0s autopkgtest [22:06:51]: starting date and time: 2025-03-15 22:06:51+0000 0s autopkgtest [22:06:51]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [22:06:51]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.48wtm6dr/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc --apt-upgrade r-cran-etm --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glibc/2.41-1ubuntu2 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor builder-cpu2-ram4-disk20 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-18.secgroup --name adt-plucky-amd64-r-cran-etm-20250315-220651-juju-7f2275-prod-proposed-migration-environment-2-c9e94c77-1fe7-423f-ad91-0eeabd75be50 --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration-amd64 -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 57s autopkgtest [22:07:48]: testbed dpkg architecture: amd64 58s autopkgtest [22:07:49]: testbed apt version: 2.9.31ubuntu1 58s autopkgtest [22:07:49]: @@@@@@@@@@@@@@@@@@@@ test bed setup 58s autopkgtest [22:07:49]: testbed release detected to be: None 59s autopkgtest [22:07:50]: updating testbed package index (apt update) 59s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 60s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 60s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 60s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 60s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [44.1 kB] 60s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [14.5 kB] 60s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [369 kB] 60s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [85.7 kB] 60s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [67.4 kB] 60s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 c-n-f Metadata [1852 B] 60s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 c-n-f Metadata [116 B] 60s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [174 kB] 60s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [342 kB] 60s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 c-n-f Metadata [15.3 kB] 60s Get:15 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [8544 B] 60s Get:16 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [16.1 kB] 60s Get:17 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 c-n-f Metadata [628 B] 60s Fetched 1265 kB in 1s (1469 kB/s) 62s Reading package lists... 62s Reading package lists... 63s Building dependency tree... 63s Reading state information... 63s Calculating upgrade... 64s Calculating upgrade... 64s The following package was automatically installed and is no longer required: 64s libnl-genl-3-200 64s Use 'sudo apt autoremove' to remove it. 64s The following NEW packages will be installed: 64s bpftool libdebuginfod-common libdebuginfod1t64 linux-headers-6.14.0-10 64s linux-headers-6.14.0-10-generic linux-image-6.14.0-10-generic 64s linux-modules-6.14.0-10-generic linux-modules-extra-6.14.0-10-generic 64s linux-perf linux-tools-6.14.0-10 linux-tools-6.14.0-10-generic pnp.ids 64s The following packages will be upgraded: 64s apparmor apt apt-utils binutils binutils-common binutils-x86-64-linux-gnu 64s cloud-init cloud-init-base curl dosfstools exfatprogs fwupd gcc-15-base 64s gir1.2-girepository-2.0 gir1.2-glib-2.0 htop hwdata initramfs-tools 64s initramfs-tools-bin initramfs-tools-core libapparmor1 libapt-pkg7.0 64s libassuan9 libatomic1 libaudit-common libaudit1 libbinutils libbrotli1 64s libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libctf-nobfd0 libctf0 64s libcurl3t64-gnutls libcurl4t64 libestr0 libftdi1-2 libfwupd3 libgcc-s1 64s libgirepository-1.0-1 libglib2.0-0t64 libglib2.0-data libgpgme11t64 64s libgprofng0 libjemalloc2 liblz4-1 liblzma5 libmm-glib0 libncurses6 64s libncursesw6 libnewt0.52 libnl-3-200 libnl-genl-3-200 libnl-route-3-200 64s libnss-systemd libpam-systemd libparted2t64 libpci3 libpython3-stdlib 64s libpython3.13 libpython3.13-minimal libpython3.13-stdlib libseccomp2 64s libselinux1 libsemanage-common libsemanage2 libsframe1 libsqlite3-0 64s libstdc++6 libsystemd-shared libsystemd0 libtinfo6 libudev1 libxml2 64s linux-firmware linux-generic linux-headers-generic linux-headers-virtual 64s linux-image-generic linux-image-virtual linux-libc-dev linux-tools-common 64s linux-virtual locales media-types ncurses-base ncurses-bin ncurses-term 64s parted pci.ids pciutils pinentry-curses python-apt-common python3 64s python3-apt python3-bcrypt python3-cffi-backend python3-dbus python3-gi 64s python3-jinja2 python3-lazr.uri python3-markupsafe python3-minimal 64s python3-newt python3-rpds-py python3-systemd python3-yaml python3.13 64s python3.13-gdbm python3.13-minimal rsync rsyslog strace systemd 64s systemd-cryptsetup systemd-resolved systemd-sysv systemd-timesyncd 64s ubuntu-kernel-accessories ubuntu-minimal ubuntu-standard udev whiptail 64s xz-utils 64s 126 upgraded, 12 newly installed, 0 to remove and 0 not upgraded. 64s Need to get 829 MB of archives. 64s After this operation, 325 MB of additional disk space will be used. 64s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 ncurses-bin amd64 6.5+20250216-2 [194 kB] 64s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libc-dev-bin amd64 2.41-1ubuntu1 [24.7 kB] 64s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 libc6-dev amd64 2.41-1ubuntu1 [2182 kB] 65s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 locales all 2.41-1ubuntu1 [4246 kB] 65s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 libc6 amd64 2.41-1ubuntu1 [3327 kB] 65s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 libc-bin amd64 2.41-1ubuntu1 [701 kB] 65s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-libc-dev amd64 6.14.0-10.10 [1723 kB] 65s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 libatomic1 amd64 15-20250222-0ubuntu1 [10.4 kB] 65s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-15-base amd64 15-20250222-0ubuntu1 [53.4 kB] 65s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 libgcc-s1 amd64 15-20250222-0ubuntu1 [77.8 kB] 65s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 libstdc++6 amd64 15-20250222-0ubuntu1 [798 kB] 65s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 ncurses-base all 6.5+20250216-2 [25.9 kB] 65s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 ncurses-term all 6.5+20250216-2 [276 kB] 65s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 liblz4-1 amd64 1.10.0-4 [66.4 kB] 65s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 liblzma5 amd64 5.6.4-1 [157 kB] 65s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 libsystemd0 amd64 257.3-1ubuntu3 [595 kB] 65s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 libnss-systemd amd64 257.3-1ubuntu3 [199 kB] 65s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 systemd-sysv amd64 257.3-1ubuntu3 [11.9 kB] 65s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 systemd-resolved amd64 257.3-1ubuntu3 [345 kB] 65s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 libpam-systemd amd64 257.3-1ubuntu3 [302 kB] 65s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 libsystemd-shared amd64 257.3-1ubuntu3 [2371 kB] 65s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 systemd amd64 257.3-1ubuntu3 [3052 kB] 65s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 systemd-timesyncd amd64 257.3-1ubuntu3 [42.1 kB] 65s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 systemd-cryptsetup amd64 257.3-1ubuntu3 [124 kB] 65s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 udev amd64 257.3-1ubuntu3 [1404 kB] 65s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 libudev1 amd64 257.3-1ubuntu3 [215 kB] 65s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 libaudit-common all 1:4.0.2-2ubuntu2 [6628 B] 65s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 libcap-ng0 amd64 0.8.5-4build1 [15.6 kB] 65s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 libaudit1 amd64 1:4.0.2-2ubuntu2 [54.0 kB] 65s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 libseccomp2 amd64 2.5.5-1ubuntu6 [53.5 kB] 65s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 libselinux1 amd64 3.7-3ubuntu3 [87.3 kB] 65s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 libapparmor1 amd64 4.1.0~beta5-0ubuntu8 [55.0 kB] 65s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 libapt-pkg7.0 amd64 2.9.33 [1138 kB] 65s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 apt amd64 2.9.33 [1439 kB] 65s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 apt-utils amd64 2.9.33 [222 kB] 65s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-minimal amd64 3.13.2-2 [27.7 kB] 65s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 python3 amd64 3.13.2-2 [24.0 kB] 65s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13 amd64 3.13.2-2 [2341 kB] 65s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 media-types all 13.0.0 [29.9 kB] 65s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 libncurses6 amd64 6.5+20250216-2 [126 kB] 65s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 libncursesw6 amd64 6.5+20250216-2 [165 kB] 65s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 libtinfo6 amd64 6.5+20250216-2 [119 kB] 65s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 libsqlite3-0 amd64 3.46.1-2 [715 kB] 65s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13 amd64 3.13.2-2 [735 kB] 66s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-minimal amd64 3.13.2-2 [2365 kB] 66s Get:46 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-minimal amd64 3.13.2-2 [883 kB] 66s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-stdlib amd64 3.13.2-2 [2066 kB] 66s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3-stdlib amd64 3.13.2-2 [10.4 kB] 66s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 rsync amd64 3.4.1+ds1-3 [482 kB] 66s Get:50 http://ftpmaster.internal/ubuntu plucky/main amd64 libdebuginfod-common all 0.192-4 [15.4 kB] 66s Get:51 http://ftpmaster.internal/ubuntu plucky/main amd64 libsemanage-common all 3.7-2.1build1 [7268 B] 66s Get:52 http://ftpmaster.internal/ubuntu plucky/main amd64 libsemanage2 amd64 3.7-2.1build1 [106 kB] 66s Get:53 http://ftpmaster.internal/ubuntu plucky/main amd64 libassuan9 amd64 3.0.2-2 [43.1 kB] 66s Get:54 http://ftpmaster.internal/ubuntu plucky/main amd64 gir1.2-girepository-2.0 amd64 1.83.4-1 [25.3 kB] 66s Get:55 http://ftpmaster.internal/ubuntu plucky/main amd64 gir1.2-glib-2.0 amd64 2.84.0-1 [184 kB] 66s Get:56 http://ftpmaster.internal/ubuntu plucky/main amd64 libglib2.0-0t64 amd64 2.84.0-1 [1669 kB] 66s Get:57 http://ftpmaster.internal/ubuntu plucky/main amd64 libgirepository-1.0-1 amd64 1.83.4-1 [89.5 kB] 66s Get:58 http://ftpmaster.internal/ubuntu plucky/main amd64 libestr0 amd64 0.1.11-2 [8340 B] 66s Get:59 http://ftpmaster.internal/ubuntu plucky/main amd64 libglib2.0-data all 2.84.0-1 [53.0 kB] 66s Get:60 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-newt amd64 0.52.24-4ubuntu2 [21.1 kB] 66s Get:61 http://ftpmaster.internal/ubuntu plucky/main amd64 libnewt0.52 amd64 0.52.24-4ubuntu2 [55.7 kB] 66s Get:62 http://ftpmaster.internal/ubuntu plucky/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2ubuntu5 [772 kB] 66s Get:63 http://ftpmaster.internal/ubuntu plucky/main amd64 python-apt-common all 2.9.9build1 [21.3 kB] 66s Get:64 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-apt amd64 2.9.9build1 [172 kB] 66s Get:65 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-cffi-backend amd64 1.17.1-2build2 [96.6 kB] 66s Get:66 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-dbus amd64 1.3.2-5build5 [102 kB] 66s Get:67 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-gi amd64 3.50.0-4build1 [252 kB] 66s Get:68 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-yaml amd64 6.0.2-1build2 [144 kB] 66s Get:69 http://ftpmaster.internal/ubuntu plucky/main amd64 rsyslog amd64 8.2412.0-2ubuntu2 [555 kB] 66s Get:70 http://ftpmaster.internal/ubuntu plucky/main amd64 whiptail amd64 0.52.24-4ubuntu2 [19.1 kB] 66s Get:71 http://ftpmaster.internal/ubuntu plucky/main amd64 ubuntu-minimal amd64 1.549 [11.5 kB] 66s Get:72 http://ftpmaster.internal/ubuntu plucky/main amd64 apparmor amd64 4.1.0~beta5-0ubuntu8 [701 kB] 66s Get:73 http://ftpmaster.internal/ubuntu plucky/main amd64 dosfstools amd64 4.2-1.2 [95.0 kB] 66s Get:74 http://ftpmaster.internal/ubuntu plucky/main amd64 libnl-genl-3-200 amd64 3.7.0-1 [12.2 kB] 66s Get:75 http://ftpmaster.internal/ubuntu plucky/main amd64 libnl-route-3-200 amd64 3.7.0-1 [191 kB] 66s Get:76 http://ftpmaster.internal/ubuntu plucky/main amd64 libnl-3-200 amd64 3.7.0-1 [64.9 kB] 66s Get:77 http://ftpmaster.internal/ubuntu plucky/main amd64 parted amd64 3.6-5 [53.9 kB] 66s Get:78 http://ftpmaster.internal/ubuntu plucky/main amd64 libparted2t64 amd64 3.6-5 [158 kB] 66s Get:79 http://ftpmaster.internal/ubuntu plucky/main amd64 pci.ids all 0.0~2025.03.09-1 [285 kB] 66s Get:80 http://ftpmaster.internal/ubuntu plucky/main amd64 pciutils amd64 1:3.13.0-2 [110 kB] 66s Get:81 http://ftpmaster.internal/ubuntu plucky/main amd64 libpci3 amd64 1:3.13.0-2 [39.8 kB] 66s Get:82 http://ftpmaster.internal/ubuntu plucky/main amd64 strace amd64 6.13+ds-1ubuntu1 [622 kB] 66s Get:83 http://ftpmaster.internal/ubuntu plucky/main amd64 xz-utils amd64 5.6.4-1 [278 kB] 66s Get:84 http://ftpmaster.internal/ubuntu plucky/main amd64 ubuntu-standard amd64 1.549 [11.5 kB] 66s Get:85 http://ftpmaster.internal/ubuntu plucky/main amd64 libgprofng0 amd64 2.44-3ubuntu1 [886 kB] 66s Get:86 http://ftpmaster.internal/ubuntu plucky/main amd64 libctf0 amd64 2.44-3ubuntu1 [96.5 kB] 66s Get:87 http://ftpmaster.internal/ubuntu plucky/main amd64 libctf-nobfd0 amd64 2.44-3ubuntu1 [98.9 kB] 66s Get:88 http://ftpmaster.internal/ubuntu plucky/main amd64 binutils-x86-64-linux-gnu amd64 2.44-3ubuntu1 [1108 kB] 66s Get:89 http://ftpmaster.internal/ubuntu plucky/main amd64 libbinutils amd64 2.44-3ubuntu1 [585 kB] 66s Get:90 http://ftpmaster.internal/ubuntu plucky/main amd64 binutils amd64 2.44-3ubuntu1 [208 kB] 66s Get:91 http://ftpmaster.internal/ubuntu plucky/main amd64 binutils-common amd64 2.44-3ubuntu1 [215 kB] 66s Get:92 http://ftpmaster.internal/ubuntu plucky/main amd64 libsframe1 amd64 2.44-3ubuntu1 [14.8 kB] 66s Get:93 http://ftpmaster.internal/ubuntu plucky/main amd64 hwdata all 0.393-3 [1562 B] 66s Get:94 http://ftpmaster.internal/ubuntu plucky/main amd64 pnp.ids all 0.393-3 [29.5 kB] 66s Get:95 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-tools-common all 6.14.0-10.10 [295 kB] 66s Get:96 http://ftpmaster.internal/ubuntu plucky/main amd64 bpftool amd64 7.6.0+6.14.0-10.10 [1147 kB] 66s Get:97 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-markupsafe amd64 2.1.5-1build4 [13.4 kB] 66s Get:98 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 66s Get:99 http://ftpmaster.internal/ubuntu plucky/main amd64 cloud-init-base all 25.1-0ubuntu3 [616 kB] 66s Get:100 http://ftpmaster.internal/ubuntu plucky/main amd64 libbrotli1 amd64 1.1.0-2build4 [365 kB] 66s Get:101 http://ftpmaster.internal/ubuntu plucky/main amd64 curl amd64 8.12.1-3ubuntu1 [258 kB] 66s Get:102 http://ftpmaster.internal/ubuntu plucky/main amd64 libcurl4t64 amd64 8.12.1-3ubuntu1 [437 kB] 67s Get:103 http://ftpmaster.internal/ubuntu plucky/main amd64 exfatprogs amd64 1.2.8-1 [76.3 kB] 67s Get:104 http://ftpmaster.internal/ubuntu plucky/main amd64 libcurl3t64-gnutls amd64 8.12.1-3ubuntu1 [432 kB] 67s Get:105 http://ftpmaster.internal/ubuntu plucky/main amd64 fwupd amd64 2.0.6-4 [5408 kB] 67s Get:106 http://ftpmaster.internal/ubuntu plucky/main amd64 libfwupd3 amd64 2.0.6-4 [136 kB] 67s Get:107 http://ftpmaster.internal/ubuntu plucky/main amd64 libmm-glib0 amd64 1.23.4-0ubuntu3 [251 kB] 67s Get:108 http://ftpmaster.internal/ubuntu plucky/main amd64 htop amd64 3.4.0-2 [195 kB] 67s Get:109 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-firmware amd64 20250310.git9e1370d3-0ubuntu1 [571 MB] 92s Get:110 http://ftpmaster.internal/ubuntu plucky/main amd64 initramfs-tools all 0.146ubuntu1 [7920 B] 92s Get:111 http://ftpmaster.internal/ubuntu plucky/main amd64 initramfs-tools-core all 0.146ubuntu1 [51.9 kB] 92s Get:112 http://ftpmaster.internal/ubuntu plucky/main amd64 initramfs-tools-bin amd64 0.146ubuntu1 [26.2 kB] 92s Get:113 http://ftpmaster.internal/ubuntu plucky/main amd64 libdebuginfod1t64 amd64 0.192-4 [21.0 kB] 92s Get:114 http://ftpmaster.internal/ubuntu plucky/main amd64 libftdi1-2 amd64 1.5-8build1 [30.2 kB] 92s Get:115 http://ftpmaster.internal/ubuntu plucky/main amd64 libgpgme11t64 amd64 1.24.2-1ubuntu2 [155 kB] 92s Get:116 http://ftpmaster.internal/ubuntu plucky/main amd64 libjemalloc2 amd64 5.3.0-3 [277 kB] 92s Get:117 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-modules-6.14.0-10-generic amd64 6.14.0-10.10 [41.2 MB] 94s Get:118 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-image-6.14.0-10-generic amd64 6.14.0-10.10 [15.3 MB] 94s Get:119 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-modules-extra-6.14.0-10-generic amd64 6.14.0-10.10 [120 MB] 99s Get:120 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-generic amd64 6.14.0-10.10 [1730 B] 99s Get:121 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-image-generic amd64 6.14.0-10.10 [11.1 kB] 99s Get:122 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-virtual amd64 6.14.0-10.10 [1722 B] 99s Get:123 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-image-virtual amd64 6.14.0-10.10 [11.1 kB] 99s Get:124 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-virtual amd64 6.14.0-10.10 [1642 B] 99s Get:125 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-6.14.0-10 all 6.14.0-10.10 [14.2 MB] 100s Get:126 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-6.14.0-10-generic amd64 6.14.0-10.10 [3915 kB] 100s Get:127 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-generic amd64 6.14.0-10.10 [11.0 kB] 100s Get:128 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-perf amd64 6.14.0-10.10 [4122 kB] 100s Get:129 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-tools-6.14.0-10 amd64 6.14.0-10.10 [1394 kB] 100s Get:130 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-tools-6.14.0-10-generic amd64 6.14.0-10.10 [830 B] 100s Get:131 http://ftpmaster.internal/ubuntu plucky/main amd64 pinentry-curses amd64 1.3.1-2ubuntu3 [42.3 kB] 100s Get:132 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-lazr.uri all 1.0.6-6 [13.7 kB] 100s Get:133 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-rpds-py amd64 0.21.0-2ubuntu2 [278 kB] 100s Get:134 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-systemd amd64 235-1build6 [43.9 kB] 100s Get:135 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-gdbm amd64 3.13.2-2 [31.9 kB] 100s Get:136 http://ftpmaster.internal/ubuntu plucky/main amd64 ubuntu-kernel-accessories amd64 1.549 [11.2 kB] 100s Get:137 http://ftpmaster.internal/ubuntu plucky/main amd64 cloud-init all 25.1-0ubuntu3 [2100 B] 100s Get:138 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-bcrypt amd64 4.2.0-2.1build1 [221 kB] 101s Preconfiguring packages ... 101s Fetched 829 MB in 36s (22.9 MB/s) 101s (Reading database ... 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(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 ... 109146 files and directories currently installed.) 110s Preparing to unpack .../0-libsqlite3-0_3.46.1-2_amd64.deb ... 110s Unpacking libsqlite3-0:amd64 (3.46.1-2) over (3.46.1-1) ... 110s Preparing to unpack .../1-python3.13_3.13.2-2_amd64.deb ... 110s Unpacking python3.13 (3.13.2-2) over (3.13.2-1) ... 110s Preparing to unpack .../2-python3.13-minimal_3.13.2-2_amd64.deb ... 110s Unpacking python3.13-minimal (3.13.2-2) over (3.13.2-1) ... 111s Preparing to unpack .../3-libpython3.13-minimal_3.13.2-2_amd64.deb ... 111s Unpacking libpython3.13-minimal:amd64 (3.13.2-2) over (3.13.2-1) ... 111s Preparing to unpack .../4-libpython3.13-stdlib_3.13.2-2_amd64.deb ... 111s Unpacking libpython3.13-stdlib:amd64 (3.13.2-2) over (3.13.2-1) ... 111s Preparing to unpack .../5-libpython3-stdlib_3.13.2-2_amd64.deb ... 111s Unpacking libpython3-stdlib:amd64 (3.13.2-2) over (3.13.2-1) ... 111s Preparing to unpack .../6-rsync_3.4.1+ds1-3_amd64.deb ... 111s Unpacking rsync (3.4.1+ds1-3) over (3.4.1-0syncable1) ... 111s Selecting previously unselected package libdebuginfod-common. 111s Preparing to unpack .../7-libdebuginfod-common_0.192-4_all.deb ... 111s Unpacking libdebuginfod-common (0.192-4) ... 111s Preparing to unpack .../8-libsemanage-common_3.7-2.1build1_all.deb ... 111s Unpacking libsemanage-common (3.7-2.1build1) over (3.7-2.1) ... 111s Setting up libsemanage-common (3.7-2.1build1) ... 111s (Reading database ... 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(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 ... 109155 files and directories currently installed.) 112s Preparing to unpack .../00-gir1.2-girepository-2.0_1.83.4-1_amd64.deb ... 112s Unpacking gir1.2-girepository-2.0:amd64 (1.83.4-1) over (1.82.0-4) ... 112s Preparing to unpack .../01-gir1.2-glib-2.0_2.84.0-1_amd64.deb ... 112s Unpacking gir1.2-glib-2.0:amd64 (2.84.0-1) over (2.83.5-1) ... 112s Preparing to unpack .../02-libglib2.0-0t64_2.84.0-1_amd64.deb ... 112s Unpacking libglib2.0-0t64:amd64 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.../23-parted_3.6-5_amd64.deb ... 115s Unpacking parted (3.6-5) over (3.6-4build1) ... 115s Preparing to unpack .../24-libparted2t64_3.6-5_amd64.deb ... 115s Adding 'diversion of /lib/x86_64-linux-gnu/libparted.so.2 to /lib/x86_64-linux-gnu/libparted.so.2.usr-is-merged by libparted2t64' 115s Adding 'diversion of /lib/x86_64-linux-gnu/libparted.so.2.0.5 to /lib/x86_64-linux-gnu/libparted.so.2.0.5.usr-is-merged by libparted2t64' 115s Unpacking libparted2t64:amd64 (3.6-5) over (3.6-4build1) ... 115s Preparing to unpack .../25-pci.ids_0.0~2025.03.09-1_all.deb ... 115s Unpacking pci.ids (0.0~2025.03.09-1) over (0.0~2025.02.12-1) ... 115s Preparing to unpack .../26-pciutils_1%3a3.13.0-2_amd64.deb ... 115s Unpacking pciutils (1:3.13.0-2) over (1:3.13.0-1) ... 115s Preparing to unpack .../27-libpci3_1%3a3.13.0-2_amd64.deb ... 115s Unpacking libpci3:amd64 (1:3.13.0-2) over (1:3.13.0-1) ... 115s Preparing to unpack .../28-strace_6.13+ds-1ubuntu1_amd64.deb ... 115s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 115s Preparing to unpack .../29-xz-utils_5.6.4-1_amd64.deb ... 115s Unpacking xz-utils (5.6.4-1) over (5.6.3-1) ... 116s Preparing to unpack .../30-ubuntu-standard_1.549_amd64.deb ... 116s Unpacking ubuntu-standard (1.549) over (1.548) ... 116s Preparing to unpack .../31-libgprofng0_2.44-3ubuntu1_amd64.deb ... 116s Unpacking libgprofng0:amd64 (2.44-3ubuntu1) over (2.44-2ubuntu1) ... 116s Preparing to unpack .../32-libctf0_2.44-3ubuntu1_amd64.deb ... 116s Unpacking libctf0:amd64 (2.44-3ubuntu1) over (2.44-2ubuntu1) ... 116s Preparing to unpack .../33-libctf-nobfd0_2.44-3ubuntu1_amd64.deb ... 116s Unpacking libctf-nobfd0:amd64 (2.44-3ubuntu1) over (2.44-2ubuntu1) ... 116s Preparing to unpack .../34-binutils-x86-64-linux-gnu_2.44-3ubuntu1_amd64.deb ... 116s Unpacking binutils-x86-64-linux-gnu (2.44-3ubuntu1) over (2.44-2ubuntu1) ... 116s Preparing to unpack .../35-libbinutils_2.44-3ubuntu1_amd64.deb ... 116s Unpacking libbinutils:amd64 (2.44-3ubuntu1) over (2.44-2ubuntu1) ... 116s Preparing to unpack .../36-binutils_2.44-3ubuntu1_amd64.deb ... 116s Unpacking binutils (2.44-3ubuntu1) over (2.44-2ubuntu1) ... 116s Preparing to unpack .../37-binutils-common_2.44-3ubuntu1_amd64.deb ... 116s Unpacking binutils-common:amd64 (2.44-3ubuntu1) over (2.44-2ubuntu1) ... 116s Preparing to unpack .../38-libsframe1_2.44-3ubuntu1_amd64.deb ... 116s Unpacking libsframe1:amd64 (2.44-3ubuntu1) over (2.44-2ubuntu1) ... 116s Preparing to unpack .../39-hwdata_0.393-3_all.deb ... 116s Unpacking hwdata (0.393-3) over (0.392-1) ... 116s Selecting previously unselected package pnp.ids. 116s Preparing to unpack .../40-pnp.ids_0.393-3_all.deb ... 116s Unpacking pnp.ids (0.393-3) ... 116s Preparing to unpack .../41-linux-tools-common_6.14.0-10.10_all.deb ... 116s Unpacking linux-tools-common (6.14.0-10.10) over (6.12.0-16.16) ... 116s Selecting previously unselected package bpftool. 116s Preparing to unpack .../42-bpftool_7.6.0+6.14.0-10.10_amd64.deb ... 116s Unpacking bpftool (7.6.0+6.14.0-10.10) ... 116s Preparing to unpack .../43-python3-markupsafe_2.1.5-1build4_amd64.deb ... 116s Unpacking python3-markupsafe (2.1.5-1build4) over (2.1.5-1build3) ... 116s Preparing to unpack .../44-python3-jinja2_3.1.5-2ubuntu1_all.deb ... 117s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 117s Preparing to unpack .../45-cloud-init-base_25.1-0ubuntu3_all.deb ... 117s Unpacking cloud-init-base (25.1-0ubuntu3) over (25.1-0ubuntu2) ... 117s Preparing to unpack .../46-libbrotli1_1.1.0-2build4_amd64.deb ... 117s Unpacking libbrotli1:amd64 (1.1.0-2build4) over (1.1.0-2build3) ... 117s Preparing to unpack .../47-curl_8.12.1-3ubuntu1_amd64.deb ... 117s Unpacking curl (8.12.1-3ubuntu1) over (8.12.1-2ubuntu1) ... 117s Preparing to unpack .../48-libcurl4t64_8.12.1-3ubuntu1_amd64.deb ... 117s Unpacking libcurl4t64:amd64 (8.12.1-3ubuntu1) over (8.12.1-2ubuntu1) ... 117s Preparing to unpack .../49-exfatprogs_1.2.8-1_amd64.deb ... 117s Unpacking exfatprogs (1.2.8-1) over (1.2.7-3) ... 117s Preparing to unpack .../50-libcurl3t64-gnutls_8.12.1-3ubuntu1_amd64.deb ... 117s Unpacking libcurl3t64-gnutls:amd64 (8.12.1-3ubuntu1) over (8.12.1-2ubuntu1) ... 117s Preparing to unpack .../51-fwupd_2.0.6-4_amd64.deb ... 118s Unpacking fwupd (2.0.6-4) over (2.0.6-3) ... 118s Preparing to unpack .../52-libfwupd3_2.0.6-4_amd64.deb ... 118s Unpacking libfwupd3:amd64 (2.0.6-4) over (2.0.6-3) ... 118s Preparing to unpack .../53-libmm-glib0_1.23.4-0ubuntu3_amd64.deb ... 118s Unpacking libmm-glib0:amd64 (1.23.4-0ubuntu3) over (1.23.4-0ubuntu2) ... 118s Preparing to unpack .../54-htop_3.4.0-2_amd64.deb ... 118s Unpacking htop (3.4.0-2) over (3.3.0-5) ... 118s Preparing to unpack .../55-linux-firmware_20250310.git9e1370d3-0ubuntu1_amd64.deb ... 118s Unpacking linux-firmware (20250310.git9e1370d3-0ubuntu1) over (20250204.git0fd450ee-0ubuntu1) ... 122s Preparing to unpack .../56-initramfs-tools_0.146ubuntu1_all.deb ... 122s Unpacking initramfs-tools (0.146ubuntu1) over (0.145ubuntu3) ... 122s Preparing to unpack .../57-initramfs-tools-core_0.146ubuntu1_all.deb ... 122s Unpacking initramfs-tools-core (0.146ubuntu1) over (0.145ubuntu3) ... 122s Preparing to unpack .../58-initramfs-tools-bin_0.146ubuntu1_amd64.deb ... 122s Unpacking initramfs-tools-bin (0.146ubuntu1) over (0.145ubuntu3) ... 122s Selecting previously unselected package libdebuginfod1t64:amd64. 122s Preparing to unpack .../59-libdebuginfod1t64_0.192-4_amd64.deb ... 122s Unpacking libdebuginfod1t64:amd64 (0.192-4) ... 122s Preparing to unpack .../60-libftdi1-2_1.5-8build1_amd64.deb ... 122s Unpacking libftdi1-2:amd64 (1.5-8build1) over (1.5-8) ... 122s Preparing to unpack .../61-libgpgme11t64_1.24.2-1ubuntu2_amd64.deb ... 122s Unpacking libgpgme11t64:amd64 (1.24.2-1ubuntu2) over (1.24.2-1ubuntu1) ... 122s Preparing to unpack .../62-libjemalloc2_5.3.0-3_amd64.deb ... 122s Unpacking libjemalloc2:amd64 (5.3.0-3) over (5.3.0-2build1) ... 122s Selecting previously unselected package linux-modules-6.14.0-10-generic. 122s Preparing to unpack .../63-linux-modules-6.14.0-10-generic_6.14.0-10.10_amd64.deb ... 122s Unpacking linux-modules-6.14.0-10-generic (6.14.0-10.10) ... 123s Selecting previously unselected package linux-image-6.14.0-10-generic. 123s Preparing to unpack .../64-linux-image-6.14.0-10-generic_6.14.0-10.10_amd64.deb ... 123s Unpacking linux-image-6.14.0-10-generic (6.14.0-10.10) ... 123s Selecting previously unselected package linux-modules-extra-6.14.0-10-generic. 123s Preparing to unpack .../65-linux-modules-extra-6.14.0-10-generic_6.14.0-10.10_amd64.deb ... 123s Unpacking linux-modules-extra-6.14.0-10-generic (6.14.0-10.10) ... 125s Preparing to unpack .../66-linux-generic_6.14.0-10.10_amd64.deb ... 125s Unpacking linux-generic (6.14.0-10.10) over (6.12.0-16.16+2) ... 125s Preparing to unpack .../67-linux-image-generic_6.14.0-10.10_amd64.deb ... 125s Unpacking linux-image-generic (6.14.0-10.10) over (6.12.0-16.16+2) ... 125s Preparing to unpack .../68-linux-virtual_6.14.0-10.10_amd64.deb ... 125s Unpacking linux-virtual (6.14.0-10.10) over (6.12.0-16.16+2) ... 125s Preparing to unpack .../69-linux-image-virtual_6.14.0-10.10_amd64.deb ... 125s Unpacking linux-image-virtual (6.14.0-10.10) over (6.12.0-16.16+2) ... 125s Preparing to unpack .../70-linux-headers-virtual_6.14.0-10.10_amd64.deb ... 125s Unpacking linux-headers-virtual (6.14.0-10.10) over (6.12.0-16.16+2) ... 125s Selecting previously unselected package linux-headers-6.14.0-10. 125s Preparing to unpack .../71-linux-headers-6.14.0-10_6.14.0-10.10_all.deb ... 125s Unpacking linux-headers-6.14.0-10 (6.14.0-10.10) ... 128s Selecting previously unselected package linux-headers-6.14.0-10-generic. 128s Preparing to unpack .../72-linux-headers-6.14.0-10-generic_6.14.0-10.10_amd64.deb ... 128s Unpacking linux-headers-6.14.0-10-generic (6.14.0-10.10) ... 130s Preparing to unpack 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(1.0.6-6) over (1.0.6-5) ... 131s Preparing to unpack .../79-python3-rpds-py_0.21.0-2ubuntu2_amd64.deb ... 131s Unpacking python3-rpds-py (0.21.0-2ubuntu2) over (0.21.0-2ubuntu1) ... 131s Preparing to unpack .../80-python3-systemd_235-1build6_amd64.deb ... 131s Unpacking python3-systemd (235-1build6) over (235-1build5) ... 131s Preparing to unpack .../81-python3.13-gdbm_3.13.2-2_amd64.deb ... 131s Unpacking python3.13-gdbm (3.13.2-2) over (3.13.2-1) ... 131s Preparing to unpack .../82-ubuntu-kernel-accessories_1.549_amd64.deb ... 131s Unpacking ubuntu-kernel-accessories (1.549) over (1.548) ... 131s Preparing to unpack .../83-cloud-init_25.1-0ubuntu3_all.deb ... 131s Unpacking cloud-init (25.1-0ubuntu3) over (25.1-0ubuntu2) ... 131s Preparing to unpack .../84-python3-bcrypt_4.2.0-2.1build1_amd64.deb ... 131s Unpacking python3-bcrypt (4.2.0-2.1build1) over (4.2.0-2.1) ... 131s Setting up linux-headers-6.14.0-10 (6.14.0-10.10) ... 131s Setting up media-types (13.0.0) ... 131s Installing new version of config file /etc/mime.types ... 131s Setting up linux-headers-6.14.0-10-generic (6.14.0-10.10) ... 131s Setting up ubuntu-kernel-accessories (1.549) ... 131s Setting up libapparmor1:amd64 (4.1.0~beta5-0ubuntu8) ... 131s Setting up pci.ids (0.0~2025.03.09-1) ... 131s Setting up libnewt0.52:amd64 (0.52.24-4ubuntu2) ... 131s Setting up apt-utils (2.9.33) ... 131s Setting up libdebuginfod-common (0.192-4) ... 131s Setting up exfatprogs (1.2.8-1) ... 131s Setting up linux-firmware (20250310.git9e1370d3-0ubuntu1) ... 131s Setting up bpftool (7.6.0+6.14.0-10.10) ... 131s Setting up libestr0:amd64 (0.1.11-2) ... 131s Setting up libbrotli1:amd64 (1.1.0-2build4) ... 131s Setting up libsqlite3-0:amd64 (3.46.1-2) ... 131s Setting up dosfstools (4.2-1.2) ... 131s Setting up rsyslog (8.2412.0-2ubuntu2) ... 132s info: The user `syslog' is already a member of `adm'. 133s Setting up binutils-common:amd64 (2.44-3ubuntu1) ... 133s Setting up libcurl3t64-gnutls:amd64 (8.12.1-3ubuntu1) ... 133s Setting up linux-libc-dev:amd64 (6.14.0-10.10) ... 133s Setting up libctf-nobfd0:amd64 (2.44-3ubuntu1) ... 133s Setting up systemd (257.3-1ubuntu3) ... 133s /usr/lib/tmpfiles.d/legacy.conf:14: Duplicate line for path "/run/lock", ignoring. 133s Created symlink '/run/systemd/system/tmp.mount' → '/dev/null'. 133s /usr/lib/tmpfiles.d/legacy.conf:14: Duplicate line for path "/run/lock", ignoring. 134s Setting up libparted2t64:amd64 (3.6-5) ... 134s Removing 'diversion of /lib/x86_64-linux-gnu/libparted.so.2 to /lib/x86_64-linux-gnu/libparted.so.2.usr-is-merged by libparted2t64' 134s Removing 'diversion of /lib/x86_64-linux-gnu/libparted.so.2.0.5 to /lib/x86_64-linux-gnu/libparted.so.2.0.5.usr-is-merged by libparted2t64' 134s Setting up linux-headers-generic (6.14.0-10.10) ... 134s Setting up libjemalloc2:amd64 (5.3.0-3) ... 134s Setting up locales (2.41-1ubuntu1) ... 134s Installing new version of config file /etc/locale.alias ... 135s Generating locales (this might take a while)... 137s en_US.UTF-8... done 137s Generation complete. 137s Setting up libsframe1:amd64 (2.44-3ubuntu1) ... 137s Setting up libpython3.13-minimal:amd64 (3.13.2-2) ... 137s Setting up apparmor (4.1.0~beta5-0ubuntu8) ... 137s Installing new version of config file /etc/apparmor.d/fusermount3 ... 137s Installing new version of config file /etc/apparmor.d/lsusb ... 137s Installing new version of config file /etc/apparmor.d/openvpn ... 139s Reloading AppArmor profiles 140s Setting up libftdi1-2:amd64 (1.5-8build1) ... 140s Setting up libglib2.0-data (2.84.0-1) ... 140s Setting up systemd-cryptsetup (257.3-1ubuntu3) ... 140s Setting up libncurses6:amd64 (6.5+20250216-2) ... 140s Setting up strace (6.13+ds-1ubuntu1) ... 140s Setting up xz-utils (5.6.4-1) ... 140s Setting up systemd-timesyncd (257.3-1ubuntu3) ... 141s systemd-time-wait-sync.service is a disabled or a static unit not running, not starting it. 141s Setting up libatomic1:amd64 (15-20250222-0ubuntu1) ... 141s Setting up udev (257.3-1ubuntu3) ... 142s Setting up linux-modules-6.14.0-10-generic (6.14.0-10.10) ... 145s Setting up libncursesw6:amd64 (6.5+20250216-2) ... 145s Setting up libpci3:amd64 (1:3.13.0-2) ... 145s Setting up whiptail (0.52.24-4ubuntu2) ... 145s Setting up python-apt-common (2.9.9build1) ... 145s Setting up pnp.ids (0.393-3) ... 145s Setting up libnl-3-200:amd64 (3.7.0-1) ... 145s Setting up python3.13-minimal (3.13.2-2) ... 146s Setting up libgpgme11t64:amd64 (1.24.2-1ubuntu2) ... 146s Setting up libbinutils:amd64 (2.44-3ubuntu1) ... 146s Setting up libc-dev-bin (2.41-1ubuntu1) ... 146s Setting up libpython3.13-stdlib:amd64 (3.13.2-2) ... 146s Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2ubuntu5) ... 146s Setting up rsync (3.4.1+ds1-3) ... 147s rsync.service is a disabled or a static unit not running, not starting it. 147s Setting up python3.13-gdbm (3.13.2-2) ... 147s Setting up libpython3-stdlib:amd64 (3.13.2-2) ... 147s Setting up systemd-resolved (257.3-1ubuntu3) ... 148s Setting up initramfs-tools-bin (0.146ubuntu1) ... 148s Setting up ncurses-term (6.5+20250216-2) ... 148s Setting up libctf0:amd64 (2.44-3ubuntu1) ... 148s Setting up libpython3.13:amd64 (3.13.2-2) ... 148s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 148s Setting up libdebuginfod1t64:amd64 (0.192-4) ... 148s Setting up systemd-sysv (257.3-1ubuntu3) ... 148s Setting up linux-headers-virtual (6.14.0-10.10) ... 148s Setting up libcurl4t64:amd64 (8.12.1-3ubuntu1) ... 148s Setting up python3.13 (3.13.2-2) ... 149s Setting up htop (3.4.0-2) ... 149s Setting up linux-image-6.14.0-10-generic (6.14.0-10.10) ... 152s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.12.0-16-generic 152s I: /boot/initrd.img.old is now a symlink to initrd.img-6.12.0-16-generic 152s I: /boot/vmlinuz is now a symlink to vmlinuz-6.14.0-10-generic 152s I: /boot/initrd.img is now a symlink to initrd.img-6.14.0-10-generic 152s Setting up parted (3.6-5) ... 152s Setting up libnss-systemd:amd64 (257.3-1ubuntu3) ... 152s Setting up python3 (3.13.2-2) ... 152s Setting up python3-newt:amd64 (0.52.24-4ubuntu2) ... 152s Setting up python3-markupsafe (2.1.5-1build4) ... 152s Setting up linux-modules-extra-6.14.0-10-generic (6.14.0-10.10) ... 155s Setting up libnl-route-3-200:amd64 (3.7.0-1) ... 155s Setting up hwdata (0.393-3) ... 155s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 156s Setting up libglib2.0-0t64:amd64 (2.84.0-1) ... 156s No schema files found: doing nothing. 156s Setting up libgprofng0:amd64 (2.44-3ubuntu1) ... 156s Setting up linux-perf (6.14.0-10.10) ... 156s Setting up gir1.2-glib-2.0:amd64 (2.84.0-1) ... 156s Setting up pciutils (1:3.13.0-2) ... 156s Setting up python3-rpds-py (0.21.0-2ubuntu2) ... 156s Setting up libmm-glib0:amd64 (1.23.4-0ubuntu3) ... 156s Setting up libnl-genl-3-200:amd64 (3.7.0-1) ... 156s Setting up libpam-systemd:amd64 (257.3-1ubuntu3) ... 156s Setting up libc6-dev:amd64 (2.41-1ubuntu1) ... 156s Setting up libgirepository-1.0-1:amd64 (1.83.4-1) ... 156s Setting up curl (8.12.1-3ubuntu1) ... 156s Setting up linux-image-virtual (6.14.0-10.10) ... 156s Setting up initramfs-tools-core (0.146ubuntu1) ... 156s Setting up linux-tools-common (6.14.0-10.10) ... 156s Setting up python3-systemd (235-1build6) ... 156s Setting up python3-cffi-backend:amd64 (1.17.1-2build2) ... 156s Setting up binutils-x86-64-linux-gnu (2.44-3ubuntu1) ... 156s Setting up linux-image-generic (6.14.0-10.10) ... 156s Setting up python3-dbus (1.3.2-5build5) ... 156s Setting up linux-tools-6.14.0-10 (6.14.0-10.10) ... 156s Setting up initramfs-tools (0.146ubuntu1) ... 156s Installing new version of config file /etc/kernel/postinst.d/initramfs-tools ... 156s Installing new version of config file /etc/kernel/postrm.d/initramfs-tools ... 156s update-initramfs: deferring update (trigger activated) 156s Setting up linux-generic (6.14.0-10.10) ... 156s Setting up ubuntu-minimal (1.549) ... 156s Setting up python3-apt (2.9.9build1) ... 156s Setting up python3-bcrypt (4.2.0-2.1build1) ... 157s Setting up python3-yaml (6.0.2-1build2) ... 157s Setting up libfwupd3:amd64 (2.0.6-4) ... 157s Setting up python3-lazr.uri (1.0.6-6) ... 157s Setting up binutils (2.44-3ubuntu1) ... 157s Setting up ubuntu-standard (1.549) ... 157s Setting up cloud-init-base (25.1-0ubuntu3) ... 159s Setting up linux-virtual (6.14.0-10.10) ... 159s Setting up gir1.2-girepository-2.0:amd64 (1.83.4-1) ... 159s Setting up python3-gi (3.50.0-4build1) ... 159s Setting up linux-tools-6.14.0-10-generic (6.14.0-10.10) ... 159s Setting up fwupd (2.0.6-4) ... 160s fwupd-refresh.service is a disabled or a static unit not running, not starting it. 160s Setting up cloud-init (25.1-0ubuntu3) ... 160s Processing triggers for man-db (2.13.0-1) ... 163s Processing triggers for dbus (1.16.2-1ubuntu1) ... 163s Processing triggers for shared-mime-info (2.4-5) ... 163s Warning: program compiled against libxml 212 using older 209 163s Processing triggers for libc-bin (2.41-1ubuntu1) ... 163s Processing triggers for linux-image-6.14.0-10-generic (6.14.0-10.10) ... 163s /etc/kernel/postinst.d/initramfs-tools: 163s update-initramfs: Generating /boot/initrd.img-6.14.0-10-generic 163s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 177s /etc/kernel/postinst.d/zz-update-grub: 177s Sourcing file `/etc/default/grub' 177s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 177s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg' 177s Generating grub configuration file ... 177s Found linux image: /boot/vmlinuz-6.14.0-10-generic 177s Found initrd image: /boot/initrd.img-6.14.0-10-generic 178s Found linux image: /boot/vmlinuz-6.12.0-16-generic 178s Found initrd image: /boot/initrd.img-6.12.0-16-generic 178s Found linux image: /boot/vmlinuz-6.11.0-8-generic 178s Found initrd image: /boot/initrd.img-6.11.0-8-generic 178s Warning: os-prober will not be executed to detect other bootable partitions. 178s Systems on them will not be added to the GRUB boot configuration. 178s Check GRUB_DISABLE_OS_PROBER documentation entry. 178s Adding boot menu entry for UEFI Firmware Settings ... 178s done 178s Processing triggers for initramfs-tools (0.146ubuntu1) ... 178s update-initramfs: Generating /boot/initrd.img-6.14.0-10-generic 178s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 194s Reading package lists... 194s Building dependency tree... 194s Reading state information... 195s Solving dependencies... 195s The following packages will be REMOVED: 195s libnl-genl-3-200* libnsl2* libpython3.12-minimal* libpython3.12-stdlib* 195s libpython3.12t64* linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 195s linux-headers-6.12.0-16* linux-headers-6.12.0-16-generic* 195s linux-image-6.11.0-8-generic* linux-image-6.12.0-16-generic* 195s linux-modules-6.11.0-8-generic* linux-modules-6.12.0-16-generic* 195s linux-modules-extra-6.12.0-16-generic* linux-tools-6.11.0-8* 195s linux-tools-6.11.0-8-generic* linux-tools-6.12.0-16* 195s linux-tools-6.12.0-16-generic* 196s 0 upgraded, 0 newly installed, 18 to remove and 5 not upgraded. 196s After this operation, 545 MB disk space will be freed. 196s (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 ... 148643 files and directories currently installed.) 196s Removing libnl-genl-3-200:amd64 (3.7.0-1) ... 196s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 196s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 196s Removing libpython3.12t64:amd64 (3.12.9-1) ... 196s Removing libpython3.12-stdlib:amd64 (3.12.9-1) ... 196s Removing libnsl2:amd64 (1.3.0-3build3) ... 196s Removing libpython3.12-minimal:amd64 (3.12.9-1) ... 196s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 197s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 200s Removing linux-headers-6.12.0-16-generic (6.12.0-16.16) ... 201s Removing linux-headers-6.12.0-16 (6.12.0-16.16) ... 204s Removing linux-image-6.11.0-8-generic (6.11.0-8.8) ... 204s /etc/kernel/postrm.d/initramfs-tools: 204s update-initramfs: Deleting /boot/initrd.img-6.11.0-8-generic 205s /etc/kernel/postrm.d/zz-update-grub: 205s Sourcing file `/etc/default/grub' 205s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 205s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg' 205s Generating grub configuration file ... 205s Found linux image: /boot/vmlinuz-6.14.0-10-generic 205s Found initrd image: /boot/initrd.img-6.14.0-10-generic 206s Found linux image: /boot/vmlinuz-6.12.0-16-generic 206s Found initrd image: /boot/initrd.img-6.12.0-16-generic 206s Warning: os-prober will not be executed to detect other bootable partitions. 206s Systems on them will not be added to the GRUB boot configuration. 206s Check GRUB_DISABLE_OS_PROBER documentation entry. 206s Adding boot menu entry for UEFI Firmware Settings ... 206s done 206s Removing linux-image-6.12.0-16-generic (6.12.0-16.16) ... 206s W: Removing the running kernel 206s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.14.0-10-generic 206s I: /boot/initrd.img.old is now a symlink to initrd.img-6.14.0-10-generic 206s /etc/kernel/postrm.d/initramfs-tools: 206s update-initramfs: Deleting /boot/initrd.img-6.12.0-16-generic 206s /etc/kernel/postrm.d/zz-update-grub: 206s Sourcing file `/etc/default/grub' 206s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 206s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg' 206s Generating grub configuration file ... 207s Found linux image: /boot/vmlinuz-6.14.0-10-generic 207s Found initrd image: /boot/initrd.img-6.14.0-10-generic 207s Warning: os-prober will not be executed to detect other bootable partitions. 207s Systems on them will not be added to the GRUB boot configuration. 207s Check GRUB_DISABLE_OS_PROBER documentation entry. 207s Adding boot menu entry for UEFI Firmware Settings ... 207s done 207s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 207s Removing linux-modules-extra-6.12.0-16-generic (6.12.0-16.16) ... 210s Removing linux-modules-6.12.0-16-generic (6.12.0-16.16) ... 210s Removing linux-tools-6.12.0-16-generic (6.12.0-16.16) ... 210s Removing linux-tools-6.12.0-16 (6.12.0-16.16) ... 210s Processing triggers for libc-bin (2.41-1ubuntu1) ... 210s (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 ... 76972 files and directories currently installed.) 210s Purging configuration files for linux-image-6.11.0-8-generic (6.11.0-8.8) ... 210s Purging configuration files for libpython3.12-minimal:amd64 (3.12.9-1) ... 211s Purging configuration files for linux-modules-extra-6.12.0-16-generic (6.12.0-16.16) ... 211s Purging configuration files for linux-modules-6.12.0-16-generic (6.12.0-16.16) ... 211s dpkg: warning: while removing linux-modules-6.12.0-16-generic, directory '/lib/modules/6.12.0-16-generic' not empty so not removed 211s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 211s Purging configuration files for linux-image-6.12.0-16-generic (6.12.0-16.16) ... 211s rmdir: failed to remove '/lib/modules/6.12.0-16-generic': Directory not empty 211s autopkgtest [22:10:22]: upgrading testbed (apt dist-upgrade and autopurge) 211s Reading package lists... 212s Building dependency tree... 212s Reading state information... 212s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 212s Starting 2 pkgProblemResolver with broken count: 0 212s Done 213s Entering ResolveByKeep 213s 214s Calculating upgrade... 214s The following packages will be upgraded: 214s libc-bin libc-dev-bin libc6 libc6-dev locales 214s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 214s Need to get 10.5 MB of archives. 214s After this operation, 1024 B of additional disk space will be used. 214s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc6-dev amd64 2.41-1ubuntu2 [2183 kB] 215s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc-dev-bin amd64 2.41-1ubuntu2 [24.7 kB] 215s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc6 amd64 2.41-1ubuntu2 [3327 kB] 215s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc-bin amd64 2.41-1ubuntu2 [700 kB] 215s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 locales all 2.41-1ubuntu2 [4246 kB] 216s Preconfiguring packages ... 216s Fetched 10.5 MB in 2s (6688 kB/s) 216s (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 ... 76968 files and directories currently installed.) 216s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_amd64.deb ... 216s Unpacking libc6-dev:amd64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 216s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_amd64.deb ... 216s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 217s Preparing to unpack .../libc6_2.41-1ubuntu2_amd64.deb ... 217s Unpacking libc6:amd64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 217s Setting up libc6:amd64 (2.41-1ubuntu2) ... 217s (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 ... 76968 files and directories currently installed.) 217s Preparing to unpack .../libc-bin_2.41-1ubuntu2_amd64.deb ... 217s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 217s Setting up libc-bin (2.41-1ubuntu2) ... 218s (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 ... 76968 files and directories currently installed.) 218s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 218s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 218s Setting up locales (2.41-1ubuntu2) ... 219s Generating locales (this might take a while)... 221s en_US.UTF-8... done 221s Generation complete. 221s Setting up libc-dev-bin (2.41-1ubuntu2) ... 221s Setting up libc6-dev:amd64 (2.41-1ubuntu2) ... 221s Processing triggers for man-db (2.13.0-1) ... 222s Processing triggers for systemd (257.3-1ubuntu3) ... 223s Reading package lists... 223s Building dependency tree... 223s Reading state information... 224s Starting pkgProblemResolver with broken count: 0 224s Starting 2 pkgProblemResolver with broken count: 0 224s Done 224s Solving dependencies... 225s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 225s autopkgtest [22:10:36]: rebooting testbed after setup commands that affected boot 248s autopkgtest [22:10:59]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP PREEMPT_DYNAMIC Wed Mar 12 16:07:00 UTC 2025 251s autopkgtest [22:11:02]: @@@@@@@@@@@@@@@@@@@@ apt-source r-cran-etm 254s Get:1 http://ftpmaster.internal/ubuntu plucky/universe r-cran-etm 1.1.1-1 (dsc) [2148 B] 254s Get:2 http://ftpmaster.internal/ubuntu plucky/universe r-cran-etm 1.1.1-1 (tar) [242 kB] 254s Get:3 http://ftpmaster.internal/ubuntu plucky/universe r-cran-etm 1.1.1-1 (diff) [3564 B] 254s gpgv: Signature made Fri Sep 18 09:39:57 2020 UTC 254s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 254s gpgv: issuer "tille@debian.org" 254s gpgv: Can't check signature: No public key 254s dpkg-source: warning: cannot verify inline signature for ./r-cran-etm_1.1.1-1.dsc: no acceptable signature found 254s autopkgtest [22:11:05]: testing package r-cran-etm version 1.1.1-1 254s autopkgtest [22:11:05]: build not needed 256s autopkgtest [22:11:07]: test run-unit-test: preparing testbed 257s Reading package lists... 257s Building dependency tree... 257s Reading state information... 257s Starting pkgProblemResolver with broken count: 0 257s Starting 2 pkgProblemResolver with broken count: 0 257s Done 258s The following NEW packages will be installed: 258s fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono libblas3 258s libcairo2 libdatrie1 libdeflate0 libfontconfig1 libgfortran5 libgomp1 258s libgraphite2-3 libharfbuzz0b libice6 libjbig0 libjpeg-turbo8 libjpeg8 258s liblapack3 liblerc4 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 258s libpaper-utils libpaper2 libpixman-1-0 libsharpyuv0 libsm6 libtcl8.6 258s libthai-data libthai0 libtiff6 libtk8.6 libwebp7 libxcb-render0 libxcb-shm0 258s libxft2 libxrender1 libxss1 libxt6t64 littler r-base-core r-cran-data.table 258s r-cran-dbi r-cran-etm r-cran-kmi r-cran-lattice r-cran-littler r-cran-matrix 258s r-cran-mitools r-cran-pkgkitten r-cran-rcpp r-cran-rcpparmadillo 258s r-cran-survival unzip x11-common xdg-utils zip 258s 0 upgraded, 57 newly installed, 0 to remove and 0 not upgraded. 258s Need to get 62.0 MB of archives. 258s After this operation, 129 MB of additional disk space will be used. 258s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB] 259s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-core all 2.37-8 [835 kB] 259s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig-config amd64 2.15.0-2ubuntu1 [37.4 kB] 259s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontconfig1 amd64 2.15.0-2ubuntu1 [164 kB] 259s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig amd64 2.15.0-2ubuntu1 [180 kB] 259s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.1-2 [359 kB] 260s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 libpixman-1-0 amd64 0.44.0-3 [427 kB] 260s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-render0 amd64 1.17.0-2 [16.2 kB] 260s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-shm0 amd64 1.17.0-2 [5758 B] 260s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 libxrender1 amd64 1:0.9.10-1.1build1 [19.0 kB] 260s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 libcairo2 amd64 1.18.2-2 [569 kB] 260s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 libdatrie1 amd64 0.2.13-3build1 [19.0 kB] 260s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate0 amd64 1.23-1 [64.1 kB] 260s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 15-20250222-0ubuntu1 [919 kB] 260s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 libgomp1 amd64 15-20250222-0ubuntu1 [148 kB] 260s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB] 260s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 libharfbuzz0b amd64 10.2.0-1 [543 kB] 260s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 260s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 libice6 amd64 2:1.1.1-1 [44.1 kB] 260s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg-turbo8 amd64 2.1.5-3ubuntu2 [179 kB] 260s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 260s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.1-2 [3179 kB] 261s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 liblerc4 amd64 4.0.0+ds-5ubuntu1 [271 kB] 261s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 libthai-data all 0.1.29-2build1 [158 kB] 261s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 libthai0 amd64 0.1.29-2build1 [18.9 kB] 261s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 libpango-1.0-0 amd64 1.56.2-1 [255 kB] 261s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 libpangoft2-1.0-0 amd64 1.56.2-1 [52.6 kB] 261s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 libpangocairo-1.0-0 amd64 1.56.2-1 [29.1 kB] 261s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 libpaper2 amd64 2.2.5-0.3 [17.4 kB] 261s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 libpaper-utils amd64 2.2.5-0.3 [15.5 kB] 261s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [25.9 kB] 261s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 libsm6 amd64 2:1.2.4-1 [17.4 kB] 261s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 libtcl8.6 amd64 8.6.16+dfsg-1 [1086 kB] 261s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB] 261s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebp7 amd64 1.5.0-0.1 [378 kB] 261s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 libtiff6 amd64 4.5.1+git230720-4ubuntu4 [200 kB] 261s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 libxft2 amd64 2.3.6-1build1 [45.3 kB] 261s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 libxss1 amd64 1:1.2.3-1build3 [7204 B] 261s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 libtk8.6 amd64 8.6.16-1 [868 kB] 261s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 libxt6t64 amd64 1:1.2.1-1.2build1 [171 kB] 261s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 zip amd64 3.0-14ubuntu2 [185 kB] 261s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 unzip amd64 6.0-28ubuntu6 [181 kB] 261s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 xdg-utils all 1.2.1-2ubuntu1 [66.0 kB] 261s Get:44 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-base-core amd64 4.4.3-1 [28.9 MB] 263s Get:45 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-littler amd64 0.3.20-2 [96.6 kB] 263s Get:46 http://ftpmaster.internal/ubuntu plucky/universe amd64 littler all 0.3.20-2 [2554 B] 263s Get:47 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-data.table amd64 1.17.0+dfsg-1 [2168 kB] 263s Get:48 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-dbi all 1.2.3-1 [853 kB] 263s Get:49 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-lattice amd64 0.22-6-1 [1340 kB] 263s Get:50 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-matrix amd64 1.7-3-1 [4349 kB] 263s Get:51 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-survival amd64 3.8-3-1 [8239 kB] 263s Get:52 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-pkgkitten all 0.2.4-1 [27.2 kB] 263s Get:53 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-rcpp amd64 1.0.14-1 [1998 kB] 264s Get:54 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-rcpparmadillo amd64 14.2.3-1-1 [864 kB] 264s Get:55 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-etm amd64 1.1.1-1 [478 kB] 264s Get:56 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-mitools all 2.4-2build1 [265 kB] 264s Get:57 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-kmi all 0.5.5-2build1 [78.3 kB] 264s Preconfiguring packages ... 264s Fetched 62.0 MB in 6s (11.2 MB/s) 264s Selecting previously unselected package fonts-dejavu-mono. 264s (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 ... 76968 files and directories currently installed.) 264s Preparing to unpack .../00-fonts-dejavu-mono_2.37-8_all.deb ... 264s Unpacking fonts-dejavu-mono (2.37-8) ... 265s Selecting previously unselected package fonts-dejavu-core. 265s Preparing to unpack .../01-fonts-dejavu-core_2.37-8_all.deb ... 265s Unpacking fonts-dejavu-core (2.37-8) ... 265s Selecting previously unselected package fontconfig-config. 265s Preparing to unpack .../02-fontconfig-config_2.15.0-2ubuntu1_amd64.deb ... 265s Unpacking fontconfig-config (2.15.0-2ubuntu1) ... 265s Selecting previously unselected package libfontconfig1:amd64. 265s Preparing to unpack .../03-libfontconfig1_2.15.0-2ubuntu1_amd64.deb ... 265s Unpacking libfontconfig1:amd64 (2.15.0-2ubuntu1) ... 265s Selecting previously unselected package fontconfig. 265s Preparing to unpack .../04-fontconfig_2.15.0-2ubuntu1_amd64.deb ... 265s Unpacking fontconfig (2.15.0-2ubuntu1) ... 265s Selecting previously unselected package libblas3:amd64. 265s Preparing to unpack .../05-libblas3_3.12.1-2_amd64.deb ... 265s Unpacking libblas3:amd64 (3.12.1-2) ... 265s Selecting previously unselected package libpixman-1-0:amd64. 265s Preparing to unpack .../06-libpixman-1-0_0.44.0-3_amd64.deb ... 265s Unpacking libpixman-1-0:amd64 (0.44.0-3) ... 265s Selecting previously unselected package libxcb-render0:amd64. 265s Preparing to unpack .../07-libxcb-render0_1.17.0-2_amd64.deb ... 265s Unpacking libxcb-render0:amd64 (1.17.0-2) ... 265s Selecting previously unselected package libxcb-shm0:amd64. 265s Preparing to unpack .../08-libxcb-shm0_1.17.0-2_amd64.deb ... 265s Unpacking libxcb-shm0:amd64 (1.17.0-2) ... 265s Selecting previously unselected package libxrender1:amd64. 265s Preparing to unpack .../09-libxrender1_1%3a0.9.10-1.1build1_amd64.deb ... 265s Unpacking libxrender1:amd64 (1:0.9.10-1.1build1) ... 265s Selecting previously unselected package libcairo2:amd64. 265s Preparing to unpack .../10-libcairo2_1.18.2-2_amd64.deb ... 265s Unpacking libcairo2:amd64 (1.18.2-2) ... 265s Selecting previously unselected package libdatrie1:amd64. 265s Preparing to unpack .../11-libdatrie1_0.2.13-3build1_amd64.deb ... 265s Unpacking libdatrie1:amd64 (0.2.13-3build1) ... 265s Selecting previously unselected package libdeflate0:amd64. 265s Preparing to unpack .../12-libdeflate0_1.23-1_amd64.deb ... 265s Unpacking libdeflate0:amd64 (1.23-1) ... 265s Selecting previously unselected package libgfortran5:amd64. 265s Preparing to unpack .../13-libgfortran5_15-20250222-0ubuntu1_amd64.deb ... 265s Unpacking libgfortran5:amd64 (15-20250222-0ubuntu1) ... 265s Selecting previously unselected package libgomp1:amd64. 265s Preparing to unpack .../14-libgomp1_15-20250222-0ubuntu1_amd64.deb ... 265s Unpacking libgomp1:amd64 (15-20250222-0ubuntu1) ... 265s Selecting previously unselected package libgraphite2-3:amd64. 265s Preparing to unpack .../15-libgraphite2-3_1.3.14-2ubuntu1_amd64.deb ... 265s Unpacking libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 265s Selecting previously unselected package libharfbuzz0b:amd64. 265s Preparing to unpack .../16-libharfbuzz0b_10.2.0-1_amd64.deb ... 265s Unpacking libharfbuzz0b:amd64 (10.2.0-1) ... 265s Selecting previously unselected package x11-common. 266s Preparing to unpack .../17-x11-common_1%3a7.7+23ubuntu3_all.deb ... 266s Unpacking x11-common (1:7.7+23ubuntu3) ... 266s Selecting previously unselected package libice6:amd64. 266s Preparing to unpack .../18-libice6_2%3a1.1.1-1_amd64.deb ... 266s Unpacking libice6:amd64 (2:1.1.1-1) ... 266s Selecting previously unselected package libjpeg-turbo8:amd64. 266s Preparing to unpack .../19-libjpeg-turbo8_2.1.5-3ubuntu2_amd64.deb ... 266s Unpacking libjpeg-turbo8:amd64 (2.1.5-3ubuntu2) ... 266s Selecting previously unselected package libjpeg8:amd64. 266s Preparing to unpack .../20-libjpeg8_8c-2ubuntu11_amd64.deb ... 266s Unpacking libjpeg8:amd64 (8c-2ubuntu11) ... 266s Selecting previously unselected package liblapack3:amd64. 266s Preparing to unpack .../21-liblapack3_3.12.1-2_amd64.deb ... 266s Unpacking liblapack3:amd64 (3.12.1-2) ... 266s Selecting previously unselected package liblerc4:amd64. 266s Preparing to unpack .../22-liblerc4_4.0.0+ds-5ubuntu1_amd64.deb ... 266s Unpacking liblerc4:amd64 (4.0.0+ds-5ubuntu1) ... 266s Selecting previously unselected package libthai-data. 266s Preparing to unpack .../23-libthai-data_0.1.29-2build1_all.deb ... 266s Unpacking libthai-data (0.1.29-2build1) ... 266s Selecting previously unselected package libthai0:amd64. 266s Preparing to unpack .../24-libthai0_0.1.29-2build1_amd64.deb ... 266s Unpacking libthai0:amd64 (0.1.29-2build1) ... 266s Selecting previously unselected package libpango-1.0-0:amd64. 266s Preparing to unpack .../25-libpango-1.0-0_1.56.2-1_amd64.deb ... 266s Unpacking libpango-1.0-0:amd64 (1.56.2-1) ... 266s Selecting previously unselected package libpangoft2-1.0-0:amd64. 266s Preparing to unpack .../26-libpangoft2-1.0-0_1.56.2-1_amd64.deb ... 266s Unpacking libpangoft2-1.0-0:amd64 (1.56.2-1) ... 266s Selecting previously unselected package libpangocairo-1.0-0:amd64. 266s Preparing to unpack .../27-libpangocairo-1.0-0_1.56.2-1_amd64.deb ... 266s Unpacking libpangocairo-1.0-0:amd64 (1.56.2-1) ... 266s Selecting previously unselected package libpaper2:amd64. 266s Preparing to unpack .../28-libpaper2_2.2.5-0.3_amd64.deb ... 266s Unpacking libpaper2:amd64 (2.2.5-0.3) ... 266s Selecting previously unselected package libpaper-utils. 266s Preparing to unpack .../29-libpaper-utils_2.2.5-0.3_amd64.deb ... 266s Unpacking libpaper-utils (2.2.5-0.3) ... 266s Selecting previously unselected package libsharpyuv0:amd64. 266s Preparing to unpack .../30-libsharpyuv0_1.5.0-0.1_amd64.deb ... 266s Unpacking libsharpyuv0:amd64 (1.5.0-0.1) ... 266s Selecting previously unselected package libsm6:amd64. 266s Preparing to unpack .../31-libsm6_2%3a1.2.4-1_amd64.deb ... 266s Unpacking libsm6:amd64 (2:1.2.4-1) ... 266s Selecting previously unselected package libtcl8.6:amd64. 266s Preparing to unpack .../32-libtcl8.6_8.6.16+dfsg-1_amd64.deb ... 266s Unpacking libtcl8.6:amd64 (8.6.16+dfsg-1) ... 266s Selecting previously unselected package libjbig0:amd64. 266s Preparing to unpack .../33-libjbig0_2.1-6.1ubuntu2_amd64.deb ... 266s Unpacking libjbig0:amd64 (2.1-6.1ubuntu2) ... 266s Selecting previously unselected package libwebp7:amd64. 266s Preparing to unpack .../34-libwebp7_1.5.0-0.1_amd64.deb ... 266s Unpacking libwebp7:amd64 (1.5.0-0.1) ... 266s Selecting previously unselected package libtiff6:amd64. 266s Preparing to unpack .../35-libtiff6_4.5.1+git230720-4ubuntu4_amd64.deb ... 266s Unpacking libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ... 266s Selecting previously unselected package libxft2:amd64. 266s Preparing to unpack .../36-libxft2_2.3.6-1build1_amd64.deb ... 266s Unpacking libxft2:amd64 (2.3.6-1build1) ... 266s Selecting previously unselected package libxss1:amd64. 266s Preparing to unpack .../37-libxss1_1%3a1.2.3-1build3_amd64.deb ... 266s Unpacking libxss1:amd64 (1:1.2.3-1build3) ... 266s Selecting previously unselected package libtk8.6:amd64. 266s Preparing to unpack .../38-libtk8.6_8.6.16-1_amd64.deb ... 266s Unpacking libtk8.6:amd64 (8.6.16-1) ... 266s Selecting previously unselected package libxt6t64:amd64. 266s Preparing to unpack .../39-libxt6t64_1%3a1.2.1-1.2build1_amd64.deb ... 266s Unpacking libxt6t64:amd64 (1:1.2.1-1.2build1) ... 267s Selecting previously unselected package zip. 267s Preparing to unpack .../40-zip_3.0-14ubuntu2_amd64.deb ... 267s Unpacking zip (3.0-14ubuntu2) ... 267s Selecting previously unselected package unzip. 267s Preparing to unpack .../41-unzip_6.0-28ubuntu6_amd64.deb ... 267s Unpacking unzip (6.0-28ubuntu6) ... 267s Selecting previously unselected package xdg-utils. 267s Preparing to unpack .../42-xdg-utils_1.2.1-2ubuntu1_all.deb ... 267s Unpacking xdg-utils (1.2.1-2ubuntu1) ... 267s Selecting previously unselected package r-base-core. 267s Preparing to unpack .../43-r-base-core_4.4.3-1_amd64.deb ... 267s Unpacking r-base-core (4.4.3-1) ... 267s Selecting previously unselected package r-cran-littler. 267s Preparing to unpack .../44-r-cran-littler_0.3.20-2_amd64.deb ... 267s Unpacking r-cran-littler (0.3.20-2) ... 267s Selecting previously unselected package littler. 267s Preparing to unpack .../45-littler_0.3.20-2_all.deb ... 267s Unpacking littler (0.3.20-2) ... 267s Selecting previously unselected package r-cran-data.table. 267s Preparing to unpack .../46-r-cran-data.table_1.17.0+dfsg-1_amd64.deb ... 267s Unpacking r-cran-data.table (1.17.0+dfsg-1) ... 267s Selecting previously unselected package r-cran-dbi. 267s Preparing to unpack .../47-r-cran-dbi_1.2.3-1_all.deb ... 267s Unpacking r-cran-dbi (1.2.3-1) ... 267s Selecting previously unselected package r-cran-lattice. 267s Preparing to unpack .../48-r-cran-lattice_0.22-6-1_amd64.deb ... 267s Unpacking r-cran-lattice (0.22-6-1) ... 267s Selecting previously unselected package r-cran-matrix. 267s Preparing to unpack .../49-r-cran-matrix_1.7-3-1_amd64.deb ... 267s Unpacking r-cran-matrix (1.7-3-1) ... 268s Selecting previously unselected package r-cran-survival. 268s Preparing to unpack .../50-r-cran-survival_3.8-3-1_amd64.deb ... 268s Unpacking r-cran-survival (3.8-3-1) ... 268s Selecting previously unselected package r-cran-pkgkitten. 268s Preparing to unpack .../51-r-cran-pkgkitten_0.2.4-1_all.deb ... 268s Unpacking r-cran-pkgkitten (0.2.4-1) ... 268s Selecting previously unselected package r-cran-rcpp. 268s Preparing to unpack .../52-r-cran-rcpp_1.0.14-1_amd64.deb ... 268s Unpacking r-cran-rcpp (1.0.14-1) ... 268s Selecting previously unselected package r-cran-rcpparmadillo. 268s Preparing to unpack .../53-r-cran-rcpparmadillo_14.2.3-1-1_amd64.deb ... 268s Unpacking r-cran-rcpparmadillo (14.2.3-1-1) ... 268s Selecting previously unselected package r-cran-etm. 268s Preparing to unpack .../54-r-cran-etm_1.1.1-1_amd64.deb ... 268s Unpacking r-cran-etm (1.1.1-1) ... 268s Selecting previously unselected package r-cran-mitools. 268s Preparing to unpack .../55-r-cran-mitools_2.4-2build1_all.deb ... 268s Unpacking r-cran-mitools (2.4-2build1) ... 268s Selecting previously unselected package r-cran-kmi. 268s Preparing to unpack .../56-r-cran-kmi_0.5.5-2build1_all.deb ... 268s Unpacking r-cran-kmi (0.5.5-2build1) ... 268s Setting up libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 268s Setting up libpixman-1-0:amd64 (0.44.0-3) ... 268s Setting up libsharpyuv0:amd64 (1.5.0-0.1) ... 268s Setting up liblerc4:amd64 (4.0.0+ds-5ubuntu1) ... 268s Setting up libxrender1:amd64 (1:0.9.10-1.1build1) ... 268s Setting up libdatrie1:amd64 (0.2.13-3build1) ... 268s Setting up libxcb-render0:amd64 (1.17.0-2) ... 268s Setting up unzip (6.0-28ubuntu6) ... 268s Setting up x11-common (1:7.7+23ubuntu3) ... 269s Setting up libdeflate0:amd64 (1.23-1) ... 269s Setting up libxcb-shm0:amd64 (1.17.0-2) ... 269s Setting up libgomp1:amd64 (15-20250222-0ubuntu1) ... 269s Setting up libjbig0:amd64 (2.1-6.1ubuntu2) ... 269s Setting up zip (3.0-14ubuntu2) ... 269s Setting up libblas3:amd64 (3.12.1-2) ... 269s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode 269s Setting up fonts-dejavu-mono (2.37-8) ... 269s Setting up libtcl8.6:amd64 (8.6.16+dfsg-1) ... 269s Setting up fonts-dejavu-core (2.37-8) ... 269s Setting up libjpeg-turbo8:amd64 (2.1.5-3ubuntu2) ... 269s Setting up libgfortran5:amd64 (15-20250222-0ubuntu1) ... 269s Setting up libwebp7:amd64 (1.5.0-0.1) ... 269s Setting up libharfbuzz0b:amd64 (10.2.0-1) ... 269s Setting up libthai-data (0.1.29-2build1) ... 269s Setting up libxss1:amd64 (1:1.2.3-1build3) ... 269s Setting up libpaper2:amd64 (2.2.5-0.3) ... 269s Setting up xdg-utils (1.2.1-2ubuntu1) ... 269s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode 269s Setting up libjpeg8:amd64 (8c-2ubuntu11) ... 269s Setting up libice6:amd64 (2:1.1.1-1) ... 269s Setting up liblapack3:amd64 (3.12.1-2) ... 269s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode 269s Setting up fontconfig-config (2.15.0-2ubuntu1) ... 269s Setting up libpaper-utils (2.2.5-0.3) ... 269s Setting up libthai0:amd64 (0.1.29-2build1) ... 269s Setting up 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(1.17.0+dfsg-1) ... 272s Setting up r-cran-matrix (1.7-3-1) ... 272s Setting up r-cran-rcpparmadillo (14.2.3-1-1) ... 272s Setting up r-cran-mitools (2.4-2build1) ... 272s Setting up r-cran-survival (3.8-3-1) ... 272s Setting up r-cran-kmi (0.5.5-2build1) ... 272s Setting up r-cran-etm (1.1.1-1) ... 272s Processing triggers for man-db (2.13.0-1) ... 273s Processing triggers for install-info (7.1.1-1) ... 274s Processing triggers for libc-bin (2.41-1ubuntu2) ... 275s autopkgtest [22:11:26]: test run-unit-test: [----------------------- 275s BEGIN TEST test.etmCIF.R 275s 275s R version 4.4.3 (2025-02-28) -- "Trophy Case" 275s Copyright (C) 2025 The R Foundation for Statistical Computing 275s Platform: x86_64-pc-linux-gnu 275s 275s R is free software and comes with ABSOLUTELY NO WARRANTY. 275s You are welcome to redistribute it under certain conditions. 275s Type 'license()' or 'licence()' for distribution details. 275s 275s R is a collaborative project with many contributors. 275s Type 'contributors()' for more information and 275s 'citation()' on how to cite R or R packages in publications. 275s 275s Type 'demo()' for some demos, 'help()' for on-line help, or 275s 'help.start()' for an HTML browser interface to help. 275s Type 'q()' to quit R. 275s 275s > ### test file for etmCIF. 275s > ### Really simple tests and comparison with etm 275s > 275s > old <- options(digits = 5) 275s > 275s > require(etm) 275s Loading required package: etm 277s > 277s > if (!require(survival, quietly = TRUE)) { 277s + print("The following tests require the 'survival' package") 277s + } else { 277s + 277s + data(abortion) 277s + 277s + from <- rep(0, nrow(abortion)) 277s + to <- abortion$cause 277s + entry <- abortion$entry 277s + exit <- abortion$exit 277s + id <- 1:nrow(abortion) 277s + data <- data.frame(id, from, to, entry, exit, group = abortion$group) 277s + 277s + ## Computation of the CIFs with etm 277s + tra <- matrix(FALSE, 4, 4) 277s + tra[1, 2:4] <- TRUE 277s + 277s + cif.control <- etm(data[data$group == 0, ], c("0", "1", "2", "3"), 277s + tra, NULL, 0) 277s + cif.exposed <- etm(data[data$group == 1, ], c("0", "1", "2", "3"), 277s + tra, NULL, 0) 277s + 277s + 277s + ## Computation of the CIFs with etmCIF 277s + netm <- etmCIF(Surv(entry, exit, cause != 0) ~ group, abortion, 277s + etype = cause, failcode = 3) 277s + 277s + ### let's do some comparisons :-) 277s + 277s + all.equal(trprob(cif.control, "0 3"), netm[[1]]$est["0", "3", ]) 277s + all.equal(trprob(cif.control, "0 2"), netm[[1]]$est["0", "2", ]) 277s + all.equal(trprob(cif.control, "0 1"), netm[[1]]$est["0", "1", ]) 277s + 277s + all.equal(trprob(cif.exposed, "0 3"), netm[[2]]$est["0", "3", ]) 277s + all.equal(trprob(cif.exposed, "0 2"), netm[[2]]$est["0", "2", ]) 277s + all.equal(trprob(cif.exposed, "0 1"), netm[[2]]$est["0", "1", ]) 277s + 277s + 277s + all.equal(trcov(cif.control, "0 3"), netm[[1]]$cov["0 3", "0 3", ]) 277s + all.equal(trcov(cif.control, "0 2"), netm[[1]]$cov["0 2", "0 2", ]) 277s + all.equal(trcov(cif.control, "0 1"), netm[[1]]$cov["0 1", "0 1", ]) 277s + 277s + all.equal(trcov(cif.exposed, "0 3"), netm[[2]]$cov["0 3", "0 3", ]) 277s + all.equal(trcov(cif.exposed, "0 2"), netm[[2]]$cov["0 2", "0 2", ]) 277s + all.equal(trcov(cif.exposed, "0 1"), netm[[2]]$cov["0 1", "0 1", ]) 277s + 277s + 277s + netm 277s + 277s + ## test on the summary 277s + snetm <- summary(netm) 277s + 277s + snetm 277s + 277s + all.equal(unname(trprob(cif.control, "0 3")), snetm[[1]][[3]]$P) 277s + all.equal(unname(trprob(cif.control, "0 2")), snetm[[1]][[2]]$P) 277s + all.equal(unname(trprob(cif.control, "0 1")), snetm[[1]][[1]]$P) 277s + 277s + all.equal(unname(trprob(cif.exposed, "0 3")), snetm[[2]][[3]]$P) 277s + all.equal(unname(trprob(cif.exposed, "0 2")), snetm[[2]][[2]]$P) 277s + all.equal(unname(trprob(cif.exposed, "0 1")), snetm[[2]][[1]]$P) 277s + 277s + scif.control <- summary(cif.control, ci.fun = "cloglog") 277s + scif.exposed <- summary(cif.exposed, ci.fun = "cloglog") 277s + 277s + all.equal(scif.control[[4]]$lower, snetm[[1]][[3]]$lower) 277s + all.equal(scif.control[[4]]$upper, snetm[[1]][[3]]$upper) 277s + 277s + all.equal(scif.exposed[[4]]$lower, snetm[[2]][[3]]$lower) 277s + all.equal(scif.exposed[[4]]$upper, snetm[[2]][[3]]$upper) 277s + } 277s [1] TRUE 277s > 277s > ### test with factors in the input 277s > abortion$status <- with(abortion, ifelse(cause == 2, "life birth", 277s + ifelse(cause == 1, "ETOP", "spontaneous abortion"))) 277s > 277s > abortion$status <- factor(abortion$status) 277s > 277s > netm.factor <- etmCIF(Surv(entry, exit, status != "cens") ~ group, abortion, 277s + etype = status, failcode = "spontaneous abortion") 277s > 277s > 277s > all.equal(trprob(cif.control, "0 3"), netm.factor[[1]]$est["0", "spontaneous abortion", ]) 277s [1] TRUE 277s > all.equal(trprob(cif.control, "0 2"), netm.factor[[1]]$est["0", "life birth", ]) 277s [1] TRUE 277s > 277s > netm.factor 277s Call: etmCIF(formula = Surv(entry, exit, status != "cens") ~ group, 277s data = abortion, etype = status, failcode = "spontaneous abortion") 277s 277s Covariate: group 277s levels: 0 1 277s 277s 277s group = 0 277s time P se(P) n.event 277s CIF ETOP 43 0.040159 0.0092578 20 277s CIF life birth 43 0.799059 0.0221865 924 277s CIF spontaneous abortion 43 0.160781 0.0213261 69 277s 277s group = 1 277s time P se(P) n.event 277s CIF ETOP 42 0.28511 0.042493 38 277s CIF life birth 42 0.35257 0.042139 92 277s CIF spontaneous abortion 42 0.36232 0.049473 43 277s > 277s > summary(netm.factor) 277s 277s group=0 277s 277s CIF ETOP 277s P time var lower upper n.risk n.event 277s 0.000000 6 0.0000e+00 0.000000 0.000000 117 0 277s 0.038955 13 8.4440e-05 0.024488 0.061694 645 1 277s 0.040159 26 8.5707e-05 0.025513 0.062939 846 0 277s 0.040159 36 8.5707e-05 0.025513 0.062939 876 0 277s 0.040159 40 8.5707e-05 0.025513 0.062939 554 0 277s 0.040159 43 8.5707e-05 0.025513 0.062939 6 0 277s 277s CIF life birth 277s P time var lower upper n.risk n.event 277s 0.000000 6 0.0000e+00 0.000000 0.000000 117 0 277s 0.000000 13 0.0000e+00 0.000000 0.000000 645 0 277s 0.000000 26 0.0000e+00 0.000000 0.000000 846 0 277s 0.053197 36 4.6195e-05 0.041379 0.068268 876 25 277s 0.563121 40 3.8801e-04 0.524924 0.602021 554 280 277s 0.799059 43 4.9224e-04 0.753969 0.840613 6 6 277s 277s CIF spontaneous abortion 277s P time var lower upper n.risk n.event 277s 0.034188 6 0.00028222 0.01297 0.088523 117 4 277s 0.150468 13 0.00045513 0.11360 0.197901 645 1 277s 0.159904 26 0.00045498 0.12274 0.206925 846 1 277s 0.160781 36 0.00045480 0.12360 0.207757 876 1 277s 0.160781 40 0.00045480 0.12360 0.207757 554 0 277s 0.160781 43 0.00045480 0.12360 0.207757 6 0 277s 277s 277s group=1 277s 277s CIF ETOP 277s P time var lower upper n.risk n.event 277s 0.00000 6 0.0000000 0.00000 0.00000 35 0 277s 0.26048 13 0.0017854 0.18795 0.35425 90 0 277s 0.28115 21 0.0018028 0.20742 0.37423 93 1 277s 0.28511 34 0.0018057 0.21116 0.37806 89 0 277s 0.28511 39 0.0018057 0.21116 0.37806 59 0 277s 0.28511 42 0.0018057 0.21116 0.37806 6 0 277s 277s CIF life birth 277s P time var lower upper n.risk n.event 277s 0.000000 6 0.0000e+00 0.000000 0.000000 35 0 277s 0.000000 13 0.0000e+00 0.000000 0.000000 90 0 277s 0.000000 21 0.0000e+00 0.000000 0.000000 93 0 277s 0.023073 34 9.0514e-05 0.010252 0.051504 89 2 277s 0.180156 39 8.0126e-04 0.131765 0.243663 59 13 277s 0.352565 42 1.7757e-03 0.276882 0.441775 6 6 277s 277s CIF spontaneous abortion 277s P time var lower upper n.risk n.event 277s 0.057143 6 0.0015394 0.014605 0.20968 35 2 277s 0.333246 13 0.0025280 0.245337 0.44216 90 4 277s 0.350702 21 0.0024827 0.262769 0.45762 93 0 277s 0.358492 34 0.0024593 0.270627 0.46448 89 0 277s 0.358492 39 0.0024593 0.270627 0.46448 59 0 277s 0.362323 42 0.0024476 0.274499 0.46785 6 0 277s 277s > 277s > ### test with group as a character vector 277s > abortion$ttt <- with(abortion, ifelse(group == 0, "control", "exposed")) 277s > abortion$ttt <- factor(abortion$ttt) 277s > 277s > netm.ttt <- etmCIF(Surv(entry, exit, status != "cens") ~ ttt, abortion, 277s + etype = status, failcode = "spontaneous abortion") 277s > 277s > all.equal(trprob(cif.control, "0 3"), netm.ttt[[1]]$est["0", "spontaneous abortion", ]) 277s [1] TRUE 277s > all.equal(trprob(cif.control, "0 2"), netm.ttt[[1]]$est["0", "life birth", ]) 277s [1] TRUE 277s > 277s > netm.ttt 277s Call: etmCIF(formula = Surv(entry, exit, status != "cens") ~ ttt, data = abortion, 277s etype = status, failcode = "spontaneous abortion") 277s 277s Covariate: ttt 277s levels: control exposed 277s 277s 277s ttt = control 277s time P se(P) n.event 277s CIF ETOP 43 0.040159 0.0092578 20 277s CIF life birth 43 0.799059 0.0221865 924 277s CIF spontaneous abortion 43 0.160781 0.0213261 69 277s 277s ttt = exposed 277s time P se(P) n.event 277s CIF ETOP 42 0.28511 0.042493 38 277s CIF life birth 42 0.35257 0.042139 92 277s CIF spontaneous abortion 42 0.36232 0.049473 43 277s > 277s > summary(netm.ttt) 277s 277s ttt=control 277s 277s CIF ETOP 277s P time var lower upper n.risk n.event 277s 0.000000 6 0.0000e+00 0.000000 0.000000 117 0 277s 0.038955 13 8.4440e-05 0.024488 0.061694 645 1 277s 0.040159 26 8.5707e-05 0.025513 0.062939 846 0 277s 0.040159 36 8.5707e-05 0.025513 0.062939 876 0 277s 0.040159 40 8.5707e-05 0.025513 0.062939 554 0 277s 0.040159 43 8.5707e-05 0.025513 0.062939 6 0 277s 277s CIF life birth 277s P time var lower upper n.risk n.event 277s 0.000000 6 0.0000e+00 0.000000 0.000000 117 0 277s 0.000000 13 0.0000e+00 0.000000 0.000000 645 0 277s 0.000000 26 0.0000e+00 0.000000 0.000000 846 0 277s 0.053197 36 4.6195e-05 0.041379 0.068268 876 25 277s 0.563121 40 3.8801e-04 0.524924 0.602021 554 280 277s 0.799059 43 4.9224e-04 0.753969 0.840613 6 6 277s 277s CIF spontaneous abortion 277s P time var lower upper n.risk n.event 277s 0.034188 6 0.00028222 0.01297 0.088523 117 4 277s 0.150468 13 0.00045513 0.11360 0.197901 645 1 277s 0.159904 26 0.00045498 0.12274 0.206925 846 1 277s 0.160781 36 0.00045480 0.12360 0.207757 876 1 277s 0.160781 40 0.00045480 0.12360 0.207757 554 0 277s 0.160781 43 0.00045480 0.12360 0.207757 6 0 277s 277s 277s ttt=exposed 277s 277s CIF ETOP 277s P time var lower upper n.risk n.event 277s 0.00000 6 0.0000000 0.00000 0.00000 35 0 277s 0.26048 13 0.0017854 0.18795 0.35425 90 0 277s 0.28115 21 0.0018028 0.20742 0.37423 93 1 277s 0.28511 34 0.0018057 0.21116 0.37806 89 0 277s 0.28511 39 0.0018057 0.21116 0.37806 59 0 277s 0.28511 42 0.0018057 0.21116 0.37806 6 0 277s 277s CIF life birth 277s P time var lower upper n.risk n.event 277s 0.000000 6 0.0000e+00 0.000000 0.000000 35 0 277s 0.000000 13 0.0000e+00 0.000000 0.000000 90 0 277s 0.000000 21 0.0000e+00 0.000000 0.000000 93 0 277s 0.023073 34 9.0514e-05 0.010252 0.051504 89 2 277s 0.180156 39 8.0126e-04 0.131765 0.243663 59 13 277s 0.352565 42 1.7757e-03 0.276882 0.441775 6 6 277s 277s CIF spontaneous abortion 277s P time var lower upper n.risk n.event 277s 0.057143 6 0.0015394 0.014605 0.20968 35 2 277s 0.333246 13 0.0025280 0.245337 0.44216 90 4 277s 0.350702 21 0.0024827 0.262769 0.45762 93 0 277s 0.358492 34 0.0024593 0.270627 0.46448 89 0 277s 0.358492 39 0.0024593 0.270627 0.46448 59 0 277s 0.362323 42 0.0024476 0.274499 0.46785 6 0 277s 277s > 277s > 277s > ### A couple of comparisons with simulated data 277s > set.seed(1313) 277s > time <- rexp(100) 277s > to <- rbinom(100, 2, prob = c(1/3, 1/3, 1/3)) 277s > from <- rep(11, 100) 277s > id <- 1:100 277s > cov <- rbinom(100, 1, 0.5) 277s > 277s > dat.s <- data.frame(id, time, from, to, cov) 277s > 277s > traa <- matrix(FALSE, 3, 3) 277s > traa[1, 2:3] <- TRUE 277s > 277s > aa0 <- etm(dat.s[dat.s$cov == 0, ], c("11", "1", "2"), traa, "0", 0) 277s > aa1 <- etm(dat.s[dat.s$cov == 1, ], c("11", "1", "2"), traa, "0", 0) 277s > aa <- etm(dat.s, c("11", "1", "2"), traa, "0", 0) 277s > 277s > test <- etmCIF(Surv(time, to != 0) ~ 1, dat.s, etype = to) 277s > 277s > test.c <- etmCIF(Surv(time, to != 0) ~ cov, dat.s, etype = to) 277s > 277s > all.equal(trprob(aa, "11 1"), test[[1]]$est["0", "1", ]) 277s [1] TRUE 277s > all.equal(trprob(aa, "11 2"), test[[1]]$est["0", "2", ]) 277s [1] TRUE 277s > 277s > all.equal(trprob(aa0, "11 1"), test.c[[1]]$est["0", "1", ]) 277s [1] TRUE 277s > all.equal(trprob(aa0, "11 2"), test.c[[1]]$est["0", "2", ]) 277s [1] TRUE 277s > 277s > all.equal(trprob(aa1, "11 1"), test.c[[2]]$est["0", "1", ]) 277s [1] TRUE 277s > all.equal(trprob(aa1, "11 2"), test.c[[2]]$est["0", "2", ]) 277s [1] TRUE 277s > 277s > test 277s Call: etmCIF(formula = Surv(time, to != 0) ~ 1, data = dat.s, etype = to) 277s 277s time P se(P) n.event 277s CIF 1 4.9088 0.809108 0.079680 45 277s CIF 2 4.9088 0.096618 0.032905 8 277s > 277s > test.c 277s Call: etmCIF(formula = Surv(time, to != 0) ~ cov, data = dat.s, etype = to) 277s 277s Covariate: cov 277s levels: 0 1 277s 277s 277s cov = 0 277s time P se(P) n.event 277s CIF 1 2.1708 0.70246 0.105797 19 277s CIF 2 2.1708 0.11144 0.053384 4 277s 277s cov = 1 277s time P se(P) n.event 277s CIF 1 4.9088 0.80787 0.094051 26 277s CIF 2 4.9088 0.08436 0.040769 4 277s > 277s > summary(test) 277s 277s 277s 277s CIF 1 277s P time var lower upper n.risk n.event 277s 0.01000 0.0092099 0.0000990 0.0014147 0.068863 100 1 277s 0.11430 0.2663096 0.0010542 0.0649454 0.196993 81 1 277s 0.23451 0.7303091 0.0020436 0.1591107 0.337736 54 1 277s 0.40425 1.4299939 0.0032996 0.3020445 0.525741 29 1 277s 0.54593 2.0647206 0.0040836 0.4269008 0.673605 16 1 277s 0.80911 4.9087561 0.0063489 0.6359544 0.933733 2 1 277s 277s CIF 2 277s P time var lower upper n.risk n.event 277s 0.000000 0.0092099 0.00000000 0.000000 0.000000 100 0 277s 0.031657 0.2663096 0.00032353 0.010320 0.094942 81 0 277s 0.067029 0.7303091 0.00070366 0.030598 0.143503 54 0 277s 0.096618 1.4299939 0.00108275 0.049082 0.185474 29 0 277s 0.096618 2.0647206 0.00108275 0.049082 0.185474 16 0 277s 0.096618 4.9087561 0.00108275 0.049082 0.185474 2 0 277s 277s > summary(test.c) 277s 277s cov=0 277s 277s CIF 1 277s P time var lower upper n.risk n.event 277s 0.022222 0.0092099 0.00048285 0.0031605 0.14747 45 1 277s 0.092222 0.2982439 0.00193603 0.0355971 0.22762 36 0 277s 0.226684 0.7021938 0.00450954 0.1241760 0.39250 24 1 277s 0.378128 1.4299939 0.00760870 0.2337884 0.57145 13 1 277s 0.505736 1.6148774 0.00895330 0.3388425 0.69885 10 1 277s 0.702465 2.1708375 0.01119294 0.4944890 0.88399 3 1 277s 277s CIF 2 277s P time var lower upper n.risk n.event 277s 0.000000 0.0092099 0.0000000 0.000000 0.00000 45 0 277s 0.048441 0.2982439 0.0011168 0.012337 0.18013 36 1 277s 0.076411 0.7021938 0.0018104 0.025202 0.21928 24 0 277s 0.111440 1.4299939 0.0028499 0.042676 0.27392 13 0 277s 0.111440 1.6148774 0.0028499 0.042676 0.27392 10 0 277s 0.111440 2.1708375 0.0028499 0.042676 0.27392 3 0 277s 277s 277s cov=1 277s 277s CIF 1 277s P time var lower upper n.risk n.event 277s 0.018182 0.066692 0.00032457 0.0025813 0.12214 55 1 277s 0.112392 0.263808 0.00187215 0.0520925 0.23333 45 1 277s 0.241023 0.730309 0.00374499 0.1440057 0.38685 31 1 277s 0.401201 1.066913 0.00570788 0.2714008 0.56421 19 1 277s 0.592334 2.366275 0.00775985 0.4286230 0.76273 8 1 277s 0.807871 4.908756 0.00884554 0.6023185 0.94771 2 1 277s 277s CIF 2 277s P time var lower upper n.risk n.event 277s 0.000000 0.066692 0.00000000 0.000000 0.00000 55 0 277s 0.037434 0.263808 0.00067458 0.009494 0.14152 45 0 277s 0.059341 0.730309 0.00111295 0.019447 0.17351 31 0 277s 0.084360 1.066913 0.00166213 0.032211 0.21119 19 0 277s 0.084360 2.366275 0.00166213 0.032211 0.21119 8 0 277s 0.084360 4.908756 0.00166213 0.032211 0.21119 2 0 277s 277s > 277s > options(old) 277s > 277s BEGIN TEST tests.etm.R 277s 277s R version 4.4.3 (2025-02-28) -- "Trophy Case" 277s Copyright (C) 2025 The R Foundation for Statistical Computing 277s Platform: x86_64-pc-linux-gnu 277s 277s R is free software and comes with ABSOLUTELY NO WARRANTY. 277s You are welcome to redistribute it under certain conditions. 277s Type 'license()' or 'licence()' for distribution details. 277s 277s R is a collaborative project with many contributors. 277s Type 'contributors()' for more information and 277s 'citation()' on how to cite R or R packages in publications. 277s 277s Type 'demo()' for some demos, 'help()' for on-line help, or 277s 'help.start()' for an HTML browser interface to help. 277s Type 'q()' to quit R. 277s 277s > require(etm) 277s Loading required package: etm 279s > 279s > ## Print with a bit less precision to avoid lots of notes in the comparison 279s > old <- options(digits = 4) 279s > 279s > ### Simple test 279s > 279s > time <- id <- 1:10 279s > from <- rep(0, 10) 279s > to <- rep(1, 10) 279s > 279s > data1 <- data.frame(id, from, to, time) 279s > tra1 <- matrix(FALSE, 2, 2) 279s > tra1[1, 2] <- TRUE 279s > 279s > etm1 <- etm(data1, c("0", "1"), tra1, NULL, 0) 279s Loading required package: survival 279s > 279s > all.equal(as.vector(trprob(etm1, "0 0")), cumprod((10:1 - 1) / (10:1))) 279s [1] TRUE 279s > 279s > etm1$cov["0 0", "0 0", ] 279s 1 2 3 4 5 6 7 8 9 10 279s 0.009 0.016 0.021 0.024 0.025 0.024 0.021 0.016 0.009 0.000 279s > 279s > all.equal(etm1$cov["0 0", "0 0",], trcov(etm1, "0 0")) 279s [1] TRUE 279s > 279s > ### A simple test from AHR's author, where the first time is censored 279s > if (!require(survival)) { 279s + stop("This test requires the survival package") 279s + } 279s > 279s > data <- data.frame(id=1:10, time=1:10, from=0, to=1, status=TRUE) 279s > 279s > tra <- matrix(FALSE, nrow=2, ncol=2) 279s > tra[1, 2] <- TRUE 279s > 279s > data$to[1] <- "cens" 279s > data$status[1] <- FALSE 279s > 279s > fit.km <- survfit(Surv(time, status) ~ 1, data=data) 279s > fit.etm <- etm(data, c("0","1"), tra, "cens", s=0, t="last", covariance=FALSE) 279s > 279s > all.equal(fit.km$surv[data$status], fit.etm$est[1,1,], check.attributes = FALSE) 279s [1] TRUE 279s > 279s > data$to[2] <- "cens" 279s > data$status[2] <- FALSE 279s > 279s > fit.km <- survfit(Surv(time, status) ~ 1, data=data) 279s > fit.etm <- etm(data, c("0","1"), tra, "cens", s=0, t="last", covariance=FALSE) 279s > 279s > all.equal(fit.km$surv[data$status], fit.etm$est[1,1,], check.attributes = FALSE) 279s [1] TRUE 279s > 279s > ### a bit more complicated 279s > 279s > time <- id <- 1:10 279s > from <- rep(0, 10) 279s > to <- rep(c(1, 2), 5) 279s > data2 <- data.frame(id, from, to, time) 279s > 279s > tra2 <- matrix(FALSE, 3, 3) 279s > tra2[1, 2:3] <- TRUE 279s > 279s > etm2 <- etm(data2, c("0", "1", "2"), tra2, NULL, 0) 279s > 279s > aa <- table(time, to) 279s > 279s > cif1 <- cumsum(aa[, 1] / 10) 279s > cif2 <- cumsum(aa[, 2] / 10) 279s > surv <- cumprod((10:1 - 1) / (10:1)) 279s > 279s > all.equal(trprob(etm2, "0 1"), cif1) 279s [1] TRUE 279s > all.equal(trprob(etm2, "0 2"), cif2) 279s [1] TRUE 279s > all.equal(as.vector(trprob(etm2, "0 0")), surv) 279s [1] TRUE 279s > 279s > ## a test on id 279s > data2$id <- letters[1:10] 279s > 279s > etm3 <- etm(data2, c("0", "1", "2"), tra2, NULL, 0) 279s > 279s > all.equal(trprob(etm2, "0 1"), trprob(etm3, "0 1")) 279s [1] TRUE 279s > all.equal(trprob(etm2, "0 2"), trprob(etm3, "0 2")) 279s [1] TRUE 279s > all.equal(trprob(etm2, "0 0"), trprob(etm3, "0 0")) 279s [1] TRUE 279s > 279s > 279s > ### Test on sir.cont 279s > 279s > data(sir.cont) 279s > 279s > ## Modification for patients entering and leaving a state 279s > ## at the same date 279s > ## Change on ventilation status is considered 279s > ## to happen before end of hospital stay 279s > sir.cont <- sir.cont[order(sir.cont$id, sir.cont$time), ] 279s > for (i in 2:nrow(sir.cont)) { 279s + if (sir.cont$id[i]==sir.cont$id[i-1]) { 279s + if (sir.cont$time[i]==sir.cont$time[i-1]) { 279s + sir.cont$time[i-1] <- sir.cont$time[i-1] - 0.5 279s + } 279s + } 279s + } 279s > 279s > ### Computation of the transition probabilities 279s > ## Possible transitions. 279s > tra <- matrix(ncol=3,nrow=3,FALSE) 279s > tra[1, 2:3] <- TRUE 279s > tra[2, c(1, 3)] <- TRUE 279s > 279s > ## etm 279s > prob.sir <- etm(sir.cont, c("0", "1", "2"), tra, "cens", 1) 279s > 279s > prob.sir 279s Multistate model with 2 transient state(s) 279s and 1 absorbing state(s) 279s 279s Possible transitions: 279s from to 279s 0 1 279s 0 2 279s 1 0 279s 1 2 279s 279s Estimate of P(1, 183) 279s 0 1 2 279s 0 0 0 1 279s 1 0 0 1 279s 2 0 0 1 279s 279s > 279s > summ.sir <- summary(prob.sir) 279s > all.equal(summ.sir[['0 1']]$P, as.vector(trprob(prob.sir, "0 1"))) 279s [1] TRUE 279s > subset(summ.sir[[3]],time<183) # issue with precision on different architectures 279s P time var lower upper n.risk n.event 279s 1.5 0.0000 1.5 0.000e+00 0.00000 0.0000 394 0 279s 2 0.1187 2.0 2.641e-04 0.08683 0.1505 396 47 279s 2.5 0.1187 2.5 2.641e-04 0.08683 0.1505 364 0 279s 3 0.2454 3.0 4.465e-04 0.20398 0.2868 365 54 279s 3.5 0.2454 3.5 4.465e-04 0.20398 0.2868 328 0 279s 4 0.3806 4.0 5.416e-04 0.33501 0.4262 331 62 279s 4.5 0.3806 4.5 5.416e-04 0.33501 0.4262 280 0 279s 5 0.4792 5.0 5.480e-04 0.43333 0.5251 283 48 279s 5.5 0.4792 5.5 5.480e-04 0.43333 0.5251 248 0 279s 6 0.5693 6.0 5.141e-04 0.52482 0.6137 249 47 279s 7 0.6350 7.0 4.665e-04 0.59266 0.6773 212 36 279s 8 0.6795 8.0 4.202e-04 0.63931 0.7197 195 27 279s 8.5 0.6795 8.5 4.202e-04 0.63931 0.7197 172 0 279s 9 0.7325 9.0 3.580e-04 0.69541 0.7696 173 34 279s 10 0.7647 10.0 3.141e-04 0.72992 0.7994 148 21 279s 10.5 0.7647 10.5 3.141e-04 0.72992 0.7994 135 0 279s 11 0.7895 11.0 2.790e-04 0.75674 0.8222 136 18 279s 12 0.8138 12.0 2.420e-04 0.78330 0.8443 129 18 279s 12.5 0.8138 12.5 2.420e-04 0.78330 0.8443 117 0 279s 13 0.8294 13.0 2.182e-04 0.80045 0.8584 118 13 279s 14 0.8452 14.0 1.938e-04 0.81789 0.8725 115 14 279s 15 0.8625 15.0 1.670e-04 0.83714 0.8878 106 15 279s 16 0.8723 16.0 1.522e-04 0.84807 0.8964 93 9 279s 17 0.8852 17.0 1.330e-04 0.86256 0.9078 86 12 279s 17.5 0.8852 17.5 1.330e-04 0.86256 0.9078 77 0 279s 18 0.8960 18.0 1.168e-04 0.87484 0.9172 76 9 279s 19 0.9029 19.0 1.070e-04 0.88261 0.9232 71 7 279s 20 0.9125 20.0 9.367e-05 0.89356 0.9315 64 10 279s 21 0.9161 21.0 8.878e-05 0.89768 0.9346 57 4 279s 22 0.9226 22.0 7.996e-05 0.90504 0.9401 55 6 279s 23 0.9261 23.0 7.537e-05 0.90904 0.9431 51 4 279s 23.5 0.9261 23.5 7.537e-05 0.90904 0.9431 49 0 279s 24 0.9354 24.0 6.292e-05 0.91982 0.9509 50 9 279s 25 0.9385 25.0 5.878e-05 0.92352 0.9536 42 3 279s 26 0.9429 26.0 5.326e-05 0.92863 0.9572 39 5 279s 27 0.9477 27.0 4.749e-05 0.93417 0.9612 35 6 279s 27.5 0.9477 27.5 4.749e-05 0.93417 0.9612 29 0 279s 28 0.9531 28.0 4.093e-05 0.94059 0.9657 30 5 279s 29 0.9567 29.0 3.668e-05 0.94485 0.9686 31 4 279s 30 0.9592 30.0 3.384e-05 0.94779 0.9706 28 3 279s 30.5 0.9592 30.5 3.384e-05 0.94779 0.9706 29 0 279s 31 0.9642 31.0 2.821e-05 0.95383 0.9746 30 6 279s 32 0.9649 32.0 2.752e-05 0.95458 0.9751 25 1 279s 33 0.9669 33.0 2.533e-05 0.95708 0.9768 24 2 279s 34 0.9685 34.0 2.368e-05 0.95900 0.9781 26 2 279s 35 0.9697 35.0 2.252e-05 0.96036 0.9790 28 2 279s 36 0.9702 36.0 2.194e-05 0.96104 0.9794 26 1 279s 37 0.9718 37.0 2.043e-05 0.96290 0.9806 26 2 279s 38 0.9739 38.0 1.831e-05 0.96555 0.9823 25 4 279s 38.5 0.9739 38.5 1.831e-05 0.96555 0.9823 21 0 279s 39 0.9760 39.0 1.643e-05 0.96802 0.9839 23 3 279s 40 0.9769 40.0 1.558e-05 0.96918 0.9847 19 1 279s 41 0.9774 41.0 1.512e-05 0.96981 0.9851 22 1 279s 42 0.9779 42.0 1.476e-05 0.97032 0.9854 22 0 279s 43 0.9798 43.0 1.308e-05 0.97271 0.9869 22 3 279s 44 0.9803 44.0 1.265e-05 0.97333 0.9873 21 1 279s 45 0.9817 45.0 1.157e-05 0.97499 0.9883 19 1 279s 46 0.9822 46.0 1.116e-05 0.97561 0.9887 17 1 279s 47 0.9831 47.0 1.037e-05 0.97683 0.9895 18 2 279s 48 0.9836 48.0 9.987e-06 0.97743 0.9898 17 1 279s 49 0.9841 49.0 9.669e-06 0.97796 0.9901 17 0 279s 50 0.9845 50.0 9.297e-06 0.97856 0.9905 17 1 279s 50.5 0.9845 50.5 9.297e-06 0.97856 0.9905 16 0 279s 51 0.9860 51.0 8.214e-06 0.98037 0.9916 17 3 279s 52 0.9870 52.0 7.513e-06 0.98159 0.9923 14 2 279s 53 0.9879 53.0 6.875e-06 0.98276 0.9930 12 1 279s 54 0.9889 54.0 6.214e-06 0.98397 0.9937 12 2 279s 55 0.9903 55.0 5.254e-06 0.98581 0.9948 10 3 279s 56 0.9913 56.0 4.667e-06 0.98703 0.9955 6 1 279s 57 0.9917 57.0 4.364e-06 0.98765 0.9958 5 1 279s 58 0.9922 58.0 4.064e-06 0.98828 0.9962 4 1 279s 59 0.9927 59.0 3.769e-06 0.98891 0.9965 3 1 279s 60 0.9932 60.0 3.488e-06 0.98953 0.9969 3 1 279s 62 0.9937 62.0 3.230e-06 0.99016 0.9972 2 0 279s 63 0.9942 63.0 2.956e-06 0.99079 0.9975 2 1 279s 68 0.9942 68.0 2.956e-06 0.99079 0.9975 1 0 279s 70 0.9946 70.0 2.694e-06 0.99143 0.9979 2 1 279s 78 0.9951 78.0 2.442e-06 0.99207 0.9982 1 0 279s 80 0.9951 80.0 2.442e-06 0.99207 0.9982 1 0 279s 85 0.9966 85.0 1.695e-06 0.99404 0.9991 2 0 279s 89 0.9966 89.0 1.695e-06 0.99404 0.9991 2 0 279s 90 0.9966 90.0 1.695e-06 0.99404 0.9991 1 0 279s 95 0.9971 95.0 1.448e-06 0.99472 0.9994 2 0 279s 100 0.9976 100.0 1.203e-06 0.99542 0.9997 3 0 279s 101 0.9981 101.0 9.592e-07 0.99613 1.0000 3 1 279s 108 0.9985 108.0 7.169e-07 0.99688 1.0000 2 1 279s 113 0.9990 113.0 4.764e-07 0.99767 1.0000 1 0 279s 116 0.9990 116.0 4.764e-07 0.99767 1.0000 1 0 279s 124 0.9990 124.0 4.764e-07 0.99767 1.0000 2 0 279s 164 0.9990 164.0 4.764e-07 0.99767 1.0000 0 0 279s > 279s > ## gonna play a bit with the state names 279s > dd <- sir.cont 279s > dd$from <- ifelse(dd$from == 0, "initial state", "ventilation") 279s > dd$to <- as.character(dd$to) 279s > for (i in seq_len(nrow(dd))) { 279s + dd$to[i] <- switch(dd$to[i], 279s + "0" = "initial state", 279s + "1" = "ventilation", 279s + "2" = "end of story", 279s + "cens" = "cens" 279s + ) 279s + } 279s > 279s > test <- etm(dd, c("initial state", "ventilation", "end of story"), tra, "cens", 1) 279s > 279s > all.equal(test$est["initial state", "initial state", ], 279s + prob.sir$est["0", "0", ]) 279s [1] TRUE 279s > all.equal(trprob(test, "initial state initial state"), trprob(prob.sir, "0 0")) 279s [1] TRUE 279s > all.equal(trprob(test, "initial state ventilation"), trprob(prob.sir, "0 1")) 279s [1] TRUE 279s > all.equal(trprob(test, "initial state end of story"), trprob(prob.sir, "0 2")) 279s [1] TRUE 279s > 279s > all.equal(trcov(test, "initial state end of story"), trcov(prob.sir, "0 2")) 279s [1] TRUE 279s > 279s > aa <- summary(test) 279s > all.equal(summ.sir[[6]], aa[[6]]) 279s [1] TRUE 279s > all.equal(summ.sir[[4]], aa[[4]]) 279s [1] TRUE 279s > 279s > ### Test on abortion data 279s > 279s > data(abortion) 279s > 279s > from <- rep(0, nrow(abortion)) 279s > to <- abortion$cause 279s > entry <- abortion$entry 279s > exit <- abortion$exit 279s > id <- 1:nrow(abortion) 279s > data <- data.frame(id, from, to, entry, exit, group = abortion$group) 279s > 279s > ## Computation of the CIFs 279s > tra <- matrix(FALSE, 4, 4) 279s > tra[1, 2:4] <- TRUE 279s > 279s > cif.control <- etm(data[data$group == 0, ], c("0", "1", "2", "3"), 279s + tra, NULL, 0) 279s > cif.exposed <- etm(data[data$group == 1, ], c("0", "1", "2", "3"), 279s + tra, NULL, 0) 279s > 279s > all.equal(trprob(cif.control, "0 1"), cif.control$est["0", "1", ]) 279s [1] TRUE 279s > all.equal(trcov(cif.control, c("0 1", "0 2")), cif.control$cov["0 1", "0 2", ]) 279s [1] TRUE 279s > 279s > trprob(cif.control, "0 1") 279s 6 7 8 9 10 11 12 13 279s 0.000000 0.007401 0.014881 0.026509 0.033208 0.037694 0.037694 0.038955 279s 14 17 19 21 24 25 26 30 279s 0.040159 0.040159 0.040159 0.040159 0.040159 0.040159 0.040159 0.040159 279s 31 32 33 34 35 36 37 38 279s 0.040159 0.040159 0.040159 0.040159 0.040159 0.040159 0.040159 0.040159 279s 39 40 41 42 43 279s 0.040159 0.040159 0.040159 0.040159 0.040159 279s > trprob(cif.control, "0 2") 279s 6 7 8 9 10 11 12 13 279s 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 279s 14 17 19 21 24 25 26 30 279s 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.003657 279s 31 32 33 34 35 36 37 38 279s 0.006371 0.008175 0.013543 0.023317 0.031260 0.053197 0.084529 0.179163 279s 39 40 41 42 43 279s 0.322016 0.563121 0.742227 0.793893 0.799059 279s > trprob(cif.control, "0 0") 279s 6 7 8 9 10 11 12 13 279s 0.965812 0.932508 0.887628 0.862433 0.838989 0.822538 0.813099 0.810578 279s 14 17 19 21 24 25 26 30 279s 0.806964 0.805874 0.803810 0.802804 0.801837 0.800883 0.799937 0.796280 279s 31 32 33 34 35 36 37 38 279s 0.793565 0.791762 0.786394 0.776620 0.768677 0.745862 0.714531 0.619897 279s 39 40 41 42 43 279s 0.477043 0.235938 0.056832 0.005167 0.000000 279s > 279s > trcov(cif.control, "0 1") 279s 6 7 8 9 10 11 12 13 279s 0.000e+00 2.719e-05 4.533e-05 6.665e-05 7.698e-05 8.304e-05 8.304e-05 8.444e-05 279s 14 17 19 21 24 25 26 30 279s 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 279s 31 32 33 34 35 36 37 38 279s 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 279s 39 40 41 42 43 279s 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 279s > trcov(cif.control, "0 2") 279s 6 7 8 9 10 11 12 13 279s 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 279s 14 17 19 21 24 25 26 30 279s 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 3.338e-06 279s 31 32 33 34 35 36 37 38 279s 5.784e-06 7.401e-06 1.216e-05 2.072e-05 2.758e-05 4.619e-05 7.202e-05 1.461e-04 279s 39 40 41 42 43 279s 2.470e-04 3.880e-04 4.702e-04 4.903e-04 4.922e-04 279s > trcov(cif.control, "0 0") 279s 6 7 8 9 10 11 12 13 279s 2.822e-04 3.821e-04 4.527e-04 4.748e-04 4.875e-04 4.927e-04 4.941e-04 4.942e-04 279s 14 17 19 21 24 25 26 30 279s 4.941e-04 4.940e-04 4.936e-04 4.933e-04 4.931e-04 4.928e-04 4.926e-04 4.914e-04 279s 31 32 33 34 35 36 37 38 279s 4.905e-04 4.899e-04 4.880e-04 4.846e-04 4.816e-04 4.729e-04 4.601e-04 4.176e-04 279s 39 40 41 42 43 279s 3.425e-04 1.865e-04 4.797e-05 4.441e-06 0.000e+00 279s > 279s > aa <- summary(cif.control) 279s > aa$"0 1" 279s P time var lower upper n.risk n.event 279s 6 0.000000 6 0.000e+00 0.000000 0.00000 117 0 279s 7 0.007401 7 2.719e-05 0.000000 0.01762 261 2 279s 8 0.014881 8 4.533e-05 0.001685 0.02808 374 3 279s 9 0.026509 9 6.665e-05 0.010508 0.04251 458 6 279s 10 0.033208 10 7.698e-05 0.016011 0.05040 515 4 279s 11 0.037694 11 8.304e-05 0.019834 0.05555 561 3 279s 12 0.037694 12 8.304e-05 0.019834 0.05555 610 0 279s 13 0.038955 13 8.444e-05 0.020944 0.05697 645 1 279s 14 0.040159 14 8.571e-05 0.022014 0.05830 673 1 279s 17 0.040159 17 8.571e-05 0.022014 0.05830 740 0 279s 19 0.040159 19 8.571e-05 0.022014 0.05830 781 0 279s 21 0.040159 21 8.571e-05 0.022014 0.05830 799 0 279s 24 0.040159 24 8.571e-05 0.022014 0.05830 830 0 279s 25 0.040159 25 8.571e-05 0.022014 0.05830 841 0 279s 26 0.040159 26 8.571e-05 0.022014 0.05830 846 0 279s 30 0.040159 30 8.571e-05 0.022014 0.05830 875 0 279s 31 0.040159 31 8.571e-05 0.022014 0.05830 880 0 279s 32 0.040159 32 8.571e-05 0.022014 0.05830 880 0 279s 33 0.040159 33 8.571e-05 0.022014 0.05830 885 0 279s 34 0.040159 34 8.571e-05 0.022014 0.05830 885 0 279s 35 0.040159 35 8.571e-05 0.022014 0.05830 880 0 279s 36 0.040159 36 8.571e-05 0.022014 0.05830 876 0 279s 37 0.040159 37 8.571e-05 0.022014 0.05830 857 0 279s 38 0.040159 38 8.571e-05 0.022014 0.05830 823 0 279s 39 0.040159 39 8.571e-05 0.022014 0.05830 716 0 279s 40 0.040159 40 8.571e-05 0.022014 0.05830 554 0 279s 41 0.040159 41 8.571e-05 0.022014 0.05830 274 0 279s 42 0.040159 42 8.571e-05 0.022014 0.05830 66 0 279s 43 0.040159 43 8.571e-05 0.022014 0.05830 6 0 279s > all.equal(aa$"0 1"$P, as.vector(trprob(cif.control, "0 1"))) 279s [1] TRUE 279s > 279s > ### test on los data 279s > 279s > data(los.data) # in package changeLOS 279s > 279s > ## putting los.data in the long format (see changeLOS) 279s > my.observ <- prepare.los.data(x=los.data) 279s > 279s > tra <- matrix(FALSE, 4, 4) 279s > tra[1, 2:4] <- TRUE 279s > tra[2, 3:4] <- TRUE 279s > 279s > tr.prob <- etm(my.observ, c("0","1","2","3"), tra, NULL, 0) 279s > 279s > tr.prob 279s Multistate model with 2 transient state(s) 279s and 2 absorbing state(s) 279s 279s Possible transitions: 279s from to 279s 0 1 279s 0 2 279s 0 3 279s 1 2 279s 1 3 279s 279s Estimate of P(0, 82) 279s 0 1 2 3 279s 0 0 0 0.7474 0.2526 279s 1 0 0 0.7073 0.2927 279s 2 0 0 1.0000 0.0000 279s 3 0 0 0.0000 1.0000 279s 279s > summary(tr.prob) 279s Transition 0 0 279s P time var lower upper n.risk n.event 279s 0.882275 3 1.374e-04 0.8593018 0.905248 756 0 279s 0.112434 15 1.320e-04 0.0899155 0.134952 90 0 279s 0.031746 27 4.066e-05 0.0192484 0.044244 26 0 279s 0.006614 41 8.690e-06 0.0008359 0.012392 5 0 279s 0.002646 61 3.490e-06 0.0000000 0.006307 3 0 279s 0.000000 82 0.000e+00 0.0000000 0.000000 1 0 279s 279s Transition 0 1 279s P time var lower upper n.risk n.event 279s 0.017196 3 2.235e-05 0.0079289 0.02646 756 13 279s 0.063492 15 7.865e-05 0.0461099 0.08087 90 0 279s 0.030423 27 3.902e-05 0.0181805 0.04267 26 1 279s 0.015873 41 2.066e-05 0.0069637 0.02478 5 0 279s 0.005291 61 6.962e-06 0.0001197 0.01046 3 0 279s 0.000000 82 0.000e+00 0.0000000 0.00000 1 0 279s 279s Transition 0 2 279s P time var lower upper n.risk n.event 279s 0.08466 3 0.0001025 0.06481 0.1045 756 64 279s 0.62302 15 0.0003107 0.58847 0.6576 90 4 279s 0.69841 27 0.0002786 0.66570 0.7311 26 1 279s 0.72751 41 0.0002622 0.69578 0.7593 5 0 279s 0.74074 61 0.0002540 0.70950 0.7720 3 1 279s 0.74735 82 0.0002498 0.71638 0.7783 1 1 279s 279s Transition 0 3 279s P time var lower upper n.risk n.event 279s 0.01587 3 2.066e-05 0.006964 0.02478 756 12 279s 0.20106 15 2.125e-04 0.172489 0.22963 90 1 279s 0.23942 27 2.409e-04 0.208999 0.26984 26 0 279s 0.25000 41 2.480e-04 0.219133 0.28087 5 0 279s 0.25132 61 2.489e-04 0.220402 0.28224 3 0 279s 0.25265 82 2.498e-04 0.221671 0.28362 1 0 279s 279s Transition 1 1 279s P time var lower upper n.risk n.event 279s 1.00000 3 0.000e+00 1.00000 1.00000 0 0 279s 0.38661 15 2.358e-03 0.29143 0.48179 51 0 279s 0.12119 27 7.842e-04 0.06630 0.17607 23 0 279s 0.04593 41 2.405e-04 0.01554 0.07633 14 0 279s 0.01531 61 6.579e-05 0.00000 0.03121 4 0 279s 0.00000 82 0.000e+00 0.00000 0.00000 0 0 279s 279s Transition 1 2 279s P time var lower upper n.risk n.event 279s 0.0000 3 0.000000 0.0000 0.0000 0 0 279s 0.4107 15 0.002590 0.3110 0.5104 51 2 279s 0.6082 27 0.002254 0.5151 0.7012 23 1 279s 0.6652 41 0.002064 0.5761 0.7542 14 2 279s 0.6920 61 0.002000 0.6043 0.7796 4 0 279s 0.7073 82 0.001984 0.6200 0.7946 0 0 279s 279s Transition 1 3 279s P time var lower upper n.risk n.event 279s 0.0000 3 0.000000 0.0000 0.0000 0 0 279s 0.2027 15 0.001784 0.1199 0.2855 51 1 279s 0.2706 27 0.001968 0.1837 0.3576 23 0 279s 0.2889 41 0.001982 0.2016 0.3761 14 0 279s 0.2927 61 0.001984 0.2054 0.3800 4 0 279s 0.2927 82 0.001984 0.2054 0.3800 0 0 279s 279s > 279s > cLOS <- etm::clos(tr.prob, aw = TRUE) 279s > 279s > cLOS 279s The expected change in length of stay is: 279s 1.975 279s 279s Alternative weighting: 279s 279s Expected change in LOS with weight.1: 2.097 279s Expected change in LOS with weight.other: 1.951 279s > 279s > 279s > ### Tests on pseudo values 279s > t_pseudo <- closPseudo(my.observ, c("0","1","2","3"), tra, NULL, 279s + formula = ~ 1, aw = TRUE) 294s > 294s > cLOS$e.phi == t_pseudo$theta[, "e.phi"] 294s [,1] 294s [1,] TRUE 294s > cLOS$e.phi.weights.1 == t_pseudo$theta[, "e.phi.weights.1"] 294s [,1] 294s [1,] TRUE 294s > cLOS$e.phi.weights.other == t_pseudo$theta[, "e.phi.weights.other"] 294s [,1] 294s [1,] TRUE 294s > 294s > mean(t_pseudo$pseudoData$ps.e.phi) 294s [1] 1.968 294s > 294s > ### tests on etmprep 294s > 294s > ### creation of fake data in the wild format, following an illness-death model 294s > ## transition times 294s > tdisease <- c(3, 4, 3, 6, 8, 9) 294s > tdeath <- c(6, 9, 8, 6, 8, 9) 294s > 294s > ## transition status 294s > stat.disease <- c(1, 1, 1, 0, 0, 0) 294s > stat.death <- c(1, 1, 1, 1, 1, 0) 294s > 294s > ## a covariate that we want to keep in the new data 294s > set.seed(1313) 294s > cova <- rbinom(6, 1, 0.5) 294s > 294s > dat <- data.frame(tdisease, tdeath, 294s + stat.disease, stat.death, 294s + cova) 294s > 294s > ## Possible transitions 295s > tra <- matrix(FALSE, 3, 3) 295s > tra[1, 2:3] <- TRUE 295s > tra[2, 3] <- TRUE 295s > 295s > ## data preparation 295s > newdat <- etmprep(c(NA, "tdisease", "tdeath"), 295s + c(NA, "stat.disease", "stat.death"), 295s + data = dat, tra = tra, 295s + cens.name = "cens", keep = "cova") 295s > 295s > newdat 295s id entry exit from to cova 295s 1 1 0 3 0 1 1 295s 2 1 3 6 1 2 1 295s 3 2 0 4 0 1 0 295s 4 2 4 9 1 2 0 295s 5 3 0 3 0 1 1 295s 6 3 3 8 1 2 1 295s 7 4 0 6 0 2 0 295s 8 5 0 8 0 2 1 295s 9 6 0 9 0 cens 1 295s > 295s > ref <- data.frame(id = c(1, 1, 2, 2, 3, 3, 4, 5, 6), 295s + entry = c(0, 3, 0, 4, 0, 3, 0, 0, 0), 295s + exit = c(3, 6, 4, 9, 3, 8, 6, 8, 9), 295s + from = c(0, 1, 0, 1, 0, 1, 0, 0, 0), 295s + to = c(rep(c(1, 2), 3), 2, 2, "cens"), 295s + cova = c(1, 1, 0, 0, 1, 1, 0, 1, 1)) 295s > ref$from <- factor(as.character(ref$from), levels = c("0", "1", "2", "cens")) 295s > ref$to <- factor(as.character(ref$to), levels = c("0", "1", "2", "cens")) 295s > 295s > all.equal(ref, newdat) 295s [1] TRUE 295s > 295s > 295s > ###################################### 295s > ### Test the stratified calls 295s > ###################################### 295s > 295s > if (require("kmi", quietly = TRUE)) { 295s + library(etm) 295s + 295s + data(icu.pneu) 295s + my.icu.pneu <- icu.pneu 295s + 295s + my.icu.pneu <- my.icu.pneu[order(my.icu.pneu$id, my.icu.pneu$start), ] 295s + masque <- diff(my.icu.pneu$id) 295s + 295s + my.icu.pneu$from <- 0 295s + my.icu.pneu$from[c(1, masque) == 0] <- 1 295s + 295s + my.icu.pneu$to2 <- my.icu.pneu$event 295s + my.icu.pneu$to2[my.icu.pneu$status == 0] <- "cens" 295s + my.icu.pneu$to2[c(masque, 1) == 0] <- 1 295s + 295s + 295s + my.icu.pneu$to <- ifelse(my.icu.pneu$to2 %in% c(2, 3), 2, 295s + my.icu.pneu$to2) 295s + 295s + my.icu.pneu <- my.icu.pneu[, c("id", "start", "stop", "from", "to", 295s + "to2", "age", "sex")] 295s + names(my.icu.pneu)[c(2, 3)] <- c("entry", "exit") 295s + 295s + bouh_strat <- etm(my.icu.pneu, c("0", "1", "2"), tra_ill(), "cens", 0, strata = "sex") 295s + 295s + bouh_female <- etm(my.icu.pneu[my.icu.pneu$sex == "F", ], 295s + c("0", "1", "2"), tra_ill(), "cens", 0) 295s + 295s + all(bouh_strat[[1]]$est == bouh_female$est) 295s + 295s + ## Test the summary 295s + the_summary <- summary(bouh_strat) 295s + the_summary 295s + 295s + ## Test trprob 295s + all(trprob(bouh_strat, "0 1")[[1]] == trprob(bouh_female, "0 1")) 295s + all(trprob(bouh_strat, "0 1", c(0, 5, 10, 15))[[1]] == trprob(bouh_female, "0 1", c(0, 5, 10, 15))) 295s + 295s + ## Test trcov 295s + all(trcov(bouh_strat, "0 1")[[1]] == trcov(bouh_female, "0 1")) 295s + all(trcov(bouh_strat, c("0 1", "0 2"))[[1]] == trcov(bouh_female, c("0 1", "0 2"))) 295s + all(trcov(bouh_strat, "0 1", c(0, 5, 10, 15))[[1]] == trcov(bouh_female, "0 1", c(0, 5, 10, 15))) 295s + } else { 295s + print("These tests require the kmi package") 295s + } 295s [1] TRUE 295s > 295s > options(old) 295s > 295s autopkgtest [22:11:46]: test run-unit-test: -----------------------] 296s run-unit-test PASS 296s autopkgtest [22:11:47]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 296s autopkgtest [22:11:47]: test pkg-r-autopkgtest: preparing testbed 296s Reading package lists... 297s Building dependency tree... 297s Reading state information... 297s Starting pkgProblemResolver with broken count: 0 297s Starting 2 pkgProblemResolver with broken count: 0 297s Done 298s The following NEW packages will be installed: 298s build-essential cpp cpp-14 cpp-14-x86-64-linux-gnu cpp-x86-64-linux-gnu 298s dctrl-tools g++ g++-14 g++-14-x86-64-linux-gnu g++-x86-64-linux-gnu gcc 298s gcc-14 gcc-14-x86-64-linux-gnu gcc-x86-64-linux-gnu gfortran gfortran-14 298s gfortran-14-x86-64-linux-gnu gfortran-x86-64-linux-gnu icu-devtools libasan8 298s libblas-dev libbz2-dev libcc1-0 libdeflate-dev libgcc-14-dev 298s libgfortran-14-dev libhwasan0 libicu-dev libisl23 libitm1 libjpeg-dev 298s libjpeg-turbo8-dev libjpeg8-dev liblapack-dev liblsan0 liblzma-dev libmpc3 298s libncurses-dev libpcre2-16-0 libpcre2-32-0 libpcre2-dev libpcre2-posix3 298s libpkgconf3 libpng-dev libquadmath0 libreadline-dev libstdc++-14-dev 298s libtirpc-dev libtsan2 libubsan1 pkg-r-autopkgtest pkgconf pkgconf-bin 298s r-base-dev r-cran-backports r-cran-broom r-cran-cli r-cran-colorspace 298s r-cran-cpp11 r-cran-dplyr r-cran-fansi r-cran-farver r-cran-geepack 298s r-cran-generics r-cran-ggplot2 r-cran-glue r-cran-gtable r-cran-isoband 298s r-cran-labeling r-cran-lifecycle r-cran-magrittr r-cran-mass r-cran-mgcv 298s r-cran-munsell r-cran-nlme r-cran-pillar r-cran-pkgconfig r-cran-purrr 298s r-cran-r6 r-cran-rcolorbrewer r-cran-rlang r-cran-scales r-cran-stringi 298s r-cran-stringr r-cran-tibble r-cran-tidyr r-cran-tidyselect r-cran-utf8 298s r-cran-vctrs r-cran-viridislite r-cran-withr zlib1g-dev 298s 0 upgraded, 92 newly installed, 0 to remove and 0 not upgraded. 298s Need to get 134 MB of archives. 298s After this operation, 413 MB of additional disk space will be used. 298s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 libisl23 amd64 0.27-1 [685 kB] 298s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libmpc3 amd64 1.3.1-1build2 [55.3 kB] 298s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-14-x86-64-linux-gnu amd64 14.2.0-17ubuntu3 [11.9 MB] 299s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-14 amd64 14.2.0-17ubuntu3 [1030 B] 299s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-x86-64-linux-gnu amd64 4:14.2.0-1ubuntu1 [5586 B] 299s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp amd64 4:14.2.0-1ubuntu1 [22.4 kB] 299s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 libcc1-0 amd64 15-20250222-0ubuntu1 [47.0 kB] 299s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 libitm1 amd64 15-20250222-0ubuntu1 [28.6 kB] 299s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 libasan8 amd64 15-20250222-0ubuntu1 [3055 kB] 299s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 liblsan0 amd64 15-20250222-0ubuntu1 [1355 kB] 299s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 libtsan2 amd64 15-20250222-0ubuntu1 [2756 kB] 299s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 libubsan1 amd64 15-20250222-0ubuntu1 [1205 kB] 299s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 libhwasan0 amd64 15-20250222-0ubuntu1 [1677 kB] 299s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 libquadmath0 amd64 15-20250222-0ubuntu1 [152 kB] 299s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 libgcc-14-dev amd64 14.2.0-17ubuntu3 [2816 kB] 300s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-14-x86-64-linux-gnu amd64 14.2.0-17ubuntu3 [23.3 MB] 300s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-14 amd64 14.2.0-17ubuntu3 [536 kB] 300s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-x86-64-linux-gnu amd64 4:14.2.0-1ubuntu1 [1208 B] 300s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc amd64 4:14.2.0-1ubuntu1 [5004 B] 300s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 libstdc++-14-dev amd64 14.2.0-17ubuntu3 [2486 kB] 301s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-14-x86-64-linux-gnu amd64 14.2.0-17ubuntu3 [13.4 MB] 301s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-14 amd64 14.2.0-17ubuntu3 [21.8 kB] 301s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-x86-64-linux-gnu amd64 4:14.2.0-1ubuntu1 [968 B] 301s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 g++ amd64 4:14.2.0-1ubuntu1 [1100 B] 301s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 build-essential amd64 12.10ubuntu1 [4928 B] 301s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 dctrl-tools amd64 2.24-3build3 [106 kB] 301s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran-14-dev amd64 14.2.0-17ubuntu3 [966 kB] 301s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 gfortran-14-x86-64-linux-gnu amd64 14.2.0-17ubuntu3 [12.6 MB] 302s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 gfortran-14 amd64 14.2.0-17ubuntu3 [13.6 kB] 302s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 gfortran-x86-64-linux-gnu amd64 4:14.2.0-1ubuntu1 [1022 B] 302s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 gfortran amd64 4:14.2.0-1ubuntu1 [1174 B] 302s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 icu-devtools amd64 76.1-1ubuntu2 [237 kB] 302s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas-dev amd64 3.12.1-2 [338 kB] 302s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 libbz2-dev amd64 1.0.8-6 [33.8 kB] 302s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate-dev amd64 1.23-1 [71.7 kB] 302s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 libicu-dev amd64 76.1-1ubuntu2 [12.6 MB] 302s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg-turbo8-dev amd64 2.1.5-3ubuntu2 [324 kB] 302s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg8-dev amd64 8c-2ubuntu11 [1484 B] 302s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg-dev amd64 8c-2ubuntu11 [1482 B] 302s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack-dev amd64 3.12.1-2 [6489 kB] 302s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 libncurses-dev amd64 6.5+20250216-2 [424 kB] 302s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 libpcre2-16-0 amd64 10.45-1 [268 kB] 302s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 libpcre2-32-0 amd64 10.45-1 [251 kB] 302s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 libpcre2-posix3 amd64 10.45-1 [7204 B] 302s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 libpcre2-dev amd64 10.45-1 [908 kB] 302s Get:46 http://ftpmaster.internal/ubuntu plucky/main amd64 libpkgconf3 amd64 1.8.1-4 [32.3 kB] 302s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1ubuntu1 [895 kB] 302s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 libpng-dev amd64 1.6.47-1 [298 kB] 302s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 libreadline-dev amd64 8.2-6 [184 kB] 302s Get:50 http://ftpmaster.internal/ubuntu plucky/main amd64 liblzma-dev amd64 5.6.4-1 [189 kB] 302s Get:51 http://ftpmaster.internal/ubuntu plucky/main amd64 pkgconf-bin amd64 1.8.1-4 [21.6 kB] 302s Get:52 http://ftpmaster.internal/ubuntu plucky/main amd64 pkgconf amd64 1.8.1-4 [16.8 kB] 302s Get:53 http://ftpmaster.internal/ubuntu plucky/main amd64 libtirpc-dev amd64 1.3.4+ds-1.3 [193 kB] 302s Get:54 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-base-dev all 4.4.3-1 [4176 B] 302s Get:55 http://ftpmaster.internal/ubuntu plucky/universe amd64 pkg-r-autopkgtest all 20231212ubuntu1 [6448 B] 302s Get:56 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-backports amd64 1.5.0-2 [121 kB] 302s Get:57 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-cli amd64 3.6.4-1 [1394 kB] 302s Get:58 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-generics all 0.1.3-1 [81.3 kB] 302s Get:59 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-glue amd64 1.8.0-1 [164 kB] 302s Get:60 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-rlang amd64 1.1.5-1 [1719 kB] 303s Get:61 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB] 303s Get:62 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-magrittr amd64 2.0.3-1 [154 kB] 303s Get:63 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-utf8 amd64 1.2.4-1 [140 kB] 303s Get:64 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-vctrs amd64 0.6.5-1 [1335 kB] 303s Get:65 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-pillar all 1.10.1+dfsg-1 [453 kB] 303s Get:66 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-r6 all 2.6.1-1 [101 kB] 303s Get:67 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-fansi amd64 1.0.5-1 [619 kB] 303s Get:68 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-pkgconfig all 2.0.3-2build1 [19.7 kB] 303s Get:69 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-tibble amd64 3.2.1+dfsg-3 [419 kB] 303s Get:70 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-withr all 3.0.2+dfsg-1 [214 kB] 303s Get:71 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-tidyselect amd64 1.2.1+dfsg-1 [222 kB] 303s Get:72 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-dplyr amd64 1.1.4-4 [1536 kB] 303s Get:73 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-purrr amd64 1.0.4-1 [552 kB] 303s Get:74 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-stringi amd64 1.8.4-1build1 [927 kB] 303s Get:75 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-stringr all 1.5.1-1 [290 kB] 303s Get:76 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-cpp11 all 0.5.2-1 [233 kB] 303s Get:77 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-tidyr amd64 1.3.1-1 [1156 kB] 303s Get:78 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-broom all 1.0.7+dfsg-1 [1802 kB] 303s Get:79 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-colorspace amd64 2.1-1+dfsg-1 [1563 kB] 303s Get:80 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-farver amd64 2.1.2-1 [1355 kB] 303s Get:81 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-mass amd64 7.3-64-1 [1114 kB] 303s Get:82 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-geepack amd64 1.3.12-1 [389 kB] 303s Get:83 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-gtable all 0.3.6+dfsg-1 [199 kB] 303s Get:84 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-isoband amd64 0.2.7-1 [1481 kB] 303s Get:85 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-nlme amd64 3.1.167-1 [2320 kB] 303s Get:86 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-mgcv amd64 1.9-1-1 [3252 kB] 303s Get:87 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-labeling all 0.4.3-1 [62.1 kB] 303s Get:88 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-munsell all 0.5.1-1 [213 kB] 303s Get:89 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-rcolorbrewer all 1.1-3-1build1 [55.4 kB] 303s Get:90 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-viridislite all 0.4.2-2 [1088 kB] 303s Get:91 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-scales all 1.3.0-1 [603 kB] 303s Get:92 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-ggplot2 all 3.5.1+dfsg-1 [3940 kB] 304s Fetched 134 MB in 6s (23.9 MB/s) 304s Selecting previously unselected package libisl23:amd64. 304s (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 ... 81548 files and directories currently installed.) 304s Preparing to unpack .../00-libisl23_0.27-1_amd64.deb ... 304s Unpacking libisl23:amd64 (0.27-1) ... 304s Selecting previously unselected package libmpc3:amd64. 304s Preparing to unpack .../01-libmpc3_1.3.1-1build2_amd64.deb ... 304s Unpacking libmpc3:amd64 (1.3.1-1build2) ... 304s Selecting previously unselected package cpp-14-x86-64-linux-gnu. 304s Preparing to unpack .../02-cpp-14-x86-64-linux-gnu_14.2.0-17ubuntu3_amd64.deb ... 304s Unpacking cpp-14-x86-64-linux-gnu (14.2.0-17ubuntu3) ... 305s Selecting previously unselected package cpp-14. 305s Preparing to unpack .../03-cpp-14_14.2.0-17ubuntu3_amd64.deb ... 305s Unpacking cpp-14 (14.2.0-17ubuntu3) ... 305s Selecting previously unselected package cpp-x86-64-linux-gnu. 305s Preparing to unpack .../04-cpp-x86-64-linux-gnu_4%3a14.2.0-1ubuntu1_amd64.deb ... 305s Unpacking cpp-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ... 305s Selecting previously unselected package cpp. 305s Preparing to unpack .../05-cpp_4%3a14.2.0-1ubuntu1_amd64.deb ... 305s Unpacking cpp (4:14.2.0-1ubuntu1) ... 305s Selecting previously unselected package libcc1-0:amd64. 305s Preparing to unpack .../06-libcc1-0_15-20250222-0ubuntu1_amd64.deb ... 305s Unpacking libcc1-0:amd64 (15-20250222-0ubuntu1) ... 305s Selecting previously unselected package libitm1:amd64. 305s Preparing to unpack .../07-libitm1_15-20250222-0ubuntu1_amd64.deb ... 305s Unpacking libitm1:amd64 (15-20250222-0ubuntu1) ... 305s Selecting previously unselected package libasan8:amd64. 305s Preparing to unpack .../08-libasan8_15-20250222-0ubuntu1_amd64.deb ... 305s Unpacking libasan8:amd64 (15-20250222-0ubuntu1) ... 305s Selecting previously unselected package liblsan0:amd64. 305s Preparing to unpack .../09-liblsan0_15-20250222-0ubuntu1_amd64.deb ... 305s Unpacking liblsan0:amd64 (15-20250222-0ubuntu1) ... 305s Selecting previously unselected package libtsan2:amd64. 305s Preparing to unpack .../10-libtsan2_15-20250222-0ubuntu1_amd64.deb ... 305s Unpacking libtsan2:amd64 (15-20250222-0ubuntu1) ... 305s Selecting previously unselected package libubsan1:amd64. 305s Preparing to unpack .../11-libubsan1_15-20250222-0ubuntu1_amd64.deb ... 305s Unpacking libubsan1:amd64 (15-20250222-0ubuntu1) ... 305s Selecting previously unselected package libhwasan0:amd64. 305s Preparing to unpack .../12-libhwasan0_15-20250222-0ubuntu1_amd64.deb ... 305s Unpacking libhwasan0:amd64 (15-20250222-0ubuntu1) ... 305s Selecting previously unselected package libquadmath0:amd64. 305s Preparing to unpack .../13-libquadmath0_15-20250222-0ubuntu1_amd64.deb ... 305s Unpacking libquadmath0:amd64 (15-20250222-0ubuntu1) ... 305s Selecting previously unselected package libgcc-14-dev:amd64. 305s Preparing to unpack .../14-libgcc-14-dev_14.2.0-17ubuntu3_amd64.deb ... 305s Unpacking libgcc-14-dev:amd64 (14.2.0-17ubuntu3) ... 305s Selecting previously unselected package gcc-14-x86-64-linux-gnu. 305s Preparing to unpack .../15-gcc-14-x86-64-linux-gnu_14.2.0-17ubuntu3_amd64.deb ... 305s Unpacking gcc-14-x86-64-linux-gnu (14.2.0-17ubuntu3) ... 306s Selecting previously unselected package gcc-14. 306s Preparing to unpack .../16-gcc-14_14.2.0-17ubuntu3_amd64.deb ... 306s Unpacking gcc-14 (14.2.0-17ubuntu3) ... 306s Selecting previously unselected package gcc-x86-64-linux-gnu. 306s Preparing to unpack .../17-gcc-x86-64-linux-gnu_4%3a14.2.0-1ubuntu1_amd64.deb ... 306s Unpacking gcc-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ... 306s Selecting previously unselected package gcc. 306s Preparing to unpack .../18-gcc_4%3a14.2.0-1ubuntu1_amd64.deb ... 306s Unpacking gcc (4:14.2.0-1ubuntu1) ... 306s Selecting previously unselected package libstdc++-14-dev:amd64. 306s Preparing to unpack .../19-libstdc++-14-dev_14.2.0-17ubuntu3_amd64.deb ... 306s Unpacking libstdc++-14-dev:amd64 (14.2.0-17ubuntu3) ... 306s Selecting previously unselected package g++-14-x86-64-linux-gnu. 306s Preparing to unpack .../20-g++-14-x86-64-linux-gnu_14.2.0-17ubuntu3_amd64.deb ... 306s Unpacking g++-14-x86-64-linux-gnu (14.2.0-17ubuntu3) ... 307s Selecting previously unselected package g++-14. 307s Preparing to unpack .../21-g++-14_14.2.0-17ubuntu3_amd64.deb ... 307s Unpacking g++-14 (14.2.0-17ubuntu3) ... 307s Selecting previously unselected package g++-x86-64-linux-gnu. 307s Preparing to unpack .../22-g++-x86-64-linux-gnu_4%3a14.2.0-1ubuntu1_amd64.deb ... 307s Unpacking g++-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ... 307s Selecting previously unselected package g++. 307s Preparing to unpack .../23-g++_4%3a14.2.0-1ubuntu1_amd64.deb ... 307s Unpacking g++ (4:14.2.0-1ubuntu1) ... 307s Selecting previously unselected package build-essential. 307s Preparing to unpack .../24-build-essential_12.10ubuntu1_amd64.deb ... 307s Unpacking build-essential (12.10ubuntu1) ... 307s Selecting previously unselected package dctrl-tools. 307s Preparing to unpack .../25-dctrl-tools_2.24-3build3_amd64.deb ... 307s Unpacking dctrl-tools (2.24-3build3) ... 307s Selecting previously unselected package libgfortran-14-dev:amd64. 307s Preparing to unpack .../26-libgfortran-14-dev_14.2.0-17ubuntu3_amd64.deb ... 307s Unpacking libgfortran-14-dev:amd64 (14.2.0-17ubuntu3) ... 307s Selecting previously unselected package gfortran-14-x86-64-linux-gnu. 307s Preparing to unpack .../27-gfortran-14-x86-64-linux-gnu_14.2.0-17ubuntu3_amd64.deb ... 307s Unpacking gfortran-14-x86-64-linux-gnu (14.2.0-17ubuntu3) ... 307s Selecting previously unselected package gfortran-14. 307s Preparing to unpack .../28-gfortran-14_14.2.0-17ubuntu3_amd64.deb ... 307s Unpacking gfortran-14 (14.2.0-17ubuntu3) ... 307s Selecting previously unselected package gfortran-x86-64-linux-gnu. 307s Preparing to unpack .../29-gfortran-x86-64-linux-gnu_4%3a14.2.0-1ubuntu1_amd64.deb ... 307s Unpacking gfortran-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ... 307s Selecting previously unselected package gfortran. 307s Preparing to unpack .../30-gfortran_4%3a14.2.0-1ubuntu1_amd64.deb ... 307s Unpacking gfortran (4:14.2.0-1ubuntu1) ... 307s Selecting previously unselected package icu-devtools. 307s Preparing to unpack .../31-icu-devtools_76.1-1ubuntu2_amd64.deb ... 307s Unpacking icu-devtools (76.1-1ubuntu2) ... 307s Selecting previously unselected package libblas-dev:amd64. 307s Preparing to unpack .../32-libblas-dev_3.12.1-2_amd64.deb ... 307s Unpacking libblas-dev:amd64 (3.12.1-2) ... 307s Selecting previously unselected package libbz2-dev:amd64. 307s Preparing to unpack .../33-libbz2-dev_1.0.8-6_amd64.deb ... 307s Unpacking libbz2-dev:amd64 (1.0.8-6) ... 307s Selecting previously unselected package libdeflate-dev:amd64. 307s Preparing to unpack .../34-libdeflate-dev_1.23-1_amd64.deb ... 307s Unpacking libdeflate-dev:amd64 (1.23-1) ... 307s Selecting previously unselected package libicu-dev:amd64. 308s Preparing to unpack .../35-libicu-dev_76.1-1ubuntu2_amd64.deb ... 308s Unpacking libicu-dev:amd64 (76.1-1ubuntu2) ... 308s Selecting previously unselected package libjpeg-turbo8-dev:amd64. 308s Preparing to unpack .../36-libjpeg-turbo8-dev_2.1.5-3ubuntu2_amd64.deb ... 308s Unpacking libjpeg-turbo8-dev:amd64 (2.1.5-3ubuntu2) ... 308s Selecting previously unselected package libjpeg8-dev:amd64. 308s Preparing to unpack .../37-libjpeg8-dev_8c-2ubuntu11_amd64.deb ... 308s Unpacking libjpeg8-dev:amd64 (8c-2ubuntu11) ... 308s Selecting previously unselected package libjpeg-dev:amd64. 308s Preparing to unpack .../38-libjpeg-dev_8c-2ubuntu11_amd64.deb ... 308s Unpacking libjpeg-dev:amd64 (8c-2ubuntu11) ... 308s Selecting previously unselected package liblapack-dev:amd64. 308s Preparing to unpack .../39-liblapack-dev_3.12.1-2_amd64.deb ... 308s Unpacking liblapack-dev:amd64 (3.12.1-2) ... 308s Selecting previously unselected package libncurses-dev:amd64. 308s Preparing to unpack .../40-libncurses-dev_6.5+20250216-2_amd64.deb ... 308s Unpacking libncurses-dev:amd64 (6.5+20250216-2) ... 308s Selecting previously unselected package libpcre2-16-0:amd64. 308s Preparing to unpack .../41-libpcre2-16-0_10.45-1_amd64.deb ... 308s Unpacking libpcre2-16-0:amd64 (10.45-1) ... 308s Selecting previously unselected package libpcre2-32-0:amd64. 308s Preparing to unpack .../42-libpcre2-32-0_10.45-1_amd64.deb ... 308s Unpacking libpcre2-32-0:amd64 (10.45-1) ... 308s Selecting previously unselected package libpcre2-posix3:amd64. 308s Preparing to unpack .../43-libpcre2-posix3_10.45-1_amd64.deb ... 308s Unpacking libpcre2-posix3:amd64 (10.45-1) ... 308s Selecting previously unselected package libpcre2-dev:amd64. 308s Preparing to unpack .../44-libpcre2-dev_10.45-1_amd64.deb ... 308s Unpacking libpcre2-dev:amd64 (10.45-1) ... 308s Selecting previously unselected package libpkgconf3:amd64. 308s Preparing to unpack .../45-libpkgconf3_1.8.1-4_amd64.deb ... 308s Unpacking libpkgconf3:amd64 (1.8.1-4) ... 309s Selecting previously unselected package zlib1g-dev:amd64. 309s Preparing to unpack .../46-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1ubuntu1_amd64.deb ... 309s Unpacking zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 309s Selecting previously unselected package libpng-dev:amd64. 309s Preparing to unpack .../47-libpng-dev_1.6.47-1_amd64.deb ... 309s Unpacking libpng-dev:amd64 (1.6.47-1) ... 309s Selecting previously unselected package libreadline-dev:amd64. 309s Preparing to unpack .../48-libreadline-dev_8.2-6_amd64.deb ... 309s Unpacking libreadline-dev:amd64 (8.2-6) ... 309s Selecting previously unselected package liblzma-dev:amd64. 309s Preparing to unpack .../49-liblzma-dev_5.6.4-1_amd64.deb ... 309s Unpacking liblzma-dev:amd64 (5.6.4-1) ... 309s Selecting previously unselected package pkgconf-bin. 309s Preparing to unpack .../50-pkgconf-bin_1.8.1-4_amd64.deb ... 309s Unpacking pkgconf-bin (1.8.1-4) ... 309s Selecting previously unselected package pkgconf:amd64. 309s Preparing to unpack .../51-pkgconf_1.8.1-4_amd64.deb ... 309s Unpacking pkgconf:amd64 (1.8.1-4) ... 309s Selecting previously unselected package libtirpc-dev:amd64. 309s Preparing to unpack .../52-libtirpc-dev_1.3.4+ds-1.3_amd64.deb ... 309s Unpacking libtirpc-dev:amd64 (1.3.4+ds-1.3) ... 309s Selecting previously unselected package r-base-dev. 309s Preparing to unpack .../53-r-base-dev_4.4.3-1_all.deb ... 309s Unpacking r-base-dev (4.4.3-1) ... 309s Selecting previously unselected package pkg-r-autopkgtest. 309s Preparing to unpack .../54-pkg-r-autopkgtest_20231212ubuntu1_all.deb ... 309s Unpacking pkg-r-autopkgtest (20231212ubuntu1) ... 309s Selecting previously unselected package r-cran-backports. 309s Preparing to unpack .../55-r-cran-backports_1.5.0-2_amd64.deb ... 309s Unpacking r-cran-backports (1.5.0-2) ... 309s Selecting previously unselected package r-cran-cli. 309s Preparing to unpack .../56-r-cran-cli_3.6.4-1_amd64.deb ... 309s Unpacking r-cran-cli (3.6.4-1) ... 309s Selecting previously unselected package r-cran-generics. 309s Preparing to unpack .../57-r-cran-generics_0.1.3-1_all.deb ... 309s Unpacking r-cran-generics (0.1.3-1) ... 309s Selecting previously unselected package r-cran-glue. 309s Preparing to unpack .../58-r-cran-glue_1.8.0-1_amd64.deb ... 309s Unpacking r-cran-glue (1.8.0-1) ... 309s Selecting previously unselected package r-cran-rlang. 309s Preparing to unpack .../59-r-cran-rlang_1.1.5-1_amd64.deb ... 309s Unpacking r-cran-rlang (1.1.5-1) ... 309s Selecting previously unselected package r-cran-lifecycle. 309s Preparing to unpack .../60-r-cran-lifecycle_1.0.4+dfsg-1_all.deb ... 309s Unpacking r-cran-lifecycle (1.0.4+dfsg-1) ... 309s Selecting previously unselected package r-cran-magrittr. 309s Preparing to unpack .../61-r-cran-magrittr_2.0.3-1_amd64.deb ... 309s Unpacking r-cran-magrittr (2.0.3-1) ... 309s Selecting previously unselected package r-cran-utf8. 309s Preparing to unpack .../62-r-cran-utf8_1.2.4-1_amd64.deb ... 309s Unpacking r-cran-utf8 (1.2.4-1) ... 309s Selecting previously unselected package r-cran-vctrs. 309s Preparing to unpack .../63-r-cran-vctrs_0.6.5-1_amd64.deb ... 309s Unpacking r-cran-vctrs (0.6.5-1) ... 310s Selecting previously unselected package r-cran-pillar. 310s Preparing to unpack .../64-r-cran-pillar_1.10.1+dfsg-1_all.deb ... 310s Unpacking r-cran-pillar (1.10.1+dfsg-1) ... 310s Selecting previously unselected package r-cran-r6. 310s Preparing to unpack .../65-r-cran-r6_2.6.1-1_all.deb ... 310s Unpacking r-cran-r6 (2.6.1-1) ... 310s Selecting previously unselected package r-cran-fansi. 310s Preparing to unpack .../66-r-cran-fansi_1.0.5-1_amd64.deb ... 310s Unpacking r-cran-fansi (1.0.5-1) ... 310s Selecting previously unselected package r-cran-pkgconfig. 310s Preparing to unpack .../67-r-cran-pkgconfig_2.0.3-2build1_all.deb ... 310s Unpacking r-cran-pkgconfig (2.0.3-2build1) ... 310s Selecting previously unselected package r-cran-tibble. 310s Preparing to unpack .../68-r-cran-tibble_3.2.1+dfsg-3_amd64.deb ... 310s Unpacking r-cran-tibble (3.2.1+dfsg-3) ... 310s Selecting previously unselected package r-cran-withr. 310s Preparing to unpack .../69-r-cran-withr_3.0.2+dfsg-1_all.deb ... 310s Unpacking r-cran-withr (3.0.2+dfsg-1) ... 310s Selecting previously unselected package r-cran-tidyselect. 310s Preparing to unpack .../70-r-cran-tidyselect_1.2.1+dfsg-1_amd64.deb ... 310s Unpacking r-cran-tidyselect (1.2.1+dfsg-1) ... 310s Selecting previously unselected package r-cran-dplyr. 310s Preparing to unpack .../71-r-cran-dplyr_1.1.4-4_amd64.deb ... 310s Unpacking r-cran-dplyr (1.1.4-4) ... 310s Selecting previously unselected package r-cran-purrr. 310s Preparing to unpack .../72-r-cran-purrr_1.0.4-1_amd64.deb ... 310s Unpacking r-cran-purrr (1.0.4-1) ... 310s Selecting previously unselected package r-cran-stringi. 310s Preparing to unpack .../73-r-cran-stringi_1.8.4-1build1_amd64.deb ... 310s Unpacking r-cran-stringi (1.8.4-1build1) ... 310s Selecting previously unselected package r-cran-stringr. 310s Preparing to unpack .../74-r-cran-stringr_1.5.1-1_all.deb ... 310s Unpacking r-cran-stringr (1.5.1-1) ... 310s Selecting previously unselected package r-cran-cpp11. 310s Preparing to unpack .../75-r-cran-cpp11_0.5.2-1_all.deb ... 310s Unpacking r-cran-cpp11 (0.5.2-1) ... 310s Selecting previously unselected package r-cran-tidyr. 310s Preparing to unpack .../76-r-cran-tidyr_1.3.1-1_amd64.deb ... 310s Unpacking r-cran-tidyr (1.3.1-1) ... 310s Selecting previously unselected package r-cran-broom. 310s Preparing to unpack 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... 311s Setting up g++-14-x86-64-linux-gnu (14.2.0-17ubuntu3) ... 311s Setting up g++-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ... 311s Setting up g++-14 (14.2.0-17ubuntu3) ... 311s Setting up gfortran-14 (14.2.0-17ubuntu3) ... 311s Setting up r-cran-geepack (1.3.12-1) ... 311s Setting up gfortran-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ... 311s Setting up gcc (4:14.2.0-1ubuntu1) ... 311s Setting up g++ (4:14.2.0-1ubuntu1) ... 311s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 311s Setting up build-essential (12.10ubuntu1) ... 311s Setting up gfortran (4:14.2.0-1ubuntu1) ... 311s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode 311s 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 311s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode 311s 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 311s Setting up r-base-dev (4.4.3-1) ... 311s Setting up pkg-r-autopkgtest (20231212ubuntu1) ... 311s Processing triggers for libc-bin (2.41-1ubuntu2) ... 311s Processing triggers for man-db (2.13.0-1) ... 313s Processing triggers for install-info (7.1.1-1) ... 314s autopkgtest [22:12:05]: test pkg-r-autopkgtest: /usr/share/dh-r/pkg-r-autopkgtest 314s autopkgtest [22:12:05]: test pkg-r-autopkgtest: [----------------------- 314s Test: Try to load the R library etm 314s 314s R version 4.4.3 (2025-02-28) -- "Trophy Case" 314s Copyright (C) 2025 The R Foundation for Statistical Computing 314s Platform: x86_64-pc-linux-gnu 314s 314s R is free software and comes with ABSOLUTELY NO WARRANTY. 314s You are welcome to redistribute it under certain conditions. 314s Type 'license()' or 'licence()' for distribution details. 314s 314s R is a collaborative project with many contributors. 314s Type 'contributors()' for more information and 314s 'citation()' on how to cite R or R packages in publications. 314s 314s Type 'demo()' for some demos, 'help()' for on-line help, or 314s 'help.start()' for an HTML browser interface to help. 314s Type 'q()' to quit R. 314s 315s > library('etm') 316s > 316s > 316s Other tests are currently unsupported! 316s They will be progressively added. 316s autopkgtest [22:12:07]: test pkg-r-autopkgtest: -----------------------] 317s pkg-r-autopkgtest PASS 317s autopkgtest [22:12:08]: test pkg-r-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 317s autopkgtest [22:12:08]: @@@@@@@@@@@@@@@@@@@@ summary 317s run-unit-test PASS 317s pkg-r-autopkgtest PASS 324s nova [W] Skipping flock for amd64 324s Creating nova instance adt-plucky-amd64-r-cran-etm-20250315-220651-juju-7f2275-prod-proposed-migration-environment-2-c9e94c77-1fe7-423f-ad91-0eeabd75be50 from image adt/ubuntu-plucky-amd64-server-20250304.img (UUID 9c7d4da5-d95f-4c85-ac1f-51eb37e75c4c)... 324s nova [W] Timed out waiting for bb0f9866-2cb0-4e58-bb12-97749ef7076c to get deleted.