0s autopkgtest [23:18:52]: starting date and time: 2026-02-09 23:18:52+0000 0s autopkgtest [23:18:52]: git checkout: 508d4a25 a-v-ssh wait_for_ssh: demote "ssh connection failed" to a debug message 0s autopkgtest [23:18:52]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.pnymc19f/out --timeout-copy=6000 --setup-commands 'ln -s /dev/null /etc/systemd/system/bluetooth.service; printf "http_proxy=http://squid.internal:3128\nhttps_proxy=http://squid.internal:3128\nno_proxy=127.0.0.1,127.0.1.1,localhost,localdomain,internal,login.ubuntu.com,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com\n" >> /etc/environment' --apt-pocket=proposed=src:r-cran-ggplot2 --apt-upgrade r-cran-etm --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=r-cran-ggplot2/4.0.2+dfsg-1 -- lxd -r lxd-armhf-10.145.243.210 lxd-armhf-10.145.243.210:autopkgtest/ubuntu/resolute/armhf 23s autopkgtest [23:19:15]: testbed dpkg architecture: armhf 25s autopkgtest [23:19:17]: testbed apt version: 3.1.15 30s autopkgtest [23:19:22]: @@@@@@@@@@@@@@@@@@@@ test bed setup 32s autopkgtest [23:19:24]: testbed release detected to be: None 39s autopkgtest [23:19:31]: updating testbed package index (apt update) 42s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 43s Get:2 http://ftpmaster.internal/ubuntu resolute InRelease [124 kB] 43s Get:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease [124 kB] 43s Get:4 http://ftpmaster.internal/ubuntu resolute-security InRelease [124 kB] 44s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [1645 kB] 47s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [29.4 kB] 47s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [176 kB] 48s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf Packages [246 kB] 48s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/universe armhf Packages [1405 kB] 52s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse armhf Packages [7452 B] 52s Get:11 http://ftpmaster.internal/ubuntu resolute/restricted Sources [15.1 kB] 52s Get:12 http://ftpmaster.internal/ubuntu resolute/universe Sources [21.4 MB] 89s Get:13 http://ftpmaster.internal/ubuntu resolute/main Sources [1398 kB] 91s Get:14 http://ftpmaster.internal/ubuntu resolute/main armhf Packages [1374 kB] 94s Get:15 http://ftpmaster.internal/ubuntu resolute/universe armhf Packages [15.3 MB] 123s Fetched 43.5 MB in 1min 21s (536 kB/s) 124s Reading package lists... 130s autopkgtest [23:21:02]: upgrading testbed (apt dist-upgrade and autopurge) 132s Reading package lists... 132s Building dependency tree... 132s Reading state information... 132s Calculating upgrade... 133s The following packages will be upgraded: 133s cryptsetup-bin dracut-install iproute2 iptables libcryptsetup12 libip4tc2 133s libip6tc2 libxtables12 wget 133s 9 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 133s Need to get 2407 kB of archives. 133s After this operation, 152 kB of additional disk space will be used. 133s Get:1 http://ftpmaster.internal/ubuntu resolute/main armhf iptables armhf 1.8.11-2ubuntu3 [345 kB] 134s Get:2 http://ftpmaster.internal/ubuntu resolute/main armhf libip4tc2 armhf 1.8.11-2ubuntu3 [22.0 kB] 134s Get:3 http://ftpmaster.internal/ubuntu resolute/main armhf libip6tc2 armhf 1.8.11-2ubuntu3 [22.3 kB] 134s Get:4 http://ftpmaster.internal/ubuntu resolute/main armhf libxtables12 armhf 1.8.11-2ubuntu3 [33.5 kB] 134s Get:5 http://ftpmaster.internal/ubuntu resolute/main armhf iproute2 armhf 6.18.0-1ubuntu1 [1123 kB] 135s Get:6 http://ftpmaster.internal/ubuntu resolute/main armhf libcryptsetup12 armhf 2:2.8.0-1ubuntu3 [254 kB] 136s Get:7 http://ftpmaster.internal/ubuntu resolute/main armhf wget armhf 1.25.0-2ubuntu4 [327 kB] 136s Get:8 http://ftpmaster.internal/ubuntu resolute/main armhf cryptsetup-bin armhf 2:2.8.0-1ubuntu3 [232 kB] 137s Get:9 http://ftpmaster.internal/ubuntu resolute/main armhf dracut-install armhf 109-11ubuntu1 [47.9 kB] 137s Preconfiguring packages ... 137s Fetched 2407 kB in 4s (598 kB/s) 137s (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 ... 68683 files and directories currently installed.) 137s Preparing to unpack .../0-iptables_1.8.11-2ubuntu3_armhf.deb ... 137s Unpacking iptables (1.8.11-2ubuntu3) over (1.8.11-2ubuntu2) ... 137s Preparing to unpack .../1-libip4tc2_1.8.11-2ubuntu3_armhf.deb ... 137s Unpacking libip4tc2:armhf (1.8.11-2ubuntu3) over (1.8.11-2ubuntu2) ... 137s Preparing to unpack .../2-libip6tc2_1.8.11-2ubuntu3_armhf.deb ... 137s Unpacking libip6tc2:armhf (1.8.11-2ubuntu3) over (1.8.11-2ubuntu2) ... 137s Preparing to unpack .../3-libxtables12_1.8.11-2ubuntu3_armhf.deb ... 137s Unpacking libxtables12:armhf (1.8.11-2ubuntu3) over (1.8.11-2ubuntu2) ... 137s Preparing to unpack .../4-iproute2_6.18.0-1ubuntu1_armhf.deb ... 138s Unpacking iproute2 (6.18.0-1ubuntu1) over (6.16.0-1ubuntu3) ... 138s Preparing to unpack .../5-libcryptsetup12_2%3a2.8.0-1ubuntu3_armhf.deb ... 138s Unpacking libcryptsetup12:armhf (2:2.8.0-1ubuntu3) over (2:2.8.0-1ubuntu2) ... 138s Preparing to unpack .../6-wget_1.25.0-2ubuntu4_armhf.deb ... 138s Unpacking wget (1.25.0-2ubuntu4) over (1.25.0-2ubuntu3) ... 138s Preparing to unpack .../7-cryptsetup-bin_2%3a2.8.0-1ubuntu3_armhf.deb ... 138s Unpacking cryptsetup-bin (2:2.8.0-1ubuntu3) over (2:2.8.0-1ubuntu2) ... 138s Preparing to unpack .../8-dracut-install_109-11ubuntu1_armhf.deb ... 138s Unpacking dracut-install (109-11ubuntu1) over (109-9ubuntu1) ... 138s Setting up libip4tc2:armhf (1.8.11-2ubuntu3) ... 138s Setting up wget (1.25.0-2ubuntu4) ... 138s Setting up libip6tc2:armhf (1.8.11-2ubuntu3) ... 138s Setting up libxtables12:armhf (1.8.11-2ubuntu3) ... 138s Setting up dracut-install (109-11ubuntu1) ... 138s Setting up libcryptsetup12:armhf (2:2.8.0-1ubuntu3) ... 138s Setting up cryptsetup-bin (2:2.8.0-1ubuntu3) ... 138s Setting up iptables (1.8.11-2ubuntu3) ... 138s Setting up iproute2 (6.18.0-1ubuntu1) ... 138s Processing triggers for man-db (2.13.1-1build1) ... 139s Processing triggers for install-info (7.2-5) ... 139s Processing triggers for libc-bin (2.42-2ubuntu4) ... 142s Reading package lists... 142s Building dependency tree... 142s Reading state information... 142s Solving dependencies... 142s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 144s autopkgtest [23:21:16]: rebooting testbed after setup commands that affected boot 195s autopkgtest [23:22:07]: testbed running kernel: Linux 6.8.0-87-generic #88~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Tue Oct 14 14:00:09 UTC 2 225s autopkgtest [23:22:37]: @@@@@@@@@@@@@@@@@@@@ apt-source r-cran-etm 236s Get:1 http://ftpmaster.internal/ubuntu resolute/universe r-cran-etm 1.1.1-1build1 (dsc) [2147 B] 236s Get:2 http://ftpmaster.internal/ubuntu resolute/universe r-cran-etm 1.1.1-1build1 (tar) [242 kB] 236s Get:3 http://ftpmaster.internal/ubuntu resolute/universe r-cran-etm 1.1.1-1build1 (diff) [3672 B] 237s gpgv: Signature made Fri Nov 28 21:46:53 2025 UTC 237s gpgv: using RSA key 92FE4F8B40CADC4ECCD60C1F5961FDBE9C619809 237s gpgv: Can't check signature: No public key 237s dpkg-source: warning: cannot verify inline signature for ./r-cran-etm_1.1.1-1build1.dsc: no acceptable signature found 237s autopkgtest [23:22:49]: testing package r-cran-etm version 1.1.1-1build1 239s autopkgtest [23:22:51]: build not needed 243s autopkgtest [23:22:55]: test run-unit-test: preparing testbed 245s Reading package lists... 245s Building dependency tree... 245s Reading state information... 245s Solving dependencies... 246s The following NEW packages will be installed: 246s fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono libblas3 246s libcairo2 libdatrie1 libdeflate0 libfontconfig1 libfreetype6 libgfortran5 246s libgomp1 libgraphite2-3 libharfbuzz0b libice6 libjbig0 libjpeg-turbo8 246s libjpeg8 liblapack3 liblerc4 libpango-1.0-0 libpangocairo-1.0-0 246s libpangoft2-1.0-0 libpaper-utils libpaper2 libpixman-1-0 libsharpyuv0 libsm6 246s libtcl8.6 libthai-data libthai0 libtiff6 libtk8.6 libwebp7 libxcb-render0 246s libxcb-shm0 libxft2 libxrender1 libxss1 libxt6t64 r-base-core 246s r-cran-data.table r-cran-dbi r-cran-etm r-cran-kmi r-cran-lattice 246s r-cran-littler r-cran-matrix r-cran-mitools r-cran-pkgkitten r-cran-rcpp 246s r-cran-rcpparmadillo r-cran-survival unzip x11-common xdg-utils zip 246s 0 upgraded, 57 newly installed, 0 to remove and 0 not upgraded. 246s Need to get 58.6 MB of archives. 246s After this operation, 116 MB of additional disk space will be used. 246s Get:1 http://ftpmaster.internal/ubuntu resolute/main armhf libfreetype6 armhf 2.14.1+dfsg-2 [345 kB] 247s Get:2 http://ftpmaster.internal/ubuntu resolute/main armhf fonts-dejavu-mono all 2.37-8build1 [502 kB] 248s Get:3 http://ftpmaster.internal/ubuntu resolute/main armhf fonts-dejavu-core all 2.37-8build1 [834 kB] 250s Get:4 http://ftpmaster.internal/ubuntu resolute/main armhf fontconfig-config armhf 2.17.1-3ubuntu1 [38.5 kB] 250s Get:5 http://ftpmaster.internal/ubuntu resolute/main armhf libfontconfig1 armhf 2.17.1-3ubuntu1 [117 kB] 250s Get:6 http://ftpmaster.internal/ubuntu resolute/main armhf fontconfig armhf 2.17.1-3ubuntu1 [180 kB] 251s Get:7 http://ftpmaster.internal/ubuntu resolute/main armhf libblas3 armhf 3.12.1-7ubuntu1 [133 kB] 251s Get:8 http://ftpmaster.internal/ubuntu resolute/main armhf libpixman-1-0 armhf 0.46.4-1 [196 kB] 252s Get:9 http://ftpmaster.internal/ubuntu resolute/main armhf libxcb-render0 armhf 1.17.0-2ubuntu1 [15.5 kB] 252s Get:10 http://ftpmaster.internal/ubuntu resolute/main armhf libxcb-shm0 armhf 1.17.0-2ubuntu1 [5956 B] 252s Get:11 http://ftpmaster.internal/ubuntu resolute/main armhf libxrender1 armhf 1:0.9.12-1 [16.6 kB] 252s Get:12 http://ftpmaster.internal/ubuntu resolute/main armhf libcairo2 armhf 1.18.4-3 [489 kB] 253s Get:13 http://ftpmaster.internal/ubuntu resolute/main armhf libdatrie1 armhf 0.2.14-1 [16.4 kB] 253s Get:14 http://ftpmaster.internal/ubuntu resolute/main armhf libdeflate0 armhf 1.23-2build1 [38.8 kB] 253s Get:15 http://ftpmaster.internal/ubuntu resolute/main armhf libgfortran5 armhf 15.2.0-12ubuntu1 [334 kB] 254s Get:16 http://ftpmaster.internal/ubuntu resolute/main armhf libgomp1 armhf 15.2.0-12ubuntu1 [129 kB] 255s Get:17 http://ftpmaster.internal/ubuntu resolute/main armhf libgraphite2-3 armhf 1.3.14-11ubuntu1 [65.2 kB] 255s Get:18 http://ftpmaster.internal/ubuntu resolute/main armhf libharfbuzz0b armhf 12.3.2-1 [501 kB] 256s Get:19 http://ftpmaster.internal/ubuntu resolute/main armhf x11-common all 1:7.7+24ubuntu1 [22.4 kB] 256s Get:20 http://ftpmaster.internal/ubuntu resolute/main armhf libice6 armhf 2:1.1.1-1build1 [37.5 kB] 256s Get:21 http://ftpmaster.internal/ubuntu resolute/main armhf libjpeg-turbo8 armhf 2.1.5-4ubuntu3 [129 kB] 256s Get:22 http://ftpmaster.internal/ubuntu resolute/main armhf libjpeg8 armhf 8c-2ubuntu11 [2148 B] 256s Get:23 http://ftpmaster.internal/ubuntu resolute/main armhf liblapack3 armhf 3.12.1-7ubuntu1 [2090 kB] 260s Get:24 http://ftpmaster.internal/ubuntu resolute/main armhf liblerc4 armhf 4.0.0+ds-5ubuntu2 [162 kB] 260s Get:25 http://ftpmaster.internal/ubuntu resolute/main armhf libthai-data all 0.1.30-1 [155 kB] 261s Get:26 http://ftpmaster.internal/ubuntu resolute/main armhf libthai0 armhf 0.1.30-1 [15.4 kB] 261s Get:27 http://ftpmaster.internal/ubuntu resolute/main armhf libpango-1.0-0 armhf 1.57.0-1 [218 kB] 261s Get:28 http://ftpmaster.internal/ubuntu resolute/main armhf libpangoft2-1.0-0 armhf 1.57.0-1 [45.2 kB] 261s Get:29 http://ftpmaster.internal/ubuntu resolute/main armhf libpangocairo-1.0-0 armhf 1.57.0-1 [25.3 kB] 261s Get:30 http://ftpmaster.internal/ubuntu resolute/main armhf libpaper2 armhf 2.2.5-0.3build1 [16.3 kB] 261s Get:31 http://ftpmaster.internal/ubuntu resolute/main armhf libpaper-utils armhf 2.2.5-0.3build1 [14.2 kB] 261s Get:32 http://ftpmaster.internal/ubuntu resolute/main armhf libsharpyuv0 armhf 1.5.0-0.1build1 [16.3 kB] 261s Get:33 http://ftpmaster.internal/ubuntu resolute/main armhf libsm6 armhf 2:1.2.6-1build1 [15.3 kB] 261s Get:34 http://ftpmaster.internal/ubuntu resolute/main armhf libtcl8.6 armhf 8.6.17+dfsg-1build1 [918 kB] 263s Get:35 http://ftpmaster.internal/ubuntu resolute/main armhf libjbig0 armhf 2.1-6.1ubuntu3 [25.3 kB] 263s Get:36 http://ftpmaster.internal/ubuntu resolute/main armhf libwebp7 armhf 1.5.0-0.1build1 [189 kB] 263s Get:37 http://ftpmaster.internal/ubuntu resolute/main armhf libtiff6 armhf 4.7.0-3ubuntu3 [188 kB] 264s Get:38 http://ftpmaster.internal/ubuntu resolute/main armhf libxft2 armhf 2.3.6-1build2 [37.2 kB] 264s Get:39 http://ftpmaster.internal/ubuntu resolute/main armhf libxss1 armhf 1:1.2.3-1build4 [6328 B] 264s Get:40 http://ftpmaster.internal/ubuntu resolute/main armhf libtk8.6 armhf 8.6.17-1 [694 kB] 265s Get:41 http://ftpmaster.internal/ubuntu resolute/main armhf libxt6t64 armhf 1:1.2.1-1.3 [145 kB] 265s Get:42 http://ftpmaster.internal/ubuntu resolute/main armhf zip armhf 3.0-15ubuntu3 [164 kB] 265s Get:43 http://ftpmaster.internal/ubuntu resolute/main armhf unzip armhf 6.0-29ubuntu1 [167 kB] 266s Get:44 http://ftpmaster.internal/ubuntu resolute/main armhf xdg-utils all 1.2.1-2ubuntu2 [66.1 kB] 266s Get:45 http://ftpmaster.internal/ubuntu resolute/universe armhf r-base-core armhf 4.5.2-1ubuntu2 [28.5 MB] 315s Get:46 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-data.table armhf 1.17.0+dfsg-1 [2111 kB] 319s Get:47 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-dbi all 1.2.3-1build1 [855 kB] 321s Get:48 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-lattice armhf 0.22-7-1 [1365 kB] 323s Get:49 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-matrix armhf 1.7-4-1 [4139 kB] 330s Get:50 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-survival armhf 3.8-6-1 [8253 kB] 343s Get:51 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-littler armhf 0.3.22-1 [81.0 kB] 343s Get:52 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-pkgkitten all 0.2.4-1 [27.2 kB] 343s Get:53 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-rcpp armhf 1.1.0-1 [2009 kB] 346s Get:54 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-rcpparmadillo armhf 15.2.3-1-1 [915 kB] 347s Get:55 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-etm armhf 1.1.1-1build1 [482 kB] 348s Get:56 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-mitools all 2.4-2build2 [266 kB] 349s Get:57 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-kmi all 0.5.5-2build2 [78.9 kB] 349s Preconfiguring packages ... 349s Fetched 58.6 MB in 1min 43s (567 kB/s) 349s Selecting previously unselected package libfreetype6:armhf. 349s (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 ... 68686 files and directories currently installed.) 349s Preparing to unpack .../00-libfreetype6_2.14.1+dfsg-2_armhf.deb ... 349s Unpacking libfreetype6:armhf (2.14.1+dfsg-2) ... 349s Selecting previously unselected package fonts-dejavu-mono. 349s Preparing to unpack .../01-fonts-dejavu-mono_2.37-8build1_all.deb ... 349s Unpacking fonts-dejavu-mono (2.37-8build1) ... 350s Selecting previously unselected package fonts-dejavu-core. 350s Preparing to unpack .../02-fonts-dejavu-core_2.37-8build1_all.deb ... 350s Unpacking fonts-dejavu-core (2.37-8build1) ... 350s Selecting previously unselected package fontconfig-config. 350s Preparing to unpack .../03-fontconfig-config_2.17.1-3ubuntu1_armhf.deb ... 350s Unpacking fontconfig-config (2.17.1-3ubuntu1) ... 350s Selecting previously unselected package libfontconfig1:armhf. 350s Preparing to unpack .../04-libfontconfig1_2.17.1-3ubuntu1_armhf.deb ... 350s Unpacking libfontconfig1:armhf (2.17.1-3ubuntu1) ... 350s Selecting previously unselected package fontconfig. 350s Preparing to unpack .../05-fontconfig_2.17.1-3ubuntu1_armhf.deb ... 350s Unpacking fontconfig (2.17.1-3ubuntu1) ... 350s Selecting previously unselected package libblas3:armhf. 350s Preparing to unpack .../06-libblas3_3.12.1-7ubuntu1_armhf.deb ... 350s Unpacking libblas3:armhf (3.12.1-7ubuntu1) ... 350s Selecting previously unselected package libpixman-1-0:armhf. 350s Preparing to unpack .../07-libpixman-1-0_0.46.4-1_armhf.deb ... 350s Unpacking libpixman-1-0:armhf (0.46.4-1) ... 350s Selecting previously unselected package libxcb-render0:armhf. 350s Preparing to unpack .../08-libxcb-render0_1.17.0-2ubuntu1_armhf.deb ... 350s Unpacking libxcb-render0:armhf (1.17.0-2ubuntu1) ... 350s Selecting previously unselected package libxcb-shm0:armhf. 350s Preparing to unpack .../09-libxcb-shm0_1.17.0-2ubuntu1_armhf.deb ... 350s Unpacking libxcb-shm0:armhf (1.17.0-2ubuntu1) ... 350s Selecting previously unselected package libxrender1:armhf. 350s Preparing to unpack .../10-libxrender1_1%3a0.9.12-1_armhf.deb ... 350s Unpacking libxrender1:armhf (1:0.9.12-1) ... 350s Selecting previously unselected package libcairo2:armhf. 350s Preparing to unpack .../11-libcairo2_1.18.4-3_armhf.deb ... 350s Unpacking libcairo2:armhf (1.18.4-3) ... 350s Selecting previously unselected package libdatrie1:armhf. 350s Preparing to unpack .../12-libdatrie1_0.2.14-1_armhf.deb ... 350s Unpacking libdatrie1:armhf (0.2.14-1) ... 350s Selecting previously unselected package libdeflate0:armhf. 350s Preparing to unpack .../13-libdeflate0_1.23-2build1_armhf.deb ... 350s Unpacking libdeflate0:armhf (1.23-2build1) ... 351s Selecting previously unselected package libgfortran5:armhf. 351s Preparing to unpack .../14-libgfortran5_15.2.0-12ubuntu1_armhf.deb ... 351s Unpacking libgfortran5:armhf (15.2.0-12ubuntu1) ... 351s Selecting previously unselected package libgomp1:armhf. 351s Preparing to unpack .../15-libgomp1_15.2.0-12ubuntu1_armhf.deb ... 351s Unpacking libgomp1:armhf (15.2.0-12ubuntu1) ... 351s Selecting previously unselected package libgraphite2-3:armhf. 351s Preparing to unpack .../16-libgraphite2-3_1.3.14-11ubuntu1_armhf.deb ... 351s Unpacking libgraphite2-3:armhf (1.3.14-11ubuntu1) ... 351s Selecting previously unselected package libharfbuzz0b:armhf. 351s Preparing to unpack .../17-libharfbuzz0b_12.3.2-1_armhf.deb ... 351s Unpacking libharfbuzz0b:armhf (12.3.2-1) ... 351s Selecting previously unselected package x11-common. 351s Preparing to unpack .../18-x11-common_1%3a7.7+24ubuntu1_all.deb ... 351s Unpacking x11-common (1:7.7+24ubuntu1) ... 351s Selecting previously unselected package libice6:armhf. 351s Preparing to unpack .../19-libice6_2%3a1.1.1-1build1_armhf.deb ... 351s Unpacking libice6:armhf (2:1.1.1-1build1) ... 351s Selecting previously unselected package libjpeg-turbo8:armhf. 351s Preparing to unpack .../20-libjpeg-turbo8_2.1.5-4ubuntu3_armhf.deb ... 351s Unpacking libjpeg-turbo8:armhf (2.1.5-4ubuntu3) ... 351s Selecting previously unselected package libjpeg8:armhf. 351s Preparing to unpack .../21-libjpeg8_8c-2ubuntu11_armhf.deb ... 351s Unpacking libjpeg8:armhf (8c-2ubuntu11) ... 351s Selecting previously unselected package liblapack3:armhf. 351s Preparing to unpack .../22-liblapack3_3.12.1-7ubuntu1_armhf.deb ... 351s Unpacking liblapack3:armhf (3.12.1-7ubuntu1) ... 351s Selecting previously unselected package liblerc4:armhf. 351s Preparing to unpack .../23-liblerc4_4.0.0+ds-5ubuntu2_armhf.deb ... 351s Unpacking liblerc4:armhf (4.0.0+ds-5ubuntu2) ... 351s Selecting previously unselected package libthai-data. 351s Preparing to unpack .../24-libthai-data_0.1.30-1_all.deb ... 351s Unpacking libthai-data (0.1.30-1) ... 351s Selecting previously unselected package libthai0:armhf. 351s Preparing to unpack .../25-libthai0_0.1.30-1_armhf.deb ... 351s Unpacking libthai0:armhf (0.1.30-1) ... 351s Selecting previously unselected package libpango-1.0-0:armhf. 351s Preparing to unpack .../26-libpango-1.0-0_1.57.0-1_armhf.deb ... 351s Unpacking libpango-1.0-0:armhf (1.57.0-1) ... 351s Selecting previously unselected package libpangoft2-1.0-0:armhf. 351s Preparing to unpack .../27-libpangoft2-1.0-0_1.57.0-1_armhf.deb ... 351s Unpacking libpangoft2-1.0-0:armhf (1.57.0-1) ... 351s Selecting previously unselected package libpangocairo-1.0-0:armhf. 351s Preparing to unpack .../28-libpangocairo-1.0-0_1.57.0-1_armhf.deb ... 351s Unpacking 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Creating config file /etc/R/Renviron with new version 356s Setting up r-cran-lattice (0.22-7-1) ... 356s Setting up r-cran-pkgkitten (0.2.4-1) ... 356s Setting up r-cran-littler (0.3.22-1) ... 356s Setting up r-cran-rcpp (1.1.0-1) ... 356s Setting up r-cran-dbi (1.2.3-1build1) ... 356s Setting up r-cran-data.table (1.17.0+dfsg-1) ... 356s Setting up r-cran-matrix (1.7-4-1) ... 356s Setting up r-cran-rcpparmadillo (15.2.3-1-1) ... 356s Setting up r-cran-mitools (2.4-2build2) ... 356s Setting up r-cran-survival (3.8-6-1) ... 356s Setting up r-cran-kmi (0.5.5-2build2) ... 356s Setting up r-cran-etm (1.1.1-1build1) ... 356s Processing triggers for man-db (2.13.1-1build1) ... 357s Processing triggers for install-info (7.2-5) ... 357s Processing triggers for libc-bin (2.42-2ubuntu4) ... 365s autopkgtest [23:24:57]: test run-unit-test: [----------------------- 367s BEGIN TEST test.etmCIF.R 367s 367s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 367s Copyright (C) 2025 The R Foundation for Statistical Computing 367s Platform: arm-unknown-linux-gnueabihf (32-bit) 367s 367s R is free software and comes with ABSOLUTELY NO WARRANTY. 367s You are welcome to redistribute it under certain conditions. 367s Type 'license()' or 'licence()' for distribution details. 367s 367s R is a collaborative project with many contributors. 367s Type 'contributors()' for more information and 367s 'citation()' on how to cite R or R packages in publications. 367s 367s Type 'demo()' for some demos, 'help()' for on-line help, or 367s 'help.start()' for an HTML browser interface to help. 367s Type 'q()' to quit R. 367s 367s Loading required package: etm 367s > ### test file for etmCIF. 367s > ### Really simple tests and comparison with etm 367s > 367s > old <- options(digits = 5) 367s > 367s > require(etm) 368s > 368s > if (!require(survival, quietly = TRUE)) { 368s + print("The following tests require the 'survival' package") 368s + } else { 368s + 368s + data(abortion) 368s + 368s + from <- rep(0, nrow(abortion)) 368s + to <- abortion$cause 368s + entry <- abortion$entry 368s + exit <- abortion$exit 368s + id <- 1:nrow(abortion) 368s + data <- data.frame(id, from, to, entry, exit, group = abortion$group) 368s + 368s + ## Computation of the CIFs with etm 368s + tra <- matrix(FALSE, 4, 4) 368s + tra[1, 2:4] <- TRUE 368s + 368s + cif.control <- etm(data[data$group == 0, ], c("0", "1", "2", "3"), 368s + tra, NULL, 0) 368s + cif.exposed <- etm(data[data$group == 1, ], c("0", "1", "2", "3"), 368s + tra, NULL, 0) 368s + 368s + 368s + ## Computation of the CIFs with etmCIF 368s + netm <- etmCIF(Surv(entry, exit, cause != 0) ~ group, abortion, 368s + etype = cause, failcode = 3) 368s + 368s + ### let's do some comparisons :-) 368s + 368s + all.equal(trprob(cif.control, "0 3"), netm[[1]]$est["0", "3", ]) 368s + all.equal(trprob(cif.control, "0 2"), netm[[1]]$est["0", "2", ]) 368s + all.equal(trprob(cif.control, "0 1"), netm[[1]]$est["0", "1", ]) 368s + 368s + all.equal(trprob(cif.exposed, "0 3"), netm[[2]]$est["0", "3", ]) 368s + all.equal(trprob(cif.exposed, "0 2"), netm[[2]]$est["0", "2", ]) 368s + all.equal(trprob(cif.exposed, "0 1"), netm[[2]]$est["0", "1", ]) 368s + 368s + 368s + all.equal(trcov(cif.control, "0 3"), netm[[1]]$cov["0 3", "0 3", ]) 368s + all.equal(trcov(cif.control, "0 2"), netm[[1]]$cov["0 2", "0 2", ]) 368s + all.equal(trcov(cif.control, "0 1"), netm[[1]]$cov["0 1", "0 1", ]) 368s + 368s + all.equal(trcov(cif.exposed, "0 3"), netm[[2]]$cov["0 3", "0 3", ]) 368s + all.equal(trcov(cif.exposed, "0 2"), netm[[2]]$cov["0 2", "0 2", ]) 368s + all.equal(trcov(cif.exposed, "0 1"), netm[[2]]$cov["0 1", "0 1", ]) 368s + 368s + 368s + netm 368s + 368s + ## test on the summary 368s + snetm <- summary(netm) 368s + 368s + snetm 368s + 368s + all.equal(unname(trprob(cif.control, "0 3")), snetm[[1]][[3]]$P) 368s + all.equal(unname(trprob(cif.control, "0 2")), snetm[[1]][[2]]$P) 368s + all.equal(unname(trprob(cif.control, "0 1")), snetm[[1]][[1]]$P) 368s + 368s + all.equal(unname(trprob(cif.exposed, "0 3")), snetm[[2]][[3]]$P) 368s + all.equal(unname(trprob(cif.exposed, "0 2")), snetm[[2]][[2]]$P) 368s + all.equal(unname(trprob(cif.exposed, "0 1")), snetm[[2]][[1]]$P) 368s + 368s + scif.control <- summary(cif.control, ci.fun = "cloglog") 368s + scif.exposed <- summary(cif.exposed, ci.fun = "cloglog") 368s + 368s + all.equal(scif.control[[4]]$lower, snetm[[1]][[3]]$lower) 368s + all.equal(scif.control[[4]]$upper, snetm[[1]][[3]]$upper) 368s + 368s + all.equal(scif.exposed[[4]]$lower, snetm[[2]][[3]]$lower) 368s + all.equal(scif.exposed[[4]]$upper, snetm[[2]][[3]]$upper) 368s + } 368s [1] TRUE 368s > 368s > ### test with factors in the input 368s > abortion$status <- with(abortion, ifelse(cause == 2, "life birth", 368s + ifelse(cause == 1, "ETOP", "spontaneous abortion"))) 368s > 368s > abortion$status <- factor(abortion$status) 368s > 368s > netm.factor <- etmCIF(Surv(entry, exit, status != "cens") ~ group, abortion, 368s + etype = status, failcode = "spontaneous abortion") 368s > 368s > 368s > all.equal(trprob(cif.control, "0 3"), netm.factor[[1]]$est["0", "spontaneous abortion", ]) 368s [1] TRUE 368s > all.equal(trprob(cif.control, "0 2"), netm.factor[[1]]$est["0", "life birth", ]) 368s [1] TRUE 368s > 368s > netm.factor 368s Call: etmCIF(formula = Surv(entry, exit, status != "cens") ~ group, 368s data = abortion, etype = status, failcode = "spontaneous abortion") 368s 368s Covariate: group 368s levels: 0 1 368s 368s 368s group = 0 368s time P se(P) n.event 368s CIF ETOP 43 0.040159 0.0092578 20 368s CIF life birth 43 0.799059 0.0221865 924 368s CIF spontaneous abortion 43 0.160781 0.0213261 69 368s 368s group = 1 368s time P se(P) n.event 368s CIF ETOP 42 0.28511 0.042493 38 368s CIF life birth 42 0.35257 0.042139 92 368s CIF spontaneous abortion 42 0.36232 0.049473 43 368s > 368s > summary(netm.factor) 368s 368s group=0 368s 368s CIF ETOP 368s P time var lower upper n.risk n.event 368s 0.000000 6 0.0000e+00 0.000000 0.000000 117 0 368s 0.038955 13 8.4440e-05 0.024488 0.061694 645 1 368s 0.040159 26 8.5707e-05 0.025513 0.062939 846 0 368s 0.040159 36 8.5707e-05 0.025513 0.062939 876 0 368s 0.040159 40 8.5707e-05 0.025513 0.062939 554 0 368s 0.040159 43 8.5707e-05 0.025513 0.062939 6 0 368s 368s CIF life birth 368s P time var lower upper n.risk n.event 368s 0.000000 6 0.0000e+00 0.000000 0.000000 117 0 368s 0.000000 13 0.0000e+00 0.000000 0.000000 645 0 368s 0.000000 26 0.0000e+00 0.000000 0.000000 846 0 368s 0.053197 36 4.6195e-05 0.041379 0.068268 876 25 368s 0.563121 40 3.8801e-04 0.524924 0.602021 554 280 368s 0.799059 43 4.9224e-04 0.753969 0.840613 6 6 368s 368s CIF spontaneous abortion 368s P time var lower upper n.risk n.event 368s 0.034188 6 0.00028222 0.01297 0.088523 117 4 368s 0.150468 13 0.00045513 0.11360 0.197901 645 1 368s 0.159904 26 0.00045498 0.12274 0.206925 846 1 368s 0.160781 36 0.00045480 0.12360 0.207757 876 1 368s 0.160781 40 0.00045480 0.12360 0.207757 554 0 368s 0.160781 43 0.00045480 0.12360 0.207757 6 0 368s 368s 368s group=1 368s 368s CIF ETOP 368s P time var lower upper n.risk n.event 368s 0.00000 6 0.0000000 0.00000 0.00000 35 0 368s 0.26048 13 0.0017854 0.18795 0.35425 90 0 368s 0.28115 21 0.0018028 0.20742 0.37423 93 1 368s 0.28511 34 0.0018057 0.21116 0.37806 89 0 368s 0.28511 39 0.0018057 0.21116 0.37806 59 0 368s 0.28511 42 0.0018057 0.21116 0.37806 6 0 368s 368s CIF life birth 368s P time var lower upper n.risk n.event 368s 0.000000 6 0.0000e+00 0.000000 0.000000 35 0 368s 0.000000 13 0.0000e+00 0.000000 0.000000 90 0 368s 0.000000 21 0.0000e+00 0.000000 0.000000 93 0 368s 0.023073 34 9.0514e-05 0.010252 0.051504 89 2 368s 0.180156 39 8.0126e-04 0.131765 0.243663 59 13 368s 0.352565 42 1.7757e-03 0.276882 0.441775 6 6 368s 368s CIF spontaneous abortion 368s P time var lower upper n.risk n.event 368s 0.057143 6 0.0015394 0.014605 0.20968 35 2 368s 0.333246 13 0.0025280 0.245337 0.44216 90 4 368s 0.350702 21 0.0024827 0.262769 0.45762 93 0 368s 0.358492 34 0.0024593 0.270627 0.46448 89 0 368s 0.358492 39 0.0024593 0.270627 0.46448 59 0 368s 0.362323 42 0.0024476 0.274499 0.46785 6 0 368s 368s > 368s > ### test with group as a character vector 368s > abortion$ttt <- with(abortion, ifelse(group == 0, "control", "exposed")) 368s > abortion$ttt <- factor(abortion$ttt) 368s > 368s > netm.ttt <- etmCIF(Surv(entry, exit, status != "cens") ~ ttt, abortion, 368s + etype = status, failcode = "spontaneous abortion") 368s > 368s > all.equal(trprob(cif.control, "0 3"), netm.ttt[[1]]$est["0", "spontaneous abortion", ]) 368s [1] TRUE 368s > all.equal(trprob(cif.control, "0 2"), netm.ttt[[1]]$est["0", "life birth", ]) 368s [1] TRUE 368s > 368s > netm.ttt 368s Call: etmCIF(formula = Surv(entry, exit, status != "cens") ~ ttt, data = abortion, 368s etype = status, failcode = "spontaneous abortion") 368s 368s Covariate: ttt 368s levels: control exposed 368s 368s 368s ttt = control 368s time P se(P) n.event 368s CIF ETOP 43 0.040159 0.0092578 20 368s CIF life birth 43 0.799059 0.0221865 924 368s CIF spontaneous abortion 43 0.160781 0.0213261 69 368s 368s ttt = exposed 368s time P se(P) n.event 368s CIF ETOP 42 0.28511 0.042493 38 368s CIF life birth 42 0.35257 0.042139 92 368s CIF spontaneous abortion 42 0.36232 0.049473 43 368s > 368s > summary(netm.ttt) 368s 368s ttt=control 368s 368s CIF ETOP 368s P time var lower upper n.risk n.event 368s 0.000000 6 0.0000e+00 0.000000 0.000000 117 0 368s 0.038955 13 8.4440e-05 0.024488 0.061694 645 1 368s 0.040159 26 8.5707e-05 0.025513 0.062939 846 0 368s 0.040159 36 8.5707e-05 0.025513 0.062939 876 0 368s 0.040159 40 8.5707e-05 0.025513 0.062939 554 0 368s 0.040159 43 8.5707e-05 0.025513 0.062939 6 0 368s 368s CIF life birth 368s P time var lower upper n.risk n.event 368s 0.000000 6 0.0000e+00 0.000000 0.000000 117 0 368s 0.000000 13 0.0000e+00 0.000000 0.000000 645 0 368s 0.000000 26 0.0000e+00 0.000000 0.000000 846 0 368s 0.053197 36 4.6195e-05 0.041379 0.068268 876 25 368s 0.563121 40 3.8801e-04 0.524924 0.602021 554 280 368s 0.799059 43 4.9224e-04 0.753969 0.840613 6 6 368s 368s CIF spontaneous abortion 368s P time var lower upper n.risk n.event 368s 0.034188 6 0.00028222 0.01297 0.088523 117 4 368s 0.150468 13 0.00045513 0.11360 0.197901 645 1 368s 0.159904 26 0.00045498 0.12274 0.206925 846 1 368s 0.160781 36 0.00045480 0.12360 0.207757 876 1 368s 0.160781 40 0.00045480 0.12360 0.207757 554 0 368s 0.160781 43 0.00045480 0.12360 0.207757 6 0 368s 368s 368s ttt=exposed 368s 368s CIF ETOP 368s P time var lower upper n.risk n.event 368s 0.00000 6 0.0000000 0.00000 0.00000 35 0 368s 0.26048 13 0.0017854 0.18795 0.35425 90 0 368s 0.28115 21 0.0018028 0.20742 0.37423 93 1 368s 0.28511 34 0.0018057 0.21116 0.37806 89 0 368s 0.28511 39 0.0018057 0.21116 0.37806 59 0 368s 0.28511 42 0.0018057 0.21116 0.37806 6 0 368s 368s CIF life birth 368s P time var lower upper n.risk n.event 368s 0.000000 6 0.0000e+00 0.000000 0.000000 35 0 368s 0.000000 13 0.0000e+00 0.000000 0.000000 90 0 368s 0.000000 21 0.0000e+00 0.000000 0.000000 93 0 368s 0.023073 34 9.0514e-05 0.010252 0.051504 89 2 368s 0.180156 39 8.0126e-04 0.131765 0.243663 59 13 368s 0.352565 42 1.7757e-03 0.276882 0.441775 6 6 368s 368s CIF spontaneous abortion 368s P time var lower upper n.risk n.event 368s 0.057143 6 0.0015394 0.014605 0.20968 35 2 368s 0.333246 13 0.0025280 0.245337 0.44216 90 4 368s 0.350702 21 0.0024827 0.262769 0.45762 93 0 368s 0.358492 34 0.0024593 0.270627 0.46448 89 0 368s 0.358492 39 0.0024593 0.270627 0.46448 59 0 368s 0.362323 42 0.0024476 0.274499 0.46785 6 0 368s 368s > 368s > 368s > ### A couple of comparisons with simulated data 368s > set.seed(1313) 368s > time <- rexp(100) 368s > to <- rbinom(100, 2, prob = c(1/3, 1/3, 1/3)) 368s > from <- rep(11, 100) 368s > id <- 1:100 368s > cov <- rbinom(100, 1, 0.5) 368s > 368s > dat.s <- data.frame(id, time, from, to, cov) 368s > 368s > traa <- matrix(FALSE, 3, 3) 368s > traa[1, 2:3] <- TRUE 368s > 368s > aa0 <- etm(dat.s[dat.s$cov == 0, ], c("11", "1", "2"), traa, "0", 0) 368s > aa1 <- etm(dat.s[dat.s$cov == 1, ], c("11", "1", "2"), traa, "0", 0) 368s > aa <- etm(dat.s, c("11", "1", "2"), traa, "0", 0) 368s > 368s > test <- etmCIF(Surv(time, to != 0) ~ 1, dat.s, etype = to) 368s > 368s > test.c <- etmCIF(Surv(time, to != 0) ~ cov, dat.s, etype = to) 368s > 368s > all.equal(trprob(aa, "11 1"), test[[1]]$est["0", "1", ]) 368s [1] TRUE 368s > all.equal(trprob(aa, "11 2"), test[[1]]$est["0", "2", ]) 368s [1] TRUE 368s > 368s > all.equal(trprob(aa0, "11 1"), test.c[[1]]$est["0", "1", ]) 368s [1] TRUE 368s > all.equal(trprob(aa0, "11 2"), test.c[[1]]$est["0", "2", ]) 368s [1] TRUE 368s > 368s > all.equal(trprob(aa1, "11 1"), test.c[[2]]$est["0", "1", ]) 368s [1] TRUE 368s > all.equal(trprob(aa1, "11 2"), test.c[[2]]$est["0", "2", ]) 368s [1] TRUE 368s > 368s > test 368s Call: etmCIF(formula = Surv(time, to != 0) ~ 1, data = dat.s, etype = to) 368s 368s time P se(P) n.event 368s CIF 1 4.9088 0.809108 0.079680 45 368s CIF 2 4.9088 0.096618 0.032905 8 368s > 368s > test.c 368s Call: etmCIF(formula = Surv(time, to != 0) ~ cov, data = dat.s, etype = to) 368s 368s Covariate: cov 368s levels: 0 1 368s 368s 368s cov = 0 368s time P se(P) n.event 368s CIF 1 2.1708 0.70246 0.105797 19 368s CIF 2 2.1708 0.11144 0.053384 4 368s 368s cov = 1 368s time P se(P) n.event 368s CIF 1 4.9088 0.80787 0.094051 26 368s CIF 2 4.9088 0.08436 0.040769 4 368s > 368s > summary(test) 368s 368s 368s 368s CIF 1 368s P time var lower upper n.risk n.event 368s 0.01000 0.0092099 0.0000990 0.0014147 0.068863 100 1 368s 0.11430 0.2663096 0.0010542 0.0649454 0.196993 81 1 368s 0.23451 0.7303091 0.0020436 0.1591107 0.337736 54 1 368s 0.40425 1.4299939 0.0032996 0.3020445 0.525741 29 1 368s 0.54593 2.0647206 0.0040836 0.4269008 0.673605 16 1 368s 0.80911 4.9087561 0.0063489 0.6359544 0.933733 2 1 368s 368s CIF 2 368s P time var lower upper n.risk n.event 368s 0.000000 0.0092099 0.00000000 0.000000 0.000000 100 0 368s 0.031657 0.2663096 0.00032353 0.010320 0.094942 81 0 368s 0.067029 0.7303091 0.00070366 0.030598 0.143503 54 0 368s 0.096618 1.4299939 0.00108275 0.049082 0.185474 29 0 368s 0.096618 2.0647206 0.00108275 0.049082 0.185474 16 0 368s 0.096618 4.9087561 0.00108275 0.049082 0.185474 2 0 368s 368s > summary(test.c) 368s 368s cov=0 368s 368s CIF 1 368s P time var lower upper n.risk n.event 368s 0.022222 0.0092099 0.00048285 0.0031605 0.14747 45 1 368s 0.092222 0.2982439 0.00193603 0.0355971 0.22762 36 0 368s 0.226684 0.7021938 0.00450954 0.1241760 0.39250 24 1 368s 0.378128 1.4299939 0.00760870 0.2337884 0.57145 13 1 368s 0.505736 1.6148774 0.00895330 0.3388425 0.69885 10 1 368s 0.702465 2.1708375 0.01119294 0.4944890 0.88399 3 1 368s 368s CIF 2 368s P time var lower upper n.risk n.event 368s 0.000000 0.0092099 0.0000000 0.000000 0.00000 45 0 368s 0.048441 0.2982439 0.0011168 0.012337 0.18013 36 1 368s 0.076411 0.7021938 0.0018104 0.025202 0.21928 24 0 368s 0.111440 1.4299939 0.0028499 0.042676 0.27392 13 0 368s 0.111440 1.6148774 0.0028499 0.042676 0.27392 10 0 368s 0.111440 2.1708375 0.0028499 0.042676 0.27392 3 0 368s 368s 368s cov=1 368s 368s CIF 1 368s P time var lower upper n.risk n.event 368s 0.018182 0.066692 0.00032457 0.0025813 0.12214 55 1 368s 0.112392 0.263808 0.00187215 0.0520925 0.23333 45 1 368s 0.241023 0.730309 0.00374499 0.1440057 0.38685 31 1 368s 0.401201 1.066913 0.00570788 0.2714008 0.56421 19 1 368s 0.592334 2.366275 0.00775985 0.4286230 0.76273 8 1 368s 0.807871 4.908756 0.00884554 0.6023185 0.94771 2 1 368s 368s CIF 2 368s P time var lower upper n.risk n.event 368s 0.000000 0.066692 0.00000000 0.000000 0.00000 55 0 368s 0.037434 0.263808 0.00067458 0.009494 0.14152 45 0 368s 0.059341 0.730309 0.00111295 0.019447 0.17351 31 0 368s 0.084360 1.066913 0.00166213 0.032211 0.21119 19 0 368s 0.084360 2.366275 0.00166213 0.032211 0.21119 8 0 368s 0.084360 4.908756 0.00166213 0.032211 0.21119 2 0 368s 368s > 368s > options(old) 368s > 368s BEGIN TEST tests.etm.R 368s 368s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 368s Copyright (C) 2025 The R Foundation for Statistical Computing 368s Platform: arm-unknown-linux-gnueabihf (32-bit) 368s 368s R is free software and comes with ABSOLUTELY NO WARRANTY. 368s You are welcome to redistribute it under certain conditions. 368s Type 'license()' or 'licence()' for distribution details. 368s 368s R is a collaborative project with many contributors. 368s Type 'contributors()' for more information and 368s 'citation()' on how to cite R or R packages in publications. 368s 368s Type 'demo()' for some demos, 'help()' for on-line help, or 368s 'help.start()' for an HTML browser interface to help. 368s Type 'q()' to quit R. 368s 369s > require(etm) 369s Loading required package: etm 370s > 370s > ## Print with a bit less precision to avoid lots of notes in the comparison 370s > old <- options(digits = 4) 370s > 370s > ### Simple test 370s > 370s > time <- id <- 1:10 370s > from <- rep(0, 10) 370s > to <- rep(1, 10) 370s > 370s > data1 <- data.frame(id, from, to, time) 370s > tra1 <- matrix(FALSE, 2, 2) 370s > tra1[1, 2] <- TRUE 370s > 370s > etm1 <- etm(data1, c("0", "1"), tra1, NULL, 0) 370s > 370s > all.equal(as.vector(trprob(etm1, "0 0")), cumprod((10:1 - 1) / (10:1))) 370s [1] TRUE 370s > 370s > etm1$cov["0 0", "0 0", ] 370s 1 2 3 4 5 6 7 8 9 10 370s 0.009 0.016 0.021 0.024 0.025 0.024 0.021 0.016 0.009 0.000 370s > 370s > all.equal(etm1$cov["0 0", "0 0",], trcov(etm1, "0 0")) 370s [1] TRUE 370s > 370s > ### A simple test from AHR's author, where the first time is censored 370s > if (!require(survival)) { 370s + stop("This test requires the survival package") 370s + } 370s Loading required package: survival 370s > 370s > data <- data.frame(id=1:10, time=1:10, from=0, to=1, status=TRUE) 370s > 370s > tra <- matrix(FALSE, nrow=2, ncol=2) 370s > tra[1, 2] <- TRUE 370s > 370s > data$to[1] <- "cens" 370s > data$status[1] <- FALSE 370s > 370s > fit.km <- survfit(Surv(time, status) ~ 1, data=data) 370s > fit.etm <- etm(data, c("0","1"), tra, "cens", s=0, t="last", covariance=FALSE) 370s > 370s > all.equal(fit.km$surv[data$status], fit.etm$est[1,1,], check.attributes = FALSE) 370s [1] TRUE 370s > 370s > data$to[2] <- "cens" 370s > data$status[2] <- FALSE 370s > 370s > fit.km <- survfit(Surv(time, status) ~ 1, data=data) 370s > fit.etm <- etm(data, c("0","1"), tra, "cens", s=0, t="last", covariance=FALSE) 370s > 370s > all.equal(fit.km$surv[data$status], fit.etm$est[1,1,], check.attributes = FALSE) 370s [1] TRUE 370s > 370s > ### a bit more complicated 370s > 370s > time <- id <- 1:10 370s > from <- rep(0, 10) 370s > to <- rep(c(1, 2), 5) 370s > data2 <- data.frame(id, from, to, time) 370s > 370s > tra2 <- matrix(FALSE, 3, 3) 370s > tra2[1, 2:3] <- TRUE 370s > 370s > etm2 <- etm(data2, c("0", "1", "2"), tra2, NULL, 0) 370s > 370s > aa <- table(time, to) 370s > 370s > cif1 <- cumsum(aa[, 1] / 10) 370s > cif2 <- cumsum(aa[, 2] / 10) 370s > surv <- cumprod((10:1 - 1) / (10:1)) 370s > 370s > all.equal(trprob(etm2, "0 1"), cif1) 370s [1] TRUE 370s > all.equal(trprob(etm2, "0 2"), cif2) 370s [1] TRUE 370s > all.equal(as.vector(trprob(etm2, "0 0")), surv) 370s [1] TRUE 370s > 370s > ## a test on id 370s > data2$id <- letters[1:10] 370s > 370s > etm3 <- etm(data2, c("0", "1", "2"), tra2, NULL, 0) 370s > 370s > all.equal(trprob(etm2, "0 1"), trprob(etm3, "0 1")) 370s [1] TRUE 370s > all.equal(trprob(etm2, "0 2"), trprob(etm3, "0 2")) 370s [1] TRUE 370s > all.equal(trprob(etm2, "0 0"), trprob(etm3, "0 0")) 370s [1] TRUE 370s > 370s > 370s > ### Test on sir.cont 370s > 370s > data(sir.cont) 370s > 370s > ## Modification for patients entering and leaving a state 370s > ## at the same date 370s > ## Change on ventilation status is considered 370s > ## to happen before end of hospital stay 370s > sir.cont <- sir.cont[order(sir.cont$id, sir.cont$time), ] 370s > for (i in 2:nrow(sir.cont)) { 370s + if (sir.cont$id[i]==sir.cont$id[i-1]) { 370s + if (sir.cont$time[i]==sir.cont$time[i-1]) { 370s + sir.cont$time[i-1] <- sir.cont$time[i-1] - 0.5 370s + } 370s + } 370s + } 370s > 370s > ### Computation of the transition probabilities 370s > ## Possible transitions. 370s > tra <- matrix(ncol=3,nrow=3,FALSE) 370s > tra[1, 2:3] <- TRUE 370s > tra[2, c(1, 3)] <- TRUE 370s > 370s > ## etm 370s > prob.sir <- etm(sir.cont, c("0", "1", "2"), tra, "cens", 1) 370s > 370s > prob.sir 370s Multistate model with 2 transient state(s) 370s and 1 absorbing state(s) 370s 370s Possible transitions: 370s from to 370s 0 1 370s 0 2 370s 1 0 370s 1 2 370s 370s Estimate of P(1, 183) 370s 0 1 2 370s 0 0 0 1 370s 1 0 0 1 370s 2 0 0 1 370s 370s > 370s > summ.sir <- summary(prob.sir) 370s > all.equal(summ.sir[['0 1']]$P, as.vector(trprob(prob.sir, "0 1"))) 370s [1] TRUE 370s > subset(summ.sir[[3]],time<183) # issue with precision on different architectures 370s P time var lower upper n.risk n.event 370s 1.5 0.0000 1.5 0.000e+00 0.00000 0.0000 394 0 370s 2 0.1187 2.0 2.641e-04 0.08683 0.1505 396 47 370s 2.5 0.1187 2.5 2.641e-04 0.08683 0.1505 364 0 370s 3 0.2454 3.0 4.465e-04 0.20398 0.2868 365 54 370s 3.5 0.2454 3.5 4.465e-04 0.20398 0.2868 328 0 370s 4 0.3806 4.0 5.416e-04 0.33501 0.4262 331 62 370s 4.5 0.3806 4.5 5.416e-04 0.33501 0.4262 280 0 370s 5 0.4792 5.0 5.480e-04 0.43333 0.5251 283 48 370s 5.5 0.4792 5.5 5.480e-04 0.43333 0.5251 248 0 370s 6 0.5693 6.0 5.141e-04 0.52482 0.6137 249 47 370s 7 0.6350 7.0 4.665e-04 0.59266 0.6773 212 36 370s 8 0.6795 8.0 4.202e-04 0.63931 0.7197 195 27 370s 8.5 0.6795 8.5 4.202e-04 0.63931 0.7197 172 0 370s 9 0.7325 9.0 3.580e-04 0.69541 0.7696 173 34 370s 10 0.7647 10.0 3.141e-04 0.72992 0.7994 148 21 370s 10.5 0.7647 10.5 3.141e-04 0.72992 0.7994 135 0 370s 11 0.7895 11.0 2.790e-04 0.75674 0.8222 136 18 370s 12 0.8138 12.0 2.420e-04 0.78330 0.8443 129 18 370s 12.5 0.8138 12.5 2.420e-04 0.78330 0.8443 117 0 370s 13 0.8294 13.0 2.182e-04 0.80045 0.8584 118 13 370s 14 0.8452 14.0 1.938e-04 0.81789 0.8725 115 14 370s 15 0.8625 15.0 1.670e-04 0.83714 0.8878 106 15 370s 16 0.8723 16.0 1.522e-04 0.84807 0.8964 93 9 370s 17 0.8852 17.0 1.330e-04 0.86256 0.9078 86 12 370s 17.5 0.8852 17.5 1.330e-04 0.86256 0.9078 77 0 370s 18 0.8960 18.0 1.168e-04 0.87484 0.9172 76 9 370s 19 0.9029 19.0 1.070e-04 0.88261 0.9232 71 7 370s 20 0.9125 20.0 9.367e-05 0.89356 0.9315 64 10 370s 21 0.9161 21.0 8.878e-05 0.89768 0.9346 57 4 370s 22 0.9226 22.0 7.996e-05 0.90504 0.9401 55 6 370s 23 0.9261 23.0 7.537e-05 0.90904 0.9431 51 4 370s 23.5 0.9261 23.5 7.537e-05 0.90904 0.9431 49 0 370s 24 0.9354 24.0 6.292e-05 0.91982 0.9509 50 9 370s 25 0.9385 25.0 5.878e-05 0.92352 0.9536 42 3 370s 26 0.9429 26.0 5.326e-05 0.92863 0.9572 39 5 370s 27 0.9477 27.0 4.749e-05 0.93417 0.9612 35 6 370s 27.5 0.9477 27.5 4.749e-05 0.93417 0.9612 29 0 370s 28 0.9531 28.0 4.093e-05 0.94059 0.9657 30 5 370s 29 0.9567 29.0 3.668e-05 0.94485 0.9686 31 4 370s 30 0.9592 30.0 3.384e-05 0.94779 0.9706 28 3 370s 30.5 0.9592 30.5 3.384e-05 0.94779 0.9706 29 0 370s 31 0.9642 31.0 2.821e-05 0.95383 0.9746 30 6 370s 32 0.9649 32.0 2.752e-05 0.95458 0.9751 25 1 370s 33 0.9669 33.0 2.533e-05 0.95708 0.9768 24 2 370s 34 0.9685 34.0 2.368e-05 0.95900 0.9781 26 2 370s 35 0.9697 35.0 2.252e-05 0.96036 0.9790 28 2 370s 36 0.9702 36.0 2.194e-05 0.96104 0.9794 26 1 370s 37 0.9718 37.0 2.043e-05 0.96290 0.9806 26 2 370s 38 0.9739 38.0 1.831e-05 0.96555 0.9823 25 4 370s 38.5 0.9739 38.5 1.831e-05 0.96555 0.9823 21 0 370s 39 0.9760 39.0 1.643e-05 0.96802 0.9839 23 3 370s 40 0.9769 40.0 1.558e-05 0.96918 0.9847 19 1 370s 41 0.9774 41.0 1.512e-05 0.96981 0.9851 22 1 370s 42 0.9779 42.0 1.476e-05 0.97032 0.9854 22 0 370s 43 0.9798 43.0 1.308e-05 0.97271 0.9869 22 3 370s 44 0.9803 44.0 1.265e-05 0.97333 0.9873 21 1 370s 45 0.9817 45.0 1.157e-05 0.97499 0.9883 19 1 370s 46 0.9822 46.0 1.116e-05 0.97561 0.9887 17 1 370s 47 0.9831 47.0 1.037e-05 0.97683 0.9895 18 2 370s 48 0.9836 48.0 9.987e-06 0.97743 0.9898 17 1 370s 49 0.9841 49.0 9.669e-06 0.97796 0.9901 17 0 370s 50 0.9845 50.0 9.297e-06 0.97856 0.9905 17 1 370s 50.5 0.9845 50.5 9.297e-06 0.97856 0.9905 16 0 370s 51 0.9860 51.0 8.214e-06 0.98037 0.9916 17 3 370s 52 0.9870 52.0 7.513e-06 0.98159 0.9923 14 2 370s 53 0.9879 53.0 6.875e-06 0.98276 0.9930 12 1 370s 54 0.9889 54.0 6.214e-06 0.98397 0.9937 12 2 370s 55 0.9903 55.0 5.254e-06 0.98581 0.9948 10 3 370s 56 0.9913 56.0 4.667e-06 0.98703 0.9955 6 1 370s 57 0.9917 57.0 4.364e-06 0.98765 0.9958 5 1 370s 58 0.9922 58.0 4.064e-06 0.98828 0.9962 4 1 370s 59 0.9927 59.0 3.769e-06 0.98891 0.9965 3 1 370s 60 0.9932 60.0 3.488e-06 0.98953 0.9969 3 1 370s 62 0.9937 62.0 3.230e-06 0.99016 0.9972 2 0 370s 63 0.9942 63.0 2.956e-06 0.99079 0.9975 2 1 370s 68 0.9942 68.0 2.956e-06 0.99079 0.9975 1 0 370s 70 0.9946 70.0 2.694e-06 0.99143 0.9979 2 1 370s 78 0.9951 78.0 2.442e-06 0.99207 0.9982 1 0 370s 80 0.9951 80.0 2.442e-06 0.99207 0.9982 1 0 370s 85 0.9966 85.0 1.695e-06 0.99404 0.9991 2 0 370s 89 0.9966 89.0 1.695e-06 0.99404 0.9991 2 0 370s 90 0.9966 90.0 1.695e-06 0.99404 0.9991 1 0 370s 95 0.9971 95.0 1.448e-06 0.99472 0.9994 2 0 370s 100 0.9976 100.0 1.203e-06 0.99542 0.9997 3 0 370s 101 0.9981 101.0 9.592e-07 0.99613 1.0000 3 1 370s 108 0.9985 108.0 7.169e-07 0.99688 1.0000 2 1 370s 113 0.9990 113.0 4.764e-07 0.99767 1.0000 1 0 370s 116 0.9990 116.0 4.764e-07 0.99767 1.0000 1 0 370s 124 0.9990 124.0 4.764e-07 0.99767 1.0000 2 0 370s 164 0.9990 164.0 4.764e-07 0.99767 1.0000 0 0 370s > 370s > ## gonna play a bit with the state names 370s > dd <- sir.cont 370s > dd$from <- ifelse(dd$from == 0, "initial state", "ventilation") 370s > dd$to <- as.character(dd$to) 370s > for (i in seq_len(nrow(dd))) { 370s + dd$to[i] <- switch(dd$to[i], 370s + "0" = "initial state", 370s + "1" = "ventilation", 370s + "2" = "end of story", 370s + "cens" = "cens" 370s + ) 370s + } 370s > 370s > test <- etm(dd, c("initial state", "ventilation", "end of story"), tra, "cens", 1) 370s > 370s > all.equal(test$est["initial state", "initial state", ], 370s + prob.sir$est["0", "0", ]) 370s [1] TRUE 370s > all.equal(trprob(test, "initial state initial state"), trprob(prob.sir, "0 0")) 370s [1] TRUE 370s > all.equal(trprob(test, "initial state ventilation"), trprob(prob.sir, "0 1")) 370s [1] TRUE 370s > all.equal(trprob(test, "initial state end of story"), trprob(prob.sir, "0 2")) 370s [1] TRUE 370s > 370s > all.equal(trcov(test, "initial state end of story"), trcov(prob.sir, "0 2")) 370s [1] TRUE 370s > 370s > aa <- summary(test) 370s > all.equal(summ.sir[[6]], aa[[6]]) 370s [1] TRUE 370s > all.equal(summ.sir[[4]], aa[[4]]) 370s [1] TRUE 370s > 370s > ### Test on abortion data 370s > 370s > data(abortion) 370s > 370s > from <- rep(0, nrow(abortion)) 370s > to <- abortion$cause 370s > entry <- abortion$entry 370s > exit <- abortion$exit 370s > id <- 1:nrow(abortion) 370s > data <- data.frame(id, from, to, entry, exit, group = abortion$group) 370s > 370s > ## Computation of the CIFs 370s > tra <- matrix(FALSE, 4, 4) 370s > tra[1, 2:4] <- TRUE 370s > 370s > cif.control <- etm(data[data$group == 0, ], c("0", "1", "2", "3"), 370s + tra, NULL, 0) 370s > cif.exposed <- etm(data[data$group == 1, ], c("0", "1", "2", "3"), 370s + tra, NULL, 0) 370s > 370s > all.equal(trprob(cif.control, "0 1"), cif.control$est["0", "1", ]) 370s [1] TRUE 370s > all.equal(trcov(cif.control, c("0 1", "0 2")), cif.control$cov["0 1", "0 2", ]) 370s [1] TRUE 370s > 370s > trprob(cif.control, "0 1") 370s 6 7 8 9 10 11 12 13 370s 0.000000 0.007401 0.014881 0.026509 0.033208 0.037694 0.037694 0.038955 370s 14 17 19 21 24 25 26 30 370s 0.040159 0.040159 0.040159 0.040159 0.040159 0.040159 0.040159 0.040159 370s 31 32 33 34 35 36 37 38 370s 0.040159 0.040159 0.040159 0.040159 0.040159 0.040159 0.040159 0.040159 370s 39 40 41 42 43 370s 0.040159 0.040159 0.040159 0.040159 0.040159 370s > trprob(cif.control, "0 2") 370s 6 7 8 9 10 11 12 13 370s 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 370s 14 17 19 21 24 25 26 30 370s 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.003657 370s 31 32 33 34 35 36 37 38 370s 0.006371 0.008175 0.013543 0.023317 0.031260 0.053197 0.084529 0.179163 370s 39 40 41 42 43 370s 0.322016 0.563121 0.742227 0.793893 0.799059 370s > trprob(cif.control, "0 0") 370s 6 7 8 9 10 11 12 13 370s 0.965812 0.932508 0.887628 0.862433 0.838989 0.822538 0.813099 0.810578 370s 14 17 19 21 24 25 26 30 370s 0.806964 0.805874 0.803810 0.802804 0.801837 0.800883 0.799937 0.796280 370s 31 32 33 34 35 36 37 38 370s 0.793565 0.791762 0.786394 0.776620 0.768677 0.745862 0.714531 0.619897 370s 39 40 41 42 43 370s 0.477043 0.235938 0.056832 0.005167 0.000000 370s > 370s > trcov(cif.control, "0 1") 370s 6 7 8 9 10 11 12 13 370s 0.000e+00 2.719e-05 4.533e-05 6.665e-05 7.698e-05 8.304e-05 8.304e-05 8.444e-05 370s 14 17 19 21 24 25 26 30 370s 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 370s 31 32 33 34 35 36 37 38 370s 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 370s 39 40 41 42 43 370s 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 370s > trcov(cif.control, "0 2") 370s 6 7 8 9 10 11 12 13 370s 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 370s 14 17 19 21 24 25 26 30 370s 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 3.338e-06 370s 31 32 33 34 35 36 37 38 370s 5.784e-06 7.401e-06 1.216e-05 2.072e-05 2.758e-05 4.619e-05 7.202e-05 1.461e-04 370s 39 40 41 42 43 370s 2.470e-04 3.880e-04 4.702e-04 4.903e-04 4.922e-04 370s > trcov(cif.control, "0 0") 370s 6 7 8 9 10 11 12 13 370s 2.822e-04 3.821e-04 4.527e-04 4.748e-04 4.875e-04 4.927e-04 4.941e-04 4.942e-04 370s 14 17 19 21 24 25 26 30 370s 4.941e-04 4.940e-04 4.936e-04 4.933e-04 4.931e-04 4.928e-04 4.926e-04 4.914e-04 370s 31 32 33 34 35 36 37 38 370s 4.905e-04 4.899e-04 4.880e-04 4.846e-04 4.816e-04 4.729e-04 4.601e-04 4.176e-04 370s 39 40 41 42 43 370s 3.425e-04 1.865e-04 4.797e-05 4.441e-06 0.000e+00 370s > 370s > aa <- summary(cif.control) 370s > aa$"0 1" 370s P time var lower upper n.risk n.event 370s 6 0.000000 6 0.000e+00 0.000000 0.00000 117 0 370s 7 0.007401 7 2.719e-05 0.000000 0.01762 261 2 370s 8 0.014881 8 4.533e-05 0.001685 0.02808 374 3 370s 9 0.026509 9 6.665e-05 0.010508 0.04251 458 6 370s 10 0.033208 10 7.698e-05 0.016011 0.05040 515 4 370s 11 0.037694 11 8.304e-05 0.019834 0.05555 561 3 370s 12 0.037694 12 8.304e-05 0.019834 0.05555 610 0 370s 13 0.038955 13 8.444e-05 0.020944 0.05697 645 1 370s 14 0.040159 14 8.571e-05 0.022014 0.05830 673 1 370s 17 0.040159 17 8.571e-05 0.022014 0.05830 740 0 370s 19 0.040159 19 8.571e-05 0.022014 0.05830 781 0 370s 21 0.040159 21 8.571e-05 0.022014 0.05830 799 0 370s 24 0.040159 24 8.571e-05 0.022014 0.05830 830 0 370s 25 0.040159 25 8.571e-05 0.022014 0.05830 841 0 370s 26 0.040159 26 8.571e-05 0.022014 0.05830 846 0 370s 30 0.040159 30 8.571e-05 0.022014 0.05830 875 0 370s 31 0.040159 31 8.571e-05 0.022014 0.05830 880 0 370s 32 0.040159 32 8.571e-05 0.022014 0.05830 880 0 370s 33 0.040159 33 8.571e-05 0.022014 0.05830 885 0 370s 34 0.040159 34 8.571e-05 0.022014 0.05830 885 0 370s 35 0.040159 35 8.571e-05 0.022014 0.05830 880 0 370s 36 0.040159 36 8.571e-05 0.022014 0.05830 876 0 370s 37 0.040159 37 8.571e-05 0.022014 0.05830 857 0 370s 38 0.040159 38 8.571e-05 0.022014 0.05830 823 0 370s 39 0.040159 39 8.571e-05 0.022014 0.05830 716 0 370s 40 0.040159 40 8.571e-05 0.022014 0.05830 554 0 370s 41 0.040159 41 8.571e-05 0.022014 0.05830 274 0 370s 42 0.040159 42 8.571e-05 0.022014 0.05830 66 0 370s 43 0.040159 43 8.571e-05 0.022014 0.05830 6 0 370s > all.equal(aa$"0 1"$P, as.vector(trprob(cif.control, "0 1"))) 370s [1] TRUE 370s > 370s > ### test on los data 370s > 370s > data(los.data) # in package changeLOS 370s > 370s > ## putting los.data in the long format (see changeLOS) 370s > my.observ <- prepare.los.data(x=los.data) 370s > 370s > tra <- matrix(FALSE, 4, 4) 370s > tra[1, 2:4] <- TRUE 370s > tra[2, 3:4] <- TRUE 370s > 370s > tr.prob <- etm(my.observ, c("0","1","2","3"), tra, NULL, 0) 370s > 370s > tr.prob 370s Multistate model with 2 transient state(s) 370s and 2 absorbing state(s) 370s 370s Possible transitions: 370s from to 370s 0 1 370s 0 2 370s 0 3 370s 1 2 370s 1 3 370s 370s Estimate of P(0, 82) 370s 0 1 2 3 370s 0 0 0 0.7474 0.2526 370s 1 0 0 0.7073 0.2927 370s 2 0 0 1.0000 0.0000 370s 3 0 0 0.0000 1.0000 370s 370s > summary(tr.prob) 370s Transition 0 0 370s P time var lower upper n.risk n.event 370s 0.882275 3 1.374e-04 0.8593018 0.905248 756 0 370s 0.112434 15 1.320e-04 0.0899155 0.134952 90 0 370s 0.031746 27 4.066e-05 0.0192484 0.044244 26 0 370s 0.006614 41 8.690e-06 0.0008359 0.012392 5 0 370s 0.002646 61 3.490e-06 0.0000000 0.006307 3 0 370s 0.000000 82 0.000e+00 0.0000000 0.000000 1 0 370s 370s Transition 0 1 370s P time var lower upper n.risk n.event 370s 0.017196 3 2.235e-05 0.0079289 0.02646 756 13 370s 0.063492 15 7.865e-05 0.0461099 0.08087 90 0 370s 0.030423 27 3.902e-05 0.0181805 0.04267 26 1 370s 0.015873 41 2.066e-05 0.0069637 0.02478 5 0 370s 0.005291 61 6.962e-06 0.0001197 0.01046 3 0 370s 0.000000 82 0.000e+00 0.0000000 0.00000 1 0 370s 370s Transition 0 2 370s P time var lower upper n.risk n.event 370s 0.08466 3 0.0001025 0.06481 0.1045 756 64 370s 0.62302 15 0.0003107 0.58847 0.6576 90 4 370s 0.69841 27 0.0002786 0.66570 0.7311 26 1 370s 0.72751 41 0.0002622 0.69578 0.7593 5 0 370s 0.74074 61 0.0002540 0.70950 0.7720 3 1 370s 0.74735 82 0.0002498 0.71638 0.7783 1 1 370s 370s Transition 0 3 370s P time var lower upper n.risk n.event 370s 0.01587 3 2.066e-05 0.006964 0.02478 756 12 370s 0.20106 15 2.125e-04 0.172489 0.22963 90 1 370s 0.23942 27 2.409e-04 0.208999 0.26984 26 0 370s 0.25000 41 2.480e-04 0.219133 0.28087 5 0 370s 0.25132 61 2.489e-04 0.220402 0.28224 3 0 370s 0.25265 82 2.498e-04 0.221671 0.28362 1 0 370s 370s Transition 1 1 370s P time var lower upper n.risk n.event 370s 1.00000 3 0.000e+00 1.00000 1.00000 0 0 370s 0.38661 15 2.358e-03 0.29143 0.48179 51 0 370s 0.12119 27 7.842e-04 0.06630 0.17607 23 0 370s 0.04593 41 2.405e-04 0.01554 0.07633 14 0 370s 0.01531 61 6.579e-05 0.00000 0.03121 4 0 370s 0.00000 82 0.000e+00 0.00000 0.00000 0 0 370s 370s Transition 1 2 370s P time var lower upper n.risk n.event 370s 0.0000 3 0.000000 0.0000 0.0000 0 0 370s 0.4107 15 0.002590 0.3110 0.5104 51 2 370s 0.6082 27 0.002254 0.5151 0.7012 23 1 370s 0.6652 41 0.002064 0.5761 0.7542 14 2 370s 0.6920 61 0.002000 0.6043 0.7796 4 0 370s 0.7073 82 0.001984 0.6200 0.7946 0 0 370s 370s Transition 1 3 370s P time var lower upper n.risk n.event 370s 0.0000 3 0.000000 0.0000 0.0000 0 0 370s 0.2027 15 0.001784 0.1199 0.2855 51 1 370s 0.2706 27 0.001968 0.1837 0.3576 23 0 370s 0.2889 41 0.001982 0.2016 0.3761 14 0 370s 0.2927 61 0.001984 0.2054 0.3800 4 0 370s 0.2927 82 0.001984 0.2054 0.3800 0 0 370s 370s > 370s > cLOS <- etm::clos(tr.prob, aw = TRUE) 370s > 370s > cLOS 370s The expected change in length of stay is: 370s 1.975 370s 370s Alternative weighting: 370s 370s Expected change in LOS with weight.1: 2.097 370s Expected change in LOS with weight.other: 1.951 370s > 370s > 370s > ### Tests on pseudo values 370s > t_pseudo <- closPseudo(my.observ, c("0","1","2","3"), tra, NULL, 370s + formula = ~ 1, aw = TRUE) 385s > 385s > cLOS$e.phi == t_pseudo$theta[, "e.phi"] 385s [,1] 385s [1,] TRUE 385s > cLOS$e.phi.weights.1 == t_pseudo$theta[, "e.phi.weights.1"] 385s [,1] 385s [1,] TRUE 385s > cLOS$e.phi.weights.other == t_pseudo$theta[, "e.phi.weights.other"] 385s [,1] 385s [1,] TRUE 385s > 385s > mean(t_pseudo$pseudoData$ps.e.phi) 385s [1] 1.968 385s > 385s > ### tests on etmprep 385s > 385s > ### creation of fake data in the wild format, following an illness-death model 385s > ## transition times 385s > tdisease <- c(3, 4, 3, 6, 8, 9) 385s > tdeath <- c(6, 9, 8, 6, 8, 9) 385s > 385s > ## transition status 385s > stat.disease <- c(1, 1, 1, 0, 0, 0) 385s > stat.death <- c(1, 1, 1, 1, 1, 0) 385s > 385s > ## a covariate that we want to keep in the new data 385s > set.seed(1313) 385s > cova <- rbinom(6, 1, 0.5) 385s > 385s > dat <- data.frame(tdisease, tdeath, 385s + stat.disease, stat.death, 385s + cova) 385s > 385s > ## Possible transitions 385s > tra <- matrix(FALSE, 3, 3) 385s > tra[1, 2:3] <- TRUE 385s > tra[2, 3] <- TRUE 385s > 385s > ## data preparation 385s > newdat <- etmprep(c(NA, "tdisease", "tdeath"), 385s + c(NA, "stat.disease", "stat.death"), 385s + data = dat, tra = tra, 385s + cens.name = "cens", keep = "cova") 385s > 385s > newdat 385s id entry exit from to cova 385s 1 1 0 3 0 1 1 385s 2 1 3 6 1 2 1 385s 3 2 0 4 0 1 0 385s 4 2 4 9 1 2 0 385s 5 3 0 3 0 1 1 385s 6 3 3 8 1 2 1 385s 7 4 0 6 0 2 0 385s 8 5 0 8 0 2 1 385s 9 6 0 9 0 cens 1 385s > 385s > ref <- data.frame(id = c(1, 1, 2, 2, 3, 3, 4, 5, 6), 385s + entry = c(0, 3, 0, 4, 0, 3, 0, 0, 0), 385s + exit = c(3, 6, 4, 9, 3, 8, 6, 8, 9), 385s + from = c(0, 1, 0, 1, 0, 1, 0, 0, 0), 385s + to = c(rep(c(1, 2), 3), 2, 2, "cens"), 385s + cova = c(1, 1, 0, 0, 1, 1, 0, 1, 1)) 385s > ref$from <- factor(as.character(ref$from), levels = c("0", "1", "2", "cens")) 385s > ref$to <- factor(as.character(ref$to), levels = c("0", "1", "2", "cens")) 385s > 385s > all.equal(ref, newdat) 385s [1] TRUE 385s > 385s > 385s > ###################################### 385s > ### Test the stratified calls 385s > ###################################### 385s > 385s > if (require("kmi", quietly = TRUE)) { 385s + library(etm) 385s + 385s + data(icu.pneu) 385s + my.icu.pneu <- icu.pneu 385s + 385s + my.icu.pneu <- my.icu.pneu[order(my.icu.pneu$id, my.icu.pneu$start), ] 385s + masque <- diff(my.icu.pneu$id) 385s + 385s + my.icu.pneu$from <- 0 385s + my.icu.pneu$from[c(1, masque) == 0] <- 1 385s + 385s + my.icu.pneu$to2 <- my.icu.pneu$event 385s + my.icu.pneu$to2[my.icu.pneu$status == 0] <- "cens" 385s + my.icu.pneu$to2[c(masque, 1) == 0] <- 1 385s + 385s + 385s + my.icu.pneu$to <- ifelse(my.icu.pneu$to2 %in% c(2, 3), 2, 385s + my.icu.pneu$to2) 385s + 385s + my.icu.pneu <- my.icu.pneu[, c("id", "start", "stop", "from", "to", 385s + "to2", "age", "sex")] 385s + names(my.icu.pneu)[c(2, 3)] <- c("entry", "exit") 385s + 385s + bouh_strat <- etm(my.icu.pneu, c("0", "1", "2"), tra_ill(), "cens", 0, strata = "sex") 385s + 385s + bouh_female <- etm(my.icu.pneu[my.icu.pneu$sex == "F", ], 385s + c("0", "1", "2"), tra_ill(), "cens", 0) 385s + 385s + all(bouh_strat[[1]]$est == bouh_female$est) 385s + 385s + ## Test the summary 385s + the_summary <- summary(bouh_strat) 385s + the_summary 385s + 385s + ## Test trprob 385s + all(trprob(bouh_strat, "0 1")[[1]] == trprob(bouh_female, "0 1")) 385s + all(trprob(bouh_strat, "0 1", c(0, 5, 10, 15))[[1]] == trprob(bouh_female, "0 1", c(0, 5, 10, 15))) 385s + 385s + ## Test trcov 385s + all(trcov(bouh_strat, "0 1")[[1]] == trcov(bouh_female, "0 1")) 385s + all(trcov(bouh_strat, c("0 1", "0 2"))[[1]] == trcov(bouh_female, c("0 1", "0 2"))) 385s + all(trcov(bouh_strat, "0 1", c(0, 5, 10, 15))[[1]] == trcov(bouh_female, "0 1", c(0, 5, 10, 15))) 385s + } else { 385s + print("These tests require the kmi package") 385s + } 386s [1] TRUE 386s > 386s > options(old) 386s > 386s autopkgtest [23:25:18]: test run-unit-test: -----------------------] 390s autopkgtest [23:25:22]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 390s run-unit-test PASS 394s autopkgtest [23:25:26]: test pkg-r-autopkgtest: preparing testbed 396s Reading package lists... 396s Building dependency tree... 396s Reading state information... 396s Solving dependencies... 397s The following NEW packages will be installed: 397s build-essential cpp cpp-15 cpp-15-arm-linux-gnueabihf 397s cpp-arm-linux-gnueabihf dctrl-tools g++ g++-15 g++-15-arm-linux-gnueabihf 397s g++-arm-linux-gnueabihf gcc gcc-15 gcc-15-arm-linux-gnueabihf 397s gcc-arm-linux-gnueabihf gfortran gfortran-15 gfortran-15-arm-linux-gnueabihf 397s gfortran-arm-linux-gnueabihf icu-devtools libasan8 libblas-dev libbz2-dev 397s libc-dev-bin libc6-dev libcc1-0 libcrypt-dev libdeflate-dev libgcc-15-dev 397s libgfortran-15-dev libicu-dev libisl23 libjpeg-dev libjpeg-turbo8-dev 397s libjpeg8-dev liblapack-dev liblzma-dev libmpc3 libncurses-dev libpcre2-16-0 397s libpcre2-32-0 libpcre2-dev libpcre2-posix3 libpkgconf3 libpng-dev 397s libreadline-dev libstdc++-15-dev libtirpc-dev libubsan1 libzstd-dev 397s linux-libc-dev pkg-r-autopkgtest pkgconf pkgconf-bin r-base-dev 397s r-cran-backports r-cran-broom r-cran-cli r-cran-cpp11 r-cran-dplyr 397s r-cran-fansi r-cran-farver r-cran-geepack r-cran-generics r-cran-ggplot2 397s r-cran-glue r-cran-gtable r-cran-isoband r-cran-labeling r-cran-lifecycle 397s r-cran-magrittr r-cran-mass r-cran-pillar r-cran-pkgconfig r-cran-purrr 397s r-cran-r6 r-cran-rcolorbrewer r-cran-rlang r-cran-s7 r-cran-scales 397s r-cran-stringi r-cran-stringr r-cran-tibble r-cran-tidyr r-cran-tidyselect 397s r-cran-utf8 r-cran-vctrs r-cran-viridislite r-cran-withr rpcsvc-proto 397s zlib1g-dev 397s 0 upgraded, 90 newly installed, 0 to remove and 0 not upgraded. 397s Need to get 108 MB of archives. 397s After this operation, 296 MB of additional disk space will be used. 397s Get:1 http://ftpmaster.internal/ubuntu resolute/main armhf libc-dev-bin armhf 2.42-2ubuntu4 [21.8 kB] 397s Get:2 http://ftpmaster.internal/ubuntu resolute/main armhf linux-libc-dev armhf 6.19.0-3.3 [1804 kB] 404s Get:3 http://ftpmaster.internal/ubuntu resolute/main armhf libcrypt-dev armhf 1:4.5.1-1 [128 kB] 405s Get:4 http://ftpmaster.internal/ubuntu resolute/main armhf rpcsvc-proto armhf 1.4.3-1build1 [62.6 kB] 405s Get:5 http://ftpmaster.internal/ubuntu resolute/main armhf libc6-dev armhf 2.42-2ubuntu4 [1416 kB] 409s Get:6 http://ftpmaster.internal/ubuntu resolute/main armhf libisl23 armhf 0.27-1build1 [553 kB] 410s Get:7 http://ftpmaster.internal/ubuntu resolute/main armhf libmpc3 armhf 1.3.1-2 [47.0 kB] 410s Get:8 http://ftpmaster.internal/ubuntu resolute/main armhf cpp-15-arm-linux-gnueabihf armhf 15.2.0-12ubuntu1 [10.1 MB] 427s Get:9 http://ftpmaster.internal/ubuntu resolute/main armhf cpp-15 armhf 15.2.0-12ubuntu1 [1032 B] 427s Get:10 http://ftpmaster.internal/ubuntu resolute/main armhf cpp-arm-linux-gnueabihf armhf 4:15.2.0-4ubuntu1 [5756 B] 427s Get:11 http://ftpmaster.internal/ubuntu resolute/main armhf cpp armhf 4:15.2.0-4ubuntu1 [22.4 kB] 427s Get:12 http://ftpmaster.internal/ubuntu resolute/main armhf libcc1-0 armhf 15.2.0-12ubuntu1 [43.5 kB] 427s Get:13 http://ftpmaster.internal/ubuntu resolute/main armhf libasan8 armhf 15.2.0-12ubuntu1 [2949 kB] 432s Get:14 http://ftpmaster.internal/ubuntu resolute/main armhf libubsan1 armhf 15.2.0-12ubuntu1 [1187 kB] 434s Get:15 http://ftpmaster.internal/ubuntu resolute/main armhf libgcc-15-dev armhf 15.2.0-12ubuntu1 [898 kB] 435s Get:16 http://ftpmaster.internal/ubuntu resolute/main armhf gcc-15-arm-linux-gnueabihf armhf 15.2.0-12ubuntu1 [19.5 MB] 470s Get:17 http://ftpmaster.internal/ubuntu resolute/main armhf gcc-15 armhf 15.2.0-12ubuntu1 [499 kB] 471s Get:18 http://ftpmaster.internal/ubuntu resolute/main armhf gcc-arm-linux-gnueabihf armhf 4:15.2.0-4ubuntu1 [1220 B] 471s Get:19 http://ftpmaster.internal/ubuntu resolute/main armhf gcc armhf 4:15.2.0-4ubuntu1 [5022 B] 471s Get:20 http://ftpmaster.internal/ubuntu resolute/main armhf libstdc++-15-dev armhf 15.2.0-12ubuntu1 [2638 kB] 476s Get:21 http://ftpmaster.internal/ubuntu resolute/main armhf g++-15-arm-linux-gnueabihf armhf 15.2.0-12ubuntu1 [11.4 MB] 499s Get:22 http://ftpmaster.internal/ubuntu resolute/main armhf g++-15 armhf 15.2.0-12ubuntu1 [25.3 kB] 499s Get:23 http://ftpmaster.internal/ubuntu resolute/main armhf g++-arm-linux-gnueabihf armhf 4:15.2.0-4ubuntu1 [968 B] 499s Get:24 http://ftpmaster.internal/ubuntu resolute/main armhf g++ armhf 4:15.2.0-4ubuntu1 [1086 B] 499s Get:25 http://ftpmaster.internal/ubuntu resolute/main armhf build-essential armhf 12.12ubuntu2 [5256 B] 499s Get:26 http://ftpmaster.internal/ubuntu resolute/main armhf dctrl-tools armhf 2.24-3build4 [95.0 kB] 499s Get:27 http://ftpmaster.internal/ubuntu resolute/main armhf libgfortran-15-dev armhf 15.2.0-12ubuntu1 [380 kB] 500s Get:28 http://ftpmaster.internal/ubuntu resolute/main armhf gfortran-15-arm-linux-gnueabihf armhf 15.2.0-12ubuntu1 [10.7 MB] 517s Get:29 http://ftpmaster.internal/ubuntu resolute/main armhf gfortran-15 armhf 15.2.0-12ubuntu1 [18.1 kB] 517s Get:30 http://ftpmaster.internal/ubuntu resolute/main armhf gfortran-arm-linux-gnueabihf armhf 4:15.2.0-4ubuntu1 [1020 B] 517s Get:31 http://ftpmaster.internal/ubuntu resolute/main armhf gfortran armhf 4:15.2.0-4ubuntu1 [1162 B] 517s Get:32 http://ftpmaster.internal/ubuntu resolute/main armhf icu-devtools armhf 78.2-1ubuntu1 [203 kB] 518s Get:33 http://ftpmaster.internal/ubuntu resolute/main armhf libblas-dev armhf 3.12.1-7ubuntu1 [141 kB] 518s Get:34 http://ftpmaster.internal/ubuntu resolute/main armhf libbz2-dev armhf 1.0.8-6build2 [31.2 kB] 518s Get:35 http://ftpmaster.internal/ubuntu resolute/main armhf libdeflate-dev armhf 1.23-2build1 [45.1 kB] 518s Get:36 http://ftpmaster.internal/ubuntu resolute/main armhf libicu-dev armhf 78.2-1ubuntu1 [12.2 MB] 541s Get:37 http://ftpmaster.internal/ubuntu resolute/main armhf libjpeg-turbo8-dev armhf 2.1.5-4ubuntu3 [265 kB] 541s Get:38 http://ftpmaster.internal/ubuntu resolute/main armhf libjpeg8-dev armhf 8c-2ubuntu11 [1484 B] 541s Get:39 http://ftpmaster.internal/ubuntu resolute/main armhf libjpeg-dev armhf 8c-2ubuntu11 [1482 B] 541s Get:40 http://ftpmaster.internal/ubuntu resolute/main armhf liblapack-dev armhf 3.12.1-7ubuntu1 [2207 kB] 545s Get:41 http://ftpmaster.internal/ubuntu resolute/main armhf libncurses-dev armhf 6.6+20251231-1 [348 kB] 546s Get:42 http://ftpmaster.internal/ubuntu resolute/main armhf libpcre2-16-0 armhf 10.46-1 [206 kB] 546s Get:43 http://ftpmaster.internal/ubuntu resolute/main armhf libpcre2-32-0 armhf 10.46-1 [197 kB] 547s Get:44 http://ftpmaster.internal/ubuntu resolute/main armhf libpcre2-posix3 armhf 10.46-1 [6286 B] 547s Get:45 http://ftpmaster.internal/ubuntu resolute/main armhf libpcre2-dev armhf 10.46-1 [744 kB] 548s Get:46 http://ftpmaster.internal/ubuntu resolute/main armhf libpkgconf3 armhf 1.8.1-4build1 [26.6 kB] 548s Get:47 http://ftpmaster.internal/ubuntu resolute/main armhf zlib1g-dev armhf 1:1.3.dfsg+really1.3.1-1ubuntu2 [881 kB] 550s Get:48 http://ftpmaster.internal/ubuntu resolute/main armhf libpng-dev armhf 1.6.54-1 [252 kB] 550s Get:49 http://ftpmaster.internal/ubuntu resolute/main armhf libreadline-dev armhf 8.3-3 [165 kB] 550s Get:50 http://ftpmaster.internal/ubuntu resolute/main armhf libzstd-dev armhf 1.5.7+dfsg-3 [342 kB] 551s Get:51 http://ftpmaster.internal/ubuntu resolute/main armhf liblzma-dev armhf 5.8.2-2 [167 kB] 551s Get:52 http://ftpmaster.internal/ubuntu resolute/main armhf pkgconf-bin armhf 1.8.1-4build1 [21.4 kB] 551s Get:53 http://ftpmaster.internal/ubuntu resolute/main armhf pkgconf armhf 1.8.1-4build1 [16.8 kB] 551s Get:54 http://ftpmaster.internal/ubuntu resolute/main armhf libtirpc-dev armhf 1.3.6+ds-1 [184 kB] 552s Get:55 http://ftpmaster.internal/ubuntu resolute/universe armhf r-base-dev all 4.5.2-1ubuntu2 [1880 B] 552s Get:56 http://ftpmaster.internal/ubuntu resolute/universe armhf pkg-r-autopkgtest all 20250812 [6158 B] 552s Get:57 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-backports armhf 1.5.0-2 [121 kB] 552s Get:58 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-cli armhf 3.6.4-1 [1377 kB] 554s Get:59 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-generics all 0.1.4-1 [84.0 kB] 554s Get:60 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-glue armhf 1.8.0-1 [162 kB] 555s Get:61 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-rlang armhf 1.1.5-3 [1700 kB] 558s Get:62 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-lifecycle all 1.0.5+dfsg-1 [120 kB] 558s Get:63 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-magrittr armhf 2.0.3-1 [154 kB] 558s Get:64 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-utf8 armhf 1.2.4-1 [136 kB] 558s Get:65 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-vctrs armhf 0.6.5-1 [1310 kB] 561s Get:66 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-pillar all 1.11.1+dfsg-1 [456 kB] 561s Get:67 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-r6 all 2.6.1-1 [101 kB] 562s Get:68 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-fansi armhf 1.0.6-2 [620 kB] 563s Get:69 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-pkgconfig all 2.0.3-2build2 [20.4 kB] 563s Get:70 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-tibble armhf 3.2.1+dfsg-3 [420 kB] 563s Get:71 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-withr all 3.0.2+dfsg-1 [214 kB] 564s Get:72 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-tidyselect armhf 1.2.1+dfsg-1 [222 kB] 564s Get:73 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-dplyr armhf 1.1.4-4 [1533 kB] 566s Get:74 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-purrr armhf 1.0.4-1 [550 kB] 567s Get:75 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-stringi armhf 1.8.4-1build2 [884 kB] 569s Get:76 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-stringr all 1.5.1-1 [290 kB] 570s Get:77 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-cpp11 all 0.5.3-1 [242 kB] 570s Get:78 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-tidyr armhf 1.3.1-1 [1152 kB] 573s Get:79 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-broom all 1.0.12+dfsg-1 [1708 kB] 576s Get:80 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-farver armhf 2.1.2-1 [1355 kB] 578s Get:81 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-mass armhf 7.3-65-1 [1108 kB] 580s Get:82 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-geepack armhf 1.3.12-1 [365 kB] 581s Get:83 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-gtable all 0.3.6+dfsg-1 [199 kB] 581s Get:84 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-isoband armhf 0.2.7-1 [1477 kB] 584s Get:85 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-s7 armhf 0.2.0-1 [328 kB] 584s Get:86 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-labeling all 0.4.3-1 [62.1 kB] 584s Get:87 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-rcolorbrewer all 1.1-3-1build2 [54.0 kB] 584s Get:88 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-viridislite all 0.4.3-1 [1088 kB] 586s Get:89 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-scales all 1.4.0-1 [725 kB] 587s Get:90 http://ftpmaster.internal/ubuntu resolute-proposed/universe armhf r-cran-ggplot2 all 4.0.2+dfsg-1 [4941 kB] 596s Fetched 108 MB in 3min 19s (545 kB/s) 596s Selecting previously unselected package libc-dev-bin. 596s (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 ... 73886 files and directories currently installed.) 596s Preparing to unpack .../00-libc-dev-bin_2.42-2ubuntu4_armhf.deb ... 596s Unpacking libc-dev-bin (2.42-2ubuntu4) ... 596s Selecting previously unselected package linux-libc-dev:armhf. 596s Preparing to unpack .../01-linux-libc-dev_6.19.0-3.3_armhf.deb ... 596s Unpacking linux-libc-dev:armhf (6.19.0-3.3) ... 596s Selecting previously unselected package libcrypt-dev:armhf. 596s Preparing to unpack .../02-libcrypt-dev_1%3a4.5.1-1_armhf.deb ... 596s Unpacking libcrypt-dev:armhf (1:4.5.1-1) ... 596s Selecting previously unselected package rpcsvc-proto. 596s Preparing to unpack .../03-rpcsvc-proto_1.4.3-1build1_armhf.deb ... 596s Unpacking rpcsvc-proto (1.4.3-1build1) ... 596s Selecting previously unselected package libc6-dev:armhf. 597s Preparing to unpack .../04-libc6-dev_2.42-2ubuntu4_armhf.deb ... 597s Unpacking libc6-dev:armhf (2.42-2ubuntu4) ... 597s Selecting previously unselected package libisl23:armhf. 597s Preparing to unpack .../05-libisl23_0.27-1build1_armhf.deb ... 597s Unpacking libisl23:armhf (0.27-1build1) ... 597s Selecting previously unselected package libmpc3:armhf. 597s Preparing to unpack .../06-libmpc3_1.3.1-2_armhf.deb ... 597s Unpacking libmpc3:armhf (1.3.1-2) ... 597s Selecting previously unselected package cpp-15-arm-linux-gnueabihf. 597s Preparing to unpack .../07-cpp-15-arm-linux-gnueabihf_15.2.0-12ubuntu1_armhf.deb ... 597s Unpacking cpp-15-arm-linux-gnueabihf (15.2.0-12ubuntu1) ... 597s Selecting previously unselected package cpp-15. 597s Preparing to unpack .../08-cpp-15_15.2.0-12ubuntu1_armhf.deb ... 597s Unpacking cpp-15 (15.2.0-12ubuntu1) ... 597s Selecting previously unselected package cpp-arm-linux-gnueabihf. 597s Preparing to unpack .../09-cpp-arm-linux-gnueabihf_4%3a15.2.0-4ubuntu1_armhf.deb ... 597s Unpacking cpp-arm-linux-gnueabihf (4:15.2.0-4ubuntu1) ... 597s Selecting previously unselected package cpp. 597s Preparing to unpack .../10-cpp_4%3a15.2.0-4ubuntu1_armhf.deb ... 597s Unpacking cpp (4:15.2.0-4ubuntu1) ... 597s Selecting previously unselected package libcc1-0:armhf. 597s Preparing to unpack .../11-libcc1-0_15.2.0-12ubuntu1_armhf.deb ... 597s Unpacking libcc1-0:armhf (15.2.0-12ubuntu1) ... 597s Selecting previously unselected package libasan8:armhf. 597s Preparing to unpack .../12-libasan8_15.2.0-12ubuntu1_armhf.deb ... 597s Unpacking libasan8:armhf (15.2.0-12ubuntu1) ... 597s Selecting previously unselected package libubsan1:armhf. 597s Preparing to unpack .../13-libubsan1_15.2.0-12ubuntu1_armhf.deb ... 597s Unpacking libubsan1:armhf (15.2.0-12ubuntu1) ... 597s Selecting previously unselected package libgcc-15-dev:armhf. 597s Preparing to unpack .../14-libgcc-15-dev_15.2.0-12ubuntu1_armhf.deb ... 597s Unpacking libgcc-15-dev:armhf (15.2.0-12ubuntu1) ... 597s Selecting previously unselected package gcc-15-arm-linux-gnueabihf. 597s Preparing to unpack .../15-gcc-15-arm-linux-gnueabihf_15.2.0-12ubuntu1_armhf.deb ... 597s Unpacking gcc-15-arm-linux-gnueabihf (15.2.0-12ubuntu1) ... 598s Selecting previously unselected package gcc-15. 598s Preparing to unpack .../16-gcc-15_15.2.0-12ubuntu1_armhf.deb ... 598s Unpacking gcc-15 (15.2.0-12ubuntu1) ... 598s Selecting previously unselected package gcc-arm-linux-gnueabihf. 598s Preparing to unpack .../17-gcc-arm-linux-gnueabihf_4%3a15.2.0-4ubuntu1_armhf.deb ... 598s Unpacking gcc-arm-linux-gnueabihf (4:15.2.0-4ubuntu1) ... 598s Selecting previously unselected package gcc. 598s Preparing to unpack .../18-gcc_4%3a15.2.0-4ubuntu1_armhf.deb ... 598s Unpacking gcc (4:15.2.0-4ubuntu1) ... 598s Selecting previously unselected package libstdc++-15-dev:armhf. 598s Preparing to unpack .../19-libstdc++-15-dev_15.2.0-12ubuntu1_armhf.deb ... 598s Unpacking libstdc++-15-dev:armhf (15.2.0-12ubuntu1) ... 598s Selecting previously unselected package g++-15-arm-linux-gnueabihf. 598s Preparing to unpack .../20-g++-15-arm-linux-gnueabihf_15.2.0-12ubuntu1_armhf.deb ... 598s Unpacking g++-15-arm-linux-gnueabihf (15.2.0-12ubuntu1) ... 598s Selecting previously unselected package g++-15. 598s Preparing to unpack .../21-g++-15_15.2.0-12ubuntu1_armhf.deb ... 598s Unpacking g++-15 (15.2.0-12ubuntu1) ... 598s Selecting previously unselected package g++-arm-linux-gnueabihf. 598s Preparing to unpack .../22-g++-arm-linux-gnueabihf_4%3a15.2.0-4ubuntu1_armhf.deb ... 598s Unpacking g++-arm-linux-gnueabihf (4:15.2.0-4ubuntu1) ... 598s Selecting previously unselected package g++. 598s Preparing to unpack .../23-g++_4%3a15.2.0-4ubuntu1_armhf.deb ... 598s Unpacking g++ (4:15.2.0-4ubuntu1) ... 598s Selecting previously unselected package build-essential. 598s Preparing to unpack .../24-build-essential_12.12ubuntu2_armhf.deb ... 598s Unpacking build-essential (12.12ubuntu2) ... 599s Selecting previously unselected package dctrl-tools. 599s Preparing to unpack .../25-dctrl-tools_2.24-3build4_armhf.deb ... 599s Unpacking dctrl-tools (2.24-3build4) ... 599s Selecting previously unselected package libgfortran-15-dev:armhf. 599s Preparing to unpack .../26-libgfortran-15-dev_15.2.0-12ubuntu1_armhf.deb ... 599s Unpacking libgfortran-15-dev:armhf (15.2.0-12ubuntu1) ... 599s Selecting previously unselected package gfortran-15-arm-linux-gnueabihf. 599s Preparing to unpack .../27-gfortran-15-arm-linux-gnueabihf_15.2.0-12ubuntu1_armhf.deb ... 599s Unpacking gfortran-15-arm-linux-gnueabihf (15.2.0-12ubuntu1) ... 599s Selecting previously unselected package gfortran-15. 599s Preparing to unpack .../28-gfortran-15_15.2.0-12ubuntu1_armhf.deb ... 599s Unpacking gfortran-15 (15.2.0-12ubuntu1) ... 599s Selecting previously unselected package gfortran-arm-linux-gnueabihf. 599s Preparing to unpack .../29-gfortran-arm-linux-gnueabihf_4%3a15.2.0-4ubuntu1_armhf.deb ... 599s Unpacking gfortran-arm-linux-gnueabihf (4:15.2.0-4ubuntu1) ... 599s Selecting previously unselected package gfortran. 599s Preparing to unpack .../30-gfortran_4%3a15.2.0-4ubuntu1_armhf.deb ... 599s Unpacking gfortran (4:15.2.0-4ubuntu1) ... 599s Selecting previously unselected package icu-devtools. 599s Preparing to unpack .../31-icu-devtools_78.2-1ubuntu1_armhf.deb ... 599s Unpacking icu-devtools (78.2-1ubuntu1) ... 599s Selecting previously unselected package libblas-dev:armhf. 599s Preparing to unpack .../32-libblas-dev_3.12.1-7ubuntu1_armhf.deb ... 599s Unpacking libblas-dev:armhf (3.12.1-7ubuntu1) ... 599s Selecting previously unselected package libbz2-dev:armhf. 599s Preparing to unpack .../33-libbz2-dev_1.0.8-6build2_armhf.deb ... 599s Unpacking libbz2-dev:armhf (1.0.8-6build2) ... 599s Selecting previously unselected package libdeflate-dev:armhf. 599s Preparing to unpack .../34-libdeflate-dev_1.23-2build1_armhf.deb ... 599s Unpacking libdeflate-dev:armhf (1.23-2build1) ... 599s Selecting previously unselected package libicu-dev:armhf. 599s Preparing to unpack .../35-libicu-dev_78.2-1ubuntu1_armhf.deb ... 599s Unpacking libicu-dev:armhf (78.2-1ubuntu1) ... 599s Selecting previously unselected package libjpeg-turbo8-dev:armhf. 599s Preparing to unpack .../36-libjpeg-turbo8-dev_2.1.5-4ubuntu3_armhf.deb ... 599s Unpacking libjpeg-turbo8-dev:armhf (2.1.5-4ubuntu3) ... 600s Selecting previously unselected package libjpeg8-dev:armhf. 600s Preparing to unpack .../37-libjpeg8-dev_8c-2ubuntu11_armhf.deb ... 600s Unpacking libjpeg8-dev:armhf (8c-2ubuntu11) ... 600s Selecting previously unselected package libjpeg-dev:armhf. 600s Preparing to unpack .../38-libjpeg-dev_8c-2ubuntu11_armhf.deb ... 600s Unpacking libjpeg-dev:armhf (8c-2ubuntu11) ... 600s Selecting previously unselected package liblapack-dev:armhf. 600s Preparing to unpack .../39-liblapack-dev_3.12.1-7ubuntu1_armhf.deb ... 600s Unpacking liblapack-dev:armhf (3.12.1-7ubuntu1) ... 600s Selecting previously unselected package libncurses-dev:armhf. 600s Preparing to unpack .../40-libncurses-dev_6.6+20251231-1_armhf.deb ... 600s Unpacking libncurses-dev:armhf (6.6+20251231-1) ... 600s Selecting previously unselected package libpcre2-16-0:armhf. 600s Preparing to unpack .../41-libpcre2-16-0_10.46-1_armhf.deb ... 600s Unpacking libpcre2-16-0:armhf (10.46-1) ... 600s Selecting previously unselected package libpcre2-32-0:armhf. 600s Preparing to unpack .../42-libpcre2-32-0_10.46-1_armhf.deb ... 600s Unpacking libpcre2-32-0:armhf (10.46-1) ... 600s Selecting previously unselected package libpcre2-posix3:armhf. 600s Preparing to unpack .../43-libpcre2-posix3_10.46-1_armhf.deb ... 600s Unpacking libpcre2-posix3:armhf (10.46-1) ... 600s Selecting previously unselected package libpcre2-dev:armhf. 600s Preparing to unpack .../44-libpcre2-dev_10.46-1_armhf.deb ... 600s Unpacking libpcre2-dev:armhf (10.46-1) ... 600s Selecting previously unselected package libpkgconf3:armhf. 600s Preparing to unpack .../45-libpkgconf3_1.8.1-4build1_armhf.deb ... 600s Unpacking libpkgconf3:armhf (1.8.1-4build1) ... 600s Selecting previously unselected package zlib1g-dev:armhf. 600s Preparing to unpack .../46-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1ubuntu2_armhf.deb ... 600s Unpacking zlib1g-dev:armhf (1:1.3.dfsg+really1.3.1-1ubuntu2) ... 600s Selecting previously unselected package libpng-dev:armhf. 600s Preparing to unpack .../47-libpng-dev_1.6.54-1_armhf.deb ... 600s Unpacking libpng-dev:armhf (1.6.54-1) ... 600s Selecting previously unselected package libreadline-dev:armhf. 600s Preparing to unpack .../48-libreadline-dev_8.3-3_armhf.deb ... 600s Unpacking libreadline-dev:armhf (8.3-3) ... 600s Selecting previously unselected package libzstd-dev:armhf. 600s Preparing to unpack .../49-libzstd-dev_1.5.7+dfsg-3_armhf.deb ... 600s Unpacking libzstd-dev:armhf (1.5.7+dfsg-3) ... 600s Selecting previously unselected package liblzma-dev:armhf. 600s Preparing to unpack .../50-liblzma-dev_5.8.2-2_armhf.deb ... 600s Unpacking liblzma-dev:armhf (5.8.2-2) ... 600s Selecting previously unselected package pkgconf-bin. 600s Preparing to unpack .../51-pkgconf-bin_1.8.1-4build1_armhf.deb ... 600s Unpacking pkgconf-bin (1.8.1-4build1) ... 600s Selecting previously unselected package pkgconf:armhf. 600s Preparing to unpack .../52-pkgconf_1.8.1-4build1_armhf.deb ... 600s Unpacking pkgconf:armhf (1.8.1-4build1) ... 600s Selecting previously unselected package libtirpc-dev:armhf. 600s Preparing to unpack .../53-libtirpc-dev_1.3.6+ds-1_armhf.deb ... 600s Unpacking libtirpc-dev:armhf (1.3.6+ds-1) ... 600s Selecting previously unselected package r-base-dev. 600s Preparing to unpack .../54-r-base-dev_4.5.2-1ubuntu2_all.deb ... 600s Unpacking r-base-dev (4.5.2-1ubuntu2) ... 600s Selecting previously unselected package pkg-r-autopkgtest. 600s Preparing to unpack .../55-pkg-r-autopkgtest_20250812_all.deb ... 600s Unpacking pkg-r-autopkgtest (20250812) ... 600s Selecting previously unselected package r-cran-backports. 600s Preparing to unpack .../56-r-cran-backports_1.5.0-2_armhf.deb ... 600s Unpacking r-cran-backports (1.5.0-2) ... 600s Selecting previously unselected package r-cran-cli. 600s Preparing to unpack .../57-r-cran-cli_3.6.4-1_armhf.deb ... 600s Unpacking r-cran-cli (3.6.4-1) ... 601s Selecting previously unselected package r-cran-generics. 601s Preparing to unpack .../58-r-cran-generics_0.1.4-1_all.deb ... 601s Unpacking r-cran-generics (0.1.4-1) ... 601s Selecting previously unselected package r-cran-glue. 601s Preparing to unpack .../59-r-cran-glue_1.8.0-1_armhf.deb ... 601s Unpacking r-cran-glue (1.8.0-1) ... 601s Selecting previously unselected package r-cran-rlang. 601s Preparing to unpack .../60-r-cran-rlang_1.1.5-3_armhf.deb ... 601s Unpacking r-cran-rlang (1.1.5-3) ... 601s Selecting previously unselected package r-cran-lifecycle. 601s Preparing to unpack .../61-r-cran-lifecycle_1.0.5+dfsg-1_all.deb ... 601s Unpacking r-cran-lifecycle (1.0.5+dfsg-1) ... 601s Selecting previously unselected package r-cran-magrittr. 601s Preparing to unpack .../62-r-cran-magrittr_2.0.3-1_armhf.deb ... 601s Unpacking r-cran-magrittr (2.0.3-1) ... 601s Selecting previously unselected package r-cran-utf8. 601s Preparing to unpack .../63-r-cran-utf8_1.2.4-1_armhf.deb ... 601s Unpacking r-cran-utf8 (1.2.4-1) ... 601s Selecting previously unselected package r-cran-vctrs. 601s Preparing to unpack .../64-r-cran-vctrs_0.6.5-1_armhf.deb ... 601s Unpacking r-cran-vctrs (0.6.5-1) ... 601s Selecting previously unselected package r-cran-pillar. 601s Preparing to unpack .../65-r-cran-pillar_1.11.1+dfsg-1_all.deb ... 601s Unpacking r-cran-pillar (1.11.1+dfsg-1) ... 601s Selecting previously unselected package r-cran-r6. 601s Preparing to unpack .../66-r-cran-r6_2.6.1-1_all.deb ... 601s Unpacking r-cran-r6 (2.6.1-1) ... 601s Selecting previously unselected package r-cran-fansi. 601s Preparing to unpack .../67-r-cran-fansi_1.0.6-2_armhf.deb ... 601s Unpacking r-cran-fansi (1.0.6-2) ... 601s Selecting previously unselected package r-cran-pkgconfig. 602s Preparing to unpack .../68-r-cran-pkgconfig_2.0.3-2build2_all.deb ... 602s Unpacking r-cran-pkgconfig (2.0.3-2build2) ... 602s Selecting previously unselected package r-cran-tibble. 602s Preparing to unpack .../69-r-cran-tibble_3.2.1+dfsg-3_armhf.deb ... 602s Unpacking r-cran-tibble (3.2.1+dfsg-3) ... 602s Selecting previously unselected package r-cran-withr. 602s Preparing to unpack .../70-r-cran-withr_3.0.2+dfsg-1_all.deb ... 602s Unpacking r-cran-withr (3.0.2+dfsg-1) ... 602s Selecting previously unselected package r-cran-tidyselect. 602s Preparing to unpack .../71-r-cran-tidyselect_1.2.1+dfsg-1_armhf.deb ... 602s Unpacking r-cran-tidyselect (1.2.1+dfsg-1) ... 602s Selecting previously unselected package r-cran-dplyr. 602s Preparing to unpack .../72-r-cran-dplyr_1.1.4-4_armhf.deb ... 602s Unpacking r-cran-dplyr (1.1.4-4) ... 602s Selecting previously unselected package r-cran-purrr. 602s Preparing to unpack .../73-r-cran-purrr_1.0.4-1_armhf.deb ... 602s Unpacking r-cran-purrr (1.0.4-1) ... 602s Selecting previously unselected package r-cran-stringi. 602s Preparing to unpack .../74-r-cran-stringi_1.8.4-1build2_armhf.deb ... 602s Unpacking r-cran-stringi (1.8.4-1build2) ... 602s Selecting previously unselected package r-cran-stringr. 602s Preparing to unpack .../75-r-cran-stringr_1.5.1-1_all.deb ... 602s Unpacking r-cran-stringr (1.5.1-1) ... 602s Selecting previously unselected package r-cran-cpp11. 602s Preparing to unpack .../76-r-cran-cpp11_0.5.3-1_all.deb ... 602s Unpacking r-cran-cpp11 (0.5.3-1) ... 602s Selecting previously unselected package r-cran-tidyr. 602s Preparing to unpack .../77-r-cran-tidyr_1.3.1-1_armhf.deb ... 602s Unpacking r-cran-tidyr (1.3.1-1) ... 602s Selecting previously unselected package r-cran-broom. 602s Preparing to unpack .../78-r-cran-broom_1.0.12+dfsg-1_all.deb ... 602s Unpacking r-cran-broom (1.0.12+dfsg-1) ... 602s Selecting previously unselected package r-cran-farver. 602s Preparing to unpack .../79-r-cran-farver_2.1.2-1_armhf.deb ... 602s Unpacking r-cran-farver (2.1.2-1) ... 602s Selecting previously unselected package r-cran-mass. 602s Preparing to unpack .../80-r-cran-mass_7.3-65-1_armhf.deb ... 602s Unpacking r-cran-mass (7.3-65-1) ... 602s Selecting previously unselected package r-cran-geepack. 602s Preparing to unpack .../81-r-cran-geepack_1.3.12-1_armhf.deb ... 602s Unpacking r-cran-geepack (1.3.12-1) ... 602s Selecting previously unselected package r-cran-gtable. 602s Preparing to unpack .../82-r-cran-gtable_0.3.6+dfsg-1_all.deb ... 602s Unpacking r-cran-gtable (0.3.6+dfsg-1) ... 602s Selecting previously unselected package r-cran-isoband. 602s Preparing to unpack .../83-r-cran-isoband_0.2.7-1_armhf.deb ... 602s Unpacking r-cran-isoband (0.2.7-1) ... 602s Selecting previously unselected package r-cran-s7. 602s Preparing to unpack .../84-r-cran-s7_0.2.0-1_armhf.deb ... 602s Unpacking r-cran-s7 (0.2.0-1) ... 602s Selecting previously unselected package r-cran-labeling. 602s Preparing to unpack .../85-r-cran-labeling_0.4.3-1_all.deb ... 602s Unpacking r-cran-labeling (0.4.3-1) ... 602s Selecting previously unselected package r-cran-rcolorbrewer. 602s Preparing to unpack .../86-r-cran-rcolorbrewer_1.1-3-1build2_all.deb ... 602s Unpacking r-cran-rcolorbrewer (1.1-3-1build2) ... 602s Selecting previously unselected package r-cran-viridislite. 602s Preparing to unpack .../87-r-cran-viridislite_0.4.3-1_all.deb ... 602s Unpacking r-cran-viridislite (0.4.3-1) ... 603s Selecting previously unselected package r-cran-scales. 603s Preparing to unpack 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libtirpc-dev:armhf (1.3.6+ds-1) ... 603s Setting up libpkgconf3:armhf (1.8.1-4build1) ... 603s Setting up rpcsvc-proto (1.4.3-1build1) ... 603s Setting up r-cran-stringi (1.8.4-1build2) ... 603s Setting up r-cran-s7 (0.2.0-1) ... 603s Setting up r-cran-cpp11 (0.5.3-1) ... 603s Setting up r-cran-rcolorbrewer (1.1-3-1build2) ... 603s Setting up r-cran-isoband (0.2.7-1) ... 603s Setting up libmpc3:armhf (1.3.1-2) ... 603s Setting up r-cran-gtable (0.3.6+dfsg-1) ... 603s Setting up r-cran-labeling (0.4.3-1) ... 603s Setting up icu-devtools (78.2-1ubuntu1) ... 603s Setting up pkgconf-bin (1.8.1-4build1) ... 603s Setting up r-cran-farver (2.1.2-1) ... 603s Setting up liblzma-dev:armhf (5.8.2-2) ... 603s Setting up libubsan1:armhf (15.2.0-12ubuntu1) ... 603s Setting up libpcre2-posix3:armhf (10.46-1) ... 603s Setting up r-cran-viridislite (0.4.3-1) ... 603s Setting up libcrypt-dev:armhf (1:4.5.1-1) ... 603s Setting up libasan8:armhf (15.2.0-12ubuntu1) ... 603s Setting up r-cran-r6 (2.6.1-1) ... 603s Setting up libisl23:armhf (0.27-1build1) ... 603s Setting up libc-dev-bin (2.42-2ubuntu4) ... 603s Setting up libdeflate-dev:armhf (1.23-2build1) ... 603s Setting up cpp-15-arm-linux-gnueabihf (15.2.0-12ubuntu1) ... 603s Setting up r-cran-magrittr (2.0.3-1) ... 603s Setting up libcc1-0:armhf (15.2.0-12ubuntu1) ... 603s Setting up r-cran-vctrs (0.6.5-1) ... 603s Setting up cpp-arm-linux-gnueabihf (4:15.2.0-4ubuntu1) ... 603s Setting up libblas-dev:armhf (3.12.1-7ubuntu1) ... 603s update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so to provide /usr/lib/arm-linux-gnueabihf/libblas.so (libblas.so-arm-linux-gnueabihf) in auto mode 603s Setting up dctrl-tools (2.24-3build4) ... 603s Setting up r-cran-pillar (1.11.1+dfsg-1) ... 603s Setting up libgcc-15-dev:armhf (15.2.0-12ubuntu1) ... 603s Setting up r-cran-stringr (1.5.1-1) ... 603s Setting up gcc-15-arm-linux-gnueabihf (15.2.0-12ubuntu1) ... 603s Setting up r-cran-tibble (3.2.1+dfsg-3) ... 603s Setting up libgfortran-15-dev:armhf (15.2.0-12ubuntu1) ... 603s Setting up pkgconf:armhf (1.8.1-4build1) ... 603s Setting up r-cran-tidyselect (1.2.1+dfsg-1) ... 603s Setting up r-cran-scales (1.4.0-1) ... 603s Setting up liblapack-dev:armhf (3.12.1-7ubuntu1) ... 603s update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so to provide /usr/lib/arm-linux-gnueabihf/liblapack.so (liblapack.so-arm-linux-gnueabihf) in auto mode 603s Setting up r-cran-purrr (1.0.4-1) ... 603s Setting up cpp-15 (15.2.0-12ubuntu1) ... 603s Setting up cpp (4:15.2.0-4ubuntu1) ... 603s Setting up libc6-dev:armhf (2.42-2ubuntu4) ... 603s Setting up r-cran-dplyr (1.1.4-4) ... 603s Setting up libicu-dev:armhf (78.2-1ubuntu1) ... 603s Setting up libbz2-dev:armhf (1.0.8-6build2) ... 603s Setting up gcc-arm-linux-gnueabihf (4:15.2.0-4ubuntu1) ... 603s Setting up libjpeg-turbo8-dev:armhf (2.1.5-4ubuntu3) ... 603s Setting up libncurses-dev:armhf (6.6+20251231-1) ... 603s Setting up gfortran-15-arm-linux-gnueabihf (15.2.0-12ubuntu1) ... 603s Setting up libpcre2-dev:armhf (10.46-1) ... 603s Setting up r-cran-ggplot2 (4.0.2+dfsg-1) ... 603s Setting up libreadline-dev:armhf (8.3-3) ... 603s Setting up gfortran-arm-linux-gnueabihf (4:15.2.0-4ubuntu1) ... 603s Setting up gcc-15 (15.2.0-12ubuntu1) ... 603s Setting up libstdc++-15-dev:armhf (15.2.0-12ubuntu1) ... 603s Setting up r-cran-tidyr (1.3.1-1) ... 603s Setting up zlib1g-dev:armhf (1:1.3.dfsg+really1.3.1-1ubuntu2) ... 603s Setting up libjpeg8-dev:armhf (8c-2ubuntu11) ... 603s Setting up gfortran-15 (15.2.0-12ubuntu1) ... 603s Setting up libpng-dev:armhf (1.6.54-1) ... 603s Setting up libjpeg-dev:armhf (8c-2ubuntu11) ... 603s Setting up g++-15-arm-linux-gnueabihf (15.2.0-12ubuntu1) ... 603s Setting up gcc (4:15.2.0-4ubuntu1) ... 603s Setting up r-cran-broom (1.0.12+dfsg-1) ... 603s Setting up g++-15 (15.2.0-12ubuntu1) ... 603s Setting up g++-arm-linux-gnueabihf (4:15.2.0-4ubuntu1) ... 603s Setting up r-cran-geepack (1.3.12-1) ... 603s Setting up gfortran (4:15.2.0-4ubuntu1) ... 603s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode 603s 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 603s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode 603s 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 603s Setting up g++ (4:15.2.0-4ubuntu1) ... 603s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 603s Setting up build-essential (12.12ubuntu2) ... 603s Setting up r-base-dev (4.5.2-1ubuntu2) ... 603s Setting up pkg-r-autopkgtest (20250812) ... 603s Processing triggers for libc-bin (2.42-2ubuntu4) ... 603s Processing triggers for man-db (2.13.1-1build1) ... 604s Processing triggers for install-info (7.2-5) ... 612s autopkgtest [23:29:04]: test pkg-r-autopkgtest: /usr/share/dh-r/pkg-r-autopkgtest 612s autopkgtest [23:29:04]: test pkg-r-autopkgtest: [----------------------- 614s Test: Try to load the R library etm 614s 614s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 614s Copyright (C) 2025 The R Foundation for Statistical Computing 614s Platform: arm-unknown-linux-gnueabihf (32-bit) 614s 614s R is free software and comes with ABSOLUTELY NO WARRANTY. 614s You are welcome to redistribute it under certain conditions. 614s Type 'license()' or 'licence()' for distribution details. 614s 614s R is a collaborative project with many contributors. 614s Type 'contributors()' for more information and 614s 'citation()' on how to cite R or R packages in publications. 614s 614s Type 'demo()' for some demos, 'help()' for on-line help, or 614s 'help.start()' for an HTML browser interface to help. 614s Type 'q()' to quit R. 614s 614s > library('etm') 615s > 616s autopkgtest [23:29:08]: test pkg-r-autopkgtest: -----------------------] 619s autopkgtest [23:29:11]: test pkg-r-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 619s pkg-r-autopkgtest PASS 623s autopkgtest [23:29:15]: @@@@@@@@@@@@@@@@@@@@ summary 623s run-unit-test PASS 623s pkg-r-autopkgtest PASS