0s autopkgtest [18:26:25]: starting date and time: 2024-03-16 18:26:25+0000 0s autopkgtest [18:26:25]: git checkout: b506e79c ssh-setup/nova: fix ARCH having two lines of data 0s autopkgtest [18:26:25]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work._40p761q/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:r-base,src:curl,src:glib2.0,src:libpng1.6,src:libpsl,src:libtirpc,src:libxt,src:openssl,src:orthanc-python,src:readline,src:wp2latex --apt-upgrade r-cran-etm --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=r-base/4.3.3-2build1 curl/8.5.0-2ubuntu7 glib2.0/2.79.3-3ubuntu5 libpng1.6/1.6.43-3 libpsl/0.21.2-1.1 libtirpc/1.3.4+ds-1.1 libxt/1:1.2.1-1.2 openssl/3.0.13-0ubuntu1 orthanc-python/4.1+ds-2build3 readline/8.2-3.1 wp2latex/4.4~ds-1build1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos02-arm64-12.secgroup --name adt-noble-arm64-r-cran-etm-20240316-182625-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 103s autopkgtest [18:28:08]: testbed dpkg architecture: arm64 103s autopkgtest [18:28:08]: testbed apt version: 2.7.12 103s autopkgtest [18:28:08]: @@@@@@@@@@@@@@@@@@@@ test bed setup 104s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 105s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3682 kB] 107s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [51.4 kB] 107s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [474 kB] 107s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 107s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [646 kB] 107s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 107s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [33.6 kB] 107s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 107s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [4006 kB] 108s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 108s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [55.5 kB] 108s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 113s Fetched 9084 kB in 4s (2186 kB/s) 114s Reading package lists... 118s Reading package lists... 119s Building dependency tree... 119s Reading state information... 120s Calculating upgrade... 121s The following packages will be REMOVED: 121s libglib2.0-0 libssl3 121s The following NEW packages will be installed: 121s libglib2.0-0t64 libssl3t64 xdg-user-dirs 121s The following packages have been kept back: 121s curl 121s The following packages will be upgraded: 121s gir1.2-glib-2.0 libglib2.0-data libtirpc-common openssl readline-common 121s 5 upgraded, 3 newly installed, 2 to remove and 1 not upgraded. 121s Need to get 4592 kB of archives. 121s After this operation, 211 kB of additional disk space will be used. 121s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 gir1.2-glib-2.0 arm64 2.79.3-3ubuntu5 [182 kB] 121s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libglib2.0-0t64 arm64 2.79.3-3ubuntu5 [1527 kB] 121s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 openssl arm64 3.0.13-0ubuntu1 [983 kB] 121s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libssl3t64 arm64 3.0.13-0ubuntu1 [1770 kB] 121s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libglib2.0-data all 2.79.3-3ubuntu5 [46.6 kB] 121s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libtirpc-common all 1.3.4+ds-1.1 [8018 B] 121s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 readline-common all 8.2-3.1 [56.4 kB] 121s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 xdg-user-dirs arm64 0.18-1 [18.1 kB] 122s Fetched 4592 kB in 1s (6000 kB/s) 122s (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 ... 75850 files and directories currently installed.) 122s Preparing to unpack .../gir1.2-glib-2.0_2.79.3-3ubuntu5_arm64.deb ... 122s Unpacking gir1.2-glib-2.0:arm64 (2.79.3-3ubuntu5) over (2.79.2-1~ubuntu1) ... 123s dpkg: libglib2.0-0:arm64: dependency problems, but removing anyway as you requested: 123s udisks2 depends on libglib2.0-0 (>= 2.77.0). 123s shared-mime-info depends on libglib2.0-0 (>= 2.75.3). 123s python3-gi depends on libglib2.0-0 (>= 2.77.0). 123s python3-dbus depends on libglib2.0-0 (>= 2.16.0). 123s netplan.io depends on libglib2.0-0 (>= 2.70.0). 123s netplan-generator depends on libglib2.0-0 (>= 2.70.0). 123s libxmlb2:arm64 depends on libglib2.0-0 (>= 2.54.0). 123s libvolume-key1:arm64 depends on libglib2.0-0 (>= 2.18.0). 123s libudisks2-0:arm64 depends on libglib2.0-0 (>= 2.75.3). 123s libqrtr-glib0:arm64 depends on libglib2.0-0 (>= 2.56). 123s libqmi-proxy depends on libglib2.0-0 (>= 2.30.0). 123s libqmi-glib5:arm64 depends on libglib2.0-0 (>= 2.54.0). 123s libpolkit-gobject-1-0:arm64 depends on libglib2.0-0 (>= 2.38.0). 123s libpolkit-agent-1-0:arm64 depends on libglib2.0-0 (>= 2.38.0). 123s libnetplan0:arm64 depends on libglib2.0-0 (>= 2.75.3). 123s libmm-glib0:arm64 depends on libglib2.0-0 (>= 2.62.0). 123s libmbim-proxy depends on libglib2.0-0 (>= 2.56). 123s libmbim-glib4:arm64 depends on libglib2.0-0 (>= 2.56). 123s libjson-glib-1.0-0:arm64 depends on libglib2.0-0 (>= 2.75.3). 123s libjcat1:arm64 depends on libglib2.0-0 (>= 2.75.3). 123s libgusb2:arm64 depends on libglib2.0-0 (>= 2.75.3). 123s libgudev-1.0-0:arm64 depends on libglib2.0-0 (>= 2.38.0). 123s libgirepository-1.0-1:arm64 depends on libglib2.0-0 (>= 2.79.0). 123s libfwupd2:arm64 depends on libglib2.0-0 (>= 2.79.0). 123s libblockdev3:arm64 depends on libglib2.0-0 (>= 2.42.2). 123s libblockdev-utils3:arm64 depends on libglib2.0-0 (>= 2.75.3). 123s libblockdev-swap3:arm64 depends on libglib2.0-0 (>= 2.42.2). 123s libblockdev-part3:arm64 depends on libglib2.0-0 (>= 2.42.2). 123s libblockdev-nvme3:arm64 depends on libglib2.0-0 (>= 2.42.2). 123s libblockdev-mdraid3:arm64 depends on libglib2.0-0 (>= 2.42.2). 123s libblockdev-loop3:arm64 depends on libglib2.0-0 (>= 2.42.2). 123s libblockdev-fs3:arm64 depends on libglib2.0-0 (>= 2.42.2). 123s libblockdev-crypto3:arm64 depends on libglib2.0-0 (>= 2.42.2). 123s fwupd depends on libglib2.0-0 (>= 2.79.0). 123s bolt depends on libglib2.0-0 (>= 2.56.0). 123s 123s (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 ... 75850 files and directories currently installed.) 123s Removing libglib2.0-0:arm64 (2.79.2-1~ubuntu1) ... 123s Selecting previously unselected package libglib2.0-0t64:arm64. 123s (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 ... 75825 files and directories currently installed.) 123s Preparing to unpack .../libglib2.0-0t64_2.79.3-3ubuntu5_arm64.deb ... 123s libglib2.0-0t64.preinst: Removing /var/lib/dpkg/info/libglib2.0-0:arm64.postrm to avoid loss of /usr/share/glib-2.0/schemas/gschemas.compiled... 123s removed '/var/lib/dpkg/info/libglib2.0-0:arm64.postrm' 123s Unpacking libglib2.0-0t64:arm64 (2.79.3-3ubuntu5) ... 123s Preparing to unpack .../openssl_3.0.13-0ubuntu1_arm64.deb ... 123s Unpacking openssl (3.0.13-0ubuntu1) over (3.0.10-1ubuntu4) ... 124s dpkg: libssl3:arm64: dependency problems, but removing anyway as you requested: 124s wget depends on libssl3 (>= 3.0.0). 124s u-boot-tools depends on libssl3 (>= 3.0.0). 124s tnftp depends on libssl3 (>= 3.0.0). 124s tcpdump depends on libssl3 (>= 3.0.0). 124s systemd-resolved depends on libssl3 (>= 3.0.0). 124s systemd depends on libssl3 (>= 3.0.0). 124s sudo depends on libssl3 (>= 3.0.0). 124s sbsigntool depends on libssl3 (>= 3.0.0). 124s rsync depends on libssl3 (>= 3.0.0). 124s python3-cryptography depends on libssl3 (>= 3.0.0). 124s openssh-server depends on libssl3 (>= 3.0.10). 124s openssh-client depends on libssl3 (>= 3.0.10). 124s mtd-utils depends on libssl3 (>= 3.0.0). 124s mokutil depends on libssl3 (>= 3.0.0). 124s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 124s libsystemd-shared:arm64 depends on libssl3 (>= 3.0.0). 124s libssh-4:arm64 depends on libssl3 (>= 3.0.0). 124s libsasl2-modules:arm64 depends on libssl3 (>= 3.0.0). 124s libsasl2-2:arm64 depends on libssl3 (>= 3.0.0). 124s libpython3.12-minimal:arm64 depends on libssl3 (>= 3.0.0). 124s libpython3.11-minimal:arm64 depends on libssl3 (>= 3.0.0). 124s libnvme1 depends on libssl3 (>= 3.0.0). 124s libkrb5-3:arm64 depends on libssl3 (>= 3.0.0). 124s libkmod2:arm64 depends on libssl3 (>= 3.0.0). 124s libfido2-1:arm64 depends on libssl3 (>= 3.0.0). 124s libcurl4:arm64 depends on libssl3 (>= 3.0.0). 124s libcryptsetup12:arm64 depends on libssl3 (>= 3.0.0). 124s kmod depends on libssl3 (>= 3.0.0). 124s dhcpcd-base depends on libssl3 (>= 3.0.0). 124s bind9-libs:arm64 depends on libssl3 (>= 3.0.0). 124s 124s (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 ... 75850 files and directories currently installed.) 124s Removing libssl3:arm64 (3.0.10-1ubuntu4) ... 124s Selecting previously unselected package libssl3t64:arm64. 124s (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 ... 75839 files and directories currently installed.) 124s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu1_arm64.deb ... 124s Unpacking libssl3t64:arm64 (3.0.13-0ubuntu1) ... 124s Preparing to unpack .../libglib2.0-data_2.79.3-3ubuntu5_all.deb ... 124s Unpacking libglib2.0-data (2.79.3-3ubuntu5) over (2.79.2-1~ubuntu1) ... 124s Preparing to unpack .../libtirpc-common_1.3.4+ds-1.1_all.deb ... 124s Unpacking libtirpc-common (1.3.4+ds-1.1) over (1.3.4+ds-1build1) ... 124s Preparing to unpack .../readline-common_8.2-3.1_all.deb ... 124s Unpacking readline-common (8.2-3.1) over (8.2-3) ... 124s Selecting previously unselected package xdg-user-dirs. 124s Preparing to unpack .../xdg-user-dirs_0.18-1_arm64.deb ... 124s Unpacking xdg-user-dirs (0.18-1) ... 124s Setting up xdg-user-dirs (0.18-1) ... 124s Setting up libssl3t64:arm64 (3.0.13-0ubuntu1) ... 124s Setting up libtirpc-common (1.3.4+ds-1.1) ... 124s Setting up libglib2.0-0t64:arm64 (2.79.3-3ubuntu5) ... 124s No schema files found: doing nothing. 124s Setting up libglib2.0-data (2.79.3-3ubuntu5) ... 124s Setting up gir1.2-glib-2.0:arm64 (2.79.3-3ubuntu5) ... 124s Setting up openssl (3.0.13-0ubuntu1) ... 124s Setting up readline-common (8.2-3.1) ... 124s Processing triggers for man-db (2.12.0-3) ... 125s Processing triggers for install-info (7.1-3) ... 126s Processing triggers for libc-bin (2.39-0ubuntu2) ... 126s Reading package lists... 127s Building dependency tree... 127s Reading state information... 128s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 129s Hit:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease 129s Hit:2 http://ftpmaster.internal/ubuntu noble InRelease 129s Hit:3 http://ftpmaster.internal/ubuntu noble-updates InRelease 129s Hit:4 http://ftpmaster.internal/ubuntu noble-security InRelease 134s Reading package lists... 134s Reading package lists... 135s Building dependency tree... 135s Reading state information... 136s Calculating upgrade... 137s The following packages have been kept back: 137s curl 137s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 137s Reading package lists... 138s Building dependency tree... 138s Reading state information... 139s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 143s autopkgtest [18:28:48]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 143s autopkgtest [18:28:48]: @@@@@@@@@@@@@@@@@@@@ apt-source r-cran-etm 145s Get:1 http://ftpmaster.internal/ubuntu noble/universe r-cran-etm 1.1.1-1 (dsc) [2148 B] 145s Get:2 http://ftpmaster.internal/ubuntu noble/universe r-cran-etm 1.1.1-1 (tar) [242 kB] 145s Get:3 http://ftpmaster.internal/ubuntu noble/universe r-cran-etm 1.1.1-1 (diff) [3564 B] 146s gpgv: Signature made Fri Sep 18 09:39:57 2020 UTC 146s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 146s gpgv: issuer "tille@debian.org" 146s gpgv: Can't check signature: No public key 146s dpkg-source: warning: cannot verify inline signature for ./r-cran-etm_1.1.1-1.dsc: no acceptable signature found 146s autopkgtest [18:28:51]: testing package r-cran-etm version 1.1.1-1 146s autopkgtest [18:28:51]: build not needed 148s autopkgtest [18:28:53]: test run-unit-test: preparing testbed 149s Reading package lists... 150s Building dependency tree... 150s Reading state information... 151s Starting pkgProblemResolver with broken count: 0 151s Starting 2 pkgProblemResolver with broken count: 0 151s Done 153s The following additional packages will be installed: 153s curl fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono 153s libblas3 libcairo2 libcurl4t64 libdatrie1 libdeflate0 libfontconfig1 153s libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libice6 libjbig0 153s libjpeg-turbo8 libjpeg8 liblapack3 liblerc4 libpango-1.0-0 153s libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpixman-1-0 153s libpng16-16t64 libpsl5t64 libreadline8t64 libsharpyuv0 libsm6 libtcl8.6 153s libthai-data libthai0 libtiff6 libtirpc3t64 libtk8.6 libwebp7 libxcb-render0 153s libxcb-shm0 libxft2 libxrender1 libxss1 libxt6t64 littler r-base-core 153s r-cran-data.table r-cran-dbi r-cran-etm r-cran-kmi r-cran-lattice 153s r-cran-littler r-cran-matrix r-cran-mitools r-cran-pkgkitten r-cran-rcpp 153s r-cran-rcpparmadillo r-cran-survival unzip x11-common xdg-utils zip 153s Suggested packages: 153s tcl8.6 tk8.6 elpa-ess r-doc-info | r-doc-pdf r-mathlib r-base-html 153s r-cran-rmysql r-cran-ggplot2 r-cran-geepack r-cran-getopt r-cran-rodbc 153s r-cran-foreign r-cran-inline 153s Recommended packages: 153s r-recommended r-base-dev r-doc-html r-cran-bit64 r-cran-bit r-cran-curl 153s r-cran-r.utils r-cran-xts r-cran-nanotime r-cran-zoo r-cran-yaml 153s r-cran-knitr r-cran-rmarkdown libfile-mimeinfo-perl libnet-dbus-perl 153s libx11-protocol-perl x11-utils x11-xserver-utils 153s The following packages will be REMOVED: 153s libcurl4 libpng16-16 libpsl5 libreadline8 libtirpc3 153s The following NEW packages will be installed: 153s autopkgtest-satdep fontconfig fontconfig-config fonts-dejavu-core 153s fonts-dejavu-mono libblas3 libcairo2 libcurl4t64 libdatrie1 libdeflate0 153s libfontconfig1 libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libice6 153s libjbig0 libjpeg-turbo8 libjpeg8 liblapack3 liblerc4 libpango-1.0-0 153s libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpixman-1-0 153s libpng16-16t64 libpsl5t64 libreadline8t64 libsharpyuv0 libsm6 libtcl8.6 153s libthai-data libthai0 libtiff6 libtirpc3t64 libtk8.6 libwebp7 libxcb-render0 153s libxcb-shm0 libxft2 libxrender1 libxss1 libxt6t64 littler r-base-core 153s r-cran-data.table r-cran-dbi r-cran-etm r-cran-kmi r-cran-lattice 153s r-cran-littler r-cran-matrix r-cran-mitools r-cran-pkgkitten r-cran-rcpp 153s r-cran-rcpparmadillo r-cran-survival unzip x11-common xdg-utils zip 153s The following packages will be upgraded: 153s curl 153s 1 upgraded, 63 newly installed, 5 to remove and 0 not upgraded. 153s Need to get 55.3 MB/55.3 MB of archives. 153s After this operation, 114 MB of additional disk space will be used. 153s Get:1 /tmp/autopkgtest.a0lvW0/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [716 B] 153s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libpsl5t64 arm64 0.21.2-1.1 [57.4 kB] 154s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 curl arm64 8.5.0-2ubuntu7 [222 kB] 154s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libcurl4t64 arm64 8.5.0-2ubuntu7 [332 kB] 154s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libpng16-16t64 arm64 1.6.43-3 [185 kB] 154s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libreadline8t64 arm64 8.2-3.1 [153 kB] 154s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libtirpc3t64 arm64 1.3.4+ds-1.1 [83.5 kB] 154s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 154s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 154s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig-config arm64 2.15.0-1ubuntu1 [37.0 kB] 154s Get:11 http://ftpmaster.internal/ubuntu noble/main arm64 libfontconfig1 arm64 2.15.0-1ubuntu1 [142 kB] 154s Get:12 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig arm64 2.15.0-1ubuntu1 [190 kB] 154s Get:13 http://ftpmaster.internal/ubuntu noble/main arm64 libblas3 arm64 3.12.0-3 [143 kB] 154s Get:14 http://ftpmaster.internal/ubuntu noble/main arm64 libpixman-1-0 arm64 0.42.2-1 [193 kB] 154s Get:15 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-render0 arm64 1.15-1 [16.1 kB] 154s Get:16 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-shm0 arm64 1.15-1 [5780 B] 154s Get:17 http://ftpmaster.internal/ubuntu noble/main arm64 libxrender1 arm64 1:0.9.10-1.1 [19.1 kB] 154s Get:18 http://ftpmaster.internal/ubuntu noble/main arm64 libcairo2 arm64 1.18.0-1 [550 kB] 154s Get:19 http://ftpmaster.internal/ubuntu noble/main arm64 libdatrie1 arm64 0.2.13-3 [21.7 kB] 154s Get:20 http://ftpmaster.internal/ubuntu noble/main arm64 libdeflate0 arm64 1.19-1 [43.4 kB] 154s Get:21 http://ftpmaster.internal/ubuntu noble/main arm64 libgfortran5 arm64 14-20240303-1ubuntu1 [444 kB] 154s Get:22 http://ftpmaster.internal/ubuntu noble/main arm64 libgomp1 arm64 14-20240303-1ubuntu1 [144 kB] 154s Get:23 http://ftpmaster.internal/ubuntu noble/main arm64 libgraphite2-3 arm64 1.3.14-2 [81.5 kB] 154s Get:24 http://ftpmaster.internal/ubuntu noble/main arm64 libharfbuzz0b arm64 8.3.0-2 [463 kB] 154s Get:25 http://ftpmaster.internal/ubuntu noble/main arm64 x11-common all 1:7.7+23ubuntu2 [23.4 kB] 154s Get:26 http://ftpmaster.internal/ubuntu noble/main arm64 libice6 arm64 2:1.0.10-1build2 [41.7 kB] 154s Get:27 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg-turbo8 arm64 2.1.5-2ubuntu1 [160 kB] 154s Get:28 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 154s Get:29 http://ftpmaster.internal/ubuntu noble/main arm64 liblapack3 arm64 3.12.0-3 [2241 kB] 154s Get:30 http://ftpmaster.internal/ubuntu noble/main arm64 liblerc4 arm64 4.0.0+ds-4ubuntu1 [153 kB] 154s Get:31 http://ftpmaster.internal/ubuntu noble/main arm64 libthai-data all 0.1.29-2 [158 kB] 154s Get:32 http://ftpmaster.internal/ubuntu noble/main arm64 libthai0 arm64 0.1.29-2 [18.1 kB] 154s Get:33 http://ftpmaster.internal/ubuntu noble/main arm64 libpango-1.0-0 arm64 1.51.0+ds-4 [226 kB] 154s Get:34 http://ftpmaster.internal/ubuntu noble/main arm64 libpangoft2-1.0-0 arm64 1.51.0+ds-4 [41.2 kB] 154s Get:35 http://ftpmaster.internal/ubuntu noble/main arm64 libpangocairo-1.0-0 arm64 1.51.0+ds-4 [27.6 kB] 154s Get:36 http://ftpmaster.internal/ubuntu noble/main arm64 libpaper1 arm64 1.1.29 [13.1 kB] 154s Get:37 http://ftpmaster.internal/ubuntu noble/main arm64 libpaper-utils arm64 1.1.29 [8480 B] 154s Get:38 http://ftpmaster.internal/ubuntu noble/main arm64 libsharpyuv0 arm64 1.3.2-0.4 [14.4 kB] 154s Get:39 http://ftpmaster.internal/ubuntu noble/main arm64 libsm6 arm64 2:1.2.3-1build2 [16.1 kB] 154s Get:40 http://ftpmaster.internal/ubuntu noble/main arm64 libtcl8.6 arm64 8.6.13+dfsg-2 [980 kB] 154s Get:41 http://ftpmaster.internal/ubuntu noble/main arm64 libjbig0 arm64 2.1-6.1ubuntu1 [28.9 kB] 154s Get:42 http://ftpmaster.internal/ubuntu noble/main arm64 libwebp7 arm64 1.3.2-0.4 [191 kB] 154s Get:43 http://ftpmaster.internal/ubuntu noble/main arm64 libtiff6 arm64 4.5.1+git230720-3ubuntu1 [226 kB] 154s Get:44 http://ftpmaster.internal/ubuntu noble/main arm64 libxft2 arm64 2.3.6-1 [43.3 kB] 154s Get:45 http://ftpmaster.internal/ubuntu noble/main arm64 libxss1 arm64 1:1.2.3-1build2 [8252 B] 154s Get:46 http://ftpmaster.internal/ubuntu noble/main arm64 libtk8.6 arm64 8.6.13-2 [760 kB] 154s Get:47 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libxt6t64 arm64 1:1.2.1-1.2 [168 kB] 154s Get:48 http://ftpmaster.internal/ubuntu noble/main arm64 zip arm64 3.0-13 [172 kB] 154s Get:49 http://ftpmaster.internal/ubuntu noble/main arm64 unzip arm64 6.0-28ubuntu3 [171 kB] 154s Get:50 http://ftpmaster.internal/ubuntu noble/main arm64 xdg-utils all 1.1.3-4.1ubuntu3 [62.0 kB] 154s Get:51 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 r-base-core arm64 4.3.3-2build1 [26.8 MB] 155s Get:52 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-littler arm64 0.3.19-1 [93.4 kB] 155s Get:53 http://ftpmaster.internal/ubuntu noble/universe arm64 littler all 0.3.19-1 [2472 B] 155s Get:54 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-data.table arm64 1.14.10+dfsg-1 [1844 kB] 155s Get:55 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-dbi all 1.2.2-1 [823 kB] 155s Get:56 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-lattice arm64 0.22-5-1 [1342 kB] 155s Get:57 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-matrix arm64 1.6-5-1 [3776 kB] 156s Get:58 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-survival arm64 3.5-8-1 [6116 kB] 156s Get:59 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-pkgkitten all 0.2.3-1 [25.1 kB] 156s Get:60 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-rcpp arm64 1.0.12-1 [1971 kB] 156s Get:61 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-rcpparmadillo arm64 0.12.8.0.0-1 [859 kB] 156s Get:62 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-etm arm64 1.1.1-1 [469 kB] 156s Get:63 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-mitools all 2.4-2build1 [265 kB] 156s Get:64 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-kmi all 0.5.5-2build1 [78.3 kB] 157s Preconfiguring packages ... 157s Fetched 55.3 MB in 3s (20.8 MB/s) 157s dpkg: libpsl5:arm64: dependency problems, but removing anyway as you requested: 157s wget depends on libpsl5 (>= 0.16.0). 157s libcurl4:arm64 depends on libpsl5 (>= 0.16.0). 157s libcurl3-gnutls:arm64 depends on libpsl5 (>= 0.16.0). 157s 157s (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 ... 75866 files and directories currently installed.) 157s Removing libpsl5:arm64 (0.21.2-1build1) ... 157s Selecting previously unselected package libpsl5t64:arm64. 157s (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 ... 75861 files and directories currently installed.) 157s Preparing to unpack .../libpsl5t64_0.21.2-1.1_arm64.deb ... 157s Unpacking libpsl5t64:arm64 (0.21.2-1.1) ... 158s Preparing to unpack .../curl_8.5.0-2ubuntu7_arm64.deb ... 158s Unpacking curl (8.5.0-2ubuntu7) over (8.5.0-2ubuntu2) ... 158s (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 ... 75867 files and directories currently installed.) 158s Removing libcurl4:arm64 (8.5.0-2ubuntu2) ... 158s Selecting previously unselected package libcurl4t64:arm64. 158s (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 ... 75862 files and directories currently installed.) 158s Preparing to unpack .../libcurl4t64_8.5.0-2ubuntu7_arm64.deb ... 158s Unpacking libcurl4t64:arm64 (8.5.0-2ubuntu7) ... 158s dpkg: libpng16-16:arm64: dependency problems, but removing anyway as you requested: 158s libplymouth5:arm64 depends on libpng16-16 (>= 1.6.2). 158s libfreetype6:arm64 depends on libpng16-16 (>= 1.6.2-1). 158s 158s (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 ... 75868 files and directories currently installed.) 158s Removing libpng16-16:arm64 (1.6.43-1) ... 158s Selecting previously unselected package libpng16-16t64:arm64. 158s (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 ... 75858 files and directories currently installed.) 158s Preparing to unpack .../libpng16-16t64_1.6.43-3_arm64.deb ... 158s Unpacking libpng16-16t64:arm64 (1.6.43-3) ... 158s dpkg: libreadline8:arm64: dependency problems, but removing anyway as you requested: 158s parted depends on libreadline8 (>= 6.0). 158s libpython3.12-stdlib:arm64 depends on libreadline8 (>= 7.0~beta). 158s libpython3.11-stdlib:arm64 depends on libreadline8 (>= 7.0~beta). 158s gpgsm depends on libreadline8 (>= 6.0). 158s gpgconf depends on libreadline8 (>= 6.0). 158s gpg depends on libreadline8 (>= 6.0). 158s gawk depends on libreadline8 (>= 6.0). 158s fdisk depends on libreadline8 (>= 6.0). 158s 159s (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 ... 75869 files and directories currently installed.) 159s Removing libreadline8:arm64 (8.2-3) ... 159s Selecting previously unselected package libreadline8t64:arm64. 159s (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 ... 75857 files and directories currently installed.) 159s Preparing to unpack .../libreadline8t64_8.2-3.1_arm64.deb ... 159s Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' 159s Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8.2 to /lib/aarch64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' 159s Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' 159s Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8.2 to /lib/aarch64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' 159s Unpacking libreadline8t64:arm64 (8.2-3.1) ... 159s dpkg: libtirpc3:arm64: dependency problems, but removing anyway as you requested: 159s lsof depends on libtirpc3 (>= 1.0.2). 159s libpython3.12-stdlib:arm64 depends on libtirpc3 (>= 1.0.2). 159s libpython3.11-stdlib:arm64 depends on libtirpc3 (>= 1.0.2). 159s libnsl2:arm64 depends on libtirpc3 (>= 1.0.2). 159s iproute2 depends on libtirpc3 (>= 1.0.2). 159s 159s (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 ... 75877 files and directories currently installed.) 159s Removing libtirpc3:arm64 (1.3.4+ds-1build1) ... 159s Selecting previously unselected package libtirpc3t64:arm64. 159s (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 ... 75871 files and directories currently installed.) 159s Preparing to unpack .../00-libtirpc3t64_1.3.4+ds-1.1_arm64.deb ... 159s Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3 to /lib/aarch64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' 159s Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3.0.0 to /lib/aarch64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' 159s Unpacking libtirpc3t64:arm64 (1.3.4+ds-1.1) ... 159s Selecting previously unselected package fonts-dejavu-mono. 159s Preparing to unpack .../01-fonts-dejavu-mono_2.37-8_all.deb ... 159s Unpacking fonts-dejavu-mono (2.37-8) ... 159s Selecting previously unselected package fonts-dejavu-core. 159s Preparing to unpack .../02-fonts-dejavu-core_2.37-8_all.deb ... 160s Unpacking fonts-dejavu-core (2.37-8) ... 160s Selecting previously unselected package fontconfig-config. 160s Preparing to unpack .../03-fontconfig-config_2.15.0-1ubuntu1_arm64.deb ... 160s Unpacking fontconfig-config (2.15.0-1ubuntu1) ... 160s Selecting previously unselected package libfontconfig1:arm64. 160s Preparing to unpack .../04-libfontconfig1_2.15.0-1ubuntu1_arm64.deb ... 160s Unpacking libfontconfig1:arm64 (2.15.0-1ubuntu1) ... 160s Selecting previously unselected package fontconfig. 160s Preparing to unpack .../05-fontconfig_2.15.0-1ubuntu1_arm64.deb ... 160s Unpacking fontconfig (2.15.0-1ubuntu1) ... 160s Selecting previously unselected package libblas3:arm64. 160s Preparing to unpack .../06-libblas3_3.12.0-3_arm64.deb ... 160s Unpacking libblas3:arm64 (3.12.0-3) ... 161s Selecting previously unselected package libpixman-1-0:arm64. 161s Preparing to unpack .../07-libpixman-1-0_0.42.2-1_arm64.deb ... 161s Unpacking libpixman-1-0:arm64 (0.42.2-1) ... 161s Selecting previously unselected package libxcb-render0:arm64. 161s Preparing to unpack .../08-libxcb-render0_1.15-1_arm64.deb ... 161s Unpacking libxcb-render0:arm64 (1.15-1) ... 161s Selecting previously unselected package libxcb-shm0:arm64. 161s Preparing to unpack .../09-libxcb-shm0_1.15-1_arm64.deb ... 161s Unpacking libxcb-shm0:arm64 (1.15-1) ... 161s Selecting previously unselected package libxrender1:arm64. 161s Preparing to unpack .../10-libxrender1_1%3a0.9.10-1.1_arm64.deb ... 161s Unpacking libxrender1:arm64 (1:0.9.10-1.1) ... 161s Selecting previously unselected package libcairo2:arm64. 161s Preparing to unpack .../11-libcairo2_1.18.0-1_arm64.deb ... 161s Unpacking libcairo2:arm64 (1.18.0-1) ... 161s Selecting previously unselected package libdatrie1:arm64. 161s Preparing to unpack .../12-libdatrie1_0.2.13-3_arm64.deb ... 161s Unpacking libdatrie1:arm64 (0.2.13-3) ... 161s Selecting previously unselected package libdeflate0:arm64. 161s Preparing to unpack .../13-libdeflate0_1.19-1_arm64.deb ... 161s Unpacking libdeflate0:arm64 (1.19-1) ... 161s Selecting previously unselected package libgfortran5:arm64. 161s Preparing to unpack .../14-libgfortran5_14-20240303-1ubuntu1_arm64.deb ... 161s Unpacking libgfortran5:arm64 (14-20240303-1ubuntu1) ... 161s Selecting previously unselected package libgomp1:arm64. 161s Preparing to unpack .../15-libgomp1_14-20240303-1ubuntu1_arm64.deb ... 161s Unpacking libgomp1:arm64 (14-20240303-1ubuntu1) ... 161s Selecting previously unselected package libgraphite2-3:arm64. 161s Preparing to unpack .../16-libgraphite2-3_1.3.14-2_arm64.deb ... 161s Unpacking libgraphite2-3:arm64 (1.3.14-2) ... 161s Selecting previously unselected package libharfbuzz0b:arm64. 162s Preparing to unpack .../17-libharfbuzz0b_8.3.0-2_arm64.deb ... 162s Unpacking libharfbuzz0b:arm64 (8.3.0-2) ... 162s Selecting previously unselected package x11-common. 162s Preparing to unpack .../18-x11-common_1%3a7.7+23ubuntu2_all.deb ... 162s Unpacking x11-common (1:7.7+23ubuntu2) ... 162s Selecting previously unselected package libice6:arm64. 162s Preparing to unpack .../19-libice6_2%3a1.0.10-1build2_arm64.deb ... 162s Unpacking libice6:arm64 (2:1.0.10-1build2) ... 162s Selecting previously unselected package libjpeg-turbo8:arm64. 162s Preparing to unpack .../20-libjpeg-turbo8_2.1.5-2ubuntu1_arm64.deb ... 162s Unpacking libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ... 162s Selecting previously unselected package libjpeg8:arm64. 162s Preparing to unpack .../21-libjpeg8_8c-2ubuntu11_arm64.deb ... 162s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 162s Selecting previously unselected package liblapack3:arm64. 162s Preparing to unpack .../22-liblapack3_3.12.0-3_arm64.deb ... 162s Unpacking liblapack3:arm64 (3.12.0-3) ... 162s Selecting previously unselected package liblerc4:arm64. 162s Preparing to unpack .../23-liblerc4_4.0.0+ds-4ubuntu1_arm64.deb ... 162s Unpacking liblerc4:arm64 (4.0.0+ds-4ubuntu1) ... 162s Selecting previously unselected package libthai-data. 162s Preparing to unpack .../24-libthai-data_0.1.29-2_all.deb ... 162s Unpacking libthai-data (0.1.29-2) ... 162s Selecting previously unselected package libthai0:arm64. 162s Preparing to unpack .../25-libthai0_0.1.29-2_arm64.deb ... 162s Unpacking libthai0:arm64 (0.1.29-2) ... 162s Selecting previously unselected package libpango-1.0-0:arm64. 162s Preparing to unpack .../26-libpango-1.0-0_1.51.0+ds-4_arm64.deb ... 162s Unpacking libpango-1.0-0:arm64 (1.51.0+ds-4) ... 163s Selecting previously unselected package libpangoft2-1.0-0:arm64. 163s Preparing to unpack .../27-libpangoft2-1.0-0_1.51.0+ds-4_arm64.deb ... 163s Unpacking libpangoft2-1.0-0:arm64 (1.51.0+ds-4) ... 163s Selecting previously unselected package libpangocairo-1.0-0:arm64. 163s Preparing to unpack .../28-libpangocairo-1.0-0_1.51.0+ds-4_arm64.deb ... 163s Unpacking libpangocairo-1.0-0:arm64 (1.51.0+ds-4) ... 163s Selecting previously unselected package libpaper1:arm64. 163s Preparing to unpack .../29-libpaper1_1.1.29_arm64.deb ... 163s Unpacking libpaper1:arm64 (1.1.29) ... 163s Selecting previously unselected package libpaper-utils. 163s Preparing to unpack .../30-libpaper-utils_1.1.29_arm64.deb ... 163s Unpacking libpaper-utils (1.1.29) ... 163s Selecting previously unselected package libsharpyuv0:arm64. 163s Preparing to unpack .../31-libsharpyuv0_1.3.2-0.4_arm64.deb ... 163s Unpacking libsharpyuv0:arm64 (1.3.2-0.4) ... 163s Selecting previously unselected package libsm6:arm64. 163s Preparing to unpack .../32-libsm6_2%3a1.2.3-1build2_arm64.deb ... 163s Unpacking libsm6:arm64 (2:1.2.3-1build2) ... 163s Selecting previously unselected package libtcl8.6:arm64. 163s Preparing to unpack .../33-libtcl8.6_8.6.13+dfsg-2_arm64.deb ... 163s Unpacking libtcl8.6:arm64 (8.6.13+dfsg-2) ... 163s Selecting previously unselected package libjbig0:arm64. 163s Preparing to unpack .../34-libjbig0_2.1-6.1ubuntu1_arm64.deb ... 163s Unpacking libjbig0:arm64 (2.1-6.1ubuntu1) ... 163s Selecting previously unselected package libwebp7:arm64. 163s Preparing to unpack .../35-libwebp7_1.3.2-0.4_arm64.deb ... 163s Unpacking libwebp7:arm64 (1.3.2-0.4) ... 163s Selecting previously unselected package libtiff6:arm64. 163s Preparing to unpack .../36-libtiff6_4.5.1+git230720-3ubuntu1_arm64.deb ... 163s Unpacking libtiff6:arm64 (4.5.1+git230720-3ubuntu1) ... 163s Selecting previously unselected package libxft2:arm64. 163s Preparing to unpack .../37-libxft2_2.3.6-1_arm64.deb ... 163s Unpacking libxft2:arm64 (2.3.6-1) ... 164s Selecting previously unselected package libxss1:arm64. 164s Preparing to unpack .../38-libxss1_1%3a1.2.3-1build2_arm64.deb ... 164s Unpacking libxss1:arm64 (1:1.2.3-1build2) ... 164s Selecting previously unselected package libtk8.6:arm64. 164s Preparing to unpack .../39-libtk8.6_8.6.13-2_arm64.deb ... 164s Unpacking libtk8.6:arm64 (8.6.13-2) ... 164s Selecting previously unselected package libxt6t64:arm64. 164s Preparing to unpack .../40-libxt6t64_1%3a1.2.1-1.2_arm64.deb ... 164s Unpacking libxt6t64:arm64 (1:1.2.1-1.2) ... 164s Selecting previously unselected package zip. 164s Preparing to unpack .../41-zip_3.0-13_arm64.deb ... 164s Unpacking zip (3.0-13) ... 164s Selecting previously unselected package unzip. 164s Preparing to unpack .../42-unzip_6.0-28ubuntu3_arm64.deb ... 164s Unpacking unzip (6.0-28ubuntu3) ... 164s Selecting previously unselected package xdg-utils. 164s Preparing to unpack .../43-xdg-utils_1.1.3-4.1ubuntu3_all.deb ... 164s Unpacking xdg-utils (1.1.3-4.1ubuntu3) ... 164s Selecting previously unselected package r-base-core. 164s Preparing to unpack .../44-r-base-core_4.3.3-2build1_arm64.deb ... 164s Unpacking 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Type 'license()' or 'licence()' for distribution details. 186s 186s R is a collaborative project with many contributors. 186s Type 'contributors()' for more information and 186s 'citation()' on how to cite R or R packages in publications. 186s 186s Type 'demo()' for some demos, 'help()' for on-line help, or 186s 'help.start()' for an HTML browser interface to help. 186s Type 'q()' to quit R. 186s 186s > ### test file for etmCIF. 186s > ### Really simple tests and comparison with etm 186s > 186s > old <- options(digits = 5) 186s > 186s > require(etm) 186s Loading required package: etm 189s > 189s > if (!require(survival, quietly = TRUE)) { 189s + print("The following tests require the 'survival' package") 189s + } else { 189s + 189s + data(abortion) 189s + 189s + from <- rep(0, nrow(abortion)) 189s + to <- abortion$cause 189s + entry <- abortion$entry 189s + exit <- abortion$exit 189s + id <- 1:nrow(abortion) 189s + data <- data.frame(id, from, to, entry, exit, group = abortion$group) 189s + 189s + ## Computation of the CIFs with etm 189s + tra <- matrix(FALSE, 4, 4) 189s + tra[1, 2:4] <- TRUE 189s + 189s + cif.control <- etm(data[data$group == 0, ], c("0", "1", "2", "3"), 189s + tra, NULL, 0) 189s + cif.exposed <- etm(data[data$group == 1, ], c("0", "1", "2", "3"), 189s + tra, NULL, 0) 189s + 189s + 189s + ## Computation of the CIFs with etmCIF 189s + netm <- etmCIF(Surv(entry, exit, cause != 0) ~ group, abortion, 189s + etype = cause, failcode = 3) 189s + 189s + ### let's do some comparisons :-) 189s + 189s + all.equal(trprob(cif.control, "0 3"), netm[[1]]$est["0", "3", ]) 189s + all.equal(trprob(cif.control, "0 2"), netm[[1]]$est["0", "2", ]) 189s + all.equal(trprob(cif.control, "0 1"), netm[[1]]$est["0", "1", ]) 189s + 189s + all.equal(trprob(cif.exposed, "0 3"), netm[[2]]$est["0", "3", ]) 189s + all.equal(trprob(cif.exposed, "0 2"), netm[[2]]$est["0", "2", ]) 189s + all.equal(trprob(cif.exposed, "0 1"), netm[[2]]$est["0", "1", ]) 189s + 189s + 189s + all.equal(trcov(cif.control, "0 3"), netm[[1]]$cov["0 3", "0 3", ]) 189s + all.equal(trcov(cif.control, "0 2"), netm[[1]]$cov["0 2", "0 2", ]) 189s + all.equal(trcov(cif.control, "0 1"), netm[[1]]$cov["0 1", "0 1", ]) 189s + 189s + all.equal(trcov(cif.exposed, "0 3"), netm[[2]]$cov["0 3", "0 3", ]) 189s + all.equal(trcov(cif.exposed, "0 2"), netm[[2]]$cov["0 2", "0 2", ]) 189s + all.equal(trcov(cif.exposed, "0 1"), netm[[2]]$cov["0 1", "0 1", ]) 189s + 189s + 189s + netm 189s + 189s + ## test on the summary 189s + snetm <- summary(netm) 189s + 189s + snetm 189s + 189s + all.equal(unname(trprob(cif.control, "0 3")), snetm[[1]][[3]]$P) 189s + all.equal(unname(trprob(cif.control, "0 2")), snetm[[1]][[2]]$P) 189s + all.equal(unname(trprob(cif.control, "0 1")), snetm[[1]][[1]]$P) 189s + 189s + all.equal(unname(trprob(cif.exposed, "0 3")), snetm[[2]][[3]]$P) 189s + all.equal(unname(trprob(cif.exposed, "0 2")), snetm[[2]][[2]]$P) 189s + all.equal(unname(trprob(cif.exposed, "0 1")), snetm[[2]][[1]]$P) 189s + 189s + scif.control <- summary(cif.control, ci.fun = "cloglog") 189s + scif.exposed <- summary(cif.exposed, ci.fun = "cloglog") 189s + 189s + all.equal(scif.control[[4]]$lower, snetm[[1]][[3]]$lower) 189s + all.equal(scif.control[[4]]$upper, snetm[[1]][[3]]$upper) 189s + 189s + all.equal(scif.exposed[[4]]$lower, snetm[[2]][[3]]$lower) 189s + all.equal(scif.exposed[[4]]$upper, snetm[[2]][[3]]$upper) 189s + } 189s [1] TRUE 189s > 189s > ### test with factors in the input 189s > abortion$status <- with(abortion, ifelse(cause == 2, "life birth", 189s + ifelse(cause == 1, "ETOP", "spontaneous abortion"))) 189s > 189s > abortion$status <- factor(abortion$status) 189s > 189s > netm.factor <- etmCIF(Surv(entry, exit, status != "cens") ~ group, abortion, 189s + etype = status, failcode = "spontaneous abortion") 190s > 190s > 190s > all.equal(trprob(cif.control, "0 3"), netm.factor[[1]]$est["0", "spontaneous abortion", ]) 190s [1] TRUE 190s > all.equal(trprob(cif.control, "0 2"), netm.factor[[1]]$est["0", "life birth", ]) 190s [1] TRUE 190s > 190s > netm.factor 190s Call: etmCIF(formula = Surv(entry, exit, status != "cens") ~ group, 190s data = abortion, etype = status, failcode = "spontaneous abortion") 190s 190s Covariate: group 190s levels: 0 1 190s 190s 190s group = 0 190s time P se(P) n.event 190s CIF ETOP 43 0.040159 0.0092578 20 190s CIF life birth 43 0.799059 0.0221865 924 190s CIF spontaneous abortion 43 0.160781 0.0213261 69 190s 190s group = 1 190s time P se(P) n.event 190s CIF ETOP 42 0.28511 0.042493 38 190s CIF life birth 42 0.35257 0.042139 92 190s CIF spontaneous abortion 42 0.36232 0.049473 43 190s > 190s > summary(netm.factor) 190s 190s group=0 190s 190s CIF ETOP 190s P time var lower upper n.risk n.event 190s 0.000000 6 0.0000e+00 0.000000 0.000000 117 0 190s 0.038955 13 8.4440e-05 0.024488 0.061694 645 1 190s 0.040159 26 8.5707e-05 0.025513 0.062939 846 0 190s 0.040159 36 8.5707e-05 0.025513 0.062939 876 0 190s 0.040159 40 8.5707e-05 0.025513 0.062939 554 0 190s 0.040159 43 8.5707e-05 0.025513 0.062939 6 0 190s 190s CIF life birth 190s P time var lower upper n.risk n.event 190s 0.000000 6 0.0000e+00 0.000000 0.000000 117 0 190s 0.000000 13 0.0000e+00 0.000000 0.000000 645 0 190s 0.000000 26 0.0000e+00 0.000000 0.000000 846 0 190s 0.053197 36 4.6195e-05 0.041379 0.068268 876 25 190s 0.563121 40 3.8801e-04 0.524924 0.602021 554 280 190s 0.799059 43 4.9224e-04 0.753969 0.840613 6 6 190s 190s CIF spontaneous abortion 190s P time var lower upper n.risk n.event 190s 0.034188 6 0.00028222 0.01297 0.088523 117 4 190s 0.150468 13 0.00045513 0.11360 0.197901 645 1 190s 0.159904 26 0.00045498 0.12274 0.206925 846 1 190s 0.160781 36 0.00045480 0.12360 0.207757 876 1 190s 0.160781 40 0.00045480 0.12360 0.207757 554 0 190s 0.160781 43 0.00045480 0.12360 0.207757 6 0 190s 190s 190s group=1 190s 190s CIF ETOP 190s P time var lower upper n.risk n.event 190s 0.00000 6 0.0000000 0.00000 0.00000 35 0 190s 0.26048 13 0.0017854 0.18795 0.35425 90 0 190s 0.28115 21 0.0018028 0.20742 0.37423 93 1 190s 0.28511 34 0.0018057 0.21116 0.37806 89 0 190s 0.28511 39 0.0018057 0.21116 0.37806 59 0 190s 0.28511 42 0.0018057 0.21116 0.37806 6 0 190s 190s CIF life birth 190s P time var lower upper n.risk n.event 190s 0.000000 6 0.0000e+00 0.000000 0.000000 35 0 190s 0.000000 13 0.0000e+00 0.000000 0.000000 90 0 190s 0.000000 21 0.0000e+00 0.000000 0.000000 93 0 190s 0.023073 34 9.0514e-05 0.010252 0.051504 89 2 190s 0.180156 39 8.0126e-04 0.131765 0.243663 59 13 190s 0.352565 42 1.7757e-03 0.276882 0.441775 6 6 190s 190s CIF spontaneous abortion 190s P time var lower upper n.risk n.event 190s 0.057143 6 0.0015394 0.014605 0.20968 35 2 190s 0.333246 13 0.0025280 0.245337 0.44216 90 4 190s 0.350702 21 0.0024827 0.262769 0.45762 93 0 190s 0.358492 34 0.0024593 0.270627 0.46448 89 0 190s 0.358492 39 0.0024593 0.270627 0.46448 59 0 190s 0.362323 42 0.0024476 0.274499 0.46785 6 0 190s 190s > 190s > ### test with group as a character vector 190s > abortion$ttt <- with(abortion, ifelse(group == 0, "control", "exposed")) 190s > abortion$ttt <- factor(abortion$ttt) 190s > 190s > netm.ttt <- etmCIF(Surv(entry, exit, status != "cens") ~ ttt, abortion, 190s + etype = status, failcode = "spontaneous abortion") 190s > 190s > all.equal(trprob(cif.control, "0 3"), netm.ttt[[1]]$est["0", "spontaneous abortion", ]) 190s [1] TRUE 190s > all.equal(trprob(cif.control, "0 2"), netm.ttt[[1]]$est["0", "life birth", ]) 190s [1] TRUE 190s > 190s > netm.ttt 190s Call: etmCIF(formula = Surv(entry, exit, status != "cens") ~ ttt, data = abortion, 190s etype = status, failcode = "spontaneous abortion") 190s 190s Covariate: ttt 190s levels: control exposed 190s 190s 190s ttt = control 190s time P se(P) n.event 190s CIF ETOP 43 0.040159 0.0092578 20 190s CIF life birth 43 0.799059 0.0221865 924 190s CIF spontaneous abortion 43 0.160781 0.0213261 69 190s 190s ttt = exposed 190s time P se(P) n.event 190s CIF ETOP 42 0.28511 0.042493 38 190s CIF life birth 42 0.35257 0.042139 92 190s CIF spontaneous abortion 42 0.36232 0.049473 43 190s > 190s > summary(netm.ttt) 190s 190s ttt=control 190s 190s CIF ETOP 190s P time var lower upper n.risk n.event 190s 0.000000 6 0.0000e+00 0.000000 0.000000 117 0 190s 0.038955 13 8.4440e-05 0.024488 0.061694 645 1 190s 0.040159 26 8.5707e-05 0.025513 0.062939 846 0 190s 0.040159 36 8.5707e-05 0.025513 0.062939 876 0 190s 0.040159 40 8.5707e-05 0.025513 0.062939 554 0 190s 0.040159 43 8.5707e-05 0.025513 0.062939 6 0 190s 190s CIF life birth 190s P time var lower upper n.risk n.event 190s 0.000000 6 0.0000e+00 0.000000 0.000000 117 0 190s 0.000000 13 0.0000e+00 0.000000 0.000000 645 0 190s 0.000000 26 0.0000e+00 0.000000 0.000000 846 0 190s 0.053197 36 4.6195e-05 0.041379 0.068268 876 25 190s 0.563121 40 3.8801e-04 0.524924 0.602021 554 280 190s 0.799059 43 4.9224e-04 0.753969 0.840613 6 6 190s 190s CIF spontaneous abortion 190s P time var lower upper n.risk n.event 190s 0.034188 6 0.00028222 0.01297 0.088523 117 4 190s 0.150468 13 0.00045513 0.11360 0.197901 645 1 190s 0.159904 26 0.00045498 0.12274 0.206925 846 1 190s 0.160781 36 0.00045480 0.12360 0.207757 876 1 190s 0.160781 40 0.00045480 0.12360 0.207757 554 0 190s 0.160781 43 0.00045480 0.12360 0.207757 6 0 190s 190s 190s ttt=exposed 190s 190s CIF ETOP 190s P time var lower upper n.risk n.event 190s 0.00000 6 0.0000000 0.00000 0.00000 35 0 190s 0.26048 13 0.0017854 0.18795 0.35425 90 0 190s 0.28115 21 0.0018028 0.20742 0.37423 93 1 190s 0.28511 34 0.0018057 0.21116 0.37806 89 0 190s 0.28511 39 0.0018057 0.21116 0.37806 59 0 190s 0.28511 42 0.0018057 0.21116 0.37806 6 0 190s 190s CIF life birth 190s P time var lower upper n.risk n.event 190s 0.000000 6 0.0000e+00 0.000000 0.000000 35 0 190s 0.000000 13 0.0000e+00 0.000000 0.000000 90 0 190s 0.000000 21 0.0000e+00 0.000000 0.000000 93 0 190s 0.023073 34 9.0514e-05 0.010252 0.051504 89 2 190s 0.180156 39 8.0126e-04 0.131765 0.243663 59 13 190s 0.352565 42 1.7757e-03 0.276882 0.441775 6 6 190s 190s CIF spontaneous abortion 190s P time var lower upper n.risk n.event 190s 0.057143 6 0.0015394 0.014605 0.20968 35 2 190s 0.333246 13 0.0025280 0.245337 0.44216 90 4 190s 0.350702 21 0.0024827 0.262769 0.45762 93 0 190s 0.358492 34 0.0024593 0.270627 0.46448 89 0 190s 0.358492 39 0.0024593 0.270627 0.46448 59 0 190s 0.362323 42 0.0024476 0.274499 0.46785 6 0 190s 190s > 190s > 190s > ### A couple of comparisons with simulated data 190s > set.seed(1313) 190s > time <- rexp(100) 190s > to <- rbinom(100, 2, prob = c(1/3, 1/3, 1/3)) 190s > from <- rep(11, 100) 190s > id <- 1:100 190s > cov <- rbinom(100, 1, 0.5) 190s > 190s > dat.s <- data.frame(id, time, from, to, cov) 190s > 190s > traa <- matrix(FALSE, 3, 3) 190s > traa[1, 2:3] <- TRUE 190s > 190s > aa0 <- etm(dat.s[dat.s$cov == 0, ], c("11", "1", "2"), traa, "0", 0) 190s > aa1 <- etm(dat.s[dat.s$cov == 1, ], c("11", "1", "2"), traa, "0", 0) 190s > aa <- etm(dat.s, c("11", "1", "2"), traa, "0", 0) 190s > 190s > test <- etmCIF(Surv(time, to != 0) ~ 1, dat.s, etype = to) 190s > 190s > test.c <- etmCIF(Surv(time, to != 0) ~ cov, dat.s, etype = to) 190s > 190s > all.equal(trprob(aa, "11 1"), test[[1]]$est["0", "1", ]) 190s [1] TRUE 190s > all.equal(trprob(aa, "11 2"), test[[1]]$est["0", "2", ]) 190s [1] TRUE 190s > 190s > all.equal(trprob(aa0, "11 1"), test.c[[1]]$est["0", "1", ]) 190s [1] TRUE 190s > all.equal(trprob(aa0, "11 2"), test.c[[1]]$est["0", "2", ]) 190s [1] TRUE 190s > 190s > all.equal(trprob(aa1, "11 1"), test.c[[2]]$est["0", "1", ]) 190s [1] TRUE 190s > all.equal(trprob(aa1, "11 2"), test.c[[2]]$est["0", "2", ]) 190s [1] TRUE 190s > 190s > test 190s Call: etmCIF(formula = Surv(time, to != 0) ~ 1, data = dat.s, etype = to) 190s 190s time P se(P) n.event 190s CIF 1 4.9088 0.809108 0.079680 45 190s CIF 2 4.9088 0.096618 0.032905 8 190s > 190s > test.c 190s Call: etmCIF(formula = Surv(time, to != 0) ~ cov, data = dat.s, etype = to) 190s 190s Covariate: cov 190s levels: 0 1 190s 190s 190s cov = 0 190s time P se(P) n.event 190s CIF 1 2.1708 0.70246 0.105797 19 190s CIF 2 2.1708 0.11144 0.053384 4 190s 190s cov = 1 190s time P se(P) n.event 190s CIF 1 4.9088 0.80787 0.094051 26 190s CIF 2 4.9088 0.08436 0.040769 4 190s > 190s > summary(test) 190s 190s 190s 190s CIF 1 190s P time var lower upper n.risk n.event 190s 0.01000 0.0092099 0.0000990 0.0014147 0.068863 100 1 190s 0.11430 0.2663096 0.0010542 0.0649454 0.196993 81 1 190s 0.23451 0.7303091 0.0020436 0.1591107 0.337736 54 1 190s 0.40425 1.4299939 0.0032996 0.3020445 0.525741 29 1 190s 0.54593 2.0647206 0.0040836 0.4269008 0.673605 16 1 190s 0.80911 4.9087561 0.0063489 0.6359544 0.933733 2 1 190s 190s CIF 2 190s P time var lower upper n.risk n.event 190s 0.000000 0.0092099 0.00000000 0.000000 0.000000 100 0 190s 0.031657 0.2663096 0.00032353 0.010320 0.094942 81 0 190s 0.067029 0.7303091 0.00070366 0.030598 0.143503 54 0 190s 0.096618 1.4299939 0.00108275 0.049082 0.185474 29 0 190s 0.096618 2.0647206 0.00108275 0.049082 0.185474 16 0 190s 0.096618 4.9087561 0.00108275 0.049082 0.185474 2 0 190s 190s > summary(test.c) 190s 190s cov=0 190s 190s CIF 1 190s P time var lower upper n.risk n.event 190s 0.022222 0.0092099 0.00048285 0.0031605 0.14747 45 1 190s 0.092222 0.2982439 0.00193603 0.0355971 0.22762 36 0 190s 0.226684 0.7021938 0.00450954 0.1241760 0.39250 24 1 190s 0.378128 1.4299939 0.00760870 0.2337884 0.57145 13 1 190s 0.505736 1.6148774 0.00895330 0.3388425 0.69885 10 1 190s 0.702465 2.1708375 0.01119294 0.4944890 0.88399 3 1 190s 190s CIF 2 190s P time var lower upper n.risk n.event 190s 0.000000 0.0092099 0.0000000 0.000000 0.00000 45 0 190s 0.048441 0.2982439 0.0011168 0.012337 0.18013 36 1 190s 0.076411 0.7021938 0.0018104 0.025202 0.21928 24 0 190s 0.111440 1.4299939 0.0028499 0.042676 0.27392 13 0 190s 0.111440 1.6148774 0.0028499 0.042676 0.27392 10 0 190s 0.111440 2.1708375 0.0028499 0.042676 0.27392 3 0 190s 190s 190s cov=1 190s 190s CIF 1 190s P time var lower upper n.risk n.event 190s 0.018182 0.066692 0.00032457 0.0025813 0.12214 55 1 190s 0.112392 0.263808 0.00187215 0.0520925 0.23333 45 1 190s 0.241023 0.730309 0.00374499 0.1440057 0.38685 31 1 190s 0.401201 1.066913 0.00570788 0.2714008 0.56421 19 1 190s 0.592334 2.366275 0.00775985 0.4286230 0.76273 8 1 190s 0.807871 4.908756 0.00884554 0.6023185 0.94771 2 1 190s 190s CIF 2 190s P time var lower upper n.risk n.event 190s 0.000000 0.066692 0.00000000 0.000000 0.00000 55 0 190s 0.037434 0.263808 0.00067458 0.009494 0.14152 45 0 190s 0.059341 0.730309 0.00111295 0.019447 0.17351 31 0 190s 0.084360 1.066913 0.00166213 0.032211 0.21119 19 0 190s 0.084360 2.366275 0.00166213 0.032211 0.21119 8 0 190s 0.084360 4.908756 0.00166213 0.032211 0.21119 2 0 190s 190s > 190s > options(old) 190s > 190s BEGIN TEST tests.etm.R 190s 190s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 190s Copyright (C) 2024 The R Foundation for Statistical Computing 190s Platform: aarch64-unknown-linux-gnu (64-bit) 190s 190s R is free software and comes with ABSOLUTELY NO WARRANTY. 190s You are welcome to redistribute it under certain conditions. 190s Type 'license()' or 'licence()' for distribution details. 190s 190s R is a collaborative project with many contributors. 190s Type 'contributors()' for more information and 190s 'citation()' on how to cite R or R packages in publications. 190s 190s Type 'demo()' for some demos, 'help()' for on-line help, or 190s 'help.start()' for an HTML browser interface to help. 190s Type 'q()' to quit R. 190s 191s > require(etm) 191s Loading required package: etm 193s > 193s > ## Print with a bit less precision to avoid lots of notes in the comparison 193s > old <- options(digits = 4) 193s > 193s > ### Simple test 193s > 193s > time <- id <- 1:10 193s > from <- rep(0, 10) 193s > to <- rep(1, 10) 193s > 193s > data1 <- data.frame(id, from, to, time) 193s > tra1 <- matrix(FALSE, 2, 2) 194s > tra1[1, 2] <- TRUE 194s > 194s > etm1 <- etm(data1, c("0", "1"), tra1, NULL, 0) 194s > 194s > all.equal(as.vector(trprob(etm1, "0 0")), cumprod((10:1 - 1) / (10:1))) 194s [1] TRUE 194s > 194s > etm1$cov["0 0", "0 0", ] 194s 1 2 3 4 5 6 7 8 9 10 194s 0.009 0.016 0.021 0.024 0.025 0.024 0.021 0.016 0.009 0.000 194s > 194s > all.equal(etm1$cov["0 0", "0 0",], trcov(etm1, "0 0")) 194s [1] TRUE 194s > 194s > ### A simple test from AHR's author, where the first time is censored 194s > if (!require(survival)) { 194s + stop("This test requires the survival package") 194s + } 194s Loading required package: survival 194s > 194s > data <- data.frame(id=1:10, time=1:10, from=0, to=1, status=TRUE) 194s > 194s > tra <- matrix(FALSE, nrow=2, ncol=2) 194s > tra[1, 2] <- TRUE 194s > 194s > data$to[1] <- "cens" 194s > data$status[1] <- FALSE 194s > 194s > fit.km <- survfit(Surv(time, status) ~ 1, data=data) 194s > fit.etm <- etm(data, c("0","1"), tra, "cens", s=0, t="last", covariance=FALSE) 194s > 194s > all.equal(fit.km$surv[data$status], fit.etm$est[1,1,], check.attributes = FALSE) 194s [1] TRUE 194s > 194s > data$to[2] <- "cens" 194s > data$status[2] <- FALSE 194s > 194s > fit.km <- survfit(Surv(time, status) ~ 1, data=data) 194s > fit.etm <- etm(data, c("0","1"), tra, "cens", s=0, t="last", covariance=FALSE) 194s > 194s > all.equal(fit.km$surv[data$status], fit.etm$est[1,1,], check.attributes = FALSE) 194s [1] TRUE 194s > 194s > ### a bit more complicated 194s > 194s > time <- id <- 1:10 194s > from <- rep(0, 10) 194s > to <- rep(c(1, 2), 5) 194s > data2 <- data.frame(id, from, to, time) 194s > 194s > tra2 <- matrix(FALSE, 3, 3) 194s > tra2[1, 2:3] <- TRUE 194s > 194s > etm2 <- etm(data2, c("0", "1", "2"), tra2, NULL, 0) 194s > 194s > aa <- table(time, to) 194s > 194s > cif1 <- cumsum(aa[, 1] / 10) 194s > cif2 <- cumsum(aa[, 2] / 10) 194s > surv <- cumprod((10:1 - 1) / (10:1)) 194s > 194s > all.equal(trprob(etm2, "0 1"), cif1) 194s [1] TRUE 194s > all.equal(trprob(etm2, "0 2"), cif2) 194s [1] TRUE 194s > all.equal(as.vector(trprob(etm2, "0 0")), surv) 194s [1] TRUE 194s > 194s > ## a test on id 194s > data2$id <- letters[1:10] 194s > 194s > etm3 <- etm(data2, c("0", "1", "2"), tra2, NULL, 0) 194s > 194s > all.equal(trprob(etm2, "0 1"), trprob(etm3, "0 1")) 194s [1] TRUE 194s > all.equal(trprob(etm2, "0 2"), trprob(etm3, "0 2")) 194s [1] TRUE 194s > all.equal(trprob(etm2, "0 0"), trprob(etm3, "0 0")) 194s [1] TRUE 194s > 194s > 194s > ### Test on sir.cont 194s > 194s > data(sir.cont) 194s > 194s > ## Modification for patients entering and leaving a state 194s > ## at the same date 194s > ## Change on ventilation status is considered 194s > ## to happen before end of hospital stay 194s > sir.cont <- sir.cont[order(sir.cont$id, sir.cont$time), ] 194s > for (i in 2:nrow(sir.cont)) { 194s + if (sir.cont$id[i]==sir.cont$id[i-1]) { 194s + if (sir.cont$time[i]==sir.cont$time[i-1]) { 194s + sir.cont$time[i-1] <- sir.cont$time[i-1] - 0.5 194s + } 194s + } 194s + } 194s > 194s > ### Computation of the transition probabilities 194s > ## Possible transitions. 194s > tra <- matrix(ncol=3,nrow=3,FALSE) 194s > tra[1, 2:3] <- TRUE 194s > tra[2, c(1, 3)] <- TRUE 194s > 194s > ## etm 194s > prob.sir <- etm(sir.cont, c("0", "1", "2"), tra, "cens", 1) 194s > 194s > prob.sir 194s Multistate model with 2 transient state(s) 194s and 1 absorbing state(s) 194s 194s Possible transitions: 194s from to 194s 0 1 194s 0 2 194s 1 0 194s 1 2 194s 194s Estimate of P(1, 183) 194s 0 1 2 194s 0 0 0 1 194s 1 0 0 1 194s 2 0 0 1 194s 194s > 194s > summ.sir <- summary(prob.sir) 194s > all.equal(summ.sir[['0 1']]$P, as.vector(trprob(prob.sir, "0 1"))) 194s [1] TRUE 194s > subset(summ.sir[[3]],time<183) # issue with precision on different architectures 194s P time var lower upper n.risk n.event 194s 1.5 0.0000 1.5 0.000e+00 0.00000 0.0000 394 0 194s 2 0.1187 2.0 2.641e-04 0.08683 0.1505 396 47 194s 2.5 0.1187 2.5 2.641e-04 0.08683 0.1505 364 0 194s 3 0.2454 3.0 4.465e-04 0.20398 0.2868 365 54 194s 3.5 0.2454 3.5 4.465e-04 0.20398 0.2868 328 0 194s 4 0.3806 4.0 5.416e-04 0.33501 0.4262 331 62 194s 4.5 0.3806 4.5 5.416e-04 0.33501 0.4262 280 0 194s 5 0.4792 5.0 5.480e-04 0.43333 0.5251 283 48 194s 5.5 0.4792 5.5 5.480e-04 0.43333 0.5251 248 0 194s 6 0.5693 6.0 5.141e-04 0.52482 0.6137 249 47 194s 7 0.6350 7.0 4.665e-04 0.59266 0.6773 212 36 194s 8 0.6795 8.0 4.202e-04 0.63931 0.7197 195 27 194s 8.5 0.6795 8.5 4.202e-04 0.63931 0.7197 172 0 194s 9 0.7325 9.0 3.580e-04 0.69541 0.7696 173 34 194s 10 0.7647 10.0 3.141e-04 0.72992 0.7994 148 21 194s 10.5 0.7647 10.5 3.141e-04 0.72992 0.7994 135 0 194s 11 0.7895 11.0 2.790e-04 0.75674 0.8222 136 18 194s 12 0.8138 12.0 2.420e-04 0.78330 0.8443 129 18 194s 12.5 0.8138 12.5 2.420e-04 0.78330 0.8443 117 0 194s 13 0.8294 13.0 2.182e-04 0.80045 0.8584 118 13 194s 14 0.8452 14.0 1.938e-04 0.81789 0.8725 115 14 194s 15 0.8625 15.0 1.670e-04 0.83714 0.8878 106 15 194s 16 0.8723 16.0 1.522e-04 0.84807 0.8964 93 9 194s 17 0.8852 17.0 1.330e-04 0.86256 0.9078 86 12 194s 17.5 0.8852 17.5 1.330e-04 0.86256 0.9078 77 0 194s 18 0.8960 18.0 1.168e-04 0.87484 0.9172 76 9 194s 19 0.9029 19.0 1.070e-04 0.88261 0.9232 71 7 194s 20 0.9125 20.0 9.367e-05 0.89356 0.9315 64 10 194s 21 0.9161 21.0 8.878e-05 0.89768 0.9346 57 4 194s 22 0.9226 22.0 7.996e-05 0.90504 0.9401 55 6 194s 23 0.9261 23.0 7.537e-05 0.90904 0.9431 51 4 194s 23.5 0.9261 23.5 7.537e-05 0.90904 0.9431 49 0 194s 24 0.9354 24.0 6.292e-05 0.91982 0.9509 50 9 194s 25 0.9385 25.0 5.878e-05 0.92352 0.9536 42 3 194s 26 0.9429 26.0 5.326e-05 0.92863 0.9572 39 5 194s 27 0.9477 27.0 4.749e-05 0.93417 0.9612 35 6 194s 27.5 0.9477 27.5 4.749e-05 0.93417 0.9612 29 0 194s 28 0.9531 28.0 4.093e-05 0.94059 0.9657 30 5 194s 29 0.9567 29.0 3.668e-05 0.94485 0.9686 31 4 194s 30 0.9592 30.0 3.384e-05 0.94779 0.9706 28 3 194s 30.5 0.9592 30.5 3.384e-05 0.94779 0.9706 29 0 194s 31 0.9642 31.0 2.821e-05 0.95383 0.9746 30 6 194s 32 0.9649 32.0 2.752e-05 0.95458 0.9751 25 1 194s 33 0.9669 33.0 2.533e-05 0.95708 0.9768 24 2 194s 34 0.9685 34.0 2.368e-05 0.95900 0.9781 26 2 194s 35 0.9697 35.0 2.252e-05 0.96036 0.9790 28 2 194s 36 0.9702 36.0 2.194e-05 0.96104 0.9794 26 1 194s 37 0.9718 37.0 2.043e-05 0.96290 0.9806 26 2 194s 38 0.9739 38.0 1.831e-05 0.96555 0.9823 25 4 194s 38.5 0.9739 38.5 1.831e-05 0.96555 0.9823 21 0 194s 39 0.9760 39.0 1.643e-05 0.96802 0.9839 23 3 194s 40 0.9769 40.0 1.558e-05 0.96918 0.9847 19 1 194s 41 0.9774 41.0 1.512e-05 0.96981 0.9851 22 1 194s 42 0.9779 42.0 1.476e-05 0.97032 0.9854 22 0 194s 43 0.9798 43.0 1.308e-05 0.97271 0.9869 22 3 194s 44 0.9803 44.0 1.265e-05 0.97333 0.9873 21 1 194s 45 0.9817 45.0 1.157e-05 0.97499 0.9883 19 1 194s 46 0.9822 46.0 1.116e-05 0.97561 0.9887 17 1 194s 47 0.9831 47.0 1.037e-05 0.97683 0.9895 18 2 194s 48 0.9836 48.0 9.987e-06 0.97743 0.9898 17 1 194s 49 0.9841 49.0 9.669e-06 0.97796 0.9901 17 0 194s 50 0.9845 50.0 9.297e-06 0.97856 0.9905 17 1 194s 50.5 0.9845 50.5 9.297e-06 0.97856 0.9905 16 0 194s 51 0.9860 51.0 8.214e-06 0.98037 0.9916 17 3 194s 52 0.9870 52.0 7.513e-06 0.98159 0.9923 14 2 194s 53 0.9879 53.0 6.875e-06 0.98276 0.9930 12 1 194s 54 0.9889 54.0 6.214e-06 0.98397 0.9937 12 2 194s 55 0.9903 55.0 5.254e-06 0.98581 0.9948 10 3 194s 56 0.9913 56.0 4.667e-06 0.98703 0.9955 6 1 194s 57 0.9917 57.0 4.364e-06 0.98765 0.9958 5 1 194s 58 0.9922 58.0 4.064e-06 0.98828 0.9962 4 1 194s 59 0.9927 59.0 3.769e-06 0.98891 0.9965 3 1 194s 60 0.9932 60.0 3.488e-06 0.98953 0.9969 3 1 194s 62 0.9937 62.0 3.230e-06 0.99016 0.9972 2 0 194s 63 0.9942 63.0 2.956e-06 0.99079 0.9975 2 1 194s 68 0.9942 68.0 2.956e-06 0.99079 0.9975 1 0 194s 70 0.9946 70.0 2.694e-06 0.99143 0.9979 2 1 194s 78 0.9951 78.0 2.442e-06 0.99207 0.9982 1 0 194s 80 0.9951 80.0 2.442e-06 0.99207 0.9982 1 0 194s 85 0.9966 85.0 1.695e-06 0.99404 0.9991 2 0 194s 89 0.9966 89.0 1.695e-06 0.99404 0.9991 2 0 194s 90 0.9966 90.0 1.695e-06 0.99404 0.9991 1 0 194s 95 0.9971 95.0 1.448e-06 0.99472 0.9994 2 0 194s 100 0.9976 100.0 1.203e-06 0.99542 0.9997 3 0 194s 101 0.9981 101.0 9.592e-07 0.99613 1.0000 3 1 194s 108 0.9985 108.0 7.169e-07 0.99688 1.0000 2 1 194s 113 0.9990 113.0 4.764e-07 0.99767 1.0000 1 0 194s 116 0.9990 116.0 4.764e-07 0.99767 1.0000 1 0 194s 124 0.9990 124.0 4.764e-07 0.99767 1.0000 2 0 194s 164 0.9990 164.0 4.764e-07 0.99767 1.0000 0 0 194s > 194s > ## gonna play a bit with the state names 194s > dd <- sir.cont 194s > dd$from <- ifelse(dd$from == 0, "initial state", "ventilation") 194s > dd$to <- as.character(dd$to) 194s > for (i in seq_len(nrow(dd))) { 194s + dd$to[i] <- switch(dd$to[i], 194s + "0" = "initial state", 194s + "1" = "ventilation", 194s + "2" = "end of story", 194s + "cens" = "cens" 194s + ) 194s + } 194s > 194s > test <- etm(dd, c("initial state", "ventilation", "end of story"), tra, "cens", 1) 194s > 194s > all.equal(test$est["initial state", "initial state", ], 194s + prob.sir$est["0", "0", ]) 194s [1] TRUE 194s > all.equal(trprob(test, "initial state initial state"), trprob(prob.sir, "0 0")) 194s [1] TRUE 194s > all.equal(trprob(test, "initial state ventilation"), trprob(prob.sir, "0 1")) 194s [1] TRUE 194s > all.equal(trprob(test, "initial state end of story"), trprob(prob.sir, "0 2")) 194s [1] TRUE 194s > 194s > all.equal(trcov(test, "initial state end of story"), trcov(prob.sir, "0 2")) 194s [1] TRUE 194s > 194s > aa <- summary(test) 194s > all.equal(summ.sir[[6]], aa[[6]]) 194s [1] TRUE 194s > all.equal(summ.sir[[4]], aa[[4]]) 194s [1] TRUE 194s > 194s > ### Test on abortion data 194s > 194s > data(abortion) 194s > 194s > from <- rep(0, nrow(abortion)) 194s > to <- abortion$cause 194s > entry <- abortion$entry 194s > exit <- abortion$exit 194s > id <- 1:nrow(abortion) 194s > data <- data.frame(id, from, to, entry, exit, group = abortion$group) 194s > 194s > ## Computation of the CIFs 194s > tra <- matrix(FALSE, 4, 4) 194s > tra[1, 2:4] <- TRUE 194s > 194s > cif.control <- etm(data[data$group == 0, ], c("0", "1", "2", "3"), 194s + tra, NULL, 0) 194s > cif.exposed <- etm(data[data$group == 1, ], c("0", "1", "2", "3"), 194s + tra, NULL, 0) 194s > 194s > all.equal(trprob(cif.control, "0 1"), cif.control$est["0", "1", ]) 194s [1] TRUE 194s > all.equal(trcov(cif.control, c("0 1", "0 2")), cif.control$cov["0 1", "0 2", ]) 194s [1] TRUE 194s > 194s > trprob(cif.control, "0 1") 194s 6 7 8 9 10 11 12 13 194s 0.000000 0.007401 0.014881 0.026509 0.033208 0.037694 0.037694 0.038955 194s 14 17 19 21 24 25 26 30 194s 0.040159 0.040159 0.040159 0.040159 0.040159 0.040159 0.040159 0.040159 194s 31 32 33 34 35 36 37 38 194s 0.040159 0.040159 0.040159 0.040159 0.040159 0.040159 0.040159 0.040159 194s 39 40 41 42 43 194s 0.040159 0.040159 0.040159 0.040159 0.040159 194s > trprob(cif.control, "0 2") 194s 6 7 8 9 10 11 12 13 194s 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 194s 14 17 19 21 24 25 26 30 194s 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.003657 194s 31 32 33 34 35 36 37 38 194s 0.006371 0.008175 0.013543 0.023317 0.031260 0.053197 0.084529 0.179163 194s 39 40 41 42 43 194s 0.322016 0.563121 0.742227 0.793893 0.799059 194s > trprob(cif.control, "0 0") 194s 6 7 8 9 10 11 12 13 194s 0.965812 0.932508 0.887628 0.862433 0.838989 0.822538 0.813099 0.810578 194s 14 17 19 21 24 25 26 30 194s 0.806964 0.805874 0.803810 0.802804 0.801837 0.800883 0.799937 0.796280 194s 31 32 33 34 35 36 37 38 194s 0.793565 0.791762 0.786394 0.776620 0.768677 0.745862 0.714531 0.619897 194s 39 40 41 42 43 194s 0.477043 0.235938 0.056832 0.005167 0.000000 194s > 194s > trcov(cif.control, "0 1") 194s 6 7 8 9 10 11 12 13 194s 0.000e+00 2.719e-05 4.533e-05 6.665e-05 7.698e-05 8.304e-05 8.304e-05 8.444e-05 194s 14 17 19 21 24 25 26 30 194s 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 194s 31 32 33 34 35 36 37 38 194s 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 194s 39 40 41 42 43 194s 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 194s > trcov(cif.control, "0 2") 194s 6 7 8 9 10 11 12 13 194s 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 194s 14 17 19 21 24 25 26 30 194s 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 3.338e-06 194s 31 32 33 34 35 36 37 38 194s 5.784e-06 7.401e-06 1.216e-05 2.072e-05 2.758e-05 4.619e-05 7.202e-05 1.461e-04 194s 39 40 41 42 43 194s 2.470e-04 3.880e-04 4.702e-04 4.903e-04 4.922e-04 194s > trcov(cif.control, "0 0") 194s 6 7 8 9 10 11 12 13 194s 2.822e-04 3.821e-04 4.527e-04 4.748e-04 4.875e-04 4.927e-04 4.941e-04 4.942e-04 194s 14 17 19 21 24 25 26 30 194s 4.941e-04 4.940e-04 4.936e-04 4.933e-04 4.931e-04 4.928e-04 4.926e-04 4.914e-04 194s 31 32 33 34 35 36 37 38 194s 4.905e-04 4.899e-04 4.880e-04 4.846e-04 4.816e-04 4.729e-04 4.601e-04 4.176e-04 194s 39 40 41 42 43 194s 3.425e-04 1.865e-04 4.797e-05 4.441e-06 0.000e+00 194s > 194s > aa <- summary(cif.control) 194s > aa$"0 1" 194s P time var lower upper n.risk n.event 194s 6 0.000000 6 0.000e+00 0.000000 0.00000 117 0 194s 7 0.007401 7 2.719e-05 0.000000 0.01762 261 2 194s 8 0.014881 8 4.533e-05 0.001685 0.02808 374 3 194s 9 0.026509 9 6.665e-05 0.010508 0.04251 458 6 194s 10 0.033208 10 7.698e-05 0.016011 0.05040 515 4 194s 11 0.037694 11 8.304e-05 0.019834 0.05555 561 3 194s 12 0.037694 12 8.304e-05 0.019834 0.05555 610 0 194s 13 0.038955 13 8.444e-05 0.020944 0.05697 645 1 194s 14 0.040159 14 8.571e-05 0.022014 0.05830 673 1 194s 17 0.040159 17 8.571e-05 0.022014 0.05830 740 0 194s 19 0.040159 19 8.571e-05 0.022014 0.05830 781 0 194s 21 0.040159 21 8.571e-05 0.022014 0.05830 799 0 194s 24 0.040159 24 8.571e-05 0.022014 0.05830 830 0 194s 25 0.040159 25 8.571e-05 0.022014 0.05830 841 0 194s 26 0.040159 26 8.571e-05 0.022014 0.05830 846 0 194s 30 0.040159 30 8.571e-05 0.022014 0.05830 875 0 194s 31 0.040159 31 8.571e-05 0.022014 0.05830 880 0 194s 32 0.040159 32 8.571e-05 0.022014 0.05830 880 0 194s 33 0.040159 33 8.571e-05 0.022014 0.05830 885 0 194s 34 0.040159 34 8.571e-05 0.022014 0.05830 885 0 194s 35 0.040159 35 8.571e-05 0.022014 0.05830 880 0 194s 36 0.040159 36 8.571e-05 0.022014 0.05830 876 0 194s 37 0.040159 37 8.571e-05 0.022014 0.05830 857 0 194s 38 0.040159 38 8.571e-05 0.022014 0.05830 823 0 194s 39 0.040159 39 8.571e-05 0.022014 0.05830 716 0 194s 40 0.040159 40 8.571e-05 0.022014 0.05830 554 0 194s 41 0.040159 41 8.571e-05 0.022014 0.05830 274 0 194s 42 0.040159 42 8.571e-05 0.022014 0.05830 66 0 194s 43 0.040159 43 8.571e-05 0.022014 0.05830 6 0 194s > all.equal(aa$"0 1"$P, as.vector(trprob(cif.control, "0 1"))) 194s [1] TRUE 194s > 194s > ### test on los data 194s > 194s > data(los.data) # in package changeLOS 194s > 194s > ## putting los.data in the long format (see changeLOS) 194s > my.observ <- prepare.los.data(x=los.data) 194s > 194s > tra <- matrix(FALSE, 4, 4) 194s > tra[1, 2:4] <- TRUE 194s > tra[2, 3:4] <- TRUE 194s > 194s > tr.prob <- etm(my.observ, c("0","1","2","3"), tra, NULL, 0) 194s > 194s > tr.prob 194s Multistate model with 2 transient state(s) 194s and 2 absorbing state(s) 194s 194s Possible transitions: 194s from to 194s 0 1 194s 0 2 194s 0 3 194s 1 2 194s 1 3 194s 194s Estimate of P(0, 82) 194s 0 1 2 3 194s 0 0 0 0.7474 0.2526 194s 1 0 0 0.7073 0.2927 194s 2 0 0 1.0000 0.0000 194s 3 0 0 0.0000 1.0000 194s 194s > summary(tr.prob) 194s Transition 0 0 194s P time var lower upper n.risk n.event 194s 0.882275 3 1.374e-04 0.8593018 0.905248 756 0 194s 0.112434 15 1.320e-04 0.0899155 0.134952 90 0 194s 0.031746 27 4.066e-05 0.0192484 0.044244 26 0 194s 0.006614 41 8.690e-06 0.0008359 0.012392 5 0 194s 0.002646 61 3.490e-06 0.0000000 0.006307 3 0 194s 0.000000 82 0.000e+00 0.0000000 0.000000 1 0 194s 194s Transition 0 1 194s P time var lower upper n.risk n.event 194s 0.017196 3 2.235e-05 0.0079289 0.02646 756 13 194s 0.063492 15 7.865e-05 0.0461099 0.08087 90 0 194s 0.030423 27 3.902e-05 0.0181805 0.04267 26 1 194s 0.015873 41 2.066e-05 0.0069637 0.02478 5 0 194s 0.005291 61 6.962e-06 0.0001197 0.01046 3 0 194s 0.000000 82 0.000e+00 0.0000000 0.00000 1 0 194s 194s Transition 0 2 194s P time var lower upper n.risk n.event 194s 0.08466 3 0.0001025 0.06481 0.1045 756 64 194s 0.62302 15 0.0003107 0.58847 0.6576 90 4 194s 0.69841 27 0.0002786 0.66570 0.7311 26 1 194s 0.72751 41 0.0002622 0.69578 0.7593 5 0 194s 0.74074 61 0.0002540 0.70950 0.7720 3 1 194s 0.74735 82 0.0002498 0.71638 0.7783 1 1 194s 194s Transition 0 3 194s P time var lower upper n.risk n.event 194s 0.01587 3 2.066e-05 0.006964 0.02478 756 12 194s 0.20106 15 2.125e-04 0.172489 0.22963 90 1 194s 0.23942 27 2.409e-04 0.208999 0.26984 26 0 194s 0.25000 41 2.480e-04 0.219133 0.28087 5 0 194s 0.25132 61 2.489e-04 0.220402 0.28224 3 0 194s 0.25265 82 2.498e-04 0.221671 0.28362 1 0 194s 194s Transition 1 1 194s P time var lower upper n.risk n.event 194s 1.00000 3 0.000e+00 1.00000 1.00000 0 0 194s 0.38661 15 2.358e-03 0.29143 0.48179 51 0 194s 0.12119 27 7.842e-04 0.06630 0.17607 23 0 194s 0.04593 41 2.405e-04 0.01554 0.07633 14 0 194s 0.01531 61 6.579e-05 0.00000 0.03121 4 0 194s 0.00000 82 0.000e+00 0.00000 0.00000 0 0 194s 194s Transition 1 2 194s P time var lower upper n.risk n.event 194s 0.0000 3 0.000000 0.0000 0.0000 0 0 194s 0.4107 15 0.002590 0.3110 0.5104 51 2 194s 0.6082 27 0.002254 0.5151 0.7012 23 1 194s 0.6652 41 0.002064 0.5761 0.7542 14 2 194s 0.6920 61 0.002000 0.6043 0.7796 4 0 194s 0.7073 82 0.001984 0.6200 0.7946 0 0 194s 194s Transition 1 3 194s P time var lower upper n.risk n.event 194s 0.0000 3 0.000000 0.0000 0.0000 0 0 194s 0.2027 15 0.001784 0.1199 0.2855 51 1 194s 0.2706 27 0.001968 0.1837 0.3576 23 0 194s 0.2889 41 0.001982 0.2016 0.3761 14 0 194s 0.2927 61 0.001984 0.2054 0.3800 4 0 194s 0.2927 82 0.001984 0.2054 0.3800 0 0 194s 194s > 194s > cLOS <- etm::clos(tr.prob, aw = TRUE) 194s > 194s > cLOS 194s The expected change in length of stay is: 194s 1.975 194s 194s Alternative weighting: 194s 194s Expected change in LOS with weight.1: 2.097 194s Expected change in LOS with weight.other: 1.951 194s > 194s > 194s > ### Tests on pseudo values 194s > t_pseudo <- closPseudo(my.observ, c("0","1","2","3"), tra, NULL, 194s + formula = ~ 1, aw = TRUE) 235s > 235s > cLOS$e.phi == t_pseudo$theta[, "e.phi"] 235s [,1] 235s [1,] TRUE 235s > cLOS$e.phi.weights.1 == t_pseudo$theta[, "e.phi.weights.1"] 235s [,1] 235s [1,] TRUE 235s > cLOS$e.phi.weights.other == t_pseudo$theta[, "e.phi.weights.other"] 235s [,1] 235s [1,] TRUE 235s > 235s > mean(t_pseudo$pseudoData$ps.e.phi) 235s [1] 1.968 235s > 235s > ### tests on etmprep 235s > 235s > ### creation of fake data in the wild format, following an illness-death model 235s > ## transition times 235s > tdisease <- c(3, 4, 3, 6, 8, 9) 235s > tdeath <- c(6, 9, 8, 6, 8, 9) 235s > 235s > ## transition status 235s > stat.disease <- c(1, 1, 1, 0, 0, 0) 235s > stat.death <- c(1, 1, 1, 1, 1, 0) 235s > 235s > ## a covariate that we want to keep in the new data 235s > set.seed(1313) 235s > cova <- rbinom(6, 1, 0.5) 235s > 235s > dat <- data.frame(tdisease, tdeath, 235s + stat.disease, stat.death, 235s + cova) 235s > 235s > ## Possible transitions 235s > tra <- matrix(FALSE, 3, 3) 235s > tra[1, 2:3] <- TRUE 235s > tra[2, 3] <- TRUE 235s > 235s > ## data preparation 235s > newdat <- etmprep(c(NA, "tdisease", "tdeath"), 235s + c(NA, "stat.disease", "stat.death"), 235s + data = dat, tra = tra, 235s + cens.name = "cens", keep = "cova") 235s > 235s > newdat 235s id entry exit from to cova 235s 1 1 0 3 0 1 1 235s 2 1 3 6 1 2 1 235s 3 2 0 4 0 1 0 235s 4 2 4 9 1 2 0 235s 5 3 0 3 0 1 1 235s 6 3 3 8 1 2 1 235s 7 4 0 6 0 2 0 235s 8 5 0 8 0 2 1 235s 9 6 0 9 0 cens 1 235s > 235s > ref <- data.frame(id = c(1, 1, 2, 2, 3, 3, 4, 5, 6), 235s + entry = c(0, 3, 0, 4, 0, 3, 0, 0, 0), 235s + exit = c(3, 6, 4, 9, 3, 8, 6, 8, 9), 235s + from = c(0, 1, 0, 1, 0, 1, 0, 0, 0), 235s + to = c(rep(c(1, 2), 3), 2, 2, "cens"), 235s + cova = c(1, 1, 0, 0, 1, 1, 0, 1, 1)) 235s > ref$from <- factor(as.character(ref$from), levels = c("0", "1", "2", "cens")) 235s > ref$to <- factor(as.character(ref$to), levels = c("0", "1", "2", "cens")) 235s > 235s > all.equal(ref, newdat) 235s [1] TRUE 235s > 235s > 235s > ###################################### 235s > ### Test the stratified calls 235s > ###################################### 235s > 235s > if (require("kmi", quietly = TRUE)) { 235s + library(etm) 235s + 235s + data(icu.pneu) 235s + my.icu.pneu <- icu.pneu 235s + 235s + my.icu.pneu <- my.icu.pneu[order(my.icu.pneu$id, my.icu.pneu$start), ] 235s + masque <- diff(my.icu.pneu$id) 235s + 235s + my.icu.pneu$from <- 0 235s + my.icu.pneu$from[c(1, masque) == 0] <- 1 235s + 235s + my.icu.pneu$to2 <- my.icu.pneu$event 235s + my.icu.pneu$to2[my.icu.pneu$status == 0] <- "cens" 235s + my.icu.pneu$to2[c(masque, 1) == 0] <- 1 235s + 235s + 235s + my.icu.pneu$to <- ifelse(my.icu.pneu$to2 %in% c(2, 3), 2, 235s + my.icu.pneu$to2) 235s + 235s + my.icu.pneu <- my.icu.pneu[, c("id", "start", "stop", "from", "to", 235s + "to2", "age", "sex")] 235s + names(my.icu.pneu)[c(2, 3)] <- c("entry", "exit") 235s + 235s + bouh_strat <- etm(my.icu.pneu, c("0", "1", "2"), tra_ill(), "cens", 0, strata = "sex") 235s + 235s + bouh_female <- etm(my.icu.pneu[my.icu.pneu$sex == "F", ], 235s + c("0", "1", "2"), tra_ill(), "cens", 0) 235s + 235s + all(bouh_strat[[1]]$est == bouh_female$est) 235s + 235s + ## Test the summary 235s + the_summary <- summary(bouh_strat) 235s + the_summary 235s + 235s + ## Test trprob 235s + all(trprob(bouh_strat, "0 1")[[1]] == trprob(bouh_female, "0 1")) 235s + all(trprob(bouh_strat, "0 1", c(0, 5, 10, 15))[[1]] == trprob(bouh_female, "0 1", c(0, 5, 10, 15))) 235s + 235s + ## Test trcov 235s + all(trcov(bouh_strat, "0 1")[[1]] == trcov(bouh_female, "0 1")) 235s + all(trcov(bouh_strat, c("0 1", "0 2"))[[1]] == trcov(bouh_female, c("0 1", "0 2"))) 235s + all(trcov(bouh_strat, "0 1", c(0, 5, 10, 15))[[1]] == trcov(bouh_female, "0 1", c(0, 5, 10, 15))) 235s + } else { 235s + print("These tests require the kmi package") 235s + } 236s [1] TRUE 236s > 236s > options(old) 236s > 236s autopkgtest [18:30:21]: test run-unit-test: -----------------------] 237s run-unit-test PASS 237s autopkgtest [18:30:22]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 237s autopkgtest [18:30:22]: test pkg-r-autopkgtest: preparing testbed 239s Reading package lists... 240s Building dependency tree... 240s Reading state information... 241s Starting pkgProblemResolver with broken count: 0 241s Starting 2 pkgProblemResolver with broken count: 0 241s Done 243s The following additional packages will be installed: 243s build-essential cpp cpp-13 cpp-13-aarch64-linux-gnu cpp-aarch64-linux-gnu 243s dctrl-tools g++ g++-13 g++-13-aarch64-linux-gnu g++-aarch64-linux-gnu gcc 243s gcc-13 gcc-13-aarch64-linux-gnu gcc-aarch64-linux-gnu gfortran gfortran-13 243s gfortran-13-aarch64-linux-gnu gfortran-aarch64-linux-gnu icu-devtools 243s libasan8 libatomic1 libblas-dev libbz2-dev libc-dev-bin libc6-dev libcc1-0 243s libcrypt-dev libgcc-13-dev libgfortran-13-dev libhwasan0 libicu-dev libisl23 243s libitm1 libjpeg-dev libjpeg-turbo8-dev libjpeg8-dev liblapack-dev liblsan0 243s liblzma-dev libmpc3 libncurses-dev libnsl-dev libpcre2-16-0 libpcre2-32-0 243s libpcre2-dev libpcre2-posix3 libpkgconf3 libpng-dev libreadline-dev 243s libstdc++-13-dev libtirpc-dev libtsan2 libubsan1 linux-libc-dev pkg-config 243s pkg-r-autopkgtest pkgconf pkgconf-bin r-base-dev r-cran-backports 243s r-cran-broom r-cran-cli r-cran-colorspace r-cran-cpp11 r-cran-dplyr 243s r-cran-ellipsis r-cran-fansi r-cran-farver r-cran-geepack r-cran-generics 243s r-cran-ggplot2 r-cran-glue r-cran-gtable r-cran-isoband r-cran-labeling 243s r-cran-lifecycle r-cran-magrittr r-cran-mass r-cran-mgcv r-cran-munsell 243s r-cran-nlme r-cran-pillar r-cran-pkgconfig r-cran-purrr r-cran-r6 243s r-cran-rcolorbrewer r-cran-rlang r-cran-scales r-cran-stringi r-cran-stringr 243s r-cran-tibble r-cran-tidyr r-cran-tidyselect r-cran-utf8 r-cran-vctrs 243s r-cran-viridislite r-cran-withr rpcsvc-proto zlib1g-dev 243s Suggested packages: 243s cpp-doc gcc-13-locales cpp-13-doc debtags gcc-13-doc gcc-multilib 243s manpages-dev autoconf automake libtool flex bison gdb gcc-doc 243s gdb-aarch64-linux-gnu gfortran-doc gfortran-13-doc libcoarrays-dev 243s liblapack-doc glibc-doc icu-doc liblzma-doc ncurses-doc readline-doc 243s libstdc++-13-doc texlive-base texlive-latex-base texlive-plain-generic 243s texlive-fonts-recommended texlive-fonts-extra texlive-extra-utils 243s texlive-latex-recommended texlive-latex-extra texinfo r-cran-aer 243s r-cran-bbmle r-cran-boot r-cran-car r-cran-cardata r-cran-caret 243s r-cran-cluster r-cran-cmprsk r-cran-coda r-cran-covr r-cran-e1071 243s r-cran-emmeans r-cran-epir r-cran-gam r-cran-gee r-cran-glmnet r-cran-gmm 243s r-cran-hmisc r-cran-irlba r-cran-interp r-cran-knitr r-cran-ks r-cran-lavaan 243s r-cran-leaps r-cran-lme4 r-cran-lmtest r-cran-lsmeans r-cran-maps 243s r-cran-mclust r-cran-metafor r-cran-modeldata r-cran-multcomp r-cran-network 243s r-cran-nnet r-cran-ordinal r-cran-plm r-cran-psych r-cran-quantreg 243s r-cran-rmarkdown r-cran-robust r-cran-robustbase r-cran-rsample 243s r-cran-sandwich r-cran-sp r-cran-spdep r-cran-spatialreg r-cran-spelling 243s r-cran-survey r-cran-systemfit r-cran-tseries r-cran-zoo r-cran-kernsmooth 243s r-cran-kernlab r-cran-mvtnorm r-cran-vcd r-cran-shiny r-cran-shinyjs 243s r-cran-png r-cran-jpeg r-cran-viridis r-cran-magick r-cran-sf r-cran-bit64 243s r-cran-formattable r-cran-nanotime r-cran-palmerpenguins r-cran-units 243s r-cran-vdiffr r-cran-testthat r-cran-bench r-cran-blob r-cran-brio 243s r-cran-callr r-cran-crayon r-cran-evaluate r-cran-here r-cran-hms 243s r-cran-htmltools r-cran-pkgbuild r-cran-pkgload 243s Recommended packages: 243s bzip2-doc manpages manpages-dev libc-devtools libpng-tools r-cran-testthat 243s r-cran-callr r-cran-covr r-cran-crayon r-cran-digest r-cran-htmltools 243s r-cran-htmlwidgets r-cran-knitr r-cran-mockery r-cran-processx r-cran-ps 243s r-cran-rmarkdown r-cran-rprojroot r-cran-rstudioapi r-cran-whoami 243s r-cran-bench r-cran-brio r-cran-decor r-cran-desc r-cran-lobstr 243s r-cran-progress r-cran-dbplyr r-cran-rmysql r-cran-rpostgresql 243s r-cran-rsqlite r-cran-unitizer r-cran-pkgload r-cran-hexbin r-cran-hmisc 243s r-cran-mapproj r-cran-maps r-cran-multcomp r-cran-profvis r-cran-quantreg 243s r-cran-ragg r-cran-rpart r-cran-sf r-cran-svglite r-cran-vdiffr r-cran-xml2 243s r-cran-waldo r-cran-lintr r-cran-tidyverse r-cran-lubridate r-cran-httr 243s r-cran-fs r-cran-usethis r-cran-bit64 r-cran-dichromat r-cran-hms 243s r-cran-mockr r-cran-formattable r-cran-readr r-cran-pkgdown r-cran-zeallot 243s The following NEW packages will be installed: 243s autopkgtest-satdep build-essential cpp cpp-13 cpp-13-aarch64-linux-gnu 243s cpp-aarch64-linux-gnu dctrl-tools g++ g++-13 g++-13-aarch64-linux-gnu 243s g++-aarch64-linux-gnu gcc gcc-13 gcc-13-aarch64-linux-gnu 243s gcc-aarch64-linux-gnu gfortran gfortran-13 gfortran-13-aarch64-linux-gnu 243s gfortran-aarch64-linux-gnu icu-devtools libasan8 libatomic1 libblas-dev 243s libbz2-dev libc-dev-bin libc6-dev libcc1-0 libcrypt-dev libgcc-13-dev 243s libgfortran-13-dev libhwasan0 libicu-dev libisl23 libitm1 libjpeg-dev 243s libjpeg-turbo8-dev libjpeg8-dev liblapack-dev liblsan0 liblzma-dev libmpc3 243s libncurses-dev libnsl-dev libpcre2-16-0 libpcre2-32-0 libpcre2-dev 243s libpcre2-posix3 libpkgconf3 libpng-dev libreadline-dev libstdc++-13-dev 243s libtirpc-dev libtsan2 libubsan1 linux-libc-dev pkg-config pkg-r-autopkgtest 243s pkgconf pkgconf-bin r-base-dev r-cran-backports r-cran-broom r-cran-cli 243s r-cran-colorspace r-cran-cpp11 r-cran-dplyr r-cran-ellipsis r-cran-fansi 243s r-cran-farver r-cran-geepack r-cran-generics r-cran-ggplot2 r-cran-glue 243s r-cran-gtable r-cran-isoband r-cran-labeling r-cran-lifecycle 243s r-cran-magrittr r-cran-mass r-cran-mgcv r-cran-munsell r-cran-nlme 243s r-cran-pillar r-cran-pkgconfig r-cran-purrr r-cran-r6 r-cran-rcolorbrewer 243s r-cran-rlang r-cran-scales r-cran-stringi r-cran-stringr r-cran-tibble 243s r-cran-tidyr r-cran-tidyselect r-cran-utf8 r-cran-vctrs r-cran-viridislite 243s r-cran-withr rpcsvc-proto zlib1g-dev 243s 0 upgraded, 100 newly installed, 0 to remove and 0 not upgraded. 243s Need to get 123 MB/123 MB of archives. 243s After this operation, 392 MB of additional disk space will be used. 243s Get:1 /tmp/autopkgtest.a0lvW0/2-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [736 B] 243s Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 libc-dev-bin arm64 2.39-0ubuntu2 [19.7 kB] 243s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 linux-libc-dev arm64 6.8.0-11.11 [1569 kB] 244s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 libcrypt-dev arm64 1:4.4.36-4 [136 kB] 244s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libtirpc-dev arm64 1.3.4+ds-1.1 [201 kB] 244s Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 libnsl-dev arm64 1.3.0-3 [71.9 kB] 244s Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 rpcsvc-proto arm64 1.4.2-0ubuntu6 [65.4 kB] 244s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 libc6-dev arm64 2.39-0ubuntu2 [1596 kB] 244s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 libisl23 arm64 0.26-3 [713 kB] 244s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 libmpc3 arm64 1.3.1-1 [55.3 kB] 244s Get:11 http://ftpmaster.internal/ubuntu noble/main arm64 cpp-13-aarch64-linux-gnu arm64 13.2.0-17ubuntu2 [10.3 MB] 244s Get:12 http://ftpmaster.internal/ubuntu noble/main arm64 cpp-13 arm64 13.2.0-17ubuntu2 [1028 B] 244s Get:13 http://ftpmaster.internal/ubuntu noble/main arm64 cpp-aarch64-linux-gnu arm64 4:13.2.0-7ubuntu1 [5316 B] 244s Get:14 http://ftpmaster.internal/ubuntu noble/main arm64 cpp arm64 4:13.2.0-7ubuntu1 [22.4 kB] 244s Get:15 http://ftpmaster.internal/ubuntu noble/main arm64 libcc1-0 arm64 14-20240303-1ubuntu1 [44.7 kB] 244s Get:16 http://ftpmaster.internal/ubuntu noble/main arm64 libitm1 arm64 14-20240303-1ubuntu1 [27.7 kB] 244s Get:17 http://ftpmaster.internal/ubuntu noble/main arm64 libatomic1 arm64 14-20240303-1ubuntu1 [11.4 kB] 244s Get:18 http://ftpmaster.internal/ubuntu noble/main arm64 libasan8 arm64 14-20240303-1ubuntu1 [2919 kB] 244s Get:19 http://ftpmaster.internal/ubuntu noble/main arm64 liblsan0 arm64 14-20240303-1ubuntu1 [1282 kB] 244s Get:20 http://ftpmaster.internal/ubuntu noble/main arm64 libtsan2 arm64 14-20240303-1ubuntu1 [2687 kB] 245s Get:21 http://ftpmaster.internal/ubuntu noble/main arm64 libubsan1 arm64 14-20240303-1ubuntu1 [1151 kB] 245s Get:22 http://ftpmaster.internal/ubuntu noble/main arm64 libhwasan0 arm64 14-20240303-1ubuntu1 [1597 kB] 245s Get:23 http://ftpmaster.internal/ubuntu noble/main arm64 libgcc-13-dev arm64 13.2.0-17ubuntu2 [2464 kB] 245s Get:24 http://ftpmaster.internal/ubuntu noble/main arm64 gcc-13-aarch64-linux-gnu arm64 13.2.0-17ubuntu2 [20.1 MB] 245s Get:25 http://ftpmaster.internal/ubuntu noble/main arm64 gcc-13 arm64 13.2.0-17ubuntu2 [467 kB] 245s Get:26 http://ftpmaster.internal/ubuntu noble/main arm64 gcc-aarch64-linux-gnu arm64 4:13.2.0-7ubuntu1 [1198 B] 245s Get:27 http://ftpmaster.internal/ubuntu noble/main arm64 gcc arm64 4:13.2.0-7ubuntu1 [5018 B] 245s Get:28 http://ftpmaster.internal/ubuntu noble/main arm64 libstdc++-13-dev arm64 13.2.0-17ubuntu2 [2322 kB] 245s Get:29 http://ftpmaster.internal/ubuntu noble/main arm64 g++-13-aarch64-linux-gnu arm64 13.2.0-17ubuntu2 [11.7 MB] 246s Get:30 http://ftpmaster.internal/ubuntu noble/main arm64 g++-13 arm64 13.2.0-17ubuntu2 [14.4 kB] 246s Get:31 http://ftpmaster.internal/ubuntu noble/main arm64 g++-aarch64-linux-gnu arm64 4:13.2.0-7ubuntu1 [962 B] 246s Get:32 http://ftpmaster.internal/ubuntu noble/main arm64 g++ arm64 4:13.2.0-7ubuntu1 [1082 B] 246s Get:33 http://ftpmaster.internal/ubuntu noble/main arm64 build-essential arm64 12.10ubuntu1 [4932 B] 246s Get:34 http://ftpmaster.internal/ubuntu noble/main arm64 dctrl-tools arm64 2.24-3build2 [65.2 kB] 246s Get:35 http://ftpmaster.internal/ubuntu noble/main arm64 libgfortran-13-dev arm64 13.2.0-17ubuntu2 [478 kB] 246s Get:36 http://ftpmaster.internal/ubuntu noble/main arm64 gfortran-13-aarch64-linux-gnu arm64 13.2.0-17ubuntu2 [10.8 MB] 246s Get:37 http://ftpmaster.internal/ubuntu noble/main arm64 gfortran-13 arm64 13.2.0-17ubuntu2 [10.3 kB] 246s Get:38 http://ftpmaster.internal/ubuntu noble/main arm64 gfortran-aarch64-linux-gnu arm64 4:13.2.0-7ubuntu1 [1022 B] 246s Get:39 http://ftpmaster.internal/ubuntu noble/main arm64 gfortran arm64 4:13.2.0-7ubuntu1 [1164 B] 246s Get:40 http://ftpmaster.internal/ubuntu noble/main arm64 icu-devtools arm64 74.2-1ubuntu1 [209 kB] 246s Get:41 http://ftpmaster.internal/ubuntu noble/main arm64 libblas-dev arm64 3.12.0-3 [111 kB] 246s Get:42 http://ftpmaster.internal/ubuntu noble/main arm64 libbz2-dev arm64 1.0.8-5ubuntu1 [35.8 kB] 246s Get:43 http://ftpmaster.internal/ubuntu noble/main arm64 libicu-dev arm64 74.2-1ubuntu1 [11.9 MB] 246s Get:44 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg-turbo8-dev arm64 2.1.5-2ubuntu1 [304 kB] 246s Get:45 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg8-dev arm64 8c-2ubuntu11 [1484 B] 246s Get:46 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg-dev arm64 8c-2ubuntu11 [1482 B] 246s Get:47 http://ftpmaster.internal/ubuntu noble/main arm64 liblapack-dev arm64 3.12.0-3 [4293 kB] 246s Get:48 http://ftpmaster.internal/ubuntu noble/main arm64 libncurses-dev arm64 6.4+20240113-1ubuntu1 [385 kB] 246s Get:49 http://ftpmaster.internal/ubuntu noble/main arm64 libpcre2-16-0 arm64 10.42-4ubuntu1 [195 kB] 246s Get:50 http://ftpmaster.internal/ubuntu noble/main arm64 libpcre2-32-0 arm64 10.42-4ubuntu1 [183 kB] 246s Get:51 http://ftpmaster.internal/ubuntu noble/main arm64 libpcre2-posix3 arm64 10.42-4ubuntu1 [6654 B] 246s Get:52 http://ftpmaster.internal/ubuntu noble/main arm64 libpcre2-dev arm64 10.42-4ubuntu1 [679 kB] 246s Get:53 http://ftpmaster.internal/ubuntu noble/main arm64 libpkgconf3 arm64 1.8.1-2 [31.2 kB] 246s Get:54 http://ftpmaster.internal/ubuntu noble/main arm64 zlib1g-dev arm64 1:1.3.dfsg-3ubuntu1 [895 kB] 246s Get:55 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libpng-dev arm64 1.6.43-3 [267 kB] 246s Get:56 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libreadline-dev arm64 8.2-3.1 [177 kB] 246s Get:57 http://ftpmaster.internal/ubuntu noble/main arm64 pkgconf-bin arm64 1.8.1-2 [20.4 kB] 246s Get:58 http://ftpmaster.internal/ubuntu noble/main arm64 pkgconf arm64 1.8.1-2 [16.7 kB] 246s Get:59 http://ftpmaster.internal/ubuntu noble/main arm64 pkg-config arm64 1.8.1-2 [7170 B] 246s Get:60 http://ftpmaster.internal/ubuntu noble/main arm64 liblzma-dev arm64 5.4.5-0.3 [209 kB] 246s Get:61 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 r-base-dev all 4.3.3-2build1 [4334 B] 246s Get:62 http://ftpmaster.internal/ubuntu noble/universe arm64 pkg-r-autopkgtest all 20231212ubuntu1 [6448 B] 246s Get:63 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-backports arm64 1.4.1-1 [101 kB] 246s Get:64 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-cli arm64 3.6.2-1 [1377 kB] 246s Get:65 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-generics all 0.1.3-1 [81.3 kB] 246s Get:66 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-glue arm64 1.7.0-1 [154 kB] 246s Get:67 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-rlang arm64 1.1.3-1 [1663 kB] 247s Get:68 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB] 247s Get:69 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-magrittr arm64 2.0.3-1 [154 kB] 247s Get:70 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-fansi arm64 1.0.5-1 [616 kB] 247s Get:71 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-utf8 arm64 1.2.4-1 [140 kB] 247s Get:72 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-vctrs arm64 0.6.5-1 [1327 kB] 247s Get:73 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-pillar all 1.9.0+dfsg-1 [464 kB] 247s Get:74 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-r6 all 2.5.1-1 [99.0 kB] 247s Get:75 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-pkgconfig all 2.0.3-2build1 [19.7 kB] 247s Get:76 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-tibble arm64 3.2.1+dfsg-2 [415 kB] 247s Get:77 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-withr all 2.5.0-1 [225 kB] 247s Get:78 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-tidyselect arm64 1.2.0+dfsg-1 [218 kB] 247s Get:79 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-dplyr arm64 1.1.4-1 [1513 kB] 247s Get:80 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-ellipsis arm64 0.3.2-2 [35.5 kB] 247s Get:81 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-purrr arm64 1.0.2-1 [501 kB] 247s Get:82 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-stringi arm64 1.8.3-1 [869 kB] 247s Get:83 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-stringr all 1.5.1-1 [290 kB] 247s Get:84 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-cpp11 all 0.4.7-1 [266 kB] 247s Get:85 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-tidyr arm64 1.3.1-1 [1154 kB] 247s Get:86 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-broom all 1.0.5+dfsg-1 [1729 kB] 247s Get:87 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-colorspace arm64 2.1-0+dfsg-1 [1540 kB] 247s Get:88 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-farver arm64 2.1.1-1 [1336 kB] 247s Get:89 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-mass arm64 7.3-60.0.1-1 [1119 kB] 247s Get:90 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-geepack arm64 1.3.10-1 [366 kB] 247s Get:91 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-gtable all 0.3.4+dfsg-1 [191 kB] 247s Get:92 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-isoband arm64 0.2.7-1 [1481 kB] 247s Get:93 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-nlme arm64 3.1.164-1 [2259 kB] 247s Get:94 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-mgcv arm64 1.9-1-1 [3248 kB] 247s Get:95 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-labeling all 0.4.3-1 [62.1 kB] 247s Get:96 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-munsell all 0.5.0-2build1 [208 kB] 247s Get:97 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-rcolorbrewer all 1.1-3-1build1 [55.4 kB] 247s Get:98 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-viridislite all 0.4.2-2 [1088 kB] 247s Get:99 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-scales all 1.3.0-1 [603 kB] 247s Get:100 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-ggplot2 all 3.4.4+dfsg-1 [3411 kB] 249s Fetched 123 MB in 4s (29.9 MB/s) 249s Selecting previously unselected package libc-dev-bin. 249s (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 ... 80156 files and directories currently installed.) 249s Preparing to unpack .../00-libc-dev-bin_2.39-0ubuntu2_arm64.deb ... 249s Unpacking libc-dev-bin (2.39-0ubuntu2) ... 249s Selecting previously unselected package linux-libc-dev:arm64. 249s Preparing to unpack .../01-linux-libc-dev_6.8.0-11.11_arm64.deb ... 249s Unpacking linux-libc-dev:arm64 (6.8.0-11.11) ... 249s Selecting previously unselected package libcrypt-dev:arm64. 249s Preparing to unpack .../02-libcrypt-dev_1%3a4.4.36-4_arm64.deb ... 249s Unpacking libcrypt-dev:arm64 (1:4.4.36-4) ... 249s Selecting previously unselected package libtirpc-dev:arm64. 249s Preparing to unpack .../03-libtirpc-dev_1.3.4+ds-1.1_arm64.deb ... 249s Unpacking libtirpc-dev:arm64 (1.3.4+ds-1.1) ... 250s Selecting previously unselected package libnsl-dev:arm64. 250s Preparing to unpack .../04-libnsl-dev_1.3.0-3_arm64.deb ... 250s Unpacking libnsl-dev:arm64 (1.3.0-3) ... 250s Selecting previously unselected package rpcsvc-proto. 250s Preparing to unpack .../05-rpcsvc-proto_1.4.2-0ubuntu6_arm64.deb ... 250s Unpacking rpcsvc-proto (1.4.2-0ubuntu6) ... 250s Selecting previously unselected package libc6-dev:arm64. 250s Preparing to unpack .../06-libc6-dev_2.39-0ubuntu2_arm64.deb ... 250s Unpacking libc6-dev:arm64 (2.39-0ubuntu2) ... 250s Selecting previously unselected package libisl23:arm64. 250s Preparing to unpack .../07-libisl23_0.26-3_arm64.deb ... 250s Unpacking libisl23:arm64 (0.26-3) ... 250s Selecting previously unselected package libmpc3:arm64. 250s Preparing to unpack .../08-libmpc3_1.3.1-1_arm64.deb ... 250s Unpacking libmpc3:arm64 (1.3.1-1) ... 250s Selecting previously unselected package cpp-13-aarch64-linux-gnu. 250s Preparing to unpack .../09-cpp-13-aarch64-linux-gnu_13.2.0-17ubuntu2_arm64.deb ... 250s Unpacking cpp-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 251s Selecting previously unselected package cpp-13. 251s Preparing to unpack .../10-cpp-13_13.2.0-17ubuntu2_arm64.deb ... 251s Unpacking cpp-13 (13.2.0-17ubuntu2) ... 251s Selecting previously unselected package cpp-aarch64-linux-gnu. 251s Preparing to unpack .../11-cpp-aarch64-linux-gnu_4%3a13.2.0-7ubuntu1_arm64.deb ... 251s Unpacking cpp-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 251s Selecting previously unselected package cpp. 251s Preparing to unpack .../12-cpp_4%3a13.2.0-7ubuntu1_arm64.deb ... 251s Unpacking cpp (4:13.2.0-7ubuntu1) ... 251s Selecting previously unselected package libcc1-0:arm64. 251s Preparing to unpack .../13-libcc1-0_14-20240303-1ubuntu1_arm64.deb ... 251s Unpacking libcc1-0:arm64 (14-20240303-1ubuntu1) ... 251s Selecting previously unselected package libitm1:arm64. 251s Preparing to unpack .../14-libitm1_14-20240303-1ubuntu1_arm64.deb ... 251s Unpacking libitm1:arm64 (14-20240303-1ubuntu1) ... 251s Selecting previously unselected package libatomic1:arm64. 251s Preparing to unpack .../15-libatomic1_14-20240303-1ubuntu1_arm64.deb ... 251s Unpacking libatomic1:arm64 (14-20240303-1ubuntu1) ... 251s Selecting previously unselected package libasan8:arm64. 251s Preparing to unpack .../16-libasan8_14-20240303-1ubuntu1_arm64.deb ... 251s Unpacking libasan8:arm64 (14-20240303-1ubuntu1) ... 252s Selecting previously unselected package liblsan0:arm64. 252s Preparing to unpack .../17-liblsan0_14-20240303-1ubuntu1_arm64.deb ... 252s Unpacking liblsan0:arm64 (14-20240303-1ubuntu1) ... 252s Selecting previously unselected package libtsan2:arm64. 252s Preparing to unpack .../18-libtsan2_14-20240303-1ubuntu1_arm64.deb ... 252s Unpacking libtsan2:arm64 (14-20240303-1ubuntu1) ... 252s Selecting previously unselected package libubsan1:arm64. 252s Preparing to unpack .../19-libubsan1_14-20240303-1ubuntu1_arm64.deb ... 252s Unpacking libubsan1:arm64 (14-20240303-1ubuntu1) ... 252s Selecting previously unselected package libhwasan0:arm64. 252s Preparing to unpack .../20-libhwasan0_14-20240303-1ubuntu1_arm64.deb ... 252s Unpacking libhwasan0:arm64 (14-20240303-1ubuntu1) ... 252s Selecting previously unselected package libgcc-13-dev:arm64. 252s Preparing to unpack .../21-libgcc-13-dev_13.2.0-17ubuntu2_arm64.deb ... 252s Unpacking libgcc-13-dev:arm64 (13.2.0-17ubuntu2) ... 253s Selecting previously unselected package gcc-13-aarch64-linux-gnu. 253s Preparing to unpack .../22-gcc-13-aarch64-linux-gnu_13.2.0-17ubuntu2_arm64.deb ... 253s Unpacking gcc-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 254s Selecting previously unselected package gcc-13. 254s Preparing to unpack .../23-gcc-13_13.2.0-17ubuntu2_arm64.deb ... 254s Unpacking gcc-13 (13.2.0-17ubuntu2) ... 254s Selecting previously unselected package gcc-aarch64-linux-gnu. 254s Preparing to unpack .../24-gcc-aarch64-linux-gnu_4%3a13.2.0-7ubuntu1_arm64.deb ... 254s Unpacking gcc-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 254s Selecting previously unselected package gcc. 254s Preparing to unpack .../25-gcc_4%3a13.2.0-7ubuntu1_arm64.deb ... 254s Unpacking gcc (4:13.2.0-7ubuntu1) ... 254s Selecting previously unselected package libstdc++-13-dev:arm64. 254s Preparing to unpack .../26-libstdc++-13-dev_13.2.0-17ubuntu2_arm64.deb ... 254s Unpacking libstdc++-13-dev:arm64 (13.2.0-17ubuntu2) ... 255s Selecting previously unselected package g++-13-aarch64-linux-gnu. 255s Preparing to unpack .../27-g++-13-aarch64-linux-gnu_13.2.0-17ubuntu2_arm64.deb ... 255s Unpacking g++-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 255s Selecting previously unselected package g++-13. 255s Preparing to unpack .../28-g++-13_13.2.0-17ubuntu2_arm64.deb ... 255s Unpacking g++-13 (13.2.0-17ubuntu2) ... 255s Selecting previously unselected package g++-aarch64-linux-gnu. 255s Preparing to unpack .../29-g++-aarch64-linux-gnu_4%3a13.2.0-7ubuntu1_arm64.deb ... 255s Unpacking g++-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 255s Selecting previously unselected package g++. 256s Preparing to unpack .../30-g++_4%3a13.2.0-7ubuntu1_arm64.deb ... 256s Unpacking g++ (4:13.2.0-7ubuntu1) ... 256s Selecting previously unselected package build-essential. 256s Preparing to unpack .../31-build-essential_12.10ubuntu1_arm64.deb ... 256s Unpacking build-essential (12.10ubuntu1) ... 256s Selecting previously unselected package dctrl-tools. 256s Preparing to unpack .../32-dctrl-tools_2.24-3build2_arm64.deb ... 256s Unpacking dctrl-tools (2.24-3build2) ... 256s Selecting previously unselected package libgfortran-13-dev:arm64. 256s Preparing to unpack .../33-libgfortran-13-dev_13.2.0-17ubuntu2_arm64.deb ... 256s Unpacking libgfortran-13-dev:arm64 (13.2.0-17ubuntu2) ... 256s Selecting previously unselected package gfortran-13-aarch64-linux-gnu. 256s Preparing to unpack .../34-gfortran-13-aarch64-linux-gnu_13.2.0-17ubuntu2_arm64.deb ... 256s Unpacking gfortran-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 257s Selecting previously unselected package gfortran-13. 257s Preparing to unpack .../35-gfortran-13_13.2.0-17ubuntu2_arm64.deb ... 257s Unpacking gfortran-13 (13.2.0-17ubuntu2) ... 257s Selecting previously unselected package gfortran-aarch64-linux-gnu. 257s Preparing to unpack .../36-gfortran-aarch64-linux-gnu_4%3a13.2.0-7ubuntu1_arm64.deb ... 257s Unpacking gfortran-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 257s Selecting previously unselected package gfortran. 257s Preparing to unpack .../37-gfortran_4%3a13.2.0-7ubuntu1_arm64.deb ... 257s Unpacking gfortran (4:13.2.0-7ubuntu1) ... 257s Selecting previously unselected package icu-devtools. 257s Preparing to unpack .../38-icu-devtools_74.2-1ubuntu1_arm64.deb ... 257s Unpacking icu-devtools (74.2-1ubuntu1) ... 257s Selecting previously unselected package libblas-dev:arm64. 257s Preparing to unpack .../39-libblas-dev_3.12.0-3_arm64.deb ... 257s Unpacking libblas-dev:arm64 (3.12.0-3) ... 257s Selecting previously unselected package libbz2-dev:arm64. 257s Preparing to unpack .../40-libbz2-dev_1.0.8-5ubuntu1_arm64.deb ... 257s Unpacking libbz2-dev:arm64 (1.0.8-5ubuntu1) ... 257s Selecting previously unselected package libicu-dev:arm64. 257s Preparing to unpack .../41-libicu-dev_74.2-1ubuntu1_arm64.deb ... 257s Unpacking libicu-dev:arm64 (74.2-1ubuntu1) ... 258s Selecting previously unselected package libjpeg-turbo8-dev:arm64. 258s Preparing to unpack .../42-libjpeg-turbo8-dev_2.1.5-2ubuntu1_arm64.deb ... 258s Unpacking libjpeg-turbo8-dev:arm64 (2.1.5-2ubuntu1) ... 258s Selecting previously unselected package libjpeg8-dev:arm64. 258s Preparing to unpack .../43-libjpeg8-dev_8c-2ubuntu11_arm64.deb ... 258s Unpacking libjpeg8-dev:arm64 (8c-2ubuntu11) ... 258s Selecting previously unselected package libjpeg-dev:arm64. 258s Preparing to unpack .../44-libjpeg-dev_8c-2ubuntu11_arm64.deb ... 258s Unpacking libjpeg-dev:arm64 (8c-2ubuntu11) ... 258s Selecting previously unselected package liblapack-dev:arm64. 258s Preparing to unpack .../45-liblapack-dev_3.12.0-3_arm64.deb ... 258s Unpacking liblapack-dev:arm64 (3.12.0-3) ... 259s Selecting previously unselected package libncurses-dev:arm64. 259s Preparing to unpack .../46-libncurses-dev_6.4+20240113-1ubuntu1_arm64.deb ... 259s Unpacking libncurses-dev:arm64 (6.4+20240113-1ubuntu1) ... 259s Selecting previously unselected package libpcre2-16-0:arm64. 259s Preparing to unpack .../47-libpcre2-16-0_10.42-4ubuntu1_arm64.deb ... 259s Unpacking libpcre2-16-0:arm64 (10.42-4ubuntu1) ... 259s Selecting previously unselected package libpcre2-32-0:arm64. 259s Preparing to unpack .../48-libpcre2-32-0_10.42-4ubuntu1_arm64.deb ... 259s Unpacking libpcre2-32-0:arm64 (10.42-4ubuntu1) ... 259s Selecting previously unselected package libpcre2-posix3:arm64. 259s Preparing to unpack .../49-libpcre2-posix3_10.42-4ubuntu1_arm64.deb ... 259s Unpacking libpcre2-posix3:arm64 (10.42-4ubuntu1) ... 259s Selecting previously unselected package libpcre2-dev:arm64. 259s Preparing to unpack .../50-libpcre2-dev_10.42-4ubuntu1_arm64.deb ... 259s Unpacking libpcre2-dev:arm64 (10.42-4ubuntu1) ... 259s Selecting previously unselected package libpkgconf3:arm64. 259s Preparing to unpack .../51-libpkgconf3_1.8.1-2_arm64.deb ... 259s Unpacking libpkgconf3:arm64 (1.8.1-2) ... 259s Selecting previously unselected package zlib1g-dev:arm64. 259s Preparing to unpack .../52-zlib1g-dev_1%3a1.3.dfsg-3ubuntu1_arm64.deb ... 259s Unpacking zlib1g-dev:arm64 (1:1.3.dfsg-3ubuntu1) ... 260s Selecting previously unselected package libpng-dev:arm64. 260s Preparing to unpack .../53-libpng-dev_1.6.43-3_arm64.deb ... 260s Unpacking libpng-dev:arm64 (1.6.43-3) ... 260s Selecting previously unselected package libreadline-dev:arm64. 260s Preparing to unpack .../54-libreadline-dev_8.2-3.1_arm64.deb ... 260s Unpacking libreadline-dev:arm64 (8.2-3.1) ... 260s Selecting previously unselected package pkgconf-bin. 260s Preparing to unpack .../55-pkgconf-bin_1.8.1-2_arm64.deb ... 260s Unpacking pkgconf-bin (1.8.1-2) ... 260s Selecting previously unselected package pkgconf:arm64. 260s Preparing to unpack .../56-pkgconf_1.8.1-2_arm64.deb ... 260s Unpacking pkgconf:arm64 (1.8.1-2) ... 260s Selecting previously unselected package pkg-config:arm64. 260s Preparing to unpack .../57-pkg-config_1.8.1-2_arm64.deb ... 260s Unpacking pkg-config:arm64 (1.8.1-2) ... 260s Selecting previously unselected package liblzma-dev:arm64. 260s Preparing to unpack .../58-liblzma-dev_5.4.5-0.3_arm64.deb ... 260s Unpacking liblzma-dev:arm64 (5.4.5-0.3) ... 260s Selecting previously unselected package r-base-dev. 260s Preparing to unpack .../59-r-base-dev_4.3.3-2build1_all.deb ... 260s Unpacking r-base-dev (4.3.3-2build1) ... 260s Selecting previously unselected package pkg-r-autopkgtest. 260s Preparing to unpack .../60-pkg-r-autopkgtest_20231212ubuntu1_all.deb ... 260s Unpacking pkg-r-autopkgtest (20231212ubuntu1) ... 260s Selecting previously unselected package r-cran-backports. 260s Preparing to unpack .../61-r-cran-backports_1.4.1-1_arm64.deb ... 260s Unpacking r-cran-backports (1.4.1-1) ... 260s Selecting previously unselected package r-cran-cli. 260s Preparing to unpack .../62-r-cran-cli_3.6.2-1_arm64.deb ... 260s Unpacking r-cran-cli (3.6.2-1) ... 261s Selecting previously unselected package r-cran-generics. 261s Preparing to unpack .../63-r-cran-generics_0.1.3-1_all.deb ... 261s Unpacking r-cran-generics (0.1.3-1) ... 261s Selecting previously unselected package r-cran-glue. 261s Preparing to unpack .../64-r-cran-glue_1.7.0-1_arm64.deb ... 261s Unpacking r-cran-glue (1.7.0-1) ... 261s Selecting previously unselected package r-cran-rlang. 261s Preparing to unpack .../65-r-cran-rlang_1.1.3-1_arm64.deb ... 261s Unpacking r-cran-rlang (1.1.3-1) ... 261s Selecting previously unselected package r-cran-lifecycle. 261s Preparing to unpack .../66-r-cran-lifecycle_1.0.4+dfsg-1_all.deb ... 261s Unpacking r-cran-lifecycle (1.0.4+dfsg-1) ... 261s Selecting previously unselected package r-cran-magrittr. 261s Preparing to unpack .../67-r-cran-magrittr_2.0.3-1_arm64.deb ... 261s Unpacking r-cran-magrittr (2.0.3-1) ... 261s Selecting previously unselected package r-cran-fansi. 261s Preparing to unpack .../68-r-cran-fansi_1.0.5-1_arm64.deb ... 261s Unpacking r-cran-fansi (1.0.5-1) ... 262s Selecting previously unselected package r-cran-utf8. 262s Preparing to unpack .../69-r-cran-utf8_1.2.4-1_arm64.deb ... 262s Unpacking r-cran-utf8 (1.2.4-1) ... 262s Selecting previously unselected package r-cran-vctrs. 262s Preparing to unpack .../70-r-cran-vctrs_0.6.5-1_arm64.deb ... 262s Unpacking r-cran-vctrs (0.6.5-1) ... 262s Selecting previously unselected package r-cran-pillar. 262s Preparing to unpack .../71-r-cran-pillar_1.9.0+dfsg-1_all.deb ... 262s Unpacking r-cran-pillar (1.9.0+dfsg-1) ... 262s Selecting previously unselected package r-cran-r6. 262s Preparing to unpack .../72-r-cran-r6_2.5.1-1_all.deb ... 262s Unpacking r-cran-r6 (2.5.1-1) ... 262s Selecting previously unselected package r-cran-pkgconfig. 262s Preparing to unpack .../73-r-cran-pkgconfig_2.0.3-2build1_all.deb ... 262s Unpacking r-cran-pkgconfig (2.0.3-2build1) ... 262s Selecting previously unselected package r-cran-tibble. 262s Preparing to unpack .../74-r-cran-tibble_3.2.1+dfsg-2_arm64.deb ... 262s Unpacking r-cran-tibble (3.2.1+dfsg-2) ... 262s Selecting previously unselected package r-cran-withr. 262s Preparing to unpack .../75-r-cran-withr_2.5.0-1_all.deb ... 262s Unpacking r-cran-withr (2.5.0-1) ... 263s Selecting previously unselected package r-cran-tidyselect. 263s Preparing to unpack .../76-r-cran-tidyselect_1.2.0+dfsg-1_arm64.deb ... 263s Unpacking r-cran-tidyselect (1.2.0+dfsg-1) ... 263s Selecting previously unselected package r-cran-dplyr. 263s Preparing to unpack .../77-r-cran-dplyr_1.1.4-1_arm64.deb ... 263s Unpacking r-cran-dplyr (1.1.4-1) ... 263s Selecting previously unselected package r-cran-ellipsis. 263s Preparing to unpack .../78-r-cran-ellipsis_0.3.2-2_arm64.deb ... 263s Unpacking r-cran-ellipsis (0.3.2-2) ... 263s Selecting previously unselected package r-cran-purrr. 263s Preparing to unpack .../79-r-cran-purrr_1.0.2-1_arm64.deb ... 263s Unpacking r-cran-purrr (1.0.2-1) ... 263s Selecting previously unselected package r-cran-stringi. 263s Preparing to unpack .../80-r-cran-stringi_1.8.3-1_arm64.deb ... 263s Unpacking r-cran-stringi (1.8.3-1) ... 263s Selecting previously unselected package r-cran-stringr. 263s Preparing to unpack .../81-r-cran-stringr_1.5.1-1_all.deb ... 263s Unpacking r-cran-stringr (1.5.1-1) ... 263s Selecting previously unselected package r-cran-cpp11. 263s Preparing to unpack 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unselected package r-cran-geepack. 264s Preparing to unpack .../88-r-cran-geepack_1.3.10-1_arm64.deb ... 264s Unpacking r-cran-geepack (1.3.10-1) ... 264s Selecting previously unselected package r-cran-gtable. 265s Preparing to unpack .../89-r-cran-gtable_0.3.4+dfsg-1_all.deb ... 265s Unpacking r-cran-gtable (0.3.4+dfsg-1) ... 265s Selecting previously unselected package r-cran-isoband. 265s Preparing to unpack .../90-r-cran-isoband_0.2.7-1_arm64.deb ... 265s Unpacking r-cran-isoband (0.2.7-1) ... 265s Selecting previously unselected package r-cran-nlme. 265s Preparing to unpack .../91-r-cran-nlme_3.1.164-1_arm64.deb ... 265s Unpacking r-cran-nlme (3.1.164-1) ... 265s Selecting previously unselected package r-cran-mgcv. 265s Preparing to unpack .../92-r-cran-mgcv_1.9-1-1_arm64.deb ... 265s Unpacking r-cran-mgcv (1.9-1-1) ... 265s Selecting previously unselected package r-cran-labeling. 265s Preparing to unpack .../93-r-cran-labeling_0.4.3-1_all.deb ... 265s Unpacking r-cran-labeling (0.4.3-1) ... 265s Selecting previously unselected package r-cran-munsell. 265s Preparing to unpack .../94-r-cran-munsell_0.5.0-2build1_all.deb ... 265s Unpacking r-cran-munsell (0.5.0-2build1) ... 265s Selecting previously unselected package r-cran-rcolorbrewer. 265s Preparing to unpack .../95-r-cran-rcolorbrewer_1.1-3-1build1_all.deb ... 265s Unpacking r-cran-rcolorbrewer (1.1-3-1build1) ... 265s Selecting previously unselected package r-cran-viridislite. 265s Preparing to unpack .../96-r-cran-viridislite_0.4.2-2_all.deb ... 265s Unpacking r-cran-viridislite (0.4.2-2) ... 265s Selecting previously unselected package r-cran-scales. 265s Preparing to unpack .../97-r-cran-scales_1.3.0-1_all.deb ... 265s Unpacking r-cran-scales (1.3.0-1) ... 266s Selecting previously unselected package r-cran-ggplot2. 266s Preparing to unpack .../98-r-cran-ggplot2_3.4.4+dfsg-1_all.deb ... 266s Unpacking r-cran-ggplot2 (3.4.4+dfsg-1) ... 266s Selecting previously unselected package autopkgtest-satdep. 266s Preparing to unpack .../99-2-autopkgtest-satdep.deb ... 266s Unpacking autopkgtest-satdep (0) ... 266s Setting up r-cran-rlang (1.1.3-1) ... 266s Setting up r-cran-withr (2.5.0-1) ... 266s Setting up r-cran-backports (1.4.1-1) ... 266s Setting up r-cran-generics (0.1.3-1) ... 266s Setting up r-cran-fansi (1.0.5-1) ... 266s Setting up r-cran-mass (7.3-60.0.1-1) ... 266s Setting up linux-libc-dev:arm64 (6.8.0-11.11) ... 266s Setting up r-cran-glue (1.7.0-1) ... 266s Setting up r-cran-cli (3.6.2-1) ... 266s Setting up r-cran-lifecycle (1.0.4+dfsg-1) ... 266s Setting up libpcre2-16-0:arm64 (10.42-4ubuntu1) ... 266s Setting up r-cran-pkgconfig (2.0.3-2build1) ... 266s Setting up libpcre2-32-0:arm64 (10.42-4ubuntu1) ... 266s Setting up r-cran-utf8 (1.2.4-1) ... 266s Setting up libtirpc-dev:arm64 (1.3.4+ds-1.1) ... 266s Setting up libpkgconf3:arm64 (1.8.1-2) ... 266s Setting up r-cran-colorspace (2.1-0+dfsg-1) ... 266s Setting up rpcsvc-proto (1.4.2-0ubuntu6) ... 266s Setting up r-cran-stringi (1.8.3-1) ... 266s Setting up r-cran-cpp11 (0.4.7-1) ... 266s Setting up r-cran-rcolorbrewer (1.1-3-1build1) ... 266s Setting up r-cran-isoband (0.2.7-1) ... 266s Setting up libmpc3:arm64 (1.3.1-1) ... 266s Setting up r-cran-gtable (0.3.4+dfsg-1) ... 266s Setting up libatomic1:arm64 (14-20240303-1ubuntu1) ... 266s Setting up r-cran-labeling (0.4.3-1) ... 266s Setting up icu-devtools (74.2-1ubuntu1) ... 266s Setting up pkgconf-bin (1.8.1-2) ... 266s Setting up r-cran-nlme (3.1.164-1) ... 266s Setting up r-cran-farver (2.1.1-1) ... 266s Setting up liblzma-dev:arm64 (5.4.5-0.3) ... 266s Setting up libubsan1:arm64 (14-20240303-1ubuntu1) ... 266s Setting up r-cran-mgcv (1.9-1-1) ... 266s Setting up libpcre2-posix3:arm64 (10.42-4ubuntu1) ... 266s Setting up libnsl-dev:arm64 (1.3.0-3) ... 266s Setting up r-cran-viridislite (0.4.2-2) ... 266s Setting up libhwasan0:arm64 (14-20240303-1ubuntu1) ... 266s Setting up libcrypt-dev:arm64 (1:4.4.36-4) ... 266s Setting up libasan8:arm64 (14-20240303-1ubuntu1) ... 266s Setting up libtsan2:arm64 (14-20240303-1ubuntu1) ... 266s Setting up r-cran-r6 (2.5.1-1) ... 266s Setting up libisl23:arm64 (0.26-3) ... 266s Setting up libc-dev-bin (2.39-0ubuntu2) ... 266s Setting up r-cran-magrittr (2.0.3-1) ... 266s Setting up libcc1-0:arm64 (14-20240303-1ubuntu1) ... 266s Setting up r-cran-vctrs (0.6.5-1) ... 266s Setting up liblsan0:arm64 (14-20240303-1ubuntu1) ... 266s Setting up libblas-dev:arm64 (3.12.0-3) ... 266s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so to provide /usr/lib/aarch64-linux-gnu/libblas.so (libblas.so-aarch64-linux-gnu) in auto mode 266s Setting up dctrl-tools (2.24-3build2) ... 266s Setting up libitm1:arm64 (14-20240303-1ubuntu1) ... 266s Setting up r-cran-pillar (1.9.0+dfsg-1) ... 266s Setting up r-cran-ellipsis (0.3.2-2) ... 266s Setting up r-cran-stringr (1.5.1-1) ... 266s Setting up cpp-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 266s Setting up r-cran-munsell (0.5.0-2build1) ... 266s Setting up r-cran-tibble (3.2.1+dfsg-2) ... 266s Setting up pkgconf:arm64 (1.8.1-2) ... 266s Setting up r-cran-tidyselect (1.2.0+dfsg-1) ... 266s Setting up cpp-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 266s Setting up r-cran-scales (1.3.0-1) ... 266s Setting up liblapack-dev:arm64 (3.12.0-3) ... 266s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so to provide /usr/lib/aarch64-linux-gnu/liblapack.so (liblapack.so-aarch64-linux-gnu) in auto mode 266s Setting up r-cran-purrr (1.0.2-1) ... 266s Setting up pkg-config:arm64 (1.8.1-2) ... 266s Setting up libgcc-13-dev:arm64 (13.2.0-17ubuntu2) ... 266s Setting up libc6-dev:arm64 (2.39-0ubuntu2) ... 266s Setting up r-cran-dplyr (1.1.4-1) ... 266s Setting up libgfortran-13-dev:arm64 (13.2.0-17ubuntu2) ... 266s Setting up libicu-dev:arm64 (74.2-1ubuntu1) ... 266s Setting up libstdc++-13-dev:arm64 (13.2.0-17ubuntu2) ... 266s Setting up libbz2-dev:arm64 (1.0.8-5ubuntu1) ... 266s Setting up libjpeg-turbo8-dev:arm64 (2.1.5-2ubuntu1) ... 266s Setting up libncurses-dev:arm64 (6.4+20240113-1ubuntu1) ... 266s Setting up libpcre2-dev:arm64 (10.42-4ubuntu1) ... 266s Setting up cpp-13 (13.2.0-17ubuntu2) ... 266s Setting up r-cran-ggplot2 (3.4.4+dfsg-1) ... 266s Setting up gcc-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 266s Setting up libreadline-dev:arm64 (8.2-3.1) ... 266s Setting up gcc-13 (13.2.0-17ubuntu2) ... 266s Setting up r-cran-tidyr (1.3.1-1) ... 266s Setting up zlib1g-dev:arm64 (1:1.3.dfsg-3ubuntu1) ... 266s Setting up cpp (4:13.2.0-7ubuntu1) ... 266s Setting up libjpeg8-dev:arm64 (8c-2ubuntu11) ... 266s Setting up g++-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 266s Setting up gcc-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 267s Setting up g++-13 (13.2.0-17ubuntu2) ... 267s Setting up libpng-dev:arm64 (1.6.43-3) ... 267s Setting up libjpeg-dev:arm64 (8c-2ubuntu11) ... 267s Setting up gfortran-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 267s Setting up gcc (4:13.2.0-7ubuntu1) ... 267s Setting up r-cran-broom (1.0.5+dfsg-1) ... 267s Setting up gfortran-13 (13.2.0-17ubuntu2) ... 267s Setting up g++-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 267s Setting up gfortran-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 267s Setting up r-cran-geepack (1.3.10-1) ... 267s Setting up gfortran (4:13.2.0-7ubuntu1) ... 267s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode 267s update-alternatives: warning: skip creation of /usr/share/man/man1/f95.1.gz because associated file /usr/share/man/man1/gfortran.1.gz (of link group f95) doesn't exist 267s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode 267s 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 267s Setting up g++ (4:13.2.0-7ubuntu1) ... 267s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 267s Setting up build-essential (12.10ubuntu1) ... 267s Setting up r-base-dev (4.3.3-2build1) ... 267s Setting up pkg-r-autopkgtest (20231212ubuntu1) ... 267s Setting up autopkgtest-satdep (0) ... 267s Processing triggers for man-db (2.12.0-3) ... 268s Processing triggers for install-info (7.1-3) ... 268s Processing triggers for libc-bin (2.39-0ubuntu2) ... 275s (Reading database ... 87702 files and directories currently installed.) 275s Removing autopkgtest-satdep (0) ... 276s autopkgtest [18:31:01]: test pkg-r-autopkgtest: /usr/share/dh-r/pkg-r-autopkgtest 276s autopkgtest [18:31:01]: test pkg-r-autopkgtest: [----------------------- 276s Test: Try to load the R library etm 276s 276s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 276s Copyright (C) 2024 The R Foundation for Statistical Computing 276s Platform: aarch64-unknown-linux-gnu (64-bit) 276s 276s R is free software and comes with ABSOLUTELY NO WARRANTY. 276s You are welcome to redistribute it under certain conditions. 276s Type 'license()' or 'licence()' for distribution details. 276s 276s R is a collaborative project with many contributors. 276s Type 'contributors()' for more information and 276s 'citation()' on how to cite R or R packages in publications. 276s 276s Type 'demo()' for some demos, 'help()' for on-line help, or 276s 'help.start()' for an HTML browser interface to help. 276s Type 'q()' to quit R. 276s 277s > library('etm') 280s > 280s > 280s Other tests are currently unsupported! 280s They will be progressively added. 281s autopkgtest [18:31:06]: test pkg-r-autopkgtest: -----------------------] 281s autopkgtest [18:31:06]: test pkg-r-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 281s pkg-r-autopkgtest PASS 282s autopkgtest [18:31:07]: @@@@@@@@@@@@@@@@@@@@ summary 282s run-unit-test PASS 282s pkg-r-autopkgtest PASS 293s Creating nova instance adt-noble-arm64-r-cran-etm-20240316-182625-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-arm64-server-20240316.img (UUID 9d2e92bf-2787-45c2-ae22-99fb4bcc175e)...