0s autopkgtest [16:05:38]: starting date and time: 2025-03-15 16:05:38+0000 0s autopkgtest [16:05:38]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [16:05:38]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.p4sdnt7a/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,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com\n" >> /etc/environment' --apt-pocket=proposed=src:glibc --apt-upgrade r-cran-etm --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glibc/2.41-1ubuntu2 -- lxd -r lxd-armhf-10.145.243.115 lxd-armhf-10.145.243.115:autopkgtest/ubuntu/plucky/armhf 21s autopkgtest [16:05:59]: testbed dpkg architecture: armhf 23s autopkgtest [16:06:01]: testbed apt version: 2.9.33 27s autopkgtest [16:06:05]: @@@@@@@@@@@@@@@@@@@@ test bed setup 28s autopkgtest [16:06:06]: testbed release detected to be: None 36s autopkgtest [16:06:14]: updating testbed package index (apt update) 38s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 38s Get:2 http://ftpmaster.internal/ubuntu plucky InRelease [257 kB] 39s Get:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease [126 kB] 39s Get:4 http://ftpmaster.internal/ubuntu plucky-security InRelease [126 kB] 39s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 39s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [379 kB] 40s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [99.7 kB] 40s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf Packages [114 kB] 40s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf c-n-f Metadata [1832 B] 40s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted armhf c-n-f Metadata [116 B] 40s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf Packages [312 kB] 41s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf c-n-f Metadata [11.1 kB] 41s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf Packages [3472 B] 41s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf c-n-f Metadata [240 B] 41s Get:15 http://ftpmaster.internal/ubuntu plucky/universe Sources [21.0 MB] 66s Get:16 http://ftpmaster.internal/ubuntu plucky/main Sources [1394 kB] 68s Get:17 http://ftpmaster.internal/ubuntu plucky/multiverse Sources [299 kB] 68s Get:18 http://ftpmaster.internal/ubuntu plucky/main armhf Packages [1378 kB] 70s Get:19 http://ftpmaster.internal/ubuntu plucky/main armhf c-n-f Metadata [29.4 kB] 70s Get:20 http://ftpmaster.internal/ubuntu plucky/restricted armhf c-n-f Metadata [108 B] 70s Get:21 http://ftpmaster.internal/ubuntu plucky/universe armhf Packages [15.1 MB] 88s Get:22 http://ftpmaster.internal/ubuntu plucky/multiverse armhf Packages [172 kB] 90s Fetched 41.0 MB in 51s (797 kB/s) 91s Reading package lists... 96s autopkgtest [16:07:14]: upgrading testbed (apt dist-upgrade and autopurge) 98s Reading package lists... 98s Building dependency tree... 98s Reading state information... 99s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 99s Starting 2 pkgProblemResolver with broken count: 0 99s Done 100s Entering ResolveByKeep 100s 101s Calculating upgrade... 101s The following packages will be upgraded: 101s libc-bin libc6 locales pinentry-curses python3-jinja2 sos strace 101s 7 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 101s Need to get 8683 kB of archives. 101s After this operation, 23.6 kB of additional disk space will be used. 101s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libc6 armhf 2.41-1ubuntu2 [2932 kB] 105s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libc-bin armhf 2.41-1ubuntu2 [545 kB] 106s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf locales all 2.41-1ubuntu2 [4246 kB] 111s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf strace armhf 6.13+ds-1ubuntu1 [445 kB] 111s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf pinentry-curses armhf 1.3.1-2ubuntu3 [40.6 kB] 111s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 112s Get:7 http://ftpmaster.internal/ubuntu plucky/main armhf sos all 4.9.0-5 [365 kB] 112s Preconfiguring packages ... 113s Fetched 8683 kB in 11s (796 kB/s) 113s (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 ... 64655 files and directories currently installed.) 113s Preparing to unpack .../libc6_2.41-1ubuntu2_armhf.deb ... 113s Unpacking libc6:armhf (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 113s Setting up libc6:armhf (2.41-1ubuntu2) ... 113s (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 ... 64655 files and directories currently installed.) 113s Preparing to unpack .../libc-bin_2.41-1ubuntu2_armhf.deb ... 113s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 113s Setting up libc-bin (2.41-1ubuntu2) ... 114s (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 ... 64655 files and directories currently installed.) 114s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 114s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 114s Preparing to unpack .../strace_6.13+ds-1ubuntu1_armhf.deb ... 114s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 114s Preparing to unpack .../pinentry-curses_1.3.1-2ubuntu3_armhf.deb ... 114s Unpacking pinentry-curses (1.3.1-2ubuntu3) over (1.3.1-2ubuntu2) ... 114s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 114s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 114s Preparing to unpack .../archives/sos_4.9.0-5_all.deb ... 114s Unpacking sos (4.9.0-5) over (4.9.0-4) ... 115s Setting up sos (4.9.0-5) ... 115s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 115s Setting up locales (2.41-1ubuntu2) ... 116s Generating locales (this might take a while)... 118s en_US.UTF-8... done 118s Generation complete. 118s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 118s Setting up strace (6.13+ds-1ubuntu1) ... 118s Processing triggers for man-db (2.13.0-1) ... 119s Processing triggers for systemd (257.3-1ubuntu3) ... 123s Reading package lists... 123s Building dependency tree... 123s Reading state information... 124s Starting pkgProblemResolver with broken count: 0 124s Starting 2 pkgProblemResolver with broken count: 0 124s Done 124s Solving dependencies... 125s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 128s autopkgtest [16:07:46]: rebooting testbed after setup commands that affected boot 172s autopkgtest [16:08:30]: testbed running kernel: Linux 6.8.0-52-generic #53~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Wed Jan 15 18:10:51 UTC 2 197s autopkgtest [16:08:55]: @@@@@@@@@@@@@@@@@@@@ apt-source r-cran-etm 207s Get:1 http://ftpmaster.internal/ubuntu plucky/universe r-cran-etm 1.1.1-1 (dsc) [2148 B] 207s Get:2 http://ftpmaster.internal/ubuntu plucky/universe r-cran-etm 1.1.1-1 (tar) [242 kB] 207s Get:3 http://ftpmaster.internal/ubuntu plucky/universe r-cran-etm 1.1.1-1 (diff) [3564 B] 207s gpgv: Signature made Fri Sep 18 09:39:57 2020 UTC 207s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 207s gpgv: issuer "tille@debian.org" 207s gpgv: Can't check signature: No public key 207s dpkg-source: warning: cannot verify inline signature for ./r-cran-etm_1.1.1-1.dsc: no acceptable signature found 207s autopkgtest [16:09:05]: testing package r-cran-etm version 1.1.1-1 209s autopkgtest [16:09:07]: build not needed 212s autopkgtest [16:09:10]: test run-unit-test: preparing testbed 214s Reading package lists... 214s Building dependency tree... 214s Reading state information... 214s Starting pkgProblemResolver with broken count: 0 214s Starting 2 pkgProblemResolver with broken count: 0 214s Done 215s The following NEW packages will be installed: 215s fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono libblas3 215s libcairo2 libdatrie1 libdeflate0 libfontconfig1 libfreetype6 libgfortran5 215s libgomp1 libgraphite2-3 libharfbuzz0b libice6 libjbig0 libjpeg-turbo8 215s libjpeg8 liblapack3 liblerc4 libpango-1.0-0 libpangocairo-1.0-0 215s libpangoft2-1.0-0 libpaper-utils libpaper2 libpixman-1-0 libsharpyuv0 libsm6 215s libtcl8.6 libthai-data libthai0 libtiff6 libtk8.6 libwebp7 libxcb-render0 215s libxcb-shm0 libxft2 libxrender1 libxss1 libxt6t64 littler r-base-core 215s r-cran-data.table r-cran-dbi r-cran-etm r-cran-kmi r-cran-lattice 215s r-cran-littler r-cran-matrix r-cran-mitools r-cran-pkgkitten r-cran-rcpp 215s r-cran-rcpparmadillo r-cran-survival unzip x11-common xdg-utils zip 215s 0 upgraded, 58 newly installed, 0 to remove and 0 not upgraded. 215s Need to get 57.9 MB of archives. 215s After this operation, 112 MB of additional disk space will be used. 215s Get:1 http://ftpmaster.internal/ubuntu plucky/main armhf libfreetype6 armhf 2.13.3+dfsg-1 [330 kB] 216s Get:2 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-dejavu-mono all 2.37-8 [502 kB] 217s Get:3 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-dejavu-core all 2.37-8 [835 kB] 218s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf fontconfig-config armhf 2.15.0-2ubuntu1 [37.5 kB] 218s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf libfontconfig1 armhf 2.15.0-2ubuntu1 [114 kB] 218s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf fontconfig armhf 2.15.0-2ubuntu1 [190 kB] 219s Get:7 http://ftpmaster.internal/ubuntu plucky/main armhf libblas3 armhf 3.12.1-2 [132 kB] 219s Get:8 http://ftpmaster.internal/ubuntu plucky/main armhf libpixman-1-0 armhf 0.44.0-3 [183 kB] 219s Get:9 http://ftpmaster.internal/ubuntu plucky/main armhf libxcb-render0 armhf 1.17.0-2 [15.3 kB] 219s Get:10 http://ftpmaster.internal/ubuntu plucky/main armhf libxcb-shm0 armhf 1.17.0-2 [5774 B] 219s Get:11 http://ftpmaster.internal/ubuntu plucky/main armhf libxrender1 armhf 1:0.9.10-1.1build1 [16.0 kB] 219s Get:12 http://ftpmaster.internal/ubuntu plucky/main armhf libcairo2 armhf 1.18.2-2 [484 kB] 220s Get:13 http://ftpmaster.internal/ubuntu plucky/main armhf libdatrie1 armhf 0.2.13-3build1 [15.7 kB] 220s Get:14 http://ftpmaster.internal/ubuntu plucky/main armhf libdeflate0 armhf 1.23-1 [38.5 kB] 220s Get:15 http://ftpmaster.internal/ubuntu plucky/main armhf libgfortran5 armhf 15-20250222-0ubuntu1 [330 kB] 221s Get:16 http://ftpmaster.internal/ubuntu plucky/main armhf libgomp1 armhf 15-20250222-0ubuntu1 [128 kB] 221s Get:17 http://ftpmaster.internal/ubuntu plucky/main armhf libgraphite2-3 armhf 1.3.14-2ubuntu1 [64.8 kB] 221s Get:18 http://ftpmaster.internal/ubuntu plucky/main armhf libharfbuzz0b armhf 10.2.0-1 [464 kB] 222s Get:19 http://ftpmaster.internal/ubuntu plucky/main armhf x11-common all 1:7.7+23ubuntu3 [21.7 kB] 222s Get:20 http://ftpmaster.internal/ubuntu plucky/main armhf libice6 armhf 2:1.1.1-1 [36.5 kB] 222s Get:21 http://ftpmaster.internal/ubuntu plucky/main armhf libjpeg-turbo8 armhf 2.1.5-3ubuntu2 [127 kB] 222s Get:22 http://ftpmaster.internal/ubuntu plucky/main armhf libjpeg8 armhf 8c-2ubuntu11 [2148 B] 222s Get:23 http://ftpmaster.internal/ubuntu plucky/main armhf liblapack3 armhf 3.12.1-2 [2091 kB] 226s Get:24 http://ftpmaster.internal/ubuntu plucky/main armhf liblerc4 armhf 4.0.0+ds-5ubuntu1 [160 kB] 226s Get:25 http://ftpmaster.internal/ubuntu plucky/main armhf libthai-data all 0.1.29-2build1 [158 kB] 226s Get:26 http://ftpmaster.internal/ubuntu plucky/main armhf libthai0 armhf 0.1.29-2build1 [15.2 kB] 226s Get:27 http://ftpmaster.internal/ubuntu plucky/main armhf libpango-1.0-0 armhf 1.56.2-1 [216 kB] 227s Get:28 http://ftpmaster.internal/ubuntu plucky/main armhf libpangoft2-1.0-0 armhf 1.56.2-1 [43.6 kB] 227s Get:29 http://ftpmaster.internal/ubuntu plucky/main armhf libpangocairo-1.0-0 armhf 1.56.2-1 [25.1 kB] 227s Get:30 http://ftpmaster.internal/ubuntu plucky/main armhf libpaper2 armhf 2.2.5-0.3 [16.3 kB] 227s Get:31 http://ftpmaster.internal/ubuntu plucky/main armhf libpaper-utils armhf 2.2.5-0.3 [14.2 kB] 227s Get:32 http://ftpmaster.internal/ubuntu plucky/main armhf libsharpyuv0 armhf 1.5.0-0.1 [16.4 kB] 227s Get:33 http://ftpmaster.internal/ubuntu plucky/main armhf libsm6 armhf 2:1.2.4-1 [15.1 kB] 227s Get:34 http://ftpmaster.internal/ubuntu plucky/main armhf libtcl8.6 armhf 8.6.16+dfsg-1 [909 kB] 228s Get:35 http://ftpmaster.internal/ubuntu plucky/main armhf libjbig0 armhf 2.1-6.1ubuntu2 [24.9 kB] 228s Get:36 http://ftpmaster.internal/ubuntu plucky/main armhf libwebp7 armhf 1.5.0-0.1 [188 kB] 229s Get:37 http://ftpmaster.internal/ubuntu plucky/main armhf libtiff6 armhf 4.5.1+git230720-4ubuntu4 [179 kB] 229s Get:38 http://ftpmaster.internal/ubuntu plucky/main armhf libxft2 armhf 2.3.6-1build1 [37.4 kB] 229s Get:39 http://ftpmaster.internal/ubuntu plucky/main armhf libxss1 armhf 1:1.2.3-1build3 [6500 B] 229s Get:40 http://ftpmaster.internal/ubuntu plucky/main armhf libtk8.6 armhf 8.6.16-1 [686 kB] 230s Get:41 http://ftpmaster.internal/ubuntu plucky/main armhf libxt6t64 armhf 1:1.2.1-1.2build1 [145 kB] 231s Get:42 http://ftpmaster.internal/ubuntu plucky/main armhf zip armhf 3.0-14ubuntu2 [164 kB] 231s Get:43 http://ftpmaster.internal/ubuntu plucky/main armhf unzip armhf 6.0-28ubuntu6 [167 kB] 231s Get:44 http://ftpmaster.internal/ubuntu plucky/main armhf xdg-utils all 1.2.1-2ubuntu1 [66.0 kB] 231s Get:45 http://ftpmaster.internal/ubuntu plucky/universe armhf r-base-core armhf 4.4.3-1 [28.2 MB] 281s Get:46 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-littler armhf 0.3.20-2 [90.9 kB] 282s Get:47 http://ftpmaster.internal/ubuntu plucky/universe armhf littler all 0.3.20-2 [2554 B] 282s Get:48 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-data.table armhf 1.17.0+dfsg-1 [2111 kB] 285s Get:49 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-dbi all 1.2.3-1 [853 kB] 287s Get:50 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-lattice armhf 0.22-6-1 [1363 kB] 289s Get:51 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-matrix armhf 1.7-3-1 [4039 kB] 296s Get:52 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-survival armhf 3.8-3-1 [8196 kB] 311s Get:53 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-pkgkitten all 0.2.4-1 [27.2 kB] 311s Get:54 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-rcpp armhf 1.0.14-1 [1976 kB] 314s Get:55 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-rcpparmadillo armhf 14.2.3-1-1 [842 kB] 316s Get:56 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-etm armhf 1.1.1-1 [470 kB] 317s Get:57 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-mitools all 2.4-2build1 [265 kB] 317s Get:58 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-kmi all 0.5.5-2build1 [78.3 kB] 318s Preconfiguring packages ... 318s Fetched 57.9 MB in 1min 42s (567 kB/s) 318s Selecting previously unselected package libfreetype6:armhf. 318s (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 ... 64655 files and directories currently installed.) 318s Preparing to unpack .../00-libfreetype6_2.13.3+dfsg-1_armhf.deb ... 318s Unpacking libfreetype6:armhf (2.13.3+dfsg-1) ... 318s Selecting previously unselected package fonts-dejavu-mono. 318s Preparing to unpack .../01-fonts-dejavu-mono_2.37-8_all.deb ... 318s Unpacking fonts-dejavu-mono (2.37-8) ... 318s Selecting previously unselected package fonts-dejavu-core. 318s Preparing to unpack .../02-fonts-dejavu-core_2.37-8_all.deb ... 318s Unpacking fonts-dejavu-core (2.37-8) ... 318s Selecting previously unselected package fontconfig-config. 318s Preparing to unpack .../03-fontconfig-config_2.15.0-2ubuntu1_armhf.deb ... 318s Unpacking fontconfig-config (2.15.0-2ubuntu1) ... 318s Selecting previously unselected package libfontconfig1:armhf. 318s Preparing to unpack .../04-libfontconfig1_2.15.0-2ubuntu1_armhf.deb ... 318s Unpacking libfontconfig1:armhf (2.15.0-2ubuntu1) ... 318s Selecting previously unselected package fontconfig. 318s Preparing to unpack .../05-fontconfig_2.15.0-2ubuntu1_armhf.deb ... 318s Unpacking fontconfig (2.15.0-2ubuntu1) ... 318s Selecting previously unselected package libblas3:armhf. 318s Preparing to unpack .../06-libblas3_3.12.1-2_armhf.deb ... 318s Unpacking libblas3:armhf (3.12.1-2) ... 318s Selecting previously unselected package libpixman-1-0:armhf. 318s Preparing to unpack .../07-libpixman-1-0_0.44.0-3_armhf.deb ... 318s Unpacking libpixman-1-0:armhf (0.44.0-3) ... 318s Selecting previously unselected package libxcb-render0:armhf. 318s Preparing to unpack .../08-libxcb-render0_1.17.0-2_armhf.deb ... 318s Unpacking libxcb-render0:armhf (1.17.0-2) ... 318s Selecting previously unselected package libxcb-shm0:armhf. 318s Preparing to unpack .../09-libxcb-shm0_1.17.0-2_armhf.deb ... 318s Unpacking libxcb-shm0:armhf (1.17.0-2) ... 319s Selecting previously unselected package libxrender1:armhf. 319s Preparing to unpack .../10-libxrender1_1%3a0.9.10-1.1build1_armhf.deb ... 319s Unpacking libxrender1:armhf (1:0.9.10-1.1build1) ... 319s Selecting previously unselected package libcairo2:armhf. 319s Preparing to unpack .../11-libcairo2_1.18.2-2_armhf.deb ... 319s Unpacking libcairo2:armhf (1.18.2-2) ... 319s Selecting previously unselected package libdatrie1:armhf. 319s Preparing to unpack .../12-libdatrie1_0.2.13-3build1_armhf.deb ... 319s Unpacking libdatrie1:armhf (0.2.13-3build1) ... 319s Selecting previously unselected package libdeflate0:armhf. 319s Preparing to unpack .../13-libdeflate0_1.23-1_armhf.deb ... 319s Unpacking libdeflate0:armhf (1.23-1) ... 319s Selecting previously unselected package libgfortran5:armhf. 319s Preparing to unpack .../14-libgfortran5_15-20250222-0ubuntu1_armhf.deb ... 319s Unpacking libgfortran5:armhf (15-20250222-0ubuntu1) ... 319s Selecting previously unselected package libgomp1:armhf. 319s Preparing to unpack .../15-libgomp1_15-20250222-0ubuntu1_armhf.deb ... 319s Unpacking libgomp1:armhf (15-20250222-0ubuntu1) ... 319s Selecting previously unselected package libgraphite2-3:armhf. 319s Preparing to unpack .../16-libgraphite2-3_1.3.14-2ubuntu1_armhf.deb ... 319s Unpacking libgraphite2-3:armhf (1.3.14-2ubuntu1) ... 319s Selecting previously unselected package libharfbuzz0b:armhf. 319s Preparing to unpack .../17-libharfbuzz0b_10.2.0-1_armhf.deb ... 319s Unpacking libharfbuzz0b:armhf (10.2.0-1) ... 319s Selecting previously unselected package x11-common. 319s Preparing to unpack .../18-x11-common_1%3a7.7+23ubuntu3_all.deb ... 319s Unpacking x11-common (1:7.7+23ubuntu3) ... 319s Selecting previously unselected package libice6:armhf. 319s Preparing to unpack .../19-libice6_2%3a1.1.1-1_armhf.deb ... 319s Unpacking libice6:armhf (2:1.1.1-1) ... 319s Selecting previously unselected package libjpeg-turbo8:armhf. 319s Preparing to unpack .../20-libjpeg-turbo8_2.1.5-3ubuntu2_armhf.deb ... 319s Unpacking libjpeg-turbo8:armhf (2.1.5-3ubuntu2) ... 319s Selecting previously unselected package libjpeg8:armhf. 319s Preparing to unpack .../21-libjpeg8_8c-2ubuntu11_armhf.deb ... 319s Unpacking libjpeg8:armhf (8c-2ubuntu11) ... 319s Selecting previously unselected package liblapack3:armhf. 319s Preparing to unpack .../22-liblapack3_3.12.1-2_armhf.deb ... 319s Unpacking liblapack3:armhf (3.12.1-2) ... 319s Selecting previously unselected package liblerc4:armhf. 319s Preparing to unpack .../23-liblerc4_4.0.0+ds-5ubuntu1_armhf.deb ... 319s Unpacking liblerc4:armhf 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(0.22-6-1) ... 324s Setting up r-cran-pkgkitten (0.2.4-1) ... 324s Setting up r-cran-littler (0.3.20-2) ... 324s Setting up r-cran-rcpp (1.0.14-1) ... 324s Setting up littler (0.3.20-2) ... 324s Setting up r-cran-dbi (1.2.3-1) ... 324s Setting up r-cran-data.table (1.17.0+dfsg-1) ... 324s Setting up r-cran-matrix (1.7-3-1) ... 324s Setting up r-cran-rcpparmadillo (14.2.3-1-1) ... 324s Setting up r-cran-mitools (2.4-2build1) ... 324s Setting up r-cran-survival (3.8-3-1) ... 324s Setting up r-cran-kmi (0.5.5-2build1) ... 324s Setting up r-cran-etm (1.1.1-1) ... 324s Processing triggers for man-db (2.13.0-1) ... 325s Processing triggers for install-info (7.1.1-1) ... 325s Processing triggers for libc-bin (2.41-1ubuntu2) ... 333s autopkgtest [16:11:11]: test run-unit-test: [----------------------- 335s BEGIN TEST test.etmCIF.R 335s 335s R version 4.4.3 (2025-02-28) -- "Trophy Case" 335s Copyright (C) 2025 The R Foundation for Statistical Computing 335s Platform: arm-unknown-linux-gnueabihf (32-bit) 335s 335s R is free software and comes with ABSOLUTELY NO WARRANTY. 335s You are welcome to redistribute it under certain conditions. 335s Type 'license()' or 'licence()' for distribution details. 335s 335s R is a collaborative project with many contributors. 335s Type 'contributors()' for more information and 335s 'citation()' on how to cite R or R packages in publications. 335s 335s Type 'demo()' for some demos, 'help()' for on-line help, or 335s 'help.start()' for an HTML browser interface to help. 335s Type 'q()' to quit R. 335s 335s Loading required package: etm 335s > ### test file for etmCIF. 335s > ### Really simple tests and comparison with etm 335s > 335s > old <- options(digits = 5) 335s > 335s > require(etm) 336s > 336s > if (!require(survival, quietly = TRUE)) { 336s + print("The following tests require the 'survival' package") 336s + } else { 336s + 336s + data(abortion) 336s + 336s + from <- rep(0, nrow(abortion)) 336s + to <- abortion$cause 336s + entry <- abortion$entry 336s + exit <- abortion$exit 336s + id <- 1:nrow(abortion) 336s + data <- data.frame(id, from, to, entry, exit, group = abortion$group) 336s + 336s + ## Computation of the CIFs with etm 336s + tra <- matrix(FALSE, 4, 4) 336s + tra[1, 2:4] <- TRUE 336s + 336s + cif.control <- etm(data[data$group == 0, ], c("0", "1", "2", "3"), 336s + tra, NULL, 0) 336s + cif.exposed <- etm(data[data$group == 1, ], c("0", "1", "2", "3"), 336s + tra, NULL, 0) 336s + 336s + 336s + ## Computation of the CIFs with etmCIF 336s + netm <- etmCIF(Surv(entry, exit, cause != 0) ~ group, abortion, 336s + etype = cause, failcode = 3) 336s + 336s + ### let's do some comparisons :-) 336s + 336s + all.equal(trprob(cif.control, "0 3"), netm[[1]]$est["0", "3", ]) 336s + all.equal(trprob(cif.control, "0 2"), netm[[1]]$est["0", "2", ]) 336s + all.equal(trprob(cif.control, "0 1"), netm[[1]]$est["0", "1", ]) 336s + 336s + all.equal(trprob(cif.exposed, "0 3"), netm[[2]]$est["0", "3", ]) 336s + all.equal(trprob(cif.exposed, "0 2"), netm[[2]]$est["0", "2", ]) 336s + all.equal(trprob(cif.exposed, "0 1"), netm[[2]]$est["0", "1", ]) 336s + 336s + 336s + all.equal(trcov(cif.control, "0 3"), netm[[1]]$cov["0 3", "0 3", ]) 336s + all.equal(trcov(cif.control, "0 2"), netm[[1]]$cov["0 2", "0 2", ]) 336s + all.equal(trcov(cif.control, "0 1"), netm[[1]]$cov["0 1", "0 1", ]) 336s + 336s + all.equal(trcov(cif.exposed, "0 3"), netm[[2]]$cov["0 3", "0 3", ]) 336s + all.equal(trcov(cif.exposed, "0 2"), netm[[2]]$cov["0 2", "0 2", ]) 336s + all.equal(trcov(cif.exposed, "0 1"), netm[[2]]$cov["0 1", "0 1", ]) 336s + 336s + 336s + netm 336s + 336s + ## test on the summary 336s + snetm <- summary(netm) 336s + 336s + snetm 336s + 336s + all.equal(unname(trprob(cif.control, "0 3")), snetm[[1]][[3]]$P) 336s + all.equal(unname(trprob(cif.control, "0 2")), snetm[[1]][[2]]$P) 336s + all.equal(unname(trprob(cif.control, "0 1")), snetm[[1]][[1]]$P) 336s + 336s + all.equal(unname(trprob(cif.exposed, "0 3")), snetm[[2]][[3]]$P) 336s + all.equal(unname(trprob(cif.exposed, "0 2")), snetm[[2]][[2]]$P) 336s + all.equal(unname(trprob(cif.exposed, "0 1")), snetm[[2]][[1]]$P) 336s + 336s + scif.control <- summary(cif.control, ci.fun = "cloglog") 336s + scif.exposed <- summary(cif.exposed, ci.fun = "cloglog") 336s + 336s + all.equal(scif.control[[4]]$lower, snetm[[1]][[3]]$lower) 336s + all.equal(scif.control[[4]]$upper, snetm[[1]][[3]]$upper) 336s + 336s + all.equal(scif.exposed[[4]]$lower, snetm[[2]][[3]]$lower) 336s + all.equal(scif.exposed[[4]]$upper, snetm[[2]][[3]]$upper) 336s + } 336s [1] TRUE 336s > 336s > ### test with factors in the input 336s > abortion$status <- with(abortion, ifelse(cause == 2, "life birth", 336s + ifelse(cause == 1, "ETOP", "spontaneous abortion"))) 336s > 336s > abortion$status <- factor(abortion$status) 336s > 336s > netm.factor <- etmCIF(Surv(entry, exit, status != "cens") ~ group, abortion, 336s + etype = status, failcode = "spontaneous abortion") 336s > 336s > 336s > all.equal(trprob(cif.control, "0 3"), netm.factor[[1]]$est["0", "spontaneous abortion", ]) 336s [1] TRUE 336s > all.equal(trprob(cif.control, "0 2"), netm.factor[[1]]$est["0", "life birth", ]) 336s [1] TRUE 336s > 336s > netm.factor 336s Call: etmCIF(formula = Surv(entry, exit, status != "cens") ~ group, 336s data = abortion, etype = status, failcode = "spontaneous abortion") 336s 336s Covariate: group 336s levels: 0 1 336s 336s 336s group = 0 336s time P se(P) n.event 336s CIF ETOP 43 0.040159 0.0092578 20 336s CIF life birth 43 0.799059 0.0221865 924 336s CIF spontaneous abortion 43 0.160781 0.0213261 69 336s 336s group = 1 336s time P se(P) n.event 336s CIF ETOP 42 0.28511 0.042493 38 336s CIF life birth 42 0.35257 0.042139 92 336s CIF spontaneous abortion 42 0.36232 0.049473 43 336s > 336s > summary(netm.factor) 336s 336s group=0 336s 336s CIF ETOP 336s P time var lower upper n.risk n.event 336s 0.000000 6 0.0000e+00 0.000000 0.000000 117 0 336s 0.038955 13 8.4440e-05 0.024488 0.061694 645 1 336s 0.040159 26 8.5707e-05 0.025513 0.062939 846 0 336s 0.040159 36 8.5707e-05 0.025513 0.062939 876 0 336s 0.040159 40 8.5707e-05 0.025513 0.062939 554 0 336s 0.040159 43 8.5707e-05 0.025513 0.062939 6 0 336s 336s CIF life birth 336s P time var lower upper n.risk n.event 336s 0.000000 6 0.0000e+00 0.000000 0.000000 117 0 336s 0.000000 13 0.0000e+00 0.000000 0.000000 645 0 336s 0.000000 26 0.0000e+00 0.000000 0.000000 846 0 336s 0.053197 36 4.6195e-05 0.041379 0.068268 876 25 336s 0.563121 40 3.8801e-04 0.524924 0.602021 554 280 336s 0.799059 43 4.9224e-04 0.753969 0.840613 6 6 336s 336s CIF spontaneous abortion 336s P time var lower upper n.risk n.event 336s 0.034188 6 0.00028222 0.01297 0.088523 117 4 336s 0.150468 13 0.00045513 0.11360 0.197901 645 1 336s 0.159904 26 0.00045498 0.12274 0.206925 846 1 336s 0.160781 36 0.00045480 0.12360 0.207757 876 1 336s 0.160781 40 0.00045480 0.12360 0.207757 554 0 336s 0.160781 43 0.00045480 0.12360 0.207757 6 0 336s 336s 336s group=1 336s 336s CIF ETOP 336s P time var lower upper n.risk n.event 336s 0.00000 6 0.0000000 0.00000 0.00000 35 0 336s 0.26048 13 0.0017854 0.18795 0.35425 90 0 336s 0.28115 21 0.0018028 0.20742 0.37423 93 1 336s 0.28511 34 0.0018057 0.21116 0.37806 89 0 336s 0.28511 39 0.0018057 0.21116 0.37806 59 0 336s 0.28511 42 0.0018057 0.21116 0.37806 6 0 336s 336s CIF life birth 336s P time var lower upper n.risk n.event 336s 0.000000 6 0.0000e+00 0.000000 0.000000 35 0 336s 0.000000 13 0.0000e+00 0.000000 0.000000 90 0 336s 0.000000 21 0.0000e+00 0.000000 0.000000 93 0 336s 0.023073 34 9.0514e-05 0.010252 0.051504 89 2 336s 0.180156 39 8.0126e-04 0.131765 0.243663 59 13 336s 0.352565 42 1.7757e-03 0.276882 0.441775 6 6 336s 336s CIF spontaneous abortion 336s P time var lower upper n.risk n.event 336s 0.057143 6 0.0015394 0.014605 0.20968 35 2 336s 0.333246 13 0.0025280 0.245337 0.44216 90 4 336s 0.350702 21 0.0024827 0.262769 0.45762 93 0 336s 0.358492 34 0.0024593 0.270627 0.46448 89 0 336s 0.358492 39 0.0024593 0.270627 0.46448 59 0 336s 0.362323 42 0.0024476 0.274499 0.46785 6 0 336s 336s > 336s > ### test with group as a character vector 336s > abortion$ttt <- with(abortion, ifelse(group == 0, "control", "exposed")) 336s > abortion$ttt <- factor(abortion$ttt) 336s > 336s > netm.ttt <- etmCIF(Surv(entry, exit, status != "cens") ~ ttt, abortion, 336s + etype = status, failcode = "spontaneous abortion") 336s > 336s > all.equal(trprob(cif.control, "0 3"), netm.ttt[[1]]$est["0", "spontaneous abortion", ]) 336s [1] TRUE 336s > all.equal(trprob(cif.control, "0 2"), netm.ttt[[1]]$est["0", "life birth", ]) 336s [1] TRUE 336s > 336s > netm.ttt 336s Call: etmCIF(formula = Surv(entry, exit, status != "cens") ~ ttt, data = abortion, 336s etype = status, failcode = "spontaneous abortion") 336s 336s Covariate: ttt 336s levels: control exposed 336s 336s 336s ttt = control 336s time P se(P) n.event 336s CIF ETOP 43 0.040159 0.0092578 20 336s CIF life birth 43 0.799059 0.0221865 924 336s CIF spontaneous abortion 43 0.160781 0.0213261 69 336s 336s ttt = exposed 336s time P se(P) n.event 336s CIF ETOP 42 0.28511 0.042493 38 336s CIF life birth 42 0.35257 0.042139 92 336s CIF spontaneous abortion 42 0.36232 0.049473 43 336s > 336s > summary(netm.ttt) 336s 336s ttt=control 336s 336s CIF ETOP 336s P time var lower upper n.risk n.event 336s 0.000000 6 0.0000e+00 0.000000 0.000000 117 0 336s 0.038955 13 8.4440e-05 0.024488 0.061694 645 1 336s 0.040159 26 8.5707e-05 0.025513 0.062939 846 0 336s 0.040159 36 8.5707e-05 0.025513 0.062939 876 0 336s 0.040159 40 8.5707e-05 0.025513 0.062939 554 0 336s 0.040159 43 8.5707e-05 0.025513 0.062939 6 0 336s 336s CIF life birth 336s P time var lower upper n.risk n.event 336s 0.000000 6 0.0000e+00 0.000000 0.000000 117 0 336s 0.000000 13 0.0000e+00 0.000000 0.000000 645 0 336s 0.000000 26 0.0000e+00 0.000000 0.000000 846 0 336s 0.053197 36 4.6195e-05 0.041379 0.068268 876 25 336s 0.563121 40 3.8801e-04 0.524924 0.602021 554 280 336s 0.799059 43 4.9224e-04 0.753969 0.840613 6 6 336s 336s CIF spontaneous abortion 336s P time var lower upper n.risk n.event 336s 0.034188 6 0.00028222 0.01297 0.088523 117 4 336s 0.150468 13 0.00045513 0.11360 0.197901 645 1 336s 0.159904 26 0.00045498 0.12274 0.206925 846 1 336s 0.160781 36 0.00045480 0.12360 0.207757 876 1 336s 0.160781 40 0.00045480 0.12360 0.207757 554 0 336s 0.160781 43 0.00045480 0.12360 0.207757 6 0 336s 336s 336s ttt=exposed 336s 336s CIF ETOP 336s P time var lower upper n.risk n.event 336s 0.00000 6 0.0000000 0.00000 0.00000 35 0 336s 0.26048 13 0.0017854 0.18795 0.35425 90 0 336s 0.28115 21 0.0018028 0.20742 0.37423 93 1 336s 0.28511 34 0.0018057 0.21116 0.37806 89 0 336s 0.28511 39 0.0018057 0.21116 0.37806 59 0 336s 0.28511 42 0.0018057 0.21116 0.37806 6 0 336s 336s CIF life birth 336s P time var lower upper n.risk n.event 336s 0.000000 6 0.0000e+00 0.000000 0.000000 35 0 336s 0.000000 13 0.0000e+00 0.000000 0.000000 90 0 336s 0.000000 21 0.0000e+00 0.000000 0.000000 93 0 336s 0.023073 34 9.0514e-05 0.010252 0.051504 89 2 336s 0.180156 39 8.0126e-04 0.131765 0.243663 59 13 336s 0.352565 42 1.7757e-03 0.276882 0.441775 6 6 336s 336s CIF spontaneous abortion 336s P time var lower upper n.risk n.event 336s 0.057143 6 0.0015394 0.014605 0.20968 35 2 336s 0.333246 13 0.0025280 0.245337 0.44216 90 4 336s 0.350702 21 0.0024827 0.262769 0.45762 93 0 336s 0.358492 34 0.0024593 0.270627 0.46448 89 0 336s 0.358492 39 0.0024593 0.270627 0.46448 59 0 336s 0.362323 42 0.0024476 0.274499 0.46785 6 0 336s 336s > 336s > 336s > ### A couple of comparisons with simulated data 336s > set.seed(1313) 336s > time <- rexp(100) 336s > to <- rbinom(100, 2, prob = c(1/3, 1/3, 1/3)) 336s > from <- rep(11, 100) 336s > id <- 1:100 336s > cov <- rbinom(100, 1, 0.5) 336s > 336s > dat.s <- data.frame(id, time, from, to, cov) 336s > 336s > traa <- matrix(FALSE, 3, 3) 336s > traa[1, 2:3] <- TRUE 336s > 336s > aa0 <- etm(dat.s[dat.s$cov == 0, ], c("11", "1", "2"), traa, "0", 0) 336s > aa1 <- etm(dat.s[dat.s$cov == 1, ], c("11", "1", "2"), traa, "0", 0) 336s > aa <- etm(dat.s, c("11", "1", "2"), traa, "0", 0) 336s > 336s > test <- etmCIF(Surv(time, to != 0) ~ 1, dat.s, etype = to) 336s > 336s > test.c <- etmCIF(Surv(time, to != 0) ~ cov, dat.s, etype = to) 336s > 336s > all.equal(trprob(aa, "11 1"), test[[1]]$est["0", "1", ]) 336s [1] TRUE 336s > all.equal(trprob(aa, "11 2"), test[[1]]$est["0", "2", ]) 336s [1] TRUE 336s > 336s > all.equal(trprob(aa0, "11 1"), test.c[[1]]$est["0", "1", ]) 336s [1] TRUE 336s > all.equal(trprob(aa0, "11 2"), test.c[[1]]$est["0", "2", ]) 336s [1] TRUE 336s > 336s > all.equal(trprob(aa1, "11 1"), test.c[[2]]$est["0", "1", ]) 336s [1] TRUE 336s > all.equal(trprob(aa1, "11 2"), test.c[[2]]$est["0", "2", ]) 336s [1] TRUE 336s > 336s > test 336s Call: etmCIF(formula = Surv(time, to != 0) ~ 1, data = dat.s, etype = to) 336s 336s time P se(P) n.event 336s CIF 1 4.9088 0.809108 0.079680 45 336s CIF 2 4.9088 0.096618 0.032905 8 336s > 336s > test.c 336s Call: etmCIF(formula = Surv(time, to != 0) ~ cov, data = dat.s, etype = to) 336s 336s Covariate: cov 336s levels: 0 1 336s 336s 336s cov = 0 336s time P se(P) n.event 336s CIF 1 2.1708 0.70246 0.105797 19 336s CIF 2 2.1708 0.11144 0.053384 4 336s 336s cov = 1 336s time P se(P) n.event 336s CIF 1 4.9088 0.80787 0.094051 26 336s CIF 2 4.9088 0.08436 0.040769 4 336s > 336s > summary(test) 336s 336s 336s 336s CIF 1 336s P time var lower upper n.risk n.event 336s 0.01000 0.0092099 0.0000990 0.0014147 0.068863 100 1 336s 0.11430 0.2663096 0.0010542 0.0649454 0.196993 81 1 336s 0.23451 0.7303091 0.0020436 0.1591107 0.337736 54 1 336s 0.40425 1.4299939 0.0032996 0.3020445 0.525741 29 1 336s 0.54593 2.0647206 0.0040836 0.4269008 0.673605 16 1 336s 0.80911 4.9087561 0.0063489 0.6359544 0.933733 2 1 336s 336s CIF 2 336s P time var lower upper n.risk n.event 336s 0.000000 0.0092099 0.00000000 0.000000 0.000000 100 0 336s 0.031657 0.2663096 0.00032353 0.010320 0.094942 81 0 336s 0.067029 0.7303091 0.00070366 0.030598 0.143503 54 0 336s 0.096618 1.4299939 0.00108275 0.049082 0.185474 29 0 336s 0.096618 2.0647206 0.00108275 0.049082 0.185474 16 0 336s 0.096618 4.9087561 0.00108275 0.049082 0.185474 2 0 336s 336s > summary(test.c) 336s 336s cov=0 336s 336s CIF 1 336s P time var lower upper n.risk n.event 336s 0.022222 0.0092099 0.00048285 0.0031605 0.14747 45 1 336s 0.092222 0.2982439 0.00193603 0.0355971 0.22762 36 0 336s 0.226684 0.7021938 0.00450954 0.1241760 0.39250 24 1 336s 0.378128 1.4299939 0.00760870 0.2337884 0.57145 13 1 336s 0.505736 1.6148774 0.00895330 0.3388425 0.69885 10 1 336s 0.702465 2.1708375 0.01119294 0.4944890 0.88399 3 1 336s 336s CIF 2 336s P time var lower upper n.risk n.event 336s 0.000000 0.0092099 0.0000000 0.000000 0.00000 45 0 336s 0.048441 0.2982439 0.0011168 0.012337 0.18013 36 1 336s 0.076411 0.7021938 0.0018104 0.025202 0.21928 24 0 336s 0.111440 1.4299939 0.0028499 0.042676 0.27392 13 0 336s 0.111440 1.6148774 0.0028499 0.042676 0.27392 10 0 336s 0.111440 2.1708375 0.0028499 0.042676 0.27392 3 0 336s 336s 336s cov=1 336s 336s CIF 1 336s P time var lower upper n.risk n.event 336s 0.018182 0.066692 0.00032457 0.0025813 0.12214 55 1 336s 0.112392 0.263808 0.00187215 0.0520925 0.23333 45 1 336s 0.241023 0.730309 0.00374499 0.1440057 0.38685 31 1 336s 0.401201 1.066913 0.00570788 0.2714008 0.56421 19 1 336s 0.592334 2.366275 0.00775985 0.4286230 0.76273 8 1 336s 0.807871 4.908756 0.00884554 0.6023185 0.94771 2 1 336s 336s CIF 2 336s P time var lower upper n.risk n.event 336s 0.000000 0.066692 0.00000000 0.000000 0.00000 55 0 336s 0.037434 0.263808 0.00067458 0.009494 0.14152 45 0 336s 0.059341 0.730309 0.00111295 0.019447 0.17351 31 0 336s 0.084360 1.066913 0.00166213 0.032211 0.21119 19 0 336s 0.084360 2.366275 0.00166213 0.032211 0.21119 8 0 336s 0.084360 4.908756 0.00166213 0.032211 0.21119 2 0 336s 336s > 336s > options(old) 336s > 336s BEGIN TEST tests.etm.R 336s 336s R version 4.4.3 (2025-02-28) -- "Trophy Case" 336s Copyright (C) 2025 The R Foundation for Statistical Computing 336s Platform: arm-unknown-linux-gnueabihf (32-bit) 336s 336s R is free software and comes with ABSOLUTELY NO WARRANTY. 336s You are welcome to redistribute it under certain conditions. 336s Type 'license()' or 'licence()' for distribution details. 336s 336s R is a collaborative project with many contributors. 336s Type 'contributors()' for more information and 336s 'citation()' on how to cite R or R packages in publications. 336s 336s Type 'demo()' for some demos, 'help()' for on-line help, or 336s 'help.start()' for an HTML browser interface to help. 336s Type 'q()' to quit R. 336s 337s > require(etm) 337s Loading required package: etm 338s > 338s > ## Print with a bit less precision to avoid lots of notes in the comparison 338s > old <- options(digits = 4) 338s > 338s > ### Simple test 338s > 338s > time <- id <- 1:10 338s > from <- rep(0, 10) 338s > to <- rep(1, 10) 338s > 338s > data1 <- data.frame(id, from, to, time) 338s > tra1 <- matrix(FALSE, 2, 2) 338s > tra1[1, 2] <- TRUE 338s > 338s > etm1 <- etm(data1, c("0", "1"), tra1, NULL, 0) 338s > 338s > all.equal(as.vector(trprob(etm1, "0 0")), cumprod((10:1 - 1) / (10:1))) 338s Loading required package: survival 338s [1] TRUE 338s > 338s > etm1$cov["0 0", "0 0", ] 338s 1 2 3 4 5 6 7 8 9 10 338s 0.009 0.016 0.021 0.024 0.025 0.024 0.021 0.016 0.009 0.000 338s > 338s > all.equal(etm1$cov["0 0", "0 0",], trcov(etm1, "0 0")) 338s [1] TRUE 338s > 338s > ### A simple test from AHR's author, where the first time is censored 338s > if (!require(survival)) { 338s + stop("This test requires the survival package") 338s + } 338s > 338s > data <- data.frame(id=1:10, time=1:10, from=0, to=1, status=TRUE) 338s > 338s > tra <- matrix(FALSE, nrow=2, ncol=2) 338s > tra[1, 2] <- TRUE 338s > 338s > data$to[1] <- "cens" 338s > data$status[1] <- FALSE 338s > 338s > fit.km <- survfit(Surv(time, status) ~ 1, data=data) 338s > fit.etm <- etm(data, c("0","1"), tra, "cens", s=0, t="last", covariance=FALSE) 338s > 338s > all.equal(fit.km$surv[data$status], fit.etm$est[1,1,], check.attributes = FALSE) 338s [1] TRUE 338s > 338s > data$to[2] <- "cens" 338s > data$status[2] <- FALSE 338s > 338s > fit.km <- survfit(Surv(time, status) ~ 1, data=data) 338s > fit.etm <- etm(data, c("0","1"), tra, "cens", s=0, t="last", covariance=FALSE) 338s > 338s > all.equal(fit.km$surv[data$status], fit.etm$est[1,1,], check.attributes = FALSE) 338s [1] TRUE 338s > 338s > ### a bit more complicated 338s > 338s > time <- id <- 1:10 338s > from <- rep(0, 10) 338s > to <- rep(c(1, 2), 5) 338s > data2 <- data.frame(id, from, to, time) 338s > 338s > tra2 <- matrix(FALSE, 3, 3) 338s > tra2[1, 2:3] <- TRUE 338s > 338s > etm2 <- etm(data2, c("0", "1", "2"), tra2, NULL, 0) 338s > 338s > aa <- table(time, to) 338s > 338s > cif1 <- cumsum(aa[, 1] / 10) 338s > cif2 <- cumsum(aa[, 2] / 10) 338s > surv <- cumprod((10:1 - 1) / (10:1)) 338s > 338s > all.equal(trprob(etm2, "0 1"), cif1) 338s [1] TRUE 338s > all.equal(trprob(etm2, "0 2"), cif2) 338s [1] TRUE 338s > all.equal(as.vector(trprob(etm2, "0 0")), surv) 338s [1] TRUE 338s > 338s > ## a test on id 338s > data2$id <- letters[1:10] 338s > 338s > etm3 <- etm(data2, c("0", "1", "2"), tra2, NULL, 0) 338s > 338s > all.equal(trprob(etm2, "0 1"), trprob(etm3, "0 1")) 338s [1] TRUE 338s > all.equal(trprob(etm2, "0 2"), trprob(etm3, "0 2")) 338s [1] TRUE 338s > all.equal(trprob(etm2, "0 0"), trprob(etm3, "0 0")) 338s [1] TRUE 338s > 338s > 338s > ### Test on sir.cont 338s > 338s > data(sir.cont) 338s > 338s > ## Modification for patients entering and leaving a state 338s > ## at the same date 338s > ## Change on ventilation status is considered 338s > ## to happen before end of hospital stay 338s > sir.cont <- sir.cont[order(sir.cont$id, sir.cont$time), ] 338s > for (i in 2:nrow(sir.cont)) { 338s + if (sir.cont$id[i]==sir.cont$id[i-1]) { 338s + if (sir.cont$time[i]==sir.cont$time[i-1]) { 338s + sir.cont$time[i-1] <- sir.cont$time[i-1] - 0.5 338s + } 338s + } 338s + } 338s > 338s > ### Computation of the transition probabilities 338s > ## Possible transitions. 338s > tra <- matrix(ncol=3,nrow=3,FALSE) 338s > tra[1, 2:3] <- TRUE 338s > tra[2, c(1, 3)] <- TRUE 338s > 338s > ## etm 338s > prob.sir <- etm(sir.cont, c("0", "1", "2"), tra, "cens", 1) 338s > 338s > prob.sir 338s Multistate model with 2 transient state(s) 338s and 1 absorbing state(s) 338s 338s Possible transitions: 338s from to 338s 0 1 338s 0 2 338s 1 0 338s 1 2 338s 338s Estimate of P(1, 183) 338s 0 1 2 338s 0 0 0 1 338s 1 0 0 1 338s 2 0 0 1 338s 338s > 338s > summ.sir <- summary(prob.sir) 338s > all.equal(summ.sir[['0 1']]$P, as.vector(trprob(prob.sir, "0 1"))) 338s [1] TRUE 338s > subset(summ.sir[[3]],time<183) # issue with precision on different architectures 338s P time var lower upper n.risk n.event 338s 1.5 0.0000 1.5 0.000e+00 0.00000 0.0000 394 0 338s 2 0.1187 2.0 2.641e-04 0.08683 0.1505 396 47 338s 2.5 0.1187 2.5 2.641e-04 0.08683 0.1505 364 0 338s 3 0.2454 3.0 4.465e-04 0.20398 0.2868 365 54 338s 3.5 0.2454 3.5 4.465e-04 0.20398 0.2868 328 0 338s 4 0.3806 4.0 5.416e-04 0.33501 0.4262 331 62 338s 4.5 0.3806 4.5 5.416e-04 0.33501 0.4262 280 0 338s 5 0.4792 5.0 5.480e-04 0.43333 0.5251 283 48 338s 5.5 0.4792 5.5 5.480e-04 0.43333 0.5251 248 0 338s 6 0.5693 6.0 5.141e-04 0.52482 0.6137 249 47 338s 7 0.6350 7.0 4.665e-04 0.59266 0.6773 212 36 338s 8 0.6795 8.0 4.202e-04 0.63931 0.7197 195 27 338s 8.5 0.6795 8.5 4.202e-04 0.63931 0.7197 172 0 338s 9 0.7325 9.0 3.580e-04 0.69541 0.7696 173 34 338s 10 0.7647 10.0 3.141e-04 0.72992 0.7994 148 21 338s 10.5 0.7647 10.5 3.141e-04 0.72992 0.7994 135 0 338s 11 0.7895 11.0 2.790e-04 0.75674 0.8222 136 18 338s 12 0.8138 12.0 2.420e-04 0.78330 0.8443 129 18 338s 12.5 0.8138 12.5 2.420e-04 0.78330 0.8443 117 0 338s 13 0.8294 13.0 2.182e-04 0.80045 0.8584 118 13 338s 14 0.8452 14.0 1.938e-04 0.81789 0.8725 115 14 338s 15 0.8625 15.0 1.670e-04 0.83714 0.8878 106 15 338s 16 0.8723 16.0 1.522e-04 0.84807 0.8964 93 9 338s 17 0.8852 17.0 1.330e-04 0.86256 0.9078 86 12 338s 17.5 0.8852 17.5 1.330e-04 0.86256 0.9078 77 0 338s 18 0.8960 18.0 1.168e-04 0.87484 0.9172 76 9 338s 19 0.9029 19.0 1.070e-04 0.88261 0.9232 71 7 338s 20 0.9125 20.0 9.367e-05 0.89356 0.9315 64 10 338s 21 0.9161 21.0 8.878e-05 0.89768 0.9346 57 4 338s 22 0.9226 22.0 7.996e-05 0.90504 0.9401 55 6 338s 23 0.9261 23.0 7.537e-05 0.90904 0.9431 51 4 338s 23.5 0.9261 23.5 7.537e-05 0.90904 0.9431 49 0 338s 24 0.9354 24.0 6.292e-05 0.91982 0.9509 50 9 338s 25 0.9385 25.0 5.878e-05 0.92352 0.9536 42 3 338s 26 0.9429 26.0 5.326e-05 0.92863 0.9572 39 5 338s 27 0.9477 27.0 4.749e-05 0.93417 0.9612 35 6 338s 27.5 0.9477 27.5 4.749e-05 0.93417 0.9612 29 0 338s 28 0.9531 28.0 4.093e-05 0.94059 0.9657 30 5 338s 29 0.9567 29.0 3.668e-05 0.94485 0.9686 31 4 338s 30 0.9592 30.0 3.384e-05 0.94779 0.9706 28 3 338s 30.5 0.9592 30.5 3.384e-05 0.94779 0.9706 29 0 338s 31 0.9642 31.0 2.821e-05 0.95383 0.9746 30 6 338s 32 0.9649 32.0 2.752e-05 0.95458 0.9751 25 1 338s 33 0.9669 33.0 2.533e-05 0.95708 0.9768 24 2 338s 34 0.9685 34.0 2.368e-05 0.95900 0.9781 26 2 338s 35 0.9697 35.0 2.252e-05 0.96036 0.9790 28 2 338s 36 0.9702 36.0 2.194e-05 0.96104 0.9794 26 1 338s 37 0.9718 37.0 2.043e-05 0.96290 0.9806 26 2 338s 38 0.9739 38.0 1.831e-05 0.96555 0.9823 25 4 338s 38.5 0.9739 38.5 1.831e-05 0.96555 0.9823 21 0 338s 39 0.9760 39.0 1.643e-05 0.96802 0.9839 23 3 338s 40 0.9769 40.0 1.558e-05 0.96918 0.9847 19 1 338s 41 0.9774 41.0 1.512e-05 0.96981 0.9851 22 1 338s 42 0.9779 42.0 1.476e-05 0.97032 0.9854 22 0 338s 43 0.9798 43.0 1.308e-05 0.97271 0.9869 22 3 338s 44 0.9803 44.0 1.265e-05 0.97333 0.9873 21 1 338s 45 0.9817 45.0 1.157e-05 0.97499 0.9883 19 1 338s 46 0.9822 46.0 1.116e-05 0.97561 0.9887 17 1 338s 47 0.9831 47.0 1.037e-05 0.97683 0.9895 18 2 338s 48 0.9836 48.0 9.987e-06 0.97743 0.9898 17 1 338s 49 0.9841 49.0 9.669e-06 0.97796 0.9901 17 0 338s 50 0.9845 50.0 9.297e-06 0.97856 0.9905 17 1 338s 50.5 0.9845 50.5 9.297e-06 0.97856 0.9905 16 0 338s 51 0.9860 51.0 8.214e-06 0.98037 0.9916 17 3 338s 52 0.9870 52.0 7.513e-06 0.98159 0.9923 14 2 338s 53 0.9879 53.0 6.875e-06 0.98276 0.9930 12 1 338s 54 0.9889 54.0 6.214e-06 0.98397 0.9937 12 2 338s 55 0.9903 55.0 5.254e-06 0.98581 0.9948 10 3 338s 56 0.9913 56.0 4.667e-06 0.98703 0.9955 6 1 338s 57 0.9917 57.0 4.364e-06 0.98765 0.9958 5 1 338s 58 0.9922 58.0 4.064e-06 0.98828 0.9962 4 1 338s 59 0.9927 59.0 3.769e-06 0.98891 0.9965 3 1 338s 60 0.9932 60.0 3.488e-06 0.98953 0.9969 3 1 338s 62 0.9937 62.0 3.230e-06 0.99016 0.9972 2 0 338s 63 0.9942 63.0 2.956e-06 0.99079 0.9975 2 1 338s 68 0.9942 68.0 2.956e-06 0.99079 0.9975 1 0 338s 70 0.9946 70.0 2.694e-06 0.99143 0.9979 2 1 338s 78 0.9951 78.0 2.442e-06 0.99207 0.9982 1 0 338s 80 0.9951 80.0 2.442e-06 0.99207 0.9982 1 0 338s 85 0.9966 85.0 1.695e-06 0.99404 0.9991 2 0 338s 89 0.9966 89.0 1.695e-06 0.99404 0.9991 2 0 338s 90 0.9966 90.0 1.695e-06 0.99404 0.9991 1 0 338s 95 0.9971 95.0 1.448e-06 0.99472 0.9994 2 0 338s 100 0.9976 100.0 1.203e-06 0.99542 0.9997 3 0 338s 101 0.9981 101.0 9.592e-07 0.99613 1.0000 3 1 338s 108 0.9985 108.0 7.169e-07 0.99688 1.0000 2 1 338s 113 0.9990 113.0 4.764e-07 0.99767 1.0000 1 0 338s 116 0.9990 116.0 4.764e-07 0.99767 1.0000 1 0 338s 124 0.9990 124.0 4.764e-07 0.99767 1.0000 2 0 338s 164 0.9990 164.0 4.764e-07 0.99767 1.0000 0 0 338s > 338s > ## gonna play a bit with the state names 338s > dd <- sir.cont 338s > dd$from <- ifelse(dd$from == 0, "initial state", "ventilation") 338s > dd$to <- as.character(dd$to) 338s > for (i in seq_len(nrow(dd))) { 338s + dd$to[i] <- switch(dd$to[i], 338s + "0" = "initial state", 338s + "1" = "ventilation", 338s + "2" = "end of story", 338s + "cens" = "cens" 338s + ) 338s + } 338s > 338s > test <- etm(dd, c("initial state", "ventilation", "end of story"), tra, "cens", 1) 338s > 338s > all.equal(test$est["initial state", "initial state", ], 338s + prob.sir$est["0", "0", ]) 338s [1] TRUE 338s > all.equal(trprob(test, "initial state initial state"), trprob(prob.sir, "0 0")) 338s [1] TRUE 338s > all.equal(trprob(test, "initial state ventilation"), trprob(prob.sir, "0 1")) 338s [1] TRUE 338s > all.equal(trprob(test, "initial state end of story"), trprob(prob.sir, "0 2")) 338s [1] TRUE 338s > 338s > all.equal(trcov(test, "initial state end of story"), trcov(prob.sir, "0 2")) 338s [1] TRUE 338s > 338s > aa <- summary(test) 338s > all.equal(summ.sir[[6]], aa[[6]]) 338s [1] TRUE 338s > all.equal(summ.sir[[4]], aa[[4]]) 338s [1] TRUE 338s > 338s > ### Test on abortion data 338s > 338s > data(abortion) 338s > 338s > from <- rep(0, nrow(abortion)) 338s > to <- abortion$cause 338s > entry <- abortion$entry 338s > exit <- abortion$exit 338s > id <- 1:nrow(abortion) 338s > data <- data.frame(id, from, to, entry, exit, group = abortion$group) 338s > 338s > ## Computation of the CIFs 338s > tra <- matrix(FALSE, 4, 4) 338s > tra[1, 2:4] <- TRUE 338s > 338s > cif.control <- etm(data[data$group == 0, ], c("0", "1", "2", "3"), 338s + tra, NULL, 0) 338s > cif.exposed <- etm(data[data$group == 1, ], c("0", "1", "2", "3"), 338s + tra, NULL, 0) 338s > 338s > all.equal(trprob(cif.control, "0 1"), cif.control$est["0", "1", ]) 338s [1] TRUE 338s > all.equal(trcov(cif.control, c("0 1", "0 2")), cif.control$cov["0 1", "0 2", ]) 338s [1] TRUE 338s > 338s > trprob(cif.control, "0 1") 338s 6 7 8 9 10 11 12 13 338s 0.000000 0.007401 0.014881 0.026509 0.033208 0.037694 0.037694 0.038955 338s 14 17 19 21 24 25 26 30 338s 0.040159 0.040159 0.040159 0.040159 0.040159 0.040159 0.040159 0.040159 338s 31 32 33 34 35 36 37 38 338s 0.040159 0.040159 0.040159 0.040159 0.040159 0.040159 0.040159 0.040159 338s 39 40 41 42 43 338s 0.040159 0.040159 0.040159 0.040159 0.040159 338s > trprob(cif.control, "0 2") 338s 6 7 8 9 10 11 12 13 338s 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 338s 14 17 19 21 24 25 26 30 338s 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.003657 338s 31 32 33 34 35 36 37 38 338s 0.006371 0.008175 0.013543 0.023317 0.031260 0.053197 0.084529 0.179163 338s 39 40 41 42 43 338s 0.322016 0.563121 0.742227 0.793893 0.799059 338s > trprob(cif.control, "0 0") 338s 6 7 8 9 10 11 12 13 338s 0.965812 0.932508 0.887628 0.862433 0.838989 0.822538 0.813099 0.810578 338s 14 17 19 21 24 25 26 30 338s 0.806964 0.805874 0.803810 0.802804 0.801837 0.800883 0.799937 0.796280 338s 31 32 33 34 35 36 37 38 338s 0.793565 0.791762 0.786394 0.776620 0.768677 0.745862 0.714531 0.619897 338s 39 40 41 42 43 338s 0.477043 0.235938 0.056832 0.005167 0.000000 338s > 338s > trcov(cif.control, "0 1") 338s 6 7 8 9 10 11 12 13 338s 0.000e+00 2.719e-05 4.533e-05 6.665e-05 7.698e-05 8.304e-05 8.304e-05 8.444e-05 338s 14 17 19 21 24 25 26 30 338s 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 338s 31 32 33 34 35 36 37 38 338s 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 338s 39 40 41 42 43 338s 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 338s > trcov(cif.control, "0 2") 338s 6 7 8 9 10 11 12 13 338s 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 338s 14 17 19 21 24 25 26 30 338s 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 3.338e-06 338s 31 32 33 34 35 36 37 38 338s 5.784e-06 7.401e-06 1.216e-05 2.072e-05 2.758e-05 4.619e-05 7.202e-05 1.461e-04 338s 39 40 41 42 43 338s 2.470e-04 3.880e-04 4.702e-04 4.903e-04 4.922e-04 338s > trcov(cif.control, "0 0") 338s 6 7 8 9 10 11 12 13 338s 2.822e-04 3.821e-04 4.527e-04 4.748e-04 4.875e-04 4.927e-04 4.941e-04 4.942e-04 338s 14 17 19 21 24 25 26 30 338s 4.941e-04 4.940e-04 4.936e-04 4.933e-04 4.931e-04 4.928e-04 4.926e-04 4.914e-04 338s 31 32 33 34 35 36 37 38 338s 4.905e-04 4.899e-04 4.880e-04 4.846e-04 4.816e-04 4.729e-04 4.601e-04 4.176e-04 338s 39 40 41 42 43 338s 3.425e-04 1.865e-04 4.797e-05 4.441e-06 0.000e+00 338s > 338s > aa <- summary(cif.control) 338s > aa$"0 1" 338s P time var lower upper n.risk n.event 338s 6 0.000000 6 0.000e+00 0.000000 0.00000 117 0 338s 7 0.007401 7 2.719e-05 0.000000 0.01762 261 2 338s 8 0.014881 8 4.533e-05 0.001685 0.02808 374 3 338s 9 0.026509 9 6.665e-05 0.010508 0.04251 458 6 338s 10 0.033208 10 7.698e-05 0.016011 0.05040 515 4 338s 11 0.037694 11 8.304e-05 0.019834 0.05555 561 3 338s 12 0.037694 12 8.304e-05 0.019834 0.05555 610 0 338s 13 0.038955 13 8.444e-05 0.020944 0.05697 645 1 338s 14 0.040159 14 8.571e-05 0.022014 0.05830 673 1 338s 17 0.040159 17 8.571e-05 0.022014 0.05830 740 0 338s 19 0.040159 19 8.571e-05 0.022014 0.05830 781 0 338s 21 0.040159 21 8.571e-05 0.022014 0.05830 799 0 338s 24 0.040159 24 8.571e-05 0.022014 0.05830 830 0 338s 25 0.040159 25 8.571e-05 0.022014 0.05830 841 0 338s 26 0.040159 26 8.571e-05 0.022014 0.05830 846 0 338s 30 0.040159 30 8.571e-05 0.022014 0.05830 875 0 338s 31 0.040159 31 8.571e-05 0.022014 0.05830 880 0 338s 32 0.040159 32 8.571e-05 0.022014 0.05830 880 0 338s 33 0.040159 33 8.571e-05 0.022014 0.05830 885 0 338s 34 0.040159 34 8.571e-05 0.022014 0.05830 885 0 338s 35 0.040159 35 8.571e-05 0.022014 0.05830 880 0 338s 36 0.040159 36 8.571e-05 0.022014 0.05830 876 0 338s 37 0.040159 37 8.571e-05 0.022014 0.05830 857 0 338s 38 0.040159 38 8.571e-05 0.022014 0.05830 823 0 338s 39 0.040159 39 8.571e-05 0.022014 0.05830 716 0 338s 40 0.040159 40 8.571e-05 0.022014 0.05830 554 0 338s 41 0.040159 41 8.571e-05 0.022014 0.05830 274 0 338s 42 0.040159 42 8.571e-05 0.022014 0.05830 66 0 338s 43 0.040159 43 8.571e-05 0.022014 0.05830 6 0 338s > all.equal(aa$"0 1"$P, as.vector(trprob(cif.control, "0 1"))) 338s [1] TRUE 338s > 338s > ### test on los data 338s > 338s > data(los.data) # in package changeLOS 338s > 338s > ## putting los.data in the long format (see changeLOS) 338s > my.observ <- prepare.los.data(x=los.data) 338s > 338s > tra <- matrix(FALSE, 4, 4) 338s > tra[1, 2:4] <- TRUE 338s > tra[2, 3:4] <- TRUE 338s > 338s > tr.prob <- etm(my.observ, c("0","1","2","3"), tra, NULL, 0) 338s > 338s > tr.prob 338s Multistate model with 2 transient state(s) 338s and 2 absorbing state(s) 338s 338s Possible transitions: 338s from to 338s 0 1 338s 0 2 338s 0 3 338s 1 2 338s 1 3 338s 338s Estimate of P(0, 82) 338s 0 1 2 3 338s 0 0 0 0.7474 0.2526 338s 1 0 0 0.7073 0.2927 338s 2 0 0 1.0000 0.0000 338s 3 0 0 0.0000 1.0000 338s 338s > summary(tr.prob) 338s Transition 0 0 338s P time var lower upper n.risk n.event 338s 0.882275 3 1.374e-04 0.8593018 0.905248 756 0 338s 0.112434 15 1.320e-04 0.0899155 0.134952 90 0 338s 0.031746 27 4.066e-05 0.0192484 0.044244 26 0 338s 0.006614 41 8.690e-06 0.0008359 0.012392 5 0 338s 0.002646 61 3.490e-06 0.0000000 0.006307 3 0 338s 0.000000 82 0.000e+00 0.0000000 0.000000 1 0 338s 338s Transition 0 1 338s P time var lower upper n.risk n.event 338s 0.017196 3 2.235e-05 0.0079289 0.02646 756 13 338s 0.063492 15 7.865e-05 0.0461099 0.08087 90 0 338s 0.030423 27 3.902e-05 0.0181805 0.04267 26 1 338s 0.015873 41 2.066e-05 0.0069637 0.02478 5 0 338s 0.005291 61 6.962e-06 0.0001197 0.01046 3 0 338s 0.000000 82 0.000e+00 0.0000000 0.00000 1 0 338s 338s Transition 0 2 338s P time var lower upper n.risk n.event 338s 0.08466 3 0.0001025 0.06481 0.1045 756 64 338s 0.62302 15 0.0003107 0.58847 0.6576 90 4 338s 0.69841 27 0.0002786 0.66570 0.7311 26 1 338s 0.72751 41 0.0002622 0.69578 0.7593 5 0 338s 0.74074 61 0.0002540 0.70950 0.7720 3 1 338s 0.74735 82 0.0002498 0.71638 0.7783 1 1 338s 338s Transition 0 3 338s P time var lower upper n.risk n.event 338s 0.01587 3 2.066e-05 0.006964 0.02478 756 12 338s 0.20106 15 2.125e-04 0.172489 0.22963 90 1 338s 0.23942 27 2.409e-04 0.208999 0.26984 26 0 338s 0.25000 41 2.480e-04 0.219133 0.28087 5 0 338s 0.25132 61 2.489e-04 0.220402 0.28224 3 0 338s 0.25265 82 2.498e-04 0.221671 0.28362 1 0 338s 338s Transition 1 1 338s P time var lower upper n.risk n.event 338s 1.00000 3 0.000e+00 1.00000 1.00000 0 0 338s 0.38661 15 2.358e-03 0.29143 0.48179 51 0 338s 0.12119 27 7.842e-04 0.06630 0.17607 23 0 338s 0.04593 41 2.405e-04 0.01554 0.07633 14 0 338s 0.01531 61 6.579e-05 0.00000 0.03121 4 0 338s 0.00000 82 0.000e+00 0.00000 0.00000 0 0 338s 338s Transition 1 2 338s P time var lower upper n.risk n.event 338s 0.0000 3 0.000000 0.0000 0.0000 0 0 338s 0.4107 15 0.002590 0.3110 0.5104 51 2 338s 0.6082 27 0.002254 0.5151 0.7012 23 1 338s 0.6652 41 0.002064 0.5761 0.7542 14 2 338s 0.6920 61 0.002000 0.6043 0.7796 4 0 338s 0.7073 82 0.001984 0.6200 0.7946 0 0 338s 338s Transition 1 3 338s P time var lower upper n.risk n.event 338s 0.0000 3 0.000000 0.0000 0.0000 0 0 338s 0.2027 15 0.001784 0.1199 0.2855 51 1 338s 0.2706 27 0.001968 0.1837 0.3576 23 0 338s 0.2889 41 0.001982 0.2016 0.3761 14 0 338s 0.2927 61 0.001984 0.2054 0.3800 4 0 338s 0.2927 82 0.001984 0.2054 0.3800 0 0 338s 338s > 338s > cLOS <- etm::clos(tr.prob, aw = TRUE) 338s > 338s > cLOS 338s The expected change in length of stay is: 338s 1.975 338s 338s Alternative weighting: 338s 338s Expected change in LOS with weight.1: 2.097 338s Expected change in LOS with weight.other: 1.951 338s > 338s > 338s > ### Tests on pseudo values 338s > t_pseudo <- closPseudo(my.observ, c("0","1","2","3"), tra, NULL, 338s + formula = ~ 1, aw = TRUE) 356s > 356s > cLOS$e.phi == t_pseudo$theta[, "e.phi"] 356s [,1] 356s [1,] TRUE 356s > cLOS$e.phi.weights.1 == t_pseudo$theta[, "e.phi.weights.1"] 356s [,1] 356s [1,] TRUE 356s > cLOS$e.phi.weights.other == t_pseudo$theta[, "e.phi.weights.other"] 356s [,1] 356s [1,] TRUE 356s > 356s > mean(t_pseudo$pseudoData$ps.e.phi) 356s [1] 1.968 356s > 356s > ### tests on etmprep 356s > 356s > ### creation of fake data in the wild format, following an illness-death model 356s > ## transition times 356s > tdisease <- c(3, 4, 3, 6, 8, 9) 356s > tdeath <- c(6, 9, 8, 6, 8, 9) 356s > 356s > ## transition status 356s > stat.disease <- c(1, 1, 1, 0, 0, 0) 356s > stat.death <- c(1, 1, 1, 1, 1, 0) 356s > 356s > ## a covariate that we want to keep in the new data 356s > set.seed(1313) 356s > cova <- rbinom(6, 1, 0.5) 356s > 356s > dat <- data.frame(tdisease, tdeath, 356s + stat.disease, stat.death, 356s + cova) 356s > 356s > ## Possible transitions 356s > tra <- matrix(FALSE, 3, 3) 356s > tra[1, 2:3] <- TRUE 356s > tra[2, 3] <- TRUE 356s > 356s > ## data preparation 356s > newdat <- etmprep(c(NA, "tdisease", "tdeath"), 356s + c(NA, "stat.disease", "stat.death"), 356s + data = dat, tra = tra, 356s + cens.name = "cens", keep = "cova") 356s > 356s > newdat 356s id entry exit from to cova 356s 1 1 0 3 0 1 1 356s 2 1 3 6 1 2 1 356s 3 2 0 4 0 1 0 356s 4 2 4 9 1 2 0 356s 5 3 0 3 0 1 1 356s 6 3 3 8 1 2 1 356s 7 4 0 6 0 2 0 356s 8 5 0 8 0 2 1 356s 9 6 0 9 0 cens 1 356s > 356s > ref <- data.frame(id = c(1, 1, 2, 2, 3, 3, 4, 5, 6), 356s + entry = c(0, 3, 0, 4, 0, 3, 0, 0, 0), 356s + exit = c(3, 6, 4, 9, 3, 8, 6, 8, 9), 356s + from = c(0, 1, 0, 1, 0, 1, 0, 0, 0), 356s + to = c(rep(c(1, 2), 3), 2, 2, "cens"), 356s + cova = c(1, 1, 0, 0, 1, 1, 0, 1, 1)) 356s > ref$from <- factor(as.character(ref$from), levels = c("0", "1", "2", "cens")) 356s > ref$to <- factor(as.character(ref$to), levels = c("0", "1", "2", "cens")) 356s > 356s > all.equal(ref, newdat) 356s [1] TRUE 356s > 356s > 356s > ###################################### 356s > ### Test the stratified calls 356s > ###################################### 356s > 356s > if (require("kmi", quietly = TRUE)) { 356s + library(etm) 356s + 356s + data(icu.pneu) 356s + my.icu.pneu <- icu.pneu 356s + 356s + my.icu.pneu <- my.icu.pneu[order(my.icu.pneu$id, my.icu.pneu$start), ] 356s + masque <- diff(my.icu.pneu$id) 356s + 356s + my.icu.pneu$from <- 0 356s + my.icu.pneu$from[c(1, masque) == 0] <- 1 356s + 356s + my.icu.pneu$to2 <- my.icu.pneu$event 356s + my.icu.pneu$to2[my.icu.pneu$status == 0] <- "cens" 356s + my.icu.pneu$to2[c(masque, 1) == 0] <- 1 356s + 356s + 356s + my.icu.pneu$to <- ifelse(my.icu.pneu$to2 %in% c(2, 3), 2, 356s + my.icu.pneu$to2) 356s + 356s + my.icu.pneu <- my.icu.pneu[, c("id", "start", "stop", "from", "to", 356s + "to2", "age", "sex")] 356s + names(my.icu.pneu)[c(2, 3)] <- c("entry", "exit") 356s + 356s + bouh_strat <- etm(my.icu.pneu, c("0", "1", "2"), tra_ill(), "cens", 0, strata = "sex") 356s + 356s + bouh_female <- etm(my.icu.pneu[my.icu.pneu$sex == "F", ], 356s + c("0", "1", "2"), tra_ill(), "cens", 0) 356s + 356s + all(bouh_strat[[1]]$est == bouh_female$est) 356s + 356s + ## Test the summary 356s + the_summary <- summary(bouh_strat) 356s + the_summary 356s + 356s + ## Test trprob 356s + all(trprob(bouh_strat, "0 1")[[1]] == trprob(bouh_female, "0 1")) 356s + all(trprob(bouh_strat, "0 1", c(0, 5, 10, 15))[[1]] == trprob(bouh_female, "0 1", c(0, 5, 10, 15))) 356s + 356s + ## Test trcov 356s + all(trcov(bouh_strat, "0 1")[[1]] == trcov(bouh_female, "0 1")) 356s + all(trcov(bouh_strat, c("0 1", "0 2"))[[1]] == trcov(bouh_female, c("0 1", "0 2"))) 356s + all(trcov(bouh_strat, "0 1", c(0, 5, 10, 15))[[1]] == trcov(bouh_female, "0 1", c(0, 5, 10, 15))) 356s + } else { 356s + print("These tests require the kmi package") 356s + } 356s [1] TRUE 356s > 356s > options(old) 356s > 357s autopkgtest [16:11:35]: test run-unit-test: -----------------------] 360s run-unit-test PASS 360s autopkgtest [16:11:38]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 364s autopkgtest [16:11:42]: test pkg-r-autopkgtest: preparing testbed 366s Reading package lists... 366s Building dependency tree... 366s Reading state information... 366s Starting pkgProblemResolver with broken count: 0 366s Starting 2 pkgProblemResolver with broken count: 0 366s Done 367s The following NEW packages will be installed: 367s build-essential cpp cpp-14 cpp-14-arm-linux-gnueabihf 367s cpp-arm-linux-gnueabihf dctrl-tools g++ g++-14 g++-14-arm-linux-gnueabihf 367s g++-arm-linux-gnueabihf gcc gcc-14 gcc-14-arm-linux-gnueabihf 367s gcc-arm-linux-gnueabihf gfortran gfortran-14 gfortran-14-arm-linux-gnueabihf 367s gfortran-arm-linux-gnueabihf icu-devtools libasan8 libblas-dev libbz2-dev 367s libc-dev-bin libc6-dev libcc1-0 libcrypt-dev libdeflate-dev libgcc-14-dev 367s libgfortran-14-dev libicu-dev libisl23 libjpeg-dev libjpeg-turbo8-dev 367s libjpeg8-dev liblapack-dev liblzma-dev libmpc3 libncurses-dev libpcre2-16-0 367s libpcre2-32-0 libpcre2-dev libpcre2-posix3 libpkgconf3 libpng-dev 367s libreadline-dev libstdc++-14-dev libtirpc-dev libubsan1 linux-libc-dev 367s pkg-r-autopkgtest pkgconf pkgconf-bin r-base-dev r-cran-backports 367s r-cran-broom r-cran-cli r-cran-colorspace r-cran-cpp11 r-cran-dplyr 367s r-cran-fansi r-cran-farver r-cran-geepack r-cran-generics r-cran-ggplot2 367s r-cran-glue r-cran-gtable r-cran-isoband r-cran-labeling r-cran-lifecycle 367s r-cran-magrittr r-cran-mass r-cran-mgcv r-cran-munsell r-cran-nlme 367s r-cran-pillar r-cran-pkgconfig r-cran-purrr r-cran-r6 r-cran-rcolorbrewer 367s r-cran-rlang r-cran-scales r-cran-stringi r-cran-stringr r-cran-tibble 367s r-cran-tidyr r-cran-tidyselect r-cran-utf8 r-cran-vctrs r-cran-viridislite 367s r-cran-withr rpcsvc-proto zlib1g-dev 368s 0 upgraded, 92 newly installed, 0 to remove and 0 not upgraded. 368s Need to get 109 MB of archives. 368s After this operation, 292 MB of additional disk space will be used. 368s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libc-dev-bin armhf 2.41-1ubuntu2 [23.0 kB] 368s Get:2 http://ftpmaster.internal/ubuntu plucky/main armhf linux-libc-dev armhf 6.14.0-10.10 [1683 kB] 369s Get:3 http://ftpmaster.internal/ubuntu plucky/main armhf libcrypt-dev armhf 1:4.4.38-1 [120 kB] 370s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf rpcsvc-proto armhf 1.4.2-0ubuntu7 [62.2 kB] 370s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libc6-dev armhf 2.41-1ubuntu2 [1396 kB] 371s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf libisl23 armhf 0.27-1 [546 kB] 372s Get:7 http://ftpmaster.internal/ubuntu plucky/main armhf libmpc3 armhf 1.3.1-1build2 [47.1 kB] 372s Get:8 http://ftpmaster.internal/ubuntu plucky/main armhf cpp-14-arm-linux-gnueabihf armhf 14.2.0-17ubuntu3 [9220 kB] 383s Get:9 http://ftpmaster.internal/ubuntu plucky/main armhf cpp-14 armhf 14.2.0-17ubuntu3 [1030 B] 383s Get:10 http://ftpmaster.internal/ubuntu plucky/main armhf cpp-arm-linux-gnueabihf armhf 4:14.2.0-1ubuntu1 [5578 B] 383s Get:11 http://ftpmaster.internal/ubuntu plucky/main armhf cpp armhf 4:14.2.0-1ubuntu1 [22.4 kB] 383s Get:12 http://ftpmaster.internal/ubuntu plucky/main armhf libcc1-0 armhf 15-20250222-0ubuntu1 [38.9 kB] 383s Get:13 http://ftpmaster.internal/ubuntu plucky/main armhf libasan8 armhf 15-20250222-0ubuntu1 [2955 kB] 387s Get:14 http://ftpmaster.internal/ubuntu plucky/main armhf libubsan1 armhf 15-20250222-0ubuntu1 [1191 kB] 388s Get:15 http://ftpmaster.internal/ubuntu plucky/main armhf libgcc-14-dev armhf 14.2.0-17ubuntu3 [897 kB] 389s Get:16 http://ftpmaster.internal/ubuntu plucky/main armhf gcc-14-arm-linux-gnueabihf armhf 14.2.0-17ubuntu3 [18.0 MB] 411s Get:17 http://ftpmaster.internal/ubuntu plucky/main armhf gcc-14 armhf 14.2.0-17ubuntu3 [506 kB] 411s Get:18 http://ftpmaster.internal/ubuntu plucky/main armhf gcc-arm-linux-gnueabihf armhf 4:14.2.0-1ubuntu1 [1218 B] 411s Get:19 http://ftpmaster.internal/ubuntu plucky/main armhf gcc armhf 4:14.2.0-1ubuntu1 [5004 B] 411s Get:20 http://ftpmaster.internal/ubuntu plucky/main armhf libstdc++-14-dev armhf 14.2.0-17ubuntu3 [2573 kB] 415s Get:21 http://ftpmaster.internal/ubuntu plucky/main armhf g++-14-arm-linux-gnueabihf armhf 14.2.0-17ubuntu3 [10.5 MB] 427s Get:22 http://ftpmaster.internal/ubuntu plucky/main armhf g++-14 armhf 14.2.0-17ubuntu3 [21.8 kB] 427s Get:23 http://ftpmaster.internal/ubuntu plucky/main armhf g++-arm-linux-gnueabihf armhf 4:14.2.0-1ubuntu1 [966 B] 427s Get:24 http://ftpmaster.internal/ubuntu plucky/main armhf g++ armhf 4:14.2.0-1ubuntu1 [1084 B] 427s Get:25 http://ftpmaster.internal/ubuntu plucky/main armhf build-essential armhf 12.10ubuntu1 [4928 B] 427s Get:26 http://ftpmaster.internal/ubuntu plucky/main armhf dctrl-tools armhf 2.24-3build3 [94.7 kB] 427s Get:27 http://ftpmaster.internal/ubuntu plucky/main armhf libgfortran-14-dev armhf 14.2.0-17ubuntu3 [370 kB] 427s Get:28 http://ftpmaster.internal/ubuntu plucky/main armhf gfortran-14-arm-linux-gnueabihf armhf 14.2.0-17ubuntu3 [9763 kB] 438s Get:29 http://ftpmaster.internal/ubuntu plucky/main armhf gfortran-14 armhf 14.2.0-17ubuntu3 [13.6 kB] 438s Get:30 http://ftpmaster.internal/ubuntu plucky/main armhf gfortran-arm-linux-gnueabihf armhf 4:14.2.0-1ubuntu1 [1026 B] 438s Get:31 http://ftpmaster.internal/ubuntu plucky/main armhf gfortran armhf 4:14.2.0-1ubuntu1 [1166 B] 438s Get:32 http://ftpmaster.internal/ubuntu plucky/main armhf icu-devtools armhf 76.1-1ubuntu2 [206 kB] 439s Get:33 http://ftpmaster.internal/ubuntu plucky/main armhf libblas-dev armhf 3.12.1-2 [141 kB] 439s Get:34 http://ftpmaster.internal/ubuntu plucky/main armhf libbz2-dev armhf 1.0.8-6 [30.9 kB] 439s Get:35 http://ftpmaster.internal/ubuntu plucky/main armhf libdeflate-dev armhf 1.23-1 [45.0 kB] 439s Get:36 http://ftpmaster.internal/ubuntu plucky/main armhf libicu-dev armhf 76.1-1ubuntu2 [12.0 MB] 452s Get:37 http://ftpmaster.internal/ubuntu plucky/main armhf libjpeg-turbo8-dev armhf 2.1.5-3ubuntu2 [265 kB] 452s Get:38 http://ftpmaster.internal/ubuntu plucky/main armhf libjpeg8-dev armhf 8c-2ubuntu11 [1484 B] 452s Get:39 http://ftpmaster.internal/ubuntu plucky/main armhf libjpeg-dev armhf 8c-2ubuntu11 [1482 B] 452s Get:40 http://ftpmaster.internal/ubuntu plucky/main armhf liblapack-dev armhf 3.12.1-2 [2207 kB] 455s Get:41 http://ftpmaster.internal/ubuntu plucky/main armhf libncurses-dev armhf 6.5+20250216-2 [345 kB] 455s Get:42 http://ftpmaster.internal/ubuntu plucky/main armhf libpcre2-16-0 armhf 10.45-1 [207 kB] 456s Get:43 http://ftpmaster.internal/ubuntu plucky/main armhf libpcre2-32-0 armhf 10.45-1 [197 kB] 456s Get:44 http://ftpmaster.internal/ubuntu plucky/main armhf libpcre2-posix3 armhf 10.45-1 [6300 B] 456s Get:45 http://ftpmaster.internal/ubuntu plucky/main armhf libpcre2-dev armhf 10.45-1 [752 kB] 457s Get:46 http://ftpmaster.internal/ubuntu plucky/main armhf libpkgconf3 armhf 1.8.1-4 [26.6 kB] 457s Get:47 http://ftpmaster.internal/ubuntu plucky/main armhf zlib1g-dev armhf 1:1.3.dfsg+really1.3.1-1ubuntu1 [880 kB] 458s Get:48 http://ftpmaster.internal/ubuntu plucky/main armhf libpng-dev armhf 1.6.47-1 [251 kB] 458s Get:49 http://ftpmaster.internal/ubuntu plucky/main armhf libreadline-dev armhf 8.2-6 [153 kB] 458s Get:50 http://ftpmaster.internal/ubuntu plucky/main armhf liblzma-dev armhf 5.6.4-1 [166 kB] 458s Get:51 http://ftpmaster.internal/ubuntu plucky/main armhf pkgconf-bin armhf 1.8.1-4 [21.2 kB] 458s Get:52 http://ftpmaster.internal/ubuntu plucky/main armhf pkgconf armhf 1.8.1-4 [16.8 kB] 458s Get:53 http://ftpmaster.internal/ubuntu plucky/main armhf libtirpc-dev armhf 1.3.4+ds-1.3 [184 kB] 458s Get:54 http://ftpmaster.internal/ubuntu plucky/universe armhf r-base-dev all 4.4.3-1 [4176 B] 458s Get:55 http://ftpmaster.internal/ubuntu plucky/universe armhf pkg-r-autopkgtest all 20231212ubuntu1 [6448 B] 458s Get:56 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-backports armhf 1.5.0-2 [121 kB] 459s Get:57 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-cli armhf 3.6.4-1 [1377 kB] 460s Get:58 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-generics all 0.1.3-1 [81.3 kB] 460s Get:59 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-glue armhf 1.8.0-1 [162 kB] 460s Get:60 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-rlang armhf 1.1.5-1 [1701 kB] 462s Get:61 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB] 462s Get:62 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-magrittr armhf 2.0.3-1 [154 kB] 462s Get:63 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-utf8 armhf 1.2.4-1 [136 kB] 462s Get:64 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-vctrs armhf 0.6.5-1 [1310 kB] 465s Get:65 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-pillar all 1.10.1+dfsg-1 [453 kB] 469s Get:66 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-r6 all 2.6.1-1 [101 kB] 470s Get:67 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-fansi armhf 1.0.5-1 [611 kB] 472s Get:68 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-pkgconfig all 2.0.3-2build1 [19.7 kB] 472s Get:69 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-tibble armhf 3.2.1+dfsg-3 [420 kB] 473s Get:70 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-withr all 3.0.2+dfsg-1 [214 kB] 473s Get:71 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-tidyselect armhf 1.2.1+dfsg-1 [222 kB] 473s Get:72 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-dplyr armhf 1.1.4-4 [1533 kB] 476s Get:73 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-purrr armhf 1.0.4-1 [550 kB] 476s Get:74 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-stringi armhf 1.8.4-1build1 [887 kB] 477s Get:75 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-stringr all 1.5.1-1 [290 kB] 477s Get:76 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-cpp11 all 0.5.2-1 [233 kB] 478s Get:77 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-tidyr armhf 1.3.1-1 [1152 kB] 479s Get:78 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-broom all 1.0.7+dfsg-1 [1802 kB] 481s Get:79 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-colorspace armhf 2.1-1+dfsg-1 [1561 kB] 483s Get:80 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-farver armhf 2.1.2-1 [1355 kB] 484s Get:81 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-mass armhf 7.3-64-1 [1105 kB] 486s Get:82 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-geepack armhf 1.3.12-1 [365 kB] 486s Get:83 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-gtable all 0.3.6+dfsg-1 [199 kB] 486s Get:84 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-isoband armhf 0.2.7-1 [1477 kB] 488s Get:85 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-nlme armhf 3.1.167-1 [2306 kB] 490s Get:86 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-mgcv armhf 1.9-1-1 [3205 kB] 494s Get:87 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-labeling all 0.4.3-1 [62.1 kB] 494s Get:88 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-munsell all 0.5.1-1 [213 kB] 494s Get:89 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-rcolorbrewer all 1.1-3-1build1 [55.4 kB] 494s Get:90 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-viridislite all 0.4.2-2 [1088 kB] 496s Get:91 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-scales all 1.3.0-1 [603 kB] 496s Get:92 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-ggplot2 all 3.5.1+dfsg-1 [3940 kB] 501s Fetched 109 MB in 2min 13s (822 kB/s) 501s Selecting previously unselected package libc-dev-bin. 501s (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 ... 69199 files and directories currently installed.) 501s Preparing to unpack .../00-libc-dev-bin_2.41-1ubuntu2_armhf.deb ... 501s Unpacking libc-dev-bin (2.41-1ubuntu2) ... 501s Selecting previously unselected package linux-libc-dev:armhf. 501s Preparing to unpack .../01-linux-libc-dev_6.14.0-10.10_armhf.deb ... 501s Unpacking linux-libc-dev:armhf (6.14.0-10.10) ... 501s Selecting previously unselected package libcrypt-dev:armhf. 501s Preparing to unpack .../02-libcrypt-dev_1%3a4.4.38-1_armhf.deb ... 501s Unpacking libcrypt-dev:armhf (1:4.4.38-1) ... 501s Selecting previously unselected package rpcsvc-proto. 501s Preparing to unpack .../03-rpcsvc-proto_1.4.2-0ubuntu7_armhf.deb ... 501s Unpacking rpcsvc-proto (1.4.2-0ubuntu7) ... 501s Selecting previously unselected package libc6-dev:armhf. 501s Preparing to unpack .../04-libc6-dev_2.41-1ubuntu2_armhf.deb ... 501s Unpacking libc6-dev:armhf (2.41-1ubuntu2) ... 501s Selecting previously unselected package libisl23:armhf. 501s Preparing to unpack .../05-libisl23_0.27-1_armhf.deb ... 501s Unpacking libisl23:armhf (0.27-1) ... 501s Selecting previously unselected package libmpc3:armhf. 501s Preparing to unpack .../06-libmpc3_1.3.1-1build2_armhf.deb ... 501s Unpacking libmpc3:armhf (1.3.1-1build2) ... 501s Selecting previously unselected package cpp-14-arm-linux-gnueabihf. 501s Preparing to unpack .../07-cpp-14-arm-linux-gnueabihf_14.2.0-17ubuntu3_armhf.deb ... 501s Unpacking cpp-14-arm-linux-gnueabihf (14.2.0-17ubuntu3) ... 502s Selecting previously unselected package cpp-14. 502s Preparing to unpack .../08-cpp-14_14.2.0-17ubuntu3_armhf.deb ... 502s Unpacking cpp-14 (14.2.0-17ubuntu3) ... 502s Selecting previously unselected package cpp-arm-linux-gnueabihf. 502s Preparing to unpack .../09-cpp-arm-linux-gnueabihf_4%3a14.2.0-1ubuntu1_armhf.deb ... 502s Unpacking cpp-arm-linux-gnueabihf (4:14.2.0-1ubuntu1) ... 502s Selecting previously unselected package cpp. 502s Preparing to unpack .../10-cpp_4%3a14.2.0-1ubuntu1_armhf.deb ... 502s Unpacking cpp (4:14.2.0-1ubuntu1) ... 502s Selecting previously unselected package libcc1-0:armhf. 502s Preparing to unpack .../11-libcc1-0_15-20250222-0ubuntu1_armhf.deb ... 502s Unpacking libcc1-0:armhf (15-20250222-0ubuntu1) ... 502s Selecting previously unselected package libasan8:armhf. 502s Preparing to unpack .../12-libasan8_15-20250222-0ubuntu1_armhf.deb ... 502s Unpacking libasan8:armhf (15-20250222-0ubuntu1) ... 502s Selecting previously unselected package libubsan1:armhf. 502s Preparing to unpack .../13-libubsan1_15-20250222-0ubuntu1_armhf.deb ... 502s Unpacking libubsan1:armhf (15-20250222-0ubuntu1) ... 502s Selecting previously unselected package libgcc-14-dev:armhf. 502s Preparing to unpack .../14-libgcc-14-dev_14.2.0-17ubuntu3_armhf.deb ... 502s Unpacking libgcc-14-dev:armhf (14.2.0-17ubuntu3) ... 502s Selecting previously unselected package gcc-14-arm-linux-gnueabihf. 502s Preparing to unpack .../15-gcc-14-arm-linux-gnueabihf_14.2.0-17ubuntu3_armhf.deb ... 502s Unpacking gcc-14-arm-linux-gnueabihf (14.2.0-17ubuntu3) ... 502s Selecting previously unselected package gcc-14. 502s Preparing to unpack .../16-gcc-14_14.2.0-17ubuntu3_armhf.deb ... 502s Unpacking gcc-14 (14.2.0-17ubuntu3) ... 503s Selecting previously unselected package gcc-arm-linux-gnueabihf. 503s Preparing to unpack .../17-gcc-arm-linux-gnueabihf_4%3a14.2.0-1ubuntu1_armhf.deb ... 503s Unpacking gcc-arm-linux-gnueabihf (4:14.2.0-1ubuntu1) ... 503s Selecting previously unselected package gcc. 503s Preparing to unpack .../18-gcc_4%3a14.2.0-1ubuntu1_armhf.deb ... 503s Unpacking gcc (4:14.2.0-1ubuntu1) ... 503s Selecting previously unselected package libstdc++-14-dev:armhf. 503s Preparing to unpack .../19-libstdc++-14-dev_14.2.0-17ubuntu3_armhf.deb ... 503s Unpacking libstdc++-14-dev:armhf (14.2.0-17ubuntu3) ... 503s Selecting previously unselected package g++-14-arm-linux-gnueabihf. 503s Preparing to unpack .../20-g++-14-arm-linux-gnueabihf_14.2.0-17ubuntu3_armhf.deb ... 503s Unpacking g++-14-arm-linux-gnueabihf (14.2.0-17ubuntu3) ... 503s Selecting previously unselected package g++-14. 503s Preparing to unpack .../21-g++-14_14.2.0-17ubuntu3_armhf.deb ... 503s Unpacking g++-14 (14.2.0-17ubuntu3) ... 503s Selecting previously unselected package g++-arm-linux-gnueabihf. 503s Preparing to unpack .../22-g++-arm-linux-gnueabihf_4%3a14.2.0-1ubuntu1_armhf.deb ... 503s Unpacking g++-arm-linux-gnueabihf (4:14.2.0-1ubuntu1) ... 503s Selecting previously unselected package g++. 503s Preparing to unpack .../23-g++_4%3a14.2.0-1ubuntu1_armhf.deb ... 503s Unpacking g++ (4:14.2.0-1ubuntu1) ... 503s Selecting previously unselected package build-essential. 503s Preparing to unpack .../24-build-essential_12.10ubuntu1_armhf.deb ... 503s Unpacking build-essential (12.10ubuntu1) ... 503s Selecting previously unselected package dctrl-tools. 503s Preparing to unpack .../25-dctrl-tools_2.24-3build3_armhf.deb ... 503s Unpacking dctrl-tools (2.24-3build3) ... 503s Selecting previously unselected package libgfortran-14-dev:armhf. 503s Preparing to unpack .../26-libgfortran-14-dev_14.2.0-17ubuntu3_armhf.deb ... 503s Unpacking libgfortran-14-dev:armhf (14.2.0-17ubuntu3) ... 503s Selecting previously unselected package gfortran-14-arm-linux-gnueabihf. 503s Preparing to unpack .../27-gfortran-14-arm-linux-gnueabihf_14.2.0-17ubuntu3_armhf.deb ... 503s Unpacking gfortran-14-arm-linux-gnueabihf (14.2.0-17ubuntu3) ... 503s Selecting previously unselected package gfortran-14. 503s Preparing to unpack .../28-gfortran-14_14.2.0-17ubuntu3_armhf.deb ... 503s Unpacking gfortran-14 (14.2.0-17ubuntu3) ... 504s Selecting previously unselected package gfortran-arm-linux-gnueabihf. 504s Preparing to unpack .../29-gfortran-arm-linux-gnueabihf_4%3a14.2.0-1ubuntu1_armhf.deb ... 504s Unpacking gfortran-arm-linux-gnueabihf (4:14.2.0-1ubuntu1) ... 504s Selecting previously unselected package gfortran. 504s Preparing to unpack .../30-gfortran_4%3a14.2.0-1ubuntu1_armhf.deb ... 504s Unpacking gfortran (4:14.2.0-1ubuntu1) ... 504s Selecting previously unselected package icu-devtools. 504s Preparing to unpack .../31-icu-devtools_76.1-1ubuntu2_armhf.deb ... 504s Unpacking icu-devtools (76.1-1ubuntu2) ... 504s Selecting previously unselected package libblas-dev:armhf. 504s Preparing to unpack .../32-libblas-dev_3.12.1-2_armhf.deb ... 504s Unpacking libblas-dev:armhf (3.12.1-2) ... 504s Selecting previously unselected package libbz2-dev:armhf. 504s Preparing to unpack .../33-libbz2-dev_1.0.8-6_armhf.deb ... 504s Unpacking libbz2-dev:armhf (1.0.8-6) ... 504s Selecting previously unselected package libdeflate-dev:armhf. 504s Preparing to unpack .../34-libdeflate-dev_1.23-1_armhf.deb ... 504s Unpacking libdeflate-dev:armhf (1.23-1) ... 504s Selecting previously unselected package libicu-dev:armhf. 504s Preparing to unpack .../35-libicu-dev_76.1-1ubuntu2_armhf.deb ... 504s Unpacking libicu-dev:armhf (76.1-1ubuntu2) ... 504s Selecting previously unselected package libjpeg-turbo8-dev:armhf. 504s Preparing to unpack .../36-libjpeg-turbo8-dev_2.1.5-3ubuntu2_armhf.deb ... 504s Unpacking libjpeg-turbo8-dev:armhf (2.1.5-3ubuntu2) ... 504s Selecting previously unselected package libjpeg8-dev:armhf. 504s Preparing to unpack .../37-libjpeg8-dev_8c-2ubuntu11_armhf.deb ... 504s Unpacking libjpeg8-dev:armhf (8c-2ubuntu11) ... 504s Selecting previously unselected package libjpeg-dev:armhf. 504s Preparing to unpack .../38-libjpeg-dev_8c-2ubuntu11_armhf.deb ... 504s Unpacking libjpeg-dev:armhf (8c-2ubuntu11) ... 504s Selecting previously unselected package liblapack-dev:armhf. 504s Preparing to unpack .../39-liblapack-dev_3.12.1-2_armhf.deb ... 504s Unpacking liblapack-dev:armhf (3.12.1-2) ... 504s Selecting previously unselected package libncurses-dev:armhf. 504s Preparing to unpack .../40-libncurses-dev_6.5+20250216-2_armhf.deb ... 504s Unpacking libncurses-dev:armhf (6.5+20250216-2) ... 504s Selecting previously unselected package libpcre2-16-0:armhf. 504s Preparing to unpack .../41-libpcre2-16-0_10.45-1_armhf.deb ... 504s Unpacking libpcre2-16-0:armhf (10.45-1) ... 504s Selecting previously unselected package libpcre2-32-0:armhf. 504s Preparing to unpack .../42-libpcre2-32-0_10.45-1_armhf.deb ... 504s Unpacking libpcre2-32-0:armhf (10.45-1) ... 504s Selecting previously unselected package libpcre2-posix3:armhf. 504s Preparing to unpack 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Unpacking libreadline-dev:armhf (8.2-6) ... 505s Selecting previously unselected package liblzma-dev:armhf. 505s Preparing to unpack .../49-liblzma-dev_5.6.4-1_armhf.deb ... 505s Unpacking liblzma-dev:armhf (5.6.4-1) ... 505s Selecting previously unselected package pkgconf-bin. 505s Preparing to unpack .../50-pkgconf-bin_1.8.1-4_armhf.deb ... 505s Unpacking pkgconf-bin (1.8.1-4) ... 505s Selecting previously unselected package pkgconf:armhf. 505s Preparing to unpack .../51-pkgconf_1.8.1-4_armhf.deb ... 505s Unpacking pkgconf:armhf (1.8.1-4) ... 505s Selecting previously unselected package libtirpc-dev:armhf. 505s Preparing to unpack .../52-libtirpc-dev_1.3.4+ds-1.3_armhf.deb ... 505s Unpacking libtirpc-dev:armhf (1.3.4+ds-1.3) ... 505s Selecting previously unselected package r-base-dev. 505s Preparing to unpack .../53-r-base-dev_4.4.3-1_all.deb ... 505s Unpacking r-base-dev (4.4.3-1) ... 505s Selecting previously unselected package pkg-r-autopkgtest. 505s Preparing to unpack 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package r-cran-lifecycle. 505s Preparing to unpack .../60-r-cran-lifecycle_1.0.4+dfsg-1_all.deb ... 505s Unpacking r-cran-lifecycle (1.0.4+dfsg-1) ... 505s Selecting previously unselected package r-cran-magrittr. 505s Preparing to unpack .../61-r-cran-magrittr_2.0.3-1_armhf.deb ... 505s Unpacking r-cran-magrittr (2.0.3-1) ... 505s Selecting previously unselected package r-cran-utf8. 505s Preparing to unpack .../62-r-cran-utf8_1.2.4-1_armhf.deb ... 505s Unpacking r-cran-utf8 (1.2.4-1) ... 505s Selecting previously unselected package r-cran-vctrs. 505s Preparing to unpack .../63-r-cran-vctrs_0.6.5-1_armhf.deb ... 505s Unpacking r-cran-vctrs (0.6.5-1) ... 505s Selecting previously unselected package r-cran-pillar. 505s Preparing to unpack .../64-r-cran-pillar_1.10.1+dfsg-1_all.deb ... 505s Unpacking r-cran-pillar (1.10.1+dfsg-1) ... 505s Selecting previously unselected package r-cran-r6. 505s Preparing to unpack .../65-r-cran-r6_2.6.1-1_all.deb ... 505s Unpacking r-cran-r6 (2.6.1-1) ... 505s Selecting previously unselected package r-cran-fansi. 505s Preparing to unpack .../66-r-cran-fansi_1.0.5-1_armhf.deb ... 505s Unpacking r-cran-fansi (1.0.5-1) ... 506s Selecting previously unselected package r-cran-pkgconfig. 506s Preparing to unpack .../67-r-cran-pkgconfig_2.0.3-2build1_all.deb ... 506s Unpacking r-cran-pkgconfig (2.0.3-2build1) ... 506s Selecting previously unselected package r-cran-tibble. 506s Preparing to unpack .../68-r-cran-tibble_3.2.1+dfsg-3_armhf.deb ... 506s Unpacking r-cran-tibble (3.2.1+dfsg-3) ... 506s Selecting previously unselected package r-cran-withr. 506s Preparing to unpack .../69-r-cran-withr_3.0.2+dfsg-1_all.deb ... 506s Unpacking r-cran-withr (3.0.2+dfsg-1) ... 506s Selecting previously unselected package r-cran-tidyselect. 506s Preparing to unpack .../70-r-cran-tidyselect_1.2.1+dfsg-1_armhf.deb ... 506s Unpacking r-cran-tidyselect (1.2.1+dfsg-1) ... 506s Selecting previously unselected package r-cran-dplyr. 506s Preparing to unpack .../71-r-cran-dplyr_1.1.4-4_armhf.deb ... 506s Unpacking r-cran-dplyr (1.1.4-4) ... 506s Selecting previously unselected package r-cran-purrr. 506s Preparing to unpack .../72-r-cran-purrr_1.0.4-1_armhf.deb ... 506s Unpacking r-cran-purrr (1.0.4-1) ... 506s Selecting previously unselected package r-cran-stringi. 506s Preparing to unpack .../73-r-cran-stringi_1.8.4-1build1_armhf.deb ... 506s Unpacking r-cran-stringi (1.8.4-1build1) ... 506s Selecting previously unselected package r-cran-stringr. 506s Preparing to unpack .../74-r-cran-stringr_1.5.1-1_all.deb ... 506s Unpacking r-cran-stringr (1.5.1-1) ... 506s Selecting previously unselected package r-cran-cpp11. 506s Preparing to unpack .../75-r-cran-cpp11_0.5.2-1_all.deb ... 506s Unpacking r-cran-cpp11 (0.5.2-1) ... 506s Selecting previously unselected package r-cran-tidyr. 506s Preparing to unpack .../76-r-cran-tidyr_1.3.1-1_armhf.deb ... 506s Unpacking r-cran-tidyr (1.3.1-1) ... 506s Selecting previously unselected package r-cran-broom. 506s Preparing to unpack .../77-r-cran-broom_1.0.7+dfsg-1_all.deb ... 506s Unpacking r-cran-broom (1.0.7+dfsg-1) ... 506s Selecting previously unselected package r-cran-colorspace. 506s Preparing to unpack .../78-r-cran-colorspace_2.1-1+dfsg-1_armhf.deb ... 506s Unpacking r-cran-colorspace (2.1-1+dfsg-1) ... 506s Selecting previously unselected package r-cran-farver. 506s Preparing to unpack .../79-r-cran-farver_2.1.2-1_armhf.deb ... 506s Unpacking r-cran-farver (2.1.2-1) ... 506s Selecting previously unselected package r-cran-mass. 506s Preparing to unpack .../80-r-cran-mass_7.3-64-1_armhf.deb ... 506s Unpacking r-cran-mass (7.3-64-1) ... 506s Selecting previously unselected package r-cran-geepack. 506s Preparing to unpack .../81-r-cran-geepack_1.3.12-1_armhf.deb ... 506s Unpacking r-cran-geepack (1.3.12-1) ... 506s Selecting previously unselected package r-cran-gtable. 506s Preparing to unpack .../82-r-cran-gtable_0.3.6+dfsg-1_all.deb ... 506s Unpacking r-cran-gtable 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(1.8.0-1) ... 507s Setting up r-cran-cli (3.6.4-1) ... 507s Setting up r-cran-lifecycle (1.0.4+dfsg-1) ... 507s Setting up libpcre2-16-0:armhf (10.45-1) ... 507s Setting up r-cran-pkgconfig (2.0.3-2build1) ... 507s Setting up libpcre2-32-0:armhf (10.45-1) ... 507s Setting up r-cran-utf8 (1.2.4-1) ... 507s Setting up libtirpc-dev:armhf (1.3.4+ds-1.3) ... 507s Setting up libpkgconf3:armhf (1.8.1-4) ... 507s Setting up r-cran-colorspace (2.1-1+dfsg-1) ... 507s Setting up rpcsvc-proto (1.4.2-0ubuntu7) ... 507s Setting up r-cran-stringi (1.8.4-1build1) ... 507s Setting up r-cran-cpp11 (0.5.2-1) ... 507s Setting up r-cran-rcolorbrewer (1.1-3-1build1) ... 507s Setting up r-cran-isoband (0.2.7-1) ... 507s Setting up libmpc3:armhf (1.3.1-1build2) ... 507s Setting up r-cran-gtable (0.3.6+dfsg-1) ... 507s Setting up r-cran-labeling (0.4.3-1) ... 507s Setting up icu-devtools (76.1-1ubuntu2) ... 507s Setting up pkgconf-bin (1.8.1-4) ... 507s Setting up r-cran-nlme (3.1.167-1) ... 507s Setting up r-cran-farver (2.1.2-1) ... 507s Setting up liblzma-dev:armhf (5.6.4-1) ... 507s Setting up libubsan1:armhf (15-20250222-0ubuntu1) ... 507s Setting up r-cran-mgcv (1.9-1-1) ... 507s Setting up libpcre2-posix3:armhf (10.45-1) ... 507s Setting up r-cran-viridislite (0.4.2-2) ... 507s Setting up libcrypt-dev:armhf (1:4.4.38-1) ... 507s Setting up libasan8:armhf (15-20250222-0ubuntu1) ... 507s Setting up r-cran-r6 (2.6.1-1) ... 507s Setting up libgcc-14-dev:armhf (14.2.0-17ubuntu3) ... 507s Setting up libisl23:armhf (0.27-1) ... 507s Setting up libc-dev-bin (2.41-1ubuntu2) ... 507s Setting up libdeflate-dev:armhf (1.23-1) ... 507s Setting up r-cran-magrittr (2.0.3-1) ... 507s Setting up libcc1-0:armhf (15-20250222-0ubuntu1) ... 507s Setting up r-cran-vctrs (0.6.5-1) ... 507s Setting up libblas-dev:armhf (3.12.1-2) ... 507s 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 507s Setting up dctrl-tools (2.24-3build3) ... 507s Setting up cpp-14-arm-linux-gnueabihf (14.2.0-17ubuntu3) ... 507s Setting up r-cran-pillar (1.10.1+dfsg-1) ... 507s Setting up libgfortran-14-dev:armhf (14.2.0-17ubuntu3) ... 507s Setting up r-cran-stringr (1.5.1-1) ... 507s Setting up r-cran-munsell (0.5.1-1) ... 507s Setting up r-cran-tibble (3.2.1+dfsg-3) ... 507s Setting up gcc-14-arm-linux-gnueabihf (14.2.0-17ubuntu3) ... 507s Setting up pkgconf:armhf (1.8.1-4) ... 507s Setting up r-cran-tidyselect (1.2.1+dfsg-1) ... 507s Setting up r-cran-scales (1.3.0-1) ... 507s Setting up liblapack-dev:armhf (3.12.1-2) ... 507s 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 507s Setting up r-cran-purrr (1.0.4-1) ... 507s Setting up cpp-14 (14.2.0-17ubuntu3) ... 507s Setting up libc6-dev:armhf (2.41-1ubuntu2) ... 507s Setting up r-cran-dplyr (1.1.4-4) ... 507s Setting up libstdc++-14-dev:armhf (14.2.0-17ubuntu3) ... 507s Setting up libicu-dev:armhf (76.1-1ubuntu2) ... 507s Setting up cpp-arm-linux-gnueabihf (4:14.2.0-1ubuntu1) ... 507s Setting up gfortran-14-arm-linux-gnueabihf (14.2.0-17ubuntu3) ... 507s Setting up libbz2-dev:armhf (1.0.8-6) ... 507s Setting up gcc-arm-linux-gnueabihf (4:14.2.0-1ubuntu1) ... 507s Setting up g++-14-arm-linux-gnueabihf (14.2.0-17ubuntu3) ... 507s Setting up libjpeg-turbo8-dev:armhf (2.1.5-3ubuntu2) ... 507s Setting up libncurses-dev:armhf (6.5+20250216-2) ... 507s Setting up libpcre2-dev:armhf (10.45-1) ... 507s Setting up r-cran-ggplot2 (3.5.1+dfsg-1) ... 507s Setting up libreadline-dev:armhf (8.2-6) ... 507s Setting up gcc-14 (14.2.0-17ubuntu3) ... 507s Setting up gfortran-arm-linux-gnueabihf (4:14.2.0-1ubuntu1) ... 507s Setting up r-cran-tidyr (1.3.1-1) ... 507s Setting up zlib1g-dev:armhf (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 507s Setting up cpp (4:14.2.0-1ubuntu1) ... 507s Setting up g++-14 (14.2.0-17ubuntu3) ... 507s Setting up libjpeg8-dev:armhf (8c-2ubuntu11) ... 507s Setting up gfortran-14 (14.2.0-17ubuntu3) ... 507s Setting up g++-arm-linux-gnueabihf (4:14.2.0-1ubuntu1) ... 507s Setting up libpng-dev:armhf (1.6.47-1) ... 507s Setting up libjpeg-dev:armhf (8c-2ubuntu11) ... 507s Setting up gcc (4:14.2.0-1ubuntu1) ... 507s Setting up r-cran-broom (1.0.7+dfsg-1) ... 507s Setting up g++ (4:14.2.0-1ubuntu1) ... 507s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 507s Setting up build-essential (12.10ubuntu1) ... 507s Setting up r-cran-geepack (1.3.12-1) ... 507s Setting up gfortran (4:14.2.0-1ubuntu1) ... 507s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode 507s 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 507s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode 507s 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 507s Setting up r-base-dev (4.4.3-1) ... 507s Setting up pkg-r-autopkgtest (20231212ubuntu1) ... 507s Processing triggers for libc-bin (2.41-1ubuntu2) ... 507s Processing triggers for man-db (2.13.0-1) ... 508s Processing triggers for install-info (7.1.1-1) ... 516s autopkgtest [16:14:14]: test pkg-r-autopkgtest: /usr/share/dh-r/pkg-r-autopkgtest 516s autopkgtest [16:14:14]: test pkg-r-autopkgtest: [----------------------- 518s Test: Try to load the R library etm 518s 518s R version 4.4.3 (2025-02-28) -- "Trophy Case" 518s Copyright (C) 2025 The R Foundation for Statistical Computing 518s Platform: arm-unknown-linux-gnueabihf (32-bit) 518s 518s R is free software and comes with ABSOLUTELY NO WARRANTY. 518s You are welcome to redistribute it under certain conditions. 518s Type 'license()' or 'licence()' for distribution details. 518s 518s R is a collaborative project with many contributors. 518s Type 'contributors()' for more information and 518s 'citation()' on how to cite R or R packages in publications. 518s 518s Type 'demo()' for some demos, 'help()' for on-line help, or 518s 'help.start()' for an HTML browser interface to help. 518s Type 'q()' to quit R. 518s 518s > library('etm') 519s > 519s > 519s Other tests are currently unsupported! 519s They will be progressively added. 520s autopkgtest [16:14:18]: test pkg-r-autopkgtest: -----------------------] 523s pkg-r-autopkgtest PASS 523s autopkgtest [16:14:21]: test pkg-r-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 527s autopkgtest [16:14:25]: @@@@@@@@@@@@@@@@@@@@ summary 527s run-unit-test PASS 527s pkg-r-autopkgtest PASS