0s autopkgtest [23:36:16]: starting date and time: 2026-02-09 23:36:16+0000 0s autopkgtest [23:36:16]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [23:36:16]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.eaqx39hb/out --timeout-copy=6000 --needs-internet=try --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:r-cran-ggplot2 --apt-upgrade r-cran-etm --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=r-cran-ggplot2/4.0.2+dfsg-1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-cpu2-ram4-disk20-arm64 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@sto01-arm64-1.secgroup --name adt-resolute-arm64-r-cran-etm-20260209-233616-juju-7f2275-prod-proposed-migration-environment-20-d698e0af-6e46-469e-8b37-df62d33cfe95 --image adt/ubuntu-resolute-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-autopkgtest-workers-arm64 -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 4s Creating nova instance adt-resolute-arm64-r-cran-etm-20260209-233616-juju-7f2275-prod-proposed-migration-environment-20-d698e0af-6e46-469e-8b37-df62d33cfe95 from image adt/ubuntu-resolute-arm64-server-20260209.img (UUID 793037ca-75af-461b-82de-f8081300b2e3)... 121s autopkgtest [23:38:17]: testbed dpkg architecture: arm64 121s autopkgtest [23:38:17]: testbed apt version: 3.1.15 122s autopkgtest [23:38:18]: @@@@@@@@@@@@@@@@@@@@ test bed setup 122s autopkgtest [23:38:18]: testbed release detected to be: None 123s autopkgtest [23:38:19]: updating testbed package index (apt update) 123s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 123s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 123s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 123s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 123s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [176 kB] 123s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [29.4 kB] 123s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [1645 kB] 126s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 Packages [246 kB] 126s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 c-n-f Metadata [6216 B] 126s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/restricted arm64 c-n-f Metadata [304 B] 126s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 Packages [1580 kB] 130s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 c-n-f Metadata [32.0 kB] 130s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse arm64 Packages [21.7 kB] 130s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse arm64 c-n-f Metadata [688 B] 132s Fetched 3862 kB in 7s (518 kB/s) 133s Reading package lists... 133s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 133s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 133s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 133s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 134s Reading package lists... 134s Reading package lists... 134s Building dependency tree... 134s Reading state information... 135s Calculating upgrade... 135s The following packages will be upgraded: 135s cryptsetup-bin dracut-install iproute2 iptables libcryptsetup12 libip4tc2 135s libip6tc2 libxtables12 wget 135s 9 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 135s Need to get 2534 kB of archives. 135s After this operation, 18.4 kB of additional disk space will be used. 135s Get:1 http://ftpmaster.internal/ubuntu resolute/main arm64 iptables arm64 1.8.11-2ubuntu3 [386 kB] 135s Get:2 http://ftpmaster.internal/ubuntu resolute/main arm64 libip4tc2 arm64 1.8.11-2ubuntu3 [24.3 kB] 135s Get:3 http://ftpmaster.internal/ubuntu resolute/main arm64 libip6tc2 arm64 1.8.11-2ubuntu3 [24.7 kB] 135s Get:4 http://ftpmaster.internal/ubuntu resolute/main arm64 libxtables12 arm64 1.8.11-2ubuntu3 [36.7 kB] 135s Get:5 http://ftpmaster.internal/ubuntu resolute/main arm64 iproute2 arm64 6.18.0-1ubuntu1 [1171 kB] 138s Get:6 http://ftpmaster.internal/ubuntu resolute/main arm64 libcryptsetup12 arm64 2:2.8.0-1ubuntu3 [274 kB] 138s Get:7 http://ftpmaster.internal/ubuntu resolute/main arm64 wget arm64 1.25.0-2ubuntu4 [344 kB] 138s Get:8 http://ftpmaster.internal/ubuntu resolute/main arm64 cryptsetup-bin arm64 2:2.8.0-1ubuntu3 [227 kB] 138s Get:9 http://ftpmaster.internal/ubuntu resolute/main arm64 dracut-install arm64 109-11ubuntu1 [45.3 kB] 138s dpkg-preconfigure: unable to re-open stdin: No such file or directory 138s Fetched 2534 kB in 2s (1027 kB/s) 138s (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 ... 136597 files and directories currently installed.) 138s Preparing to unpack .../0-iptables_1.8.11-2ubuntu3_arm64.deb ... 138s Unpacking iptables (1.8.11-2ubuntu3) over (1.8.11-2ubuntu2) ... 138s Preparing to unpack .../1-libip4tc2_1.8.11-2ubuntu3_arm64.deb ... 138s Unpacking libip4tc2:arm64 (1.8.11-2ubuntu3) over (1.8.11-2ubuntu2) ... 139s Preparing to unpack .../2-libip6tc2_1.8.11-2ubuntu3_arm64.deb ... 139s Unpacking libip6tc2:arm64 (1.8.11-2ubuntu3) over (1.8.11-2ubuntu2) ... 139s Preparing to unpack .../3-libxtables12_1.8.11-2ubuntu3_arm64.deb ... 139s Unpacking libxtables12:arm64 (1.8.11-2ubuntu3) over (1.8.11-2ubuntu2) ... 139s Preparing to unpack .../4-iproute2_6.18.0-1ubuntu1_arm64.deb ... 139s Unpacking iproute2 (6.18.0-1ubuntu1) over (6.16.0-1ubuntu3) ... 139s Preparing to unpack .../5-libcryptsetup12_2%3a2.8.0-1ubuntu3_arm64.deb ... 139s Unpacking libcryptsetup12:arm64 (2:2.8.0-1ubuntu3) over (2:2.8.0-1ubuntu2) ... 139s Preparing to unpack .../6-wget_1.25.0-2ubuntu4_arm64.deb ... 139s Unpacking wget (1.25.0-2ubuntu4) over (1.25.0-2ubuntu3) ... 139s Preparing to unpack .../7-cryptsetup-bin_2%3a2.8.0-1ubuntu3_arm64.deb ... 139s Unpacking cryptsetup-bin (2:2.8.0-1ubuntu3) over (2:2.8.0-1ubuntu2) ... 139s Preparing to unpack .../8-dracut-install_109-11ubuntu1_arm64.deb ... 139s Unpacking dracut-install (109-11ubuntu1) over (109-9ubuntu1) ... 139s Setting up libip4tc2:arm64 (1.8.11-2ubuntu3) ... 139s Setting up wget (1.25.0-2ubuntu4) ... 139s Setting up libip6tc2:arm64 (1.8.11-2ubuntu3) ... 139s Setting up libxtables12:arm64 (1.8.11-2ubuntu3) ... 139s Setting up dracut-install (109-11ubuntu1) ... 139s Setting up libcryptsetup12:arm64 (2:2.8.0-1ubuntu3) ... 139s Setting up cryptsetup-bin (2:2.8.0-1ubuntu3) ... 139s Setting up iptables (1.8.11-2ubuntu3) ... 139s Setting up iproute2 (6.18.0-1ubuntu1) ... 140s Processing triggers for man-db (2.13.1-1build1) ... 141s Processing triggers for install-info (7.2-5) ... 141s Processing triggers for libc-bin (2.42-2ubuntu4) ... 141s autopkgtest [23:38:37]: upgrading testbed (apt dist-upgrade and autopurge) 141s Reading package lists... 141s Building dependency tree... 141s Reading state information... 142s Calculating upgrade... 142s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 142s Reading package lists... 142s Building dependency tree... 142s Reading state information... 143s Solving dependencies... 143s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 145s autopkgtest [23:38:41]: testbed running kernel: Linux 6.19.0-3-generic #3-Ubuntu SMP PREEMPT_DYNAMIC Fri Jan 23 19:46:27 UTC 2026 146s autopkgtest [23:38:42]: @@@@@@@@@@@@@@@@@@@@ apt-source r-cran-etm 147s Get:1 http://ftpmaster.internal/ubuntu resolute/universe r-cran-etm 1.1.1-1build1 (dsc) [2147 B] 147s Get:2 http://ftpmaster.internal/ubuntu resolute/universe r-cran-etm 1.1.1-1build1 (tar) [242 kB] 147s Get:3 http://ftpmaster.internal/ubuntu resolute/universe r-cran-etm 1.1.1-1build1 (diff) [3672 B] 147s gpgv: Signature made Fri Nov 28 21:46:53 2025 UTC 147s gpgv: using RSA key 92FE4F8B40CADC4ECCD60C1F5961FDBE9C619809 147s gpgv: Can't check signature: No public key 147s dpkg-source: warning: cannot verify inline signature for ./r-cran-etm_1.1.1-1build1.dsc: no acceptable signature found 147s autopkgtest [23:38:43]: testing package r-cran-etm version 1.1.1-1build1 147s autopkgtest [23:38:43]: build not needed 149s autopkgtest [23:38:45]: test run-unit-test: preparing testbed 149s Reading package lists... 149s Building dependency tree... 149s Reading state information... 150s Solving dependencies... 150s The following NEW packages will be installed: 150s fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono libblas3 150s libcairo2 libdatrie1 libdeflate0 libfontconfig1 libgfortran5 libgomp1 150s libgraphite2-3 libharfbuzz0b libice6 libjbig0 libjpeg-turbo8 libjpeg8 150s liblapack3 liblerc4 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 150s libpaper-utils libpaper2 libpixman-1-0 libsharpyuv0 libsm6 libtcl8.6 150s libthai-data libthai0 libtiff6 libtk8.6 libwebp7 libxcb-render0 libxcb-shm0 150s libxft2 libxrender1 libxss1 libxt6t64 r-base-core r-cran-data.table 150s r-cran-dbi r-cran-etm r-cran-kmi r-cran-lattice r-cran-littler r-cran-matrix 150s r-cran-mitools r-cran-pkgkitten r-cran-rcpp r-cran-rcpparmadillo 150s r-cran-survival unzip x11-common xdg-utils zip 150s 0 upgraded, 56 newly installed, 0 to remove and 0 not upgraded. 150s Need to get 59.3 MB of archives. 150s After this operation, 125 MB of additional disk space will be used. 150s Get:1 http://ftpmaster.internal/ubuntu resolute/main arm64 fonts-dejavu-mono all 2.37-8build1 [502 kB] 150s Get:2 http://ftpmaster.internal/ubuntu resolute/main arm64 fonts-dejavu-core all 2.37-8build1 [834 kB] 152s Get:3 http://ftpmaster.internal/ubuntu resolute/main arm64 fontconfig-config arm64 2.17.1-3ubuntu1 [38.5 kB] 152s Get:4 http://ftpmaster.internal/ubuntu resolute/main arm64 libfontconfig1 arm64 2.17.1-3ubuntu1 [144 kB] 152s Get:5 http://ftpmaster.internal/ubuntu resolute/main arm64 fontconfig arm64 2.17.1-3ubuntu1 [181 kB] 152s Get:6 http://ftpmaster.internal/ubuntu resolute/main arm64 libblas3 arm64 3.12.1-7ubuntu1 [181 kB] 152s Get:7 http://ftpmaster.internal/ubuntu resolute/main arm64 libpixman-1-0 arm64 0.46.4-1 [204 kB] 152s Get:8 http://ftpmaster.internal/ubuntu resolute/main arm64 libxcb-render0 arm64 1.17.0-2ubuntu1 [16.4 kB] 152s Get:9 http://ftpmaster.internal/ubuntu resolute/main arm64 libxcb-shm0 arm64 1.17.0-2ubuntu1 [5938 B] 152s Get:10 http://ftpmaster.internal/ubuntu resolute/main arm64 libxrender1 arm64 1:0.9.12-1 [19.5 kB] 152s Get:11 http://ftpmaster.internal/ubuntu resolute/main arm64 libcairo2 arm64 1.18.4-3 [556 kB] 154s Get:12 http://ftpmaster.internal/ubuntu resolute/main arm64 libdatrie1 arm64 0.2.14-1 [19.6 kB] 154s Get:13 http://ftpmaster.internal/ubuntu resolute/main arm64 libdeflate0 arm64 1.23-2build1 [46.8 kB] 154s Get:14 http://ftpmaster.internal/ubuntu resolute/main arm64 libgfortran5 arm64 15.2.0-12ubuntu1 [451 kB] 154s Get:15 http://ftpmaster.internal/ubuntu resolute/main arm64 libgomp1 arm64 15.2.0-12ubuntu1 [147 kB] 154s Get:16 http://ftpmaster.internal/ubuntu resolute/main arm64 libgraphite2-3 arm64 1.3.14-11ubuntu1 [72.1 kB] 154s Get:17 http://ftpmaster.internal/ubuntu resolute/main arm64 libharfbuzz0b arm64 12.3.2-1 [510 kB] 154s Get:18 http://ftpmaster.internal/ubuntu resolute/main arm64 x11-common all 1:7.7+24ubuntu1 [22.4 kB] 154s Get:19 http://ftpmaster.internal/ubuntu resolute/main arm64 libice6 arm64 2:1.1.1-1build1 [43.0 kB] 154s Get:20 http://ftpmaster.internal/ubuntu resolute/main arm64 libjpeg-turbo8 arm64 2.1.5-4ubuntu3 [161 kB] 154s Get:21 http://ftpmaster.internal/ubuntu resolute/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 154s Get:22 http://ftpmaster.internal/ubuntu resolute/main arm64 liblapack3 arm64 3.12.1-7ubuntu1 [2299 kB] 159s Get:23 http://ftpmaster.internal/ubuntu resolute/main arm64 liblerc4 arm64 4.0.0+ds-5ubuntu2 [174 kB] 159s Get:24 http://ftpmaster.internal/ubuntu resolute/main arm64 libthai-data all 0.1.30-1 [155 kB] 159s Get:25 http://ftpmaster.internal/ubuntu resolute/main arm64 libthai0 arm64 0.1.30-1 [18.3 kB] 159s Get:26 http://ftpmaster.internal/ubuntu resolute/main arm64 libpango-1.0-0 arm64 1.57.0-1 [238 kB] 159s Get:27 http://ftpmaster.internal/ubuntu resolute/main arm64 libpangoft2-1.0-0 arm64 1.57.0-1 [51.5 kB] 159s Get:28 http://ftpmaster.internal/ubuntu resolute/main arm64 libpangocairo-1.0-0 arm64 1.57.0-1 [27.9 kB] 159s Get:29 http://ftpmaster.internal/ubuntu resolute/main arm64 libpaper2 arm64 2.2.5-0.3build1 [17.3 kB] 159s Get:30 http://ftpmaster.internal/ubuntu resolute/main arm64 libpaper-utils arm64 2.2.5-0.3build1 [15.4 kB] 159s Get:31 http://ftpmaster.internal/ubuntu resolute/main arm64 libsharpyuv0 arm64 1.5.0-0.1build1 [16.7 kB] 159s Get:32 http://ftpmaster.internal/ubuntu resolute/main arm64 libsm6 arm64 2:1.2.6-1build1 [16.8 kB] 159s Get:33 http://ftpmaster.internal/ubuntu resolute/main arm64 libtcl8.6 arm64 8.6.17+dfsg-1build1 [983 kB] 161s Get:34 http://ftpmaster.internal/ubuntu resolute/main arm64 libjbig0 arm64 2.1-6.1ubuntu3 [29.2 kB] 161s Get:35 http://ftpmaster.internal/ubuntu resolute/main arm64 libwebp7 arm64 1.5.0-0.1build1 [205 kB] 161s Get:36 http://ftpmaster.internal/ubuntu resolute/main arm64 libtiff6 arm64 4.7.0-3ubuntu3 [196 kB] 161s Get:37 http://ftpmaster.internal/ubuntu resolute/main arm64 libxft2 arm64 2.3.6-1build2 [43.2 kB] 161s Get:38 http://ftpmaster.internal/ubuntu resolute/main arm64 libxss1 arm64 1:1.2.3-1build4 [7102 B] 161s Get:39 http://ftpmaster.internal/ubuntu resolute/main arm64 libtk8.6 arm64 8.6.17-1 [811 kB] 162s Get:40 http://ftpmaster.internal/ubuntu resolute/main arm64 libxt6t64 arm64 1:1.2.1-1.3 [168 kB] 162s Get:41 http://ftpmaster.internal/ubuntu resolute/main arm64 zip arm64 3.0-15ubuntu3 [170 kB] 162s Get:42 http://ftpmaster.internal/ubuntu resolute/main arm64 unzip arm64 6.0-29ubuntu1 [176 kB] 162s Get:43 http://ftpmaster.internal/ubuntu resolute/main arm64 xdg-utils all 1.2.1-2ubuntu2 [66.1 kB] 162s Get:44 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-base-core arm64 4.5.2-1ubuntu2 [28.6 MB] 215s Get:45 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-data.table arm64 1.17.0+dfsg-1 [2129 kB] 218s Get:46 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-dbi all 1.2.3-1build1 [855 kB] 220s Get:47 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-lattice arm64 0.22-7-1 [1365 kB] 222s Get:48 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-matrix arm64 1.7-4-1 [4146 kB] 229s Get:49 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-survival arm64 3.8-6-1 [8270 kB] 243s Get:50 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-littler arm64 0.3.22-1 [85.1 kB] 243s Get:51 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-pkgkitten all 0.2.4-1 [27.2 kB] 243s Get:52 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-rcpp arm64 1.1.0-1 [2011 kB] 247s Get:53 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-rcpparmadillo arm64 15.2.3-1-1 [916 kB] 248s Get:54 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-etm arm64 1.1.1-1build1 [478 kB] 249s Get:55 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-mitools all 2.4-2build2 [266 kB] 249s Get:56 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-kmi all 0.5.5-2build2 [78.9 kB] 250s Preconfiguring packages ... 250s Fetched 59.3 MB in 1min 39s (598 kB/s) 250s Selecting previously unselected package fonts-dejavu-mono. 250s (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 ... 136600 files and directories currently installed.) 250s Preparing to unpack .../00-fonts-dejavu-mono_2.37-8build1_all.deb ... 250s Unpacking fonts-dejavu-mono (2.37-8build1) ... 250s Selecting previously unselected package fonts-dejavu-core. 250s Preparing to unpack .../01-fonts-dejavu-core_2.37-8build1_all.deb ... 250s Unpacking fonts-dejavu-core (2.37-8build1) ... 250s Selecting previously unselected package fontconfig-config. 250s Preparing to unpack .../02-fontconfig-config_2.17.1-3ubuntu1_arm64.deb ... 250s Unpacking fontconfig-config (2.17.1-3ubuntu1) ... 250s Selecting previously unselected package libfontconfig1:arm64. 250s Preparing to unpack .../03-libfontconfig1_2.17.1-3ubuntu1_arm64.deb ... 250s Unpacking libfontconfig1:arm64 (2.17.1-3ubuntu1) ... 250s Selecting previously unselected package fontconfig. 250s Preparing to unpack .../04-fontconfig_2.17.1-3ubuntu1_arm64.deb ... 250s Unpacking fontconfig (2.17.1-3ubuntu1) ... 250s Selecting previously unselected package libblas3:arm64. 250s Preparing to unpack .../05-libblas3_3.12.1-7ubuntu1_arm64.deb ... 250s Unpacking libblas3:arm64 (3.12.1-7ubuntu1) ... 250s Selecting previously unselected package libpixman-1-0:arm64. 250s Preparing to unpack .../06-libpixman-1-0_0.46.4-1_arm64.deb ... 250s Unpacking libpixman-1-0:arm64 (0.46.4-1) ... 250s Selecting previously unselected package libxcb-render0:arm64. 250s Preparing to unpack .../07-libxcb-render0_1.17.0-2ubuntu1_arm64.deb ... 250s Unpacking libxcb-render0:arm64 (1.17.0-2ubuntu1) ... 250s Selecting previously unselected package libxcb-shm0:arm64. 250s Preparing to unpack .../08-libxcb-shm0_1.17.0-2ubuntu1_arm64.deb ... 250s Unpacking libxcb-shm0:arm64 (1.17.0-2ubuntu1) ... 250s Selecting previously unselected package libxrender1:arm64. 250s Preparing to unpack .../09-libxrender1_1%3a0.9.12-1_arm64.deb ... 250s Unpacking libxrender1:arm64 (1:0.9.12-1) ... 250s Selecting previously unselected package libcairo2:arm64. 250s Preparing to unpack .../10-libcairo2_1.18.4-3_arm64.deb ... 250s Unpacking libcairo2:arm64 (1.18.4-3) ... 250s Selecting previously unselected package libdatrie1:arm64. 251s Preparing to unpack .../11-libdatrie1_0.2.14-1_arm64.deb ... 251s Unpacking libdatrie1:arm64 (0.2.14-1) ... 251s Selecting previously unselected package libdeflate0:arm64. 251s Preparing to unpack .../12-libdeflate0_1.23-2build1_arm64.deb ... 251s Unpacking libdeflate0:arm64 (1.23-2build1) ... 251s Selecting previously unselected package libgfortran5:arm64. 251s Preparing to unpack .../13-libgfortran5_15.2.0-12ubuntu1_arm64.deb ... 251s Unpacking libgfortran5:arm64 (15.2.0-12ubuntu1) ... 251s Selecting previously unselected package libgomp1:arm64. 251s Preparing to unpack .../14-libgomp1_15.2.0-12ubuntu1_arm64.deb ... 251s Unpacking libgomp1:arm64 (15.2.0-12ubuntu1) ... 251s Selecting previously unselected package libgraphite2-3:arm64. 251s Preparing to unpack .../15-libgraphite2-3_1.3.14-11ubuntu1_arm64.deb ... 251s Unpacking libgraphite2-3:arm64 (1.3.14-11ubuntu1) ... 251s Selecting previously unselected package libharfbuzz0b:arm64. 251s Preparing to unpack .../16-libharfbuzz0b_12.3.2-1_arm64.deb ... 251s Unpacking libharfbuzz0b:arm64 (12.3.2-1) ... 251s Selecting previously unselected package x11-common. 251s Preparing to unpack .../17-x11-common_1%3a7.7+24ubuntu1_all.deb ... 251s Unpacking x11-common (1:7.7+24ubuntu1) ... 251s Selecting previously unselected package libice6:arm64. 251s Preparing to unpack .../18-libice6_2%3a1.1.1-1build1_arm64.deb ... 251s Unpacking libice6:arm64 (2:1.1.1-1build1) ... 251s Selecting previously unselected package libjpeg-turbo8:arm64. 251s Preparing to unpack .../19-libjpeg-turbo8_2.1.5-4ubuntu3_arm64.deb ... 251s Unpacking libjpeg-turbo8:arm64 (2.1.5-4ubuntu3) ... 251s Selecting previously unselected package libjpeg8:arm64. 251s Preparing to unpack .../20-libjpeg8_8c-2ubuntu11_arm64.deb ... 251s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 251s Selecting previously unselected package liblapack3:arm64. 251s Preparing to unpack .../21-liblapack3_3.12.1-7ubuntu1_arm64.deb ... 251s Unpacking liblapack3:arm64 (3.12.1-7ubuntu1) ... 251s Selecting previously unselected package liblerc4:arm64. 251s Preparing to unpack .../22-liblerc4_4.0.0+ds-5ubuntu2_arm64.deb ... 251s Unpacking liblerc4:arm64 (4.0.0+ds-5ubuntu2) ... 251s Selecting previously unselected package libthai-data. 251s Preparing to unpack .../23-libthai-data_0.1.30-1_all.deb ... 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r-cran-rcpparmadillo (15.2.3-1-1) ... 256s Setting up r-cran-mitools (2.4-2build2) ... 256s Setting up r-cran-survival (3.8-6-1) ... 256s Setting up r-cran-kmi (0.5.5-2build2) ... 256s Setting up r-cran-etm (1.1.1-1build1) ... 256s Processing triggers for man-db (2.13.1-1build1) ... 257s Processing triggers for install-info (7.2-5) ... 257s Processing triggers for libc-bin (2.42-2ubuntu4) ... 258s autopkgtest [23:40:34]: test run-unit-test: [----------------------- 258s BEGIN TEST test.etmCIF.R 258s 258s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 258s Copyright (C) 2025 The R Foundation for Statistical Computing 258s Platform: aarch64-unknown-linux-gnu 258s 258s R is free software and comes with ABSOLUTELY NO WARRANTY. 258s You are welcome to redistribute it under certain conditions. 258s Type 'license()' or 'licence()' for distribution details. 258s 258s R is a collaborative project with many contributors. 258s Type 'contributors()' for more information and 258s 'citation()' on how to cite R or R packages in publications. 258s 258s Type 'demo()' for some demos, 'help()' for on-line help, or 258s 'help.start()' for an HTML browser interface to help. 258s Type 'q()' to quit R. 258s 258s > ### test file for etmCIF. 258s > ### Really simple tests and comparison with etm 258s > 258s > old <- options(digits = 5) 258s > 258s > require(etm) 258s Loading required package: etm 259s > 259s > if (!require(survival, quietly = TRUE)) { 259s + print("The following tests require the 'survival' package") 259s + } else { 259s + 259s + data(abortion) 259s + 259s + from <- rep(0, nrow(abortion)) 259s + to <- abortion$cause 259s + entry <- abortion$entry 259s + exit <- abortion$exit 259s + id <- 1:nrow(abortion) 259s + data <- data.frame(id, from, to, entry, exit, group = abortion$group) 259s + 259s + ## Computation of the CIFs with etm 259s + tra <- matrix(FALSE, 4, 4) 259s + tra[1, 2:4] <- TRUE 259s + 259s + cif.control <- etm(data[data$group == 0, ], c("0", "1", "2", "3"), 259s + tra, NULL, 0) 259s + cif.exposed <- etm(data[data$group == 1, ], c("0", "1", "2", "3"), 259s + tra, NULL, 0) 259s + 259s + 259s + ## Computation of the CIFs with etmCIF 259s + netm <- etmCIF(Surv(entry, exit, cause != 0) ~ group, abortion, 259s + etype = cause, failcode = 3) 259s + 259s + ### let's do some comparisons :-) 259s + 259s + all.equal(trprob(cif.control, "0 3"), netm[[1]]$est["0", "3", ]) 259s + all.equal(trprob(cif.control, "0 2"), netm[[1]]$est["0", "2", ]) 259s + all.equal(trprob(cif.control, "0 1"), netm[[1]]$est["0", "1", ]) 259s + 259s + all.equal(trprob(cif.exposed, "0 3"), netm[[2]]$est["0", "3", ]) 259s + all.equal(trprob(cif.exposed, "0 2"), netm[[2]]$est["0", "2", ]) 259s + all.equal(trprob(cif.exposed, "0 1"), netm[[2]]$est["0", "1", ]) 259s + 259s + 259s + all.equal(trcov(cif.control, "0 3"), netm[[1]]$cov["0 3", "0 3", ]) 259s + all.equal(trcov(cif.control, "0 2"), netm[[1]]$cov["0 2", "0 2", ]) 259s + all.equal(trcov(cif.control, "0 1"), netm[[1]]$cov["0 1", "0 1", ]) 259s + 259s + all.equal(trcov(cif.exposed, "0 3"), netm[[2]]$cov["0 3", "0 3", ]) 259s + all.equal(trcov(cif.exposed, "0 2"), netm[[2]]$cov["0 2", "0 2", ]) 259s + all.equal(trcov(cif.exposed, "0 1"), netm[[2]]$cov["0 1", "0 1", ]) 259s + 259s + 259s + netm 259s + 259s + ## test on the summary 259s + snetm <- summary(netm) 259s + 259s + snetm 259s + 259s + all.equal(unname(trprob(cif.control, "0 3")), snetm[[1]][[3]]$P) 259s + all.equal(unname(trprob(cif.control, "0 2")), snetm[[1]][[2]]$P) 259s + all.equal(unname(trprob(cif.control, "0 1")), snetm[[1]][[1]]$P) 259s + 259s + all.equal(unname(trprob(cif.exposed, "0 3")), snetm[[2]][[3]]$P) 259s + all.equal(unname(trprob(cif.exposed, "0 2")), snetm[[2]][[2]]$P) 259s + all.equal(unname(trprob(cif.exposed, "0 1")), snetm[[2]][[1]]$P) 259s + 259s + scif.control <- summary(cif.control, ci.fun = "cloglog") 259s + scif.exposed <- summary(cif.exposed, ci.fun = "cloglog") 259s + 259s + all.equal(scif.control[[4]]$lower, snetm[[1]][[3]]$lower) 259s + all.equal(scif.control[[4]]$upper, snetm[[1]][[3]]$upper) 259s + 259s + all.equal(scif.exposed[[4]]$lower, snetm[[2]][[3]]$lower) 259s + all.equal(scif.exposed[[4]]$upper, snetm[[2]][[3]]$upper) 259s + } 260s [1] TRUE 260s > 260s > ### test with factors in the input 260s > abortion$status <- with(abortion, ifelse(cause == 2, "life birth", 260s + ifelse(cause == 1, "ETOP", "spontaneous abortion"))) 260s > 260s > abortion$status <- factor(abortion$status) 260s > 260s > netm.factor <- etmCIF(Surv(entry, exit, status != "cens") ~ group, abortion, 260s + etype = status, failcode = "spontaneous abortion") 260s > 260s > 260s > all.equal(trprob(cif.control, "0 3"), netm.factor[[1]]$est["0", "spontaneous abortion", ]) 260s [1] TRUE 260s > all.equal(trprob(cif.control, "0 2"), netm.factor[[1]]$est["0", "life birth", ]) 260s [1] TRUE 260s > 260s > netm.factor 260s Call: etmCIF(formula = Surv(entry, exit, status != "cens") ~ group, 260s data = abortion, etype = status, failcode = "spontaneous abortion") 260s 260s Covariate: group 260s levels: 0 1 260s 260s 260s group = 0 260s time P se(P) n.event 260s CIF ETOP 43 0.040159 0.0092578 20 260s CIF life birth 43 0.799059 0.0221865 924 260s CIF spontaneous abortion 43 0.160781 0.0213261 69 260s 260s group = 1 260s time P se(P) n.event 260s CIF ETOP 42 0.28511 0.042493 38 260s CIF life birth 42 0.35257 0.042139 92 260s CIF spontaneous abortion 42 0.36232 0.049473 43 260s > 260s > summary(netm.factor) 260s 260s group=0 260s 260s CIF ETOP 260s P time var lower upper n.risk n.event 260s 0.000000 6 0.0000e+00 0.000000 0.000000 117 0 260s 0.038955 13 8.4440e-05 0.024488 0.061694 645 1 260s 0.040159 26 8.5707e-05 0.025513 0.062939 846 0 260s 0.040159 36 8.5707e-05 0.025513 0.062939 876 0 260s 0.040159 40 8.5707e-05 0.025513 0.062939 554 0 260s 0.040159 43 8.5707e-05 0.025513 0.062939 6 0 260s 260s CIF life birth 260s P time var lower upper n.risk n.event 260s 0.000000 6 0.0000e+00 0.000000 0.000000 117 0 260s 0.000000 13 0.0000e+00 0.000000 0.000000 645 0 260s 0.000000 26 0.0000e+00 0.000000 0.000000 846 0 260s 0.053197 36 4.6195e-05 0.041379 0.068268 876 25 260s 0.563121 40 3.8801e-04 0.524924 0.602021 554 280 260s 0.799059 43 4.9224e-04 0.753969 0.840613 6 6 260s 260s CIF spontaneous abortion 260s P time var lower upper n.risk n.event 260s 0.034188 6 0.00028222 0.01297 0.088523 117 4 260s 0.150468 13 0.00045513 0.11360 0.197901 645 1 260s 0.159904 26 0.00045498 0.12274 0.206925 846 1 260s 0.160781 36 0.00045480 0.12360 0.207757 876 1 260s 0.160781 40 0.00045480 0.12360 0.207757 554 0 260s 0.160781 43 0.00045480 0.12360 0.207757 6 0 260s 260s 260s group=1 260s 260s CIF ETOP 260s P time var lower upper n.risk n.event 260s 0.00000 6 0.0000000 0.00000 0.00000 35 0 260s 0.26048 13 0.0017854 0.18795 0.35425 90 0 260s 0.28115 21 0.0018028 0.20742 0.37423 93 1 260s 0.28511 34 0.0018057 0.21116 0.37806 89 0 260s 0.28511 39 0.0018057 0.21116 0.37806 59 0 260s 0.28511 42 0.0018057 0.21116 0.37806 6 0 260s 260s CIF life birth 260s P time var lower upper n.risk n.event 260s 0.000000 6 0.0000e+00 0.000000 0.000000 35 0 260s 0.000000 13 0.0000e+00 0.000000 0.000000 90 0 260s 0.000000 21 0.0000e+00 0.000000 0.000000 93 0 260s 0.023073 34 9.0514e-05 0.010252 0.051504 89 2 260s 0.180156 39 8.0126e-04 0.131765 0.243663 59 13 260s 0.352565 42 1.7757e-03 0.276882 0.441775 6 6 260s 260s CIF spontaneous abortion 260s P time var lower upper n.risk n.event 260s 0.057143 6 0.0015394 0.014605 0.20968 35 2 260s 0.333246 13 0.0025280 0.245337 0.44216 90 4 260s 0.350702 21 0.0024827 0.262769 0.45762 93 0 260s 0.358492 34 0.0024593 0.270627 0.46448 89 0 260s 0.358492 39 0.0024593 0.270627 0.46448 59 0 260s 0.362323 42 0.0024476 0.274499 0.46785 6 0 260s 260s > 260s > ### test with group as a character vector 260s > abortion$ttt <- with(abortion, ifelse(group == 0, "control", "exposed")) 260s > abortion$ttt <- factor(abortion$ttt) 260s > 260s > netm.ttt <- etmCIF(Surv(entry, exit, status != "cens") ~ ttt, abortion, 260s + etype = status, failcode = "spontaneous abortion") 260s > 260s > all.equal(trprob(cif.control, "0 3"), netm.ttt[[1]]$est["0", "spontaneous abortion", ]) 260s [1] TRUE 260s > all.equal(trprob(cif.control, "0 2"), netm.ttt[[1]]$est["0", "life birth", ]) 260s [1] TRUE 260s > 260s > netm.ttt 260s Call: etmCIF(formula = Surv(entry, exit, status != "cens") ~ ttt, data = abortion, 260s etype = status, failcode = "spontaneous abortion") 260s 260s Covariate: ttt 260s levels: control exposed 260s 260s 260s ttt = control 260s time P se(P) n.event 260s CIF ETOP 43 0.040159 0.0092578 20 260s CIF life birth 43 0.799059 0.0221865 924 260s CIF spontaneous abortion 43 0.160781 0.0213261 69 260s 260s ttt = exposed 260s time P se(P) n.event 260s CIF ETOP 42 0.28511 0.042493 38 260s CIF life birth 42 0.35257 0.042139 92 260s CIF spontaneous abortion 42 0.36232 0.049473 43 260s > 260s > summary(netm.ttt) 260s 260s ttt=control 260s 260s CIF ETOP 260s P time var lower upper n.risk n.event 260s 0.000000 6 0.0000e+00 0.000000 0.000000 117 0 260s 0.038955 13 8.4440e-05 0.024488 0.061694 645 1 260s 0.040159 26 8.5707e-05 0.025513 0.062939 846 0 260s 0.040159 36 8.5707e-05 0.025513 0.062939 876 0 260s 0.040159 40 8.5707e-05 0.025513 0.062939 554 0 260s 0.040159 43 8.5707e-05 0.025513 0.062939 6 0 260s 260s CIF life birth 260s P time var lower upper n.risk n.event 260s 0.000000 6 0.0000e+00 0.000000 0.000000 117 0 260s 0.000000 13 0.0000e+00 0.000000 0.000000 645 0 260s 0.000000 26 0.0000e+00 0.000000 0.000000 846 0 260s 0.053197 36 4.6195e-05 0.041379 0.068268 876 25 260s 0.563121 40 3.8801e-04 0.524924 0.602021 554 280 260s 0.799059 43 4.9224e-04 0.753969 0.840613 6 6 260s 260s CIF spontaneous abortion 260s P time var lower upper n.risk n.event 260s 0.034188 6 0.00028222 0.01297 0.088523 117 4 260s 0.150468 13 0.00045513 0.11360 0.197901 645 1 260s 0.159904 26 0.00045498 0.12274 0.206925 846 1 260s 0.160781 36 0.00045480 0.12360 0.207757 876 1 260s 0.160781 40 0.00045480 0.12360 0.207757 554 0 260s 0.160781 43 0.00045480 0.12360 0.207757 6 0 260s 260s 260s ttt=exposed 260s 260s CIF ETOP 260s P time var lower upper n.risk n.event 260s 0.00000 6 0.0000000 0.00000 0.00000 35 0 260s 0.26048 13 0.0017854 0.18795 0.35425 90 0 260s 0.28115 21 0.0018028 0.20742 0.37423 93 1 260s 0.28511 34 0.0018057 0.21116 0.37806 89 0 260s 0.28511 39 0.0018057 0.21116 0.37806 59 0 260s 0.28511 42 0.0018057 0.21116 0.37806 6 0 260s 260s CIF life birth 260s P time var lower upper n.risk n.event 260s 0.000000 6 0.0000e+00 0.000000 0.000000 35 0 260s 0.000000 13 0.0000e+00 0.000000 0.000000 90 0 260s 0.000000 21 0.0000e+00 0.000000 0.000000 93 0 260s 0.023073 34 9.0514e-05 0.010252 0.051504 89 2 260s 0.180156 39 8.0126e-04 0.131765 0.243663 59 13 260s 0.352565 42 1.7757e-03 0.276882 0.441775 6 6 260s 260s CIF spontaneous abortion 260s P time var lower upper n.risk n.event 260s 0.057143 6 0.0015394 0.014605 0.20968 35 2 260s 0.333246 13 0.0025280 0.245337 0.44216 90 4 260s 0.350702 21 0.0024827 0.262769 0.45762 93 0 260s 0.358492 34 0.0024593 0.270627 0.46448 89 0 260s 0.358492 39 0.0024593 0.270627 0.46448 59 0 260s 0.362323 42 0.0024476 0.274499 0.46785 6 0 260s 260s > 260s > 260s > ### A couple of comparisons with simulated data 260s > set.seed(1313) 260s > time <- rexp(100) 260s > to <- rbinom(100, 2, prob = c(1/3, 1/3, 1/3)) 260s > from <- rep(11, 100) 260s > id <- 1:100 260s > cov <- rbinom(100, 1, 0.5) 260s > 260s > dat.s <- data.frame(id, time, from, to, cov) 260s > 260s > traa <- matrix(FALSE, 3, 3) 260s > traa[1, 2:3] <- TRUE 260s > 260s > aa0 <- etm(dat.s[dat.s$cov == 0, ], c("11", "1", "2"), traa, "0", 0) 260s > aa1 <- etm(dat.s[dat.s$cov == 1, ], c("11", "1", "2"), traa, "0", 0) 260s > aa <- etm(dat.s, c("11", "1", "2"), traa, "0", 0) 260s > 260s > test <- etmCIF(Surv(time, to != 0) ~ 1, dat.s, etype = to) 260s > 260s > test.c <- etmCIF(Surv(time, to != 0) ~ cov, dat.s, etype = to) 260s > 260s > all.equal(trprob(aa, "11 1"), test[[1]]$est["0", "1", ]) 260s [1] TRUE 260s > all.equal(trprob(aa, "11 2"), test[[1]]$est["0", "2", ]) 260s [1] TRUE 260s > 260s > all.equal(trprob(aa0, "11 1"), test.c[[1]]$est["0", "1", ]) 260s [1] TRUE 260s > all.equal(trprob(aa0, "11 2"), test.c[[1]]$est["0", "2", ]) 260s [1] TRUE 260s > 260s > all.equal(trprob(aa1, "11 1"), test.c[[2]]$est["0", "1", ]) 260s [1] TRUE 260s > all.equal(trprob(aa1, "11 2"), test.c[[2]]$est["0", "2", ]) 260s [1] TRUE 260s > 260s > test 260s Call: etmCIF(formula = Surv(time, to != 0) ~ 1, data = dat.s, etype = to) 260s 260s time P se(P) n.event 260s CIF 1 4.9088 0.809108 0.079680 45 260s CIF 2 4.9088 0.096618 0.032905 8 260s > 260s > test.c 260s Call: etmCIF(formula = Surv(time, to != 0) ~ cov, data = dat.s, etype = to) 260s 260s Covariate: cov 260s levels: 0 1 260s 260s 260s cov = 0 260s time P se(P) n.event 260s CIF 1 2.1708 0.70246 0.105797 19 260s CIF 2 2.1708 0.11144 0.053384 4 260s 260s cov = 1 260s time P se(P) n.event 260s CIF 1 4.9088 0.80787 0.094051 26 260s CIF 2 4.9088 0.08436 0.040769 4 260s > 260s > summary(test) 260s 260s 260s 260s CIF 1 260s P time var lower upper n.risk n.event 260s 0.01000 0.0092099 0.0000990 0.0014147 0.068863 100 1 260s 0.11430 0.2663096 0.0010542 0.0649454 0.196993 81 1 260s 0.23451 0.7303091 0.0020436 0.1591107 0.337736 54 1 260s 0.40425 1.4299939 0.0032996 0.3020445 0.525741 29 1 260s 0.54593 2.0647206 0.0040836 0.4269008 0.673605 16 1 260s 0.80911 4.9087561 0.0063489 0.6359544 0.933733 2 1 260s 260s CIF 2 260s P time var lower upper n.risk n.event 260s 0.000000 0.0092099 0.00000000 0.000000 0.000000 100 0 260s 0.031657 0.2663096 0.00032353 0.010320 0.094942 81 0 260s 0.067029 0.7303091 0.00070366 0.030598 0.143503 54 0 260s 0.096618 1.4299939 0.00108275 0.049082 0.185474 29 0 260s 0.096618 2.0647206 0.00108275 0.049082 0.185474 16 0 260s 0.096618 4.9087561 0.00108275 0.049082 0.185474 2 0 260s 260s > summary(test.c) 260s 260s cov=0 260s 260s CIF 1 260s P time var lower upper n.risk n.event 260s 0.022222 0.0092099 0.00048285 0.0031605 0.14747 45 1 260s 0.092222 0.2982439 0.00193603 0.0355971 0.22762 36 0 260s 0.226684 0.7021938 0.00450954 0.1241760 0.39250 24 1 260s 0.378128 1.4299939 0.00760870 0.2337884 0.57145 13 1 260s 0.505736 1.6148774 0.00895330 0.3388425 0.69885 10 1 260s 0.702465 2.1708375 0.01119294 0.4944890 0.88399 3 1 260s 260s CIF 2 260s P time var lower upper n.risk n.event 260s 0.000000 0.0092099 0.0000000 0.000000 0.00000 45 0 260s 0.048441 0.2982439 0.0011168 0.012337 0.18013 36 1 260s 0.076411 0.7021938 0.0018104 0.025202 0.21928 24 0 260s 0.111440 1.4299939 0.0028499 0.042676 0.27392 13 0 260s 0.111440 1.6148774 0.0028499 0.042676 0.27392 10 0 260s 0.111440 2.1708375 0.0028499 0.042676 0.27392 3 0 260s 260s 260s cov=1 260s 260s CIF 1 260s P time var lower upper n.risk n.event 260s 0.018182 0.066692 0.00032457 0.0025813 0.12214 55 1 260s 0.112392 0.263808 0.00187215 0.0520925 0.23333 45 1 260s 0.241023 0.730309 0.00374499 0.1440057 0.38685 31 1 260s 0.401201 1.066913 0.00570788 0.2714008 0.56421 19 1 260s 0.592334 2.366275 0.00775985 0.4286230 0.76273 8 1 260s 0.807871 4.908756 0.00884554 0.6023185 0.94771 2 1 260s 260s CIF 2 260s P time var lower upper n.risk n.event 260s 0.000000 0.066692 0.00000000 0.000000 0.00000 55 0 260s 0.037434 0.263808 0.00067458 0.009494 0.14152 45 0 260s 0.059341 0.730309 0.00111295 0.019447 0.17351 31 0 260s 0.084360 1.066913 0.00166213 0.032211 0.21119 19 0 260s 0.084360 2.366275 0.00166213 0.032211 0.21119 8 0 260s 0.084360 4.908756 0.00166213 0.032211 0.21119 2 0 260s 260s > 260s > options(old) 260s > 260s BEGIN TEST tests.etm.R 260s 260s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 260s Copyright (C) 2025 The R Foundation for Statistical Computing 260s Platform: aarch64-unknown-linux-gnu 260s 260s R is free software and comes with ABSOLUTELY NO WARRANTY. 260s You are welcome to redistribute it under certain conditions. 260s Type 'license()' or 'licence()' for distribution details. 260s 260s R is a collaborative project with many contributors. 260s Type 'contributors()' for more information and 260s 'citation()' on how to cite R or R packages in publications. 260s 260s Type 'demo()' for some demos, 'help()' for on-line help, or 260s 'help.start()' for an HTML browser interface to help. 260s Type 'q()' to quit R. 260s 260s > require(etm) 260s Loading required package: etm 261s > 261s > ## Print with a bit less precision to avoid lots of notes in the comparison 261s > old <- options(digits = 4) 261s > 261s > ### Simple test 261s > 261s > time <- id <- 1:10 261s > from <- rep(0, 10) 261s > to <- rep(1, 10) 261s > 261s > data1 <- data.frame(id, from, to, time) 261s > tra1 <- matrix(FALSE, 2, 2) 261s > tra1[1, 2] <- TRUE 261s > 261s > etm1 <- etm(data1, c("0", "1"), tra1, NULL, 0) 261s > 261s > all.equal(as.vector(trprob(etm1, "0 0")), cumprod((10:1 - 1) / (10:1))) 261s [1] TRUE 261s > 261s > etm1$cov["0 0", "0 0", ] 261s 1 2 3 4 5 6 7 8 9 10 261s 0.009 0.016 0.021 0.024 0.025 0.024 0.021 0.016 0.009 0.000 261s > 261s > all.equal(etm1$cov["0 0", "0 0",], trcov(etm1, "0 0")) 261s Loading required package: survival 261s [1] TRUE 261s > 261s > ### A simple test from AHR's author, where the first time is censored 261s > if (!require(survival)) { 261s + stop("This test requires the survival package") 261s + } 261s > 261s > data <- data.frame(id=1:10, time=1:10, from=0, to=1, status=TRUE) 261s > 261s > tra <- matrix(FALSE, nrow=2, ncol=2) 261s > tra[1, 2] <- TRUE 261s > 261s > data$to[1] <- "cens" 261s > data$status[1] <- FALSE 261s > 261s > fit.km <- survfit(Surv(time, status) ~ 1, data=data) 261s > fit.etm <- etm(data, c("0","1"), tra, "cens", s=0, t="last", covariance=FALSE) 261s > 261s > all.equal(fit.km$surv[data$status], fit.etm$est[1,1,], check.attributes = FALSE) 261s [1] TRUE 261s > 261s > data$to[2] <- "cens" 261s > data$status[2] <- FALSE 261s > 261s > fit.km <- survfit(Surv(time, status) ~ 1, data=data) 261s > fit.etm <- etm(data, c("0","1"), tra, "cens", s=0, t="last", covariance=FALSE) 261s > 261s > all.equal(fit.km$surv[data$status], fit.etm$est[1,1,], check.attributes = FALSE) 261s [1] TRUE 261s > 261s > ### a bit more complicated 261s > 261s > time <- id <- 1:10 261s > from <- rep(0, 10) 261s > to <- rep(c(1, 2), 5) 261s > data2 <- data.frame(id, from, to, time) 261s > 261s > tra2 <- matrix(FALSE, 3, 3) 261s > tra2[1, 2:3] <- TRUE 261s > 261s > etm2 <- etm(data2, c("0", "1", "2"), tra2, NULL, 0) 261s > 261s > aa <- table(time, to) 261s > 261s > cif1 <- cumsum(aa[, 1] / 10) 261s > cif2 <- cumsum(aa[, 2] / 10) 261s > surv <- cumprod((10:1 - 1) / (10:1)) 261s > 261s > all.equal(trprob(etm2, "0 1"), cif1) 261s [1] TRUE 261s > all.equal(trprob(etm2, "0 2"), cif2) 261s [1] TRUE 261s > all.equal(as.vector(trprob(etm2, "0 0")), surv) 261s [1] TRUE 261s > 261s > ## a test on id 261s > data2$id <- letters[1:10] 261s > 261s > etm3 <- etm(data2, c("0", "1", "2"), tra2, NULL, 0) 261s > 261s > all.equal(trprob(etm2, "0 1"), trprob(etm3, "0 1")) 261s [1] TRUE 261s > all.equal(trprob(etm2, "0 2"), trprob(etm3, "0 2")) 261s [1] TRUE 261s > all.equal(trprob(etm2, "0 0"), trprob(etm3, "0 0")) 261s [1] TRUE 261s > 261s > 261s > ### Test on sir.cont 261s > 261s > data(sir.cont) 261s > 261s > ## Modification for patients entering and leaving a state 261s > ## at the same date 261s > ## Change on ventilation status is considered 261s > ## to happen before end of hospital stay 261s > sir.cont <- sir.cont[order(sir.cont$id, sir.cont$time), ] 261s > for (i in 2:nrow(sir.cont)) { 261s + if (sir.cont$id[i]==sir.cont$id[i-1]) { 261s + if (sir.cont$time[i]==sir.cont$time[i-1]) { 261s + sir.cont$time[i-1] <- sir.cont$time[i-1] - 0.5 261s + } 261s + } 261s + } 261s > 261s > ### Computation of the transition probabilities 261s > ## Possible transitions. 261s > tra <- matrix(ncol=3,nrow=3,FALSE) 261s > tra[1, 2:3] <- TRUE 261s > tra[2, c(1, 3)] <- TRUE 261s > 261s > ## etm 261s > prob.sir <- etm(sir.cont, c("0", "1", "2"), tra, "cens", 1) 261s > 261s > prob.sir 261s Multistate model with 2 transient state(s) 261s and 1 absorbing state(s) 261s 261s Possible transitions: 261s from to 261s 0 1 261s 0 2 261s 1 0 261s 1 2 261s 261s Estimate of P(1, 183) 261s 0 1 2 261s 0 0 0 1 261s 1 0 0 1 261s 2 0 0 1 261s 261s > 261s > summ.sir <- summary(prob.sir) 261s > all.equal(summ.sir[['0 1']]$P, as.vector(trprob(prob.sir, "0 1"))) 261s [1] TRUE 261s > subset(summ.sir[[3]],time<183) # issue with precision on different architectures 261s P time var lower upper n.risk n.event 261s 1.5 0.0000 1.5 0.000e+00 0.00000 0.0000 394 0 261s 2 0.1187 2.0 2.641e-04 0.08683 0.1505 396 47 261s 2.5 0.1187 2.5 2.641e-04 0.08683 0.1505 364 0 261s 3 0.2454 3.0 4.465e-04 0.20398 0.2868 365 54 261s 3.5 0.2454 3.5 4.465e-04 0.20398 0.2868 328 0 261s 4 0.3806 4.0 5.416e-04 0.33501 0.4262 331 62 261s 4.5 0.3806 4.5 5.416e-04 0.33501 0.4262 280 0 261s 5 0.4792 5.0 5.480e-04 0.43333 0.5251 283 48 261s 5.5 0.4792 5.5 5.480e-04 0.43333 0.5251 248 0 261s 6 0.5693 6.0 5.141e-04 0.52482 0.6137 249 47 261s 7 0.6350 7.0 4.665e-04 0.59266 0.6773 212 36 261s 8 0.6795 8.0 4.202e-04 0.63931 0.7197 195 27 261s 8.5 0.6795 8.5 4.202e-04 0.63931 0.7197 172 0 261s 9 0.7325 9.0 3.580e-04 0.69541 0.7696 173 34 261s 10 0.7647 10.0 3.141e-04 0.72992 0.7994 148 21 261s 10.5 0.7647 10.5 3.141e-04 0.72992 0.7994 135 0 261s 11 0.7895 11.0 2.790e-04 0.75674 0.8222 136 18 261s 12 0.8138 12.0 2.420e-04 0.78330 0.8443 129 18 261s 12.5 0.8138 12.5 2.420e-04 0.78330 0.8443 117 0 261s 13 0.8294 13.0 2.182e-04 0.80045 0.8584 118 13 261s 14 0.8452 14.0 1.938e-04 0.81789 0.8725 115 14 261s 15 0.8625 15.0 1.670e-04 0.83714 0.8878 106 15 261s 16 0.8723 16.0 1.522e-04 0.84807 0.8964 93 9 261s 17 0.8852 17.0 1.330e-04 0.86256 0.9078 86 12 261s 17.5 0.8852 17.5 1.330e-04 0.86256 0.9078 77 0 261s 18 0.8960 18.0 1.168e-04 0.87484 0.9172 76 9 261s 19 0.9029 19.0 1.070e-04 0.88261 0.9232 71 7 261s 20 0.9125 20.0 9.367e-05 0.89356 0.9315 64 10 261s 21 0.9161 21.0 8.878e-05 0.89768 0.9346 57 4 261s 22 0.9226 22.0 7.996e-05 0.90504 0.9401 55 6 261s 23 0.9261 23.0 7.537e-05 0.90904 0.9431 51 4 261s 23.5 0.9261 23.5 7.537e-05 0.90904 0.9431 49 0 261s 24 0.9354 24.0 6.292e-05 0.91982 0.9509 50 9 261s 25 0.9385 25.0 5.878e-05 0.92352 0.9536 42 3 261s 26 0.9429 26.0 5.326e-05 0.92863 0.9572 39 5 261s 27 0.9477 27.0 4.749e-05 0.93417 0.9612 35 6 261s 27.5 0.9477 27.5 4.749e-05 0.93417 0.9612 29 0 261s 28 0.9531 28.0 4.093e-05 0.94059 0.9657 30 5 261s 29 0.9567 29.0 3.668e-05 0.94485 0.9686 31 4 261s 30 0.9592 30.0 3.384e-05 0.94779 0.9706 28 3 261s 30.5 0.9592 30.5 3.384e-05 0.94779 0.9706 29 0 261s 31 0.9642 31.0 2.821e-05 0.95383 0.9746 30 6 261s 32 0.9649 32.0 2.752e-05 0.95458 0.9751 25 1 261s 33 0.9669 33.0 2.533e-05 0.95708 0.9768 24 2 261s 34 0.9685 34.0 2.368e-05 0.95900 0.9781 26 2 261s 35 0.9697 35.0 2.252e-05 0.96036 0.9790 28 2 261s 36 0.9702 36.0 2.194e-05 0.96104 0.9794 26 1 261s 37 0.9718 37.0 2.043e-05 0.96290 0.9806 26 2 261s 38 0.9739 38.0 1.831e-05 0.96555 0.9823 25 4 261s 38.5 0.9739 38.5 1.831e-05 0.96555 0.9823 21 0 261s 39 0.9760 39.0 1.643e-05 0.96802 0.9839 23 3 261s 40 0.9769 40.0 1.558e-05 0.96918 0.9847 19 1 261s 41 0.9774 41.0 1.512e-05 0.96981 0.9851 22 1 261s 42 0.9779 42.0 1.476e-05 0.97032 0.9854 22 0 261s 43 0.9798 43.0 1.308e-05 0.97271 0.9869 22 3 261s 44 0.9803 44.0 1.265e-05 0.97333 0.9873 21 1 261s 45 0.9817 45.0 1.157e-05 0.97499 0.9883 19 1 261s 46 0.9822 46.0 1.116e-05 0.97561 0.9887 17 1 261s 47 0.9831 47.0 1.037e-05 0.97683 0.9895 18 2 261s 48 0.9836 48.0 9.987e-06 0.97743 0.9898 17 1 261s 49 0.9841 49.0 9.669e-06 0.97796 0.9901 17 0 261s 50 0.9845 50.0 9.297e-06 0.97856 0.9905 17 1 261s 50.5 0.9845 50.5 9.297e-06 0.97856 0.9905 16 0 261s 51 0.9860 51.0 8.214e-06 0.98037 0.9916 17 3 261s 52 0.9870 52.0 7.513e-06 0.98159 0.9923 14 2 261s 53 0.9879 53.0 6.875e-06 0.98276 0.9930 12 1 261s 54 0.9889 54.0 6.214e-06 0.98397 0.9937 12 2 261s 55 0.9903 55.0 5.254e-06 0.98581 0.9948 10 3 261s 56 0.9913 56.0 4.667e-06 0.98703 0.9955 6 1 261s 57 0.9917 57.0 4.364e-06 0.98765 0.9958 5 1 261s 58 0.9922 58.0 4.064e-06 0.98828 0.9962 4 1 261s 59 0.9927 59.0 3.769e-06 0.98891 0.9965 3 1 261s 60 0.9932 60.0 3.488e-06 0.98953 0.9969 3 1 261s 62 0.9937 62.0 3.230e-06 0.99016 0.9972 2 0 261s 63 0.9942 63.0 2.956e-06 0.99079 0.9975 2 1 261s 68 0.9942 68.0 2.956e-06 0.99079 0.9975 1 0 261s 70 0.9946 70.0 2.694e-06 0.99143 0.9979 2 1 261s 78 0.9951 78.0 2.442e-06 0.99207 0.9982 1 0 261s 80 0.9951 80.0 2.442e-06 0.99207 0.9982 1 0 261s 85 0.9966 85.0 1.695e-06 0.99404 0.9991 2 0 261s 89 0.9966 89.0 1.695e-06 0.99404 0.9991 2 0 261s 90 0.9966 90.0 1.695e-06 0.99404 0.9991 1 0 261s 95 0.9971 95.0 1.448e-06 0.99472 0.9994 2 0 261s 100 0.9976 100.0 1.203e-06 0.99542 0.9997 3 0 261s 101 0.9981 101.0 9.592e-07 0.99613 1.0000 3 1 261s 108 0.9985 108.0 7.169e-07 0.99688 1.0000 2 1 261s 113 0.9990 113.0 4.764e-07 0.99767 1.0000 1 0 261s 116 0.9990 116.0 4.764e-07 0.99767 1.0000 1 0 261s 124 0.9990 124.0 4.764e-07 0.99767 1.0000 2 0 261s 164 0.9990 164.0 4.764e-07 0.99767 1.0000 0 0 261s > 261s > ## gonna play a bit with the state names 261s > dd <- sir.cont 261s > dd$from <- ifelse(dd$from == 0, "initial state", "ventilation") 261s > dd$to <- as.character(dd$to) 261s > for (i in seq_len(nrow(dd))) { 261s + dd$to[i] <- switch(dd$to[i], 261s + "0" = "initial state", 261s + "1" = "ventilation", 261s + "2" = "end of story", 261s + "cens" = "cens" 261s + ) 261s + } 261s > 261s > test <- etm(dd, c("initial state", "ventilation", "end of story"), tra, "cens", 1) 261s > 261s > all.equal(test$est["initial state", "initial state", ], 261s + prob.sir$est["0", "0", ]) 261s [1] TRUE 261s > all.equal(trprob(test, "initial state initial state"), trprob(prob.sir, "0 0")) 261s [1] TRUE 261s > all.equal(trprob(test, "initial state ventilation"), trprob(prob.sir, "0 1")) 261s [1] TRUE 261s > all.equal(trprob(test, "initial state end of story"), trprob(prob.sir, "0 2")) 261s [1] TRUE 261s > 261s > all.equal(trcov(test, "initial state end of story"), trcov(prob.sir, "0 2")) 261s [1] TRUE 261s > 261s > aa <- summary(test) 261s > all.equal(summ.sir[[6]], aa[[6]]) 261s [1] TRUE 261s > all.equal(summ.sir[[4]], aa[[4]]) 261s [1] TRUE 261s > 261s > ### Test on abortion data 261s > 261s > data(abortion) 261s > 261s > from <- rep(0, nrow(abortion)) 261s > to <- abortion$cause 261s > entry <- abortion$entry 261s > exit <- abortion$exit 261s > id <- 1:nrow(abortion) 261s > data <- data.frame(id, from, to, entry, exit, group = abortion$group) 261s > 261s > ## Computation of the CIFs 261s > tra <- matrix(FALSE, 4, 4) 261s > tra[1, 2:4] <- TRUE 261s > 261s > cif.control <- etm(data[data$group == 0, ], c("0", "1", "2", "3"), 261s + tra, NULL, 0) 261s > cif.exposed <- etm(data[data$group == 1, ], c("0", "1", "2", "3"), 261s + tra, NULL, 0) 261s > 261s > all.equal(trprob(cif.control, "0 1"), cif.control$est["0", "1", ]) 261s [1] TRUE 261s > all.equal(trcov(cif.control, c("0 1", "0 2")), cif.control$cov["0 1", "0 2", ]) 261s [1] TRUE 261s > 261s > trprob(cif.control, "0 1") 261s 6 7 8 9 10 11 12 13 261s 0.000000 0.007401 0.014881 0.026509 0.033208 0.037694 0.037694 0.038955 261s 14 17 19 21 24 25 26 30 261s 0.040159 0.040159 0.040159 0.040159 0.040159 0.040159 0.040159 0.040159 261s 31 32 33 34 35 36 37 38 261s 0.040159 0.040159 0.040159 0.040159 0.040159 0.040159 0.040159 0.040159 261s 39 40 41 42 43 261s 0.040159 0.040159 0.040159 0.040159 0.040159 261s > trprob(cif.control, "0 2") 261s 6 7 8 9 10 11 12 13 261s 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 261s 14 17 19 21 24 25 26 30 261s 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.003657 261s 31 32 33 34 35 36 37 38 261s 0.006371 0.008175 0.013543 0.023317 0.031260 0.053197 0.084529 0.179163 261s 39 40 41 42 43 261s 0.322016 0.563121 0.742227 0.793893 0.799059 261s > trprob(cif.control, "0 0") 261s 6 7 8 9 10 11 12 13 261s 0.965812 0.932508 0.887628 0.862433 0.838989 0.822538 0.813099 0.810578 261s 14 17 19 21 24 25 26 30 261s 0.806964 0.805874 0.803810 0.802804 0.801837 0.800883 0.799937 0.796280 261s 31 32 33 34 35 36 37 38 261s 0.793565 0.791762 0.786394 0.776620 0.768677 0.745862 0.714531 0.619897 261s 39 40 41 42 43 261s 0.477043 0.235938 0.056832 0.005167 0.000000 261s > 261s > trcov(cif.control, "0 1") 261s 6 7 8 9 10 11 12 13 261s 0.000e+00 2.719e-05 4.533e-05 6.665e-05 7.698e-05 8.304e-05 8.304e-05 8.444e-05 261s 14 17 19 21 24 25 26 30 261s 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 261s 31 32 33 34 35 36 37 38 261s 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 261s 39 40 41 42 43 261s 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 261s > trcov(cif.control, "0 2") 261s 6 7 8 9 10 11 12 13 261s 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 261s 14 17 19 21 24 25 26 30 261s 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 3.338e-06 261s 31 32 33 34 35 36 37 38 261s 5.784e-06 7.401e-06 1.216e-05 2.072e-05 2.758e-05 4.619e-05 7.202e-05 1.461e-04 261s 39 40 41 42 43 261s 2.470e-04 3.880e-04 4.702e-04 4.903e-04 4.922e-04 261s > trcov(cif.control, "0 0") 261s 6 7 8 9 10 11 12 13 261s 2.822e-04 3.821e-04 4.527e-04 4.748e-04 4.875e-04 4.927e-04 4.941e-04 4.942e-04 261s 14 17 19 21 24 25 26 30 261s 4.941e-04 4.940e-04 4.936e-04 4.933e-04 4.931e-04 4.928e-04 4.926e-04 4.914e-04 261s 31 32 33 34 35 36 37 38 261s 4.905e-04 4.899e-04 4.880e-04 4.846e-04 4.816e-04 4.729e-04 4.601e-04 4.176e-04 261s 39 40 41 42 43 261s 3.425e-04 1.865e-04 4.797e-05 4.441e-06 0.000e+00 261s > 261s > aa <- summary(cif.control) 261s > aa$"0 1" 261s P time var lower upper n.risk n.event 261s 6 0.000000 6 0.000e+00 0.000000 0.00000 117 0 261s 7 0.007401 7 2.719e-05 0.000000 0.01762 261 2 261s 8 0.014881 8 4.533e-05 0.001685 0.02808 374 3 261s 9 0.026509 9 6.665e-05 0.010508 0.04251 458 6 261s 10 0.033208 10 7.698e-05 0.016011 0.05040 515 4 261s 11 0.037694 11 8.304e-05 0.019834 0.05555 561 3 261s 12 0.037694 12 8.304e-05 0.019834 0.05555 610 0 261s 13 0.038955 13 8.444e-05 0.020944 0.05697 645 1 261s 14 0.040159 14 8.571e-05 0.022014 0.05830 673 1 261s 17 0.040159 17 8.571e-05 0.022014 0.05830 740 0 261s 19 0.040159 19 8.571e-05 0.022014 0.05830 781 0 261s 21 0.040159 21 8.571e-05 0.022014 0.05830 799 0 261s 24 0.040159 24 8.571e-05 0.022014 0.05830 830 0 261s 25 0.040159 25 8.571e-05 0.022014 0.05830 841 0 261s 26 0.040159 26 8.571e-05 0.022014 0.05830 846 0 261s 30 0.040159 30 8.571e-05 0.022014 0.05830 875 0 261s 31 0.040159 31 8.571e-05 0.022014 0.05830 880 0 261s 32 0.040159 32 8.571e-05 0.022014 0.05830 880 0 261s 33 0.040159 33 8.571e-05 0.022014 0.05830 885 0 261s 34 0.040159 34 8.571e-05 0.022014 0.05830 885 0 261s 35 0.040159 35 8.571e-05 0.022014 0.05830 880 0 261s 36 0.040159 36 8.571e-05 0.022014 0.05830 876 0 261s 37 0.040159 37 8.571e-05 0.022014 0.05830 857 0 261s 38 0.040159 38 8.571e-05 0.022014 0.05830 823 0 261s 39 0.040159 39 8.571e-05 0.022014 0.05830 716 0 261s 40 0.040159 40 8.571e-05 0.022014 0.05830 554 0 261s 41 0.040159 41 8.571e-05 0.022014 0.05830 274 0 261s 42 0.040159 42 8.571e-05 0.022014 0.05830 66 0 261s 43 0.040159 43 8.571e-05 0.022014 0.05830 6 0 261s > all.equal(aa$"0 1"$P, as.vector(trprob(cif.control, "0 1"))) 261s [1] TRUE 261s > 261s > ### test on los data 261s > 261s > data(los.data) # in package changeLOS 261s > 261s > ## putting los.data in the long format (see changeLOS) 261s > my.observ <- prepare.los.data(x=los.data) 261s > 261s > tra <- matrix(FALSE, 4, 4) 261s > tra[1, 2:4] <- TRUE 261s > tra[2, 3:4] <- TRUE 261s > 261s > tr.prob <- etm(my.observ, c("0","1","2","3"), tra, NULL, 0) 261s > 261s > tr.prob 261s Multistate model with 2 transient state(s) 261s and 2 absorbing state(s) 261s 261s Possible transitions: 261s from to 261s 0 1 261s 0 2 261s 0 3 261s 1 2 261s 1 3 261s 261s Estimate of P(0, 82) 261s 0 1 2 3 261s 0 0 0 0.7474 0.2526 261s 1 0 0 0.7073 0.2927 261s 2 0 0 1.0000 0.0000 261s 3 0 0 0.0000 1.0000 261s 261s > summary(tr.prob) 261s Transition 0 0 261s P time var lower upper n.risk n.event 261s 0.882275 3 1.374e-04 0.8593018 0.905248 756 0 261s 0.112434 15 1.320e-04 0.0899155 0.134952 90 0 261s 0.031746 27 4.066e-05 0.0192484 0.044244 26 0 261s 0.006614 41 8.690e-06 0.0008359 0.012392 5 0 261s 0.002646 61 3.490e-06 0.0000000 0.006307 3 0 261s 0.000000 82 0.000e+00 0.0000000 0.000000 1 0 261s 261s Transition 0 1 261s P time var lower upper n.risk n.event 261s 0.017196 3 2.235e-05 0.0079289 0.02646 756 13 261s 0.063492 15 7.865e-05 0.0461099 0.08087 90 0 261s 0.030423 27 3.902e-05 0.0181805 0.04267 26 1 261s 0.015873 41 2.066e-05 0.0069637 0.02478 5 0 261s 0.005291 61 6.962e-06 0.0001197 0.01046 3 0 261s 0.000000 82 0.000e+00 0.0000000 0.00000 1 0 261s 261s Transition 0 2 261s P time var lower upper n.risk n.event 261s 0.08466 3 0.0001025 0.06481 0.1045 756 64 261s 0.62302 15 0.0003107 0.58847 0.6576 90 4 261s 0.69841 27 0.0002786 0.66570 0.7311 26 1 261s 0.72751 41 0.0002622 0.69578 0.7593 5 0 261s 0.74074 61 0.0002540 0.70950 0.7720 3 1 261s 0.74735 82 0.0002498 0.71638 0.7783 1 1 261s 261s Transition 0 3 261s P time var lower upper n.risk n.event 261s 0.01587 3 2.066e-05 0.006964 0.02478 756 12 261s 0.20106 15 2.125e-04 0.172489 0.22963 90 1 261s 0.23942 27 2.409e-04 0.208999 0.26984 26 0 261s 0.25000 41 2.480e-04 0.219133 0.28087 5 0 261s 0.25132 61 2.489e-04 0.220402 0.28224 3 0 261s 0.25265 82 2.498e-04 0.221671 0.28362 1 0 261s 261s Transition 1 1 261s P time var lower upper n.risk n.event 261s 1.00000 3 0.000e+00 1.00000 1.00000 0 0 261s 0.38661 15 2.358e-03 0.29143 0.48179 51 0 261s 0.12119 27 7.842e-04 0.06630 0.17607 23 0 261s 0.04593 41 2.405e-04 0.01554 0.07633 14 0 261s 0.01531 61 6.579e-05 0.00000 0.03121 4 0 261s 0.00000 82 0.000e+00 0.00000 0.00000 0 0 261s 261s Transition 1 2 261s P time var lower upper n.risk n.event 261s 0.0000 3 0.000000 0.0000 0.0000 0 0 261s 0.4107 15 0.002590 0.3110 0.5104 51 2 261s 0.6082 27 0.002254 0.5151 0.7012 23 1 261s 0.6652 41 0.002064 0.5761 0.7542 14 2 261s 0.6920 61 0.002000 0.6043 0.7796 4 0 261s 0.7073 82 0.001984 0.6200 0.7946 0 0 261s 261s Transition 1 3 261s P time var lower upper n.risk n.event 261s 0.0000 3 0.000000 0.0000 0.0000 0 0 261s 0.2027 15 0.001784 0.1199 0.2855 51 1 261s 0.2706 27 0.001968 0.1837 0.3576 23 0 261s 0.2889 41 0.001982 0.2016 0.3761 14 0 261s 0.2927 61 0.001984 0.2054 0.3800 4 0 261s 0.2927 82 0.001984 0.2054 0.3800 0 0 261s 261s > 261s > cLOS <- etm::clos(tr.prob, aw = TRUE) 261s > 261s > cLOS 261s The expected change in length of stay is: 261s 1.975 261s 261s Alternative weighting: 261s 261s Expected change in LOS with weight.1: 2.097 261s Expected change in LOS with weight.other: 1.951 261s > 261s > 261s > ### Tests on pseudo values 261s > t_pseudo <- closPseudo(my.observ, c("0","1","2","3"), tra, NULL, 261s + formula = ~ 1, aw = TRUE) 277s > 277s > cLOS$e.phi == t_pseudo$theta[, "e.phi"] 277s [,1] 277s [1,] TRUE 277s > cLOS$e.phi.weights.1 == t_pseudo$theta[, "e.phi.weights.1"] 277s [,1] 277s [1,] TRUE 277s > cLOS$e.phi.weights.other == t_pseudo$theta[, "e.phi.weights.other"] 277s [,1] 277s [1,] TRUE 277s > 277s > mean(t_pseudo$pseudoData$ps.e.phi) 277s [1] 1.968 277s > 277s > ### tests on etmprep 277s > 277s > ### creation of fake data in the wild format, following an illness-death model 277s > ## transition times 277s > tdisease <- c(3, 4, 3, 6, 8, 9) 277s > tdeath <- c(6, 9, 8, 6, 8, 9) 277s > 277s > ## transition status 277s > stat.disease <- c(1, 1, 1, 0, 0, 0) 277s > stat.death <- c(1, 1, 1, 1, 1, 0) 277s > 277s > ## a covariate that we want to keep in the new data 277s > set.seed(1313) 277s > cova <- rbinom(6, 1, 0.5) 277s > 277s > dat <- data.frame(tdisease, tdeath, 277s + stat.disease, stat.death, 277s + cova) 277s > 277s > ## Possible transitions 277s > tra <- matrix(FALSE, 3, 3) 277s > tra[1, 2:3] <- TRUE 277s > tra[2, 3] <- TRUE 277s > 277s > ## data preparation 277s > newdat <- etmprep(c(NA, "tdisease", "tdeath"), 277s + c(NA, "stat.disease", "stat.death"), 277s + data = dat, tra = tra, 277s + cens.name = "cens", keep = "cova") 277s > 277s > newdat 277s id entry exit from to cova 277s 1 1 0 3 0 1 1 277s 2 1 3 6 1 2 1 277s 3 2 0 4 0 1 0 277s 4 2 4 9 1 2 0 277s 5 3 0 3 0 1 1 277s 6 3 3 8 1 2 1 277s 7 4 0 6 0 2 0 277s 8 5 0 8 0 2 1 277s 9 6 0 9 0 cens 1 277s > 277s > ref <- data.frame(id = c(1, 1, 2, 2, 3, 3, 4, 5, 6), 277s + entry = c(0, 3, 0, 4, 0, 3, 0, 0, 0), 277s + exit = c(3, 6, 4, 9, 3, 8, 6, 8, 9), 277s + from = c(0, 1, 0, 1, 0, 1, 0, 0, 0), 277s + to = c(rep(c(1, 2), 3), 2, 2, "cens"), 277s + cova = c(1, 1, 0, 0, 1, 1, 0, 1, 1)) 277s > ref$from <- factor(as.character(ref$from), levels = c("0", "1", "2", "cens")) 277s > ref$to <- factor(as.character(ref$to), levels = c("0", "1", "2", "cens")) 277s > 277s > all.equal(ref, newdat) 277s [1] TRUE 277s > 277s > 277s > ###################################### 277s > ### Test the stratified calls 277s > ###################################### 277s > 277s > if (require("kmi", quietly = TRUE)) { 277s + library(etm) 277s + 277s + data(icu.pneu) 277s + my.icu.pneu <- icu.pneu 277s + 277s + my.icu.pneu <- my.icu.pneu[order(my.icu.pneu$id, my.icu.pneu$start), ] 277s + masque <- diff(my.icu.pneu$id) 277s + 277s + my.icu.pneu$from <- 0 277s + my.icu.pneu$from[c(1, masque) == 0] <- 1 277s + 277s + my.icu.pneu$to2 <- my.icu.pneu$event 277s + my.icu.pneu$to2[my.icu.pneu$status == 0] <- "cens" 277s + my.icu.pneu$to2[c(masque, 1) == 0] <- 1 277s + 277s + 277s + my.icu.pneu$to <- ifelse(my.icu.pneu$to2 %in% c(2, 3), 2, 277s + my.icu.pneu$to2) 277s + 277s + my.icu.pneu <- my.icu.pneu[, c("id", "start", "stop", "from", "to", 277s + "to2", "age", "sex")] 277s + names(my.icu.pneu)[c(2, 3)] <- c("entry", "exit") 277s + 277s + bouh_strat <- etm(my.icu.pneu, c("0", "1", "2"), tra_ill(), "cens", 0, strata = "sex") 277s + 277s + bouh_female <- etm(my.icu.pneu[my.icu.pneu$sex == "F", ], 277s + c("0", "1", "2"), tra_ill(), "cens", 0) 277s + 277s + all(bouh_strat[[1]]$est == bouh_female$est) 277s + 277s + ## Test the summary 277s + the_summary <- summary(bouh_strat) 277s + the_summary 277s + 277s + ## Test trprob 277s + all(trprob(bouh_strat, "0 1")[[1]] == trprob(bouh_female, "0 1")) 277s + all(trprob(bouh_strat, "0 1", c(0, 5, 10, 15))[[1]] == trprob(bouh_female, "0 1", c(0, 5, 10, 15))) 277s + 277s + ## Test trcov 277s + all(trcov(bouh_strat, "0 1")[[1]] == trcov(bouh_female, "0 1")) 277s + all(trcov(bouh_strat, c("0 1", "0 2"))[[1]] == trcov(bouh_female, c("0 1", "0 2"))) 277s + all(trcov(bouh_strat, "0 1", c(0, 5, 10, 15))[[1]] == trcov(bouh_female, "0 1", c(0, 5, 10, 15))) 277s + } else { 277s + print("These tests require the kmi package") 277s + } 277s [1] TRUE 277s > 277s > options(old) 277s > 277s autopkgtest [23:40:53]: test run-unit-test: -----------------------] 278s run-unit-test PASS 278s autopkgtest [23:40:54]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 278s autopkgtest [23:40:54]: test pkg-r-autopkgtest: preparing testbed 278s Reading package lists... 278s Building dependency tree... 278s Reading state information... 279s Solving dependencies... 279s The following NEW packages will be installed: 279s build-essential cpp cpp-15 cpp-15-aarch64-linux-gnu cpp-aarch64-linux-gnu 279s dctrl-tools g++ g++-15 g++-15-aarch64-linux-gnu g++-aarch64-linux-gnu gcc 279s gcc-15 gcc-15-aarch64-linux-gnu gcc-aarch64-linux-gnu gfortran gfortran-15 279s gfortran-15-aarch64-linux-gnu gfortran-aarch64-linux-gnu icu-devtools 279s libasan8 libblas-dev libbz2-dev libc-dev-bin libc6-dev libcc1-0 libcrypt-dev 279s libdeflate-dev libgcc-15-dev libgfortran-15-dev libhwasan0 libicu-dev 279s libisl23 libitm1 libjpeg-dev libjpeg-turbo8-dev libjpeg8-dev liblapack-dev 279s liblsan0 liblzma-dev libmpc3 libncurses-dev libpcre2-16-0 libpcre2-32-0 279s libpcre2-dev libpcre2-posix3 libpkgconf3 libpng-dev libreadline-dev 279s libstdc++-15-dev libtirpc-dev libtsan2 libubsan1 libzstd-dev linux-libc-dev 279s pkg-r-autopkgtest pkgconf pkgconf-bin r-base-dev r-cran-backports 279s r-cran-broom r-cran-cli r-cran-cpp11 r-cran-dplyr r-cran-fansi r-cran-farver 279s r-cran-geepack r-cran-generics r-cran-ggplot2 r-cran-glue r-cran-gtable 279s r-cran-isoband r-cran-labeling r-cran-lifecycle r-cran-magrittr r-cran-mass 279s r-cran-pillar r-cran-pkgconfig r-cran-purrr r-cran-r6 r-cran-rcolorbrewer 279s r-cran-rlang r-cran-s7 r-cran-scales r-cran-stringi r-cran-stringr 279s r-cran-tibble r-cran-tidyr r-cran-tidyselect r-cran-utf8 r-cran-vctrs 279s r-cran-viridislite r-cran-withr rpcsvc-proto zlib1g-dev 279s 0 upgraded, 94 newly installed, 0 to remove and 0 not upgraded. 279s Need to get 128 MB of archives. 279s After this operation, 421 MB of additional disk space will be used. 279s Get:1 http://ftpmaster.internal/ubuntu resolute/main arm64 libc-dev-bin arm64 2.42-2ubuntu4 [22.5 kB] 279s Get:2 http://ftpmaster.internal/ubuntu resolute/main arm64 linux-libc-dev arm64 6.19.0-3.3 [1819 kB] 282s Get:3 http://ftpmaster.internal/ubuntu resolute/main arm64 libcrypt-dev arm64 1:4.5.1-1 [123 kB] 282s Get:4 http://ftpmaster.internal/ubuntu resolute/main arm64 rpcsvc-proto arm64 1.4.3-1build1 [65.6 kB] 282s Get:5 http://ftpmaster.internal/ubuntu resolute/main arm64 libc6-dev arm64 2.42-2ubuntu4 [1765 kB] 285s Get:6 http://ftpmaster.internal/ubuntu resolute/main arm64 libisl23 arm64 0.27-1build1 [676 kB] 287s Get:7 http://ftpmaster.internal/ubuntu resolute/main arm64 libmpc3 arm64 1.3.1-2 [55.6 kB] 287s Get:8 http://ftpmaster.internal/ubuntu resolute/main arm64 cpp-15-aarch64-linux-gnu arm64 15.2.0-12ubuntu1 [11.7 MB] 310s Get:9 http://ftpmaster.internal/ubuntu resolute/main arm64 cpp-15 arm64 15.2.0-12ubuntu1 [1030 B] 310s Get:10 http://ftpmaster.internal/ubuntu resolute/main arm64 cpp-aarch64-linux-gnu arm64 4:15.2.0-4ubuntu1 [5736 B] 310s Get:11 http://ftpmaster.internal/ubuntu resolute/main arm64 cpp arm64 4:15.2.0-4ubuntu1 [22.4 kB] 310s Get:12 http://ftpmaster.internal/ubuntu resolute/main arm64 libcc1-0 arm64 15.2.0-12ubuntu1 [49.0 kB] 310s Get:13 http://ftpmaster.internal/ubuntu resolute/main arm64 libitm1 arm64 15.2.0-12ubuntu1 [27.8 kB] 310s Get:14 http://ftpmaster.internal/ubuntu resolute/main arm64 libasan8 arm64 15.2.0-12ubuntu1 [2920 kB] 317s Get:15 http://ftpmaster.internal/ubuntu resolute/main arm64 liblsan0 arm64 15.2.0-12ubuntu1 [1316 kB] 321s Get:16 http://ftpmaster.internal/ubuntu resolute/main arm64 libtsan2 arm64 15.2.0-12ubuntu1 [2688 kB] 330s Get:17 http://ftpmaster.internal/ubuntu resolute/main arm64 libubsan1 arm64 15.2.0-12ubuntu1 [1175 kB] 334s Get:18 http://ftpmaster.internal/ubuntu resolute/main arm64 libhwasan0 arm64 15.2.0-12ubuntu1 [1638 kB] 337s Get:19 http://ftpmaster.internal/ubuntu resolute/main arm64 libgcc-15-dev arm64 15.2.0-12ubuntu1 [2600 kB] 343s Get:20 http://ftpmaster.internal/ubuntu resolute/main arm64 gcc-15-aarch64-linux-gnu arm64 15.2.0-12ubuntu1 [23.1 MB] 389s Get:21 http://ftpmaster.internal/ubuntu resolute/main arm64 gcc-15 arm64 15.2.0-12ubuntu1 [519 kB] 389s Get:22 http://ftpmaster.internal/ubuntu resolute/main arm64 gcc-aarch64-linux-gnu arm64 4:15.2.0-4ubuntu1 [1206 B] 389s Get:23 http://ftpmaster.internal/ubuntu resolute/main arm64 gcc arm64 4:15.2.0-4ubuntu1 [5016 B] 389s Get:24 http://ftpmaster.internal/ubuntu resolute/main arm64 libstdc++-15-dev arm64 15.2.0-12ubuntu1 [2549 kB] 393s Get:25 http://ftpmaster.internal/ubuntu resolute/main arm64 g++-15-aarch64-linux-gnu arm64 15.2.0-12ubuntu1 [13.2 MB] 416s Get:26 http://ftpmaster.internal/ubuntu resolute/main arm64 g++-15 arm64 15.2.0-12ubuntu1 [25.3 kB] 416s Get:27 http://ftpmaster.internal/ubuntu resolute/main arm64 g++-aarch64-linux-gnu arm64 4:15.2.0-4ubuntu1 [956 B] 416s Get:28 http://ftpmaster.internal/ubuntu resolute/main arm64 g++ arm64 4:15.2.0-4ubuntu1 [1080 B] 416s Get:29 http://ftpmaster.internal/ubuntu resolute/main arm64 build-essential arm64 12.12ubuntu2 [5254 B] 416s Get:30 http://ftpmaster.internal/ubuntu resolute/main arm64 dctrl-tools arm64 2.24-3build4 [102 kB] 416s Get:31 http://ftpmaster.internal/ubuntu resolute/main arm64 libgfortran-15-dev arm64 15.2.0-12ubuntu1 [490 kB] 416s Get:32 http://ftpmaster.internal/ubuntu resolute/main arm64 gfortran-15-aarch64-linux-gnu arm64 15.2.0-12ubuntu1 [12.5 MB] 439s Get:33 http://ftpmaster.internal/ubuntu resolute/main arm64 gfortran-15 arm64 15.2.0-12ubuntu1 [18.1 kB] 439s Get:34 http://ftpmaster.internal/ubuntu resolute/main arm64 gfortran-aarch64-linux-gnu arm64 4:15.2.0-4ubuntu1 [1022 B] 439s Get:35 http://ftpmaster.internal/ubuntu resolute/main arm64 gfortran arm64 4:15.2.0-4ubuntu1 [1160 B] 439s Get:36 http://ftpmaster.internal/ubuntu resolute/main arm64 icu-devtools arm64 78.2-1ubuntu1 [207 kB] 439s Get:37 http://ftpmaster.internal/ubuntu resolute/main arm64 libblas-dev arm64 3.12.1-7ubuntu1 [160 kB] 439s Get:38 http://ftpmaster.internal/ubuntu resolute/main arm64 libbz2-dev arm64 1.0.8-6build2 [34.9 kB] 439s Get:39 http://ftpmaster.internal/ubuntu resolute/main arm64 libdeflate-dev arm64 1.23-2build1 [54.3 kB] 440s Get:40 http://ftpmaster.internal/ubuntu resolute/main arm64 libicu-dev arm64 78.2-1ubuntu1 [12.5 MB] 462s Get:41 http://ftpmaster.internal/ubuntu resolute/main arm64 libjpeg-turbo8-dev arm64 2.1.5-4ubuntu3 [301 kB] 462s Get:42 http://ftpmaster.internal/ubuntu resolute/main arm64 libjpeg8-dev arm64 8c-2ubuntu11 [1484 B] 462s Get:43 http://ftpmaster.internal/ubuntu resolute/main arm64 libjpeg-dev arm64 8c-2ubuntu11 [1482 B] 462s Get:44 http://ftpmaster.internal/ubuntu resolute/main arm64 liblapack-dev arm64 3.12.1-7ubuntu1 [4456 kB] 470s Get:45 http://ftpmaster.internal/ubuntu resolute/main arm64 libncurses-dev arm64 6.6+20251231-1 [391 kB] 470s Get:46 http://ftpmaster.internal/ubuntu resolute/main arm64 libpcre2-16-0 arm64 10.46-1 [225 kB] 470s Get:47 http://ftpmaster.internal/ubuntu resolute/main arm64 libpcre2-32-0 arm64 10.46-1 [213 kB] 470s Get:48 http://ftpmaster.internal/ubuntu resolute/main arm64 libpcre2-posix3 arm64 10.46-1 [7300 B] 470s Get:49 http://ftpmaster.internal/ubuntu resolute/main arm64 libpcre2-dev arm64 10.46-1 [772 kB] 471s Get:50 http://ftpmaster.internal/ubuntu resolute/main arm64 libpkgconf3 arm64 1.8.1-4build1 [33.7 kB] 471s Get:51 http://ftpmaster.internal/ubuntu resolute/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1ubuntu2 [899 kB] 473s Get:52 http://ftpmaster.internal/ubuntu resolute/main arm64 libpng-dev arm64 1.6.54-1 [268 kB] 473s Get:53 http://ftpmaster.internal/ubuntu resolute/main arm64 libreadline-dev arm64 8.3-3 [199 kB] 473s Get:54 http://ftpmaster.internal/ubuntu resolute/main arm64 libzstd-dev arm64 1.5.7+dfsg-3 [349 kB] 473s Get:55 http://ftpmaster.internal/ubuntu resolute/main arm64 liblzma-dev arm64 5.8.2-2 [180 kB] 473s Get:56 http://ftpmaster.internal/ubuntu resolute/main arm64 pkgconf-bin arm64 1.8.1-4build1 [21.7 kB] 473s Get:57 http://ftpmaster.internal/ubuntu resolute/main arm64 pkgconf arm64 1.8.1-4build1 [16.8 kB] 473s Get:58 http://ftpmaster.internal/ubuntu resolute/main arm64 libtirpc-dev arm64 1.3.6+ds-1 [202 kB] 473s Get:59 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-base-dev all 4.5.2-1ubuntu2 [1880 B] 473s Get:60 http://ftpmaster.internal/ubuntu resolute/universe arm64 pkg-r-autopkgtest all 20250812 [6158 B] 473s Get:61 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-backports arm64 1.5.0-2 [121 kB] 473s Get:62 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-cli arm64 3.6.4-1 [1374 kB] 475s Get:63 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-generics all 0.1.4-1 [84.0 kB] 475s Get:64 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-glue arm64 1.8.0-1 [163 kB] 476s Get:65 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-rlang arm64 1.1.5-3 [1706 kB] 479s Get:66 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-lifecycle all 1.0.5+dfsg-1 [120 kB] 479s Get:67 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-magrittr arm64 2.0.3-1 [154 kB] 479s Get:68 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-utf8 arm64 1.2.4-1 [140 kB] 479s Get:69 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-vctrs arm64 0.6.5-1 [1327 kB] 481s Get:70 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-pillar all 1.11.1+dfsg-1 [456 kB] 481s Get:71 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-r6 all 2.6.1-1 [101 kB] 481s Get:72 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-fansi arm64 1.0.6-2 [627 kB] 482s Get:73 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-pkgconfig all 2.0.3-2build2 [20.4 kB] 482s Get:74 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-tibble arm64 3.2.1+dfsg-3 [420 kB] 482s Get:75 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-withr all 3.0.2+dfsg-1 [214 kB] 482s Get:76 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-tidyselect arm64 1.2.1+dfsg-1 [222 kB] 482s Get:77 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-dplyr arm64 1.1.4-4 [1534 kB] 486s Get:78 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-purrr arm64 1.0.4-1 [552 kB] 488s Get:79 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-stringi arm64 1.8.4-1build2 [901 kB] 490s Get:80 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-stringr all 1.5.1-1 [290 kB] 490s Get:81 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-cpp11 all 0.5.3-1 [242 kB] 490s Get:82 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-tidyr arm64 1.3.1-1 [1154 kB] 492s Get:83 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-broom all 1.0.12+dfsg-1 [1708 kB] 495s Get:84 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-farver arm64 2.1.2-1 [1344 kB] 497s Get:85 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-mass arm64 7.3-65-1 [1109 kB] 499s Get:86 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-geepack arm64 1.3.12-1 [377 kB] 499s Get:87 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-gtable all 0.3.6+dfsg-1 [199 kB] 499s Get:88 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-isoband arm64 0.2.7-1 [1481 kB] 502s Get:89 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-s7 arm64 0.2.0-1 [329 kB] 502s Get:90 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-labeling all 0.4.3-1 [62.1 kB] 502s Get:91 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-rcolorbrewer all 1.1-3-1build2 [54.0 kB] 502s Get:92 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-viridislite all 0.4.3-1 [1088 kB] 504s Get:93 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-scales all 1.4.0-1 [725 kB] 505s Get:94 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 r-cran-ggplot2 all 4.0.2+dfsg-1 [4941 kB] 514s Fetched 128 MB in 3min 55s (545 kB/s) 514s Selecting previously unselected package libc-dev-bin. 515s (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 ... 141794 files and directories currently installed.) 515s Preparing to unpack .../00-libc-dev-bin_2.42-2ubuntu4_arm64.deb ... 515s Unpacking libc-dev-bin (2.42-2ubuntu4) ... 515s Selecting previously unselected package linux-libc-dev:arm64. 515s Preparing to unpack .../01-linux-libc-dev_6.19.0-3.3_arm64.deb ... 515s Unpacking linux-libc-dev:arm64 (6.19.0-3.3) ... 515s Selecting previously unselected package libcrypt-dev:arm64. 515s Preparing to unpack .../02-libcrypt-dev_1%3a4.5.1-1_arm64.deb ... 515s Unpacking libcrypt-dev:arm64 (1:4.5.1-1) ... 515s Selecting previously unselected package rpcsvc-proto. 515s Preparing to unpack .../03-rpcsvc-proto_1.4.3-1build1_arm64.deb ... 515s Unpacking rpcsvc-proto (1.4.3-1build1) ... 515s Selecting previously unselected package libc6-dev:arm64. 515s Preparing to unpack .../04-libc6-dev_2.42-2ubuntu4_arm64.deb ... 515s Unpacking libc6-dev:arm64 (2.42-2ubuntu4) ... 515s Selecting previously unselected package libisl23:arm64. 515s Preparing to unpack .../05-libisl23_0.27-1build1_arm64.deb ... 515s Unpacking libisl23:arm64 (0.27-1build1) ... 515s Selecting previously unselected package libmpc3:arm64. 515s Preparing to unpack .../06-libmpc3_1.3.1-2_arm64.deb ... 515s Unpacking libmpc3:arm64 (1.3.1-2) ... 515s Selecting previously unselected package cpp-15-aarch64-linux-gnu. 515s Preparing to unpack .../07-cpp-15-aarch64-linux-gnu_15.2.0-12ubuntu1_arm64.deb ... 515s Unpacking cpp-15-aarch64-linux-gnu (15.2.0-12ubuntu1) ... 515s Selecting previously unselected package cpp-15. 515s Preparing to unpack .../08-cpp-15_15.2.0-12ubuntu1_arm64.deb ... 515s Unpacking cpp-15 (15.2.0-12ubuntu1) ... 515s Selecting previously unselected package cpp-aarch64-linux-gnu. 515s Preparing to unpack .../09-cpp-aarch64-linux-gnu_4%3a15.2.0-4ubuntu1_arm64.deb ... 515s Unpacking cpp-aarch64-linux-gnu (4:15.2.0-4ubuntu1) ... 515s Selecting previously unselected package cpp. 515s Preparing to unpack .../10-cpp_4%3a15.2.0-4ubuntu1_arm64.deb ... 515s Unpacking cpp (4:15.2.0-4ubuntu1) ... 515s Selecting previously unselected package libcc1-0:arm64. 515s Preparing to unpack .../11-libcc1-0_15.2.0-12ubuntu1_arm64.deb ... 515s Unpacking libcc1-0:arm64 (15.2.0-12ubuntu1) ... 515s Selecting previously unselected package libitm1:arm64. 515s Preparing to unpack .../12-libitm1_15.2.0-12ubuntu1_arm64.deb ... 515s Unpacking libitm1:arm64 (15.2.0-12ubuntu1) ... 515s Selecting previously unselected package libasan8:arm64. 515s Preparing to unpack .../13-libasan8_15.2.0-12ubuntu1_arm64.deb ... 515s Unpacking libasan8:arm64 (15.2.0-12ubuntu1) ... 516s Selecting previously unselected package liblsan0:arm64. 516s Preparing to unpack .../14-liblsan0_15.2.0-12ubuntu1_arm64.deb ... 516s Unpacking liblsan0:arm64 (15.2.0-12ubuntu1) ... 516s Selecting previously unselected package libtsan2:arm64. 516s Preparing to unpack .../15-libtsan2_15.2.0-12ubuntu1_arm64.deb ... 516s Unpacking libtsan2:arm64 (15.2.0-12ubuntu1) ... 516s Selecting previously unselected package libubsan1:arm64. 516s Preparing to unpack .../16-libubsan1_15.2.0-12ubuntu1_arm64.deb ... 516s Unpacking libubsan1:arm64 (15.2.0-12ubuntu1) ... 516s Selecting previously unselected package libhwasan0:arm64. 516s Preparing to unpack .../17-libhwasan0_15.2.0-12ubuntu1_arm64.deb ... 516s Unpacking libhwasan0:arm64 (15.2.0-12ubuntu1) ... 516s Selecting previously unselected package libgcc-15-dev:arm64. 516s Preparing to unpack .../18-libgcc-15-dev_15.2.0-12ubuntu1_arm64.deb ... 516s Unpacking libgcc-15-dev:arm64 (15.2.0-12ubuntu1) ... 516s Selecting previously unselected package gcc-15-aarch64-linux-gnu. 516s Preparing to unpack .../19-gcc-15-aarch64-linux-gnu_15.2.0-12ubuntu1_arm64.deb ... 516s Unpacking gcc-15-aarch64-linux-gnu (15.2.0-12ubuntu1) ... 516s Selecting previously unselected package gcc-15. 516s Preparing to unpack .../20-gcc-15_15.2.0-12ubuntu1_arm64.deb ... 516s Unpacking gcc-15 (15.2.0-12ubuntu1) ... 516s Selecting previously unselected package gcc-aarch64-linux-gnu. 516s Preparing to unpack .../21-gcc-aarch64-linux-gnu_4%3a15.2.0-4ubuntu1_arm64.deb ... 516s Unpacking gcc-aarch64-linux-gnu (4:15.2.0-4ubuntu1) ... 516s Selecting previously unselected package gcc. 516s Preparing to unpack .../22-gcc_4%3a15.2.0-4ubuntu1_arm64.deb ... 516s Unpacking gcc (4:15.2.0-4ubuntu1) ... 516s Selecting previously unselected package libstdc++-15-dev:arm64. 517s Preparing to unpack .../23-libstdc++-15-dev_15.2.0-12ubuntu1_arm64.deb ... 517s Unpacking libstdc++-15-dev:arm64 (15.2.0-12ubuntu1) ... 517s Selecting previously unselected package g++-15-aarch64-linux-gnu. 517s Preparing to unpack .../24-g++-15-aarch64-linux-gnu_15.2.0-12ubuntu1_arm64.deb ... 517s Unpacking g++-15-aarch64-linux-gnu (15.2.0-12ubuntu1) ... 517s Selecting previously unselected package g++-15. 517s Preparing to unpack .../25-g++-15_15.2.0-12ubuntu1_arm64.deb ... 517s Unpacking g++-15 (15.2.0-12ubuntu1) ... 517s Selecting previously unselected package g++-aarch64-linux-gnu. 517s Preparing to unpack .../26-g++-aarch64-linux-gnu_4%3a15.2.0-4ubuntu1_arm64.deb ... 517s Unpacking g++-aarch64-linux-gnu (4:15.2.0-4ubuntu1) ... 517s Selecting previously unselected package g++. 517s Preparing to unpack .../27-g++_4%3a15.2.0-4ubuntu1_arm64.deb ... 517s Unpacking g++ (4:15.2.0-4ubuntu1) ... 517s Selecting previously unselected package build-essential. 517s Preparing to unpack .../28-build-essential_12.12ubuntu2_arm64.deb ... 517s Unpacking build-essential (12.12ubuntu2) ... 517s Selecting previously unselected package dctrl-tools. 517s Preparing to unpack .../29-dctrl-tools_2.24-3build4_arm64.deb ... 517s Unpacking dctrl-tools (2.24-3build4) ... 517s Selecting previously unselected package libgfortran-15-dev:arm64. 517s Preparing to unpack .../30-libgfortran-15-dev_15.2.0-12ubuntu1_arm64.deb ... 517s Unpacking libgfortran-15-dev:arm64 (15.2.0-12ubuntu1) ... 517s Selecting previously unselected package gfortran-15-aarch64-linux-gnu. 517s Preparing to unpack .../31-gfortran-15-aarch64-linux-gnu_15.2.0-12ubuntu1_arm64.deb ... 517s Unpacking gfortran-15-aarch64-linux-gnu (15.2.0-12ubuntu1) ... 517s Selecting previously unselected package gfortran-15. 517s Preparing to unpack .../32-gfortran-15_15.2.0-12ubuntu1_arm64.deb ... 517s Unpacking gfortran-15 (15.2.0-12ubuntu1) ... 517s Selecting previously unselected package gfortran-aarch64-linux-gnu. 518s Preparing to unpack .../33-gfortran-aarch64-linux-gnu_4%3a15.2.0-4ubuntu1_arm64.deb ... 518s Unpacking gfortran-aarch64-linux-gnu (4:15.2.0-4ubuntu1) ... 518s Selecting previously unselected package gfortran. 518s Preparing to unpack .../34-gfortran_4%3a15.2.0-4ubuntu1_arm64.deb ... 518s Unpacking gfortran (4:15.2.0-4ubuntu1) ... 518s Selecting previously unselected package icu-devtools. 518s Preparing to unpack .../35-icu-devtools_78.2-1ubuntu1_arm64.deb ... 518s Unpacking icu-devtools (78.2-1ubuntu1) ... 518s Selecting previously unselected package libblas-dev:arm64. 518s Preparing to unpack .../36-libblas-dev_3.12.1-7ubuntu1_arm64.deb ... 518s Unpacking libblas-dev:arm64 (3.12.1-7ubuntu1) ... 518s Selecting previously unselected package libbz2-dev:arm64. 518s Preparing to unpack .../37-libbz2-dev_1.0.8-6build2_arm64.deb ... 518s Unpacking libbz2-dev:arm64 (1.0.8-6build2) ... 518s Selecting previously unselected package libdeflate-dev:arm64. 518s Preparing to unpack .../38-libdeflate-dev_1.23-2build1_arm64.deb ... 518s Unpacking libdeflate-dev:arm64 (1.23-2build1) ... 518s Selecting previously unselected package libicu-dev:arm64. 518s Preparing to unpack .../39-libicu-dev_78.2-1ubuntu1_arm64.deb ... 518s Unpacking libicu-dev:arm64 (78.2-1ubuntu1) ... 518s Selecting previously unselected package libjpeg-turbo8-dev:arm64. 518s Preparing to unpack .../40-libjpeg-turbo8-dev_2.1.5-4ubuntu3_arm64.deb ... 518s Unpacking libjpeg-turbo8-dev:arm64 (2.1.5-4ubuntu3) ... 518s Selecting previously unselected package libjpeg8-dev:arm64. 518s Preparing to unpack .../41-libjpeg8-dev_8c-2ubuntu11_arm64.deb ... 518s Unpacking libjpeg8-dev:arm64 (8c-2ubuntu11) ... 518s Selecting previously unselected package libjpeg-dev:arm64. 518s Preparing to unpack .../42-libjpeg-dev_8c-2ubuntu11_arm64.deb ... 518s Unpacking libjpeg-dev:arm64 (8c-2ubuntu11) ... 518s Selecting previously unselected package liblapack-dev:arm64. 518s Preparing to unpack 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Selecting previously unselected package r-cran-fansi. 520s Preparing to unpack .../71-r-cran-fansi_1.0.6-2_arm64.deb ... 520s Unpacking r-cran-fansi (1.0.6-2) ... 520s Selecting previously unselected package r-cran-pkgconfig. 520s Preparing to unpack .../72-r-cran-pkgconfig_2.0.3-2build2_all.deb ... 520s Unpacking r-cran-pkgconfig (2.0.3-2build2) ... 520s Selecting previously unselected package r-cran-tibble. 520s Preparing to unpack .../73-r-cran-tibble_3.2.1+dfsg-3_arm64.deb ... 520s Unpacking r-cran-tibble (3.2.1+dfsg-3) ... 520s Selecting previously unselected package r-cran-withr. 520s Preparing to unpack .../74-r-cran-withr_3.0.2+dfsg-1_all.deb ... 520s Unpacking r-cran-withr (3.0.2+dfsg-1) ... 520s Selecting previously unselected package r-cran-tidyselect. 520s Preparing to unpack .../75-r-cran-tidyselect_1.2.1+dfsg-1_arm64.deb ... 520s Unpacking r-cran-tidyselect (1.2.1+dfsg-1) ... 520s Selecting previously unselected package r-cran-dplyr. 520s Preparing to unpack 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Setting up libc-dev-bin (2.42-2ubuntu4) ... 521s Setting up libdeflate-dev:arm64 (1.23-2build1) ... 521s Setting up r-cran-magrittr (2.0.3-1) ... 521s Setting up libcc1-0:arm64 (15.2.0-12ubuntu1) ... 521s Setting up r-cran-vctrs (0.6.5-1) ... 521s Setting up liblsan0:arm64 (15.2.0-12ubuntu1) ... 521s Setting up libblas-dev:arm64 (3.12.1-7ubuntu1) ... 521s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so to provide /usr/lib/aarch64-linux-gnu/libblas.so (libblas.so-aarch64-linux-gnu) in auto mode 521s Setting up dctrl-tools (2.24-3build4) ... 521s Setting up libitm1:arm64 (15.2.0-12ubuntu1) ... 521s Setting up r-cran-pillar (1.11.1+dfsg-1) ... 521s Setting up cpp-15-aarch64-linux-gnu (15.2.0-12ubuntu1) ... 521s Setting up libgcc-15-dev:arm64 (15.2.0-12ubuntu1) ... 521s Setting up r-cran-stringr (1.5.1-1) ... 521s Setting up r-cran-tibble (3.2.1+dfsg-3) ... 521s Setting up libgfortran-15-dev:arm64 (15.2.0-12ubuntu1) ... 521s Setting up pkgconf:arm64 (1.8.1-4build1) ... 521s Setting up r-cran-tidyselect (1.2.1+dfsg-1) ... 521s Setting up cpp-aarch64-linux-gnu (4:15.2.0-4ubuntu1) ... 521s Setting up r-cran-scales (1.4.0-1) ... 521s Setting up liblapack-dev:arm64 (3.12.1-7ubuntu1) ... 521s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so to provide /usr/lib/aarch64-linux-gnu/liblapack.so (liblapack.so-aarch64-linux-gnu) in auto mode 521s Setting up r-cran-purrr (1.0.4-1) ... 521s Setting up cpp-15 (15.2.0-12ubuntu1) ... 521s Setting up cpp (4:15.2.0-4ubuntu1) ... 521s Setting up libc6-dev:arm64 (2.42-2ubuntu4) ... 521s Setting up r-cran-dplyr (1.1.4-4) ... 521s Setting up libicu-dev:arm64 (78.2-1ubuntu1) ... 521s Setting up libbz2-dev:arm64 (1.0.8-6build2) ... 521s Setting up libjpeg-turbo8-dev:arm64 (2.1.5-4ubuntu3) ... 521s Setting up libncurses-dev:arm64 (6.6+20251231-1) ... 521s Setting up gcc-15-aarch64-linux-gnu (15.2.0-12ubuntu1) ... 521s Setting up libpcre2-dev:arm64 (10.46-1) ... 521s Setting up r-cran-ggplot2 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(1.3.12-1) ... 521s Setting up gfortran (4:15.2.0-4ubuntu1) ... 521s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode 521s 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 521s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode 521s 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 521s Setting up g++ (4:15.2.0-4ubuntu1) ... 521s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 521s Setting up build-essential (12.12ubuntu2) ... 521s Setting up r-base-dev (4.5.2-1ubuntu2) ... 521s Setting up pkg-r-autopkgtest (20250812) ... 521s Processing triggers for libc-bin (2.42-2ubuntu4) ... 521s Processing triggers for man-db (2.13.1-1build1) ... 522s Processing triggers for install-info (7.2-5) ... 523s autopkgtest [23:44:59]: test pkg-r-autopkgtest: /usr/share/dh-r/pkg-r-autopkgtest 523s autopkgtest [23:44:59]: test pkg-r-autopkgtest: [----------------------- 523s Test: Try to load the R library etm 523s 523s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 523s Copyright (C) 2025 The R Foundation for Statistical Computing 523s Platform: aarch64-unknown-linux-gnu 523s 523s R is free software and comes with ABSOLUTELY NO WARRANTY. 523s You are welcome to redistribute it under certain conditions. 523s Type 'license()' or 'licence()' for distribution details. 523s 523s R is a collaborative project with many contributors. 523s Type 'contributors()' for more information and 523s 'citation()' on how to cite R or R packages in publications. 523s 523s Type 'demo()' for some demos, 'help()' for on-line help, or 523s 'help.start()' for an HTML browser interface to help. 523s Type 'q()' to quit R. 523s 523s > library('etm') 524s > 524s autopkgtest [23:45:00]: test pkg-r-autopkgtest: -----------------------] 525s pkg-r-autopkgtest PASS 525s autopkgtest [23:45:01]: test pkg-r-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 525s autopkgtest [23:45:01]: @@@@@@@@@@@@@@@@@@@@ summary 525s run-unit-test PASS 525s pkg-r-autopkgtest PASS