0s autopkgtest [23:13:47]: starting date and time: 2026-02-09 23:13:47+0000 0s autopkgtest [23:13:47]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [23:13:47]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.ia4si4w_/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-ppc64el --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@sto01-ppc64el-11.secgroup --name adt-resolute-ppc64el-r-cran-etm-20260209-231347-juju-7f2275-prod-proposed-migration-environment-2-4b298ea7-d011-4df7-82a2-2e92c00f0163 --image adt/ubuntu-resolute-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-autopkgtest-workers-ppc64el -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 3s Creating nova instance adt-resolute-ppc64el-r-cran-etm-20260209-231347-juju-7f2275-prod-proposed-migration-environment-2-4b298ea7-d011-4df7-82a2-2e92c00f0163 from image adt/ubuntu-resolute-ppc64el-server-20260209.img (UUID f7f31435-4cd1-4090-aa55-59cfefa097ca)... 84s autopkgtest [23:15:11]: testbed dpkg architecture: ppc64el 84s autopkgtest [23:15:11]: testbed apt version: 3.1.15 85s autopkgtest [23:15:12]: @@@@@@@@@@@@@@@@@@@@ test bed setup 85s autopkgtest [23:15:12]: testbed release detected to be: None 86s autopkgtest [23:15:13]: updating testbed package index (apt update) 86s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 86s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 86s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 86s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 86s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [176 kB] 86s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [29.4 kB] 86s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [1645 kB] 88s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main ppc64el Packages [246 kB] 88s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/universe ppc64el Packages [1534 kB] 90s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse ppc64el Packages [19.4 kB] 90s Fetched 3774 kB in 5s (822 kB/s) 91s Reading package lists... 92s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 92s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 92s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 92s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 93s Reading package lists... 93s Reading package lists... 93s Building dependency tree... 93s Reading state information... 93s Calculating upgrade... 93s The following packages will be upgraded: 93s cryptsetup-bin dracut-install iproute2 iptables libcryptsetup12 libip4tc2 93s libip6tc2 libxtables12 wget 93s 9 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 93s Need to get 3125 kB of archives. 93s After this operation, 78.8 kB of additional disk space will be used. 93s Get:1 http://ftpmaster.internal/ubuntu resolute/main ppc64el iptables ppc64el 1.8.11-2ubuntu3 [464 kB] 93s Get:2 http://ftpmaster.internal/ubuntu resolute/main ppc64el libip4tc2 ppc64el 1.8.11-2ubuntu3 [27.8 kB] 93s Get:3 http://ftpmaster.internal/ubuntu resolute/main ppc64el libip6tc2 ppc64el 1.8.11-2ubuntu3 [28.2 kB] 93s Get:4 http://ftpmaster.internal/ubuntu resolute/main ppc64el libxtables12 ppc64el 1.8.11-2ubuntu3 [41.2 kB] 93s Get:5 http://ftpmaster.internal/ubuntu resolute/main ppc64el iproute2 ppc64el 6.18.0-1ubuntu1 [1458 kB] 95s Get:6 http://ftpmaster.internal/ubuntu resolute/main ppc64el libcryptsetup12 ppc64el 2:2.8.0-1ubuntu3 [404 kB] 95s Get:7 http://ftpmaster.internal/ubuntu resolute/main ppc64el wget ppc64el 1.25.0-2ubuntu4 [401 kB] 95s Get:8 http://ftpmaster.internal/ubuntu resolute/main ppc64el cryptsetup-bin ppc64el 2:2.8.0-1ubuntu3 [250 kB] 95s Get:9 http://ftpmaster.internal/ubuntu resolute/main ppc64el dracut-install ppc64el 109-11ubuntu1 [51.3 kB] 96s dpkg-preconfigure: unable to re-open stdin: No such file or directory 96s Fetched 3125 kB in 2s (1457 kB/s) 96s (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 ... 122003 files and directories currently installed.) 96s Preparing to unpack .../0-iptables_1.8.11-2ubuntu3_ppc64el.deb ... 96s Unpacking iptables (1.8.11-2ubuntu3) over (1.8.11-2ubuntu2) ... 96s Preparing to unpack .../1-libip4tc2_1.8.11-2ubuntu3_ppc64el.deb ... 96s Unpacking libip4tc2:ppc64el (1.8.11-2ubuntu3) over (1.8.11-2ubuntu2) ... 96s Preparing to unpack .../2-libip6tc2_1.8.11-2ubuntu3_ppc64el.deb ... 96s Unpacking libip6tc2:ppc64el (1.8.11-2ubuntu3) over (1.8.11-2ubuntu2) ... 96s Preparing to unpack .../3-libxtables12_1.8.11-2ubuntu3_ppc64el.deb ... 96s Unpacking libxtables12:ppc64el (1.8.11-2ubuntu3) over (1.8.11-2ubuntu2) ... 96s Preparing to unpack .../4-iproute2_6.18.0-1ubuntu1_ppc64el.deb ... 96s Unpacking iproute2 (6.18.0-1ubuntu1) over (6.16.0-1ubuntu3) ... 97s Preparing to unpack .../5-libcryptsetup12_2%3a2.8.0-1ubuntu3_ppc64el.deb ... 97s Unpacking libcryptsetup12:ppc64el (2:2.8.0-1ubuntu3) over (2:2.8.0-1ubuntu2) ... 97s Preparing to unpack .../6-wget_1.25.0-2ubuntu4_ppc64el.deb ... 97s Unpacking wget (1.25.0-2ubuntu4) over (1.25.0-2ubuntu3) ... 97s Preparing to unpack .../7-cryptsetup-bin_2%3a2.8.0-1ubuntu3_ppc64el.deb ... 97s Unpacking cryptsetup-bin (2:2.8.0-1ubuntu3) over (2:2.8.0-1ubuntu2) ... 97s Preparing to unpack .../8-dracut-install_109-11ubuntu1_ppc64el.deb ... 97s Unpacking dracut-install (109-11ubuntu1) over (109-9ubuntu1) ... 97s Setting up libip4tc2:ppc64el (1.8.11-2ubuntu3) ... 97s Setting up wget (1.25.0-2ubuntu4) ... 97s Setting up libip6tc2:ppc64el (1.8.11-2ubuntu3) ... 97s Setting up libxtables12:ppc64el (1.8.11-2ubuntu3) ... 97s Setting up dracut-install (109-11ubuntu1) ... 97s Setting up libcryptsetup12:ppc64el (2:2.8.0-1ubuntu3) ... 97s Setting up cryptsetup-bin (2:2.8.0-1ubuntu3) ... 97s Setting up iptables (1.8.11-2ubuntu3) ... 97s Setting up iproute2 (6.18.0-1ubuntu1) ... 97s Processing triggers for man-db (2.13.1-1build1) ... 99s Processing triggers for install-info (7.2-5) ... 99s Processing triggers for libc-bin (2.42-2ubuntu4) ... 99s autopkgtest [23:15:26]: upgrading testbed (apt dist-upgrade and autopurge) 99s Reading package lists... 99s Building dependency tree... 99s Reading state information... 100s Calculating upgrade... 100s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 100s Reading package lists... 100s Building dependency tree... 100s Reading state information... 100s Solving dependencies... 100s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 102s autopkgtest [23:15:29]: testbed running kernel: Linux 6.19.0-3-generic #3-Ubuntu SMP PREEMPT_DYNAMIC Fri Jan 23 20:13:51 UTC 2026 103s autopkgtest [23:15:30]: @@@@@@@@@@@@@@@@@@@@ apt-source r-cran-etm 104s Get:1 http://ftpmaster.internal/ubuntu resolute/universe r-cran-etm 1.1.1-1build1 (dsc) [2147 B] 104s Get:2 http://ftpmaster.internal/ubuntu resolute/universe r-cran-etm 1.1.1-1build1 (tar) [242 kB] 104s Get:3 http://ftpmaster.internal/ubuntu resolute/universe r-cran-etm 1.1.1-1build1 (diff) [3672 B] 104s gpgv: Signature made Fri Nov 28 21:46:53 2025 UTC 104s gpgv: using RSA key 92FE4F8B40CADC4ECCD60C1F5961FDBE9C619809 104s gpgv: Can't check signature: No public key 104s dpkg-source: warning: cannot verify inline signature for ./r-cran-etm_1.1.1-1build1.dsc: no acceptable signature found 104s autopkgtest [23:15:31]: testing package r-cran-etm version 1.1.1-1build1 105s autopkgtest [23:15:32]: build not needed 108s autopkgtest [23:15:35]: test run-unit-test: preparing testbed 108s Reading package lists... 109s Building dependency tree... 109s Reading state information... 109s Solving dependencies... 109s The following NEW packages will be installed: 109s fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono libblas3 109s libcairo2 libdatrie1 libdeflate0 libfontconfig1 libgfortran5 libgomp1 109s libgraphite2-3 libharfbuzz0b libice6 libjbig0 libjpeg-turbo8 libjpeg8 109s liblapack3 liblerc4 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 109s libpaper-utils libpaper2 libpixman-1-0 libsharpyuv0 libsm6 libtcl8.6 109s libthai-data libthai0 libtiff6 libtk8.6 libwebp7 libxcb-render0 libxcb-shm0 109s libxft2 libxrender1 libxss1 libxt6t64 r-base-core r-cran-data.table 109s r-cran-dbi r-cran-etm r-cran-kmi r-cran-lattice r-cran-littler r-cran-matrix 109s r-cran-mitools r-cran-pkgkitten r-cran-rcpp r-cran-rcpparmadillo 109s r-cran-survival unzip x11-common xdg-utils zip 109s 0 upgraded, 56 newly installed, 0 to remove and 0 not upgraded. 109s Need to get 63.2 MB of archives. 109s After this operation, 138 MB of additional disk space will be used. 109s Get:1 http://ftpmaster.internal/ubuntu resolute/main ppc64el fonts-dejavu-mono all 2.37-8build1 [502 kB] 109s Get:2 http://ftpmaster.internal/ubuntu resolute/main ppc64el fonts-dejavu-core all 2.37-8build1 [834 kB] 110s Get:3 http://ftpmaster.internal/ubuntu resolute/main ppc64el fontconfig-config ppc64el 2.17.1-3ubuntu1 [38.5 kB] 110s Get:4 http://ftpmaster.internal/ubuntu resolute/main ppc64el libfontconfig1 ppc64el 2.17.1-3ubuntu1 [193 kB] 110s Get:5 http://ftpmaster.internal/ubuntu resolute/main ppc64el fontconfig ppc64el 2.17.1-3ubuntu1 [182 kB] 110s Get:6 http://ftpmaster.internal/ubuntu resolute/main ppc64el libblas3 ppc64el 3.12.1-7ubuntu1 [291 kB] 110s Get:7 http://ftpmaster.internal/ubuntu resolute/main ppc64el libpixman-1-0 ppc64el 0.46.4-1 [347 kB] 110s Get:8 http://ftpmaster.internal/ubuntu resolute/main ppc64el libxcb-render0 ppc64el 1.17.0-2ubuntu1 [17.4 kB] 110s Get:9 http://ftpmaster.internal/ubuntu resolute/main ppc64el libxcb-shm0 ppc64el 1.17.0-2ubuntu1 [6072 B] 110s Get:10 http://ftpmaster.internal/ubuntu resolute/main ppc64el libxrender1 ppc64el 1:0.9.12-1 [23.0 kB] 110s Get:11 http://ftpmaster.internal/ubuntu resolute/main ppc64el libcairo2 ppc64el 1.18.4-3 [759 kB] 111s Get:12 http://ftpmaster.internal/ubuntu resolute/main ppc64el libdatrie1 ppc64el 0.2.14-1 [22.7 kB] 111s Get:13 http://ftpmaster.internal/ubuntu resolute/main ppc64el libdeflate0 ppc64el 1.23-2build1 [64.1 kB] 111s Get:14 http://ftpmaster.internal/ubuntu resolute/main ppc64el libgfortran5 ppc64el 15.2.0-12ubuntu1 [620 kB] 112s Get:15 http://ftpmaster.internal/ubuntu resolute/main ppc64el libgomp1 ppc64el 15.2.0-12ubuntu1 [169 kB] 112s Get:16 http://ftpmaster.internal/ubuntu resolute/main ppc64el libgraphite2-3 ppc64el 1.3.14-11ubuntu1 [85.3 kB] 112s Get:17 http://ftpmaster.internal/ubuntu resolute/main ppc64el libharfbuzz0b ppc64el 12.3.2-1 [663 kB] 113s Get:18 http://ftpmaster.internal/ubuntu resolute/main ppc64el x11-common all 1:7.7+24ubuntu1 [22.4 kB] 113s Get:19 http://ftpmaster.internal/ubuntu resolute/main ppc64el libice6 ppc64el 2:1.1.1-1build1 [51.9 kB] 113s Get:20 http://ftpmaster.internal/ubuntu resolute/main ppc64el libjpeg-turbo8 ppc64el 2.1.5-4ubuntu3 [214 kB] 113s Get:21 http://ftpmaster.internal/ubuntu resolute/main ppc64el libjpeg8 ppc64el 8c-2ubuntu11 [2148 B] 113s Get:22 http://ftpmaster.internal/ubuntu resolute/main ppc64el liblapack3 ppc64el 3.12.1-7ubuntu1 [2960 kB] 118s Get:23 http://ftpmaster.internal/ubuntu resolute/main ppc64el liblerc4 ppc64el 4.0.0+ds-5ubuntu2 [315 kB] 118s Get:24 http://ftpmaster.internal/ubuntu resolute/main ppc64el libthai-data all 0.1.30-1 [155 kB] 118s Get:25 http://ftpmaster.internal/ubuntu resolute/main ppc64el libthai0 ppc64el 0.1.30-1 [22.5 kB] 118s Get:26 http://ftpmaster.internal/ubuntu resolute/main ppc64el libpango-1.0-0 ppc64el 1.57.0-1 [283 kB] 118s Get:27 http://ftpmaster.internal/ubuntu resolute/main ppc64el libpangoft2-1.0-0 ppc64el 1.57.0-1 [61.2 kB] 118s Get:28 http://ftpmaster.internal/ubuntu resolute/main ppc64el libpangocairo-1.0-0 ppc64el 1.57.0-1 [31.0 kB] 118s Get:29 http://ftpmaster.internal/ubuntu resolute/main ppc64el libpaper2 ppc64el 2.2.5-0.3build1 [18.1 kB] 118s Get:30 http://ftpmaster.internal/ubuntu resolute/main ppc64el libpaper-utils ppc64el 2.2.5-0.3build1 [15.7 kB] 118s Get:31 http://ftpmaster.internal/ubuntu resolute/main ppc64el libsharpyuv0 ppc64el 1.5.0-0.1build1 [24.7 kB] 118s Get:32 http://ftpmaster.internal/ubuntu resolute/main ppc64el libsm6 ppc64el 2:1.2.6-1build1 [18.6 kB] 118s Get:33 http://ftpmaster.internal/ubuntu resolute/main ppc64el libtcl8.6 ppc64el 8.6.17+dfsg-1build1 [1239 kB] 119s Get:34 http://ftpmaster.internal/ubuntu resolute/main ppc64el libjbig0 ppc64el 2.1-6.1ubuntu3 [37.1 kB] 119s Get:35 http://ftpmaster.internal/ubuntu resolute/main ppc64el libwebp7 ppc64el 1.5.0-0.1build1 [330 kB] 119s Get:36 http://ftpmaster.internal/ubuntu resolute/main ppc64el libtiff6 ppc64el 4.7.0-3ubuntu3 [307 kB] 119s Get:37 http://ftpmaster.internal/ubuntu resolute/main ppc64el libxft2 ppc64el 2.3.6-1build2 [61.6 kB] 119s Get:38 http://ftpmaster.internal/ubuntu resolute/main ppc64el libxss1 ppc64el 1:1.2.3-1build4 [7470 B] 119s Get:39 http://ftpmaster.internal/ubuntu resolute/main ppc64el libtk8.6 ppc64el 8.6.17-1 [968 kB] 120s Get:40 http://ftpmaster.internal/ubuntu resolute/main ppc64el libxt6t64 ppc64el 1:1.2.1-1.3 [203 kB] 120s Get:41 http://ftpmaster.internal/ubuntu resolute/main ppc64el zip ppc64el 3.0-15ubuntu3 [198 kB] 120s Get:42 http://ftpmaster.internal/ubuntu resolute/main ppc64el unzip ppc64el 6.0-29ubuntu1 [200 kB] 120s Get:43 http://ftpmaster.internal/ubuntu resolute/main ppc64el xdg-utils all 1.2.1-2ubuntu2 [66.1 kB] 120s Get:44 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-base-core ppc64el 4.5.2-1ubuntu2 [29.3 MB] 160s Get:45 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-data.table ppc64el 1.17.0+dfsg-1 [2197 kB] 163s Get:46 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-dbi all 1.2.3-1build1 [855 kB] 164s Get:47 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-lattice ppc64el 0.22-7-1 [1366 kB] 166s Get:48 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-matrix ppc64el 1.7-4-1 [4584 kB] 172s Get:49 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-survival ppc64el 3.8-6-1 [8312 kB] 184s Get:50 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-littler ppc64el 0.3.22-1 [85.5 kB] 184s Get:51 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-pkgkitten all 0.2.4-1 [27.2 kB] 184s Get:52 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-rcpp ppc64el 1.1.0-1 [2037 kB] 188s Get:53 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-rcpparmadillo ppc64el 15.2.3-1-1 [935 kB] 189s Get:54 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-etm ppc64el 1.1.1-1build1 [506 kB] 189s Get:55 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-mitools all 2.4-2build2 [266 kB] 189s Get:56 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-kmi all 0.5.5-2build2 [78.9 kB] 189s Preconfiguring packages ... 189s Fetched 63.2 MB in 1min 20s (788 kB/s) 189s Selecting previously unselected package fonts-dejavu-mono. 189s (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 ... 122006 files and directories currently installed.) 189s Preparing to unpack .../00-fonts-dejavu-mono_2.37-8build1_all.deb ... 189s Unpacking fonts-dejavu-mono (2.37-8build1) ... 189s Selecting previously unselected package fonts-dejavu-core. 189s Preparing to unpack .../01-fonts-dejavu-core_2.37-8build1_all.deb ... 189s Unpacking fonts-dejavu-core (2.37-8build1) ... 189s Selecting previously unselected package fontconfig-config. 189s Preparing to unpack .../02-fontconfig-config_2.17.1-3ubuntu1_ppc64el.deb ... 190s Unpacking fontconfig-config (2.17.1-3ubuntu1) ... 190s Selecting previously unselected package libfontconfig1:ppc64el. 190s Preparing to unpack .../03-libfontconfig1_2.17.1-3ubuntu1_ppc64el.deb ... 190s Unpacking libfontconfig1:ppc64el (2.17.1-3ubuntu1) ... 190s Selecting previously unselected package fontconfig. 190s Preparing to unpack .../04-fontconfig_2.17.1-3ubuntu1_ppc64el.deb ... 190s Unpacking fontconfig (2.17.1-3ubuntu1) ... 190s Selecting previously unselected package libblas3:ppc64el. 190s Preparing to unpack .../05-libblas3_3.12.1-7ubuntu1_ppc64el.deb ... 190s Unpacking libblas3:ppc64el (3.12.1-7ubuntu1) ... 190s Selecting previously unselected package libpixman-1-0:ppc64el. 190s Preparing to unpack .../06-libpixman-1-0_0.46.4-1_ppc64el.deb ... 190s Unpacking libpixman-1-0:ppc64el (0.46.4-1) ... 190s Selecting previously unselected package libxcb-render0:ppc64el. 190s Preparing to unpack .../07-libxcb-render0_1.17.0-2ubuntu1_ppc64el.deb ... 190s Unpacking libxcb-render0:ppc64el (1.17.0-2ubuntu1) ... 190s Selecting previously unselected package libxcb-shm0:ppc64el. 190s Preparing to unpack .../08-libxcb-shm0_1.17.0-2ubuntu1_ppc64el.deb ... 190s Unpacking libxcb-shm0:ppc64el (1.17.0-2ubuntu1) ... 190s Selecting previously unselected package libxrender1:ppc64el. 190s Preparing to unpack .../09-libxrender1_1%3a0.9.12-1_ppc64el.deb ... 190s Unpacking libxrender1:ppc64el (1:0.9.12-1) ... 190s Selecting previously unselected package libcairo2:ppc64el. 190s Preparing to unpack .../10-libcairo2_1.18.4-3_ppc64el.deb ... 190s Unpacking libcairo2:ppc64el (1.18.4-3) ... 190s Selecting previously unselected package libdatrie1:ppc64el. 190s Preparing to unpack .../11-libdatrie1_0.2.14-1_ppc64el.deb ... 190s Unpacking libdatrie1:ppc64el (0.2.14-1) ... 190s Selecting previously unselected package libdeflate0:ppc64el. 190s Preparing to unpack .../12-libdeflate0_1.23-2build1_ppc64el.deb ... 190s Unpacking libdeflate0:ppc64el (1.23-2build1) ... 190s Selecting previously unselected package libgfortran5:ppc64el. 190s Preparing to unpack .../13-libgfortran5_15.2.0-12ubuntu1_ppc64el.deb ... 190s Unpacking libgfortran5:ppc64el (15.2.0-12ubuntu1) ... 190s Selecting previously unselected package libgomp1:ppc64el. 190s Preparing to unpack .../14-libgomp1_15.2.0-12ubuntu1_ppc64el.deb ... 190s Unpacking libgomp1:ppc64el (15.2.0-12ubuntu1) ... 190s Selecting previously unselected package libgraphite2-3:ppc64el. 190s Preparing to unpack .../15-libgraphite2-3_1.3.14-11ubuntu1_ppc64el.deb ... 190s Unpacking libgraphite2-3:ppc64el (1.3.14-11ubuntu1) ... 190s Selecting previously unselected package libharfbuzz0b:ppc64el. 190s Preparing to unpack .../16-libharfbuzz0b_12.3.2-1_ppc64el.deb ... 190s Unpacking libharfbuzz0b:ppc64el (12.3.2-1) ... 190s Selecting previously unselected package x11-common. 190s Preparing to unpack .../17-x11-common_1%3a7.7+24ubuntu1_all.deb ... 190s Unpacking x11-common (1:7.7+24ubuntu1) ... 190s Selecting previously unselected package libice6:ppc64el. 190s Preparing to unpack .../18-libice6_2%3a1.1.1-1build1_ppc64el.deb ... 190s Unpacking libice6:ppc64el (2:1.1.1-1build1) ... 190s Selecting previously unselected package libjpeg-turbo8:ppc64el. 190s Preparing to unpack .../19-libjpeg-turbo8_2.1.5-4ubuntu3_ppc64el.deb ... 190s Unpacking libjpeg-turbo8:ppc64el (2.1.5-4ubuntu3) ... 190s Selecting previously unselected package libjpeg8:ppc64el. 190s Preparing to unpack .../20-libjpeg8_8c-2ubuntu11_ppc64el.deb ... 190s Unpacking libjpeg8:ppc64el (8c-2ubuntu11) ... 190s Selecting previously unselected package liblapack3:ppc64el. 190s Preparing to unpack .../21-liblapack3_3.12.1-7ubuntu1_ppc64el.deb ... 190s Unpacking liblapack3:ppc64el (3.12.1-7ubuntu1) ... 190s Selecting previously unselected package liblerc4:ppc64el. 190s Preparing to unpack .../22-liblerc4_4.0.0+ds-5ubuntu2_ppc64el.deb ... 190s Unpacking liblerc4:ppc64el (4.0.0+ds-5ubuntu2) 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Creating config file /etc/R/Renviron with new version 195s Setting up r-cran-lattice (0.22-7-1) ... 195s Setting up r-cran-pkgkitten (0.2.4-1) ... 195s Setting up r-cran-littler (0.3.22-1) ... 195s Setting up r-cran-rcpp (1.1.0-1) ... 195s Setting up r-cran-dbi (1.2.3-1build1) ... 195s Setting up r-cran-data.table (1.17.0+dfsg-1) ... 195s Setting up r-cran-matrix (1.7-4-1) ... 195s Setting up r-cran-rcpparmadillo (15.2.3-1-1) ... 195s Setting up r-cran-mitools (2.4-2build2) ... 195s Setting up r-cran-survival (3.8-6-1) ... 195s Setting up r-cran-kmi (0.5.5-2build2) ... 195s Setting up r-cran-etm (1.1.1-1build1) ... 195s Processing triggers for man-db (2.13.1-1build1) ... 196s Processing triggers for install-info (7.2-5) ... 196s Processing triggers for libc-bin (2.42-2ubuntu4) ... 197s autopkgtest [23:17:04]: test run-unit-test: [----------------------- 197s BEGIN TEST test.etmCIF.R 197s 197s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 197s Copyright (C) 2025 The R Foundation for Statistical Computing 197s Platform: powerpc64le-unknown-linux-gnu 197s 197s R is free software and comes with ABSOLUTELY NO WARRANTY. 197s You are welcome to redistribute it under certain conditions. 197s Type 'license()' or 'licence()' for distribution details. 197s 197s R is a collaborative project with many contributors. 197s Type 'contributors()' for more information and 197s 'citation()' on how to cite R or R packages in publications. 197s 197s Type 'demo()' for some demos, 'help()' for on-line help, or 197s 'help.start()' for an HTML browser interface to help. 197s Type 'q()' to quit R. 197s 198s > ### test file for etmCIF. 198s > ### Really simple tests and comparison with etm 198s > 198s > old <- options(digits = 5) 198s > 198s > require(etm) 198s Loading required package: etm 199s > 199s > if (!require(survival, quietly = TRUE)) { 199s + print("The following tests require the 'survival' package") 199s + } else { 199s + 199s + data(abortion) 199s + 199s + from <- rep(0, nrow(abortion)) 199s + to <- abortion$cause 199s + entry <- abortion$entry 199s + exit <- abortion$exit 199s + id <- 1:nrow(abortion) 199s + data <- data.frame(id, from, to, entry, exit, group = abortion$group) 199s + 199s + ## Computation of the CIFs with etm 199s + tra <- matrix(FALSE, 4, 4) 199s + tra[1, 2:4] <- TRUE 199s + 199s + cif.control <- etm(data[data$group == 0, ], c("0", "1", "2", "3"), 199s + tra, NULL, 0) 199s + cif.exposed <- etm(data[data$group == 1, ], c("0", "1", "2", "3"), 199s + tra, NULL, 0) 199s + 199s + 199s + ## Computation of the CIFs with etmCIF 199s + netm <- etmCIF(Surv(entry, exit, cause != 0) ~ group, abortion, 199s + etype = cause, failcode = 3) 199s + 199s + ### let's do some comparisons :-) 199s + 199s + all.equal(trprob(cif.control, "0 3"), netm[[1]]$est["0", "3", ]) 199s + all.equal(trprob(cif.control, "0 2"), netm[[1]]$est["0", "2", ]) 199s + all.equal(trprob(cif.control, "0 1"), netm[[1]]$est["0", "1", ]) 199s + 199s + all.equal(trprob(cif.exposed, "0 3"), netm[[2]]$est["0", "3", ]) 199s + all.equal(trprob(cif.exposed, "0 2"), netm[[2]]$est["0", "2", ]) 199s + all.equal(trprob(cif.exposed, "0 1"), netm[[2]]$est["0", "1", ]) 199s + 199s + 199s + all.equal(trcov(cif.control, "0 3"), netm[[1]]$cov["0 3", "0 3", ]) 199s + all.equal(trcov(cif.control, "0 2"), netm[[1]]$cov["0 2", "0 2", ]) 199s + all.equal(trcov(cif.control, "0 1"), netm[[1]]$cov["0 1", "0 1", ]) 199s + 199s + all.equal(trcov(cif.exposed, "0 3"), netm[[2]]$cov["0 3", "0 3", ]) 199s + all.equal(trcov(cif.exposed, "0 2"), netm[[2]]$cov["0 2", "0 2", ]) 199s + all.equal(trcov(cif.exposed, "0 1"), netm[[2]]$cov["0 1", "0 1", ]) 199s + 199s + 199s + netm 199s + 199s + ## test on the summary 199s + snetm <- summary(netm) 199s + 199s + snetm 199s + 199s + all.equal(unname(trprob(cif.control, "0 3")), snetm[[1]][[3]]$P) 199s + all.equal(unname(trprob(cif.control, "0 2")), snetm[[1]][[2]]$P) 199s + all.equal(unname(trprob(cif.control, "0 1")), snetm[[1]][[1]]$P) 199s + 199s + all.equal(unname(trprob(cif.exposed, "0 3")), snetm[[2]][[3]]$P) 199s + all.equal(unname(trprob(cif.exposed, "0 2")), snetm[[2]][[2]]$P) 199s + all.equal(unname(trprob(cif.exposed, "0 1")), snetm[[2]][[1]]$P) 199s + 199s + scif.control <- summary(cif.control, ci.fun = "cloglog") 199s + scif.exposed <- summary(cif.exposed, ci.fun = "cloglog") 199s + 199s + all.equal(scif.control[[4]]$lower, snetm[[1]][[3]]$lower) 199s + all.equal(scif.control[[4]]$upper, snetm[[1]][[3]]$upper) 199s + 199s + all.equal(scif.exposed[[4]]$lower, snetm[[2]][[3]]$lower) 199s + all.equal(scif.exposed[[4]]$upper, snetm[[2]][[3]]$upper) 199s + } 199s [1] TRUE 199s > 199s > ### test with factors in the input 199s > abortion$status <- with(abortion, ifelse(cause == 2, "life birth", 199s + ifelse(cause == 1, "ETOP", "spontaneous abortion"))) 199s > 199s > abortion$status <- factor(abortion$status) 199s > 199s > netm.factor <- etmCIF(Surv(entry, exit, status != "cens") ~ group, abortion, 199s + etype = status, failcode = "spontaneous abortion") 199s > 199s > 199s > all.equal(trprob(cif.control, "0 3"), netm.factor[[1]]$est["0", "spontaneous abortion", ]) 199s [1] TRUE 199s > all.equal(trprob(cif.control, "0 2"), netm.factor[[1]]$est["0", "life birth", ]) 199s [1] TRUE 199s > 199s > netm.factor 199s Call: etmCIF(formula = Surv(entry, exit, status != "cens") ~ group, 199s data = abortion, etype = status, failcode = "spontaneous abortion") 199s 199s Covariate: group 199s levels: 0 1 199s 199s 199s group = 0 199s time P se(P) n.event 199s CIF ETOP 43 0.040159 0.0092578 20 199s CIF life birth 43 0.799059 0.0221865 924 199s CIF spontaneous abortion 43 0.160781 0.0213261 69 199s 199s group = 1 199s time P se(P) n.event 199s CIF ETOP 42 0.28511 0.042493 38 199s CIF life birth 42 0.35257 0.042139 92 199s CIF spontaneous abortion 42 0.36232 0.049473 43 199s > 199s > summary(netm.factor) 199s 199s group=0 199s 199s CIF ETOP 199s P time var lower upper n.risk n.event 199s 0.000000 6 0.0000e+00 0.000000 0.000000 117 0 199s 0.038955 13 8.4440e-05 0.024488 0.061694 645 1 199s 0.040159 26 8.5707e-05 0.025513 0.062939 846 0 199s 0.040159 36 8.5707e-05 0.025513 0.062939 876 0 199s 0.040159 40 8.5707e-05 0.025513 0.062939 554 0 199s 0.040159 43 8.5707e-05 0.025513 0.062939 6 0 199s 199s CIF life birth 199s P time var lower upper n.risk n.event 199s 0.000000 6 0.0000e+00 0.000000 0.000000 117 0 199s 0.000000 13 0.0000e+00 0.000000 0.000000 645 0 199s 0.000000 26 0.0000e+00 0.000000 0.000000 846 0 199s 0.053197 36 4.6195e-05 0.041379 0.068268 876 25 199s 0.563121 40 3.8801e-04 0.524924 0.602021 554 280 199s 0.799059 43 4.9224e-04 0.753969 0.840613 6 6 199s 199s CIF spontaneous abortion 199s P time var lower upper n.risk n.event 199s 0.034188 6 0.00028222 0.01297 0.088523 117 4 199s 0.150468 13 0.00045513 0.11360 0.197901 645 1 199s 0.159904 26 0.00045498 0.12274 0.206925 846 1 199s 0.160781 36 0.00045480 0.12360 0.207757 876 1 199s 0.160781 40 0.00045480 0.12360 0.207757 554 0 199s 0.160781 43 0.00045480 0.12360 0.207757 6 0 199s 199s 199s group=1 199s 199s CIF ETOP 199s P time var lower upper n.risk n.event 199s 0.00000 6 0.0000000 0.00000 0.00000 35 0 199s 0.26048 13 0.0017854 0.18795 0.35425 90 0 199s 0.28115 21 0.0018028 0.20742 0.37423 93 1 199s 0.28511 34 0.0018057 0.21116 0.37806 89 0 199s 0.28511 39 0.0018057 0.21116 0.37806 59 0 199s 0.28511 42 0.0018057 0.21116 0.37806 6 0 199s 199s CIF life birth 199s P time var lower upper n.risk n.event 199s 0.000000 6 0.0000e+00 0.000000 0.000000 35 0 199s 0.000000 13 0.0000e+00 0.000000 0.000000 90 0 199s 0.000000 21 0.0000e+00 0.000000 0.000000 93 0 199s 0.023073 34 9.0514e-05 0.010252 0.051504 89 2 199s 0.180156 39 8.0126e-04 0.131765 0.243663 59 13 199s 0.352565 42 1.7757e-03 0.276882 0.441775 6 6 199s 199s CIF spontaneous abortion 199s P time var lower upper n.risk n.event 199s 0.057143 6 0.0015394 0.014605 0.20968 35 2 199s 0.333246 13 0.0025280 0.245337 0.44216 90 4 199s 0.350702 21 0.0024827 0.262769 0.45762 93 0 199s 0.358492 34 0.0024593 0.270627 0.46448 89 0 199s 0.358492 39 0.0024593 0.270627 0.46448 59 0 199s 0.362323 42 0.0024476 0.274499 0.46785 6 0 199s 199s > 199s > ### test with group as a character vector 199s > abortion$ttt <- with(abortion, ifelse(group == 0, "control", "exposed")) 199s > abortion$ttt <- factor(abortion$ttt) 199s > 199s > netm.ttt <- etmCIF(Surv(entry, exit, status != "cens") ~ ttt, abortion, 199s + etype = status, failcode = "spontaneous abortion") 199s > 199s > all.equal(trprob(cif.control, "0 3"), netm.ttt[[1]]$est["0", "spontaneous abortion", ]) 199s [1] TRUE 199s > all.equal(trprob(cif.control, "0 2"), netm.ttt[[1]]$est["0", "life birth", ]) 199s [1] TRUE 199s > 199s > netm.ttt 199s Call: etmCIF(formula = Surv(entry, exit, status != "cens") ~ ttt, data = abortion, 199s etype = status, failcode = "spontaneous abortion") 199s 199s Covariate: ttt 199s levels: control exposed 199s 199s 199s ttt = control 199s time P se(P) n.event 199s CIF ETOP 43 0.040159 0.0092578 20 199s CIF life birth 43 0.799059 0.0221865 924 199s CIF spontaneous abortion 43 0.160781 0.0213261 69 199s 199s ttt = exposed 199s time P se(P) n.event 199s CIF ETOP 42 0.28511 0.042493 38 199s CIF life birth 42 0.35257 0.042139 92 199s CIF spontaneous abortion 42 0.36232 0.049473 43 199s > 199s > summary(netm.ttt) 199s 199s ttt=control 199s 199s CIF ETOP 199s P time var lower upper n.risk n.event 199s 0.000000 6 0.0000e+00 0.000000 0.000000 117 0 199s 0.038955 13 8.4440e-05 0.024488 0.061694 645 1 199s 0.040159 26 8.5707e-05 0.025513 0.062939 846 0 199s 0.040159 36 8.5707e-05 0.025513 0.062939 876 0 199s 0.040159 40 8.5707e-05 0.025513 0.062939 554 0 199s 0.040159 43 8.5707e-05 0.025513 0.062939 6 0 199s 199s CIF life birth 199s P time var lower upper n.risk n.event 199s 0.000000 6 0.0000e+00 0.000000 0.000000 117 0 199s 0.000000 13 0.0000e+00 0.000000 0.000000 645 0 199s 0.000000 26 0.0000e+00 0.000000 0.000000 846 0 199s 0.053197 36 4.6195e-05 0.041379 0.068268 876 25 199s 0.563121 40 3.8801e-04 0.524924 0.602021 554 280 199s 0.799059 43 4.9224e-04 0.753969 0.840613 6 6 199s 199s CIF spontaneous abortion 199s P time var lower upper n.risk n.event 199s 0.034188 6 0.00028222 0.01297 0.088523 117 4 199s 0.150468 13 0.00045513 0.11360 0.197901 645 1 199s 0.159904 26 0.00045498 0.12274 0.206925 846 1 199s 0.160781 36 0.00045480 0.12360 0.207757 876 1 199s 0.160781 40 0.00045480 0.12360 0.207757 554 0 199s 0.160781 43 0.00045480 0.12360 0.207757 6 0 199s 199s 199s ttt=exposed 199s 199s CIF ETOP 199s P time var lower upper n.risk n.event 199s 0.00000 6 0.0000000 0.00000 0.00000 35 0 199s 0.26048 13 0.0017854 0.18795 0.35425 90 0 199s 0.28115 21 0.0018028 0.20742 0.37423 93 1 199s 0.28511 34 0.0018057 0.21116 0.37806 89 0 199s 0.28511 39 0.0018057 0.21116 0.37806 59 0 199s 0.28511 42 0.0018057 0.21116 0.37806 6 0 199s 199s CIF life birth 199s P time var lower upper n.risk n.event 199s 0.000000 6 0.0000e+00 0.000000 0.000000 35 0 199s 0.000000 13 0.0000e+00 0.000000 0.000000 90 0 199s 0.000000 21 0.0000e+00 0.000000 0.000000 93 0 199s 0.023073 34 9.0514e-05 0.010252 0.051504 89 2 199s 0.180156 39 8.0126e-04 0.131765 0.243663 59 13 199s 0.352565 42 1.7757e-03 0.276882 0.441775 6 6 199s 199s CIF spontaneous abortion 199s P time var lower upper n.risk n.event 199s 0.057143 6 0.0015394 0.014605 0.20968 35 2 199s 0.333246 13 0.0025280 0.245337 0.44216 90 4 199s 0.350702 21 0.0024827 0.262769 0.45762 93 0 199s 0.358492 34 0.0024593 0.270627 0.46448 89 0 199s 0.358492 39 0.0024593 0.270627 0.46448 59 0 199s 0.362323 42 0.0024476 0.274499 0.46785 6 0 199s 199s > 199s > 199s > ### A couple of comparisons with simulated data 199s > set.seed(1313) 199s > time <- rexp(100) 199s > to <- rbinom(100, 2, prob = c(1/3, 1/3, 1/3)) 199s > from <- rep(11, 100) 199s > id <- 1:100 199s > cov <- rbinom(100, 1, 0.5) 199s > 199s > dat.s <- data.frame(id, time, from, to, cov) 199s > 199s > traa <- matrix(FALSE, 3, 3) 199s > traa[1, 2:3] <- TRUE 199s > 199s > aa0 <- etm(dat.s[dat.s$cov == 0, ], c("11", "1", "2"), traa, "0", 0) 199s > aa1 <- etm(dat.s[dat.s$cov == 1, ], c("11", "1", "2"), traa, "0", 0) 199s > aa <- etm(dat.s, c("11", "1", "2"), traa, "0", 0) 199s > 199s > test <- etmCIF(Surv(time, to != 0) ~ 1, dat.s, etype = to) 199s > 199s > test.c <- etmCIF(Surv(time, to != 0) ~ cov, dat.s, etype = to) 199s > 199s > all.equal(trprob(aa, "11 1"), test[[1]]$est["0", "1", ]) 199s [1] TRUE 199s > all.equal(trprob(aa, "11 2"), test[[1]]$est["0", "2", ]) 199s [1] TRUE 199s > 199s > all.equal(trprob(aa0, "11 1"), test.c[[1]]$est["0", "1", ]) 199s [1] TRUE 199s > all.equal(trprob(aa0, "11 2"), test.c[[1]]$est["0", "2", ]) 199s [1] TRUE 199s > 199s > all.equal(trprob(aa1, "11 1"), test.c[[2]]$est["0", "1", ]) 199s [1] TRUE 199s > all.equal(trprob(aa1, "11 2"), test.c[[2]]$est["0", "2", ]) 199s [1] TRUE 199s > 199s > test 199s Call: etmCIF(formula = Surv(time, to != 0) ~ 1, data = dat.s, etype = to) 199s 199s time P se(P) n.event 199s CIF 1 4.9088 0.809108 0.079680 45 199s CIF 2 4.9088 0.096618 0.032905 8 199s > 199s > test.c 199s Call: etmCIF(formula = Surv(time, to != 0) ~ cov, data = dat.s, etype = to) 199s 199s Covariate: cov 199s levels: 0 1 199s 199s 199s cov = 0 199s time P se(P) n.event 199s CIF 1 2.1708 0.70246 0.105797 19 199s CIF 2 2.1708 0.11144 0.053384 4 199s 199s cov = 1 199s time P se(P) n.event 199s CIF 1 4.9088 0.80787 0.094051 26 199s CIF 2 4.9088 0.08436 0.040769 4 199s > 199s > summary(test) 199s 199s 199s 199s CIF 1 199s P time var lower upper n.risk n.event 199s 0.01000 0.0092099 0.0000990 0.0014147 0.068863 100 1 199s 0.11430 0.2663096 0.0010542 0.0649454 0.196993 81 1 199s 0.23451 0.7303091 0.0020436 0.1591107 0.337736 54 1 199s 0.40425 1.4299939 0.0032996 0.3020445 0.525741 29 1 199s 0.54593 2.0647206 0.0040836 0.4269008 0.673605 16 1 199s 0.80911 4.9087561 0.0063489 0.6359544 0.933733 2 1 199s 199s CIF 2 199s P time var lower upper n.risk n.event 199s 0.000000 0.0092099 0.00000000 0.000000 0.000000 100 0 199s 0.031657 0.2663096 0.00032353 0.010320 0.094942 81 0 199s 0.067029 0.7303091 0.00070366 0.030598 0.143503 54 0 199s 0.096618 1.4299939 0.00108275 0.049082 0.185474 29 0 199s 0.096618 2.0647206 0.00108275 0.049082 0.185474 16 0 199s 0.096618 4.9087561 0.00108275 0.049082 0.185474 2 0 199s 199s > summary(test.c) 199s 199s cov=0 199s 199s CIF 1 199s P time var lower upper n.risk n.event 199s 0.022222 0.0092099 0.00048285 0.0031605 0.14747 45 1 199s 0.092222 0.2982439 0.00193603 0.0355971 0.22762 36 0 199s 0.226684 0.7021938 0.00450954 0.1241760 0.39250 24 1 199s 0.378128 1.4299939 0.00760870 0.2337884 0.57145 13 1 199s 0.505736 1.6148774 0.00895330 0.3388425 0.69885 10 1 199s 0.702465 2.1708375 0.01119294 0.4944890 0.88399 3 1 199s 199s CIF 2 199s P time var lower upper n.risk n.event 199s 0.000000 0.0092099 0.0000000 0.000000 0.00000 45 0 199s 0.048441 0.2982439 0.0011168 0.012337 0.18013 36 1 199s 0.076411 0.7021938 0.0018104 0.025202 0.21928 24 0 199s 0.111440 1.4299939 0.0028499 0.042676 0.27392 13 0 199s 0.111440 1.6148774 0.0028499 0.042676 0.27392 10 0 199s 0.111440 2.1708375 0.0028499 0.042676 0.27392 3 0 199s 199s 199s cov=1 199s 199s CIF 1 199s P time var lower upper n.risk n.event 199s 0.018182 0.066692 0.00032457 0.0025813 0.12214 55 1 199s 0.112392 0.263808 0.00187215 0.0520925 0.23333 45 1 199s 0.241023 0.730309 0.00374499 0.1440057 0.38685 31 1 199s 0.401201 1.066913 0.00570788 0.2714008 0.56421 19 1 199s 0.592334 2.366275 0.00775985 0.4286230 0.76273 8 1 199s 0.807871 4.908756 0.00884554 0.6023185 0.94771 2 1 199s 199s CIF 2 199s P time var lower upper n.risk n.event 199s 0.000000 0.066692 0.00000000 0.000000 0.00000 55 0 199s 0.037434 0.263808 0.00067458 0.009494 0.14152 45 0 199s 0.059341 0.730309 0.00111295 0.019447 0.17351 31 0 199s 0.084360 1.066913 0.00166213 0.032211 0.21119 19 0 199s 0.084360 2.366275 0.00166213 0.032211 0.21119 8 0 199s 0.084360 4.908756 0.00166213 0.032211 0.21119 2 0 199s 199s > 199s > options(old) 199s > 199s BEGIN TEST tests.etm.R 199s 199s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 199s Copyright (C) 2025 The R Foundation for Statistical Computing 199s Platform: powerpc64le-unknown-linux-gnu 199s 199s R is free software and comes with ABSOLUTELY NO WARRANTY. 199s You are welcome to redistribute it under certain conditions. 199s Type 'license()' or 'licence()' for distribution details. 199s 199s R is a collaborative project with many contributors. 199s Type 'contributors()' for more information and 199s 'citation()' on how to cite R or R packages in publications. 199s 199s Type 'demo()' for some demos, 'help()' for on-line help, or 199s 'help.start()' for an HTML browser interface to help. 199s Type 'q()' to quit R. 199s 199s > require(etm) 199s Loading required package: etm 200s > 200s > ## Print with a bit less precision to avoid lots of notes in the comparison 200s > old <- options(digits = 4) 200s > 200s > ### Simple test 200s > 200s > time <- id <- 1:10 200s > from <- rep(0, 10) 200s > to <- rep(1, 10) 200s > 200s > data1 <- data.frame(id, from, to, time) 200s > tra1 <- matrix(FALSE, 2, 2) 200s > tra1[1, 2] <- TRUE 200s > 200s > etm1 <- etm(data1, c("0", "1"), tra1, NULL, 0) 200s > 200s > all.equal(as.vector(trprob(etm1, "0 0")), cumprod((10:1 - 1) / (10:1))) 200s [1] TRUE 200s > 200s > etm1$cov["0 0", "0 0", ] 200s 1 2 3 4 5 6 7 8 9 10 200s 0.009 0.016 0.021 0.024 0.025 0.024 0.021 0.016 0.009 0.000 200s > 200s > all.equal(etm1$cov["0 0", "0 0",], trcov(etm1, "0 0")) 200s [1] TRUE 200s > 200s > ### A simple test from AHR's author, where the first time is censored 200s > if (!require(survival)) { 200s + stop("This test requires the survival package") 200s + } 200s > 200s > data <- data.frame(id=1:10, time=1:10, from=0, to=1, status=TRUE) 200s > 200s > tra <- matrix(FALSE, nrow=2, ncol=2) 200s > tra[1, 2] <- TRUE 200s > 200s > data$to[1] <- "cens" 200s > data$status[1] <- FALSE 200s > 200s > fit.km <- survfit(Surv(time, status) ~ 1, data=data) 200s > fit.etm <- etm(data, c("0","1"), tra, "cens", s=0, t="last", covariance=FALSE) 200s Loading required package: survival 200s > 200s > all.equal(fit.km$surv[data$status], fit.etm$est[1,1,], check.attributes = FALSE) 200s [1] TRUE 200s > 200s > data$to[2] <- "cens" 200s > data$status[2] <- FALSE 200s > 200s > fit.km <- survfit(Surv(time, status) ~ 1, data=data) 200s > fit.etm <- etm(data, c("0","1"), tra, "cens", s=0, t="last", covariance=FALSE) 200s > 200s > all.equal(fit.km$surv[data$status], fit.etm$est[1,1,], check.attributes = FALSE) 200s [1] TRUE 200s > 200s > ### a bit more complicated 200s > 200s > time <- id <- 1:10 200s > from <- rep(0, 10) 200s > to <- rep(c(1, 2), 5) 200s > data2 <- data.frame(id, from, to, time) 200s > 200s > tra2 <- matrix(FALSE, 3, 3) 200s > tra2[1, 2:3] <- TRUE 200s > 200s > etm2 <- etm(data2, c("0", "1", "2"), tra2, NULL, 0) 200s > 200s > aa <- table(time, to) 200s > 200s > cif1 <- cumsum(aa[, 1] / 10) 200s > cif2 <- cumsum(aa[, 2] / 10) 200s > surv <- cumprod((10:1 - 1) / (10:1)) 200s > 200s > all.equal(trprob(etm2, "0 1"), cif1) 200s [1] TRUE 200s > all.equal(trprob(etm2, "0 2"), cif2) 200s [1] TRUE 200s > all.equal(as.vector(trprob(etm2, "0 0")), surv) 200s [1] TRUE 200s > 200s > ## a test on id 200s > data2$id <- letters[1:10] 200s > 200s > etm3 <- etm(data2, c("0", "1", "2"), tra2, NULL, 0) 200s > 200s > all.equal(trprob(etm2, "0 1"), trprob(etm3, "0 1")) 200s [1] TRUE 200s > all.equal(trprob(etm2, "0 2"), trprob(etm3, "0 2")) 200s [1] TRUE 200s > all.equal(trprob(etm2, "0 0"), trprob(etm3, "0 0")) 200s [1] TRUE 200s > 200s > 200s > ### Test on sir.cont 200s > 200s > data(sir.cont) 200s > 200s > ## Modification for patients entering and leaving a state 200s > ## at the same date 200s > ## Change on ventilation status is considered 200s > ## to happen before end of hospital stay 200s > sir.cont <- sir.cont[order(sir.cont$id, sir.cont$time), ] 200s > for (i in 2:nrow(sir.cont)) { 200s + if (sir.cont$id[i]==sir.cont$id[i-1]) { 200s + if (sir.cont$time[i]==sir.cont$time[i-1]) { 200s + sir.cont$time[i-1] <- sir.cont$time[i-1] - 0.5 200s + } 200s + } 200s + } 200s > 200s > ### Computation of the transition probabilities 200s > ## Possible transitions. 200s > tra <- matrix(ncol=3,nrow=3,FALSE) 200s > tra[1, 2:3] <- TRUE 200s > tra[2, c(1, 3)] <- TRUE 200s > 200s > ## etm 200s > prob.sir <- etm(sir.cont, c("0", "1", "2"), tra, "cens", 1) 200s > 200s > prob.sir 200s Multistate model with 2 transient state(s) 200s and 1 absorbing state(s) 200s 200s Possible transitions: 200s from to 200s 0 1 200s 0 2 200s 1 0 200s 1 2 200s 200s Estimate of P(1, 183) 200s 0 1 2 200s 0 0 0 1 200s 1 0 0 1 200s 2 0 0 1 200s 200s > 200s > summ.sir <- summary(prob.sir) 200s > all.equal(summ.sir[['0 1']]$P, as.vector(trprob(prob.sir, "0 1"))) 200s [1] TRUE 200s > subset(summ.sir[[3]],time<183) # issue with precision on different architectures 200s P time var lower upper n.risk n.event 200s 1.5 0.0000 1.5 0.000e+00 0.00000 0.0000 394 0 200s 2 0.1187 2.0 2.641e-04 0.08683 0.1505 396 47 200s 2.5 0.1187 2.5 2.641e-04 0.08683 0.1505 364 0 200s 3 0.2454 3.0 4.465e-04 0.20398 0.2868 365 54 200s 3.5 0.2454 3.5 4.465e-04 0.20398 0.2868 328 0 200s 4 0.3806 4.0 5.416e-04 0.33501 0.4262 331 62 200s 4.5 0.3806 4.5 5.416e-04 0.33501 0.4262 280 0 200s 5 0.4792 5.0 5.480e-04 0.43333 0.5251 283 48 200s 5.5 0.4792 5.5 5.480e-04 0.43333 0.5251 248 0 200s 6 0.5693 6.0 5.141e-04 0.52482 0.6137 249 47 200s 7 0.6350 7.0 4.665e-04 0.59266 0.6773 212 36 200s 8 0.6795 8.0 4.202e-04 0.63931 0.7197 195 27 200s 8.5 0.6795 8.5 4.202e-04 0.63931 0.7197 172 0 200s 9 0.7325 9.0 3.580e-04 0.69541 0.7696 173 34 200s 10 0.7647 10.0 3.141e-04 0.72992 0.7994 148 21 200s 10.5 0.7647 10.5 3.141e-04 0.72992 0.7994 135 0 200s 11 0.7895 11.0 2.790e-04 0.75674 0.8222 136 18 200s 12 0.8138 12.0 2.420e-04 0.78330 0.8443 129 18 200s 12.5 0.8138 12.5 2.420e-04 0.78330 0.8443 117 0 200s 13 0.8294 13.0 2.182e-04 0.80045 0.8584 118 13 200s 14 0.8452 14.0 1.938e-04 0.81789 0.8725 115 14 200s 15 0.8625 15.0 1.670e-04 0.83714 0.8878 106 15 200s 16 0.8723 16.0 1.522e-04 0.84807 0.8964 93 9 200s 17 0.8852 17.0 1.330e-04 0.86256 0.9078 86 12 200s 17.5 0.8852 17.5 1.330e-04 0.86256 0.9078 77 0 200s 18 0.8960 18.0 1.168e-04 0.87484 0.9172 76 9 200s 19 0.9029 19.0 1.070e-04 0.88261 0.9232 71 7 200s 20 0.9125 20.0 9.367e-05 0.89356 0.9315 64 10 200s 21 0.9161 21.0 8.878e-05 0.89768 0.9346 57 4 200s 22 0.9226 22.0 7.996e-05 0.90504 0.9401 55 6 200s 23 0.9261 23.0 7.537e-05 0.90904 0.9431 51 4 200s 23.5 0.9261 23.5 7.537e-05 0.90904 0.9431 49 0 200s 24 0.9354 24.0 6.292e-05 0.91982 0.9509 50 9 200s 25 0.9385 25.0 5.878e-05 0.92352 0.9536 42 3 200s 26 0.9429 26.0 5.326e-05 0.92863 0.9572 39 5 200s 27 0.9477 27.0 4.749e-05 0.93417 0.9612 35 6 200s 27.5 0.9477 27.5 4.749e-05 0.93417 0.9612 29 0 200s 28 0.9531 28.0 4.093e-05 0.94059 0.9657 30 5 200s 29 0.9567 29.0 3.668e-05 0.94485 0.9686 31 4 200s 30 0.9592 30.0 3.384e-05 0.94779 0.9706 28 3 200s 30.5 0.9592 30.5 3.384e-05 0.94779 0.9706 29 0 200s 31 0.9642 31.0 2.821e-05 0.95383 0.9746 30 6 200s 32 0.9649 32.0 2.752e-05 0.95458 0.9751 25 1 200s 33 0.9669 33.0 2.533e-05 0.95708 0.9768 24 2 200s 34 0.9685 34.0 2.368e-05 0.95900 0.9781 26 2 200s 35 0.9697 35.0 2.252e-05 0.96036 0.9790 28 2 200s 36 0.9702 36.0 2.194e-05 0.96104 0.9794 26 1 200s 37 0.9718 37.0 2.043e-05 0.96290 0.9806 26 2 200s 38 0.9739 38.0 1.831e-05 0.96555 0.9823 25 4 200s 38.5 0.9739 38.5 1.831e-05 0.96555 0.9823 21 0 200s 39 0.9760 39.0 1.643e-05 0.96802 0.9839 23 3 200s 40 0.9769 40.0 1.558e-05 0.96918 0.9847 19 1 200s 41 0.9774 41.0 1.512e-05 0.96981 0.9851 22 1 200s 42 0.9779 42.0 1.476e-05 0.97032 0.9854 22 0 200s 43 0.9798 43.0 1.308e-05 0.97271 0.9869 22 3 200s 44 0.9803 44.0 1.265e-05 0.97333 0.9873 21 1 200s 45 0.9817 45.0 1.157e-05 0.97499 0.9883 19 1 200s 46 0.9822 46.0 1.116e-05 0.97561 0.9887 17 1 200s 47 0.9831 47.0 1.037e-05 0.97683 0.9895 18 2 200s 48 0.9836 48.0 9.987e-06 0.97743 0.9898 17 1 200s 49 0.9841 49.0 9.669e-06 0.97796 0.9901 17 0 200s 50 0.9845 50.0 9.297e-06 0.97856 0.9905 17 1 200s 50.5 0.9845 50.5 9.297e-06 0.97856 0.9905 16 0 200s 51 0.9860 51.0 8.214e-06 0.98037 0.9916 17 3 200s 52 0.9870 52.0 7.513e-06 0.98159 0.9923 14 2 200s 53 0.9879 53.0 6.875e-06 0.98276 0.9930 12 1 200s 54 0.9889 54.0 6.214e-06 0.98397 0.9937 12 2 200s 55 0.9903 55.0 5.254e-06 0.98581 0.9948 10 3 200s 56 0.9913 56.0 4.667e-06 0.98703 0.9955 6 1 200s 57 0.9917 57.0 4.364e-06 0.98765 0.9958 5 1 200s 58 0.9922 58.0 4.064e-06 0.98828 0.9962 4 1 200s 59 0.9927 59.0 3.769e-06 0.98891 0.9965 3 1 200s 60 0.9932 60.0 3.488e-06 0.98953 0.9969 3 1 200s 62 0.9937 62.0 3.230e-06 0.99016 0.9972 2 0 200s 63 0.9942 63.0 2.956e-06 0.99079 0.9975 2 1 200s 68 0.9942 68.0 2.956e-06 0.99079 0.9975 1 0 200s 70 0.9946 70.0 2.694e-06 0.99143 0.9979 2 1 200s 78 0.9951 78.0 2.442e-06 0.99207 0.9982 1 0 200s 80 0.9951 80.0 2.442e-06 0.99207 0.9982 1 0 200s 85 0.9966 85.0 1.695e-06 0.99404 0.9991 2 0 200s 89 0.9966 89.0 1.695e-06 0.99404 0.9991 2 0 200s 90 0.9966 90.0 1.695e-06 0.99404 0.9991 1 0 200s 95 0.9971 95.0 1.448e-06 0.99472 0.9994 2 0 200s 100 0.9976 100.0 1.203e-06 0.99542 0.9997 3 0 200s 101 0.9981 101.0 9.592e-07 0.99613 1.0000 3 1 200s 108 0.9985 108.0 7.169e-07 0.99688 1.0000 2 1 200s 113 0.9990 113.0 4.764e-07 0.99767 1.0000 1 0 200s 116 0.9990 116.0 4.764e-07 0.99767 1.0000 1 0 200s 124 0.9990 124.0 4.764e-07 0.99767 1.0000 2 0 200s 164 0.9990 164.0 4.764e-07 0.99767 1.0000 0 0 200s > 200s > ## gonna play a bit with the state names 200s > dd <- sir.cont 200s > dd$from <- ifelse(dd$from == 0, "initial state", "ventilation") 200s > dd$to <- as.character(dd$to) 200s > for (i in seq_len(nrow(dd))) { 200s + dd$to[i] <- switch(dd$to[i], 200s + "0" = "initial state", 200s + "1" = "ventilation", 200s + "2" = "end of story", 200s + "cens" = "cens" 200s + ) 200s + } 200s > 200s > test <- etm(dd, c("initial state", "ventilation", "end of story"), tra, "cens", 1) 200s > 200s > all.equal(test$est["initial state", "initial state", ], 200s + prob.sir$est["0", "0", ]) 200s [1] TRUE 200s > all.equal(trprob(test, "initial state initial state"), trprob(prob.sir, "0 0")) 200s [1] TRUE 200s > all.equal(trprob(test, "initial state ventilation"), trprob(prob.sir, "0 1")) 200s [1] TRUE 200s > all.equal(trprob(test, "initial state end of story"), trprob(prob.sir, "0 2")) 200s [1] TRUE 200s > 200s > all.equal(trcov(test, "initial state end of story"), trcov(prob.sir, "0 2")) 200s [1] TRUE 200s > 200s > aa <- summary(test) 200s > all.equal(summ.sir[[6]], aa[[6]]) 200s [1] TRUE 200s > all.equal(summ.sir[[4]], aa[[4]]) 200s [1] TRUE 200s > 200s > ### Test on abortion data 200s > 200s > data(abortion) 200s > 200s > from <- rep(0, nrow(abortion)) 200s > to <- abortion$cause 200s > entry <- abortion$entry 200s > exit <- abortion$exit 200s > id <- 1:nrow(abortion) 200s > data <- data.frame(id, from, to, entry, exit, group = abortion$group) 200s > 200s > ## Computation of the CIFs 200s > tra <- matrix(FALSE, 4, 4) 200s > tra[1, 2:4] <- TRUE 200s > 200s > cif.control <- etm(data[data$group == 0, ], c("0", "1", "2", "3"), 200s + tra, NULL, 0) 200s > cif.exposed <- etm(data[data$group == 1, ], c("0", "1", "2", "3"), 200s + tra, NULL, 0) 200s > 200s > all.equal(trprob(cif.control, "0 1"), cif.control$est["0", "1", ]) 200s [1] TRUE 200s > all.equal(trcov(cif.control, c("0 1", "0 2")), cif.control$cov["0 1", "0 2", ]) 200s [1] TRUE 200s > 200s > trprob(cif.control, "0 1") 200s 6 7 8 9 10 11 12 13 200s 0.000000 0.007401 0.014881 0.026509 0.033208 0.037694 0.037694 0.038955 200s 14 17 19 21 24 25 26 30 200s 0.040159 0.040159 0.040159 0.040159 0.040159 0.040159 0.040159 0.040159 200s 31 32 33 34 35 36 37 38 200s 0.040159 0.040159 0.040159 0.040159 0.040159 0.040159 0.040159 0.040159 200s 39 40 41 42 43 200s 0.040159 0.040159 0.040159 0.040159 0.040159 200s > trprob(cif.control, "0 2") 200s 6 7 8 9 10 11 12 13 200s 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 200s 14 17 19 21 24 25 26 30 200s 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.003657 200s 31 32 33 34 35 36 37 38 200s 0.006371 0.008175 0.013543 0.023317 0.031260 0.053197 0.084529 0.179163 200s 39 40 41 42 43 200s 0.322016 0.563121 0.742227 0.793893 0.799059 200s > trprob(cif.control, "0 0") 200s 6 7 8 9 10 11 12 13 200s 0.965812 0.932508 0.887628 0.862433 0.838989 0.822538 0.813099 0.810578 200s 14 17 19 21 24 25 26 30 200s 0.806964 0.805874 0.803810 0.802804 0.801837 0.800883 0.799937 0.796280 200s 31 32 33 34 35 36 37 38 200s 0.793565 0.791762 0.786394 0.776620 0.768677 0.745862 0.714531 0.619897 200s 39 40 41 42 43 200s 0.477043 0.235938 0.056832 0.005167 0.000000 200s > 200s > trcov(cif.control, "0 1") 200s 6 7 8 9 10 11 12 13 200s 0.000e+00 2.719e-05 4.533e-05 6.665e-05 7.698e-05 8.304e-05 8.304e-05 8.444e-05 200s 14 17 19 21 24 25 26 30 200s 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 200s 31 32 33 34 35 36 37 38 200s 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 200s 39 40 41 42 43 200s 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 200s > trcov(cif.control, "0 2") 200s 6 7 8 9 10 11 12 13 200s 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 200s 14 17 19 21 24 25 26 30 200s 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 3.338e-06 200s 31 32 33 34 35 36 37 38 200s 5.784e-06 7.401e-06 1.216e-05 2.072e-05 2.758e-05 4.619e-05 7.202e-05 1.461e-04 200s 39 40 41 42 43 200s 2.470e-04 3.880e-04 4.702e-04 4.903e-04 4.922e-04 200s > trcov(cif.control, "0 0") 200s 6 7 8 9 10 11 12 13 200s 2.822e-04 3.821e-04 4.527e-04 4.748e-04 4.875e-04 4.927e-04 4.941e-04 4.942e-04 200s 14 17 19 21 24 25 26 30 200s 4.941e-04 4.940e-04 4.936e-04 4.933e-04 4.931e-04 4.928e-04 4.926e-04 4.914e-04 200s 31 32 33 34 35 36 37 38 200s 4.905e-04 4.899e-04 4.880e-04 4.846e-04 4.816e-04 4.729e-04 4.601e-04 4.176e-04 200s 39 40 41 42 43 200s 3.425e-04 1.865e-04 4.797e-05 4.441e-06 0.000e+00 200s > 200s > aa <- summary(cif.control) 200s > aa$"0 1" 200s P time var lower upper n.risk n.event 200s 6 0.000000 6 0.000e+00 0.000000 0.00000 117 0 200s 7 0.007401 7 2.719e-05 0.000000 0.01762 261 2 200s 8 0.014881 8 4.533e-05 0.001685 0.02808 374 3 200s 9 0.026509 9 6.665e-05 0.010508 0.04251 458 6 200s 10 0.033208 10 7.698e-05 0.016011 0.05040 515 4 200s 11 0.037694 11 8.304e-05 0.019834 0.05555 561 3 200s 12 0.037694 12 8.304e-05 0.019834 0.05555 610 0 200s 13 0.038955 13 8.444e-05 0.020944 0.05697 645 1 200s 14 0.040159 14 8.571e-05 0.022014 0.05830 673 1 200s 17 0.040159 17 8.571e-05 0.022014 0.05830 740 0 200s 19 0.040159 19 8.571e-05 0.022014 0.05830 781 0 200s 21 0.040159 21 8.571e-05 0.022014 0.05830 799 0 200s 24 0.040159 24 8.571e-05 0.022014 0.05830 830 0 200s 25 0.040159 25 8.571e-05 0.022014 0.05830 841 0 200s 26 0.040159 26 8.571e-05 0.022014 0.05830 846 0 200s 30 0.040159 30 8.571e-05 0.022014 0.05830 875 0 200s 31 0.040159 31 8.571e-05 0.022014 0.05830 880 0 200s 32 0.040159 32 8.571e-05 0.022014 0.05830 880 0 200s 33 0.040159 33 8.571e-05 0.022014 0.05830 885 0 200s 34 0.040159 34 8.571e-05 0.022014 0.05830 885 0 200s 35 0.040159 35 8.571e-05 0.022014 0.05830 880 0 200s 36 0.040159 36 8.571e-05 0.022014 0.05830 876 0 200s 37 0.040159 37 8.571e-05 0.022014 0.05830 857 0 200s 38 0.040159 38 8.571e-05 0.022014 0.05830 823 0 200s 39 0.040159 39 8.571e-05 0.022014 0.05830 716 0 200s 40 0.040159 40 8.571e-05 0.022014 0.05830 554 0 200s 41 0.040159 41 8.571e-05 0.022014 0.05830 274 0 200s 42 0.040159 42 8.571e-05 0.022014 0.05830 66 0 200s 43 0.040159 43 8.571e-05 0.022014 0.05830 6 0 200s > all.equal(aa$"0 1"$P, as.vector(trprob(cif.control, "0 1"))) 200s [1] TRUE 200s > 200s > ### test on los data 200s > 200s > data(los.data) # in package changeLOS 200s > 200s > ## putting los.data in the long format (see changeLOS) 200s > my.observ <- prepare.los.data(x=los.data) 200s > 200s > tra <- matrix(FALSE, 4, 4) 200s > tra[1, 2:4] <- TRUE 200s > tra[2, 3:4] <- TRUE 200s > 200s > tr.prob <- etm(my.observ, c("0","1","2","3"), tra, NULL, 0) 200s > 200s > tr.prob 200s Multistate model with 2 transient state(s) 200s and 2 absorbing state(s) 200s 200s Possible transitions: 200s from to 200s 0 1 200s 0 2 200s 0 3 200s 1 2 200s 1 3 200s 200s Estimate of P(0, 82) 200s 0 1 2 3 200s 0 0 0 0.7474 0.2526 200s 1 0 0 0.7073 0.2927 200s 2 0 0 1.0000 0.0000 200s 3 0 0 0.0000 1.0000 200s 200s > summary(tr.prob) 200s Transition 0 0 200s P time var lower upper n.risk n.event 200s 0.882275 3 1.374e-04 0.8593018 0.905248 756 0 200s 0.112434 15 1.320e-04 0.0899155 0.134952 90 0 200s 0.031746 27 4.066e-05 0.0192484 0.044244 26 0 200s 0.006614 41 8.690e-06 0.0008359 0.012392 5 0 200s 0.002646 61 3.490e-06 0.0000000 0.006307 3 0 200s 0.000000 82 0.000e+00 0.0000000 0.000000 1 0 200s 200s Transition 0 1 200s P time var lower upper n.risk n.event 200s 0.017196 3 2.235e-05 0.0079289 0.02646 756 13 200s 0.063492 15 7.865e-05 0.0461099 0.08087 90 0 200s 0.030423 27 3.902e-05 0.0181805 0.04267 26 1 200s 0.015873 41 2.066e-05 0.0069637 0.02478 5 0 200s 0.005291 61 6.962e-06 0.0001197 0.01046 3 0 200s 0.000000 82 0.000e+00 0.0000000 0.00000 1 0 200s 200s Transition 0 2 200s P time var lower upper n.risk n.event 200s 0.08466 3 0.0001025 0.06481 0.1045 756 64 200s 0.62302 15 0.0003107 0.58847 0.6576 90 4 200s 0.69841 27 0.0002786 0.66570 0.7311 26 1 200s 0.72751 41 0.0002622 0.69578 0.7593 5 0 200s 0.74074 61 0.0002540 0.70950 0.7720 3 1 200s 0.74735 82 0.0002498 0.71638 0.7783 1 1 200s 200s Transition 0 3 200s P time var lower upper n.risk n.event 200s 0.01587 3 2.066e-05 0.006964 0.02478 756 12 200s 0.20106 15 2.125e-04 0.172489 0.22963 90 1 200s 0.23942 27 2.409e-04 0.208999 0.26984 26 0 200s 0.25000 41 2.480e-04 0.219133 0.28087 5 0 200s 0.25132 61 2.489e-04 0.220402 0.28224 3 0 200s 0.25265 82 2.498e-04 0.221671 0.28362 1 0 200s 200s Transition 1 1 200s P time var lower upper n.risk n.event 200s 1.00000 3 0.000e+00 1.00000 1.00000 0 0 200s 0.38661 15 2.358e-03 0.29143 0.48179 51 0 200s 0.12119 27 7.842e-04 0.06630 0.17607 23 0 200s 0.04593 41 2.405e-04 0.01554 0.07633 14 0 200s 0.01531 61 6.579e-05 0.00000 0.03121 4 0 200s 0.00000 82 0.000e+00 0.00000 0.00000 0 0 200s 200s Transition 1 2 200s P time var lower upper n.risk n.event 200s 0.0000 3 0.000000 0.0000 0.0000 0 0 200s 0.4107 15 0.002590 0.3110 0.5104 51 2 200s 0.6082 27 0.002254 0.5151 0.7012 23 1 200s 0.6652 41 0.002064 0.5761 0.7542 14 2 200s 0.6920 61 0.002000 0.6043 0.7796 4 0 200s 0.7073 82 0.001984 0.6200 0.7946 0 0 200s 200s Transition 1 3 200s P time var lower upper n.risk n.event 200s 0.0000 3 0.000000 0.0000 0.0000 0 0 200s 0.2027 15 0.001784 0.1199 0.2855 51 1 200s 0.2706 27 0.001968 0.1837 0.3576 23 0 200s 0.2889 41 0.001982 0.2016 0.3761 14 0 200s 0.2927 61 0.001984 0.2054 0.3800 4 0 200s 0.2927 82 0.001984 0.2054 0.3800 0 0 200s 200s > 200s > cLOS <- etm::clos(tr.prob, aw = TRUE) 200s > 200s > cLOS 200s The expected change in length of stay is: 200s 1.975 200s 200s Alternative weighting: 200s 200s Expected change in LOS with weight.1: 2.097 200s Expected change in LOS with weight.other: 1.951 200s > 200s > 200s > ### Tests on pseudo values 200s > t_pseudo <- closPseudo(my.observ, c("0","1","2","3"), tra, NULL, 200s + formula = ~ 1, aw = TRUE) 214s > 214s > cLOS$e.phi == t_pseudo$theta[, "e.phi"] 214s [,1] 214s [1,] TRUE 214s > cLOS$e.phi.weights.1 == t_pseudo$theta[, "e.phi.weights.1"] 214s [,1] 214s [1,] TRUE 214s > cLOS$e.phi.weights.other == t_pseudo$theta[, "e.phi.weights.other"] 214s [,1] 214s [1,] TRUE 214s > 214s > mean(t_pseudo$pseudoData$ps.e.phi) 214s [1] 1.968 214s > 214s > ### tests on etmprep 214s > 214s > ### creation of fake data in the wild format, following an illness-death model 214s > ## transition times 214s > tdisease <- c(3, 4, 3, 6, 8, 9) 214s > tdeath <- c(6, 9, 8, 6, 8, 9) 214s > 214s > ## transition status 214s > stat.disease <- c(1, 1, 1, 0, 0, 0) 214s > stat.death <- c(1, 1, 1, 1, 1, 0) 214s > 214s > ## a covariate that we want to keep in the new data 214s > set.seed(1313) 214s > cova <- rbinom(6, 1, 0.5) 214s > 214s > dat <- data.frame(tdisease, tdeath, 214s + stat.disease, stat.death, 214s + cova) 214s > 214s > ## Possible transitions 214s > tra <- matrix(FALSE, 3, 3) 214s > tra[1, 2:3] <- TRUE 214s > tra[2, 3] <- TRUE 214s > 214s > ## data preparation 214s > newdat <- etmprep(c(NA, "tdisease", "tdeath"), 214s + c(NA, "stat.disease", "stat.death"), 214s + data = dat, tra = tra, 214s + cens.name = "cens", keep = "cova") 214s > 214s > newdat 214s id entry exit from to cova 214s 1 1 0 3 0 1 1 214s 2 1 3 6 1 2 1 214s 3 2 0 4 0 1 0 214s 4 2 4 9 1 2 0 214s 5 3 0 3 0 1 1 214s 6 3 3 8 1 2 1 214s 7 4 0 6 0 2 0 214s 8 5 0 8 0 2 1 214s 9 6 0 9 0 cens 1 214s > 214s > ref <- data.frame(id = c(1, 1, 2, 2, 3, 3, 4, 5, 6), 214s + entry = c(0, 3, 0, 4, 0, 3, 0, 0, 0), 214s + exit = c(3, 6, 4, 9, 3, 8, 6, 8, 9), 214s + from = c(0, 1, 0, 1, 0, 1, 0, 0, 0), 214s + to = c(rep(c(1, 2), 3), 2, 2, "cens"), 214s + cova = c(1, 1, 0, 0, 1, 1, 0, 1, 1)) 214s > ref$from <- factor(as.character(ref$from), levels = c("0", "1", "2", "cens")) 214s > ref$to <- factor(as.character(ref$to), levels = c("0", "1", "2", "cens")) 214s > 214s > all.equal(ref, newdat) 214s [1] TRUE 214s > 214s > 214s > ###################################### 214s > ### Test the stratified calls 214s > ###################################### 214s > 214s > if (require("kmi", quietly = TRUE)) { 214s + library(etm) 214s + 214s + data(icu.pneu) 214s + my.icu.pneu <- icu.pneu 214s + 214s + my.icu.pneu <- my.icu.pneu[order(my.icu.pneu$id, my.icu.pneu$start), ] 214s + masque <- diff(my.icu.pneu$id) 214s + 214s + my.icu.pneu$from <- 0 214s + my.icu.pneu$from[c(1, masque) == 0] <- 1 214s + 214s + my.icu.pneu$to2 <- my.icu.pneu$event 214s + my.icu.pneu$to2[my.icu.pneu$status == 0] <- "cens" 214s + my.icu.pneu$to2[c(masque, 1) == 0] <- 1 214s + 214s + 214s + my.icu.pneu$to <- ifelse(my.icu.pneu$to2 %in% c(2, 3), 2, 214s + my.icu.pneu$to2) 214s + 214s + my.icu.pneu <- my.icu.pneu[, c("id", "start", "stop", "from", "to", 214s + "to2", "age", "sex")] 214s + names(my.icu.pneu)[c(2, 3)] <- c("entry", "exit") 214s + 214s + bouh_strat <- etm(my.icu.pneu, c("0", "1", "2"), tra_ill(), "cens", 0, strata = "sex") 214s + 214s + bouh_female <- etm(my.icu.pneu[my.icu.pneu$sex == "F", ], 214s + c("0", "1", "2"), tra_ill(), "cens", 0) 214s + 214s + all(bouh_strat[[1]]$est == bouh_female$est) 214s + 214s + ## Test the summary 214s + the_summary <- summary(bouh_strat) 214s + the_summary 214s + 214s + ## Test trprob 214s + all(trprob(bouh_strat, "0 1")[[1]] == trprob(bouh_female, "0 1")) 214s + all(trprob(bouh_strat, "0 1", c(0, 5, 10, 15))[[1]] == trprob(bouh_female, "0 1", c(0, 5, 10, 15))) 214s + 214s + ## Test trcov 214s + all(trcov(bouh_strat, "0 1")[[1]] == trcov(bouh_female, "0 1")) 214s + all(trcov(bouh_strat, c("0 1", "0 2"))[[1]] == trcov(bouh_female, c("0 1", "0 2"))) 214s + all(trcov(bouh_strat, "0 1", c(0, 5, 10, 15))[[1]] == trcov(bouh_female, "0 1", c(0, 5, 10, 15))) 214s + } else { 214s + print("These tests require the kmi package") 214s + } 214s [1] TRUE 214s > 214s > options(old) 214s > 214s autopkgtest [23:17:21]: test run-unit-test: -----------------------] 214s run-unit-test PASS 214s autopkgtest [23:17:21]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 215s autopkgtest [23:17:22]: test pkg-r-autopkgtest: preparing testbed 215s Reading package lists... 215s Building dependency tree... 215s Reading state information... 215s Solving dependencies... 215s The following NEW packages will be installed: 215s build-essential cpp cpp-15 cpp-15-powerpc64le-linux-gnu 215s cpp-powerpc64le-linux-gnu dctrl-tools g++ g++-15 215s g++-15-powerpc64le-linux-gnu g++-powerpc64le-linux-gnu gcc gcc-15 215s gcc-15-powerpc64le-linux-gnu gcc-powerpc64le-linux-gnu gfortran gfortran-15 215s gfortran-15-powerpc64le-linux-gnu gfortran-powerpc64le-linux-gnu 215s icu-devtools libasan8 libblas-dev libbz2-dev libc-dev-bin libc6-dev libcc1-0 215s libcrypt-dev libdeflate-dev libgcc-15-dev libgfortran-15-dev libicu-dev 215s libisl23 libitm1 libjpeg-dev libjpeg-turbo8-dev libjpeg8-dev liblapack-dev 215s liblsan0 liblzma-dev libmpc3 libncurses-dev libpcre2-16-0 libpcre2-32-0 215s libpcre2-dev libpcre2-posix3 libpkgconf3 libpng-dev libquadmath0 215s libreadline-dev libstdc++-15-dev libtirpc-dev libtsan2 libubsan1 libzstd-dev 215s linux-libc-dev pkg-r-autopkgtest pkgconf pkgconf-bin r-base-dev 215s r-cran-backports r-cran-broom r-cran-cli r-cran-cpp11 r-cran-dplyr 215s r-cran-fansi r-cran-farver r-cran-geepack r-cran-generics r-cran-ggplot2 215s r-cran-glue r-cran-gtable r-cran-isoband r-cran-labeling r-cran-lifecycle 215s r-cran-magrittr r-cran-mass r-cran-pillar r-cran-pkgconfig r-cran-purrr 215s r-cran-r6 r-cran-rcolorbrewer r-cran-rlang r-cran-s7 r-cran-scales 215s r-cran-stringi r-cran-stringr r-cran-tibble r-cran-tidyr r-cran-tidyselect 215s r-cran-utf8 r-cran-vctrs r-cran-viridislite r-cran-withr rpcsvc-proto 215s zlib1g-dev 215s 0 upgraded, 94 newly installed, 0 to remove and 0 not upgraded. 215s Need to get 129 MB of archives. 215s After this operation, 434 MB of additional disk space will be used. 215s Get:1 http://ftpmaster.internal/ubuntu resolute/main ppc64el libc-dev-bin ppc64el 2.42-2ubuntu4 [23.9 kB] 215s Get:2 http://ftpmaster.internal/ubuntu resolute/main ppc64el linux-libc-dev ppc64el 6.19.0-3.3 [1832 kB] 218s Get:3 http://ftpmaster.internal/ubuntu resolute/main ppc64el libcrypt-dev ppc64el 1:4.5.1-1 [162 kB] 218s Get:4 http://ftpmaster.internal/ubuntu resolute/main ppc64el rpcsvc-proto ppc64el 1.4.3-1build1 [84.2 kB] 218s Get:5 http://ftpmaster.internal/ubuntu resolute/main ppc64el libc6-dev ppc64el 2.42-2ubuntu4 [2080 kB] 221s Get:6 http://ftpmaster.internal/ubuntu resolute/main ppc64el libisl23 ppc64el 0.27-1build1 [893 kB] 222s Get:7 http://ftpmaster.internal/ubuntu resolute/main ppc64el libmpc3 ppc64el 1.3.1-2 [62.5 kB] 222s Get:8 http://ftpmaster.internal/ubuntu resolute/main ppc64el cpp-15-powerpc64le-linux-gnu ppc64el 15.2.0-12ubuntu1 [11.4 MB] 241s Get:9 http://ftpmaster.internal/ubuntu resolute/main ppc64el cpp-15 ppc64el 15.2.0-12ubuntu1 [1038 B] 241s Get:10 http://ftpmaster.internal/ubuntu resolute/main ppc64el cpp-powerpc64le-linux-gnu ppc64el 4:15.2.0-4ubuntu1 [5746 B] 241s Get:11 http://ftpmaster.internal/ubuntu resolute/main ppc64el cpp ppc64el 4:15.2.0-4ubuntu1 [22.4 kB] 241s Get:12 http://ftpmaster.internal/ubuntu resolute/main ppc64el libcc1-0 ppc64el 15.2.0-12ubuntu1 [49.0 kB] 241s Get:13 http://ftpmaster.internal/ubuntu resolute/main ppc64el libitm1 ppc64el 15.2.0-12ubuntu1 [32.2 kB] 241s Get:14 http://ftpmaster.internal/ubuntu resolute/main ppc64el libasan8 ppc64el 15.2.0-12ubuntu1 [3006 kB] 247s Get:15 http://ftpmaster.internal/ubuntu resolute/main ppc64el liblsan0 ppc64el 15.2.0-12ubuntu1 [1374 kB] 249s Get:16 http://ftpmaster.internal/ubuntu resolute/main ppc64el libtsan2 ppc64el 15.2.0-12ubuntu1 [2729 kB] 253s Get:17 http://ftpmaster.internal/ubuntu resolute/main ppc64el libubsan1 ppc64el 15.2.0-12ubuntu1 [1231 kB] 255s Get:18 http://ftpmaster.internal/ubuntu resolute/main ppc64el libquadmath0 ppc64el 15.2.0-12ubuntu1 [160 kB] 255s Get:19 http://ftpmaster.internal/ubuntu resolute/main ppc64el libgcc-15-dev ppc64el 15.2.0-12ubuntu1 [1670 kB] 258s Get:20 http://ftpmaster.internal/ubuntu resolute/main ppc64el gcc-15-powerpc64le-linux-gnu ppc64el 15.2.0-12ubuntu1 [22.4 MB] 292s Get:21 http://ftpmaster.internal/ubuntu resolute/main ppc64el gcc-15 ppc64el 15.2.0-12ubuntu1 [530 kB] 293s Get:22 http://ftpmaster.internal/ubuntu resolute/main ppc64el gcc-powerpc64le-linux-gnu ppc64el 4:15.2.0-4ubuntu1 [1220 B] 293s Get:23 http://ftpmaster.internal/ubuntu resolute/main ppc64el gcc ppc64el 4:15.2.0-4ubuntu1 [5032 B] 293s Get:24 http://ftpmaster.internal/ubuntu resolute/main ppc64el libstdc++-15-dev ppc64el 15.2.0-12ubuntu1 [2747 kB] 300s Get:25 http://ftpmaster.internal/ubuntu resolute/main ppc64el g++-15-powerpc64le-linux-gnu ppc64el 15.2.0-12ubuntu1 [13.0 MB] 321s Get:26 http://ftpmaster.internal/ubuntu resolute/main ppc64el g++-15 ppc64el 15.2.0-12ubuntu1 [25.3 kB] 321s Get:27 http://ftpmaster.internal/ubuntu resolute/main ppc64el g++-powerpc64le-linux-gnu ppc64el 4:15.2.0-4ubuntu1 [970 B] 321s Get:28 http://ftpmaster.internal/ubuntu resolute/main ppc64el g++ ppc64el 4:15.2.0-4ubuntu1 [1092 B] 321s Get:29 http://ftpmaster.internal/ubuntu resolute/main ppc64el build-essential ppc64el 12.12ubuntu2 [5256 B] 321s Get:30 http://ftpmaster.internal/ubuntu resolute/main ppc64el dctrl-tools ppc64el 2.24-3build4 [108 kB] 321s Get:31 http://ftpmaster.internal/ubuntu resolute/main ppc64el libgfortran-15-dev ppc64el 15.2.0-12ubuntu1 [651 kB] 322s Get:32 http://ftpmaster.internal/ubuntu resolute/main ppc64el gfortran-15-powerpc64le-linux-gnu ppc64el 15.2.0-12ubuntu1 [12.3 MB] 342s Get:33 http://ftpmaster.internal/ubuntu resolute/main ppc64el gfortran-15 ppc64el 15.2.0-12ubuntu1 [18.1 kB] 342s Get:34 http://ftpmaster.internal/ubuntu resolute/main ppc64el gfortran-powerpc64le-linux-gnu ppc64el 4:15.2.0-4ubuntu1 [1020 B] 342s Get:35 http://ftpmaster.internal/ubuntu resolute/main ppc64el gfortran ppc64el 4:15.2.0-4ubuntu1 [1166 B] 342s Get:36 http://ftpmaster.internal/ubuntu resolute/main ppc64el icu-devtools ppc64el 78.2-1ubuntu1 [246 kB] 342s Get:37 http://ftpmaster.internal/ubuntu resolute/main ppc64el libblas-dev ppc64el 3.12.1-7ubuntu1 [306 kB] 342s Get:38 http://ftpmaster.internal/ubuntu resolute/main ppc64el libbz2-dev ppc64el 1.0.8-6build2 [50.0 kB] 343s Get:39 http://ftpmaster.internal/ubuntu resolute/main ppc64el libdeflate-dev ppc64el 1.23-2build1 [71.8 kB] 343s Get:40 http://ftpmaster.internal/ubuntu resolute/main ppc64el libicu-dev ppc64el 78.2-1ubuntu1 [13.3 MB] 368s Get:41 http://ftpmaster.internal/ubuntu resolute/main ppc64el libjpeg-turbo8-dev ppc64el 2.1.5-4ubuntu3 [358 kB] 368s Get:42 http://ftpmaster.internal/ubuntu resolute/main ppc64el libjpeg8-dev ppc64el 8c-2ubuntu11 [1484 B] 368s Get:43 http://ftpmaster.internal/ubuntu resolute/main ppc64el libjpeg-dev ppc64el 8c-2ubuntu11 [1486 B] 368s Get:44 http://ftpmaster.internal/ubuntu resolute/main ppc64el liblapack-dev ppc64el 3.12.1-7ubuntu1 [6357 kB] 379s Get:45 http://ftpmaster.internal/ubuntu resolute/main ppc64el libncurses-dev ppc64el 6.6+20251231-1 [505 kB] 379s Get:46 http://ftpmaster.internal/ubuntu resolute/main ppc64el libpcre2-16-0 ppc64el 10.46-1 [292 kB] 379s Get:47 http://ftpmaster.internal/ubuntu resolute/main ppc64el libpcre2-32-0 ppc64el 10.46-1 [275 kB] 379s Get:48 http://ftpmaster.internal/ubuntu resolute/main ppc64el libpcre2-posix3 ppc64el 10.46-1 [7334 B] 379s Get:49 http://ftpmaster.internal/ubuntu resolute/main ppc64el libpcre2-dev ppc64el 10.46-1 [937 kB] 381s Get:50 http://ftpmaster.internal/ubuntu resolute/main ppc64el libpkgconf3 ppc64el 1.8.1-4build1 [37.9 kB] 381s Get:51 http://ftpmaster.internal/ubuntu resolute/main ppc64el zlib1g-dev ppc64el 1:1.3.dfsg+really1.3.1-1ubuntu2 [903 kB] 382s Get:52 http://ftpmaster.internal/ubuntu resolute/main ppc64el libpng-dev ppc64el 1.6.54-1 [326 kB] 382s Get:53 http://ftpmaster.internal/ubuntu resolute/main ppc64el libreadline-dev ppc64el 8.3-3 [252 kB] 382s Get:54 http://ftpmaster.internal/ubuntu resolute/main ppc64el libzstd-dev ppc64el 1.5.7+dfsg-3 [528 kB] 383s Get:55 http://ftpmaster.internal/ubuntu resolute/main ppc64el liblzma-dev ppc64el 5.8.2-2 [210 kB] 383s Get:56 http://ftpmaster.internal/ubuntu resolute/main ppc64el pkgconf-bin ppc64el 1.8.1-4build1 [22.7 kB] 383s Get:57 http://ftpmaster.internal/ubuntu resolute/main ppc64el pkgconf ppc64el 1.8.1-4build1 [16.8 kB] 383s Get:58 http://ftpmaster.internal/ubuntu resolute/main ppc64el libtirpc-dev ppc64el 1.3.6+ds-1 [223 kB] 383s Get:59 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-base-dev all 4.5.2-1ubuntu2 [1880 B] 383s Get:60 http://ftpmaster.internal/ubuntu resolute/universe ppc64el pkg-r-autopkgtest all 20250812 [6158 B] 383s Get:61 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-backports ppc64el 1.5.0-2 [122 kB] 383s Get:62 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-cli ppc64el 3.6.4-1 [1411 kB] 386s Get:63 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-generics all 0.1.4-1 [84.0 kB] 386s Get:64 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-glue ppc64el 1.8.0-1 [165 kB] 386s Get:65 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-rlang ppc64el 1.1.5-3 [1738 kB] 389s Get:66 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-lifecycle all 1.0.5+dfsg-1 [120 kB] 389s Get:67 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-magrittr ppc64el 2.0.3-1 [154 kB] 389s Get:68 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-utf8 ppc64el 1.2.4-1 [148 kB] 389s Get:69 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-vctrs ppc64el 0.6.5-1 [1399 kB] 391s Get:70 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-pillar all 1.11.1+dfsg-1 [456 kB] 391s Get:71 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-r6 all 2.6.1-1 [101 kB] 391s Get:72 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-fansi ppc64el 1.0.6-2 [637 kB] 392s Get:73 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-pkgconfig all 2.0.3-2build2 [20.4 kB] 392s Get:74 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-tibble ppc64el 3.2.1+dfsg-3 [420 kB] 392s Get:75 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-withr all 3.0.2+dfsg-1 [214 kB] 392s Get:76 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-tidyselect ppc64el 1.2.1+dfsg-1 [222 kB] 392s Get:77 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-dplyr ppc64el 1.1.4-4 [1542 kB] 394s Get:78 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-purrr ppc64el 1.0.4-1 [555 kB] 396s Get:79 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-stringi ppc64el 1.8.4-1build2 [947 kB] 398s Get:80 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-stringr all 1.5.1-1 [290 kB] 398s Get:81 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-cpp11 all 0.5.3-1 [242 kB] 398s Get:82 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-tidyr ppc64el 1.3.1-1 [1163 kB] 400s Get:83 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-broom all 1.0.12+dfsg-1 [1708 kB] 403s Get:84 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-farver ppc64el 2.1.2-1 [1389 kB] 407s Get:85 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-mass ppc64el 7.3-65-1 [1116 kB] 410s Get:86 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-geepack ppc64el 1.3.12-1 [413 kB] 411s Get:87 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-gtable all 0.3.6+dfsg-1 [199 kB] 411s Get:88 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-isoband ppc64el 0.2.7-1 [1486 kB] 415s Get:89 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-s7 ppc64el 0.2.0-1 [330 kB] 415s Get:90 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-labeling all 0.4.3-1 [62.1 kB] 415s Get:91 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-rcolorbrewer all 1.1-3-1build2 [54.0 kB] 415s Get:92 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-viridislite all 0.4.3-1 [1088 kB] 418s Get:93 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-scales all 1.4.0-1 [725 kB] 419s Get:94 http://ftpmaster.internal/ubuntu resolute-proposed/universe ppc64el r-cran-ggplot2 all 4.0.2+dfsg-1 [4941 kB] 431s Fetched 129 MB in 3min 35s (602 kB/s) 431s Selecting previously unselected package libc-dev-bin. 431s (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 ... 127200 files and directories currently installed.) 431s Preparing to unpack .../00-libc-dev-bin_2.42-2ubuntu4_ppc64el.deb ... 431s Unpacking libc-dev-bin (2.42-2ubuntu4) ... 431s Selecting previously unselected package linux-libc-dev:ppc64el. 431s Preparing to unpack .../01-linux-libc-dev_6.19.0-3.3_ppc64el.deb ... 431s Unpacking linux-libc-dev:ppc64el (6.19.0-3.3) ... 431s Selecting previously unselected package libcrypt-dev:ppc64el. 431s Preparing to unpack .../02-libcrypt-dev_1%3a4.5.1-1_ppc64el.deb ... 431s Unpacking libcrypt-dev:ppc64el (1:4.5.1-1) ... 431s Selecting previously unselected package rpcsvc-proto. 431s Preparing to unpack .../03-rpcsvc-proto_1.4.3-1build1_ppc64el.deb ... 431s Unpacking rpcsvc-proto (1.4.3-1build1) ... 431s Selecting previously unselected package libc6-dev:ppc64el. 431s Preparing to unpack .../04-libc6-dev_2.42-2ubuntu4_ppc64el.deb ... 431s Unpacking libc6-dev:ppc64el (2.42-2ubuntu4) ... 431s Selecting previously unselected package libisl23:ppc64el. 431s Preparing to unpack .../05-libisl23_0.27-1build1_ppc64el.deb ... 431s Unpacking libisl23:ppc64el (0.27-1build1) ... 431s Selecting previously unselected package libmpc3:ppc64el. 431s Preparing to unpack .../06-libmpc3_1.3.1-2_ppc64el.deb ... 431s Unpacking libmpc3:ppc64el (1.3.1-2) ... 431s Selecting previously unselected package cpp-15-powerpc64le-linux-gnu. 431s Preparing to unpack .../07-cpp-15-powerpc64le-linux-gnu_15.2.0-12ubuntu1_ppc64el.deb ... 431s Unpacking cpp-15-powerpc64le-linux-gnu (15.2.0-12ubuntu1) ... 431s Selecting previously unselected package cpp-15. 431s Preparing to unpack .../08-cpp-15_15.2.0-12ubuntu1_ppc64el.deb ... 431s Unpacking cpp-15 (15.2.0-12ubuntu1) ... 431s Selecting previously unselected package cpp-powerpc64le-linux-gnu. 431s Preparing to unpack .../09-cpp-powerpc64le-linux-gnu_4%3a15.2.0-4ubuntu1_ppc64el.deb ... 431s Unpacking cpp-powerpc64le-linux-gnu (4:15.2.0-4ubuntu1) ... 431s Selecting previously unselected package cpp. 431s Preparing to unpack .../10-cpp_4%3a15.2.0-4ubuntu1_ppc64el.deb ... 431s Unpacking cpp (4:15.2.0-4ubuntu1) ... 431s Selecting previously unselected package libcc1-0:ppc64el. 431s Preparing to unpack .../11-libcc1-0_15.2.0-12ubuntu1_ppc64el.deb ... 431s Unpacking libcc1-0:ppc64el (15.2.0-12ubuntu1) ... 431s Selecting previously unselected package libitm1:ppc64el. 431s Preparing to unpack .../12-libitm1_15.2.0-12ubuntu1_ppc64el.deb ... 431s Unpacking libitm1:ppc64el (15.2.0-12ubuntu1) ... 431s Selecting previously unselected package libasan8:ppc64el. 431s Preparing to unpack .../13-libasan8_15.2.0-12ubuntu1_ppc64el.deb ... 431s Unpacking libasan8:ppc64el (15.2.0-12ubuntu1) ... 431s Selecting previously unselected package liblsan0:ppc64el. 431s Preparing to unpack .../14-liblsan0_15.2.0-12ubuntu1_ppc64el.deb ... 431s Unpacking liblsan0:ppc64el (15.2.0-12ubuntu1) ... 431s Selecting previously unselected package libtsan2:ppc64el. 431s Preparing to unpack .../15-libtsan2_15.2.0-12ubuntu1_ppc64el.deb ... 431s Unpacking libtsan2:ppc64el (15.2.0-12ubuntu1) ... 431s Selecting previously unselected package libubsan1:ppc64el. 431s Preparing to unpack .../16-libubsan1_15.2.0-12ubuntu1_ppc64el.deb ... 431s Unpacking libubsan1:ppc64el (15.2.0-12ubuntu1) ... 431s Selecting previously unselected package libquadmath0:ppc64el. 431s Preparing to unpack .../17-libquadmath0_15.2.0-12ubuntu1_ppc64el.deb ... 431s Unpacking libquadmath0:ppc64el (15.2.0-12ubuntu1) ... 432s Selecting previously unselected package libgcc-15-dev:ppc64el. 432s Preparing to unpack .../18-libgcc-15-dev_15.2.0-12ubuntu1_ppc64el.deb ... 432s Unpacking libgcc-15-dev:ppc64el (15.2.0-12ubuntu1) ... 432s Selecting previously unselected package gcc-15-powerpc64le-linux-gnu. 432s Preparing to unpack .../19-gcc-15-powerpc64le-linux-gnu_15.2.0-12ubuntu1_ppc64el.deb ... 432s Unpacking gcc-15-powerpc64le-linux-gnu (15.2.0-12ubuntu1) ... 432s Selecting previously unselected package gcc-15. 432s Preparing to unpack .../20-gcc-15_15.2.0-12ubuntu1_ppc64el.deb ... 432s Unpacking gcc-15 (15.2.0-12ubuntu1) ... 432s Selecting previously unselected package gcc-powerpc64le-linux-gnu. 432s Preparing to unpack .../21-gcc-powerpc64le-linux-gnu_4%3a15.2.0-4ubuntu1_ppc64el.deb ... 432s Unpacking gcc-powerpc64le-linux-gnu (4:15.2.0-4ubuntu1) ... 432s Selecting previously unselected package gcc. 432s Preparing to unpack .../22-gcc_4%3a15.2.0-4ubuntu1_ppc64el.deb ... 432s Unpacking gcc (4:15.2.0-4ubuntu1) ... 432s Selecting previously unselected package libstdc++-15-dev:ppc64el. 432s Preparing to unpack .../23-libstdc++-15-dev_15.2.0-12ubuntu1_ppc64el.deb ... 432s Unpacking libstdc++-15-dev:ppc64el (15.2.0-12ubuntu1) ... 432s Selecting previously unselected package g++-15-powerpc64le-linux-gnu. 432s Preparing to unpack .../24-g++-15-powerpc64le-linux-gnu_15.2.0-12ubuntu1_ppc64el.deb ... 432s Unpacking g++-15-powerpc64le-linux-gnu (15.2.0-12ubuntu1) ... 432s Selecting previously unselected package g++-15. 432s Preparing to unpack .../25-g++-15_15.2.0-12ubuntu1_ppc64el.deb ... 432s Unpacking g++-15 (15.2.0-12ubuntu1) ... 432s Selecting previously unselected package g++-powerpc64le-linux-gnu. 432s Preparing to unpack .../26-g++-powerpc64le-linux-gnu_4%3a15.2.0-4ubuntu1_ppc64el.deb ... 432s Unpacking g++-powerpc64le-linux-gnu (4:15.2.0-4ubuntu1) ... 432s Selecting previously unselected package g++. 432s Preparing to unpack .../27-g++_4%3a15.2.0-4ubuntu1_ppc64el.deb ... 432s Unpacking g++ (4:15.2.0-4ubuntu1) ... 432s Selecting previously unselected package build-essential. 432s Preparing to unpack .../28-build-essential_12.12ubuntu2_ppc64el.deb ... 432s Unpacking build-essential (12.12ubuntu2) ... 432s Selecting previously unselected package dctrl-tools. 432s Preparing to unpack .../29-dctrl-tools_2.24-3build4_ppc64el.deb ... 432s Unpacking dctrl-tools (2.24-3build4) ... 432s Selecting previously unselected package libgfortran-15-dev:ppc64el. 432s Preparing to unpack .../30-libgfortran-15-dev_15.2.0-12ubuntu1_ppc64el.deb ... 432s Unpacking libgfortran-15-dev:ppc64el (15.2.0-12ubuntu1) ... 432s Selecting previously unselected package gfortran-15-powerpc64le-linux-gnu. 432s Preparing to unpack .../31-gfortran-15-powerpc64le-linux-gnu_15.2.0-12ubuntu1_ppc64el.deb ... 432s Unpacking gfortran-15-powerpc64le-linux-gnu (15.2.0-12ubuntu1) ... 433s Selecting previously unselected package gfortran-15. 433s Preparing to unpack .../32-gfortran-15_15.2.0-12ubuntu1_ppc64el.deb ... 433s Unpacking gfortran-15 (15.2.0-12ubuntu1) ... 433s Selecting previously unselected package gfortran-powerpc64le-linux-gnu. 433s Preparing to unpack .../33-gfortran-powerpc64le-linux-gnu_4%3a15.2.0-4ubuntu1_ppc64el.deb ... 433s Unpacking gfortran-powerpc64le-linux-gnu (4:15.2.0-4ubuntu1) ... 433s Selecting previously unselected package gfortran. 433s Preparing to unpack .../34-gfortran_4%3a15.2.0-4ubuntu1_ppc64el.deb ... 433s Unpacking gfortran (4:15.2.0-4ubuntu1) ... 433s Selecting previously unselected package icu-devtools. 433s Preparing to unpack .../35-icu-devtools_78.2-1ubuntu1_ppc64el.deb ... 433s Unpacking icu-devtools (78.2-1ubuntu1) ... 433s Selecting previously unselected package libblas-dev:ppc64el. 433s Preparing to unpack .../36-libblas-dev_3.12.1-7ubuntu1_ppc64el.deb ... 433s Unpacking libblas-dev:ppc64el (3.12.1-7ubuntu1) ... 433s Selecting previously unselected package libbz2-dev:ppc64el. 433s Preparing to unpack .../37-libbz2-dev_1.0.8-6build2_ppc64el.deb ... 433s Unpacking libbz2-dev:ppc64el (1.0.8-6build2) ... 433s Selecting previously unselected package libdeflate-dev:ppc64el. 433s Preparing to unpack .../38-libdeflate-dev_1.23-2build1_ppc64el.deb ... 433s Unpacking libdeflate-dev:ppc64el (1.23-2build1) ... 433s Selecting previously unselected package libicu-dev:ppc64el. 433s Preparing to unpack .../39-libicu-dev_78.2-1ubuntu1_ppc64el.deb ... 433s Unpacking libicu-dev:ppc64el (78.2-1ubuntu1) ... 433s Selecting previously unselected package libjpeg-turbo8-dev:ppc64el. 433s Preparing to unpack .../40-libjpeg-turbo8-dev_2.1.5-4ubuntu3_ppc64el.deb ... 433s Unpacking libjpeg-turbo8-dev:ppc64el (2.1.5-4ubuntu3) ... 433s Selecting previously unselected package libjpeg8-dev:ppc64el. 433s Preparing to unpack .../41-libjpeg8-dev_8c-2ubuntu11_ppc64el.deb ... 433s Unpacking libjpeg8-dev:ppc64el (8c-2ubuntu11) ... 433s Selecting previously unselected package libjpeg-dev:ppc64el. 433s Preparing to unpack .../42-libjpeg-dev_8c-2ubuntu11_ppc64el.deb ... 433s Unpacking libjpeg-dev:ppc64el (8c-2ubuntu11) ... 433s Selecting previously unselected package liblapack-dev:ppc64el. 433s Preparing to unpack .../43-liblapack-dev_3.12.1-7ubuntu1_ppc64el.deb ... 433s Unpacking liblapack-dev:ppc64el (3.12.1-7ubuntu1) ... 433s Selecting previously unselected package libncurses-dev:ppc64el. 433s Preparing to unpack .../44-libncurses-dev_6.6+20251231-1_ppc64el.deb ... 433s Unpacking libncurses-dev:ppc64el (6.6+20251231-1) ... 433s Selecting previously unselected package libpcre2-16-0:ppc64el. 433s Preparing to unpack .../45-libpcre2-16-0_10.46-1_ppc64el.deb ... 433s Unpacking libpcre2-16-0:ppc64el (10.46-1) ... 433s Selecting previously unselected package libpcre2-32-0:ppc64el. 433s Preparing to unpack .../46-libpcre2-32-0_10.46-1_ppc64el.deb ... 433s Unpacking libpcre2-32-0:ppc64el (10.46-1) ... 433s Selecting previously unselected package libpcre2-posix3:ppc64el. 433s Preparing to unpack .../47-libpcre2-posix3_10.46-1_ppc64el.deb ... 433s Unpacking libpcre2-posix3:ppc64el (10.46-1) ... 433s Selecting previously unselected package libpcre2-dev:ppc64el. 433s Preparing to unpack .../48-libpcre2-dev_10.46-1_ppc64el.deb ... 433s Unpacking libpcre2-dev:ppc64el (10.46-1) ... 433s Selecting previously unselected package libpkgconf3:ppc64el. 433s Preparing to unpack .../49-libpkgconf3_1.8.1-4build1_ppc64el.deb ... 433s Unpacking libpkgconf3:ppc64el (1.8.1-4build1) ... 433s Selecting previously unselected package zlib1g-dev:ppc64el. 433s Preparing to unpack .../50-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1ubuntu2_ppc64el.deb ... 433s Unpacking zlib1g-dev:ppc64el (1:1.3.dfsg+really1.3.1-1ubuntu2) ... 433s Selecting previously unselected package libpng-dev:ppc64el. 433s Preparing to unpack .../51-libpng-dev_1.6.54-1_ppc64el.deb ... 433s Unpacking libpng-dev:ppc64el (1.6.54-1) ... 433s Selecting previously unselected package libreadline-dev:ppc64el. 433s Preparing to unpack .../52-libreadline-dev_8.3-3_ppc64el.deb ... 433s Unpacking libreadline-dev:ppc64el (8.3-3) ... 433s Selecting previously unselected package libzstd-dev:ppc64el. 433s Preparing to unpack .../53-libzstd-dev_1.5.7+dfsg-3_ppc64el.deb ... 433s Unpacking libzstd-dev:ppc64el (1.5.7+dfsg-3) ... 434s Selecting previously unselected package liblzma-dev:ppc64el. 434s Preparing to unpack .../54-liblzma-dev_5.8.2-2_ppc64el.deb ... 434s Unpacking liblzma-dev:ppc64el (5.8.2-2) ... 434s Selecting previously unselected package pkgconf-bin. 434s Preparing to unpack .../55-pkgconf-bin_1.8.1-4build1_ppc64el.deb ... 434s Unpacking pkgconf-bin (1.8.1-4build1) ... 434s Selecting previously unselected package pkgconf:ppc64el. 434s Preparing to unpack .../56-pkgconf_1.8.1-4build1_ppc64el.deb ... 434s Unpacking pkgconf:ppc64el (1.8.1-4build1) ... 434s Selecting previously unselected package libtirpc-dev:ppc64el. 434s Preparing to unpack .../57-libtirpc-dev_1.3.6+ds-1_ppc64el.deb ... 434s Unpacking libtirpc-dev:ppc64el (1.3.6+ds-1) ... 434s Selecting previously unselected package r-base-dev. 434s Preparing to unpack .../58-r-base-dev_4.5.2-1ubuntu2_all.deb ... 434s Unpacking r-base-dev (4.5.2-1ubuntu2) ... 434s Selecting previously unselected package pkg-r-autopkgtest. 434s Preparing to unpack .../59-pkg-r-autopkgtest_20250812_all.deb ... 434s Unpacking pkg-r-autopkgtest (20250812) ... 434s Selecting previously unselected package r-cran-backports. 434s Preparing to unpack .../60-r-cran-backports_1.5.0-2_ppc64el.deb ... 434s Unpacking r-cran-backports (1.5.0-2) ... 434s Selecting previously unselected package r-cran-cli. 434s Preparing to unpack .../61-r-cran-cli_3.6.4-1_ppc64el.deb ... 434s Unpacking r-cran-cli (3.6.4-1) ... 434s Selecting previously unselected package r-cran-generics. 434s Preparing to unpack .../62-r-cran-generics_0.1.4-1_all.deb ... 434s Unpacking r-cran-generics (0.1.4-1) ... 434s Selecting previously unselected package r-cran-glue. 434s Preparing to unpack .../63-r-cran-glue_1.8.0-1_ppc64el.deb ... 434s Unpacking r-cran-glue (1.8.0-1) ... 434s Selecting previously unselected package r-cran-rlang. 434s Preparing to unpack .../64-r-cran-rlang_1.1.5-3_ppc64el.deb ... 434s Unpacking r-cran-rlang (1.1.5-3) ... 434s Selecting previously unselected package r-cran-lifecycle. 434s Preparing to unpack .../65-r-cran-lifecycle_1.0.5+dfsg-1_all.deb ... 434s Unpacking r-cran-lifecycle (1.0.5+dfsg-1) ... 434s Selecting previously unselected package r-cran-magrittr. 434s Preparing to unpack .../66-r-cran-magrittr_2.0.3-1_ppc64el.deb ... 434s Unpacking r-cran-magrittr (2.0.3-1) ... 434s Selecting previously unselected package r-cran-utf8. 434s Preparing to unpack .../67-r-cran-utf8_1.2.4-1_ppc64el.deb ... 434s Unpacking r-cran-utf8 (1.2.4-1) ... 434s Selecting previously unselected package r-cran-vctrs. 434s Preparing to unpack .../68-r-cran-vctrs_0.6.5-1_ppc64el.deb ... 434s Unpacking r-cran-vctrs (0.6.5-1) ... 434s Selecting previously unselected package r-cran-pillar. 434s Preparing to unpack .../69-r-cran-pillar_1.11.1+dfsg-1_all.deb ... 434s Unpacking r-cran-pillar (1.11.1+dfsg-1) ... 434s Selecting previously unselected package r-cran-r6. 434s Preparing to unpack .../70-r-cran-r6_2.6.1-1_all.deb ... 434s Unpacking r-cran-r6 (2.6.1-1) ... 434s Selecting previously unselected package r-cran-fansi. 434s Preparing to unpack .../71-r-cran-fansi_1.0.6-2_ppc64el.deb ... 434s Unpacking r-cran-fansi (1.0.6-2) ... 434s Selecting previously unselected package r-cran-pkgconfig. 434s Preparing to unpack .../72-r-cran-pkgconfig_2.0.3-2build2_all.deb ... 434s Unpacking r-cran-pkgconfig (2.0.3-2build2) ... 434s Selecting previously unselected package r-cran-tibble. 434s Preparing to unpack .../73-r-cran-tibble_3.2.1+dfsg-3_ppc64el.deb ... 434s Unpacking r-cran-tibble (3.2.1+dfsg-3) ... 434s Selecting previously unselected package r-cran-withr. 434s Preparing to unpack .../74-r-cran-withr_3.0.2+dfsg-1_all.deb ... 434s Unpacking r-cran-withr (3.0.2+dfsg-1) ... 434s Selecting previously unselected package r-cran-tidyselect. 434s Preparing to unpack .../75-r-cran-tidyselect_1.2.1+dfsg-1_ppc64el.deb ... 434s Unpacking r-cran-tidyselect (1.2.1+dfsg-1) ... 434s Selecting previously unselected package r-cran-dplyr. 434s Preparing to unpack .../76-r-cran-dplyr_1.1.4-4_ppc64el.deb ... 434s Unpacking r-cran-dplyr (1.1.4-4) ... 434s Selecting previously unselected package r-cran-purrr. 434s Preparing to unpack .../77-r-cran-purrr_1.0.4-1_ppc64el.deb ... 434s Unpacking r-cran-purrr (1.0.4-1) ... 434s Selecting previously unselected package r-cran-stringi. 434s Preparing to unpack .../78-r-cran-stringi_1.8.4-1build2_ppc64el.deb ... 434s Unpacking r-cran-stringi (1.8.4-1build2) ... 434s Selecting previously unselected package r-cran-stringr. 434s Preparing to unpack .../79-r-cran-stringr_1.5.1-1_all.deb ... 434s Unpacking r-cran-stringr (1.5.1-1) ... 434s Selecting previously unselected package r-cran-cpp11. 434s Preparing to unpack .../80-r-cran-cpp11_0.5.3-1_all.deb ... 434s Unpacking r-cran-cpp11 (0.5.3-1) ... 434s Selecting previously unselected package r-cran-tidyr. 434s Preparing to unpack .../81-r-cran-tidyr_1.3.1-1_ppc64el.deb ... 434s Unpacking r-cran-tidyr (1.3.1-1) ... 434s Selecting previously unselected package r-cran-broom. 434s Preparing to unpack .../82-r-cran-broom_1.0.12+dfsg-1_all.deb ... 434s Unpacking r-cran-broom (1.0.12+dfsg-1) ... 434s Selecting previously unselected package r-cran-farver. 434s Preparing to unpack .../83-r-cran-farver_2.1.2-1_ppc64el.deb ... 434s Unpacking r-cran-farver (2.1.2-1) ... 434s Selecting previously unselected package r-cran-mass. 434s Preparing to unpack .../84-r-cran-mass_7.3-65-1_ppc64el.deb ... 434s Unpacking r-cran-mass (7.3-65-1) ... 434s Selecting previously unselected package r-cran-geepack. 434s Preparing to unpack .../85-r-cran-geepack_1.3.12-1_ppc64el.deb ... 434s Unpacking r-cran-geepack (1.3.12-1) ... 435s Selecting previously unselected package r-cran-gtable. 435s Preparing to unpack .../86-r-cran-gtable_0.3.6+dfsg-1_all.deb ... 435s Unpacking r-cran-gtable (0.3.6+dfsg-1) ... 435s Selecting previously unselected package r-cran-isoband. 435s Preparing to unpack .../87-r-cran-isoband_0.2.7-1_ppc64el.deb ... 435s Unpacking r-cran-isoband (0.2.7-1) ... 435s Selecting previously unselected package r-cran-s7. 435s Preparing to unpack .../88-r-cran-s7_0.2.0-1_ppc64el.deb ... 435s Unpacking r-cran-s7 (0.2.0-1) ... 435s Selecting previously unselected package r-cran-labeling. 435s Preparing to unpack .../89-r-cran-labeling_0.4.3-1_all.deb ... 435s Unpacking r-cran-labeling (0.4.3-1) ... 435s Selecting previously unselected package r-cran-rcolorbrewer. 435s Preparing to unpack .../90-r-cran-rcolorbrewer_1.1-3-1build2_all.deb ... 435s Unpacking r-cran-rcolorbrewer (1.1-3-1build2) ... 435s Selecting previously unselected package r-cran-viridislite. 435s Preparing to unpack .../91-r-cran-viridislite_0.4.3-1_all.deb ... 435s Unpacking r-cran-viridislite (0.4.3-1) ... 435s Selecting previously unselected package r-cran-scales. 435s Preparing to unpack .../92-r-cran-scales_1.4.0-1_all.deb ... 435s Unpacking r-cran-scales (1.4.0-1) ... 435s Selecting previously unselected package r-cran-ggplot2. 435s Preparing to unpack .../93-r-cran-ggplot2_4.0.2+dfsg-1_all.deb ... 435s Unpacking r-cran-ggplot2 (4.0.2+dfsg-1) ... 435s Setting up r-cran-rlang (1.1.5-3) ... 435s Setting up libzstd-dev:ppc64el (1.5.7+dfsg-3) ... 435s Setting up r-cran-withr (3.0.2+dfsg-1) ... 435s Setting up r-cran-backports (1.5.0-2) ... 435s Setting up r-cran-generics (0.1.4-1) ... 435s Setting up r-cran-fansi (1.0.6-2) ... 435s Setting up r-cran-mass (7.3-65-1) ... 435s Setting up linux-libc-dev:ppc64el (6.19.0-3.3) ... 435s Setting up r-cran-glue (1.8.0-1) ... 435s Setting up r-cran-cli (3.6.4-1) ... 435s Setting up r-cran-lifecycle (1.0.5+dfsg-1) ... 435s Setting up libpcre2-16-0:ppc64el (10.46-1) ... 435s Setting up r-cran-pkgconfig (2.0.3-2build2) ... 435s Setting up libpcre2-32-0:ppc64el (10.46-1) ... 435s Setting up r-cran-utf8 (1.2.4-1) ... 435s Setting up libtirpc-dev:ppc64el (1.3.6+ds-1) ... 435s Setting up libpkgconf3:ppc64el (1.8.1-4build1) ... 435s Setting up rpcsvc-proto (1.4.3-1build1) ... 435s Setting up r-cran-stringi (1.8.4-1build2) ... 435s Setting up r-cran-s7 (0.2.0-1) ... 435s Setting up r-cran-cpp11 (0.5.3-1) ... 435s Setting up r-cran-rcolorbrewer (1.1-3-1build2) ... 435s Setting up r-cran-isoband (0.2.7-1) ... 435s Setting up libquadmath0:ppc64el (15.2.0-12ubuntu1) ... 435s Setting up libmpc3:ppc64el (1.3.1-2) ... 435s Setting up r-cran-gtable (0.3.6+dfsg-1) ... 435s Setting up r-cran-labeling (0.4.3-1) ... 435s Setting up icu-devtools (78.2-1ubuntu1) ... 435s Setting up pkgconf-bin (1.8.1-4build1) ... 435s Setting up r-cran-farver (2.1.2-1) ... 435s Setting up liblzma-dev:ppc64el (5.8.2-2) ... 435s Setting up libubsan1:ppc64el (15.2.0-12ubuntu1) ... 435s Setting up libpcre2-posix3:ppc64el (10.46-1) ... 435s Setting up r-cran-viridislite (0.4.3-1) ... 435s Setting up libcrypt-dev:ppc64el (1:4.5.1-1) ... 435s Setting up libasan8:ppc64el (15.2.0-12ubuntu1) ... 435s Setting up libtsan2:ppc64el (15.2.0-12ubuntu1) ... 435s Setting up r-cran-r6 (2.6.1-1) ... 435s Setting up libisl23:ppc64el (0.27-1build1) ... 435s Setting up libc-dev-bin (2.42-2ubuntu4) ... 435s Setting up libdeflate-dev:ppc64el (1.23-2build1) ... 435s Setting up r-cran-magrittr (2.0.3-1) ... 435s Setting up libcc1-0:ppc64el (15.2.0-12ubuntu1) ... 435s Setting up r-cran-vctrs (0.6.5-1) ... 435s Setting up liblsan0:ppc64el (15.2.0-12ubuntu1) ... 435s Setting up libblas-dev:ppc64el (3.12.1-7ubuntu1) ... 435s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/blas/libblas.so to provide /usr/lib/powerpc64le-linux-gnu/libblas.so (libblas.so-powerpc64le-linux-gnu) in auto mode 435s Setting up dctrl-tools (2.24-3build4) ... 435s Setting up libitm1:ppc64el (15.2.0-12ubuntu1) ... 435s Setting up r-cran-pillar (1.11.1+dfsg-1) ... 435s Setting up libgcc-15-dev:ppc64el (15.2.0-12ubuntu1) ... 435s Setting up r-cran-stringr (1.5.1-1) ... 435s Setting up r-cran-tibble (3.2.1+dfsg-3) ... 435s Setting up libgfortran-15-dev:ppc64el (15.2.0-12ubuntu1) ... 435s Setting up pkgconf:ppc64el (1.8.1-4build1) ... 435s Setting up r-cran-tidyselect (1.2.1+dfsg-1) ... 435s Setting up cpp-15-powerpc64le-linux-gnu (15.2.0-12ubuntu1) ... 435s Setting up r-cran-scales (1.4.0-1) ... 435s Setting up liblapack-dev:ppc64el (3.12.1-7ubuntu1) ... 435s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/lapack/liblapack.so to provide /usr/lib/powerpc64le-linux-gnu/liblapack.so (liblapack.so-powerpc64le-linux-gnu) in auto mode 435s Setting up r-cran-purrr (1.0.4-1) ... 435s Setting up cpp-15 (15.2.0-12ubuntu1) ... 435s Setting up libc6-dev:ppc64el (2.42-2ubuntu4) ... 435s Setting up r-cran-dplyr (1.1.4-4) ... 435s Setting up libicu-dev:ppc64el (78.2-1ubuntu1) ... 435s Setting up cpp-powerpc64le-linux-gnu (4:15.2.0-4ubuntu1) ... 435s Setting up libbz2-dev:ppc64el (1.0.8-6build2) ... 435s Setting up libjpeg-turbo8-dev:ppc64el (2.1.5-4ubuntu3) ... 435s Setting up libncurses-dev:ppc64el (6.6+20251231-1) ... 435s Setting up libpcre2-dev:ppc64el (10.46-1) ... 435s Setting up gcc-15-powerpc64le-linux-gnu (15.2.0-12ubuntu1) ... 435s Setting up r-cran-ggplot2 (4.0.2+dfsg-1) ... 435s Setting up libreadline-dev:ppc64el (8.3-3) ... 435s Setting up gcc-15 (15.2.0-12ubuntu1) ... 435s Setting up libstdc++-15-dev:ppc64el (15.2.0-12ubuntu1) ... 435s Setting up gcc-powerpc64le-linux-gnu (4:15.2.0-4ubuntu1) ... 435s Setting up gfortran-15-powerpc64le-linux-gnu (15.2.0-12ubuntu1) ... 435s Setting up r-cran-tidyr (1.3.1-1) ... 435s Setting up zlib1g-dev:ppc64el (1:1.3.dfsg+really1.3.1-1ubuntu2) ... 435s Setting up cpp (4:15.2.0-4ubuntu1) ... 435s Setting up libjpeg8-dev:ppc64el (8c-2ubuntu11) ... 435s Setting up gfortran-15 (15.2.0-12ubuntu1) ... 435s Setting up g++-15-powerpc64le-linux-gnu (15.2.0-12ubuntu1) ... 435s Setting up libpng-dev:ppc64el (1.6.54-1) ... 435s Setting up libjpeg-dev:ppc64el (8c-2ubuntu11) ... 435s Setting up gcc (4:15.2.0-4ubuntu1) ... 435s Setting up gfortran-powerpc64le-linux-gnu (4:15.2.0-4ubuntu1) ... 435s Setting up r-cran-broom (1.0.12+dfsg-1) ... 435s Setting up g++-15 (15.2.0-12ubuntu1) ... 435s Setting up g++-powerpc64le-linux-gnu (4:15.2.0-4ubuntu1) ... 435s Setting up r-cran-geepack (1.3.12-1) ... 435s Setting up gfortran (4:15.2.0-4ubuntu1) ... 435s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode 435s 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 435s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode 435s 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 435s Setting up g++ (4:15.2.0-4ubuntu1) ... 435s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 435s Setting up build-essential (12.12ubuntu2) ... 435s Setting up r-base-dev (4.5.2-1ubuntu2) ... 435s Setting up pkg-r-autopkgtest (20250812) ... 435s Processing triggers for libc-bin (2.42-2ubuntu4) ... 435s Processing triggers for man-db (2.13.1-1build1) ... 436s Processing triggers for install-info (7.2-5) ... 437s autopkgtest [23:21:04]: test pkg-r-autopkgtest: /usr/share/dh-r/pkg-r-autopkgtest 437s autopkgtest [23:21:04]: test pkg-r-autopkgtest: [----------------------- 437s Test: Try to load the R library etm 437s 437s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 437s Copyright (C) 2025 The R Foundation for Statistical Computing 437s Platform: powerpc64le-unknown-linux-gnu 437s 437s R is free software and comes with ABSOLUTELY NO WARRANTY. 437s You are welcome to redistribute it under certain conditions. 437s Type 'license()' or 'licence()' for distribution details. 437s 437s R is a collaborative project with many contributors. 437s Type 'contributors()' for more information and 437s 'citation()' on how to cite R or R packages in publications. 437s 437s Type 'demo()' for some demos, 'help()' for on-line help, or 437s 'help.start()' for an HTML browser interface to help. 437s Type 'q()' to quit R. 437s 438s > library('etm') 439s > 439s autopkgtest [23:21:06]: test pkg-r-autopkgtest: -----------------------] 439s pkg-r-autopkgtest PASS 439s autopkgtest [23:21:06]: test pkg-r-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 440s autopkgtest [23:21:07]: @@@@@@@@@@@@@@@@@@@@ summary 440s run-unit-test PASS 440s pkg-r-autopkgtest PASS