0s autopkgtest [17:59:34]: starting date and time: 2025-03-15 17:59:34+0000
0s autopkgtest [17:59:34]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production'
0s autopkgtest [17:59:34]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.lx23frwh/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-s390x --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-s390x-5.secgroup --name adt-plucky-s390x-r-cran-etm-20250315-175934-juju-7f2275-prod-proposed-migration-environment-15-389e059e-c8db-4df6-88e7-d96e3beb5301 --image adt/ubuntu-plucky-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration-s390x -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/
117s autopkgtest [18:01:31]: testbed dpkg architecture: s390x
117s autopkgtest [18:01:31]: testbed apt version: 2.9.33
117s autopkgtest [18:01:31]: @@@@@@@@@@@@@@@@@@@@ test bed setup
118s autopkgtest [18:01:32]: testbed release detected to be: None
118s autopkgtest [18:01:32]: updating testbed package index (apt update)
119s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB]
119s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease
119s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease
119s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease
119s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [379 kB]
120s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [99.7 kB]
120s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB]
120s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x Packages [113 kB]
120s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x c-n-f Metadata [1824 B]
120s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted s390x c-n-f Metadata [116 B]
120s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x Packages [320 kB]
120s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x c-n-f Metadata [13.4 kB]
120s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x Packages [3776 B]
120s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x c-n-f Metadata [240 B]
120s Fetched 1073 kB in 2s (632 kB/s)
121s Reading package lists...
122s + lsb_release --codename --short
122s + RELEASE=plucky
122s + cat
122s + [ plucky != trusty ]
122s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y --allow-downgrades -o Dpkg::Options::=--force-confnew dist-upgrade
122s Reading package lists...
122s Building dependency tree...
122s Reading state information...
122s Calculating upgrade...
122s Calculating upgrade...
122s The following packages were automatically installed and are no longer required:
122s libnsl2 libpython3.12-minimal libpython3.12-stdlib libpython3.12t64
122s linux-headers-6.11.0-8 linux-headers-6.11.0-8-generic
122s linux-modules-6.11.0-8-generic linux-tools-6.11.0-8
122s linux-tools-6.11.0-8-generic
122s Use 'sudo apt autoremove' to remove them.
122s The following packages will be upgraded:
122s pinentry-curses python3-jinja2 strace
122s 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
122s Need to get 652 kB of archives.
122s After this operation, 27.6 kB of additional disk space will be used.
122s Get:1 http://ftpmaster.internal/ubuntu plucky/main s390x strace s390x 6.13+ds-1ubuntu1 [500 kB]
123s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x pinentry-curses s390x 1.3.1-2ubuntu3 [42.9 kB]
123s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x python3-jinja2 all 3.1.5-2ubuntu1 [109 kB]
123s Fetched 652 kB in 1s (714 kB/s)
123s (Reading database ...
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(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 81428 files and directories currently installed.)
123s Preparing to unpack .../strace_6.13+ds-1ubuntu1_s390x.deb ...
123s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ...
123s Preparing to unpack .../pinentry-curses_1.3.1-2ubuntu3_s390x.deb ...
123s Unpacking pinentry-curses (1.3.1-2ubuntu3) over (1.3.1-2ubuntu2) ...
123s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ...
123s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ...
123s Setting up pinentry-curses (1.3.1-2ubuntu3) ...
123s Setting up python3-jinja2 (3.1.5-2ubuntu1) ...
124s Setting up strace (6.13+ds-1ubuntu1) ...
124s Processing triggers for man-db (2.13.0-1) ...
124s + rm /etc/apt/preferences.d/force-downgrade-to-release.pref
124s + /usr/lib/apt/apt-helper analyze-pattern ?true
124s + uname -r
124s + sed s/\./\\./g
124s + running_kernel_pattern=^linux-.*6\.14\.0-10-generic.*
124s + apt list ?obsolete
124s + tail -n+2
124s + grep -v ^linux-.*6\.14\.0-10-generic.*+ cut -d/ -f1
124s
124s + obsolete_pkgs=linux-headers-6.11.0-8-generic
124s linux-headers-6.11.0-8
124s linux-modules-6.11.0-8-generic
124s linux-tools-6.11.0-8-generic
124s linux-tools-6.11.0-8
124s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y purge --autoremove linux-headers-6.11.0-8-generic linux-headers-6.11.0-8 linux-modules-6.11.0-8-generic linux-tools-6.11.0-8-generic linux-tools-6.11.0-8
124s Reading package lists...
124s Building dependency tree...
124s Reading state information...
125s Solving dependencies...
125s The following packages will be REMOVED:
125s libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64*
125s linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic*
125s linux-modules-6.11.0-8-generic* linux-tools-6.11.0-8*
125s linux-tools-6.11.0-8-generic*
125s 0 upgraded, 0 newly installed, 9 to remove and 5 not upgraded.
125s After this operation, 167 MB disk space will be freed.
125s (Reading database ...
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(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 ... 81428 files and directories currently installed.)
125s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ...
125s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ...
125s Removing libpython3.12t64:s390x (3.12.9-1) ...
125s Removing libpython3.12-stdlib:s390x (3.12.9-1) ...
125s Removing libnsl2:s390x (1.3.0-3build3) ...
125s Removing libpython3.12-minimal:s390x (3.12.9-1) ...
125s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ...
125s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ...
126s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ...
126s Processing triggers for libc-bin (2.41-1ubuntu1) ...
126s (Reading database ...
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(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 56328 files and directories currently installed.)
126s Purging configuration files for libpython3.12-minimal:s390x (3.12.9-1) ...
126s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ...
126s + grep -q trusty /etc/lsb-release
126s + [ ! -d /usr/share/doc/unattended-upgrades ]
126s + [ ! -d /usr/share/doc/lxd ]
126s + [ ! -d /usr/share/doc/lxd-client ]
127s + [ ! -d /usr/share/doc/snapd ]
127s + type iptables
127s + cat
127s + chmod 755 /etc/rc.local
127s + . /etc/rc.local
127s + iptables -w -t mangle -A FORWARD -p tcp --tcp-flags SYN,RST SYN -j TCPMSS --clamp-mss-to-pmtu
127s + iptables -A OUTPUT -d 10.255.255.1/32 -p tcp -j DROP
127s + iptables -A OUTPUT -d 10.255.255.2/32 -p tcp -j DROP
127s + uname -m
127s + [ s390x = ppc64le ]
127s + [ -d /run/systemd/system ]
127s + systemd-detect-virt --quiet --vm
127s + mkdir -p /etc/systemd/system/systemd-random-seed.service.d/
127s + cat
127s + grep -q lz4 /etc/initramfs-tools/initramfs.conf
127s + echo COMPRESS=lz4
127s autopkgtest [18:01:41]: upgrading testbed (apt dist-upgrade and autopurge)
127s Reading package lists...
127s Building dependency tree...
127s Reading state information...
127s Calculating upgrade...Starting pkgProblemResolver with broken count: 0
127s Starting 2 pkgProblemResolver with broken count: 0
127s Done
127s Entering ResolveByKeep
127s
127s Calculating upgrade...
128s The following packages will be upgraded:
128s libc-bin libc-dev-bin libc6 libc6-dev locales
128s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
128s Need to get 9512 kB of archives.
128s After this operation, 8192 B of additional disk space will be used.
128s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc6-dev s390x 2.41-1ubuntu2 [1678 kB]
130s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc-dev-bin s390x 2.41-1ubuntu2 [24.3 kB]
130s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc6 s390x 2.41-1ubuntu2 [2892 kB]
132s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc-bin s390x 2.41-1ubuntu2 [671 kB]
133s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x locales all 2.41-1ubuntu2 [4246 kB]
138s Preconfiguring packages ...
138s Fetched 9512 kB in 10s (975 kB/s)
138s (Reading database ...
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(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 56326 files and directories currently installed.)
138s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_s390x.deb ...
138s Unpacking libc6-dev:s390x (2.41-1ubuntu2) over (2.41-1ubuntu1) ...
138s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_s390x.deb ...
138s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ...
138s Preparing to unpack .../libc6_2.41-1ubuntu2_s390x.deb ...
138s Unpacking libc6:s390x (2.41-1ubuntu2) over (2.41-1ubuntu1) ...
138s Setting up libc6:s390x (2.41-1ubuntu2) ...
138s (Reading database ...
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(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 56326 files and directories currently installed.)
138s Preparing to unpack .../libc-bin_2.41-1ubuntu2_s390x.deb ...
138s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ...
138s Setting up libc-bin (2.41-1ubuntu2) ...
138s (Reading database ...
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(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 ... 56326 files and directories currently installed.)
138s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ...
138s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ...
138s Setting up locales (2.41-1ubuntu2) ...
139s Generating locales (this might take a while)...
140s en_US.UTF-8... done
140s Generation complete.
140s Setting up libc-dev-bin (2.41-1ubuntu2) ...
140s Setting up libc6-dev:s390x (2.41-1ubuntu2) ...
140s Processing triggers for man-db (2.13.0-1) ...
140s Processing triggers for systemd (257.3-1ubuntu3) ...
141s Reading package lists...
141s Building dependency tree...
141s Reading state information...
142s Starting pkgProblemResolver with broken count: 0
142s Starting 2 pkgProblemResolver with broken count: 0
142s Done
142s Solving dependencies...
142s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
142s autopkgtest [18:01:56]: rebooting testbed after setup commands that affected boot
162s autopkgtest [18:02:16]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP Wed Mar 12 14:53:49 UTC 2025
164s autopkgtest [18:02:18]: @@@@@@@@@@@@@@@@@@@@ apt-source r-cran-etm
166s Get:1 http://ftpmaster.internal/ubuntu plucky/universe r-cran-etm 1.1.1-1 (dsc) [2148 B]
166s Get:2 http://ftpmaster.internal/ubuntu plucky/universe r-cran-etm 1.1.1-1 (tar) [242 kB]
166s Get:3 http://ftpmaster.internal/ubuntu plucky/universe r-cran-etm 1.1.1-1 (diff) [3564 B]
166s gpgv: Signature made Fri Sep 18 09:39:57 2020 UTC
166s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
166s gpgv: issuer "tille@debian.org"
166s gpgv: Can't check signature: No public key
166s dpkg-source: warning: cannot verify inline signature for ./r-cran-etm_1.1.1-1.dsc: no acceptable signature found
166s autopkgtest [18:02:20]: testing package r-cran-etm version 1.1.1-1
167s autopkgtest [18:02:21]: build not needed
170s autopkgtest [18:02:24]: test run-unit-test: preparing testbed
171s Reading package lists...
171s Building dependency tree...
171s Reading state information...
171s Starting pkgProblemResolver with broken count: 0
171s Starting 2 pkgProblemResolver with broken count: 0
171s Done
171s The following NEW packages will be installed:
171s fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono libblas3
171s libcairo2 libdatrie1 libdeflate0 libfontconfig1 libfreetype6 libgfortran5
171s libgomp1 libgraphite2-3 libharfbuzz0b libice6 libjbig0 libjpeg-turbo8
171s libjpeg8 liblapack3 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0
171s libpaper-utils libpaper2 libpixman-1-0 libsharpyuv0 libsm6 libtcl8.6
171s libthai-data libthai0 libtiff6 libtk8.6 libwebp7 libxcb-render0 libxcb-shm0
171s libxft2 libxrender1 libxss1 libxt6t64 littler r-base-core r-cran-data.table
171s r-cran-dbi r-cran-etm r-cran-kmi r-cran-lattice r-cran-littler r-cran-matrix
171s r-cran-mitools r-cran-pkgkitten r-cran-rcpp r-cran-rcpparmadillo
171s r-cran-survival unzip x11-common xdg-utils zip
171s 0 upgraded, 57 newly installed, 0 to remove and 0 not upgraded.
171s Need to get 60.9 MB of archives.
171s After this operation, 125 MB of additional disk space will be used.
171s Get:1 http://ftpmaster.internal/ubuntu plucky/main s390x libfreetype6 s390x 2.13.3+dfsg-1 [431 kB]
172s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x fonts-dejavu-mono all 2.37-8 [502 kB]
172s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x fonts-dejavu-core all 2.37-8 [835 kB]
173s Get:4 http://ftpmaster.internal/ubuntu plucky/main s390x fontconfig-config s390x 2.15.0-2ubuntu1 [37.5 kB]
173s Get:5 http://ftpmaster.internal/ubuntu plucky/main s390x libfontconfig1 s390x 2.15.0-2ubuntu1 [150 kB]
173s Get:6 http://ftpmaster.internal/ubuntu plucky/main s390x fontconfig s390x 2.15.0-2ubuntu1 [191 kB]
173s Get:7 http://ftpmaster.internal/ubuntu plucky/main s390x libblas3 s390x 3.12.1-2 [252 kB]
173s Get:8 http://ftpmaster.internal/ubuntu plucky/main s390x libpixman-1-0 s390x 0.44.0-3 [201 kB]
174s Get:9 http://ftpmaster.internal/ubuntu plucky/main s390x libxcb-render0 s390x 1.17.0-2 [17.0 kB]
174s Get:10 http://ftpmaster.internal/ubuntu plucky/main s390x libxcb-shm0 s390x 1.17.0-2 [5862 B]
174s Get:11 http://ftpmaster.internal/ubuntu plucky/main s390x libxrender1 s390x 1:0.9.10-1.1build1 [20.4 kB]
174s Get:12 http://ftpmaster.internal/ubuntu plucky/main s390x libcairo2 s390x 1.18.2-2 [580 kB]
174s Get:13 http://ftpmaster.internal/ubuntu plucky/main s390x libdatrie1 s390x 0.2.13-3build1 [20.6 kB]
174s Get:14 http://ftpmaster.internal/ubuntu plucky/main s390x libdeflate0 s390x 1.23-1 [46.1 kB]
174s Get:15 http://ftpmaster.internal/ubuntu plucky/main s390x libgfortran5 s390x 15-20250222-0ubuntu1 [620 kB]
175s Get:16 http://ftpmaster.internal/ubuntu plucky/main s390x libgomp1 s390x 15-20250222-0ubuntu1 [152 kB]
175s Get:17 http://ftpmaster.internal/ubuntu plucky/main s390x libgraphite2-3 s390x 1.3.14-2ubuntu1 [79.8 kB]
175s Get:18 http://ftpmaster.internal/ubuntu plucky/main s390x libharfbuzz0b s390x 10.2.0-1 [538 kB]
175s Get:19 http://ftpmaster.internal/ubuntu plucky/main s390x x11-common all 1:7.7+23ubuntu3 [21.7 kB]
175s Get:20 http://ftpmaster.internal/ubuntu plucky/main s390x libice6 s390x 2:1.1.1-1 [45.4 kB]
175s Get:21 http://ftpmaster.internal/ubuntu plucky/main s390x libjpeg-turbo8 s390x 2.1.5-3ubuntu2 [147 kB]
175s Get:22 http://ftpmaster.internal/ubuntu plucky/main s390x libjpeg8 s390x 8c-2ubuntu11 [2146 B]
175s Get:23 http://ftpmaster.internal/ubuntu plucky/main s390x liblapack3 s390x 3.12.1-2 [2971 kB]
178s Get:24 http://ftpmaster.internal/ubuntu plucky/main s390x libthai-data all 0.1.29-2build1 [158 kB]
178s Get:25 http://ftpmaster.internal/ubuntu plucky/main s390x libthai0 s390x 0.1.29-2build1 [20.7 kB]
178s Get:26 http://ftpmaster.internal/ubuntu plucky/main s390x libpango-1.0-0 s390x 1.56.2-1 [253 kB]
178s Get:27 http://ftpmaster.internal/ubuntu plucky/main s390x libpangoft2-1.0-0 s390x 1.56.2-1 [50.2 kB]
178s Get:28 http://ftpmaster.internal/ubuntu plucky/main s390x libpangocairo-1.0-0 s390x 1.56.2-1 [28.2 kB]
178s Get:29 http://ftpmaster.internal/ubuntu plucky/main s390x libpaper2 s390x 2.2.5-0.3 [17.2 kB]
178s Get:30 http://ftpmaster.internal/ubuntu plucky/main s390x libpaper-utils s390x 2.2.5-0.3 [15.3 kB]
178s Get:31 http://ftpmaster.internal/ubuntu plucky/main s390x libsharpyuv0 s390x 1.5.0-0.1 [16.7 kB]
178s Get:32 http://ftpmaster.internal/ubuntu plucky/main s390x libsm6 s390x 2:1.2.4-1 [18.4 kB]
178s Get:33 http://ftpmaster.internal/ubuntu plucky/main s390x libtcl8.6 s390x 8.6.16+dfsg-1 [1034 kB]
179s Get:34 http://ftpmaster.internal/ubuntu plucky/main s390x libjbig0 s390x 2.1-6.1ubuntu2 [33.1 kB]
179s Get:35 http://ftpmaster.internal/ubuntu plucky/main s390x libwebp7 s390x 1.5.0-0.1 [210 kB]
179s Get:36 http://ftpmaster.internal/ubuntu plucky/main s390x libtiff6 s390x 4.5.1+git230720-4ubuntu4 [217 kB]
180s Get:37 http://ftpmaster.internal/ubuntu plucky/main s390x libxft2 s390x 2.3.6-1build1 [49.6 kB]
180s Get:38 http://ftpmaster.internal/ubuntu plucky/main s390x libxss1 s390x 1:1.2.3-1build3 [7396 B]
180s Get:39 http://ftpmaster.internal/ubuntu plucky/main s390x libtk8.6 s390x 8.6.16-1 [830 kB]
180s Get:40 http://ftpmaster.internal/ubuntu plucky/main s390x libxt6t64 s390x 1:1.2.1-1.2build1 [184 kB]
181s Get:41 http://ftpmaster.internal/ubuntu plucky/main s390x zip s390x 3.0-14ubuntu2 [187 kB]
181s Get:42 http://ftpmaster.internal/ubuntu plucky/main s390x unzip s390x 6.0-28ubuntu6 [186 kB]
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216s Get:55 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-etm s390x 1.1.1-1 [474 kB]
217s Get:56 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-mitools all 2.4-2build1 [265 kB]
217s Get:57 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-kmi all 0.5.5-2build1 [78.3 kB]
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223s autopkgtest [18:03:17]: test run-unit-test: [-----------------------
224s BEGIN TEST test.etmCIF.R
224s
224s R version 4.4.3 (2025-02-28) -- "Trophy Case"
224s Copyright (C) 2025 The R Foundation for Statistical Computing
224s Platform: s390x-ibm-linux-gnu
224s
224s R is free software and comes with ABSOLUTELY NO WARRANTY.
224s You are welcome to redistribute it under certain conditions.
224s Type 'license()' or 'licence()' for distribution details.
224s
224s R is a collaborative project with many contributors.
224s Type 'contributors()' for more information and
224s 'citation()' on how to cite R or R packages in publications.
224s
224s Type 'demo()' for some demos, 'help()' for on-line help, or
224s 'help.start()' for an HTML browser interface to help.
224s Type 'q()' to quit R.
224s
224s > ### test file for etmCIF.
224s > ### Really simple tests and comparison with etm
224s >
224s > old <- options(digits = 5)
224s >
224s > require(etm)
224s Loading required package: etm
225s >
225s > if (!require(survival, quietly = TRUE)) {
225s + print("The following tests require the 'survival' package")
225s + } else {
225s +
225s + data(abortion)
225s +
225s + from <- rep(0, nrow(abortion))
225s + to <- abortion$cause
225s + entry <- abortion$entry
225s + exit <- abortion$exit
225s + id <- 1:nrow(abortion)
225s + data <- data.frame(id, from, to, entry, exit, group = abortion$group)
225s +
225s + ## Computation of the CIFs with etm
225s + tra <- matrix(FALSE, 4, 4)
225s + tra[1, 2:4] <- TRUE
225s +
225s + cif.control <- etm(data[data$group == 0, ], c("0", "1", "2", "3"),
225s + tra, NULL, 0)
225s + cif.exposed <- etm(data[data$group == 1, ], c("0", "1", "2", "3"),
225s + tra, NULL, 0)
225s +
225s +
225s + ## Computation of the CIFs with etmCIF
225s + netm <- etmCIF(Surv(entry, exit, cause != 0) ~ group, abortion,
225s + etype = cause, failcode = 3)
225s +
225s + ### let's do some comparisons :-)
225s +
225s + all.equal(trprob(cif.control, "0 3"), netm[[1]]$est["0", "3", ])
225s + all.equal(trprob(cif.control, "0 2"), netm[[1]]$est["0", "2", ])
225s + all.equal(trprob(cif.control, "0 1"), netm[[1]]$est["0", "1", ])
225s +
225s + all.equal(trprob(cif.exposed, "0 3"), netm[[2]]$est["0", "3", ])
225s + all.equal(trprob(cif.exposed, "0 2"), netm[[2]]$est["0", "2", ])
225s + all.equal(trprob(cif.exposed, "0 1"), netm[[2]]$est["0", "1", ])
225s +
225s +
225s + all.equal(trcov(cif.control, "0 3"), netm[[1]]$cov["0 3", "0 3", ])
225s + all.equal(trcov(cif.control, "0 2"), netm[[1]]$cov["0 2", "0 2", ])
225s + all.equal(trcov(cif.control, "0 1"), netm[[1]]$cov["0 1", "0 1", ])
225s +
225s + all.equal(trcov(cif.exposed, "0 3"), netm[[2]]$cov["0 3", "0 3", ])
225s + all.equal(trcov(cif.exposed, "0 2"), netm[[2]]$cov["0 2", "0 2", ])
225s + all.equal(trcov(cif.exposed, "0 1"), netm[[2]]$cov["0 1", "0 1", ])
225s +
225s +
225s + netm
225s +
225s + ## test on the summary
225s + snetm <- summary(netm)
225s +
225s + snetm
225s +
225s + all.equal(unname(trprob(cif.control, "0 3")), snetm[[1]][[3]]$P)
225s + all.equal(unname(trprob(cif.control, "0 2")), snetm[[1]][[2]]$P)
225s + all.equal(unname(trprob(cif.control, "0 1")), snetm[[1]][[1]]$P)
225s +
225s + all.equal(unname(trprob(cif.exposed, "0 3")), snetm[[2]][[3]]$P)
225s + all.equal(unname(trprob(cif.exposed, "0 2")), snetm[[2]][[2]]$P)
225s + all.equal(unname(trprob(cif.exposed, "0 1")), snetm[[2]][[1]]$P)
225s +
225s + scif.control <- summary(cif.control, ci.fun = "cloglog")
225s + scif.exposed <- summary(cif.exposed, ci.fun = "cloglog")
225s +
225s + all.equal(scif.control[[4]]$lower, snetm[[1]][[3]]$lower)
225s + all.equal(scif.control[[4]]$upper, snetm[[1]][[3]]$upper)
225s +
225s + all.equal(scif.exposed[[4]]$lower, snetm[[2]][[3]]$lower)
225s + all.equal(scif.exposed[[4]]$upper, snetm[[2]][[3]]$upper)
225s + }
225s [1] TRUE
225s >
225s > ### test with factors in the input
225s > abortion$status <- with(abortion, ifelse(cause == 2, "life birth",
225s + ifelse(cause == 1, "ETOP", "spontaneous abortion")))
225s >
225s > abortion$status <- factor(abortion$status)
225s >
225s > netm.factor <- etmCIF(Surv(entry, exit, status != "cens") ~ group, abortion,
225s + etype = status, failcode = "spontaneous abortion")
225s >
225s >
225s > all.equal(trprob(cif.control, "0 3"), netm.factor[[1]]$est["0", "spontaneous abortion", ])
225s [1] TRUE
225s > all.equal(trprob(cif.control, "0 2"), netm.factor[[1]]$est["0", "life birth", ])
225s [1] TRUE
225s >
225s > netm.factor
225s Call: etmCIF(formula = Surv(entry, exit, status != "cens") ~ group,
225s data = abortion, etype = status, failcode = "spontaneous abortion")
225s
225s Covariate: group
225s levels: 0 1
225s
225s
225s group = 0
225s time P se(P) n.event
225s CIF ETOP 43 0.040159 0.0092578 20
225s CIF life birth 43 0.799059 0.0221865 924
225s CIF spontaneous abortion 43 0.160781 0.0213261 69
225s
225s group = 1
225s time P se(P) n.event
225s CIF ETOP 42 0.28511 0.042493 38
225s CIF life birth 42 0.35257 0.042139 92
225s CIF spontaneous abortion 42 0.36232 0.049473 43
225s >
225s > summary(netm.factor)
225s
225s group=0
225s
225s CIF ETOP
225s P time var lower upper n.risk n.event
225s 0.000000 6 0.0000e+00 0.000000 0.000000 117 0
225s 0.038955 13 8.4440e-05 0.024488 0.061694 645 1
225s 0.040159 26 8.5707e-05 0.025513 0.062939 846 0
225s 0.040159 36 8.5707e-05 0.025513 0.062939 876 0
225s 0.040159 40 8.5707e-05 0.025513 0.062939 554 0
225s 0.040159 43 8.5707e-05 0.025513 0.062939 6 0
225s
225s CIF life birth
225s P time var lower upper n.risk n.event
225s 0.000000 6 0.0000e+00 0.000000 0.000000 117 0
225s 0.000000 13 0.0000e+00 0.000000 0.000000 645 0
225s 0.000000 26 0.0000e+00 0.000000 0.000000 846 0
225s 0.053197 36 4.6195e-05 0.041379 0.068268 876 25
225s 0.563121 40 3.8801e-04 0.524924 0.602021 554 280
225s 0.799059 43 4.9224e-04 0.753969 0.840613 6 6
225s
225s CIF spontaneous abortion
225s P time var lower upper n.risk n.event
225s 0.034188 6 0.00028222 0.01297 0.088523 117 4
225s 0.150468 13 0.00045513 0.11360 0.197901 645 1
225s 0.159904 26 0.00045498 0.12274 0.206925 846 1
225s 0.160781 36 0.00045480 0.12360 0.207757 876 1
225s 0.160781 40 0.00045480 0.12360 0.207757 554 0
225s 0.160781 43 0.00045480 0.12360 0.207757 6 0
225s
225s
225s group=1
225s
225s CIF ETOP
225s P time var lower upper n.risk n.event
225s 0.00000 6 0.0000000 0.00000 0.00000 35 0
225s 0.26048 13 0.0017854 0.18795 0.35425 90 0
225s 0.28115 21 0.0018028 0.20742 0.37423 93 1
225s 0.28511 34 0.0018057 0.21116 0.37806 89 0
225s 0.28511 39 0.0018057 0.21116 0.37806 59 0
225s 0.28511 42 0.0018057 0.21116 0.37806 6 0
225s
225s CIF life birth
225s P time var lower upper n.risk n.event
225s 0.000000 6 0.0000e+00 0.000000 0.000000 35 0
225s 0.000000 13 0.0000e+00 0.000000 0.000000 90 0
225s 0.000000 21 0.0000e+00 0.000000 0.000000 93 0
225s 0.023073 34 9.0514e-05 0.010252 0.051504 89 2
225s 0.180156 39 8.0126e-04 0.131765 0.243663 59 13
225s 0.352565 42 1.7757e-03 0.276882 0.441775 6 6
225s
225s CIF spontaneous abortion
225s P time var lower upper n.risk n.event
225s 0.057143 6 0.0015394 0.014605 0.20968 35 2
225s 0.333246 13 0.0025280 0.245337 0.44216 90 4
225s 0.350702 21 0.0024827 0.262769 0.45762 93 0
225s 0.358492 34 0.0024593 0.270627 0.46448 89 0
225s 0.358492 39 0.0024593 0.270627 0.46448 59 0
225s 0.362323 42 0.0024476 0.274499 0.46785 6 0
225s
225s >
225s > ### test with group as a character vector
225s > abortion$ttt <- with(abortion, ifelse(group == 0, "control", "exposed"))
225s > abortion$ttt <- factor(abortion$ttt)
225s >
225s > netm.ttt <- etmCIF(Surv(entry, exit, status != "cens") ~ ttt, abortion,
225s + etype = status, failcode = "spontaneous abortion")
225s >
225s > all.equal(trprob(cif.control, "0 3"), netm.ttt[[1]]$est["0", "spontaneous abortion", ])
225s [1] TRUE
225s > all.equal(trprob(cif.control, "0 2"), netm.ttt[[1]]$est["0", "life birth", ])
225s [1] TRUE
225s >
225s > netm.ttt
225s Call: etmCIF(formula = Surv(entry, exit, status != "cens") ~ ttt, data = abortion,
225s etype = status, failcode = "spontaneous abortion")
225s
225s Covariate: ttt
225s levels: control exposed
225s
225s
225s ttt = control
225s time P se(P) n.event
225s CIF ETOP 43 0.040159 0.0092578 20
225s CIF life birth 43 0.799059 0.0221865 924
225s CIF spontaneous abortion 43 0.160781 0.0213261 69
225s
225s ttt = exposed
225s time P se(P) n.event
225s CIF ETOP 42 0.28511 0.042493 38
225s CIF life birth 42 0.35257 0.042139 92
225s CIF spontaneous abortion 42 0.36232 0.049473 43
225s >
225s > summary(netm.ttt)
225s
225s ttt=control
225s
225s CIF ETOP
225s P time var lower upper n.risk n.event
225s 0.000000 6 0.0000e+00 0.000000 0.000000 117 0
225s 0.038955 13 8.4440e-05 0.024488 0.061694 645 1
225s 0.040159 26 8.5707e-05 0.025513 0.062939 846 0
225s 0.040159 36 8.5707e-05 0.025513 0.062939 876 0
225s 0.040159 40 8.5707e-05 0.025513 0.062939 554 0
225s 0.040159 43 8.5707e-05 0.025513 0.062939 6 0
225s
225s CIF life birth
225s P time var lower upper n.risk n.event
225s 0.000000 6 0.0000e+00 0.000000 0.000000 117 0
225s 0.000000 13 0.0000e+00 0.000000 0.000000 645 0
225s 0.000000 26 0.0000e+00 0.000000 0.000000 846 0
225s 0.053197 36 4.6195e-05 0.041379 0.068268 876 25
225s 0.563121 40 3.8801e-04 0.524924 0.602021 554 280
225s 0.799059 43 4.9224e-04 0.753969 0.840613 6 6
225s
225s CIF spontaneous abortion
225s P time var lower upper n.risk n.event
225s 0.034188 6 0.00028222 0.01297 0.088523 117 4
225s 0.150468 13 0.00045513 0.11360 0.197901 645 1
225s 0.159904 26 0.00045498 0.12274 0.206925 846 1
225s 0.160781 36 0.00045480 0.12360 0.207757 876 1
225s 0.160781 40 0.00045480 0.12360 0.207757 554 0
225s 0.160781 43 0.00045480 0.12360 0.207757 6 0
225s
225s
225s ttt=exposed
225s
225s CIF ETOP
225s P time var lower upper n.risk n.event
225s 0.00000 6 0.0000000 0.00000 0.00000 35 0
225s 0.26048 13 0.0017854 0.18795 0.35425 90 0
225s 0.28115 21 0.0018028 0.20742 0.37423 93 1
225s 0.28511 34 0.0018057 0.21116 0.37806 89 0
225s 0.28511 39 0.0018057 0.21116 0.37806 59 0
225s 0.28511 42 0.0018057 0.21116 0.37806 6 0
225s
225s CIF life birth
225s P time var lower upper n.risk n.event
225s 0.000000 6 0.0000e+00 0.000000 0.000000 35 0
225s 0.000000 13 0.0000e+00 0.000000 0.000000 90 0
225s 0.000000 21 0.0000e+00 0.000000 0.000000 93 0
225s 0.023073 34 9.0514e-05 0.010252 0.051504 89 2
225s 0.180156 39 8.0126e-04 0.131765 0.243663 59 13
225s 0.352565 42 1.7757e-03 0.276882 0.441775 6 6
225s
225s CIF spontaneous abortion
225s P time var lower upper n.risk n.event
225s 0.057143 6 0.0015394 0.014605 0.20968 35 2
225s 0.333246 13 0.0025280 0.245337 0.44216 90 4
225s 0.350702 21 0.0024827 0.262769 0.45762 93 0
225s 0.358492 34 0.0024593 0.270627 0.46448 89 0
225s 0.358492 39 0.0024593 0.270627 0.46448 59 0
225s 0.362323 42 0.0024476 0.274499 0.46785 6 0
225s
225s >
225s >
225s > ### A couple of comparisons with simulated data
225s > set.seed(1313)
225s > time <- rexp(100)
225s > to <- rbinom(100, 2, prob = c(1/3, 1/3, 1/3))
225s > from <- rep(11, 100)
225s > id <- 1:100
225s > cov <- rbinom(100, 1, 0.5)
225s >
225s > dat.s <- data.frame(id, time, from, to, cov)
225s >
225s > traa <- matrix(FALSE, 3, 3)
225s > traa[1, 2:3] <- TRUE
225s >
225s > aa0 <- etm(dat.s[dat.s$cov == 0, ], c("11", "1", "2"), traa, "0", 0)
225s > aa1 <- etm(dat.s[dat.s$cov == 1, ], c("11", "1", "2"), traa, "0", 0)
225s > aa <- etm(dat.s, c("11", "1", "2"), traa, "0", 0)
225s >
225s > test <- etmCIF(Surv(time, to != 0) ~ 1, dat.s, etype = to)
225s >
225s > test.c <- etmCIF(Surv(time, to != 0) ~ cov, dat.s, etype = to)
225s >
225s > all.equal(trprob(aa, "11 1"), test[[1]]$est["0", "1", ])
225s [1] TRUE
225s > all.equal(trprob(aa, "11 2"), test[[1]]$est["0", "2", ])
225s [1] TRUE
225s >
225s > all.equal(trprob(aa0, "11 1"), test.c[[1]]$est["0", "1", ])
225s [1] TRUE
225s > all.equal(trprob(aa0, "11 2"), test.c[[1]]$est["0", "2", ])
225s [1] TRUE
225s >
225s > all.equal(trprob(aa1, "11 1"), test.c[[2]]$est["0", "1", ])
225s [1] TRUE
225s > all.equal(trprob(aa1, "11 2"), test.c[[2]]$est["0", "2", ])
225s [1] TRUE
225s >
225s > test
225s Call: etmCIF(formula = Surv(time, to != 0) ~ 1, data = dat.s, etype = to)
225s
225s time P se(P) n.event
225s CIF 1 4.9088 0.809108 0.079680 45
225s CIF 2 4.9088 0.096618 0.032905 8
225s >
225s > test.c
225s Call: etmCIF(formula = Surv(time, to != 0) ~ cov, data = dat.s, etype = to)
225s
225s Covariate: cov
225s levels: 0 1
225s
225s
225s cov = 0
225s time P se(P) n.event
225s CIF 1 2.1708 0.70246 0.105797 19
225s CIF 2 2.1708 0.11144 0.053384 4
225s
225s cov = 1
225s time P se(P) n.event
225s CIF 1 4.9088 0.80787 0.094051 26
225s CIF 2 4.9088 0.08436 0.040769 4
225s >
225s > summary(test)
225s
225s
225s
225s CIF 1
225s P time var lower upper n.risk n.event
225s 0.01000 0.0092099 0.0000990 0.0014147 0.068863 100 1
225s 0.11430 0.2663096 0.0010542 0.0649454 0.196993 81 1
225s 0.23451 0.7303091 0.0020436 0.1591107 0.337736 54 1
225s 0.40425 1.4299939 0.0032996 0.3020445 0.525741 29 1
225s 0.54593 2.0647206 0.0040836 0.4269008 0.673605 16 1
225s 0.80911 4.9087561 0.0063489 0.6359544 0.933733 2 1
225s
225s CIF 2
225s P time var lower upper n.risk n.event
225s 0.000000 0.0092099 0.00000000 0.000000 0.000000 100 0
225s 0.031657 0.2663096 0.00032353 0.010320 0.094942 81 0
225s 0.067029 0.7303091 0.00070366 0.030598 0.143503 54 0
225s 0.096618 1.4299939 0.00108275 0.049082 0.185474 29 0
225s 0.096618 2.0647206 0.00108275 0.049082 0.185474 16 0
225s 0.096618 4.9087561 0.00108275 0.049082 0.185474 2 0
225s
225s > summary(test.c)
225s
225s cov=0
225s
225s CIF 1
225s P time var lower upper n.risk n.event
225s 0.022222 0.0092099 0.00048285 0.0031605 0.14747 45 1
225s 0.092222 0.2982439 0.00193603 0.0355971 0.22762 36 0
225s 0.226684 0.7021938 0.00450954 0.1241760 0.39250 24 1
225s 0.378128 1.4299939 0.00760870 0.2337884 0.57145 13 1
225s 0.505736 1.6148774 0.00895330 0.3388425 0.69885 10 1
225s 0.702465 2.1708375 0.01119294 0.4944890 0.88399 3 1
225s
225s CIF 2
225s P time var lower upper n.risk n.event
225s 0.000000 0.0092099 0.0000000 0.000000 0.00000 45 0
225s 0.048441 0.2982439 0.0011168 0.012337 0.18013 36 1
225s 0.076411 0.7021938 0.0018104 0.025202 0.21928 24 0
225s 0.111440 1.4299939 0.0028499 0.042676 0.27392 13 0
225s 0.111440 1.6148774 0.0028499 0.042676 0.27392 10 0
225s 0.111440 2.1708375 0.0028499 0.042676 0.27392 3 0
225s
225s
225s cov=1
225s
225s CIF 1
225s P time var lower upper n.risk n.event
225s 0.018182 0.066692 0.00032457 0.0025813 0.12214 55 1
225s 0.112392 0.263808 0.00187215 0.0520925 0.23333 45 1
225s 0.241023 0.730309 0.00374499 0.1440057 0.38685 31 1
225s 0.401201 1.066913 0.00570788 0.2714008 0.56421 19 1
225s 0.592334 2.366275 0.00775985 0.4286230 0.76273 8 1
225s 0.807871 4.908756 0.00884554 0.6023185 0.94771 2 1
225s
225s CIF 2
225s P time var lower upper n.risk n.event
225s 0.000000 0.066692 0.00000000 0.000000 0.00000 55 0
225s 0.037434 0.263808 0.00067458 0.009494 0.14152 45 0
225s 0.059341 0.730309 0.00111295 0.019447 0.17351 31 0
225s 0.084360 1.066913 0.00166213 0.032211 0.21119 19 0
225s 0.084360 2.366275 0.00166213 0.032211 0.21119 8 0
225s 0.084360 4.908756 0.00166213 0.032211 0.21119 2 0
225s
225s >
225s > options(old)
225s >
225s BEGIN TEST tests.etm.R
225s
225s R version 4.4.3 (2025-02-28) -- "Trophy Case"
225s Copyright (C) 2025 The R Foundation for Statistical Computing
225s Platform: s390x-ibm-linux-gnu
225s
225s R is free software and comes with ABSOLUTELY NO WARRANTY.
225s You are welcome to redistribute it under certain conditions.
225s Type 'license()' or 'licence()' for distribution details.
225s
225s R is a collaborative project with many contributors.
225s Type 'contributors()' for more information and
225s 'citation()' on how to cite R or R packages in publications.
225s
225s Type 'demo()' for some demos, 'help()' for on-line help, or
225s 'help.start()' for an HTML browser interface to help.
225s Type 'q()' to quit R.
225s
225s > require(etm)
225s Loading required package: etm
226s >
226s > ## Print with a bit less precision to avoid lots of notes in the comparison
226s > old <- options(digits = 4)
226s >
226s > ### Simple test
226s >
226s > time <- id <- 1:10
226s > from <- rep(0, 10)
226s > to <- rep(1, 10)
226s >
226s > data1 <- data.frame(id, from, to, time)
226s > tra1 <- matrix(FALSE, 2, 2)
226s > tra1[1, 2] <- TRUE
226s >
226s > etm1 <- etm(data1, c("0", "1"), tra1, NULL, 0)
226s >
226s > all.equal(as.vector(trprob(etm1, "0 0")), cumprod((10:1 - 1) / (10:1)))
226s [1] TRUE
226s >
226s > etm1$cov["0 0", "0 0", ]
226s 1 2 3 4 5 6 7 8 9 10
226s 0.009 0.016 0.021 0.024 0.025 0.024 0.021 0.016 0.009 0.000
226s >
226s > all.equal(etm1$cov["0 0", "0 0",], trcov(etm1, "0 0"))
226s [1] TRUE
226s >
226s > ### A simple test from AHR's author, where the first time is censored
226s > if (!require(survival)) {
226s + stop("This test requires the survival package")
226s + }
226s >
226s > data <- data.frame(id=1:10, time=1:10, from=0, to=1, status=TRUE)
226s >
226s > Loading required package: survival
226s tra <- matrix(FALSE, nrow=2, ncol=2)
226s > tra[1, 2] <- TRUE
226s >
226s > data$to[1] <- "cens"
226s > data$status[1] <- FALSE
226s >
226s > fit.km <- survfit(Surv(time, status) ~ 1, data=data)
226s > fit.etm <- etm(data, c("0","1"), tra, "cens", s=0, t="last", covariance=FALSE)
226s >
226s > all.equal(fit.km$surv[data$status], fit.etm$est[1,1,], check.attributes = FALSE)
226s [1] TRUE
226s >
226s > data$to[2] <- "cens"
226s > data$status[2] <- FALSE
226s >
226s > fit.km <- survfit(Surv(time, status) ~ 1, data=data)
226s > fit.etm <- etm(data, c("0","1"), tra, "cens", s=0, t="last", covariance=FALSE)
226s >
226s > all.equal(fit.km$surv[data$status], fit.etm$est[1,1,], check.attributes = FALSE)
226s [1] TRUE
226s >
226s > ### a bit more complicated
226s >
226s > time <- id <- 1:10
226s > from <- rep(0, 10)
226s > to <- rep(c(1, 2), 5)
226s > data2 <- data.frame(id, from, to, time)
226s >
226s > tra2 <- matrix(FALSE, 3, 3)
226s > tra2[1, 2:3] <- TRUE
226s >
226s > etm2 <- etm(data2, c("0", "1", "2"), tra2, NULL, 0)
226s >
226s > aa <- table(time, to)
226s >
226s > cif1 <- cumsum(aa[, 1] / 10)
226s > cif2 <- cumsum(aa[, 2] / 10)
226s > surv <- cumprod((10:1 - 1) / (10:1))
226s >
226s > all.equal(trprob(etm2, "0 1"), cif1)
226s [1] TRUE
226s > all.equal(trprob(etm2, "0 2"), cif2)
226s [1] TRUE
226s > all.equal(as.vector(trprob(etm2, "0 0")), surv)
226s [1] TRUE
226s >
226s > ## a test on id
226s > data2$id <- letters[1:10]
226s >
226s > etm3 <- etm(data2, c("0", "1", "2"), tra2, NULL, 0)
226s >
226s > all.equal(trprob(etm2, "0 1"), trprob(etm3, "0 1"))
226s [1] TRUE
226s > all.equal(trprob(etm2, "0 2"), trprob(etm3, "0 2"))
226s [1] TRUE
226s > all.equal(trprob(etm2, "0 0"), trprob(etm3, "0 0"))
226s [1] TRUE
226s >
226s >
226s > ### Test on sir.cont
226s >
226s > data(sir.cont)
226s >
226s > ## Modification for patients entering and leaving a state
226s > ## at the same date
226s > ## Change on ventilation status is considered
226s > ## to happen before end of hospital stay
226s > sir.cont <- sir.cont[order(sir.cont$id, sir.cont$time), ]
226s > for (i in 2:nrow(sir.cont)) {
226s + if (sir.cont$id[i]==sir.cont$id[i-1]) {
226s + if (sir.cont$time[i]==sir.cont$time[i-1]) {
226s + sir.cont$time[i-1] <- sir.cont$time[i-1] - 0.5
226s + }
226s + }
226s + }
226s >
226s > ### Computation of the transition probabilities
226s > ## Possible transitions.
226s > tra <- matrix(ncol=3,nrow=3,FALSE)
226s > tra[1, 2:3] <- TRUE
226s > tra[2, c(1, 3)] <- TRUE
226s >
226s > ## etm
226s > prob.sir <- etm(sir.cont, c("0", "1", "2"), tra, "cens", 1)
226s >
226s > prob.sir
226s Multistate model with 2 transient state(s)
226s and 1 absorbing state(s)
226s
226s Possible transitions:
226s from to
226s 0 1
226s 0 2
226s 1 0
226s 1 2
226s
226s Estimate of P(1, 183)
226s 0 1 2
226s 0 0 0 1
226s 1 0 0 1
226s 2 0 0 1
226s
226s >
226s > summ.sir <- summary(prob.sir)
226s > all.equal(summ.sir[['0 1']]$P, as.vector(trprob(prob.sir, "0 1")))
226s [1] TRUE
226s > subset(summ.sir[[3]],time<183) # issue with precision on different architectures
226s P time var lower upper n.risk n.event
226s 1.5 0.0000 1.5 0.000e+00 0.00000 0.0000 394 0
226s 2 0.1187 2.0 2.641e-04 0.08683 0.1505 396 47
226s 2.5 0.1187 2.5 2.641e-04 0.08683 0.1505 364 0
226s 3 0.2454 3.0 4.465e-04 0.20398 0.2868 365 54
226s 3.5 0.2454 3.5 4.465e-04 0.20398 0.2868 328 0
226s 4 0.3806 4.0 5.416e-04 0.33501 0.4262 331 62
226s 4.5 0.3806 4.5 5.416e-04 0.33501 0.4262 280 0
226s 5 0.4792 5.0 5.480e-04 0.43333 0.5251 283 48
226s 5.5 0.4792 5.5 5.480e-04 0.43333 0.5251 248 0
226s 6 0.5693 6.0 5.141e-04 0.52482 0.6137 249 47
226s 7 0.6350 7.0 4.665e-04 0.59266 0.6773 212 36
226s 8 0.6795 8.0 4.202e-04 0.63931 0.7197 195 27
226s 8.5 0.6795 8.5 4.202e-04 0.63931 0.7197 172 0
226s 9 0.7325 9.0 3.580e-04 0.69541 0.7696 173 34
226s 10 0.7647 10.0 3.141e-04 0.72992 0.7994 148 21
226s 10.5 0.7647 10.5 3.141e-04 0.72992 0.7994 135 0
226s 11 0.7895 11.0 2.790e-04 0.75674 0.8222 136 18
226s 12 0.8138 12.0 2.420e-04 0.78330 0.8443 129 18
226s 12.5 0.8138 12.5 2.420e-04 0.78330 0.8443 117 0
226s 13 0.8294 13.0 2.182e-04 0.80045 0.8584 118 13
226s 14 0.8452 14.0 1.938e-04 0.81789 0.8725 115 14
226s 15 0.8625 15.0 1.670e-04 0.83714 0.8878 106 15
226s 16 0.8723 16.0 1.522e-04 0.84807 0.8964 93 9
226s 17 0.8852 17.0 1.330e-04 0.86256 0.9078 86 12
226s 17.5 0.8852 17.5 1.330e-04 0.86256 0.9078 77 0
226s 18 0.8960 18.0 1.168e-04 0.87484 0.9172 76 9
226s 19 0.9029 19.0 1.070e-04 0.88261 0.9232 71 7
226s 20 0.9125 20.0 9.367e-05 0.89356 0.9315 64 10
226s 21 0.9161 21.0 8.878e-05 0.89768 0.9346 57 4
226s 22 0.9226 22.0 7.996e-05 0.90504 0.9401 55 6
226s 23 0.9261 23.0 7.537e-05 0.90904 0.9431 51 4
226s 23.5 0.9261 23.5 7.537e-05 0.90904 0.9431 49 0
226s 24 0.9354 24.0 6.292e-05 0.91982 0.9509 50 9
226s 25 0.9385 25.0 5.878e-05 0.92352 0.9536 42 3
226s 26 0.9429 26.0 5.326e-05 0.92863 0.9572 39 5
226s 27 0.9477 27.0 4.749e-05 0.93417 0.9612 35 6
226s 27.5 0.9477 27.5 4.749e-05 0.93417 0.9612 29 0
226s 28 0.9531 28.0 4.093e-05 0.94059 0.9657 30 5
226s 29 0.9567 29.0 3.668e-05 0.94485 0.9686 31 4
226s 30 0.9592 30.0 3.384e-05 0.94779 0.9706 28 3
226s 30.5 0.9592 30.5 3.384e-05 0.94779 0.9706 29 0
226s 31 0.9642 31.0 2.821e-05 0.95383 0.9746 30 6
226s 32 0.9649 32.0 2.752e-05 0.95458 0.9751 25 1
226s 33 0.9669 33.0 2.533e-05 0.95708 0.9768 24 2
226s 34 0.9685 34.0 2.368e-05 0.95900 0.9781 26 2
226s 35 0.9697 35.0 2.252e-05 0.96036 0.9790 28 2
226s 36 0.9702 36.0 2.194e-05 0.96104 0.9794 26 1
226s 37 0.9718 37.0 2.043e-05 0.96290 0.9806 26 2
226s 38 0.9739 38.0 1.831e-05 0.96555 0.9823 25 4
226s 38.5 0.9739 38.5 1.831e-05 0.96555 0.9823 21 0
226s 39 0.9760 39.0 1.643e-05 0.96802 0.9839 23 3
226s 40 0.9769 40.0 1.558e-05 0.96918 0.9847 19 1
226s 41 0.9774 41.0 1.512e-05 0.96981 0.9851 22 1
226s 42 0.9779 42.0 1.476e-05 0.97032 0.9854 22 0
226s 43 0.9798 43.0 1.308e-05 0.97271 0.9869 22 3
226s 44 0.9803 44.0 1.265e-05 0.97333 0.9873 21 1
226s 45 0.9817 45.0 1.157e-05 0.97499 0.9883 19 1
226s 46 0.9822 46.0 1.116e-05 0.97561 0.9887 17 1
226s 47 0.9831 47.0 1.037e-05 0.97683 0.9895 18 2
226s 48 0.9836 48.0 9.987e-06 0.97743 0.9898 17 1
226s 49 0.9841 49.0 9.669e-06 0.97796 0.9901 17 0
226s 50 0.9845 50.0 9.297e-06 0.97856 0.9905 17 1
226s 50.5 0.9845 50.5 9.297e-06 0.97856 0.9905 16 0
226s 51 0.9860 51.0 8.214e-06 0.98037 0.9916 17 3
226s 52 0.9870 52.0 7.513e-06 0.98159 0.9923 14 2
226s 53 0.9879 53.0 6.875e-06 0.98276 0.9930 12 1
226s 54 0.9889 54.0 6.214e-06 0.98397 0.9937 12 2
226s 55 0.9903 55.0 5.254e-06 0.98581 0.9948 10 3
226s 56 0.9913 56.0 4.667e-06 0.98703 0.9955 6 1
226s 57 0.9917 57.0 4.364e-06 0.98765 0.9958 5 1
226s 58 0.9922 58.0 4.064e-06 0.98828 0.9962 4 1
226s 59 0.9927 59.0 3.769e-06 0.98891 0.9965 3 1
226s 60 0.9932 60.0 3.488e-06 0.98953 0.9969 3 1
226s 62 0.9937 62.0 3.230e-06 0.99016 0.9972 2 0
226s 63 0.9942 63.0 2.956e-06 0.99079 0.9975 2 1
226s 68 0.9942 68.0 2.956e-06 0.99079 0.9975 1 0
226s 70 0.9946 70.0 2.694e-06 0.99143 0.9979 2 1
226s 78 0.9951 78.0 2.442e-06 0.99207 0.9982 1 0
226s 80 0.9951 80.0 2.442e-06 0.99207 0.9982 1 0
226s 85 0.9966 85.0 1.695e-06 0.99404 0.9991 2 0
226s 89 0.9966 89.0 1.695e-06 0.99404 0.9991 2 0
226s 90 0.9966 90.0 1.695e-06 0.99404 0.9991 1 0
226s 95 0.9971 95.0 1.448e-06 0.99472 0.9994 2 0
226s 100 0.9976 100.0 1.203e-06 0.99542 0.9997 3 0
226s 101 0.9981 101.0 9.592e-07 0.99613 1.0000 3 1
226s 108 0.9985 108.0 7.169e-07 0.99688 1.0000 2 1
226s 113 0.9990 113.0 4.764e-07 0.99767 1.0000 1 0
226s 116 0.9990 116.0 4.764e-07 0.99767 1.0000 1 0
226s 124 0.9990 124.0 4.764e-07 0.99767 1.0000 2 0
226s 164 0.9990 164.0 4.764e-07 0.99767 1.0000 0 0
226s >
226s > ## gonna play a bit with the state names
226s > dd <- sir.cont
226s > dd$from <- ifelse(dd$from == 0, "initial state", "ventilation")
226s > dd$to <- as.character(dd$to)
226s > for (i in seq_len(nrow(dd))) {
226s + dd$to[i] <- switch(dd$to[i],
226s + "0" = "initial state",
226s + "1" = "ventilation",
226s + "2" = "end of story",
226s + "cens" = "cens"
226s + )
226s + }
226s >
226s > test <- etm(dd, c("initial state", "ventilation", "end of story"), tra, "cens", 1)
226s >
226s > all.equal(test$est["initial state", "initial state", ],
226s + prob.sir$est["0", "0", ])
226s [1] TRUE
226s > all.equal(trprob(test, "initial state initial state"), trprob(prob.sir, "0 0"))
226s [1] TRUE
226s > all.equal(trprob(test, "initial state ventilation"), trprob(prob.sir, "0 1"))
226s [1] TRUE
226s > all.equal(trprob(test, "initial state end of story"), trprob(prob.sir, "0 2"))
226s [1] TRUE
226s >
226s > all.equal(trcov(test, "initial state end of story"), trcov(prob.sir, "0 2"))
226s [1] TRUE
226s >
226s > aa <- summary(test)
226s > all.equal(summ.sir[[6]], aa[[6]])
226s [1] TRUE
226s > all.equal(summ.sir[[4]], aa[[4]])
226s [1] TRUE
226s >
226s > ### Test on abortion data
226s >
226s > data(abortion)
226s >
226s > from <- rep(0, nrow(abortion))
226s > to <- abortion$cause
226s > entry <- abortion$entry
226s > exit <- abortion$exit
226s > id <- 1:nrow(abortion)
226s > data <- data.frame(id, from, to, entry, exit, group = abortion$group)
226s >
226s > ## Computation of the CIFs
226s > tra <- matrix(FALSE, 4, 4)
226s > tra[1, 2:4] <- TRUE
226s >
226s > cif.control <- etm(data[data$group == 0, ], c("0", "1", "2", "3"),
226s + tra, NULL, 0)
226s > cif.exposed <- etm(data[data$group == 1, ], c("0", "1", "2", "3"),
226s + tra, NULL, 0)
226s >
226s > all.equal(trprob(cif.control, "0 1"), cif.control$est["0", "1", ])
226s [1] TRUE
226s > all.equal(trcov(cif.control, c("0 1", "0 2")), cif.control$cov["0 1", "0 2", ])
226s [1] TRUE
226s >
226s > trprob(cif.control, "0 1")
226s 6 7 8 9 10 11 12 13
226s 0.000000 0.007401 0.014881 0.026509 0.033208 0.037694 0.037694 0.038955
226s 14 17 19 21 24 25 26 30
226s 0.040159 0.040159 0.040159 0.040159 0.040159 0.040159 0.040159 0.040159
226s 31 32 33 34 35 36 37 38
226s 0.040159 0.040159 0.040159 0.040159 0.040159 0.040159 0.040159 0.040159
226s 39 40 41 42 43
226s 0.040159 0.040159 0.040159 0.040159 0.040159
226s > trprob(cif.control, "0 2")
226s 6 7 8 9 10 11 12 13
226s 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
226s 14 17 19 21 24 25 26 30
226s 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.003657
226s 31 32 33 34 35 36 37 38
226s 0.006371 0.008175 0.013543 0.023317 0.031260 0.053197 0.084529 0.179163
226s 39 40 41 42 43
226s 0.322016 0.563121 0.742227 0.793893 0.799059
226s > trprob(cif.control, "0 0")
226s 6 7 8 9 10 11 12 13
226s 0.965812 0.932508 0.887628 0.862433 0.838989 0.822538 0.813099 0.810578
226s 14 17 19 21 24 25 26 30
226s 0.806964 0.805874 0.803810 0.802804 0.801837 0.800883 0.799937 0.796280
226s 31 32 33 34 35 36 37 38
226s 0.793565 0.791762 0.786394 0.776620 0.768677 0.745862 0.714531 0.619897
226s 39 40 41 42 43
226s 0.477043 0.235938 0.056832 0.005167 0.000000
226s >
226s > trcov(cif.control, "0 1")
226s 6 7 8 9 10 11 12 13
226s 0.000e+00 2.719e-05 4.533e-05 6.665e-05 7.698e-05 8.304e-05 8.304e-05 8.444e-05
226s 14 17 19 21 24 25 26 30
226s 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05
226s 31 32 33 34 35 36 37 38
226s 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05
226s 39 40 41 42 43
226s 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05
226s > trcov(cif.control, "0 2")
226s 6 7 8 9 10 11 12 13
226s 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00
226s 14 17 19 21 24 25 26 30
226s 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 3.338e-06
226s 31 32 33 34 35 36 37 38
226s 5.784e-06 7.401e-06 1.216e-05 2.072e-05 2.758e-05 4.619e-05 7.202e-05 1.461e-04
226s 39 40 41 42 43
226s 2.470e-04 3.880e-04 4.702e-04 4.903e-04 4.922e-04
226s > trcov(cif.control, "0 0")
226s 6 7 8 9 10 11 12 13
226s 2.822e-04 3.821e-04 4.527e-04 4.748e-04 4.875e-04 4.927e-04 4.941e-04 4.942e-04
226s 14 17 19 21 24 25 26 30
226s 4.941e-04 4.940e-04 4.936e-04 4.933e-04 4.931e-04 4.928e-04 4.926e-04 4.914e-04
226s 31 32 33 34 35 36 37 38
226s 4.905e-04 4.899e-04 4.880e-04 4.846e-04 4.816e-04 4.729e-04 4.601e-04 4.176e-04
226s 39 40 41 42 43
226s 3.425e-04 1.865e-04 4.797e-05 4.441e-06 0.000e+00
226s >
226s > aa <- summary(cif.control)
226s > aa$"0 1"
226s P time var lower upper n.risk n.event
226s 6 0.000000 6 0.000e+00 0.000000 0.00000 117 0
226s 7 0.007401 7 2.719e-05 0.000000 0.01762 261 2
226s 8 0.014881 8 4.533e-05 0.001685 0.02808 374 3
226s 9 0.026509 9 6.665e-05 0.010508 0.04251 458 6
226s 10 0.033208 10 7.698e-05 0.016011 0.05040 515 4
226s 11 0.037694 11 8.304e-05 0.019834 0.05555 561 3
226s 12 0.037694 12 8.304e-05 0.019834 0.05555 610 0
226s 13 0.038955 13 8.444e-05 0.020944 0.05697 645 1
226s 14 0.040159 14 8.571e-05 0.022014 0.05830 673 1
226s 17 0.040159 17 8.571e-05 0.022014 0.05830 740 0
226s 19 0.040159 19 8.571e-05 0.022014 0.05830 781 0
226s 21 0.040159 21 8.571e-05 0.022014 0.05830 799 0
226s 24 0.040159 24 8.571e-05 0.022014 0.05830 830 0
226s 25 0.040159 25 8.571e-05 0.022014 0.05830 841 0
226s 26 0.040159 26 8.571e-05 0.022014 0.05830 846 0
226s 30 0.040159 30 8.571e-05 0.022014 0.05830 875 0
226s 31 0.040159 31 8.571e-05 0.022014 0.05830 880 0
226s 32 0.040159 32 8.571e-05 0.022014 0.05830 880 0
226s 33 0.040159 33 8.571e-05 0.022014 0.05830 885 0
226s 34 0.040159 34 8.571e-05 0.022014 0.05830 885 0
226s 35 0.040159 35 8.571e-05 0.022014 0.05830 880 0
226s 36 0.040159 36 8.571e-05 0.022014 0.05830 876 0
226s 37 0.040159 37 8.571e-05 0.022014 0.05830 857 0
226s 38 0.040159 38 8.571e-05 0.022014 0.05830 823 0
226s 39 0.040159 39 8.571e-05 0.022014 0.05830 716 0
226s 40 0.040159 40 8.571e-05 0.022014 0.05830 554 0
226s 41 0.040159 41 8.571e-05 0.022014 0.05830 274 0
226s 42 0.040159 42 8.571e-05 0.022014 0.05830 66 0
226s 43 0.040159 43 8.571e-05 0.022014 0.05830 6 0
226s > all.equal(aa$"0 1"$P, as.vector(trprob(cif.control, "0 1")))
226s [1] TRUE
226s >
226s > ### test on los data
226s >
226s > data(los.data) # in package changeLOS
226s >
226s > ## putting los.data in the long format (see changeLOS)
226s > my.observ <- prepare.los.data(x=los.data)
226s >
226s > tra <- matrix(FALSE, 4, 4)
226s > tra[1, 2:4] <- TRUE
226s > tra[2, 3:4] <- TRUE
226s >
226s > tr.prob <- etm(my.observ, c("0","1","2","3"), tra, NULL, 0)
226s >
226s > tr.prob
226s Multistate model with 2 transient state(s)
226s and 2 absorbing state(s)
226s
226s Possible transitions:
226s from to
226s 0 1
226s 0 2
226s 0 3
226s 1 2
226s 1 3
226s
226s Estimate of P(0, 82)
226s 0 1 2 3
226s 0 0 0 0.7474 0.2526
226s 1 0 0 0.7073 0.2927
226s 2 0 0 1.0000 0.0000
226s 3 0 0 0.0000 1.0000
226s
226s > summary(tr.prob)
226s Transition 0 0
226s P time var lower upper n.risk n.event
226s 0.882275 3 1.374e-04 0.8593018 0.905248 756 0
226s 0.112434 15 1.320e-04 0.0899155 0.134952 90 0
226s 0.031746 27 4.066e-05 0.0192484 0.044244 26 0
226s 0.006614 41 8.690e-06 0.0008359 0.012392 5 0
226s 0.002646 61 3.490e-06 0.0000000 0.006307 3 0
226s 0.000000 82 0.000e+00 0.0000000 0.000000 1 0
226s
226s Transition 0 1
226s P time var lower upper n.risk n.event
226s 0.017196 3 2.235e-05 0.0079289 0.02646 756 13
226s 0.063492 15 7.865e-05 0.0461099 0.08087 90 0
226s 0.030423 27 3.902e-05 0.0181805 0.04267 26 1
226s 0.015873 41 2.066e-05 0.0069637 0.02478 5 0
226s 0.005291 61 6.962e-06 0.0001197 0.01046 3 0
226s 0.000000 82 0.000e+00 0.0000000 0.00000 1 0
226s
226s Transition 0 2
226s P time var lower upper n.risk n.event
226s 0.08466 3 0.0001025 0.06481 0.1045 756 64
226s 0.62302 15 0.0003107 0.58847 0.6576 90 4
226s 0.69841 27 0.0002786 0.66570 0.7311 26 1
226s 0.72751 41 0.0002622 0.69578 0.7593 5 0
226s 0.74074 61 0.0002540 0.70950 0.7720 3 1
226s 0.74735 82 0.0002498 0.71638 0.7783 1 1
226s
226s Transition 0 3
226s P time var lower upper n.risk n.event
226s 0.01587 3 2.066e-05 0.006964 0.02478 756 12
226s 0.20106 15 2.125e-04 0.172489 0.22963 90 1
226s 0.23942 27 2.409e-04 0.208999 0.26984 26 0
226s 0.25000 41 2.480e-04 0.219133 0.28087 5 0
226s 0.25132 61 2.489e-04 0.220402 0.28224 3 0
226s 0.25265 82 2.498e-04 0.221671 0.28362 1 0
226s
226s Transition 1 1
226s P time var lower upper n.risk n.event
226s 1.00000 3 0.000e+00 1.00000 1.00000 0 0
226s 0.38661 15 2.358e-03 0.29143 0.48179 51 0
226s 0.12119 27 7.842e-04 0.06630 0.17607 23 0
226s 0.04593 41 2.405e-04 0.01554 0.07633 14 0
226s 0.01531 61 6.579e-05 0.00000 0.03121 4 0
226s 0.00000 82 0.000e+00 0.00000 0.00000 0 0
226s
226s Transition 1 2
226s P time var lower upper n.risk n.event
226s 0.0000 3 0.000000 0.0000 0.0000 0 0
226s 0.4107 15 0.002590 0.3110 0.5104 51 2
226s 0.6082 27 0.002254 0.5151 0.7012 23 1
226s 0.6652 41 0.002064 0.5761 0.7542 14 2
226s 0.6920 61 0.002000 0.6043 0.7796 4 0
226s 0.7073 82 0.001984 0.6200 0.7946 0 0
226s
226s Transition 1 3
226s P time var lower upper n.risk n.event
226s 0.0000 3 0.000000 0.0000 0.0000 0 0
226s 0.2027 15 0.001784 0.1199 0.2855 51 1
226s 0.2706 27 0.001968 0.1837 0.3576 23 0
226s 0.2889 41 0.001982 0.2016 0.3761 14 0
226s 0.2927 61 0.001984 0.2054 0.3800 4 0
226s 0.2927 82 0.001984 0.2054 0.3800 0 0
226s
226s >
226s > cLOS <- etm::clos(tr.prob, aw = TRUE)
226s >
226s > cLOS
226s The expected change in length of stay is:
226s 1.975
226s
226s Alternative weighting:
226s
226s Expected change in LOS with weight.1: 2.097
226s Expected change in LOS with weight.other: 1.951
226s >
226s >
226s > ### Tests on pseudo values
226s > t_pseudo <- closPseudo(my.observ, c("0","1","2","3"), tra, NULL,
226s + formula = ~ 1, aw = TRUE)
237s >
237s > cLOS$e.phi == t_pseudo$theta[, "e.phi"]
237s [,1]
237s [1,] TRUE
237s > cLOS$e.phi.weights.1 == t_pseudo$theta[, "e.phi.weights.1"]
237s [,1]
237s [1,] TRUE
237s > cLOS$e.phi.weights.other == t_pseudo$theta[, "e.phi.weights.other"]
237s [,1]
237s [1,] TRUE
237s >
237s > mean(t_pseudo$pseudoData$ps.e.phi)
237s [1] 1.968
237s >
237s > ### tests on etmprep
237s >
237s > ### creation of fake data in the wild format, following an illness-death model
237s > ## transition times
237s > tdisease <- c(3, 4, 3, 6, 8, 9)
237s > tdeath <- c(6, 9, 8, 6, 8, 9)
237s >
237s > ## transition status
237s > stat.disease <- c(1, 1, 1, 0, 0, 0)
237s > stat.death <- c(1, 1, 1, 1, 1, 0)
237s >
237s > ## a covariate that we want to keep in the new data
237s > set.seed(1313)
237s > cova <- rbinom(6, 1, 0.5)
237s >
237s > dat <- data.frame(tdisease, tdeath,
237s + stat.disease, stat.death,
237s + cova)
237s >
237s > ## Possible transitions
237s > tra <- matrix(FALSE, 3, 3)
237s > tra[1, 2:3] <- TRUE
237s > tra[2, 3] <- TRUE
237s >
237s > ## data preparation
237s > newdat <- etmprep(c(NA, "tdisease", "tdeath"),
237s + c(NA, "stat.disease", "stat.death"),
237s + data = dat, tra = tra,
237s + cens.name = "cens", keep = "cova")
237s >
237s > newdat
237s id entry exit from to cova
237s 1 1 0 3 0 1 1
237s 2 1 3 6 1 2 1
237s 3 2 0 4 0 1 0
237s 4 2 4 9 1 2 0
237s 5 3 0 3 0 1 1
237s 6 3 3 8 1 2 1
237s 7 4 0 6 0 2 0
237s 8 5 0 8 0 2 1
237s 9 6 0 9 0 cens 1
237s >
237s > ref <- data.frame(id = c(1, 1, 2, 2, 3, 3, 4, 5, 6),
237s + entry = c(0, 3, 0, 4, 0, 3, 0, 0, 0),
237s + exit = c(3, 6, 4, 9, 3, 8, 6, 8, 9),
237s + from = c(0, 1, 0, 1, 0, 1, 0, 0, 0),
237s + to = c(rep(c(1, 2), 3), 2, 2, "cens"),
237s + cova = c(1, 1, 0, 0, 1, 1, 0, 1, 1))
237s > ref$from <- factor(as.character(ref$from), levels = c("0", "1", "2", "cens"))
237s > ref$to <- factor(as.character(ref$to), levels = c("0", "1", "2", "cens"))
237s >
237s > all.equal(ref, newdat)
237s [1] TRUE
237s >
237s >
237s > ######################################
237s > ### Test the stratified calls
237s > ######################################
237s >
237s > if (require("kmi", quietly = TRUE)) {
237s + library(etm)
237s +
237s + data(icu.pneu)
237s + my.icu.pneu <- icu.pneu
237s +
237s + my.icu.pneu <- my.icu.pneu[order(my.icu.pneu$id, my.icu.pneu$start), ]
237s + masque <- diff(my.icu.pneu$id)
237s +
237s + my.icu.pneu$from <- 0
237s + my.icu.pneu$from[c(1, masque) == 0] <- 1
237s +
237s + my.icu.pneu$to2 <- my.icu.pneu$event
237s + my.icu.pneu$to2[my.icu.pneu$status == 0] <- "cens"
237s + my.icu.pneu$to2[c(masque, 1) == 0] <- 1
237s +
237s +
237s + my.icu.pneu$to <- ifelse(my.icu.pneu$to2 %in% c(2, 3), 2,
237s + my.icu.pneu$to2)
237s +
237s + my.icu.pneu <- my.icu.pneu[, c("id", "start", "stop", "from", "to",
237s + "to2", "age", "sex")]
237s + names(my.icu.pneu)[c(2, 3)] <- c("entry", "exit")
237s +
237s + bouh_strat <- etm(my.icu.pneu, c("0", "1", "2"), tra_ill(), "cens", 0, strata = "sex")
237s +
237s + bouh_female <- etm(my.icu.pneu[my.icu.pneu$sex == "F", ],
237s + c("0", "1", "2"), tra_ill(), "cens", 0)
237s +
237s + all(bouh_strat[[1]]$est == bouh_female$est)
237s +
237s + ## Test the summary
237s + the_summary <- summary(bouh_strat)
237s + the_summary
237s +
237s + ## Test trprob
237s + all(trprob(bouh_strat, "0 1")[[1]] == trprob(bouh_female, "0 1"))
237s + all(trprob(bouh_strat, "0 1", c(0, 5, 10, 15))[[1]] == trprob(bouh_female, "0 1", c(0, 5, 10, 15)))
237s +
237s + ## Test trcov
237s + all(trcov(bouh_strat, "0 1")[[1]] == trcov(bouh_female, "0 1"))
237s + all(trcov(bouh_strat, c("0 1", "0 2"))[[1]] == trcov(bouh_female, c("0 1", "0 2")))
237s + all(trcov(bouh_strat, "0 1", c(0, 5, 10, 15))[[1]] == trcov(bouh_female, "0 1", c(0, 5, 10, 15)))
237s + } else {
237s + print("These tests require the kmi package")
237s + }
237s [1] TRUE
237s >
237s > options(old)
237s >
237s autopkgtest [18:03:31]: test run-unit-test: -----------------------]
238s autopkgtest [18:03:32]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - -
238s run-unit-test PASS
238s autopkgtest [18:03:32]: test pkg-r-autopkgtest: preparing testbed
238s Reading package lists...
239s Building dependency tree...
239s Reading state information...
239s Starting pkgProblemResolver with broken count: 0
239s Starting 2 pkgProblemResolver with broken count: 0
239s Done
239s The following NEW packages will be installed:
239s build-essential cpp cpp-14 cpp-14-s390x-linux-gnu cpp-s390x-linux-gnu
239s dctrl-tools g++ g++-14 g++-14-s390x-linux-gnu g++-s390x-linux-gnu gcc gcc-14
239s gcc-14-s390x-linux-gnu gcc-s390x-linux-gnu gfortran gfortran-14
239s gfortran-14-s390x-linux-gnu gfortran-s390x-linux-gnu icu-devtools libasan8
239s libblas-dev libbz2-dev libcc1-0 libdeflate-dev libgcc-14-dev
239s libgfortran-14-dev libicu-dev libisl23 libitm1 libjpeg-dev
239s libjpeg-turbo8-dev libjpeg8-dev liblapack-dev liblzma-dev libmpc3
239s libncurses-dev libpcre2-16-0 libpcre2-32-0 libpcre2-dev libpcre2-posix3
239s libpkgconf3 libpng-dev libreadline-dev libstdc++-14-dev libtirpc-dev
239s libubsan1 pkg-r-autopkgtest pkgconf pkgconf-bin r-base-dev r-cran-backports
239s r-cran-broom r-cran-cli r-cran-colorspace r-cran-cpp11 r-cran-dplyr
239s r-cran-fansi r-cran-farver r-cran-geepack r-cran-generics r-cran-ggplot2
239s r-cran-glue r-cran-gtable r-cran-isoband r-cran-labeling r-cran-lifecycle
239s r-cran-magrittr r-cran-mass r-cran-mgcv r-cran-munsell r-cran-nlme
239s r-cran-pillar r-cran-pkgconfig r-cran-purrr r-cran-r6 r-cran-rcolorbrewer
239s r-cran-rlang r-cran-scales r-cran-stringi r-cran-stringr r-cran-tibble
239s r-cran-tidyr r-cran-tidyselect r-cran-utf8 r-cran-vctrs r-cran-viridislite
239s r-cran-withr zlib1g-dev
239s 0 upgraded, 88 newly installed, 0 to remove and 0 not upgraded.
239s Need to get 114 MB of archives.
239s After this operation, 329 MB of additional disk space will be used.
239s Get:1 http://ftpmaster.internal/ubuntu plucky/main s390x libisl23 s390x 0.27-1 [704 kB]
241s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x libmpc3 s390x 1.3.1-1build2 [57.8 kB]
241s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x cpp-14-s390x-linux-gnu s390x 14.2.0-17ubuntu3 [9572 kB]
250s Get:4 http://ftpmaster.internal/ubuntu plucky/main s390x cpp-14 s390x 14.2.0-17ubuntu3 [1028 B]
250s Get:5 http://ftpmaster.internal/ubuntu plucky/main s390x cpp-s390x-linux-gnu s390x 4:14.2.0-1ubuntu1 [5556 B]
250s Get:6 http://ftpmaster.internal/ubuntu plucky/main s390x cpp s390x 4:14.2.0-1ubuntu1 [22.4 kB]
250s Get:7 http://ftpmaster.internal/ubuntu plucky/main s390x libcc1-0 s390x 15-20250222-0ubuntu1 [49.2 kB]
250s Get:8 http://ftpmaster.internal/ubuntu plucky/main s390x libitm1 s390x 15-20250222-0ubuntu1 [31.2 kB]
250s Get:9 http://ftpmaster.internal/ubuntu plucky/main s390x libasan8 s390x 15-20250222-0ubuntu1 [2970 kB]
253s Get:10 http://ftpmaster.internal/ubuntu plucky/main s390x libubsan1 s390x 15-20250222-0ubuntu1 [1212 kB]
254s Get:11 http://ftpmaster.internal/ubuntu plucky/main s390x libgcc-14-dev s390x 14.2.0-17ubuntu3 [1037 kB]
255s Get:12 http://ftpmaster.internal/ubuntu plucky/main s390x gcc-14-s390x-linux-gnu s390x 14.2.0-17ubuntu3 [18.7 MB]
273s Get:13 http://ftpmaster.internal/ubuntu plucky/main s390x gcc-14 s390x 14.2.0-17ubuntu3 [526 kB]
273s Get:14 http://ftpmaster.internal/ubuntu plucky/main s390x gcc-s390x-linux-gnu s390x 4:14.2.0-1ubuntu1 [1204 B]
273s Get:15 http://ftpmaster.internal/ubuntu plucky/main s390x gcc s390x 4:14.2.0-1ubuntu1 [5004 B]
273s Get:16 http://ftpmaster.internal/ubuntu plucky/main s390x libstdc++-14-dev s390x 14.2.0-17ubuntu3 [2611 kB]
276s Get:17 http://ftpmaster.internal/ubuntu plucky/main s390x g++-14-s390x-linux-gnu s390x 14.2.0-17ubuntu3 [11.0 MB]
288s Get:18 http://ftpmaster.internal/ubuntu plucky/main s390x g++-14 s390x 14.2.0-17ubuntu3 [21.8 kB]
288s Get:19 http://ftpmaster.internal/ubuntu plucky/main s390x g++-s390x-linux-gnu s390x 4:14.2.0-1ubuntu1 [956 B]
288s Get:20 http://ftpmaster.internal/ubuntu plucky/main s390x g++ s390x 4:14.2.0-1ubuntu1 [1080 B]
288s Get:21 http://ftpmaster.internal/ubuntu plucky/main s390x build-essential s390x 12.10ubuntu1 [4930 B]
288s Get:22 http://ftpmaster.internal/ubuntu plucky/main s390x dctrl-tools s390x 2.24-3build3 [106 kB]
288s Get:23 http://ftpmaster.internal/ubuntu plucky/main s390x libgfortran-14-dev s390x 14.2.0-17ubuntu3 [654 kB]
289s Get:24 http://ftpmaster.internal/ubuntu plucky/main s390x gfortran-14-s390x-linux-gnu s390x 14.2.0-17ubuntu3 [10.3 MB]
297s Get:25 http://ftpmaster.internal/ubuntu plucky/main s390x gfortran-14 s390x 14.2.0-17ubuntu3 [13.6 kB]
297s Get:26 http://ftpmaster.internal/ubuntu plucky/main s390x gfortran-s390x-linux-gnu s390x 4:14.2.0-1ubuntu1 [1012 B]
297s Get:27 http://ftpmaster.internal/ubuntu plucky/main s390x gfortran s390x 4:14.2.0-1ubuntu1 [1160 B]
297s Get:28 http://ftpmaster.internal/ubuntu plucky/main s390x icu-devtools s390x 76.1-1ubuntu2 [225 kB]
298s Get:29 http://ftpmaster.internal/ubuntu plucky/main s390x libblas-dev s390x 3.12.1-2 [254 kB]
298s Get:30 http://ftpmaster.internal/ubuntu plucky/main s390x libbz2-dev s390x 1.0.8-6 [39.1 kB]
298s Get:31 http://ftpmaster.internal/ubuntu plucky/main s390x libdeflate-dev s390x 1.23-1 [52.2 kB]
298s Get:32 http://ftpmaster.internal/ubuntu plucky/main s390x libicu-dev s390x 76.1-1ubuntu2 [12.2 MB]
308s Get:33 http://ftpmaster.internal/ubuntu plucky/main s390x libjpeg-turbo8-dev s390x 2.1.5-3ubuntu2 [281 kB]
308s Get:34 http://ftpmaster.internal/ubuntu plucky/main s390x libjpeg8-dev s390x 8c-2ubuntu11 [1484 B]
308s Get:35 http://ftpmaster.internal/ubuntu plucky/main s390x libjpeg-dev s390x 8c-2ubuntu11 [1484 B]
308s Get:36 http://ftpmaster.internal/ubuntu plucky/main s390x liblapack-dev s390x 3.12.1-2 [5967 kB]
313s Get:37 http://ftpmaster.internal/ubuntu plucky/main s390x libncurses-dev s390x 6.5+20250216-2 [407 kB]
314s Get:38 http://ftpmaster.internal/ubuntu plucky/main s390x libpcre2-16-0 s390x 10.45-1 [259 kB]
314s Get:39 http://ftpmaster.internal/ubuntu plucky/main s390x libpcre2-32-0 s390x 10.45-1 [245 kB]
314s Get:40 http://ftpmaster.internal/ubuntu plucky/main s390x libpcre2-posix3 s390x 10.45-1 [7080 B]
314s Get:41 http://ftpmaster.internal/ubuntu plucky/main s390x libpcre2-dev s390x 10.45-1 [899 kB]
315s Get:42 http://ftpmaster.internal/ubuntu plucky/main s390x libpkgconf3 s390x 1.8.1-4 [31.2 kB]
315s Get:43 http://ftpmaster.internal/ubuntu plucky/main s390x zlib1g-dev s390x 1:1.3.dfsg+really1.3.1-1ubuntu1 [898 kB]
315s Get:44 http://ftpmaster.internal/ubuntu plucky/main s390x libpng-dev s390x 1.6.47-1 [278 kB]
316s Get:45 http://ftpmaster.internal/ubuntu plucky/main s390x libreadline-dev s390x 8.2-6 [187 kB]
316s Get:46 http://ftpmaster.internal/ubuntu plucky/main s390x liblzma-dev s390x 5.6.4-1 [183 kB]
316s Get:47 http://ftpmaster.internal/ubuntu plucky/main s390x pkgconf-bin s390x 1.8.1-4 [21.5 kB]
316s Get:48 http://ftpmaster.internal/ubuntu plucky/main s390x pkgconf s390x 1.8.1-4 [16.7 kB]
316s Get:49 http://ftpmaster.internal/ubuntu plucky/main s390x libtirpc-dev s390x 1.3.4+ds-1.3 [196 kB]
316s Get:50 http://ftpmaster.internal/ubuntu plucky/universe s390x r-base-dev all 4.4.3-1 [4176 B]
316s Get:51 http://ftpmaster.internal/ubuntu plucky/universe s390x pkg-r-autopkgtest all 20231212ubuntu1 [6448 B]
316s Get:52 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-backports s390x 1.5.0-2 [121 kB]
316s Get:53 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-cli s390x 3.6.4-1 [1379 kB]
317s Get:54 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-generics all 0.1.3-1 [81.3 kB]
317s Get:55 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-glue s390x 1.8.0-1 [164 kB]
318s Get:56 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-rlang s390x 1.1.5-1 [1713 kB]
319s Get:57 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB]
319s Get:58 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-magrittr s390x 2.0.3-1 [154 kB]
319s Get:59 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-utf8 s390x 1.2.4-1 [143 kB]
320s Get:60 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-vctrs s390x 0.6.5-1 [1448 kB]
321s Get:61 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-pillar all 1.10.1+dfsg-1 [453 kB]
321s Get:62 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-r6 all 2.6.1-1 [101 kB]
321s Get:63 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-fansi s390x 1.0.5-1 [615 kB]
322s Get:64 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-pkgconfig all 2.0.3-2build1 [19.7 kB]
322s Get:65 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-tibble s390x 3.2.1+dfsg-3 [420 kB]
322s Get:66 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-withr all 3.0.2+dfsg-1 [214 kB]
322s Get:67 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-tidyselect s390x 1.2.1+dfsg-1 [222 kB]
323s Get:68 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-dplyr s390x 1.1.4-4 [1537 kB]
325s Get:69 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-purrr s390x 1.0.4-1 [553 kB]
325s Get:70 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-stringi s390x 1.8.4-1build1 [917 kB]
325s Get:71 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-stringr all 1.5.1-1 [290 kB]
326s Get:72 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-cpp11 all 0.5.2-1 [233 kB]
326s Get:73 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-tidyr s390x 1.3.1-1 [1157 kB]
327s Get:74 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-broom all 1.0.7+dfsg-1 [1802 kB]
329s Get:75 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-colorspace s390x 2.1-1+dfsg-1 [1567 kB]
331s Get:76 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-farver s390x 2.1.2-1 [1353 kB]
332s Get:77 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-mass s390x 7.3-64-1 [1113 kB]
333s Get:78 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-geepack s390x 1.3.12-1 [425 kB]
335s Get:79 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-gtable all 0.3.6+dfsg-1 [199 kB]
335s Get:80 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-isoband s390x 0.2.7-1 [1481 kB]
335s Get:81 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-nlme s390x 3.1.167-1 [2323 kB]
338s Get:82 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-mgcv s390x 1.9-1-1 [3348 kB]
342s Get:83 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-labeling all 0.4.3-1 [62.1 kB]
342s Get:84 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-munsell all 0.5.1-1 [213 kB]
342s Get:85 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-rcolorbrewer all 1.1-3-1build1 [55.4 kB]
342s Get:86 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-viridislite all 0.4.2-2 [1088 kB]
343s Get:87 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-scales all 1.3.0-1 [603 kB]
343s Get:88 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-ggplot2 all 3.5.1+dfsg-1 [3940 kB]
348s Fetched 114 MB in 1min 48s (1052 kB/s)
348s Selecting previously unselected package libisl23:s390x.
348s (Reading database ...
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348s Preparing to unpack .../00-libisl23_0.27-1_s390x.deb ...
348s Unpacking libisl23:s390x (0.27-1) ...
348s Selecting previously unselected package libmpc3:s390x.
348s Preparing to unpack .../01-libmpc3_1.3.1-1build2_s390x.deb ...
348s Unpacking libmpc3:s390x (1.3.1-1build2) ...
348s Selecting previously unselected package cpp-14-s390x-linux-gnu.
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349s Unpacking g++-s390x-linux-gnu (4:14.2.0-1ubuntu1) ...
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349s Preparing to unpack .../19-g++_4%3a14.2.0-1ubuntu1_s390x.deb ...
349s Unpacking g++ (4:14.2.0-1ubuntu1) ...
349s Selecting previously unselected package build-essential.
349s Preparing to unpack .../20-build-essential_12.10ubuntu1_s390x.deb ...
349s Unpacking build-essential (12.10ubuntu1) ...
349s Selecting previously unselected package dctrl-tools.
349s Preparing to unpack .../21-dctrl-tools_2.24-3build3_s390x.deb ...
349s Unpacking dctrl-tools (2.24-3build3) ...
349s Selecting previously unselected package libgfortran-14-dev:s390x.
349s Preparing to unpack .../22-libgfortran-14-dev_14.2.0-17ubuntu3_s390x.deb ...
349s Unpacking libgfortran-14-dev:s390x (14.2.0-17ubuntu3) ...
349s Selecting previously unselected package gfortran-14-s390x-linux-gnu.
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349s Unpacking gfortran-14-s390x-linux-gnu (14.2.0-17ubuntu3) ...
349s Selecting previously unselected package gfortran-14.
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349s Selecting previously unselected package gfortran-s390x-linux-gnu.
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349s Unpacking gfortran-s390x-linux-gnu (4:14.2.0-1ubuntu1) ...
349s Selecting previously unselected package gfortran.
349s Preparing to unpack .../26-gfortran_4%3a14.2.0-1ubuntu1_s390x.deb ...
349s Unpacking gfortran (4:14.2.0-1ubuntu1) ...
349s Selecting previously unselected package icu-devtools.
349s Preparing to unpack .../27-icu-devtools_76.1-1ubuntu2_s390x.deb ...
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349s Selecting previously unselected package libblas-dev:s390x.
349s Preparing to unpack .../28-libblas-dev_3.12.1-2_s390x.deb ...
349s Unpacking libblas-dev:s390x (3.12.1-2) ...
349s Selecting previously unselected package libbz2-dev:s390x.
349s Preparing to unpack .../29-libbz2-dev_1.0.8-6_s390x.deb ...
349s Unpacking libbz2-dev:s390x (1.0.8-6) ...
349s Selecting previously unselected package libdeflate-dev:s390x.
349s Preparing to unpack .../30-libdeflate-dev_1.23-1_s390x.deb ...
349s Unpacking libdeflate-dev:s390x (1.23-1) ...
349s Selecting previously unselected package libicu-dev:s390x.
349s Preparing to unpack .../31-libicu-dev_76.1-1ubuntu2_s390x.deb ...
349s Unpacking libicu-dev:s390x (76.1-1ubuntu2) ...
349s Selecting previously unselected package libjpeg-turbo8-dev:s390x.
349s Preparing to unpack .../32-libjpeg-turbo8-dev_2.1.5-3ubuntu2_s390x.deb ...
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349s Selecting previously unselected package libjpeg8-dev:s390x.
349s Preparing to unpack .../33-libjpeg8-dev_8c-2ubuntu11_s390x.deb ...
349s Unpacking libjpeg8-dev:s390x (8c-2ubuntu11) ...
349s Selecting previously unselected package libjpeg-dev:s390x.
349s Preparing to unpack .../34-libjpeg-dev_8c-2ubuntu11_s390x.deb ...
349s Unpacking libjpeg-dev:s390x (8c-2ubuntu11) ...
349s Selecting previously unselected package liblapack-dev:s390x.
349s Preparing to unpack .../35-liblapack-dev_3.12.1-2_s390x.deb ...
349s Unpacking liblapack-dev:s390x (3.12.1-2) ...
349s Selecting previously unselected package libncurses-dev:s390x.
349s Preparing to unpack .../36-libncurses-dev_6.5+20250216-2_s390x.deb ...
349s Unpacking libncurses-dev:s390x (6.5+20250216-2) ...
349s Selecting previously unselected package libpcre2-16-0:s390x.
349s Preparing to unpack .../37-libpcre2-16-0_10.45-1_s390x.deb ...
349s Unpacking libpcre2-16-0:s390x (10.45-1) ...
349s Selecting previously unselected package libpcre2-32-0:s390x.
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349s Unpacking libpcre2-32-0:s390x (10.45-1) ...
349s Selecting previously unselected package libpcre2-posix3:s390x.
349s Preparing to unpack .../39-libpcre2-posix3_10.45-1_s390x.deb ...
349s Unpacking libpcre2-posix3:s390x (10.45-1) ...
349s Selecting previously unselected package libpcre2-dev:s390x.
349s Preparing to unpack .../40-libpcre2-dev_10.45-1_s390x.deb ...
349s Unpacking libpcre2-dev:s390x (10.45-1) ...
349s Selecting previously unselected package libpkgconf3:s390x.
349s Preparing to unpack .../41-libpkgconf3_1.8.1-4_s390x.deb ...
349s Unpacking libpkgconf3:s390x (1.8.1-4) ...
349s Selecting previously unselected package zlib1g-dev:s390x.
349s Preparing to unpack .../42-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1ubuntu1_s390x.deb ...
349s Unpacking zlib1g-dev:s390x (1:1.3.dfsg+really1.3.1-1ubuntu1) ...
349s Selecting previously unselected package libpng-dev:s390x.
349s Preparing to unpack .../43-libpng-dev_1.6.47-1_s390x.deb ...
349s Unpacking libpng-dev:s390x (1.6.47-1) ...
349s Selecting previously unselected package libreadline-dev:s390x.
349s Preparing to unpack .../44-libreadline-dev_8.2-6_s390x.deb ...
349s Unpacking libreadline-dev:s390x (8.2-6) ...
349s Selecting previously unselected package liblzma-dev:s390x.
349s Preparing to unpack .../45-liblzma-dev_5.6.4-1_s390x.deb ...
349s Unpacking liblzma-dev:s390x (5.6.4-1) ...
349s Selecting previously unselected package pkgconf-bin.
349s Preparing to unpack .../46-pkgconf-bin_1.8.1-4_s390x.deb ...
349s Unpacking pkgconf-bin (1.8.1-4) ...
349s Selecting previously unselected package pkgconf:s390x.
349s Preparing to unpack .../47-pkgconf_1.8.1-4_s390x.deb ...
349s Unpacking pkgconf:s390x (1.8.1-4) ...
349s Selecting previously unselected package libtirpc-dev:s390x.
349s Preparing to unpack .../48-libtirpc-dev_1.3.4+ds-1.3_s390x.deb ...
349s Unpacking libtirpc-dev:s390x (1.3.4+ds-1.3) ...
349s Selecting previously unselected package r-base-dev.
349s Preparing to unpack .../49-r-base-dev_4.4.3-1_all.deb ...
349s Unpacking r-base-dev (4.4.3-1) ...
349s Selecting previously unselected package pkg-r-autopkgtest.
349s Preparing to unpack .../50-pkg-r-autopkgtest_20231212ubuntu1_all.deb ...
349s Unpacking pkg-r-autopkgtest (20231212ubuntu1) ...
349s Selecting previously unselected package r-cran-backports.
349s Preparing to unpack .../51-r-cran-backports_1.5.0-2_s390x.deb ...
349s Unpacking r-cran-backports (1.5.0-2) ...
349s Selecting previously unselected package r-cran-cli.
349s Preparing to unpack .../52-r-cran-cli_3.6.4-1_s390x.deb ...
349s Unpacking r-cran-cli (3.6.4-1) ...
350s Selecting previously unselected package r-cran-generics.
350s Preparing to unpack .../53-r-cran-generics_0.1.3-1_all.deb ...
350s Unpacking r-cran-generics (0.1.3-1) ...
350s Selecting previously unselected package r-cran-glue.
350s Preparing to unpack .../54-r-cran-glue_1.8.0-1_s390x.deb ...
350s Unpacking r-cran-glue (1.8.0-1) ...
350s Selecting previously unselected package r-cran-rlang.
350s Preparing to unpack .../55-r-cran-rlang_1.1.5-1_s390x.deb ...
350s Unpacking r-cran-rlang (1.1.5-1) ...
350s Selecting previously unselected package r-cran-lifecycle.
350s Preparing to unpack .../56-r-cran-lifecycle_1.0.4+dfsg-1_all.deb ...
350s Unpacking r-cran-lifecycle (1.0.4+dfsg-1) ...
350s Selecting previously unselected package r-cran-magrittr.
350s Preparing to unpack .../57-r-cran-magrittr_2.0.3-1_s390x.deb ...
350s Unpacking r-cran-magrittr (2.0.3-1) ...
350s Selecting previously unselected package r-cran-utf8.
350s Preparing to unpack .../58-r-cran-utf8_1.2.4-1_s390x.deb ...
350s Unpacking r-cran-utf8 (1.2.4-1) ...
350s Selecting previously unselected package r-cran-vctrs.
350s Preparing to unpack .../59-r-cran-vctrs_0.6.5-1_s390x.deb ...
350s Unpacking r-cran-vctrs (0.6.5-1) ...
350s Selecting previously unselected package r-cran-pillar.
350s Preparing to unpack .../60-r-cran-pillar_1.10.1+dfsg-1_all.deb ...
350s Unpacking r-cran-pillar (1.10.1+dfsg-1) ...
350s Selecting previously unselected package r-cran-r6.
350s Preparing to unpack .../61-r-cran-r6_2.6.1-1_all.deb ...
350s Unpacking r-cran-r6 (2.6.1-1) ...
350s Selecting previously unselected package r-cran-fansi.
350s Preparing to unpack .../62-r-cran-fansi_1.0.5-1_s390x.deb ...
350s Unpacking r-cran-fansi (1.0.5-1) ...
350s Selecting previously unselected package r-cran-pkgconfig.
350s Preparing to unpack .../63-r-cran-pkgconfig_2.0.3-2build1_all.deb ...
350s Unpacking r-cran-pkgconfig (2.0.3-2build1) ...
350s Selecting previously unselected package r-cran-tibble.
350s Preparing to unpack .../64-r-cran-tibble_3.2.1+dfsg-3_s390x.deb ...
350s Unpacking r-cran-tibble (3.2.1+dfsg-3) ...
350s Selecting previously unselected package r-cran-withr.
350s Preparing to unpack .../65-r-cran-withr_3.0.2+dfsg-1_all.deb ...
350s Unpacking r-cran-withr (3.0.2+dfsg-1) ...
350s Selecting previously unselected package r-cran-tidyselect.
350s Preparing to unpack .../66-r-cran-tidyselect_1.2.1+dfsg-1_s390x.deb ...
350s Unpacking r-cran-tidyselect (1.2.1+dfsg-1) ...
350s Selecting previously unselected package r-cran-dplyr.
350s Preparing to unpack .../67-r-cran-dplyr_1.1.4-4_s390x.deb ...
350s Unpacking r-cran-dplyr (1.1.4-4) ...
350s Selecting previously unselected package r-cran-purrr.
350s Preparing to unpack .../68-r-cran-purrr_1.0.4-1_s390x.deb ...
350s Unpacking r-cran-purrr (1.0.4-1) ...
350s Selecting previously unselected package r-cran-stringi.
350s Preparing to unpack .../69-r-cran-stringi_1.8.4-1build1_s390x.deb ...
350s Unpacking r-cran-stringi (1.8.4-1build1) ...
350s Selecting previously unselected package r-cran-stringr.
350s Preparing to unpack .../70-r-cran-stringr_1.5.1-1_all.deb ...
350s Unpacking r-cran-stringr (1.5.1-1) ...
350s Selecting previously unselected package r-cran-cpp11.
350s Preparing to unpack .../71-r-cran-cpp11_0.5.2-1_all.deb ...
350s Unpacking r-cran-cpp11 (0.5.2-1) ...
350s Selecting previously unselected package r-cran-tidyr.
350s Preparing to unpack .../72-r-cran-tidyr_1.3.1-1_s390x.deb ...
350s Unpacking r-cran-tidyr (1.3.1-1) ...
350s Selecting previously unselected package r-cran-broom.
350s Preparing to unpack .../73-r-cran-broom_1.0.7+dfsg-1_all.deb ...
350s Unpacking r-cran-broom (1.0.7+dfsg-1) ...
350s Selecting previously unselected package r-cran-colorspace.
350s Preparing to unpack .../74-r-cran-colorspace_2.1-1+dfsg-1_s390x.deb ...
350s Unpacking r-cran-colorspace (2.1-1+dfsg-1) ...
350s Selecting previously unselected package r-cran-farver.
350s Preparing to unpack .../75-r-cran-farver_2.1.2-1_s390x.deb ...
350s Unpacking r-cran-farver (2.1.2-1) ...
350s Selecting previously unselected package r-cran-mass.
350s Preparing to unpack .../76-r-cran-mass_7.3-64-1_s390x.deb ...
350s Unpacking r-cran-mass (7.3-64-1) ...
350s Selecting previously unselected package r-cran-geepack.
350s Preparing to unpack .../77-r-cran-geepack_1.3.12-1_s390x.deb ...
350s Unpacking r-cran-geepack (1.3.12-1) ...
350s Selecting previously unselected package r-cran-gtable.
350s Preparing to unpack .../78-r-cran-gtable_0.3.6+dfsg-1_all.deb ...
350s Unpacking r-cran-gtable (0.3.6+dfsg-1) ...
350s Selecting previously unselected package r-cran-isoband.
350s Preparing to unpack .../79-r-cran-isoband_0.2.7-1_s390x.deb ...
350s Unpacking r-cran-isoband (0.2.7-1) ...
350s Selecting previously unselected package r-cran-nlme.
350s Preparing to unpack .../80-r-cran-nlme_3.1.167-1_s390x.deb ...
350s Unpacking r-cran-nlme (3.1.167-1) ...
350s Selecting previously unselected package r-cran-mgcv.
350s Preparing to unpack .../81-r-cran-mgcv_1.9-1-1_s390x.deb ...
350s Unpacking r-cran-mgcv (1.9-1-1) ...
350s Selecting previously unselected package r-cran-labeling.
350s Preparing to unpack .../82-r-cran-labeling_0.4.3-1_all.deb ...
350s Unpacking r-cran-labeling (0.4.3-1) ...
350s Selecting previously unselected package r-cran-munsell.
350s Preparing to unpack .../83-r-cran-munsell_0.5.1-1_all.deb ...
350s Unpacking r-cran-munsell (0.5.1-1) ...
350s Selecting previously unselected package r-cran-rcolorbrewer.
350s Preparing to unpack .../84-r-cran-rcolorbrewer_1.1-3-1build1_all.deb ...
350s Unpacking r-cran-rcolorbrewer (1.1-3-1build1) ...
350s Selecting previously unselected package r-cran-viridislite.
350s Preparing to unpack .../85-r-cran-viridislite_0.4.2-2_all.deb ...
350s Unpacking r-cran-viridislite (0.4.2-2) ...
350s Selecting previously unselected package r-cran-scales.
350s Preparing to unpack .../86-r-cran-scales_1.3.0-1_all.deb ...
350s Unpacking r-cran-scales (1.3.0-1) ...
350s Selecting previously unselected package r-cran-ggplot2.
350s Preparing to unpack .../87-r-cran-ggplot2_3.5.1+dfsg-1_all.deb ...
350s Unpacking r-cran-ggplot2 (3.5.1+dfsg-1) ...
350s Setting up libjpeg-turbo8-dev:s390x (2.1.5-3ubuntu2) ...
350s Setting up libncurses-dev:s390x (6.5+20250216-2) ...
350s Setting up r-cran-rlang (1.1.5-1) ...
350s Setting up r-cran-withr (3.0.2+dfsg-1) ...
350s Setting up r-cran-backports (1.5.0-2) ...
350s Setting up r-cran-generics (0.1.3-1) ...
350s Setting up r-cran-fansi (1.0.5-1) ...
350s Setting up r-cran-mass (7.3-64-1) ...
350s Setting up libreadline-dev:s390x (8.2-6) ...
350s Setting up r-cran-glue (1.8.0-1) ...
350s Setting up r-cran-cli (3.6.4-1) ...
350s Setting up r-cran-lifecycle (1.0.4+dfsg-1) ...
350s Setting up libpcre2-16-0:s390x (10.45-1) ...
350s Setting up r-cran-pkgconfig (2.0.3-2build1) ...
350s Setting up libpcre2-32-0:s390x (10.45-1) ...
350s Setting up r-cran-utf8 (1.2.4-1) ...
350s Setting up libtirpc-dev:s390x (1.3.4+ds-1.3) ...
350s Setting up libpkgconf3:s390x (1.8.1-4) ...
350s Setting up r-cran-colorspace (2.1-1+dfsg-1) ...
350s Setting up r-cran-stringi (1.8.4-1build1) ...
350s Setting up r-cran-cpp11 (0.5.2-1) ...
350s Setting up r-cran-rcolorbrewer (1.1-3-1build1) ...
350s Setting up r-cran-isoband (0.2.7-1) ...
350s Setting up libmpc3:s390x (1.3.1-1build2) ...
350s Setting up r-cran-gtable (0.3.6+dfsg-1) ...
350s Setting up r-cran-labeling (0.4.3-1) ...
350s Setting up icu-devtools (76.1-1ubuntu2) ...
350s Setting up pkgconf-bin (1.8.1-4) ...
350s Setting up r-cran-nlme (3.1.167-1) ...
350s Setting up r-cran-farver (2.1.2-1) ...
350s Setting up liblzma-dev:s390x (5.6.4-1) ...
350s Setting up libubsan1:s390x (15-20250222-0ubuntu1) ...
350s Setting up zlib1g-dev:s390x (1:1.3.dfsg+really1.3.1-1ubuntu1) ...
350s Setting up r-cran-mgcv (1.9-1-1) ...
350s Setting up libpcre2-posix3:s390x (10.45-1) ...
350s Setting up r-cran-viridislite (0.4.2-2) ...
350s Setting up libasan8:s390x (15-20250222-0ubuntu1) ...
350s Setting up r-cran-r6 (2.6.1-1) ...
350s Setting up libjpeg8-dev:s390x (8c-2ubuntu11) ...
350s Setting up libisl23:s390x (0.27-1) ...
350s Setting up libdeflate-dev:s390x (1.23-1) ...
350s Setting up libicu-dev:s390x (76.1-1ubuntu2) ...
350s Setting up r-cran-magrittr (2.0.3-1) ...
350s Setting up libcc1-0:s390x (15-20250222-0ubuntu1) ...
350s Setting up r-cran-vctrs (0.6.5-1) ...
350s Setting up libblas-dev:s390x (3.12.1-2) ...
350s update-alternatives: using /usr/lib/s390x-linux-gnu/blas/libblas.so to provide /usr/lib/s390x-linux-gnu/libblas.so (libblas.so-s390x-linux-gnu) in auto mode
350s Setting up dctrl-tools (2.24-3build3) ...
350s Setting up libitm1:s390x (15-20250222-0ubuntu1) ...
350s Setting up libbz2-dev:s390x (1.0.8-6) ...
350s Setting up r-cran-pillar (1.10.1+dfsg-1) ...
350s Setting up r-cran-stringr (1.5.1-1) ...
350s Setting up libpcre2-dev:s390x (10.45-1) ...
350s Setting up libpng-dev:s390x (1.6.47-1) ...
350s Setting up r-cran-munsell (0.5.1-1) ...
350s Setting up r-cran-tibble (3.2.1+dfsg-3) ...
350s Setting up libjpeg-dev:s390x (8c-2ubuntu11) ...
350s Setting up pkgconf:s390x (1.8.1-4) ...
350s Setting up r-cran-tidyselect (1.2.1+dfsg-1) ...
350s Setting up r-cran-scales (1.3.0-1) ...
350s Setting up liblapack-dev:s390x (3.12.1-2) ...
350s update-alternatives: using /usr/lib/s390x-linux-gnu/lapack/liblapack.so to provide /usr/lib/s390x-linux-gnu/liblapack.so (liblapack.so-s390x-linux-gnu) in auto mode
350s Setting up r-cran-purrr (1.0.4-1) ...
350s Setting up cpp-14-s390x-linux-gnu (14.2.0-17ubuntu3) ...
350s Setting up cpp-14 (14.2.0-17ubuntu3) ...
350s Setting up r-cran-dplyr (1.1.4-4) ...
350s Setting up libgcc-14-dev:s390x (14.2.0-17ubuntu3) ...
350s Setting up libstdc++-14-dev:s390x (14.2.0-17ubuntu3) ...
350s Setting up libgfortran-14-dev:s390x (14.2.0-17ubuntu3) ...
350s Setting up cpp-s390x-linux-gnu (4:14.2.0-1ubuntu1) ...
350s Setting up r-cran-ggplot2 (3.5.1+dfsg-1) ...
350s Setting up gcc-14-s390x-linux-gnu (14.2.0-17ubuntu3) ...
350s Setting up gcc-s390x-linux-gnu (4:14.2.0-1ubuntu1) ...
350s Setting up g++-14-s390x-linux-gnu (14.2.0-17ubuntu3) ...
350s Setting up r-cran-tidyr (1.3.1-1) ...
350s Setting up cpp (4:14.2.0-1ubuntu1) ...
350s Setting up gfortran-14-s390x-linux-gnu (14.2.0-17ubuntu3) ...
350s Setting up g++-s390x-linux-gnu (4:14.2.0-1ubuntu1) ...
350s Setting up gcc-14 (14.2.0-17ubuntu3) ...
350s Setting up r-cran-broom (1.0.7+dfsg-1) ...
350s Setting up g++-14 (14.2.0-17ubuntu3) ...
350s Setting up gfortran-14 (14.2.0-17ubuntu3) ...
350s Setting up gfortran-s390x-linux-gnu (4:14.2.0-1ubuntu1) ...
350s Setting up r-cran-geepack (1.3.12-1) ...
350s Setting up gcc (4:14.2.0-1ubuntu1) ...
350s Setting up g++ (4:14.2.0-1ubuntu1) ...
350s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode
350s Setting up build-essential (12.10ubuntu1) ...
350s Setting up gfortran (4:14.2.0-1ubuntu1) ...
350s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode
350s 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
350s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode
350s 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
350s Setting up r-base-dev (4.4.3-1) ...
350s Setting up pkg-r-autopkgtest (20231212ubuntu1) ...
350s Processing triggers for libc-bin (2.41-1ubuntu2) ...
350s Processing triggers for man-db (2.13.0-1) ...
351s Processing triggers for install-info (7.1.1-1) ...
352s autopkgtest [18:05:26]: test pkg-r-autopkgtest: /usr/share/dh-r/pkg-r-autopkgtest
352s autopkgtest [18:05:26]: test pkg-r-autopkgtest: [-----------------------
352s Test: Try to load the R library etm
352s
352s R version 4.4.3 (2025-02-28) -- "Trophy Case"
352s Copyright (C) 2025 The R Foundation for Statistical Computing
352s Platform: s390x-ibm-linux-gnu
352s
352s R is free software and comes with ABSOLUTELY NO WARRANTY.
352s You are welcome to redistribute it under certain conditions.
352s Type 'license()' or 'licence()' for distribution details.
352s
352s R is a collaborative project with many contributors.
352s Type 'contributors()' for more information and
352s 'citation()' on how to cite R or R packages in publications.
352s
352s Type 'demo()' for some demos, 'help()' for on-line help, or
352s 'help.start()' for an HTML browser interface to help.
352s Type 'q()' to quit R.
352s
352s > library('etm')
353s >
353s >
353s Other tests are currently unsupported!
353s They will be progressively added.
354s autopkgtest [18:05:28]: test pkg-r-autopkgtest: -----------------------]
354s autopkgtest [18:05:28]: test pkg-r-autopkgtest: - - - - - - - - - - results - - - - - - - - - -
354s pkg-r-autopkgtest PASS
354s autopkgtest [18:05:28]: @@@@@@@@@@@@@@@@@@@@ summary
354s run-unit-test PASS
354s pkg-r-autopkgtest PASS
360s nova [W] Using flock in prodstack6-s390x
360s Creating nova instance adt-plucky-s390x-r-cran-etm-20250315-175934-juju-7f2275-prod-proposed-migration-environment-15-389e059e-c8db-4df6-88e7-d96e3beb5301 from image adt/ubuntu-plucky-s390x-server-20250315.img (UUID 3d3557fa-fd0f-4bba-9b89-8d5964e09f61)...
360s nova [W] Timed out waiting for 449a5370-486b-488b-ac67-fab31e3128c9 to get deleted.