0s autopkgtest [13:04:55]: starting date and time: 2024-03-20 13:04:55+0000 0s autopkgtest [13:04:55]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [13:04:55]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.gpunvukv/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:r-cran-rcpparmadillo --apt-upgrade r-cran-etm --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=r-cran-rcpparmadillo/0.12.8.1.0-1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@lcy02-25.secgroup --name adt-noble-amd64-r-cran-etm-20240320-130455-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/ 78s autopkgtest [13:06:13]: testbed dpkg architecture: amd64 78s autopkgtest [13:06:13]: testbed apt version: 2.7.12 78s autopkgtest [13:06:13]: @@@@@@@@@@@@@@@@@@@@ test bed setup 78s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 78s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 78s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [497 kB] 78s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3767 kB] 79s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [52.7 kB] 79s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main i386 Packages [451 kB] 79s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 Packages [697 kB] 79s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 c-n-f Metadata [3508 B] 79s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted i386 Packages [6700 B] 79s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/restricted amd64 Packages [36.6 kB] 79s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/restricted amd64 c-n-f Metadata [116 B] 79s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 Packages [4291 kB] 79s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/universe i386 Packages [1325 kB] 79s Get:14 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 c-n-f Metadata [9396 B] 79s Get:15 http://ftpmaster.internal/ubuntu noble-proposed/multiverse i386 Packages [16.2 kB] 79s Get:16 http://ftpmaster.internal/ubuntu noble-proposed/multiverse amd64 Packages [67.2 kB] 79s Get:17 http://ftpmaster.internal/ubuntu noble-proposed/multiverse amd64 c-n-f Metadata [196 B] 82s Fetched 11.3 MB in 1s (8022 kB/s) 82s Reading package lists... 84s Reading package lists... 84s Building dependency tree... 84s Reading state information... 84s Calculating upgrade... 85s The following packages will be upgraded: 85s ubuntu-minimal ubuntu-standard 85s 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 85s Need to get 21.5 kB of archives. 85s After this operation, 0 B of additional disk space will be used. 85s Get:1 http://ftpmaster.internal/ubuntu noble/main amd64 ubuntu-minimal amd64 1.536build1 [10.7 kB] 85s Get:2 http://ftpmaster.internal/ubuntu noble/main amd64 ubuntu-standard amd64 1.536build1 [10.7 kB] 85s Fetched 21.5 kB in 0s (1136 kB/s) 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 ... 71803 files and directories currently installed.) 85s Preparing to unpack .../ubuntu-minimal_1.536build1_amd64.deb ... 85s Unpacking ubuntu-minimal (1.536build1) over (1.536) ... 85s Preparing to unpack .../ubuntu-standard_1.536build1_amd64.deb ... 85s Unpacking ubuntu-standard (1.536build1) over (1.536) ... 85s Setting up ubuntu-minimal (1.536build1) ... 85s Setting up ubuntu-standard (1.536build1) ... 85s Reading package lists... 86s Building dependency tree... 86s Reading state information... 86s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 86s Hit:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease 86s Hit:2 http://ftpmaster.internal/ubuntu noble InRelease 86s Hit:3 http://ftpmaster.internal/ubuntu noble-updates InRelease 86s Hit:4 http://ftpmaster.internal/ubuntu noble-security InRelease 88s Reading package lists... 88s Reading package lists... 88s Building dependency tree... 88s Reading state information... 89s 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. 90s autopkgtest [13:06:25]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 00:29:05 UTC 2024 90s autopkgtest [13:06:25]: @@@@@@@@@@@@@@@@@@@@ apt-source r-cran-etm 91s Get:1 http://ftpmaster.internal/ubuntu noble/universe r-cran-etm 1.1.1-1 (dsc) [2148 B] 91s Get:2 http://ftpmaster.internal/ubuntu noble/universe r-cran-etm 1.1.1-1 (tar) [242 kB] 91s Get:3 http://ftpmaster.internal/ubuntu noble/universe r-cran-etm 1.1.1-1 (diff) [3564 B] 91s gpgv: Signature made Fri Sep 18 09:39:57 2020 UTC 91s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 91s gpgv: issuer "tille@debian.org" 91s gpgv: Can't check signature: No public key 91s dpkg-source: warning: cannot verify inline signature for ./r-cran-etm_1.1.1-1.dsc: no acceptable signature found 91s autopkgtest [13:06:26]: testing package r-cran-etm version 1.1.1-1 91s autopkgtest [13:06:26]: build not needed 92s autopkgtest [13:06:27]: test run-unit-test: preparing testbed 94s Reading package lists... 94s Building dependency tree... 94s Reading state information... 95s Starting pkgProblemResolver with broken count: 0 95s Starting 2 pkgProblemResolver with broken count: 0 95s Done 95s The following additional packages will be installed: 95s fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono libblas3 95s libcairo2 libdatrie1 libdeflate0 libfontconfig1 libgfortran5 libgomp1 95s libgraphite2-3 libharfbuzz0b libice6 libjbig0 libjpeg-turbo8 libjpeg8 95s liblapack3 liblerc4 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 95s libpaper-utils libpaper1 libpixman-1-0 libsharpyuv0 libsm6 libtcl8.6 95s libthai-data libthai0 libtiff6 libtk8.6 libwebp7 libxcb-render0 libxcb-shm0 95s libxft2 libxrender1 libxss1 libxt6 littler r-base-core r-cran-data.table 95s r-cran-dbi r-cran-etm r-cran-kmi r-cran-lattice r-cran-littler r-cran-matrix 95s r-cran-mitools r-cran-pkgkitten r-cran-rcpp r-cran-rcpparmadillo 95s r-cran-survival unzip x11-common xdg-utils zip 95s Suggested packages: 95s tcl8.6 tk8.6 elpa-ess r-doc-info | r-doc-pdf r-mathlib r-base-html 95s r-cran-rmysql r-cran-ggplot2 r-cran-geepack r-cran-getopt r-cran-rodbc 95s r-cran-foreign r-cran-inline 95s Recommended packages: 95s r-recommended r-base-dev r-doc-html r-cran-bit64 r-cran-bit r-cran-curl 95s r-cran-r.utils r-cran-xts r-cran-nanotime r-cran-zoo r-cran-yaml 95s r-cran-knitr r-cran-rmarkdown libfile-mimeinfo-perl libnet-dbus-perl 95s libx11-protocol-perl x11-utils x11-xserver-utils 95s The following NEW packages will be installed: 95s autopkgtest-satdep fontconfig fontconfig-config fonts-dejavu-core 95s fonts-dejavu-mono libblas3 libcairo2 libdatrie1 libdeflate0 libfontconfig1 95s libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libice6 libjbig0 95s libjpeg-turbo8 libjpeg8 liblapack3 liblerc4 libpango-1.0-0 95s libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpixman-1-0 95s libsharpyuv0 libsm6 libtcl8.6 libthai-data libthai0 libtiff6 libtk8.6 95s libwebp7 libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxss1 libxt6 95s littler r-base-core r-cran-data.table r-cran-dbi r-cran-etm r-cran-kmi 95s r-cran-lattice r-cran-littler r-cran-matrix r-cran-mitools r-cran-pkgkitten 95s r-cran-rcpp r-cran-rcpparmadillo r-cran-survival unzip x11-common xdg-utils 95s zip 96s 0 upgraded, 58 newly installed, 0 to remove and 0 not upgraded. 96s Need to get 55.7 MB/55.7 MB of archives. 96s After this operation, 116 MB of additional disk space will be used. 96s Get:1 /tmp/autopkgtest.GQasZm/1-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [712 B] 96s Get:2 http://ftpmaster.internal/ubuntu noble/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB] 96s Get:3 http://ftpmaster.internal/ubuntu noble/main amd64 fonts-dejavu-core all 2.37-8 [835 kB] 96s Get:4 http://ftpmaster.internal/ubuntu noble/main amd64 fontconfig-config amd64 2.15.0-1ubuntu1 [36.9 kB] 96s Get:5 http://ftpmaster.internal/ubuntu noble/main amd64 libfontconfig1 amd64 2.15.0-1ubuntu1 [139 kB] 96s Get:6 http://ftpmaster.internal/ubuntu noble/main amd64 fontconfig amd64 2.15.0-1ubuntu1 [180 kB] 96s Get:7 http://ftpmaster.internal/ubuntu noble/main amd64 libblas3 amd64 3.12.0-3 [238 kB] 96s Get:8 http://ftpmaster.internal/ubuntu noble/main amd64 libpixman-1-0 amd64 0.42.2-1 [268 kB] 96s Get:9 http://ftpmaster.internal/ubuntu noble/main amd64 libxcb-render0 amd64 1.15-1 [16.3 kB] 96s Get:10 http://ftpmaster.internal/ubuntu noble/main amd64 libxcb-shm0 amd64 1.15-1 [5740 B] 96s Get:11 http://ftpmaster.internal/ubuntu noble/main amd64 libxrender1 amd64 1:0.9.10-1.1 [20.0 kB] 96s Get:12 http://ftpmaster.internal/ubuntu noble/main amd64 libcairo2 amd64 1.18.0-1 [572 kB] 96s Get:13 http://ftpmaster.internal/ubuntu noble/main amd64 libdatrie1 amd64 0.2.13-3 [20.9 kB] 96s Get:14 http://ftpmaster.internal/ubuntu noble/main amd64 libdeflate0 amd64 1.19-1 [43.7 kB] 96s Get:15 http://ftpmaster.internal/ubuntu noble/main amd64 libgfortran5 amd64 14-20240303-1ubuntu1 [924 kB] 96s Get:16 http://ftpmaster.internal/ubuntu noble/main amd64 libgomp1 amd64 14-20240303-1ubuntu1 [147 kB] 96s Get:17 http://ftpmaster.internal/ubuntu noble/main amd64 libgraphite2-3 amd64 1.3.14-2 [83.1 kB] 96s Get:18 http://ftpmaster.internal/ubuntu noble/main amd64 libharfbuzz0b amd64 8.3.0-2 [469 kB] 96s Get:19 http://ftpmaster.internal/ubuntu noble/main amd64 x11-common all 1:7.7+23ubuntu2 [23.4 kB] 96s Get:20 http://ftpmaster.internal/ubuntu noble/main amd64 libice6 amd64 2:1.0.10-1build2 [42.6 kB] 96s Get:21 http://ftpmaster.internal/ubuntu noble/main amd64 libjpeg-turbo8 amd64 2.1.5-2ubuntu1 [147 kB] 96s Get:22 http://ftpmaster.internal/ubuntu noble/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 96s Get:23 http://ftpmaster.internal/ubuntu noble/main amd64 liblapack3 amd64 3.12.0-3 [2649 kB] 96s Get:24 http://ftpmaster.internal/ubuntu noble/main amd64 liblerc4 amd64 4.0.0+ds-4ubuntu1 [184 kB] 96s Get:25 http://ftpmaster.internal/ubuntu noble/main amd64 libthai-data all 0.1.29-2 [158 kB] 96s Get:26 http://ftpmaster.internal/ubuntu noble/main amd64 libthai0 amd64 0.1.29-2 [18.8 kB] 96s Get:27 http://ftpmaster.internal/ubuntu noble/main amd64 libpango-1.0-0 amd64 1.51.0+ds-4 [228 kB] 96s Get:28 http://ftpmaster.internal/ubuntu noble/main amd64 libpangoft2-1.0-0 amd64 1.51.0+ds-4 [42.1 kB] 96s Get:29 http://ftpmaster.internal/ubuntu noble/main amd64 libpangocairo-1.0-0 amd64 1.51.0+ds-4 [29.0 kB] 96s Get:30 http://ftpmaster.internal/ubuntu noble/main amd64 libpaper1 amd64 1.1.29 [13.4 kB] 96s Get:31 http://ftpmaster.internal/ubuntu noble/main amd64 libpaper-utils amd64 1.1.29 [8658 B] 96s Get:32 http://ftpmaster.internal/ubuntu noble/main amd64 libsharpyuv0 amd64 1.3.2-0.4 [15.6 kB] 96s Get:33 http://ftpmaster.internal/ubuntu noble/main amd64 libsm6 amd64 2:1.2.3-1build2 [16.7 kB] 96s Get:34 http://ftpmaster.internal/ubuntu noble/main amd64 libtcl8.6 amd64 8.6.13+dfsg-2 [984 kB] 96s Get:35 http://ftpmaster.internal/ubuntu noble/main amd64 libjbig0 amd64 2.1-6.1ubuntu1 [29.3 kB] 96s Get:36 http://ftpmaster.internal/ubuntu noble/main amd64 libwebp7 amd64 1.3.2-0.4 [230 kB] 96s Get:37 http://ftpmaster.internal/ubuntu noble/main amd64 libtiff6 amd64 4.5.1+git230720-3ubuntu1 [232 kB] 96s Get:38 http://ftpmaster.internal/ubuntu noble/main amd64 libxft2 amd64 2.3.6-1 [44.5 kB] 96s Get:39 http://ftpmaster.internal/ubuntu noble/main amd64 libxss1 amd64 1:1.2.3-1build2 [8476 B] 96s Get:40 http://ftpmaster.internal/ubuntu noble/main amd64 libtk8.6 amd64 8.6.13-2 [776 kB] 96s Get:41 http://ftpmaster.internal/ubuntu noble/main amd64 libxt6 amd64 1:1.2.1-1.1 [173 kB] 96s Get:42 http://ftpmaster.internal/ubuntu noble/main amd64 zip amd64 3.0-13 [176 kB] 96s Get:43 http://ftpmaster.internal/ubuntu noble/main amd64 unzip amd64 6.0-28ubuntu3 [174 kB] 96s Get:44 http://ftpmaster.internal/ubuntu noble/main amd64 xdg-utils all 1.1.3-4.1ubuntu3 [62.0 kB] 96s Get:45 http://ftpmaster.internal/ubuntu noble/universe amd64 r-base-core amd64 4.3.2-1build1 [27.0 MB] 96s Get:46 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-littler amd64 0.3.19-1 [94.1 kB] 96s Get:47 http://ftpmaster.internal/ubuntu noble/universe amd64 littler all 0.3.19-1 [2472 B] 96s Get:48 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-data.table amd64 1.14.10+dfsg-1 [1837 kB] 96s Get:49 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-dbi all 1.2.2-1 [823 kB] 96s Get:50 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-lattice amd64 0.22-5-1 [1342 kB] 96s Get:51 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-matrix amd64 1.6-5-1 [3830 kB] 96s Get:52 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-survival amd64 3.5-8-1 [6120 kB] 96s Get:53 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-pkgkitten all 0.2.3-1 [25.1 kB] 96s Get:54 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-rcpp amd64 1.0.12-1 [1981 kB] 96s Get:55 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 r-cran-rcpparmadillo amd64 0.12.8.1.0-1 [862 kB] 96s Get:56 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-etm amd64 1.1.1-1 [478 kB] 96s Get:57 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-mitools all 2.4-2build1 [265 kB] 96s Get:58 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-kmi all 0.5.5-2build1 [78.3 kB] 96s Preconfiguring packages ... 96s Fetched 55.7 MB in 0s (122 MB/s) 96s Selecting previously unselected package fonts-dejavu-mono. 96s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 71803 files and directories currently installed.) 96s Preparing to unpack .../00-fonts-dejavu-mono_2.37-8_all.deb ... 96s Unpacking fonts-dejavu-mono (2.37-8) ... 96s Selecting previously unselected package fonts-dejavu-core. 96s Preparing to unpack .../01-fonts-dejavu-core_2.37-8_all.deb ... 96s Unpacking fonts-dejavu-core (2.37-8) ... 96s Selecting previously unselected package fontconfig-config. 97s Preparing to unpack .../02-fontconfig-config_2.15.0-1ubuntu1_amd64.deb ... 97s Unpacking fontconfig-config (2.15.0-1ubuntu1) ... 97s Selecting previously unselected package libfontconfig1:amd64. 97s Preparing to unpack .../03-libfontconfig1_2.15.0-1ubuntu1_amd64.deb ... 97s Unpacking libfontconfig1:amd64 (2.15.0-1ubuntu1) ... 97s Selecting previously unselected package fontconfig. 97s Preparing to unpack .../04-fontconfig_2.15.0-1ubuntu1_amd64.deb ... 97s Unpacking fontconfig (2.15.0-1ubuntu1) ... 97s Selecting previously unselected package libblas3:amd64. 97s Preparing to unpack .../05-libblas3_3.12.0-3_amd64.deb ... 97s Unpacking libblas3:amd64 (3.12.0-3) ... 97s Selecting previously unselected package libpixman-1-0:amd64. 97s Preparing to unpack .../06-libpixman-1-0_0.42.2-1_amd64.deb ... 97s Unpacking libpixman-1-0:amd64 (0.42.2-1) ... 97s Selecting previously unselected package libxcb-render0:amd64. 97s Preparing to unpack .../07-libxcb-render0_1.15-1_amd64.deb ... 97s Unpacking libxcb-render0:amd64 (1.15-1) ... 97s Selecting previously unselected package libxcb-shm0:amd64. 97s Preparing to unpack .../08-libxcb-shm0_1.15-1_amd64.deb ... 97s Unpacking libxcb-shm0:amd64 (1.15-1) ... 97s Selecting previously unselected package libxrender1:amd64. 97s Preparing to unpack .../09-libxrender1_1%3a0.9.10-1.1_amd64.deb ... 97s Unpacking libxrender1:amd64 (1:0.9.10-1.1) ... 97s Selecting previously unselected package libcairo2:amd64. 97s Preparing to unpack .../10-libcairo2_1.18.0-1_amd64.deb ... 97s Unpacking libcairo2:amd64 (1.18.0-1) ... 97s Selecting previously unselected package libdatrie1:amd64. 97s Preparing to unpack .../11-libdatrie1_0.2.13-3_amd64.deb ... 97s Unpacking libdatrie1:amd64 (0.2.13-3) ... 97s Selecting previously unselected package libdeflate0:amd64. 97s Preparing to unpack .../12-libdeflate0_1.19-1_amd64.deb ... 97s Unpacking libdeflate0:amd64 (1.19-1) ... 97s Selecting previously unselected package libgfortran5:amd64. 97s Preparing to unpack .../13-libgfortran5_14-20240303-1ubuntu1_amd64.deb ... 97s Unpacking libgfortran5:amd64 (14-20240303-1ubuntu1) ... 97s Selecting previously unselected package libgomp1:amd64. 97s Preparing to unpack .../14-libgomp1_14-20240303-1ubuntu1_amd64.deb ... 97s Unpacking libgomp1:amd64 (14-20240303-1ubuntu1) ... 97s Selecting previously unselected package libgraphite2-3:amd64. 97s Preparing to unpack .../15-libgraphite2-3_1.3.14-2_amd64.deb ... 97s Unpacking libgraphite2-3:amd64 (1.3.14-2) ... 97s Selecting previously unselected package libharfbuzz0b:amd64. 97s Preparing to unpack .../16-libharfbuzz0b_8.3.0-2_amd64.deb ... 97s Unpacking libharfbuzz0b:amd64 (8.3.0-2) ... 97s Selecting previously unselected package x11-common. 97s Preparing to unpack .../17-x11-common_1%3a7.7+23ubuntu2_all.deb ... 97s Unpacking x11-common (1:7.7+23ubuntu2) ... 97s Selecting previously unselected package libice6:amd64. 97s Preparing to unpack .../18-libice6_2%3a1.0.10-1build2_amd64.deb ... 97s Unpacking libice6:amd64 (2:1.0.10-1build2) ... 97s Selecting previously unselected package libjpeg-turbo8:amd64. 97s Preparing to unpack .../19-libjpeg-turbo8_2.1.5-2ubuntu1_amd64.deb ... 97s Unpacking libjpeg-turbo8:amd64 (2.1.5-2ubuntu1) ... 97s Selecting previously unselected package libjpeg8:amd64. 97s Preparing to unpack .../20-libjpeg8_8c-2ubuntu11_amd64.deb ... 97s Unpacking libjpeg8:amd64 (8c-2ubuntu11) ... 97s Selecting previously unselected package liblapack3:amd64. 97s Preparing to unpack .../21-liblapack3_3.12.0-3_amd64.deb ... 97s Unpacking liblapack3:amd64 (3.12.0-3) ... 97s Selecting previously unselected package liblerc4:amd64. 97s Preparing to unpack .../22-liblerc4_4.0.0+ds-4ubuntu1_amd64.deb ... 97s Unpacking liblerc4:amd64 (4.0.0+ds-4ubuntu1) ... 97s Selecting previously unselected package libthai-data. 97s Preparing to unpack .../23-libthai-data_0.1.29-2_all.deb ... 97s Unpacking libthai-data (0.1.29-2) ... 97s Selecting previously unselected package libthai0:amd64. 97s Preparing to unpack .../24-libthai0_0.1.29-2_amd64.deb ... 97s Unpacking libthai0:amd64 (0.1.29-2) ... 97s Selecting previously unselected package libpango-1.0-0:amd64. 97s Preparing to unpack .../25-libpango-1.0-0_1.51.0+ds-4_amd64.deb ... 97s Unpacking libpango-1.0-0:amd64 (1.51.0+ds-4) ... 97s Selecting previously unselected package libpangoft2-1.0-0:amd64. 97s Preparing to unpack .../26-libpangoft2-1.0-0_1.51.0+ds-4_amd64.deb ... 97s Unpacking libpangoft2-1.0-0:amd64 (1.51.0+ds-4) ... 97s Selecting previously unselected package libpangocairo-1.0-0:amd64. 97s Preparing to unpack .../27-libpangocairo-1.0-0_1.51.0+ds-4_amd64.deb ... 97s Unpacking libpangocairo-1.0-0:amd64 (1.51.0+ds-4) ... 97s Selecting previously unselected package libpaper1:amd64. 97s Preparing to unpack .../28-libpaper1_1.1.29_amd64.deb ... 97s Unpacking libpaper1:amd64 (1.1.29) ... 98s Selecting previously unselected package libpaper-utils. 98s Preparing to unpack .../29-libpaper-utils_1.1.29_amd64.deb ... 98s 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Type 'license()' or 'licence()' for distribution details. 107s 107s R is a collaborative project with many contributors. 107s Type 'contributors()' for more information and 107s 'citation()' on how to cite R or R packages in publications. 107s 107s Type 'demo()' for some demos, 'help()' for on-line help, or 107s 'help.start()' for an HTML browser interface to help. 107s Type 'q()' to quit R. 107s 108s Loading required package: etm 108s > ### test file for etmCIF. 108s > ### Really simple tests and comparison with etm 108s > 108s > old <- options(digits = 5) 108s > 108s > require(etm) 109s > 109s > if (!require(survival, quietly = TRUE)) { 109s + print("The following tests require the 'survival' package") 109s + } else { 109s + 109s + data(abortion) 109s + 109s + from <- rep(0, nrow(abortion)) 109s + to <- abortion$cause 109s + entry <- abortion$entry 109s + exit <- abortion$exit 109s + id <- 1:nrow(abortion) 109s + data <- data.frame(id, from, to, entry, exit, group = abortion$group) 109s + 109s + ## Computation of the CIFs with etm 109s + tra <- matrix(FALSE, 4, 4) 109s + tra[1, 2:4] <- TRUE 109s + 109s + cif.control <- etm(data[data$group == 0, ], c("0", "1", "2", "3"), 109s + tra, NULL, 0) 109s + cif.exposed <- etm(data[data$group == 1, ], c("0", "1", "2", "3"), 109s + tra, NULL, 0) 109s + 109s + 109s + ## Computation of the CIFs with etmCIF 109s + netm <- etmCIF(Surv(entry, exit, cause != 0) ~ group, abortion, 109s + etype = cause, failcode = 3) 109s + 109s + ### let's do some comparisons :-) 109s + 109s + all.equal(trprob(cif.control, "0 3"), netm[[1]]$est["0", "3", ]) 109s + all.equal(trprob(cif.control, "0 2"), netm[[1]]$est["0", "2", ]) 109s + all.equal(trprob(cif.control, "0 1"), netm[[1]]$est["0", "1", ]) 109s + 109s + all.equal(trprob(cif.exposed, "0 3"), netm[[2]]$est["0", "3", ]) 109s + all.equal(trprob(cif.exposed, "0 2"), netm[[2]]$est["0", "2", ]) 109s + all.equal(trprob(cif.exposed, "0 1"), netm[[2]]$est["0", "1", ]) 109s + 109s + 109s + all.equal(trcov(cif.control, "0 3"), netm[[1]]$cov["0 3", "0 3", ]) 109s + all.equal(trcov(cif.control, "0 2"), netm[[1]]$cov["0 2", "0 2", ]) 109s + all.equal(trcov(cif.control, "0 1"), netm[[1]]$cov["0 1", "0 1", ]) 109s + 109s + all.equal(trcov(cif.exposed, "0 3"), netm[[2]]$cov["0 3", "0 3", ]) 109s + all.equal(trcov(cif.exposed, "0 2"), netm[[2]]$cov["0 2", "0 2", ]) 109s + all.equal(trcov(cif.exposed, "0 1"), netm[[2]]$cov["0 1", "0 1", ]) 109s + 109s + 109s + netm 109s + 109s + ## test on the summary 109s + snetm <- summary(netm) 109s + 109s + snetm 109s + 109s + all.equal(unname(trprob(cif.control, "0 3")), snetm[[1]][[3]]$P) 109s + all.equal(unname(trprob(cif.control, "0 2")), snetm[[1]][[2]]$P) 109s + all.equal(unname(trprob(cif.control, "0 1")), snetm[[1]][[1]]$P) 109s + 109s + all.equal(unname(trprob(cif.exposed, "0 3")), snetm[[2]][[3]]$P) 109s + all.equal(unname(trprob(cif.exposed, "0 2")), snetm[[2]][[2]]$P) 109s + all.equal(unname(trprob(cif.exposed, "0 1")), snetm[[2]][[1]]$P) 109s + 109s + scif.control <- summary(cif.control, ci.fun = "cloglog") 109s + scif.exposed <- summary(cif.exposed, ci.fun = "cloglog") 109s + 109s + all.equal(scif.control[[4]]$lower, snetm[[1]][[3]]$lower) 109s + all.equal(scif.control[[4]]$upper, snetm[[1]][[3]]$upper) 109s + 109s + all.equal(scif.exposed[[4]]$lower, snetm[[2]][[3]]$lower) 109s + all.equal(scif.exposed[[4]]$upper, snetm[[2]][[3]]$upper) 109s + } 109s [1] TRUE 109s > 109s > ### test with factors in the input 109s > abortion$status <- with(abortion, ifelse(cause == 2, "life birth", 109s + ifelse(cause == 1, "ETOP", "spontaneous abortion"))) 109s > 109s > abortion$status <- factor(abortion$status) 109s > 109s > netm.factor <- etmCIF(Surv(entry, exit, status != "cens") ~ group, abortion, 109s + etype = status, failcode = "spontaneous abortion") 109s > 109s > 109s > all.equal(trprob(cif.control, "0 3"), netm.factor[[1]]$est["0", "spontaneous abortion", ]) 109s [1] TRUE 109s > all.equal(trprob(cif.control, "0 2"), netm.factor[[1]]$est["0", "life birth", ]) 109s [1] TRUE 109s > 109s > netm.factor 109s Call: etmCIF(formula = Surv(entry, exit, status != "cens") ~ group, 109s data = abortion, etype = status, failcode = "spontaneous abortion") 109s 109s Covariate: group 109s levels: 0 1 109s 109s 109s group = 0 109s time P se(P) n.event 109s CIF ETOP 43 0.040159 0.0092578 20 109s CIF life birth 43 0.799059 0.0221865 924 109s CIF spontaneous abortion 43 0.160781 0.0213261 69 109s 109s group = 1 109s time P se(P) n.event 109s CIF ETOP 42 0.28511 0.042493 38 109s CIF life birth 42 0.35257 0.042139 92 109s CIF spontaneous abortion 42 0.36232 0.049473 43 109s > 109s > summary(netm.factor) 109s 109s group=0 109s 109s CIF ETOP 109s P time var lower upper n.risk n.event 109s 0.000000 6 0.0000e+00 0.000000 0.000000 117 0 109s 0.038955 13 8.4440e-05 0.024488 0.061694 645 1 109s 0.040159 26 8.5707e-05 0.025513 0.062939 846 0 109s 0.040159 36 8.5707e-05 0.025513 0.062939 876 0 109s 0.040159 40 8.5707e-05 0.025513 0.062939 554 0 109s 0.040159 43 8.5707e-05 0.025513 0.062939 6 0 109s 109s CIF life birth 109s P time var lower upper n.risk n.event 109s 0.000000 6 0.0000e+00 0.000000 0.000000 117 0 109s 0.000000 13 0.0000e+00 0.000000 0.000000 645 0 109s 0.000000 26 0.0000e+00 0.000000 0.000000 846 0 109s 0.053197 36 4.6195e-05 0.041379 0.068268 876 25 109s 0.563121 40 3.8801e-04 0.524924 0.602021 554 280 109s 0.799059 43 4.9224e-04 0.753969 0.840613 6 6 109s 109s CIF spontaneous abortion 109s P time var lower upper n.risk n.event 109s 0.034188 6 0.00028222 0.01297 0.088523 117 4 109s 0.150468 13 0.00045513 0.11360 0.197901 645 1 109s 0.159904 26 0.00045498 0.12274 0.206925 846 1 109s 0.160781 36 0.00045480 0.12360 0.207757 876 1 109s 0.160781 40 0.00045480 0.12360 0.207757 554 0 109s 0.160781 43 0.00045480 0.12360 0.207757 6 0 109s 109s 109s group=1 109s 109s CIF ETOP 109s P time var lower upper n.risk n.event 109s 0.00000 6 0.0000000 0.00000 0.00000 35 0 109s 0.26048 13 0.0017854 0.18795 0.35425 90 0 109s 0.28115 21 0.0018028 0.20742 0.37423 93 1 109s 0.28511 34 0.0018057 0.21116 0.37806 89 0 109s 0.28511 39 0.0018057 0.21116 0.37806 59 0 109s 0.28511 42 0.0018057 0.21116 0.37806 6 0 109s 109s CIF life birth 109s P time var lower upper n.risk n.event 109s 0.000000 6 0.0000e+00 0.000000 0.000000 35 0 109s 0.000000 13 0.0000e+00 0.000000 0.000000 90 0 109s 0.000000 21 0.0000e+00 0.000000 0.000000 93 0 109s 0.023073 34 9.0514e-05 0.010252 0.051504 89 2 109s 0.180156 39 8.0126e-04 0.131765 0.243663 59 13 109s 0.352565 42 1.7757e-03 0.276882 0.441775 6 6 109s 109s CIF spontaneous abortion 109s P time var lower upper n.risk n.event 109s 0.057143 6 0.0015394 0.014605 0.20968 35 2 109s 0.333246 13 0.0025280 0.245337 0.44216 90 4 109s 0.350702 21 0.0024827 0.262769 0.45762 93 0 109s 0.358492 34 0.0024593 0.270627 0.46448 89 0 109s 0.358492 39 0.0024593 0.270627 0.46448 59 0 109s 0.362323 42 0.0024476 0.274499 0.46785 6 0 109s 109s > 109s > ### test with group as a character vector 109s > abortion$ttt <- with(abortion, ifelse(group == 0, "control", "exposed")) 109s > abortion$ttt <- factor(abortion$ttt) 109s > 109s > netm.ttt <- etmCIF(Surv(entry, exit, status != "cens") ~ ttt, abortion, 109s + etype = status, failcode = "spontaneous abortion") 109s > 109s > all.equal(trprob(cif.control, "0 3"), netm.ttt[[1]]$est["0", "spontaneous abortion", ]) 109s [1] TRUE 109s > all.equal(trprob(cif.control, "0 2"), netm.ttt[[1]]$est["0", "life birth", ]) 109s [1] TRUE 109s > 109s > netm.ttt 109s Call: etmCIF(formula = Surv(entry, exit, status != "cens") ~ ttt, data = abortion, 109s etype = status, failcode = "spontaneous abortion") 109s 109s Covariate: ttt 109s levels: control exposed 109s 109s 109s ttt = control 109s time P se(P) n.event 109s CIF ETOP 43 0.040159 0.0092578 20 109s CIF life birth 43 0.799059 0.0221865 924 109s CIF spontaneous abortion 43 0.160781 0.0213261 69 109s 109s ttt = exposed 109s time P se(P) n.event 109s CIF ETOP 42 0.28511 0.042493 38 109s CIF life birth 42 0.35257 0.042139 92 109s CIF spontaneous abortion 42 0.36232 0.049473 43 109s > 109s > summary(netm.ttt) 109s 109s ttt=control 109s 109s CIF ETOP 109s P time var lower upper n.risk n.event 109s 0.000000 6 0.0000e+00 0.000000 0.000000 117 0 109s 0.038955 13 8.4440e-05 0.024488 0.061694 645 1 109s 0.040159 26 8.5707e-05 0.025513 0.062939 846 0 109s 0.040159 36 8.5707e-05 0.025513 0.062939 876 0 109s 0.040159 40 8.5707e-05 0.025513 0.062939 554 0 109s 0.040159 43 8.5707e-05 0.025513 0.062939 6 0 109s 109s CIF life birth 109s P time var lower upper n.risk n.event 109s 0.000000 6 0.0000e+00 0.000000 0.000000 117 0 109s 0.000000 13 0.0000e+00 0.000000 0.000000 645 0 109s 0.000000 26 0.0000e+00 0.000000 0.000000 846 0 109s 0.053197 36 4.6195e-05 0.041379 0.068268 876 25 109s 0.563121 40 3.8801e-04 0.524924 0.602021 554 280 109s 0.799059 43 4.9224e-04 0.753969 0.840613 6 6 109s 109s CIF spontaneous abortion 109s P time var lower upper n.risk n.event 109s 0.034188 6 0.00028222 0.01297 0.088523 117 4 109s 0.150468 13 0.00045513 0.11360 0.197901 645 1 109s 0.159904 26 0.00045498 0.12274 0.206925 846 1 109s 0.160781 36 0.00045480 0.12360 0.207757 876 1 109s 0.160781 40 0.00045480 0.12360 0.207757 554 0 109s 0.160781 43 0.00045480 0.12360 0.207757 6 0 109s 109s 109s ttt=exposed 109s 109s CIF ETOP 109s P time var lower upper n.risk n.event 109s 0.00000 6 0.0000000 0.00000 0.00000 35 0 109s 0.26048 13 0.0017854 0.18795 0.35425 90 0 109s 0.28115 21 0.0018028 0.20742 0.37423 93 1 109s 0.28511 34 0.0018057 0.21116 0.37806 89 0 109s 0.28511 39 0.0018057 0.21116 0.37806 59 0 109s 0.28511 42 0.0018057 0.21116 0.37806 6 0 109s 109s CIF life birth 109s P time var lower upper n.risk n.event 109s 0.000000 6 0.0000e+00 0.000000 0.000000 35 0 109s 0.000000 13 0.0000e+00 0.000000 0.000000 90 0 109s 0.000000 21 0.0000e+00 0.000000 0.000000 93 0 109s 0.023073 34 9.0514e-05 0.010252 0.051504 89 2 109s 0.180156 39 8.0126e-04 0.131765 0.243663 59 13 109s 0.352565 42 1.7757e-03 0.276882 0.441775 6 6 109s 109s CIF spontaneous abortion 109s P time var lower upper n.risk n.event 109s 0.057143 6 0.0015394 0.014605 0.20968 35 2 109s 0.333246 13 0.0025280 0.245337 0.44216 90 4 109s 0.350702 21 0.0024827 0.262769 0.45762 93 0 109s 0.358492 34 0.0024593 0.270627 0.46448 89 0 109s 0.358492 39 0.0024593 0.270627 0.46448 59 0 109s 0.362323 42 0.0024476 0.274499 0.46785 6 0 109s 109s > 109s > 109s > ### A couple of comparisons with simulated data 109s > set.seed(1313) 109s > time <- rexp(100) 109s > to <- rbinom(100, 2, prob = c(1/3, 1/3, 1/3)) 109s > from <- rep(11, 100) 109s > id <- 1:100 109s > cov <- rbinom(100, 1, 0.5) 109s > 109s > dat.s <- data.frame(id, time, from, to, cov) 109s > 109s > traa <- matrix(FALSE, 3, 3) 109s > traa[1, 2:3] <- TRUE 109s > 109s > aa0 <- etm(dat.s[dat.s$cov == 0, ], c("11", "1", "2"), traa, "0", 0) 109s > aa1 <- etm(dat.s[dat.s$cov == 1, ], c("11", "1", "2"), traa, "0", 0) 109s > aa <- etm(dat.s, c("11", "1", "2"), traa, "0", 0) 109s > 109s > test <- etmCIF(Surv(time, to != 0) ~ 1, dat.s, etype = to) 109s > 109s > test.c <- etmCIF(Surv(time, to != 0) ~ cov, dat.s, etype = to) 109s > 109s > all.equal(trprob(aa, "11 1"), test[[1]]$est["0", "1", ]) 109s [1] TRUE 109s > all.equal(trprob(aa, "11 2"), test[[1]]$est["0", "2", ]) 109s [1] TRUE 109s > 109s > all.equal(trprob(aa0, "11 1"), test.c[[1]]$est["0", "1", ]) 109s [1] TRUE 109s > all.equal(trprob(aa0, "11 2"), test.c[[1]]$est["0", "2", ]) 109s [1] TRUE 109s > 109s > all.equal(trprob(aa1, "11 1"), test.c[[2]]$est["0", "1", ]) 109s [1] TRUE 109s > all.equal(trprob(aa1, "11 2"), test.c[[2]]$est["0", "2", ]) 109s [1] TRUE 109s > 109s > test 109s Call: etmCIF(formula = Surv(time, to != 0) ~ 1, data = dat.s, etype = to) 109s 109s time P se(P) n.event 109s CIF 1 4.9088 0.809108 0.079680 45 109s CIF 2 4.9088 0.096618 0.032905 8 109s > 109s > test.c 109s Call: etmCIF(formula = Surv(time, to != 0) ~ cov, data = dat.s, etype = to) 109s 109s Covariate: cov 109s levels: 0 1 109s 109s 109s cov = 0 109s time P se(P) n.event 109s CIF 1 2.1708 0.70246 0.105797 19 109s CIF 2 2.1708 0.11144 0.053384 4 109s 109s cov = 1 109s time P se(P) n.event 109s CIF 1 4.9088 0.80787 0.094051 26 109s CIF 2 4.9088 0.08436 0.040769 4 109s > 109s > summary(test) 109s 109s 109s 109s CIF 1 109s P time var lower upper n.risk n.event 109s 0.01000 0.0092099 0.0000990 0.0014147 0.068863 100 1 109s 0.11430 0.2663096 0.0010542 0.0649454 0.196993 81 1 109s 0.23451 0.7303091 0.0020436 0.1591107 0.337736 54 1 109s 0.40425 1.4299939 0.0032996 0.3020445 0.525741 29 1 109s 0.54593 2.0647206 0.0040836 0.4269008 0.673605 16 1 109s 0.80911 4.9087561 0.0063489 0.6359544 0.933733 2 1 109s 109s CIF 2 109s P time var lower upper n.risk n.event 109s 0.000000 0.0092099 0.00000000 0.000000 0.000000 100 0 109s 0.031657 0.2663096 0.00032353 0.010320 0.094942 81 0 109s 0.067029 0.7303091 0.00070366 0.030598 0.143503 54 0 109s 0.096618 1.4299939 0.00108275 0.049082 0.185474 29 0 109s 0.096618 2.0647206 0.00108275 0.049082 0.185474 16 0 109s 0.096618 4.9087561 0.00108275 0.049082 0.185474 2 0 109s 109s > summary(test.c) 109s 109s cov=0 109s 109s CIF 1 109s P time var lower upper n.risk n.event 109s 0.022222 0.0092099 0.00048285 0.0031605 0.14747 45 1 109s 0.092222 0.2982439 0.00193603 0.0355971 0.22762 36 0 109s 0.226684 0.7021938 0.00450954 0.1241760 0.39250 24 1 109s 0.378128 1.4299939 0.00760870 0.2337884 0.57145 13 1 109s 0.505736 1.6148774 0.00895330 0.3388425 0.69885 10 1 109s 0.702465 2.1708375 0.01119294 0.4944890 0.88399 3 1 109s 109s CIF 2 109s P time var lower upper n.risk n.event 109s 0.000000 0.0092099 0.0000000 0.000000 0.00000 45 0 109s 0.048441 0.2982439 0.0011168 0.012337 0.18013 36 1 109s 0.076411 0.7021938 0.0018104 0.025202 0.21928 24 0 109s 0.111440 1.4299939 0.0028499 0.042676 0.27392 13 0 109s 0.111440 1.6148774 0.0028499 0.042676 0.27392 10 0 109s 0.111440 2.1708375 0.0028499 0.042676 0.27392 3 0 109s 109s 109s cov=1 109s 109s CIF 1 109s P time var lower upper n.risk n.event 109s 0.018182 0.066692 0.00032457 0.0025813 0.12214 55 1 109s 0.112392 0.263808 0.00187215 0.0520925 0.23333 45 1 109s 0.241023 0.730309 0.00374499 0.1440057 0.38685 31 1 109s 0.401201 1.066913 0.00570788 0.2714008 0.56421 19 1 109s 0.592334 2.366275 0.00775985 0.4286230 0.76273 8 1 109s 0.807871 4.908756 0.00884554 0.6023185 0.94771 2 1 109s 109s CIF 2 109s P time var lower upper n.risk n.event 109s 0.000000 0.066692 0.00000000 0.000000 0.00000 55 0 109s 0.037434 0.263808 0.00067458 0.009494 0.14152 45 0 109s 0.059341 0.730309 0.00111295 0.019447 0.17351 31 0 109s 0.084360 1.066913 0.00166213 0.032211 0.21119 19 0 109s 0.084360 2.366275 0.00166213 0.032211 0.21119 8 0 109s 0.084360 4.908756 0.00166213 0.032211 0.21119 2 0 109s 109s > 109s > options(old) 109s > 109s BEGIN TEST tests.etm.R 109s 109s R version 4.3.2 (2023-10-31) -- "Eye Holes" 109s Copyright (C) 2023 The R Foundation for Statistical Computing 109s Platform: x86_64-pc-linux-gnu (64-bit) 109s 109s R is free software and comes with ABSOLUTELY NO WARRANTY. 109s You are welcome to redistribute it under certain conditions. 109s Type 'license()' or 'licence()' for distribution details. 109s 109s R is a collaborative project with many contributors. 109s Type 'contributors()' for more information and 109s 'citation()' on how to cite R or R packages in publications. 109s 109s Type 'demo()' for some demos, 'help()' for on-line help, or 109s 'help.start()' for an HTML browser interface to help. 109s Type 'q()' to quit R. 109s 109s > require(etm) 109s Loading required package: etm 110s > 110s > ## Print with a bit less precision to avoid lots of notes in the comparison 110s > old <- options(digits = 4) 110s > 110s > ### Simple test 110s > 110s > time <- id <- 1:10 110s > from <- rep(0, 10) 110s > to <- rep(1, 10) 110s > 110s > data1 <- data.frame(id, from, to, time) 110s > tra1 <- matrix(FALSE, 2, 2) 110s > tra1[1, 2] <- TRUE 110s > 110s > etm1 <- etm(data1, c("0", "1"), tra1, NULL, 0) 110s > 110s > all.equal(as.vector(trprob(etm1, "0 0")), cumprod((10:1 - 1) / (10:1))) 110s [1] TRUE 110s > 110s > etm1$cov["0 0", "0 0", ] 110s 1 2 3 4 5 6 7 8 9 10 110s 0.009 0.016 0.021 0.024 0.025 0.024 0.021 0.016 0.009 0.000 110s > 110s > all.equal(etm1$cov["0 0", "0 0",], trcov(etm1, "0 0")) 110s [1] TRUE 110s > 110s > ### A simple test from AHR's author, where the first time is censored 110s > if (!require(survival)) { 110s + stop("This test requires the survival package") 110s + } 110s Loading required package: survival 110s > 110s > data <- data.frame(id=1:10, time=1:10, from=0, to=1, status=TRUE) 110s > 110s > tra <- matrix(FALSE, nrow=2, ncol=2) 110s > tra[1, 2] <- TRUE 110s > 110s > data$to[1] <- "cens" 110s > data$status[1] <- FALSE 110s > 110s > fit.km <- survfit(Surv(time, status) ~ 1, data=data) 110s > fit.etm <- etm(data, c("0","1"), tra, "cens", s=0, t="last", covariance=FALSE) 110s > 110s > all.equal(fit.km$surv[data$status], fit.etm$est[1,1,], check.attributes = FALSE) 110s [1] TRUE 110s > 110s > data$to[2] <- "cens" 110s > data$status[2] <- FALSE 110s > 110s > fit.km <- survfit(Surv(time, status) ~ 1, data=data) 110s > fit.etm <- etm(data, c("0","1"), tra, "cens", s=0, t="last", covariance=FALSE) 110s > 110s > all.equal(fit.km$surv[data$status], fit.etm$est[1,1,], check.attributes = FALSE) 110s [1] TRUE 110s > 110s > ### a bit more complicated 110s > 110s > time <- id <- 1:10 110s > from <- rep(0, 10) 110s > to <- rep(c(1, 2), 5) 110s > data2 <- data.frame(id, from, to, time) 110s > 110s > tra2 <- matrix(FALSE, 3, 3) 110s > tra2[1, 2:3] <- TRUE 110s > 110s > etm2 <- etm(data2, c("0", "1", "2"), tra2, NULL, 0) 110s > 110s > aa <- table(time, to) 110s > 110s > cif1 <- cumsum(aa[, 1] / 10) 110s > cif2 <- cumsum(aa[, 2] / 10) 110s > surv <- cumprod((10:1 - 1) / (10:1)) 110s > 110s > all.equal(trprob(etm2, "0 1"), cif1) 110s [1] TRUE 110s > all.equal(trprob(etm2, "0 2"), cif2) 110s [1] TRUE 110s > all.equal(as.vector(trprob(etm2, "0 0")), surv) 110s [1] TRUE 110s > 110s > ## a test on id 110s > data2$id <- letters[1:10] 110s > 110s > etm3 <- etm(data2, c("0", "1", "2"), tra2, NULL, 0) 110s > 110s > all.equal(trprob(etm2, "0 1"), trprob(etm3, "0 1")) 110s [1] TRUE 110s > all.equal(trprob(etm2, "0 2"), trprob(etm3, "0 2")) 110s [1] TRUE 110s > all.equal(trprob(etm2, "0 0"), trprob(etm3, "0 0")) 110s [1] TRUE 110s > 110s > 110s > ### Test on sir.cont 110s > 110s > data(sir.cont) 110s > 110s > ## Modification for patients entering and leaving a state 110s > ## at the same date 110s > ## Change on ventilation status is considered 110s > ## to happen before end of hospital stay 110s > sir.cont <- sir.cont[order(sir.cont$id, sir.cont$time), ] 110s > for (i in 2:nrow(sir.cont)) { 110s + if (sir.cont$id[i]==sir.cont$id[i-1]) { 110s + if (sir.cont$time[i]==sir.cont$time[i-1]) { 110s + sir.cont$time[i-1] <- sir.cont$time[i-1] - 0.5 110s + } 110s + } 110s + } 110s > 110s > ### Computation of the transition probabilities 110s > ## Possible transitions. 110s > tra <- matrix(ncol=3,nrow=3,FALSE) 110s > tra[1, 2:3] <- TRUE 110s > tra[2, c(1, 3)] <- TRUE 110s > 110s > ## etm 110s > prob.sir <- etm(sir.cont, c("0", "1", "2"), tra, "cens", 1) 110s > 110s > prob.sir 110s Multistate model with 2 transient state(s) 110s and 1 absorbing state(s) 110s 110s Possible transitions: 110s from to 110s 0 1 110s 0 2 110s 1 0 110s 1 2 110s 110s Estimate of P(1, 183) 110s 0 1 2 110s 0 0 0 1 110s 1 0 0 1 110s 2 0 0 1 110s 110s > 110s > summ.sir <- summary(prob.sir) 110s > all.equal(summ.sir[['0 1']]$P, as.vector(trprob(prob.sir, "0 1"))) 110s [1] TRUE 110s > subset(summ.sir[[3]],time<183) # issue with precision on different architectures 110s P time var lower upper n.risk n.event 110s 1.5 0.0000 1.5 0.000e+00 0.00000 0.0000 394 0 110s 2 0.1187 2.0 2.641e-04 0.08683 0.1505 396 47 110s 2.5 0.1187 2.5 2.641e-04 0.08683 0.1505 364 0 110s 3 0.2454 3.0 4.465e-04 0.20398 0.2868 365 54 110s 3.5 0.2454 3.5 4.465e-04 0.20398 0.2868 328 0 110s 4 0.3806 4.0 5.416e-04 0.33501 0.4262 331 62 110s 4.5 0.3806 4.5 5.416e-04 0.33501 0.4262 280 0 110s 5 0.4792 5.0 5.480e-04 0.43333 0.5251 283 48 110s 5.5 0.4792 5.5 5.480e-04 0.43333 0.5251 248 0 110s 6 0.5693 6.0 5.141e-04 0.52482 0.6137 249 47 110s 7 0.6350 7.0 4.665e-04 0.59266 0.6773 212 36 110s 8 0.6795 8.0 4.202e-04 0.63931 0.7197 195 27 110s 8.5 0.6795 8.5 4.202e-04 0.63931 0.7197 172 0 110s 9 0.7325 9.0 3.580e-04 0.69541 0.7696 173 34 110s 10 0.7647 10.0 3.141e-04 0.72992 0.7994 148 21 110s 10.5 0.7647 10.5 3.141e-04 0.72992 0.7994 135 0 110s 11 0.7895 11.0 2.790e-04 0.75674 0.8222 136 18 110s 12 0.8138 12.0 2.420e-04 0.78330 0.8443 129 18 110s 12.5 0.8138 12.5 2.420e-04 0.78330 0.8443 117 0 110s 13 0.8294 13.0 2.182e-04 0.80045 0.8584 118 13 110s 14 0.8452 14.0 1.938e-04 0.81789 0.8725 115 14 110s 15 0.8625 15.0 1.670e-04 0.83714 0.8878 106 15 110s 16 0.8723 16.0 1.522e-04 0.84807 0.8964 93 9 110s 17 0.8852 17.0 1.330e-04 0.86256 0.9078 86 12 110s 17.5 0.8852 17.5 1.330e-04 0.86256 0.9078 77 0 110s 18 0.8960 18.0 1.168e-04 0.87484 0.9172 76 9 110s 19 0.9029 19.0 1.070e-04 0.88261 0.9232 71 7 110s 20 0.9125 20.0 9.367e-05 0.89356 0.9315 64 10 110s 21 0.9161 21.0 8.878e-05 0.89768 0.9346 57 4 110s 22 0.9226 22.0 7.996e-05 0.90504 0.9401 55 6 110s 23 0.9261 23.0 7.537e-05 0.90904 0.9431 51 4 110s 23.5 0.9261 23.5 7.537e-05 0.90904 0.9431 49 0 110s 24 0.9354 24.0 6.292e-05 0.91982 0.9509 50 9 110s 25 0.9385 25.0 5.878e-05 0.92352 0.9536 42 3 110s 26 0.9429 26.0 5.326e-05 0.92863 0.9572 39 5 110s 27 0.9477 27.0 4.749e-05 0.93417 0.9612 35 6 110s 27.5 0.9477 27.5 4.749e-05 0.93417 0.9612 29 0 110s 28 0.9531 28.0 4.093e-05 0.94059 0.9657 30 5 110s 29 0.9567 29.0 3.668e-05 0.94485 0.9686 31 4 110s 30 0.9592 30.0 3.384e-05 0.94779 0.9706 28 3 110s 30.5 0.9592 30.5 3.384e-05 0.94779 0.9706 29 0 110s 31 0.9642 31.0 2.821e-05 0.95383 0.9746 30 6 110s 32 0.9649 32.0 2.752e-05 0.95458 0.9751 25 1 110s 33 0.9669 33.0 2.533e-05 0.95708 0.9768 24 2 110s 34 0.9685 34.0 2.368e-05 0.95900 0.9781 26 2 110s 35 0.9697 35.0 2.252e-05 0.96036 0.9790 28 2 110s 36 0.9702 36.0 2.194e-05 0.96104 0.9794 26 1 110s 37 0.9718 37.0 2.043e-05 0.96290 0.9806 26 2 110s 38 0.9739 38.0 1.831e-05 0.96555 0.9823 25 4 110s 38.5 0.9739 38.5 1.831e-05 0.96555 0.9823 21 0 110s 39 0.9760 39.0 1.643e-05 0.96802 0.9839 23 3 110s 40 0.9769 40.0 1.558e-05 0.96918 0.9847 19 1 110s 41 0.9774 41.0 1.512e-05 0.96981 0.9851 22 1 110s 42 0.9779 42.0 1.476e-05 0.97032 0.9854 22 0 110s 43 0.9798 43.0 1.308e-05 0.97271 0.9869 22 3 110s 44 0.9803 44.0 1.265e-05 0.97333 0.9873 21 1 110s 45 0.9817 45.0 1.157e-05 0.97499 0.9883 19 1 110s 46 0.9822 46.0 1.116e-05 0.97561 0.9887 17 1 110s 47 0.9831 47.0 1.037e-05 0.97683 0.9895 18 2 110s 48 0.9836 48.0 9.987e-06 0.97743 0.9898 17 1 110s 49 0.9841 49.0 9.669e-06 0.97796 0.9901 17 0 110s 50 0.9845 50.0 9.297e-06 0.97856 0.9905 17 1 110s 50.5 0.9845 50.5 9.297e-06 0.97856 0.9905 16 0 110s 51 0.9860 51.0 8.214e-06 0.98037 0.9916 17 3 110s 52 0.9870 52.0 7.513e-06 0.98159 0.9923 14 2 110s 53 0.9879 53.0 6.875e-06 0.98276 0.9930 12 1 110s 54 0.9889 54.0 6.214e-06 0.98397 0.9937 12 2 110s 55 0.9903 55.0 5.254e-06 0.98581 0.9948 10 3 110s 56 0.9913 56.0 4.667e-06 0.98703 0.9955 6 1 110s 57 0.9917 57.0 4.364e-06 0.98765 0.9958 5 1 110s 58 0.9922 58.0 4.064e-06 0.98828 0.9962 4 1 110s 59 0.9927 59.0 3.769e-06 0.98891 0.9965 3 1 110s 60 0.9932 60.0 3.488e-06 0.98953 0.9969 3 1 110s 62 0.9937 62.0 3.230e-06 0.99016 0.9972 2 0 110s 63 0.9942 63.0 2.956e-06 0.99079 0.9975 2 1 110s 68 0.9942 68.0 2.956e-06 0.99079 0.9975 1 0 110s 70 0.9946 70.0 2.694e-06 0.99143 0.9979 2 1 110s 78 0.9951 78.0 2.442e-06 0.99207 0.9982 1 0 110s 80 0.9951 80.0 2.442e-06 0.99207 0.9982 1 0 110s 85 0.9966 85.0 1.695e-06 0.99404 0.9991 2 0 110s 89 0.9966 89.0 1.695e-06 0.99404 0.9991 2 0 110s 90 0.9966 90.0 1.695e-06 0.99404 0.9991 1 0 110s 95 0.9971 95.0 1.448e-06 0.99472 0.9994 2 0 110s 100 0.9976 100.0 1.203e-06 0.99542 0.9997 3 0 110s 101 0.9981 101.0 9.592e-07 0.99613 1.0000 3 1 110s 108 0.9985 108.0 7.169e-07 0.99688 1.0000 2 1 110s 113 0.9990 113.0 4.764e-07 0.99767 1.0000 1 0 110s 116 0.9990 116.0 4.764e-07 0.99767 1.0000 1 0 110s 124 0.9990 124.0 4.764e-07 0.99767 1.0000 2 0 110s 164 0.9990 164.0 4.764e-07 0.99767 1.0000 0 0 110s > 110s > ## gonna play a bit with the state names 110s > dd <- sir.cont 110s > dd$from <- ifelse(dd$from == 0, "initial state", "ventilation") 110s > dd$to <- as.character(dd$to) 110s > for (i in seq_len(nrow(dd))) { 110s + dd$to[i] <- switch(dd$to[i], 110s + "0" = "initial state", 110s + "1" = "ventilation", 110s + "2" = "end of story", 110s + "cens" = "cens" 110s + ) 110s + } 110s > 110s > test <- etm(dd, c("initial state", "ventilation", "end of story"), tra, "cens", 1) 111s > 111s > all.equal(test$est["initial state", "initial state", ], 111s + prob.sir$est["0", "0", ]) 111s [1] TRUE 111s > all.equal(trprob(test, "initial state initial state"), trprob(prob.sir, "0 0")) 111s [1] TRUE 111s > all.equal(trprob(test, "initial state ventilation"), trprob(prob.sir, "0 1")) 111s [1] TRUE 111s > all.equal(trprob(test, "initial state end of story"), trprob(prob.sir, "0 2")) 111s [1] TRUE 111s > 111s > all.equal(trcov(test, "initial state end of story"), trcov(prob.sir, "0 2")) 111s [1] TRUE 111s > 111s > aa <- summary(test) 111s > all.equal(summ.sir[[6]], aa[[6]]) 111s [1] TRUE 111s > all.equal(summ.sir[[4]], aa[[4]]) 111s [1] TRUE 111s > 111s > ### Test on abortion data 111s > 111s > data(abortion) 111s > 111s > from <- rep(0, nrow(abortion)) 111s > to <- abortion$cause 111s > entry <- abortion$entry 111s > exit <- abortion$exit 111s > id <- 1:nrow(abortion) 111s > data <- data.frame(id, from, to, entry, exit, group = abortion$group) 111s > 111s > ## Computation of the CIFs 111s > tra <- matrix(FALSE, 4, 4) 111s > tra[1, 2:4] <- TRUE 111s > 111s > cif.control <- etm(data[data$group == 0, ], c("0", "1", "2", "3"), 111s + tra, NULL, 0) 111s > cif.exposed <- etm(data[data$group == 1, ], c("0", "1", "2", "3"), 111s + tra, NULL, 0) 111s > 111s > all.equal(trprob(cif.control, "0 1"), cif.control$est["0", "1", ]) 111s [1] TRUE 111s > all.equal(trcov(cif.control, c("0 1", "0 2")), cif.control$cov["0 1", "0 2", ]) 111s [1] TRUE 111s > 111s > trprob(cif.control, "0 1") 111s 6 7 8 9 10 11 12 13 111s 0.000000 0.007401 0.014881 0.026509 0.033208 0.037694 0.037694 0.038955 111s 14 17 19 21 24 25 26 30 111s 0.040159 0.040159 0.040159 0.040159 0.040159 0.040159 0.040159 0.040159 111s 31 32 33 34 35 36 37 38 111s 0.040159 0.040159 0.040159 0.040159 0.040159 0.040159 0.040159 0.040159 111s 39 40 41 42 43 111s 0.040159 0.040159 0.040159 0.040159 0.040159 111s > trprob(cif.control, "0 2") 111s 6 7 8 9 10 11 12 13 111s 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 111s 14 17 19 21 24 25 26 30 111s 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.003657 111s 31 32 33 34 35 36 37 38 111s 0.006371 0.008175 0.013543 0.023317 0.031260 0.053197 0.084529 0.179163 111s 39 40 41 42 43 111s 0.322016 0.563121 0.742227 0.793893 0.799059 111s > trprob(cif.control, "0 0") 111s 6 7 8 9 10 11 12 13 111s 0.965812 0.932508 0.887628 0.862433 0.838989 0.822538 0.813099 0.810578 111s 14 17 19 21 24 25 26 30 111s 0.806964 0.805874 0.803810 0.802804 0.801837 0.800883 0.799937 0.796280 111s 31 32 33 34 35 36 37 38 111s 0.793565 0.791762 0.786394 0.776620 0.768677 0.745862 0.714531 0.619897 111s 39 40 41 42 43 111s 0.477043 0.235938 0.056832 0.005167 0.000000 111s > 111s > trcov(cif.control, "0 1") 111s 6 7 8 9 10 11 12 13 111s 0.000e+00 2.719e-05 4.533e-05 6.665e-05 7.698e-05 8.304e-05 8.304e-05 8.444e-05 111s 14 17 19 21 24 25 26 30 111s 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 111s 31 32 33 34 35 36 37 38 111s 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 111s 39 40 41 42 43 111s 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 111s > trcov(cif.control, "0 2") 111s 6 7 8 9 10 11 12 13 111s 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 111s 14 17 19 21 24 25 26 30 111s 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 3.338e-06 111s 31 32 33 34 35 36 37 38 111s 5.784e-06 7.401e-06 1.216e-05 2.072e-05 2.758e-05 4.619e-05 7.202e-05 1.461e-04 111s 39 40 41 42 43 111s 2.470e-04 3.880e-04 4.702e-04 4.903e-04 4.922e-04 111s > trcov(cif.control, "0 0") 111s 6 7 8 9 10 11 12 13 111s 2.822e-04 3.821e-04 4.527e-04 4.748e-04 4.875e-04 4.927e-04 4.941e-04 4.942e-04 111s 14 17 19 21 24 25 26 30 111s 4.941e-04 4.940e-04 4.936e-04 4.933e-04 4.931e-04 4.928e-04 4.926e-04 4.914e-04 111s 31 32 33 34 35 36 37 38 111s 4.905e-04 4.899e-04 4.880e-04 4.846e-04 4.816e-04 4.729e-04 4.601e-04 4.176e-04 111s 39 40 41 42 43 111s 3.425e-04 1.865e-04 4.797e-05 4.441e-06 0.000e+00 111s > 111s > aa <- summary(cif.control) 111s > aa$"0 1" 111s P time var lower upper n.risk n.event 111s 6 0.000000 6 0.000e+00 0.000000 0.00000 117 0 111s 7 0.007401 7 2.719e-05 0.000000 0.01762 261 2 111s 8 0.014881 8 4.533e-05 0.001685 0.02808 374 3 111s 9 0.026509 9 6.665e-05 0.010508 0.04251 458 6 111s 10 0.033208 10 7.698e-05 0.016011 0.05040 515 4 111s 11 0.037694 11 8.304e-05 0.019834 0.05555 561 3 111s 12 0.037694 12 8.304e-05 0.019834 0.05555 610 0 111s 13 0.038955 13 8.444e-05 0.020944 0.05697 645 1 111s 14 0.040159 14 8.571e-05 0.022014 0.05830 673 1 111s 17 0.040159 17 8.571e-05 0.022014 0.05830 740 0 111s 19 0.040159 19 8.571e-05 0.022014 0.05830 781 0 111s 21 0.040159 21 8.571e-05 0.022014 0.05830 799 0 111s 24 0.040159 24 8.571e-05 0.022014 0.05830 830 0 111s 25 0.040159 25 8.571e-05 0.022014 0.05830 841 0 111s 26 0.040159 26 8.571e-05 0.022014 0.05830 846 0 111s 30 0.040159 30 8.571e-05 0.022014 0.05830 875 0 111s 31 0.040159 31 8.571e-05 0.022014 0.05830 880 0 111s 32 0.040159 32 8.571e-05 0.022014 0.05830 880 0 111s 33 0.040159 33 8.571e-05 0.022014 0.05830 885 0 111s 34 0.040159 34 8.571e-05 0.022014 0.05830 885 0 111s 35 0.040159 35 8.571e-05 0.022014 0.05830 880 0 111s 36 0.040159 36 8.571e-05 0.022014 0.05830 876 0 111s 37 0.040159 37 8.571e-05 0.022014 0.05830 857 0 111s 38 0.040159 38 8.571e-05 0.022014 0.05830 823 0 111s 39 0.040159 39 8.571e-05 0.022014 0.05830 716 0 111s 40 0.040159 40 8.571e-05 0.022014 0.05830 554 0 111s 41 0.040159 41 8.571e-05 0.022014 0.05830 274 0 111s 42 0.040159 42 8.571e-05 0.022014 0.05830 66 0 111s 43 0.040159 43 8.571e-05 0.022014 0.05830 6 0 111s > all.equal(aa$"0 1"$P, as.vector(trprob(cif.control, "0 1"))) 111s [1] TRUE 111s > 111s > ### test on los data 111s > 111s > data(los.data) # in package changeLOS 111s > 111s > ## putting los.data in the long format (see changeLOS) 111s > my.observ <- prepare.los.data(x=los.data) 111s > 111s > tra <- matrix(FALSE, 4, 4) 111s > tra[1, 2:4] <- TRUE 111s > tra[2, 3:4] <- TRUE 111s > 111s > tr.prob <- etm(my.observ, c("0","1","2","3"), tra, NULL, 0) 111s > 111s > tr.prob 111s Multistate model with 2 transient state(s) 111s and 2 absorbing state(s) 111s 111s Possible transitions: 111s from to 111s 0 1 111s 0 2 111s 0 3 111s 1 2 111s 1 3 111s 111s Estimate of P(0, 82) 111s 0 1 2 3 111s 0 0 0 0.7474 0.2526 111s 1 0 0 0.7073 0.2927 111s 2 0 0 1.0000 0.0000 111s 3 0 0 0.0000 1.0000 111s 111s > summary(tr.prob) 111s Transition 0 0 111s P time var lower upper n.risk n.event 111s 0.882275 3 1.374e-04 0.8593018 0.905248 756 0 111s 0.112434 15 1.320e-04 0.0899155 0.134952 90 0 111s 0.031746 27 4.066e-05 0.0192484 0.044244 26 0 111s 0.006614 41 8.690e-06 0.0008359 0.012392 5 0 111s 0.002646 61 3.490e-06 0.0000000 0.006307 3 0 111s 0.000000 82 0.000e+00 0.0000000 0.000000 1 0 111s 111s Transition 0 1 111s P time var lower upper n.risk n.event 111s 0.017196 3 2.235e-05 0.0079289 0.02646 756 13 111s 0.063492 15 7.865e-05 0.0461099 0.08087 90 0 111s 0.030423 27 3.902e-05 0.0181805 0.04267 26 1 111s 0.015873 41 2.066e-05 0.0069637 0.02478 5 0 111s 0.005291 61 6.962e-06 0.0001197 0.01046 3 0 111s 0.000000 82 0.000e+00 0.0000000 0.00000 1 0 111s 111s Transition 0 2 111s P time var lower upper n.risk n.event 111s 0.08466 3 0.0001025 0.06481 0.1045 756 64 111s 0.62302 15 0.0003107 0.58847 0.6576 90 4 111s 0.69841 27 0.0002786 0.66570 0.7311 26 1 111s 0.72751 41 0.0002622 0.69578 0.7593 5 0 111s 0.74074 61 0.0002540 0.70950 0.7720 3 1 111s 0.74735 82 0.0002498 0.71638 0.7783 1 1 111s 111s Transition 0 3 111s P time var lower upper n.risk n.event 111s 0.01587 3 2.066e-05 0.006964 0.02478 756 12 111s 0.20106 15 2.125e-04 0.172489 0.22963 90 1 111s 0.23942 27 2.409e-04 0.208999 0.26984 26 0 111s 0.25000 41 2.480e-04 0.219133 0.28087 5 0 111s 0.25132 61 2.489e-04 0.220402 0.28224 3 0 111s 0.25265 82 2.498e-04 0.221671 0.28362 1 0 111s 111s Transition 1 1 111s P time var lower upper n.risk n.event 111s 1.00000 3 0.000e+00 1.00000 1.00000 0 0 111s 0.38661 15 2.358e-03 0.29143 0.48179 51 0 111s 0.12119 27 7.842e-04 0.06630 0.17607 23 0 111s 0.04593 41 2.405e-04 0.01554 0.07633 14 0 111s 0.01531 61 6.579e-05 0.00000 0.03121 4 0 111s 0.00000 82 0.000e+00 0.00000 0.00000 0 0 111s 111s Transition 1 2 111s P time var lower upper n.risk n.event 111s 0.0000 3 0.000000 0.0000 0.0000 0 0 111s 0.4107 15 0.002590 0.3110 0.5104 51 2 111s 0.6082 27 0.002254 0.5151 0.7012 23 1 111s 0.6652 41 0.002064 0.5761 0.7542 14 2 111s 0.6920 61 0.002000 0.6043 0.7796 4 0 111s 0.7073 82 0.001984 0.6200 0.7946 0 0 111s 111s Transition 1 3 111s P time var lower upper n.risk n.event 111s 0.0000 3 0.000000 0.0000 0.0000 0 0 111s 0.2027 15 0.001784 0.1199 0.2855 51 1 111s 0.2706 27 0.001968 0.1837 0.3576 23 0 111s 0.2889 41 0.001982 0.2016 0.3761 14 0 111s 0.2927 61 0.001984 0.2054 0.3800 4 0 111s 0.2927 82 0.001984 0.2054 0.3800 0 0 111s 111s > 111s > cLOS <- etm::clos(tr.prob, aw = TRUE) 111s > 111s > cLOS 111s The expected change in length of stay is: 111s 1.975 111s 111s Alternative weighting: 111s 111s Expected change in LOS with weight.1: 2.097 111s Expected change in LOS with weight.other: 1.951 111s > 111s > 111s > ### Tests on pseudo values 111s > t_pseudo <- closPseudo(my.observ, c("0","1","2","3"), tra, NULL, 111s + formula = ~ 1, aw = TRUE) 123s > 123s > cLOS$e.phi == t_pseudo$theta[, "e.phi"] 123s [,1] 123s [1,] TRUE 123s > cLOS$e.phi.weights.1 == t_pseudo$theta[, "e.phi.weights.1"] 123s [,1] 123s [1,] TRUE 123s > cLOS$e.phi.weights.other == t_pseudo$theta[, "e.phi.weights.other"] 123s [,1] 123s [1,] TRUE 123s > 123s > mean(t_pseudo$pseudoData$ps.e.phi) 123s [1] 1.968 123s > 123s > ### tests on etmprep 123s > 123s > ### creation of fake data in the wild format, following an illness-death model 123s > ## transition times 123s > tdisease <- c(3, 4, 3, 6, 8, 9) 123s > tdeath <- c(6, 9, 8, 6, 8, 9) 123s > 123s > ## transition status 123s > stat.disease <- c(1, 1, 1, 0, 0, 0) 123s > stat.death <- c(1, 1, 1, 1, 1, 0) 123s > 123s > ## a covariate that we want to keep in the new data 123s > set.seed(1313) 123s > cova <- rbinom(6, 1, 0.5) 123s > 123s > dat <- data.frame(tdisease, tdeath, 123s + stat.disease, stat.death, 123s + cova) 123s > 123s > ## Possible transitions 123s > tra <- matrix(FALSE, 3, 3) 123s > tra[1, 2:3] <- TRUE 123s > tra[2, 3] <- TRUE 123s > 123s > ## data preparation 123s > newdat <- etmprep(c(NA, "tdisease", "tdeath"), 123s + c(NA, "stat.disease", "stat.death"), 123s + data = dat, tra = tra, 123s + cens.name = "cens", keep = "cova") 123s > 123s > newdat 123s id entry exit from to cova 123s 1 1 0 3 0 1 1 123s 2 1 3 6 1 2 1 123s 3 2 0 4 0 1 0 123s 4 2 4 9 1 2 0 123s 5 3 0 3 0 1 1 123s 6 3 3 8 1 2 1 123s 7 4 0 6 0 2 0 123s 8 5 0 8 0 2 1 123s 9 6 0 9 0 cens 1 123s > 123s > ref <- data.frame(id = c(1, 1, 2, 2, 3, 3, 4, 5, 6), 123s + entry = c(0, 3, 0, 4, 0, 3, 0, 0, 0), 123s + exit = c(3, 6, 4, 9, 3, 8, 6, 8, 9), 123s + from = c(0, 1, 0, 1, 0, 1, 0, 0, 0), 123s + to = c(rep(c(1, 2), 3), 2, 2, "cens"), 123s + cova = c(1, 1, 0, 0, 1, 1, 0, 1, 1)) 123s > ref$from <- factor(as.character(ref$from), levels = c("0", "1", "2", "cens")) 123s > ref$to <- factor(as.character(ref$to), levels = c("0", "1", "2", "cens")) 123s > 123s > all.equal(ref, newdat) 123s [1] TRUE 123s > 123s > 123s > ###################################### 123s > ### Test the stratified calls 123s > ###################################### 123s > 123s > if (require("kmi", quietly = TRUE)) { 123s + library(etm) 123s + 123s + data(icu.pneu) 123s + my.icu.pneu <- icu.pneu 123s + 123s + my.icu.pneu <- my.icu.pneu[order(my.icu.pneu$id, my.icu.pneu$start), ] 123s + masque <- diff(my.icu.pneu$id) 123s + 123s + my.icu.pneu$from <- 0 123s + my.icu.pneu$from[c(1, masque) == 0] <- 1 123s + 123s + my.icu.pneu$to2 <- my.icu.pneu$event 123s + my.icu.pneu$to2[my.icu.pneu$status == 0] <- "cens" 123s + my.icu.pneu$to2[c(masque, 1) == 0] <- 1 123s + 123s + 123s + my.icu.pneu$to <- ifelse(my.icu.pneu$to2 %in% c(2, 3), 2, 123s + my.icu.pneu$to2) 123s + 123s + my.icu.pneu <- my.icu.pneu[, c("id", "start", "stop", "from", "to", 123s + "to2", "age", "sex")] 123s + names(my.icu.pneu)[c(2, 3)] <- c("entry", "exit") 123s + 123s + bouh_strat <- etm(my.icu.pneu, c("0", "1", "2"), tra_ill(), "cens", 0, strata = "sex") 123s + 123s + bouh_female <- etm(my.icu.pneu[my.icu.pneu$sex == "F", ], 123s + c("0", "1", "2"), tra_ill(), "cens", 0) 123s + 123s + all(bouh_strat[[1]]$est == bouh_female$est) 123s + 123s + ## Test the summary 123s + the_summary <- summary(bouh_strat) 123s + the_summary 123s + 123s + ## Test trprob 123s + all(trprob(bouh_strat, "0 1")[[1]] == trprob(bouh_female, "0 1")) 123s + all(trprob(bouh_strat, "0 1", c(0, 5, 10, 15))[[1]] == trprob(bouh_female, "0 1", c(0, 5, 10, 15))) 123s + 123s + ## Test trcov 123s + all(trcov(bouh_strat, "0 1")[[1]] == trcov(bouh_female, "0 1")) 123s + all(trcov(bouh_strat, c("0 1", "0 2"))[[1]] == trcov(bouh_female, c("0 1", "0 2"))) 123s + all(trcov(bouh_strat, "0 1", c(0, 5, 10, 15))[[1]] == trcov(bouh_female, "0 1", c(0, 5, 10, 15))) 123s + } else { 123s + print("These tests require the kmi package") 123s + } 123s [1] TRUE 123s > 123s > options(old) 123s > 123s autopkgtest [13:06:58]: test run-unit-test: -----------------------] 123s autopkgtest [13:06:58]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 123s run-unit-test PASS 123s autopkgtest [13:06:58]: test pkg-r-autopkgtest: preparing testbed 132s Reading package lists... 132s Building dependency tree... 132s Reading state information... 132s Starting pkgProblemResolver with broken count: 0 132s Starting 2 pkgProblemResolver with broken count: 0 132s Done 133s The following additional packages will be installed: 133s build-essential cpp cpp-13 cpp-13-x86-64-linux-gnu cpp-x86-64-linux-gnu 133s dctrl-tools g++ g++-13 g++-13-x86-64-linux-gnu g++-x86-64-linux-gnu gcc 133s gcc-13 gcc-13-x86-64-linux-gnu gcc-x86-64-linux-gnu gfortran gfortran-13 133s gfortran-13-x86-64-linux-gnu gfortran-x86-64-linux-gnu icu-devtools libasan8 133s libatomic1 libblas-dev libbz2-dev libc-dev-bin libc6-dev libcc1-0 133s libcrypt-dev libgcc-13-dev libgfortran-13-dev libhwasan0 libicu-dev libisl23 133s libitm1 libjpeg-dev libjpeg-turbo8-dev libjpeg8-dev liblapack-dev liblsan0 133s liblzma-dev libmpc3 libncurses-dev libnsl-dev libpcre2-16-0 libpcre2-32-0 133s libpcre2-dev libpcre2-posix3 libpkgconf3 libpng-dev libquadmath0 133s libreadline-dev libstdc++-13-dev libtirpc-dev libtsan2 libubsan1 133s linux-libc-dev pkg-config pkg-r-autopkgtest pkgconf pkgconf-bin r-base-dev 133s r-cran-backports r-cran-broom r-cran-cli r-cran-colorspace r-cran-cpp11 133s r-cran-dplyr r-cran-ellipsis r-cran-fansi r-cran-farver r-cran-geepack 133s r-cran-generics r-cran-ggplot2 r-cran-glue r-cran-gtable r-cran-isoband 133s r-cran-labeling r-cran-lifecycle r-cran-magrittr r-cran-mass r-cran-mgcv 133s r-cran-munsell r-cran-nlme r-cran-pillar r-cran-pkgconfig r-cran-purrr 133s r-cran-r6 r-cran-rcolorbrewer r-cran-rlang r-cran-scales r-cran-stringi 133s r-cran-stringr r-cran-tibble r-cran-tidyr r-cran-tidyselect r-cran-utf8 133s r-cran-vctrs r-cran-viridislite r-cran-withr rpcsvc-proto zlib1g-dev 133s Suggested packages: 133s cpp-doc gcc-13-locales cpp-13-doc debtags g++-multilib g++-13-multilib 133s gcc-13-doc gcc-multilib manpages-dev autoconf automake libtool flex bison 133s gdb gcc-doc gcc-13-multilib gdb-x86-64-linux-gnu gfortran-multilib 133s gfortran-doc gfortran-13-multilib gfortran-13-doc libcoarrays-dev 133s liblapack-doc glibc-doc icu-doc liblzma-doc ncurses-doc readline-doc 133s libstdc++-13-doc texlive-base texlive-latex-base texlive-plain-generic 133s texlive-fonts-recommended texlive-fonts-extra texlive-extra-utils 133s texlive-latex-recommended texlive-latex-extra texinfo r-cran-aer 133s r-cran-bbmle r-cran-boot r-cran-car r-cran-cardata r-cran-caret 133s r-cran-cluster r-cran-cmprsk r-cran-coda r-cran-covr r-cran-e1071 133s r-cran-emmeans r-cran-epir r-cran-gam r-cran-gee r-cran-glmnet r-cran-gmm 133s r-cran-hmisc r-cran-irlba r-cran-interp r-cran-knitr r-cran-ks r-cran-lavaan 133s r-cran-leaps r-cran-lme4 r-cran-lmtest r-cran-lsmeans r-cran-maps 133s r-cran-mclust r-cran-metafor r-cran-modeldata r-cran-multcomp r-cran-network 133s r-cran-nnet r-cran-ordinal r-cran-plm r-cran-psych r-cran-quantreg 133s r-cran-rmarkdown r-cran-robust r-cran-robustbase r-cran-rsample 133s r-cran-sandwich r-cran-sp r-cran-spdep r-cran-spatialreg r-cran-spelling 133s r-cran-survey r-cran-systemfit r-cran-tseries r-cran-zoo r-cran-kernsmooth 133s r-cran-kernlab r-cran-mvtnorm r-cran-vcd r-cran-shiny r-cran-shinyjs 133s r-cran-png r-cran-jpeg r-cran-viridis r-cran-magick r-cran-sf r-cran-bit64 133s r-cran-formattable r-cran-nanotime r-cran-palmerpenguins r-cran-units 133s r-cran-vdiffr r-cran-testthat r-cran-bench r-cran-blob r-cran-brio 133s r-cran-callr r-cran-crayon r-cran-evaluate r-cran-here r-cran-hms 133s r-cran-htmltools r-cran-pkgbuild r-cran-pkgload 133s Recommended packages: 133s bzip2-doc manpages manpages-dev libc-devtools libpng-tools r-cran-testthat 133s r-cran-callr r-cran-covr r-cran-crayon r-cran-digest r-cran-htmltools 133s r-cran-htmlwidgets r-cran-knitr r-cran-mockery r-cran-processx r-cran-ps 133s r-cran-rmarkdown r-cran-rprojroot r-cran-rstudioapi r-cran-whoami 133s r-cran-bench r-cran-brio r-cran-decor r-cran-desc r-cran-lobstr 133s r-cran-progress r-cran-dbplyr r-cran-rmysql r-cran-rpostgresql 133s r-cran-rsqlite r-cran-unitizer r-cran-pkgload r-cran-hexbin r-cran-hmisc 133s r-cran-mapproj r-cran-maps r-cran-multcomp r-cran-profvis r-cran-quantreg 133s r-cran-ragg r-cran-rpart r-cran-sf r-cran-svglite r-cran-vdiffr r-cran-xml2 133s r-cran-waldo r-cran-lintr r-cran-tidyverse r-cran-lubridate r-cran-httr 133s r-cran-fs r-cran-usethis r-cran-bit64 r-cran-dichromat r-cran-hms 133s r-cran-mockr r-cran-formattable r-cran-readr r-cran-pkgdown r-cran-zeallot 133s The following NEW packages will be installed: 133s autopkgtest-satdep build-essential cpp cpp-13 cpp-13-x86-64-linux-gnu 133s cpp-x86-64-linux-gnu dctrl-tools g++ g++-13 g++-13-x86-64-linux-gnu 133s g++-x86-64-linux-gnu gcc gcc-13 gcc-13-x86-64-linux-gnu gcc-x86-64-linux-gnu 133s gfortran gfortran-13 gfortran-13-x86-64-linux-gnu gfortran-x86-64-linux-gnu 133s icu-devtools libasan8 libatomic1 libblas-dev libbz2-dev libc-dev-bin 133s libc6-dev libcc1-0 libcrypt-dev libgcc-13-dev libgfortran-13-dev libhwasan0 133s libicu-dev libisl23 libitm1 libjpeg-dev libjpeg-turbo8-dev libjpeg8-dev 133s liblapack-dev liblsan0 liblzma-dev libmpc3 libncurses-dev libnsl-dev 133s libpcre2-16-0 libpcre2-32-0 libpcre2-dev libpcre2-posix3 libpkgconf3 133s libpng-dev libquadmath0 libreadline-dev libstdc++-13-dev libtirpc-dev 133s libtsan2 libubsan1 linux-libc-dev pkg-config pkg-r-autopkgtest pkgconf 133s pkgconf-bin r-base-dev r-cran-backports r-cran-broom r-cran-cli 133s r-cran-colorspace r-cran-cpp11 r-cran-dplyr r-cran-ellipsis r-cran-fansi 133s r-cran-farver r-cran-geepack r-cran-generics r-cran-ggplot2 r-cran-glue 133s r-cran-gtable r-cran-isoband r-cran-labeling r-cran-lifecycle 133s r-cran-magrittr r-cran-mass r-cran-mgcv r-cran-munsell r-cran-nlme 133s r-cran-pillar r-cran-pkgconfig r-cran-purrr r-cran-r6 r-cran-rcolorbrewer 133s r-cran-rlang r-cran-scales r-cran-stringi r-cran-stringr r-cran-tibble 133s r-cran-tidyr r-cran-tidyselect r-cran-utf8 r-cran-vctrs r-cran-viridislite 133s r-cran-withr rpcsvc-proto zlib1g-dev 133s 0 upgraded, 101 newly installed, 0 to remove and 0 not upgraded. 133s Need to get 130 MB/130 MB of archives. 133s After this operation, 424 MB of additional disk space will be used. 133s Get:1 /tmp/autopkgtest.GQasZm/2-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [736 B] 133s Get:2 http://ftpmaster.internal/ubuntu noble/main amd64 libc-dev-bin amd64 2.39-0ubuntu2 [20.4 kB] 133s Get:3 http://ftpmaster.internal/ubuntu noble/main amd64 linux-libc-dev amd64 6.8.0-11.11 [1595 kB] 133s Get:4 http://ftpmaster.internal/ubuntu noble/main amd64 libcrypt-dev amd64 1:4.4.36-4 [128 kB] 133s Get:5 http://ftpmaster.internal/ubuntu noble/main amd64 libtirpc-dev amd64 1.3.4+ds-1build1 [222 kB] 133s Get:6 http://ftpmaster.internal/ubuntu noble/main amd64 libnsl-dev amd64 1.3.0-3 [71.2 kB] 133s Get:7 http://ftpmaster.internal/ubuntu noble/main amd64 rpcsvc-proto amd64 1.4.2-0ubuntu6 [68.5 kB] 133s Get:8 http://ftpmaster.internal/ubuntu noble/main amd64 libc6-dev amd64 2.39-0ubuntu2 [2126 kB] 133s Get:9 http://ftpmaster.internal/ubuntu noble/main amd64 libisl23 amd64 0.26-3 [741 kB] 133s Get:10 http://ftpmaster.internal/ubuntu noble/main amd64 libmpc3 amd64 1.3.1-1 [54.1 kB] 133s Get:11 http://ftpmaster.internal/ubuntu noble/main amd64 cpp-13-x86-64-linux-gnu amd64 13.2.0-17ubuntu2 [11.2 MB] 133s Get:12 http://ftpmaster.internal/ubuntu noble/main amd64 cpp-13 amd64 13.2.0-17ubuntu2 [1030 B] 133s Get:13 http://ftpmaster.internal/ubuntu noble/main amd64 cpp-x86-64-linux-gnu amd64 4:13.2.0-7ubuntu1 [5326 B] 133s Get:14 http://ftpmaster.internal/ubuntu noble/main amd64 cpp amd64 4:13.2.0-7ubuntu1 [22.4 kB] 133s Get:15 http://ftpmaster.internal/ubuntu noble/main amd64 libcc1-0 amd64 14-20240303-1ubuntu1 [47.7 kB] 133s Get:16 http://ftpmaster.internal/ubuntu noble/main amd64 libitm1 amd64 14-20240303-1ubuntu1 [29.1 kB] 133s Get:17 http://ftpmaster.internal/ubuntu noble/main amd64 libatomic1 amd64 14-20240303-1ubuntu1 [10.4 kB] 133s Get:18 http://ftpmaster.internal/ubuntu noble/main amd64 libasan8 amd64 14-20240303-1ubuntu1 [3026 kB] 133s Get:19 http://ftpmaster.internal/ubuntu noble/main amd64 liblsan0 amd64 14-20240303-1ubuntu1 [1310 kB] 133s Get:20 http://ftpmaster.internal/ubuntu noble/main amd64 libtsan2 amd64 14-20240303-1ubuntu1 [2732 kB] 133s Get:21 http://ftpmaster.internal/ubuntu noble/main amd64 libubsan1 amd64 14-20240303-1ubuntu1 [1172 kB] 133s Get:22 http://ftpmaster.internal/ubuntu noble/main amd64 libhwasan0 amd64 14-20240303-1ubuntu1 [1629 kB] 134s Get:23 http://ftpmaster.internal/ubuntu noble/main amd64 libquadmath0 amd64 14-20240303-1ubuntu1 [155 kB] 134s Get:24 http://ftpmaster.internal/ubuntu noble/main amd64 libgcc-13-dev amd64 13.2.0-17ubuntu2 [2687 kB] 134s Get:25 http://ftpmaster.internal/ubuntu noble/main amd64 gcc-13-x86-64-linux-gnu amd64 13.2.0-17ubuntu2 [21.9 MB] 134s Get:26 http://ftpmaster.internal/ubuntu noble/main amd64 gcc-13 amd64 13.2.0-17ubuntu2 [477 kB] 134s Get:27 http://ftpmaster.internal/ubuntu noble/main amd64 gcc-x86-64-linux-gnu amd64 4:13.2.0-7ubuntu1 [1212 B] 134s Get:28 http://ftpmaster.internal/ubuntu noble/main amd64 gcc amd64 4:13.2.0-7ubuntu1 [5018 B] 134s Get:29 http://ftpmaster.internal/ubuntu noble/main amd64 libstdc++-13-dev amd64 13.2.0-17ubuntu2 [2340 kB] 134s Get:30 http://ftpmaster.internal/ubuntu noble/main amd64 g++-13-x86-64-linux-gnu amd64 13.2.0-17ubuntu2 [12.5 MB] 134s Get:31 http://ftpmaster.internal/ubuntu noble/main amd64 g++-13 amd64 13.2.0-17ubuntu2 [14.5 kB] 134s Get:32 http://ftpmaster.internal/ubuntu noble/main amd64 g++-x86-64-linux-gnu amd64 4:13.2.0-7ubuntu1 [964 B] 134s Get:33 http://ftpmaster.internal/ubuntu noble/main amd64 g++ amd64 4:13.2.0-7ubuntu1 [1100 B] 134s Get:34 http://ftpmaster.internal/ubuntu noble/main amd64 build-essential amd64 12.10ubuntu1 [4928 B] 134s Get:35 http://ftpmaster.internal/ubuntu noble/main amd64 dctrl-tools amd64 2.24-3build2 [66.9 kB] 134s Get:36 http://ftpmaster.internal/ubuntu noble/main amd64 libgfortran-13-dev amd64 13.2.0-17ubuntu2 [942 kB] 134s Get:37 http://ftpmaster.internal/ubuntu noble/main amd64 gfortran-13-x86-64-linux-gnu amd64 13.2.0-17ubuntu2 [11.6 MB] 134s Get:38 http://ftpmaster.internal/ubuntu noble/main amd64 gfortran-13 amd64 13.2.0-17ubuntu2 [10.3 kB] 134s Get:39 http://ftpmaster.internal/ubuntu noble/main amd64 gfortran-x86-64-linux-gnu amd64 4:13.2.0-7ubuntu1 [1024 B] 134s Get:40 http://ftpmaster.internal/ubuntu noble/main amd64 gfortran amd64 4:13.2.0-7ubuntu1 [1176 B] 134s Get:41 http://ftpmaster.internal/ubuntu noble/main amd64 icu-devtools amd64 74.2-1ubuntu1 [212 kB] 134s Get:42 http://ftpmaster.internal/ubuntu noble/main amd64 libblas-dev amd64 3.12.0-3 [170 kB] 134s Get:43 http://ftpmaster.internal/ubuntu noble/main amd64 libbz2-dev amd64 1.0.8-5ubuntu1 [33.6 kB] 134s Get:44 http://ftpmaster.internal/ubuntu noble/main amd64 libicu-dev amd64 74.2-1ubuntu1 [11.9 MB] 134s Get:45 http://ftpmaster.internal/ubuntu noble/main amd64 libjpeg-turbo8-dev amd64 2.1.5-2ubuntu1 [294 kB] 134s Get:46 http://ftpmaster.internal/ubuntu noble/main amd64 libjpeg8-dev amd64 8c-2ubuntu11 [1484 B] 134s Get:47 http://ftpmaster.internal/ubuntu noble/main amd64 libjpeg-dev amd64 8c-2ubuntu11 [1482 B] 134s Get:48 http://ftpmaster.internal/ubuntu noble/main amd64 liblapack-dev amd64 3.12.0-3 [5196 kB] 134s Get:49 http://ftpmaster.internal/ubuntu noble/main amd64 libncurses-dev amd64 6.4+20240113-1ubuntu1 [384 kB] 134s Get:50 http://ftpmaster.internal/ubuntu noble/main amd64 libpcre2-16-0 amd64 10.42-4ubuntu1 [211 kB] 134s Get:51 http://ftpmaster.internal/ubuntu noble/main amd64 libpcre2-32-0 amd64 10.42-4ubuntu1 [198 kB] 134s Get:52 http://ftpmaster.internal/ubuntu noble/main amd64 libpcre2-posix3 amd64 10.42-4ubuntu1 [6808 B] 134s Get:53 http://ftpmaster.internal/ubuntu noble/main amd64 libpcre2-dev amd64 10.42-4ubuntu1 [743 kB] 134s Get:54 http://ftpmaster.internal/ubuntu noble/main amd64 libpkgconf3 amd64 1.8.1-2 [31.1 kB] 134s Get:55 http://ftpmaster.internal/ubuntu noble/main amd64 zlib1g-dev amd64 1:1.3.dfsg-3ubuntu1 [896 kB] 134s Get:56 http://ftpmaster.internal/ubuntu noble/main amd64 libpng-dev amd64 1.6.43-1 [264 kB] 134s Get:57 http://ftpmaster.internal/ubuntu noble/main amd64 libreadline-dev amd64 8.2-3 [167 kB] 134s Get:58 http://ftpmaster.internal/ubuntu noble/main amd64 pkgconf-bin amd64 1.8.1-2 [20.7 kB] 134s Get:59 http://ftpmaster.internal/ubuntu noble/main amd64 pkgconf amd64 1.8.1-2 [16.8 kB] 134s Get:60 http://ftpmaster.internal/ubuntu noble/main amd64 pkg-config amd64 1.8.1-2 [7170 B] 134s Get:61 http://ftpmaster.internal/ubuntu noble/main amd64 liblzma-dev amd64 5.4.5-0.3 [205 kB] 134s Get:62 http://ftpmaster.internal/ubuntu noble/universe amd64 r-base-dev all 4.3.2-1build1 [4336 B] 134s Get:63 http://ftpmaster.internal/ubuntu noble/universe amd64 pkg-r-autopkgtest all 20231212ubuntu1 [6448 B] 134s Get:64 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-backports amd64 1.4.1-1 [101 kB] 134s Get:65 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-cli amd64 3.6.2-1 [1380 kB] 134s Get:66 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-generics all 0.1.3-1 [81.3 kB] 134s Get:67 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-glue amd64 1.7.0-1 [154 kB] 134s Get:68 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-rlang amd64 1.1.3-1 [1663 kB] 134s Get:69 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB] 134s Get:70 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-magrittr amd64 2.0.3-1 [154 kB] 134s Get:71 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-fansi amd64 1.0.5-1 [619 kB] 134s Get:72 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-utf8 amd64 1.2.4-1 [140 kB] 134s Get:73 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-vctrs amd64 0.6.5-1 [1335 kB] 134s Get:74 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-pillar all 1.9.0+dfsg-1 [464 kB] 134s Get:75 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-r6 all 2.5.1-1 [99.0 kB] 134s Get:76 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-pkgconfig all 2.0.3-2build1 [19.7 kB] 134s Get:77 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-tibble amd64 3.2.1+dfsg-2 [415 kB] 134s Get:78 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-withr all 2.5.0-1 [225 kB] 134s Get:79 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-tidyselect amd64 1.2.0+dfsg-1 [218 kB] 134s Get:80 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-dplyr amd64 1.1.4-1 [1515 kB] 134s Get:81 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-ellipsis amd64 0.3.2-2 [35.6 kB] 134s Get:82 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-purrr amd64 1.0.2-1 [502 kB] 134s Get:83 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-stringi amd64 1.8.3-1 [873 kB] 134s Get:84 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-stringr all 1.5.1-1 [290 kB] 134s Get:85 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-cpp11 all 0.4.7-1 [266 kB] 134s Get:86 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-tidyr amd64 1.3.1-1 [1156 kB] 134s Get:87 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-broom all 1.0.5+dfsg-1 [1729 kB] 134s Get:88 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-colorspace amd64 2.1-0+dfsg-1 [1541 kB] 134s Get:89 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-farver amd64 2.1.1-1 [1353 kB] 134s Get:90 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-mass amd64 7.3-60.0.1-1 [1119 kB] 134s Get:91 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-geepack amd64 1.3.10-1 [377 kB] 134s Get:92 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-gtable all 0.3.4+dfsg-1 [191 kB] 134s Get:93 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-isoband amd64 0.2.7-1 [1481 kB] 134s Get:94 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-nlme amd64 3.1.164-1 [2260 kB] 134s Get:95 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-mgcv amd64 1.9-1-1 [3252 kB] 134s Get:96 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-labeling all 0.4.3-1 [62.1 kB] 134s Get:97 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-munsell all 0.5.0-2build1 [208 kB] 134s Get:98 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-rcolorbrewer all 1.1-3-1build1 [55.4 kB] 134s Get:99 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-viridislite all 0.4.2-2 [1088 kB] 134s Get:100 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-scales all 1.3.0-1 [603 kB] 134s Get:101 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-ggplot2 all 3.4.4+dfsg-1 [3411 kB] 135s Fetched 130 MB in 1s (111 MB/s) 135s Selecting previously unselected package libc-dev-bin. 135s (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 ... 76118 files and directories currently installed.) 135s Preparing to unpack .../000-libc-dev-bin_2.39-0ubuntu2_amd64.deb ... 135s Unpacking libc-dev-bin (2.39-0ubuntu2) ... 135s Selecting previously unselected package linux-libc-dev:amd64. 135s Preparing to unpack .../001-linux-libc-dev_6.8.0-11.11_amd64.deb ... 135s Unpacking linux-libc-dev:amd64 (6.8.0-11.11) ... 135s Selecting previously unselected package libcrypt-dev:amd64. 135s Preparing to unpack .../002-libcrypt-dev_1%3a4.4.36-4_amd64.deb ... 135s Unpacking libcrypt-dev:amd64 (1:4.4.36-4) ... 135s Selecting previously unselected package libtirpc-dev:amd64. 135s Preparing to unpack .../003-libtirpc-dev_1.3.4+ds-1build1_amd64.deb ... 135s Unpacking libtirpc-dev:amd64 (1.3.4+ds-1build1) ... 135s Selecting previously unselected package libnsl-dev:amd64. 135s Preparing to unpack .../004-libnsl-dev_1.3.0-3_amd64.deb ... 135s Unpacking libnsl-dev:amd64 (1.3.0-3) ... 135s Selecting previously unselected package rpcsvc-proto. 135s Preparing to unpack .../005-rpcsvc-proto_1.4.2-0ubuntu6_amd64.deb ... 135s Unpacking rpcsvc-proto (1.4.2-0ubuntu6) ... 135s Selecting previously unselected package libc6-dev:amd64. 135s Preparing to unpack .../006-libc6-dev_2.39-0ubuntu2_amd64.deb ... 135s Unpacking libc6-dev:amd64 (2.39-0ubuntu2) ... 135s Selecting previously unselected package libisl23:amd64. 135s Preparing to unpack .../007-libisl23_0.26-3_amd64.deb ... 135s Unpacking libisl23:amd64 (0.26-3) ... 135s Selecting previously unselected package libmpc3:amd64. 135s Preparing to unpack .../008-libmpc3_1.3.1-1_amd64.deb ... 135s Unpacking libmpc3:amd64 (1.3.1-1) ... 135s Selecting previously unselected package cpp-13-x86-64-linux-gnu. 135s Preparing to unpack .../009-cpp-13-x86-64-linux-gnu_13.2.0-17ubuntu2_amd64.deb ... 135s Unpacking cpp-13-x86-64-linux-gnu (13.2.0-17ubuntu2) ... 135s Selecting previously unselected package cpp-13. 135s Preparing to unpack .../010-cpp-13_13.2.0-17ubuntu2_amd64.deb ... 135s Unpacking cpp-13 (13.2.0-17ubuntu2) ... 136s Selecting previously unselected package cpp-x86-64-linux-gnu. 136s Preparing to unpack .../011-cpp-x86-64-linux-gnu_4%3a13.2.0-7ubuntu1_amd64.deb ... 136s Unpacking cpp-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ... 136s Selecting previously unselected package cpp. 136s Preparing to unpack .../012-cpp_4%3a13.2.0-7ubuntu1_amd64.deb ... 136s Unpacking cpp (4:13.2.0-7ubuntu1) ... 136s Selecting previously unselected package libcc1-0:amd64. 136s Preparing to unpack .../013-libcc1-0_14-20240303-1ubuntu1_amd64.deb ... 136s Unpacking libcc1-0:amd64 (14-20240303-1ubuntu1) ... 136s Selecting previously unselected package libitm1:amd64. 136s Preparing to unpack .../014-libitm1_14-20240303-1ubuntu1_amd64.deb ... 136s Unpacking libitm1:amd64 (14-20240303-1ubuntu1) ... 136s Selecting previously unselected package libatomic1:amd64. 136s Preparing to unpack .../015-libatomic1_14-20240303-1ubuntu1_amd64.deb ... 136s Unpacking libatomic1:amd64 (14-20240303-1ubuntu1) ... 136s Selecting previously unselected package libasan8:amd64. 136s Preparing to unpack .../016-libasan8_14-20240303-1ubuntu1_amd64.deb ... 136s Unpacking libasan8:amd64 (14-20240303-1ubuntu1) ... 136s Selecting previously unselected package liblsan0:amd64. 136s Preparing to unpack .../017-liblsan0_14-20240303-1ubuntu1_amd64.deb ... 136s Unpacking liblsan0:amd64 (14-20240303-1ubuntu1) ... 136s Selecting previously unselected package libtsan2:amd64. 136s Preparing to unpack .../018-libtsan2_14-20240303-1ubuntu1_amd64.deb ... 136s Unpacking libtsan2:amd64 (14-20240303-1ubuntu1) ... 136s Selecting previously unselected package libubsan1:amd64. 136s Preparing to unpack .../019-libubsan1_14-20240303-1ubuntu1_amd64.deb ... 136s Unpacking libubsan1:amd64 (14-20240303-1ubuntu1) ... 136s Selecting previously unselected package libhwasan0:amd64. 136s Preparing to unpack .../020-libhwasan0_14-20240303-1ubuntu1_amd64.deb ... 136s Unpacking libhwasan0:amd64 (14-20240303-1ubuntu1) ... 136s Selecting previously unselected package libquadmath0:amd64. 136s Preparing to unpack .../021-libquadmath0_14-20240303-1ubuntu1_amd64.deb ... 136s Unpacking libquadmath0:amd64 (14-20240303-1ubuntu1) ... 136s Selecting previously unselected package libgcc-13-dev:amd64. 136s Preparing to unpack .../022-libgcc-13-dev_13.2.0-17ubuntu2_amd64.deb ... 136s Unpacking libgcc-13-dev:amd64 (13.2.0-17ubuntu2) ... 136s Selecting previously unselected package gcc-13-x86-64-linux-gnu. 136s Preparing to unpack .../023-gcc-13-x86-64-linux-gnu_13.2.0-17ubuntu2_amd64.deb ... 136s Unpacking gcc-13-x86-64-linux-gnu (13.2.0-17ubuntu2) ... 137s Selecting previously unselected package gcc-13. 137s Preparing to unpack .../024-gcc-13_13.2.0-17ubuntu2_amd64.deb ... 137s Unpacking gcc-13 (13.2.0-17ubuntu2) ... 137s Selecting previously unselected package gcc-x86-64-linux-gnu. 137s Preparing to unpack .../025-gcc-x86-64-linux-gnu_4%3a13.2.0-7ubuntu1_amd64.deb ... 137s Unpacking gcc-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ... 137s Selecting previously unselected package gcc. 137s Preparing to unpack .../026-gcc_4%3a13.2.0-7ubuntu1_amd64.deb ... 137s Unpacking gcc (4:13.2.0-7ubuntu1) ... 137s Selecting previously unselected package libstdc++-13-dev:amd64. 137s Preparing to unpack .../027-libstdc++-13-dev_13.2.0-17ubuntu2_amd64.deb ... 137s Unpacking libstdc++-13-dev:amd64 (13.2.0-17ubuntu2) ... 137s Selecting previously unselected package g++-13-x86-64-linux-gnu. 137s Preparing to unpack .../028-g++-13-x86-64-linux-gnu_13.2.0-17ubuntu2_amd64.deb ... 137s Unpacking g++-13-x86-64-linux-gnu (13.2.0-17ubuntu2) ... 137s Selecting previously unselected package g++-13. 137s Preparing to unpack .../029-g++-13_13.2.0-17ubuntu2_amd64.deb ... 137s Unpacking g++-13 (13.2.0-17ubuntu2) ... 137s Selecting previously unselected package g++-x86-64-linux-gnu. 137s Preparing to unpack .../030-g++-x86-64-linux-gnu_4%3a13.2.0-7ubuntu1_amd64.deb ... 137s Unpacking g++-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ... 137s Selecting previously unselected package g++. 137s Preparing to unpack .../031-g++_4%3a13.2.0-7ubuntu1_amd64.deb ... 137s Unpacking g++ (4:13.2.0-7ubuntu1) ... 137s Selecting previously unselected package build-essential. 137s Preparing to unpack .../032-build-essential_12.10ubuntu1_amd64.deb ... 137s Unpacking build-essential (12.10ubuntu1) ... 137s Selecting previously unselected package dctrl-tools. 137s Preparing to unpack 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package gfortran. 138s Preparing to unpack .../038-gfortran_4%3a13.2.0-7ubuntu1_amd64.deb ... 138s Unpacking gfortran (4:13.2.0-7ubuntu1) ... 138s Selecting previously unselected package icu-devtools. 138s Preparing to unpack .../039-icu-devtools_74.2-1ubuntu1_amd64.deb ... 138s Unpacking icu-devtools (74.2-1ubuntu1) ... 138s Selecting previously unselected package libblas-dev:amd64. 138s Preparing to unpack .../040-libblas-dev_3.12.0-3_amd64.deb ... 138s Unpacking libblas-dev:amd64 (3.12.0-3) ... 138s Selecting previously unselected package libbz2-dev:amd64. 138s Preparing to unpack .../041-libbz2-dev_1.0.8-5ubuntu1_amd64.deb ... 138s Unpacking libbz2-dev:amd64 (1.0.8-5ubuntu1) ... 138s Selecting previously unselected package libicu-dev:amd64. 138s Preparing to unpack .../042-libicu-dev_74.2-1ubuntu1_amd64.deb ... 138s Unpacking libicu-dev:amd64 (74.2-1ubuntu1) ... 138s Selecting previously unselected package libjpeg-turbo8-dev:amd64. 138s Preparing to unpack .../043-libjpeg-turbo8-dev_2.1.5-2ubuntu1_amd64.deb ... 138s Unpacking libjpeg-turbo8-dev:amd64 (2.1.5-2ubuntu1) ... 138s Selecting previously unselected package libjpeg8-dev:amd64. 138s Preparing to unpack .../044-libjpeg8-dev_8c-2ubuntu11_amd64.deb ... 138s Unpacking libjpeg8-dev:amd64 (8c-2ubuntu11) ... 138s Selecting previously unselected package libjpeg-dev:amd64. 138s Preparing to unpack .../045-libjpeg-dev_8c-2ubuntu11_amd64.deb ... 138s Unpacking libjpeg-dev:amd64 (8c-2ubuntu11) ... 138s Selecting previously unselected package liblapack-dev:amd64. 138s Preparing to unpack .../046-liblapack-dev_3.12.0-3_amd64.deb ... 138s Unpacking liblapack-dev:amd64 (3.12.0-3) ... 138s Selecting previously unselected package libncurses-dev:amd64. 138s Preparing to unpack .../047-libncurses-dev_6.4+20240113-1ubuntu1_amd64.deb ... 138s Unpacking libncurses-dev:amd64 (6.4+20240113-1ubuntu1) ... 138s Selecting previously unselected package libpcre2-16-0:amd64. 138s Preparing to unpack .../048-libpcre2-16-0_10.42-4ubuntu1_amd64.deb ... 138s Unpacking libpcre2-16-0:amd64 (10.42-4ubuntu1) ... 138s Selecting previously unselected package libpcre2-32-0:amd64. 138s Preparing to unpack .../049-libpcre2-32-0_10.42-4ubuntu1_amd64.deb ... 138s Unpacking libpcre2-32-0:amd64 (10.42-4ubuntu1) ... 138s Selecting previously unselected package libpcre2-posix3:amd64. 138s Preparing to unpack .../050-libpcre2-posix3_10.42-4ubuntu1_amd64.deb ... 138s Unpacking libpcre2-posix3:amd64 (10.42-4ubuntu1) ... 138s Selecting previously unselected package libpcre2-dev:amd64. 138s Preparing to unpack .../051-libpcre2-dev_10.42-4ubuntu1_amd64.deb ... 138s Unpacking libpcre2-dev:amd64 (10.42-4ubuntu1) ... 138s Selecting previously unselected package libpkgconf3:amd64. 138s Preparing to unpack .../052-libpkgconf3_1.8.1-2_amd64.deb ... 138s Unpacking libpkgconf3:amd64 (1.8.1-2) ... 138s Selecting previously unselected package zlib1g-dev:amd64. 138s Preparing to unpack .../053-zlib1g-dev_1%3a1.3.dfsg-3ubuntu1_amd64.deb ... 138s Unpacking zlib1g-dev:amd64 (1:1.3.dfsg-3ubuntu1) ... 138s Selecting previously unselected package libpng-dev:amd64. 138s Preparing to unpack .../054-libpng-dev_1.6.43-1_amd64.deb ... 138s Unpacking libpng-dev:amd64 (1.6.43-1) ... 139s Selecting previously unselected package libreadline-dev:amd64. 139s Preparing to unpack .../055-libreadline-dev_8.2-3_amd64.deb ... 139s Unpacking libreadline-dev:amd64 (8.2-3) ... 139s Selecting previously unselected package pkgconf-bin. 139s Preparing to unpack .../056-pkgconf-bin_1.8.1-2_amd64.deb ... 139s Unpacking pkgconf-bin (1.8.1-2) ... 139s Selecting previously unselected package pkgconf:amd64. 139s Preparing to unpack .../057-pkgconf_1.8.1-2_amd64.deb ... 139s Unpacking pkgconf:amd64 (1.8.1-2) ... 139s Selecting previously unselected package pkg-config:amd64. 139s Preparing to unpack .../058-pkg-config_1.8.1-2_amd64.deb ... 139s Unpacking pkg-config:amd64 (1.8.1-2) ... 139s Selecting previously unselected package liblzma-dev:amd64. 139s Preparing to unpack .../059-liblzma-dev_5.4.5-0.3_amd64.deb ... 139s Unpacking liblzma-dev:amd64 (5.4.5-0.3) ... 139s Selecting previously unselected package r-base-dev. 139s Preparing to unpack .../060-r-base-dev_4.3.2-1build1_all.deb ... 139s Unpacking r-base-dev (4.3.2-1build1) ... 139s Selecting previously unselected package pkg-r-autopkgtest. 139s Preparing to unpack .../061-pkg-r-autopkgtest_20231212ubuntu1_all.deb ... 139s Unpacking pkg-r-autopkgtest (20231212ubuntu1) ... 139s Selecting previously unselected package r-cran-backports. 139s Preparing to unpack .../062-r-cran-backports_1.4.1-1_amd64.deb ... 139s Unpacking r-cran-backports (1.4.1-1) ... 139s Selecting previously unselected package r-cran-cli. 139s Preparing to unpack .../063-r-cran-cli_3.6.2-1_amd64.deb ... 139s Unpacking r-cran-cli (3.6.2-1) ... 139s Selecting previously unselected package r-cran-generics. 139s Preparing to unpack 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package r-cran-utf8. 139s Preparing to unpack .../070-r-cran-utf8_1.2.4-1_amd64.deb ... 139s Unpacking r-cran-utf8 (1.2.4-1) ... 139s Selecting previously unselected package r-cran-vctrs. 139s Preparing to unpack .../071-r-cran-vctrs_0.6.5-1_amd64.deb ... 139s Unpacking r-cran-vctrs (0.6.5-1) ... 139s Selecting previously unselected package r-cran-pillar. 139s Preparing to unpack .../072-r-cran-pillar_1.9.0+dfsg-1_all.deb ... 139s Unpacking r-cran-pillar (1.9.0+dfsg-1) ... 139s Selecting previously unselected package r-cran-r6. 139s Preparing to unpack .../073-r-cran-r6_2.5.1-1_all.deb ... 139s Unpacking r-cran-r6 (2.5.1-1) ... 139s Selecting previously unselected package r-cran-pkgconfig. 139s Preparing to unpack .../074-r-cran-pkgconfig_2.0.3-2build1_all.deb ... 139s Unpacking r-cran-pkgconfig (2.0.3-2build1) ... 139s Selecting previously unselected package r-cran-tibble. 139s Preparing to unpack .../075-r-cran-tibble_3.2.1+dfsg-2_amd64.deb ... 139s Unpacking r-cran-tibble (3.2.1+dfsg-2) ... 139s Selecting previously unselected package r-cran-withr. 139s Preparing to unpack .../076-r-cran-withr_2.5.0-1_all.deb ... 139s Unpacking r-cran-withr (2.5.0-1) ... 139s Selecting previously unselected package r-cran-tidyselect. 139s Preparing to unpack .../077-r-cran-tidyselect_1.2.0+dfsg-1_amd64.deb ... 139s Unpacking r-cran-tidyselect (1.2.0+dfsg-1) ... 139s Selecting previously unselected package r-cran-dplyr. 139s Preparing to unpack .../078-r-cran-dplyr_1.1.4-1_amd64.deb ... 139s Unpacking r-cran-dplyr (1.1.4-1) ... 139s Selecting previously unselected package r-cran-ellipsis. 139s Preparing to unpack .../079-r-cran-ellipsis_0.3.2-2_amd64.deb ... 139s Unpacking r-cran-ellipsis (0.3.2-2) ... 140s Selecting previously unselected package r-cran-purrr. 140s Preparing to unpack .../080-r-cran-purrr_1.0.2-1_amd64.deb ... 140s Unpacking r-cran-purrr (1.0.2-1) ... 140s Selecting previously unselected package r-cran-stringi. 140s Preparing to unpack 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unselected package r-cran-farver. 140s Preparing to unpack .../087-r-cran-farver_2.1.1-1_amd64.deb ... 140s Unpacking r-cran-farver (2.1.1-1) ... 140s Selecting previously unselected package r-cran-mass. 140s Preparing to unpack .../088-r-cran-mass_7.3-60.0.1-1_amd64.deb ... 140s Unpacking r-cran-mass (7.3-60.0.1-1) ... 140s Selecting previously unselected package r-cran-geepack. 140s Preparing to unpack .../089-r-cran-geepack_1.3.10-1_amd64.deb ... 140s Unpacking r-cran-geepack (1.3.10-1) ... 140s Selecting previously unselected package r-cran-gtable. 140s Preparing to unpack .../090-r-cran-gtable_0.3.4+dfsg-1_all.deb ... 140s Unpacking r-cran-gtable (0.3.4+dfsg-1) ... 140s Selecting previously unselected package r-cran-isoband. 140s Preparing to unpack .../091-r-cran-isoband_0.2.7-1_amd64.deb ... 140s Unpacking r-cran-isoband (0.2.7-1) ... 140s Selecting previously unselected package r-cran-nlme. 140s Preparing to unpack .../092-r-cran-nlme_3.1.164-1_amd64.deb ... 140s Unpacking r-cran-nlme (3.1.164-1) ... 140s Selecting previously unselected package r-cran-mgcv. 140s Preparing to unpack .../093-r-cran-mgcv_1.9-1-1_amd64.deb ... 140s Unpacking r-cran-mgcv (1.9-1-1) ... 140s Selecting previously unselected package r-cran-labeling. 140s Preparing to unpack .../094-r-cran-labeling_0.4.3-1_all.deb ... 140s Unpacking r-cran-labeling (0.4.3-1) ... 140s Selecting previously unselected package r-cran-munsell. 140s Preparing to unpack .../095-r-cran-munsell_0.5.0-2build1_all.deb ... 140s Unpacking r-cran-munsell (0.5.0-2build1) ... 140s Selecting previously unselected package r-cran-rcolorbrewer. 140s Preparing to unpack .../096-r-cran-rcolorbrewer_1.1-3-1build1_all.deb ... 140s Unpacking r-cran-rcolorbrewer (1.1-3-1build1) ... 140s Selecting previously unselected package r-cran-viridislite. 140s Preparing to unpack .../097-r-cran-viridislite_0.4.2-2_all.deb ... 140s Unpacking r-cran-viridislite (0.4.2-2) ... 140s Selecting previously unselected package r-cran-scales. 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141s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode 141s 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 141s Setting up g++ (4:13.2.0-7ubuntu1) ... 141s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 141s Setting up build-essential (12.10ubuntu1) ... 141s Setting up r-base-dev (4.3.2-1build1) ... 141s Setting up pkg-r-autopkgtest (20231212ubuntu1) ... 141s Setting up autopkgtest-satdep (0) ... 141s Processing triggers for man-db (2.12.0-3) ... 141s Processing triggers for install-info (7.1-3) ... 142s Processing triggers for libc-bin (2.39-0ubuntu2) ... 144s (Reading database ... 83812 files and directories currently installed.) 144s Removing autopkgtest-satdep (0) ... 144s autopkgtest [13:07:19]: test pkg-r-autopkgtest: /usr/share/dh-r/pkg-r-autopkgtest 144s autopkgtest [13:07:19]: test pkg-r-autopkgtest: [----------------------- 144s Test: Try to load the R library etm 144s 144s R version 4.3.2 (2023-10-31) -- "Eye Holes" 144s Copyright (C) 2023 The R Foundation for Statistical Computing 144s Platform: x86_64-pc-linux-gnu (64-bit) 144s 144s R is free software and comes with ABSOLUTELY NO WARRANTY. 144s You are welcome to redistribute it under certain conditions. 144s Type 'license()' or 'licence()' for distribution details. 144s 144s R is a collaborative project with many contributors. 144s Type 'contributors()' for more information and 144s 'citation()' on how to cite R or R packages in publications. 144s 144s Type 'demo()' for some demos, 'help()' for on-line help, or 144s 'help.start()' for an HTML browser interface to help. 144s Type 'q()' to quit R. 144s 144s > library('etm') 146s > 146s > 146s Other tests are currently unsupported! 146s They will be progressively added. 146s autopkgtest [13:07:21]: test pkg-r-autopkgtest: -----------------------] 146s autopkgtest [13:07:21]: test pkg-r-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 146s pkg-r-autopkgtest PASS 146s autopkgtest [13:07:21]: @@@@@@@@@@@@@@@@@@@@ summary 146s run-unit-test PASS 146s pkg-r-autopkgtest PASS 158s Creating nova instance adt-noble-amd64-r-cran-etm-20240320-130455-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-amd64-server-20240319.img (UUID 7b50f403-c8dd-4ed1-a25c-18c4799f5a5b)...