0s autopkgtest [22:57:17]: starting date and time: 2026-02-09 22:57:17+0000 0s autopkgtest [22:57:17]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [22:57:17]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.awe9dbfu/out --timeout-copy=6000 --needs-internet=try --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:lattice --apt-upgrade r-cran-etm --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=lattice/0.22-9-1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-cpu2-ram4-disk20-arm64 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@sto01-arm64-23.secgroup --name adt-resolute-arm64-r-cran-etm-20260209-225716-juju-7f2275-prod-proposed-migration-environment-15-cae1ef2a-fce4-4205-bec9-6f3079b5948e --image adt/ubuntu-resolute-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-autopkgtest-workers-arm64 -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 3s Creating nova instance adt-resolute-arm64-r-cran-etm-20260209-225716-juju-7f2275-prod-proposed-migration-environment-15-cae1ef2a-fce4-4205-bec9-6f3079b5948e from image adt/ubuntu-resolute-arm64-server-20260209.img (UUID 793037ca-75af-461b-82de-f8081300b2e3)... 111s autopkgtest [22:59:08]: testbed dpkg architecture: arm64 111s autopkgtest [22:59:08]: testbed apt version: 3.1.15 112s autopkgtest [22:59:09]: @@@@@@@@@@@@@@@@@@@@ test bed setup 112s autopkgtest [22:59:09]: testbed release detected to be: None 113s autopkgtest [22:59:10]: updating testbed package index (apt update) 113s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 113s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 113s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 113s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 113s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [176 kB] 113s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [1645 kB] 118s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [29.4 kB] 118s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 Packages [246 kB] 118s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 c-n-f Metadata [6216 B] 118s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/restricted arm64 c-n-f Metadata [304 B] 118s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 Packages [1580 kB] 120s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 c-n-f Metadata [32.0 kB] 121s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse arm64 Packages [21.7 kB] 121s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse arm64 c-n-f Metadata [688 B] 122s Fetched 3862 kB in 8s (496 kB/s) 123s Reading package lists... 123s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 123s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 124s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 124s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 124s Reading package lists... 124s Reading package lists... 125s Building dependency tree... 125s Reading state information... 125s Calculating upgrade... 125s The following packages will be upgraded: 125s cryptsetup-bin dracut-install iproute2 iptables libcryptsetup12 libip4tc2 125s libip6tc2 libxtables12 wget 125s 9 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 125s Need to get 2534 kB of archives. 125s After this operation, 18.4 kB of additional disk space will be used. 125s Get:1 http://ftpmaster.internal/ubuntu resolute/main arm64 iptables arm64 1.8.11-2ubuntu3 [386 kB] 125s Get:2 http://ftpmaster.internal/ubuntu resolute/main arm64 libip4tc2 arm64 1.8.11-2ubuntu3 [24.3 kB] 125s Get:3 http://ftpmaster.internal/ubuntu resolute/main arm64 libip6tc2 arm64 1.8.11-2ubuntu3 [24.7 kB] 125s Get:4 http://ftpmaster.internal/ubuntu resolute/main arm64 libxtables12 arm64 1.8.11-2ubuntu3 [36.7 kB] 126s Get:5 http://ftpmaster.internal/ubuntu resolute/main arm64 iproute2 arm64 6.18.0-1ubuntu1 [1171 kB] 128s Get:6 http://ftpmaster.internal/ubuntu resolute/main arm64 libcryptsetup12 arm64 2:2.8.0-1ubuntu3 [274 kB] 128s Get:7 http://ftpmaster.internal/ubuntu resolute/main arm64 wget arm64 1.25.0-2ubuntu4 [344 kB] 128s Get:8 http://ftpmaster.internal/ubuntu resolute/main arm64 cryptsetup-bin arm64 2:2.8.0-1ubuntu3 [227 kB] 128s Get:9 http://ftpmaster.internal/ubuntu resolute/main arm64 dracut-install arm64 109-11ubuntu1 [45.3 kB] 128s dpkg-preconfigure: unable to re-open stdin: No such file or directory 128s Fetched 2534 kB in 2s (1197 kB/s) 128s (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.) 128s Preparing to unpack .../0-iptables_1.8.11-2ubuntu3_arm64.deb ... 128s Unpacking iptables (1.8.11-2ubuntu3) over (1.8.11-2ubuntu2) ... 128s Preparing to unpack .../1-libip4tc2_1.8.11-2ubuntu3_arm64.deb ... 128s Unpacking libip4tc2:arm64 (1.8.11-2ubuntu3) over (1.8.11-2ubuntu2) ... 128s Preparing to unpack .../2-libip6tc2_1.8.11-2ubuntu3_arm64.deb ... 128s Unpacking libip6tc2:arm64 (1.8.11-2ubuntu3) over (1.8.11-2ubuntu2) ... 129s Preparing to unpack .../3-libxtables12_1.8.11-2ubuntu3_arm64.deb ... 129s Unpacking libxtables12:arm64 (1.8.11-2ubuntu3) over (1.8.11-2ubuntu2) ... 129s Preparing to unpack .../4-iproute2_6.18.0-1ubuntu1_arm64.deb ... 129s Unpacking iproute2 (6.18.0-1ubuntu1) over (6.16.0-1ubuntu3) ... 129s Preparing to unpack .../5-libcryptsetup12_2%3a2.8.0-1ubuntu3_arm64.deb ... 129s Unpacking libcryptsetup12:arm64 (2:2.8.0-1ubuntu3) over (2:2.8.0-1ubuntu2) ... 129s Preparing to unpack .../6-wget_1.25.0-2ubuntu4_arm64.deb ... 129s Unpacking wget (1.25.0-2ubuntu4) over (1.25.0-2ubuntu3) ... 129s Preparing to unpack .../7-cryptsetup-bin_2%3a2.8.0-1ubuntu3_arm64.deb ... 129s Unpacking cryptsetup-bin (2:2.8.0-1ubuntu3) over (2:2.8.0-1ubuntu2) ... 129s Preparing to unpack .../8-dracut-install_109-11ubuntu1_arm64.deb ... 129s Unpacking dracut-install (109-11ubuntu1) over (109-9ubuntu1) ... 129s Setting up libip4tc2:arm64 (1.8.11-2ubuntu3) ... 129s Setting up wget (1.25.0-2ubuntu4) ... 129s Setting up libip6tc2:arm64 (1.8.11-2ubuntu3) ... 129s Setting up libxtables12:arm64 (1.8.11-2ubuntu3) ... 129s Setting up dracut-install (109-11ubuntu1) ... 129s Setting up libcryptsetup12:arm64 (2:2.8.0-1ubuntu3) ... 129s Setting up cryptsetup-bin (2:2.8.0-1ubuntu3) ... 129s Setting up iptables (1.8.11-2ubuntu3) ... 129s Setting up iproute2 (6.18.0-1ubuntu1) ... 130s Processing triggers for man-db (2.13.1-1build1) ... 131s Processing triggers for install-info (7.2-5) ... 131s Processing triggers for libc-bin (2.42-2ubuntu4) ... 131s autopkgtest [22:59:28]: upgrading testbed (apt dist-upgrade and autopurge) 131s Reading package lists... 131s Building dependency tree... 131s Reading state information... 132s Calculating upgrade... 132s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 132s Reading package lists... 132s Building dependency tree... 132s Reading state information... 133s Solving dependencies... 133s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 135s autopkgtest [22:59:32]: testbed running kernel: Linux 6.19.0-3-generic #3-Ubuntu SMP PREEMPT_DYNAMIC Fri Jan 23 19:46:27 UTC 2026 136s autopkgtest [22:59:33]: @@@@@@@@@@@@@@@@@@@@ apt-source r-cran-etm 137s Get:1 http://ftpmaster.internal/ubuntu resolute/universe r-cran-etm 1.1.1-1build1 (dsc) [2147 B] 137s Get:2 http://ftpmaster.internal/ubuntu resolute/universe r-cran-etm 1.1.1-1build1 (tar) [242 kB] 137s Get:3 http://ftpmaster.internal/ubuntu resolute/universe r-cran-etm 1.1.1-1build1 (diff) [3672 B] 137s gpgv: Signature made Fri Nov 28 21:46:53 2025 UTC 137s gpgv: using RSA key 92FE4F8B40CADC4ECCD60C1F5961FDBE9C619809 137s gpgv: Can't check signature: No public key 137s dpkg-source: warning: cannot verify inline signature for ./r-cran-etm_1.1.1-1build1.dsc: no acceptable signature found 137s autopkgtest [22:59:34]: testing package r-cran-etm version 1.1.1-1build1 138s autopkgtest [22:59:35]: build not needed 139s autopkgtest [22:59:36]: test run-unit-test: preparing testbed 139s Reading package lists... 139s Building dependency tree... 139s Reading state information... 139s Solving dependencies... 140s The following NEW packages will be installed: 140s fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono libblas3 140s libcairo2 libdatrie1 libdeflate0 libfontconfig1 libgfortran5 libgomp1 140s libgraphite2-3 libharfbuzz0b libice6 libjbig0 libjpeg-turbo8 libjpeg8 140s liblapack3 liblerc4 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 140s libpaper-utils libpaper2 libpixman-1-0 libsharpyuv0 libsm6 libtcl8.6 140s libthai-data libthai0 libtiff6 libtk8.6 libwebp7 libxcb-render0 libxcb-shm0 140s libxft2 libxrender1 libxss1 libxt6t64 r-base-core r-cran-data.table 140s r-cran-dbi r-cran-etm r-cran-kmi r-cran-lattice r-cran-littler r-cran-matrix 140s r-cran-mitools r-cran-pkgkitten r-cran-rcpp r-cran-rcpparmadillo 140s r-cran-survival unzip x11-common xdg-utils zip 140s 0 upgraded, 56 newly installed, 0 to remove and 0 not upgraded. 140s Need to get 59.4 MB of archives. 140s After this operation, 125 MB of additional disk space will be used. 140s Get:1 http://ftpmaster.internal/ubuntu resolute/main arm64 fonts-dejavu-mono all 2.37-8build1 [502 kB] 140s Get:2 http://ftpmaster.internal/ubuntu resolute/main arm64 fonts-dejavu-core all 2.37-8build1 [834 kB] 141s Get:3 http://ftpmaster.internal/ubuntu resolute/main arm64 fontconfig-config arm64 2.17.1-3ubuntu1 [38.5 kB] 141s Get:4 http://ftpmaster.internal/ubuntu resolute/main arm64 libfontconfig1 arm64 2.17.1-3ubuntu1 [144 kB] 141s Get:5 http://ftpmaster.internal/ubuntu resolute/main arm64 fontconfig arm64 2.17.1-3ubuntu1 [181 kB] 141s Get:6 http://ftpmaster.internal/ubuntu resolute/main arm64 libblas3 arm64 3.12.1-7ubuntu1 [181 kB] 141s Get:7 http://ftpmaster.internal/ubuntu resolute/main arm64 libpixman-1-0 arm64 0.46.4-1 [204 kB] 141s Get:8 http://ftpmaster.internal/ubuntu resolute/main arm64 libxcb-render0 arm64 1.17.0-2ubuntu1 [16.4 kB] 141s Get:9 http://ftpmaster.internal/ubuntu resolute/main arm64 libxcb-shm0 arm64 1.17.0-2ubuntu1 [5938 B] 141s Get:10 http://ftpmaster.internal/ubuntu resolute/main arm64 libxrender1 arm64 1:0.9.12-1 [19.5 kB] 141s Get:11 http://ftpmaster.internal/ubuntu resolute/main arm64 libcairo2 arm64 1.18.4-3 [556 kB] 142s Get:12 http://ftpmaster.internal/ubuntu resolute/main arm64 libdatrie1 arm64 0.2.14-1 [19.6 kB] 142s Get:13 http://ftpmaster.internal/ubuntu resolute/main arm64 libdeflate0 arm64 1.23-2build1 [46.8 kB] 142s Get:14 http://ftpmaster.internal/ubuntu resolute/main arm64 libgfortran5 arm64 15.2.0-12ubuntu1 [451 kB] 142s Get:15 http://ftpmaster.internal/ubuntu resolute/main arm64 libgomp1 arm64 15.2.0-12ubuntu1 [147 kB] 142s Get:16 http://ftpmaster.internal/ubuntu resolute/main arm64 libgraphite2-3 arm64 1.3.14-11ubuntu1 [72.1 kB] 142s Get:17 http://ftpmaster.internal/ubuntu resolute/main arm64 libharfbuzz0b arm64 12.3.2-1 [510 kB] 142s Get:18 http://ftpmaster.internal/ubuntu resolute/main arm64 x11-common all 1:7.7+24ubuntu1 [22.4 kB] 142s Get:19 http://ftpmaster.internal/ubuntu resolute/main arm64 libice6 arm64 2:1.1.1-1build1 [43.0 kB] 142s Get:20 http://ftpmaster.internal/ubuntu resolute/main arm64 libjpeg-turbo8 arm64 2.1.5-4ubuntu3 [161 kB] 143s Get:21 http://ftpmaster.internal/ubuntu resolute/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 143s Get:22 http://ftpmaster.internal/ubuntu resolute/main arm64 liblapack3 arm64 3.12.1-7ubuntu1 [2299 kB] 147s Get:23 http://ftpmaster.internal/ubuntu resolute/main arm64 liblerc4 arm64 4.0.0+ds-5ubuntu2 [174 kB] 147s Get:24 http://ftpmaster.internal/ubuntu resolute/main arm64 libthai-data all 0.1.30-1 [155 kB] 147s Get:25 http://ftpmaster.internal/ubuntu resolute/main arm64 libthai0 arm64 0.1.30-1 [18.3 kB] 147s Get:26 http://ftpmaster.internal/ubuntu resolute/main arm64 libpango-1.0-0 arm64 1.57.0-1 [238 kB] 147s Get:27 http://ftpmaster.internal/ubuntu resolute/main arm64 libpangoft2-1.0-0 arm64 1.57.0-1 [51.5 kB] 147s Get:28 http://ftpmaster.internal/ubuntu resolute/main arm64 libpangocairo-1.0-0 arm64 1.57.0-1 [27.9 kB] 147s Get:29 http://ftpmaster.internal/ubuntu resolute/main arm64 libpaper2 arm64 2.2.5-0.3build1 [17.3 kB] 147s Get:30 http://ftpmaster.internal/ubuntu resolute/main arm64 libpaper-utils arm64 2.2.5-0.3build1 [15.4 kB] 147s Get:31 http://ftpmaster.internal/ubuntu resolute/main arm64 libsharpyuv0 arm64 1.5.0-0.1build1 [16.7 kB] 147s Get:32 http://ftpmaster.internal/ubuntu resolute/main arm64 libsm6 arm64 2:1.2.6-1build1 [16.8 kB] 147s Get:33 http://ftpmaster.internal/ubuntu resolute/main arm64 libtcl8.6 arm64 8.6.17+dfsg-1build1 [983 kB] 148s Get:34 http://ftpmaster.internal/ubuntu resolute/main arm64 libjbig0 arm64 2.1-6.1ubuntu3 [29.2 kB] 148s Get:35 http://ftpmaster.internal/ubuntu resolute/main arm64 libwebp7 arm64 1.5.0-0.1build1 [205 kB] 148s Get:36 http://ftpmaster.internal/ubuntu resolute/main arm64 libtiff6 arm64 4.7.0-3ubuntu3 [196 kB] 148s Get:37 http://ftpmaster.internal/ubuntu resolute/main arm64 libxft2 arm64 2.3.6-1build2 [43.2 kB] 148s Get:38 http://ftpmaster.internal/ubuntu resolute/main arm64 libxss1 arm64 1:1.2.3-1build4 [7102 B] 148s Get:39 http://ftpmaster.internal/ubuntu resolute/main arm64 libtk8.6 arm64 8.6.17-1 [811 kB] 150s Get:40 http://ftpmaster.internal/ubuntu resolute/main arm64 libxt6t64 arm64 1:1.2.1-1.3 [168 kB] 150s Get:41 http://ftpmaster.internal/ubuntu resolute/main arm64 zip arm64 3.0-15ubuntu3 [170 kB] 150s Get:42 http://ftpmaster.internal/ubuntu resolute/main arm64 unzip arm64 6.0-29ubuntu1 [176 kB] 150s Get:43 http://ftpmaster.internal/ubuntu resolute/main arm64 xdg-utils all 1.2.1-2ubuntu2 [66.1 kB] 150s Get:44 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-base-core arm64 4.5.2-1ubuntu2 [28.6 MB] 197s Get:45 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-data.table arm64 1.17.0+dfsg-1 [2129 kB] 201s Get:46 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-dbi all 1.2.3-1build1 [855 kB] 203s Get:47 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 r-cran-lattice arm64 0.22-9-1 [1399 kB] 206s Get:48 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-matrix arm64 1.7-4-1 [4146 kB] 212s Get:49 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-survival arm64 3.8-6-1 [8270 kB] 225s Get:50 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-littler arm64 0.3.22-1 [85.1 kB] 225s Get:51 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-pkgkitten all 0.2.4-1 [27.2 kB] 225s Get:52 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-rcpp arm64 1.1.0-1 [2011 kB] 228s Get:53 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-rcpparmadillo arm64 15.2.3-1-1 [916 kB] 229s Get:54 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-etm arm64 1.1.1-1build1 [478 kB] 230s Get:55 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-mitools all 2.4-2build2 [266 kB] 230s Get:56 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-kmi all 0.5.5-2build2 [78.9 kB] 230s Preconfiguring packages ... 231s Fetched 59.4 MB in 1min 30s (657 kB/s) 231s Selecting previously unselected package fonts-dejavu-mono. 231s (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.) 231s Preparing to unpack .../00-fonts-dejavu-mono_2.37-8build1_all.deb ... 231s Unpacking fonts-dejavu-mono (2.37-8build1) ... 231s Selecting previously unselected package fonts-dejavu-core. 231s Preparing to unpack .../01-fonts-dejavu-core_2.37-8build1_all.deb ... 231s Unpacking fonts-dejavu-core (2.37-8build1) ... 231s Selecting previously unselected package fontconfig-config. 231s Preparing to unpack .../02-fontconfig-config_2.17.1-3ubuntu1_arm64.deb ... 231s Unpacking fontconfig-config (2.17.1-3ubuntu1) ... 231s Selecting previously unselected package libfontconfig1:arm64. 231s Preparing to unpack .../03-libfontconfig1_2.17.1-3ubuntu1_arm64.deb ... 231s Unpacking libfontconfig1:arm64 (2.17.1-3ubuntu1) ... 231s Selecting previously unselected package fontconfig. 231s Preparing to unpack .../04-fontconfig_2.17.1-3ubuntu1_arm64.deb ... 231s Unpacking fontconfig (2.17.1-3ubuntu1) ... 231s Selecting previously unselected package libblas3:arm64. 231s Preparing to unpack .../05-libblas3_3.12.1-7ubuntu1_arm64.deb ... 231s Unpacking libblas3:arm64 (3.12.1-7ubuntu1) ... 231s Selecting previously unselected package libpixman-1-0:arm64. 231s Preparing to unpack .../06-libpixman-1-0_0.46.4-1_arm64.deb ... 231s Unpacking libpixman-1-0:arm64 (0.46.4-1) ... 231s Selecting previously unselected package libxcb-render0:arm64. 231s Preparing to unpack .../07-libxcb-render0_1.17.0-2ubuntu1_arm64.deb ... 231s Unpacking libxcb-render0:arm64 (1.17.0-2ubuntu1) ... 231s Selecting previously unselected package libxcb-shm0:arm64. 231s Preparing to unpack .../08-libxcb-shm0_1.17.0-2ubuntu1_arm64.deb ... 231s Unpacking libxcb-shm0:arm64 (1.17.0-2ubuntu1) ... 231s Selecting previously unselected package libxrender1:arm64. 231s Preparing to unpack .../09-libxrender1_1%3a0.9.12-1_arm64.deb ... 231s Unpacking libxrender1:arm64 (1:0.9.12-1) ... 231s Selecting previously unselected package libcairo2:arm64. 231s Preparing to unpack .../10-libcairo2_1.18.4-3_arm64.deb ... 231s Unpacking libcairo2:arm64 (1.18.4-3) ... 231s Selecting previously unselected package libdatrie1:arm64. 231s Preparing to unpack .../11-libdatrie1_0.2.14-1_arm64.deb ... 231s Unpacking libdatrie1:arm64 (0.2.14-1) ... 231s Selecting previously unselected package libdeflate0:arm64. 232s Preparing to unpack .../12-libdeflate0_1.23-2build1_arm64.deb ... 232s Unpacking libdeflate0:arm64 (1.23-2build1) ... 232s Selecting previously unselected package libgfortran5:arm64. 232s Preparing to unpack .../13-libgfortran5_15.2.0-12ubuntu1_arm64.deb ... 232s Unpacking libgfortran5:arm64 (15.2.0-12ubuntu1) ... 232s Selecting previously unselected package libgomp1:arm64. 232s Preparing to unpack .../14-libgomp1_15.2.0-12ubuntu1_arm64.deb ... 232s Unpacking libgomp1:arm64 (15.2.0-12ubuntu1) ... 232s Selecting previously unselected package libgraphite2-3:arm64. 232s Preparing to unpack .../15-libgraphite2-3_1.3.14-11ubuntu1_arm64.deb ... 232s Unpacking libgraphite2-3:arm64 (1.3.14-11ubuntu1) ... 232s Selecting previously unselected package libharfbuzz0b:arm64. 232s Preparing to unpack .../16-libharfbuzz0b_12.3.2-1_arm64.deb ... 232s Unpacking libharfbuzz0b:arm64 (12.3.2-1) ... 232s Selecting previously unselected package x11-common. 232s Preparing to unpack .../17-x11-common_1%3a7.7+24ubuntu1_all.deb ... 232s Unpacking x11-common (1:7.7+24ubuntu1) ... 232s Selecting previously unselected package libice6:arm64. 232s Preparing to unpack .../18-libice6_2%3a1.1.1-1build1_arm64.deb ... 232s Unpacking libice6:arm64 (2:1.1.1-1build1) ... 232s Selecting previously unselected package libjpeg-turbo8:arm64. 232s Preparing to unpack .../19-libjpeg-turbo8_2.1.5-4ubuntu3_arm64.deb ... 232s Unpacking libjpeg-turbo8:arm64 (2.1.5-4ubuntu3) ... 232s Selecting previously unselected package libjpeg8:arm64. 232s Preparing to unpack .../20-libjpeg8_8c-2ubuntu11_arm64.deb ... 232s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 232s Selecting previously unselected package liblapack3:arm64. 232s Preparing to unpack .../21-liblapack3_3.12.1-7ubuntu1_arm64.deb ... 232s Unpacking liblapack3:arm64 (3.12.1-7ubuntu1) ... 232s Selecting previously unselected package liblerc4:arm64. 232s Preparing to unpack .../22-liblerc4_4.0.0+ds-5ubuntu2_arm64.deb ... 232s Unpacking liblerc4:arm64 (4.0.0+ds-5ubuntu2) ... 232s Selecting previously unselected package libthai-data. 232s Preparing to unpack .../23-libthai-data_0.1.30-1_all.deb ... 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r-cran-rcpparmadillo (15.2.3-1-1) ... 237s Setting up r-cran-mitools (2.4-2build2) ... 237s Setting up r-cran-survival (3.8-6-1) ... 237s Setting up r-cran-kmi (0.5.5-2build2) ... 237s Setting up r-cran-etm (1.1.1-1build1) ... 237s Processing triggers for man-db (2.13.1-1build1) ... 238s Processing triggers for install-info (7.2-5) ... 238s Processing triggers for libc-bin (2.42-2ubuntu4) ... 239s autopkgtest [23:01:16]: test run-unit-test: [----------------------- 239s BEGIN TEST test.etmCIF.R 239s 239s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 239s Copyright (C) 2025 The R Foundation for Statistical Computing 239s Platform: aarch64-unknown-linux-gnu 239s 239s R is free software and comes with ABSOLUTELY NO WARRANTY. 239s You are welcome to redistribute it under certain conditions. 239s Type 'license()' or 'licence()' for distribution details. 239s 239s R is a collaborative project with many contributors. 239s Type 'contributors()' for more information and 239s 'citation()' on how to cite R or R packages in publications. 239s 239s Type 'demo()' for some demos, 'help()' for on-line help, or 239s 'help.start()' for an HTML browser interface to help. 239s Type 'q()' to quit R. 239s 239s > ### test file for etmCIF. 239s > ### Really simple tests and comparison with etm 239s > 239s > old <- options(digits = 5) 239s > 239s > require(etm) 239s Loading required package: etm 240s > 240s > if (!require(survival, quietly = TRUE)) { 240s + print("The following tests require the 'survival' package") 240s + } else { 240s + 240s + data(abortion) 240s + 240s + from <- rep(0, nrow(abortion)) 240s + to <- abortion$cause 240s + entry <- abortion$entry 240s + exit <- abortion$exit 240s + id <- 1:nrow(abortion) 240s + data <- data.frame(id, from, to, entry, exit, group = abortion$group) 240s + 240s + ## Computation of the CIFs with etm 240s + tra <- matrix(FALSE, 4, 4) 240s + tra[1, 2:4] <- TRUE 240s + 240s + cif.control <- etm(data[data$group == 0, ], c("0", "1", "2", "3"), 240s + tra, NULL, 0) 240s + cif.exposed <- etm(data[data$group == 1, ], c("0", "1", "2", "3"), 240s + tra, NULL, 0) 240s + 240s + 240s + ## Computation of the CIFs with etmCIF 240s + netm <- etmCIF(Surv(entry, exit, cause != 0) ~ group, abortion, 240s + etype = cause, failcode = 3) 240s + 240s + ### let's do some comparisons :-) 240s + 240s + all.equal(trprob(cif.control, "0 3"), netm[[1]]$est["0", "3", ]) 240s + all.equal(trprob(cif.control, "0 2"), netm[[1]]$est["0", "2", ]) 240s + all.equal(trprob(cif.control, "0 1"), netm[[1]]$est["0", "1", ]) 240s + 240s + all.equal(trprob(cif.exposed, "0 3"), netm[[2]]$est["0", "3", ]) 240s + all.equal(trprob(cif.exposed, "0 2"), netm[[2]]$est["0", "2", ]) 240s + all.equal(trprob(cif.exposed, "0 1"), netm[[2]]$est["0", "1", ]) 240s + 240s + 240s + all.equal(trcov(cif.control, "0 3"), netm[[1]]$cov["0 3", "0 3", ]) 240s + all.equal(trcov(cif.control, "0 2"), netm[[1]]$cov["0 2", "0 2", ]) 240s + all.equal(trcov(cif.control, "0 1"), netm[[1]]$cov["0 1", "0 1", ]) 240s + 240s + all.equal(trcov(cif.exposed, "0 3"), netm[[2]]$cov["0 3", "0 3", ]) 240s + all.equal(trcov(cif.exposed, "0 2"), netm[[2]]$cov["0 2", "0 2", ]) 240s + all.equal(trcov(cif.exposed, "0 1"), netm[[2]]$cov["0 1", "0 1", ]) 240s + 240s + 240s + netm 240s + 240s + ## test on the summary 240s + snetm <- summary(netm) 240s + 240s + snetm 240s + 240s + all.equal(unname(trprob(cif.control, "0 3")), snetm[[1]][[3]]$P) 240s + all.equal(unname(trprob(cif.control, "0 2")), snetm[[1]][[2]]$P) 240s + all.equal(unname(trprob(cif.control, "0 1")), snetm[[1]][[1]]$P) 240s + 240s + all.equal(unname(trprob(cif.exposed, "0 3")), snetm[[2]][[3]]$P) 240s + all.equal(unname(trprob(cif.exposed, "0 2")), snetm[[2]][[2]]$P) 240s + all.equal(unname(trprob(cif.exposed, "0 1")), snetm[[2]][[1]]$P) 240s + 240s + scif.control <- summary(cif.control, ci.fun = "cloglog") 240s + scif.exposed <- summary(cif.exposed, ci.fun = "cloglog") 240s + 240s + all.equal(scif.control[[4]]$lower, snetm[[1]][[3]]$lower) 240s + all.equal(scif.control[[4]]$upper, snetm[[1]][[3]]$upper) 240s + 240s + all.equal(scif.exposed[[4]]$lower, snetm[[2]][[3]]$lower) 240s + all.equal(scif.exposed[[4]]$upper, snetm[[2]][[3]]$upper) 240s + } 240s [1] TRUE 240s > 240s > ### test with factors in the input 240s > abortion$status <- with(abortion, ifelse(cause == 2, "life birth", 240s + ifelse(cause == 1, "ETOP", "spontaneous abortion"))) 240s > 240s > abortion$status <- factor(abortion$status) 240s > 240s > netm.factor <- etmCIF(Surv(entry, exit, status != "cens") ~ group, abortion, 240s + etype = status, failcode = "spontaneous abortion") 240s > 240s > 240s > all.equal(trprob(cif.control, "0 3"), netm.factor[[1]]$est["0", "spontaneous abortion", ]) 240s [1] TRUE 240s > all.equal(trprob(cif.control, "0 2"), netm.factor[[1]]$est["0", "life birth", ]) 240s [1] TRUE 240s > 240s > netm.factor 240s Call: etmCIF(formula = Surv(entry, exit, status != "cens") ~ group, 240s data = abortion, etype = status, failcode = "spontaneous abortion") 240s 240s Covariate: group 240s levels: 0 1 240s 240s 240s group = 0 240s time P se(P) n.event 240s CIF ETOP 43 0.040159 0.0092578 20 240s CIF life birth 43 0.799059 0.0221865 924 240s CIF spontaneous abortion 43 0.160781 0.0213261 69 240s 240s group = 1 240s time P se(P) n.event 240s CIF ETOP 42 0.28511 0.042493 38 240s CIF life birth 42 0.35257 0.042139 92 240s CIF spontaneous abortion 42 0.36232 0.049473 43 240s > 240s > summary(netm.factor) 240s 240s group=0 240s 240s CIF ETOP 240s P time var lower upper n.risk n.event 240s 0.000000 6 0.0000e+00 0.000000 0.000000 117 0 240s 0.038955 13 8.4440e-05 0.024488 0.061694 645 1 240s 0.040159 26 8.5707e-05 0.025513 0.062939 846 0 240s 0.040159 36 8.5707e-05 0.025513 0.062939 876 0 240s 0.040159 40 8.5707e-05 0.025513 0.062939 554 0 240s 0.040159 43 8.5707e-05 0.025513 0.062939 6 0 240s 240s CIF life birth 240s P time var lower upper n.risk n.event 240s 0.000000 6 0.0000e+00 0.000000 0.000000 117 0 240s 0.000000 13 0.0000e+00 0.000000 0.000000 645 0 240s 0.000000 26 0.0000e+00 0.000000 0.000000 846 0 240s 0.053197 36 4.6195e-05 0.041379 0.068268 876 25 240s 0.563121 40 3.8801e-04 0.524924 0.602021 554 280 240s 0.799059 43 4.9224e-04 0.753969 0.840613 6 6 240s 240s CIF spontaneous abortion 240s P time var lower upper n.risk n.event 240s 0.034188 6 0.00028222 0.01297 0.088523 117 4 240s 0.150468 13 0.00045513 0.11360 0.197901 645 1 240s 0.159904 26 0.00045498 0.12274 0.206925 846 1 240s 0.160781 36 0.00045480 0.12360 0.207757 876 1 240s 0.160781 40 0.00045480 0.12360 0.207757 554 0 240s 0.160781 43 0.00045480 0.12360 0.207757 6 0 240s 240s 240s group=1 240s 240s CIF ETOP 240s P time var lower upper n.risk n.event 240s 0.00000 6 0.0000000 0.00000 0.00000 35 0 240s 0.26048 13 0.0017854 0.18795 0.35425 90 0 240s 0.28115 21 0.0018028 0.20742 0.37423 93 1 240s 0.28511 34 0.0018057 0.21116 0.37806 89 0 240s 0.28511 39 0.0018057 0.21116 0.37806 59 0 240s 0.28511 42 0.0018057 0.21116 0.37806 6 0 240s 240s CIF life birth 240s P time var lower upper n.risk n.event 240s 0.000000 6 0.0000e+00 0.000000 0.000000 35 0 240s 0.000000 13 0.0000e+00 0.000000 0.000000 90 0 240s 0.000000 21 0.0000e+00 0.000000 0.000000 93 0 240s 0.023073 34 9.0514e-05 0.010252 0.051504 89 2 240s 0.180156 39 8.0126e-04 0.131765 0.243663 59 13 240s 0.352565 42 1.7757e-03 0.276882 0.441775 6 6 240s 240s CIF spontaneous abortion 240s P time var lower upper n.risk n.event 240s 0.057143 6 0.0015394 0.014605 0.20968 35 2 240s 0.333246 13 0.0025280 0.245337 0.44216 90 4 240s 0.350702 21 0.0024827 0.262769 0.45762 93 0 240s 0.358492 34 0.0024593 0.270627 0.46448 89 0 240s 0.358492 39 0.0024593 0.270627 0.46448 59 0 240s 0.362323 42 0.0024476 0.274499 0.46785 6 0 240s 240s > 240s > ### test with group as a character vector 240s > abortion$ttt <- with(abortion, ifelse(group == 0, "control", "exposed")) 240s > abortion$ttt <- factor(abortion$ttt) 240s > 240s > netm.ttt <- etmCIF(Surv(entry, exit, status != "cens") ~ ttt, abortion, 240s + etype = status, failcode = "spontaneous abortion") 241s > 241s > all.equal(trprob(cif.control, "0 3"), netm.ttt[[1]]$est["0", "spontaneous abortion", ]) 241s [1] TRUE 241s > all.equal(trprob(cif.control, "0 2"), netm.ttt[[1]]$est["0", "life birth", ]) 241s [1] TRUE 241s > 241s > netm.ttt 241s Call: etmCIF(formula = Surv(entry, exit, status != "cens") ~ ttt, data = abortion, 241s etype = status, failcode = "spontaneous abortion") 241s 241s Covariate: ttt 241s levels: control exposed 241s 241s 241s ttt = control 241s time P se(P) n.event 241s CIF ETOP 43 0.040159 0.0092578 20 241s CIF life birth 43 0.799059 0.0221865 924 241s CIF spontaneous abortion 43 0.160781 0.0213261 69 241s 241s ttt = exposed 241s time P se(P) n.event 241s CIF ETOP 42 0.28511 0.042493 38 241s CIF life birth 42 0.35257 0.042139 92 241s CIF spontaneous abortion 42 0.36232 0.049473 43 241s > 241s > summary(netm.ttt) 241s 241s ttt=control 241s 241s CIF ETOP 241s P time var lower upper n.risk n.event 241s 0.000000 6 0.0000e+00 0.000000 0.000000 117 0 241s 0.038955 13 8.4440e-05 0.024488 0.061694 645 1 241s 0.040159 26 8.5707e-05 0.025513 0.062939 846 0 241s 0.040159 36 8.5707e-05 0.025513 0.062939 876 0 241s 0.040159 40 8.5707e-05 0.025513 0.062939 554 0 241s 0.040159 43 8.5707e-05 0.025513 0.062939 6 0 241s 241s CIF life birth 241s P time var lower upper n.risk n.event 241s 0.000000 6 0.0000e+00 0.000000 0.000000 117 0 241s 0.000000 13 0.0000e+00 0.000000 0.000000 645 0 241s 0.000000 26 0.0000e+00 0.000000 0.000000 846 0 241s 0.053197 36 4.6195e-05 0.041379 0.068268 876 25 241s 0.563121 40 3.8801e-04 0.524924 0.602021 554 280 241s 0.799059 43 4.9224e-04 0.753969 0.840613 6 6 241s 241s CIF spontaneous abortion 241s P time var lower upper n.risk n.event 241s 0.034188 6 0.00028222 0.01297 0.088523 117 4 241s 0.150468 13 0.00045513 0.11360 0.197901 645 1 241s 0.159904 26 0.00045498 0.12274 0.206925 846 1 241s 0.160781 36 0.00045480 0.12360 0.207757 876 1 241s 0.160781 40 0.00045480 0.12360 0.207757 554 0 241s 0.160781 43 0.00045480 0.12360 0.207757 6 0 241s 241s 241s ttt=exposed 241s 241s CIF ETOP 241s P time var lower upper n.risk n.event 241s 0.00000 6 0.0000000 0.00000 0.00000 35 0 241s 0.26048 13 0.0017854 0.18795 0.35425 90 0 241s 0.28115 21 0.0018028 0.20742 0.37423 93 1 241s 0.28511 34 0.0018057 0.21116 0.37806 89 0 241s 0.28511 39 0.0018057 0.21116 0.37806 59 0 241s 0.28511 42 0.0018057 0.21116 0.37806 6 0 241s 241s CIF life birth 241s P time var lower upper n.risk n.event 241s 0.000000 6 0.0000e+00 0.000000 0.000000 35 0 241s 0.000000 13 0.0000e+00 0.000000 0.000000 90 0 241s 0.000000 21 0.0000e+00 0.000000 0.000000 93 0 241s 0.023073 34 9.0514e-05 0.010252 0.051504 89 2 241s 0.180156 39 8.0126e-04 0.131765 0.243663 59 13 241s 0.352565 42 1.7757e-03 0.276882 0.441775 6 6 241s 241s CIF spontaneous abortion 241s P time var lower upper n.risk n.event 241s 0.057143 6 0.0015394 0.014605 0.20968 35 2 241s 0.333246 13 0.0025280 0.245337 0.44216 90 4 241s 0.350702 21 0.0024827 0.262769 0.45762 93 0 241s 0.358492 34 0.0024593 0.270627 0.46448 89 0 241s 0.358492 39 0.0024593 0.270627 0.46448 59 0 241s 0.362323 42 0.0024476 0.274499 0.46785 6 0 241s 241s > 241s > 241s > ### A couple of comparisons with simulated data 241s > set.seed(1313) 241s > time <- rexp(100) 241s > to <- rbinom(100, 2, prob = c(1/3, 1/3, 1/3)) 241s > from <- rep(11, 100) 241s > id <- 1:100 241s > cov <- rbinom(100, 1, 0.5) 241s > 241s > dat.s <- data.frame(id, time, from, to, cov) 241s > 241s > traa <- matrix(FALSE, 3, 3) 241s > traa[1, 2:3] <- TRUE 241s > 241s > aa0 <- etm(dat.s[dat.s$cov == 0, ], c("11", "1", "2"), traa, "0", 0) 241s > aa1 <- etm(dat.s[dat.s$cov == 1, ], c("11", "1", "2"), traa, "0", 0) 241s > aa <- etm(dat.s, c("11", "1", "2"), traa, "0", 0) 241s > 241s > test <- etmCIF(Surv(time, to != 0) ~ 1, dat.s, etype = to) 241s > 241s > test.c <- etmCIF(Surv(time, to != 0) ~ cov, dat.s, etype = to) 241s > 241s > all.equal(trprob(aa, "11 1"), test[[1]]$est["0", "1", ]) 241s [1] TRUE 241s > all.equal(trprob(aa, "11 2"), test[[1]]$est["0", "2", ]) 241s [1] TRUE 241s > 241s > all.equal(trprob(aa0, "11 1"), test.c[[1]]$est["0", "1", ]) 241s [1] TRUE 241s > all.equal(trprob(aa0, "11 2"), test.c[[1]]$est["0", "2", ]) 241s [1] TRUE 241s > 241s > all.equal(trprob(aa1, "11 1"), test.c[[2]]$est["0", "1", ]) 241s [1] TRUE 241s > all.equal(trprob(aa1, "11 2"), test.c[[2]]$est["0", "2", ]) 241s [1] TRUE 241s > 241s > test 241s Call: etmCIF(formula = Surv(time, to != 0) ~ 1, data = dat.s, etype = to) 241s 241s time P se(P) n.event 241s CIF 1 4.9088 0.809108 0.079680 45 241s CIF 2 4.9088 0.096618 0.032905 8 241s > 241s > test.c 241s Call: etmCIF(formula = Surv(time, to != 0) ~ cov, data = dat.s, etype = to) 241s 241s Covariate: cov 241s levels: 0 1 241s 241s 241s cov = 0 241s time P se(P) n.event 241s CIF 1 2.1708 0.70246 0.105797 19 241s CIF 2 2.1708 0.11144 0.053384 4 241s 241s cov = 1 241s time P se(P) n.event 241s CIF 1 4.9088 0.80787 0.094051 26 241s CIF 2 4.9088 0.08436 0.040769 4 241s > 241s > summary(test) 241s 241s 241s 241s CIF 1 241s P time var lower upper n.risk n.event 241s 0.01000 0.0092099 0.0000990 0.0014147 0.068863 100 1 241s 0.11430 0.2663096 0.0010542 0.0649454 0.196993 81 1 241s 0.23451 0.7303091 0.0020436 0.1591107 0.337736 54 1 241s 0.40425 1.4299939 0.0032996 0.3020445 0.525741 29 1 241s 0.54593 2.0647206 0.0040836 0.4269008 0.673605 16 1 241s 0.80911 4.9087561 0.0063489 0.6359544 0.933733 2 1 241s 241s CIF 2 241s P time var lower upper n.risk n.event 241s 0.000000 0.0092099 0.00000000 0.000000 0.000000 100 0 241s 0.031657 0.2663096 0.00032353 0.010320 0.094942 81 0 241s 0.067029 0.7303091 0.00070366 0.030598 0.143503 54 0 241s 0.096618 1.4299939 0.00108275 0.049082 0.185474 29 0 241s 0.096618 2.0647206 0.00108275 0.049082 0.185474 16 0 241s 0.096618 4.9087561 0.00108275 0.049082 0.185474 2 0 241s 241s > summary(test.c) 241s 241s cov=0 241s 241s CIF 1 241s P time var lower upper n.risk n.event 241s 0.022222 0.0092099 0.00048285 0.0031605 0.14747 45 1 241s 0.092222 0.2982439 0.00193603 0.0355971 0.22762 36 0 241s 0.226684 0.7021938 0.00450954 0.1241760 0.39250 24 1 241s 0.378128 1.4299939 0.00760870 0.2337884 0.57145 13 1 241s 0.505736 1.6148774 0.00895330 0.3388425 0.69885 10 1 241s 0.702465 2.1708375 0.01119294 0.4944890 0.88399 3 1 241s 241s CIF 2 241s P time var lower upper n.risk n.event 241s 0.000000 0.0092099 0.0000000 0.000000 0.00000 45 0 241s 0.048441 0.2982439 0.0011168 0.012337 0.18013 36 1 241s 0.076411 0.7021938 0.0018104 0.025202 0.21928 24 0 241s 0.111440 1.4299939 0.0028499 0.042676 0.27392 13 0 241s 0.111440 1.6148774 0.0028499 0.042676 0.27392 10 0 241s 0.111440 2.1708375 0.0028499 0.042676 0.27392 3 0 241s 241s 241s cov=1 241s 241s CIF 1 241s P time var lower upper n.risk n.event 241s 0.018182 0.066692 0.00032457 0.0025813 0.12214 55 1 241s 0.112392 0.263808 0.00187215 0.0520925 0.23333 45 1 241s 0.241023 0.730309 0.00374499 0.1440057 0.38685 31 1 241s 0.401201 1.066913 0.00570788 0.2714008 0.56421 19 1 241s 0.592334 2.366275 0.00775985 0.4286230 0.76273 8 1 241s 0.807871 4.908756 0.00884554 0.6023185 0.94771 2 1 241s 241s CIF 2 241s P time var lower upper n.risk n.event 241s 0.000000 0.066692 0.00000000 0.000000 0.00000 55 0 241s 0.037434 0.263808 0.00067458 0.009494 0.14152 45 0 241s 0.059341 0.730309 0.00111295 0.019447 0.17351 31 0 241s 0.084360 1.066913 0.00166213 0.032211 0.21119 19 0 241s 0.084360 2.366275 0.00166213 0.032211 0.21119 8 0 241s 0.084360 4.908756 0.00166213 0.032211 0.21119 2 0 241s 241s > 241s > options(old) 241s > 241s BEGIN TEST tests.etm.R 241s 241s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 241s Copyright (C) 2025 The R Foundation for Statistical Computing 241s Platform: aarch64-unknown-linux-gnu 241s 241s R is free software and comes with ABSOLUTELY NO WARRANTY. 241s You are welcome to redistribute it under certain conditions. 241s Type 'license()' or 'licence()' for distribution details. 241s 241s R is a collaborative project with many contributors. 241s Type 'contributors()' for more information and 241s 'citation()' on how to cite R or R packages in publications. 241s 241s Type 'demo()' for some demos, 'help()' for on-line help, or 241s 'help.start()' for an HTML browser interface to help. 241s Type 'q()' to quit R. 241s 241s > require(etm) 241s Loading required package: etm 242s > 242s > ## Print with a bit less precision to avoid lots of notes in the comparison 242s > old <- options(digits = 4) 242s > 242s > ### Simple test 242s > 242s > time <- id <- 1:10 242s > from <- rep(0, 10) 242s > to <- rep(1, 10) 242s > 242s > data1 <- data.frame(id, from, to, time) 242s > tra1 <- matrix(FALSE, 2, 2) 242s > tra1[1, 2] <- TRUE 242s > 242s > etm1 <- etm(data1, c("0", "1"), tra1, NULL, 0) 242s > 242s > all.equal(as.vector(trprob(etm1, "0 0")), cumprod((10:1 - 1) / (10:1))) 242s [1] TRUE 242s > 242s > etm1$cov["0 0", "0 0", ] 242s 1 2 3 4 5 6 7 8 9 10 242s 0.009 0.016 0.021 0.024 0.025 0.024 0.021 0.016 0.009 0.000 242s > 242s > all.equal(etm1$cov["0 0", "0 0",], trcov(etm1, "0 0")) 242s [1] TRUE 242s > 242s > ### A simple test from AHR's author, where the first time is censored 242s > if (!require(survival)) { 242s + stop("This test requires the survival package") 242s + } 242s > 242s > data <- data.frame(id=1:10, time=1:10, from=0, to=1, status=TRUE) 242s Loading required package: survival 242s > 242s > tra <- matrix(FALSE, nrow=2, ncol=2) 242s > tra[1, 2] <- TRUE 242s > 242s > data$to[1] <- "cens" 242s > data$status[1] <- FALSE 242s > 242s > fit.km <- survfit(Surv(time, status) ~ 1, data=data) 242s > fit.etm <- etm(data, c("0","1"), tra, "cens", s=0, t="last", covariance=FALSE) 242s > 242s > all.equal(fit.km$surv[data$status], fit.etm$est[1,1,], check.attributes = FALSE) 242s [1] TRUE 242s > 242s > data$to[2] <- "cens" 242s > data$status[2] <- FALSE 242s > 242s > fit.km <- survfit(Surv(time, status) ~ 1, data=data) 242s > fit.etm <- etm(data, c("0","1"), tra, "cens", s=0, t="last", covariance=FALSE) 242s > 242s > all.equal(fit.km$surv[data$status], fit.etm$est[1,1,], check.attributes = FALSE) 242s [1] TRUE 242s > 242s > ### a bit more complicated 242s > 242s > time <- id <- 1:10 242s > from <- rep(0, 10) 242s > to <- rep(c(1, 2), 5) 242s > data2 <- data.frame(id, from, to, time) 242s > 242s > tra2 <- matrix(FALSE, 3, 3) 242s > tra2[1, 2:3] <- TRUE 242s > 242s > etm2 <- etm(data2, c("0", "1", "2"), tra2, NULL, 0) 242s > 242s > aa <- table(time, to) 242s > 242s > cif1 <- cumsum(aa[, 1] / 10) 242s > cif2 <- cumsum(aa[, 2] / 10) 242s > surv <- cumprod((10:1 - 1) / (10:1)) 242s > 242s > all.equal(trprob(etm2, "0 1"), cif1) 242s [1] TRUE 242s > all.equal(trprob(etm2, "0 2"), cif2) 242s [1] TRUE 242s > all.equal(as.vector(trprob(etm2, "0 0")), surv) 242s [1] TRUE 242s > 242s > ## a test on id 242s > data2$id <- letters[1:10] 242s > 242s > etm3 <- etm(data2, c("0", "1", "2"), tra2, NULL, 0) 242s > 242s > all.equal(trprob(etm2, "0 1"), trprob(etm3, "0 1")) 242s [1] TRUE 242s > all.equal(trprob(etm2, "0 2"), trprob(etm3, "0 2")) 242s [1] TRUE 242s > all.equal(trprob(etm2, "0 0"), trprob(etm3, "0 0")) 242s [1] TRUE 242s > 242s > 242s > ### Test on sir.cont 242s > 242s > data(sir.cont) 242s > 242s > ## Modification for patients entering and leaving a state 242s > ## at the same date 242s > ## Change on ventilation status is considered 242s > ## to happen before end of hospital stay 242s > sir.cont <- sir.cont[order(sir.cont$id, sir.cont$time), ] 242s > for (i in 2:nrow(sir.cont)) { 242s + if (sir.cont$id[i]==sir.cont$id[i-1]) { 242s + if (sir.cont$time[i]==sir.cont$time[i-1]) { 242s + sir.cont$time[i-1] <- sir.cont$time[i-1] - 0.5 242s + } 242s + } 242s + } 242s > 242s > ### Computation of the transition probabilities 242s > ## Possible transitions. 242s > tra <- matrix(ncol=3,nrow=3,FALSE) 242s > tra[1, 2:3] <- TRUE 242s > tra[2, c(1, 3)] <- TRUE 242s > 242s > ## etm 242s > prob.sir <- etm(sir.cont, c("0", "1", "2"), tra, "cens", 1) 242s > 242s > prob.sir 242s Multistate model with 2 transient state(s) 242s and 1 absorbing state(s) 242s 242s Possible transitions: 242s from to 242s 0 1 242s 0 2 242s 1 0 242s 1 2 242s 242s Estimate of P(1, 183) 242s 0 1 2 242s 0 0 0 1 242s 1 0 0 1 242s 2 0 0 1 242s 242s > 242s > summ.sir <- summary(prob.sir) 242s > all.equal(summ.sir[['0 1']]$P, as.vector(trprob(prob.sir, "0 1"))) 242s [1] TRUE 242s > subset(summ.sir[[3]],time<183) # issue with precision on different architectures 242s P time var lower upper n.risk n.event 242s 1.5 0.0000 1.5 0.000e+00 0.00000 0.0000 394 0 242s 2 0.1187 2.0 2.641e-04 0.08683 0.1505 396 47 242s 2.5 0.1187 2.5 2.641e-04 0.08683 0.1505 364 0 242s 3 0.2454 3.0 4.465e-04 0.20398 0.2868 365 54 242s 3.5 0.2454 3.5 4.465e-04 0.20398 0.2868 328 0 242s 4 0.3806 4.0 5.416e-04 0.33501 0.4262 331 62 242s 4.5 0.3806 4.5 5.416e-04 0.33501 0.4262 280 0 242s 5 0.4792 5.0 5.480e-04 0.43333 0.5251 283 48 242s 5.5 0.4792 5.5 5.480e-04 0.43333 0.5251 248 0 242s 6 0.5693 6.0 5.141e-04 0.52482 0.6137 249 47 242s 7 0.6350 7.0 4.665e-04 0.59266 0.6773 212 36 242s 8 0.6795 8.0 4.202e-04 0.63931 0.7197 195 27 242s 8.5 0.6795 8.5 4.202e-04 0.63931 0.7197 172 0 242s 9 0.7325 9.0 3.580e-04 0.69541 0.7696 173 34 242s 10 0.7647 10.0 3.141e-04 0.72992 0.7994 148 21 242s 10.5 0.7647 10.5 3.141e-04 0.72992 0.7994 135 0 242s 11 0.7895 11.0 2.790e-04 0.75674 0.8222 136 18 242s 12 0.8138 12.0 2.420e-04 0.78330 0.8443 129 18 242s 12.5 0.8138 12.5 2.420e-04 0.78330 0.8443 117 0 242s 13 0.8294 13.0 2.182e-04 0.80045 0.8584 118 13 242s 14 0.8452 14.0 1.938e-04 0.81789 0.8725 115 14 242s 15 0.8625 15.0 1.670e-04 0.83714 0.8878 106 15 242s 16 0.8723 16.0 1.522e-04 0.84807 0.8964 93 9 242s 17 0.8852 17.0 1.330e-04 0.86256 0.9078 86 12 242s 17.5 0.8852 17.5 1.330e-04 0.86256 0.9078 77 0 242s 18 0.8960 18.0 1.168e-04 0.87484 0.9172 76 9 242s 19 0.9029 19.0 1.070e-04 0.88261 0.9232 71 7 242s 20 0.9125 20.0 9.367e-05 0.89356 0.9315 64 10 242s 21 0.9161 21.0 8.878e-05 0.89768 0.9346 57 4 242s 22 0.9226 22.0 7.996e-05 0.90504 0.9401 55 6 242s 23 0.9261 23.0 7.537e-05 0.90904 0.9431 51 4 242s 23.5 0.9261 23.5 7.537e-05 0.90904 0.9431 49 0 242s 24 0.9354 24.0 6.292e-05 0.91982 0.9509 50 9 242s 25 0.9385 25.0 5.878e-05 0.92352 0.9536 42 3 242s 26 0.9429 26.0 5.326e-05 0.92863 0.9572 39 5 242s 27 0.9477 27.0 4.749e-05 0.93417 0.9612 35 6 242s 27.5 0.9477 27.5 4.749e-05 0.93417 0.9612 29 0 242s 28 0.9531 28.0 4.093e-05 0.94059 0.9657 30 5 242s 29 0.9567 29.0 3.668e-05 0.94485 0.9686 31 4 242s 30 0.9592 30.0 3.384e-05 0.94779 0.9706 28 3 242s 30.5 0.9592 30.5 3.384e-05 0.94779 0.9706 29 0 242s 31 0.9642 31.0 2.821e-05 0.95383 0.9746 30 6 242s 32 0.9649 32.0 2.752e-05 0.95458 0.9751 25 1 242s 33 0.9669 33.0 2.533e-05 0.95708 0.9768 24 2 242s 34 0.9685 34.0 2.368e-05 0.95900 0.9781 26 2 242s 35 0.9697 35.0 2.252e-05 0.96036 0.9790 28 2 242s 36 0.9702 36.0 2.194e-05 0.96104 0.9794 26 1 242s 37 0.9718 37.0 2.043e-05 0.96290 0.9806 26 2 242s 38 0.9739 38.0 1.831e-05 0.96555 0.9823 25 4 242s 38.5 0.9739 38.5 1.831e-05 0.96555 0.9823 21 0 242s 39 0.9760 39.0 1.643e-05 0.96802 0.9839 23 3 242s 40 0.9769 40.0 1.558e-05 0.96918 0.9847 19 1 242s 41 0.9774 41.0 1.512e-05 0.96981 0.9851 22 1 242s 42 0.9779 42.0 1.476e-05 0.97032 0.9854 22 0 242s 43 0.9798 43.0 1.308e-05 0.97271 0.9869 22 3 242s 44 0.9803 44.0 1.265e-05 0.97333 0.9873 21 1 242s 45 0.9817 45.0 1.157e-05 0.97499 0.9883 19 1 242s 46 0.9822 46.0 1.116e-05 0.97561 0.9887 17 1 242s 47 0.9831 47.0 1.037e-05 0.97683 0.9895 18 2 242s 48 0.9836 48.0 9.987e-06 0.97743 0.9898 17 1 242s 49 0.9841 49.0 9.669e-06 0.97796 0.9901 17 0 242s 50 0.9845 50.0 9.297e-06 0.97856 0.9905 17 1 242s 50.5 0.9845 50.5 9.297e-06 0.97856 0.9905 16 0 242s 51 0.9860 51.0 8.214e-06 0.98037 0.9916 17 3 242s 52 0.9870 52.0 7.513e-06 0.98159 0.9923 14 2 242s 53 0.9879 53.0 6.875e-06 0.98276 0.9930 12 1 242s 54 0.9889 54.0 6.214e-06 0.98397 0.9937 12 2 242s 55 0.9903 55.0 5.254e-06 0.98581 0.9948 10 3 242s 56 0.9913 56.0 4.667e-06 0.98703 0.9955 6 1 242s 57 0.9917 57.0 4.364e-06 0.98765 0.9958 5 1 242s 58 0.9922 58.0 4.064e-06 0.98828 0.9962 4 1 242s 59 0.9927 59.0 3.769e-06 0.98891 0.9965 3 1 242s 60 0.9932 60.0 3.488e-06 0.98953 0.9969 3 1 242s 62 0.9937 62.0 3.230e-06 0.99016 0.9972 2 0 242s 63 0.9942 63.0 2.956e-06 0.99079 0.9975 2 1 242s 68 0.9942 68.0 2.956e-06 0.99079 0.9975 1 0 242s 70 0.9946 70.0 2.694e-06 0.99143 0.9979 2 1 242s 78 0.9951 78.0 2.442e-06 0.99207 0.9982 1 0 242s 80 0.9951 80.0 2.442e-06 0.99207 0.9982 1 0 242s 85 0.9966 85.0 1.695e-06 0.99404 0.9991 2 0 242s 89 0.9966 89.0 1.695e-06 0.99404 0.9991 2 0 242s 90 0.9966 90.0 1.695e-06 0.99404 0.9991 1 0 242s 95 0.9971 95.0 1.448e-06 0.99472 0.9994 2 0 242s 100 0.9976 100.0 1.203e-06 0.99542 0.9997 3 0 242s 101 0.9981 101.0 9.592e-07 0.99613 1.0000 3 1 242s 108 0.9985 108.0 7.169e-07 0.99688 1.0000 2 1 242s 113 0.9990 113.0 4.764e-07 0.99767 1.0000 1 0 242s 116 0.9990 116.0 4.764e-07 0.99767 1.0000 1 0 242s 124 0.9990 124.0 4.764e-07 0.99767 1.0000 2 0 242s 164 0.9990 164.0 4.764e-07 0.99767 1.0000 0 0 242s > 242s > ## gonna play a bit with the state names 242s > dd <- sir.cont 242s > dd$from <- ifelse(dd$from == 0, "initial state", "ventilation") 242s > dd$to <- as.character(dd$to) 242s > for (i in seq_len(nrow(dd))) { 242s + dd$to[i] <- switch(dd$to[i], 242s + "0" = "initial state", 242s + "1" = "ventilation", 242s + "2" = "end of story", 242s + "cens" = "cens" 242s + ) 242s + } 242s > 242s > test <- etm(dd, c("initial state", "ventilation", "end of story"), tra, "cens", 1) 242s > 242s > all.equal(test$est["initial state", "initial state", ], 242s + prob.sir$est["0", "0", ]) 242s [1] TRUE 242s > all.equal(trprob(test, "initial state initial state"), trprob(prob.sir, "0 0")) 242s [1] TRUE 242s > all.equal(trprob(test, "initial state ventilation"), trprob(prob.sir, "0 1")) 242s [1] TRUE 242s > all.equal(trprob(test, "initial state end of story"), trprob(prob.sir, "0 2")) 242s [1] TRUE 242s > 242s > all.equal(trcov(test, "initial state end of story"), trcov(prob.sir, "0 2")) 242s [1] TRUE 242s > 242s > aa <- summary(test) 242s > all.equal(summ.sir[[6]], aa[[6]]) 242s [1] TRUE 242s > all.equal(summ.sir[[4]], aa[[4]]) 242s [1] TRUE 242s > 242s > ### Test on abortion data 242s > 242s > data(abortion) 242s > 242s > from <- rep(0, nrow(abortion)) 242s > to <- abortion$cause 242s > entry <- abortion$entry 242s > exit <- abortion$exit 242s > id <- 1:nrow(abortion) 242s > data <- data.frame(id, from, to, entry, exit, group = abortion$group) 242s > 242s > ## Computation of the CIFs 242s > tra <- matrix(FALSE, 4, 4) 242s > tra[1, 2:4] <- TRUE 242s > 242s > cif.control <- etm(data[data$group == 0, ], c("0", "1", "2", "3"), 242s + tra, NULL, 0) 242s > cif.exposed <- etm(data[data$group == 1, ], c("0", "1", "2", "3"), 242s + tra, NULL, 0) 242s > 242s > all.equal(trprob(cif.control, "0 1"), cif.control$est["0", "1", ]) 242s [1] TRUE 242s > all.equal(trcov(cif.control, c("0 1", "0 2")), cif.control$cov["0 1", "0 2", ]) 242s [1] TRUE 242s > 242s > trprob(cif.control, "0 1") 242s 6 7 8 9 10 11 12 13 242s 0.000000 0.007401 0.014881 0.026509 0.033208 0.037694 0.037694 0.038955 242s 14 17 19 21 24 25 26 30 242s 0.040159 0.040159 0.040159 0.040159 0.040159 0.040159 0.040159 0.040159 242s 31 32 33 34 35 36 37 38 242s 0.040159 0.040159 0.040159 0.040159 0.040159 0.040159 0.040159 0.040159 242s 39 40 41 42 43 242s 0.040159 0.040159 0.040159 0.040159 0.040159 242s > trprob(cif.control, "0 2") 242s 6 7 8 9 10 11 12 13 242s 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 242s 14 17 19 21 24 25 26 30 242s 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.003657 242s 31 32 33 34 35 36 37 38 242s 0.006371 0.008175 0.013543 0.023317 0.031260 0.053197 0.084529 0.179163 242s 39 40 41 42 43 242s 0.322016 0.563121 0.742227 0.793893 0.799059 242s > trprob(cif.control, "0 0") 242s 6 7 8 9 10 11 12 13 242s 0.965812 0.932508 0.887628 0.862433 0.838989 0.822538 0.813099 0.810578 242s 14 17 19 21 24 25 26 30 242s 0.806964 0.805874 0.803810 0.802804 0.801837 0.800883 0.799937 0.796280 242s 31 32 33 34 35 36 37 38 242s 0.793565 0.791762 0.786394 0.776620 0.768677 0.745862 0.714531 0.619897 242s 39 40 41 42 43 242s 0.477043 0.235938 0.056832 0.005167 0.000000 242s > 242s > trcov(cif.control, "0 1") 242s 6 7 8 9 10 11 12 13 242s 0.000e+00 2.719e-05 4.533e-05 6.665e-05 7.698e-05 8.304e-05 8.304e-05 8.444e-05 242s 14 17 19 21 24 25 26 30 242s 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 242s 31 32 33 34 35 36 37 38 242s 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 242s 39 40 41 42 43 242s 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 242s > trcov(cif.control, "0 2") 242s 6 7 8 9 10 11 12 13 242s 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 242s 14 17 19 21 24 25 26 30 242s 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 3.338e-06 242s 31 32 33 34 35 36 37 38 242s 5.784e-06 7.401e-06 1.216e-05 2.072e-05 2.758e-05 4.619e-05 7.202e-05 1.461e-04 242s 39 40 41 42 43 242s 2.470e-04 3.880e-04 4.702e-04 4.903e-04 4.922e-04 242s > trcov(cif.control, "0 0") 242s 6 7 8 9 10 11 12 13 242s 2.822e-04 3.821e-04 4.527e-04 4.748e-04 4.875e-04 4.927e-04 4.941e-04 4.942e-04 242s 14 17 19 21 24 25 26 30 242s 4.941e-04 4.940e-04 4.936e-04 4.933e-04 4.931e-04 4.928e-04 4.926e-04 4.914e-04 242s 31 32 33 34 35 36 37 38 242s 4.905e-04 4.899e-04 4.880e-04 4.846e-04 4.816e-04 4.729e-04 4.601e-04 4.176e-04 242s 39 40 41 42 43 242s 3.425e-04 1.865e-04 4.797e-05 4.441e-06 0.000e+00 242s > 242s > aa <- summary(cif.control) 242s > aa$"0 1" 242s P time var lower upper n.risk n.event 242s 6 0.000000 6 0.000e+00 0.000000 0.00000 117 0 242s 7 0.007401 7 2.719e-05 0.000000 0.01762 261 2 242s 8 0.014881 8 4.533e-05 0.001685 0.02808 374 3 242s 9 0.026509 9 6.665e-05 0.010508 0.04251 458 6 242s 10 0.033208 10 7.698e-05 0.016011 0.05040 515 4 242s 11 0.037694 11 8.304e-05 0.019834 0.05555 561 3 242s 12 0.037694 12 8.304e-05 0.019834 0.05555 610 0 242s 13 0.038955 13 8.444e-05 0.020944 0.05697 645 1 242s 14 0.040159 14 8.571e-05 0.022014 0.05830 673 1 242s 17 0.040159 17 8.571e-05 0.022014 0.05830 740 0 242s 19 0.040159 19 8.571e-05 0.022014 0.05830 781 0 242s 21 0.040159 21 8.571e-05 0.022014 0.05830 799 0 242s 24 0.040159 24 8.571e-05 0.022014 0.05830 830 0 242s 25 0.040159 25 8.571e-05 0.022014 0.05830 841 0 242s 26 0.040159 26 8.571e-05 0.022014 0.05830 846 0 242s 30 0.040159 30 8.571e-05 0.022014 0.05830 875 0 242s 31 0.040159 31 8.571e-05 0.022014 0.05830 880 0 242s 32 0.040159 32 8.571e-05 0.022014 0.05830 880 0 242s 33 0.040159 33 8.571e-05 0.022014 0.05830 885 0 242s 34 0.040159 34 8.571e-05 0.022014 0.05830 885 0 242s 35 0.040159 35 8.571e-05 0.022014 0.05830 880 0 242s 36 0.040159 36 8.571e-05 0.022014 0.05830 876 0 242s 37 0.040159 37 8.571e-05 0.022014 0.05830 857 0 242s 38 0.040159 38 8.571e-05 0.022014 0.05830 823 0 242s 39 0.040159 39 8.571e-05 0.022014 0.05830 716 0 242s 40 0.040159 40 8.571e-05 0.022014 0.05830 554 0 242s 41 0.040159 41 8.571e-05 0.022014 0.05830 274 0 242s 42 0.040159 42 8.571e-05 0.022014 0.05830 66 0 242s 43 0.040159 43 8.571e-05 0.022014 0.05830 6 0 242s > all.equal(aa$"0 1"$P, as.vector(trprob(cif.control, "0 1"))) 242s [1] TRUE 242s > 242s > ### test on los data 242s > 242s > data(los.data) # in package changeLOS 242s > 242s > ## putting los.data in the long format (see changeLOS) 242s > my.observ <- prepare.los.data(x=los.data) 242s > 242s > tra <- matrix(FALSE, 4, 4) 242s > tra[1, 2:4] <- TRUE 242s > tra[2, 3:4] <- TRUE 242s > 242s > tr.prob <- etm(my.observ, c("0","1","2","3"), tra, NULL, 0) 242s > 242s > tr.prob 242s Multistate model with 2 transient state(s) 242s and 2 absorbing state(s) 242s 242s Possible transitions: 242s from to 242s 0 1 242s 0 2 242s 0 3 242s 1 2 242s 1 3 242s 242s Estimate of P(0, 82) 242s 0 1 2 3 242s 0 0 0 0.7474 0.2526 242s 1 0 0 0.7073 0.2927 242s 2 0 0 1.0000 0.0000 242s 3 0 0 0.0000 1.0000 242s 242s > summary(tr.prob) 242s Transition 0 0 242s P time var lower upper n.risk n.event 242s 0.882275 3 1.374e-04 0.8593018 0.905248 756 0 242s 0.112434 15 1.320e-04 0.0899155 0.134952 90 0 242s 0.031746 27 4.066e-05 0.0192484 0.044244 26 0 242s 0.006614 41 8.690e-06 0.0008359 0.012392 5 0 242s 0.002646 61 3.490e-06 0.0000000 0.006307 3 0 242s 0.000000 82 0.000e+00 0.0000000 0.000000 1 0 242s 242s Transition 0 1 242s P time var lower upper n.risk n.event 242s 0.017196 3 2.235e-05 0.0079289 0.02646 756 13 242s 0.063492 15 7.865e-05 0.0461099 0.08087 90 0 242s 0.030423 27 3.902e-05 0.0181805 0.04267 26 1 242s 0.015873 41 2.066e-05 0.0069637 0.02478 5 0 242s 0.005291 61 6.962e-06 0.0001197 0.01046 3 0 242s 0.000000 82 0.000e+00 0.0000000 0.00000 1 0 242s 242s Transition 0 2 242s P time var lower upper n.risk n.event 242s 0.08466 3 0.0001025 0.06481 0.1045 756 64 242s 0.62302 15 0.0003107 0.58847 0.6576 90 4 242s 0.69841 27 0.0002786 0.66570 0.7311 26 1 242s 0.72751 41 0.0002622 0.69578 0.7593 5 0 242s 0.74074 61 0.0002540 0.70950 0.7720 3 1 242s 0.74735 82 0.0002498 0.71638 0.7783 1 1 242s 242s Transition 0 3 242s P time var lower upper n.risk n.event 242s 0.01587 3 2.066e-05 0.006964 0.02478 756 12 242s 0.20106 15 2.125e-04 0.172489 0.22963 90 1 242s 0.23942 27 2.409e-04 0.208999 0.26984 26 0 242s 0.25000 41 2.480e-04 0.219133 0.28087 5 0 242s 0.25132 61 2.489e-04 0.220402 0.28224 3 0 242s 0.25265 82 2.498e-04 0.221671 0.28362 1 0 242s 242s Transition 1 1 242s P time var lower upper n.risk n.event 242s 1.00000 3 0.000e+00 1.00000 1.00000 0 0 242s 0.38661 15 2.358e-03 0.29143 0.48179 51 0 242s 0.12119 27 7.842e-04 0.06630 0.17607 23 0 242s 0.04593 41 2.405e-04 0.01554 0.07633 14 0 242s 0.01531 61 6.579e-05 0.00000 0.03121 4 0 242s 0.00000 82 0.000e+00 0.00000 0.00000 0 0 242s 242s Transition 1 2 242s P time var lower upper n.risk n.event 242s 0.0000 3 0.000000 0.0000 0.0000 0 0 242s 0.4107 15 0.002590 0.3110 0.5104 51 2 242s 0.6082 27 0.002254 0.5151 0.7012 23 1 242s 0.6652 41 0.002064 0.5761 0.7542 14 2 242s 0.6920 61 0.002000 0.6043 0.7796 4 0 242s 0.7073 82 0.001984 0.6200 0.7946 0 0 242s 242s Transition 1 3 242s P time var lower upper n.risk n.event 242s 0.0000 3 0.000000 0.0000 0.0000 0 0 242s 0.2027 15 0.001784 0.1199 0.2855 51 1 242s 0.2706 27 0.001968 0.1837 0.3576 23 0 242s 0.2889 41 0.001982 0.2016 0.3761 14 0 242s 0.2927 61 0.001984 0.2054 0.3800 4 0 242s 0.2927 82 0.001984 0.2054 0.3800 0 0 242s 242s > 242s > cLOS <- etm::clos(tr.prob, aw = TRUE) 242s > 242s > cLOS 242s The expected change in length of stay is: 242s 1.975 242s 242s Alternative weighting: 242s 242s Expected change in LOS with weight.1: 2.097 242s Expected change in LOS with weight.other: 1.951 242s > 242s > 242s > ### Tests on pseudo values 242s > t_pseudo <- closPseudo(my.observ, c("0","1","2","3"), tra, NULL, 242s + formula = ~ 1, aw = TRUE) 257s > 257s > cLOS$e.phi == t_pseudo$theta[, "e.phi"] 257s [,1] 257s [1,] TRUE 257s > cLOS$e.phi.weights.1 == t_pseudo$theta[, "e.phi.weights.1"] 257s [,1] 257s [1,] TRUE 257s > cLOS$e.phi.weights.other == t_pseudo$theta[, "e.phi.weights.other"] 257s [,1] 257s [1,] TRUE 257s > 257s > mean(t_pseudo$pseudoData$ps.e.phi) 257s [1] 1.968 257s > 257s > ### tests on etmprep 257s > 257s > ### creation of fake data in the wild format, following an illness-death model 257s > ## transition times 257s > tdisease <- c(3, 4, 3, 6, 8, 9) 257s > tdeath <- c(6, 9, 8, 6, 8, 9) 257s > 257s > ## transition status 257s > stat.disease <- c(1, 1, 1, 0, 0, 0) 257s > stat.death <- c(1, 1, 1, 1, 1, 0) 257s > 257s > ## a covariate that we want to keep in the new data 257s > set.seed(1313) 257s > cova <- rbinom(6, 1, 0.5) 257s > 257s > dat <- data.frame(tdisease, tdeath, 257s + stat.disease, stat.death, 257s + cova) 257s > 257s > ## Possible transitions 257s > tra <- matrix(FALSE, 3, 3) 257s > tra[1, 2:3] <- TRUE 257s > tra[2, 3] <- TRUE 257s > 257s > ## data preparation 257s > newdat <- etmprep(c(NA, "tdisease", "tdeath"), 257s + c(NA, "stat.disease", "stat.death"), 257s + data = dat, tra = tra, 257s + cens.name = "cens", keep = "cova") 257s > 257s > newdat 257s id entry exit from to cova 257s 1 1 0 3 0 1 1 257s 2 1 3 6 1 2 1 257s 3 2 0 4 0 1 0 257s 4 2 4 9 1 2 0 257s 5 3 0 3 0 1 1 257s 6 3 3 8 1 2 1 257s 7 4 0 6 0 2 0 257s 8 5 0 8 0 2 1 257s 9 6 0 9 0 cens 1 257s > 257s > ref <- data.frame(id = c(1, 1, 2, 2, 3, 3, 4, 5, 6), 257s + entry = c(0, 3, 0, 4, 0, 3, 0, 0, 0), 257s + exit = c(3, 6, 4, 9, 3, 8, 6, 8, 9), 257s + from = c(0, 1, 0, 1, 0, 1, 0, 0, 0), 257s + to = c(rep(c(1, 2), 3), 2, 2, "cens"), 257s + cova = c(1, 1, 0, 0, 1, 1, 0, 1, 1)) 257s > ref$from <- factor(as.character(ref$from), levels = c("0", "1", "2", "cens")) 257s > ref$to <- factor(as.character(ref$to), levels = c("0", "1", "2", "cens")) 257s > 257s > all.equal(ref, newdat) 257s [1] TRUE 257s > 257s > 257s > ###################################### 257s > ### Test the stratified calls 257s > ###################################### 257s > 257s > if (require("kmi", quietly = TRUE)) { 257s + library(etm) 257s + 257s + data(icu.pneu) 257s + my.icu.pneu <- icu.pneu 257s + 257s + my.icu.pneu <- my.icu.pneu[order(my.icu.pneu$id, my.icu.pneu$start), ] 257s + masque <- diff(my.icu.pneu$id) 257s + 257s + my.icu.pneu$from <- 0 257s + my.icu.pneu$from[c(1, masque) == 0] <- 1 257s + 257s + my.icu.pneu$to2 <- my.icu.pneu$event 257s + my.icu.pneu$to2[my.icu.pneu$status == 0] <- "cens" 257s + my.icu.pneu$to2[c(masque, 1) == 0] <- 1 257s + 257s + 257s + my.icu.pneu$to <- ifelse(my.icu.pneu$to2 %in% c(2, 3), 2, 257s + my.icu.pneu$to2) 257s + 257s + my.icu.pneu <- my.icu.pneu[, c("id", "start", "stop", "from", "to", 257s + "to2", "age", "sex")] 257s + names(my.icu.pneu)[c(2, 3)] <- c("entry", "exit") 257s + 257s + bouh_strat <- etm(my.icu.pneu, c("0", "1", "2"), tra_ill(), "cens", 0, strata = "sex") 257s + 257s + bouh_female <- etm(my.icu.pneu[my.icu.pneu$sex == "F", ], 257s + c("0", "1", "2"), tra_ill(), "cens", 0) 257s + 257s + all(bouh_strat[[1]]$est == bouh_female$est) 257s + 257s + ## Test the summary 257s + the_summary <- summary(bouh_strat) 257s + the_summary 257s + 257s + ## Test trprob 257s + all(trprob(bouh_strat, "0 1")[[1]] == trprob(bouh_female, "0 1")) 257s + all(trprob(bouh_strat, "0 1", c(0, 5, 10, 15))[[1]] == trprob(bouh_female, "0 1", c(0, 5, 10, 15))) 257s + 257s + ## Test trcov 257s + all(trcov(bouh_strat, "0 1")[[1]] == trcov(bouh_female, "0 1")) 257s + all(trcov(bouh_strat, c("0 1", "0 2"))[[1]] == trcov(bouh_female, c("0 1", "0 2"))) 257s + all(trcov(bouh_strat, "0 1", c(0, 5, 10, 15))[[1]] == trcov(bouh_female, "0 1", c(0, 5, 10, 15))) 257s + } else { 257s + print("These tests require the kmi package") 257s + } 257s [1] TRUE 257s > 257s > options(old) 257s > 258s autopkgtest [23:01:35]: test run-unit-test: -----------------------] 258s run-unit-test PASS 258s autopkgtest [23:01:35]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 258s autopkgtest [23:01:35]: test pkg-r-autopkgtest: preparing testbed 259s Reading package lists... 259s Building dependency tree... 259s Reading state information... 259s Solving dependencies... 259s The following NEW packages will be installed: 259s build-essential cpp cpp-15 cpp-15-aarch64-linux-gnu cpp-aarch64-linux-gnu 259s dctrl-tools g++ g++-15 g++-15-aarch64-linux-gnu g++-aarch64-linux-gnu gcc 259s gcc-15 gcc-15-aarch64-linux-gnu gcc-aarch64-linux-gnu gfortran gfortran-15 259s gfortran-15-aarch64-linux-gnu gfortran-aarch64-linux-gnu icu-devtools 259s libasan8 libblas-dev libbz2-dev libc-dev-bin libc6-dev libcc1-0 libcrypt-dev 259s libdeflate-dev libgcc-15-dev libgfortran-15-dev libhwasan0 libicu-dev 259s libisl23 libitm1 libjpeg-dev libjpeg-turbo8-dev libjpeg8-dev liblapack-dev 259s liblsan0 liblzma-dev libmpc3 libncurses-dev libpcre2-16-0 libpcre2-32-0 259s libpcre2-dev libpcre2-posix3 libpkgconf3 libpng-dev libreadline-dev 259s libstdc++-15-dev libtirpc-dev libtsan2 libubsan1 libzstd-dev linux-libc-dev 259s pkg-r-autopkgtest pkgconf pkgconf-bin r-base-dev r-cran-backports 259s r-cran-broom r-cran-cli r-cran-cpp11 r-cran-dplyr r-cran-fansi r-cran-farver 259s r-cran-geepack r-cran-generics r-cran-ggplot2 r-cran-glue r-cran-gtable 259s r-cran-isoband r-cran-labeling r-cran-lifecycle r-cran-magrittr r-cran-mass 259s r-cran-mgcv r-cran-nlme r-cran-pillar r-cran-pkgconfig r-cran-purrr 259s r-cran-r6 r-cran-rcolorbrewer r-cran-rlang r-cran-scales r-cran-stringi 259s r-cran-stringr r-cran-tibble r-cran-tidyr r-cran-tidyselect r-cran-utf8 259s r-cran-vctrs r-cran-viridislite r-cran-withr rpcsvc-proto zlib1g-dev 259s 0 upgraded, 95 newly installed, 0 to remove and 0 not upgraded. 259s Need to get 133 MB of archives. 259s After this operation, 425 MB of additional disk space will be used. 259s Get:1 http://ftpmaster.internal/ubuntu resolute/main arm64 libc-dev-bin arm64 2.42-2ubuntu4 [22.5 kB] 259s Get:2 http://ftpmaster.internal/ubuntu resolute/main arm64 linux-libc-dev arm64 6.19.0-3.3 [1819 kB] 263s Get:3 http://ftpmaster.internal/ubuntu resolute/main arm64 libcrypt-dev arm64 1:4.5.1-1 [123 kB] 263s Get:4 http://ftpmaster.internal/ubuntu resolute/main arm64 rpcsvc-proto arm64 1.4.3-1build1 [65.6 kB] 263s Get:5 http://ftpmaster.internal/ubuntu resolute/main arm64 libc6-dev arm64 2.42-2ubuntu4 [1765 kB] 269s Get:6 http://ftpmaster.internal/ubuntu resolute/main arm64 libisl23 arm64 0.27-1build1 [676 kB] 269s Get:7 http://ftpmaster.internal/ubuntu resolute/main arm64 libmpc3 arm64 1.3.1-2 [55.6 kB] 269s Get:8 http://ftpmaster.internal/ubuntu resolute/main arm64 cpp-15-aarch64-linux-gnu arm64 15.2.0-12ubuntu1 [11.7 MB] 290s Get:9 http://ftpmaster.internal/ubuntu resolute/main arm64 cpp-15 arm64 15.2.0-12ubuntu1 [1030 B] 290s Get:10 http://ftpmaster.internal/ubuntu resolute/main arm64 cpp-aarch64-linux-gnu arm64 4:15.2.0-4ubuntu1 [5736 B] 290s Get:11 http://ftpmaster.internal/ubuntu resolute/main arm64 cpp arm64 4:15.2.0-4ubuntu1 [22.4 kB] 290s Get:12 http://ftpmaster.internal/ubuntu resolute/main arm64 libcc1-0 arm64 15.2.0-12ubuntu1 [49.0 kB] 290s Get:13 http://ftpmaster.internal/ubuntu resolute/main arm64 libitm1 arm64 15.2.0-12ubuntu1 [27.8 kB] 290s Get:14 http://ftpmaster.internal/ubuntu resolute/main arm64 libasan8 arm64 15.2.0-12ubuntu1 [2920 kB] 295s Get:15 http://ftpmaster.internal/ubuntu resolute/main arm64 liblsan0 arm64 15.2.0-12ubuntu1 [1316 kB] 298s Get:16 http://ftpmaster.internal/ubuntu resolute/main arm64 libtsan2 arm64 15.2.0-12ubuntu1 [2688 kB] 302s Get:17 http://ftpmaster.internal/ubuntu resolute/main arm64 libubsan1 arm64 15.2.0-12ubuntu1 [1175 kB] 304s Get:18 http://ftpmaster.internal/ubuntu resolute/main arm64 libhwasan0 arm64 15.2.0-12ubuntu1 [1638 kB] 307s Get:19 http://ftpmaster.internal/ubuntu resolute/main arm64 libgcc-15-dev arm64 15.2.0-12ubuntu1 [2600 kB] 311s Get:20 http://ftpmaster.internal/ubuntu resolute/main arm64 gcc-15-aarch64-linux-gnu arm64 15.2.0-12ubuntu1 [23.1 MB] 353s Get:21 http://ftpmaster.internal/ubuntu resolute/main arm64 gcc-15 arm64 15.2.0-12ubuntu1 [519 kB] 353s Get:22 http://ftpmaster.internal/ubuntu resolute/main arm64 gcc-aarch64-linux-gnu arm64 4:15.2.0-4ubuntu1 [1206 B] 353s Get:23 http://ftpmaster.internal/ubuntu resolute/main arm64 gcc arm64 4:15.2.0-4ubuntu1 [5016 B] 353s Get:24 http://ftpmaster.internal/ubuntu resolute/main arm64 libstdc++-15-dev arm64 15.2.0-12ubuntu1 [2549 kB] 358s Get:25 http://ftpmaster.internal/ubuntu resolute/main arm64 g++-15-aarch64-linux-gnu arm64 15.2.0-12ubuntu1 [13.2 MB] 384s Get:26 http://ftpmaster.internal/ubuntu resolute/main arm64 g++-15 arm64 15.2.0-12ubuntu1 [25.3 kB] 384s Get:27 http://ftpmaster.internal/ubuntu resolute/main arm64 g++-aarch64-linux-gnu arm64 4:15.2.0-4ubuntu1 [956 B] 384s Get:28 http://ftpmaster.internal/ubuntu resolute/main arm64 g++ arm64 4:15.2.0-4ubuntu1 [1080 B] 384s Get:29 http://ftpmaster.internal/ubuntu resolute/main arm64 build-essential arm64 12.12ubuntu2 [5254 B] 384s Get:30 http://ftpmaster.internal/ubuntu resolute/main arm64 dctrl-tools arm64 2.24-3build4 [102 kB] 384s Get:31 http://ftpmaster.internal/ubuntu resolute/main arm64 libgfortran-15-dev arm64 15.2.0-12ubuntu1 [490 kB] 384s Get:32 http://ftpmaster.internal/ubuntu resolute/main arm64 gfortran-15-aarch64-linux-gnu arm64 15.2.0-12ubuntu1 [12.5 MB] 408s Get:33 http://ftpmaster.internal/ubuntu resolute/main arm64 gfortran-15 arm64 15.2.0-12ubuntu1 [18.1 kB] 408s Get:34 http://ftpmaster.internal/ubuntu resolute/main arm64 gfortran-aarch64-linux-gnu arm64 4:15.2.0-4ubuntu1 [1022 B] 408s Get:35 http://ftpmaster.internal/ubuntu resolute/main arm64 gfortran arm64 4:15.2.0-4ubuntu1 [1160 B] 408s Get:36 http://ftpmaster.internal/ubuntu resolute/main arm64 icu-devtools arm64 78.2-1ubuntu1 [207 kB] 408s Get:37 http://ftpmaster.internal/ubuntu resolute/main arm64 libblas-dev arm64 3.12.1-7ubuntu1 [160 kB] 408s Get:38 http://ftpmaster.internal/ubuntu resolute/main arm64 libbz2-dev arm64 1.0.8-6build2 [34.9 kB] 408s Get:39 http://ftpmaster.internal/ubuntu resolute/main arm64 libdeflate-dev arm64 1.23-2build1 [54.3 kB] 409s Get:40 http://ftpmaster.internal/ubuntu resolute/main arm64 libicu-dev arm64 78.2-1ubuntu1 [12.5 MB] 432s Get:41 http://ftpmaster.internal/ubuntu resolute/main arm64 libjpeg-turbo8-dev arm64 2.1.5-4ubuntu3 [301 kB] 432s Get:42 http://ftpmaster.internal/ubuntu resolute/main arm64 libjpeg8-dev arm64 8c-2ubuntu11 [1484 B] 432s Get:43 http://ftpmaster.internal/ubuntu resolute/main arm64 libjpeg-dev arm64 8c-2ubuntu11 [1482 B] 432s Get:44 http://ftpmaster.internal/ubuntu resolute/main arm64 liblapack-dev arm64 3.12.1-7ubuntu1 [4456 kB] 446s Get:45 http://ftpmaster.internal/ubuntu resolute/main arm64 libncurses-dev arm64 6.6+20251231-1 [391 kB] 446s Get:46 http://ftpmaster.internal/ubuntu resolute/main arm64 libpcre2-16-0 arm64 10.46-1 [225 kB] 446s Get:47 http://ftpmaster.internal/ubuntu resolute/main arm64 libpcre2-32-0 arm64 10.46-1 [213 kB] 446s Get:48 http://ftpmaster.internal/ubuntu resolute/main arm64 libpcre2-posix3 arm64 10.46-1 [7300 B] 446s Get:49 http://ftpmaster.internal/ubuntu resolute/main arm64 libpcre2-dev arm64 10.46-1 [772 kB] 448s Get:50 http://ftpmaster.internal/ubuntu resolute/main arm64 libpkgconf3 arm64 1.8.1-4build1 [33.7 kB] 448s Get:51 http://ftpmaster.internal/ubuntu resolute/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1ubuntu2 [899 kB] 450s Get:52 http://ftpmaster.internal/ubuntu resolute/main arm64 libpng-dev arm64 1.6.54-1 [268 kB] 450s Get:53 http://ftpmaster.internal/ubuntu resolute/main arm64 libreadline-dev arm64 8.3-3 [199 kB] 450s Get:54 http://ftpmaster.internal/ubuntu resolute/main arm64 libzstd-dev arm64 1.5.7+dfsg-3 [349 kB] 450s Get:55 http://ftpmaster.internal/ubuntu resolute/main arm64 liblzma-dev arm64 5.8.2-2 [180 kB] 450s Get:56 http://ftpmaster.internal/ubuntu resolute/main arm64 pkgconf-bin arm64 1.8.1-4build1 [21.7 kB] 450s Get:57 http://ftpmaster.internal/ubuntu resolute/main arm64 pkgconf arm64 1.8.1-4build1 [16.8 kB] 450s Get:58 http://ftpmaster.internal/ubuntu resolute/main arm64 libtirpc-dev arm64 1.3.6+ds-1 [202 kB] 450s Get:59 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-base-dev all 4.5.2-1ubuntu2 [1880 B] 450s Get:60 http://ftpmaster.internal/ubuntu resolute/universe arm64 pkg-r-autopkgtest all 20250812 [6158 B] 450s Get:61 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-backports arm64 1.5.0-2 [121 kB] 450s Get:62 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-cli arm64 3.6.4-1 [1374 kB] 452s Get:63 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-generics all 0.1.4-1 [84.0 kB] 453s Get:64 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-glue arm64 1.8.0-1 [163 kB] 453s Get:65 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-rlang arm64 1.1.5-3 [1706 kB] 456s Get:66 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-lifecycle all 1.0.5+dfsg-1 [120 kB] 456s Get:67 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-magrittr arm64 2.0.3-1 [154 kB] 456s Get:68 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-utf8 arm64 1.2.4-1 [140 kB] 456s Get:69 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-vctrs arm64 0.6.5-1 [1327 kB] 459s Get:70 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-pillar all 1.11.1+dfsg-1 [456 kB] 459s Get:71 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-r6 all 2.6.1-1 [101 kB] 459s Get:72 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-fansi arm64 1.0.6-2 [627 kB] 460s Get:73 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-pkgconfig all 2.0.3-2build2 [20.4 kB] 460s Get:74 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-tibble arm64 3.2.1+dfsg-3 [420 kB] 460s Get:75 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-withr all 3.0.2+dfsg-1 [214 kB] 460s Get:76 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-tidyselect arm64 1.2.1+dfsg-1 [222 kB] 460s Get:77 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-dplyr arm64 1.1.4-4 [1534 kB] 463s Get:78 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-purrr arm64 1.0.4-1 [552 kB] 464s Get:79 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-stringi arm64 1.8.4-1build2 [901 kB] 466s Get:80 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-stringr all 1.5.1-1 [290 kB] 466s Get:81 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-cpp11 all 0.5.3-1 [242 kB] 466s Get:82 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-tidyr arm64 1.3.1-1 [1154 kB] 468s Get:83 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-broom all 1.0.12+dfsg-1 [1708 kB] 473s Get:84 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-farver arm64 2.1.2-1 [1344 kB] 477s Get:85 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-mass arm64 7.3-65-1 [1109 kB] 480s Get:86 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-geepack arm64 1.3.12-1 [377 kB] 480s Get:87 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-gtable all 0.3.6+dfsg-1 [199 kB] 481s Get:88 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-isoband arm64 0.2.7-1 [1481 kB] 486s Get:89 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-nlme arm64 3.1.168-1 [2310 kB] 490s Get:90 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-mgcv arm64 1.9-4-1 [3546 kB] 495s Get:91 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-labeling all 0.4.3-1 [62.1 kB] 495s Get:92 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-rcolorbrewer all 1.1-3-1build2 [54.0 kB] 495s Get:93 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-viridislite all 0.4.3-1 [1088 kB] 498s Get:94 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-scales all 1.4.0-1 [725 kB] 498s Get:95 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-ggplot2 all 3.5.1+dfsg-1 [3940 kB] 505s Fetched 133 MB in 4min 5s (542 kB/s) 505s Selecting previously unselected package libc-dev-bin. 505s (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 ... 141796 files and directories currently installed.) 505s Preparing to unpack .../00-libc-dev-bin_2.42-2ubuntu4_arm64.deb ... 505s Unpacking libc-dev-bin (2.42-2ubuntu4) ... 505s Selecting previously unselected package linux-libc-dev:arm64. 505s Preparing to unpack .../01-linux-libc-dev_6.19.0-3.3_arm64.deb ... 505s Unpacking linux-libc-dev:arm64 (6.19.0-3.3) ... 505s Selecting previously unselected package libcrypt-dev:arm64. 505s Preparing to unpack .../02-libcrypt-dev_1%3a4.5.1-1_arm64.deb ... 505s Unpacking libcrypt-dev:arm64 (1:4.5.1-1) ... 505s Selecting previously unselected package rpcsvc-proto. 505s Preparing to unpack .../03-rpcsvc-proto_1.4.3-1build1_arm64.deb ... 505s Unpacking rpcsvc-proto (1.4.3-1build1) ... 505s Selecting previously unselected package libc6-dev:arm64. 505s Preparing to unpack .../04-libc6-dev_2.42-2ubuntu4_arm64.deb ... 505s Unpacking libc6-dev:arm64 (2.42-2ubuntu4) ... 505s Selecting previously unselected package libisl23:arm64. 505s Preparing to unpack .../05-libisl23_0.27-1build1_arm64.deb ... 505s Unpacking libisl23:arm64 (0.27-1build1) ... 505s Selecting previously unselected package libmpc3:arm64. 505s Preparing to unpack .../06-libmpc3_1.3.1-2_arm64.deb ... 505s Unpacking libmpc3:arm64 (1.3.1-2) ... 505s Selecting previously unselected package cpp-15-aarch64-linux-gnu. 505s Preparing to unpack .../07-cpp-15-aarch64-linux-gnu_15.2.0-12ubuntu1_arm64.deb ... 505s Unpacking cpp-15-aarch64-linux-gnu (15.2.0-12ubuntu1) ... 505s Selecting previously unselected package cpp-15. 505s Preparing to unpack .../08-cpp-15_15.2.0-12ubuntu1_arm64.deb ... 505s Unpacking cpp-15 (15.2.0-12ubuntu1) ... 505s Selecting previously unselected package cpp-aarch64-linux-gnu. 505s Preparing to unpack .../09-cpp-aarch64-linux-gnu_4%3a15.2.0-4ubuntu1_arm64.deb ... 505s Unpacking cpp-aarch64-linux-gnu (4:15.2.0-4ubuntu1) ... 505s Selecting previously unselected package cpp. 506s Preparing to unpack .../10-cpp_4%3a15.2.0-4ubuntu1_arm64.deb ... 506s Unpacking cpp (4:15.2.0-4ubuntu1) ... 506s Selecting previously unselected package libcc1-0:arm64. 506s Preparing to unpack .../11-libcc1-0_15.2.0-12ubuntu1_arm64.deb ... 506s Unpacking libcc1-0:arm64 (15.2.0-12ubuntu1) ... 506s Selecting previously unselected package libitm1:arm64. 506s Preparing to unpack .../12-libitm1_15.2.0-12ubuntu1_arm64.deb ... 506s Unpacking libitm1:arm64 (15.2.0-12ubuntu1) ... 506s Selecting previously unselected package libasan8:arm64. 506s Preparing to unpack .../13-libasan8_15.2.0-12ubuntu1_arm64.deb ... 506s Unpacking libasan8:arm64 (15.2.0-12ubuntu1) ... 506s Selecting previously unselected package liblsan0:arm64. 506s Preparing to unpack .../14-liblsan0_15.2.0-12ubuntu1_arm64.deb ... 506s Unpacking liblsan0:arm64 (15.2.0-12ubuntu1) ... 506s Selecting previously unselected package libtsan2:arm64. 506s Preparing to unpack .../15-libtsan2_15.2.0-12ubuntu1_arm64.deb ... 506s Unpacking libtsan2:arm64 (15.2.0-12ubuntu1) ... 506s Selecting previously unselected package libubsan1:arm64. 506s Preparing to unpack .../16-libubsan1_15.2.0-12ubuntu1_arm64.deb ... 506s Unpacking libubsan1:arm64 (15.2.0-12ubuntu1) ... 506s Selecting previously unselected package libhwasan0:arm64. 506s Preparing to unpack .../17-libhwasan0_15.2.0-12ubuntu1_arm64.deb ... 506s Unpacking libhwasan0:arm64 (15.2.0-12ubuntu1) ... 506s Selecting previously unselected package libgcc-15-dev:arm64. 506s Preparing to unpack .../18-libgcc-15-dev_15.2.0-12ubuntu1_arm64.deb ... 506s Unpacking libgcc-15-dev:arm64 (15.2.0-12ubuntu1) ... 506s Selecting previously unselected package gcc-15-aarch64-linux-gnu. 506s Preparing to unpack .../19-gcc-15-aarch64-linux-gnu_15.2.0-12ubuntu1_arm64.deb ... 506s Unpacking gcc-15-aarch64-linux-gnu (15.2.0-12ubuntu1) ... 507s Selecting previously unselected package gcc-15. 507s Preparing to unpack .../20-gcc-15_15.2.0-12ubuntu1_arm64.deb ... 507s Unpacking gcc-15 (15.2.0-12ubuntu1) ... 507s Selecting previously unselected package gcc-aarch64-linux-gnu. 507s Preparing to unpack .../21-gcc-aarch64-linux-gnu_4%3a15.2.0-4ubuntu1_arm64.deb ... 507s Unpacking gcc-aarch64-linux-gnu (4:15.2.0-4ubuntu1) ... 507s Selecting previously unselected package gcc. 507s Preparing to unpack .../22-gcc_4%3a15.2.0-4ubuntu1_arm64.deb ... 507s Unpacking gcc (4:15.2.0-4ubuntu1) ... 507s Selecting previously unselected package libstdc++-15-dev:arm64. 507s Preparing to unpack .../23-libstdc++-15-dev_15.2.0-12ubuntu1_arm64.deb ... 507s Unpacking libstdc++-15-dev:arm64 (15.2.0-12ubuntu1) ... 507s Selecting previously unselected package g++-15-aarch64-linux-gnu. 507s Preparing to unpack .../24-g++-15-aarch64-linux-gnu_15.2.0-12ubuntu1_arm64.deb ... 507s Unpacking g++-15-aarch64-linux-gnu (15.2.0-12ubuntu1) ... 507s Selecting previously unselected package g++-15. 507s Preparing to unpack .../25-g++-15_15.2.0-12ubuntu1_arm64.deb ... 507s Unpacking g++-15 (15.2.0-12ubuntu1) ... 507s Selecting previously unselected package g++-aarch64-linux-gnu. 507s Preparing to unpack .../26-g++-aarch64-linux-gnu_4%3a15.2.0-4ubuntu1_arm64.deb ... 507s Unpacking g++-aarch64-linux-gnu (4:15.2.0-4ubuntu1) ... 507s Selecting previously unselected package g++. 507s Preparing to unpack .../27-g++_4%3a15.2.0-4ubuntu1_arm64.deb ... 507s Unpacking g++ (4:15.2.0-4ubuntu1) ... 507s Selecting previously unselected package build-essential. 507s Preparing to unpack .../28-build-essential_12.12ubuntu2_arm64.deb ... 507s Unpacking build-essential (12.12ubuntu2) ... 507s Selecting previously unselected package dctrl-tools. 507s Preparing to unpack .../29-dctrl-tools_2.24-3build4_arm64.deb ... 507s Unpacking dctrl-tools (2.24-3build4) ... 507s Selecting previously unselected package libgfortran-15-dev:arm64. 507s Preparing to unpack .../30-libgfortran-15-dev_15.2.0-12ubuntu1_arm64.deb ... 507s Unpacking libgfortran-15-dev:arm64 (15.2.0-12ubuntu1) ... 508s Selecting previously unselected package gfortran-15-aarch64-linux-gnu. 508s Preparing to unpack .../31-gfortran-15-aarch64-linux-gnu_15.2.0-12ubuntu1_arm64.deb ... 508s Unpacking gfortran-15-aarch64-linux-gnu (15.2.0-12ubuntu1) ... 508s Selecting previously unselected package gfortran-15. 508s Preparing to unpack .../32-gfortran-15_15.2.0-12ubuntu1_arm64.deb ... 508s Unpacking gfortran-15 (15.2.0-12ubuntu1) ... 508s Selecting previously unselected package gfortran-aarch64-linux-gnu. 508s Preparing to unpack .../33-gfortran-aarch64-linux-gnu_4%3a15.2.0-4ubuntu1_arm64.deb ... 508s Unpacking gfortran-aarch64-linux-gnu (4:15.2.0-4ubuntu1) ... 508s Selecting previously unselected package gfortran. 508s Preparing to unpack .../34-gfortran_4%3a15.2.0-4ubuntu1_arm64.deb ... 508s Unpacking gfortran (4:15.2.0-4ubuntu1) ... 508s Selecting previously unselected package icu-devtools. 508s Preparing to unpack .../35-icu-devtools_78.2-1ubuntu1_arm64.deb ... 508s Unpacking icu-devtools (78.2-1ubuntu1) ... 508s Selecting previously unselected package libblas-dev:arm64. 508s Preparing to unpack .../36-libblas-dev_3.12.1-7ubuntu1_arm64.deb ... 508s Unpacking libblas-dev:arm64 (3.12.1-7ubuntu1) ... 508s Selecting previously unselected package libbz2-dev:arm64. 508s Preparing to unpack .../37-libbz2-dev_1.0.8-6build2_arm64.deb ... 508s Unpacking libbz2-dev:arm64 (1.0.8-6build2) ... 508s Selecting previously unselected package libdeflate-dev:arm64. 508s Preparing to unpack .../38-libdeflate-dev_1.23-2build1_arm64.deb ... 508s Unpacking libdeflate-dev:arm64 (1.23-2build1) ... 508s Selecting previously unselected package libicu-dev:arm64. 508s Preparing to unpack .../39-libicu-dev_78.2-1ubuntu1_arm64.deb ... 508s Unpacking libicu-dev:arm64 (78.2-1ubuntu1) ... 508s Selecting previously unselected package libjpeg-turbo8-dev:arm64. 508s Preparing to unpack .../40-libjpeg-turbo8-dev_2.1.5-4ubuntu3_arm64.deb ... 508s Unpacking libjpeg-turbo8-dev:arm64 (2.1.5-4ubuntu3) ... 508s Selecting previously unselected package libjpeg8-dev:arm64. 508s Preparing to unpack .../41-libjpeg8-dev_8c-2ubuntu11_arm64.deb ... 508s Unpacking libjpeg8-dev:arm64 (8c-2ubuntu11) ... 508s Selecting previously unselected package libjpeg-dev:arm64. 508s Preparing to unpack .../42-libjpeg-dev_8c-2ubuntu11_arm64.deb ... 508s Unpacking libjpeg-dev:arm64 (8c-2ubuntu11) ... 509s Selecting previously unselected package liblapack-dev:arm64. 509s Preparing to unpack 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Setting up r-base-dev (4.5.2-1ubuntu2) ... 512s Setting up pkg-r-autopkgtest (20250812) ... 512s Processing triggers for libc-bin (2.42-2ubuntu4) ... 512s Processing triggers for man-db (2.13.1-1build1) ... 513s Processing triggers for install-info (7.2-5) ... 514s autopkgtest [23:05:51]: test pkg-r-autopkgtest: /usr/share/dh-r/pkg-r-autopkgtest 514s autopkgtest [23:05:51]: test pkg-r-autopkgtest: [----------------------- 514s Test: Try to load the R library etm 514s 514s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 514s Copyright (C) 2025 The R Foundation for Statistical Computing 514s Platform: aarch64-unknown-linux-gnu 514s 514s R is free software and comes with ABSOLUTELY NO WARRANTY. 514s You are welcome to redistribute it under certain conditions. 514s Type 'license()' or 'licence()' for distribution details. 514s 514s R is a collaborative project with many contributors. 514s Type 'contributors()' for more information and 514s 'citation()' on how to cite R or R packages in publications. 514s 514s Type 'demo()' for some demos, 'help()' for on-line help, or 514s 'help.start()' for an HTML browser interface to help. 514s Type 'q()' to quit R. 514s 514s > library('etm') 515s > 515s autopkgtest [23:05:52]: test pkg-r-autopkgtest: -----------------------] 516s pkg-r-autopkgtest PASS 516s autopkgtest [23:05:53]: test pkg-r-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 516s autopkgtest [23:05:53]: @@@@@@@@@@@@@@@@@@@@ summary 516s run-unit-test PASS 516s pkg-r-autopkgtest PASS