0s autopkgtest [15:24:16]: starting date and time: 2025-03-15 15:24:16+0000 0s autopkgtest [15:24:16]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [15:24:16]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.6ik0q6v4/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc --apt-upgrade r-cran-etm --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glibc/2.41-1ubuntu2 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-arm64-4.secgroup --name adt-plucky-arm64-r-cran-etm-20250315-152416-juju-7f2275-prod-proposed-migration-environment-2-76dbb60c-80c0-4b97-bdfd-ff1dbef18f99 --image adt/ubuntu-plucky-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 171s autopkgtest [15:27:07]: testbed dpkg architecture: arm64 171s autopkgtest [15:27:07]: testbed apt version: 2.9.33 171s autopkgtest [15:27:07]: @@@@@@@@@@@@@@@@@@@@ test bed setup 172s autopkgtest [15:27:08]: testbed release detected to be: None 173s autopkgtest [15:27:09]: updating testbed package index (apt update) 173s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 173s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 173s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 173s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 173s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [101 kB] 174s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 174s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [404 kB] 174s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [78.2 kB] 174s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 c-n-f Metadata [1976 B] 174s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 c-n-f Metadata [116 B] 174s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [346 kB] 174s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 c-n-f Metadata [15.8 kB] 174s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [4948 B] 174s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 c-n-f Metadata [572 B] 175s Fetched 1094 kB in 1s (784 kB/s) 176s Reading package lists... 177s Reading package lists... 177s Building dependency tree... 177s Reading state information... 178s Calculating upgrade... 178s Calculating upgrade... 179s The following packages will be upgraded: 179s python3-jinja2 strace 179s 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 179s Need to get 608 kB of archives. 179s After this operation, 11.3 kB of additional disk space will be used. 179s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 strace arm64 6.13+ds-1ubuntu1 [499 kB] 179s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 180s Fetched 608 kB in 1s (780 kB/s) 180s (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 ... 117701 files and directories currently installed.) 180s Preparing to unpack .../strace_6.13+ds-1ubuntu1_arm64.deb ... 180s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 181s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 181s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 181s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 181s Setting up strace (6.13+ds-1ubuntu1) ... 181s Processing triggers for man-db (2.13.0-1) ... 182s Reading package lists... 182s Building dependency tree... 182s Reading state information... 183s Solving dependencies... 183s The following packages will be REMOVED: 183s libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64* 183s libunwind8* linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 183s linux-image-6.11.0-8-generic* linux-modules-6.11.0-8-generic* 183s linux-tools-6.11.0-8* linux-tools-6.11.0-8-generic* 184s 0 upgraded, 0 newly installed, 11 to remove and 5 not upgraded. 184s After this operation, 267 MB disk space will be freed. 184s (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 ... 117701 files and directories currently installed.) 184s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 184s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 184s Removing libpython3.12t64:arm64 (3.12.9-1) ... 184s Removing libpython3.12-stdlib:arm64 (3.12.9-1) ... 184s Removing libnsl2:arm64 (1.3.0-3build3) ... 184s Removing libpython3.12-minimal:arm64 (3.12.9-1) ... 184s Removing libunwind8:arm64 (1.6.2-3.1) ... 184s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 185s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 187s Removing linux-image-6.11.0-8-generic (6.11.0-8.8) ... 187s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.14.0-10-generic 187s I: /boot/initrd.img.old is now a symlink to initrd.img-6.14.0-10-generic 187s /etc/kernel/postrm.d/initramfs-tools: 187s update-initramfs: Deleting /boot/initrd.img-6.11.0-8-generic 187s /etc/kernel/postrm.d/zz-flash-kernel: 187s flash-kernel: Kernel 6.11.0-8-generic has been removed. 187s flash-kernel: A higher version (6.14.0-10-generic) is still installed, no reflashing required. 187s /etc/kernel/postrm.d/zz-update-grub: 187s Sourcing file `/etc/default/grub' 187s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 187s Generating grub configuration file ... 188s Found linux image: /boot/vmlinuz-6.14.0-10-generic 188s Found initrd image: /boot/initrd.img-6.14.0-10-generic 188s Warning: os-prober will not be executed to detect other bootable partitions. 188s Systems on them will not be added to the GRUB boot configuration. 188s Check GRUB_DISABLE_OS_PROBER documentation entry. 188s Adding boot menu entry for UEFI Firmware Settings ... 188s done 188s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 188s Processing triggers for libc-bin (2.41-1ubuntu1) ... 188s (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 ... 81650 files and directories currently installed.) 188s Purging configuration files for linux-image-6.11.0-8-generic (6.11.0-8.8) ... 188s Purging configuration files for libpython3.12-minimal:arm64 (3.12.9-1) ... 189s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 189s autopkgtest [15:27:25]: upgrading testbed (apt dist-upgrade and autopurge) 189s Reading package lists... 189s Building dependency tree... 189s Reading state information... 190s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 190s Starting 2 pkgProblemResolver with broken count: 0 190s Done 191s Entering ResolveByKeep 191s 191s Calculating upgrade... 192s The following packages will be upgraded: 192s libc-bin libc-dev-bin libc6 libc6-dev locales 192s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 192s Need to get 9530 kB of archives. 192s After this operation, 0 B of additional disk space will be used. 192s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6-dev arm64 2.41-1ubuntu2 [1750 kB] 193s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-dev-bin arm64 2.41-1ubuntu2 [24.0 kB] 193s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6 arm64 2.41-1ubuntu2 [2910 kB] 196s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-bin arm64 2.41-1ubuntu2 [600 kB] 196s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 locales all 2.41-1ubuntu2 [4246 kB] 200s Preconfiguring packages ... 200s Fetched 9530 kB in 7s (1299 kB/s) 200s (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 ... 81647 files and directories currently installed.) 200s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_arm64.deb ... 200s Unpacking libc6-dev:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 200s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_arm64.deb ... 200s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 200s Preparing to unpack .../libc6_2.41-1ubuntu2_arm64.deb ... 200s Unpacking libc6:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 201s Setting up libc6:arm64 (2.41-1ubuntu2) ... 201s (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 ... 81647 files and directories currently installed.) 201s Preparing to unpack .../libc-bin_2.41-1ubuntu2_arm64.deb ... 201s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 201s Setting up libc-bin (2.41-1ubuntu2) ... 201s (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 ... 81647 files and directories currently installed.) 201s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 201s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 201s Setting up locales (2.41-1ubuntu2) ... 202s Generating locales (this might take a while)... 204s en_US.UTF-8... done 204s Generation complete. 204s Setting up libc-dev-bin (2.41-1ubuntu2) ... 204s Setting up libc6-dev:arm64 (2.41-1ubuntu2) ... 204s Processing triggers for man-db (2.13.0-1) ... 205s Processing triggers for systemd (257.3-1ubuntu3) ... 206s Reading package lists... 206s Building dependency tree... 206s Reading state information... 207s Starting pkgProblemResolver with broken count: 0 207s Starting 2 pkgProblemResolver with broken count: 0 207s Done 207s Solving dependencies... 208s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 208s autopkgtest [15:27:44]: rebooting testbed after setup commands that affected boot 232s autopkgtest [15:28:08]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP PREEMPT_DYNAMIC Wed Mar 12 15:45:31 UTC 2025 235s autopkgtest [15:28:11]: @@@@@@@@@@@@@@@@@@@@ apt-source r-cran-etm 238s Get:1 http://ftpmaster.internal/ubuntu plucky/universe r-cran-etm 1.1.1-1 (dsc) [2148 B] 238s Get:2 http://ftpmaster.internal/ubuntu plucky/universe r-cran-etm 1.1.1-1 (tar) [242 kB] 238s Get:3 http://ftpmaster.internal/ubuntu plucky/universe r-cran-etm 1.1.1-1 (diff) [3564 B] 238s gpgv: Signature made Fri Sep 18 09:39:57 2020 UTC 238s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 238s gpgv: issuer "tille@debian.org" 238s gpgv: Can't check signature: No public key 238s dpkg-source: warning: cannot verify inline signature for ./r-cran-etm_1.1.1-1.dsc: no acceptable signature found 238s autopkgtest [15:28:14]: testing package r-cran-etm version 1.1.1-1 239s autopkgtest [15:28:15]: build not needed 241s autopkgtest [15:28:17]: test run-unit-test: preparing testbed 241s Reading package lists... 242s Building dependency tree... 242s Reading state information... 242s Starting pkgProblemResolver with broken count: 0 242s Starting 2 pkgProblemResolver with broken count: 0 242s Done 243s The following NEW packages will be installed: 243s fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono libblas3 243s libcairo2 libdatrie1 libdeflate0 libfontconfig1 libgfortran5 libgomp1 243s libgraphite2-3 libharfbuzz0b libice6 libjbig0 libjpeg-turbo8 libjpeg8 243s liblapack3 liblerc4 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 243s libpaper-utils libpaper2 libpixman-1-0 libsharpyuv0 libsm6 libtcl8.6 243s libthai-data libthai0 libtiff6 libtk8.6 libwebp7 libxcb-render0 libxcb-shm0 243s libxft2 libxrender1 libxss1 libxt6t64 littler r-base-core r-cran-data.table 243s r-cran-dbi r-cran-etm r-cran-kmi r-cran-lattice r-cran-littler r-cran-matrix 243s r-cran-mitools r-cran-pkgkitten r-cran-rcpp r-cran-rcpparmadillo 243s r-cran-survival unzip x11-common xdg-utils zip 243s 0 upgraded, 57 newly installed, 0 to remove and 0 not upgraded. 243s Need to get 58.7 MB of archives. 243s After this operation, 123 MB of additional disk space will be used. 243s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 244s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 245s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig-config arm64 2.15.0-2ubuntu1 [37.5 kB] 245s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 libfontconfig1 arm64 2.15.0-2ubuntu1 [144 kB] 245s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig arm64 2.15.0-2ubuntu1 [191 kB] 246s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.1-2 [161 kB] 246s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 libpixman-1-0 arm64 0.44.0-3 [197 kB] 246s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-render0 arm64 1.17.0-2 [16.6 kB] 246s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-shm0 arm64 1.17.0-2 [5884 B] 246s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 libxrender1 arm64 1:0.9.10-1.1build1 [18.8 kB] 246s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 libcairo2 arm64 1.18.2-2 [560 kB] 247s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 libdatrie1 arm64 0.2.13-3build1 [19.2 kB] 247s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate0 arm64 1.23-1 [46.2 kB] 247s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 15-20250222-0ubuntu1 [444 kB] 247s Get:15 http://ftpmaster.internal/ubuntu plucky/main arm64 libgomp1 arm64 15-20250222-0ubuntu1 [146 kB] 247s Get:16 http://ftpmaster.internal/ubuntu plucky/main arm64 libgraphite2-3 arm64 1.3.14-2ubuntu1 [70.6 kB] 247s Get:17 http://ftpmaster.internal/ubuntu plucky/main arm64 libharfbuzz0b arm64 10.2.0-1 [490 kB] 248s Get:18 http://ftpmaster.internal/ubuntu plucky/main arm64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 248s Get:19 http://ftpmaster.internal/ubuntu plucky/main arm64 libice6 arm64 2:1.1.1-1 [42.3 kB] 248s Get:20 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg-turbo8 arm64 2.1.5-3ubuntu2 [165 kB] 248s Get:21 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 248s Get:22 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.1-2 [2307 kB] 250s Get:23 http://ftpmaster.internal/ubuntu plucky/main arm64 liblerc4 arm64 4.0.0+ds-5ubuntu1 [167 kB] 250s Get:24 http://ftpmaster.internal/ubuntu plucky/main arm64 libthai-data all 0.1.29-2build1 [158 kB] 250s Get:25 http://ftpmaster.internal/ubuntu plucky/main arm64 libthai0 arm64 0.1.29-2build1 [18.2 kB] 251s Get:26 http://ftpmaster.internal/ubuntu plucky/main arm64 libpango-1.0-0 arm64 1.56.2-1 [237 kB] 251s Get:27 http://ftpmaster.internal/ubuntu plucky/main arm64 libpangoft2-1.0-0 arm64 1.56.2-1 [49.5 kB] 251s Get:28 http://ftpmaster.internal/ubuntu plucky/main arm64 libpangocairo-1.0-0 arm64 1.56.2-1 [27.6 kB] 251s Get:29 http://ftpmaster.internal/ubuntu plucky/main arm64 libpaper2 arm64 2.2.5-0.3 [17.3 kB] 251s Get:30 http://ftpmaster.internal/ubuntu plucky/main arm64 libpaper-utils arm64 2.2.5-0.3 [15.4 kB] 251s Get:31 http://ftpmaster.internal/ubuntu plucky/main arm64 libsharpyuv0 arm64 1.5.0-0.1 [16.9 kB] 251s Get:32 http://ftpmaster.internal/ubuntu plucky/main arm64 libsm6 arm64 2:1.2.4-1 [16.4 kB] 251s Get:33 http://ftpmaster.internal/ubuntu plucky/main arm64 libtcl8.6 arm64 8.6.16+dfsg-1 [987 kB] 252s Get:34 http://ftpmaster.internal/ubuntu plucky/main arm64 libjbig0 arm64 2.1-6.1ubuntu2 [29.3 kB] 252s Get:35 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebp7 arm64 1.5.0-0.1 [194 kB] 252s Get:36 http://ftpmaster.internal/ubuntu plucky/main arm64 libtiff6 arm64 4.5.1+git230720-4ubuntu4 [193 kB] 252s Get:37 http://ftpmaster.internal/ubuntu plucky/main arm64 libxft2 arm64 2.3.6-1build1 [44.1 kB] 252s Get:38 http://ftpmaster.internal/ubuntu plucky/main arm64 libxss1 arm64 1:1.2.3-1build3 [7244 B] 252s Get:39 http://ftpmaster.internal/ubuntu plucky/main arm64 libtk8.6 arm64 8.6.16-1 [776 kB] 253s Get:40 http://ftpmaster.internal/ubuntu plucky/main arm64 libxt6t64 arm64 1:1.2.1-1.2build1 [168 kB] 253s Get:41 http://ftpmaster.internal/ubuntu plucky/main arm64 zip arm64 3.0-14ubuntu2 [173 kB] 253s Get:42 http://ftpmaster.internal/ubuntu plucky/main arm64 unzip arm64 6.0-28ubuntu6 [178 kB] 253s Get:43 http://ftpmaster.internal/ubuntu plucky/main arm64 xdg-utils all 1.2.1-2ubuntu1 [66.0 kB] 253s Get:44 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-base-core arm64 4.4.3-1 [28.4 MB] 283s Get:45 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-littler arm64 0.3.20-2 [96.1 kB] 283s Get:46 http://ftpmaster.internal/ubuntu plucky/universe arm64 littler all 0.3.20-2 [2554 B] 283s Get:47 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-data.table arm64 1.17.0+dfsg-1 [2129 kB] 285s Get:48 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-dbi all 1.2.3-1 [853 kB] 286s Get:49 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-lattice arm64 0.22-6-1 [1363 kB] 288s Get:50 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-matrix arm64 1.7-3-1 [4045 kB] 293s Get:51 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-survival arm64 3.8-3-1 [8213 kB] 302s Get:52 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-pkgkitten all 0.2.4-1 [27.2 kB] 302s Get:53 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-rcpp arm64 1.0.14-1 [1978 kB] 304s Get:54 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-rcpparmadillo arm64 14.2.3-1-1 [843 kB] 305s Get:55 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-etm arm64 1.1.1-1 [469 kB] 306s Get:56 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-mitools all 2.4-2build1 [265 kB] 306s Get:57 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-kmi all 0.5.5-2build1 [78.3 kB] 307s Preconfiguring packages ... 307s Fetched 58.7 MB in 1min 3s (933 kB/s) 307s Selecting previously unselected package fonts-dejavu-mono. 307s (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 ... 81647 files and directories currently installed.) 307s Preparing to unpack .../00-fonts-dejavu-mono_2.37-8_all.deb ... 307s Unpacking fonts-dejavu-mono (2.37-8) ... 307s Selecting previously unselected package fonts-dejavu-core. 307s Preparing to unpack .../01-fonts-dejavu-core_2.37-8_all.deb ... 307s Unpacking fonts-dejavu-core (2.37-8) ... 307s Selecting previously unselected package fontconfig-config. 307s Preparing to unpack .../02-fontconfig-config_2.15.0-2ubuntu1_arm64.deb ... 308s Unpacking fontconfig-config (2.15.0-2ubuntu1) ... 308s Selecting previously unselected package libfontconfig1:arm64. 308s Preparing to unpack .../03-libfontconfig1_2.15.0-2ubuntu1_arm64.deb ... 308s Unpacking libfontconfig1:arm64 (2.15.0-2ubuntu1) ... 308s Selecting previously unselected package fontconfig. 308s Preparing to unpack .../04-fontconfig_2.15.0-2ubuntu1_arm64.deb ... 308s Unpacking fontconfig (2.15.0-2ubuntu1) ... 308s Selecting previously unselected package libblas3:arm64. 308s Preparing to unpack .../05-libblas3_3.12.1-2_arm64.deb ... 308s Unpacking libblas3:arm64 (3.12.1-2) ... 308s Selecting previously unselected package libpixman-1-0:arm64. 308s Preparing to unpack .../06-libpixman-1-0_0.44.0-3_arm64.deb ... 308s Unpacking libpixman-1-0:arm64 (0.44.0-3) ... 308s Selecting previously unselected package libxcb-render0:arm64. 308s Preparing to unpack .../07-libxcb-render0_1.17.0-2_arm64.deb ... 308s Unpacking 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(1.17.0+dfsg-1) ... 314s Setting up r-cran-matrix (1.7-3-1) ... 314s Setting up r-cran-rcpparmadillo (14.2.3-1-1) ... 314s Setting up r-cran-mitools (2.4-2build1) ... 314s Setting up r-cran-survival (3.8-3-1) ... 314s Setting up r-cran-kmi (0.5.5-2build1) ... 314s Setting up r-cran-etm (1.1.1-1) ... 314s Processing triggers for man-db (2.13.0-1) ... 315s Processing triggers for install-info (7.1.1-1) ... 315s Processing triggers for libc-bin (2.41-1ubuntu2) ... 317s autopkgtest [15:29:33]: test run-unit-test: [----------------------- 317s BEGIN TEST test.etmCIF.R 317s 317s R version 4.4.3 (2025-02-28) -- "Trophy Case" 317s Copyright (C) 2025 The R Foundation for Statistical Computing 317s Platform: aarch64-unknown-linux-gnu 317s 317s R is free software and comes with ABSOLUTELY NO WARRANTY. 317s You are welcome to redistribute it under certain conditions. 317s Type 'license()' or 'licence()' for distribution details. 317s 317s R is a collaborative project with many contributors. 317s Type 'contributors()' for more information and 317s 'citation()' on how to cite R or R packages in publications. 317s 317s Type 'demo()' for some demos, 'help()' for on-line help, or 317s 'help.start()' for an HTML browser interface to help. 317s Type 'q()' to quit R. 317s 317s > ### test file for etmCIF. 317s > ### Really simple tests and comparison with etm 317s > 317s > old <- options(digits = 5) 317s > 317s > require(etm) 317s Loading required package: etm 318s > 318s > if (!require(survival, quietly = TRUE)) { 318s + print("The following tests require the 'survival' package") 318s + } else { 318s + 318s + data(abortion) 318s + 318s + from <- rep(0, nrow(abortion)) 318s + to <- abortion$cause 318s + entry <- abortion$entry 318s + exit <- abortion$exit 318s + id <- 1:nrow(abortion) 318s + data <- data.frame(id, from, to, entry, exit, group = abortion$group) 318s + 318s + ## Computation of the CIFs with etm 318s + tra <- matrix(FALSE, 4, 4) 318s + tra[1, 2:4] <- TRUE 318s + 318s + cif.control <- etm(data[data$group == 0, ], c("0", "1", "2", "3"), 318s + tra, NULL, 0) 318s + cif.exposed <- etm(data[data$group == 1, ], c("0", "1", "2", "3"), 318s + tra, NULL, 0) 318s + 318s + 318s + ## Computation of the CIFs with etmCIF 318s + netm <- etmCIF(Surv(entry, exit, cause != 0) ~ group, abortion, 318s + etype = cause, failcode = 3) 318s + 318s + ### let's do some comparisons :-) 318s + 318s + all.equal(trprob(cif.control, "0 3"), netm[[1]]$est["0", "3", ]) 318s + all.equal(trprob(cif.control, "0 2"), netm[[1]]$est["0", "2", ]) 318s + all.equal(trprob(cif.control, "0 1"), netm[[1]]$est["0", "1", ]) 318s + 318s + all.equal(trprob(cif.exposed, "0 3"), netm[[2]]$est["0", "3", ]) 318s + all.equal(trprob(cif.exposed, "0 2"), netm[[2]]$est["0", "2", ]) 318s + all.equal(trprob(cif.exposed, "0 1"), netm[[2]]$est["0", "1", ]) 318s + 318s + 318s + all.equal(trcov(cif.control, "0 3"), netm[[1]]$cov["0 3", "0 3", ]) 318s + all.equal(trcov(cif.control, "0 2"), netm[[1]]$cov["0 2", "0 2", ]) 318s + all.equal(trcov(cif.control, "0 1"), netm[[1]]$cov["0 1", "0 1", ]) 318s + 318s + all.equal(trcov(cif.exposed, "0 3"), netm[[2]]$cov["0 3", "0 3", ]) 318s + all.equal(trcov(cif.exposed, "0 2"), netm[[2]]$cov["0 2", "0 2", ]) 318s + all.equal(trcov(cif.exposed, "0 1"), netm[[2]]$cov["0 1", "0 1", ]) 318s + 318s + 318s + netm 318s + 318s + ## test on the summary 318s + snetm <- summary(netm) 318s + 318s + snetm 318s + 318s + all.equal(unname(trprob(cif.control, "0 3")), snetm[[1]][[3]]$P) 318s + all.equal(unname(trprob(cif.control, "0 2")), snetm[[1]][[2]]$P) 318s + all.equal(unname(trprob(cif.control, "0 1")), snetm[[1]][[1]]$P) 318s + 318s + all.equal(unname(trprob(cif.exposed, "0 3")), snetm[[2]][[3]]$P) 318s + all.equal(unname(trprob(cif.exposed, "0 2")), snetm[[2]][[2]]$P) 318s + all.equal(unname(trprob(cif.exposed, "0 1")), snetm[[2]][[1]]$P) 318s + 318s + scif.control <- summary(cif.control, ci.fun = "cloglog") 318s + scif.exposed <- summary(cif.exposed, ci.fun = "cloglog") 318s + 318s + all.equal(scif.control[[4]]$lower, snetm[[1]][[3]]$lower) 318s + all.equal(scif.control[[4]]$upper, snetm[[1]][[3]]$upper) 318s + 318s + all.equal(scif.exposed[[4]]$lower, snetm[[2]][[3]]$lower) 318s + all.equal(scif.exposed[[4]]$upper, snetm[[2]][[3]]$upper) 318s + } 319s [1] TRUE 319s > 319s > ### test with factors in the input 319s > abortion$status <- with(abortion, ifelse(cause == 2, "life birth", 319s + ifelse(cause == 1, "ETOP", "spontaneous abortion"))) 319s > 319s > abortion$status <- factor(abortion$status) 319s > 319s > netm.factor <- etmCIF(Surv(entry, exit, status != "cens") ~ group, abortion, 319s + etype = status, failcode = "spontaneous abortion") 319s > 319s > 319s > all.equal(trprob(cif.control, "0 3"), netm.factor[[1]]$est["0", "spontaneous abortion", ]) 319s [1] TRUE 319s > all.equal(trprob(cif.control, "0 2"), netm.factor[[1]]$est["0", "life birth", ]) 319s [1] TRUE 319s > 319s > netm.factor 319s Call: etmCIF(formula = Surv(entry, exit, status != "cens") ~ group, 319s data = abortion, etype = status, failcode = "spontaneous abortion") 319s 319s Covariate: group 319s levels: 0 1 319s 319s 319s group = 0 319s time P se(P) n.event 319s CIF ETOP 43 0.040159 0.0092578 20 319s CIF life birth 43 0.799059 0.0221865 924 319s CIF spontaneous abortion 43 0.160781 0.0213261 69 319s 319s group = 1 319s time P se(P) n.event 319s CIF ETOP 42 0.28511 0.042493 38 319s CIF life birth 42 0.35257 0.042139 92 319s CIF spontaneous abortion 42 0.36232 0.049473 43 319s > 319s > summary(netm.factor) 319s 319s group=0 319s 319s CIF ETOP 319s P time var lower upper n.risk n.event 319s 0.000000 6 0.0000e+00 0.000000 0.000000 117 0 319s 0.038955 13 8.4440e-05 0.024488 0.061694 645 1 319s 0.040159 26 8.5707e-05 0.025513 0.062939 846 0 319s 0.040159 36 8.5707e-05 0.025513 0.062939 876 0 319s 0.040159 40 8.5707e-05 0.025513 0.062939 554 0 319s 0.040159 43 8.5707e-05 0.025513 0.062939 6 0 319s 319s CIF life birth 319s P time var lower upper n.risk n.event 319s 0.000000 6 0.0000e+00 0.000000 0.000000 117 0 319s 0.000000 13 0.0000e+00 0.000000 0.000000 645 0 319s 0.000000 26 0.0000e+00 0.000000 0.000000 846 0 319s 0.053197 36 4.6195e-05 0.041379 0.068268 876 25 319s 0.563121 40 3.8801e-04 0.524924 0.602021 554 280 319s 0.799059 43 4.9224e-04 0.753969 0.840613 6 6 319s 319s CIF spontaneous abortion 319s P time var lower upper n.risk n.event 319s 0.034188 6 0.00028222 0.01297 0.088523 117 4 319s 0.150468 13 0.00045513 0.11360 0.197901 645 1 319s 0.159904 26 0.00045498 0.12274 0.206925 846 1 319s 0.160781 36 0.00045480 0.12360 0.207757 876 1 319s 0.160781 40 0.00045480 0.12360 0.207757 554 0 319s 0.160781 43 0.00045480 0.12360 0.207757 6 0 319s 319s 319s group=1 319s 319s CIF ETOP 319s P time var lower upper n.risk n.event 319s 0.00000 6 0.0000000 0.00000 0.00000 35 0 319s 0.26048 13 0.0017854 0.18795 0.35425 90 0 319s 0.28115 21 0.0018028 0.20742 0.37423 93 1 319s 0.28511 34 0.0018057 0.21116 0.37806 89 0 319s 0.28511 39 0.0018057 0.21116 0.37806 59 0 319s 0.28511 42 0.0018057 0.21116 0.37806 6 0 319s 319s CIF life birth 319s P time var lower upper n.risk n.event 319s 0.000000 6 0.0000e+00 0.000000 0.000000 35 0 319s 0.000000 13 0.0000e+00 0.000000 0.000000 90 0 319s 0.000000 21 0.0000e+00 0.000000 0.000000 93 0 319s 0.023073 34 9.0514e-05 0.010252 0.051504 89 2 319s 0.180156 39 8.0126e-04 0.131765 0.243663 59 13 319s 0.352565 42 1.7757e-03 0.276882 0.441775 6 6 319s 319s CIF spontaneous abortion 319s P time var lower upper n.risk n.event 319s 0.057143 6 0.0015394 0.014605 0.20968 35 2 319s 0.333246 13 0.0025280 0.245337 0.44216 90 4 319s 0.350702 21 0.0024827 0.262769 0.45762 93 0 319s 0.358492 34 0.0024593 0.270627 0.46448 89 0 319s 0.358492 39 0.0024593 0.270627 0.46448 59 0 319s 0.362323 42 0.0024476 0.274499 0.46785 6 0 319s 319s > 319s > ### test with group as a character vector 319s > abortion$ttt <- with(abortion, ifelse(group == 0, "control", "exposed")) 319s > abortion$ttt <- factor(abortion$ttt) 319s > 319s > netm.ttt <- etmCIF(Surv(entry, exit, status != "cens") ~ ttt, abortion, 319s + etype = status, failcode = "spontaneous abortion") 319s > 319s > all.equal(trprob(cif.control, "0 3"), netm.ttt[[1]]$est["0", "spontaneous abortion", ]) 319s [1] TRUE 319s > all.equal(trprob(cif.control, "0 2"), netm.ttt[[1]]$est["0", "life birth", ]) 319s [1] TRUE 319s > 319s > netm.ttt 319s Call: etmCIF(formula = Surv(entry, exit, status != "cens") ~ ttt, data = abortion, 319s etype = status, failcode = "spontaneous abortion") 319s 319s Covariate: ttt 319s levels: control exposed 319s 319s 319s ttt = control 319s time P se(P) n.event 319s CIF ETOP 43 0.040159 0.0092578 20 319s CIF life birth 43 0.799059 0.0221865 924 319s CIF spontaneous abortion 43 0.160781 0.0213261 69 319s 319s ttt = exposed 319s time P se(P) n.event 319s CIF ETOP 42 0.28511 0.042493 38 319s CIF life birth 42 0.35257 0.042139 92 319s CIF spontaneous abortion 42 0.36232 0.049473 43 319s > 319s > summary(netm.ttt) 319s 319s ttt=control 319s 319s CIF ETOP 319s P time var lower upper n.risk n.event 319s 0.000000 6 0.0000e+00 0.000000 0.000000 117 0 319s 0.038955 13 8.4440e-05 0.024488 0.061694 645 1 319s 0.040159 26 8.5707e-05 0.025513 0.062939 846 0 319s 0.040159 36 8.5707e-05 0.025513 0.062939 876 0 319s 0.040159 40 8.5707e-05 0.025513 0.062939 554 0 319s 0.040159 43 8.5707e-05 0.025513 0.062939 6 0 319s 319s CIF life birth 319s P time var lower upper n.risk n.event 319s 0.000000 6 0.0000e+00 0.000000 0.000000 117 0 319s 0.000000 13 0.0000e+00 0.000000 0.000000 645 0 319s 0.000000 26 0.0000e+00 0.000000 0.000000 846 0 319s 0.053197 36 4.6195e-05 0.041379 0.068268 876 25 319s 0.563121 40 3.8801e-04 0.524924 0.602021 554 280 319s 0.799059 43 4.9224e-04 0.753969 0.840613 6 6 319s 319s CIF spontaneous abortion 319s P time var lower upper n.risk n.event 319s 0.034188 6 0.00028222 0.01297 0.088523 117 4 319s 0.150468 13 0.00045513 0.11360 0.197901 645 1 319s 0.159904 26 0.00045498 0.12274 0.206925 846 1 319s 0.160781 36 0.00045480 0.12360 0.207757 876 1 319s 0.160781 40 0.00045480 0.12360 0.207757 554 0 319s 0.160781 43 0.00045480 0.12360 0.207757 6 0 319s 319s 319s ttt=exposed 319s 319s CIF ETOP 319s P time var lower upper n.risk n.event 319s 0.00000 6 0.0000000 0.00000 0.00000 35 0 319s 0.26048 13 0.0017854 0.18795 0.35425 90 0 319s 0.28115 21 0.0018028 0.20742 0.37423 93 1 319s 0.28511 34 0.0018057 0.21116 0.37806 89 0 319s 0.28511 39 0.0018057 0.21116 0.37806 59 0 319s 0.28511 42 0.0018057 0.21116 0.37806 6 0 319s 319s CIF life birth 319s P time var lower upper n.risk n.event 319s 0.000000 6 0.0000e+00 0.000000 0.000000 35 0 319s 0.000000 13 0.0000e+00 0.000000 0.000000 90 0 319s 0.000000 21 0.0000e+00 0.000000 0.000000 93 0 319s 0.023073 34 9.0514e-05 0.010252 0.051504 89 2 319s 0.180156 39 8.0126e-04 0.131765 0.243663 59 13 319s 0.352565 42 1.7757e-03 0.276882 0.441775 6 6 319s 319s CIF spontaneous abortion 319s P time var lower upper n.risk n.event 319s 0.057143 6 0.0015394 0.014605 0.20968 35 2 319s 0.333246 13 0.0025280 0.245337 0.44216 90 4 319s 0.350702 21 0.0024827 0.262769 0.45762 93 0 319s 0.358492 34 0.0024593 0.270627 0.46448 89 0 319s 0.358492 39 0.0024593 0.270627 0.46448 59 0 319s 0.362323 42 0.0024476 0.274499 0.46785 6 0 319s 319s > 319s > 319s > ### A couple of comparisons with simulated data 319s > set.seed(1313) 319s > time <- rexp(100) 319s > to <- rbinom(100, 2, prob = c(1/3, 1/3, 1/3)) 319s > from <- rep(11, 100) 319s > id <- 1:100 319s > cov <- rbinom(100, 1, 0.5) 319s > 319s > dat.s <- data.frame(id, time, from, to, cov) 319s > 319s > traa <- matrix(FALSE, 3, 3) 319s > traa[1, 2:3] <- TRUE 319s > 319s > aa0 <- etm(dat.s[dat.s$cov == 0, ], c("11", "1", "2"), traa, "0", 0) 319s > aa1 <- etm(dat.s[dat.s$cov == 1, ], c("11", "1", "2"), traa, "0", 0) 319s > aa <- etm(dat.s, c("11", "1", "2"), traa, "0", 0) 319s > 319s > test <- etmCIF(Surv(time, to != 0) ~ 1, dat.s, etype = to) 319s > 319s > test.c <- etmCIF(Surv(time, to != 0) ~ cov, dat.s, etype = to) 319s > 319s > all.equal(trprob(aa, "11 1"), test[[1]]$est["0", "1", ]) 319s [1] TRUE 319s > all.equal(trprob(aa, "11 2"), test[[1]]$est["0", "2", ]) 319s [1] TRUE 319s > 319s > all.equal(trprob(aa0, "11 1"), test.c[[1]]$est["0", "1", ]) 319s [1] TRUE 319s > all.equal(trprob(aa0, "11 2"), test.c[[1]]$est["0", "2", ]) 319s [1] TRUE 319s > 319s > all.equal(trprob(aa1, "11 1"), test.c[[2]]$est["0", "1", ]) 319s [1] TRUE 319s > all.equal(trprob(aa1, "11 2"), test.c[[2]]$est["0", "2", ]) 319s [1] TRUE 319s > 319s > test 319s Call: etmCIF(formula = Surv(time, to != 0) ~ 1, data = dat.s, etype = to) 319s 319s time P se(P) n.event 319s CIF 1 4.9088 0.809108 0.079680 45 319s CIF 2 4.9088 0.096618 0.032905 8 319s > 319s > test.c 319s Call: etmCIF(formula = Surv(time, to != 0) ~ cov, data = dat.s, etype = to) 319s 319s Covariate: cov 319s levels: 0 1 319s 319s 319s cov = 0 319s time P se(P) n.event 319s CIF 1 2.1708 0.70246 0.105797 19 319s CIF 2 2.1708 0.11144 0.053384 4 319s 319s cov = 1 319s time P se(P) n.event 319s CIF 1 4.9088 0.80787 0.094051 26 319s CIF 2 4.9088 0.08436 0.040769 4 319s > 319s > summary(test) 319s 319s 319s 319s CIF 1 319s P time var lower upper n.risk n.event 319s 0.01000 0.0092099 0.0000990 0.0014147 0.068863 100 1 319s 0.11430 0.2663096 0.0010542 0.0649454 0.196993 81 1 319s 0.23451 0.7303091 0.0020436 0.1591107 0.337736 54 1 319s 0.40425 1.4299939 0.0032996 0.3020445 0.525741 29 1 319s 0.54593 2.0647206 0.0040836 0.4269008 0.673605 16 1 319s 0.80911 4.9087561 0.0063489 0.6359544 0.933733 2 1 319s 319s CIF 2 319s P time var lower upper n.risk n.event 319s 0.000000 0.0092099 0.00000000 0.000000 0.000000 100 0 319s 0.031657 0.2663096 0.00032353 0.010320 0.094942 81 0 319s 0.067029 0.7303091 0.00070366 0.030598 0.143503 54 0 319s 0.096618 1.4299939 0.00108275 0.049082 0.185474 29 0 319s 0.096618 2.0647206 0.00108275 0.049082 0.185474 16 0 319s 0.096618 4.9087561 0.00108275 0.049082 0.185474 2 0 319s 319s > summary(test.c) 319s 319s cov=0 319s 319s CIF 1 319s P time var lower upper n.risk n.event 319s 0.022222 0.0092099 0.00048285 0.0031605 0.14747 45 1 319s 0.092222 0.2982439 0.00193603 0.0355971 0.22762 36 0 319s 0.226684 0.7021938 0.00450954 0.1241760 0.39250 24 1 319s 0.378128 1.4299939 0.00760870 0.2337884 0.57145 13 1 319s 0.505736 1.6148774 0.00895330 0.3388425 0.69885 10 1 319s 0.702465 2.1708375 0.01119294 0.4944890 0.88399 3 1 319s 319s CIF 2 319s P time var lower upper n.risk n.event 319s 0.000000 0.0092099 0.0000000 0.000000 0.00000 45 0 319s 0.048441 0.2982439 0.0011168 0.012337 0.18013 36 1 319s 0.076411 0.7021938 0.0018104 0.025202 0.21928 24 0 319s 0.111440 1.4299939 0.0028499 0.042676 0.27392 13 0 319s 0.111440 1.6148774 0.0028499 0.042676 0.27392 10 0 319s 0.111440 2.1708375 0.0028499 0.042676 0.27392 3 0 319s 319s 319s cov=1 319s 319s CIF 1 319s P time var lower upper n.risk n.event 319s 0.018182 0.066692 0.00032457 0.0025813 0.12214 55 1 319s 0.112392 0.263808 0.00187215 0.0520925 0.23333 45 1 319s 0.241023 0.730309 0.00374499 0.1440057 0.38685 31 1 319s 0.401201 1.066913 0.00570788 0.2714008 0.56421 19 1 319s 0.592334 2.366275 0.00775985 0.4286230 0.76273 8 1 319s 0.807871 4.908756 0.00884554 0.6023185 0.94771 2 1 319s 319s CIF 2 319s P time var lower upper n.risk n.event 319s 0.000000 0.066692 0.00000000 0.000000 0.00000 55 0 319s 0.037434 0.263808 0.00067458 0.009494 0.14152 45 0 319s 0.059341 0.730309 0.00111295 0.019447 0.17351 31 0 319s 0.084360 1.066913 0.00166213 0.032211 0.21119 19 0 319s 0.084360 2.366275 0.00166213 0.032211 0.21119 8 0 319s 0.084360 4.908756 0.00166213 0.032211 0.21119 2 0 319s 319s > 319s > options(old) 319s > 319s BEGIN TEST tests.etm.R 319s 319s R version 4.4.3 (2025-02-28) -- "Trophy Case" 319s Copyright (C) 2025 The R Foundation for Statistical Computing 319s Platform: aarch64-unknown-linux-gnu 319s 319s R is free software and comes with ABSOLUTELY NO WARRANTY. 319s You are welcome to redistribute it under certain conditions. 319s Type 'license()' or 'licence()' for distribution details. 319s 319s R is a collaborative project with many contributors. 319s Type 'contributors()' for more information and 319s 'citation()' on how to cite R or R packages in publications. 319s 319s Type 'demo()' for some demos, 'help()' for on-line help, or 319s 'help.start()' for an HTML browser interface to help. 319s Type 'q()' to quit R. 319s 319s > require(etm) 319s Loading required package: etm 320s > 320s > ## Print with a bit less precision to avoid lots of notes in the comparison 320s > old <- options(digits = 4) 320s > 320s > ### Simple test 320s > 320s > time <- id <- 1:10 320s > from <- rep(0, 10) 320s > to <- rep(1, 10) 320s > 320s > data1 <- data.frame(id, from, to, time) 320s > tra1 <- matrix(FALSE, 2, 2) 320s > tra1[1, 2] <- TRUE 320s > 320s > etm1 <- etm(data1, c("0", "1"), tra1, NULL, 0) 320s > 320s > all.equal(as.vector(trprob(etm1, "0 0")), cumprod((10:1 - 1) / (10:1))) 320s [1] TRUE 320s > 320s > etm1$cov["0 0", "0 0", ] 320s 1 2 3 4 5 6 7 8 9 10 320s 0.009 0.016 0.021 0.024 0.025 0.024 0.021 0.016 0.009 0.000 320s > 320s > all.equal(etm1$cov["0 0", "0 0",], trcov(etm1, "0 0")) 320s [1] TRUE 320s > 320s > ### A simple test from AHR's author, where the first time is censored 320s > if (!require(survival)) { 320s + stop("This test requires the survival package") 320s + } 320s > 320s > data <- data.frame(id=1:10, time=1:10, from=0, to=1, status=TRUE) 320s > 320s > tra <- matrix(FALSE, nrow=2, ncol=2) 320s > tra[1, 2] <- TRUE 320s > 320s > data$to[1] <- "cens" 320s > data$status[1] <- FALSE 320s > 320s > fit.km <- survfit(Surv(time, status) ~ 1, data=data) 320s > fit.etm <- etm(data, c("0","1"), tra, "cens", s=0, t="last", covariance=FALSE) 320s Loading required package: survival 320s > 320s > all.equal(fit.km$surv[data$status], fit.etm$est[1,1,], check.attributes = FALSE) 320s [1] TRUE 320s > 320s > data$to[2] <- "cens" 320s > data$status[2] <- FALSE 320s > 320s > fit.km <- survfit(Surv(time, status) ~ 1, data=data) 320s > fit.etm <- etm(data, c("0","1"), tra, "cens", s=0, t="last", covariance=FALSE) 320s > 320s > all.equal(fit.km$surv[data$status], fit.etm$est[1,1,], check.attributes = FALSE) 320s [1] TRUE 320s > 320s > ### a bit more complicated 320s > 320s > time <- id <- 1:10 320s > from <- rep(0, 10) 320s > to <- rep(c(1, 2), 5) 320s > data2 <- data.frame(id, from, to, time) 320s > 320s > tra2 <- matrix(FALSE, 3, 3) 320s > tra2[1, 2:3] <- TRUE 320s > 320s > etm2 <- etm(data2, c("0", "1", "2"), tra2, NULL, 0) 320s > 320s > aa <- table(time, to) 320s > 320s > cif1 <- cumsum(aa[, 1] / 10) 320s > cif2 <- cumsum(aa[, 2] / 10) 320s > surv <- cumprod((10:1 - 1) / (10:1)) 320s > 320s > all.equal(trprob(etm2, "0 1"), cif1) 320s [1] TRUE 320s > all.equal(trprob(etm2, "0 2"), cif2) 320s [1] TRUE 320s > all.equal(as.vector(trprob(etm2, "0 0")), surv) 320s [1] TRUE 320s > 320s > ## a test on id 320s > data2$id <- letters[1:10] 320s > 320s > etm3 <- etm(data2, c("0", "1", "2"), tra2, NULL, 0) 320s > 320s > all.equal(trprob(etm2, "0 1"), trprob(etm3, "0 1")) 320s [1] TRUE 320s > all.equal(trprob(etm2, "0 2"), trprob(etm3, "0 2")) 320s [1] TRUE 320s > all.equal(trprob(etm2, "0 0"), trprob(etm3, "0 0")) 320s [1] TRUE 320s > 320s > 320s > ### Test on sir.cont 320s > 320s > data(sir.cont) 320s > 320s > ## Modification for patients entering and leaving a state 320s > ## at the same date 320s > ## Change on ventilation status is considered 320s > ## to happen before end of hospital stay 320s > sir.cont <- sir.cont[order(sir.cont$id, sir.cont$time), ] 320s > for (i in 2:nrow(sir.cont)) { 320s + if (sir.cont$id[i]==sir.cont$id[i-1]) { 320s + if (sir.cont$time[i]==sir.cont$time[i-1]) { 320s + sir.cont$time[i-1] <- sir.cont$time[i-1] - 0.5 320s + } 320s + } 320s + } 320s > 320s > ### Computation of the transition probabilities 320s > ## Possible transitions. 320s > tra <- matrix(ncol=3,nrow=3,FALSE) 320s > tra[1, 2:3] <- TRUE 320s > tra[2, c(1, 3)] <- TRUE 320s > 320s > ## etm 320s > prob.sir <- etm(sir.cont, c("0", "1", "2"), tra, "cens", 1) 320s > 320s > prob.sir 320s Multistate model with 2 transient state(s) 320s and 1 absorbing state(s) 320s 320s Possible transitions: 320s from to 320s 0 1 320s 0 2 320s 1 0 320s 1 2 320s 320s Estimate of P(1, 183) 320s 0 1 2 320s 0 0 0 1 320s 1 0 0 1 320s 2 0 0 1 320s 320s > 320s > summ.sir <- summary(prob.sir) 320s > all.equal(summ.sir[['0 1']]$P, as.vector(trprob(prob.sir, "0 1"))) 320s [1] TRUE 320s > subset(summ.sir[[3]],time<183) # issue with precision on different architectures 320s P time var lower upper n.risk n.event 320s 1.5 0.0000 1.5 0.000e+00 0.00000 0.0000 394 0 320s 2 0.1187 2.0 2.641e-04 0.08683 0.1505 396 47 320s 2.5 0.1187 2.5 2.641e-04 0.08683 0.1505 364 0 320s 3 0.2454 3.0 4.465e-04 0.20398 0.2868 365 54 320s 3.5 0.2454 3.5 4.465e-04 0.20398 0.2868 328 0 320s 4 0.3806 4.0 5.416e-04 0.33501 0.4262 331 62 320s 4.5 0.3806 4.5 5.416e-04 0.33501 0.4262 280 0 320s 5 0.4792 5.0 5.480e-04 0.43333 0.5251 283 48 320s 5.5 0.4792 5.5 5.480e-04 0.43333 0.5251 248 0 320s 6 0.5693 6.0 5.141e-04 0.52482 0.6137 249 47 320s 7 0.6350 7.0 4.665e-04 0.59266 0.6773 212 36 320s 8 0.6795 8.0 4.202e-04 0.63931 0.7197 195 27 320s 8.5 0.6795 8.5 4.202e-04 0.63931 0.7197 172 0 320s 9 0.7325 9.0 3.580e-04 0.69541 0.7696 173 34 320s 10 0.7647 10.0 3.141e-04 0.72992 0.7994 148 21 320s 10.5 0.7647 10.5 3.141e-04 0.72992 0.7994 135 0 320s 11 0.7895 11.0 2.790e-04 0.75674 0.8222 136 18 320s 12 0.8138 12.0 2.420e-04 0.78330 0.8443 129 18 320s 12.5 0.8138 12.5 2.420e-04 0.78330 0.8443 117 0 320s 13 0.8294 13.0 2.182e-04 0.80045 0.8584 118 13 320s 14 0.8452 14.0 1.938e-04 0.81789 0.8725 115 14 320s 15 0.8625 15.0 1.670e-04 0.83714 0.8878 106 15 320s 16 0.8723 16.0 1.522e-04 0.84807 0.8964 93 9 320s 17 0.8852 17.0 1.330e-04 0.86256 0.9078 86 12 320s 17.5 0.8852 17.5 1.330e-04 0.86256 0.9078 77 0 320s 18 0.8960 18.0 1.168e-04 0.87484 0.9172 76 9 320s 19 0.9029 19.0 1.070e-04 0.88261 0.9232 71 7 320s 20 0.9125 20.0 9.367e-05 0.89356 0.9315 64 10 320s 21 0.9161 21.0 8.878e-05 0.89768 0.9346 57 4 320s 22 0.9226 22.0 7.996e-05 0.90504 0.9401 55 6 320s 23 0.9261 23.0 7.537e-05 0.90904 0.9431 51 4 320s 23.5 0.9261 23.5 7.537e-05 0.90904 0.9431 49 0 320s 24 0.9354 24.0 6.292e-05 0.91982 0.9509 50 9 320s 25 0.9385 25.0 5.878e-05 0.92352 0.9536 42 3 320s 26 0.9429 26.0 5.326e-05 0.92863 0.9572 39 5 320s 27 0.9477 27.0 4.749e-05 0.93417 0.9612 35 6 320s 27.5 0.9477 27.5 4.749e-05 0.93417 0.9612 29 0 320s 28 0.9531 28.0 4.093e-05 0.94059 0.9657 30 5 320s 29 0.9567 29.0 3.668e-05 0.94485 0.9686 31 4 320s 30 0.9592 30.0 3.384e-05 0.94779 0.9706 28 3 320s 30.5 0.9592 30.5 3.384e-05 0.94779 0.9706 29 0 320s 31 0.9642 31.0 2.821e-05 0.95383 0.9746 30 6 320s 32 0.9649 32.0 2.752e-05 0.95458 0.9751 25 1 320s 33 0.9669 33.0 2.533e-05 0.95708 0.9768 24 2 320s 34 0.9685 34.0 2.368e-05 0.95900 0.9781 26 2 320s 35 0.9697 35.0 2.252e-05 0.96036 0.9790 28 2 320s 36 0.9702 36.0 2.194e-05 0.96104 0.9794 26 1 320s 37 0.9718 37.0 2.043e-05 0.96290 0.9806 26 2 320s 38 0.9739 38.0 1.831e-05 0.96555 0.9823 25 4 320s 38.5 0.9739 38.5 1.831e-05 0.96555 0.9823 21 0 320s 39 0.9760 39.0 1.643e-05 0.96802 0.9839 23 3 320s 40 0.9769 40.0 1.558e-05 0.96918 0.9847 19 1 320s 41 0.9774 41.0 1.512e-05 0.96981 0.9851 22 1 320s 42 0.9779 42.0 1.476e-05 0.97032 0.9854 22 0 320s 43 0.9798 43.0 1.308e-05 0.97271 0.9869 22 3 320s 44 0.9803 44.0 1.265e-05 0.97333 0.9873 21 1 320s 45 0.9817 45.0 1.157e-05 0.97499 0.9883 19 1 320s 46 0.9822 46.0 1.116e-05 0.97561 0.9887 17 1 320s 47 0.9831 47.0 1.037e-05 0.97683 0.9895 18 2 320s 48 0.9836 48.0 9.987e-06 0.97743 0.9898 17 1 320s 49 0.9841 49.0 9.669e-06 0.97796 0.9901 17 0 320s 50 0.9845 50.0 9.297e-06 0.97856 0.9905 17 1 320s 50.5 0.9845 50.5 9.297e-06 0.97856 0.9905 16 0 320s 51 0.9860 51.0 8.214e-06 0.98037 0.9916 17 3 320s 52 0.9870 52.0 7.513e-06 0.98159 0.9923 14 2 320s 53 0.9879 53.0 6.875e-06 0.98276 0.9930 12 1 320s 54 0.9889 54.0 6.214e-06 0.98397 0.9937 12 2 320s 55 0.9903 55.0 5.254e-06 0.98581 0.9948 10 3 320s 56 0.9913 56.0 4.667e-06 0.98703 0.9955 6 1 320s 57 0.9917 57.0 4.364e-06 0.98765 0.9958 5 1 320s 58 0.9922 58.0 4.064e-06 0.98828 0.9962 4 1 320s 59 0.9927 59.0 3.769e-06 0.98891 0.9965 3 1 320s 60 0.9932 60.0 3.488e-06 0.98953 0.9969 3 1 320s 62 0.9937 62.0 3.230e-06 0.99016 0.9972 2 0 320s 63 0.9942 63.0 2.956e-06 0.99079 0.9975 2 1 320s 68 0.9942 68.0 2.956e-06 0.99079 0.9975 1 0 320s 70 0.9946 70.0 2.694e-06 0.99143 0.9979 2 1 320s 78 0.9951 78.0 2.442e-06 0.99207 0.9982 1 0 320s 80 0.9951 80.0 2.442e-06 0.99207 0.9982 1 0 320s 85 0.9966 85.0 1.695e-06 0.99404 0.9991 2 0 320s 89 0.9966 89.0 1.695e-06 0.99404 0.9991 2 0 320s 90 0.9966 90.0 1.695e-06 0.99404 0.9991 1 0 320s 95 0.9971 95.0 1.448e-06 0.99472 0.9994 2 0 320s 100 0.9976 100.0 1.203e-06 0.99542 0.9997 3 0 320s 101 0.9981 101.0 9.592e-07 0.99613 1.0000 3 1 320s 108 0.9985 108.0 7.169e-07 0.99688 1.0000 2 1 320s 113 0.9990 113.0 4.764e-07 0.99767 1.0000 1 0 320s 116 0.9990 116.0 4.764e-07 0.99767 1.0000 1 0 320s 124 0.9990 124.0 4.764e-07 0.99767 1.0000 2 0 320s 164 0.9990 164.0 4.764e-07 0.99767 1.0000 0 0 320s > 320s > ## gonna play a bit with the state names 320s > dd <- sir.cont 320s > dd$from <- ifelse(dd$from == 0, "initial state", "ventilation") 320s > dd$to <- as.character(dd$to) 320s > for (i in seq_len(nrow(dd))) { 320s + dd$to[i] <- switch(dd$to[i], 320s + "0" = "initial state", 320s + "1" = "ventilation", 320s + "2" = "end of story", 320s + "cens" = "cens" 320s + ) 320s + } 320s > 320s > test <- etm(dd, c("initial state", "ventilation", "end of story"), tra, "cens", 1) 320s > 320s > all.equal(test$est["initial state", "initial state", ], 320s + prob.sir$est["0", "0", ]) 320s [1] TRUE 320s > all.equal(trprob(test, "initial state initial state"), trprob(prob.sir, "0 0")) 320s [1] TRUE 320s > all.equal(trprob(test, "initial state ventilation"), trprob(prob.sir, "0 1")) 320s [1] TRUE 320s > all.equal(trprob(test, "initial state end of story"), trprob(prob.sir, "0 2")) 320s [1] TRUE 320s > 320s > all.equal(trcov(test, "initial state end of story"), trcov(prob.sir, "0 2")) 320s [1] TRUE 320s > 320s > aa <- summary(test) 320s > all.equal(summ.sir[[6]], aa[[6]]) 320s [1] TRUE 320s > all.equal(summ.sir[[4]], aa[[4]]) 320s [1] TRUE 320s > 320s > ### Test on abortion data 320s > 320s > data(abortion) 320s > 320s > from <- rep(0, nrow(abortion)) 320s > to <- abortion$cause 320s > entry <- abortion$entry 320s > exit <- abortion$exit 320s > id <- 1:nrow(abortion) 320s > data <- data.frame(id, from, to, entry, exit, group = abortion$group) 320s > 320s > ## Computation of the CIFs 320s > tra <- matrix(FALSE, 4, 4) 320s > tra[1, 2:4] <- TRUE 320s > 320s > cif.control <- etm(data[data$group == 0, ], c("0", "1", "2", "3"), 320s + tra, NULL, 0) 320s > cif.exposed <- etm(data[data$group == 1, ], c("0", "1", "2", "3"), 320s + tra, NULL, 0) 321s > 321s > all.equal(trprob(cif.control, "0 1"), cif.control$est["0", "1", ]) 321s [1] TRUE 321s > all.equal(trcov(cif.control, c("0 1", "0 2")), cif.control$cov["0 1", "0 2", ]) 321s [1] TRUE 321s > 321s > trprob(cif.control, "0 1") 321s 6 7 8 9 10 11 12 13 321s 0.000000 0.007401 0.014881 0.026509 0.033208 0.037694 0.037694 0.038955 321s 14 17 19 21 24 25 26 30 321s 0.040159 0.040159 0.040159 0.040159 0.040159 0.040159 0.040159 0.040159 321s 31 32 33 34 35 36 37 38 321s 0.040159 0.040159 0.040159 0.040159 0.040159 0.040159 0.040159 0.040159 321s 39 40 41 42 43 321s 0.040159 0.040159 0.040159 0.040159 0.040159 321s > trprob(cif.control, "0 2") 321s 6 7 8 9 10 11 12 13 321s 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 321s 14 17 19 21 24 25 26 30 321s 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.003657 321s 31 32 33 34 35 36 37 38 321s 0.006371 0.008175 0.013543 0.023317 0.031260 0.053197 0.084529 0.179163 321s 39 40 41 42 43 321s 0.322016 0.563121 0.742227 0.793893 0.799059 321s > trprob(cif.control, "0 0") 321s 6 7 8 9 10 11 12 13 321s 0.965812 0.932508 0.887628 0.862433 0.838989 0.822538 0.813099 0.810578 321s 14 17 19 21 24 25 26 30 321s 0.806964 0.805874 0.803810 0.802804 0.801837 0.800883 0.799937 0.796280 321s 31 32 33 34 35 36 37 38 321s 0.793565 0.791762 0.786394 0.776620 0.768677 0.745862 0.714531 0.619897 321s 39 40 41 42 43 321s 0.477043 0.235938 0.056832 0.005167 0.000000 321s > 321s > trcov(cif.control, "0 1") 321s 6 7 8 9 10 11 12 13 321s 0.000e+00 2.719e-05 4.533e-05 6.665e-05 7.698e-05 8.304e-05 8.304e-05 8.444e-05 321s 14 17 19 21 24 25 26 30 321s 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 321s 31 32 33 34 35 36 37 38 321s 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 321s 39 40 41 42 43 321s 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 321s > trcov(cif.control, "0 2") 321s 6 7 8 9 10 11 12 13 321s 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 321s 14 17 19 21 24 25 26 30 321s 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 3.338e-06 321s 31 32 33 34 35 36 37 38 321s 5.784e-06 7.401e-06 1.216e-05 2.072e-05 2.758e-05 4.619e-05 7.202e-05 1.461e-04 321s 39 40 41 42 43 321s 2.470e-04 3.880e-04 4.702e-04 4.903e-04 4.922e-04 321s > trcov(cif.control, "0 0") 321s 6 7 8 9 10 11 12 13 321s 2.822e-04 3.821e-04 4.527e-04 4.748e-04 4.875e-04 4.927e-04 4.941e-04 4.942e-04 321s 14 17 19 21 24 25 26 30 321s 4.941e-04 4.940e-04 4.936e-04 4.933e-04 4.931e-04 4.928e-04 4.926e-04 4.914e-04 321s 31 32 33 34 35 36 37 38 321s 4.905e-04 4.899e-04 4.880e-04 4.846e-04 4.816e-04 4.729e-04 4.601e-04 4.176e-04 321s 39 40 41 42 43 321s 3.425e-04 1.865e-04 4.797e-05 4.441e-06 0.000e+00 321s > 321s > aa <- summary(cif.control) 321s > aa$"0 1" 321s P time var lower upper n.risk n.event 321s 6 0.000000 6 0.000e+00 0.000000 0.00000 117 0 321s 7 0.007401 7 2.719e-05 0.000000 0.01762 261 2 321s 8 0.014881 8 4.533e-05 0.001685 0.02808 374 3 321s 9 0.026509 9 6.665e-05 0.010508 0.04251 458 6 321s 10 0.033208 10 7.698e-05 0.016011 0.05040 515 4 321s 11 0.037694 11 8.304e-05 0.019834 0.05555 561 3 321s 12 0.037694 12 8.304e-05 0.019834 0.05555 610 0 321s 13 0.038955 13 8.444e-05 0.020944 0.05697 645 1 321s 14 0.040159 14 8.571e-05 0.022014 0.05830 673 1 321s 17 0.040159 17 8.571e-05 0.022014 0.05830 740 0 321s 19 0.040159 19 8.571e-05 0.022014 0.05830 781 0 321s 21 0.040159 21 8.571e-05 0.022014 0.05830 799 0 321s 24 0.040159 24 8.571e-05 0.022014 0.05830 830 0 321s 25 0.040159 25 8.571e-05 0.022014 0.05830 841 0 321s 26 0.040159 26 8.571e-05 0.022014 0.05830 846 0 321s 30 0.040159 30 8.571e-05 0.022014 0.05830 875 0 321s 31 0.040159 31 8.571e-05 0.022014 0.05830 880 0 321s 32 0.040159 32 8.571e-05 0.022014 0.05830 880 0 321s 33 0.040159 33 8.571e-05 0.022014 0.05830 885 0 321s 34 0.040159 34 8.571e-05 0.022014 0.05830 885 0 321s 35 0.040159 35 8.571e-05 0.022014 0.05830 880 0 321s 36 0.040159 36 8.571e-05 0.022014 0.05830 876 0 321s 37 0.040159 37 8.571e-05 0.022014 0.05830 857 0 321s 38 0.040159 38 8.571e-05 0.022014 0.05830 823 0 321s 39 0.040159 39 8.571e-05 0.022014 0.05830 716 0 321s 40 0.040159 40 8.571e-05 0.022014 0.05830 554 0 321s 41 0.040159 41 8.571e-05 0.022014 0.05830 274 0 321s 42 0.040159 42 8.571e-05 0.022014 0.05830 66 0 321s 43 0.040159 43 8.571e-05 0.022014 0.05830 6 0 321s > all.equal(aa$"0 1"$P, as.vector(trprob(cif.control, "0 1"))) 321s [1] TRUE 321s > 321s > ### test on los data 321s > 321s > data(los.data) # in package changeLOS 321s > 321s > ## putting los.data in the long format (see changeLOS) 321s > my.observ <- prepare.los.data(x=los.data) 321s > 321s > tra <- matrix(FALSE, 4, 4) 321s > tra[1, 2:4] <- TRUE 321s > tra[2, 3:4] <- TRUE 321s > 321s > tr.prob <- etm(my.observ, c("0","1","2","3"), tra, NULL, 0) 321s > 321s > tr.prob 321s Multistate model with 2 transient state(s) 321s and 2 absorbing state(s) 321s 321s Possible transitions: 321s from to 321s 0 1 321s 0 2 321s 0 3 321s 1 2 321s 1 3 321s 321s Estimate of P(0, 82) 321s 0 1 2 3 321s 0 0 0 0.7474 0.2526 321s 1 0 0 0.7073 0.2927 321s 2 0 0 1.0000 0.0000 321s 3 0 0 0.0000 1.0000 321s 321s > summary(tr.prob) 321s Transition 0 0 321s P time var lower upper n.risk n.event 321s 0.882275 3 1.374e-04 0.8593018 0.905248 756 0 321s 0.112434 15 1.320e-04 0.0899155 0.134952 90 0 321s 0.031746 27 4.066e-05 0.0192484 0.044244 26 0 321s 0.006614 41 8.690e-06 0.0008359 0.012392 5 0 321s 0.002646 61 3.490e-06 0.0000000 0.006307 3 0 321s 0.000000 82 0.000e+00 0.0000000 0.000000 1 0 321s 321s Transition 0 1 321s P time var lower upper n.risk n.event 321s 0.017196 3 2.235e-05 0.0079289 0.02646 756 13 321s 0.063492 15 7.865e-05 0.0461099 0.08087 90 0 321s 0.030423 27 3.902e-05 0.0181805 0.04267 26 1 321s 0.015873 41 2.066e-05 0.0069637 0.02478 5 0 321s 0.005291 61 6.962e-06 0.0001197 0.01046 3 0 321s 0.000000 82 0.000e+00 0.0000000 0.00000 1 0 321s 321s Transition 0 2 321s P time var lower upper n.risk n.event 321s 0.08466 3 0.0001025 0.06481 0.1045 756 64 321s 0.62302 15 0.0003107 0.58847 0.6576 90 4 321s 0.69841 27 0.0002786 0.66570 0.7311 26 1 321s 0.72751 41 0.0002622 0.69578 0.7593 5 0 321s 0.74074 61 0.0002540 0.70950 0.7720 3 1 321s 0.74735 82 0.0002498 0.71638 0.7783 1 1 321s 321s Transition 0 3 321s P time var lower upper n.risk n.event 321s 0.01587 3 2.066e-05 0.006964 0.02478 756 12 321s 0.20106 15 2.125e-04 0.172489 0.22963 90 1 321s 0.23942 27 2.409e-04 0.208999 0.26984 26 0 321s 0.25000 41 2.480e-04 0.219133 0.28087 5 0 321s 0.25132 61 2.489e-04 0.220402 0.28224 3 0 321s 0.25265 82 2.498e-04 0.221671 0.28362 1 0 321s 321s Transition 1 1 321s P time var lower upper n.risk n.event 321s 1.00000 3 0.000e+00 1.00000 1.00000 0 0 321s 0.38661 15 2.358e-03 0.29143 0.48179 51 0 321s 0.12119 27 7.842e-04 0.06630 0.17607 23 0 321s 0.04593 41 2.405e-04 0.01554 0.07633 14 0 321s 0.01531 61 6.579e-05 0.00000 0.03121 4 0 321s 0.00000 82 0.000e+00 0.00000 0.00000 0 0 321s 321s Transition 1 2 321s P time var lower upper n.risk n.event 321s 0.0000 3 0.000000 0.0000 0.0000 0 0 321s 0.4107 15 0.002590 0.3110 0.5104 51 2 321s 0.6082 27 0.002254 0.5151 0.7012 23 1 321s 0.6652 41 0.002064 0.5761 0.7542 14 2 321s 0.6920 61 0.002000 0.6043 0.7796 4 0 321s 0.7073 82 0.001984 0.6200 0.7946 0 0 321s 321s Transition 1 3 321s P time var lower upper n.risk n.event 321s 0.0000 3 0.000000 0.0000 0.0000 0 0 321s 0.2027 15 0.001784 0.1199 0.2855 51 1 321s 0.2706 27 0.001968 0.1837 0.3576 23 0 321s 0.2889 41 0.001982 0.2016 0.3761 14 0 321s 0.2927 61 0.001984 0.2054 0.3800 4 0 321s 0.2927 82 0.001984 0.2054 0.3800 0 0 321s 321s > 321s > cLOS <- etm::clos(tr.prob, aw = TRUE) 321s > 321s > cLOS 321s The expected change in length of stay is: 321s 1.975 321s 321s Alternative weighting: 321s 321s Expected change in LOS with weight.1: 2.097 321s Expected change in LOS with weight.other: 1.951 321s > 321s > 321s > ### Tests on pseudo values 321s > t_pseudo <- closPseudo(my.observ, c("0","1","2","3"), tra, NULL, 321s + formula = ~ 1, aw = TRUE) 337s > 337s > cLOS$e.phi == t_pseudo$theta[, "e.phi"] 337s [,1] 337s [1,] TRUE 337s > cLOS$e.phi.weights.1 == t_pseudo$theta[, "e.phi.weights.1"] 337s [,1] 337s [1,] TRUE 337s > cLOS$e.phi.weights.other == t_pseudo$theta[, "e.phi.weights.other"] 337s [,1] 337s [1,] TRUE 337s > 337s > mean(t_pseudo$pseudoData$ps.e.phi) 337s [1] 1.968 337s > 337s > ### tests on etmprep 337s > 337s > ### creation of fake data in the wild format, following an illness-death model 337s > ## transition times 337s > tdisease <- c(3, 4, 3, 6, 8, 9) 337s > tdeath <- c(6, 9, 8, 6, 8, 9) 337s > 337s > ## transition status 337s > stat.disease <- c(1, 1, 1, 0, 0, 0) 337s > stat.death <- c(1, 1, 1, 1, 1, 0) 337s > 337s > ## a covariate that we want to keep in the new data 337s > set.seed(1313) 337s > cova <- rbinom(6, 1, 0.5) 337s > 337s > dat <- data.frame(tdisease, tdeath, 337s + stat.disease, stat.death, 337s + cova) 337s > 337s > ## Possible transitions 337s > tra <- matrix(FALSE, 3, 3) 337s > tra[1, 2:3] <- TRUE 337s > tra[2, 3] <- TRUE 337s > 337s > ## data preparation 337s > newdat <- etmprep(c(NA, "tdisease", "tdeath"), 337s + c(NA, "stat.disease", "stat.death"), 337s + data = dat, tra = tra, 337s + cens.name = "cens", keep = "cova") 337s > 337s > newdat 337s id entry exit from to cova 337s 1 1 0 3 0 1 1 337s 2 1 3 6 1 2 1 337s 3 2 0 4 0 1 0 337s 4 2 4 9 1 2 0 337s 5 3 0 3 0 1 1 337s 6 3 3 8 1 2 1 337s 7 4 0 6 0 2 0 337s 8 5 0 8 0 2 1 337s 9 6 0 9 0 cens 1 337s > 337s > ref <- data.frame(id = c(1, 1, 2, 2, 3, 3, 4, 5, 6), 337s + entry = c(0, 3, 0, 4, 0, 3, 0, 0, 0), 337s + exit = c(3, 6, 4, 9, 3, 8, 6, 8, 9), 337s + from = c(0, 1, 0, 1, 0, 1, 0, 0, 0), 337s + to = c(rep(c(1, 2), 3), 2, 2, "cens"), 337s + cova = c(1, 1, 0, 0, 1, 1, 0, 1, 1)) 337s > ref$from <- factor(as.character(ref$from), levels = c("0", "1", "2", "cens")) 337s > ref$to <- factor(as.character(ref$to), levels = c("0", "1", "2", "cens")) 337s > 337s > all.equal(ref, newdat) 337s [1] TRUE 337s > 337s > 337s > ###################################### 337s > ### Test the stratified calls 337s > ###################################### 337s > 337s > if (require("kmi", quietly = TRUE)) { 337s + library(etm) 337s + 337s + data(icu.pneu) 337s + my.icu.pneu <- icu.pneu 337s + 337s + my.icu.pneu <- my.icu.pneu[order(my.icu.pneu$id, my.icu.pneu$start), ] 337s + masque <- diff(my.icu.pneu$id) 337s + 337s + my.icu.pneu$from <- 0 337s + my.icu.pneu$from[c(1, masque) == 0] <- 1 337s + 337s + my.icu.pneu$to2 <- my.icu.pneu$event 337s + my.icu.pneu$to2[my.icu.pneu$status == 0] <- "cens" 337s + my.icu.pneu$to2[c(masque, 1) == 0] <- 1 337s + 337s + 337s + my.icu.pneu$to <- ifelse(my.icu.pneu$to2 %in% c(2, 3), 2, 337s + my.icu.pneu$to2) 337s + 337s + my.icu.pneu <- my.icu.pneu[, c("id", "start", "stop", "from", "to", 337s + "to2", "age", "sex")] 337s + names(my.icu.pneu)[c(2, 3)] <- c("entry", "exit") 337s + 337s + bouh_strat <- etm(my.icu.pneu, c("0", "1", "2"), tra_ill(), "cens", 0, strata = "sex") 337s + 337s + bouh_female <- etm(my.icu.pneu[my.icu.pneu$sex == "F", ], 337s + c("0", "1", "2"), tra_ill(), "cens", 0) 337s + 337s + all(bouh_strat[[1]]$est == bouh_female$est) 337s + 337s + ## Test the summary 337s + the_summary <- summary(bouh_strat) 337s + the_summary 337s + 337s + ## Test trprob 337s + all(trprob(bouh_strat, "0 1")[[1]] == trprob(bouh_female, "0 1")) 337s + all(trprob(bouh_strat, "0 1", c(0, 5, 10, 15))[[1]] == trprob(bouh_female, "0 1", c(0, 5, 10, 15))) 337s + 337s + ## Test trcov 337s + all(trcov(bouh_strat, "0 1")[[1]] == trcov(bouh_female, "0 1")) 337s + all(trcov(bouh_strat, c("0 1", "0 2"))[[1]] == trcov(bouh_female, c("0 1", "0 2"))) 337s + all(trcov(bouh_strat, "0 1", c(0, 5, 10, 15))[[1]] == trcov(bouh_female, "0 1", c(0, 5, 10, 15))) 337s + } else { 337s + print("These tests require the kmi package") 337s + } 338s [1] TRUE 338s > 338s > options(old) 338s > 338s autopkgtest [15:29:54]: test run-unit-test: -----------------------] 338s autopkgtest [15:29:54]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 338s run-unit-test PASS 339s autopkgtest [15:29:55]: test pkg-r-autopkgtest: preparing testbed 339s Reading package lists... 339s Building dependency tree... 339s Reading state information... 340s Starting pkgProblemResolver with broken count: 0 340s Starting 2 pkgProblemResolver with broken count: 0 340s Done 341s The following NEW packages will be installed: 341s build-essential cpp cpp-14 cpp-14-aarch64-linux-gnu cpp-aarch64-linux-gnu 341s dctrl-tools g++ g++-14 g++-14-aarch64-linux-gnu g++-aarch64-linux-gnu gcc 341s gcc-14 gcc-14-aarch64-linux-gnu gcc-aarch64-linux-gnu gfortran gfortran-14 341s gfortran-14-aarch64-linux-gnu gfortran-aarch64-linux-gnu icu-devtools 341s libasan8 libblas-dev libbz2-dev libcc1-0 libdeflate-dev libgcc-14-dev 341s libgfortran-14-dev libhwasan0 libicu-dev libisl23 libitm1 libjpeg-dev 341s libjpeg-turbo8-dev libjpeg8-dev liblapack-dev liblsan0 liblzma-dev libmpc3 341s libncurses-dev libpcre2-16-0 libpcre2-32-0 libpcre2-dev libpcre2-posix3 341s libpkgconf3 libpng-dev libreadline-dev libstdc++-14-dev libtirpc-dev 341s libtsan2 libubsan1 pkg-r-autopkgtest pkgconf pkgconf-bin r-base-dev 341s r-cran-backports r-cran-broom r-cran-cli r-cran-colorspace r-cran-cpp11 341s r-cran-dplyr r-cran-fansi r-cran-farver r-cran-geepack r-cran-generics 341s r-cran-ggplot2 r-cran-glue r-cran-gtable r-cran-isoband r-cran-labeling 341s r-cran-lifecycle r-cran-magrittr r-cran-mass r-cran-mgcv r-cran-munsell 341s r-cran-nlme r-cran-pillar r-cran-pkgconfig r-cran-purrr r-cran-r6 341s r-cran-rcolorbrewer r-cran-rlang r-cran-scales r-cran-stringi r-cran-stringr 341s r-cran-tibble r-cran-tidyr r-cran-tidyselect r-cran-utf8 r-cran-vctrs 341s r-cran-viridislite r-cran-withr zlib1g-dev 341s 0 upgraded, 91 newly installed, 0 to remove and 0 not upgraded. 341s Need to get 124 MB of archives. 341s After this operation, 385 MB of additional disk space will be used. 341s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 libisl23 arm64 0.27-1 [676 kB] 342s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 libmpc3 arm64 1.3.1-1build2 [56.8 kB] 342s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp-14-aarch64-linux-gnu arm64 14.2.0-17ubuntu3 [10.6 MB] 353s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp-14 arm64 14.2.0-17ubuntu3 [1028 B] 353s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp-aarch64-linux-gnu arm64 4:14.2.0-1ubuntu1 [5558 B] 353s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp arm64 4:14.2.0-1ubuntu1 [22.4 kB] 353s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 libcc1-0 arm64 15-20250222-0ubuntu1 [44.2 kB] 353s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 libitm1 arm64 15-20250222-0ubuntu1 [28.0 kB] 353s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 libasan8 arm64 15-20250222-0ubuntu1 [2924 kB] 357s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 liblsan0 arm64 15-20250222-0ubuntu1 [1319 kB] 358s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 libtsan2 arm64 15-20250222-0ubuntu1 [2694 kB] 361s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 libubsan1 arm64 15-20250222-0ubuntu1 [1178 kB] 362s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 libhwasan0 arm64 15-20250222-0ubuntu1 [1642 kB] 364s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 libgcc-14-dev arm64 14.2.0-17ubuntu3 [2593 kB] 367s Get:15 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc-14-aarch64-linux-gnu arm64 14.2.0-17ubuntu3 [20.9 MB] 390s Get:16 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc-14 arm64 14.2.0-17ubuntu3 [526 kB] 391s Get:17 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc-aarch64-linux-gnu arm64 4:14.2.0-1ubuntu1 [1200 B] 391s Get:18 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc arm64 4:14.2.0-1ubuntu1 [4998 B] 391s Get:19 http://ftpmaster.internal/ubuntu plucky/main arm64 libstdc++-14-dev arm64 14.2.0-17ubuntu3 [2499 kB] 393s Get:20 http://ftpmaster.internal/ubuntu plucky/main arm64 g++-14-aarch64-linux-gnu arm64 14.2.0-17ubuntu3 [12.1 MB] 406s Get:21 http://ftpmaster.internal/ubuntu plucky/main arm64 g++-14 arm64 14.2.0-17ubuntu3 [21.8 kB] 406s Get:22 http://ftpmaster.internal/ubuntu plucky/main arm64 g++-aarch64-linux-gnu arm64 4:14.2.0-1ubuntu1 [956 B] 406s Get:23 http://ftpmaster.internal/ubuntu plucky/main arm64 g++ arm64 4:14.2.0-1ubuntu1 [1080 B] 406s Get:24 http://ftpmaster.internal/ubuntu plucky/main arm64 build-essential arm64 12.10ubuntu1 [4932 B] 406s Get:25 http://ftpmaster.internal/ubuntu plucky/main arm64 dctrl-tools arm64 2.24-3build3 [103 kB] 407s Get:26 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran-14-dev arm64 14.2.0-17ubuntu3 [498 kB] 407s Get:27 http://ftpmaster.internal/ubuntu plucky/main arm64 gfortran-14-aarch64-linux-gnu arm64 14.2.0-17ubuntu3 [11.4 MB] 419s Get:28 http://ftpmaster.internal/ubuntu plucky/main arm64 gfortran-14 arm64 14.2.0-17ubuntu3 [13.6 kB] 419s Get:29 http://ftpmaster.internal/ubuntu plucky/main arm64 gfortran-aarch64-linux-gnu arm64 4:14.2.0-1ubuntu1 [1022 B] 419s Get:30 http://ftpmaster.internal/ubuntu plucky/main arm64 gfortran arm64 4:14.2.0-1ubuntu1 [1166 B] 419s Get:31 http://ftpmaster.internal/ubuntu plucky/main arm64 icu-devtools arm64 76.1-1ubuntu2 [213 kB] 420s Get:32 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas-dev arm64 3.12.1-2 [126 kB] 420s Get:33 http://ftpmaster.internal/ubuntu plucky/main arm64 libbz2-dev arm64 1.0.8-6 [36.1 kB] 420s Get:34 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate-dev arm64 1.23-1 [53.7 kB] 420s Get:35 http://ftpmaster.internal/ubuntu plucky/main arm64 libicu-dev arm64 76.1-1ubuntu2 [12.2 MB] 434s Get:36 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg-turbo8-dev arm64 2.1.5-3ubuntu2 [306 kB] 434s Get:37 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg8-dev arm64 8c-2ubuntu11 [1484 B] 434s Get:38 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg-dev arm64 8c-2ubuntu11 [1482 B] 434s Get:39 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack-dev arm64 3.12.1-2 [4439 kB] 440s Get:40 http://ftpmaster.internal/ubuntu plucky/main arm64 libncurses-dev arm64 6.5+20250216-2 [389 kB] 440s Get:41 http://ftpmaster.internal/ubuntu plucky/main arm64 libpcre2-16-0 arm64 10.45-1 [222 kB] 440s Get:42 http://ftpmaster.internal/ubuntu plucky/main arm64 libpcre2-32-0 arm64 10.45-1 [210 kB] 441s Get:43 http://ftpmaster.internal/ubuntu plucky/main arm64 libpcre2-posix3 arm64 10.45-1 [7084 B] 441s Get:44 http://ftpmaster.internal/ubuntu plucky/main arm64 libpcre2-dev arm64 10.45-1 [768 kB] 441s Get:45 http://ftpmaster.internal/ubuntu plucky/main arm64 libpkgconf3 arm64 1.8.1-4 [31.4 kB] 441s Get:46 http://ftpmaster.internal/ubuntu plucky/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1ubuntu1 [894 kB] 443s Get:47 http://ftpmaster.internal/ubuntu plucky/main arm64 libpng-dev arm64 1.6.47-1 [269 kB] 443s Get:48 http://ftpmaster.internal/ubuntu plucky/main arm64 libreadline-dev arm64 8.2-6 [179 kB] 443s Get:49 http://ftpmaster.internal/ubuntu plucky/main arm64 liblzma-dev arm64 5.6.4-1 [180 kB] 443s Get:50 http://ftpmaster.internal/ubuntu plucky/main arm64 pkgconf-bin arm64 1.8.1-4 [20.9 kB] 443s Get:51 http://ftpmaster.internal/ubuntu plucky/main arm64 pkgconf arm64 1.8.1-4 [16.7 kB] 443s Get:52 http://ftpmaster.internal/ubuntu plucky/main arm64 libtirpc-dev arm64 1.3.4+ds-1.3 [201 kB] 443s Get:53 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-base-dev all 4.4.3-1 [4176 B] 443s Get:54 http://ftpmaster.internal/ubuntu plucky/universe arm64 pkg-r-autopkgtest all 20231212ubuntu1 [6448 B] 443s Get:55 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-backports arm64 1.5.0-2 [121 kB] 444s Get:56 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-cli arm64 3.6.4-1 [1374 kB] 445s Get:57 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-generics all 0.1.3-1 [81.3 kB] 445s Get:58 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-glue arm64 1.8.0-1 [163 kB] 445s Get:59 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-rlang arm64 1.1.5-1 [1707 kB] 447s Get:60 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB] 447s Get:61 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-magrittr arm64 2.0.3-1 [154 kB] 448s Get:62 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-utf8 arm64 1.2.4-1 [140 kB] 448s Get:63 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-vctrs arm64 0.6.5-1 [1327 kB] 449s Get:64 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-pillar all 1.10.1+dfsg-1 [453 kB] 450s Get:65 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-r6 all 2.6.1-1 [101 kB] 450s Get:66 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-fansi arm64 1.0.5-1 [616 kB] 450s Get:67 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-pkgconfig all 2.0.3-2build1 [19.7 kB] 450s Get:68 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-tibble arm64 3.2.1+dfsg-3 [420 kB] 451s Get:69 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-withr all 3.0.2+dfsg-1 [214 kB] 451s Get:70 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-tidyselect arm64 1.2.1+dfsg-1 [222 kB] 451s Get:71 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-dplyr arm64 1.1.4-4 [1534 kB] 453s Get:72 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-purrr arm64 1.0.4-1 [552 kB] 453s Get:73 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-stringi arm64 1.8.4-1build1 [902 kB] 454s Get:74 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-stringr all 1.5.1-1 [290 kB] 454s Get:75 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-cpp11 all 0.5.2-1 [233 kB] 455s Get:76 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-tidyr arm64 1.3.1-1 [1154 kB] 456s Get:77 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-broom all 1.0.7+dfsg-1 [1802 kB] 458s Get:78 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-colorspace arm64 2.1-1+dfsg-1 [1563 kB] 460s Get:79 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-farver arm64 2.1.2-1 [1344 kB] 461s Get:80 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-mass arm64 7.3-64-1 [1110 kB] 462s Get:81 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-geepack arm64 1.3.12-1 [377 kB] 463s Get:82 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-gtable all 0.3.6+dfsg-1 [199 kB] 463s Get:83 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-isoband arm64 0.2.7-1 [1481 kB] 465s Get:84 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-nlme arm64 3.1.167-1 [2311 kB] 467s Get:85 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-mgcv arm64 1.9-1-1 [3248 kB] 471s Get:86 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-labeling all 0.4.3-1 [62.1 kB] 471s Get:87 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-munsell all 0.5.1-1 [213 kB] 471s Get:88 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-rcolorbrewer all 1.1-3-1build1 [55.4 kB] 471s Get:89 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-viridislite all 0.4.2-2 [1088 kB] 472s Get:90 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-scales all 1.3.0-1 [603 kB] 473s Get:91 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-ggplot2 all 3.5.1+dfsg-1 [3940 kB] 478s Fetched 124 MB in 2min 17s (907 kB/s) 478s Selecting previously unselected package libisl23:arm64. 478s (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 ... 86185 files and directories currently installed.) 478s Preparing to unpack .../00-libisl23_0.27-1_arm64.deb ... 478s Unpacking libisl23:arm64 (0.27-1) ... 478s Selecting previously unselected package libmpc3:arm64. 478s Preparing to unpack .../01-libmpc3_1.3.1-1build2_arm64.deb ... 478s Unpacking libmpc3:arm64 (1.3.1-1build2) ... 478s Selecting previously unselected package cpp-14-aarch64-linux-gnu. 478s Preparing to unpack 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libhwasan0:arm64 (15-20250222-0ubuntu1) ... 479s Selecting previously unselected package libgcc-14-dev:arm64. 479s Preparing to unpack .../13-libgcc-14-dev_14.2.0-17ubuntu3_arm64.deb ... 479s Unpacking libgcc-14-dev:arm64 (14.2.0-17ubuntu3) ... 479s Selecting previously unselected package gcc-14-aarch64-linux-gnu. 479s Preparing to unpack .../14-gcc-14-aarch64-linux-gnu_14.2.0-17ubuntu3_arm64.deb ... 479s Unpacking gcc-14-aarch64-linux-gnu (14.2.0-17ubuntu3) ... 479s Selecting previously unselected package gcc-14. 479s Preparing to unpack .../15-gcc-14_14.2.0-17ubuntu3_arm64.deb ... 479s Unpacking gcc-14 (14.2.0-17ubuntu3) ... 479s Selecting previously unselected package gcc-aarch64-linux-gnu. 479s Preparing to unpack .../16-gcc-aarch64-linux-gnu_4%3a14.2.0-1ubuntu1_arm64.deb ... 479s Unpacking gcc-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 479s Selecting previously unselected package gcc. 479s Preparing to unpack .../17-gcc_4%3a14.2.0-1ubuntu1_arm64.deb ... 479s Unpacking gcc (4:14.2.0-1ubuntu1) ... 480s Selecting previously unselected package libstdc++-14-dev:arm64. 480s Preparing to unpack .../18-libstdc++-14-dev_14.2.0-17ubuntu3_arm64.deb ... 480s Unpacking libstdc++-14-dev:arm64 (14.2.0-17ubuntu3) ... 480s Selecting previously unselected package g++-14-aarch64-linux-gnu. 480s Preparing to unpack .../19-g++-14-aarch64-linux-gnu_14.2.0-17ubuntu3_arm64.deb ... 480s Unpacking g++-14-aarch64-linux-gnu (14.2.0-17ubuntu3) ... 480s Selecting previously unselected package g++-14. 480s Preparing to unpack .../20-g++-14_14.2.0-17ubuntu3_arm64.deb ... 480s Unpacking g++-14 (14.2.0-17ubuntu3) ... 480s Selecting previously unselected package g++-aarch64-linux-gnu. 480s Preparing to unpack .../21-g++-aarch64-linux-gnu_4%3a14.2.0-1ubuntu1_arm64.deb ... 480s Unpacking g++-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 480s Selecting previously unselected package g++. 480s Preparing to unpack .../22-g++_4%3a14.2.0-1ubuntu1_arm64.deb ... 480s Unpacking g++ (4:14.2.0-1ubuntu1) ... 480s Selecting previously unselected package build-essential. 480s Preparing to unpack .../23-build-essential_12.10ubuntu1_arm64.deb ... 480s Unpacking build-essential (12.10ubuntu1) ... 480s Selecting previously unselected package dctrl-tools. 480s Preparing to unpack .../24-dctrl-tools_2.24-3build3_arm64.deb ... 480s Unpacking dctrl-tools (2.24-3build3) ... 480s Selecting previously unselected package libgfortran-14-dev:arm64. 480s Preparing to unpack .../25-libgfortran-14-dev_14.2.0-17ubuntu3_arm64.deb ... 480s Unpacking libgfortran-14-dev:arm64 (14.2.0-17ubuntu3) ... 480s Selecting previously unselected package gfortran-14-aarch64-linux-gnu. 480s Preparing to unpack .../26-gfortran-14-aarch64-linux-gnu_14.2.0-17ubuntu3_arm64.deb ... 480s Unpacking gfortran-14-aarch64-linux-gnu (14.2.0-17ubuntu3) ... 481s Selecting previously unselected package gfortran-14. 481s Preparing to unpack .../27-gfortran-14_14.2.0-17ubuntu3_arm64.deb ... 481s Unpacking gfortran-14 (14.2.0-17ubuntu3) ... 481s Selecting previously unselected package gfortran-aarch64-linux-gnu. 481s Preparing to unpack .../28-gfortran-aarch64-linux-gnu_4%3a14.2.0-1ubuntu1_arm64.deb ... 481s Unpacking gfortran-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 481s Selecting previously unselected package gfortran. 481s Preparing to unpack .../29-gfortran_4%3a14.2.0-1ubuntu1_arm64.deb ... 481s Unpacking gfortran (4:14.2.0-1ubuntu1) ... 481s Selecting previously unselected package icu-devtools. 481s Preparing to unpack .../30-icu-devtools_76.1-1ubuntu2_arm64.deb ... 481s Unpacking icu-devtools (76.1-1ubuntu2) ... 481s Selecting previously unselected package libblas-dev:arm64. 481s Preparing to unpack .../31-libblas-dev_3.12.1-2_arm64.deb ... 481s Unpacking libblas-dev:arm64 (3.12.1-2) ... 481s Selecting previously unselected package libbz2-dev:arm64. 481s Preparing to unpack .../32-libbz2-dev_1.0.8-6_arm64.deb ... 481s Unpacking libbz2-dev:arm64 (1.0.8-6) ... 481s Selecting previously unselected package libdeflate-dev:arm64. 481s Preparing to unpack .../33-libdeflate-dev_1.23-1_arm64.deb ... 481s Unpacking libdeflate-dev:arm64 (1.23-1) ... 481s Selecting previously unselected package libicu-dev:arm64. 481s Preparing to unpack .../34-libicu-dev_76.1-1ubuntu2_arm64.deb ... 481s Unpacking libicu-dev:arm64 (76.1-1ubuntu2) ... 481s Selecting previously unselected package libjpeg-turbo8-dev:arm64. 481s Preparing to unpack .../35-libjpeg-turbo8-dev_2.1.5-3ubuntu2_arm64.deb ... 481s Unpacking libjpeg-turbo8-dev:arm64 (2.1.5-3ubuntu2) ... 481s Selecting previously unselected package libjpeg8-dev:arm64. 481s Preparing to unpack .../36-libjpeg8-dev_8c-2ubuntu11_arm64.deb ... 481s Unpacking libjpeg8-dev:arm64 (8c-2ubuntu11) ... 481s Selecting previously unselected package libjpeg-dev:arm64. 481s Preparing to unpack .../37-libjpeg-dev_8c-2ubuntu11_arm64.deb ... 481s Unpacking libjpeg-dev:arm64 (8c-2ubuntu11) ... 481s Selecting previously unselected package liblapack-dev:arm64. 481s Preparing to unpack .../38-liblapack-dev_3.12.1-2_arm64.deb ... 481s Unpacking liblapack-dev:arm64 (3.12.1-2) ... 481s Selecting previously unselected package libncurses-dev:arm64. 481s Preparing to unpack .../39-libncurses-dev_6.5+20250216-2_arm64.deb ... 481s Unpacking libncurses-dev:arm64 (6.5+20250216-2) ... 482s Selecting previously unselected package libpcre2-16-0:arm64. 482s Preparing to unpack .../40-libpcre2-16-0_10.45-1_arm64.deb ... 482s Unpacking libpcre2-16-0:arm64 (10.45-1) ... 482s Selecting previously unselected package libpcre2-32-0:arm64. 482s Preparing to unpack .../41-libpcre2-32-0_10.45-1_arm64.deb ... 482s Unpacking libpcre2-32-0:arm64 (10.45-1) ... 482s Selecting previously unselected package libpcre2-posix3:arm64. 482s Preparing to unpack .../42-libpcre2-posix3_10.45-1_arm64.deb ... 482s Unpacking libpcre2-posix3:arm64 (10.45-1) ... 482s Selecting previously unselected package libpcre2-dev:arm64. 482s Preparing to unpack .../43-libpcre2-dev_10.45-1_arm64.deb ... 482s Unpacking libpcre2-dev:arm64 (10.45-1) ... 482s Selecting previously unselected package libpkgconf3:arm64. 482s Preparing to unpack .../44-libpkgconf3_1.8.1-4_arm64.deb ... 482s Unpacking libpkgconf3:arm64 (1.8.1-4) ... 482s Selecting previously unselected package zlib1g-dev:arm64. 482s Preparing to unpack .../45-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1ubuntu1_arm64.deb ... 482s Unpacking zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 482s Selecting previously unselected package libpng-dev:arm64. 482s Preparing to unpack .../46-libpng-dev_1.6.47-1_arm64.deb ... 482s Unpacking libpng-dev:arm64 (1.6.47-1) ... 482s Selecting previously unselected package libreadline-dev:arm64. 482s Preparing to unpack .../47-libreadline-dev_8.2-6_arm64.deb ... 482s Unpacking libreadline-dev:arm64 (8.2-6) ... 482s Selecting previously unselected package liblzma-dev:arm64. 482s Preparing to unpack .../48-liblzma-dev_5.6.4-1_arm64.deb ... 482s Unpacking liblzma-dev:arm64 (5.6.4-1) ... 482s Selecting previously unselected package pkgconf-bin. 482s Preparing to unpack .../49-pkgconf-bin_1.8.1-4_arm64.deb ... 482s Unpacking pkgconf-bin (1.8.1-4) ... 482s Selecting previously unselected package pkgconf:arm64. 482s Preparing to unpack .../50-pkgconf_1.8.1-4_arm64.deb ... 482s Unpacking pkgconf:arm64 (1.8.1-4) ... 482s Selecting previously unselected package libtirpc-dev:arm64. 482s Preparing to unpack .../51-libtirpc-dev_1.3.4+ds-1.3_arm64.deb ... 482s Unpacking libtirpc-dev:arm64 (1.3.4+ds-1.3) ... 482s Selecting previously unselected package r-base-dev. 482s Preparing to unpack .../52-r-base-dev_4.4.3-1_all.deb ... 482s Unpacking r-base-dev (4.4.3-1) ... 482s Selecting previously unselected package pkg-r-autopkgtest. 482s Preparing to unpack .../53-pkg-r-autopkgtest_20231212ubuntu1_all.deb ... 482s Unpacking pkg-r-autopkgtest (20231212ubuntu1) ... 482s Selecting previously unselected package r-cran-backports. 482s Preparing to unpack .../54-r-cran-backports_1.5.0-2_arm64.deb ... 482s Unpacking r-cran-backports (1.5.0-2) ... 482s Selecting previously unselected package r-cran-cli. 482s Preparing to unpack .../55-r-cran-cli_3.6.4-1_arm64.deb ... 482s Unpacking r-cran-cli (3.6.4-1) ... 482s Selecting previously unselected package r-cran-generics. 482s Preparing to unpack .../56-r-cran-generics_0.1.3-1_all.deb ... 482s Unpacking r-cran-generics (0.1.3-1) ... 482s Selecting previously unselected package r-cran-glue. 482s Preparing to unpack .../57-r-cran-glue_1.8.0-1_arm64.deb ... 482s Unpacking r-cran-glue (1.8.0-1) ... 482s Selecting previously unselected package r-cran-rlang. 482s Preparing to unpack .../58-r-cran-rlang_1.1.5-1_arm64.deb ... 482s Unpacking r-cran-rlang (1.1.5-1) ... 482s Selecting previously unselected package r-cran-lifecycle. 482s Preparing to unpack .../59-r-cran-lifecycle_1.0.4+dfsg-1_all.deb ... 482s Unpacking r-cran-lifecycle (1.0.4+dfsg-1) ... 482s Selecting previously unselected package r-cran-magrittr. 483s Preparing to unpack .../60-r-cran-magrittr_2.0.3-1_arm64.deb ... 483s Unpacking r-cran-magrittr (2.0.3-1) ... 483s Selecting previously unselected package r-cran-utf8. 483s Preparing to unpack .../61-r-cran-utf8_1.2.4-1_arm64.deb ... 483s Unpacking r-cran-utf8 (1.2.4-1) ... 483s Selecting previously unselected package r-cran-vctrs. 483s Preparing to unpack .../62-r-cran-vctrs_0.6.5-1_arm64.deb ... 483s Unpacking r-cran-vctrs (0.6.5-1) ... 483s Selecting previously unselected package r-cran-pillar. 483s Preparing to unpack .../63-r-cran-pillar_1.10.1+dfsg-1_all.deb ... 483s Unpacking r-cran-pillar (1.10.1+dfsg-1) ... 483s Selecting previously unselected package r-cran-r6. 483s Preparing to unpack .../64-r-cran-r6_2.6.1-1_all.deb ... 483s Unpacking r-cran-r6 (2.6.1-1) ... 483s Selecting previously unselected package r-cran-fansi. 483s Preparing to unpack .../65-r-cran-fansi_1.0.5-1_arm64.deb ... 483s Unpacking r-cran-fansi (1.0.5-1) ... 483s Selecting previously unselected package r-cran-pkgconfig. 483s Preparing to unpack .../66-r-cran-pkgconfig_2.0.3-2build1_all.deb ... 483s Unpacking r-cran-pkgconfig (2.0.3-2build1) ... 483s Selecting previously unselected package r-cran-tibble. 483s Preparing to unpack .../67-r-cran-tibble_3.2.1+dfsg-3_arm64.deb ... 483s Unpacking r-cran-tibble (3.2.1+dfsg-3) ... 483s Selecting previously unselected package r-cran-withr. 483s Preparing to unpack .../68-r-cran-withr_3.0.2+dfsg-1_all.deb ... 483s Unpacking r-cran-withr (3.0.2+dfsg-1) ... 483s Selecting previously unselected package r-cran-tidyselect. 483s Preparing to unpack .../69-r-cran-tidyselect_1.2.1+dfsg-1_arm64.deb ... 483s Unpacking r-cran-tidyselect (1.2.1+dfsg-1) ... 483s Selecting previously unselected package r-cran-dplyr. 483s Preparing to unpack .../70-r-cran-dplyr_1.1.4-4_arm64.deb ... 483s Unpacking r-cran-dplyr (1.1.4-4) ... 483s Selecting previously unselected package r-cran-purrr. 483s Preparing to unpack .../71-r-cran-purrr_1.0.4-1_arm64.deb ... 483s Unpacking r-cran-purrr (1.0.4-1) ... 483s Selecting previously unselected package r-cran-stringi. 483s Preparing to unpack .../72-r-cran-stringi_1.8.4-1build1_arm64.deb ... 483s Unpacking r-cran-stringi (1.8.4-1build1) ... 483s Selecting previously unselected package r-cran-stringr. 483s Preparing to unpack .../73-r-cran-stringr_1.5.1-1_all.deb ... 483s Unpacking r-cran-stringr (1.5.1-1) ... 483s Selecting previously unselected package r-cran-cpp11. 483s Preparing to unpack .../74-r-cran-cpp11_0.5.2-1_all.deb ... 483s Unpacking r-cran-cpp11 (0.5.2-1) ... 483s Selecting previously unselected package r-cran-tidyr. 483s Preparing to unpack .../75-r-cran-tidyr_1.3.1-1_arm64.deb ... 483s Unpacking r-cran-tidyr (1.3.1-1) ... 483s Selecting previously unselected package r-cran-broom. 483s Preparing to unpack .../76-r-cran-broom_1.0.7+dfsg-1_all.deb ... 483s Unpacking r-cran-broom (1.0.7+dfsg-1) ... 483s Selecting previously unselected package r-cran-colorspace. 483s Preparing to unpack .../77-r-cran-colorspace_2.1-1+dfsg-1_arm64.deb ... 483s Unpacking r-cran-colorspace (2.1-1+dfsg-1) ... 483s Selecting previously unselected package r-cran-farver. 484s Preparing to unpack .../78-r-cran-farver_2.1.2-1_arm64.deb ... 484s Unpacking r-cran-farver (2.1.2-1) ... 484s Selecting previously unselected package r-cran-mass. 484s Preparing to unpack .../79-r-cran-mass_7.3-64-1_arm64.deb ... 484s Unpacking r-cran-mass (7.3-64-1) ... 484s Selecting previously unselected package r-cran-geepack. 484s Preparing to unpack .../80-r-cran-geepack_1.3.12-1_arm64.deb ... 484s Unpacking r-cran-geepack (1.3.12-1) ... 484s Selecting previously unselected package r-cran-gtable. 484s Preparing to unpack .../81-r-cran-gtable_0.3.6+dfsg-1_all.deb ... 484s Unpacking r-cran-gtable (0.3.6+dfsg-1) ... 484s Selecting previously unselected package r-cran-isoband. 484s Preparing to unpack .../82-r-cran-isoband_0.2.7-1_arm64.deb ... 484s Unpacking r-cran-isoband (0.2.7-1) ... 484s Selecting previously unselected package r-cran-nlme. 484s Preparing to unpack .../83-r-cran-nlme_3.1.167-1_arm64.deb ... 484s Unpacking r-cran-nlme (3.1.167-1) ... 484s Selecting previously unselected package r-cran-mgcv. 484s Preparing to unpack .../84-r-cran-mgcv_1.9-1-1_arm64.deb ... 484s Unpacking r-cran-mgcv (1.9-1-1) ... 484s Selecting previously unselected package r-cran-labeling. 484s Preparing to unpack .../85-r-cran-labeling_0.4.3-1_all.deb ... 484s Unpacking r-cran-labeling (0.4.3-1) ... 484s Selecting previously unselected package r-cran-munsell. 484s Preparing to unpack .../86-r-cran-munsell_0.5.1-1_all.deb ... 484s Unpacking r-cran-munsell (0.5.1-1) ... 484s Selecting previously unselected package r-cran-rcolorbrewer. 484s Preparing to unpack .../87-r-cran-rcolorbrewer_1.1-3-1build1_all.deb ... 484s Unpacking r-cran-rcolorbrewer (1.1-3-1build1) ... 484s Selecting previously unselected package r-cran-viridislite. 484s Preparing to unpack .../88-r-cran-viridislite_0.4.2-2_all.deb ... 484s Unpacking r-cran-viridislite (0.4.2-2) ... 484s Selecting previously unselected package r-cran-scales. 484s Preparing to unpack .../89-r-cran-scales_1.3.0-1_all.deb ... 484s Unpacking r-cran-scales (1.3.0-1) ... 484s Selecting previously unselected package r-cran-ggplot2. 484s Preparing to unpack .../90-r-cran-ggplot2_3.5.1+dfsg-1_all.deb ... 484s Unpacking r-cran-ggplot2 (3.5.1+dfsg-1) ... 484s Setting up libjpeg-turbo8-dev:arm64 (2.1.5-3ubuntu2) ... 484s Setting up libncurses-dev:arm64 (6.5+20250216-2) ... 484s Setting up r-cran-rlang (1.1.5-1) ... 484s Setting up r-cran-withr (3.0.2+dfsg-1) ... 484s Setting up r-cran-backports (1.5.0-2) ... 484s Setting up r-cran-generics (0.1.3-1) ... 484s Setting up r-cran-fansi (1.0.5-1) ... 484s Setting up r-cran-mass (7.3-64-1) ... 484s Setting up libreadline-dev:arm64 (8.2-6) ... 484s Setting up r-cran-glue (1.8.0-1) ... 484s Setting up r-cran-cli (3.6.4-1) ... 484s Setting up r-cran-lifecycle (1.0.4+dfsg-1) ... 485s Setting up libpcre2-16-0:arm64 (10.45-1) ... 485s Setting up r-cran-pkgconfig (2.0.3-2build1) ... 485s Setting up libpcre2-32-0:arm64 (10.45-1) ... 485s Setting up r-cran-utf8 (1.2.4-1) ... 485s Setting up libtirpc-dev:arm64 (1.3.4+ds-1.3) ... 485s Setting up libpkgconf3:arm64 (1.8.1-4) ... 485s Setting up r-cran-colorspace (2.1-1+dfsg-1) ... 485s Setting up r-cran-stringi (1.8.4-1build1) ... 485s Setting up r-cran-cpp11 (0.5.2-1) ... 485s Setting up r-cran-rcolorbrewer (1.1-3-1build1) ... 485s Setting up r-cran-isoband (0.2.7-1) ... 485s Setting up libmpc3:arm64 (1.3.1-1build2) ... 485s Setting up r-cran-gtable (0.3.6+dfsg-1) ... 485s Setting up r-cran-labeling (0.4.3-1) ... 485s Setting up icu-devtools (76.1-1ubuntu2) ... 485s Setting up pkgconf-bin (1.8.1-4) ... 485s Setting up r-cran-nlme (3.1.167-1) ... 485s Setting up r-cran-farver (2.1.2-1) ... 485s Setting up liblzma-dev:arm64 (5.6.4-1) ... 485s Setting up libubsan1:arm64 (15-20250222-0ubuntu1) ... 485s Setting up zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 485s Setting up r-cran-mgcv (1.9-1-1) ... 485s Setting up libpcre2-posix3:arm64 (10.45-1) ... 485s Setting up r-cran-viridislite (0.4.2-2) ... 485s Setting up libhwasan0:arm64 (15-20250222-0ubuntu1) ... 485s Setting up libasan8:arm64 (15-20250222-0ubuntu1) ... 485s Setting up libtsan2:arm64 (15-20250222-0ubuntu1) ... 485s Setting up r-cran-r6 (2.6.1-1) ... 485s Setting up libjpeg8-dev:arm64 (8c-2ubuntu11) ... 485s Setting up libisl23:arm64 (0.27-1) ... 485s Setting up libdeflate-dev:arm64 (1.23-1) ... 485s Setting up libicu-dev:arm64 (76.1-1ubuntu2) ... 485s Setting up r-cran-magrittr (2.0.3-1) ... 485s Setting up libcc1-0:arm64 (15-20250222-0ubuntu1) ... 485s Setting up r-cran-vctrs (0.6.5-1) ... 485s Setting up liblsan0:arm64 (15-20250222-0ubuntu1) ... 485s Setting up libblas-dev:arm64 (3.12.1-2) ... 485s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so to provide /usr/lib/aarch64-linux-gnu/libblas.so (libblas.so-aarch64-linux-gnu) in auto mode 485s Setting up dctrl-tools (2.24-3build3) ... 485s Setting up libitm1:arm64 (15-20250222-0ubuntu1) ... 485s Setting up libbz2-dev:arm64 (1.0.8-6) ... 485s Setting up r-cran-pillar (1.10.1+dfsg-1) ... 485s Setting up r-cran-stringr (1.5.1-1) ... 485s Setting up libpcre2-dev:arm64 (10.45-1) ... 485s Setting up libpng-dev:arm64 (1.6.47-1) ... 485s Setting up r-cran-munsell (0.5.1-1) ... 485s Setting up r-cran-tibble (3.2.1+dfsg-3) ... 485s Setting up libjpeg-dev:arm64 (8c-2ubuntu11) ... 485s Setting up pkgconf:arm64 (1.8.1-4) ... 485s Setting up r-cran-tidyselect (1.2.1+dfsg-1) ... 485s Setting up r-cran-scales (1.3.0-1) ... 485s Setting up liblapack-dev:arm64 (3.12.1-2) ... 485s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so to provide /usr/lib/aarch64-linux-gnu/liblapack.so (liblapack.so-aarch64-linux-gnu) in auto mode 485s Setting up r-cran-purrr (1.0.4-1) ... 485s Setting up cpp-14-aarch64-linux-gnu (14.2.0-17ubuntu3) ... 485s Setting up r-cran-dplyr (1.1.4-4) ... 485s Setting up libgcc-14-dev:arm64 (14.2.0-17ubuntu3) ... 485s Setting up libstdc++-14-dev:arm64 (14.2.0-17ubuntu3) ... 485s Setting up libgfortran-14-dev:arm64 (14.2.0-17ubuntu3) ... 485s Setting up r-cran-ggplot2 (3.5.1+dfsg-1) ... 485s Setting up cpp-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 485s Setting up r-cran-tidyr (1.3.1-1) ... 485s Setting up cpp-14 (14.2.0-17ubuntu3) ... 485s Setting up cpp (4:14.2.0-1ubuntu1) ... 485s Setting up gcc-14-aarch64-linux-gnu (14.2.0-17ubuntu3) ... 485s Setting up gcc-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 485s Setting up g++-14-aarch64-linux-gnu (14.2.0-17ubuntu3) ... 485s Setting up gcc-14 (14.2.0-17ubuntu3) ... 485s Setting up r-cran-broom (1.0.7+dfsg-1) ... 485s Setting up gfortran-14-aarch64-linux-gnu (14.2.0-17ubuntu3) ... 485s Setting up g++-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 485s Setting up gfortran-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 485s Setting up g++-14 (14.2.0-17ubuntu3) ... 485s Setting up gfortran-14 (14.2.0-17ubuntu3) ... 485s Setting up r-cran-geepack (1.3.12-1) ... 485s Setting up gcc (4:14.2.0-1ubuntu1) ... 485s Setting up g++ (4:14.2.0-1ubuntu1) ... 485s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 485s Setting up build-essential (12.10ubuntu1) ... 485s Setting up gfortran (4:14.2.0-1ubuntu1) ... 485s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode 485s 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 485s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode 485s 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 485s Setting up r-base-dev (4.4.3-1) ... 485s Setting up pkg-r-autopkgtest (20231212ubuntu1) ... 485s Processing triggers for libc-bin (2.41-1ubuntu2) ... 485s Processing triggers for man-db (2.13.0-1) ... 486s Processing triggers for install-info (7.1.1-1) ... 487s autopkgtest [15:32:23]: test pkg-r-autopkgtest: /usr/share/dh-r/pkg-r-autopkgtest 487s autopkgtest [15:32:23]: test pkg-r-autopkgtest: [----------------------- 487s Test: Try to load the R library etm 487s 487s R version 4.4.3 (2025-02-28) -- "Trophy Case" 487s Copyright (C) 2025 The R Foundation for Statistical Computing 487s Platform: aarch64-unknown-linux-gnu 487s 487s R is free software and comes with ABSOLUTELY NO WARRANTY. 487s You are welcome to redistribute it under certain conditions. 487s Type 'license()' or 'licence()' for distribution details. 487s 487s R is a collaborative project with many contributors. 487s Type 'contributors()' for more information and 487s 'citation()' on how to cite R or R packages in publications. 487s 487s Type 'demo()' for some demos, 'help()' for on-line help, or 487s 'help.start()' for an HTML browser interface to help. 487s Type 'q()' to quit R. 487s 487s > library('etm') 488s > 488s > 488s Other tests are currently unsupported! 488s They will be progressively added. 489s autopkgtest [15:32:25]: test pkg-r-autopkgtest: -----------------------] 489s autopkgtest [15:32:25]: test pkg-r-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 489s pkg-r-autopkgtest PASS 489s autopkgtest [15:32:25]: @@@@@@@@@@@@@@@@@@@@ summary 489s run-unit-test PASS 489s pkg-r-autopkgtest PASS 495s nova [W] Using flock in prodstack6-arm64 495s flock: timeout while waiting to get lock 495s Creating nova instance adt-plucky-arm64-r-cran-etm-20250315-152416-juju-7f2275-prod-proposed-migration-environment-2-76dbb60c-80c0-4b97-bdfd-ff1dbef18f99 from image adt/ubuntu-plucky-arm64-server-20250315.img (UUID bd6e766c-b51f-4b53-86d6-23aa4d18f524)... 495s nova [W] Timed out waiting for f401ba24-0e84-4361-941b-bdb776946ea6 to get deleted.