0s autopkgtest [22:40:51]: starting date and time: 2026-02-09 22:40:51+0000 0s autopkgtest [22:40:51]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [22:40:51]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.e9m2kg70/out --timeout-copy=6000 --needs-internet=try --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:lattice --apt-upgrade r-cran-etm --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=lattice/0.22-9-1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-cpu2-ram4-disk20-ppc64el --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@sto01-ppc64el-3.secgroup --name adt-resolute-ppc64el-r-cran-etm-20260209-224051-juju-7f2275-prod-proposed-migration-environment-2-6b8d3b7a-8a87-4dd8-9144-3d57989a3c06 --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/ 4s Creating nova instance adt-resolute-ppc64el-r-cran-etm-20260209-224051-juju-7f2275-prod-proposed-migration-environment-2-6b8d3b7a-8a87-4dd8-9144-3d57989a3c06 from image adt/ubuntu-resolute-ppc64el-server-20260209.img (UUID f7f31435-4cd1-4090-aa55-59cfefa097ca)... 131s autopkgtest [22:43:02]: testbed dpkg architecture: ppc64el 131s autopkgtest [22:43:02]: testbed apt version: 3.1.15 132s autopkgtest [22:43:03]: @@@@@@@@@@@@@@@@@@@@ test bed setup 132s autopkgtest [22:43:03]: testbed release detected to be: None 132s autopkgtest [22:43:03]: updating testbed package index (apt update) 133s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 133s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 133s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 133s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 133s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [29.4 kB] 133s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [176 kB] 133s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [1645 kB] 135s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main ppc64el Packages [246 kB] 135s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/universe ppc64el Packages [1534 kB] 137s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse ppc64el Packages [19.4 kB] 138s Fetched 3774 kB in 5s (752 kB/s) 138s Reading package lists... 139s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 139s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 139s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 139s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 140s Reading package lists... 140s Reading package lists... 140s Building dependency tree... 140s Reading state information... 140s Calculating upgrade... 141s The following packages will be upgraded: 141s cryptsetup-bin dracut-install iproute2 iptables libcryptsetup12 libip4tc2 141s libip6tc2 libxtables12 wget 141s 9 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 141s Need to get 3125 kB of archives. 141s After this operation, 78.8 kB of additional disk space will be used. 141s Get:1 http://ftpmaster.internal/ubuntu resolute/main ppc64el iptables ppc64el 1.8.11-2ubuntu3 [464 kB] 141s Get:2 http://ftpmaster.internal/ubuntu resolute/main ppc64el libip4tc2 ppc64el 1.8.11-2ubuntu3 [27.8 kB] 141s Get:3 http://ftpmaster.internal/ubuntu resolute/main ppc64el libip6tc2 ppc64el 1.8.11-2ubuntu3 [28.2 kB] 141s Get:4 http://ftpmaster.internal/ubuntu resolute/main ppc64el libxtables12 ppc64el 1.8.11-2ubuntu3 [41.2 kB] 141s Get:5 http://ftpmaster.internal/ubuntu resolute/main ppc64el iproute2 ppc64el 6.18.0-1ubuntu1 [1458 kB] 143s Get:6 http://ftpmaster.internal/ubuntu resolute/main ppc64el libcryptsetup12 ppc64el 2:2.8.0-1ubuntu3 [404 kB] 143s Get:7 http://ftpmaster.internal/ubuntu resolute/main ppc64el wget ppc64el 1.25.0-2ubuntu4 [401 kB] 143s Get:8 http://ftpmaster.internal/ubuntu resolute/main ppc64el cryptsetup-bin ppc64el 2:2.8.0-1ubuntu3 [250 kB] 143s Get:9 http://ftpmaster.internal/ubuntu resolute/main ppc64el dracut-install ppc64el 109-11ubuntu1 [51.3 kB] 143s dpkg-preconfigure: unable to re-open stdin: No such file or directory 143s Fetched 3125 kB in 2s (1345 kB/s) 144s (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.) 144s Preparing to unpack .../0-iptables_1.8.11-2ubuntu3_ppc64el.deb ... 144s Unpacking iptables (1.8.11-2ubuntu3) over (1.8.11-2ubuntu2) ... 144s Preparing to unpack .../1-libip4tc2_1.8.11-2ubuntu3_ppc64el.deb ... 144s Unpacking libip4tc2:ppc64el (1.8.11-2ubuntu3) over (1.8.11-2ubuntu2) ... 144s Preparing to unpack .../2-libip6tc2_1.8.11-2ubuntu3_ppc64el.deb ... 144s Unpacking libip6tc2:ppc64el (1.8.11-2ubuntu3) over (1.8.11-2ubuntu2) ... 144s Preparing to unpack .../3-libxtables12_1.8.11-2ubuntu3_ppc64el.deb ... 144s Unpacking libxtables12:ppc64el (1.8.11-2ubuntu3) over (1.8.11-2ubuntu2) ... 144s Preparing to unpack .../4-iproute2_6.18.0-1ubuntu1_ppc64el.deb ... 144s Unpacking iproute2 (6.18.0-1ubuntu1) over (6.16.0-1ubuntu3) ... 144s Preparing to unpack .../5-libcryptsetup12_2%3a2.8.0-1ubuntu3_ppc64el.deb ... 144s Unpacking libcryptsetup12:ppc64el (2:2.8.0-1ubuntu3) over (2:2.8.0-1ubuntu2) ... 144s Preparing to unpack .../6-wget_1.25.0-2ubuntu4_ppc64el.deb ... 144s Unpacking wget (1.25.0-2ubuntu4) over (1.25.0-2ubuntu3) ... 144s Preparing to unpack .../7-cryptsetup-bin_2%3a2.8.0-1ubuntu3_ppc64el.deb ... 144s Unpacking cryptsetup-bin (2:2.8.0-1ubuntu3) over (2:2.8.0-1ubuntu2) ... 144s Preparing to unpack .../8-dracut-install_109-11ubuntu1_ppc64el.deb ... 144s Unpacking dracut-install (109-11ubuntu1) over (109-9ubuntu1) ... 145s Setting up libip4tc2:ppc64el (1.8.11-2ubuntu3) ... 145s Setting up wget (1.25.0-2ubuntu4) ... 145s Setting up libip6tc2:ppc64el (1.8.11-2ubuntu3) ... 145s Setting up libxtables12:ppc64el (1.8.11-2ubuntu3) ... 145s Setting up dracut-install (109-11ubuntu1) ... 145s Setting up libcryptsetup12:ppc64el (2:2.8.0-1ubuntu3) ... 145s Setting up cryptsetup-bin (2:2.8.0-1ubuntu3) ... 145s Setting up iptables (1.8.11-2ubuntu3) ... 145s Setting up iproute2 (6.18.0-1ubuntu1) ... 145s Processing triggers for man-db (2.13.1-1build1) ... 146s Processing triggers for install-info (7.2-5) ... 146s Processing triggers for libc-bin (2.42-2ubuntu4) ... 146s autopkgtest [22:43:17]: upgrading testbed (apt dist-upgrade and autopurge) 146s Reading package lists... 147s Building dependency tree... 147s Reading state information... 147s Calculating upgrade... 147s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 147s Reading package lists... 147s Building dependency tree... 147s Reading state information... 147s Solving dependencies... 147s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 150s autopkgtest [22:43:21]: testbed running kernel: Linux 6.19.0-3-generic #3-Ubuntu SMP PREEMPT_DYNAMIC Fri Jan 23 20:13:51 UTC 2026 150s autopkgtest [22:43:21]: @@@@@@@@@@@@@@@@@@@@ apt-source r-cran-etm 152s Get:1 http://ftpmaster.internal/ubuntu resolute/universe r-cran-etm 1.1.1-1build1 (dsc) [2147 B] 152s Get:2 http://ftpmaster.internal/ubuntu resolute/universe r-cran-etm 1.1.1-1build1 (tar) [242 kB] 152s Get:3 http://ftpmaster.internal/ubuntu resolute/universe r-cran-etm 1.1.1-1build1 (diff) [3672 B] 152s gpgv: Signature made Fri Nov 28 21:46:53 2025 UTC 152s gpgv: using RSA key 92FE4F8B40CADC4ECCD60C1F5961FDBE9C619809 152s gpgv: Can't check signature: No public key 152s dpkg-source: warning: cannot verify inline signature for ./r-cran-etm_1.1.1-1build1.dsc: no acceptable signature found 152s autopkgtest [22:43:23]: testing package r-cran-etm version 1.1.1-1build1 153s autopkgtest [22:43:24]: build not needed 155s autopkgtest [22:43:26]: test run-unit-test: preparing testbed 155s Reading package lists... 155s Building dependency tree... 155s Reading state information... 155s Solving dependencies... 156s The following NEW packages will be installed: 156s fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono libblas3 156s libcairo2 libdatrie1 libdeflate0 libfontconfig1 libgfortran5 libgomp1 156s libgraphite2-3 libharfbuzz0b libice6 libjbig0 libjpeg-turbo8 libjpeg8 156s liblapack3 liblerc4 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 156s libpaper-utils libpaper2 libpixman-1-0 libsharpyuv0 libsm6 libtcl8.6 156s libthai-data libthai0 libtiff6 libtk8.6 libwebp7 libxcb-render0 libxcb-shm0 156s libxft2 libxrender1 libxss1 libxt6t64 r-base-core r-cran-data.table 156s r-cran-dbi r-cran-etm r-cran-kmi r-cran-lattice r-cran-littler r-cran-matrix 156s r-cran-mitools r-cran-pkgkitten r-cran-rcpp r-cran-rcpparmadillo 156s r-cran-survival unzip x11-common xdg-utils zip 156s 0 upgraded, 56 newly installed, 0 to remove and 0 not upgraded. 156s Need to get 63.2 MB of archives. 156s After this operation, 138 MB of additional disk space will be used. 156s Get:1 http://ftpmaster.internal/ubuntu resolute/main ppc64el fonts-dejavu-mono all 2.37-8build1 [502 kB] 157s Get:2 http://ftpmaster.internal/ubuntu resolute/main ppc64el fonts-dejavu-core all 2.37-8build1 [834 kB] 158s Get:3 http://ftpmaster.internal/ubuntu resolute/main ppc64el fontconfig-config ppc64el 2.17.1-3ubuntu1 [38.5 kB] 158s Get:4 http://ftpmaster.internal/ubuntu resolute/main ppc64el libfontconfig1 ppc64el 2.17.1-3ubuntu1 [193 kB] 158s Get:5 http://ftpmaster.internal/ubuntu resolute/main ppc64el fontconfig ppc64el 2.17.1-3ubuntu1 [182 kB] 158s Get:6 http://ftpmaster.internal/ubuntu resolute/main ppc64el libblas3 ppc64el 3.12.1-7ubuntu1 [291 kB] 158s Get:7 http://ftpmaster.internal/ubuntu resolute/main ppc64el libpixman-1-0 ppc64el 0.46.4-1 [347 kB] 158s Get:8 http://ftpmaster.internal/ubuntu resolute/main ppc64el libxcb-render0 ppc64el 1.17.0-2ubuntu1 [17.4 kB] 158s Get:9 http://ftpmaster.internal/ubuntu resolute/main ppc64el libxcb-shm0 ppc64el 1.17.0-2ubuntu1 [6072 B] 158s Get:10 http://ftpmaster.internal/ubuntu resolute/main ppc64el libxrender1 ppc64el 1:0.9.12-1 [23.0 kB] 158s Get:11 http://ftpmaster.internal/ubuntu resolute/main ppc64el libcairo2 ppc64el 1.18.4-3 [759 kB] 160s Get:12 http://ftpmaster.internal/ubuntu resolute/main ppc64el libdatrie1 ppc64el 0.2.14-1 [22.7 kB] 160s Get:13 http://ftpmaster.internal/ubuntu resolute/main ppc64el libdeflate0 ppc64el 1.23-2build1 [64.1 kB] 160s Get:14 http://ftpmaster.internal/ubuntu resolute/main ppc64el libgfortran5 ppc64el 15.2.0-12ubuntu1 [620 kB] 161s Get:15 http://ftpmaster.internal/ubuntu resolute/main ppc64el libgomp1 ppc64el 15.2.0-12ubuntu1 [169 kB] 161s Get:16 http://ftpmaster.internal/ubuntu resolute/main ppc64el libgraphite2-3 ppc64el 1.3.14-11ubuntu1 [85.3 kB] 161s Get:17 http://ftpmaster.internal/ubuntu resolute/main ppc64el libharfbuzz0b ppc64el 12.3.2-1 [663 kB] 162s Get:18 http://ftpmaster.internal/ubuntu resolute/main ppc64el x11-common all 1:7.7+24ubuntu1 [22.4 kB] 162s Get:19 http://ftpmaster.internal/ubuntu resolute/main ppc64el libice6 ppc64el 2:1.1.1-1build1 [51.9 kB] 162s Get:20 http://ftpmaster.internal/ubuntu resolute/main ppc64el libjpeg-turbo8 ppc64el 2.1.5-4ubuntu3 [214 kB] 162s Get:21 http://ftpmaster.internal/ubuntu resolute/main ppc64el libjpeg8 ppc64el 8c-2ubuntu11 [2148 B] 162s Get:22 http://ftpmaster.internal/ubuntu resolute/main ppc64el liblapack3 ppc64el 3.12.1-7ubuntu1 [2960 kB] 166s Get:23 http://ftpmaster.internal/ubuntu resolute/main ppc64el liblerc4 ppc64el 4.0.0+ds-5ubuntu2 [315 kB] 166s Get:24 http://ftpmaster.internal/ubuntu resolute/main ppc64el libthai-data all 0.1.30-1 [155 kB] 166s Get:25 http://ftpmaster.internal/ubuntu resolute/main ppc64el libthai0 ppc64el 0.1.30-1 [22.5 kB] 166s Get:26 http://ftpmaster.internal/ubuntu resolute/main ppc64el libpango-1.0-0 ppc64el 1.57.0-1 [283 kB] 166s Get:27 http://ftpmaster.internal/ubuntu resolute/main ppc64el libpangoft2-1.0-0 ppc64el 1.57.0-1 [61.2 kB] 166s Get:28 http://ftpmaster.internal/ubuntu resolute/main ppc64el libpangocairo-1.0-0 ppc64el 1.57.0-1 [31.0 kB] 166s Get:29 http://ftpmaster.internal/ubuntu resolute/main ppc64el libpaper2 ppc64el 2.2.5-0.3build1 [18.1 kB] 166s Get:30 http://ftpmaster.internal/ubuntu resolute/main ppc64el libpaper-utils ppc64el 2.2.5-0.3build1 [15.7 kB] 166s Get:31 http://ftpmaster.internal/ubuntu resolute/main ppc64el libsharpyuv0 ppc64el 1.5.0-0.1build1 [24.7 kB] 166s Get:32 http://ftpmaster.internal/ubuntu resolute/main ppc64el libsm6 ppc64el 2:1.2.6-1build1 [18.6 kB] 167s Get:33 http://ftpmaster.internal/ubuntu resolute/main ppc64el libtcl8.6 ppc64el 8.6.17+dfsg-1build1 [1239 kB] 168s Get:34 http://ftpmaster.internal/ubuntu resolute/main ppc64el libjbig0 ppc64el 2.1-6.1ubuntu3 [37.1 kB] 168s Get:35 http://ftpmaster.internal/ubuntu resolute/main ppc64el libwebp7 ppc64el 1.5.0-0.1build1 [330 kB] 168s Get:36 http://ftpmaster.internal/ubuntu resolute/main ppc64el libtiff6 ppc64el 4.7.0-3ubuntu3 [307 kB] 168s Get:37 http://ftpmaster.internal/ubuntu resolute/main ppc64el libxft2 ppc64el 2.3.6-1build2 [61.6 kB] 168s Get:38 http://ftpmaster.internal/ubuntu resolute/main ppc64el libxss1 ppc64el 1:1.2.3-1build4 [7470 B] 168s Get:39 http://ftpmaster.internal/ubuntu resolute/main ppc64el libtk8.6 ppc64el 8.6.17-1 [968 kB] 170s Get:40 http://ftpmaster.internal/ubuntu resolute/main ppc64el libxt6t64 ppc64el 1:1.2.1-1.3 [203 kB] 170s Get:41 http://ftpmaster.internal/ubuntu resolute/main ppc64el zip ppc64el 3.0-15ubuntu3 [198 kB] 170s Get:42 http://ftpmaster.internal/ubuntu resolute/main ppc64el unzip ppc64el 6.0-29ubuntu1 [200 kB] 170s Get:43 http://ftpmaster.internal/ubuntu resolute/main ppc64el xdg-utils all 1.2.1-2ubuntu2 [66.1 kB] 170s Get:44 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-base-core ppc64el 4.5.2-1ubuntu2 [29.3 MB] 225s Get:45 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-data.table ppc64el 1.17.0+dfsg-1 [2197 kB] 229s Get:46 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-dbi all 1.2.3-1build1 [855 kB] 230s Get:47 http://ftpmaster.internal/ubuntu resolute-proposed/universe ppc64el r-cran-lattice ppc64el 0.22-9-1 [1399 kB] 232s Get:48 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-matrix ppc64el 1.7-4-1 [4584 kB] 239s Get:49 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-survival ppc64el 3.8-6-1 [8312 kB] 254s Get:50 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-littler ppc64el 0.3.22-1 [85.5 kB] 254s Get:51 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-pkgkitten all 0.2.4-1 [27.2 kB] 254s Get:52 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-rcpp ppc64el 1.1.0-1 [2037 kB] 257s Get:53 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-rcpparmadillo ppc64el 15.2.3-1-1 [935 kB] 258s Get:54 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-etm ppc64el 1.1.1-1build1 [506 kB] 259s Get:55 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-mitools all 2.4-2build2 [266 kB] 259s Get:56 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-kmi all 0.5.5-2build2 [78.9 kB] 259s Preconfiguring packages ... 259s Fetched 63.2 MB in 1min 44s (611 kB/s) 259s Selecting previously unselected package fonts-dejavu-mono. 259s (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.) 259s Preparing to unpack .../00-fonts-dejavu-mono_2.37-8build1_all.deb ... 259s Unpacking fonts-dejavu-mono (2.37-8build1) ... 259s Selecting previously unselected package fonts-dejavu-core. 259s Preparing to unpack .../01-fonts-dejavu-core_2.37-8build1_all.deb ... 259s Unpacking fonts-dejavu-core (2.37-8build1) ... 260s Selecting previously unselected package fontconfig-config. 260s Preparing to unpack .../02-fontconfig-config_2.17.1-3ubuntu1_ppc64el.deb ... 260s Unpacking fontconfig-config (2.17.1-3ubuntu1) ... 260s Selecting previously unselected package libfontconfig1:ppc64el. 260s Preparing to unpack .../03-libfontconfig1_2.17.1-3ubuntu1_ppc64el.deb ... 260s Unpacking libfontconfig1:ppc64el (2.17.1-3ubuntu1) ... 260s Selecting previously unselected package fontconfig. 260s Preparing to unpack .../04-fontconfig_2.17.1-3ubuntu1_ppc64el.deb ... 260s Unpacking fontconfig (2.17.1-3ubuntu1) ... 260s Selecting previously unselected package libblas3:ppc64el. 260s Preparing to unpack .../05-libblas3_3.12.1-7ubuntu1_ppc64el.deb ... 260s Unpacking libblas3:ppc64el (3.12.1-7ubuntu1) ... 260s Selecting previously unselected package libpixman-1-0:ppc64el. 260s Preparing to unpack .../06-libpixman-1-0_0.46.4-1_ppc64el.deb ... 260s Unpacking libpixman-1-0:ppc64el (0.46.4-1) ... 260s Selecting previously unselected package libxcb-render0:ppc64el. 260s Preparing to unpack .../07-libxcb-render0_1.17.0-2ubuntu1_ppc64el.deb ... 260s Unpacking libxcb-render0:ppc64el (1.17.0-2ubuntu1) ... 260s Selecting previously unselected package libxcb-shm0:ppc64el. 260s Preparing to unpack .../08-libxcb-shm0_1.17.0-2ubuntu1_ppc64el.deb ... 260s Unpacking libxcb-shm0:ppc64el (1.17.0-2ubuntu1) ... 260s Selecting previously unselected package libxrender1:ppc64el. 260s Preparing to unpack .../09-libxrender1_1%3a0.9.12-1_ppc64el.deb ... 260s Unpacking libxrender1:ppc64el (1:0.9.12-1) ... 260s Selecting previously unselected package libcairo2:ppc64el. 260s Preparing to unpack .../10-libcairo2_1.18.4-3_ppc64el.deb ... 260s Unpacking libcairo2:ppc64el (1.18.4-3) ... 260s Selecting previously unselected package libdatrie1:ppc64el. 260s Preparing to unpack .../11-libdatrie1_0.2.14-1_ppc64el.deb ... 260s Unpacking libdatrie1:ppc64el (0.2.14-1) ... 260s Selecting previously unselected package libdeflate0:ppc64el. 260s Preparing to unpack .../12-libdeflate0_1.23-2build1_ppc64el.deb ... 260s Unpacking libdeflate0:ppc64el (1.23-2build1) ... 260s Selecting previously unselected package libgfortran5:ppc64el. 260s Preparing to unpack .../13-libgfortran5_15.2.0-12ubuntu1_ppc64el.deb ... 260s Unpacking libgfortran5:ppc64el (15.2.0-12ubuntu1) ... 260s Selecting previously unselected package libgomp1:ppc64el. 260s Preparing to unpack .../14-libgomp1_15.2.0-12ubuntu1_ppc64el.deb ... 260s Unpacking libgomp1:ppc64el (15.2.0-12ubuntu1) ... 260s Selecting previously unselected package libgraphite2-3:ppc64el. 260s Preparing to unpack .../15-libgraphite2-3_1.3.14-11ubuntu1_ppc64el.deb ... 260s Unpacking libgraphite2-3:ppc64el (1.3.14-11ubuntu1) ... 260s Selecting previously unselected package libharfbuzz0b:ppc64el. 260s Preparing to unpack .../16-libharfbuzz0b_12.3.2-1_ppc64el.deb ... 260s Unpacking libharfbuzz0b:ppc64el (12.3.2-1) ... 260s Selecting previously unselected package x11-common. 260s Preparing to unpack .../17-x11-common_1%3a7.7+24ubuntu1_all.deb ... 260s Unpacking x11-common (1:7.7+24ubuntu1) ... 260s Selecting previously unselected package libice6:ppc64el. 260s Preparing to unpack .../18-libice6_2%3a1.1.1-1build1_ppc64el.deb ... 260s Unpacking libice6:ppc64el (2:1.1.1-1build1) ... 260s Selecting previously unselected package libjpeg-turbo8:ppc64el. 260s Preparing to unpack .../19-libjpeg-turbo8_2.1.5-4ubuntu3_ppc64el.deb ... 260s Unpacking libjpeg-turbo8:ppc64el (2.1.5-4ubuntu3) ... 260s Selecting previously unselected package libjpeg8:ppc64el. 260s Preparing to unpack .../20-libjpeg8_8c-2ubuntu11_ppc64el.deb ... 260s Unpacking libjpeg8:ppc64el (8c-2ubuntu11) ... 260s Selecting previously unselected package liblapack3:ppc64el. 260s Preparing to unpack .../21-liblapack3_3.12.1-7ubuntu1_ppc64el.deb ... 260s Unpacking liblapack3:ppc64el (3.12.1-7ubuntu1) ... 260s Selecting previously unselected package liblerc4:ppc64el. 260s Preparing to unpack .../22-liblerc4_4.0.0+ds-5ubuntu2_ppc64el.deb ... 260s Unpacking liblerc4:ppc64el (4.0.0+ds-5ubuntu2) 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Creating config file /etc/R/Renviron with new version 264s Setting up r-cran-lattice (0.22-9-1) ... 264s Setting up r-cran-pkgkitten (0.2.4-1) ... 264s Setting up r-cran-littler (0.3.22-1) ... 264s Setting up r-cran-rcpp (1.1.0-1) ... 264s Setting up r-cran-dbi (1.2.3-1build1) ... 264s Setting up r-cran-data.table (1.17.0+dfsg-1) ... 264s Setting up r-cran-matrix (1.7-4-1) ... 264s Setting up r-cran-rcpparmadillo (15.2.3-1-1) ... 264s Setting up r-cran-mitools (2.4-2build2) ... 264s Setting up r-cran-survival (3.8-6-1) ... 264s Setting up r-cran-kmi (0.5.5-2build2) ... 264s Setting up r-cran-etm (1.1.1-1build1) ... 264s Processing triggers for man-db (2.13.1-1build1) ... 265s Processing triggers for install-info (7.2-5) ... 265s Processing triggers for libc-bin (2.42-2ubuntu4) ... 266s autopkgtest [22:45:17]: test run-unit-test: [----------------------- 266s BEGIN TEST test.etmCIF.R 266s 266s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 266s Copyright (C) 2025 The R Foundation for Statistical Computing 266s Platform: powerpc64le-unknown-linux-gnu 266s 266s R is free software and comes with ABSOLUTELY NO WARRANTY. 266s You are welcome to redistribute it under certain conditions. 266s Type 'license()' or 'licence()' for distribution details. 266s 266s R is a collaborative project with many contributors. 266s Type 'contributors()' for more information and 266s 'citation()' on how to cite R or R packages in publications. 266s 266s Type 'demo()' for some demos, 'help()' for on-line help, or 266s 'help.start()' for an HTML browser interface to help. 266s Type 'q()' to quit R. 266s 266s Loading required package: etm 266s > ### test file for etmCIF. 266s > ### Really simple tests and comparison with etm 266s > 266s > old <- options(digits = 5) 266s > 266s > require(etm) 268s > 268s > if (!require(survival, quietly = TRUE)) { 268s + print("The following tests require the 'survival' package") 268s + } else { 268s + 268s + data(abortion) 268s + 268s + from <- rep(0, nrow(abortion)) 268s + to <- abortion$cause 268s + entry <- abortion$entry 268s + exit <- abortion$exit 268s + id <- 1:nrow(abortion) 268s + data <- data.frame(id, from, to, entry, exit, group = abortion$group) 268s + 268s + ## Computation of the CIFs with etm 268s + tra <- matrix(FALSE, 4, 4) 268s + tra[1, 2:4] <- TRUE 268s + 268s + cif.control <- etm(data[data$group == 0, ], c("0", "1", "2", "3"), 268s + tra, NULL, 0) 268s + cif.exposed <- etm(data[data$group == 1, ], c("0", "1", "2", "3"), 268s + tra, NULL, 0) 268s + 268s + 268s + ## Computation of the CIFs with etmCIF 268s + netm <- etmCIF(Surv(entry, exit, cause != 0) ~ group, abortion, 268s + etype = cause, failcode = 3) 268s + 268s + ### let's do some comparisons :-) 268s + 268s + all.equal(trprob(cif.control, "0 3"), netm[[1]]$est["0", "3", ]) 268s + all.equal(trprob(cif.control, "0 2"), netm[[1]]$est["0", "2", ]) 268s + all.equal(trprob(cif.control, "0 1"), netm[[1]]$est["0", "1", ]) 268s + 268s + all.equal(trprob(cif.exposed, "0 3"), netm[[2]]$est["0", "3", ]) 268s + all.equal(trprob(cif.exposed, "0 2"), netm[[2]]$est["0", "2", ]) 268s + all.equal(trprob(cif.exposed, "0 1"), netm[[2]]$est["0", "1", ]) 268s + 268s + 268s + all.equal(trcov(cif.control, "0 3"), netm[[1]]$cov["0 3", "0 3", ]) 268s + all.equal(trcov(cif.control, "0 2"), netm[[1]]$cov["0 2", "0 2", ]) 268s + all.equal(trcov(cif.control, "0 1"), netm[[1]]$cov["0 1", "0 1", ]) 268s + 268s + all.equal(trcov(cif.exposed, "0 3"), netm[[2]]$cov["0 3", "0 3", ]) 268s + all.equal(trcov(cif.exposed, "0 2"), netm[[2]]$cov["0 2", "0 2", ]) 268s + all.equal(trcov(cif.exposed, "0 1"), netm[[2]]$cov["0 1", "0 1", ]) 268s + 268s + 268s + netm 268s + 268s + ## test on the summary 268s + snetm <- summary(netm) 268s + 268s + snetm 268s + 268s + all.equal(unname(trprob(cif.control, "0 3")), snetm[[1]][[3]]$P) 268s + all.equal(unname(trprob(cif.control, "0 2")), snetm[[1]][[2]]$P) 268s + all.equal(unname(trprob(cif.control, "0 1")), snetm[[1]][[1]]$P) 268s + 268s + all.equal(unname(trprob(cif.exposed, "0 3")), snetm[[2]][[3]]$P) 268s + all.equal(unname(trprob(cif.exposed, "0 2")), snetm[[2]][[2]]$P) 268s + all.equal(unname(trprob(cif.exposed, "0 1")), snetm[[2]][[1]]$P) 268s + 268s + scif.control <- summary(cif.control, ci.fun = "cloglog") 268s + scif.exposed <- summary(cif.exposed, ci.fun = "cloglog") 268s + 268s + all.equal(scif.control[[4]]$lower, snetm[[1]][[3]]$lower) 268s + all.equal(scif.control[[4]]$upper, snetm[[1]][[3]]$upper) 268s + 268s + all.equal(scif.exposed[[4]]$lower, snetm[[2]][[3]]$lower) 268s + all.equal(scif.exposed[[4]]$upper, snetm[[2]][[3]]$upper) 268s + } 268s [1] TRUE 268s > 268s > ### test with factors in the input 268s > abortion$status <- with(abortion, ifelse(cause == 2, "life birth", 268s + ifelse(cause == 1, "ETOP", "spontaneous abortion"))) 268s > 268s > abortion$status <- factor(abortion$status) 268s > 268s > netm.factor <- etmCIF(Surv(entry, exit, status != "cens") ~ group, abortion, 268s + etype = status, failcode = "spontaneous abortion") 268s > 268s > 268s > all.equal(trprob(cif.control, "0 3"), netm.factor[[1]]$est["0", "spontaneous abortion", ]) 268s [1] TRUE 268s > all.equal(trprob(cif.control, "0 2"), netm.factor[[1]]$est["0", "life birth", ]) 268s [1] TRUE 268s > 268s > netm.factor 268s Call: etmCIF(formula = Surv(entry, exit, status != "cens") ~ group, 268s data = abortion, etype = status, failcode = "spontaneous abortion") 268s 268s Covariate: group 268s levels: 0 1 268s 268s 268s group = 0 268s time P se(P) n.event 268s CIF ETOP 43 0.040159 0.0092578 20 268s CIF life birth 43 0.799059 0.0221865 924 268s CIF spontaneous abortion 43 0.160781 0.0213261 69 268s 268s group = 1 268s time P se(P) n.event 268s CIF ETOP 42 0.28511 0.042493 38 268s CIF life birth 42 0.35257 0.042139 92 268s CIF spontaneous abortion 42 0.36232 0.049473 43 268s > 268s > summary(netm.factor) 268s 268s group=0 268s 268s CIF ETOP 268s P time var lower upper n.risk n.event 268s 0.000000 6 0.0000e+00 0.000000 0.000000 117 0 268s 0.038955 13 8.4440e-05 0.024488 0.061694 645 1 268s 0.040159 26 8.5707e-05 0.025513 0.062939 846 0 268s 0.040159 36 8.5707e-05 0.025513 0.062939 876 0 268s 0.040159 40 8.5707e-05 0.025513 0.062939 554 0 268s 0.040159 43 8.5707e-05 0.025513 0.062939 6 0 268s 268s CIF life birth 268s P time var lower upper n.risk n.event 268s 0.000000 6 0.0000e+00 0.000000 0.000000 117 0 268s 0.000000 13 0.0000e+00 0.000000 0.000000 645 0 268s 0.000000 26 0.0000e+00 0.000000 0.000000 846 0 268s 0.053197 36 4.6195e-05 0.041379 0.068268 876 25 268s 0.563121 40 3.8801e-04 0.524924 0.602021 554 280 268s 0.799059 43 4.9224e-04 0.753969 0.840613 6 6 268s 268s CIF spontaneous abortion 268s P time var lower upper n.risk n.event 268s 0.034188 6 0.00028222 0.01297 0.088523 117 4 268s 0.150468 13 0.00045513 0.11360 0.197901 645 1 268s 0.159904 26 0.00045498 0.12274 0.206925 846 1 268s 0.160781 36 0.00045480 0.12360 0.207757 876 1 268s 0.160781 40 0.00045480 0.12360 0.207757 554 0 268s 0.160781 43 0.00045480 0.12360 0.207757 6 0 268s 268s 268s group=1 268s 268s CIF ETOP 268s P time var lower upper n.risk n.event 268s 0.00000 6 0.0000000 0.00000 0.00000 35 0 268s 0.26048 13 0.0017854 0.18795 0.35425 90 0 268s 0.28115 21 0.0018028 0.20742 0.37423 93 1 268s 0.28511 34 0.0018057 0.21116 0.37806 89 0 268s 0.28511 39 0.0018057 0.21116 0.37806 59 0 268s 0.28511 42 0.0018057 0.21116 0.37806 6 0 268s 268s CIF life birth 268s P time var lower upper n.risk n.event 268s 0.000000 6 0.0000e+00 0.000000 0.000000 35 0 268s 0.000000 13 0.0000e+00 0.000000 0.000000 90 0 268s 0.000000 21 0.0000e+00 0.000000 0.000000 93 0 268s 0.023073 34 9.0514e-05 0.010252 0.051504 89 2 268s 0.180156 39 8.0126e-04 0.131765 0.243663 59 13 268s 0.352565 42 1.7757e-03 0.276882 0.441775 6 6 268s 268s CIF spontaneous abortion 268s P time var lower upper n.risk n.event 268s 0.057143 6 0.0015394 0.014605 0.20968 35 2 268s 0.333246 13 0.0025280 0.245337 0.44216 90 4 268s 0.350702 21 0.0024827 0.262769 0.45762 93 0 268s 0.358492 34 0.0024593 0.270627 0.46448 89 0 268s 0.358492 39 0.0024593 0.270627 0.46448 59 0 268s 0.362323 42 0.0024476 0.274499 0.46785 6 0 268s 268s > 268s > ### test with group as a character vector 268s > abortion$ttt <- with(abortion, ifelse(group == 0, "control", "exposed")) 268s > abortion$ttt <- factor(abortion$ttt) 268s > 268s > netm.ttt <- etmCIF(Surv(entry, exit, status != "cens") ~ ttt, abortion, 268s + etype = status, failcode = "spontaneous abortion") 268s > 268s > all.equal(trprob(cif.control, "0 3"), netm.ttt[[1]]$est["0", "spontaneous abortion", ]) 268s [1] TRUE 268s > all.equal(trprob(cif.control, "0 2"), netm.ttt[[1]]$est["0", "life birth", ]) 268s [1] TRUE 268s > 268s > netm.ttt 268s Call: etmCIF(formula = Surv(entry, exit, status != "cens") ~ ttt, data = abortion, 268s etype = status, failcode = "spontaneous abortion") 268s 268s Covariate: ttt 268s levels: control exposed 268s 268s 268s ttt = control 268s time P se(P) n.event 268s CIF ETOP 43 0.040159 0.0092578 20 268s CIF life birth 43 0.799059 0.0221865 924 268s CIF spontaneous abortion 43 0.160781 0.0213261 69 268s 268s ttt = exposed 268s time P se(P) n.event 268s CIF ETOP 42 0.28511 0.042493 38 268s CIF life birth 42 0.35257 0.042139 92 268s CIF spontaneous abortion 42 0.36232 0.049473 43 268s > 268s > summary(netm.ttt) 268s 268s ttt=control 268s 268s CIF ETOP 268s P time var lower upper n.risk n.event 268s 0.000000 6 0.0000e+00 0.000000 0.000000 117 0 268s 0.038955 13 8.4440e-05 0.024488 0.061694 645 1 268s 0.040159 26 8.5707e-05 0.025513 0.062939 846 0 268s 0.040159 36 8.5707e-05 0.025513 0.062939 876 0 268s 0.040159 40 8.5707e-05 0.025513 0.062939 554 0 268s 0.040159 43 8.5707e-05 0.025513 0.062939 6 0 268s 268s CIF life birth 268s P time var lower upper n.risk n.event 268s 0.000000 6 0.0000e+00 0.000000 0.000000 117 0 268s 0.000000 13 0.0000e+00 0.000000 0.000000 645 0 268s 0.000000 26 0.0000e+00 0.000000 0.000000 846 0 268s 0.053197 36 4.6195e-05 0.041379 0.068268 876 25 268s 0.563121 40 3.8801e-04 0.524924 0.602021 554 280 268s 0.799059 43 4.9224e-04 0.753969 0.840613 6 6 268s 268s CIF spontaneous abortion 268s P time var lower upper n.risk n.event 268s 0.034188 6 0.00028222 0.01297 0.088523 117 4 268s 0.150468 13 0.00045513 0.11360 0.197901 645 1 268s 0.159904 26 0.00045498 0.12274 0.206925 846 1 268s 0.160781 36 0.00045480 0.12360 0.207757 876 1 268s 0.160781 40 0.00045480 0.12360 0.207757 554 0 268s 0.160781 43 0.00045480 0.12360 0.207757 6 0 268s 268s 268s ttt=exposed 268s 268s CIF ETOP 268s P time var lower upper n.risk n.event 268s 0.00000 6 0.0000000 0.00000 0.00000 35 0 268s 0.26048 13 0.0017854 0.18795 0.35425 90 0 268s 0.28115 21 0.0018028 0.20742 0.37423 93 1 268s 0.28511 34 0.0018057 0.21116 0.37806 89 0 268s 0.28511 39 0.0018057 0.21116 0.37806 59 0 268s 0.28511 42 0.0018057 0.21116 0.37806 6 0 268s 268s CIF life birth 268s P time var lower upper n.risk n.event 268s 0.000000 6 0.0000e+00 0.000000 0.000000 35 0 268s 0.000000 13 0.0000e+00 0.000000 0.000000 90 0 268s 0.000000 21 0.0000e+00 0.000000 0.000000 93 0 268s 0.023073 34 9.0514e-05 0.010252 0.051504 89 2 268s 0.180156 39 8.0126e-04 0.131765 0.243663 59 13 268s 0.352565 42 1.7757e-03 0.276882 0.441775 6 6 268s 268s CIF spontaneous abortion 268s P time var lower upper n.risk n.event 268s 0.057143 6 0.0015394 0.014605 0.20968 35 2 268s 0.333246 13 0.0025280 0.245337 0.44216 90 4 268s 0.350702 21 0.0024827 0.262769 0.45762 93 0 268s 0.358492 34 0.0024593 0.270627 0.46448 89 0 268s 0.358492 39 0.0024593 0.270627 0.46448 59 0 268s 0.362323 42 0.0024476 0.274499 0.46785 6 0 268s 268s > 268s > 268s > ### A couple of comparisons with simulated data 268s > set.seed(1313) 268s > time <- rexp(100) 268s > to <- rbinom(100, 2, prob = c(1/3, 1/3, 1/3)) 268s > from <- rep(11, 100) 268s > id <- 1:100 268s > cov <- rbinom(100, 1, 0.5) 268s > 268s > dat.s <- data.frame(id, time, from, to, cov) 268s > 268s > traa <- matrix(FALSE, 3, 3) 268s > traa[1, 2:3] <- TRUE 268s > 268s > aa0 <- etm(dat.s[dat.s$cov == 0, ], c("11", "1", "2"), traa, "0", 0) 268s > aa1 <- etm(dat.s[dat.s$cov == 1, ], c("11", "1", "2"), traa, "0", 0) 268s > aa <- etm(dat.s, c("11", "1", "2"), traa, "0", 0) 268s > 268s > test <- etmCIF(Surv(time, to != 0) ~ 1, dat.s, etype = to) 268s > 268s > test.c <- etmCIF(Surv(time, to != 0) ~ cov, dat.s, etype = to) 268s > 268s > all.equal(trprob(aa, "11 1"), test[[1]]$est["0", "1", ]) 268s [1] TRUE 268s > all.equal(trprob(aa, "11 2"), test[[1]]$est["0", "2", ]) 268s [1] TRUE 268s > 268s > all.equal(trprob(aa0, "11 1"), test.c[[1]]$est["0", "1", ]) 268s [1] TRUE 268s > all.equal(trprob(aa0, "11 2"), test.c[[1]]$est["0", "2", ]) 268s [1] TRUE 268s > 268s > all.equal(trprob(aa1, "11 1"), test.c[[2]]$est["0", "1", ]) 268s [1] TRUE 268s > all.equal(trprob(aa1, "11 2"), test.c[[2]]$est["0", "2", ]) 268s [1] TRUE 268s > 268s > test 268s Call: etmCIF(formula = Surv(time, to != 0) ~ 1, data = dat.s, etype = to) 268s 268s time P se(P) n.event 268s CIF 1 4.9088 0.809108 0.079680 45 268s CIF 2 4.9088 0.096618 0.032905 8 268s > 268s > test.c 268s Call: etmCIF(formula = Surv(time, to != 0) ~ cov, data = dat.s, etype = to) 268s 268s Covariate: cov 268s levels: 0 1 268s 268s 268s cov = 0 268s time P se(P) n.event 268s CIF 1 2.1708 0.70246 0.105797 19 268s CIF 2 2.1708 0.11144 0.053384 4 268s 268s cov = 1 268s time P se(P) n.event 268s CIF 1 4.9088 0.80787 0.094051 26 268s CIF 2 4.9088 0.08436 0.040769 4 268s > 268s > summary(test) 268s 268s 268s 268s CIF 1 268s P time var lower upper n.risk n.event 268s 0.01000 0.0092099 0.0000990 0.0014147 0.068863 100 1 268s 0.11430 0.2663096 0.0010542 0.0649454 0.196993 81 1 268s 0.23451 0.7303091 0.0020436 0.1591107 0.337736 54 1 268s 0.40425 1.4299939 0.0032996 0.3020445 0.525741 29 1 268s 0.54593 2.0647206 0.0040836 0.4269008 0.673605 16 1 268s 0.80911 4.9087561 0.0063489 0.6359544 0.933733 2 1 268s 268s CIF 2 268s P time var lower upper n.risk n.event 268s 0.000000 0.0092099 0.00000000 0.000000 0.000000 100 0 268s 0.031657 0.2663096 0.00032353 0.010320 0.094942 81 0 268s 0.067029 0.7303091 0.00070366 0.030598 0.143503 54 0 268s 0.096618 1.4299939 0.00108275 0.049082 0.185474 29 0 268s 0.096618 2.0647206 0.00108275 0.049082 0.185474 16 0 268s 0.096618 4.9087561 0.00108275 0.049082 0.185474 2 0 268s 268s > summary(test.c) 268s 268s cov=0 268s 268s CIF 1 268s P time var lower upper n.risk n.event 268s 0.022222 0.0092099 0.00048285 0.0031605 0.14747 45 1 268s 0.092222 0.2982439 0.00193603 0.0355971 0.22762 36 0 268s 0.226684 0.7021938 0.00450954 0.1241760 0.39250 24 1 268s 0.378128 1.4299939 0.00760870 0.2337884 0.57145 13 1 268s 0.505736 1.6148774 0.00895330 0.3388425 0.69885 10 1 268s 0.702465 2.1708375 0.01119294 0.4944890 0.88399 3 1 268s 268s CIF 2 268s P time var lower upper n.risk n.event 268s 0.000000 0.0092099 0.0000000 0.000000 0.00000 45 0 268s 0.048441 0.2982439 0.0011168 0.012337 0.18013 36 1 268s 0.076411 0.7021938 0.0018104 0.025202 0.21928 24 0 268s 0.111440 1.4299939 0.0028499 0.042676 0.27392 13 0 268s 0.111440 1.6148774 0.0028499 0.042676 0.27392 10 0 268s 0.111440 2.1708375 0.0028499 0.042676 0.27392 3 0 268s 268s 268s cov=1 268s 268s CIF 1 268s P time var lower upper n.risk n.event 268s 0.018182 0.066692 0.00032457 0.0025813 0.12214 55 1 268s 0.112392 0.263808 0.00187215 0.0520925 0.23333 45 1 268s 0.241023 0.730309 0.00374499 0.1440057 0.38685 31 1 268s 0.401201 1.066913 0.00570788 0.2714008 0.56421 19 1 268s 0.592334 2.366275 0.00775985 0.4286230 0.76273 8 1 268s 0.807871 4.908756 0.00884554 0.6023185 0.94771 2 1 268s 268s CIF 2 268s P time var lower upper n.risk n.event 268s 0.000000 0.066692 0.00000000 0.000000 0.00000 55 0 268s 0.037434 0.263808 0.00067458 0.009494 0.14152 45 0 268s 0.059341 0.730309 0.00111295 0.019447 0.17351 31 0 268s 0.084360 1.066913 0.00166213 0.032211 0.21119 19 0 268s 0.084360 2.366275 0.00166213 0.032211 0.21119 8 0 268s 0.084360 4.908756 0.00166213 0.032211 0.21119 2 0 268s 268s > 268s > options(old) 268s > 268s BEGIN TEST tests.etm.R 268s 268s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 268s Copyright (C) 2025 The R Foundation for Statistical Computing 268s Platform: powerpc64le-unknown-linux-gnu 268s 268s R is free software and comes with ABSOLUTELY NO WARRANTY. 268s You are welcome to redistribute it under certain conditions. 268s Type 'license()' or 'licence()' for distribution details. 268s 268s R is a collaborative project with many contributors. 268s Type 'contributors()' for more information and 268s 'citation()' on how to cite R or R packages in publications. 268s 268s Type 'demo()' for some demos, 'help()' for on-line help, or 268s 'help.start()' for an HTML browser interface to help. 268s Type 'q()' to quit R. 268s 268s > require(etm) 268s Loading required package: etm 269s > 269s > ## Print with a bit less precision to avoid lots of notes in the comparison 269s > old <- options(digits = 4) 269s > 269s > ### Simple test 269s > 269s > time <- id <- 1:10 269s > from <- rep(0, 10) 269s > to <- rep(1, 10) 269s > 269s > data1 <- data.frame(id, from, to, time) 269s > tra1 <- matrix(FALSE, 2, 2) 269s > tra1[1, 2] <- TRUE 269s > 269s > etm1 <- etm(data1, c("0", "1"), tra1, NULL, 0) 269s > 269s > all.equal(as.vector(trprob(etm1, "0 0")), cumprod((10:1 - 1) / (10:1))) 269s [1] TRUE 269s > 269s > etm1$cov["0 0", "0 0", ] 269s 1 2 3 4 5 6 7 8 9 10 269s 0.009 0.016 0.021 0.024 0.025 0.024 0.021 0.016 0.009 0.000 269s > 269s > all.equal(etm1$cov["0 0", "0 0",], trcov(etm1, "0 0")) 269s [1] TRUE 269s > 269s > ### A simple test from AHR's author, where the first time is censored 269s > if (!require(survival)) { 269s + stop("This test requires the survival package") 269s + } 269s Loading required package: survival 269s > 269s > data <- data.frame(id=1:10, time=1:10, from=0, to=1, status=TRUE) 269s > 269s > tra <- matrix(FALSE, nrow=2, ncol=2) 269s > tra[1, 2] <- TRUE 269s > 269s > data$to[1] <- "cens" 269s > data$status[1] <- FALSE 269s > 269s > fit.km <- survfit(Surv(time, status) ~ 1, data=data) 269s > fit.etm <- etm(data, c("0","1"), tra, "cens", s=0, t="last", covariance=FALSE) 269s > 269s > all.equal(fit.km$surv[data$status], fit.etm$est[1,1,], check.attributes = FALSE) 269s [1] TRUE 269s > 269s > data$to[2] <- "cens" 269s > data$status[2] <- FALSE 269s > 269s > fit.km <- survfit(Surv(time, status) ~ 1, data=data) 269s > fit.etm <- etm(data, c("0","1"), tra, "cens", s=0, t="last", covariance=FALSE) 269s > 269s > all.equal(fit.km$surv[data$status], fit.etm$est[1,1,], check.attributes = FALSE) 269s [1] TRUE 269s > 269s > ### a bit more complicated 269s > 269s > time <- id <- 1:10 269s > from <- rep(0, 10) 269s > to <- rep(c(1, 2), 5) 269s > data2 <- data.frame(id, from, to, time) 269s > 269s > tra2 <- matrix(FALSE, 3, 3) 269s > tra2[1, 2:3] <- TRUE 269s > 269s > etm2 <- etm(data2, c("0", "1", "2"), tra2, NULL, 0) 269s > 269s > aa <- table(time, to) 269s > 269s > cif1 <- cumsum(aa[, 1] / 10) 269s > cif2 <- cumsum(aa[, 2] / 10) 269s > surv <- cumprod((10:1 - 1) / (10:1)) 269s > 269s > all.equal(trprob(etm2, "0 1"), cif1) 269s [1] TRUE 269s > all.equal(trprob(etm2, "0 2"), cif2) 269s [1] TRUE 269s > all.equal(as.vector(trprob(etm2, "0 0")), surv) 269s [1] TRUE 269s > 269s > ## a test on id 269s > data2$id <- letters[1:10] 269s > 269s > etm3 <- etm(data2, c("0", "1", "2"), tra2, NULL, 0) 269s > 269s > all.equal(trprob(etm2, "0 1"), trprob(etm3, "0 1")) 269s [1] TRUE 269s > all.equal(trprob(etm2, "0 2"), trprob(etm3, "0 2")) 269s [1] TRUE 269s > all.equal(trprob(etm2, "0 0"), trprob(etm3, "0 0")) 269s [1] TRUE 269s > 269s > 269s > ### Test on sir.cont 269s > 269s > data(sir.cont) 269s > 269s > ## Modification for patients entering and leaving a state 269s > ## at the same date 269s > ## Change on ventilation status is considered 269s > ## to happen before end of hospital stay 269s > sir.cont <- sir.cont[order(sir.cont$id, sir.cont$time), ] 269s > for (i in 2:nrow(sir.cont)) { 269s + if (sir.cont$id[i]==sir.cont$id[i-1]) { 269s + if (sir.cont$time[i]==sir.cont$time[i-1]) { 269s + sir.cont$time[i-1] <- sir.cont$time[i-1] - 0.5 269s + } 269s + } 269s + } 269s > 269s > ### Computation of the transition probabilities 269s > ## Possible transitions. 269s > tra <- matrix(ncol=3,nrow=3,FALSE) 269s > tra[1, 2:3] <- TRUE 269s > tra[2, c(1, 3)] <- TRUE 269s > 269s > ## etm 269s > prob.sir <- etm(sir.cont, c("0", "1", "2"), tra, "cens", 1) 269s > 269s > prob.sir 269s Multistate model with 2 transient state(s) 269s and 1 absorbing state(s) 269s 269s Possible transitions: 269s from to 269s 0 1 269s 0 2 269s 1 0 269s 1 2 269s 269s Estimate of P(1, 183) 269s 0 1 2 269s 0 0 0 1 269s 1 0 0 1 269s 2 0 0 1 269s 269s > 269s > summ.sir <- summary(prob.sir) 269s > all.equal(summ.sir[['0 1']]$P, as.vector(trprob(prob.sir, "0 1"))) 269s [1] TRUE 269s > subset(summ.sir[[3]],time<183) # issue with precision on different architectures 269s P time var lower upper n.risk n.event 269s 1.5 0.0000 1.5 0.000e+00 0.00000 0.0000 394 0 269s 2 0.1187 2.0 2.641e-04 0.08683 0.1505 396 47 269s 2.5 0.1187 2.5 2.641e-04 0.08683 0.1505 364 0 269s 3 0.2454 3.0 4.465e-04 0.20398 0.2868 365 54 269s 3.5 0.2454 3.5 4.465e-04 0.20398 0.2868 328 0 269s 4 0.3806 4.0 5.416e-04 0.33501 0.4262 331 62 269s 4.5 0.3806 4.5 5.416e-04 0.33501 0.4262 280 0 269s 5 0.4792 5.0 5.480e-04 0.43333 0.5251 283 48 269s 5.5 0.4792 5.5 5.480e-04 0.43333 0.5251 248 0 269s 6 0.5693 6.0 5.141e-04 0.52482 0.6137 249 47 269s 7 0.6350 7.0 4.665e-04 0.59266 0.6773 212 36 269s 8 0.6795 8.0 4.202e-04 0.63931 0.7197 195 27 269s 8.5 0.6795 8.5 4.202e-04 0.63931 0.7197 172 0 269s 9 0.7325 9.0 3.580e-04 0.69541 0.7696 173 34 269s 10 0.7647 10.0 3.141e-04 0.72992 0.7994 148 21 269s 10.5 0.7647 10.5 3.141e-04 0.72992 0.7994 135 0 269s 11 0.7895 11.0 2.790e-04 0.75674 0.8222 136 18 269s 12 0.8138 12.0 2.420e-04 0.78330 0.8443 129 18 269s 12.5 0.8138 12.5 2.420e-04 0.78330 0.8443 117 0 269s 13 0.8294 13.0 2.182e-04 0.80045 0.8584 118 13 269s 14 0.8452 14.0 1.938e-04 0.81789 0.8725 115 14 269s 15 0.8625 15.0 1.670e-04 0.83714 0.8878 106 15 269s 16 0.8723 16.0 1.522e-04 0.84807 0.8964 93 9 269s 17 0.8852 17.0 1.330e-04 0.86256 0.9078 86 12 269s 17.5 0.8852 17.5 1.330e-04 0.86256 0.9078 77 0 269s 18 0.8960 18.0 1.168e-04 0.87484 0.9172 76 9 269s 19 0.9029 19.0 1.070e-04 0.88261 0.9232 71 7 269s 20 0.9125 20.0 9.367e-05 0.89356 0.9315 64 10 269s 21 0.9161 21.0 8.878e-05 0.89768 0.9346 57 4 269s 22 0.9226 22.0 7.996e-05 0.90504 0.9401 55 6 269s 23 0.9261 23.0 7.537e-05 0.90904 0.9431 51 4 269s 23.5 0.9261 23.5 7.537e-05 0.90904 0.9431 49 0 269s 24 0.9354 24.0 6.292e-05 0.91982 0.9509 50 9 269s 25 0.9385 25.0 5.878e-05 0.92352 0.9536 42 3 269s 26 0.9429 26.0 5.326e-05 0.92863 0.9572 39 5 269s 27 0.9477 27.0 4.749e-05 0.93417 0.9612 35 6 269s 27.5 0.9477 27.5 4.749e-05 0.93417 0.9612 29 0 269s 28 0.9531 28.0 4.093e-05 0.94059 0.9657 30 5 269s 29 0.9567 29.0 3.668e-05 0.94485 0.9686 31 4 269s 30 0.9592 30.0 3.384e-05 0.94779 0.9706 28 3 269s 30.5 0.9592 30.5 3.384e-05 0.94779 0.9706 29 0 269s 31 0.9642 31.0 2.821e-05 0.95383 0.9746 30 6 269s 32 0.9649 32.0 2.752e-05 0.95458 0.9751 25 1 269s 33 0.9669 33.0 2.533e-05 0.95708 0.9768 24 2 269s 34 0.9685 34.0 2.368e-05 0.95900 0.9781 26 2 269s 35 0.9697 35.0 2.252e-05 0.96036 0.9790 28 2 269s 36 0.9702 36.0 2.194e-05 0.96104 0.9794 26 1 269s 37 0.9718 37.0 2.043e-05 0.96290 0.9806 26 2 269s 38 0.9739 38.0 1.831e-05 0.96555 0.9823 25 4 269s 38.5 0.9739 38.5 1.831e-05 0.96555 0.9823 21 0 269s 39 0.9760 39.0 1.643e-05 0.96802 0.9839 23 3 269s 40 0.9769 40.0 1.558e-05 0.96918 0.9847 19 1 269s 41 0.9774 41.0 1.512e-05 0.96981 0.9851 22 1 269s 42 0.9779 42.0 1.476e-05 0.97032 0.9854 22 0 269s 43 0.9798 43.0 1.308e-05 0.97271 0.9869 22 3 269s 44 0.9803 44.0 1.265e-05 0.97333 0.9873 21 1 269s 45 0.9817 45.0 1.157e-05 0.97499 0.9883 19 1 269s 46 0.9822 46.0 1.116e-05 0.97561 0.9887 17 1 269s 47 0.9831 47.0 1.037e-05 0.97683 0.9895 18 2 269s 48 0.9836 48.0 9.987e-06 0.97743 0.9898 17 1 269s 49 0.9841 49.0 9.669e-06 0.97796 0.9901 17 0 269s 50 0.9845 50.0 9.297e-06 0.97856 0.9905 17 1 269s 50.5 0.9845 50.5 9.297e-06 0.97856 0.9905 16 0 269s 51 0.9860 51.0 8.214e-06 0.98037 0.9916 17 3 269s 52 0.9870 52.0 7.513e-06 0.98159 0.9923 14 2 269s 53 0.9879 53.0 6.875e-06 0.98276 0.9930 12 1 269s 54 0.9889 54.0 6.214e-06 0.98397 0.9937 12 2 269s 55 0.9903 55.0 5.254e-06 0.98581 0.9948 10 3 269s 56 0.9913 56.0 4.667e-06 0.98703 0.9955 6 1 269s 57 0.9917 57.0 4.364e-06 0.98765 0.9958 5 1 269s 58 0.9922 58.0 4.064e-06 0.98828 0.9962 4 1 269s 59 0.9927 59.0 3.769e-06 0.98891 0.9965 3 1 269s 60 0.9932 60.0 3.488e-06 0.98953 0.9969 3 1 269s 62 0.9937 62.0 3.230e-06 0.99016 0.9972 2 0 269s 63 0.9942 63.0 2.956e-06 0.99079 0.9975 2 1 269s 68 0.9942 68.0 2.956e-06 0.99079 0.9975 1 0 269s 70 0.9946 70.0 2.694e-06 0.99143 0.9979 2 1 269s 78 0.9951 78.0 2.442e-06 0.99207 0.9982 1 0 269s 80 0.9951 80.0 2.442e-06 0.99207 0.9982 1 0 269s 85 0.9966 85.0 1.695e-06 0.99404 0.9991 2 0 269s 89 0.9966 89.0 1.695e-06 0.99404 0.9991 2 0 269s 90 0.9966 90.0 1.695e-06 0.99404 0.9991 1 0 269s 95 0.9971 95.0 1.448e-06 0.99472 0.9994 2 0 269s 100 0.9976 100.0 1.203e-06 0.99542 0.9997 3 0 269s 101 0.9981 101.0 9.592e-07 0.99613 1.0000 3 1 269s 108 0.9985 108.0 7.169e-07 0.99688 1.0000 2 1 269s 113 0.9990 113.0 4.764e-07 0.99767 1.0000 1 0 269s 116 0.9990 116.0 4.764e-07 0.99767 1.0000 1 0 269s 124 0.9990 124.0 4.764e-07 0.99767 1.0000 2 0 269s 164 0.9990 164.0 4.764e-07 0.99767 1.0000 0 0 269s > 269s > ## gonna play a bit with the state names 269s > dd <- sir.cont 269s > dd$from <- ifelse(dd$from == 0, "initial state", "ventilation") 269s > dd$to <- as.character(dd$to) 269s > for (i in seq_len(nrow(dd))) { 269s + dd$to[i] <- switch(dd$to[i], 269s + "0" = "initial state", 269s + "1" = "ventilation", 269s + "2" = "end of story", 269s + "cens" = "cens" 269s + ) 269s + } 269s > 269s > test <- etm(dd, c("initial state", "ventilation", "end of story"), tra, "cens", 1) 269s > 269s > all.equal(test$est["initial state", "initial state", ], 269s + prob.sir$est["0", "0", ]) 269s [1] TRUE 269s > all.equal(trprob(test, "initial state initial state"), trprob(prob.sir, "0 0")) 269s [1] TRUE 269s > all.equal(trprob(test, "initial state ventilation"), trprob(prob.sir, "0 1")) 269s [1] TRUE 269s > all.equal(trprob(test, "initial state end of story"), trprob(prob.sir, "0 2")) 269s [1] TRUE 269s > 269s > all.equal(trcov(test, "initial state end of story"), trcov(prob.sir, "0 2")) 269s [1] TRUE 269s > 269s > aa <- summary(test) 269s > all.equal(summ.sir[[6]], aa[[6]]) 269s [1] TRUE 269s > all.equal(summ.sir[[4]], aa[[4]]) 269s [1] TRUE 269s > 269s > ### Test on abortion data 269s > 269s > data(abortion) 269s > 269s > from <- rep(0, nrow(abortion)) 269s > to <- abortion$cause 269s > entry <- abortion$entry 269s > exit <- abortion$exit 269s > id <- 1:nrow(abortion) 269s > data <- data.frame(id, from, to, entry, exit, group = abortion$group) 269s > 269s > ## Computation of the CIFs 269s > tra <- matrix(FALSE, 4, 4) 269s > tra[1, 2:4] <- TRUE 269s > 269s > cif.control <- etm(data[data$group == 0, ], c("0", "1", "2", "3"), 269s + tra, NULL, 0) 269s > cif.exposed <- etm(data[data$group == 1, ], c("0", "1", "2", "3"), 269s + tra, NULL, 0) 269s > 269s > all.equal(trprob(cif.control, "0 1"), cif.control$est["0", "1", ]) 269s [1] TRUE 269s > all.equal(trcov(cif.control, c("0 1", "0 2")), cif.control$cov["0 1", "0 2", ]) 269s [1] TRUE 269s > 269s > trprob(cif.control, "0 1") 269s 6 7 8 9 10 11 12 13 269s 0.000000 0.007401 0.014881 0.026509 0.033208 0.037694 0.037694 0.038955 269s 14 17 19 21 24 25 26 30 269s 0.040159 0.040159 0.040159 0.040159 0.040159 0.040159 0.040159 0.040159 269s 31 32 33 34 35 36 37 38 269s 0.040159 0.040159 0.040159 0.040159 0.040159 0.040159 0.040159 0.040159 269s 39 40 41 42 43 269s 0.040159 0.040159 0.040159 0.040159 0.040159 269s > trprob(cif.control, "0 2") 269s 6 7 8 9 10 11 12 13 269s 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 269s 14 17 19 21 24 25 26 30 269s 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.003657 269s 31 32 33 34 35 36 37 38 269s 0.006371 0.008175 0.013543 0.023317 0.031260 0.053197 0.084529 0.179163 269s 39 40 41 42 43 269s 0.322016 0.563121 0.742227 0.793893 0.799059 269s > trprob(cif.control, "0 0") 269s 6 7 8 9 10 11 12 13 269s 0.965812 0.932508 0.887628 0.862433 0.838989 0.822538 0.813099 0.810578 269s 14 17 19 21 24 25 26 30 269s 0.806964 0.805874 0.803810 0.802804 0.801837 0.800883 0.799937 0.796280 269s 31 32 33 34 35 36 37 38 269s 0.793565 0.791762 0.786394 0.776620 0.768677 0.745862 0.714531 0.619897 269s 39 40 41 42 43 269s 0.477043 0.235938 0.056832 0.005167 0.000000 269s > 269s > trcov(cif.control, "0 1") 269s 6 7 8 9 10 11 12 13 269s 0.000e+00 2.719e-05 4.533e-05 6.665e-05 7.698e-05 8.304e-05 8.304e-05 8.444e-05 269s 14 17 19 21 24 25 26 30 269s 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 269s 31 32 33 34 35 36 37 38 269s 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 269s 39 40 41 42 43 269s 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 269s > trcov(cif.control, "0 2") 269s 6 7 8 9 10 11 12 13 269s 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 269s 14 17 19 21 24 25 26 30 269s 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 3.338e-06 269s 31 32 33 34 35 36 37 38 269s 5.784e-06 7.401e-06 1.216e-05 2.072e-05 2.758e-05 4.619e-05 7.202e-05 1.461e-04 269s 39 40 41 42 43 269s 2.470e-04 3.880e-04 4.702e-04 4.903e-04 4.922e-04 269s > trcov(cif.control, "0 0") 269s 6 7 8 9 10 11 12 13 269s 2.822e-04 3.821e-04 4.527e-04 4.748e-04 4.875e-04 4.927e-04 4.941e-04 4.942e-04 269s 14 17 19 21 24 25 26 30 269s 4.941e-04 4.940e-04 4.936e-04 4.933e-04 4.931e-04 4.928e-04 4.926e-04 4.914e-04 269s 31 32 33 34 35 36 37 38 269s 4.905e-04 4.899e-04 4.880e-04 4.846e-04 4.816e-04 4.729e-04 4.601e-04 4.176e-04 269s 39 40 41 42 43 269s 3.425e-04 1.865e-04 4.797e-05 4.441e-06 0.000e+00 269s > 269s > aa <- summary(cif.control) 269s > aa$"0 1" 269s P time var lower upper n.risk n.event 269s 6 0.000000 6 0.000e+00 0.000000 0.00000 117 0 269s 7 0.007401 7 2.719e-05 0.000000 0.01762 261 2 269s 8 0.014881 8 4.533e-05 0.001685 0.02808 374 3 269s 9 0.026509 9 6.665e-05 0.010508 0.04251 458 6 269s 10 0.033208 10 7.698e-05 0.016011 0.05040 515 4 269s 11 0.037694 11 8.304e-05 0.019834 0.05555 561 3 269s 12 0.037694 12 8.304e-05 0.019834 0.05555 610 0 269s 13 0.038955 13 8.444e-05 0.020944 0.05697 645 1 269s 14 0.040159 14 8.571e-05 0.022014 0.05830 673 1 269s 17 0.040159 17 8.571e-05 0.022014 0.05830 740 0 269s 19 0.040159 19 8.571e-05 0.022014 0.05830 781 0 269s 21 0.040159 21 8.571e-05 0.022014 0.05830 799 0 269s 24 0.040159 24 8.571e-05 0.022014 0.05830 830 0 269s 25 0.040159 25 8.571e-05 0.022014 0.05830 841 0 269s 26 0.040159 26 8.571e-05 0.022014 0.05830 846 0 269s 30 0.040159 30 8.571e-05 0.022014 0.05830 875 0 269s 31 0.040159 31 8.571e-05 0.022014 0.05830 880 0 269s 32 0.040159 32 8.571e-05 0.022014 0.05830 880 0 269s 33 0.040159 33 8.571e-05 0.022014 0.05830 885 0 269s 34 0.040159 34 8.571e-05 0.022014 0.05830 885 0 269s 35 0.040159 35 8.571e-05 0.022014 0.05830 880 0 269s 36 0.040159 36 8.571e-05 0.022014 0.05830 876 0 269s 37 0.040159 37 8.571e-05 0.022014 0.05830 857 0 269s 38 0.040159 38 8.571e-05 0.022014 0.05830 823 0 269s 39 0.040159 39 8.571e-05 0.022014 0.05830 716 0 269s 40 0.040159 40 8.571e-05 0.022014 0.05830 554 0 269s 41 0.040159 41 8.571e-05 0.022014 0.05830 274 0 269s 42 0.040159 42 8.571e-05 0.022014 0.05830 66 0 269s 43 0.040159 43 8.571e-05 0.022014 0.05830 6 0 269s > all.equal(aa$"0 1"$P, as.vector(trprob(cif.control, "0 1"))) 269s [1] TRUE 269s > 269s > ### test on los data 269s > 269s > data(los.data) # in package changeLOS 269s > 269s > ## putting los.data in the long format (see changeLOS) 269s > my.observ <- prepare.los.data(x=los.data) 269s > 269s > tra <- matrix(FALSE, 4, 4) 269s > tra[1, 2:4] <- TRUE 269s > tra[2, 3:4] <- TRUE 269s > 269s > tr.prob <- etm(my.observ, c("0","1","2","3"), tra, NULL, 0) 269s > 269s > tr.prob 269s Multistate model with 2 transient state(s) 269s and 2 absorbing state(s) 269s 269s Possible transitions: 269s from to 269s 0 1 269s 0 2 269s 0 3 269s 1 2 269s 1 3 269s 269s Estimate of P(0, 82) 269s 0 1 2 3 269s 0 0 0 0.7474 0.2526 269s 1 0 0 0.7073 0.2927 269s 2 0 0 1.0000 0.0000 269s 3 0 0 0.0000 1.0000 269s 269s > summary(tr.prob) 269s Transition 0 0 269s P time var lower upper n.risk n.event 269s 0.882275 3 1.374e-04 0.8593018 0.905248 756 0 269s 0.112434 15 1.320e-04 0.0899155 0.134952 90 0 269s 0.031746 27 4.066e-05 0.0192484 0.044244 26 0 269s 0.006614 41 8.690e-06 0.0008359 0.012392 5 0 269s 0.002646 61 3.490e-06 0.0000000 0.006307 3 0 269s 0.000000 82 0.000e+00 0.0000000 0.000000 1 0 269s 269s Transition 0 1 269s P time var lower upper n.risk n.event 269s 0.017196 3 2.235e-05 0.0079289 0.02646 756 13 269s 0.063492 15 7.865e-05 0.0461099 0.08087 90 0 269s 0.030423 27 3.902e-05 0.0181805 0.04267 26 1 269s 0.015873 41 2.066e-05 0.0069637 0.02478 5 0 269s 0.005291 61 6.962e-06 0.0001197 0.01046 3 0 269s 0.000000 82 0.000e+00 0.0000000 0.00000 1 0 269s 269s Transition 0 2 269s P time var lower upper n.risk n.event 269s 0.08466 3 0.0001025 0.06481 0.1045 756 64 269s 0.62302 15 0.0003107 0.58847 0.6576 90 4 269s 0.69841 27 0.0002786 0.66570 0.7311 26 1 269s 0.72751 41 0.0002622 0.69578 0.7593 5 0 269s 0.74074 61 0.0002540 0.70950 0.7720 3 1 269s 0.74735 82 0.0002498 0.71638 0.7783 1 1 269s 269s Transition 0 3 269s P time var lower upper n.risk n.event 269s 0.01587 3 2.066e-05 0.006964 0.02478 756 12 269s 0.20106 15 2.125e-04 0.172489 0.22963 90 1 269s 0.23942 27 2.409e-04 0.208999 0.26984 26 0 269s 0.25000 41 2.480e-04 0.219133 0.28087 5 0 269s 0.25132 61 2.489e-04 0.220402 0.28224 3 0 269s 0.25265 82 2.498e-04 0.221671 0.28362 1 0 269s 269s Transition 1 1 269s P time var lower upper n.risk n.event 269s 1.00000 3 0.000e+00 1.00000 1.00000 0 0 269s 0.38661 15 2.358e-03 0.29143 0.48179 51 0 269s 0.12119 27 7.842e-04 0.06630 0.17607 23 0 269s 0.04593 41 2.405e-04 0.01554 0.07633 14 0 269s 0.01531 61 6.579e-05 0.00000 0.03121 4 0 269s 0.00000 82 0.000e+00 0.00000 0.00000 0 0 269s 269s Transition 1 2 269s P time var lower upper n.risk n.event 269s 0.0000 3 0.000000 0.0000 0.0000 0 0 269s 0.4107 15 0.002590 0.3110 0.5104 51 2 269s 0.6082 27 0.002254 0.5151 0.7012 23 1 269s 0.6652 41 0.002064 0.5761 0.7542 14 2 269s 0.6920 61 0.002000 0.6043 0.7796 4 0 269s 0.7073 82 0.001984 0.6200 0.7946 0 0 269s 269s Transition 1 3 269s P time var lower upper n.risk n.event 269s 0.0000 3 0.000000 0.0000 0.0000 0 0 269s 0.2027 15 0.001784 0.1199 0.2855 51 1 269s 0.2706 27 0.001968 0.1837 0.3576 23 0 269s 0.2889 41 0.001982 0.2016 0.3761 14 0 269s 0.2927 61 0.001984 0.2054 0.3800 4 0 269s 0.2927 82 0.001984 0.2054 0.3800 0 0 269s 269s > 269s > cLOS <- etm::clos(tr.prob, aw = TRUE) 269s > 269s > cLOS 269s The expected change in length of stay is: 269s 1.975 269s 269s Alternative weighting: 269s 269s Expected change in LOS with weight.1: 2.097 269s Expected change in LOS with weight.other: 1.951 269s > 269s > 269s > ### Tests on pseudo values 269s > t_pseudo <- closPseudo(my.observ, c("0","1","2","3"), tra, NULL, 269s + formula = ~ 1, aw = TRUE) 283s > 283s > cLOS$e.phi == t_pseudo$theta[, "e.phi"] 283s [,1] 283s [1,] TRUE 283s > cLOS$e.phi.weights.1 == t_pseudo$theta[, "e.phi.weights.1"] 283s [,1] 283s [1,] TRUE 283s > cLOS$e.phi.weights.other == t_pseudo$theta[, "e.phi.weights.other"] 283s [,1] 283s [1,] TRUE 283s > 283s > mean(t_pseudo$pseudoData$ps.e.phi) 283s [1] 1.968 283s > 283s > ### tests on etmprep 283s > 283s > ### creation of fake data in the wild format, following an illness-death model 283s > ## transition times 283s > tdisease <- c(3, 4, 3, 6, 8, 9) 283s > tdeath <- c(6, 9, 8, 6, 8, 9) 283s > 283s > ## transition status 283s > stat.disease <- c(1, 1, 1, 0, 0, 0) 283s > stat.death <- c(1, 1, 1, 1, 1, 0) 283s > 283s > ## a covariate that we want to keep in the new data 283s > set.seed(1313) 283s > cova <- rbinom(6, 1, 0.5) 283s > 283s > dat <- data.frame(tdisease, tdeath, 283s + stat.disease, stat.death, 283s + cova) 283s > 283s > ## Possible transitions 283s > tra <- matrix(FALSE, 3, 3) 283s > tra[1, 2:3] <- TRUE 283s > tra[2, 3] <- TRUE 283s > 283s > ## data preparation 283s > newdat <- etmprep(c(NA, "tdisease", "tdeath"), 283s + c(NA, "stat.disease", "stat.death"), 283s + data = dat, tra = tra, 283s + cens.name = "cens", keep = "cova") 283s > 283s > newdat 283s id entry exit from to cova 283s 1 1 0 3 0 1 1 283s 2 1 3 6 1 2 1 283s 3 2 0 4 0 1 0 283s 4 2 4 9 1 2 0 283s 5 3 0 3 0 1 1 283s 6 3 3 8 1 2 1 283s 7 4 0 6 0 2 0 283s 8 5 0 8 0 2 1 283s 9 6 0 9 0 cens 1 283s > 283s > ref <- data.frame(id = c(1, 1, 2, 2, 3, 3, 4, 5, 6), 283s + entry = c(0, 3, 0, 4, 0, 3, 0, 0, 0), 283s + exit = c(3, 6, 4, 9, 3, 8, 6, 8, 9), 283s + from = c(0, 1, 0, 1, 0, 1, 0, 0, 0), 283s + to = c(rep(c(1, 2), 3), 2, 2, "cens"), 283s + cova = c(1, 1, 0, 0, 1, 1, 0, 1, 1)) 283s > ref$from <- factor(as.character(ref$from), levels = c("0", "1", "2", "cens")) 283s > ref$to <- factor(as.character(ref$to), levels = c("0", "1", "2", "cens")) 283s > 283s > all.equal(ref, newdat) 283s [1] TRUE 283s > 283s > 283s > ###################################### 283s > ### Test the stratified calls 283s > ###################################### 283s > 283s > if (require("kmi", quietly = TRUE)) { 283s + library(etm) 283s + 283s + data(icu.pneu) 283s + my.icu.pneu <- icu.pneu 283s + 283s + my.icu.pneu <- my.icu.pneu[order(my.icu.pneu$id, my.icu.pneu$start), ] 283s + masque <- diff(my.icu.pneu$id) 283s + 283s + my.icu.pneu$from <- 0 283s + my.icu.pneu$from[c(1, masque) == 0] <- 1 283s + 283s + my.icu.pneu$to2 <- my.icu.pneu$event 283s + my.icu.pneu$to2[my.icu.pneu$status == 0] <- "cens" 283s + my.icu.pneu$to2[c(masque, 1) == 0] <- 1 283s + 283s + 283s + my.icu.pneu$to <- ifelse(my.icu.pneu$to2 %in% c(2, 3), 2, 283s + my.icu.pneu$to2) 283s + 283s + my.icu.pneu <- my.icu.pneu[, c("id", "start", "stop", "from", "to", 283s + "to2", "age", "sex")] 283s + names(my.icu.pneu)[c(2, 3)] <- c("entry", "exit") 283s + 283s + bouh_strat <- etm(my.icu.pneu, c("0", "1", "2"), tra_ill(), "cens", 0, strata = "sex") 283s + 283s + bouh_female <- etm(my.icu.pneu[my.icu.pneu$sex == "F", ], 283s + c("0", "1", "2"), tra_ill(), "cens", 0) 283s + 283s + all(bouh_strat[[1]]$est == bouh_female$est) 283s + 283s + ## Test the summary 283s + the_summary <- summary(bouh_strat) 283s + the_summary 283s + 283s + ## Test trprob 283s + all(trprob(bouh_strat, "0 1")[[1]] == trprob(bouh_female, "0 1")) 283s + all(trprob(bouh_strat, "0 1", c(0, 5, 10, 15))[[1]] == trprob(bouh_female, "0 1", c(0, 5, 10, 15))) 283s + 283s + ## Test trcov 283s + all(trcov(bouh_strat, "0 1")[[1]] == trcov(bouh_female, "0 1")) 283s + all(trcov(bouh_strat, c("0 1", "0 2"))[[1]] == trcov(bouh_female, c("0 1", "0 2"))) 283s + all(trcov(bouh_strat, "0 1", c(0, 5, 10, 15))[[1]] == trcov(bouh_female, "0 1", c(0, 5, 10, 15))) 283s + } else { 283s + print("These tests require the kmi package") 283s + } 283s [1] TRUE 283s > 283s > options(old) 283s > 284s autopkgtest [22:45:35]: test run-unit-test: -----------------------] 284s run-unit-test PASS 284s autopkgtest [22:45:35]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 284s autopkgtest [22:45:35]: test pkg-r-autopkgtest: preparing testbed 284s Reading package lists... 285s Building dependency tree... 285s Reading state information... 285s Solving dependencies... 285s The following NEW packages will be installed: 285s build-essential cpp cpp-15 cpp-15-powerpc64le-linux-gnu 285s cpp-powerpc64le-linux-gnu dctrl-tools g++ g++-15 285s g++-15-powerpc64le-linux-gnu g++-powerpc64le-linux-gnu gcc gcc-15 285s gcc-15-powerpc64le-linux-gnu gcc-powerpc64le-linux-gnu gfortran gfortran-15 285s gfortran-15-powerpc64le-linux-gnu gfortran-powerpc64le-linux-gnu 285s icu-devtools libasan8 libblas-dev libbz2-dev libc-dev-bin libc6-dev libcc1-0 285s libcrypt-dev libdeflate-dev libgcc-15-dev libgfortran-15-dev libicu-dev 285s libisl23 libitm1 libjpeg-dev libjpeg-turbo8-dev libjpeg8-dev liblapack-dev 285s liblsan0 liblzma-dev libmpc3 libncurses-dev libpcre2-16-0 libpcre2-32-0 285s libpcre2-dev libpcre2-posix3 libpkgconf3 libpng-dev libquadmath0 285s libreadline-dev libstdc++-15-dev libtirpc-dev libtsan2 libubsan1 libzstd-dev 285s linux-libc-dev pkg-r-autopkgtest pkgconf pkgconf-bin r-base-dev 285s r-cran-backports r-cran-broom r-cran-cli r-cran-cpp11 r-cran-dplyr 285s r-cran-fansi r-cran-farver r-cran-geepack r-cran-generics r-cran-ggplot2 285s r-cran-glue r-cran-gtable r-cran-isoband r-cran-labeling r-cran-lifecycle 285s r-cran-magrittr r-cran-mass r-cran-mgcv r-cran-nlme r-cran-pillar 285s r-cran-pkgconfig r-cran-purrr r-cran-r6 r-cran-rcolorbrewer r-cran-rlang 285s r-cran-scales r-cran-stringi r-cran-stringr r-cran-tibble r-cran-tidyr 285s r-cran-tidyselect r-cran-utf8 r-cran-vctrs r-cran-viridislite r-cran-withr 285s rpcsvc-proto zlib1g-dev 285s 0 upgraded, 95 newly installed, 0 to remove and 0 not upgraded. 285s Need to get 134 MB of archives. 285s After this operation, 439 MB of additional disk space will be used. 285s Get:1 http://ftpmaster.internal/ubuntu resolute/main ppc64el libc-dev-bin ppc64el 2.42-2ubuntu4 [23.9 kB] 285s Get:2 http://ftpmaster.internal/ubuntu resolute/main ppc64el linux-libc-dev ppc64el 6.19.0-3.3 [1832 kB] 288s Get:3 http://ftpmaster.internal/ubuntu resolute/main ppc64el libcrypt-dev ppc64el 1:4.5.1-1 [162 kB] 288s Get:4 http://ftpmaster.internal/ubuntu resolute/main ppc64el rpcsvc-proto ppc64el 1.4.3-1build1 [84.2 kB] 288s Get:5 http://ftpmaster.internal/ubuntu resolute/main ppc64el libc6-dev ppc64el 2.42-2ubuntu4 [2080 kB] 291s Get:6 http://ftpmaster.internal/ubuntu resolute/main ppc64el libisl23 ppc64el 0.27-1build1 [893 kB] 293s Get:7 http://ftpmaster.internal/ubuntu resolute/main ppc64el libmpc3 ppc64el 1.3.1-2 [62.5 kB] 293s Get:8 http://ftpmaster.internal/ubuntu resolute/main ppc64el cpp-15-powerpc64le-linux-gnu ppc64el 15.2.0-12ubuntu1 [11.4 MB] 310s Get:9 http://ftpmaster.internal/ubuntu resolute/main ppc64el cpp-15 ppc64el 15.2.0-12ubuntu1 [1038 B] 310s Get:10 http://ftpmaster.internal/ubuntu resolute/main ppc64el cpp-powerpc64le-linux-gnu ppc64el 4:15.2.0-4ubuntu1 [5746 B] 310s Get:11 http://ftpmaster.internal/ubuntu resolute/main ppc64el cpp ppc64el 4:15.2.0-4ubuntu1 [22.4 kB] 310s Get:12 http://ftpmaster.internal/ubuntu resolute/main ppc64el libcc1-0 ppc64el 15.2.0-12ubuntu1 [49.0 kB] 310s Get:13 http://ftpmaster.internal/ubuntu resolute/main ppc64el libitm1 ppc64el 15.2.0-12ubuntu1 [32.2 kB] 310s Get:14 http://ftpmaster.internal/ubuntu resolute/main ppc64el libasan8 ppc64el 15.2.0-12ubuntu1 [3006 kB] 315s Get:15 http://ftpmaster.internal/ubuntu resolute/main ppc64el liblsan0 ppc64el 15.2.0-12ubuntu1 [1374 kB] 317s Get:16 http://ftpmaster.internal/ubuntu resolute/main ppc64el libtsan2 ppc64el 15.2.0-12ubuntu1 [2729 kB] 322s Get:17 http://ftpmaster.internal/ubuntu resolute/main ppc64el libubsan1 ppc64el 15.2.0-12ubuntu1 [1231 kB] 324s Get:18 http://ftpmaster.internal/ubuntu resolute/main ppc64el libquadmath0 ppc64el 15.2.0-12ubuntu1 [160 kB] 324s Get:19 http://ftpmaster.internal/ubuntu resolute/main ppc64el libgcc-15-dev ppc64el 15.2.0-12ubuntu1 [1670 kB] 327s Get:20 http://ftpmaster.internal/ubuntu resolute/main ppc64el gcc-15-powerpc64le-linux-gnu ppc64el 15.2.0-12ubuntu1 [22.4 MB] 361s Get:21 http://ftpmaster.internal/ubuntu resolute/main ppc64el gcc-15 ppc64el 15.2.0-12ubuntu1 [530 kB] 362s Get:22 http://ftpmaster.internal/ubuntu resolute/main ppc64el gcc-powerpc64le-linux-gnu ppc64el 4:15.2.0-4ubuntu1 [1220 B] 362s Get:23 http://ftpmaster.internal/ubuntu resolute/main ppc64el gcc ppc64el 4:15.2.0-4ubuntu1 [5032 B] 362s Get:24 http://ftpmaster.internal/ubuntu resolute/main ppc64el libstdc++-15-dev ppc64el 15.2.0-12ubuntu1 [2747 kB] 366s Get:25 http://ftpmaster.internal/ubuntu resolute/main ppc64el g++-15-powerpc64le-linux-gnu ppc64el 15.2.0-12ubuntu1 [13.0 MB] 389s Get:26 http://ftpmaster.internal/ubuntu resolute/main ppc64el g++-15 ppc64el 15.2.0-12ubuntu1 [25.3 kB] 389s Get:27 http://ftpmaster.internal/ubuntu resolute/main ppc64el g++-powerpc64le-linux-gnu ppc64el 4:15.2.0-4ubuntu1 [970 B] 389s Get:28 http://ftpmaster.internal/ubuntu resolute/main ppc64el g++ ppc64el 4:15.2.0-4ubuntu1 [1092 B] 389s Get:29 http://ftpmaster.internal/ubuntu resolute/main ppc64el build-essential ppc64el 12.12ubuntu2 [5256 B] 389s Get:30 http://ftpmaster.internal/ubuntu resolute/main ppc64el dctrl-tools ppc64el 2.24-3build4 [108 kB] 389s Get:31 http://ftpmaster.internal/ubuntu resolute/main ppc64el libgfortran-15-dev ppc64el 15.2.0-12ubuntu1 [651 kB] 390s Get:32 http://ftpmaster.internal/ubuntu resolute/main ppc64el gfortran-15-powerpc64le-linux-gnu ppc64el 15.2.0-12ubuntu1 [12.3 MB] 413s Get:33 http://ftpmaster.internal/ubuntu resolute/main ppc64el gfortran-15 ppc64el 15.2.0-12ubuntu1 [18.1 kB] 413s Get:34 http://ftpmaster.internal/ubuntu resolute/main ppc64el gfortran-powerpc64le-linux-gnu ppc64el 4:15.2.0-4ubuntu1 [1020 B] 413s Get:35 http://ftpmaster.internal/ubuntu resolute/main ppc64el gfortran ppc64el 4:15.2.0-4ubuntu1 [1166 B] 413s Get:36 http://ftpmaster.internal/ubuntu resolute/main ppc64el icu-devtools ppc64el 78.2-1ubuntu1 [246 kB] 413s Get:37 http://ftpmaster.internal/ubuntu resolute/main ppc64el libblas-dev ppc64el 3.12.1-7ubuntu1 [306 kB] 413s Get:38 http://ftpmaster.internal/ubuntu resolute/main ppc64el libbz2-dev ppc64el 1.0.8-6build2 [50.0 kB] 413s Get:39 http://ftpmaster.internal/ubuntu resolute/main ppc64el libdeflate-dev ppc64el 1.23-2build1 [71.8 kB] 413s Get:40 http://ftpmaster.internal/ubuntu resolute/main ppc64el libicu-dev ppc64el 78.2-1ubuntu1 [13.3 MB] 436s Get:41 http://ftpmaster.internal/ubuntu resolute/main ppc64el libjpeg-turbo8-dev ppc64el 2.1.5-4ubuntu3 [358 kB] 436s Get:42 http://ftpmaster.internal/ubuntu resolute/main ppc64el libjpeg8-dev ppc64el 8c-2ubuntu11 [1484 B] 436s Get:43 http://ftpmaster.internal/ubuntu resolute/main ppc64el libjpeg-dev ppc64el 8c-2ubuntu11 [1486 B] 436s Get:44 http://ftpmaster.internal/ubuntu resolute/main ppc64el liblapack-dev ppc64el 3.12.1-7ubuntu1 [6357 kB] 446s Get:45 http://ftpmaster.internal/ubuntu resolute/main ppc64el libncurses-dev ppc64el 6.6+20251231-1 [505 kB] 446s Get:46 http://ftpmaster.internal/ubuntu resolute/main ppc64el libpcre2-16-0 ppc64el 10.46-1 [292 kB] 446s Get:47 http://ftpmaster.internal/ubuntu resolute/main ppc64el libpcre2-32-0 ppc64el 10.46-1 [275 kB] 446s Get:48 http://ftpmaster.internal/ubuntu resolute/main ppc64el libpcre2-posix3 ppc64el 10.46-1 [7334 B] 446s Get:49 http://ftpmaster.internal/ubuntu resolute/main ppc64el libpcre2-dev ppc64el 10.46-1 [937 kB] 448s Get:50 http://ftpmaster.internal/ubuntu resolute/main ppc64el libpkgconf3 ppc64el 1.8.1-4build1 [37.9 kB] 448s Get:51 http://ftpmaster.internal/ubuntu resolute/main ppc64el zlib1g-dev ppc64el 1:1.3.dfsg+really1.3.1-1ubuntu2 [903 kB] 449s Get:52 http://ftpmaster.internal/ubuntu resolute/main ppc64el libpng-dev ppc64el 1.6.54-1 [326 kB] 449s Get:53 http://ftpmaster.internal/ubuntu resolute/main ppc64el libreadline-dev ppc64el 8.3-3 [252 kB] 449s Get:54 http://ftpmaster.internal/ubuntu resolute/main ppc64el libzstd-dev ppc64el 1.5.7+dfsg-3 [528 kB] 450s Get:55 http://ftpmaster.internal/ubuntu resolute/main ppc64el liblzma-dev ppc64el 5.8.2-2 [210 kB] 450s Get:56 http://ftpmaster.internal/ubuntu resolute/main ppc64el pkgconf-bin ppc64el 1.8.1-4build1 [22.7 kB] 450s Get:57 http://ftpmaster.internal/ubuntu resolute/main ppc64el pkgconf ppc64el 1.8.1-4build1 [16.8 kB] 450s Get:58 http://ftpmaster.internal/ubuntu resolute/main ppc64el libtirpc-dev ppc64el 1.3.6+ds-1 [223 kB] 450s Get:59 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-base-dev all 4.5.2-1ubuntu2 [1880 B] 450s Get:60 http://ftpmaster.internal/ubuntu resolute/universe ppc64el pkg-r-autopkgtest all 20250812 [6158 B] 450s Get:61 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-backports ppc64el 1.5.0-2 [122 kB] 450s Get:62 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-cli ppc64el 3.6.4-1 [1411 kB] 453s Get:63 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-generics all 0.1.4-1 [84.0 kB] 453s Get:64 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-glue ppc64el 1.8.0-1 [165 kB] 453s Get:65 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-rlang ppc64el 1.1.5-3 [1738 kB] 456s Get:66 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-lifecycle all 1.0.5+dfsg-1 [120 kB] 456s Get:67 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-magrittr ppc64el 2.0.3-1 [154 kB] 456s Get:68 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-utf8 ppc64el 1.2.4-1 [148 kB] 456s Get:69 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-vctrs ppc64el 0.6.5-1 [1399 kB] 458s Get:70 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-pillar all 1.11.1+dfsg-1 [456 kB] 458s Get:71 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-r6 all 2.6.1-1 [101 kB] 458s Get:72 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-fansi ppc64el 1.0.6-2 [637 kB] 459s Get:73 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-pkgconfig all 2.0.3-2build2 [20.4 kB] 459s Get:74 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-tibble ppc64el 3.2.1+dfsg-3 [420 kB] 459s Get:75 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-withr all 3.0.2+dfsg-1 [214 kB] 459s Get:76 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-tidyselect ppc64el 1.2.1+dfsg-1 [222 kB] 459s Get:77 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-dplyr ppc64el 1.1.4-4 [1542 kB] 462s Get:78 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-purrr ppc64el 1.0.4-1 [555 kB] 462s Get:79 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-stringi ppc64el 1.8.4-1build2 [947 kB] 464s Get:80 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-stringr all 1.5.1-1 [290 kB] 464s Get:81 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-cpp11 all 0.5.3-1 [242 kB] 464s Get:82 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-tidyr ppc64el 1.3.1-1 [1163 kB] 466s Get:83 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-broom all 1.0.12+dfsg-1 [1708 kB] 469s Get:84 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-farver ppc64el 2.1.2-1 [1389 kB] 471s Get:85 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-mass ppc64el 7.3-65-1 [1116 kB] 474s Get:86 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-geepack ppc64el 1.3.12-1 [413 kB] 474s Get:87 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-gtable all 0.3.6+dfsg-1 [199 kB] 474s Get:88 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-isoband ppc64el 0.2.7-1 [1486 kB] 478s Get:89 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-nlme ppc64el 3.1.168-1 [2327 kB] 488s Get:90 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-mgcv ppc64el 1.9-4-1 [3694 kB] 490s Get:91 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-labeling all 0.4.3-1 [62.1 kB] 490s Get:92 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-rcolorbrewer all 1.1-3-1build2 [54.0 kB] 490s Get:93 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-viridislite all 0.4.3-1 [1088 kB] 492s Get:94 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-scales all 1.4.0-1 [725 kB] 493s Get:95 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-ggplot2 all 3.5.1+dfsg-1 [3940 kB] 500s Fetched 134 MB in 3min 35s (623 kB/s) 500s Selecting previously unselected package libc-dev-bin. 500s (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 ... 127202 files and directories currently installed.) 500s Preparing to unpack .../00-libc-dev-bin_2.42-2ubuntu4_ppc64el.deb ... 500s Unpacking libc-dev-bin (2.42-2ubuntu4) ... 500s Selecting previously unselected package linux-libc-dev:ppc64el. 500s Preparing to unpack .../01-linux-libc-dev_6.19.0-3.3_ppc64el.deb ... 500s Unpacking linux-libc-dev:ppc64el (6.19.0-3.3) ... 501s Selecting previously unselected package libcrypt-dev:ppc64el. 501s Preparing to unpack .../02-libcrypt-dev_1%3a4.5.1-1_ppc64el.deb ... 501s Unpacking libcrypt-dev:ppc64el (1:4.5.1-1) ... 501s Selecting previously unselected package rpcsvc-proto. 501s Preparing to unpack .../03-rpcsvc-proto_1.4.3-1build1_ppc64el.deb ... 501s Unpacking rpcsvc-proto (1.4.3-1build1) ... 501s Selecting previously unselected package libc6-dev:ppc64el. 501s Preparing to unpack .../04-libc6-dev_2.42-2ubuntu4_ppc64el.deb ... 501s Unpacking libc6-dev:ppc64el (2.42-2ubuntu4) ... 501s Selecting previously unselected package libisl23:ppc64el. 501s Preparing to unpack .../05-libisl23_0.27-1build1_ppc64el.deb ... 501s Unpacking libisl23:ppc64el (0.27-1build1) ... 501s Selecting previously unselected package libmpc3:ppc64el. 501s Preparing to unpack .../06-libmpc3_1.3.1-2_ppc64el.deb ... 501s Unpacking libmpc3:ppc64el (1.3.1-2) ... 501s Selecting previously unselected package cpp-15-powerpc64le-linux-gnu. 501s Preparing to unpack .../07-cpp-15-powerpc64le-linux-gnu_15.2.0-12ubuntu1_ppc64el.deb ... 501s Unpacking cpp-15-powerpc64le-linux-gnu (15.2.0-12ubuntu1) ... 501s Selecting previously unselected package cpp-15. 501s Preparing to unpack .../08-cpp-15_15.2.0-12ubuntu1_ppc64el.deb ... 501s Unpacking cpp-15 (15.2.0-12ubuntu1) ... 501s Selecting previously unselected package cpp-powerpc64le-linux-gnu. 501s Preparing to unpack .../09-cpp-powerpc64le-linux-gnu_4%3a15.2.0-4ubuntu1_ppc64el.deb ... 501s Unpacking cpp-powerpc64le-linux-gnu (4:15.2.0-4ubuntu1) ... 501s Selecting previously unselected package cpp. 501s Preparing to unpack .../10-cpp_4%3a15.2.0-4ubuntu1_ppc64el.deb ... 501s Unpacking cpp (4:15.2.0-4ubuntu1) ... 501s Selecting previously unselected package libcc1-0:ppc64el. 501s Preparing to unpack .../11-libcc1-0_15.2.0-12ubuntu1_ppc64el.deb ... 501s Unpacking libcc1-0:ppc64el (15.2.0-12ubuntu1) ... 501s Selecting previously unselected package libitm1:ppc64el. 501s Preparing to unpack .../12-libitm1_15.2.0-12ubuntu1_ppc64el.deb ... 501s Unpacking libitm1:ppc64el (15.2.0-12ubuntu1) ... 501s Selecting previously unselected package libasan8:ppc64el. 501s Preparing to unpack .../13-libasan8_15.2.0-12ubuntu1_ppc64el.deb ... 501s Unpacking libasan8:ppc64el (15.2.0-12ubuntu1) ... 501s Selecting previously unselected package liblsan0:ppc64el. 501s Preparing to unpack .../14-liblsan0_15.2.0-12ubuntu1_ppc64el.deb ... 501s Unpacking liblsan0:ppc64el (15.2.0-12ubuntu1) ... 501s Selecting previously unselected package libtsan2:ppc64el. 501s Preparing to unpack .../15-libtsan2_15.2.0-12ubuntu1_ppc64el.deb ... 501s Unpacking libtsan2:ppc64el (15.2.0-12ubuntu1) ... 501s Selecting previously unselected package libubsan1:ppc64el. 501s Preparing to unpack .../16-libubsan1_15.2.0-12ubuntu1_ppc64el.deb ... 501s Unpacking libubsan1:ppc64el (15.2.0-12ubuntu1) ... 501s Selecting previously unselected package libquadmath0:ppc64el. 501s Preparing to unpack .../17-libquadmath0_15.2.0-12ubuntu1_ppc64el.deb ... 501s Unpacking libquadmath0:ppc64el (15.2.0-12ubuntu1) ... 501s Selecting previously unselected package libgcc-15-dev:ppc64el. 501s Preparing to unpack .../18-libgcc-15-dev_15.2.0-12ubuntu1_ppc64el.deb ... 501s Unpacking libgcc-15-dev:ppc64el (15.2.0-12ubuntu1) ... 501s Selecting previously unselected package gcc-15-powerpc64le-linux-gnu. 501s Preparing to unpack .../19-gcc-15-powerpc64le-linux-gnu_15.2.0-12ubuntu1_ppc64el.deb ... 501s Unpacking gcc-15-powerpc64le-linux-gnu (15.2.0-12ubuntu1) ... 502s Selecting previously unselected package gcc-15. 502s Preparing to unpack .../20-gcc-15_15.2.0-12ubuntu1_ppc64el.deb ... 502s Unpacking gcc-15 (15.2.0-12ubuntu1) ... 502s Selecting previously unselected package gcc-powerpc64le-linux-gnu. 502s Preparing to unpack .../21-gcc-powerpc64le-linux-gnu_4%3a15.2.0-4ubuntu1_ppc64el.deb ... 502s Unpacking gcc-powerpc64le-linux-gnu (4:15.2.0-4ubuntu1) ... 502s Selecting previously unselected package gcc. 502s Preparing to unpack .../22-gcc_4%3a15.2.0-4ubuntu1_ppc64el.deb ... 502s Unpacking gcc (4:15.2.0-4ubuntu1) ... 502s Selecting previously unselected package libstdc++-15-dev:ppc64el. 502s Preparing to unpack .../23-libstdc++-15-dev_15.2.0-12ubuntu1_ppc64el.deb ... 502s Unpacking libstdc++-15-dev:ppc64el (15.2.0-12ubuntu1) ... 502s Selecting previously unselected package g++-15-powerpc64le-linux-gnu. 502s Preparing to unpack .../24-g++-15-powerpc64le-linux-gnu_15.2.0-12ubuntu1_ppc64el.deb ... 502s Unpacking g++-15-powerpc64le-linux-gnu (15.2.0-12ubuntu1) ... 502s Selecting previously unselected package g++-15. 502s Preparing to unpack .../25-g++-15_15.2.0-12ubuntu1_ppc64el.deb ... 502s Unpacking g++-15 (15.2.0-12ubuntu1) ... 502s Selecting previously unselected package g++-powerpc64le-linux-gnu. 502s Preparing to unpack .../26-g++-powerpc64le-linux-gnu_4%3a15.2.0-4ubuntu1_ppc64el.deb ... 502s Unpacking g++-powerpc64le-linux-gnu (4:15.2.0-4ubuntu1) ... 502s Selecting previously unselected package g++. 502s Preparing to unpack .../27-g++_4%3a15.2.0-4ubuntu1_ppc64el.deb ... 502s Unpacking g++ (4:15.2.0-4ubuntu1) ... 502s Selecting previously unselected package build-essential. 502s Preparing to unpack .../28-build-essential_12.12ubuntu2_ppc64el.deb ... 502s Unpacking build-essential (12.12ubuntu2) ... 502s Selecting previously unselected package dctrl-tools. 502s Preparing to unpack .../29-dctrl-tools_2.24-3build4_ppc64el.deb ... 502s Unpacking dctrl-tools (2.24-3build4) ... 502s Selecting previously unselected package libgfortran-15-dev:ppc64el. 502s Preparing to unpack .../30-libgfortran-15-dev_15.2.0-12ubuntu1_ppc64el.deb ... 502s Unpacking libgfortran-15-dev:ppc64el (15.2.0-12ubuntu1) ... 502s Selecting previously unselected package gfortran-15-powerpc64le-linux-gnu. 502s Preparing to unpack .../31-gfortran-15-powerpc64le-linux-gnu_15.2.0-12ubuntu1_ppc64el.deb ... 502s Unpacking gfortran-15-powerpc64le-linux-gnu (15.2.0-12ubuntu1) ... 502s Selecting previously unselected package gfortran-15. 502s Preparing to unpack .../32-gfortran-15_15.2.0-12ubuntu1_ppc64el.deb ... 502s Unpacking gfortran-15 (15.2.0-12ubuntu1) ... 502s Selecting previously unselected package gfortran-powerpc64le-linux-gnu. 502s Preparing to unpack .../33-gfortran-powerpc64le-linux-gnu_4%3a15.2.0-4ubuntu1_ppc64el.deb ... 502s Unpacking gfortran-powerpc64le-linux-gnu (4:15.2.0-4ubuntu1) ... 502s Selecting previously unselected package gfortran. 502s Preparing to unpack .../34-gfortran_4%3a15.2.0-4ubuntu1_ppc64el.deb ... 502s Unpacking gfortran (4:15.2.0-4ubuntu1) ... 502s Selecting previously unselected package icu-devtools. 502s Preparing to unpack .../35-icu-devtools_78.2-1ubuntu1_ppc64el.deb ... 502s Unpacking icu-devtools (78.2-1ubuntu1) ... 502s Selecting previously unselected package libblas-dev:ppc64el. 502s Preparing to unpack .../36-libblas-dev_3.12.1-7ubuntu1_ppc64el.deb ... 502s Unpacking libblas-dev:ppc64el (3.12.1-7ubuntu1) ... 502s Selecting previously unselected package libbz2-dev:ppc64el. 502s Preparing to unpack .../37-libbz2-dev_1.0.8-6build2_ppc64el.deb ... 502s Unpacking libbz2-dev:ppc64el (1.0.8-6build2) ... 502s Selecting previously unselected package libdeflate-dev:ppc64el. 502s Preparing to unpack .../38-libdeflate-dev_1.23-2build1_ppc64el.deb ... 502s Unpacking libdeflate-dev:ppc64el (1.23-2build1) ... 502s Selecting previously unselected package libicu-dev:ppc64el. 502s Preparing to unpack .../39-libicu-dev_78.2-1ubuntu1_ppc64el.deb ... 502s Unpacking libicu-dev:ppc64el (78.2-1ubuntu1) ... 503s Selecting previously unselected package libjpeg-turbo8-dev:ppc64el. 503s Preparing to unpack .../40-libjpeg-turbo8-dev_2.1.5-4ubuntu3_ppc64el.deb ... 503s Unpacking libjpeg-turbo8-dev:ppc64el (2.1.5-4ubuntu3) ... 503s Selecting previously unselected package libjpeg8-dev:ppc64el. 503s Preparing to unpack .../41-libjpeg8-dev_8c-2ubuntu11_ppc64el.deb ... 503s Unpacking libjpeg8-dev:ppc64el (8c-2ubuntu11) ... 503s Selecting previously unselected package libjpeg-dev:ppc64el. 503s Preparing to unpack .../42-libjpeg-dev_8c-2ubuntu11_ppc64el.deb ... 503s Unpacking libjpeg-dev:ppc64el (8c-2ubuntu11) ... 503s Selecting previously unselected package liblapack-dev:ppc64el. 503s Preparing to unpack .../43-liblapack-dev_3.12.1-7ubuntu1_ppc64el.deb ... 503s Unpacking liblapack-dev:ppc64el (3.12.1-7ubuntu1) ... 503s Selecting previously unselected package libncurses-dev:ppc64el. 503s Preparing to unpack .../44-libncurses-dev_6.6+20251231-1_ppc64el.deb ... 503s Unpacking libncurses-dev:ppc64el (6.6+20251231-1) ... 503s Selecting previously unselected package libpcre2-16-0:ppc64el. 503s Preparing to unpack .../45-libpcre2-16-0_10.46-1_ppc64el.deb ... 503s Unpacking libpcre2-16-0:ppc64el (10.46-1) ... 503s Selecting previously unselected package libpcre2-32-0:ppc64el. 503s Preparing to unpack .../46-libpcre2-32-0_10.46-1_ppc64el.deb ... 503s Unpacking libpcre2-32-0:ppc64el (10.46-1) ... 503s Selecting previously unselected package libpcre2-posix3:ppc64el. 503s Preparing to unpack .../47-libpcre2-posix3_10.46-1_ppc64el.deb ... 503s Unpacking libpcre2-posix3:ppc64el (10.46-1) ... 503s Selecting previously unselected package libpcre2-dev:ppc64el. 503s Preparing to unpack .../48-libpcre2-dev_10.46-1_ppc64el.deb ... 503s Unpacking libpcre2-dev:ppc64el (10.46-1) ... 503s Selecting previously unselected package libpkgconf3:ppc64el. 503s Preparing to unpack .../49-libpkgconf3_1.8.1-4build1_ppc64el.deb ... 503s Unpacking libpkgconf3:ppc64el (1.8.1-4build1) ... 503s Selecting previously unselected package zlib1g-dev:ppc64el. 503s Preparing to unpack .../50-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1ubuntu2_ppc64el.deb ... 503s Unpacking zlib1g-dev:ppc64el (1:1.3.dfsg+really1.3.1-1ubuntu2) ... 503s Selecting previously unselected package libpng-dev:ppc64el. 503s Preparing to unpack .../51-libpng-dev_1.6.54-1_ppc64el.deb ... 503s Unpacking libpng-dev:ppc64el (1.6.54-1) ... 503s Selecting previously unselected package libreadline-dev:ppc64el. 503s Preparing to unpack .../52-libreadline-dev_8.3-3_ppc64el.deb ... 503s Unpacking libreadline-dev:ppc64el (8.3-3) ... 503s Selecting previously unselected package libzstd-dev:ppc64el. 503s Preparing to unpack .../53-libzstd-dev_1.5.7+dfsg-3_ppc64el.deb ... 503s Unpacking libzstd-dev:ppc64el (1.5.7+dfsg-3) ... 503s Selecting previously unselected package liblzma-dev:ppc64el. 503s Preparing to unpack .../54-liblzma-dev_5.8.2-2_ppc64el.deb ... 503s Unpacking liblzma-dev:ppc64el (5.8.2-2) ... 503s Selecting previously unselected package pkgconf-bin. 503s Preparing to unpack .../55-pkgconf-bin_1.8.1-4build1_ppc64el.deb ... 503s Unpacking pkgconf-bin (1.8.1-4build1) ... 503s Selecting previously unselected package pkgconf:ppc64el. 503s Preparing to unpack .../56-pkgconf_1.8.1-4build1_ppc64el.deb ... 503s Unpacking pkgconf:ppc64el (1.8.1-4build1) ... 503s Selecting previously unselected package libtirpc-dev:ppc64el. 503s Preparing to unpack .../57-libtirpc-dev_1.3.6+ds-1_ppc64el.deb ... 503s Unpacking libtirpc-dev:ppc64el (1.3.6+ds-1) ... 503s Selecting previously unselected package r-base-dev. 503s Preparing to unpack .../58-r-base-dev_4.5.2-1ubuntu2_all.deb ... 503s Unpacking r-base-dev (4.5.2-1ubuntu2) ... 503s Selecting previously unselected package pkg-r-autopkgtest. 503s Preparing to unpack .../59-pkg-r-autopkgtest_20250812_all.deb ... 503s Unpacking pkg-r-autopkgtest (20250812) ... 503s Selecting previously unselected package r-cran-backports. 503s Preparing to unpack .../60-r-cran-backports_1.5.0-2_ppc64el.deb ... 503s Unpacking r-cran-backports (1.5.0-2) ... 503s Selecting previously unselected package r-cran-cli. 503s Preparing to unpack .../61-r-cran-cli_3.6.4-1_ppc64el.deb ... 503s Unpacking r-cran-cli (3.6.4-1) ... 503s Selecting previously unselected package r-cran-generics. 503s Preparing to unpack .../62-r-cran-generics_0.1.4-1_all.deb ... 503s Unpacking r-cran-generics (0.1.4-1) ... 503s Selecting previously unselected package r-cran-glue. 503s Preparing to unpack .../63-r-cran-glue_1.8.0-1_ppc64el.deb ... 503s Unpacking r-cran-glue (1.8.0-1) ... 503s Selecting previously unselected package r-cran-rlang. 503s Preparing to unpack .../64-r-cran-rlang_1.1.5-3_ppc64el.deb ... 503s Unpacking r-cran-rlang (1.1.5-3) ... 503s Selecting previously unselected package r-cran-lifecycle. 503s Preparing to unpack .../65-r-cran-lifecycle_1.0.5+dfsg-1_all.deb ... 503s Unpacking r-cran-lifecycle (1.0.5+dfsg-1) ... 504s Selecting previously unselected package r-cran-magrittr. 504s Preparing to unpack .../66-r-cran-magrittr_2.0.3-1_ppc64el.deb ... 504s Unpacking r-cran-magrittr (2.0.3-1) ... 504s Selecting previously unselected package r-cran-utf8. 504s Preparing to unpack .../67-r-cran-utf8_1.2.4-1_ppc64el.deb ... 504s Unpacking r-cran-utf8 (1.2.4-1) ... 504s Selecting previously unselected package r-cran-vctrs. 504s Preparing to unpack .../68-r-cran-vctrs_0.6.5-1_ppc64el.deb ... 504s Unpacking r-cran-vctrs (0.6.5-1) ... 504s Selecting previously unselected package r-cran-pillar. 504s Preparing to unpack .../69-r-cran-pillar_1.11.1+dfsg-1_all.deb ... 504s Unpacking r-cran-pillar (1.11.1+dfsg-1) ... 504s Selecting previously unselected package r-cran-r6. 504s Preparing to unpack .../70-r-cran-r6_2.6.1-1_all.deb ... 504s Unpacking r-cran-r6 (2.6.1-1) ... 504s Selecting previously unselected package r-cran-fansi. 504s Preparing to unpack .../71-r-cran-fansi_1.0.6-2_ppc64el.deb ... 504s Unpacking r-cran-fansi (1.0.6-2) ... 504s Selecting previously unselected package r-cran-pkgconfig. 504s Preparing to unpack .../72-r-cran-pkgconfig_2.0.3-2build2_all.deb ... 504s Unpacking r-cran-pkgconfig (2.0.3-2build2) ... 504s Selecting previously unselected package r-cran-tibble. 504s Preparing to unpack .../73-r-cran-tibble_3.2.1+dfsg-3_ppc64el.deb ... 504s Unpacking r-cran-tibble (3.2.1+dfsg-3) ... 504s Selecting previously unselected package r-cran-withr. 504s Preparing to unpack .../74-r-cran-withr_3.0.2+dfsg-1_all.deb ... 504s Unpacking r-cran-withr (3.0.2+dfsg-1) ... 504s Selecting previously unselected package r-cran-tidyselect. 504s Preparing to unpack .../75-r-cran-tidyselect_1.2.1+dfsg-1_ppc64el.deb ... 504s Unpacking r-cran-tidyselect (1.2.1+dfsg-1) ... 504s Selecting previously unselected package r-cran-dplyr. 504s Preparing to unpack .../76-r-cran-dplyr_1.1.4-4_ppc64el.deb ... 504s Unpacking r-cran-dplyr (1.1.4-4) ... 504s Selecting previously unselected package r-cran-purrr. 504s Preparing to unpack .../77-r-cran-purrr_1.0.4-1_ppc64el.deb ... 504s Unpacking r-cran-purrr (1.0.4-1) ... 504s Selecting previously unselected package r-cran-stringi. 504s Preparing to unpack .../78-r-cran-stringi_1.8.4-1build2_ppc64el.deb ... 504s Unpacking r-cran-stringi (1.8.4-1build2) ... 504s Selecting previously unselected package r-cran-stringr. 504s Preparing to unpack .../79-r-cran-stringr_1.5.1-1_all.deb ... 504s Unpacking r-cran-stringr (1.5.1-1) ... 504s Selecting previously unselected package r-cran-cpp11. 504s Preparing to unpack .../80-r-cran-cpp11_0.5.3-1_all.deb ... 504s Unpacking r-cran-cpp11 (0.5.3-1) ... 504s Selecting previously unselected package r-cran-tidyr. 504s Preparing to unpack .../81-r-cran-tidyr_1.3.1-1_ppc64el.deb ... 504s Unpacking r-cran-tidyr (1.3.1-1) ... 504s Selecting previously unselected package r-cran-broom. 504s Preparing to unpack .../82-r-cran-broom_1.0.12+dfsg-1_all.deb ... 504s Unpacking r-cran-broom (1.0.12+dfsg-1) ... 504s Selecting previously unselected package r-cran-farver. 504s Preparing to unpack .../83-r-cran-farver_2.1.2-1_ppc64el.deb ... 504s Unpacking r-cran-farver (2.1.2-1) ... 504s Selecting previously unselected package r-cran-mass. 504s Preparing to unpack .../84-r-cran-mass_7.3-65-1_ppc64el.deb ... 504s Unpacking r-cran-mass (7.3-65-1) ... 504s Selecting previously unselected package r-cran-geepack. 504s Preparing to unpack .../85-r-cran-geepack_1.3.12-1_ppc64el.deb ... 504s Unpacking r-cran-geepack (1.3.12-1) ... 504s Selecting previously unselected package r-cran-gtable. 504s Preparing to unpack .../86-r-cran-gtable_0.3.6+dfsg-1_all.deb ... 504s Unpacking r-cran-gtable (0.3.6+dfsg-1) ... 504s Selecting previously unselected package r-cran-isoband. 504s Preparing to unpack .../87-r-cran-isoband_0.2.7-1_ppc64el.deb ... 504s Unpacking r-cran-isoband (0.2.7-1) ... 504s Selecting previously unselected package r-cran-nlme. 504s Preparing to unpack .../88-r-cran-nlme_3.1.168-1_ppc64el.deb ... 504s Unpacking r-cran-nlme (3.1.168-1) ... 504s Selecting previously unselected package r-cran-mgcv. 504s Preparing to unpack .../89-r-cran-mgcv_1.9-4-1_ppc64el.deb ... 504s Unpacking r-cran-mgcv (1.9-4-1) ... 504s Selecting previously unselected package r-cran-labeling. 504s Preparing to unpack .../90-r-cran-labeling_0.4.3-1_all.deb ... 504s Unpacking r-cran-labeling (0.4.3-1) ... 505s Selecting previously unselected package r-cran-rcolorbrewer. 505s Preparing to unpack .../91-r-cran-rcolorbrewer_1.1-3-1build2_all.deb ... 505s Unpacking r-cran-rcolorbrewer (1.1-3-1build2) ... 505s Selecting previously unselected package r-cran-viridislite. 505s Preparing to unpack .../92-r-cran-viridislite_0.4.3-1_all.deb ... 505s Unpacking r-cran-viridislite (0.4.3-1) ... 505s Selecting previously unselected package r-cran-scales. 505s Preparing to unpack .../93-r-cran-scales_1.4.0-1_all.deb ... 505s Unpacking r-cran-scales (1.4.0-1) ... 505s Selecting previously unselected package r-cran-ggplot2. 505s Preparing to unpack .../94-r-cran-ggplot2_3.5.1+dfsg-1_all.deb ... 505s Unpacking r-cran-ggplot2 (3.5.1+dfsg-1) ... 505s Setting up r-cran-rlang (1.1.5-3) ... 505s Setting up libzstd-dev:ppc64el (1.5.7+dfsg-3) ... 505s Setting up r-cran-withr (3.0.2+dfsg-1) ... 505s Setting up r-cran-backports (1.5.0-2) ... 505s Setting up r-cran-generics (0.1.4-1) ... 505s Setting up r-cran-fansi (1.0.6-2) ... 505s Setting up r-cran-mass (7.3-65-1) ... 505s Setting up linux-libc-dev:ppc64el (6.19.0-3.3) ... 505s Setting up r-cran-glue (1.8.0-1) ... 505s Setting up r-cran-cli (3.6.4-1) ... 505s Setting up r-cran-lifecycle (1.0.5+dfsg-1) ... 505s Setting up libpcre2-16-0:ppc64el (10.46-1) ... 505s Setting up r-cran-pkgconfig (2.0.3-2build2) ... 505s Setting up libpcre2-32-0:ppc64el (10.46-1) ... 505s Setting up r-cran-utf8 (1.2.4-1) ... 505s Setting up libtirpc-dev:ppc64el (1.3.6+ds-1) ... 505s Setting up libpkgconf3:ppc64el (1.8.1-4build1) ... 505s Setting up rpcsvc-proto (1.4.3-1build1) ... 505s Setting up r-cran-stringi (1.8.4-1build2) ... 505s Setting up r-cran-cpp11 (0.5.3-1) ... 505s Setting up r-cran-rcolorbrewer (1.1-3-1build2) ... 505s Setting up r-cran-isoband (0.2.7-1) ... 505s Setting up libquadmath0:ppc64el (15.2.0-12ubuntu1) ... 505s Setting up libmpc3:ppc64el (1.3.1-2) ... 505s Setting up r-cran-gtable (0.3.6+dfsg-1) ... 505s Setting up r-cran-labeling (0.4.3-1) ... 505s Setting up icu-devtools (78.2-1ubuntu1) ... 505s Setting up pkgconf-bin (1.8.1-4build1) ... 505s Setting up r-cran-nlme (3.1.168-1) ... 505s Setting up r-cran-farver (2.1.2-1) ... 505s Setting up liblzma-dev:ppc64el (5.8.2-2) ... 505s Setting up libubsan1:ppc64el (15.2.0-12ubuntu1) ... 505s Setting up r-cran-mgcv (1.9-4-1) ... 505s Setting up libpcre2-posix3:ppc64el (10.46-1) ... 505s Setting up r-cran-viridislite (0.4.3-1) ... 505s Setting up libcrypt-dev:ppc64el (1:4.5.1-1) ... 505s Setting up libasan8:ppc64el (15.2.0-12ubuntu1) ... 505s Setting up libtsan2:ppc64el (15.2.0-12ubuntu1) ... 505s Setting up r-cran-r6 (2.6.1-1) ... 505s Setting up libisl23:ppc64el (0.27-1build1) ... 505s Setting up libc-dev-bin (2.42-2ubuntu4) ... 505s Setting up libdeflate-dev:ppc64el (1.23-2build1) ... 505s Setting up r-cran-magrittr (2.0.3-1) ... 505s Setting up libcc1-0:ppc64el (15.2.0-12ubuntu1) ... 505s Setting up r-cran-vctrs (0.6.5-1) ... 505s Setting up liblsan0:ppc64el (15.2.0-12ubuntu1) ... 505s Setting up libblas-dev:ppc64el (3.12.1-7ubuntu1) ... 505s 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 505s Setting up dctrl-tools (2.24-3build4) ... 505s Setting up libitm1:ppc64el (15.2.0-12ubuntu1) ... 505s Setting up r-cran-pillar (1.11.1+dfsg-1) ... 505s Setting up libgcc-15-dev:ppc64el (15.2.0-12ubuntu1) ... 505s Setting up r-cran-stringr (1.5.1-1) ... 505s Setting up r-cran-tibble (3.2.1+dfsg-3) ... 505s Setting up libgfortran-15-dev:ppc64el (15.2.0-12ubuntu1) ... 505s Setting up pkgconf:ppc64el (1.8.1-4build1) ... 505s Setting up r-cran-tidyselect (1.2.1+dfsg-1) ... 505s Setting up cpp-15-powerpc64le-linux-gnu (15.2.0-12ubuntu1) ... 505s Setting up r-cran-scales (1.4.0-1) ... 505s Setting up liblapack-dev:ppc64el (3.12.1-7ubuntu1) ... 505s 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 505s Setting up r-cran-purrr (1.0.4-1) ... 505s Setting up cpp-15 (15.2.0-12ubuntu1) ... 505s Setting up libc6-dev:ppc64el (2.42-2ubuntu4) ... 505s Setting up r-cran-dplyr (1.1.4-4) ... 505s Setting up libicu-dev:ppc64el (78.2-1ubuntu1) ... 505s Setting up cpp-powerpc64le-linux-gnu (4:15.2.0-4ubuntu1) ... 505s Setting up libbz2-dev:ppc64el (1.0.8-6build2) ... 505s Setting up libjpeg-turbo8-dev:ppc64el (2.1.5-4ubuntu3) ... 505s Setting up libncurses-dev:ppc64el (6.6+20251231-1) ... 505s Setting up libpcre2-dev:ppc64el (10.46-1) ... 505s Setting up gcc-15-powerpc64le-linux-gnu (15.2.0-12ubuntu1) ... 505s Setting up r-cran-ggplot2 (3.5.1+dfsg-1) ... 505s Setting up libreadline-dev:ppc64el (8.3-3) ... 505s Setting up gcc-15 (15.2.0-12ubuntu1) ... 505s Setting up libstdc++-15-dev:ppc64el (15.2.0-12ubuntu1) ... 505s Setting up gcc-powerpc64le-linux-gnu (4:15.2.0-4ubuntu1) ... 505s Setting up gfortran-15-powerpc64le-linux-gnu (15.2.0-12ubuntu1) ... 505s Setting up r-cran-tidyr (1.3.1-1) ... 505s Setting up zlib1g-dev:ppc64el (1:1.3.dfsg+really1.3.1-1ubuntu2) ... 505s Setting up cpp (4:15.2.0-4ubuntu1) ... 505s Setting up libjpeg8-dev:ppc64el (8c-2ubuntu11) ... 505s Setting up gfortran-15 (15.2.0-12ubuntu1) ... 505s Setting up g++-15-powerpc64le-linux-gnu (15.2.0-12ubuntu1) ... 505s Setting up libpng-dev:ppc64el (1.6.54-1) ... 505s Setting up libjpeg-dev:ppc64el (8c-2ubuntu11) ... 505s Setting up gcc (4:15.2.0-4ubuntu1) ... 505s Setting up gfortran-powerpc64le-linux-gnu (4:15.2.0-4ubuntu1) ... 505s Setting up r-cran-broom (1.0.12+dfsg-1) ... 505s Setting up g++-15 (15.2.0-12ubuntu1) ... 505s Setting up g++-powerpc64le-linux-gnu (4:15.2.0-4ubuntu1) ... 505s Setting up r-cran-geepack (1.3.12-1) ... 505s Setting up gfortran (4:15.2.0-4ubuntu1) ... 505s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode 505s 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 505s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode 505s 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 505s Setting up g++ (4:15.2.0-4ubuntu1) ... 505s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 505s Setting up build-essential (12.12ubuntu2) ... 505s Setting up r-base-dev (4.5.2-1ubuntu2) ... 505s Setting up pkg-r-autopkgtest (20250812) ... 505s Processing triggers for libc-bin (2.42-2ubuntu4) ... 505s Processing triggers for man-db (2.13.1-1build1) ... 506s Processing triggers for install-info (7.2-5) ... 507s autopkgtest [22:49:18]: test pkg-r-autopkgtest: /usr/share/dh-r/pkg-r-autopkgtest 507s autopkgtest [22:49:18]: test pkg-r-autopkgtest: [----------------------- 507s Test: Try to load the R library etm 507s 507s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 507s Copyright (C) 2025 The R Foundation for Statistical Computing 507s Platform: powerpc64le-unknown-linux-gnu 507s 507s R is free software and comes with ABSOLUTELY NO WARRANTY. 507s You are welcome to redistribute it under certain conditions. 507s Type 'license()' or 'licence()' for distribution details. 507s 507s R is a collaborative project with many contributors. 507s Type 'contributors()' for more information and 507s 'citation()' on how to cite R or R packages in publications. 507s 507s Type 'demo()' for some demos, 'help()' for on-line help, or 507s 'help.start()' for an HTML browser interface to help. 507s Type 'q()' to quit R. 507s 507s > library('etm') 508s > 509s autopkgtest [22:49:20]: test pkg-r-autopkgtest: -----------------------] 509s autopkgtest [22:49:20]: test pkg-r-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 509s pkg-r-autopkgtest PASS 509s autopkgtest [22:49:20]: @@@@@@@@@@@@@@@@@@@@ summary 509s run-unit-test PASS 509s pkg-r-autopkgtest PASS