0s autopkgtest [08:49:11]: starting date and time: 2024-03-26 08:49:11+0000 0s autopkgtest [08:49:11]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [08:49:11]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.nk0d22w9/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --setup-commands /home/ubuntu/autopkgtest/setup-commands/setup-testbed --apt-pocket=proposed --apt-upgrade r-cran-etm --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=r-base/4.3.3-2build1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@lcy02-19.secgroup --name adt-noble-amd64-r-cran-etm-20240326-084911-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-amd64-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,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 72s autopkgtest [08:50:23]: testbed dpkg architecture: amd64 72s autopkgtest [08:50:23]: testbed apt version: 2.7.12 72s autopkgtest [08:50:23]: @@@@@@@@@@@@@@@@@@@@ test bed setup 72s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 72s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [7592 B] 72s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [4023 kB] 72s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [56.0 kB] 72s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [495 kB] 72s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main i386 Packages [482 kB] 72s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 Packages [729 kB] 72s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 c-n-f Metadata [3508 B] 72s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted i386 Packages [6700 B] 72s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/restricted amd64 Packages [37.9 kB] 72s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/restricted amd64 c-n-f Metadata [116 B] 72s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/universe i386 Packages [1255 kB] 73s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 Packages [4385 kB] 73s Get:14 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 c-n-f Metadata [9396 B] 73s Get:15 http://ftpmaster.internal/ubuntu noble-proposed/multiverse amd64 Packages [96.8 kB] 73s Get:16 http://ftpmaster.internal/ubuntu noble-proposed/multiverse i386 Packages [28.6 kB] 73s Get:17 http://ftpmaster.internal/ubuntu noble-proposed/multiverse amd64 c-n-f Metadata [196 B] 76s Fetched 11.7 MB in 1s (8247 kB/s) 76s Reading package lists... 77s Reading package lists... 78s Building dependency tree... 78s Reading state information... 78s Calculating upgrade... 79s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 79s Reading package lists... 79s Building dependency tree... 79s Reading state information... 79s 0 upgraded, 0 newly installed, 0 to remove and 248 not upgraded. 80s sh: Attempting to set up Debian/Ubuntu apt sources automatically 80s sh: Distribution appears to be Ubuntu 81s Reading package lists... 81s Building dependency tree... 81s Reading state information... 81s eatmydata is already the newest version (131-1). 81s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 81s Reading package lists... 81s Building dependency tree... 81s Reading state information... 82s dbus is already the newest version (1.14.10-4ubuntu1). 82s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 82s Reading package lists... 82s Building dependency tree... 82s Reading state information... 82s rng-tools-debian is already the newest version (2.4). 82s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 83s Reading package lists... 83s Building dependency tree... 83s Reading state information... 83s The following packages will be REMOVED: 83s cloud-init* python3-configobj* python3-debconf* 83s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 83s After this operation, 3256 kB disk space will be freed. 83s (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 ... 71864 files and directories currently installed.) 83s Removing cloud-init (24.1.2-0ubuntu1) ... 84s Removing python3-configobj (5.0.8-3) ... 84s Removing python3-debconf (1.5.86) ... 84s Processing triggers for man-db (2.12.0-3) ... 85s (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 ... 71475 files and directories currently installed.) 85s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 85s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 85s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 85s invoke-rc.d: policy-rc.d denied execution of try-restart. 85s Reading package lists... 86s Building dependency tree... 86s Reading state information... 86s linux-generic is already the newest version (6.8.0-11.11+1). 86s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 86s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 86s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 86s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 88s Reading package lists... 88s Reading package lists... 88s Building dependency tree... 88s Reading state information... 88s Calculating upgrade... 89s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 89s Reading package lists... 89s Building dependency tree... 89s Reading state information... 89s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 89s autopkgtest [08:50:40]: rebooting testbed after setup commands that affected boot 237s autopkgtest [08:53:08]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 00:29:05 UTC 2024 237s autopkgtest [08:53:08]: @@@@@@@@@@@@@@@@@@@@ apt-source r-cran-etm 238s Get:1 http://ftpmaster.internal/ubuntu noble/universe r-cran-etm 1.1.1-1 (dsc) [2148 B] 238s Get:2 http://ftpmaster.internal/ubuntu noble/universe r-cran-etm 1.1.1-1 (tar) [242 kB] 238s Get:3 http://ftpmaster.internal/ubuntu noble/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 239s autopkgtest [08:53:10]: testing package r-cran-etm version 1.1.1-1 239s autopkgtest [08:53:10]: build not needed 241s autopkgtest [08:53:12]: test run-unit-test: preparing testbed 241s Reading package lists... 241s Building dependency tree... 241s Reading state information... 242s Starting pkgProblemResolver with broken count: 0 242s Starting 2 pkgProblemResolver with broken count: 0 242s Done 242s The following additional packages will be installed: 242s fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono libblas3 242s libcairo2 libdatrie1 libdeflate0 libfontconfig1 libgfortran5 libgomp1 242s libgraphite2-3 libharfbuzz0b libice6 libjbig0 libjpeg-turbo8 libjpeg8 242s liblapack3 liblerc4 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 242s libpaper-utils libpaper1 libpixman-1-0 libsharpyuv0 libsm6 libtcl8.6 242s libthai-data libthai0 libtiff6 libtk8.6 libwebp7 libxcb-render0 libxcb-shm0 242s libxft2 libxrender1 libxss1 libxt6 littler r-base-core r-cran-data.table 242s r-cran-dbi r-cran-etm r-cran-kmi r-cran-lattice r-cran-littler r-cran-matrix 242s r-cran-mitools r-cran-pkgkitten r-cran-rcpp r-cran-rcpparmadillo 242s r-cran-survival unzip x11-common xdg-utils zip 242s Suggested packages: 242s tcl8.6 tk8.6 elpa-ess r-doc-info | r-doc-pdf r-mathlib r-base-html 242s r-cran-rmysql r-cran-ggplot2 r-cran-geepack r-cran-getopt r-cran-rodbc 242s r-cran-foreign r-cran-inline 242s Recommended packages: 242s r-recommended r-base-dev r-doc-html r-cran-bit64 r-cran-bit r-cran-curl 242s r-cran-r.utils r-cran-xts r-cran-nanotime r-cran-zoo r-cran-yaml 242s r-cran-knitr r-cran-rmarkdown libfile-mimeinfo-perl libnet-dbus-perl 242s libx11-protocol-perl x11-utils x11-xserver-utils 242s The following NEW packages will be installed: 242s autopkgtest-satdep fontconfig fontconfig-config fonts-dejavu-core 242s fonts-dejavu-mono libblas3 libcairo2 libdatrie1 libdeflate0 libfontconfig1 242s libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libice6 libjbig0 242s libjpeg-turbo8 libjpeg8 liblapack3 liblerc4 libpango-1.0-0 242s libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpixman-1-0 242s libsharpyuv0 libsm6 libtcl8.6 libthai-data libthai0 libtiff6 libtk8.6 242s libwebp7 libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxss1 libxt6 242s littler r-base-core r-cran-data.table r-cran-dbi r-cran-etm r-cran-kmi 242s r-cran-lattice r-cran-littler r-cran-matrix r-cran-mitools r-cran-pkgkitten 242s r-cran-rcpp r-cran-rcpparmadillo r-cran-survival unzip x11-common xdg-utils 242s zip 242s 0 upgraded, 58 newly installed, 0 to remove and 0 not upgraded. 242s Need to get 55.7 MB/55.7 MB of archives. 242s After this operation, 116 MB of additional disk space will be used. 242s Get:1 /tmp/autopkgtest.UWYLfo/1-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [712 B] 242s Get:2 http://ftpmaster.internal/ubuntu noble/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB] 242s Get:3 http://ftpmaster.internal/ubuntu noble/main amd64 fonts-dejavu-core all 2.37-8 [835 kB] 242s Get:4 http://ftpmaster.internal/ubuntu noble/main amd64 fontconfig-config amd64 2.15.0-1ubuntu1 [36.9 kB] 242s Get:5 http://ftpmaster.internal/ubuntu noble/main amd64 libfontconfig1 amd64 2.15.0-1ubuntu1 [139 kB] 242s Get:6 http://ftpmaster.internal/ubuntu noble/main amd64 fontconfig amd64 2.15.0-1ubuntu1 [180 kB] 242s Get:7 http://ftpmaster.internal/ubuntu noble/main amd64 libblas3 amd64 3.12.0-3 [238 kB] 242s Get:8 http://ftpmaster.internal/ubuntu noble/main amd64 libpixman-1-0 amd64 0.42.2-1 [268 kB] 242s Get:9 http://ftpmaster.internal/ubuntu noble/main amd64 libxcb-render0 amd64 1.15-1 [16.3 kB] 242s Get:10 http://ftpmaster.internal/ubuntu noble/main amd64 libxcb-shm0 amd64 1.15-1 [5740 B] 242s Get:11 http://ftpmaster.internal/ubuntu noble/main amd64 libxrender1 amd64 1:0.9.10-1.1 [20.0 kB] 242s Get:12 http://ftpmaster.internal/ubuntu noble/main amd64 libcairo2 amd64 1.18.0-1 [572 kB] 242s Get:13 http://ftpmaster.internal/ubuntu noble/main amd64 libdatrie1 amd64 0.2.13-3 [20.9 kB] 242s Get:14 http://ftpmaster.internal/ubuntu noble/main amd64 libdeflate0 amd64 1.19-1 [43.7 kB] 242s Get:15 http://ftpmaster.internal/ubuntu noble/main amd64 libgfortran5 amd64 14-20240303-1ubuntu1 [924 kB] 242s Get:16 http://ftpmaster.internal/ubuntu noble/main amd64 libgomp1 amd64 14-20240303-1ubuntu1 [147 kB] 242s Get:17 http://ftpmaster.internal/ubuntu noble/main amd64 libgraphite2-3 amd64 1.3.14-2 [83.1 kB] 242s Get:18 http://ftpmaster.internal/ubuntu noble/main amd64 libharfbuzz0b amd64 8.3.0-2 [469 kB] 242s Get:19 http://ftpmaster.internal/ubuntu noble/main amd64 x11-common all 1:7.7+23ubuntu2 [23.4 kB] 242s Get:20 http://ftpmaster.internal/ubuntu noble/main amd64 libice6 amd64 2:1.0.10-1build2 [42.6 kB] 242s Get:21 http://ftpmaster.internal/ubuntu noble/main amd64 libjpeg-turbo8 amd64 2.1.5-2ubuntu1 [147 kB] 242s Get:22 http://ftpmaster.internal/ubuntu noble/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 242s Get:23 http://ftpmaster.internal/ubuntu noble/main amd64 liblapack3 amd64 3.12.0-3 [2649 kB] 242s Get:24 http://ftpmaster.internal/ubuntu noble/main amd64 liblerc4 amd64 4.0.0+ds-4ubuntu1 [184 kB] 242s Get:25 http://ftpmaster.internal/ubuntu noble/main amd64 libthai-data all 0.1.29-2 [158 kB] 242s Get:26 http://ftpmaster.internal/ubuntu noble/main amd64 libthai0 amd64 0.1.29-2 [18.8 kB] 242s Get:27 http://ftpmaster.internal/ubuntu noble/main amd64 libpango-1.0-0 amd64 1.51.0+ds-4 [228 kB] 242s Get:28 http://ftpmaster.internal/ubuntu noble/main amd64 libpangoft2-1.0-0 amd64 1.51.0+ds-4 [42.1 kB] 242s Get:29 http://ftpmaster.internal/ubuntu noble/main amd64 libpangocairo-1.0-0 amd64 1.51.0+ds-4 [29.0 kB] 242s Get:30 http://ftpmaster.internal/ubuntu noble/main amd64 libpaper1 amd64 1.1.29 [13.4 kB] 242s Get:31 http://ftpmaster.internal/ubuntu noble/main amd64 libpaper-utils amd64 1.1.29 [8658 B] 242s Get:32 http://ftpmaster.internal/ubuntu noble/main amd64 libsharpyuv0 amd64 1.3.2-0.4 [15.6 kB] 242s Get:33 http://ftpmaster.internal/ubuntu noble/main amd64 libsm6 amd64 2:1.2.3-1build2 [16.7 kB] 242s Get:34 http://ftpmaster.internal/ubuntu noble/main amd64 libtcl8.6 amd64 8.6.13+dfsg-2 [984 kB] 242s Get:35 http://ftpmaster.internal/ubuntu noble/main amd64 libjbig0 amd64 2.1-6.1ubuntu1 [29.3 kB] 242s Get:36 http://ftpmaster.internal/ubuntu noble/main amd64 libwebp7 amd64 1.3.2-0.4 [230 kB] 242s Get:37 http://ftpmaster.internal/ubuntu noble/main amd64 libtiff6 amd64 4.5.1+git230720-3ubuntu1 [232 kB] 242s Get:38 http://ftpmaster.internal/ubuntu noble/main amd64 libxft2 amd64 2.3.6-1 [44.5 kB] 242s Get:39 http://ftpmaster.internal/ubuntu noble/main amd64 libxss1 amd64 1:1.2.3-1build2 [8476 B] 242s Get:40 http://ftpmaster.internal/ubuntu noble/main amd64 libtk8.6 amd64 8.6.14-1 [779 kB] 242s Get:41 http://ftpmaster.internal/ubuntu noble/main amd64 libxt6 amd64 1:1.2.1-1.1 [173 kB] 242s Get:42 http://ftpmaster.internal/ubuntu noble/main amd64 zip amd64 3.0-13 [176 kB] 242s Get:43 http://ftpmaster.internal/ubuntu noble/main amd64 unzip amd64 6.0-28ubuntu3 [174 kB] 242s Get:44 http://ftpmaster.internal/ubuntu noble/main amd64 xdg-utils all 1.1.3-4.1ubuntu3 [62.0 kB] 242s Get:45 http://ftpmaster.internal/ubuntu noble/universe amd64 r-base-core amd64 4.3.2-1build1 [27.0 MB] 243s Get:46 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-littler amd64 0.3.19-1 [94.1 kB] 243s Get:47 http://ftpmaster.internal/ubuntu noble/universe amd64 littler all 0.3.19-1 [2472 B] 243s Get:48 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-data.table amd64 1.14.10+dfsg-1 [1837 kB] 243s Get:49 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-dbi all 1.2.2-1 [823 kB] 243s Get:50 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-lattice amd64 0.22-5-1 [1342 kB] 243s Get:51 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-matrix amd64 1.6-5-1 [3830 kB] 243s Get:52 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-survival amd64 3.5-8-1 [6120 kB] 243s Get:53 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-pkgkitten all 0.2.3-1 [25.1 kB] 243s Get:54 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-rcpp amd64 1.0.12-1 [1981 kB] 243s Get:55 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-rcpparmadillo amd64 0.12.8.0.0-1 [862 kB] 243s Get:56 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-etm amd64 1.1.1-1 [478 kB] 243s Get:57 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-mitools all 2.4-2build1 [265 kB] 243s Get:58 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-kmi all 0.5.5-2build1 [78.3 kB] 243s Preconfiguring packages ... 243s Fetched 55.7 MB in 1s (65.2 MB/s) 243s Selecting previously unselected package fonts-dejavu-mono. 244s (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 ... 71420 files and directories currently installed.) 244s Preparing to unpack .../00-fonts-dejavu-mono_2.37-8_all.deb ... 244s Unpacking fonts-dejavu-mono (2.37-8) ... 244s Selecting previously unselected package fonts-dejavu-core. 244s Preparing to unpack .../01-fonts-dejavu-core_2.37-8_all.deb ... 244s Unpacking fonts-dejavu-core (2.37-8) ... 244s Selecting previously unselected package fontconfig-config. 244s Preparing to unpack .../02-fontconfig-config_2.15.0-1ubuntu1_amd64.deb ... 244s Unpacking fontconfig-config (2.15.0-1ubuntu1) ... 244s Selecting previously unselected package libfontconfig1:amd64. 244s Preparing to unpack .../03-libfontconfig1_2.15.0-1ubuntu1_amd64.deb ... 244s Unpacking libfontconfig1:amd64 (2.15.0-1ubuntu1) ... 244s Selecting previously unselected package fontconfig. 244s Preparing to unpack .../04-fontconfig_2.15.0-1ubuntu1_amd64.deb ... 244s Unpacking fontconfig (2.15.0-1ubuntu1) ... 244s Selecting previously unselected package libblas3:amd64. 244s Preparing to unpack .../05-libblas3_3.12.0-3_amd64.deb ... 244s Unpacking libblas3:amd64 (3.12.0-3) ... 244s Selecting previously unselected package libpixman-1-0:amd64. 244s Preparing to unpack .../06-libpixman-1-0_0.42.2-1_amd64.deb ... 244s Unpacking libpixman-1-0:amd64 (0.42.2-1) ... 244s Selecting previously unselected package libxcb-render0:amd64. 244s Preparing to unpack .../07-libxcb-render0_1.15-1_amd64.deb ... 244s Unpacking libxcb-render0:amd64 (1.15-1) ... 244s Selecting previously unselected package libxcb-shm0:amd64. 244s Preparing to unpack .../08-libxcb-shm0_1.15-1_amd64.deb ... 244s Unpacking libxcb-shm0:amd64 (1.15-1) ... 244s Selecting previously unselected package libxrender1:amd64. 244s Preparing to unpack .../09-libxrender1_1%3a0.9.10-1.1_amd64.deb ... 244s Unpacking libxrender1:amd64 (1:0.9.10-1.1) ... 244s Selecting previously unselected package libcairo2:amd64. 244s Preparing to unpack .../10-libcairo2_1.18.0-1_amd64.deb ... 244s Unpacking libcairo2:amd64 (1.18.0-1) ... 244s Selecting previously unselected package libdatrie1:amd64. 244s Preparing to unpack .../11-libdatrie1_0.2.13-3_amd64.deb ... 244s Unpacking libdatrie1:amd64 (0.2.13-3) ... 244s Selecting previously unselected package libdeflate0:amd64. 244s Preparing to unpack .../12-libdeflate0_1.19-1_amd64.deb ... 244s Unpacking libdeflate0:amd64 (1.19-1) ... 244s Selecting previously unselected package libgfortran5:amd64. 244s Preparing to unpack .../13-libgfortran5_14-20240303-1ubuntu1_amd64.deb ... 244s Unpacking libgfortran5:amd64 (14-20240303-1ubuntu1) ... 244s Selecting previously unselected package libgomp1:amd64. 244s Preparing to unpack .../14-libgomp1_14-20240303-1ubuntu1_amd64.deb ... 244s Unpacking libgomp1:amd64 (14-20240303-1ubuntu1) ... 244s Selecting previously unselected package libgraphite2-3:amd64. 244s Preparing to unpack .../15-libgraphite2-3_1.3.14-2_amd64.deb ... 244s Unpacking libgraphite2-3:amd64 (1.3.14-2) ... 244s Selecting previously unselected package libharfbuzz0b:amd64. 244s Preparing to unpack .../16-libharfbuzz0b_8.3.0-2_amd64.deb ... 244s Unpacking libharfbuzz0b:amd64 (8.3.0-2) ... 244s Selecting previously unselected package x11-common. 244s Preparing to unpack .../17-x11-common_1%3a7.7+23ubuntu2_all.deb ... 244s Unpacking x11-common (1:7.7+23ubuntu2) ... 245s Selecting previously unselected package libice6:amd64. 245s Preparing to unpack .../18-libice6_2%3a1.0.10-1build2_amd64.deb ... 245s Unpacking libice6:amd64 (2:1.0.10-1build2) ... 245s Selecting previously unselected package libjpeg-turbo8:amd64. 245s Preparing to unpack .../19-libjpeg-turbo8_2.1.5-2ubuntu1_amd64.deb ... 245s Unpacking libjpeg-turbo8:amd64 (2.1.5-2ubuntu1) ... 245s Selecting previously unselected package libjpeg8:amd64. 245s Preparing to unpack .../20-libjpeg8_8c-2ubuntu11_amd64.deb ... 245s Unpacking libjpeg8:amd64 (8c-2ubuntu11) ... 245s Selecting previously unselected package liblapack3:amd64. 245s Preparing to unpack .../21-liblapack3_3.12.0-3_amd64.deb ... 245s Unpacking liblapack3:amd64 (3.12.0-3) ... 245s Selecting previously unselected package liblerc4:amd64. 245s Preparing to unpack .../22-liblerc4_4.0.0+ds-4ubuntu1_amd64.deb ... 245s Unpacking liblerc4:amd64 (4.0.0+ds-4ubuntu1) ... 245s Selecting previously unselected package libthai-data. 245s Preparing to unpack .../23-libthai-data_0.1.29-2_all.deb ... 245s Unpacking libthai-data 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R Foundation for Statistical Computing 254s Platform: x86_64-pc-linux-gnu (64-bit) 254s 254s R is free software and comes with ABSOLUTELY NO WARRANTY. 254s You are welcome to redistribute it under certain conditions. 254s Type 'license()' or 'licence()' for distribution details. 254s 254s R is a collaborative project with many contributors. 254s Type 'contributors()' for more information and 254s 'citation()' on how to cite R or R packages in publications. 254s 254s Type 'demo()' for some demos, 'help()' for on-line help, or 254s 'help.start()' for an HTML browser interface to help. 254s Type 'q()' to quit R. 254s 254s > ### test file for etmCIF. 254s > ### Really simple tests and comparison with etm 254s > 254s > old <- options(digits = 5) 254s > 254s > require(etm) 254s Loading required package: etm 255s > 255s > if (!require(survival, quietly = TRUE)) { 255s + print("The following tests require the 'survival' package") 255s + } else { 255s + 255s + data(abortion) 255s + 255s + from <- rep(0, nrow(abortion)) 255s + to <- abortion$cause 255s + entry <- abortion$entry 255s + exit <- abortion$exit 255s + id <- 1:nrow(abortion) 255s + data <- data.frame(id, from, to, entry, exit, group = abortion$group) 255s + 255s + ## Computation of the CIFs with etm 255s + tra <- matrix(FALSE, 4, 4) 255s + tra[1, 2:4] <- TRUE 255s + 255s + cif.control <- etm(data[data$group == 0, ], c("0", "1", "2", "3"), 255s + tra, NULL, 0) 255s + cif.exposed <- etm(data[data$group == 1, ], c("0", "1", "2", "3"), 255s + tra, NULL, 0) 255s + 255s + 255s + ## Computation of the CIFs with etmCIF 255s + netm <- etmCIF(Surv(entry, exit, cause != 0) ~ group, abortion, 255s + etype = cause, failcode = 3) 255s + 255s + ### let's do some comparisons :-) 255s + 255s + all.equal(trprob(cif.control, "0 3"), netm[[1]]$est["0", "3", ]) 255s + all.equal(trprob(cif.control, "0 2"), netm[[1]]$est["0", "2", ]) 255s + all.equal(trprob(cif.control, "0 1"), netm[[1]]$est["0", "1", ]) 255s + 255s + all.equal(trprob(cif.exposed, "0 3"), netm[[2]]$est["0", "3", ]) 255s + all.equal(trprob(cif.exposed, "0 2"), netm[[2]]$est["0", "2", ]) 255s + all.equal(trprob(cif.exposed, "0 1"), netm[[2]]$est["0", "1", ]) 255s + 255s + 255s + all.equal(trcov(cif.control, "0 3"), netm[[1]]$cov["0 3", "0 3", ]) 255s + all.equal(trcov(cif.control, "0 2"), netm[[1]]$cov["0 2", "0 2", ]) 255s + all.equal(trcov(cif.control, "0 1"), netm[[1]]$cov["0 1", "0 1", ]) 255s + 255s + all.equal(trcov(cif.exposed, "0 3"), netm[[2]]$cov["0 3", "0 3", ]) 255s + all.equal(trcov(cif.exposed, "0 2"), netm[[2]]$cov["0 2", "0 2", ]) 255s + all.equal(trcov(cif.exposed, "0 1"), netm[[2]]$cov["0 1", "0 1", ]) 255s + 255s + 255s + netm 255s + 255s + ## test on the summary 255s + snetm <- summary(netm) 255s + 255s + snetm 255s + 255s + all.equal(unname(trprob(cif.control, "0 3")), snetm[[1]][[3]]$P) 255s + all.equal(unname(trprob(cif.control, "0 2")), snetm[[1]][[2]]$P) 255s + all.equal(unname(trprob(cif.control, "0 1")), snetm[[1]][[1]]$P) 255s + 255s + all.equal(unname(trprob(cif.exposed, "0 3")), snetm[[2]][[3]]$P) 255s + all.equal(unname(trprob(cif.exposed, "0 2")), snetm[[2]][[2]]$P) 255s + all.equal(unname(trprob(cif.exposed, "0 1")), snetm[[2]][[1]]$P) 255s + 255s + scif.control <- summary(cif.control, ci.fun = "cloglog") 255s + scif.exposed <- summary(cif.exposed, ci.fun = "cloglog") 255s + 255s + all.equal(scif.control[[4]]$lower, snetm[[1]][[3]]$lower) 255s + all.equal(scif.control[[4]]$upper, snetm[[1]][[3]]$upper) 255s + 255s + all.equal(scif.exposed[[4]]$lower, snetm[[2]][[3]]$lower) 255s + all.equal(scif.exposed[[4]]$upper, snetm[[2]][[3]]$upper) 255s + } 255s [1] TRUE 255s > 255s > ### test with factors in the input 255s > abortion$status <- with(abortion, ifelse(cause == 2, "life birth", 255s + ifelse(cause == 1, "ETOP", "spontaneous abortion"))) 255s > 255s > abortion$status <- factor(abortion$status) 255s > 255s > netm.factor <- etmCIF(Surv(entry, exit, status != "cens") ~ group, abortion, 255s + etype = status, failcode = "spontaneous abortion") 255s > 255s > 255s > all.equal(trprob(cif.control, "0 3"), netm.factor[[1]]$est["0", "spontaneous abortion", ]) 255s [1] TRUE 255s > all.equal(trprob(cif.control, "0 2"), netm.factor[[1]]$est["0", "life birth", ]) 255s [1] TRUE 255s > 255s > netm.factor 255s Call: etmCIF(formula = Surv(entry, exit, status != "cens") ~ group, 255s data = abortion, etype = status, failcode = "spontaneous abortion") 255s 255s Covariate: group 255s levels: 0 1 255s 255s 255s group = 0 255s time P se(P) n.event 255s CIF ETOP 43 0.040159 0.0092578 20 255s CIF life birth 43 0.799059 0.0221865 924 255s CIF spontaneous abortion 43 0.160781 0.0213261 69 255s 255s group = 1 255s time P se(P) n.event 255s CIF ETOP 42 0.28511 0.042493 38 255s CIF life birth 42 0.35257 0.042139 92 255s CIF spontaneous abortion 42 0.36232 0.049473 43 255s > 255s > summary(netm.factor) 255s 255s group=0 255s 255s CIF ETOP 255s P time var lower upper n.risk n.event 255s 0.000000 6 0.0000e+00 0.000000 0.000000 117 0 255s 0.038955 13 8.4440e-05 0.024488 0.061694 645 1 255s 0.040159 26 8.5707e-05 0.025513 0.062939 846 0 255s 0.040159 36 8.5707e-05 0.025513 0.062939 876 0 255s 0.040159 40 8.5707e-05 0.025513 0.062939 554 0 255s 0.040159 43 8.5707e-05 0.025513 0.062939 6 0 255s 255s CIF life birth 255s P time var lower upper n.risk n.event 255s 0.000000 6 0.0000e+00 0.000000 0.000000 117 0 255s 0.000000 13 0.0000e+00 0.000000 0.000000 645 0 255s 0.000000 26 0.0000e+00 0.000000 0.000000 846 0 255s 0.053197 36 4.6195e-05 0.041379 0.068268 876 25 255s 0.563121 40 3.8801e-04 0.524924 0.602021 554 280 255s 0.799059 43 4.9224e-04 0.753969 0.840613 6 6 255s 255s CIF spontaneous abortion 255s P time var lower upper n.risk n.event 255s 0.034188 6 0.00028222 0.01297 0.088523 117 4 255s 0.150468 13 0.00045513 0.11360 0.197901 645 1 255s 0.159904 26 0.00045498 0.12274 0.206925 846 1 255s 0.160781 36 0.00045480 0.12360 0.207757 876 1 255s 0.160781 40 0.00045480 0.12360 0.207757 554 0 255s 0.160781 43 0.00045480 0.12360 0.207757 6 0 255s 255s 255s group=1 255s 255s CIF ETOP 255s P time var lower upper n.risk n.event 255s 0.00000 6 0.0000000 0.00000 0.00000 35 0 255s 0.26048 13 0.0017854 0.18795 0.35425 90 0 255s 0.28115 21 0.0018028 0.20742 0.37423 93 1 255s 0.28511 34 0.0018057 0.21116 0.37806 89 0 255s 0.28511 39 0.0018057 0.21116 0.37806 59 0 255s 0.28511 42 0.0018057 0.21116 0.37806 6 0 255s 255s CIF life birth 255s P time var lower upper n.risk n.event 255s 0.000000 6 0.0000e+00 0.000000 0.000000 35 0 255s 0.000000 13 0.0000e+00 0.000000 0.000000 90 0 255s 0.000000 21 0.0000e+00 0.000000 0.000000 93 0 255s 0.023073 34 9.0514e-05 0.010252 0.051504 89 2 255s 0.180156 39 8.0126e-04 0.131765 0.243663 59 13 255s 0.352565 42 1.7757e-03 0.276882 0.441775 6 6 255s 255s CIF spontaneous abortion 255s P time var lower upper n.risk n.event 255s 0.057143 6 0.0015394 0.014605 0.20968 35 2 255s 0.333246 13 0.0025280 0.245337 0.44216 90 4 255s 0.350702 21 0.0024827 0.262769 0.45762 93 0 255s 0.358492 34 0.0024593 0.270627 0.46448 89 0 255s 0.358492 39 0.0024593 0.270627 0.46448 59 0 255s 0.362323 42 0.0024476 0.274499 0.46785 6 0 255s 255s > 255s > ### test with group as a character vector 255s > abortion$ttt <- with(abortion, ifelse(group == 0, "control", "exposed")) 255s > abortion$ttt <- factor(abortion$ttt) 255s > 255s > netm.ttt <- etmCIF(Surv(entry, exit, status != "cens") ~ ttt, abortion, 255s + etype = status, failcode = "spontaneous abortion") 255s > 255s > all.equal(trprob(cif.control, "0 3"), netm.ttt[[1]]$est["0", "spontaneous abortion", ]) 255s [1] TRUE 255s > all.equal(trprob(cif.control, "0 2"), netm.ttt[[1]]$est["0", "life birth", ]) 255s [1] TRUE 255s > 255s > netm.ttt 255s Call: etmCIF(formula = Surv(entry, exit, status != "cens") ~ ttt, data = abortion, 255s etype = status, failcode = "spontaneous abortion") 255s 255s Covariate: ttt 255s levels: control exposed 255s 255s 255s ttt = control 255s time P se(P) n.event 255s CIF ETOP 43 0.040159 0.0092578 20 255s CIF life birth 43 0.799059 0.0221865 924 255s CIF spontaneous abortion 43 0.160781 0.0213261 69 255s 255s ttt = exposed 255s time P se(P) n.event 255s CIF ETOP 42 0.28511 0.042493 38 255s CIF life birth 42 0.35257 0.042139 92 255s CIF spontaneous abortion 42 0.36232 0.049473 43 255s > 255s > summary(netm.ttt) 255s 255s ttt=control 255s 255s CIF ETOP 255s P time var lower upper n.risk n.event 255s 0.000000 6 0.0000e+00 0.000000 0.000000 117 0 255s 0.038955 13 8.4440e-05 0.024488 0.061694 645 1 255s 0.040159 26 8.5707e-05 0.025513 0.062939 846 0 255s 0.040159 36 8.5707e-05 0.025513 0.062939 876 0 255s 0.040159 40 8.5707e-05 0.025513 0.062939 554 0 255s 0.040159 43 8.5707e-05 0.025513 0.062939 6 0 255s 255s CIF life birth 255s P time var lower upper n.risk n.event 255s 0.000000 6 0.0000e+00 0.000000 0.000000 117 0 255s 0.000000 13 0.0000e+00 0.000000 0.000000 645 0 255s 0.000000 26 0.0000e+00 0.000000 0.000000 846 0 255s 0.053197 36 4.6195e-05 0.041379 0.068268 876 25 255s 0.563121 40 3.8801e-04 0.524924 0.602021 554 280 255s 0.799059 43 4.9224e-04 0.753969 0.840613 6 6 255s 255s CIF spontaneous abortion 255s P time var lower upper n.risk n.event 255s 0.034188 6 0.00028222 0.01297 0.088523 117 4 255s 0.150468 13 0.00045513 0.11360 0.197901 645 1 255s 0.159904 26 0.00045498 0.12274 0.206925 846 1 255s 0.160781 36 0.00045480 0.12360 0.207757 876 1 255s 0.160781 40 0.00045480 0.12360 0.207757 554 0 255s 0.160781 43 0.00045480 0.12360 0.207757 6 0 255s 255s 255s ttt=exposed 255s 255s CIF ETOP 255s P time var lower upper n.risk n.event 255s 0.00000 6 0.0000000 0.00000 0.00000 35 0 255s 0.26048 13 0.0017854 0.18795 0.35425 90 0 255s 0.28115 21 0.0018028 0.20742 0.37423 93 1 255s 0.28511 34 0.0018057 0.21116 0.37806 89 0 255s 0.28511 39 0.0018057 0.21116 0.37806 59 0 255s 0.28511 42 0.0018057 0.21116 0.37806 6 0 255s 255s CIF life birth 255s P time var lower upper n.risk n.event 255s 0.000000 6 0.0000e+00 0.000000 0.000000 35 0 255s 0.000000 13 0.0000e+00 0.000000 0.000000 90 0 255s 0.000000 21 0.0000e+00 0.000000 0.000000 93 0 255s 0.023073 34 9.0514e-05 0.010252 0.051504 89 2 255s 0.180156 39 8.0126e-04 0.131765 0.243663 59 13 255s 0.352565 42 1.7757e-03 0.276882 0.441775 6 6 255s 255s CIF spontaneous abortion 255s P time var lower upper n.risk n.event 255s 0.057143 6 0.0015394 0.014605 0.20968 35 2 255s 0.333246 13 0.0025280 0.245337 0.44216 90 4 255s 0.350702 21 0.0024827 0.262769 0.45762 93 0 255s 0.358492 34 0.0024593 0.270627 0.46448 89 0 255s 0.358492 39 0.0024593 0.270627 0.46448 59 0 255s 0.362323 42 0.0024476 0.274499 0.46785 6 0 255s 255s > 255s > 255s > ### A couple of comparisons with simulated data 255s > set.seed(1313) 255s > time <- rexp(100) 255s > to <- rbinom(100, 2, prob = c(1/3, 1/3, 1/3)) 255s > from <- rep(11, 100) 255s > id <- 1:100 255s > cov <- rbinom(100, 1, 0.5) 255s > 255s > dat.s <- data.frame(id, time, from, to, cov) 255s > 255s > traa <- matrix(FALSE, 3, 3) 255s > traa[1, 2:3] <- TRUE 255s > 255s > aa0 <- etm(dat.s[dat.s$cov == 0, ], c("11", "1", "2"), traa, "0", 0) 255s > aa1 <- etm(dat.s[dat.s$cov == 1, ], c("11", "1", "2"), traa, "0", 0) 255s > aa <- etm(dat.s, c("11", "1", "2"), traa, "0", 0) 255s > 255s > test <- etmCIF(Surv(time, to != 0) ~ 1, dat.s, etype = to) 255s > 255s > test.c <- etmCIF(Surv(time, to != 0) ~ cov, dat.s, etype = to) 255s > 255s > all.equal(trprob(aa, "11 1"), test[[1]]$est["0", "1", ]) 255s [1] TRUE 255s > all.equal(trprob(aa, "11 2"), test[[1]]$est["0", "2", ]) 255s [1] TRUE 255s > 255s > all.equal(trprob(aa0, "11 1"), test.c[[1]]$est["0", "1", ]) 255s [1] TRUE 255s > all.equal(trprob(aa0, "11 2"), test.c[[1]]$est["0", "2", ]) 255s [1] TRUE 255s > 255s > all.equal(trprob(aa1, "11 1"), test.c[[2]]$est["0", "1", ]) 255s [1] TRUE 255s > all.equal(trprob(aa1, "11 2"), test.c[[2]]$est["0", "2", ]) 255s [1] TRUE 255s > 255s > test 255s Call: etmCIF(formula = Surv(time, to != 0) ~ 1, data = dat.s, etype = to) 255s 255s time P se(P) n.event 255s CIF 1 4.9088 0.809108 0.079680 45 255s CIF 2 4.9088 0.096618 0.032905 8 255s > 255s > test.c 255s Call: etmCIF(formula = Surv(time, to != 0) ~ cov, data = dat.s, etype = to) 255s 255s Covariate: cov 255s levels: 0 1 255s 255s 255s cov = 0 255s time P se(P) n.event 255s CIF 1 2.1708 0.70246 0.105797 19 255s CIF 2 2.1708 0.11144 0.053384 4 255s 255s cov = 1 255s time P se(P) n.event 255s CIF 1 4.9088 0.80787 0.094051 26 255s CIF 2 4.9088 0.08436 0.040769 4 255s > 255s > summary(test) 255s 255s 255s 255s CIF 1 255s P time var lower upper n.risk n.event 255s 0.01000 0.0092099 0.0000990 0.0014147 0.068863 100 1 255s 0.11430 0.2663096 0.0010542 0.0649454 0.196993 81 1 255s 0.23451 0.7303091 0.0020436 0.1591107 0.337736 54 1 255s 0.40425 1.4299939 0.0032996 0.3020445 0.525741 29 1 255s 0.54593 2.0647206 0.0040836 0.4269008 0.673605 16 1 255s 0.80911 4.9087561 0.0063489 0.6359544 0.933733 2 1 255s 255s CIF 2 255s P time var lower upper n.risk n.event 255s 0.000000 0.0092099 0.00000000 0.000000 0.000000 100 0 255s 0.031657 0.2663096 0.00032353 0.010320 0.094942 81 0 255s 0.067029 0.7303091 0.00070366 0.030598 0.143503 54 0 255s 0.096618 1.4299939 0.00108275 0.049082 0.185474 29 0 255s 0.096618 2.0647206 0.00108275 0.049082 0.185474 16 0 255s 0.096618 4.9087561 0.00108275 0.049082 0.185474 2 0 255s 255s > summary(test.c) 255s 255s cov=0 255s 255s CIF 1 255s P time var lower upper n.risk n.event 255s 0.022222 0.0092099 0.00048285 0.0031605 0.14747 45 1 255s 0.092222 0.2982439 0.00193603 0.0355971 0.22762 36 0 255s 0.226684 0.7021938 0.00450954 0.1241760 0.39250 24 1 255s 0.378128 1.4299939 0.00760870 0.2337884 0.57145 13 1 255s 0.505736 1.6148774 0.00895330 0.3388425 0.69885 10 1 255s 0.702465 2.1708375 0.01119294 0.4944890 0.88399 3 1 255s 255s CIF 2 255s P time var lower upper n.risk n.event 255s 0.000000 0.0092099 0.0000000 0.000000 0.00000 45 0 255s 0.048441 0.2982439 0.0011168 0.012337 0.18013 36 1 255s 0.076411 0.7021938 0.0018104 0.025202 0.21928 24 0 255s 0.111440 1.4299939 0.0028499 0.042676 0.27392 13 0 255s 0.111440 1.6148774 0.0028499 0.042676 0.27392 10 0 255s 0.111440 2.1708375 0.0028499 0.042676 0.27392 3 0 255s 255s 255s cov=1 255s 255s CIF 1 255s P time var lower upper n.risk n.event 255s 0.018182 0.066692 0.00032457 0.0025813 0.12214 55 1 255s 0.112392 0.263808 0.00187215 0.0520925 0.23333 45 1 255s 0.241023 0.730309 0.00374499 0.1440057 0.38685 31 1 255s 0.401201 1.066913 0.00570788 0.2714008 0.56421 19 1 255s 0.592334 2.366275 0.00775985 0.4286230 0.76273 8 1 255s 0.807871 4.908756 0.00884554 0.6023185 0.94771 2 1 255s 255s CIF 2 255s P time var lower upper n.risk n.event 255s 0.000000 0.066692 0.00000000 0.000000 0.00000 55 0 255s 0.037434 0.263808 0.00067458 0.009494 0.14152 45 0 255s 0.059341 0.730309 0.00111295 0.019447 0.17351 31 0 255s 0.084360 1.066913 0.00166213 0.032211 0.21119 19 0 255s 0.084360 2.366275 0.00166213 0.032211 0.21119 8 0 255s 0.084360 4.908756 0.00166213 0.032211 0.21119 2 0 255s 255s > 255s > options(old) 255s > 255s BEGIN TEST tests.etm.R 255s 255s R version 4.3.2 (2023-10-31) -- "Eye Holes" 255s Copyright (C) 2023 The R Foundation for Statistical Computing 255s Platform: x86_64-pc-linux-gnu (64-bit) 255s 255s R is free software and comes with ABSOLUTELY NO WARRANTY. 255s You are welcome to redistribute it under certain conditions. 255s Type 'license()' or 'licence()' for distribution details. 255s 255s R is a collaborative project with many contributors. 255s Type 'contributors()' for more information and 255s 'citation()' on how to cite R or R packages in publications. 255s 255s Type 'demo()' for some demos, 'help()' for on-line help, or 255s 'help.start()' for an HTML browser interface to help. 255s Type 'q()' to quit R. 255s 255s > require(etm) 255s Loading required package: etm 256s > 256s > ## Print with a bit less precision to avoid lots of notes in the comparison 256s > old <- options(digits = 4) 256s > 256s > ### Simple test 256s > 256s > time <- id <- 1:10 256s > from <- rep(0, 10) 256s > to <- rep(1, 10) 256s > 256s > data1 <- data.frame(id, from, to, time) 256s > tra1 <- matrix(FALSE, 2, 2) 256s > tra1[1, 2] <- TRUE 256s > 256s > etm1 <- etm(data1, c("0", "1"), tra1, NULL, 0) 256s > 256s > all.equal(as.vector(trprob(etm1, "0 0")), cumprod((10:1 - 1) / (10:1))) 256s [1] TRUE 256s > 256s > etm1$cov["0 0", "0 0", ] 256s 1 2 3 4 5 6 7 8 9 10 256s 0.009 0.016 0.021 0.024 0.025 0.024 0.021 0.016 0.009 0.000 256s > 256s > all.equal(etm1$cov["0 0", "0 0",], trcov(etm1, "0 0")) 256s [1] TRUE 256s > 256s > ### A simple test from AHR's author, where the first time is censored 256s > if (!require(survival)) { 256s + stop("This test requires the survival package") 256s + } 256s Loading required package: survival 256s > 256s > data <- data.frame(id=1:10, time=1:10, from=0, to=1, status=TRUE) 256s > 256s > tra <- matrix(FALSE, nrow=2, ncol=2) 256s > tra[1, 2] <- TRUE 256s > 256s > data$to[1] <- "cens" 256s > data$status[1] <- FALSE 256s > 256s > fit.km <- survfit(Surv(time, status) ~ 1, data=data) 256s > fit.etm <- etm(data, c("0","1"), tra, "cens", s=0, t="last", covariance=FALSE) 256s > 256s > all.equal(fit.km$surv[data$status], fit.etm$est[1,1,], check.attributes = FALSE) 256s [1] TRUE 256s > 256s > data$to[2] <- "cens" 256s > data$status[2] <- FALSE 256s > 256s > fit.km <- survfit(Surv(time, status) ~ 1, data=data) 256s > fit.etm <- etm(data, c("0","1"), tra, "cens", s=0, t="last", covariance=FALSE) 257s > 257s > all.equal(fit.km$surv[data$status], fit.etm$est[1,1,], check.attributes = FALSE) 257s [1] TRUE 257s > 257s > ### a bit more complicated 257s > 257s > time <- id <- 1:10 257s > from <- rep(0, 10) 257s > to <- rep(c(1, 2), 5) 257s > data2 <- data.frame(id, from, to, time) 257s > 257s > tra2 <- matrix(FALSE, 3, 3) 257s > tra2[1, 2:3] <- TRUE 257s > 257s > etm2 <- etm(data2, c("0", "1", "2"), tra2, NULL, 0) 257s > 257s > aa <- table(time, to) 257s > 257s > cif1 <- cumsum(aa[, 1] / 10) 257s > cif2 <- cumsum(aa[, 2] / 10) 257s > surv <- cumprod((10:1 - 1) / (10:1)) 257s > 257s > all.equal(trprob(etm2, "0 1"), cif1) 257s [1] TRUE 257s > all.equal(trprob(etm2, "0 2"), cif2) 257s [1] TRUE 257s > all.equal(as.vector(trprob(etm2, "0 0")), surv) 257s [1] TRUE 257s > 257s > ## a test on id 257s > data2$id <- letters[1:10] 257s > 257s > etm3 <- etm(data2, c("0", "1", "2"), tra2, NULL, 0) 257s > 257s > all.equal(trprob(etm2, "0 1"), trprob(etm3, "0 1")) 257s [1] TRUE 257s > all.equal(trprob(etm2, "0 2"), trprob(etm3, "0 2")) 257s [1] TRUE 257s > all.equal(trprob(etm2, "0 0"), trprob(etm3, "0 0")) 257s [1] TRUE 257s > 257s > 257s > ### Test on sir.cont 257s > 257s > data(sir.cont) 257s > 257s > ## Modification for patients entering and leaving a state 257s > ## at the same date 257s > ## Change on ventilation status is considered 257s > ## to happen before end of hospital stay 257s > sir.cont <- sir.cont[order(sir.cont$id, sir.cont$time), ] 257s > for (i in 2:nrow(sir.cont)) { 257s + if (sir.cont$id[i]==sir.cont$id[i-1]) { 257s + if (sir.cont$time[i]==sir.cont$time[i-1]) { 257s + sir.cont$time[i-1] <- sir.cont$time[i-1] - 0.5 257s + } 257s + } 257s + } 257s > 257s > ### Computation of the transition probabilities 257s > ## Possible transitions. 257s > tra <- matrix(ncol=3,nrow=3,FALSE) 257s > tra[1, 2:3] <- TRUE 257s > tra[2, c(1, 3)] <- TRUE 257s > 257s > ## etm 257s > prob.sir <- etm(sir.cont, c("0", "1", "2"), tra, "cens", 1) 257s > 257s > prob.sir 257s Multistate model with 2 transient state(s) 257s and 1 absorbing state(s) 257s 257s Possible transitions: 257s from to 257s 0 1 257s 0 2 257s 1 0 257s 1 2 257s 257s Estimate of P(1, 183) 257s 0 1 2 257s 0 0 0 1 257s 1 0 0 1 257s 2 0 0 1 257s 257s > 257s > summ.sir <- summary(prob.sir) 257s > all.equal(summ.sir[['0 1']]$P, as.vector(trprob(prob.sir, "0 1"))) 257s [1] TRUE 257s > subset(summ.sir[[3]],time<183) # issue with precision on different architectures 257s P time var lower upper n.risk n.event 257s 1.5 0.0000 1.5 0.000e+00 0.00000 0.0000 394 0 257s 2 0.1187 2.0 2.641e-04 0.08683 0.1505 396 47 257s 2.5 0.1187 2.5 2.641e-04 0.08683 0.1505 364 0 257s 3 0.2454 3.0 4.465e-04 0.20398 0.2868 365 54 257s 3.5 0.2454 3.5 4.465e-04 0.20398 0.2868 328 0 257s 4 0.3806 4.0 5.416e-04 0.33501 0.4262 331 62 257s 4.5 0.3806 4.5 5.416e-04 0.33501 0.4262 280 0 257s 5 0.4792 5.0 5.480e-04 0.43333 0.5251 283 48 257s 5.5 0.4792 5.5 5.480e-04 0.43333 0.5251 248 0 257s 6 0.5693 6.0 5.141e-04 0.52482 0.6137 249 47 257s 7 0.6350 7.0 4.665e-04 0.59266 0.6773 212 36 257s 8 0.6795 8.0 4.202e-04 0.63931 0.7197 195 27 257s 8.5 0.6795 8.5 4.202e-04 0.63931 0.7197 172 0 257s 9 0.7325 9.0 3.580e-04 0.69541 0.7696 173 34 257s 10 0.7647 10.0 3.141e-04 0.72992 0.7994 148 21 257s 10.5 0.7647 10.5 3.141e-04 0.72992 0.7994 135 0 257s 11 0.7895 11.0 2.790e-04 0.75674 0.8222 136 18 257s 12 0.8138 12.0 2.420e-04 0.78330 0.8443 129 18 257s 12.5 0.8138 12.5 2.420e-04 0.78330 0.8443 117 0 257s 13 0.8294 13.0 2.182e-04 0.80045 0.8584 118 13 257s 14 0.8452 14.0 1.938e-04 0.81789 0.8725 115 14 257s 15 0.8625 15.0 1.670e-04 0.83714 0.8878 106 15 257s 16 0.8723 16.0 1.522e-04 0.84807 0.8964 93 9 257s 17 0.8852 17.0 1.330e-04 0.86256 0.9078 86 12 257s 17.5 0.8852 17.5 1.330e-04 0.86256 0.9078 77 0 257s 18 0.8960 18.0 1.168e-04 0.87484 0.9172 76 9 257s 19 0.9029 19.0 1.070e-04 0.88261 0.9232 71 7 257s 20 0.9125 20.0 9.367e-05 0.89356 0.9315 64 10 257s 21 0.9161 21.0 8.878e-05 0.89768 0.9346 57 4 257s 22 0.9226 22.0 7.996e-05 0.90504 0.9401 55 6 257s 23 0.9261 23.0 7.537e-05 0.90904 0.9431 51 4 257s 23.5 0.9261 23.5 7.537e-05 0.90904 0.9431 49 0 257s 24 0.9354 24.0 6.292e-05 0.91982 0.9509 50 9 257s 25 0.9385 25.0 5.878e-05 0.92352 0.9536 42 3 257s 26 0.9429 26.0 5.326e-05 0.92863 0.9572 39 5 257s 27 0.9477 27.0 4.749e-05 0.93417 0.9612 35 6 257s 27.5 0.9477 27.5 4.749e-05 0.93417 0.9612 29 0 257s 28 0.9531 28.0 4.093e-05 0.94059 0.9657 30 5 257s 29 0.9567 29.0 3.668e-05 0.94485 0.9686 31 4 257s 30 0.9592 30.0 3.384e-05 0.94779 0.9706 28 3 257s 30.5 0.9592 30.5 3.384e-05 0.94779 0.9706 29 0 257s 31 0.9642 31.0 2.821e-05 0.95383 0.9746 30 6 257s 32 0.9649 32.0 2.752e-05 0.95458 0.9751 25 1 257s 33 0.9669 33.0 2.533e-05 0.95708 0.9768 24 2 257s 34 0.9685 34.0 2.368e-05 0.95900 0.9781 26 2 257s 35 0.9697 35.0 2.252e-05 0.96036 0.9790 28 2 257s 36 0.9702 36.0 2.194e-05 0.96104 0.9794 26 1 257s 37 0.9718 37.0 2.043e-05 0.96290 0.9806 26 2 257s 38 0.9739 38.0 1.831e-05 0.96555 0.9823 25 4 257s 38.5 0.9739 38.5 1.831e-05 0.96555 0.9823 21 0 257s 39 0.9760 39.0 1.643e-05 0.96802 0.9839 23 3 257s 40 0.9769 40.0 1.558e-05 0.96918 0.9847 19 1 257s 41 0.9774 41.0 1.512e-05 0.96981 0.9851 22 1 257s 42 0.9779 42.0 1.476e-05 0.97032 0.9854 22 0 257s 43 0.9798 43.0 1.308e-05 0.97271 0.9869 22 3 257s 44 0.9803 44.0 1.265e-05 0.97333 0.9873 21 1 257s 45 0.9817 45.0 1.157e-05 0.97499 0.9883 19 1 257s 46 0.9822 46.0 1.116e-05 0.97561 0.9887 17 1 257s 47 0.9831 47.0 1.037e-05 0.97683 0.9895 18 2 257s 48 0.9836 48.0 9.987e-06 0.97743 0.9898 17 1 257s 49 0.9841 49.0 9.669e-06 0.97796 0.9901 17 0 257s 50 0.9845 50.0 9.297e-06 0.97856 0.9905 17 1 257s 50.5 0.9845 50.5 9.297e-06 0.97856 0.9905 16 0 257s 51 0.9860 51.0 8.214e-06 0.98037 0.9916 17 3 257s 52 0.9870 52.0 7.513e-06 0.98159 0.9923 14 2 257s 53 0.9879 53.0 6.875e-06 0.98276 0.9930 12 1 257s 54 0.9889 54.0 6.214e-06 0.98397 0.9937 12 2 257s 55 0.9903 55.0 5.254e-06 0.98581 0.9948 10 3 257s 56 0.9913 56.0 4.667e-06 0.98703 0.9955 6 1 257s 57 0.9917 57.0 4.364e-06 0.98765 0.9958 5 1 257s 58 0.9922 58.0 4.064e-06 0.98828 0.9962 4 1 257s 59 0.9927 59.0 3.769e-06 0.98891 0.9965 3 1 257s 60 0.9932 60.0 3.488e-06 0.98953 0.9969 3 1 257s 62 0.9937 62.0 3.230e-06 0.99016 0.9972 2 0 257s 63 0.9942 63.0 2.956e-06 0.99079 0.9975 2 1 257s 68 0.9942 68.0 2.956e-06 0.99079 0.9975 1 0 257s 70 0.9946 70.0 2.694e-06 0.99143 0.9979 2 1 257s 78 0.9951 78.0 2.442e-06 0.99207 0.9982 1 0 257s 80 0.9951 80.0 2.442e-06 0.99207 0.9982 1 0 257s 85 0.9966 85.0 1.695e-06 0.99404 0.9991 2 0 257s 89 0.9966 89.0 1.695e-06 0.99404 0.9991 2 0 257s 90 0.9966 90.0 1.695e-06 0.99404 0.9991 1 0 257s 95 0.9971 95.0 1.448e-06 0.99472 0.9994 2 0 257s 100 0.9976 100.0 1.203e-06 0.99542 0.9997 3 0 257s 101 0.9981 101.0 9.592e-07 0.99613 1.0000 3 1 257s 108 0.9985 108.0 7.169e-07 0.99688 1.0000 2 1 257s 113 0.9990 113.0 4.764e-07 0.99767 1.0000 1 0 257s 116 0.9990 116.0 4.764e-07 0.99767 1.0000 1 0 257s 124 0.9990 124.0 4.764e-07 0.99767 1.0000 2 0 257s 164 0.9990 164.0 4.764e-07 0.99767 1.0000 0 0 257s > 257s > ## gonna play a bit with the state names 257s > dd <- sir.cont 257s > dd$from <- ifelse(dd$from == 0, "initial state", "ventilation") 257s > dd$to <- as.character(dd$to) 257s > for (i in seq_len(nrow(dd))) { 257s + dd$to[i] <- switch(dd$to[i], 257s + "0" = "initial state", 257s + "1" = "ventilation", 257s + "2" = "end of story", 257s + "cens" = "cens" 257s + ) 257s + } 257s > 257s > test <- etm(dd, c("initial state", "ventilation", "end of story"), tra, "cens", 1) 257s > 257s > all.equal(test$est["initial state", "initial state", ], 257s + prob.sir$est["0", "0", ]) 257s [1] TRUE 257s > all.equal(trprob(test, "initial state initial state"), trprob(prob.sir, "0 0")) 257s [1] TRUE 257s > all.equal(trprob(test, "initial state ventilation"), trprob(prob.sir, "0 1")) 257s [1] TRUE 257s > all.equal(trprob(test, "initial state end of story"), trprob(prob.sir, "0 2")) 257s [1] TRUE 257s > 257s > all.equal(trcov(test, "initial state end of story"), trcov(prob.sir, "0 2")) 257s [1] TRUE 257s > 257s > aa <- summary(test) 257s > all.equal(summ.sir[[6]], aa[[6]]) 257s [1] TRUE 257s > all.equal(summ.sir[[4]], aa[[4]]) 257s [1] TRUE 257s > 257s > ### Test on abortion data 257s > 257s > data(abortion) 257s > 257s > from <- rep(0, nrow(abortion)) 257s > to <- abortion$cause 257s > entry <- abortion$entry 257s > exit <- abortion$exit 257s > id <- 1:nrow(abortion) 257s > data <- data.frame(id, from, to, entry, exit, group = abortion$group) 257s > 257s > ## Computation of the CIFs 257s > tra <- matrix(FALSE, 4, 4) 257s > tra[1, 2:4] <- TRUE 257s > 257s > cif.control <- etm(data[data$group == 0, ], c("0", "1", "2", "3"), 257s + tra, NULL, 0) 257s > cif.exposed <- etm(data[data$group == 1, ], c("0", "1", "2", "3"), 257s + tra, NULL, 0) 257s > 257s > all.equal(trprob(cif.control, "0 1"), cif.control$est["0", "1", ]) 257s [1] TRUE 257s > all.equal(trcov(cif.control, c("0 1", "0 2")), cif.control$cov["0 1", "0 2", ]) 257s [1] TRUE 257s > 257s > trprob(cif.control, "0 1") 257s 6 7 8 9 10 11 12 13 257s 0.000000 0.007401 0.014881 0.026509 0.033208 0.037694 0.037694 0.038955 257s 14 17 19 21 24 25 26 30 257s 0.040159 0.040159 0.040159 0.040159 0.040159 0.040159 0.040159 0.040159 257s 31 32 33 34 35 36 37 38 257s 0.040159 0.040159 0.040159 0.040159 0.040159 0.040159 0.040159 0.040159 257s 39 40 41 42 43 257s 0.040159 0.040159 0.040159 0.040159 0.040159 257s > trprob(cif.control, "0 2") 257s 6 7 8 9 10 11 12 13 257s 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 257s 14 17 19 21 24 25 26 30 257s 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.003657 257s 31 32 33 34 35 36 37 38 257s 0.006371 0.008175 0.013543 0.023317 0.031260 0.053197 0.084529 0.179163 257s 39 40 41 42 43 257s 0.322016 0.563121 0.742227 0.793893 0.799059 257s > trprob(cif.control, "0 0") 257s 6 7 8 9 10 11 12 13 257s 0.965812 0.932508 0.887628 0.862433 0.838989 0.822538 0.813099 0.810578 257s 14 17 19 21 24 25 26 30 257s 0.806964 0.805874 0.803810 0.802804 0.801837 0.800883 0.799937 0.796280 257s 31 32 33 34 35 36 37 38 257s 0.793565 0.791762 0.786394 0.776620 0.768677 0.745862 0.714531 0.619897 257s 39 40 41 42 43 257s 0.477043 0.235938 0.056832 0.005167 0.000000 257s > 257s > trcov(cif.control, "0 1") 257s 6 7 8 9 10 11 12 13 257s 0.000e+00 2.719e-05 4.533e-05 6.665e-05 7.698e-05 8.304e-05 8.304e-05 8.444e-05 257s 14 17 19 21 24 25 26 30 257s 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 257s 31 32 33 34 35 36 37 38 257s 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 257s 39 40 41 42 43 257s 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 257s > trcov(cif.control, "0 2") 257s 6 7 8 9 10 11 12 13 257s 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 257s 14 17 19 21 24 25 26 30 257s 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 3.338e-06 257s 31 32 33 34 35 36 37 38 257s 5.784e-06 7.401e-06 1.216e-05 2.072e-05 2.758e-05 4.619e-05 7.202e-05 1.461e-04 257s 39 40 41 42 43 257s 2.470e-04 3.880e-04 4.702e-04 4.903e-04 4.922e-04 257s > trcov(cif.control, "0 0") 257s 6 7 8 9 10 11 12 13 257s 2.822e-04 3.821e-04 4.527e-04 4.748e-04 4.875e-04 4.927e-04 4.941e-04 4.942e-04 257s 14 17 19 21 24 25 26 30 257s 4.941e-04 4.940e-04 4.936e-04 4.933e-04 4.931e-04 4.928e-04 4.926e-04 4.914e-04 257s 31 32 33 34 35 36 37 38 257s 4.905e-04 4.899e-04 4.880e-04 4.846e-04 4.816e-04 4.729e-04 4.601e-04 4.176e-04 257s 39 40 41 42 43 257s 3.425e-04 1.865e-04 4.797e-05 4.441e-06 0.000e+00 257s > 257s > aa <- summary(cif.control) 257s > aa$"0 1" 257s P time var lower upper n.risk n.event 257s 6 0.000000 6 0.000e+00 0.000000 0.00000 117 0 257s 7 0.007401 7 2.719e-05 0.000000 0.01762 261 2 257s 8 0.014881 8 4.533e-05 0.001685 0.02808 374 3 257s 9 0.026509 9 6.665e-05 0.010508 0.04251 458 6 257s 10 0.033208 10 7.698e-05 0.016011 0.05040 515 4 257s 11 0.037694 11 8.304e-05 0.019834 0.05555 561 3 257s 12 0.037694 12 8.304e-05 0.019834 0.05555 610 0 257s 13 0.038955 13 8.444e-05 0.020944 0.05697 645 1 257s 14 0.040159 14 8.571e-05 0.022014 0.05830 673 1 257s 17 0.040159 17 8.571e-05 0.022014 0.05830 740 0 257s 19 0.040159 19 8.571e-05 0.022014 0.05830 781 0 257s 21 0.040159 21 8.571e-05 0.022014 0.05830 799 0 257s 24 0.040159 24 8.571e-05 0.022014 0.05830 830 0 257s 25 0.040159 25 8.571e-05 0.022014 0.05830 841 0 257s 26 0.040159 26 8.571e-05 0.022014 0.05830 846 0 257s 30 0.040159 30 8.571e-05 0.022014 0.05830 875 0 257s 31 0.040159 31 8.571e-05 0.022014 0.05830 880 0 257s 32 0.040159 32 8.571e-05 0.022014 0.05830 880 0 257s 33 0.040159 33 8.571e-05 0.022014 0.05830 885 0 257s 34 0.040159 34 8.571e-05 0.022014 0.05830 885 0 257s 35 0.040159 35 8.571e-05 0.022014 0.05830 880 0 257s 36 0.040159 36 8.571e-05 0.022014 0.05830 876 0 257s 37 0.040159 37 8.571e-05 0.022014 0.05830 857 0 257s 38 0.040159 38 8.571e-05 0.022014 0.05830 823 0 257s 39 0.040159 39 8.571e-05 0.022014 0.05830 716 0 257s 40 0.040159 40 8.571e-05 0.022014 0.05830 554 0 257s 41 0.040159 41 8.571e-05 0.022014 0.05830 274 0 257s 42 0.040159 42 8.571e-05 0.022014 0.05830 66 0 257s 43 0.040159 43 8.571e-05 0.022014 0.05830 6 0 257s > all.equal(aa$"0 1"$P, as.vector(trprob(cif.control, "0 1"))) 257s [1] TRUE 257s > 257s > ### test on los data 257s > 257s > data(los.data) # in package changeLOS 257s > 257s > ## putting los.data in the long format (see changeLOS) 257s > my.observ <- prepare.los.data(x=los.data) 257s > 257s > tra <- matrix(FALSE, 4, 4) 257s > tra[1, 2:4] <- TRUE 257s > tra[2, 3:4] <- TRUE 257s > 257s > tr.prob <- etm(my.observ, c("0","1","2","3"), tra, NULL, 0) 257s > 257s > tr.prob 257s Multistate model with 2 transient state(s) 257s and 2 absorbing state(s) 257s 257s Possible transitions: 257s from to 257s 0 1 257s 0 2 257s 0 3 257s 1 2 257s 1 3 257s 257s Estimate of P(0, 82) 257s 0 1 2 3 257s 0 0 0 0.7474 0.2526 257s 1 0 0 0.7073 0.2927 257s 2 0 0 1.0000 0.0000 257s 3 0 0 0.0000 1.0000 257s 257s > summary(tr.prob) 257s Transition 0 0 257s P time var lower upper n.risk n.event 257s 0.882275 3 1.374e-04 0.8593018 0.905248 756 0 257s 0.112434 15 1.320e-04 0.0899155 0.134952 90 0 257s 0.031746 27 4.066e-05 0.0192484 0.044244 26 0 257s 0.006614 41 8.690e-06 0.0008359 0.012392 5 0 257s 0.002646 61 3.490e-06 0.0000000 0.006307 3 0 257s 0.000000 82 0.000e+00 0.0000000 0.000000 1 0 257s 257s Transition 0 1 257s P time var lower upper n.risk n.event 257s 0.017196 3 2.235e-05 0.0079289 0.02646 756 13 257s 0.063492 15 7.865e-05 0.0461099 0.08087 90 0 257s 0.030423 27 3.902e-05 0.0181805 0.04267 26 1 257s 0.015873 41 2.066e-05 0.0069637 0.02478 5 0 257s 0.005291 61 6.962e-06 0.0001197 0.01046 3 0 257s 0.000000 82 0.000e+00 0.0000000 0.00000 1 0 257s 257s Transition 0 2 257s P time var lower upper n.risk n.event 257s 0.08466 3 0.0001025 0.06481 0.1045 756 64 257s 0.62302 15 0.0003107 0.58847 0.6576 90 4 257s 0.69841 27 0.0002786 0.66570 0.7311 26 1 257s 0.72751 41 0.0002622 0.69578 0.7593 5 0 257s 0.74074 61 0.0002540 0.70950 0.7720 3 1 257s 0.74735 82 0.0002498 0.71638 0.7783 1 1 257s 257s Transition 0 3 257s P time var lower upper n.risk n.event 257s 0.01587 3 2.066e-05 0.006964 0.02478 756 12 257s 0.20106 15 2.125e-04 0.172489 0.22963 90 1 257s 0.23942 27 2.409e-04 0.208999 0.26984 26 0 257s 0.25000 41 2.480e-04 0.219133 0.28087 5 0 257s 0.25132 61 2.489e-04 0.220402 0.28224 3 0 257s 0.25265 82 2.498e-04 0.221671 0.28362 1 0 257s 257s Transition 1 1 257s P time var lower upper n.risk n.event 257s 1.00000 3 0.000e+00 1.00000 1.00000 0 0 257s 0.38661 15 2.358e-03 0.29143 0.48179 51 0 257s 0.12119 27 7.842e-04 0.06630 0.17607 23 0 257s 0.04593 41 2.405e-04 0.01554 0.07633 14 0 257s 0.01531 61 6.579e-05 0.00000 0.03121 4 0 257s 0.00000 82 0.000e+00 0.00000 0.00000 0 0 257s 257s Transition 1 2 257s P time var lower upper n.risk n.event 257s 0.0000 3 0.000000 0.0000 0.0000 0 0 257s 0.4107 15 0.002590 0.3110 0.5104 51 2 257s 0.6082 27 0.002254 0.5151 0.7012 23 1 257s 0.6652 41 0.002064 0.5761 0.7542 14 2 257s 0.6920 61 0.002000 0.6043 0.7796 4 0 257s 0.7073 82 0.001984 0.6200 0.7946 0 0 257s 257s Transition 1 3 257s P time var lower upper n.risk n.event 257s 0.0000 3 0.000000 0.0000 0.0000 0 0 257s 0.2027 15 0.001784 0.1199 0.2855 51 1 257s 0.2706 27 0.001968 0.1837 0.3576 23 0 257s 0.2889 41 0.001982 0.2016 0.3761 14 0 257s 0.2927 61 0.001984 0.2054 0.3800 4 0 257s 0.2927 82 0.001984 0.2054 0.3800 0 0 257s 257s > 257s > cLOS <- etm::clos(tr.prob, aw = TRUE) 257s > 257s > cLOS 257s The expected change in length of stay is: 257s 1.975 257s 257s Alternative weighting: 257s 257s Expected change in LOS with weight.1: 2.097 257s Expected change in LOS with weight.other: 1.951 257s > 257s > 257s > ### Tests on pseudo values 257s > t_pseudo <- closPseudo(my.observ, c("0","1","2","3"), tra, NULL, 257s + formula = ~ 1, aw = TRUE) 268s > 268s > cLOS$e.phi == t_pseudo$theta[, "e.phi"] 268s [,1] 268s [1,] TRUE 268s > cLOS$e.phi.weights.1 == t_pseudo$theta[, "e.phi.weights.1"] 268s [,1] 268s [1,] TRUE 268s > cLOS$e.phi.weights.other == t_pseudo$theta[, "e.phi.weights.other"] 268s [,1] 268s [1,] TRUE 268s > 268s > mean(t_pseudo$pseudoData$ps.e.phi) 268s [1] 1.968 268s > 268s > ### tests on etmprep 268s > 268s > ### creation of fake data in the wild format, following an illness-death model 268s > ## transition times 268s > tdisease <- c(3, 4, 3, 6, 8, 9) 268s > tdeath <- c(6, 9, 8, 6, 8, 9) 268s > 268s > ## transition status 268s > stat.disease <- c(1, 1, 1, 0, 0, 0) 268s > stat.death <- c(1, 1, 1, 1, 1, 0) 268s > 268s > ## a covariate that we want to keep in the new data 268s > set.seed(1313) 268s > cova <- rbinom(6, 1, 0.5) 268s > 268s > dat <- data.frame(tdisease, tdeath, 268s + stat.disease, stat.death, 268s + cova) 268s > 268s > ## Possible transitions 268s > tra <- matrix(FALSE, 3, 3) 268s > tra[1, 2:3] <- TRUE 268s > tra[2, 3] <- TRUE 268s > 268s > ## data preparation 268s > newdat <- etmprep(c(NA, "tdisease", "tdeath"), 268s + c(NA, "stat.disease", "stat.death"), 268s + data = dat, tra = tra, 268s + cens.name = "cens", keep = "cova") 268s > 268s > newdat 268s id entry exit from to cova 268s 1 1 0 3 0 1 1 268s 2 1 3 6 1 2 1 268s 3 2 0 4 0 1 0 268s 4 2 4 9 1 2 0 268s 5 3 0 3 0 1 1 268s 6 3 3 8 1 2 1 268s 7 4 0 6 0 2 0 268s 8 5 0 8 0 2 1 268s 9 6 0 9 0 cens 1 268s > 268s > ref <- data.frame(id = c(1, 1, 2, 2, 3, 3, 4, 5, 6), 268s + entry = c(0, 3, 0, 4, 0, 3, 0, 0, 0), 268s + exit = c(3, 6, 4, 9, 3, 8, 6, 8, 9), 268s + from = c(0, 1, 0, 1, 0, 1, 0, 0, 0), 268s + to = c(rep(c(1, 2), 3), 2, 2, "cens"), 268s + cova = c(1, 1, 0, 0, 1, 1, 0, 1, 1)) 268s > ref$from <- factor(as.character(ref$from), levels = c("0", "1", "2", "cens")) 268s > ref$to <- factor(as.character(ref$to), levels = c("0", "1", "2", "cens")) 268s > 268s > all.equal(ref, newdat) 268s [1] TRUE 268s > 268s > 268s > ###################################### 268s > ### Test the stratified calls 268s > ###################################### 268s > 268s > if (require("kmi", quietly = TRUE)) { 268s + library(etm) 268s + 268s + data(icu.pneu) 268s + my.icu.pneu <- icu.pneu 268s + 268s + my.icu.pneu <- my.icu.pneu[order(my.icu.pneu$id, my.icu.pneu$start), ] 268s + masque <- diff(my.icu.pneu$id) 268s + 268s + my.icu.pneu$from <- 0 268s + my.icu.pneu$from[c(1, masque) == 0] <- 1 268s + 268s + my.icu.pneu$to2 <- my.icu.pneu$event 268s + my.icu.pneu$to2[my.icu.pneu$status == 0] <- "cens" 268s + my.icu.pneu$to2[c(masque, 1) == 0] <- 1 268s + 268s + 268s + my.icu.pneu$to <- ifelse(my.icu.pneu$to2 %in% c(2, 3), 2, 268s + my.icu.pneu$to2) 268s + 268s + my.icu.pneu <- my.icu.pneu[, c("id", "start", "stop", "from", "to", 268s + "to2", "age", "sex")] 268s + names(my.icu.pneu)[c(2, 3)] <- c("entry", "exit") 268s + 268s + bouh_strat <- etm(my.icu.pneu, c("0", "1", "2"), tra_ill(), "cens", 0, strata = "sex") 268s + 268s + bouh_female <- etm(my.icu.pneu[my.icu.pneu$sex == "F", ], 268s + c("0", "1", "2"), tra_ill(), "cens", 0) 268s + 268s + all(bouh_strat[[1]]$est == bouh_female$est) 268s + 268s + ## Test the summary 268s + the_summary <- summary(bouh_strat) 268s + the_summary 268s + 268s + ## Test trprob 268s + all(trprob(bouh_strat, "0 1")[[1]] == trprob(bouh_female, "0 1")) 268s + all(trprob(bouh_strat, "0 1", c(0, 5, 10, 15))[[1]] == trprob(bouh_female, "0 1", c(0, 5, 10, 15))) 268s + 268s + ## Test trcov 268s + all(trcov(bouh_strat, "0 1")[[1]] == trcov(bouh_female, "0 1")) 268s + all(trcov(bouh_strat, c("0 1", "0 2"))[[1]] == trcov(bouh_female, c("0 1", "0 2"))) 268s + all(trcov(bouh_strat, "0 1", c(0, 5, 10, 15))[[1]] == trcov(bouh_female, "0 1", c(0, 5, 10, 15))) 268s + } else { 268s + print("These tests require the kmi package") 268s + } 268s [1] TRUE 268s > 268s > options(old) 268s > 268s autopkgtest [08:53:39]: test run-unit-test: -----------------------] 268s autopkgtest [08:53:39]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 268s run-unit-test PASS 268s autopkgtest [08:53:39]: test pkg-r-autopkgtest: preparing testbed 269s Reading package lists... 269s Building dependency tree... 269s Reading state information... 269s Starting pkgProblemResolver with broken count: 0 269s Starting 2 pkgProblemResolver with broken count: 0 269s Done 270s The following additional packages will be installed: 270s build-essential cpp cpp-13 cpp-13-x86-64-linux-gnu cpp-x86-64-linux-gnu 270s dctrl-tools g++ g++-13 g++-13-x86-64-linux-gnu g++-x86-64-linux-gnu gcc 270s gcc-13 gcc-13-x86-64-linux-gnu gcc-x86-64-linux-gnu gfortran gfortran-13 270s gfortran-13-x86-64-linux-gnu gfortran-x86-64-linux-gnu icu-devtools libasan8 270s libatomic1 libblas-dev libbz2-dev libc-dev-bin libc6-dev libcc1-0 270s libcrypt-dev libgcc-13-dev libgfortran-13-dev libhwasan0 libicu-dev libisl23 270s libitm1 libjpeg-dev libjpeg-turbo8-dev libjpeg8-dev liblapack-dev liblsan0 270s liblzma-dev libmpc3 libncurses-dev libpcre2-16-0 libpcre2-32-0 libpcre2-dev 270s libpcre2-posix3 libpkgconf3 libpng-dev libquadmath0 libreadline-dev 270s libstdc++-13-dev libtsan2 libubsan1 linux-libc-dev pkg-config 270s pkg-r-autopkgtest pkgconf pkgconf-bin r-base-dev r-cran-backports 270s r-cran-broom r-cran-cli r-cran-colorspace r-cran-cpp11 r-cran-dplyr 270s r-cran-ellipsis r-cran-fansi r-cran-farver r-cran-geepack r-cran-generics 270s r-cran-ggplot2 r-cran-glue r-cran-gtable r-cran-isoband r-cran-labeling 270s r-cran-lifecycle r-cran-magrittr r-cran-mass r-cran-mgcv r-cran-munsell 270s r-cran-nlme r-cran-pillar r-cran-pkgconfig r-cran-purrr r-cran-r6 270s r-cran-rcolorbrewer r-cran-rlang r-cran-scales r-cran-stringi r-cran-stringr 270s r-cran-tibble r-cran-tidyr r-cran-tidyselect r-cran-utf8 r-cran-vctrs 270s r-cran-viridislite r-cran-withr rpcsvc-proto zlib1g-dev 270s Suggested packages: 270s cpp-doc gcc-13-locales cpp-13-doc debtags g++-multilib g++-13-multilib 270s gcc-13-doc gcc-multilib manpages-dev autoconf automake libtool flex bison 270s gdb gcc-doc gcc-13-multilib gdb-x86-64-linux-gnu gfortran-multilib 270s gfortran-doc gfortran-13-multilib gfortran-13-doc libcoarrays-dev 270s liblapack-doc glibc-doc icu-doc liblzma-doc ncurses-doc readline-doc 270s libstdc++-13-doc texlive-base texlive-latex-base texlive-plain-generic 270s texlive-fonts-recommended texlive-fonts-extra texlive-extra-utils 270s texlive-latex-recommended texlive-latex-extra texinfo r-cran-aer 270s r-cran-bbmle r-cran-boot r-cran-car r-cran-cardata r-cran-caret 270s r-cran-cluster r-cran-cmprsk r-cran-coda r-cran-covr r-cran-e1071 270s r-cran-emmeans r-cran-epir r-cran-gam r-cran-gee r-cran-glmnet r-cran-gmm 270s r-cran-hmisc r-cran-irlba r-cran-interp r-cran-knitr r-cran-ks r-cran-lavaan 270s r-cran-leaps r-cran-lme4 r-cran-lmtest r-cran-lsmeans r-cran-maps 270s r-cran-mclust r-cran-metafor r-cran-modeldata r-cran-multcomp r-cran-network 270s r-cran-nnet r-cran-ordinal r-cran-plm r-cran-psych r-cran-quantreg 270s r-cran-rmarkdown r-cran-robust r-cran-robustbase r-cran-rsample 270s r-cran-sandwich r-cran-sp r-cran-spdep r-cran-spatialreg r-cran-spelling 270s r-cran-survey r-cran-systemfit r-cran-tseries r-cran-zoo r-cran-kernsmooth 270s r-cran-kernlab r-cran-mvtnorm r-cran-vcd r-cran-shiny r-cran-shinyjs 270s r-cran-png r-cran-jpeg r-cran-viridis r-cran-magick r-cran-sf r-cran-bit64 270s r-cran-formattable r-cran-nanotime r-cran-palmerpenguins r-cran-units 270s r-cran-vdiffr r-cran-testthat r-cran-bench r-cran-blob r-cran-brio 270s r-cran-callr r-cran-crayon r-cran-evaluate r-cran-here r-cran-hms 270s r-cran-htmltools r-cran-pkgbuild r-cran-pkgload 270s Recommended packages: 270s bzip2-doc manpages manpages-dev libc-devtools libpng-tools r-cran-testthat 270s r-cran-callr r-cran-covr r-cran-crayon r-cran-digest r-cran-htmltools 270s r-cran-htmlwidgets r-cran-knitr r-cran-mockery r-cran-processx r-cran-ps 270s r-cran-rmarkdown r-cran-rprojroot r-cran-rstudioapi r-cran-whoami 270s r-cran-bench r-cran-brio r-cran-decor r-cran-desc r-cran-lobstr 270s r-cran-progress r-cran-dbplyr r-cran-rmysql r-cran-rpostgresql 270s r-cran-rsqlite r-cran-unitizer r-cran-pkgload r-cran-hexbin r-cran-hmisc 270s r-cran-mapproj r-cran-maps r-cran-multcomp r-cran-profvis r-cran-quantreg 270s r-cran-ragg r-cran-rpart r-cran-sf r-cran-svglite r-cran-vdiffr r-cran-xml2 270s r-cran-waldo r-cran-lintr r-cran-tidyverse r-cran-lubridate r-cran-httr 270s r-cran-fs r-cran-usethis r-cran-bit64 r-cran-dichromat r-cran-hms 270s r-cran-mockr r-cran-formattable r-cran-readr r-cran-pkgdown r-cran-zeallot 270s The following NEW packages will be installed: 270s autopkgtest-satdep build-essential cpp cpp-13 cpp-13-x86-64-linux-gnu 270s cpp-x86-64-linux-gnu dctrl-tools g++ g++-13 g++-13-x86-64-linux-gnu 270s g++-x86-64-linux-gnu gcc gcc-13 gcc-13-x86-64-linux-gnu gcc-x86-64-linux-gnu 270s gfortran gfortran-13 gfortran-13-x86-64-linux-gnu gfortran-x86-64-linux-gnu 270s icu-devtools libasan8 libatomic1 libblas-dev libbz2-dev libc-dev-bin 270s libc6-dev libcc1-0 libcrypt-dev libgcc-13-dev libgfortran-13-dev libhwasan0 270s libicu-dev libisl23 libitm1 libjpeg-dev libjpeg-turbo8-dev libjpeg8-dev 270s liblapack-dev liblsan0 liblzma-dev libmpc3 libncurses-dev libpcre2-16-0 270s libpcre2-32-0 libpcre2-dev libpcre2-posix3 libpkgconf3 libpng-dev 270s libquadmath0 libreadline-dev libstdc++-13-dev libtsan2 libubsan1 270s linux-libc-dev pkg-config pkg-r-autopkgtest pkgconf pkgconf-bin r-base-dev 270s r-cran-backports r-cran-broom r-cran-cli r-cran-colorspace r-cran-cpp11 270s r-cran-dplyr r-cran-ellipsis r-cran-fansi r-cran-farver r-cran-geepack 270s r-cran-generics r-cran-ggplot2 r-cran-glue r-cran-gtable r-cran-isoband 270s r-cran-labeling r-cran-lifecycle r-cran-magrittr r-cran-mass r-cran-mgcv 270s r-cran-munsell r-cran-nlme r-cran-pillar r-cran-pkgconfig r-cran-purrr 270s r-cran-r6 r-cran-rcolorbrewer r-cran-rlang r-cran-scales r-cran-stringi 270s r-cran-stringr r-cran-tibble r-cran-tidyr r-cran-tidyselect r-cran-utf8 270s r-cran-vctrs r-cran-viridislite r-cran-withr rpcsvc-proto zlib1g-dev 270s 0 upgraded, 99 newly installed, 0 to remove and 0 not upgraded. 270s Need to get 130 MB/130 MB of archives. 270s After this operation, 423 MB of additional disk space will be used. 270s Get:1 /tmp/autopkgtest.UWYLfo/2-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [732 B] 270s Get:2 http://ftpmaster.internal/ubuntu noble/main amd64 libc-dev-bin amd64 2.39-0ubuntu6 [20.4 kB] 270s Get:3 http://ftpmaster.internal/ubuntu noble/main amd64 linux-libc-dev amd64 6.8.0-11.11 [1595 kB] 270s Get:4 http://ftpmaster.internal/ubuntu noble/main amd64 libcrypt-dev amd64 1:4.4.36-4 [128 kB] 270s Get:5 http://ftpmaster.internal/ubuntu noble/main amd64 rpcsvc-proto amd64 1.4.2-0ubuntu6 [68.5 kB] 270s Get:6 http://ftpmaster.internal/ubuntu noble/main amd64 libc6-dev amd64 2.39-0ubuntu6 [2126 kB] 270s Get:7 http://ftpmaster.internal/ubuntu noble/main amd64 libisl23 amd64 0.26-3 [741 kB] 270s Get:8 http://ftpmaster.internal/ubuntu noble/main amd64 libmpc3 amd64 1.3.1-1 [54.1 kB] 270s Get:9 http://ftpmaster.internal/ubuntu noble/main amd64 cpp-13-x86-64-linux-gnu amd64 13.2.0-17ubuntu2 [11.2 MB] 270s Get:10 http://ftpmaster.internal/ubuntu noble/main amd64 cpp-13 amd64 13.2.0-17ubuntu2 [1030 B] 270s Get:11 http://ftpmaster.internal/ubuntu noble/main amd64 cpp-x86-64-linux-gnu amd64 4:13.2.0-7ubuntu1 [5326 B] 270s Get:12 http://ftpmaster.internal/ubuntu noble/main amd64 cpp amd64 4:13.2.0-7ubuntu1 [22.4 kB] 270s Get:13 http://ftpmaster.internal/ubuntu noble/main amd64 libcc1-0 amd64 14-20240303-1ubuntu1 [47.7 kB] 270s Get:14 http://ftpmaster.internal/ubuntu noble/main amd64 libitm1 amd64 14-20240303-1ubuntu1 [29.1 kB] 270s Get:15 http://ftpmaster.internal/ubuntu noble/main amd64 libatomic1 amd64 14-20240303-1ubuntu1 [10.4 kB] 270s Get:16 http://ftpmaster.internal/ubuntu noble/main amd64 libasan8 amd64 14-20240303-1ubuntu1 [3026 kB] 270s Get:17 http://ftpmaster.internal/ubuntu noble/main amd64 liblsan0 amd64 14-20240303-1ubuntu1 [1310 kB] 270s Get:18 http://ftpmaster.internal/ubuntu noble/main amd64 libtsan2 amd64 14-20240303-1ubuntu1 [2732 kB] 270s Get:19 http://ftpmaster.internal/ubuntu noble/main amd64 libubsan1 amd64 14-20240303-1ubuntu1 [1172 kB] 270s Get:20 http://ftpmaster.internal/ubuntu noble/main amd64 libhwasan0 amd64 14-20240303-1ubuntu1 [1629 kB] 270s Get:21 http://ftpmaster.internal/ubuntu noble/main amd64 libquadmath0 amd64 14-20240303-1ubuntu1 [155 kB] 270s Get:22 http://ftpmaster.internal/ubuntu noble/main amd64 libgcc-13-dev amd64 13.2.0-17ubuntu2 [2687 kB] 270s Get:23 http://ftpmaster.internal/ubuntu noble/main amd64 gcc-13-x86-64-linux-gnu amd64 13.2.0-17ubuntu2 [21.9 MB] 270s Get:24 http://ftpmaster.internal/ubuntu noble/main amd64 gcc-13 amd64 13.2.0-17ubuntu2 [477 kB] 270s Get:25 http://ftpmaster.internal/ubuntu noble/main amd64 gcc-x86-64-linux-gnu amd64 4:13.2.0-7ubuntu1 [1212 B] 270s Get:26 http://ftpmaster.internal/ubuntu noble/main amd64 gcc amd64 4:13.2.0-7ubuntu1 [5018 B] 270s Get:27 http://ftpmaster.internal/ubuntu noble/main amd64 libstdc++-13-dev amd64 13.2.0-17ubuntu2 [2340 kB] 270s Get:28 http://ftpmaster.internal/ubuntu noble/main amd64 g++-13-x86-64-linux-gnu amd64 13.2.0-17ubuntu2 [12.5 MB] 270s Get:29 http://ftpmaster.internal/ubuntu noble/main amd64 g++-13 amd64 13.2.0-17ubuntu2 [14.5 kB] 270s Get:30 http://ftpmaster.internal/ubuntu noble/main amd64 g++-x86-64-linux-gnu amd64 4:13.2.0-7ubuntu1 [964 B] 270s Get:31 http://ftpmaster.internal/ubuntu noble/main amd64 g++ amd64 4:13.2.0-7ubuntu1 [1100 B] 270s Get:32 http://ftpmaster.internal/ubuntu noble/main amd64 build-essential amd64 12.10ubuntu1 [4928 B] 270s Get:33 http://ftpmaster.internal/ubuntu noble/main amd64 dctrl-tools amd64 2.24-3build2 [66.9 kB] 270s Get:34 http://ftpmaster.internal/ubuntu noble/main amd64 libgfortran-13-dev amd64 13.2.0-17ubuntu2 [942 kB] 270s Get:35 http://ftpmaster.internal/ubuntu noble/main amd64 gfortran-13-x86-64-linux-gnu amd64 13.2.0-17ubuntu2 [11.6 MB] 271s Get:36 http://ftpmaster.internal/ubuntu noble/main amd64 gfortran-13 amd64 13.2.0-17ubuntu2 [10.3 kB] 271s Get:37 http://ftpmaster.internal/ubuntu noble/main amd64 gfortran-x86-64-linux-gnu amd64 4:13.2.0-7ubuntu1 [1024 B] 271s Get:38 http://ftpmaster.internal/ubuntu noble/main amd64 gfortran amd64 4:13.2.0-7ubuntu1 [1176 B] 271s Get:39 http://ftpmaster.internal/ubuntu noble/main amd64 icu-devtools amd64 74.2-1ubuntu1 [212 kB] 271s Get:40 http://ftpmaster.internal/ubuntu noble/main amd64 libblas-dev amd64 3.12.0-3 [170 kB] 271s Get:41 http://ftpmaster.internal/ubuntu noble/main amd64 libbz2-dev amd64 1.0.8-5ubuntu1 [33.6 kB] 271s Get:42 http://ftpmaster.internal/ubuntu noble/main amd64 libicu-dev amd64 74.2-1ubuntu1 [11.9 MB] 271s Get:43 http://ftpmaster.internal/ubuntu noble/main amd64 libjpeg-turbo8-dev amd64 2.1.5-2ubuntu1 [294 kB] 271s Get:44 http://ftpmaster.internal/ubuntu noble/main amd64 libjpeg8-dev amd64 8c-2ubuntu11 [1484 B] 271s Get:45 http://ftpmaster.internal/ubuntu noble/main amd64 libjpeg-dev amd64 8c-2ubuntu11 [1482 B] 271s Get:46 http://ftpmaster.internal/ubuntu noble/main amd64 liblapack-dev amd64 3.12.0-3 [5196 kB] 271s Get:47 http://ftpmaster.internal/ubuntu noble/main amd64 libncurses-dev amd64 6.4+20240113-1ubuntu1 [384 kB] 271s Get:48 http://ftpmaster.internal/ubuntu noble/main amd64 libpcre2-16-0 amd64 10.42-4ubuntu1 [211 kB] 271s Get:49 http://ftpmaster.internal/ubuntu noble/main amd64 libpcre2-32-0 amd64 10.42-4ubuntu1 [198 kB] 271s Get:50 http://ftpmaster.internal/ubuntu noble/main amd64 libpcre2-posix3 amd64 10.42-4ubuntu1 [6808 B] 271s Get:51 http://ftpmaster.internal/ubuntu noble/main amd64 libpcre2-dev amd64 10.42-4ubuntu1 [743 kB] 271s Get:52 http://ftpmaster.internal/ubuntu noble/main amd64 libpkgconf3 amd64 1.8.1-2 [31.1 kB] 271s Get:53 http://ftpmaster.internal/ubuntu noble/main amd64 zlib1g-dev amd64 1:1.3.dfsg-3ubuntu1 [896 kB] 271s Get:54 http://ftpmaster.internal/ubuntu noble/main amd64 libpng-dev amd64 1.6.43-1 [264 kB] 271s Get:55 http://ftpmaster.internal/ubuntu noble/main amd64 libreadline-dev amd64 8.2-3 [167 kB] 271s Get:56 http://ftpmaster.internal/ubuntu noble/main amd64 pkgconf-bin amd64 1.8.1-2 [20.7 kB] 271s Get:57 http://ftpmaster.internal/ubuntu noble/main amd64 pkgconf amd64 1.8.1-2 [16.8 kB] 271s Get:58 http://ftpmaster.internal/ubuntu noble/main amd64 pkg-config amd64 1.8.1-2 [7170 B] 271s Get:59 http://ftpmaster.internal/ubuntu noble/main amd64 liblzma-dev amd64 5.4.5-0.3 [205 kB] 271s Get:60 http://ftpmaster.internal/ubuntu noble/universe amd64 r-base-dev all 4.3.2-1build1 [4336 B] 271s Get:61 http://ftpmaster.internal/ubuntu noble/universe amd64 pkg-r-autopkgtest all 20231212ubuntu1 [6448 B] 271s Get:62 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-backports amd64 1.4.1-1 [101 kB] 271s Get:63 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-cli amd64 3.6.2-1 [1380 kB] 271s Get:64 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-generics all 0.1.3-1 [81.3 kB] 271s Get:65 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-glue amd64 1.7.0-1 [154 kB] 271s Get:66 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-rlang amd64 1.1.3-1 [1663 kB] 271s Get:67 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB] 271s Get:68 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-magrittr amd64 2.0.3-1 [154 kB] 271s Get:69 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-fansi amd64 1.0.5-1 [619 kB] 271s Get:70 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-utf8 amd64 1.2.4-1 [140 kB] 271s Get:71 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-vctrs amd64 0.6.5-1 [1335 kB] 271s Get:72 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-pillar all 1.9.0+dfsg-1 [464 kB] 271s Get:73 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-r6 all 2.5.1-1 [99.0 kB] 271s Get:74 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-pkgconfig all 2.0.3-2build1 [19.7 kB] 271s Get:75 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-tibble amd64 3.2.1+dfsg-2 [415 kB] 271s Get:76 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-withr all 2.5.0-1 [225 kB] 271s Get:77 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-tidyselect amd64 1.2.0+dfsg-1 [218 kB] 271s Get:78 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-dplyr amd64 1.1.4-1 [1515 kB] 271s Get:79 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-ellipsis amd64 0.3.2-2 [35.6 kB] 271s Get:80 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-purrr amd64 1.0.2-1 [502 kB] 271s Get:81 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-stringi amd64 1.8.3-1 [873 kB] 271s Get:82 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-stringr all 1.5.1-1 [290 kB] 271s Get:83 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-cpp11 all 0.4.7-1 [266 kB] 271s Get:84 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-tidyr amd64 1.3.1-1 [1156 kB] 271s Get:85 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-broom all 1.0.5+dfsg-1 [1729 kB] 271s Get:86 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-colorspace amd64 2.1-0+dfsg-1 [1541 kB] 271s Get:87 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-farver amd64 2.1.1-1 [1353 kB] 271s Get:88 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-mass amd64 7.3-60.0.1-1 [1119 kB] 271s Get:89 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-geepack amd64 1.3.10-1 [377 kB] 271s Get:90 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-gtable all 0.3.4+dfsg-1 [191 kB] 271s Get:91 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-isoband amd64 0.2.7-1 [1481 kB] 271s Get:92 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-nlme amd64 3.1.164-1 [2260 kB] 271s Get:93 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-mgcv amd64 1.9-1-1 [3252 kB] 271s Get:94 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-labeling all 0.4.3-1 [62.1 kB] 271s Get:95 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-munsell all 0.5.0-2build1 [208 kB] 271s Get:96 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-rcolorbrewer all 1.1-3-1build1 [55.4 kB] 271s Get:97 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-viridislite all 0.4.2-2 [1088 kB] 271s Get:98 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-scales all 1.3.0-1 [603 kB] 271s Get:99 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-ggplot2 all 3.4.4+dfsg-1 [3411 kB] 272s Fetched 130 MB in 1s (93.3 MB/s) 272s Selecting previously unselected package libc-dev-bin. 272s (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 ... 75735 files and directories currently installed.) 272s Preparing to unpack .../00-libc-dev-bin_2.39-0ubuntu6_amd64.deb ... 272s Unpacking libc-dev-bin (2.39-0ubuntu6) ... 272s Selecting previously unselected package linux-libc-dev:amd64. 272s Preparing to unpack .../01-linux-libc-dev_6.8.0-11.11_amd64.deb ... 272s Unpacking linux-libc-dev:amd64 (6.8.0-11.11) ... 272s Selecting previously unselected package libcrypt-dev:amd64. 272s Preparing to unpack .../02-libcrypt-dev_1%3a4.4.36-4_amd64.deb ... 272s Unpacking libcrypt-dev:amd64 (1:4.4.36-4) ... 272s Selecting previously unselected package rpcsvc-proto. 272s Preparing to unpack .../03-rpcsvc-proto_1.4.2-0ubuntu6_amd64.deb ... 272s Unpacking rpcsvc-proto (1.4.2-0ubuntu6) ... 272s Selecting previously unselected package libc6-dev:amd64. 272s Preparing to unpack .../04-libc6-dev_2.39-0ubuntu6_amd64.deb ... 272s Unpacking libc6-dev:amd64 (2.39-0ubuntu6) ... 272s Selecting previously unselected package libisl23:amd64. 272s Preparing to unpack .../05-libisl23_0.26-3_amd64.deb ... 272s Unpacking libisl23:amd64 (0.26-3) ... 272s Selecting previously unselected package libmpc3:amd64. 272s Preparing to unpack .../06-libmpc3_1.3.1-1_amd64.deb ... 272s Unpacking libmpc3:amd64 (1.3.1-1) ... 272s Selecting previously unselected package cpp-13-x86-64-linux-gnu. 272s Preparing to unpack .../07-cpp-13-x86-64-linux-gnu_13.2.0-17ubuntu2_amd64.deb ... 272s Unpacking cpp-13-x86-64-linux-gnu (13.2.0-17ubuntu2) ... 272s Selecting previously unselected package cpp-13. 272s Preparing to unpack .../08-cpp-13_13.2.0-17ubuntu2_amd64.deb ... 272s Unpacking cpp-13 (13.2.0-17ubuntu2) ... 272s Selecting previously unselected package cpp-x86-64-linux-gnu. 272s Preparing to unpack .../09-cpp-x86-64-linux-gnu_4%3a13.2.0-7ubuntu1_amd64.deb ... 272s Unpacking cpp-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ... 272s Selecting previously unselected package cpp. 272s Preparing to unpack .../10-cpp_4%3a13.2.0-7ubuntu1_amd64.deb ... 272s Unpacking cpp (4:13.2.0-7ubuntu1) ... 272s Selecting previously unselected package libcc1-0:amd64. 272s Preparing to unpack .../11-libcc1-0_14-20240303-1ubuntu1_amd64.deb ... 272s Unpacking libcc1-0:amd64 (14-20240303-1ubuntu1) ... 272s Selecting previously unselected package libitm1:amd64. 273s Preparing to unpack .../12-libitm1_14-20240303-1ubuntu1_amd64.deb ... 273s Unpacking libitm1:amd64 (14-20240303-1ubuntu1) ... 273s Selecting previously unselected package libatomic1:amd64. 273s Preparing to unpack .../13-libatomic1_14-20240303-1ubuntu1_amd64.deb ... 273s Unpacking libatomic1:amd64 (14-20240303-1ubuntu1) ... 273s Selecting previously unselected package libasan8:amd64. 273s Preparing to unpack .../14-libasan8_14-20240303-1ubuntu1_amd64.deb ... 273s Unpacking libasan8:amd64 (14-20240303-1ubuntu1) ... 273s Selecting previously unselected package liblsan0:amd64. 273s Preparing to unpack .../15-liblsan0_14-20240303-1ubuntu1_amd64.deb ... 273s Unpacking liblsan0:amd64 (14-20240303-1ubuntu1) ... 273s Selecting previously unselected package libtsan2:amd64. 273s Preparing to unpack .../16-libtsan2_14-20240303-1ubuntu1_amd64.deb ... 273s Unpacking libtsan2:amd64 (14-20240303-1ubuntu1) ... 273s Selecting previously unselected package libubsan1:amd64. 273s Preparing to unpack .../17-libubsan1_14-20240303-1ubuntu1_amd64.deb ... 273s Unpacking libubsan1:amd64 (14-20240303-1ubuntu1) ... 273s Selecting previously unselected package libhwasan0:amd64. 273s Preparing to unpack .../18-libhwasan0_14-20240303-1ubuntu1_amd64.deb ... 273s Unpacking libhwasan0:amd64 (14-20240303-1ubuntu1) ... 273s Selecting previously unselected package libquadmath0:amd64. 273s Preparing to unpack .../19-libquadmath0_14-20240303-1ubuntu1_amd64.deb ... 273s Unpacking libquadmath0:amd64 (14-20240303-1ubuntu1) ... 273s Selecting previously unselected package libgcc-13-dev:amd64. 273s Preparing to unpack .../20-libgcc-13-dev_13.2.0-17ubuntu2_amd64.deb ... 273s Unpacking libgcc-13-dev:amd64 (13.2.0-17ubuntu2) ... 273s Selecting previously unselected package gcc-13-x86-64-linux-gnu. 273s Preparing to unpack .../21-gcc-13-x86-64-linux-gnu_13.2.0-17ubuntu2_amd64.deb ... 273s Unpacking gcc-13-x86-64-linux-gnu (13.2.0-17ubuntu2) ... 273s Selecting previously unselected package gcc-13. 273s Preparing to unpack .../22-gcc-13_13.2.0-17ubuntu2_amd64.deb ... 273s Unpacking gcc-13 (13.2.0-17ubuntu2) ... 273s Selecting previously unselected package gcc-x86-64-linux-gnu. 273s Preparing to unpack .../23-gcc-x86-64-linux-gnu_4%3a13.2.0-7ubuntu1_amd64.deb ... 273s Unpacking gcc-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ... 273s Selecting previously unselected package gcc. 273s Preparing to unpack .../24-gcc_4%3a13.2.0-7ubuntu1_amd64.deb ... 273s Unpacking gcc (4:13.2.0-7ubuntu1) ... 273s Selecting previously unselected package libstdc++-13-dev:amd64. 273s Preparing to unpack .../25-libstdc++-13-dev_13.2.0-17ubuntu2_amd64.deb ... 273s Unpacking libstdc++-13-dev:amd64 (13.2.0-17ubuntu2) ... 274s Selecting previously unselected package g++-13-x86-64-linux-gnu. 274s Preparing to unpack .../26-g++-13-x86-64-linux-gnu_13.2.0-17ubuntu2_amd64.deb ... 274s Unpacking g++-13-x86-64-linux-gnu (13.2.0-17ubuntu2) ... 274s Selecting previously unselected package g++-13. 274s Preparing to unpack .../27-g++-13_13.2.0-17ubuntu2_amd64.deb ... 274s Unpacking g++-13 (13.2.0-17ubuntu2) ... 274s Selecting previously unselected package g++-x86-64-linux-gnu. 274s Preparing to unpack .../28-g++-x86-64-linux-gnu_4%3a13.2.0-7ubuntu1_amd64.deb ... 274s Unpacking g++-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ... 274s Selecting previously unselected package g++. 274s Preparing to unpack .../29-g++_4%3a13.2.0-7ubuntu1_amd64.deb ... 274s Unpacking g++ (4:13.2.0-7ubuntu1) ... 274s Selecting previously unselected package build-essential. 274s Preparing to unpack .../30-build-essential_12.10ubuntu1_amd64.deb ... 274s Unpacking build-essential (12.10ubuntu1) ... 274s Selecting previously unselected package dctrl-tools. 274s Preparing to unpack .../31-dctrl-tools_2.24-3build2_amd64.deb ... 274s Unpacking dctrl-tools (2.24-3build2) ... 274s Selecting previously unselected package libgfortran-13-dev:amd64. 274s Preparing to unpack .../32-libgfortran-13-dev_13.2.0-17ubuntu2_amd64.deb ... 274s Unpacking libgfortran-13-dev:amd64 (13.2.0-17ubuntu2) ... 274s Selecting previously unselected package gfortran-13-x86-64-linux-gnu. 274s Preparing to unpack .../33-gfortran-13-x86-64-linux-gnu_13.2.0-17ubuntu2_amd64.deb ... 274s Unpacking gfortran-13-x86-64-linux-gnu (13.2.0-17ubuntu2) ... 274s Selecting previously unselected package gfortran-13. 274s Preparing to unpack .../34-gfortran-13_13.2.0-17ubuntu2_amd64.deb ... 274s Unpacking gfortran-13 (13.2.0-17ubuntu2) ... 274s Selecting previously unselected package gfortran-x86-64-linux-gnu. 274s Preparing to unpack .../35-gfortran-x86-64-linux-gnu_4%3a13.2.0-7ubuntu1_amd64.deb ... 274s Unpacking gfortran-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ... 274s Selecting previously unselected package gfortran. 274s Preparing to unpack .../36-gfortran_4%3a13.2.0-7ubuntu1_amd64.deb ... 274s Unpacking gfortran (4:13.2.0-7ubuntu1) ... 274s Selecting previously unselected package icu-devtools. 274s Preparing to unpack .../37-icu-devtools_74.2-1ubuntu1_amd64.deb ... 274s Unpacking icu-devtools (74.2-1ubuntu1) ... 274s Selecting previously unselected package libblas-dev:amd64. 274s Preparing to unpack .../38-libblas-dev_3.12.0-3_amd64.deb ... 274s Unpacking libblas-dev:amd64 (3.12.0-3) ... 274s Selecting previously unselected package libbz2-dev:amd64. 274s Preparing to unpack .../39-libbz2-dev_1.0.8-5ubuntu1_amd64.deb ... 274s Unpacking libbz2-dev:amd64 (1.0.8-5ubuntu1) ... 274s Selecting previously unselected package libicu-dev:amd64. 274s Preparing to unpack .../40-libicu-dev_74.2-1ubuntu1_amd64.deb ... 274s Unpacking libicu-dev:amd64 (74.2-1ubuntu1) ... 275s Selecting previously unselected package libjpeg-turbo8-dev:amd64. 275s Preparing to unpack .../41-libjpeg-turbo8-dev_2.1.5-2ubuntu1_amd64.deb ... 275s Unpacking libjpeg-turbo8-dev:amd64 (2.1.5-2ubuntu1) ... 275s Selecting previously unselected package libjpeg8-dev:amd64. 275s Preparing to unpack .../42-libjpeg8-dev_8c-2ubuntu11_amd64.deb ... 275s Unpacking libjpeg8-dev:amd64 (8c-2ubuntu11) ... 275s Selecting previously unselected package libjpeg-dev:amd64. 275s Preparing to unpack .../43-libjpeg-dev_8c-2ubuntu11_amd64.deb ... 275s Unpacking libjpeg-dev:amd64 (8c-2ubuntu11) ... 275s Selecting previously unselected package liblapack-dev:amd64. 275s Preparing to unpack .../44-liblapack-dev_3.12.0-3_amd64.deb ... 275s Unpacking liblapack-dev:amd64 (3.12.0-3) ... 275s Selecting previously unselected package libncurses-dev:amd64. 275s Preparing to unpack .../45-libncurses-dev_6.4+20240113-1ubuntu1_amd64.deb ... 275s Unpacking libncurses-dev:amd64 (6.4+20240113-1ubuntu1) ... 275s Selecting previously unselected package libpcre2-16-0:amd64. 275s Preparing to unpack .../46-libpcre2-16-0_10.42-4ubuntu1_amd64.deb ... 275s Unpacking libpcre2-16-0:amd64 (10.42-4ubuntu1) ... 275s Selecting previously unselected package libpcre2-32-0:amd64. 275s Preparing to unpack .../47-libpcre2-32-0_10.42-4ubuntu1_amd64.deb ... 275s Unpacking libpcre2-32-0:amd64 (10.42-4ubuntu1) ... 275s Selecting previously unselected package libpcre2-posix3:amd64. 275s Preparing to unpack .../48-libpcre2-posix3_10.42-4ubuntu1_amd64.deb ... 275s Unpacking libpcre2-posix3:amd64 (10.42-4ubuntu1) ... 275s Selecting previously unselected package libpcre2-dev:amd64. 275s Preparing to unpack .../49-libpcre2-dev_10.42-4ubuntu1_amd64.deb ... 275s Unpacking libpcre2-dev:amd64 (10.42-4ubuntu1) ... 275s Selecting previously unselected package libpkgconf3:amd64. 275s Preparing to unpack .../50-libpkgconf3_1.8.1-2_amd64.deb ... 275s Unpacking libpkgconf3:amd64 (1.8.1-2) ... 275s Selecting previously unselected package zlib1g-dev:amd64. 275s Preparing to unpack .../51-zlib1g-dev_1%3a1.3.dfsg-3ubuntu1_amd64.deb ... 275s Unpacking zlib1g-dev:amd64 (1:1.3.dfsg-3ubuntu1) ... 275s Selecting previously unselected package libpng-dev:amd64. 275s Preparing to unpack .../52-libpng-dev_1.6.43-1_amd64.deb ... 275s Unpacking libpng-dev:amd64 (1.6.43-1) ... 275s Selecting previously unselected package libreadline-dev:amd64. 275s Preparing to unpack .../53-libreadline-dev_8.2-3_amd64.deb ... 275s Unpacking libreadline-dev:amd64 (8.2-3) ... 275s Selecting previously unselected package pkgconf-bin. 275s Preparing to unpack .../54-pkgconf-bin_1.8.1-2_amd64.deb ... 275s Unpacking pkgconf-bin (1.8.1-2) ... 275s Selecting previously unselected package pkgconf:amd64. 275s Preparing to unpack .../55-pkgconf_1.8.1-2_amd64.deb ... 275s Unpacking pkgconf:amd64 (1.8.1-2) ... 275s Selecting previously unselected package pkg-config:amd64. 275s Preparing to unpack .../56-pkg-config_1.8.1-2_amd64.deb ... 275s Unpacking pkg-config:amd64 (1.8.1-2) ... 275s Selecting previously unselected package liblzma-dev:amd64. 275s Preparing to unpack .../57-liblzma-dev_5.4.5-0.3_amd64.deb ... 275s Unpacking liblzma-dev:amd64 (5.4.5-0.3) ... 275s Selecting previously unselected package r-base-dev. 275s Preparing to unpack .../58-r-base-dev_4.3.2-1build1_all.deb ... 275s Unpacking r-base-dev (4.3.2-1build1) ... 275s Selecting previously unselected package pkg-r-autopkgtest. 275s Preparing to unpack .../59-pkg-r-autopkgtest_20231212ubuntu1_all.deb ... 275s Unpacking pkg-r-autopkgtest (20231212ubuntu1) ... 275s Selecting previously unselected package r-cran-backports. 275s Preparing to unpack .../60-r-cran-backports_1.4.1-1_amd64.deb ... 275s Unpacking r-cran-backports (1.4.1-1) ... 275s Selecting previously unselected package r-cran-cli. 275s Preparing to unpack .../61-r-cran-cli_3.6.2-1_amd64.deb ... 275s Unpacking r-cran-cli (3.6.2-1) ... 275s Selecting previously unselected package r-cran-generics. 275s Preparing to unpack .../62-r-cran-generics_0.1.3-1_all.deb ... 275s Unpacking r-cran-generics (0.1.3-1) ... 275s Selecting previously unselected package r-cran-glue. 275s Preparing to unpack .../63-r-cran-glue_1.7.0-1_amd64.deb ... 275s Unpacking r-cran-glue (1.7.0-1) ... 275s Selecting previously unselected package r-cran-rlang. 275s Preparing to unpack .../64-r-cran-rlang_1.1.3-1_amd64.deb ... 275s Unpacking r-cran-rlang (1.1.3-1) ... 276s Selecting previously unselected package r-cran-lifecycle. 276s Preparing to unpack .../65-r-cran-lifecycle_1.0.4+dfsg-1_all.deb ... 276s Unpacking r-cran-lifecycle (1.0.4+dfsg-1) ... 276s Selecting previously unselected package r-cran-magrittr. 276s Preparing to unpack .../66-r-cran-magrittr_2.0.3-1_amd64.deb ... 276s Unpacking r-cran-magrittr (2.0.3-1) ... 276s Selecting previously unselected package r-cran-fansi. 276s Preparing to unpack .../67-r-cran-fansi_1.0.5-1_amd64.deb ... 276s Unpacking r-cran-fansi (1.0.5-1) ... 276s Selecting previously unselected package r-cran-utf8. 276s Preparing to unpack .../68-r-cran-utf8_1.2.4-1_amd64.deb ... 276s Unpacking r-cran-utf8 (1.2.4-1) ... 276s Selecting previously unselected package r-cran-vctrs. 276s Preparing to unpack .../69-r-cran-vctrs_0.6.5-1_amd64.deb ... 276s Unpacking r-cran-vctrs (0.6.5-1) ... 276s Selecting previously unselected package r-cran-pillar. 276s Preparing to unpack .../70-r-cran-pillar_1.9.0+dfsg-1_all.deb ... 276s Unpacking r-cran-pillar (1.9.0+dfsg-1) ... 276s Selecting previously unselected package r-cran-r6. 276s Preparing to unpack .../71-r-cran-r6_2.5.1-1_all.deb ... 276s Unpacking r-cran-r6 (2.5.1-1) ... 276s Selecting previously unselected package r-cran-pkgconfig. 276s Preparing to unpack .../72-r-cran-pkgconfig_2.0.3-2build1_all.deb ... 276s Unpacking r-cran-pkgconfig (2.0.3-2build1) ... 276s Selecting previously unselected package r-cran-tibble. 276s Preparing to unpack .../73-r-cran-tibble_3.2.1+dfsg-2_amd64.deb ... 276s Unpacking r-cran-tibble (3.2.1+dfsg-2) ... 276s Selecting previously unselected package r-cran-withr. 276s Preparing to unpack .../74-r-cran-withr_2.5.0-1_all.deb ... 276s Unpacking r-cran-withr (2.5.0-1) ... 276s Selecting previously unselected package r-cran-tidyselect. 276s Preparing to unpack .../75-r-cran-tidyselect_1.2.0+dfsg-1_amd64.deb ... 276s Unpacking r-cran-tidyselect (1.2.0+dfsg-1) ... 276s Selecting previously unselected package r-cran-dplyr. 276s Preparing to unpack .../76-r-cran-dplyr_1.1.4-1_amd64.deb ... 276s Unpacking r-cran-dplyr (1.1.4-1) ... 276s Selecting previously unselected package r-cran-ellipsis. 276s Preparing to unpack .../77-r-cran-ellipsis_0.3.2-2_amd64.deb ... 276s Unpacking r-cran-ellipsis (0.3.2-2) ... 276s Selecting previously unselected package r-cran-purrr. 276s Preparing to unpack .../78-r-cran-purrr_1.0.2-1_amd64.deb ... 276s Unpacking r-cran-purrr (1.0.2-1) ... 276s Selecting previously unselected package r-cran-stringi. 276s Preparing to unpack .../79-r-cran-stringi_1.8.3-1_amd64.deb ... 276s Unpacking r-cran-stringi (1.8.3-1) ... 276s Selecting previously unselected package r-cran-stringr. 276s Preparing to unpack .../80-r-cran-stringr_1.5.1-1_all.deb ... 276s Unpacking r-cran-stringr (1.5.1-1) ... 276s Selecting previously unselected package r-cran-cpp11. 276s Preparing to unpack .../81-r-cran-cpp11_0.4.7-1_all.deb ... 276s Unpacking r-cran-cpp11 (0.4.7-1) ... 276s Selecting previously unselected package r-cran-tidyr. 276s Preparing to unpack .../82-r-cran-tidyr_1.3.1-1_amd64.deb ... 276s Unpacking r-cran-tidyr (1.3.1-1) ... 276s Selecting previously unselected package r-cran-broom. 276s Preparing to unpack .../83-r-cran-broom_1.0.5+dfsg-1_all.deb ... 276s Unpacking r-cran-broom (1.0.5+dfsg-1) ... 276s Selecting previously unselected package r-cran-colorspace. 276s Preparing to unpack .../84-r-cran-colorspace_2.1-0+dfsg-1_amd64.deb ... 276s Unpacking r-cran-colorspace (2.1-0+dfsg-1) ... 276s Selecting previously unselected package r-cran-farver. 276s Preparing to unpack .../85-r-cran-farver_2.1.1-1_amd64.deb ... 276s Unpacking r-cran-farver (2.1.1-1) ... 276s Selecting previously unselected package r-cran-mass. 276s Preparing to unpack .../86-r-cran-mass_7.3-60.0.1-1_amd64.deb ... 276s Unpacking r-cran-mass (7.3-60.0.1-1) ... 276s Selecting previously unselected package r-cran-geepack. 276s Preparing to unpack .../87-r-cran-geepack_1.3.10-1_amd64.deb ... 276s Unpacking r-cran-geepack (1.3.10-1) ... 276s Selecting previously unselected package r-cran-gtable. 276s Preparing to unpack .../88-r-cran-gtable_0.3.4+dfsg-1_all.deb ... 276s Unpacking r-cran-gtable (0.3.4+dfsg-1) ... 277s Selecting previously unselected package r-cran-isoband. 277s Preparing to unpack .../89-r-cran-isoband_0.2.7-1_amd64.deb ... 277s Unpacking r-cran-isoband (0.2.7-1) ... 277s Selecting previously unselected package r-cran-nlme. 277s Preparing to unpack .../90-r-cran-nlme_3.1.164-1_amd64.deb ... 277s Unpacking r-cran-nlme (3.1.164-1) ... 277s Selecting previously unselected package r-cran-mgcv. 277s Preparing to unpack .../91-r-cran-mgcv_1.9-1-1_amd64.deb ... 277s Unpacking r-cran-mgcv (1.9-1-1) ... 277s Selecting previously unselected package r-cran-labeling. 277s Preparing to unpack .../92-r-cran-labeling_0.4.3-1_all.deb ... 277s Unpacking r-cran-labeling (0.4.3-1) ... 277s Selecting previously unselected package r-cran-munsell. 277s Preparing to unpack .../93-r-cran-munsell_0.5.0-2build1_all.deb ... 277s Unpacking r-cran-munsell (0.5.0-2build1) ... 277s Selecting previously unselected package r-cran-rcolorbrewer. 277s Preparing to unpack .../94-r-cran-rcolorbrewer_1.1-3-1build1_all.deb ... 277s Unpacking r-cran-rcolorbrewer (1.1-3-1build1) ... 277s Selecting previously unselected package r-cran-viridislite. 277s Preparing to unpack .../95-r-cran-viridislite_0.4.2-2_all.deb ... 277s Unpacking r-cran-viridislite (0.4.2-2) ... 277s Selecting previously unselected package r-cran-scales. 277s Preparing to unpack .../96-r-cran-scales_1.3.0-1_all.deb ... 277s Unpacking r-cran-scales (1.3.0-1) ... 277s Selecting previously unselected package r-cran-ggplot2. 277s Preparing to unpack .../97-r-cran-ggplot2_3.4.4+dfsg-1_all.deb ... 277s Unpacking r-cran-ggplot2 (3.4.4+dfsg-1) ... 277s Selecting previously unselected package autopkgtest-satdep. 277s Preparing to unpack .../98-2-autopkgtest-satdep.deb ... 277s Unpacking autopkgtest-satdep (0) ... 277s Setting up r-cran-rlang (1.1.3-1) ... 277s Setting up r-cran-withr (2.5.0-1) ... 277s Setting up r-cran-backports (1.4.1-1) ... 277s Setting up r-cran-generics (0.1.3-1) ... 277s Setting up r-cran-fansi (1.0.5-1) ... 277s Setting up r-cran-mass (7.3-60.0.1-1) ... 277s Setting up linux-libc-dev:amd64 (6.8.0-11.11) ... 277s Setting up r-cran-glue (1.7.0-1) ... 277s Setting up r-cran-cli (3.6.2-1) ... 277s Setting up r-cran-lifecycle (1.0.4+dfsg-1) ... 277s Setting up libpcre2-16-0:amd64 (10.42-4ubuntu1) ... 277s Setting up r-cran-pkgconfig (2.0.3-2build1) ... 277s Setting up libpcre2-32-0:amd64 (10.42-4ubuntu1) ... 277s Setting up r-cran-utf8 (1.2.4-1) ... 277s Setting up libpkgconf3:amd64 (1.8.1-2) ... 277s Setting up r-cran-colorspace (2.1-0+dfsg-1) ... 277s Setting up rpcsvc-proto (1.4.2-0ubuntu6) ... 277s Setting up r-cran-stringi (1.8.3-1) ... 277s Setting up r-cran-cpp11 (0.4.7-1) ... 277s Setting up r-cran-rcolorbrewer (1.1-3-1build1) ... 277s Setting up r-cran-isoband (0.2.7-1) ... 277s Setting up libquadmath0:amd64 (14-20240303-1ubuntu1) ... 277s Setting up libmpc3:amd64 (1.3.1-1) ... 277s Setting up r-cran-gtable (0.3.4+dfsg-1) ... 277s Setting up libatomic1:amd64 (14-20240303-1ubuntu1) ... 277s Setting up r-cran-labeling (0.4.3-1) ... 277s Setting up icu-devtools (74.2-1ubuntu1) ... 277s Setting up pkgconf-bin (1.8.1-2) ... 277s Setting up r-cran-nlme (3.1.164-1) ... 277s Setting up r-cran-farver (2.1.1-1) ... 277s Setting up liblzma-dev:amd64 (5.4.5-0.3) ... 277s Setting up libubsan1:amd64 (14-20240303-1ubuntu1) ... 277s Setting up r-cran-mgcv (1.9-1-1) ... 277s Setting up libpcre2-posix3:amd64 (10.42-4ubuntu1) ... 277s Setting up r-cran-viridislite (0.4.2-2) ... 277s Setting up libhwasan0:amd64 (14-20240303-1ubuntu1) ... 277s Setting up libcrypt-dev:amd64 (1:4.4.36-4) ... 277s Setting up libasan8:amd64 (14-20240303-1ubuntu1) ... 277s Setting up libtsan2:amd64 (14-20240303-1ubuntu1) ... 277s Setting up r-cran-r6 (2.5.1-1) ... 277s Setting up libisl23:amd64 (0.26-3) ... 277s Setting up libc-dev-bin (2.39-0ubuntu6) ... 277s Setting up r-cran-magrittr (2.0.3-1) ... 277s Setting up libcc1-0:amd64 (14-20240303-1ubuntu1) ... 277s Setting up r-cran-vctrs (0.6.5-1) ... 277s Setting up liblsan0:amd64 (14-20240303-1ubuntu1) ... 277s Setting up libblas-dev:amd64 (3.12.0-3) ... 277s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so to provide /usr/lib/x86_64-linux-gnu/libblas.so (libblas.so-x86_64-linux-gnu) in auto mode 277s Setting up dctrl-tools (2.24-3build2) ... 277s Setting up libitm1:amd64 (14-20240303-1ubuntu1) ... 277s Setting up r-cran-pillar (1.9.0+dfsg-1) ... 277s Setting up r-cran-ellipsis (0.3.2-2) ... 277s Setting up r-cran-stringr (1.5.1-1) ... 277s Setting up cpp-13-x86-64-linux-gnu (13.2.0-17ubuntu2) ... 277s Setting up r-cran-munsell (0.5.0-2build1) ... 277s Setting up r-cran-tibble (3.2.1+dfsg-2) ... 277s Setting up pkgconf:amd64 (1.8.1-2) ... 277s Setting up r-cran-tidyselect (1.2.0+dfsg-1) ... 277s Setting up r-cran-scales (1.3.0-1) ... 277s Setting up liblapack-dev:amd64 (3.12.0-3) ... 277s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so to provide /usr/lib/x86_64-linux-gnu/liblapack.so (liblapack.so-x86_64-linux-gnu) in auto mode 277s Setting up r-cran-purrr (1.0.2-1) ... 277s Setting up pkg-config:amd64 (1.8.1-2) ... 277s Setting up libgcc-13-dev:amd64 (13.2.0-17ubuntu2) ... 277s Setting up libc6-dev:amd64 (2.39-0ubuntu6) ... 277s Setting up r-cran-dplyr (1.1.4-1) ... 277s Setting up libgfortran-13-dev:amd64 (13.2.0-17ubuntu2) ... 277s Setting up libicu-dev:amd64 (74.2-1ubuntu1) ... 277s Setting up libstdc++-13-dev:amd64 (13.2.0-17ubuntu2) ... 277s Setting up libbz2-dev:amd64 (1.0.8-5ubuntu1) ... 277s Setting up cpp-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ... 277s Setting up libjpeg-turbo8-dev:amd64 (2.1.5-2ubuntu1) ... 277s Setting up libncurses-dev:amd64 (6.4+20240113-1ubuntu1) ... 277s Setting up libpcre2-dev:amd64 (10.42-4ubuntu1) ... 277s Setting up cpp-13 (13.2.0-17ubuntu2) ... 277s Setting up r-cran-ggplot2 (3.4.4+dfsg-1) ... 277s Setting up gcc-13-x86-64-linux-gnu (13.2.0-17ubuntu2) ... 277s Setting up libreadline-dev:amd64 (8.2-3) ... 277s Setting up gfortran-13-x86-64-linux-gnu (13.2.0-17ubuntu2) ... 277s Setting up gcc-13 (13.2.0-17ubuntu2) ... 277s Setting up r-cran-tidyr (1.3.1-1) ... 277s Setting up zlib1g-dev:amd64 (1:1.3.dfsg-3ubuntu1) ... 277s Setting up cpp (4:13.2.0-7ubuntu1) ... 277s Setting up libjpeg8-dev:amd64 (8c-2ubuntu11) ... 277s Setting up g++-13-x86-64-linux-gnu (13.2.0-17ubuntu2) ... 277s Setting up gcc-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ... 277s Setting up libpng-dev:amd64 (1.6.43-1) ... 277s Setting up libjpeg-dev:amd64 (8c-2ubuntu11) ... 277s Setting up gfortran-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ... 277s Setting up gcc (4:13.2.0-7ubuntu1) ... 277s Setting up r-cran-broom (1.0.5+dfsg-1) ... 277s Setting up gfortran-13 (13.2.0-17ubuntu2) ... 277s Setting up g++-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ... 277s Setting up g++-13 (13.2.0-17ubuntu2) ... 277s Setting up r-cran-geepack (1.3.10-1) ... 277s Setting up gfortran (4:13.2.0-7ubuntu1) ... 277s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode 277s 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 277s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode 277s 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 277s Setting up g++ (4:13.2.0-7ubuntu1) ... 277s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 277s Setting up build-essential (12.10ubuntu1) ... 277s Setting up r-base-dev (4.3.2-1build1) ... 277s Setting up pkg-r-autopkgtest (20231212ubuntu1) ... 277s Setting up autopkgtest-satdep (0) ... 277s Processing triggers for man-db (2.12.0-3) ... 278s Processing triggers for install-info (7.1-3) ... 278s Processing triggers for libc-bin (2.39-0ubuntu6) ... 280s (Reading database ... 83328 files and directories currently installed.) 280s Removing autopkgtest-satdep (0) ... 280s autopkgtest [08:53:51]: test pkg-r-autopkgtest: /usr/share/dh-r/pkg-r-autopkgtest 280s autopkgtest [08:53:51]: test pkg-r-autopkgtest: [----------------------- 280s Test: Try to load the R library etm 280s 280s R version 4.3.2 (2023-10-31) -- "Eye Holes" 280s Copyright (C) 2023 The R Foundation for Statistical Computing 280s Platform: x86_64-pc-linux-gnu (64-bit) 280s 280s R is free software and comes with ABSOLUTELY NO WARRANTY. 280s You are welcome to redistribute it under certain conditions. 280s Type 'license()' or 'licence()' for distribution details. 280s 280s R is a collaborative project with many contributors. 280s Type 'contributors()' for more information and 280s 'citation()' on how to cite R or R packages in publications. 280s 280s Type 'demo()' for some demos, 'help()' for on-line help, or 280s 'help.start()' for an HTML browser interface to help. 280s Type 'q()' to quit R. 280s 280s > library('etm') 281s > 281s > 281s Other tests are currently unsupported! 281s They will be progressively added. 282s autopkgtest [08:53:53]: test pkg-r-autopkgtest: -----------------------] 282s pkg-r-autopkgtest PASS 282s autopkgtest [08:53:53]: test pkg-r-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 282s autopkgtest [08:53:53]: @@@@@@@@@@@@@@@@@@@@ summary 282s run-unit-test PASS 282s pkg-r-autopkgtest PASS 292s Creating nova instance adt-noble-amd64-r-cran-etm-20240326-084911-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-amd64-server-20240325.img (UUID ba43860b-557a-4db2-b3f0-378a99bca08c)...