0s autopkgtest [22:55:28]: starting date and time: 2026-02-09 22:55:28+0000 0s autopkgtest [22:55:28]: git checkout: 508d4a25 a-v-ssh wait_for_ssh: demote "ssh connection failed" to a debug message 0s autopkgtest [22:55:28]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.s5p9fy4v/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:lattice --apt-upgrade r-cran-etm --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=lattice/0.22-9-1 -- lxd -r lxd-armhf-10.145.243.61 lxd-armhf-10.145.243.61:autopkgtest/ubuntu/resolute/armhf 26s autopkgtest [22:55:54]: testbed dpkg architecture: armhf 27s autopkgtest [22:55:55]: testbed apt version: 3.1.15 31s autopkgtest [22:55:59]: @@@@@@@@@@@@@@@@@@@@ test bed setup 33s autopkgtest [22:56:01]: testbed release detected to be: None 41s autopkgtest [22:56:09]: updating testbed package index (apt update) 43s 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/main Sources [176 kB] 44s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [29.4 kB] 44s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [1645 kB] 47s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf Packages [246 kB] 47s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/universe armhf Packages [1405 kB] 49s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse armhf Packages [7452 B] 49s Get:11 http://ftpmaster.internal/ubuntu resolute/universe Sources [21.4 MB] 81s Get:12 http://ftpmaster.internal/ubuntu resolute/restricted Sources [15.1 kB] 81s Get:13 http://ftpmaster.internal/ubuntu resolute/main Sources [1398 kB] 84s Get:14 http://ftpmaster.internal/ubuntu resolute/main armhf Packages [1374 kB] 86s Get:15 http://ftpmaster.internal/ubuntu resolute/universe armhf Packages [15.3 MB] 112s Fetched 43.5 MB in 1min 9s (626 kB/s) 113s Reading package lists... 119s autopkgtest [22:57:27]: upgrading testbed (apt dist-upgrade and autopurge) 121s Reading package lists... 121s Building dependency tree... 121s Reading state information... 122s Calculating upgrade... 123s The following packages will be upgraded: 123s cryptsetup-bin dracut-install iproute2 iptables libcryptsetup12 libip4tc2 123s libip6tc2 libxtables12 wget 123s 9 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 123s Need to get 2407 kB of archives. 123s After this operation, 152 kB of additional disk space will be used. 123s Get:1 http://ftpmaster.internal/ubuntu resolute/main armhf iptables armhf 1.8.11-2ubuntu3 [345 kB] 123s Get:2 http://ftpmaster.internal/ubuntu resolute/main armhf libip4tc2 armhf 1.8.11-2ubuntu3 [22.0 kB] 123s Get:3 http://ftpmaster.internal/ubuntu resolute/main armhf libip6tc2 armhf 1.8.11-2ubuntu3 [22.3 kB] 124s Get:4 http://ftpmaster.internal/ubuntu resolute/main armhf libxtables12 armhf 1.8.11-2ubuntu3 [33.5 kB] 124s Get:5 http://ftpmaster.internal/ubuntu resolute/main armhf iproute2 armhf 6.18.0-1ubuntu1 [1123 kB] 125s Get:6 http://ftpmaster.internal/ubuntu resolute/main armhf libcryptsetup12 armhf 2:2.8.0-1ubuntu3 [254 kB] 126s Get:7 http://ftpmaster.internal/ubuntu resolute/main armhf wget armhf 1.25.0-2ubuntu4 [327 kB] 126s Get:8 http://ftpmaster.internal/ubuntu resolute/main armhf cryptsetup-bin armhf 2:2.8.0-1ubuntu3 [232 kB] 127s Get:9 http://ftpmaster.internal/ubuntu resolute/main armhf dracut-install armhf 109-11ubuntu1 [47.9 kB] 127s Preconfiguring packages ... 127s Fetched 2407 kB in 4s (598 kB/s) 127s (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.) 127s Preparing to unpack .../0-iptables_1.8.11-2ubuntu3_armhf.deb ... 127s Unpacking iptables (1.8.11-2ubuntu3) over (1.8.11-2ubuntu2) ... 128s Preparing to unpack .../1-libip4tc2_1.8.11-2ubuntu3_armhf.deb ... 128s Unpacking libip4tc2:armhf (1.8.11-2ubuntu3) over (1.8.11-2ubuntu2) ... 128s Preparing to unpack .../2-libip6tc2_1.8.11-2ubuntu3_armhf.deb ... 128s Unpacking libip6tc2:armhf (1.8.11-2ubuntu3) over (1.8.11-2ubuntu2) ... 128s Preparing to unpack .../3-libxtables12_1.8.11-2ubuntu3_armhf.deb ... 128s Unpacking libxtables12:armhf (1.8.11-2ubuntu3) over (1.8.11-2ubuntu2) ... 128s Preparing to unpack .../4-iproute2_6.18.0-1ubuntu1_armhf.deb ... 128s Unpacking iproute2 (6.18.0-1ubuntu1) over (6.16.0-1ubuntu3) ... 128s Preparing to unpack .../5-libcryptsetup12_2%3a2.8.0-1ubuntu3_armhf.deb ... 128s Unpacking libcryptsetup12:armhf (2:2.8.0-1ubuntu3) over (2:2.8.0-1ubuntu2) ... 128s Preparing to unpack .../6-wget_1.25.0-2ubuntu4_armhf.deb ... 128s Unpacking wget (1.25.0-2ubuntu4) over (1.25.0-2ubuntu3) ... 128s Preparing to unpack .../7-cryptsetup-bin_2%3a2.8.0-1ubuntu3_armhf.deb ... 128s Unpacking cryptsetup-bin (2:2.8.0-1ubuntu3) over (2:2.8.0-1ubuntu2) ... 128s Preparing to unpack .../8-dracut-install_109-11ubuntu1_armhf.deb ... 128s Unpacking dracut-install (109-11ubuntu1) over (109-9ubuntu1) ... 128s Setting up libip4tc2:armhf (1.8.11-2ubuntu3) ... 128s Setting up wget (1.25.0-2ubuntu4) ... 128s Setting up libip6tc2:armhf (1.8.11-2ubuntu3) ... 128s Setting up libxtables12:armhf (1.8.11-2ubuntu3) ... 128s Setting up dracut-install (109-11ubuntu1) ... 128s Setting up libcryptsetup12:armhf (2:2.8.0-1ubuntu3) ... 128s Setting up cryptsetup-bin (2:2.8.0-1ubuntu3) ... 128s Setting up iptables (1.8.11-2ubuntu3) ... 128s Setting up iproute2 (6.18.0-1ubuntu1) ... 129s Processing triggers for man-db (2.13.1-1build1) ... 130s Processing triggers for install-info (7.2-5) ... 130s Processing triggers for libc-bin (2.42-2ubuntu4) ... 132s Reading package lists... 133s Building dependency tree... 133s Reading state information... 133s Solving dependencies... 134s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 136s autopkgtest [22:57:44]: rebooting testbed after setup commands that affected boot 176s autopkgtest [22:58:24]: 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 200s autopkgtest [22:58:48]: @@@@@@@@@@@@@@@@@@@@ apt-source r-cran-etm 211s Get:1 http://ftpmaster.internal/ubuntu resolute/universe r-cran-etm 1.1.1-1build1 (dsc) [2147 B] 211s Get:2 http://ftpmaster.internal/ubuntu resolute/universe r-cran-etm 1.1.1-1build1 (tar) [242 kB] 211s Get:3 http://ftpmaster.internal/ubuntu resolute/universe r-cran-etm 1.1.1-1build1 (diff) [3672 B] 212s gpgv: Signature made Fri Nov 28 21:46:53 2025 UTC 212s gpgv: using RSA key 92FE4F8B40CADC4ECCD60C1F5961FDBE9C619809 212s gpgv: Can't check signature: No public key 212s dpkg-source: warning: cannot verify inline signature for ./r-cran-etm_1.1.1-1build1.dsc: no acceptable signature found 212s autopkgtest [22:59:00]: testing package r-cran-etm version 1.1.1-1build1 214s autopkgtest [22:59:02]: build not needed 217s autopkgtest [22:59:05]: test run-unit-test: preparing testbed 219s Reading package lists... 219s Building dependency tree... 219s Reading state information... 220s Solving dependencies... 220s The following NEW packages will be installed: 220s fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono libblas3 220s libcairo2 libdatrie1 libdeflate0 libfontconfig1 libfreetype6 libgfortran5 220s libgomp1 libgraphite2-3 libharfbuzz0b libice6 libjbig0 libjpeg-turbo8 220s libjpeg8 liblapack3 liblerc4 libpango-1.0-0 libpangocairo-1.0-0 220s libpangoft2-1.0-0 libpaper-utils libpaper2 libpixman-1-0 libsharpyuv0 libsm6 220s libtcl8.6 libthai-data libthai0 libtiff6 libtk8.6 libwebp7 libxcb-render0 220s libxcb-shm0 libxft2 libxrender1 libxss1 libxt6t64 r-base-core 220s r-cran-data.table r-cran-dbi r-cran-etm r-cran-kmi r-cran-lattice 220s r-cran-littler r-cran-matrix r-cran-mitools r-cran-pkgkitten r-cran-rcpp 220s r-cran-rcpparmadillo r-cran-survival unzip x11-common xdg-utils zip 221s 0 upgraded, 57 newly installed, 0 to remove and 0 not upgraded. 221s Need to get 58.6 MB of archives. 221s After this operation, 116 MB of additional disk space will be used. 221s Get:1 http://ftpmaster.internal/ubuntu resolute/main armhf libfreetype6 armhf 2.14.1+dfsg-2 [345 kB] 221s Get:2 http://ftpmaster.internal/ubuntu resolute/main armhf fonts-dejavu-mono all 2.37-8build1 [502 kB] 222s Get:3 http://ftpmaster.internal/ubuntu resolute/main armhf fonts-dejavu-core all 2.37-8build1 [834 kB] 225s Get:4 http://ftpmaster.internal/ubuntu resolute/main armhf fontconfig-config armhf 2.17.1-3ubuntu1 [38.5 kB] 225s Get:5 http://ftpmaster.internal/ubuntu resolute/main armhf libfontconfig1 armhf 2.17.1-3ubuntu1 [117 kB] 225s Get:6 http://ftpmaster.internal/ubuntu resolute/main armhf fontconfig armhf 2.17.1-3ubuntu1 [180 kB] 225s Get:7 http://ftpmaster.internal/ubuntu resolute/main armhf libblas3 armhf 3.12.1-7ubuntu1 [133 kB] 226s Get:8 http://ftpmaster.internal/ubuntu resolute/main armhf libpixman-1-0 armhf 0.46.4-1 [196 kB] 226s Get:9 http://ftpmaster.internal/ubuntu resolute/main armhf libxcb-render0 armhf 1.17.0-2ubuntu1 [15.5 kB] 226s Get:10 http://ftpmaster.internal/ubuntu resolute/main armhf libxcb-shm0 armhf 1.17.0-2ubuntu1 [5956 B] 226s Get:11 http://ftpmaster.internal/ubuntu resolute/main armhf libxrender1 armhf 1:0.9.12-1 [16.6 kB] 226s Get:12 http://ftpmaster.internal/ubuntu resolute/main armhf libcairo2 armhf 1.18.4-3 [489 kB] 227s Get:13 http://ftpmaster.internal/ubuntu resolute/main armhf libdatrie1 armhf 0.2.14-1 [16.4 kB] 227s Get:14 http://ftpmaster.internal/ubuntu resolute/main armhf libdeflate0 armhf 1.23-2build1 [38.8 kB] 227s Get:15 http://ftpmaster.internal/ubuntu resolute/main armhf libgfortran5 armhf 15.2.0-12ubuntu1 [334 kB] 228s Get:16 http://ftpmaster.internal/ubuntu resolute/main armhf libgomp1 armhf 15.2.0-12ubuntu1 [129 kB] 228s Get:17 http://ftpmaster.internal/ubuntu resolute/main armhf libgraphite2-3 armhf 1.3.14-11ubuntu1 [65.2 kB] 228s Get:18 http://ftpmaster.internal/ubuntu resolute/main armhf libharfbuzz0b armhf 12.3.2-1 [501 kB] 229s Get:19 http://ftpmaster.internal/ubuntu resolute/main armhf x11-common all 1:7.7+24ubuntu1 [22.4 kB] 229s Get:20 http://ftpmaster.internal/ubuntu resolute/main armhf libice6 armhf 2:1.1.1-1build1 [37.5 kB] 229s Get:21 http://ftpmaster.internal/ubuntu resolute/main armhf libjpeg-turbo8 armhf 2.1.5-4ubuntu3 [129 kB] 229s Get:22 http://ftpmaster.internal/ubuntu resolute/main armhf libjpeg8 armhf 8c-2ubuntu11 [2148 B] 229s Get:23 http://ftpmaster.internal/ubuntu resolute/main armhf liblapack3 armhf 3.12.1-7ubuntu1 [2090 kB] 233s Get:24 http://ftpmaster.internal/ubuntu resolute/main armhf liblerc4 armhf 4.0.0+ds-5ubuntu2 [162 kB] 233s Get:25 http://ftpmaster.internal/ubuntu resolute/main armhf libthai-data all 0.1.30-1 [155 kB] 233s Get:26 http://ftpmaster.internal/ubuntu resolute/main armhf libthai0 armhf 0.1.30-1 [15.4 kB] 233s Get:27 http://ftpmaster.internal/ubuntu resolute/main armhf libpango-1.0-0 armhf 1.57.0-1 [218 kB] 234s Get:28 http://ftpmaster.internal/ubuntu resolute/main armhf libpangoft2-1.0-0 armhf 1.57.0-1 [45.2 kB] 234s Get:29 http://ftpmaster.internal/ubuntu resolute/main armhf libpangocairo-1.0-0 armhf 1.57.0-1 [25.3 kB] 234s Get:30 http://ftpmaster.internal/ubuntu resolute/main armhf libpaper2 armhf 2.2.5-0.3build1 [16.3 kB] 234s Get:31 http://ftpmaster.internal/ubuntu resolute/main armhf libpaper-utils armhf 2.2.5-0.3build1 [14.2 kB] 234s Get:32 http://ftpmaster.internal/ubuntu resolute/main armhf libsharpyuv0 armhf 1.5.0-0.1build1 [16.3 kB] 234s Get:33 http://ftpmaster.internal/ubuntu resolute/main armhf libsm6 armhf 2:1.2.6-1build1 [15.3 kB] 234s Get:34 http://ftpmaster.internal/ubuntu resolute/main armhf libtcl8.6 armhf 8.6.17+dfsg-1build1 [918 kB] 235s Get:35 http://ftpmaster.internal/ubuntu resolute/main armhf libjbig0 armhf 2.1-6.1ubuntu3 [25.3 kB] 235s Get:36 http://ftpmaster.internal/ubuntu resolute/main armhf libwebp7 armhf 1.5.0-0.1build1 [189 kB] 236s Get:37 http://ftpmaster.internal/ubuntu resolute/main armhf libtiff6 armhf 4.7.0-3ubuntu3 [188 kB] 236s Get:38 http://ftpmaster.internal/ubuntu resolute/main armhf libxft2 armhf 2.3.6-1build2 [37.2 kB] 236s Get:39 http://ftpmaster.internal/ubuntu resolute/main armhf libxss1 armhf 1:1.2.3-1build4 [6328 B] 236s Get:40 http://ftpmaster.internal/ubuntu resolute/main armhf libtk8.6 armhf 8.6.17-1 [694 kB] 237s Get:41 http://ftpmaster.internal/ubuntu resolute/main armhf libxt6t64 armhf 1:1.2.1-1.3 [145 kB] 237s Get:42 http://ftpmaster.internal/ubuntu resolute/main armhf zip armhf 3.0-15ubuntu3 [164 kB] 238s Get:43 http://ftpmaster.internal/ubuntu resolute/main armhf unzip armhf 6.0-29ubuntu1 [167 kB] 238s Get:44 http://ftpmaster.internal/ubuntu resolute/main armhf xdg-utils all 1.2.1-2ubuntu2 [66.1 kB] 238s Get:45 http://ftpmaster.internal/ubuntu resolute/universe armhf r-base-core armhf 4.5.2-1ubuntu2 [28.5 MB] 302s Get:46 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-data.table armhf 1.17.0+dfsg-1 [2111 kB] 309s Get:47 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-dbi all 1.2.3-1build1 [855 kB] 310s Get:48 http://ftpmaster.internal/ubuntu resolute-proposed/universe armhf r-cran-lattice armhf 0.22-9-1 [1399 kB] 312s Get:49 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-matrix armhf 1.7-4-1 [4139 kB] 319s Get:50 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-survival armhf 3.8-6-1 [8253 kB] 332s Get:51 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-littler armhf 0.3.22-1 [81.0 kB] 332s Get:52 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-pkgkitten all 0.2.4-1 [27.2 kB] 332s Get:53 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-rcpp armhf 1.1.0-1 [2009 kB] 336s Get:54 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-rcpparmadillo armhf 15.2.3-1-1 [915 kB] 337s Get:55 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-etm armhf 1.1.1-1build1 [482 kB] 338s Get:56 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-mitools all 2.4-2build2 [266 kB] 338s Get:57 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-kmi all 0.5.5-2build2 [78.9 kB] 339s Preconfiguring packages ... 339s Fetched 58.6 MB in 1min 58s (496 kB/s) 339s Selecting previously unselected package libfreetype6:armhf. 339s (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.) 339s Preparing to unpack .../00-libfreetype6_2.14.1+dfsg-2_armhf.deb ... 339s Unpacking libfreetype6:armhf (2.14.1+dfsg-2) ... 339s Selecting previously unselected package fonts-dejavu-mono. 339s Preparing to unpack .../01-fonts-dejavu-mono_2.37-8build1_all.deb ... 339s Unpacking fonts-dejavu-mono (2.37-8build1) ... 339s Selecting previously unselected package fonts-dejavu-core. 339s Preparing to unpack .../02-fonts-dejavu-core_2.37-8build1_all.deb ... 340s Unpacking fonts-dejavu-core (2.37-8build1) ... 340s Selecting previously unselected package fontconfig-config. 340s Preparing to unpack .../03-fontconfig-config_2.17.1-3ubuntu1_armhf.deb ... 340s Unpacking fontconfig-config (2.17.1-3ubuntu1) ... 340s Selecting previously unselected package libfontconfig1:armhf. 340s Preparing to unpack .../04-libfontconfig1_2.17.1-3ubuntu1_armhf.deb ... 340s Unpacking libfontconfig1:armhf (2.17.1-3ubuntu1) ... 340s Selecting previously unselected package fontconfig. 340s Preparing to unpack .../05-fontconfig_2.17.1-3ubuntu1_armhf.deb ... 340s Unpacking fontconfig (2.17.1-3ubuntu1) ... 340s Selecting previously unselected package libblas3:armhf. 340s Preparing to unpack .../06-libblas3_3.12.1-7ubuntu1_armhf.deb ... 340s Unpacking libblas3:armhf (3.12.1-7ubuntu1) ... 340s Selecting previously unselected package libpixman-1-0:armhf. 340s Preparing to unpack .../07-libpixman-1-0_0.46.4-1_armhf.deb ... 340s Unpacking libpixman-1-0:armhf (0.46.4-1) ... 340s Selecting previously unselected package libxcb-render0:armhf. 340s Preparing to unpack .../08-libxcb-render0_1.17.0-2ubuntu1_armhf.deb ... 340s Unpacking libxcb-render0:armhf (1.17.0-2ubuntu1) ... 340s Selecting previously unselected package libxcb-shm0:armhf. 340s Preparing to unpack .../09-libxcb-shm0_1.17.0-2ubuntu1_armhf.deb ... 340s Unpacking libxcb-shm0:armhf (1.17.0-2ubuntu1) ... 340s Selecting previously unselected package libxrender1:armhf. 340s Preparing to unpack .../10-libxrender1_1%3a0.9.12-1_armhf.deb ... 340s Unpacking libxrender1:armhf (1:0.9.12-1) ... 340s Selecting previously unselected package libcairo2:armhf. 340s Preparing to unpack .../11-libcairo2_1.18.4-3_armhf.deb ... 340s Unpacking libcairo2:armhf (1.18.4-3) ... 340s Selecting previously unselected package libdatrie1:armhf. 340s Preparing to unpack .../12-libdatrie1_0.2.14-1_armhf.deb ... 340s Unpacking libdatrie1:armhf (0.2.14-1) ... 340s Selecting previously unselected package libdeflate0:armhf. 340s Preparing to unpack .../13-libdeflate0_1.23-2build1_armhf.deb ... 340s Unpacking libdeflate0:armhf (1.23-2build1) ... 341s Selecting previously unselected package libgfortran5:armhf. 341s Preparing to unpack .../14-libgfortran5_15.2.0-12ubuntu1_armhf.deb ... 341s Unpacking libgfortran5:armhf (15.2.0-12ubuntu1) ... 341s Selecting previously unselected package libgomp1:armhf. 341s Preparing to unpack .../15-libgomp1_15.2.0-12ubuntu1_armhf.deb ... 341s Unpacking libgomp1:armhf (15.2.0-12ubuntu1) ... 341s Selecting previously unselected package libgraphite2-3:armhf. 341s Preparing to unpack .../16-libgraphite2-3_1.3.14-11ubuntu1_armhf.deb ... 341s Unpacking libgraphite2-3:armhf (1.3.14-11ubuntu1) ... 341s Selecting previously unselected package libharfbuzz0b:armhf. 341s Preparing to unpack .../17-libharfbuzz0b_12.3.2-1_armhf.deb ... 341s Unpacking libharfbuzz0b:armhf (12.3.2-1) ... 341s Selecting previously unselected package x11-common. 341s Preparing to unpack .../18-x11-common_1%3a7.7+24ubuntu1_all.deb ... 341s Unpacking x11-common (1:7.7+24ubuntu1) ... 341s Selecting previously unselected package libice6:armhf. 341s Preparing to unpack .../19-libice6_2%3a1.1.1-1build1_armhf.deb ... 341s Unpacking libice6:armhf (2:1.1.1-1build1) ... 341s Selecting previously unselected package libjpeg-turbo8:armhf. 341s Preparing to unpack .../20-libjpeg-turbo8_2.1.5-4ubuntu3_armhf.deb ... 341s Unpacking libjpeg-turbo8:armhf (2.1.5-4ubuntu3) ... 341s Selecting previously unselected package libjpeg8:armhf. 341s Preparing to unpack .../21-libjpeg8_8c-2ubuntu11_armhf.deb ... 341s Unpacking libjpeg8:armhf (8c-2ubuntu11) ... 341s Selecting previously unselected package liblapack3:armhf. 341s Preparing to unpack .../22-liblapack3_3.12.1-7ubuntu1_armhf.deb ... 341s Unpacking liblapack3:armhf (3.12.1-7ubuntu1) ... 341s Selecting previously unselected package liblerc4:armhf. 341s Preparing to unpack .../23-liblerc4_4.0.0+ds-5ubuntu2_armhf.deb ... 341s Unpacking liblerc4:armhf (4.0.0+ds-5ubuntu2) ... 341s Selecting previously unselected package libthai-data. 341s Preparing to unpack .../24-libthai-data_0.1.30-1_all.deb ... 341s Unpacking libthai-data (0.1.30-1) ... 341s Selecting previously unselected package libthai0:armhf. 341s Preparing to unpack .../25-libthai0_0.1.30-1_armhf.deb ... 341s Unpacking libthai0:armhf (0.1.30-1) ... 341s Selecting previously unselected package libpango-1.0-0:armhf. 341s Preparing to unpack .../26-libpango-1.0-0_1.57.0-1_armhf.deb ... 341s Unpacking libpango-1.0-0:armhf (1.57.0-1) ... 341s Selecting previously unselected package libpangoft2-1.0-0:armhf. 341s Preparing to unpack .../27-libpangoft2-1.0-0_1.57.0-1_armhf.deb ... 341s Unpacking libpangoft2-1.0-0:armhf (1.57.0-1) ... 341s Selecting previously unselected package libpangocairo-1.0-0:armhf. 341s Preparing to unpack .../28-libpangocairo-1.0-0_1.57.0-1_armhf.deb ... 341s Unpacking 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Creating config file /etc/R/Renviron with new version 347s Setting up r-cran-lattice (0.22-9-1) ... 347s Setting up r-cran-pkgkitten (0.2.4-1) ... 347s Setting up r-cran-littler (0.3.22-1) ... 347s Setting up r-cran-rcpp (1.1.0-1) ... 347s Setting up r-cran-dbi (1.2.3-1build1) ... 347s Setting up r-cran-data.table (1.17.0+dfsg-1) ... 347s Setting up r-cran-matrix (1.7-4-1) ... 347s Setting up r-cran-rcpparmadillo (15.2.3-1-1) ... 347s Setting up r-cran-mitools (2.4-2build2) ... 347s Setting up r-cran-survival (3.8-6-1) ... 347s Setting up r-cran-kmi (0.5.5-2build2) ... 347s Setting up r-cran-etm (1.1.1-1build1) ... 347s Processing triggers for man-db (2.13.1-1build1) ... 348s Processing triggers for install-info (7.2-5) ... 348s Processing triggers for libc-bin (2.42-2ubuntu4) ... 356s autopkgtest [23:01:24]: test run-unit-test: [----------------------- 358s BEGIN TEST test.etmCIF.R 358s 358s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 358s Copyright (C) 2025 The R Foundation for Statistical Computing 358s Platform: arm-unknown-linux-gnueabihf (32-bit) 358s 358s R is free software and comes with ABSOLUTELY NO WARRANTY. 358s You are welcome to redistribute it under certain conditions. 358s Type 'license()' or 'licence()' for distribution details. 358s 358s R is a collaborative project with many contributors. 358s Type 'contributors()' for more information and 358s 'citation()' on how to cite R or R packages in publications. 358s 358s Type 'demo()' for some demos, 'help()' for on-line help, or 358s 'help.start()' for an HTML browser interface to help. 358s Type 'q()' to quit R. 358s 358s > ### test file for etmCIF. 358s > ### Really simple tests and comparison with etm 358s > 358s > old <- options(digits = 5) 358s > 358s > require(etm) 358s Loading required package: etm 360s > 360s > if (!require(survival, quietly = TRUE)) { 360s + print("The following tests require the 'survival' package") 360s + } else { 360s + 360s + data(abortion) 360s + 360s + from <- rep(0, nrow(abortion)) 360s + to <- abortion$cause 360s + entry <- abortion$entry 360s + exit <- abortion$exit 360s + id <- 1:nrow(abortion) 360s + data <- data.frame(id, from, to, entry, exit, group = abortion$group) 360s + 360s + ## Computation of the CIFs with etm 360s + tra <- matrix(FALSE, 4, 4) 360s + tra[1, 2:4] <- TRUE 360s + 360s + cif.control <- etm(data[data$group == 0, ], c("0", "1", "2", "3"), 360s + tra, NULL, 0) 360s + cif.exposed <- etm(data[data$group == 1, ], c("0", "1", "2", "3"), 360s + tra, NULL, 0) 360s + 360s + 360s + ## Computation of the CIFs with etmCIF 360s + netm <- etmCIF(Surv(entry, exit, cause != 0) ~ group, abortion, 360s + etype = cause, failcode = 3) 360s + 360s + ### let's do some comparisons :-) 360s + 360s + all.equal(trprob(cif.control, "0 3"), netm[[1]]$est["0", "3", ]) 360s + all.equal(trprob(cif.control, "0 2"), netm[[1]]$est["0", "2", ]) 360s + all.equal(trprob(cif.control, "0 1"), netm[[1]]$est["0", "1", ]) 360s + 360s + all.equal(trprob(cif.exposed, "0 3"), netm[[2]]$est["0", "3", ]) 360s + all.equal(trprob(cif.exposed, "0 2"), netm[[2]]$est["0", "2", ]) 360s + all.equal(trprob(cif.exposed, "0 1"), netm[[2]]$est["0", "1", ]) 360s + 360s + 360s + all.equal(trcov(cif.control, "0 3"), netm[[1]]$cov["0 3", "0 3", ]) 360s + all.equal(trcov(cif.control, "0 2"), netm[[1]]$cov["0 2", "0 2", ]) 360s + all.equal(trcov(cif.control, "0 1"), netm[[1]]$cov["0 1", "0 1", ]) 360s + 360s + all.equal(trcov(cif.exposed, "0 3"), netm[[2]]$cov["0 3", "0 3", ]) 360s + all.equal(trcov(cif.exposed, "0 2"), netm[[2]]$cov["0 2", "0 2", ]) 360s + all.equal(trcov(cif.exposed, "0 1"), netm[[2]]$cov["0 1", "0 1", ]) 360s + 360s + 360s + netm 360s + 360s + ## test on the summary 360s + snetm <- summary(netm) 360s + 360s + snetm 360s + 360s + all.equal(unname(trprob(cif.control, "0 3")), snetm[[1]][[3]]$P) 360s + all.equal(unname(trprob(cif.control, "0 2")), snetm[[1]][[2]]$P) 360s + all.equal(unname(trprob(cif.control, "0 1")), snetm[[1]][[1]]$P) 360s + 360s + all.equal(unname(trprob(cif.exposed, "0 3")), snetm[[2]][[3]]$P) 360s + all.equal(unname(trprob(cif.exposed, "0 2")), snetm[[2]][[2]]$P) 360s + all.equal(unname(trprob(cif.exposed, "0 1")), snetm[[2]][[1]]$P) 360s + 360s + scif.control <- summary(cif.control, ci.fun = "cloglog") 360s + scif.exposed <- summary(cif.exposed, ci.fun = "cloglog") 360s + 360s + all.equal(scif.control[[4]]$lower, snetm[[1]][[3]]$lower) 360s + all.equal(scif.control[[4]]$upper, snetm[[1]][[3]]$upper) 360s + 360s + all.equal(scif.exposed[[4]]$lower, snetm[[2]][[3]]$lower) 360s + all.equal(scif.exposed[[4]]$upper, snetm[[2]][[3]]$upper) 360s + } 360s [1] TRUE 360s > 360s > ### test with factors in the input 360s > abortion$status <- with(abortion, ifelse(cause == 2, "life birth", 360s + ifelse(cause == 1, "ETOP", "spontaneous abortion"))) 360s > 360s > abortion$status <- factor(abortion$status) 360s > 360s > netm.factor <- etmCIF(Surv(entry, exit, status != "cens") ~ group, abortion, 360s + etype = status, failcode = "spontaneous abortion") 360s > 360s > 360s > all.equal(trprob(cif.control, "0 3"), netm.factor[[1]]$est["0", "spontaneous abortion", ]) 360s [1] TRUE 360s > all.equal(trprob(cif.control, "0 2"), netm.factor[[1]]$est["0", "life birth", ]) 360s [1] TRUE 360s > 360s > netm.factor 360s Call: etmCIF(formula = Surv(entry, exit, status != "cens") ~ group, 360s data = abortion, etype = status, failcode = "spontaneous abortion") 360s 360s Covariate: group 360s levels: 0 1 360s 360s 360s group = 0 360s time P se(P) n.event 360s CIF ETOP 43 0.040159 0.0092578 20 360s CIF life birth 43 0.799059 0.0221865 924 360s CIF spontaneous abortion 43 0.160781 0.0213261 69 360s 360s group = 1 360s time P se(P) n.event 360s CIF ETOP 42 0.28511 0.042493 38 360s CIF life birth 42 0.35257 0.042139 92 360s CIF spontaneous abortion 42 0.36232 0.049473 43 360s > 360s > summary(netm.factor) 360s 360s group=0 360s 360s CIF ETOP 360s P time var lower upper n.risk n.event 360s 0.000000 6 0.0000e+00 0.000000 0.000000 117 0 360s 0.038955 13 8.4440e-05 0.024488 0.061694 645 1 360s 0.040159 26 8.5707e-05 0.025513 0.062939 846 0 360s 0.040159 36 8.5707e-05 0.025513 0.062939 876 0 360s 0.040159 40 8.5707e-05 0.025513 0.062939 554 0 360s 0.040159 43 8.5707e-05 0.025513 0.062939 6 0 360s 360s CIF life birth 360s P time var lower upper n.risk n.event 360s 0.000000 6 0.0000e+00 0.000000 0.000000 117 0 360s 0.000000 13 0.0000e+00 0.000000 0.000000 645 0 360s 0.000000 26 0.0000e+00 0.000000 0.000000 846 0 360s 0.053197 36 4.6195e-05 0.041379 0.068268 876 25 360s 0.563121 40 3.8801e-04 0.524924 0.602021 554 280 360s 0.799059 43 4.9224e-04 0.753969 0.840613 6 6 360s 360s CIF spontaneous abortion 360s P time var lower upper n.risk n.event 360s 0.034188 6 0.00028222 0.01297 0.088523 117 4 360s 0.150468 13 0.00045513 0.11360 0.197901 645 1 360s 0.159904 26 0.00045498 0.12274 0.206925 846 1 360s 0.160781 36 0.00045480 0.12360 0.207757 876 1 360s 0.160781 40 0.00045480 0.12360 0.207757 554 0 360s 0.160781 43 0.00045480 0.12360 0.207757 6 0 360s 360s 360s group=1 360s 360s CIF ETOP 360s P time var lower upper n.risk n.event 360s 0.00000 6 0.0000000 0.00000 0.00000 35 0 360s 0.26048 13 0.0017854 0.18795 0.35425 90 0 360s 0.28115 21 0.0018028 0.20742 0.37423 93 1 360s 0.28511 34 0.0018057 0.21116 0.37806 89 0 360s 0.28511 39 0.0018057 0.21116 0.37806 59 0 360s 0.28511 42 0.0018057 0.21116 0.37806 6 0 360s 360s CIF life birth 360s P time var lower upper n.risk n.event 360s 0.000000 6 0.0000e+00 0.000000 0.000000 35 0 360s 0.000000 13 0.0000e+00 0.000000 0.000000 90 0 360s 0.000000 21 0.0000e+00 0.000000 0.000000 93 0 360s 0.023073 34 9.0514e-05 0.010252 0.051504 89 2 360s 0.180156 39 8.0126e-04 0.131765 0.243663 59 13 360s 0.352565 42 1.7757e-03 0.276882 0.441775 6 6 360s 360s CIF spontaneous abortion 360s P time var lower upper n.risk n.event 360s 0.057143 6 0.0015394 0.014605 0.20968 35 2 360s 0.333246 13 0.0025280 0.245337 0.44216 90 4 360s 0.350702 21 0.0024827 0.262769 0.45762 93 0 360s 0.358492 34 0.0024593 0.270627 0.46448 89 0 360s 0.358492 39 0.0024593 0.270627 0.46448 59 0 360s 0.362323 42 0.0024476 0.274499 0.46785 6 0 360s 360s > 360s > ### test with group as a character vector 360s > abortion$ttt <- with(abortion, ifelse(group == 0, "control", "exposed")) 360s > abortion$ttt <- factor(abortion$ttt) 360s > 360s > netm.ttt <- etmCIF(Surv(entry, exit, status != "cens") ~ ttt, abortion, 360s + etype = status, failcode = "spontaneous abortion") 360s > 360s > all.equal(trprob(cif.control, "0 3"), netm.ttt[[1]]$est["0", "spontaneous abortion", ]) 360s [1] TRUE 360s > all.equal(trprob(cif.control, "0 2"), netm.ttt[[1]]$est["0", "life birth", ]) 360s [1] TRUE 360s > 360s > netm.ttt 360s Call: etmCIF(formula = Surv(entry, exit, status != "cens") ~ ttt, data = abortion, 360s etype = status, failcode = "spontaneous abortion") 360s 360s Covariate: ttt 360s levels: control exposed 360s 360s 360s ttt = control 360s time P se(P) n.event 360s CIF ETOP 43 0.040159 0.0092578 20 360s CIF life birth 43 0.799059 0.0221865 924 360s CIF spontaneous abortion 43 0.160781 0.0213261 69 360s 360s ttt = exposed 360s time P se(P) n.event 360s CIF ETOP 42 0.28511 0.042493 38 360s CIF life birth 42 0.35257 0.042139 92 360s CIF spontaneous abortion 42 0.36232 0.049473 43 360s > 360s > summary(netm.ttt) 360s 360s ttt=control 360s 360s CIF ETOP 360s P time var lower upper n.risk n.event 360s 0.000000 6 0.0000e+00 0.000000 0.000000 117 0 360s 0.038955 13 8.4440e-05 0.024488 0.061694 645 1 360s 0.040159 26 8.5707e-05 0.025513 0.062939 846 0 360s 0.040159 36 8.5707e-05 0.025513 0.062939 876 0 360s 0.040159 40 8.5707e-05 0.025513 0.062939 554 0 360s 0.040159 43 8.5707e-05 0.025513 0.062939 6 0 360s 360s CIF life birth 360s P time var lower upper n.risk n.event 360s 0.000000 6 0.0000e+00 0.000000 0.000000 117 0 360s 0.000000 13 0.0000e+00 0.000000 0.000000 645 0 360s 0.000000 26 0.0000e+00 0.000000 0.000000 846 0 360s 0.053197 36 4.6195e-05 0.041379 0.068268 876 25 360s 0.563121 40 3.8801e-04 0.524924 0.602021 554 280 360s 0.799059 43 4.9224e-04 0.753969 0.840613 6 6 360s 360s CIF spontaneous abortion 360s P time var lower upper n.risk n.event 360s 0.034188 6 0.00028222 0.01297 0.088523 117 4 360s 0.150468 13 0.00045513 0.11360 0.197901 645 1 360s 0.159904 26 0.00045498 0.12274 0.206925 846 1 360s 0.160781 36 0.00045480 0.12360 0.207757 876 1 360s 0.160781 40 0.00045480 0.12360 0.207757 554 0 360s 0.160781 43 0.00045480 0.12360 0.207757 6 0 360s 360s 360s ttt=exposed 360s 360s CIF ETOP 360s P time var lower upper n.risk n.event 360s 0.00000 6 0.0000000 0.00000 0.00000 35 0 360s 0.26048 13 0.0017854 0.18795 0.35425 90 0 360s 0.28115 21 0.0018028 0.20742 0.37423 93 1 360s 0.28511 34 0.0018057 0.21116 0.37806 89 0 360s 0.28511 39 0.0018057 0.21116 0.37806 59 0 360s 0.28511 42 0.0018057 0.21116 0.37806 6 0 360s 360s CIF life birth 360s P time var lower upper n.risk n.event 360s 0.000000 6 0.0000e+00 0.000000 0.000000 35 0 360s 0.000000 13 0.0000e+00 0.000000 0.000000 90 0 360s 0.000000 21 0.0000e+00 0.000000 0.000000 93 0 360s 0.023073 34 9.0514e-05 0.010252 0.051504 89 2 360s 0.180156 39 8.0126e-04 0.131765 0.243663 59 13 360s 0.352565 42 1.7757e-03 0.276882 0.441775 6 6 360s 360s CIF spontaneous abortion 360s P time var lower upper n.risk n.event 360s 0.057143 6 0.0015394 0.014605 0.20968 35 2 360s 0.333246 13 0.0025280 0.245337 0.44216 90 4 360s 0.350702 21 0.0024827 0.262769 0.45762 93 0 360s 0.358492 34 0.0024593 0.270627 0.46448 89 0 360s 0.358492 39 0.0024593 0.270627 0.46448 59 0 360s 0.362323 42 0.0024476 0.274499 0.46785 6 0 360s 360s > 360s > 360s > ### A couple of comparisons with simulated data 360s > set.seed(1313) 360s > time <- rexp(100) 360s > to <- rbinom(100, 2, prob = c(1/3, 1/3, 1/3)) 360s > from <- rep(11, 100) 360s > id <- 1:100 360s > cov <- rbinom(100, 1, 0.5) 360s > 360s > dat.s <- data.frame(id, time, from, to, cov) 360s > 360s > traa <- matrix(FALSE, 3, 3) 360s > traa[1, 2:3] <- TRUE 360s > 360s > aa0 <- etm(dat.s[dat.s$cov == 0, ], c("11", "1", "2"), traa, "0", 0) 360s > aa1 <- etm(dat.s[dat.s$cov == 1, ], c("11", "1", "2"), traa, "0", 0) 360s > aa <- etm(dat.s, c("11", "1", "2"), traa, "0", 0) 360s > 360s > test <- etmCIF(Surv(time, to != 0) ~ 1, dat.s, etype = to) 360s > 360s > test.c <- etmCIF(Surv(time, to != 0) ~ cov, dat.s, etype = to) 360s > 360s > all.equal(trprob(aa, "11 1"), test[[1]]$est["0", "1", ]) 360s [1] TRUE 360s > all.equal(trprob(aa, "11 2"), test[[1]]$est["0", "2", ]) 360s [1] TRUE 360s > 360s > all.equal(trprob(aa0, "11 1"), test.c[[1]]$est["0", "1", ]) 360s [1] TRUE 360s > all.equal(trprob(aa0, "11 2"), test.c[[1]]$est["0", "2", ]) 360s [1] TRUE 360s > 360s > all.equal(trprob(aa1, "11 1"), test.c[[2]]$est["0", "1", ]) 360s [1] TRUE 360s > all.equal(trprob(aa1, "11 2"), test.c[[2]]$est["0", "2", ]) 360s [1] TRUE 360s > 360s > test 360s Call: etmCIF(formula = Surv(time, to != 0) ~ 1, data = dat.s, etype = to) 360s 360s time P se(P) n.event 360s CIF 1 4.9088 0.809108 0.079680 45 360s CIF 2 4.9088 0.096618 0.032905 8 360s > 360s > test.c 360s Call: etmCIF(formula = Surv(time, to != 0) ~ cov, data = dat.s, etype = to) 360s 360s Covariate: cov 360s levels: 0 1 360s 360s 360s cov = 0 360s time P se(P) n.event 360s CIF 1 2.1708 0.70246 0.105797 19 360s CIF 2 2.1708 0.11144 0.053384 4 360s 360s cov = 1 360s time P se(P) n.event 360s CIF 1 4.9088 0.80787 0.094051 26 360s CIF 2 4.9088 0.08436 0.040769 4 360s > 360s > summary(test) 360s 360s 360s 360s CIF 1 360s P time var lower upper n.risk n.event 360s 0.01000 0.0092099 0.0000990 0.0014147 0.068863 100 1 360s 0.11430 0.2663096 0.0010542 0.0649454 0.196993 81 1 360s 0.23451 0.7303091 0.0020436 0.1591107 0.337736 54 1 360s 0.40425 1.4299939 0.0032996 0.3020445 0.525741 29 1 360s 0.54593 2.0647206 0.0040836 0.4269008 0.673605 16 1 360s 0.80911 4.9087561 0.0063489 0.6359544 0.933733 2 1 360s 360s CIF 2 360s P time var lower upper n.risk n.event 360s 0.000000 0.0092099 0.00000000 0.000000 0.000000 100 0 360s 0.031657 0.2663096 0.00032353 0.010320 0.094942 81 0 360s 0.067029 0.7303091 0.00070366 0.030598 0.143503 54 0 360s 0.096618 1.4299939 0.00108275 0.049082 0.185474 29 0 360s 0.096618 2.0647206 0.00108275 0.049082 0.185474 16 0 360s 0.096618 4.9087561 0.00108275 0.049082 0.185474 2 0 360s 360s > summary(test.c) 360s 360s cov=0 360s 360s CIF 1 360s P time var lower upper n.risk n.event 360s 0.022222 0.0092099 0.00048285 0.0031605 0.14747 45 1 360s 0.092222 0.2982439 0.00193603 0.0355971 0.22762 36 0 360s 0.226684 0.7021938 0.00450954 0.1241760 0.39250 24 1 360s 0.378128 1.4299939 0.00760870 0.2337884 0.57145 13 1 360s 0.505736 1.6148774 0.00895330 0.3388425 0.69885 10 1 360s 0.702465 2.1708375 0.01119294 0.4944890 0.88399 3 1 360s 360s CIF 2 360s P time var lower upper n.risk n.event 360s 0.000000 0.0092099 0.0000000 0.000000 0.00000 45 0 360s 0.048441 0.2982439 0.0011168 0.012337 0.18013 36 1 360s 0.076411 0.7021938 0.0018104 0.025202 0.21928 24 0 360s 0.111440 1.4299939 0.0028499 0.042676 0.27392 13 0 360s 0.111440 1.6148774 0.0028499 0.042676 0.27392 10 0 360s 0.111440 2.1708375 0.0028499 0.042676 0.27392 3 0 360s 360s 360s cov=1 360s 360s CIF 1 360s P time var lower upper n.risk n.event 360s 0.018182 0.066692 0.00032457 0.0025813 0.12214 55 1 360s 0.112392 0.263808 0.00187215 0.0520925 0.23333 45 1 360s 0.241023 0.730309 0.00374499 0.1440057 0.38685 31 1 360s 0.401201 1.066913 0.00570788 0.2714008 0.56421 19 1 360s 0.592334 2.366275 0.00775985 0.4286230 0.76273 8 1 360s 0.807871 4.908756 0.00884554 0.6023185 0.94771 2 1 360s 360s CIF 2 360s P time var lower upper n.risk n.event 360s 0.000000 0.066692 0.00000000 0.000000 0.00000 55 0 360s 0.037434 0.263808 0.00067458 0.009494 0.14152 45 0 360s 0.059341 0.730309 0.00111295 0.019447 0.17351 31 0 360s 0.084360 1.066913 0.00166213 0.032211 0.21119 19 0 360s 0.084360 2.366275 0.00166213 0.032211 0.21119 8 0 360s 0.084360 4.908756 0.00166213 0.032211 0.21119 2 0 360s 360s > 360s > options(old) 360s > 360s BEGIN TEST tests.etm.R 360s 360s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 360s Copyright (C) 2025 The R Foundation for Statistical Computing 360s Platform: arm-unknown-linux-gnueabihf (32-bit) 360s 360s R is free software and comes with ABSOLUTELY NO WARRANTY. 360s You are welcome to redistribute it under certain conditions. 360s Type 'license()' or 'licence()' for distribution details. 360s 360s R is a collaborative project with many contributors. 360s Type 'contributors()' for more information and 360s 'citation()' on how to cite R or R packages in publications. 360s 360s Type 'demo()' for some demos, 'help()' for on-line help, or 360s 'help.start()' for an HTML browser interface to help. 360s Type 'q()' to quit R. 360s 361s Loading required package: etm 361s > require(etm) 362s > 362s > ## Print with a bit less precision to avoid lots of notes in the comparison 362s > old <- options(digits = 4) 362s > 362s > ### Simple test 362s > 362s > time <- id <- 1:10 362s > from <- rep(0, 10) 362s > to <- rep(1, 10) 362s > 362s > data1 <- data.frame(id, from, to, time) 362s > tra1 <- matrix(FALSE, 2, 2) 362s > tra1[1, 2] <- TRUE 362s > 362s > etm1 <- etm(data1, c("0", "1"), tra1, NULL, 0) 362s > 362s > all.equal(as.vector(trprob(etm1, "0 0")), cumprod((10:1 - 1) / (10:1))) 362s [1] TRUE 362s > 362s > etm1$cov["0 0", "0 0", ] 362s 1 2 3 4 5 6 7 8 9 10 362s 0.009 0.016 0.021 0.024 0.025 0.024 0.021 0.016 0.009 0.000 362s > 362s > all.equal(etm1$cov["0 0", "0 0",], trcov(etm1, "0 0")) 362s [1] TRUE 362s > 362s > ### A simple test from AHR's author, where the first time is censored 362s > if (!require(survival)) { 362s + stop("This test requires the survival package") 362s Loading required package: survival 362s + } 362s > 362s > data <- data.frame(id=1:10, time=1:10, from=0, to=1, status=TRUE) 362s > 362s > tra <- matrix(FALSE, nrow=2, ncol=2) 362s > tra[1, 2] <- TRUE 362s > 362s > data$to[1] <- "cens" 362s > data$status[1] <- FALSE 362s > 362s > fit.km <- survfit(Surv(time, status) ~ 1, data=data) 362s > fit.etm <- etm(data, c("0","1"), tra, "cens", s=0, t="last", covariance=FALSE) 362s > 362s > all.equal(fit.km$surv[data$status], fit.etm$est[1,1,], check.attributes = FALSE) 362s [1] TRUE 362s > 362s > data$to[2] <- "cens" 362s > data$status[2] <- FALSE 362s > 362s > fit.km <- survfit(Surv(time, status) ~ 1, data=data) 362s > fit.etm <- etm(data, c("0","1"), tra, "cens", s=0, t="last", covariance=FALSE) 362s > 362s > all.equal(fit.km$surv[data$status], fit.etm$est[1,1,], check.attributes = FALSE) 362s [1] TRUE 362s > 362s > ### a bit more complicated 362s > 362s > time <- id <- 1:10 362s > from <- rep(0, 10) 362s > to <- rep(c(1, 2), 5) 362s > data2 <- data.frame(id, from, to, time) 362s > 362s > tra2 <- matrix(FALSE, 3, 3) 362s > tra2[1, 2:3] <- TRUE 362s > 362s > etm2 <- etm(data2, c("0", "1", "2"), tra2, NULL, 0) 362s > 362s > aa <- table(time, to) 362s > 362s > cif1 <- cumsum(aa[, 1] / 10) 362s > cif2 <- cumsum(aa[, 2] / 10) 362s > surv <- cumprod((10:1 - 1) / (10:1)) 362s > 362s > all.equal(trprob(etm2, "0 1"), cif1) 362s [1] TRUE 362s > all.equal(trprob(etm2, "0 2"), cif2) 362s [1] TRUE 362s > all.equal(as.vector(trprob(etm2, "0 0")), surv) 362s [1] TRUE 362s > 362s > ## a test on id 362s > data2$id <- letters[1:10] 362s > 362s > etm3 <- etm(data2, c("0", "1", "2"), tra2, NULL, 0) 362s > 362s > all.equal(trprob(etm2, "0 1"), trprob(etm3, "0 1")) 362s [1] TRUE 362s > all.equal(trprob(etm2, "0 2"), trprob(etm3, "0 2")) 362s [1] TRUE 362s > all.equal(trprob(etm2, "0 0"), trprob(etm3, "0 0")) 362s [1] TRUE 362s > 362s > 362s > ### Test on sir.cont 362s > 362s > data(sir.cont) 362s > 362s > ## Modification for patients entering and leaving a state 362s > ## at the same date 362s > ## Change on ventilation status is considered 362s > ## to happen before end of hospital stay 362s > sir.cont <- sir.cont[order(sir.cont$id, sir.cont$time), ] 362s > for (i in 2:nrow(sir.cont)) { 362s + if (sir.cont$id[i]==sir.cont$id[i-1]) { 362s + if (sir.cont$time[i]==sir.cont$time[i-1]) { 362s + sir.cont$time[i-1] <- sir.cont$time[i-1] - 0.5 362s + } 362s + } 362s + } 362s > 362s > ### Computation of the transition probabilities 362s > ## Possible transitions. 362s > tra <- matrix(ncol=3,nrow=3,FALSE) 362s > tra[1, 2:3] <- TRUE 362s > tra[2, c(1, 3)] <- TRUE 362s > 362s > ## etm 362s > prob.sir <- etm(sir.cont, c("0", "1", "2"), tra, "cens", 1) 362s > 362s > prob.sir 362s Multistate model with 2 transient state(s) 362s and 1 absorbing state(s) 362s 362s Possible transitions: 362s from to 362s 0 1 362s 0 2 362s 1 0 362s 1 2 362s 362s Estimate of P(1, 183) 362s 0 1 2 362s 0 0 0 1 362s 1 0 0 1 362s 2 0 0 1 362s 362s > 362s > summ.sir <- summary(prob.sir) 362s > all.equal(summ.sir[['0 1']]$P, as.vector(trprob(prob.sir, "0 1"))) 362s [1] TRUE 362s > subset(summ.sir[[3]],time<183) # issue with precision on different architectures 362s P time var lower upper n.risk n.event 362s 1.5 0.0000 1.5 0.000e+00 0.00000 0.0000 394 0 362s 2 0.1187 2.0 2.641e-04 0.08683 0.1505 396 47 362s 2.5 0.1187 2.5 2.641e-04 0.08683 0.1505 364 0 362s 3 0.2454 3.0 4.465e-04 0.20398 0.2868 365 54 362s 3.5 0.2454 3.5 4.465e-04 0.20398 0.2868 328 0 362s 4 0.3806 4.0 5.416e-04 0.33501 0.4262 331 62 362s 4.5 0.3806 4.5 5.416e-04 0.33501 0.4262 280 0 362s 5 0.4792 5.0 5.480e-04 0.43333 0.5251 283 48 362s 5.5 0.4792 5.5 5.480e-04 0.43333 0.5251 248 0 362s 6 0.5693 6.0 5.141e-04 0.52482 0.6137 249 47 362s 7 0.6350 7.0 4.665e-04 0.59266 0.6773 212 36 362s 8 0.6795 8.0 4.202e-04 0.63931 0.7197 195 27 362s 8.5 0.6795 8.5 4.202e-04 0.63931 0.7197 172 0 362s 9 0.7325 9.0 3.580e-04 0.69541 0.7696 173 34 362s 10 0.7647 10.0 3.141e-04 0.72992 0.7994 148 21 362s 10.5 0.7647 10.5 3.141e-04 0.72992 0.7994 135 0 362s 11 0.7895 11.0 2.790e-04 0.75674 0.8222 136 18 362s 12 0.8138 12.0 2.420e-04 0.78330 0.8443 129 18 362s 12.5 0.8138 12.5 2.420e-04 0.78330 0.8443 117 0 362s 13 0.8294 13.0 2.182e-04 0.80045 0.8584 118 13 362s 14 0.8452 14.0 1.938e-04 0.81789 0.8725 115 14 362s 15 0.8625 15.0 1.670e-04 0.83714 0.8878 106 15 362s 16 0.8723 16.0 1.522e-04 0.84807 0.8964 93 9 362s 17 0.8852 17.0 1.330e-04 0.86256 0.9078 86 12 362s 17.5 0.8852 17.5 1.330e-04 0.86256 0.9078 77 0 362s 18 0.8960 18.0 1.168e-04 0.87484 0.9172 76 9 362s 19 0.9029 19.0 1.070e-04 0.88261 0.9232 71 7 362s 20 0.9125 20.0 9.367e-05 0.89356 0.9315 64 10 362s 21 0.9161 21.0 8.878e-05 0.89768 0.9346 57 4 362s 22 0.9226 22.0 7.996e-05 0.90504 0.9401 55 6 362s 23 0.9261 23.0 7.537e-05 0.90904 0.9431 51 4 362s 23.5 0.9261 23.5 7.537e-05 0.90904 0.9431 49 0 362s 24 0.9354 24.0 6.292e-05 0.91982 0.9509 50 9 362s 25 0.9385 25.0 5.878e-05 0.92352 0.9536 42 3 362s 26 0.9429 26.0 5.326e-05 0.92863 0.9572 39 5 362s 27 0.9477 27.0 4.749e-05 0.93417 0.9612 35 6 362s 27.5 0.9477 27.5 4.749e-05 0.93417 0.9612 29 0 362s 28 0.9531 28.0 4.093e-05 0.94059 0.9657 30 5 362s 29 0.9567 29.0 3.668e-05 0.94485 0.9686 31 4 362s 30 0.9592 30.0 3.384e-05 0.94779 0.9706 28 3 362s 30.5 0.9592 30.5 3.384e-05 0.94779 0.9706 29 0 362s 31 0.9642 31.0 2.821e-05 0.95383 0.9746 30 6 362s 32 0.9649 32.0 2.752e-05 0.95458 0.9751 25 1 362s 33 0.9669 33.0 2.533e-05 0.95708 0.9768 24 2 362s 34 0.9685 34.0 2.368e-05 0.95900 0.9781 26 2 362s 35 0.9697 35.0 2.252e-05 0.96036 0.9790 28 2 362s 36 0.9702 36.0 2.194e-05 0.96104 0.9794 26 1 362s 37 0.9718 37.0 2.043e-05 0.96290 0.9806 26 2 362s 38 0.9739 38.0 1.831e-05 0.96555 0.9823 25 4 362s 38.5 0.9739 38.5 1.831e-05 0.96555 0.9823 21 0 362s 39 0.9760 39.0 1.643e-05 0.96802 0.9839 23 3 362s 40 0.9769 40.0 1.558e-05 0.96918 0.9847 19 1 362s 41 0.9774 41.0 1.512e-05 0.96981 0.9851 22 1 362s 42 0.9779 42.0 1.476e-05 0.97032 0.9854 22 0 362s 43 0.9798 43.0 1.308e-05 0.97271 0.9869 22 3 362s 44 0.9803 44.0 1.265e-05 0.97333 0.9873 21 1 362s 45 0.9817 45.0 1.157e-05 0.97499 0.9883 19 1 362s 46 0.9822 46.0 1.116e-05 0.97561 0.9887 17 1 362s 47 0.9831 47.0 1.037e-05 0.97683 0.9895 18 2 362s 48 0.9836 48.0 9.987e-06 0.97743 0.9898 17 1 362s 49 0.9841 49.0 9.669e-06 0.97796 0.9901 17 0 362s 50 0.9845 50.0 9.297e-06 0.97856 0.9905 17 1 362s 50.5 0.9845 50.5 9.297e-06 0.97856 0.9905 16 0 362s 51 0.9860 51.0 8.214e-06 0.98037 0.9916 17 3 362s 52 0.9870 52.0 7.513e-06 0.98159 0.9923 14 2 362s 53 0.9879 53.0 6.875e-06 0.98276 0.9930 12 1 362s 54 0.9889 54.0 6.214e-06 0.98397 0.9937 12 2 362s 55 0.9903 55.0 5.254e-06 0.98581 0.9948 10 3 362s 56 0.9913 56.0 4.667e-06 0.98703 0.9955 6 1 362s 57 0.9917 57.0 4.364e-06 0.98765 0.9958 5 1 362s 58 0.9922 58.0 4.064e-06 0.98828 0.9962 4 1 362s 59 0.9927 59.0 3.769e-06 0.98891 0.9965 3 1 362s 60 0.9932 60.0 3.488e-06 0.98953 0.9969 3 1 362s 62 0.9937 62.0 3.230e-06 0.99016 0.9972 2 0 362s 63 0.9942 63.0 2.956e-06 0.99079 0.9975 2 1 362s 68 0.9942 68.0 2.956e-06 0.99079 0.9975 1 0 362s 70 0.9946 70.0 2.694e-06 0.99143 0.9979 2 1 362s 78 0.9951 78.0 2.442e-06 0.99207 0.9982 1 0 362s 80 0.9951 80.0 2.442e-06 0.99207 0.9982 1 0 362s 85 0.9966 85.0 1.695e-06 0.99404 0.9991 2 0 362s 89 0.9966 89.0 1.695e-06 0.99404 0.9991 2 0 362s 90 0.9966 90.0 1.695e-06 0.99404 0.9991 1 0 362s 95 0.9971 95.0 1.448e-06 0.99472 0.9994 2 0 362s 100 0.9976 100.0 1.203e-06 0.99542 0.9997 3 0 362s 101 0.9981 101.0 9.592e-07 0.99613 1.0000 3 1 362s 108 0.9985 108.0 7.169e-07 0.99688 1.0000 2 1 362s 113 0.9990 113.0 4.764e-07 0.99767 1.0000 1 0 362s 116 0.9990 116.0 4.764e-07 0.99767 1.0000 1 0 362s 124 0.9990 124.0 4.764e-07 0.99767 1.0000 2 0 362s 164 0.9990 164.0 4.764e-07 0.99767 1.0000 0 0 362s > 362s > ## gonna play a bit with the state names 362s > dd <- sir.cont 362s > dd$from <- ifelse(dd$from == 0, "initial state", "ventilation") 362s > dd$to <- as.character(dd$to) 362s > for (i in seq_len(nrow(dd))) { 362s + dd$to[i] <- switch(dd$to[i], 362s + "0" = "initial state", 362s + "1" = "ventilation", 362s + "2" = "end of story", 362s + "cens" = "cens" 362s + ) 362s + } 362s > 362s > test <- etm(dd, c("initial state", "ventilation", "end of story"), tra, "cens", 1) 362s > 362s > all.equal(test$est["initial state", "initial state", ], 362s + prob.sir$est["0", "0", ]) 362s [1] TRUE 362s > all.equal(trprob(test, "initial state initial state"), trprob(prob.sir, "0 0")) 362s [1] TRUE 362s > all.equal(trprob(test, "initial state ventilation"), trprob(prob.sir, "0 1")) 362s [1] TRUE 362s > all.equal(trprob(test, "initial state end of story"), trprob(prob.sir, "0 2")) 362s [1] TRUE 362s > 362s > all.equal(trcov(test, "initial state end of story"), trcov(prob.sir, "0 2")) 362s [1] TRUE 362s > 362s > aa <- summary(test) 362s > all.equal(summ.sir[[6]], aa[[6]]) 362s [1] TRUE 362s > all.equal(summ.sir[[4]], aa[[4]]) 362s [1] TRUE 362s > 362s > ### Test on abortion data 362s > 362s > data(abortion) 362s > 362s > from <- rep(0, nrow(abortion)) 362s > to <- abortion$cause 362s > entry <- abortion$entry 362s > exit <- abortion$exit 362s > id <- 1:nrow(abortion) 362s > data <- data.frame(id, from, to, entry, exit, group = abortion$group) 362s > 362s > ## Computation of the CIFs 362s > tra <- matrix(FALSE, 4, 4) 362s > tra[1, 2:4] <- TRUE 362s > 362s > cif.control <- etm(data[data$group == 0, ], c("0", "1", "2", "3"), 362s + tra, NULL, 0) 362s > cif.exposed <- etm(data[data$group == 1, ], c("0", "1", "2", "3"), 362s + tra, NULL, 0) 362s > 362s > all.equal(trprob(cif.control, "0 1"), cif.control$est["0", "1", ]) 362s [1] TRUE 362s > all.equal(trcov(cif.control, c("0 1", "0 2")), cif.control$cov["0 1", "0 2", ]) 362s [1] TRUE 362s > 362s > trprob(cif.control, "0 1") 362s 6 7 8 9 10 11 12 13 362s 0.000000 0.007401 0.014881 0.026509 0.033208 0.037694 0.037694 0.038955 362s 14 17 19 21 24 25 26 30 362s 0.040159 0.040159 0.040159 0.040159 0.040159 0.040159 0.040159 0.040159 362s 31 32 33 34 35 36 37 38 362s 0.040159 0.040159 0.040159 0.040159 0.040159 0.040159 0.040159 0.040159 362s 39 40 41 42 43 362s 0.040159 0.040159 0.040159 0.040159 0.040159 362s > trprob(cif.control, "0 2") 362s 6 7 8 9 10 11 12 13 362s 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 362s 14 17 19 21 24 25 26 30 362s 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.003657 362s 31 32 33 34 35 36 37 38 362s 0.006371 0.008175 0.013543 0.023317 0.031260 0.053197 0.084529 0.179163 362s 39 40 41 42 43 362s 0.322016 0.563121 0.742227 0.793893 0.799059 362s > trprob(cif.control, "0 0") 362s 6 7 8 9 10 11 12 13 362s 0.965812 0.932508 0.887628 0.862433 0.838989 0.822538 0.813099 0.810578 362s 14 17 19 21 24 25 26 30 362s 0.806964 0.805874 0.803810 0.802804 0.801837 0.800883 0.799937 0.796280 362s 31 32 33 34 35 36 37 38 362s 0.793565 0.791762 0.786394 0.776620 0.768677 0.745862 0.714531 0.619897 362s 39 40 41 42 43 362s 0.477043 0.235938 0.056832 0.005167 0.000000 362s > 362s > trcov(cif.control, "0 1") 362s 6 7 8 9 10 11 12 13 362s 0.000e+00 2.719e-05 4.533e-05 6.665e-05 7.698e-05 8.304e-05 8.304e-05 8.444e-05 362s 14 17 19 21 24 25 26 30 362s 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 362s 31 32 33 34 35 36 37 38 362s 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 362s 39 40 41 42 43 362s 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 362s > trcov(cif.control, "0 2") 362s 6 7 8 9 10 11 12 13 362s 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 362s 14 17 19 21 24 25 26 30 362s 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 3.338e-06 362s 31 32 33 34 35 36 37 38 362s 5.784e-06 7.401e-06 1.216e-05 2.072e-05 2.758e-05 4.619e-05 7.202e-05 1.461e-04 362s 39 40 41 42 43 362s 2.470e-04 3.880e-04 4.702e-04 4.903e-04 4.922e-04 362s > trcov(cif.control, "0 0") 362s 6 7 8 9 10 11 12 13 362s 2.822e-04 3.821e-04 4.527e-04 4.748e-04 4.875e-04 4.927e-04 4.941e-04 4.942e-04 362s 14 17 19 21 24 25 26 30 362s 4.941e-04 4.940e-04 4.936e-04 4.933e-04 4.931e-04 4.928e-04 4.926e-04 4.914e-04 362s 31 32 33 34 35 36 37 38 362s 4.905e-04 4.899e-04 4.880e-04 4.846e-04 4.816e-04 4.729e-04 4.601e-04 4.176e-04 362s 39 40 41 42 43 362s 3.425e-04 1.865e-04 4.797e-05 4.441e-06 0.000e+00 362s > 362s > aa <- summary(cif.control) 362s > aa$"0 1" 362s P time var lower upper n.risk n.event 362s 6 0.000000 6 0.000e+00 0.000000 0.00000 117 0 362s 7 0.007401 7 2.719e-05 0.000000 0.01762 261 2 362s 8 0.014881 8 4.533e-05 0.001685 0.02808 374 3 362s 9 0.026509 9 6.665e-05 0.010508 0.04251 458 6 362s 10 0.033208 10 7.698e-05 0.016011 0.05040 515 4 362s 11 0.037694 11 8.304e-05 0.019834 0.05555 561 3 362s 12 0.037694 12 8.304e-05 0.019834 0.05555 610 0 362s 13 0.038955 13 8.444e-05 0.020944 0.05697 645 1 362s 14 0.040159 14 8.571e-05 0.022014 0.05830 673 1 362s 17 0.040159 17 8.571e-05 0.022014 0.05830 740 0 362s 19 0.040159 19 8.571e-05 0.022014 0.05830 781 0 362s 21 0.040159 21 8.571e-05 0.022014 0.05830 799 0 362s 24 0.040159 24 8.571e-05 0.022014 0.05830 830 0 362s 25 0.040159 25 8.571e-05 0.022014 0.05830 841 0 362s 26 0.040159 26 8.571e-05 0.022014 0.05830 846 0 362s 30 0.040159 30 8.571e-05 0.022014 0.05830 875 0 362s 31 0.040159 31 8.571e-05 0.022014 0.05830 880 0 362s 32 0.040159 32 8.571e-05 0.022014 0.05830 880 0 362s 33 0.040159 33 8.571e-05 0.022014 0.05830 885 0 362s 34 0.040159 34 8.571e-05 0.022014 0.05830 885 0 362s 35 0.040159 35 8.571e-05 0.022014 0.05830 880 0 362s 36 0.040159 36 8.571e-05 0.022014 0.05830 876 0 362s 37 0.040159 37 8.571e-05 0.022014 0.05830 857 0 362s 38 0.040159 38 8.571e-05 0.022014 0.05830 823 0 362s 39 0.040159 39 8.571e-05 0.022014 0.05830 716 0 362s 40 0.040159 40 8.571e-05 0.022014 0.05830 554 0 362s 41 0.040159 41 8.571e-05 0.022014 0.05830 274 0 362s 42 0.040159 42 8.571e-05 0.022014 0.05830 66 0 362s 43 0.040159 43 8.571e-05 0.022014 0.05830 6 0 362s > all.equal(aa$"0 1"$P, as.vector(trprob(cif.control, "0 1"))) 362s [1] TRUE 362s > 362s > ### test on los data 362s > 362s > data(los.data) # in package changeLOS 362s > 362s > ## putting los.data in the long format (see changeLOS) 362s > my.observ <- prepare.los.data(x=los.data) 362s > 362s > tra <- matrix(FALSE, 4, 4) 362s > tra[1, 2:4] <- TRUE 362s > tra[2, 3:4] <- TRUE 362s > 362s > tr.prob <- etm(my.observ, c("0","1","2","3"), tra, NULL, 0) 362s > 362s > tr.prob 362s Multistate model with 2 transient state(s) 362s and 2 absorbing state(s) 362s 362s Possible transitions: 362s from to 362s 0 1 362s 0 2 362s 0 3 362s 1 2 362s 1 3 362s 362s Estimate of P(0, 82) 362s 0 1 2 3 362s 0 0 0 0.7474 0.2526 362s 1 0 0 0.7073 0.2927 362s 2 0 0 1.0000 0.0000 362s 3 0 0 0.0000 1.0000 362s 362s > summary(tr.prob) 362s Transition 0 0 362s P time var lower upper n.risk n.event 362s 0.882275 3 1.374e-04 0.8593018 0.905248 756 0 362s 0.112434 15 1.320e-04 0.0899155 0.134952 90 0 362s 0.031746 27 4.066e-05 0.0192484 0.044244 26 0 362s 0.006614 41 8.690e-06 0.0008359 0.012392 5 0 362s 0.002646 61 3.490e-06 0.0000000 0.006307 3 0 362s 0.000000 82 0.000e+00 0.0000000 0.000000 1 0 362s 362s Transition 0 1 362s P time var lower upper n.risk n.event 362s 0.017196 3 2.235e-05 0.0079289 0.02646 756 13 362s 0.063492 15 7.865e-05 0.0461099 0.08087 90 0 362s 0.030423 27 3.902e-05 0.0181805 0.04267 26 1 362s 0.015873 41 2.066e-05 0.0069637 0.02478 5 0 362s 0.005291 61 6.962e-06 0.0001197 0.01046 3 0 362s 0.000000 82 0.000e+00 0.0000000 0.00000 1 0 362s 362s Transition 0 2 362s P time var lower upper n.risk n.event 362s 0.08466 3 0.0001025 0.06481 0.1045 756 64 362s 0.62302 15 0.0003107 0.58847 0.6576 90 4 362s 0.69841 27 0.0002786 0.66570 0.7311 26 1 362s 0.72751 41 0.0002622 0.69578 0.7593 5 0 362s 0.74074 61 0.0002540 0.70950 0.7720 3 1 362s 0.74735 82 0.0002498 0.71638 0.7783 1 1 362s 362s Transition 0 3 362s P time var lower upper n.risk n.event 362s 0.01587 3 2.066e-05 0.006964 0.02478 756 12 362s 0.20106 15 2.125e-04 0.172489 0.22963 90 1 362s 0.23942 27 2.409e-04 0.208999 0.26984 26 0 362s 0.25000 41 2.480e-04 0.219133 0.28087 5 0 362s 0.25132 61 2.489e-04 0.220402 0.28224 3 0 362s 0.25265 82 2.498e-04 0.221671 0.28362 1 0 362s 362s Transition 1 1 362s P time var lower upper n.risk n.event 362s 1.00000 3 0.000e+00 1.00000 1.00000 0 0 362s 0.38661 15 2.358e-03 0.29143 0.48179 51 0 362s 0.12119 27 7.842e-04 0.06630 0.17607 23 0 362s 0.04593 41 2.405e-04 0.01554 0.07633 14 0 362s 0.01531 61 6.579e-05 0.00000 0.03121 4 0 362s 0.00000 82 0.000e+00 0.00000 0.00000 0 0 362s 362s Transition 1 2 362s P time var lower upper n.risk n.event 362s 0.0000 3 0.000000 0.0000 0.0000 0 0 362s 0.4107 15 0.002590 0.3110 0.5104 51 2 362s 0.6082 27 0.002254 0.5151 0.7012 23 1 362s 0.6652 41 0.002064 0.5761 0.7542 14 2 362s 0.6920 61 0.002000 0.6043 0.7796 4 0 362s 0.7073 82 0.001984 0.6200 0.7946 0 0 362s 362s Transition 1 3 363s P time var lower upper n.risk n.event 363s 0.0000 3 0.000000 0.0000 0.0000 0 0 363s 0.2027 15 0.001784 0.1199 0.2855 51 1 363s 0.2706 27 0.001968 0.1837 0.3576 23 0 363s 0.2889 41 0.001982 0.2016 0.3761 14 0 363s 0.2927 61 0.001984 0.2054 0.3800 4 0 363s 0.2927 82 0.001984 0.2054 0.3800 0 0 363s 363s > 363s > cLOS <- etm::clos(tr.prob, aw = TRUE) 363s > 363s > cLOS 363s The expected change in length of stay is: 363s 1.975 363s 363s Alternative weighting: 363s 363s Expected change in LOS with weight.1: 2.097 363s Expected change in LOS with weight.other: 1.951 363s > 363s > 363s > ### Tests on pseudo values 363s > t_pseudo <- closPseudo(my.observ, c("0","1","2","3"), tra, NULL, 363s + 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 + } 385s [1] TRUE 385s > 385s > options(old) 385s > 385s autopkgtest [23:01:53]: test run-unit-test: -----------------------] 389s autopkgtest [23:01:57]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 389s run-unit-test PASS 393s autopkgtest [23:02:01]: test pkg-r-autopkgtest: preparing testbed 395s Reading package lists... 395s Building dependency tree... 395s 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-mgcv r-cran-nlme r-cran-pillar 397s r-cran-pkgconfig r-cran-purrr r-cran-r6 r-cran-rcolorbrewer r-cran-rlang 397s r-cran-scales r-cran-stringi r-cran-stringr r-cran-tibble r-cran-tidyr 397s r-cran-tidyselect r-cran-utf8 r-cran-vctrs r-cran-viridislite r-cran-withr 397s rpcsvc-proto zlib1g-dev 397s 0 upgraded, 91 newly installed, 0 to remove and 0 not upgraded. 397s Need to get 113 MB of archives. 397s After this operation, 300 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] 400s Get:3 http://ftpmaster.internal/ubuntu resolute/main armhf libcrypt-dev armhf 1:4.5.1-1 [128 kB] 400s Get:4 http://ftpmaster.internal/ubuntu resolute/main armhf rpcsvc-proto armhf 1.4.3-1build1 [62.6 kB] 400s Get:5 http://ftpmaster.internal/ubuntu resolute/main armhf libc6-dev armhf 2.42-2ubuntu4 [1416 kB] 403s Get:6 http://ftpmaster.internal/ubuntu resolute/main armhf libisl23 armhf 0.27-1build1 [553 kB] 404s Get:7 http://ftpmaster.internal/ubuntu resolute/main armhf libmpc3 armhf 1.3.1-2 [47.0 kB] 404s Get:8 http://ftpmaster.internal/ubuntu resolute/main armhf cpp-15-arm-linux-gnueabihf armhf 15.2.0-12ubuntu1 [10.1 MB] 422s Get:9 http://ftpmaster.internal/ubuntu resolute/main armhf cpp-15 armhf 15.2.0-12ubuntu1 [1032 B] 422s Get:10 http://ftpmaster.internal/ubuntu resolute/main armhf cpp-arm-linux-gnueabihf armhf 4:15.2.0-4ubuntu1 [5756 B] 422s Get:11 http://ftpmaster.internal/ubuntu resolute/main armhf cpp armhf 4:15.2.0-4ubuntu1 [22.4 kB] 422s Get:12 http://ftpmaster.internal/ubuntu resolute/main armhf libcc1-0 armhf 15.2.0-12ubuntu1 [43.5 kB] 422s Get:13 http://ftpmaster.internal/ubuntu resolute/main armhf libasan8 armhf 15.2.0-12ubuntu1 [2949 kB] 427s Get:14 http://ftpmaster.internal/ubuntu resolute/main armhf libubsan1 armhf 15.2.0-12ubuntu1 [1187 kB] 429s Get:15 http://ftpmaster.internal/ubuntu resolute/main armhf libgcc-15-dev armhf 15.2.0-12ubuntu1 [898 kB] 431s 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] 472s Get:18 http://ftpmaster.internal/ubuntu resolute/main armhf gcc-arm-linux-gnueabihf armhf 4:15.2.0-4ubuntu1 [1220 B] 472s Get:19 http://ftpmaster.internal/ubuntu resolute/main armhf gcc armhf 4:15.2.0-4ubuntu1 [5022 B] 472s Get:20 http://ftpmaster.internal/ubuntu resolute/main armhf libstdc++-15-dev armhf 15.2.0-12ubuntu1 [2638 kB] 482s Get:21 http://ftpmaster.internal/ubuntu resolute/main armhf g++-15-arm-linux-gnueabihf armhf 15.2.0-12ubuntu1 [11.4 MB] 503s Get:22 http://ftpmaster.internal/ubuntu resolute/main armhf g++-15 armhf 15.2.0-12ubuntu1 [25.3 kB] 503s Get:23 http://ftpmaster.internal/ubuntu resolute/main armhf g++-arm-linux-gnueabihf armhf 4:15.2.0-4ubuntu1 [968 B] 503s Get:24 http://ftpmaster.internal/ubuntu resolute/main armhf g++ armhf 4:15.2.0-4ubuntu1 [1086 B] 503s Get:25 http://ftpmaster.internal/ubuntu resolute/main armhf build-essential armhf 12.12ubuntu2 [5256 B] 503s Get:26 http://ftpmaster.internal/ubuntu resolute/main armhf dctrl-tools armhf 2.24-3build4 [95.0 kB] 503s Get:27 http://ftpmaster.internal/ubuntu resolute/main armhf libgfortran-15-dev armhf 15.2.0-12ubuntu1 [380 kB] 504s Get:28 http://ftpmaster.internal/ubuntu resolute/main armhf gfortran-15-arm-linux-gnueabihf armhf 15.2.0-12ubuntu1 [10.7 MB] 526s Get:29 http://ftpmaster.internal/ubuntu resolute/main armhf gfortran-15 armhf 15.2.0-12ubuntu1 [18.1 kB] 526s Get:30 http://ftpmaster.internal/ubuntu resolute/main armhf gfortran-arm-linux-gnueabihf armhf 4:15.2.0-4ubuntu1 [1020 B] 526s Get:31 http://ftpmaster.internal/ubuntu resolute/main armhf gfortran armhf 4:15.2.0-4ubuntu1 [1162 B] 526s Get:32 http://ftpmaster.internal/ubuntu resolute/main armhf icu-devtools armhf 78.2-1ubuntu1 [203 kB] 527s Get:33 http://ftpmaster.internal/ubuntu resolute/main armhf libblas-dev armhf 3.12.1-7ubuntu1 [141 kB] 527s Get:34 http://ftpmaster.internal/ubuntu resolute/main armhf libbz2-dev armhf 1.0.8-6build2 [31.2 kB] 527s Get:35 http://ftpmaster.internal/ubuntu resolute/main armhf libdeflate-dev armhf 1.23-2build1 [45.1 kB] 527s Get:36 http://ftpmaster.internal/ubuntu resolute/main armhf libicu-dev armhf 78.2-1ubuntu1 [12.2 MB] 550s Get:37 http://ftpmaster.internal/ubuntu resolute/main armhf libjpeg-turbo8-dev armhf 2.1.5-4ubuntu3 [265 kB] 551s Get:38 http://ftpmaster.internal/ubuntu resolute/main armhf libjpeg8-dev armhf 8c-2ubuntu11 [1484 B] 551s Get:39 http://ftpmaster.internal/ubuntu resolute/main armhf libjpeg-dev armhf 8c-2ubuntu11 [1482 B] 551s Get:40 http://ftpmaster.internal/ubuntu resolute/main armhf liblapack-dev armhf 3.12.1-7ubuntu1 [2207 kB] 557s Get:41 http://ftpmaster.internal/ubuntu resolute/main armhf libncurses-dev armhf 6.6+20251231-1 [348 kB] 558s Get:42 http://ftpmaster.internal/ubuntu resolute/main armhf libpcre2-16-0 armhf 10.46-1 [206 kB] 558s Get:43 http://ftpmaster.internal/ubuntu resolute/main armhf libpcre2-32-0 armhf 10.46-1 [197 kB] 558s Get:44 http://ftpmaster.internal/ubuntu resolute/main armhf libpcre2-posix3 armhf 10.46-1 [6286 B] 558s Get:45 http://ftpmaster.internal/ubuntu resolute/main armhf libpcre2-dev armhf 10.46-1 [744 kB] 560s Get:46 http://ftpmaster.internal/ubuntu resolute/main armhf libpkgconf3 armhf 1.8.1-4build1 [26.6 kB] 560s Get:47 http://ftpmaster.internal/ubuntu resolute/main armhf zlib1g-dev armhf 1:1.3.dfsg+really1.3.1-1ubuntu2 [881 kB] 562s Get:48 http://ftpmaster.internal/ubuntu resolute/main armhf libpng-dev armhf 1.6.54-1 [252 kB] 562s Get:49 http://ftpmaster.internal/ubuntu resolute/main armhf libreadline-dev armhf 8.3-3 [165 kB] 562s Get:50 http://ftpmaster.internal/ubuntu resolute/main armhf libzstd-dev armhf 1.5.7+dfsg-3 [342 kB] 563s Get:51 http://ftpmaster.internal/ubuntu resolute/main armhf liblzma-dev armhf 5.8.2-2 [167 kB] 563s Get:52 http://ftpmaster.internal/ubuntu resolute/main armhf pkgconf-bin armhf 1.8.1-4build1 [21.4 kB] 563s Get:53 http://ftpmaster.internal/ubuntu resolute/main armhf pkgconf armhf 1.8.1-4build1 [16.8 kB] 563s Get:54 http://ftpmaster.internal/ubuntu resolute/main armhf libtirpc-dev armhf 1.3.6+ds-1 [184 kB] 564s Get:55 http://ftpmaster.internal/ubuntu resolute/universe armhf r-base-dev all 4.5.2-1ubuntu2 [1880 B] 564s Get:56 http://ftpmaster.internal/ubuntu resolute/universe armhf pkg-r-autopkgtest all 20250812 [6158 B] 564s Get:57 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-backports armhf 1.5.0-2 [121 kB] 564s Get:58 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-cli armhf 3.6.4-1 [1377 kB] 567s Get:59 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-generics all 0.1.4-1 [84.0 kB] 567s Get:60 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-glue armhf 1.8.0-1 [162 kB] 567s Get:61 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-rlang armhf 1.1.5-3 [1700 kB] 570s Get:62 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-lifecycle all 1.0.5+dfsg-1 [120 kB] 571s Get:63 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-magrittr armhf 2.0.3-1 [154 kB] 571s Get:64 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-utf8 armhf 1.2.4-1 [136 kB] 571s Get:65 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-vctrs armhf 0.6.5-1 [1310 kB] 574s Get:66 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-pillar all 1.11.1+dfsg-1 [456 kB] 575s Get:67 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-r6 all 2.6.1-1 [101 kB] 575s Get:68 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-fansi armhf 1.0.6-2 [620 kB] 576s Get:69 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-pkgconfig all 2.0.3-2build2 [20.4 kB] 576s Get:70 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-tibble armhf 3.2.1+dfsg-3 [420 kB] 577s Get:71 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-withr all 3.0.2+dfsg-1 [214 kB] 577s Get:72 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-tidyselect armhf 1.2.1+dfsg-1 [222 kB] 578s Get:73 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-dplyr armhf 1.1.4-4 [1533 kB] 581s Get:74 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-purrr armhf 1.0.4-1 [550 kB] 582s Get:75 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-stringi armhf 1.8.4-1build2 [884 kB] 584s Get:76 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-stringr all 1.5.1-1 [290 kB] 584s Get:77 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-cpp11 all 0.5.3-1 [242 kB] 585s Get:78 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-tidyr armhf 1.3.1-1 [1152 kB] 587s Get:79 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-broom all 1.0.12+dfsg-1 [1708 kB] 590s Get:80 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-farver armhf 2.1.2-1 [1355 kB] 593s Get:81 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-mass armhf 7.3-65-1 [1108 kB] 596s Get:82 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-geepack armhf 1.3.12-1 [365 kB] 596s Get:83 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-gtable all 0.3.6+dfsg-1 [199 kB] 597s Get:84 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-isoband armhf 0.2.7-1 [1477 kB] 599s Get:85 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-nlme armhf 3.1.168-1 [2304 kB] 603s Get:86 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-mgcv armhf 1.9-4-1 [3515 kB] 608s Get:87 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-labeling all 0.4.3-1 [62.1 kB] 608s Get:88 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-rcolorbrewer all 1.1-3-1build2 [54.0 kB] 609s Get:89 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-viridislite all 0.4.3-1 [1088 kB] 610s Get:90 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-scales all 1.4.0-1 [725 kB] 611s Get:91 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-ggplot2 all 3.5.1+dfsg-1 [3940 kB] 618s Fetched 113 MB in 3min 41s (511 kB/s) 618s Selecting previously unselected package libc-dev-bin. 618s (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 ... 73888 files and directories currently installed.) 618s Preparing to unpack .../00-libc-dev-bin_2.42-2ubuntu4_armhf.deb ... 618s Unpacking libc-dev-bin (2.42-2ubuntu4) ... 618s Selecting previously unselected package linux-libc-dev:armhf. 618s Preparing to unpack .../01-linux-libc-dev_6.19.0-3.3_armhf.deb ... 618s Unpacking linux-libc-dev:armhf (6.19.0-3.3) ... 619s Selecting previously unselected package libcrypt-dev:armhf. 619s Preparing to unpack .../02-libcrypt-dev_1%3a4.5.1-1_armhf.deb ... 619s Unpacking libcrypt-dev:armhf (1:4.5.1-1) ... 619s Selecting previously unselected package rpcsvc-proto. 619s Preparing to unpack .../03-rpcsvc-proto_1.4.3-1build1_armhf.deb ... 619s Unpacking rpcsvc-proto (1.4.3-1build1) ... 619s Selecting previously unselected package libc6-dev:armhf. 619s Preparing to unpack .../04-libc6-dev_2.42-2ubuntu4_armhf.deb ... 619s Unpacking libc6-dev:armhf (2.42-2ubuntu4) ... 619s Selecting previously unselected package libisl23:armhf. 619s Preparing to unpack .../05-libisl23_0.27-1build1_armhf.deb ... 619s Unpacking libisl23:armhf (0.27-1build1) ... 619s Selecting previously unselected package libmpc3:armhf. 619s Preparing to unpack .../06-libmpc3_1.3.1-2_armhf.deb ... 619s Unpacking libmpc3:armhf (1.3.1-2) ... 619s Selecting previously unselected package cpp-15-arm-linux-gnueabihf. 619s Preparing to unpack .../07-cpp-15-arm-linux-gnueabihf_15.2.0-12ubuntu1_armhf.deb ... 619s Unpacking cpp-15-arm-linux-gnueabihf (15.2.0-12ubuntu1) ... 619s Selecting previously unselected package cpp-15. 619s Preparing to unpack .../08-cpp-15_15.2.0-12ubuntu1_armhf.deb ... 619s Unpacking cpp-15 (15.2.0-12ubuntu1) ... 619s Selecting previously unselected package cpp-arm-linux-gnueabihf. 619s Preparing to unpack .../09-cpp-arm-linux-gnueabihf_4%3a15.2.0-4ubuntu1_armhf.deb ... 619s Unpacking cpp-arm-linux-gnueabihf (4:15.2.0-4ubuntu1) ... 619s Selecting previously unselected package cpp. 619s Preparing to unpack .../10-cpp_4%3a15.2.0-4ubuntu1_armhf.deb ... 619s Unpacking cpp (4:15.2.0-4ubuntu1) ... 619s Selecting previously unselected package libcc1-0:armhf. 619s Preparing to unpack .../11-libcc1-0_15.2.0-12ubuntu1_armhf.deb ... 619s Unpacking libcc1-0:armhf (15.2.0-12ubuntu1) ... 619s Selecting previously unselected package libasan8:armhf. 620s Preparing to unpack .../12-libasan8_15.2.0-12ubuntu1_armhf.deb ... 620s Unpacking libasan8:armhf (15.2.0-12ubuntu1) ... 620s Selecting previously unselected package libubsan1:armhf. 620s Preparing to unpack .../13-libubsan1_15.2.0-12ubuntu1_armhf.deb ... 620s Unpacking libubsan1:armhf (15.2.0-12ubuntu1) ... 620s Selecting previously unselected package libgcc-15-dev:armhf. 620s Preparing to unpack .../14-libgcc-15-dev_15.2.0-12ubuntu1_armhf.deb ... 620s Unpacking libgcc-15-dev:armhf (15.2.0-12ubuntu1) ... 620s Selecting previously unselected package gcc-15-arm-linux-gnueabihf. 620s Preparing to unpack .../15-gcc-15-arm-linux-gnueabihf_15.2.0-12ubuntu1_armhf.deb ... 620s Unpacking gcc-15-arm-linux-gnueabihf (15.2.0-12ubuntu1) ... 620s Selecting previously unselected package gcc-15. 620s Preparing to unpack .../16-gcc-15_15.2.0-12ubuntu1_armhf.deb ... 620s Unpacking gcc-15 (15.2.0-12ubuntu1) ... 620s Selecting previously unselected package gcc-arm-linux-gnueabihf. 620s Preparing to unpack .../17-gcc-arm-linux-gnueabihf_4%3a15.2.0-4ubuntu1_armhf.deb ... 620s Unpacking gcc-arm-linux-gnueabihf (4:15.2.0-4ubuntu1) ... 620s Selecting previously unselected package gcc. 620s Preparing to unpack .../18-gcc_4%3a15.2.0-4ubuntu1_armhf.deb ... 620s Unpacking gcc (4:15.2.0-4ubuntu1) ... 621s Selecting previously unselected package libstdc++-15-dev:armhf. 621s Preparing to unpack .../19-libstdc++-15-dev_15.2.0-12ubuntu1_armhf.deb ... 621s Unpacking libstdc++-15-dev:armhf (15.2.0-12ubuntu1) ... 621s Selecting previously unselected package g++-15-arm-linux-gnueabihf. 621s Preparing to unpack .../20-g++-15-arm-linux-gnueabihf_15.2.0-12ubuntu1_armhf.deb ... 621s Unpacking g++-15-arm-linux-gnueabihf (15.2.0-12ubuntu1) ... 621s Selecting previously unselected package g++-15. 621s Preparing to unpack .../21-g++-15_15.2.0-12ubuntu1_armhf.deb ... 621s Unpacking g++-15 (15.2.0-12ubuntu1) ... 621s Selecting previously unselected package g++-arm-linux-gnueabihf. 621s Preparing to unpack .../22-g++-arm-linux-gnueabihf_4%3a15.2.0-4ubuntu1_armhf.deb ... 621s Unpacking g++-arm-linux-gnueabihf (4:15.2.0-4ubuntu1) ... 621s Selecting previously unselected package g++. 621s Preparing to unpack .../23-g++_4%3a15.2.0-4ubuntu1_armhf.deb ... 621s Unpacking g++ (4:15.2.0-4ubuntu1) ... 621s Selecting previously unselected package build-essential. 621s Preparing to unpack .../24-build-essential_12.12ubuntu2_armhf.deb ... 621s Unpacking build-essential (12.12ubuntu2) ... 621s Selecting previously unselected package dctrl-tools. 621s Preparing to unpack .../25-dctrl-tools_2.24-3build4_armhf.deb ... 621s Unpacking dctrl-tools (2.24-3build4) ... 621s Selecting previously unselected package libgfortran-15-dev:armhf. 621s Preparing to unpack .../26-libgfortran-15-dev_15.2.0-12ubuntu1_armhf.deb ... 621s Unpacking libgfortran-15-dev:armhf (15.2.0-12ubuntu1) ... 621s Selecting previously unselected package gfortran-15-arm-linux-gnueabihf. 621s Preparing to unpack .../27-gfortran-15-arm-linux-gnueabihf_15.2.0-12ubuntu1_armhf.deb ... 621s Unpacking gfortran-15-arm-linux-gnueabihf (15.2.0-12ubuntu1) ... 622s Selecting previously unselected package gfortran-15. 622s Preparing to unpack .../28-gfortran-15_15.2.0-12ubuntu1_armhf.deb ... 622s Unpacking gfortran-15 (15.2.0-12ubuntu1) ... 622s Selecting previously unselected package gfortran-arm-linux-gnueabihf. 622s Preparing to unpack .../29-gfortran-arm-linux-gnueabihf_4%3a15.2.0-4ubuntu1_armhf.deb ... 622s Unpacking gfortran-arm-linux-gnueabihf (4:15.2.0-4ubuntu1) ... 622s Selecting previously unselected package gfortran. 622s Preparing to unpack .../30-gfortran_4%3a15.2.0-4ubuntu1_armhf.deb ... 622s Unpacking gfortran (4:15.2.0-4ubuntu1) ... 622s Selecting previously unselected package icu-devtools. 622s Preparing to unpack .../31-icu-devtools_78.2-1ubuntu1_armhf.deb ... 622s Unpacking icu-devtools (78.2-1ubuntu1) ... 622s Selecting previously unselected package libblas-dev:armhf. 622s Preparing to unpack .../32-libblas-dev_3.12.1-7ubuntu1_armhf.deb ... 622s Unpacking libblas-dev:armhf (3.12.1-7ubuntu1) ... 622s Selecting previously unselected package libbz2-dev:armhf. 622s Preparing to unpack .../33-libbz2-dev_1.0.8-6build2_armhf.deb ... 622s Unpacking libbz2-dev:armhf (1.0.8-6build2) ... 622s Selecting previously unselected package libdeflate-dev:armhf. 622s Preparing to unpack .../34-libdeflate-dev_1.23-2build1_armhf.deb ... 622s Unpacking libdeflate-dev:armhf (1.23-2build1) ... 622s Selecting previously unselected package libicu-dev:armhf. 622s Preparing to unpack .../35-libicu-dev_78.2-1ubuntu1_armhf.deb ... 622s Unpacking libicu-dev:armhf (78.2-1ubuntu1) ... 623s Selecting previously unselected package libjpeg-turbo8-dev:armhf. 623s Preparing to unpack .../36-libjpeg-turbo8-dev_2.1.5-4ubuntu3_armhf.deb ... 623s Unpacking libjpeg-turbo8-dev:armhf (2.1.5-4ubuntu3) ... 623s Selecting previously unselected package libjpeg8-dev:armhf. 623s Preparing to unpack .../37-libjpeg8-dev_8c-2ubuntu11_armhf.deb ... 623s Unpacking libjpeg8-dev:armhf (8c-2ubuntu11) ... 623s Selecting previously unselected package libjpeg-dev:armhf. 623s Preparing to unpack .../38-libjpeg-dev_8c-2ubuntu11_armhf.deb ... 623s Unpacking libjpeg-dev:armhf (8c-2ubuntu11) ... 623s Selecting previously unselected package liblapack-dev:armhf. 623s Preparing to unpack .../39-liblapack-dev_3.12.1-7ubuntu1_armhf.deb ... 623s Unpacking liblapack-dev:armhf (3.12.1-7ubuntu1) ... 623s Selecting previously unselected package libncurses-dev:armhf. 623s Preparing to unpack .../40-libncurses-dev_6.6+20251231-1_armhf.deb ... 623s Unpacking libncurses-dev:armhf (6.6+20251231-1) ... 623s Selecting previously unselected package libpcre2-16-0:armhf. 623s Preparing to unpack .../41-libpcre2-16-0_10.46-1_armhf.deb ... 623s Unpacking libpcre2-16-0:armhf (10.46-1) ... 623s Selecting previously unselected package libpcre2-32-0:armhf. 623s Preparing to unpack .../42-libpcre2-32-0_10.46-1_armhf.deb ... 623s Unpacking libpcre2-32-0:armhf (10.46-1) ... 623s Selecting previously unselected package libpcre2-posix3:armhf. 623s Preparing to unpack .../43-libpcre2-posix3_10.46-1_armhf.deb ... 623s Unpacking libpcre2-posix3:armhf (10.46-1) ... 623s Selecting previously unselected package libpcre2-dev:armhf. 623s Preparing to unpack .../44-libpcre2-dev_10.46-1_armhf.deb ... 623s Unpacking libpcre2-dev:armhf (10.46-1) ... 623s Selecting previously unselected package libpkgconf3:armhf. 623s Preparing to unpack .../45-libpkgconf3_1.8.1-4build1_armhf.deb ... 623s Unpacking libpkgconf3:armhf (1.8.1-4build1) ... 623s Selecting previously unselected package zlib1g-dev:armhf. 623s Preparing to unpack .../46-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1ubuntu2_armhf.deb ... 623s Unpacking zlib1g-dev:armhf (1:1.3.dfsg+really1.3.1-1ubuntu2) ... 623s Selecting previously unselected package libpng-dev:armhf. 623s Preparing to unpack .../47-libpng-dev_1.6.54-1_armhf.deb ... 623s Unpacking libpng-dev:armhf (1.6.54-1) ... 624s Selecting previously unselected package libreadline-dev:armhf. 624s Preparing to unpack .../48-libreadline-dev_8.3-3_armhf.deb ... 624s Unpacking libreadline-dev:armhf (8.3-3) ... 624s Selecting previously unselected package libzstd-dev:armhf. 624s Preparing to unpack .../49-libzstd-dev_1.5.7+dfsg-3_armhf.deb ... 624s Unpacking libzstd-dev:armhf (1.5.7+dfsg-3) ... 624s Selecting previously unselected package liblzma-dev:armhf. 624s Preparing to unpack .../50-liblzma-dev_5.8.2-2_armhf.deb ... 624s Unpacking liblzma-dev:armhf (5.8.2-2) ... 624s Selecting previously unselected package pkgconf-bin. 624s Preparing to unpack .../51-pkgconf-bin_1.8.1-4build1_armhf.deb ... 624s Unpacking pkgconf-bin (1.8.1-4build1) ... 624s Selecting previously unselected package pkgconf:armhf. 624s Preparing to unpack .../52-pkgconf_1.8.1-4build1_armhf.deb ... 624s Unpacking pkgconf:armhf (1.8.1-4build1) ... 624s Selecting previously unselected package libtirpc-dev:armhf. 624s Preparing to unpack .../53-libtirpc-dev_1.3.6+ds-1_armhf.deb ... 624s Unpacking libtirpc-dev:armhf (1.3.6+ds-1) ... 624s Selecting previously unselected package r-base-dev. 624s Preparing to unpack .../54-r-base-dev_4.5.2-1ubuntu2_all.deb ... 624s Unpacking r-base-dev (4.5.2-1ubuntu2) ... 624s Selecting previously unselected package pkg-r-autopkgtest. 624s Preparing to unpack .../55-pkg-r-autopkgtest_20250812_all.deb ... 624s Unpacking pkg-r-autopkgtest (20250812) ... 624s Selecting previously unselected package r-cran-backports. 624s Preparing to unpack .../56-r-cran-backports_1.5.0-2_armhf.deb ... 624s Unpacking r-cran-backports (1.5.0-2) ... 624s Selecting previously unselected package r-cran-cli. 624s Preparing to unpack .../57-r-cran-cli_3.6.4-1_armhf.deb ... 624s Unpacking r-cran-cli (3.6.4-1) ... 624s Selecting previously unselected package r-cran-generics. 624s Preparing to unpack .../58-r-cran-generics_0.1.4-1_all.deb ... 624s Unpacking r-cran-generics (0.1.4-1) ... 624s Selecting previously unselected package r-cran-glue. 624s Preparing to unpack .../59-r-cran-glue_1.8.0-1_armhf.deb ... 624s Unpacking r-cran-glue (1.8.0-1) ... 624s Selecting previously unselected package r-cran-rlang. 624s Preparing to unpack .../60-r-cran-rlang_1.1.5-3_armhf.deb ... 624s Unpacking r-cran-rlang (1.1.5-3) ... 624s Selecting previously unselected package r-cran-lifecycle. 624s Preparing to unpack .../61-r-cran-lifecycle_1.0.5+dfsg-1_all.deb ... 624s Unpacking r-cran-lifecycle (1.0.5+dfsg-1) ... 624s Selecting previously unselected package r-cran-magrittr. 624s Preparing to unpack .../62-r-cran-magrittr_2.0.3-1_armhf.deb ... 624s Unpacking r-cran-magrittr (2.0.3-1) ... 625s Selecting previously unselected package r-cran-utf8. 625s Preparing to unpack .../63-r-cran-utf8_1.2.4-1_armhf.deb ... 625s Unpacking r-cran-utf8 (1.2.4-1) ... 625s Selecting previously unselected package r-cran-vctrs. 625s Preparing to unpack .../64-r-cran-vctrs_0.6.5-1_armhf.deb ... 625s Unpacking r-cran-vctrs (0.6.5-1) ... 625s Selecting previously unselected package r-cran-pillar. 625s Preparing to unpack .../65-r-cran-pillar_1.11.1+dfsg-1_all.deb ... 625s Unpacking r-cran-pillar (1.11.1+dfsg-1) ... 625s Selecting previously unselected package r-cran-r6. 625s Preparing to unpack .../66-r-cran-r6_2.6.1-1_all.deb ... 625s Unpacking r-cran-r6 (2.6.1-1) ... 625s Selecting previously unselected package r-cran-fansi. 625s Preparing to unpack .../67-r-cran-fansi_1.0.6-2_armhf.deb ... 625s Unpacking r-cran-fansi (1.0.6-2) ... 625s Selecting previously unselected package r-cran-pkgconfig. 625s Preparing to unpack .../68-r-cran-pkgconfig_2.0.3-2build2_all.deb ... 625s Unpacking r-cran-pkgconfig (2.0.3-2build2) ... 625s Selecting previously unselected package r-cran-tibble. 625s Preparing to unpack .../69-r-cran-tibble_3.2.1+dfsg-3_armhf.deb ... 625s Unpacking r-cran-tibble (3.2.1+dfsg-3) ... 625s Selecting previously unselected package r-cran-withr. 625s Preparing to unpack .../70-r-cran-withr_3.0.2+dfsg-1_all.deb ... 625s Unpacking r-cran-withr (3.0.2+dfsg-1) ... 625s Selecting previously unselected package r-cran-tidyselect. 625s Preparing to unpack .../71-r-cran-tidyselect_1.2.1+dfsg-1_armhf.deb ... 625s Unpacking r-cran-tidyselect (1.2.1+dfsg-1) ... 625s Selecting previously unselected package r-cran-dplyr. 625s Preparing to unpack .../72-r-cran-dplyr_1.1.4-4_armhf.deb ... 625s Unpacking r-cran-dplyr (1.1.4-4) ... 625s Selecting previously unselected package r-cran-purrr. 625s Preparing to unpack .../73-r-cran-purrr_1.0.4-1_armhf.deb ... 625s Unpacking r-cran-purrr (1.0.4-1) ... 625s Selecting previously unselected package r-cran-stringi. 625s Preparing to unpack .../74-r-cran-stringi_1.8.4-1build2_armhf.deb ... 625s Unpacking r-cran-stringi (1.8.4-1build2) ... 625s Selecting previously unselected package r-cran-stringr. 625s Preparing to unpack .../75-r-cran-stringr_1.5.1-1_all.deb ... 625s Unpacking r-cran-stringr (1.5.1-1) ... 626s Selecting previously unselected package r-cran-cpp11. 626s Preparing to unpack .../76-r-cran-cpp11_0.5.3-1_all.deb ... 626s Unpacking r-cran-cpp11 (0.5.3-1) ... 626s Selecting previously unselected package r-cran-tidyr. 626s Preparing to unpack .../77-r-cran-tidyr_1.3.1-1_armhf.deb ... 626s Unpacking r-cran-tidyr (1.3.1-1) ... 626s Selecting previously unselected package r-cran-broom. 626s Preparing to unpack .../78-r-cran-broom_1.0.12+dfsg-1_all.deb ... 626s Unpacking r-cran-broom (1.0.12+dfsg-1) ... 626s Selecting previously unselected package r-cran-farver. 626s Preparing to unpack .../79-r-cran-farver_2.1.2-1_armhf.deb ... 626s Unpacking r-cran-farver (2.1.2-1) ... 626s Selecting previously unselected package r-cran-mass. 626s Preparing to unpack .../80-r-cran-mass_7.3-65-1_armhf.deb ... 626s Unpacking r-cran-mass (7.3-65-1) ... 626s Selecting previously unselected package r-cran-geepack. 626s Preparing to unpack .../81-r-cran-geepack_1.3.12-1_armhf.deb ... 626s Unpacking r-cran-geepack (1.3.12-1) ... 626s Selecting previously unselected package r-cran-gtable. 626s Preparing to unpack .../82-r-cran-gtable_0.3.6+dfsg-1_all.deb ... 626s Unpacking r-cran-gtable (0.3.6+dfsg-1) ... 626s Selecting previously unselected package r-cran-isoband. 626s Preparing to unpack .../83-r-cran-isoband_0.2.7-1_armhf.deb ... 626s Unpacking r-cran-isoband (0.2.7-1) ... 626s Selecting previously unselected package r-cran-nlme. 626s Preparing to unpack .../84-r-cran-nlme_3.1.168-1_armhf.deb ... 626s Unpacking r-cran-nlme (3.1.168-1) ... 626s Selecting previously unselected package r-cran-mgcv. 626s Preparing to unpack .../85-r-cran-mgcv_1.9-4-1_armhf.deb ... 626s Unpacking r-cran-mgcv (1.9-4-1) ... 626s Selecting previously unselected package r-cran-labeling. 626s Preparing to unpack .../86-r-cran-labeling_0.4.3-1_all.deb ... 626s Unpacking r-cran-labeling (0.4.3-1) ... 626s Selecting previously unselected package r-cran-rcolorbrewer. 626s Preparing to unpack .../87-r-cran-rcolorbrewer_1.1-3-1build2_all.deb ... 626s Unpacking r-cran-rcolorbrewer (1.1-3-1build2) ... 626s Selecting previously unselected package r-cran-viridislite. 626s Preparing to unpack .../88-r-cran-viridislite_0.4.3-1_all.deb ... 626s Unpacking r-cran-viridislite (0.4.3-1) ... 626s Selecting previously unselected package r-cran-scales. 626s Preparing to unpack .../89-r-cran-scales_1.4.0-1_all.deb ... 626s Unpacking r-cran-scales (1.4.0-1) ... 627s Selecting previously unselected package r-cran-ggplot2. 627s Preparing to unpack .../90-r-cran-ggplot2_3.5.1+dfsg-1_all.deb ... 627s Unpacking r-cran-ggplot2 (3.5.1+dfsg-1) ... 627s Setting up r-cran-rlang (1.1.5-3) ... 627s Setting up libzstd-dev:armhf (1.5.7+dfsg-3) ... 627s Setting up r-cran-withr (3.0.2+dfsg-1) ... 627s Setting up r-cran-backports (1.5.0-2) ... 627s Setting up r-cran-generics (0.1.4-1) ... 627s Setting up r-cran-fansi (1.0.6-2) ... 627s Setting up r-cran-mass (7.3-65-1) ... 627s Setting up linux-libc-dev:armhf (6.19.0-3.3) ... 627s Setting up r-cran-glue (1.8.0-1) ... 627s Setting up r-cran-cli (3.6.4-1) ... 627s Setting up r-cran-lifecycle (1.0.5+dfsg-1) ... 627s Setting up libpcre2-16-0:armhf (10.46-1) ... 627s Setting up r-cran-pkgconfig (2.0.3-2build2) ... 627s Setting up libpcre2-32-0:armhf (10.46-1) ... 627s Setting up r-cran-utf8 (1.2.4-1) ... 627s Setting up libtirpc-dev:armhf (1.3.6+ds-1) ... 627s Setting up libpkgconf3:armhf (1.8.1-4build1) ... 627s Setting up rpcsvc-proto (1.4.3-1build1) ... 627s Setting up r-cran-stringi (1.8.4-1build2) ... 627s Setting up r-cran-cpp11 (0.5.3-1) ... 627s Setting up r-cran-rcolorbrewer (1.1-3-1build2) ... 627s Setting up r-cran-isoband (0.2.7-1) ... 627s Setting up libmpc3:armhf (1.3.1-2) ... 627s Setting up r-cran-gtable (0.3.6+dfsg-1) ... 627s Setting up r-cran-labeling (0.4.3-1) ... 627s Setting up icu-devtools (78.2-1ubuntu1) ... 627s Setting up pkgconf-bin (1.8.1-4build1) ... 627s Setting up r-cran-nlme (3.1.168-1) ... 627s Setting up r-cran-farver (2.1.2-1) ... 627s Setting up liblzma-dev:armhf (5.8.2-2) ... 627s Setting up libubsan1:armhf (15.2.0-12ubuntu1) ... 627s Setting up r-cran-mgcv (1.9-4-1) ... 627s Setting up libpcre2-posix3:armhf (10.46-1) ... 627s Setting up r-cran-viridislite (0.4.3-1) ... 627s Setting up libcrypt-dev:armhf (1:4.5.1-1) ... 627s Setting up libasan8:armhf (15.2.0-12ubuntu1) ... 627s Setting up r-cran-r6 (2.6.1-1) ... 627s Setting up libisl23:armhf (0.27-1build1) ... 627s Setting up libc-dev-bin (2.42-2ubuntu4) ... 627s Setting up libdeflate-dev:armhf (1.23-2build1) ... 627s Setting up cpp-15-arm-linux-gnueabihf (15.2.0-12ubuntu1) ... 627s Setting up r-cran-magrittr (2.0.3-1) ... 627s Setting up libcc1-0:armhf (15.2.0-12ubuntu1) ... 627s Setting up r-cran-vctrs (0.6.5-1) ... 627s Setting up cpp-arm-linux-gnueabihf (4:15.2.0-4ubuntu1) ... 627s Setting up libblas-dev:armhf (3.12.1-7ubuntu1) ... 627s 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 627s Setting up dctrl-tools (2.24-3build4) ... 627s Setting up r-cran-pillar (1.11.1+dfsg-1) ... 627s Setting up libgcc-15-dev:armhf (15.2.0-12ubuntu1) ... 627s Setting up r-cran-stringr (1.5.1-1) ... 627s Setting up gcc-15-arm-linux-gnueabihf (15.2.0-12ubuntu1) ... 627s Setting up r-cran-tibble (3.2.1+dfsg-3) ... 627s Setting up libgfortran-15-dev:armhf (15.2.0-12ubuntu1) ... 627s Setting up pkgconf:armhf (1.8.1-4build1) ... 627s Setting up r-cran-tidyselect (1.2.1+dfsg-1) ... 627s Setting up r-cran-scales (1.4.0-1) ... 627s Setting up liblapack-dev:armhf (3.12.1-7ubuntu1) ... 627s 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 627s Setting up r-cran-purrr (1.0.4-1) ... 627s Setting up cpp-15 (15.2.0-12ubuntu1) ... 627s Setting up cpp (4:15.2.0-4ubuntu1) ... 627s Setting up libc6-dev:armhf (2.42-2ubuntu4) ... 627s Setting up r-cran-dplyr (1.1.4-4) ... 627s Setting up libicu-dev:armhf (78.2-1ubuntu1) ... 627s Setting up libbz2-dev:armhf (1.0.8-6build2) ... 627s Setting up gcc-arm-linux-gnueabihf (4:15.2.0-4ubuntu1) ... 627s Setting up libjpeg-turbo8-dev:armhf (2.1.5-4ubuntu3) ... 627s Setting up libncurses-dev:armhf (6.6+20251231-1) ... 627s Setting up gfortran-15-arm-linux-gnueabihf (15.2.0-12ubuntu1) ... 627s Setting up libpcre2-dev:armhf (10.46-1) ... 627s Setting up r-cran-ggplot2 (3.5.1+dfsg-1) ... 627s Setting up libreadline-dev:armhf (8.3-3) ... 627s Setting up gfortran-arm-linux-gnueabihf (4:15.2.0-4ubuntu1) ... 627s Setting up gcc-15 (15.2.0-12ubuntu1) ... 627s Setting up libstdc++-15-dev:armhf (15.2.0-12ubuntu1) ... 627s Setting up r-cran-tidyr (1.3.1-1) ... 627s Setting up zlib1g-dev:armhf (1:1.3.dfsg+really1.3.1-1ubuntu2) ... 627s Setting up libjpeg8-dev:armhf (8c-2ubuntu11) ... 627s Setting up gfortran-15 (15.2.0-12ubuntu1) ... 627s Setting up libpng-dev:armhf (1.6.54-1) ... 627s Setting up libjpeg-dev:armhf (8c-2ubuntu11) ... 627s Setting up g++-15-arm-linux-gnueabihf (15.2.0-12ubuntu1) ... 627s Setting up gcc (4:15.2.0-4ubuntu1) ... 627s Setting up r-cran-broom (1.0.12+dfsg-1) ... 627s Setting up g++-15 (15.2.0-12ubuntu1) ... 627s Setting up g++-arm-linux-gnueabihf (4:15.2.0-4ubuntu1) ... 627s Setting up r-cran-geepack (1.3.12-1) ... 627s Setting up gfortran (4:15.2.0-4ubuntu1) ... 627s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode 627s 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 627s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode 627s 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 627s Setting up g++ (4:15.2.0-4ubuntu1) ... 627s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 627s Setting up build-essential (12.12ubuntu2) ... 627s Setting up r-base-dev (4.5.2-1ubuntu2) ... 627s Setting up pkg-r-autopkgtest (20250812) ... 627s Processing triggers for libc-bin (2.42-2ubuntu4) ... 627s Processing triggers for man-db (2.13.1-1build1) ... 628s Processing triggers for install-info (7.2-5) ... 636s autopkgtest [23:06:04]: test pkg-r-autopkgtest: /usr/share/dh-r/pkg-r-autopkgtest 636s autopkgtest [23:06:04]: test pkg-r-autopkgtest: [----------------------- 638s Test: Try to load the R library etm 639s 639s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 639s Copyright (C) 2025 The R Foundation for Statistical Computing 639s Platform: arm-unknown-linux-gnueabihf (32-bit) 639s 639s R is free software and comes with ABSOLUTELY NO WARRANTY. 639s You are welcome to redistribute it under certain conditions. 639s Type 'license()' or 'licence()' for distribution details. 639s 639s R is a collaborative project with many contributors. 639s Type 'contributors()' for more information and 639s 'citation()' on how to cite R or R packages in publications. 639s 639s Type 'demo()' for some demos, 'help()' for on-line help, or 639s 'help.start()' for an HTML browser interface to help. 639s Type 'q()' to quit R. 639s 639s > library('etm') 640s > 641s autopkgtest [23:06:09]: test pkg-r-autopkgtest: -----------------------] 645s pkg-r-autopkgtest PASS 645s autopkgtest [23:06:13]: test pkg-r-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 649s autopkgtest [23:06:17]: @@@@@@@@@@@@@@@@@@@@ summary 649s run-unit-test PASS 649s pkg-r-autopkgtest PASS