316s Get:15 http://ftpmaster.internal/ubuntu plucky/main s390x gcc s390x 4:14.2.0-1ubuntu1 [5004 B] 316s Get:16 http://ftpmaster.internal/ubuntu plucky/main s390x libstdc++-14-dev s390x 14.2.0-17ubuntu3 [2611 kB] 319s Get:17 http://ftpmaster.internal/ubuntu plucky/main s390x g++-14-s390x-linux-gnu s390x 14.2.0-17ubuntu3 [11.0 MB] 330s Get:18 http://ftpmaster.internal/ubuntu plucky/main s390x g++-14 s390x 14.2.0-17ubuntu3 [21.8 kB] 330s Get:19 http://ftpmaster.internal/ubuntu plucky/main s390x g++-s390x-linux-gnu s390x 4:14.2.0-1ubuntu1 [956 B] 330s Get:20 http://ftpmaster.internal/ubuntu plucky/main s390x g++ s390x 4:14.2.0-1ubuntu1 [1080 B] 330s Get:21 http://ftpmaster.internal/ubuntu plucky/main s390x build-essential s390x 12.10ubuntu1 [4930 B] 330s Get:22 http://ftpmaster.internal/ubuntu plucky/main s390x dctrl-tools s390x 2.24-3build3 [106 kB] 330s Get:23 http://ftpmaster.internal/ubuntu plucky/main s390x libgfortran-14-dev s390x 14.2.0-17ubuntu3 [654 kB] 331s Get:24 http://ftpmaster.internal/ubuntu plucky/main s390x gfortran-14-s390x-linux-gnu s390x 14.2.0-17ubuntu3 [10.3 MB] 340s Get:25 http://ftpmaster.internal/ubuntu plucky/main s390x gfortran-14 s390x 14.2.0-17ubuntu3 [13.6 kB] 340s Get:26 http://ftpmaster.internal/ubuntu plucky/main s390x gfortran-s390x-linux-gnu s390x 4:14.2.0-1ubuntu1 [1012 B] 340s Get:27 http://ftpmaster.internal/ubuntu plucky/main s390x gfortran s390x 4:14.2.0-1ubuntu1 [1160 B] 340s Get:28 http://ftpmaster.internal/ubuntu plucky/main s390x icu-devtools s390x 76.1-1ubuntu2 [225 kB] 340s Get:29 http://ftpmaster.internal/ubuntu plucky/main s390x libblas-dev s390x 3.12.1-2 [254 kB] 340s Get:30 http://ftpmaster.internal/ubuntu plucky/main s390x libbz2-dev s390x 1.0.8-6 [39.1 kB] 340s Get:31 http://ftpmaster.internal/ubuntu plucky/main s390x libdeflate-dev s390x 1.23-1 [52.2 kB] 341s Get:32 http://ftpmaster.internal/ubuntu plucky/main s390x libicu-dev s390x 76.1-1ubuntu2 [12.2 MB] 351s Get:33 http://ftpmaster.internal/ubuntu plucky/main s390x libjpeg-turbo8-dev s390x 2.1.5-3ubuntu2 [281 kB] 352s Get:34 http://ftpmaster.internal/ubuntu plucky/main s390x libjpeg8-dev s390x 8c-2ubuntu11 [1484 B] 352s Get:35 http://ftpmaster.internal/ubuntu plucky/main s390x libjpeg-dev s390x 8c-2ubuntu11 [1484 B] 352s Get:36 http://ftpmaster.internal/ubuntu plucky/main s390x libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 352s Get:37 http://ftpmaster.internal/ubuntu plucky/main s390x liblapack-dev s390x 3.12.1-2 [5967 kB] 357s Get:38 http://ftpmaster.internal/ubuntu plucky/main s390x libncurses-dev s390x 6.5+20250216-2 [407 kB] 358s Get:39 http://ftpmaster.internal/ubuntu plucky/main s390x libpcre2-16-0 s390x 10.45-1 [259 kB] 358s Get:40 http://ftpmaster.internal/ubuntu plucky/main s390x libpcre2-32-0 s390x 10.45-1 [245 kB] 358s Get:41 http://ftpmaster.internal/ubuntu plucky/main s390x libpcre2-posix3 s390x 10.45-1 [7080 B] 358s Get:42 http://ftpmaster.internal/ubuntu plucky/main s390x libpcre2-dev s390x 10.45-1 [899 kB] 359s Get:43 http://ftpmaster.internal/ubuntu plucky/main s390x libpkgconf3 s390x 1.8.1-4 [31.2 kB] 359s Get:44 http://ftpmaster.internal/ubuntu plucky/main s390x zlib1g-dev s390x 1:1.3.dfsg+really1.3.1-1ubuntu1 [898 kB] 360s Get:45 http://ftpmaster.internal/ubuntu plucky/main s390x libpng-dev s390x 1.6.47-1 [278 kB] 360s Get:46 http://ftpmaster.internal/ubuntu plucky/main s390x libreadline-dev s390x 8.2-6 [187 kB] 360s Get:47 http://ftpmaster.internal/ubuntu plucky/universe s390x node-html5shiv all 3.7.3+dfsg-5 [13.5 kB] 360s Get:48 http://ftpmaster.internal/ubuntu plucky/main s390x liblzma-dev s390x 5.6.4-1 [183 kB] 360s Get:49 http://ftpmaster.internal/ubuntu plucky/main s390x pkgconf-bin s390x 1.8.1-4 [21.5 kB] 360s Get:50 http://ftpmaster.internal/ubuntu plucky/main s390x pkgconf s390x 1.8.1-4 [16.7 kB] 360s Get:51 http://ftpmaster.internal/ubuntu plucky/main s390x libtirpc-dev s390x 1.3.4+ds-1.3 [196 kB] 360s Get:52 http://ftpmaster.internal/ubuntu plucky/universe s390x r-base-dev all 4.4.3-1 [4176 B] 360s Get:53 http://ftpmaster.internal/ubuntu plucky/universe s390x pkg-r-autopkgtest all 20231212ubuntu1 [6448 B] 360s Get:54 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-expm s390x 1.0-0-1 [229 kB] 361s Get:55 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-gee s390x 4.13-29-1 [78.1 kB] 361s Get:56 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-xml2 s390x 1.3.7-1 [328 kB] 361s Fetched 83.3 MB in 1min 20s (1040 kB/s) 361s Selecting previously unselected package libisl23:s390x. 361s (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 ... 61392 files and directories currently installed.) 361s Preparing to unpack .../00-libisl23_0.27-1_s390x.deb ... 361s Unpacking libisl23:s390x (0.27-1) ... 361s Selecting previously unselected package libmpc3:s390x. 361s Preparing to unpack .../01-libmpc3_1.3.1-1build2_s390x.deb ... 361s Unpacking libmpc3:s390x (1.3.1-1build2) ... 361s Selecting previously unselected package cpp-14-s390x-linux-gnu. 361s Preparing to unpack .../02-cpp-14-s390x-linux-gnu_14.2.0-17ubuntu3_s390x.deb ... 361s Unpacking cpp-14-s390x-linux-gnu (14.2.0-17ubuntu3) ... 362s Selecting previously unselected package cpp-14. 362s Preparing to unpack .../03-cpp-14_14.2.0-17ubuntu3_s390x.deb ... 362s Unpacking cpp-14 (14.2.0-17ubuntu3) ... 362s Selecting previously unselected package cpp-s390x-linux-gnu. 362s Preparing to unpack .../04-cpp-s390x-linux-gnu_4%3a14.2.0-1ubuntu1_s390x.deb ... 362s Unpacking cpp-s390x-linux-gnu (4:14.2.0-1ubuntu1) ... 362s Selecting previously unselected package cpp. 362s Preparing to unpack .../05-cpp_4%3a14.2.0-1ubuntu1_s390x.deb ... 362s Unpacking cpp (4:14.2.0-1ubuntu1) ... 362s Selecting previously unselected package libcc1-0:s390x. 362s Preparing to unpack .../06-libcc1-0_15-20250222-0ubuntu1_s390x.deb ... 362s Unpacking libcc1-0:s390x (15-20250222-0ubuntu1) ... 362s Selecting previously unselected package libitm1:s390x. 362s Preparing to unpack .../07-libitm1_15-20250222-0ubuntu1_s390x.deb ... 362s Unpacking libitm1:s390x (15-20250222-0ubuntu1) ... 362s Selecting previously unselected package libasan8:s390x. 362s Preparing to unpack .../08-libasan8_15-20250222-0ubuntu1_s390x.deb ... 362s Unpacking libasan8:s390x (15-20250222-0ubuntu1) ... 362s Selecting previously unselected package libubsan1:s390x. 362s Preparing to unpack .../09-libubsan1_15-20250222-0ubuntu1_s390x.deb ... 362s Unpacking libubsan1:s390x (15-20250222-0ubuntu1) ... 362s Selecting previously unselected package libgcc-14-dev:s390x. 362s Preparing to unpack .../10-libgcc-14-dev_14.2.0-17ubuntu3_s390x.deb ... 362s Unpacking libgcc-14-dev:s390x (14.2.0-17ubuntu3) ... 362s Selecting previously unselected package gcc-14-s390x-linux-gnu. 362s Preparing to unpack .../11-gcc-14-s390x-linux-gnu_14.2.0-17ubuntu3_s390x.deb ... 362s Unpacking gcc-14-s390x-linux-gnu (14.2.0-17ubuntu3) ... 362s Selecting previously unselected package gcc-14. 362s Preparing to unpack .../12-gcc-14_14.2.0-17ubuntu3_s390x.deb ... 362s Unpacking gcc-14 (14.2.0-17ubuntu3) ... 362s Selecting previously unselected package gcc-s390x-linux-gnu. 362s Preparing to unpack .../13-gcc-s390x-linux-gnu_4%3a14.2.0-1ubuntu1_s390x.deb ... 362s Unpacking gcc-s390x-linux-gnu (4:14.2.0-1ubuntu1) ... 362s Selecting previously unselected package gcc. 362s Preparing to unpack .../14-gcc_4%3a14.2.0-1ubuntu1_s390x.deb ... 362s Unpacking gcc (4:14.2.0-1ubuntu1) ... 362s Selecting previously unselected package libstdc++-14-dev:s390x. 362s Preparing to unpack .../15-libstdc++-14-dev_14.2.0-17ubuntu3_s390x.deb ... 362s Unpacking libstdc++-14-dev:s390x (14.2.0-17ubuntu3) ... 362s Selecting previously unselected package g++-14-s390x-linux-gnu. 362s Preparing to unpack .../16-g++-14-s390x-linux-gnu_14.2.0-17ubuntu3_s390x.deb ... 362s Unpacking g++-14-s390x-linux-gnu (14.2.0-17ubuntu3) ... 362s Selecting previously unselected package g++-14. 362s Preparing to unpack .../17-g++-14_14.2.0-17ubuntu3_s390x.deb ... 362s Unpacking g++-14 (14.2.0-17ubuntu3) ... 362s Selecting previously unselected package g++-s390x-linux-gnu. 362s Preparing to unpack .../18-g++-s390x-linux-gnu_4%3a14.2.0-1ubuntu1_s390x.deb ... 362s Unpacking g++-s390x-linux-gnu (4:14.2.0-1ubuntu1) ... 362s Selecting previously unselected package g++. 362s Preparing to unpack .../19-g++_4%3a14.2.0-1ubuntu1_s390x.deb ... 362s Unpacking g++ (4:14.2.0-1ubuntu1) ... 362s Selecting previously unselected package build-essential. 362s Preparing to unpack .../20-build-essential_12.10ubuntu1_s390x.deb ... 362s Unpacking build-essential (12.10ubuntu1) ... 362s Selecting previously unselected package dctrl-tools. 362s Preparing to unpack .../21-dctrl-tools_2.24-3build3_s390x.deb ... 362s Unpacking dctrl-tools (2.24-3build3) ... 362s Selecting previously unselected package libgfortran-14-dev:s390x. 362s Preparing to unpack .../22-libgfortran-14-dev_14.2.0-17ubuntu3_s390x.deb ... 362s Unpacking libgfortran-14-dev:s390x (14.2.0-17ubuntu3) ... 362s Selecting previously unselected package gfortran-14-s390x-linux-gnu. 362s Preparing to unpack .../23-gfortran-14-s390x-linux-gnu_14.2.0-17ubuntu3_s390x.deb ... 362s Unpacking gfortran-14-s390x-linux-gnu (14.2.0-17ubuntu3) ... 363s Selecting previously unselected package gfortran-14. 363s Preparing to unpack .../24-gfortran-14_14.2.0-17ubuntu3_s390x.deb ... 363s Unpacking gfortran-14 (14.2.0-17ubuntu3) ... 363s Selecting previously unselected package gfortran-s390x-linux-gnu. 363s Preparing to unpack .../25-gfortran-s390x-linux-gnu_4%3a14.2.0-1ubuntu1_s390x.deb ... 363s Unpacking gfortran-s390x-linux-gnu (4:14.2.0-1ubuntu1) ... 363s Selecting previously unselected package gfortran. 363s Preparing to unpack .../26-gfortran_4%3a14.2.0-1ubuntu1_s390x.deb ... 363s Unpacking gfortran (4:14.2.0-1ubuntu1) ... 363s Selecting previously unselected package icu-devtools. 363s Preparing to unpack .../27-icu-devtools_76.1-1ubuntu2_s390x.deb ... 363s Unpacking icu-devtools (76.1-1ubuntu2) ... 363s Selecting previously unselected package libblas-dev:s390x. 363s Preparing to unpack .../28-libblas-dev_3.12.1-2_s390x.deb ... 363s Unpacking libblas-dev:s390x (3.12.1-2) ... 363s Selecting previously unselected package libbz2-dev:s390x. 363s Preparing to unpack .../29-libbz2-dev_1.0.8-6_s390x.deb ... 363s Unpacking libbz2-dev:s390x (1.0.8-6) ... 363s Selecting previously unselected package libdeflate-dev:s390x. 363s Preparing to unpack .../30-libdeflate-dev_1.23-1_s390x.deb ... 363s Unpacking libdeflate-dev:s390x (1.23-1) ... 363s Selecting previously unselected package libicu-dev:s390x. 363s Preparing to unpack .../31-libicu-dev_76.1-1ubuntu2_s390x.deb ... 363s Unpacking libicu-dev:s390x (76.1-1ubuntu2) ... 363s Selecting previously unselected package libjpeg-turbo8-dev:s390x. 363s Preparing to unpack .../32-libjpeg-turbo8-dev_2.1.5-3ubuntu2_s390x.deb ... 363s Unpacking libjpeg-turbo8-dev:s390x (2.1.5-3ubuntu2) ... 363s Selecting previously unselected package libjpeg8-dev:s390x. 363s Preparing to unpack .../33-libjpeg8-dev_8c-2ubuntu11_s390x.deb ... 363s Unpacking libjpeg8-dev:s390x (8c-2ubuntu11) ... 363s Selecting previously unselected package libjpeg-dev:s390x. 363s Preparing to unpack .../34-libjpeg-dev_8c-2ubuntu11_s390x.deb ... 363s Unpacking libjpeg-dev:s390x (8c-2ubuntu11) ... 363s Selecting previously unselected package libjs-jquery. 363s Preparing to unpack .../35-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 363s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 363s Selecting previously unselected package liblapack-dev:s390x. 363s Preparing to unpack .../36-liblapack-dev_3.12.1-2_s390x.deb ... 363s Unpacking liblapack-dev:s390x (3.12.1-2) ... 363s Selecting previously unselected package libncurses-dev:s390x. 363s Preparing to unpack .../37-libncurses-dev_6.5+20250216-2_s390x.deb ... 363s Unpacking libncurses-dev:s390x (6.5+20250216-2) ... 363s Selecting previously unselected package libpcre2-16-0:s390x. 363s Preparing to unpack .../38-libpcre2-16-0_10.45-1_s390x.deb ... 363s Unpacking libpcre2-16-0:s390x (10.45-1) ... 363s Selecting previously unselected package libpcre2-32-0:s390x. 363s Preparing to unpack .../39-libpcre2-32-0_10.45-1_s390x.deb ... 363s Unpacking libpcre2-32-0:s390x (10.45-1) ... 363s Selecting previously unselected package libpcre2-posix3:s390x. 363s Preparing to unpack .../40-libpcre2-posix3_10.45-1_s390x.deb ... 363s Unpacking libpcre2-posix3:s390x (10.45-1) ... 363s Selecting previously unselected package libpcre2-dev:s390x. 363s Preparing to unpack .../41-libpcre2-dev_10.45-1_s390x.deb ... 363s Unpacking libpcre2-dev:s390x (10.45-1) ... 363s Selecting previously unselected package libpkgconf3:s390x. 363s Preparing to unpack .../42-libpkgconf3_1.8.1-4_s390x.deb ... 363s Unpacking libpkgconf3:s390x (1.8.1-4) ... 363s Selecting previously unselected package zlib1g-dev:s390x. 363s Preparing to unpack .../43-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1ubuntu1_s390x.deb ... 363s Unpacking zlib1g-dev:s390x (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 363s Selecting previously unselected package libpng-dev:s390x. 363s Preparing to unpack .../44-libpng-dev_1.6.47-1_s390x.deb ... 363s Unpacking libpng-dev:s390x (1.6.47-1) ... 363s Selecting previously unselected package libreadline-dev:s390x. 363s Preparing to unpack .../45-libreadline-dev_8.2-6_s390x.deb ... 363s Unpacking libreadline-dev:s390x (8.2-6) ... 363s Selecting previously unselected package node-html5shiv. 363s Preparing to unpack .../46-node-html5shiv_3.7.3+dfsg-5_all.deb ... 363s Unpacking node-html5shiv (3.7.3+dfsg-5) ... 363s Selecting previously unselected package liblzma-dev:s390x. 363s Preparing to unpack .../47-liblzma-dev_5.6.4-1_s390x.deb ... 363s Unpacking liblzma-dev:s390x (5.6.4-1) ... 363s Selecting previously unselected package pkgconf-bin. 363s Preparing to unpack .../48-pkgconf-bin_1.8.1-4_s390x.deb ... 363s Unpacking pkgconf-bin (1.8.1-4) ... 363s Selecting previously unselected package pkgconf:s390x. 363s Preparing to unpack .../49-pkgconf_1.8.1-4_s390x.deb ... 363s Unpacking pkgconf:s390x (1.8.1-4) ... 363s Selecting previously unselected package libtirpc-dev:s390x. 363s Preparing to unpack .../50-libtirpc-dev_1.3.4+ds-1.3_s390x.deb ... 363s Unpacking libtirpc-dev:s390x (1.3.4+ds-1.3) ... 363s Selecting previously unselected package r-base-dev. 363s Preparing to unpack .../51-r-base-dev_4.4.3-1_all.deb ... 363s Unpacking r-base-dev (4.4.3-1) ... 363s Selecting previously unselected package pkg-r-autopkgtest. 363s Preparing to unpack .../52-pkg-r-autopkgtest_20231212ubuntu1_all.deb ... 363s Unpacking pkg-r-autopkgtest (20231212ubuntu1) ... 363s Selecting previously unselected package r-cran-expm. 363s Preparing to unpack .../53-r-cran-expm_1.0-0-1_s390x.deb ... 363s Unpacking r-cran-expm (1.0-0-1) ... 363s Selecting previously unselected package r-cran-gee. 363s Preparing to unpack .../54-r-cran-gee_4.13-29-1_s390x.deb ... 363s Unpacking r-cran-gee (4.13-29-1) ... 363s Selecting previously unselected package r-cran-xml2. 363s Preparing to unpack .../55-r-cran-xml2_1.3.7-1_s390x.deb ... 363s Unpacking r-cran-xml2 (1.3.7-1) ... 363s Setting up libjpeg-turbo8-dev:s390x (2.1.5-3ubuntu2) ... 363s Setting up libncurses-dev:s390x (6.5+20250216-2) ... 363s Setting up node-html5shiv (3.7.3+dfsg-5) ... 363s Setting up r-cran-expm (1.0-0-1) ... 363s Setting up libreadline-dev:s390x (8.2-6) ... 363s Setting up libpcre2-16-0:s390x (10.45-1) ... 363s Setting up libpcre2-32-0:s390x (10.45-1) ... 363s Setting up libtirpc-dev:s390x (1.3.4+ds-1.3) ... 363s Setting up libpkgconf3:s390x (1.8.1-4) ... 363s Setting up libmpc3:s390x (1.3.1-1build2) ... 363s Setting up icu-devtools (76.1-1ubuntu2) ... 363s Setting up pkgconf-bin (1.8.1-4) ... 363s Setting up liblzma-dev:s390x (5.6.4-1) ... 363s Setting up libubsan1:s390x (15-20250222-0ubuntu1) ... 363s Setting up zlib1g-dev:s390x (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 363s Setting up libpcre2-posix3:s390x (10.45-1) ... 363s Setting up libasan8:s390x (15-20250222-0ubuntu1) ... 363s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 363s Setting up libjpeg8-dev:s390x (8c-2ubuntu11) ... 363s Setting up r-cran-gee (4.13-29-1) ... 363s Setting up libisl23:s390x (0.27-1) ... 363s Setting up libdeflate-dev:s390x (1.23-1) ... 363s Setting up libicu-dev:s390x (76.1-1ubuntu2) ... 363s Setting up libcc1-0:s390x (15-20250222-0ubuntu1) ... 363s Setting up libblas-dev:s390x (3.12.1-2) ... 363s 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 363s Setting up dctrl-tools (2.24-3build3) ... 363s Setting up libitm1:s390x (15-20250222-0ubuntu1) ... 363s Setting up libbz2-dev:s390x (1.0.8-6) ... 363s Setting up libpcre2-dev:s390x (10.45-1) ... 363s Setting up r-cran-xml2 (1.3.7-1) ... 363s Setting up libpng-dev:s390x (1.6.47-1) ... 363s Setting up libjpeg-dev:s390x (8c-2ubuntu11) ... 363s Setting up pkgconf:s390x (1.8.1-4) ... 363s Setting up liblapack-dev:s390x (3.12.1-2) ... 363s 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 363s Setting up cpp-14-s390x-linux-gnu (14.2.0-17ubuntu3) ... 363s Setting up cpp-14 (14.2.0-17ubuntu3) ... 363s Setting up libgcc-14-dev:s390x (14.2.0-17ubuntu3) ... 363s Setting up libstdc++-14-dev:s390x (14.2.0-17ubuntu3) ... 363s Setting up libgfortran-14-dev:s390x (14.2.0-17ubuntu3) ... 363s Setting up cpp-s390x-linux-gnu (4:14.2.0-1ubuntu1) ... 363s Setting up gcc-14-s390x-linux-gnu (14.2.0-17ubuntu3) ... 363s Setting up gcc-s390x-linux-gnu (4:14.2.0-1ubuntu1) ... 363s Setting up g++-14-s390x-linux-gnu (14.2.0-17ubuntu3) ... 363s Setting up cpp (4:14.2.0-1ubuntu1) ... 363s Setting up gfortran-14-s390x-linux-gnu (14.2.0-17ubuntu3) ... 363s Setting up g++-s390x-linux-gnu (4:14.2.0-1ubuntu1) ... 363s Setting up gcc-14 (14.2.0-17ubuntu3) ... 363s Setting up g++-14 (14.2.0-17ubuntu3) ... 363s Setting up gfortran-14 (14.2.0-17ubuntu3) ... 363s Setting up gfortran-s390x-linux-gnu (4:14.2.0-1ubuntu1) ... 363s Setting up gcc (4:14.2.0-1ubuntu1) ... 363s Setting up g++ (4:14.2.0-1ubuntu1) ... 363s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 363s Setting up build-essential (12.10ubuntu1) ... 363s Setting up gfortran (4:14.2.0-1ubuntu1) ... 363s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode 363s 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 363s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode 363s 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 363s Setting up r-base-dev (4.4.3-1) ... 363s Setting up pkg-r-autopkgtest (20231212ubuntu1) ... 363s Processing triggers for libc-bin (2.41-1ubuntu2) ... 363s Processing triggers for man-db (2.13.0-1) ... 364s Processing triggers for install-info (7.1.1-1) ... 365s autopkgtest [17:57:41]: test pkg-r-autopkgtest: /usr/share/dh-r/pkg-r-autopkgtest 365s autopkgtest [17:57:41]: test pkg-r-autopkgtest: [----------------------- 365s Test: Try to load the R library ape 365s 365s R version 4.4.3 (2025-02-28) -- "Trophy Case" 365s Copyright (C) 2025 The R Foundation for Statistical Computing 365s Platform: s390x-ibm-linux-gnu 365s 365s R is free software and comes with ABSOLUTELY NO WARRANTY. 365s You are welcome to redistribute it under certain conditions. 365s Type 'license()' or 'licence()' for distribution details. 365s 365s R is a collaborative project with many contributors. 365s Type 'contributors()' for more information and 365s 'citation()' on how to cite R or R packages in publications. 365s 365s Type 'demo()' for some demos, 'help()' for on-line help, or 365s 'help.start()' for an HTML browser interface to help. 365s Type 'q()' to quit R. 365s 365s > library('ape') 366s > 366s > 366s Other tests are currently unsupported! 366s They will be progressively added. 366s autopkgtest [17:57:42]: test pkg-r-autopkgtest: -----------------------] 366s pkg-r-autopkgtest PASS 366s autopkgtest [17:57:42]: test pkg-r-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 367s autopkgtest [17:57:43]: @@@@@@@@@@@@@@@@@@@@ summary 367s run-unit-test PASS 367s pkg-r-autopkgtest PASS 383s nova [W] Using flock in prodstack6-s390x 383s flock: timeout while waiting to get lock 383s Creating nova instance adt-plucky-s390x-r-cran-ape-20250315-175136-juju-7f2275-prod-proposed-migration-environment-20-a2005986-0c56-43b8-b641-ca9867251466 from image adt/ubuntu-plucky-s390x-server-20250315.img (UUID 3d3557fa-fd0f-4bba-9b89-8d5964e09f61)... 383s nova [W] Timed out waiting for df7d0cf3-1b89-45cc-8cbb-c9b115ef1e03 to get deleted.