0s autopkgtest [04:55:21]: starting date and time: 2026-02-10 04:55:21+0000 0s autopkgtest [04:55:21]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [04:55:21]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.bvvpbaw_/out --timeout-copy=6000 --needs-internet=try --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:r-cran-ggplot2 --apt-upgrade r-cran-etm --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=r-cran-ggplot2/4.0.2+dfsg-1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-cpu2-ram4-disk20-amd64 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@sto01-29.secgroup --name adt-resolute-amd64-r-cran-etm-20260210-045521-juju-7f2275-prod-proposed-migration-environment-20-87ffd1c2-2ed4-4036-a22f-a2defeb64ece --image adt/ubuntu-resolute-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-autopkgtest-workers-amd64 -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 4s Creating nova instance adt-resolute-amd64-r-cran-etm-20260210-045521-juju-7f2275-prod-proposed-migration-environment-20-87ffd1c2-2ed4-4036-a22f-a2defeb64ece from image adt/ubuntu-resolute-amd64-server-20260204.img (UUID fedf54b4-458b-493e-8072-6425c19717b4)... 76s autopkgtest [04:56:37]: testbed dpkg architecture: amd64 76s autopkgtest [04:56:37]: testbed apt version: 3.1.14 76s autopkgtest [04:56:37]: @@@@@@@@@@@@@@@@@@@@ test bed setup 76s autopkgtest [04:56:37]: testbed release detected to be: None 77s autopkgtest [04:56:38]: updating testbed package index (apt update) 77s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 77s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 77s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 77s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 77s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [181 kB] 77s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [1735 kB] 78s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [31.1 kB] 78s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 Packages [268 kB] 78s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main i386 Packages [220 kB] 78s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 c-n-f Metadata [5980 B] 78s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/restricted amd64 c-n-f Metadata [120 B] 78s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 Packages [1791 kB] 78s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/universe i386 Packages [768 kB] 78s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 c-n-f Metadata [32.6 kB] 78s Get:15 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse i386 Packages [5020 B] 78s Get:16 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 Packages [26.4 kB] 78s Get:17 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 c-n-f Metadata [996 B] 79s Fetched 5189 kB in 1s (3913 kB/s) 80s Reading package lists... 80s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 81s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 81s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 81s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 81s Reading package lists... 81s Reading package lists... 82s Building dependency tree... 82s Reading state information... 82s Calculating upgrade... 82s The following package was automatically installed and is no longer required: 82s libpython3.13 82s Use 'sudo apt autoremove' to remove it. 82s The following NEW packages will be installed: 82s gcc-16-base libpython3.14 libpython3.14-minimal libpython3.14-stdlib 82s linux-headers-6.19.0-3 linux-headers-6.19.0-3-generic 82s linux-image-6.19.0-3-generic linux-modules-6.19.0-3-generic 82s linux-tools-6.19.0-3 linux-tools-6.19.0-3-generic 82s The following packages will be upgraded: 82s 3cpio amd64-microcode apt bpftool busybox-initramfs busybox-static 82s cryptsetup-bin dash dbus dbus-bin dbus-daemon dbus-session-bus-common 82s dbus-system-bus-common dbus-user-session debianutils dmsetup dracut-install 82s ethtool findutils gir1.2-girepository-3.0 gir1.2-glib-2.0 hwdata iproute2 82s iptables less libapt-pkg7.0 libatomic1 libattr1 libbpf1 libbsd0 82s libcryptsetup12 libdbus-1-3 libdevmapper1.02.1 libdrm-amdgpu1 libdrm-common 82s libdrm2 libevent-core-2.1-7t64 libgcc-s1 libgdbm-compat4t64 libgdbm6t64 82s libgirepository-2.0-0 libglib2.0-0t64 libglib2.0-data libgpm2 libgudev-1.0-0 82s libidn2-0 libip4tc2 libip6tc2 libjansson4 libkeyutils1 liblsof0 82s libmaxminddb0 libnetfilter-conntrack3 libnpth0t64 libonig5 libpcap0.8t64 82s libpci3 libsensors-config libsensors5 libstdc++6 libusb-1.0-0 libwrap0 82s libxau6 libxkbcommon0 libxtables12 linux-generic linux-headers-generic 82s linux-headers-virtual linux-image-generic linux-image-virtual linux-perf 82s linux-tools-common linux-virtual lsof man-db mawk patch pciutils pnp.ids 82s pollinate python3-linkify-it python3-markdown-it python3-referencing sed 82s shared-mime-info tar tcpdump ubuntu-kernel-accessories ubuntu-standard wget 82s 90 upgraded, 10 newly installed, 0 to remove and 0 not upgraded. 82s Need to get 237 MB of archives. 82s After this operation, 339 MB of additional disk space will be used. 82s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 debianutils amd64 5.23.2build1 [93.3 kB] 82s Get:2 http://ftpmaster.internal/ubuntu resolute/main amd64 dash amd64 0.5.12-12ubuntu3 [96.0 kB] 82s Get:3 http://ftpmaster.internal/ubuntu resolute/main amd64 findutils amd64 4.10.0-3build2 [307 kB] 82s Get:4 http://ftpmaster.internal/ubuntu resolute/main amd64 sed amd64 4.9-2build3 [195 kB] 82s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 tar amd64 1.35+dfsg-3.1build2 [257 kB] 82s Get:6 http://ftpmaster.internal/ubuntu resolute/main amd64 libattr1 amd64 1:2.5.2-3build2 [11.4 kB] 82s Get:7 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc-16-base amd64 16-20260208-1ubuntu1 [59.7 kB] 82s Get:8 http://ftpmaster.internal/ubuntu resolute/main amd64 libgcc-s1 amd64 16-20260208-1ubuntu1 [80.3 kB] 82s Get:9 http://ftpmaster.internal/ubuntu resolute/main amd64 libbsd0 amd64 0.12.2-2build2 [42.3 kB] 82s Get:10 http://ftpmaster.internal/ubuntu resolute/main amd64 mawk amd64 1.3.4.20260129-1 [133 kB] 82s Get:11 http://ftpmaster.internal/ubuntu resolute/main amd64 libstdc++6 amd64 16-20260208-1ubuntu1 [844 kB] 83s Get:12 http://ftpmaster.internal/ubuntu resolute/main amd64 libapt-pkg7.0 amd64 3.1.15 [1151 kB] 83s Get:13 http://ftpmaster.internal/ubuntu resolute/main amd64 apt amd64 3.1.15 [1479 kB] 83s Get:14 http://ftpmaster.internal/ubuntu resolute/main amd64 dbus-system-bus-common all 1.16.2-2ubuntu3 [55.8 kB] 83s Get:15 http://ftpmaster.internal/ubuntu resolute/main amd64 dbus-session-bus-common all 1.16.2-2ubuntu3 [54.4 kB] 83s Get:16 http://ftpmaster.internal/ubuntu resolute/main amd64 dbus-user-session amd64 1.16.2-2ubuntu3 [9696 B] 83s Get:17 http://ftpmaster.internal/ubuntu resolute/main amd64 dbus-daemon amd64 1.16.2-2ubuntu3 [119 kB] 83s Get:18 http://ftpmaster.internal/ubuntu resolute/main amd64 dbus-bin amd64 1.16.2-2ubuntu3 [40.1 kB] 83s Get:19 http://ftpmaster.internal/ubuntu resolute/main amd64 dbus amd64 1.16.2-2ubuntu3 [24.2 kB] 83s Get:20 http://ftpmaster.internal/ubuntu resolute/main amd64 libdbus-1-3 amd64 1.16.2-2ubuntu3 [185 kB] 83s Get:21 http://ftpmaster.internal/ubuntu resolute/main amd64 libdevmapper1.02.1 amd64 2:1.02.205-2ubuntu3 [142 kB] 83s Get:22 http://ftpmaster.internal/ubuntu resolute/main amd64 dmsetup amd64 2:1.02.205-2ubuntu3 [79.4 kB] 83s Get:23 http://ftpmaster.internal/ubuntu resolute/main amd64 ethtool amd64 1:6.15-3build1 [318 kB] 83s Get:24 http://ftpmaster.internal/ubuntu resolute/main amd64 gir1.2-girepository-3.0 amd64 2.87.2-2 [25.2 kB] 83s Get:25 http://ftpmaster.internal/ubuntu resolute/main amd64 libgirepository-2.0-0 amd64 2.87.2-2 [76.1 kB] 83s Get:26 http://ftpmaster.internal/ubuntu resolute/main amd64 libatomic1 amd64 16-20260208-1ubuntu1 [11.4 kB] 83s Get:27 http://ftpmaster.internal/ubuntu resolute/main amd64 gir1.2-glib-2.0 amd64 2.87.2-2 [182 kB] 83s Get:28 http://ftpmaster.internal/ubuntu resolute/main amd64 libglib2.0-0t64 amd64 2.87.2-2 [1613 kB] 83s Get:29 http://ftpmaster.internal/ubuntu resolute/main amd64 libbpf1 amd64 1:1.6.2-1build1 [184 kB] 83s Get:30 http://ftpmaster.internal/ubuntu resolute/main amd64 iptables amd64 1.8.11-2ubuntu3 [381 kB] 83s Get:31 http://ftpmaster.internal/ubuntu resolute/main amd64 libip4tc2 amd64 1.8.11-2ubuntu3 [24.2 kB] 83s Get:32 http://ftpmaster.internal/ubuntu resolute/main amd64 libip6tc2 amd64 1.8.11-2ubuntu3 [24.4 kB] 83s Get:33 http://ftpmaster.internal/ubuntu resolute/main amd64 libnetfilter-conntrack3 amd64 1.1.1-1 [47.5 kB] 83s Get:34 http://ftpmaster.internal/ubuntu resolute/main amd64 libxtables12 amd64 1.8.11-2ubuntu3 [36.6 kB] 83s Get:35 http://ftpmaster.internal/ubuntu resolute/main amd64 iproute2 amd64 6.18.0-1ubuntu1 [1178 kB] 83s Get:36 http://ftpmaster.internal/ubuntu resolute/main amd64 less amd64 668-1build1 [172 kB] 83s Get:37 http://ftpmaster.internal/ubuntu resolute/main amd64 libcryptsetup12 amd64 2:2.8.0-1ubuntu3 [283 kB] 83s Get:38 http://ftpmaster.internal/ubuntu resolute/main amd64 libglib2.0-data all 2.87.2-2 [58.2 kB] 83s Get:39 http://ftpmaster.internal/ubuntu resolute/main amd64 libidn2-0 amd64 2.3.8-4build1 [67.6 kB] 83s Get:40 http://ftpmaster.internal/ubuntu resolute/main amd64 libkeyutils1 amd64 1.6.3-6ubuntu3 [10.6 kB] 83s Get:41 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-linkify-it all 2.0.3-1ubuntu3 [19.4 kB] 83s Get:42 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-markdown-it all 3.0.0-3build1 [54.4 kB] 83s Get:43 http://ftpmaster.internal/ubuntu resolute/main amd64 shared-mime-info amd64 2.4-5build3 [476 kB] 83s Get:44 http://ftpmaster.internal/ubuntu resolute/main amd64 busybox-static amd64 1:1.37.0-7ubuntu1 [1034 kB] 83s Get:45 http://ftpmaster.internal/ubuntu resolute/main amd64 libdrm-common all 2.4.131-1 [9774 B] 83s Get:46 http://ftpmaster.internal/ubuntu resolute/main amd64 libdrm2 amd64 2.4.131-1 [42.3 kB] 83s Get:47 http://ftpmaster.internal/ubuntu resolute/main amd64 libgdbm6t64 amd64 1.26-1build1 [36.5 kB] 83s Get:48 http://ftpmaster.internal/ubuntu resolute/main amd64 libgpm2 amd64 1.20.7-12build1 [14.4 kB] 83s Get:49 http://ftpmaster.internal/ubuntu resolute/main amd64 libjansson4 amd64 2.14-2build4 [33.2 kB] 83s Get:50 http://ftpmaster.internal/ubuntu resolute/main amd64 lsof amd64 4.99.4+dfsg-2build2 [239 kB] 83s Get:51 http://ftpmaster.internal/ubuntu resolute/main amd64 liblsof0 amd64 4.99.4+dfsg-2build2 [56.5 kB] 83s Get:52 http://ftpmaster.internal/ubuntu resolute/main amd64 libmaxminddb0 amd64 1.12.2-1build2 [18.9 kB] 83s Get:53 http://ftpmaster.internal/ubuntu resolute/main amd64 libpcap0.8t64 amd64 1.10.5-2ubuntu3 [154 kB] 83s Get:54 http://ftpmaster.internal/ubuntu resolute/main amd64 pciutils amd64 1:3.14.0-1build2 [95.5 kB] 83s Get:55 http://ftpmaster.internal/ubuntu resolute/main amd64 libpci3 amd64 1:3.14.0-1build2 [38.1 kB] 83s Get:56 http://ftpmaster.internal/ubuntu resolute/main amd64 libsensors-config all 1:3.6.2-2build1 [6862 B] 83s Get:57 http://ftpmaster.internal/ubuntu resolute/main amd64 libsensors5 amd64 1:3.6.2-2build1 [28.9 kB] 83s Get:58 http://ftpmaster.internal/ubuntu resolute/main amd64 libusb-1.0-0 amd64 2:1.0.29-2build1 [56.9 kB] 83s Get:59 http://ftpmaster.internal/ubuntu resolute/main amd64 libxau6 amd64 1:1.0.11-1build2 [7502 B] 83s Get:60 http://ftpmaster.internal/ubuntu resolute/main amd64 libxkbcommon0 amd64 1.13.1-1 [159 kB] 83s Get:61 http://ftpmaster.internal/ubuntu resolute/main amd64 man-db amd64 2.13.1-1build1 [1392 kB] 83s Get:62 http://ftpmaster.internal/ubuntu resolute/main amd64 tcpdump amd64 4.99.5-2ubuntu3 [477 kB] 83s Get:63 http://ftpmaster.internal/ubuntu resolute/main amd64 wget amd64 1.25.0-2ubuntu4 [353 kB] 83s Get:64 http://ftpmaster.internal/ubuntu resolute/main amd64 ubuntu-standard amd64 1.564 [13.3 kB] 83s Get:65 http://ftpmaster.internal/ubuntu resolute/main amd64 3cpio amd64 0.14.0-1ubuntu1 [285 kB] 83s Get:66 http://ftpmaster.internal/ubuntu resolute/main amd64 bpftool amd64 7.7.0+6.19.0-3.3 [1229 kB] 83s Get:67 http://ftpmaster.internal/ubuntu resolute/main amd64 busybox-initramfs amd64 1:1.37.0-7ubuntu1 [191 kB] 83s Get:68 http://ftpmaster.internal/ubuntu resolute/main amd64 cryptsetup-bin amd64 2:2.8.0-1ubuntu3 [228 kB] 83s Get:69 http://ftpmaster.internal/ubuntu resolute/main amd64 dracut-install amd64 109-11ubuntu1 [45.8 kB] 83s Get:70 http://ftpmaster.internal/ubuntu resolute/main amd64 hwdata all 0.394-1build1 [1566 B] 83s Get:71 http://ftpmaster.internal/ubuntu resolute/main amd64 pnp.ids all 0.394-1build1 [29.6 kB] 83s Get:72 http://ftpmaster.internal/ubuntu resolute/main amd64 libdrm-amdgpu1 amd64 2.4.131-1 [23.2 kB] 83s Get:73 http://ftpmaster.internal/ubuntu resolute/main amd64 libevent-core-2.1-7t64 amd64 2.1.12-stable-10build2 [93.1 kB] 83s Get:74 http://ftpmaster.internal/ubuntu resolute/main amd64 libgdbm-compat4t64 amd64 1.26-1build1 [6796 B] 83s Get:75 http://ftpmaster.internal/ubuntu resolute/main amd64 libgudev-1.0-0 amd64 1:238-7build1 [15.9 kB] 83s Get:76 http://ftpmaster.internal/ubuntu resolute/main amd64 libnpth0t64 amd64 1.8-3build1 [9302 B] 83s Get:77 http://ftpmaster.internal/ubuntu resolute/main amd64 libonig5 amd64 6.9.10-1build1 [174 kB] 83s Get:78 http://ftpmaster.internal/ubuntu resolute/main amd64 libpython3.14-minimal amd64 3.14.2-1 [920 kB] 83s Get:79 http://ftpmaster.internal/ubuntu resolute/main amd64 libpython3.14-stdlib amd64 3.14.2-1 [2398 kB] 83s Get:80 http://ftpmaster.internal/ubuntu resolute/main amd64 libpython3.14 amd64 3.14.2-1 [2568 kB] 83s Get:81 http://ftpmaster.internal/ubuntu resolute/main amd64 libwrap0 amd64 7.6.q-36build2 [48.5 kB] 83s Get:82 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-modules-6.19.0-3-generic amd64 6.19.0-3.3 [171 MB] 86s Get:83 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-image-6.19.0-3-generic amd64 6.19.0-3.3+1 [16.8 MB] 86s Get:84 http://ftpmaster.internal/ubuntu resolute/main amd64 amd64-microcode amd64 3.20251202.1ubuntu1 [459 kB] 86s Get:85 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-generic amd64 6.19.0-3.3 [1698 B] 86s Get:86 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-image-generic amd64 6.19.0-3.3 [12.2 kB] 86s Get:87 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-virtual amd64 6.19.0-3.3 [1700 B] 86s Get:88 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-image-virtual amd64 6.19.0-3.3 [12.1 kB] 86s Get:89 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-headers-virtual amd64 6.19.0-3.3 [1646 B] 86s Get:90 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-headers-6.19.0-3 all 6.19.0-3.3 [14.9 MB] 86s Get:91 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-headers-6.19.0-3-generic amd64 6.19.0-3.3 [4330 kB] 86s Get:92 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-headers-generic amd64 6.19.0-3.3 [12.0 kB] 86s Get:93 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-perf amd64 6.19.0-3.3 [4480 kB] 86s Get:94 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-tools-common all 6.19.0-3.3 [345 kB] 86s Get:95 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-tools-6.19.0-3 amd64 6.19.0-3.3 [1455 kB] 86s Get:96 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-tools-6.19.0-3-generic amd64 6.19.0-3.3 [1612 B] 86s Get:97 http://ftpmaster.internal/ubuntu resolute/main amd64 patch amd64 2.8-2build1 [95.7 kB] 86s Get:98 http://ftpmaster.internal/ubuntu resolute/main amd64 pollinate all 4.33-4ubuntu5 [14.0 kB] 86s Get:99 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-referencing all 0.36.2-1ubuntu2 [22.2 kB] 86s Get:100 http://ftpmaster.internal/ubuntu resolute/main amd64 ubuntu-kernel-accessories amd64 1.564 [13.1 kB] 87s dpkg-preconfigure: unable to re-open stdin: No such file or directory 87s Fetched 237 MB in 4s (56.1 MB/s) 87s (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 ... 83957 files and directories currently installed.) 87s Preparing to unpack .../debianutils_5.23.2build1_amd64.deb ... 87s Unpacking debianutils (5.23.2build1) over (5.23.2) ... 87s Setting up debianutils (5.23.2build1) ... 87s (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 ... 83957 files and directories currently installed.) 87s Preparing to unpack .../dash_0.5.12-12ubuntu3_amd64.deb ... 87s Unpacking dash (0.5.12-12ubuntu3) over (0.5.12-12ubuntu2) ... 87s Setting up dash (0.5.12-12ubuntu3) ... 87s (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 ... 83957 files and directories currently installed.) 87s Preparing to unpack .../findutils_4.10.0-3build2_amd64.deb ... 87s Unpacking findutils (4.10.0-3build2) over (4.10.0-3build1) ... 87s Setting up findutils (4.10.0-3build2) ... 87s (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 ... 83957 files and directories currently installed.) 87s Preparing to unpack .../sed_4.9-2build3_amd64.deb ... 87s Unpacking sed (4.9-2build3) over (4.9-2build2) ... 87s Setting up sed (4.9-2build3) ... 87s (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 ... 83957 files and directories currently installed.) 87s Preparing to unpack .../tar_1.35+dfsg-3.1build2_amd64.deb ... 87s Unpacking tar (1.35+dfsg-3.1build2) over (1.35+dfsg-3.1build1) ... 87s Setting up tar (1.35+dfsg-3.1build2) ... 87s (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 ... 83957 files and directories currently installed.) 87s Preparing to unpack .../libattr1_1%3a2.5.2-3build2_amd64.deb ... 87s Unpacking libattr1:amd64 (1:2.5.2-3build2) over (1:2.5.2-3build1) ... 87s Setting up libattr1:amd64 (1:2.5.2-3build2) ... 87s Selecting previously unselected package gcc-16-base:amd64. 88s (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 ... 83957 files and directories currently installed.) 88s Preparing to unpack .../gcc-16-base_16-20260208-1ubuntu1_amd64.deb ... 88s Unpacking gcc-16-base:amd64 (16-20260208-1ubuntu1) ... 88s Setting up gcc-16-base:amd64 (16-20260208-1ubuntu1) ... 88s (Reading database ... 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(7.7.0+6.19.0-3.3) ... 95s Setting up libip6tc2:amd64 (1.8.11-2ubuntu3) ... 95s Setting up liblsof0 (4.99.4+dfsg-2build2) ... 95s Setting up libmaxminddb0:amd64 (1.12.2-1build2) ... 95s Setting up libpython3.14-minimal:amd64 (3.14.2-1) ... 95s Setting up libsensors-config (1:3.6.2-2build1) ... 95s Setting up less (668-1build1) ... 95s Setting up linux-headers-6.19.0-3 (6.19.0-3.3) ... 95s Setting up libidn2-0:amd64 (2.3.8-4build1) ... 95s Setting up amd64-microcode (3.20251202.1ubuntu1) ... 95s amd64-microcode: microcode will be updated at next boot 95s Setting up man-db (2.13.1-1build1) ... 96s Updating database of manual pages ... 97s man-db.service is a disabled or a static unit not running, not starting it. 97s Setting up libjansson4:amd64 (2.14-2build4) ... 97s Setting up libglib2.0-data (2.87.2-2) ... 97s Setting up pollinate (4.33-4ubuntu5) ... 107s Setting up busybox-static (1:1.37.0-7ubuntu1) ... 107s Setting up libwrap0:amd64 (7.6.q-36build2) ... 107s Setting up linux-image-6.19.0-3-generic (6.19.0-3.3+1) ... 109s I: /boot/vmlinuz is now a symlink to vmlinuz-6.19.0-3-generic 109s I: /boot/initrd.img is now a symlink to initrd.img-6.19.0-3-generic 109s Setting up libdbus-1-3:amd64 (1.16.2-2ubuntu3) ... 109s Setting up libatomic1:amd64 (16-20260208-1ubuntu1) ... 109s Setting up patch (2.8-2build1) ... 109s Setting up libsensors5:amd64 (1:3.6.2-2build1) ... 109s Setting up busybox-initramfs (1:1.37.0-7ubuntu1) ... 109s Setting up libxtables12:amd64 (1.8.11-2ubuntu3) ... 109s Setting up lsof (4.99.4+dfsg-2build2) ... 109s Setting up libpci3:amd64 (1:3.14.0-1build2) ... 109s Setting up libdevmapper1.02.1:amd64 (2:1.02.205-2ubuntu3) ... 109s Setting up dracut-install (109-11ubuntu1) ... 109s Setting up dmsetup (2:1.02.205-2ubuntu3) ... 109s Setting up libnetfilter-conntrack3:amd64 (1.1.1-1) ... 109s Setting up pnp.ids (0.394-1build1) ... 109s Setting up dbus-session-bus-common (1.16.2-2ubuntu3) ... 109s Setting up python3-linkify-it (2.0.3-1ubuntu3) ... 109s Setting up libpcap0.8t64:amd64 (1.10.5-2ubuntu3) ... 109s Setting up libcryptsetup12:amd64 (2:2.8.0-1ubuntu3) ... 109s Setting up mawk (1.3.4.20260129-1) ... 109s Setting up libevent-core-2.1-7t64:amd64 (2.1.12-stable-10build2) ... 109s Setting up libusb-1.0-0:amd64 (2:1.0.29-2build1) ... 109s Setting up linux-image-virtual (6.19.0-3.3) ... 109s Setting up dbus-system-bus-common (1.16.2-2ubuntu3) ... 109s Setting up libbsd0:amd64 (0.12.2-2build2) ... 109s Setting up libdrm-common (2.4.131-1) ... 109s Setting up libstdc++6:amd64 (16-20260208-1ubuntu1) ... 109s Setting up dbus-bin (1.16.2-2ubuntu3) ... 109s Setting up libonig5:amd64 (6.9.10-1build1) ... 109s Setting up libbpf1:amd64 (1:1.6.2-1build1) ... 109s Setting up ethtool (1:6.15-3build1) ... 109s Setting up python3-referencing (0.36.2-1ubuntu2) ... 109s Setting up libxkbcommon0:amd64 (1.13.1-1) ... 109s Setting up cryptsetup-bin (2:2.8.0-1ubuntu3) ... 109s Setting up linux-headers-6.19.0-3-generic (6.19.0-3.3) ... 109s Setting up tcpdump (4.99.5-2ubuntu3) ... 109s Setting up linux-image-generic (6.19.0-3.3) ... 109s Setting up wget (1.25.0-2ubuntu4) ... 109s Setting up libpython3.14-stdlib:amd64 (3.14.2-1) ... 109s Setting up iptables (1.8.11-2ubuntu3) ... 109s Setting up iproute2 (6.18.0-1ubuntu1) ... 109s Setting up linux-headers-generic (6.19.0-3.3) ... 109s Setting up dbus-daemon (1.16.2-2ubuntu3) ... 109s Setting up hwdata (0.394-1build1) ... 109s Setting up dbus-user-session (1.16.2-2ubuntu3) ... 109s Setting up libglib2.0-0t64:amd64 (2.87.2-2) ... 109s No schema files found: doing nothing. 109s Setting up dbus (1.16.2-2ubuntu3) ... 109s A reboot is required to replace the running dbus-daemon. 109s Please reboot the system when convenient. 110s Setting up shared-mime-info (2.4-5build3) ... 110s Setting up gir1.2-glib-2.0:amd64 (2.87.2-2) ... 110s Setting up pciutils (1:3.14.0-1build2) ... 110s Setting up python3-markdown-it (3.0.0-3build1) ... 111s Setting up libdrm2:amd64 (2.4.131-1) ... 111s Setting up libpython3.14:amd64 (3.14.2-1) ... 111s Setting up libapt-pkg7.0:amd64 (3.1.15) ... 111s Setting up linux-tools-common (6.19.0-3.3) ... 111s Setting up libgudev-1.0-0:amd64 (1:238-7build1) ... 111s Setting up libdrm-amdgpu1:amd64 (2.4.131-1) ... 111s Setting up apt (3.1.15) ... 111s Setting up linux-headers-virtual (6.19.0-3.3) ... 111s Setting up linux-generic (6.19.0-3.3) ... 111s Setting up libgirepository-2.0-0:amd64 (2.87.2-2) ... 111s Setting up linux-tools-6.19.0-3 (6.19.0-3.3) ... 111s Setting up ubuntu-standard (1.564) ... 111s Setting up gir1.2-girepository-3.0:amd64 (2.87.2-2) ... 111s Setting up linux-virtual (6.19.0-3.3) ... 111s Setting up linux-perf (6.19.0-3.3) ... 111s Setting up linux-tools-6.19.0-3-generic (6.19.0-3.3) ... 111s Processing triggers for debianutils (5.23.2build1) ... 111s Processing triggers for install-info (7.2-5) ... 111s Processing triggers for initramfs-tools (0.150ubuntu7) ... 111s update-initramfs: Generating /boot/initrd.img-6.18.0-9-generic 116s Processing triggers for libc-bin (2.42-2ubuntu4) ... 116s Processing triggers for linux-image-6.19.0-3-generic (6.19.0-3.3+1) ... 116s /etc/kernel/postinst.d/initramfs-tools: 116s update-initramfs: Generating /boot/initrd.img-6.19.0-3-generic 119s /etc/kernel/postinst.d/zz-update-grub: 119s Sourcing file `/etc/default/grub' 119s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 119s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg' 119s Generating grub configuration file ... 120s Found linux image: /boot/vmlinuz-6.19.0-3-generic 120s Found initrd image: /boot/initrd.img-6.19.0-3-generic 120s Found linux image: /boot/vmlinuz-6.18.0-9-generic 120s Found initrd image: /boot/initrd.img-6.18.0-9-generic 120s Warning: os-prober will not be executed to detect other bootable partitions. 120s Systems on them will not be added to the GRUB boot configuration. 120s Check GRUB_DISABLE_OS_PROBER documentation entry. 120s Adding boot menu entry for UEFI Firmware Settings ... 120s done 120s autopkgtest [04:57:21]: upgrading testbed (apt dist-upgrade and autopurge) 121s Reading package lists... 121s Building dependency tree... 121s Reading state information... 121s Calculating upgrade... 121s The following package was automatically installed and is no longer required: 121s libpython3.13 121s Use 'sudo apt autoremove' to remove it. 121s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 121s Reading package lists... 121s Building dependency tree... 121s Reading state information... 121s Solving dependencies... 121s The following packages will be REMOVED: 121s libpython3.13* 122s 0 upgraded, 0 newly installed, 1 to remove and 0 not upgraded. 122s After this operation, 7599 kB disk space will be freed. 122s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 125273 files and directories currently installed.) 122s Removing libpython3.13:amd64 (3.13.11-1) ... 122s Processing triggers for libc-bin (2.42-2ubuntu4) ... 122s autopkgtest [04:57:23]: rebooting testbed after setup commands that affected boot 151s autopkgtest [04:57:52]: testbed running kernel: Linux 6.19.0-3-generic #3-Ubuntu SMP PREEMPT_DYNAMIC Fri Jan 23 20:01:24 UTC 2026 153s autopkgtest [04:57:54]: @@@@@@@@@@@@@@@@@@@@ apt-source r-cran-etm 154s Get:1 http://ftpmaster.internal/ubuntu resolute/universe r-cran-etm 1.1.1-1build1 (dsc) [2147 B] 154s Get:2 http://ftpmaster.internal/ubuntu resolute/universe r-cran-etm 1.1.1-1build1 (tar) [242 kB] 154s Get:3 http://ftpmaster.internal/ubuntu resolute/universe r-cran-etm 1.1.1-1build1 (diff) [3672 B] 154s gpgv: Signature made Fri Nov 28 21:46:53 2025 UTC 154s gpgv: using RSA key 92FE4F8B40CADC4ECCD60C1F5961FDBE9C619809 154s gpgv: Can't check signature: No public key 154s dpkg-source: warning: cannot verify inline signature for ./r-cran-etm_1.1.1-1build1.dsc: no acceptable signature found 154s autopkgtest [04:57:55]: testing package r-cran-etm version 1.1.1-1build1 154s autopkgtest [04:57:55]: build not needed 156s autopkgtest [04:57:57]: test run-unit-test: preparing testbed 156s Reading package lists... 156s Building dependency tree... 156s Reading state information... 156s Solving dependencies... 156s The following NEW packages will be installed: 156s fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono libblas3 156s libcairo2 libdatrie1 libdeflate0 libfontconfig1 libgfortran5 libgomp1 156s libgraphite2-3 libharfbuzz0b libice6 libjbig0 libjpeg-turbo8 libjpeg8 156s liblapack3 liblerc4 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 156s libpaper-utils libpaper2 libpixman-1-0 libsharpyuv0 libsm6 libtcl8.6 156s libthai-data libthai0 libtiff6 libtk8.6 libwebp7 libxcb-render0 libxcb-shm0 156s libxft2 libxrender1 libxss1 libxt6t64 r-base-core r-cran-data.table 156s r-cran-dbi r-cran-etm r-cran-kmi r-cran-lattice r-cran-littler r-cran-matrix 156s r-cran-mitools r-cran-pkgkitten r-cran-rcpp r-cran-rcpparmadillo 156s r-cran-survival unzip x11-common xdg-utils zip 157s 0 upgraded, 56 newly installed, 0 to remove and 0 not upgraded. 157s Need to get 61.0 MB of archives. 157s After this operation, 128 MB of additional disk space will be used. 157s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-dejavu-mono all 2.37-8build1 [502 kB] 157s Get:2 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-dejavu-core all 2.37-8build1 [834 kB] 157s Get:3 http://ftpmaster.internal/ubuntu resolute/main amd64 fontconfig-config amd64 2.17.1-3ubuntu1 [38.5 kB] 157s Get:4 http://ftpmaster.internal/ubuntu resolute/main amd64 libfontconfig1 amd64 2.17.1-3ubuntu1 [144 kB] 157s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 fontconfig amd64 2.17.1-3ubuntu1 [180 kB] 157s Get:6 http://ftpmaster.internal/ubuntu resolute/main amd64 libblas3 amd64 3.12.1-7ubuntu1 [260 kB] 157s Get:7 http://ftpmaster.internal/ubuntu resolute/main amd64 libpixman-1-0 amd64 0.46.4-1 [287 kB] 157s Get:8 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-render0 amd64 1.17.0-2ubuntu1 [16.2 kB] 157s Get:9 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-shm0 amd64 1.17.0-2ubuntu1 [5808 B] 157s Get:10 http://ftpmaster.internal/ubuntu resolute/main amd64 libxrender1 amd64 1:0.9.12-1 [19.8 kB] 157s Get:11 http://ftpmaster.internal/ubuntu resolute/main amd64 libcairo2 amd64 1.18.4-3 [579 kB] 157s Get:12 http://ftpmaster.internal/ubuntu resolute/main amd64 libdatrie1 amd64 0.2.14-1 [19.8 kB] 157s Get:13 http://ftpmaster.internal/ubuntu resolute/main amd64 libdeflate0 amd64 1.23-2build1 [51.6 kB] 157s Get:14 http://ftpmaster.internal/ubuntu resolute/main amd64 libgfortran5 amd64 16-20260208-1ubuntu1 [957 kB] 157s Get:15 http://ftpmaster.internal/ubuntu resolute/main amd64 libgomp1 amd64 16-20260208-1ubuntu1 [162 kB] 157s Get:16 http://ftpmaster.internal/ubuntu resolute/main amd64 libgraphite2-3 amd64 1.3.14-11ubuntu1 [73.7 kB] 157s Get:17 http://ftpmaster.internal/ubuntu resolute/main amd64 libharfbuzz0b amd64 12.3.2-1 [519 kB] 157s Get:18 http://ftpmaster.internal/ubuntu resolute/main amd64 x11-common all 1:7.7+24ubuntu1 [22.4 kB] 157s Get:19 http://ftpmaster.internal/ubuntu resolute/main amd64 libice6 amd64 2:1.1.1-1build1 [44.0 kB] 157s Get:20 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg-turbo8 amd64 2.1.5-4ubuntu3 [156 kB] 157s Get:21 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg8 amd64 8c-2ubuntu12 [2142 B] 157s Get:22 http://ftpmaster.internal/ubuntu resolute/main amd64 liblapack3 amd64 3.12.1-7ubuntu1 [2739 kB] 157s Get:23 http://ftpmaster.internal/ubuntu resolute/main amd64 liblerc4 amd64 4.0.0+ds-5ubuntu2 [207 kB] 157s Get:24 http://ftpmaster.internal/ubuntu resolute/main amd64 libthai-data all 0.1.30-1 [155 kB] 157s Get:25 http://ftpmaster.internal/ubuntu resolute/main amd64 libthai0 amd64 0.1.30-1 [19.2 kB] 157s Get:26 http://ftpmaster.internal/ubuntu resolute/main amd64 libpango-1.0-0 amd64 1.57.0-1 [241 kB] 157s Get:27 http://ftpmaster.internal/ubuntu resolute/main amd64 libpangoft2-1.0-0 amd64 1.57.0-1 [53.3 kB] 157s Get:28 http://ftpmaster.internal/ubuntu resolute/main amd64 libpangocairo-1.0-0 amd64 1.57.0-1 [29.0 kB] 157s Get:29 http://ftpmaster.internal/ubuntu resolute/main amd64 libpaper2 amd64 2.2.5-0.3build1 [17.3 kB] 157s Get:30 http://ftpmaster.internal/ubuntu resolute/main amd64 libpaper-utils amd64 2.2.5-0.3build1 [15.6 kB] 157s Get:31 http://ftpmaster.internal/ubuntu resolute/main amd64 libsharpyuv0 amd64 1.5.0-0.1build1 [17.6 kB] 157s Get:32 http://ftpmaster.internal/ubuntu resolute/main amd64 libsm6 amd64 2:1.2.6-1build1 [16.9 kB] 157s Get:33 http://ftpmaster.internal/ubuntu resolute/main amd64 libtcl8.6 amd64 8.6.17+dfsg-1build1 [1003 kB] 157s Get:34 http://ftpmaster.internal/ubuntu resolute/main amd64 libjbig0 amd64 2.1-6.1ubuntu3 [30.0 kB] 157s Get:35 http://ftpmaster.internal/ubuntu resolute/main amd64 libwebp7 amd64 1.5.0-0.1build1 [264 kB] 157s Get:36 http://ftpmaster.internal/ubuntu resolute/main amd64 libtiff6 amd64 4.7.0-3ubuntu3 [209 kB] 157s Get:37 http://ftpmaster.internal/ubuntu resolute/main amd64 libxft2 amd64 2.3.6-1build2 [45.1 kB] 157s Get:38 http://ftpmaster.internal/ubuntu resolute/main amd64 libxss1 amd64 1:1.2.3-1build4 [7084 B] 157s Get:39 http://ftpmaster.internal/ubuntu resolute/main amd64 libtk8.6 amd64 8.6.17-1 [823 kB] 157s Get:40 http://ftpmaster.internal/ubuntu resolute/main amd64 libxt6t64 amd64 1:1.2.1-1.3 [173 kB] 157s Get:41 http://ftpmaster.internal/ubuntu resolute/main amd64 zip amd64 3.0-15ubuntu3 [175 kB] 157s Get:42 http://ftpmaster.internal/ubuntu resolute/main amd64 unzip amd64 6.0-29ubuntu1 [180 kB] 157s Get:43 http://ftpmaster.internal/ubuntu resolute/main amd64 xdg-utils all 1.2.1-2ubuntu2 [66.1 kB] 157s Get:44 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-base-core amd64 4.5.2-1ubuntu2 [28.8 MB] 158s Get:45 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-data.table amd64 1.17.0+dfsg-1 [2168 kB] 158s Get:46 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-dbi all 1.2.3-1build1 [855 kB] 158s Get:47 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-lattice amd64 0.22-7-1 [1367 kB] 158s Get:48 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-matrix amd64 1.7-4-1 [4220 kB] 158s Get:49 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-survival amd64 3.8-6-1 [8274 kB] 159s Get:50 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-littler amd64 0.3.22-1 [85.5 kB] 159s Get:51 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-pkgkitten all 0.2.4-1 [27.2 kB] 159s Get:52 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rcpp amd64 1.1.0-1 [2021 kB] 159s Get:53 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rcpparmadillo amd64 15.2.3-1-1 [919 kB] 159s Get:54 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-etm amd64 1.1.1-1build1 [485 kB] 159s Get:55 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-mitools all 2.4-2build2 [266 kB] 159s Get:56 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-kmi all 0.5.5-2build2 [78.9 kB] 159s Preconfiguring packages ... 159s Fetched 61.0 MB in 2s (27.7 MB/s) 159s Selecting previously unselected package fonts-dejavu-mono. 159s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 125269 files and directories currently installed.) 159s Preparing to unpack .../00-fonts-dejavu-mono_2.37-8build1_all.deb ... 159s Unpacking fonts-dejavu-mono (2.37-8build1) ... 159s Selecting previously unselected package fonts-dejavu-core. 159s Preparing to unpack .../01-fonts-dejavu-core_2.37-8build1_all.deb ... 159s Unpacking fonts-dejavu-core (2.37-8build1) ... 159s Selecting previously unselected package fontconfig-config. 159s Preparing to unpack .../02-fontconfig-config_2.17.1-3ubuntu1_amd64.deb ... 159s Unpacking fontconfig-config (2.17.1-3ubuntu1) ... 159s Selecting previously unselected package libfontconfig1:amd64. 159s Preparing to unpack .../03-libfontconfig1_2.17.1-3ubuntu1_amd64.deb ... 159s Unpacking libfontconfig1:amd64 (2.17.1-3ubuntu1) ... 159s Selecting previously unselected package fontconfig. 159s Preparing to unpack .../04-fontconfig_2.17.1-3ubuntu1_amd64.deb ... 159s Unpacking fontconfig (2.17.1-3ubuntu1) ... 159s Selecting previously unselected package libblas3:amd64. 159s Preparing to unpack .../05-libblas3_3.12.1-7ubuntu1_amd64.deb ... 159s Unpacking libblas3:amd64 (3.12.1-7ubuntu1) ... 159s Selecting previously unselected package libpixman-1-0:amd64. 159s Preparing to unpack .../06-libpixman-1-0_0.46.4-1_amd64.deb ... 159s Unpacking libpixman-1-0:amd64 (0.46.4-1) ... 159s Selecting previously unselected package libxcb-render0:amd64. 159s Preparing to unpack .../07-libxcb-render0_1.17.0-2ubuntu1_amd64.deb ... 159s Unpacking libxcb-render0:amd64 (1.17.0-2ubuntu1) ... 159s Selecting previously unselected package libxcb-shm0:amd64. 159s Preparing to unpack .../08-libxcb-shm0_1.17.0-2ubuntu1_amd64.deb ... 159s Unpacking libxcb-shm0:amd64 (1.17.0-2ubuntu1) ... 159s Selecting previously unselected package libxrender1:amd64. 159s Preparing to unpack .../09-libxrender1_1%3a0.9.12-1_amd64.deb ... 159s Unpacking libxrender1:amd64 (1:0.9.12-1) ... 159s Selecting previously unselected package libcairo2:amd64. 159s Preparing to unpack .../10-libcairo2_1.18.4-3_amd64.deb ... 159s Unpacking libcairo2:amd64 (1.18.4-3) ... 159s Selecting previously unselected package libdatrie1:amd64. 159s Preparing to unpack .../11-libdatrie1_0.2.14-1_amd64.deb ... 159s Unpacking libdatrie1:amd64 (0.2.14-1) ... 159s Selecting previously unselected package libdeflate0:amd64. 159s Preparing to unpack .../12-libdeflate0_1.23-2build1_amd64.deb ... 159s Unpacking libdeflate0:amd64 (1.23-2build1) ... 159s Selecting previously unselected package libgfortran5:amd64. 159s Preparing to unpack .../13-libgfortran5_16-20260208-1ubuntu1_amd64.deb ... 159s Unpacking libgfortran5:amd64 (16-20260208-1ubuntu1) ... 159s Selecting previously unselected package libgomp1:amd64. 159s Preparing to unpack .../14-libgomp1_16-20260208-1ubuntu1_amd64.deb ... 159s Unpacking libgomp1:amd64 (16-20260208-1ubuntu1) ... 159s Selecting previously unselected package libgraphite2-3:amd64. 159s Preparing to unpack .../15-libgraphite2-3_1.3.14-11ubuntu1_amd64.deb ... 159s Unpacking libgraphite2-3:amd64 (1.3.14-11ubuntu1) ... 159s Selecting previously unselected package libharfbuzz0b:amd64. 159s Preparing to unpack .../16-libharfbuzz0b_12.3.2-1_amd64.deb ... 159s Unpacking libharfbuzz0b:amd64 (12.3.2-1) ... 159s Selecting previously unselected package x11-common. 159s Preparing to unpack .../17-x11-common_1%3a7.7+24ubuntu1_all.deb ... 159s Unpacking x11-common (1:7.7+24ubuntu1) ... 160s Selecting previously unselected package libice6:amd64. 160s Preparing to unpack .../18-libice6_2%3a1.1.1-1build1_amd64.deb ... 160s Unpacking libice6:amd64 (2:1.1.1-1build1) ... 160s Selecting previously unselected package libjpeg-turbo8:amd64. 160s Preparing to unpack .../19-libjpeg-turbo8_2.1.5-4ubuntu3_amd64.deb ... 160s Unpacking libjpeg-turbo8:amd64 (2.1.5-4ubuntu3) ... 160s Selecting previously unselected package libjpeg8:amd64. 160s Preparing to unpack .../20-libjpeg8_8c-2ubuntu12_amd64.deb ... 160s Unpacking libjpeg8:amd64 (8c-2ubuntu12) ... 160s Selecting previously unselected package liblapack3:amd64. 160s Preparing to unpack .../21-liblapack3_3.12.1-7ubuntu1_amd64.deb ... 160s Unpacking liblapack3:amd64 (3.12.1-7ubuntu1) ... 160s Selecting previously unselected package liblerc4:amd64. 160s Preparing to unpack .../22-liblerc4_4.0.0+ds-5ubuntu2_amd64.deb ... 160s Unpacking liblerc4:amd64 (4.0.0+ds-5ubuntu2) ... 160s Selecting previously unselected package libthai-data. 160s Preparing to unpack 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project with many contributors. 165s Type 'contributors()' for more information and 165s 'citation()' on how to cite R or R packages in publications. 165s 165s Type 'demo()' for some demos, 'help()' for on-line help, or 165s 'help.start()' for an HTML browser interface to help. 165s Type 'q()' to quit R. 165s 165s > ### test file for etmCIF. 165s > ### Really simple tests and comparison with etm 165s > 165s > old <- options(digits = 5) 165s > 165s > require(etm) 165s Loading required package: etm 166s > 166s > if (!require(survival, quietly = TRUE)) { 166s + print("The following tests require the 'survival' package") 166s + } else { 166s + 166s + data(abortion) 166s + 166s + from <- rep(0, nrow(abortion)) 166s + to <- abortion$cause 166s + entry <- abortion$entry 166s + exit <- abortion$exit 166s + id <- 1:nrow(abortion) 166s + data <- data.frame(id, from, to, entry, exit, group = abortion$group) 166s + 166s + ## Computation of the CIFs with etm 166s + tra <- matrix(FALSE, 4, 4) 166s + tra[1, 2:4] <- TRUE 166s + 166s + cif.control <- etm(data[data$group == 0, ], c("0", "1", "2", "3"), 166s + tra, NULL, 0) 166s + cif.exposed <- etm(data[data$group == 1, ], c("0", "1", "2", "3"), 166s + tra, NULL, 0) 166s + 166s + 166s + ## Computation of the CIFs with etmCIF 166s + netm <- etmCIF(Surv(entry, exit, cause != 0) ~ group, abortion, 166s + etype = cause, failcode = 3) 166s + 166s + ### let's do some comparisons :-) 166s + 166s + all.equal(trprob(cif.control, "0 3"), netm[[1]]$est["0", "3", ]) 166s + all.equal(trprob(cif.control, "0 2"), netm[[1]]$est["0", "2", ]) 166s + all.equal(trprob(cif.control, "0 1"), netm[[1]]$est["0", "1", ]) 166s + 166s + all.equal(trprob(cif.exposed, "0 3"), netm[[2]]$est["0", "3", ]) 166s + all.equal(trprob(cif.exposed, "0 2"), netm[[2]]$est["0", "2", ]) 166s + all.equal(trprob(cif.exposed, "0 1"), netm[[2]]$est["0", "1", ]) 166s + 166s + 166s + all.equal(trcov(cif.control, "0 3"), netm[[1]]$cov["0 3", "0 3", ]) 166s + all.equal(trcov(cif.control, "0 2"), netm[[1]]$cov["0 2", "0 2", ]) 166s + all.equal(trcov(cif.control, "0 1"), netm[[1]]$cov["0 1", "0 1", ]) 166s + 166s + all.equal(trcov(cif.exposed, "0 3"), netm[[2]]$cov["0 3", "0 3", ]) 166s + all.equal(trcov(cif.exposed, "0 2"), netm[[2]]$cov["0 2", "0 2", ]) 166s + all.equal(trcov(cif.exposed, "0 1"), netm[[2]]$cov["0 1", "0 1", ]) 166s + 166s + 166s + netm 166s + 166s + ## test on the summary 166s + snetm <- summary(netm) 166s + 166s + snetm 166s + 166s + all.equal(unname(trprob(cif.control, "0 3")), snetm[[1]][[3]]$P) 166s + all.equal(unname(trprob(cif.control, "0 2")), snetm[[1]][[2]]$P) 166s + all.equal(unname(trprob(cif.control, "0 1")), snetm[[1]][[1]]$P) 166s + 166s + all.equal(unname(trprob(cif.exposed, "0 3")), snetm[[2]][[3]]$P) 166s + all.equal(unname(trprob(cif.exposed, "0 2")), snetm[[2]][[2]]$P) 166s + all.equal(unname(trprob(cif.exposed, "0 1")), snetm[[2]][[1]]$P) 166s + 166s + scif.control <- summary(cif.control, ci.fun = "cloglog") 166s + scif.exposed <- summary(cif.exposed, ci.fun = "cloglog") 166s + 166s + all.equal(scif.control[[4]]$lower, snetm[[1]][[3]]$lower) 166s + all.equal(scif.control[[4]]$upper, snetm[[1]][[3]]$upper) 166s + 166s + all.equal(scif.exposed[[4]]$lower, snetm[[2]][[3]]$lower) 166s + all.equal(scif.exposed[[4]]$upper, snetm[[2]][[3]]$upper) 166s + } 166s [1] TRUE 166s > 166s > ### test with factors in the input 166s > abortion$status <- with(abortion, ifelse(cause == 2, "life birth", 166s + ifelse(cause == 1, "ETOP", "spontaneous abortion"))) 166s > 166s > abortion$status <- factor(abortion$status) 166s > 166s > netm.factor <- etmCIF(Surv(entry, exit, status != "cens") ~ group, abortion, 166s + etype = status, failcode = "spontaneous abortion") 166s > 166s > 166s > all.equal(trprob(cif.control, "0 3"), netm.factor[[1]]$est["0", "spontaneous abortion", ]) 166s [1] TRUE 166s > all.equal(trprob(cif.control, "0 2"), netm.factor[[1]]$est["0", "life birth", ]) 166s [1] TRUE 166s > 166s > netm.factor 166s Call: etmCIF(formula = Surv(entry, exit, status != "cens") ~ group, 166s data = abortion, etype = status, failcode = "spontaneous abortion") 166s 166s Covariate: group 166s levels: 0 1 166s 166s 166s group = 0 166s time P se(P) n.event 166s CIF ETOP 43 0.040159 0.0092578 20 166s CIF life birth 43 0.799059 0.0221865 924 166s CIF spontaneous abortion 43 0.160781 0.0213261 69 166s 166s group = 1 166s time P se(P) n.event 166s CIF ETOP 42 0.28511 0.042493 38 166s CIF life birth 42 0.35257 0.042139 92 166s CIF spontaneous abortion 42 0.36232 0.049473 43 166s > 166s > summary(netm.factor) 166s 166s group=0 166s 166s CIF ETOP 166s P time var lower upper n.risk n.event 166s 0.000000 6 0.0000e+00 0.000000 0.000000 117 0 166s 0.038955 13 8.4440e-05 0.024488 0.061694 645 1 166s 0.040159 26 8.5707e-05 0.025513 0.062939 846 0 166s 0.040159 36 8.5707e-05 0.025513 0.062939 876 0 166s 0.040159 40 8.5707e-05 0.025513 0.062939 554 0 166s 0.040159 43 8.5707e-05 0.025513 0.062939 6 0 166s 166s CIF life birth 166s P time var lower upper n.risk n.event 166s 0.000000 6 0.0000e+00 0.000000 0.000000 117 0 166s 0.000000 13 0.0000e+00 0.000000 0.000000 645 0 166s 0.000000 26 0.0000e+00 0.000000 0.000000 846 0 166s 0.053197 36 4.6195e-05 0.041379 0.068268 876 25 166s 0.563121 40 3.8801e-04 0.524924 0.602021 554 280 166s 0.799059 43 4.9224e-04 0.753969 0.840613 6 6 166s 166s CIF spontaneous abortion 166s P time var lower upper n.risk n.event 166s 0.034188 6 0.00028222 0.01297 0.088523 117 4 166s 0.150468 13 0.00045513 0.11360 0.197901 645 1 166s 0.159904 26 0.00045498 0.12274 0.206925 846 1 166s 0.160781 36 0.00045480 0.12360 0.207757 876 1 166s 0.160781 40 0.00045480 0.12360 0.207757 554 0 166s 0.160781 43 0.00045480 0.12360 0.207757 6 0 166s 166s 166s group=1 166s 166s CIF ETOP 166s P time var lower upper n.risk n.event 166s 0.00000 6 0.0000000 0.00000 0.00000 35 0 166s 0.26048 13 0.0017854 0.18795 0.35425 90 0 166s 0.28115 21 0.0018028 0.20742 0.37423 93 1 166s 0.28511 34 0.0018057 0.21116 0.37806 89 0 166s 0.28511 39 0.0018057 0.21116 0.37806 59 0 166s 0.28511 42 0.0018057 0.21116 0.37806 6 0 166s 166s CIF life birth 166s P time var lower upper n.risk n.event 166s 0.000000 6 0.0000e+00 0.000000 0.000000 35 0 166s 0.000000 13 0.0000e+00 0.000000 0.000000 90 0 166s 0.000000 21 0.0000e+00 0.000000 0.000000 93 0 166s 0.023073 34 9.0514e-05 0.010252 0.051504 89 2 166s 0.180156 39 8.0126e-04 0.131765 0.243663 59 13 166s 0.352565 42 1.7757e-03 0.276882 0.441775 6 6 166s 166s CIF spontaneous abortion 166s P time var lower upper n.risk n.event 166s 0.057143 6 0.0015394 0.014605 0.20968 35 2 166s 0.333246 13 0.0025280 0.245337 0.44216 90 4 166s 0.350702 21 0.0024827 0.262769 0.45762 93 0 166s 0.358492 34 0.0024593 0.270627 0.46448 89 0 166s 0.358492 39 0.0024593 0.270627 0.46448 59 0 166s 0.362323 42 0.0024476 0.274499 0.46785 6 0 166s 166s > 166s > ### test with group as a character vector 166s > abortion$ttt <- with(abortion, ifelse(group == 0, "control", "exposed")) 166s > abortion$ttt <- factor(abortion$ttt) 166s > 166s > netm.ttt <- etmCIF(Surv(entry, exit, status != "cens") ~ ttt, abortion, 166s + etype = status, failcode = "spontaneous abortion") 166s > 166s > all.equal(trprob(cif.control, "0 3"), netm.ttt[[1]]$est["0", "spontaneous abortion", ]) 166s [1] TRUE 166s > all.equal(trprob(cif.control, "0 2"), netm.ttt[[1]]$est["0", "life birth", ]) 166s [1] TRUE 166s > 166s > netm.ttt 166s Call: etmCIF(formula = Surv(entry, exit, status != "cens") ~ ttt, data = abortion, 166s etype = status, failcode = "spontaneous abortion") 166s 166s Covariate: ttt 166s levels: control exposed 166s 166s 166s ttt = control 166s time P se(P) n.event 166s CIF ETOP 43 0.040159 0.0092578 20 166s CIF life birth 43 0.799059 0.0221865 924 166s CIF spontaneous abortion 43 0.160781 0.0213261 69 166s 166s ttt = exposed 166s time P se(P) n.event 166s CIF ETOP 42 0.28511 0.042493 38 166s CIF life birth 42 0.35257 0.042139 92 166s CIF spontaneous abortion 42 0.36232 0.049473 43 166s > 166s > summary(netm.ttt) 166s 166s ttt=control 166s 166s CIF ETOP 166s P time var lower upper n.risk n.event 166s 0.000000 6 0.0000e+00 0.000000 0.000000 117 0 166s 0.038955 13 8.4440e-05 0.024488 0.061694 645 1 166s 0.040159 26 8.5707e-05 0.025513 0.062939 846 0 166s 0.040159 36 8.5707e-05 0.025513 0.062939 876 0 166s 0.040159 40 8.5707e-05 0.025513 0.062939 554 0 166s 0.040159 43 8.5707e-05 0.025513 0.062939 6 0 166s 166s CIF life birth 166s P time var lower upper n.risk n.event 166s 0.000000 6 0.0000e+00 0.000000 0.000000 117 0 166s 0.000000 13 0.0000e+00 0.000000 0.000000 645 0 166s 0.000000 26 0.0000e+00 0.000000 0.000000 846 0 166s 0.053197 36 4.6195e-05 0.041379 0.068268 876 25 166s 0.563121 40 3.8801e-04 0.524924 0.602021 554 280 166s 0.799059 43 4.9224e-04 0.753969 0.840613 6 6 166s 166s CIF spontaneous abortion 166s P time var lower upper n.risk n.event 166s 0.034188 6 0.00028222 0.01297 0.088523 117 4 166s 0.150468 13 0.00045513 0.11360 0.197901 645 1 166s 0.159904 26 0.00045498 0.12274 0.206925 846 1 166s 0.160781 36 0.00045480 0.12360 0.207757 876 1 166s 0.160781 40 0.00045480 0.12360 0.207757 554 0 166s 0.160781 43 0.00045480 0.12360 0.207757 6 0 166s 166s 166s ttt=exposed 166s 166s CIF ETOP 166s P time var lower upper n.risk n.event 166s 0.00000 6 0.0000000 0.00000 0.00000 35 0 166s 0.26048 13 0.0017854 0.18795 0.35425 90 0 166s 0.28115 21 0.0018028 0.20742 0.37423 93 1 166s 0.28511 34 0.0018057 0.21116 0.37806 89 0 166s 0.28511 39 0.0018057 0.21116 0.37806 59 0 166s 0.28511 42 0.0018057 0.21116 0.37806 6 0 166s 166s CIF life birth 166s P time var lower upper n.risk n.event 166s 0.000000 6 0.0000e+00 0.000000 0.000000 35 0 166s 0.000000 13 0.0000e+00 0.000000 0.000000 90 0 166s 0.000000 21 0.0000e+00 0.000000 0.000000 93 0 166s 0.023073 34 9.0514e-05 0.010252 0.051504 89 2 166s 0.180156 39 8.0126e-04 0.131765 0.243663 59 13 166s 0.352565 42 1.7757e-03 0.276882 0.441775 6 6 166s 166s CIF spontaneous abortion 166s P time var lower upper n.risk n.event 166s 0.057143 6 0.0015394 0.014605 0.20968 35 2 166s 0.333246 13 0.0025280 0.245337 0.44216 90 4 166s 0.350702 21 0.0024827 0.262769 0.45762 93 0 166s 0.358492 34 0.0024593 0.270627 0.46448 89 0 166s 0.358492 39 0.0024593 0.270627 0.46448 59 0 166s 0.362323 42 0.0024476 0.274499 0.46785 6 0 166s 166s > 166s > 166s > ### A couple of comparisons with simulated data 166s > set.seed(1313) 166s > time <- rexp(100) 166s > to <- rbinom(100, 2, prob = c(1/3, 1/3, 1/3)) 166s > from <- rep(11, 100) 166s > id <- 1:100 166s > cov <- rbinom(100, 1, 0.5) 166s > 166s > dat.s <- data.frame(id, time, from, to, cov) 166s > 166s > traa <- matrix(FALSE, 3, 3) 166s > traa[1, 2:3] <- TRUE 166s > 166s > aa0 <- etm(dat.s[dat.s$cov == 0, ], c("11", "1", "2"), traa, "0", 0) 166s > aa1 <- etm(dat.s[dat.s$cov == 1, ], c("11", "1", "2"), traa, "0", 0) 166s > aa <- etm(dat.s, c("11", "1", "2"), traa, "0", 0) 166s > 166s > test <- etmCIF(Surv(time, to != 0) ~ 1, dat.s, etype = to) 166s > 166s > test.c <- etmCIF(Surv(time, to != 0) ~ cov, dat.s, etype = to) 166s > 166s > all.equal(trprob(aa, "11 1"), test[[1]]$est["0", "1", ]) 166s [1] TRUE 166s > all.equal(trprob(aa, "11 2"), test[[1]]$est["0", "2", ]) 166s [1] TRUE 166s > 166s > all.equal(trprob(aa0, "11 1"), test.c[[1]]$est["0", "1", ]) 166s [1] TRUE 166s > all.equal(trprob(aa0, "11 2"), test.c[[1]]$est["0", "2", ]) 166s [1] TRUE 166s > 166s > all.equal(trprob(aa1, "11 1"), test.c[[2]]$est["0", "1", ]) 166s [1] TRUE 166s > all.equal(trprob(aa1, "11 2"), test.c[[2]]$est["0", "2", ]) 166s [1] TRUE 166s > 166s > test 166s Call: etmCIF(formula = Surv(time, to != 0) ~ 1, data = dat.s, etype = to) 166s 166s time P se(P) n.event 166s CIF 1 4.9088 0.809108 0.079680 45 166s CIF 2 4.9088 0.096618 0.032905 8 166s > 166s > test.c 166s Call: etmCIF(formula = Surv(time, to != 0) ~ cov, data = dat.s, etype = to) 166s 166s Covariate: cov 166s levels: 0 1 166s 166s 166s cov = 0 166s time P se(P) n.event 166s CIF 1 2.1708 0.70246 0.105797 19 166s CIF 2 2.1708 0.11144 0.053384 4 166s 166s cov = 1 166s time P se(P) n.event 166s CIF 1 4.9088 0.80787 0.094051 26 166s CIF 2 4.9088 0.08436 0.040769 4 166s > 166s > summary(test) 166s 166s 166s 166s CIF 1 166s P time var lower upper n.risk n.event 166s 0.01000 0.0092099 0.0000990 0.0014147 0.068863 100 1 166s 0.11430 0.2663096 0.0010542 0.0649454 0.196993 81 1 166s 0.23451 0.7303091 0.0020436 0.1591107 0.337736 54 1 166s 0.40425 1.4299939 0.0032996 0.3020445 0.525741 29 1 166s 0.54593 2.0647206 0.0040836 0.4269008 0.673605 16 1 166s 0.80911 4.9087561 0.0063489 0.6359544 0.933733 2 1 166s 166s CIF 2 166s P time var lower upper n.risk n.event 166s 0.000000 0.0092099 0.00000000 0.000000 0.000000 100 0 166s 0.031657 0.2663096 0.00032353 0.010320 0.094942 81 0 166s 0.067029 0.7303091 0.00070366 0.030598 0.143503 54 0 166s 0.096618 1.4299939 0.00108275 0.049082 0.185474 29 0 166s 0.096618 2.0647206 0.00108275 0.049082 0.185474 16 0 166s 0.096618 4.9087561 0.00108275 0.049082 0.185474 2 0 166s 166s > summary(test.c) 166s 166s cov=0 166s 166s CIF 1 166s P time var lower upper n.risk n.event 166s 0.022222 0.0092099 0.00048285 0.0031605 0.14747 45 1 166s 0.092222 0.2982439 0.00193603 0.0355971 0.22762 36 0 166s 0.226684 0.7021938 0.00450954 0.1241760 0.39250 24 1 166s 0.378128 1.4299939 0.00760870 0.2337884 0.57145 13 1 166s 0.505736 1.6148774 0.00895330 0.3388425 0.69885 10 1 166s 0.702465 2.1708375 0.01119294 0.4944890 0.88399 3 1 166s 166s CIF 2 166s P time var lower upper n.risk n.event 166s 0.000000 0.0092099 0.0000000 0.000000 0.00000 45 0 166s 0.048441 0.2982439 0.0011168 0.012337 0.18013 36 1 166s 0.076411 0.7021938 0.0018104 0.025202 0.21928 24 0 166s 0.111440 1.4299939 0.0028499 0.042676 0.27392 13 0 166s 0.111440 1.6148774 0.0028499 0.042676 0.27392 10 0 166s 0.111440 2.1708375 0.0028499 0.042676 0.27392 3 0 166s 166s 166s cov=1 166s 166s CIF 1 166s P time var lower upper n.risk n.event 166s 0.018182 0.066692 0.00032457 0.0025813 0.12214 55 1 166s 0.112392 0.263808 0.00187215 0.0520925 0.23333 45 1 166s 0.241023 0.730309 0.00374499 0.1440057 0.38685 31 1 166s 0.401201 1.066913 0.00570788 0.2714008 0.56421 19 1 166s 0.592334 2.366275 0.00775985 0.4286230 0.76273 8 1 166s 0.807871 4.908756 0.00884554 0.6023185 0.94771 2 1 166s 166s CIF 2 166s P time var lower upper n.risk n.event 166s 0.000000 0.066692 0.00000000 0.000000 0.00000 55 0 166s 0.037434 0.263808 0.00067458 0.009494 0.14152 45 0 166s 0.059341 0.730309 0.00111295 0.019447 0.17351 31 0 166s 0.084360 1.066913 0.00166213 0.032211 0.21119 19 0 166s 0.084360 2.366275 0.00166213 0.032211 0.21119 8 0 166s 0.084360 4.908756 0.00166213 0.032211 0.21119 2 0 166s 166s > 166s > options(old) 166s > 166s BEGIN TEST tests.etm.R 166s 166s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 166s Copyright (C) 2025 The R Foundation for Statistical Computing 166s Platform: x86_64-pc-linux-gnu 166s 166s R is free software and comes with ABSOLUTELY NO WARRANTY. 166s You are welcome to redistribute it under certain conditions. 166s Type 'license()' or 'licence()' for distribution details. 166s 166s R is a collaborative project with many contributors. 166s Type 'contributors()' for more information and 166s 'citation()' on how to cite R or R packages in publications. 166s 166s Type 'demo()' for some demos, 'help()' for on-line help, or 166s 'help.start()' for an HTML browser interface to help. 166s Type 'q()' to quit R. 166s 166s > Loading required package: etm 166s require(etm) 167s > 167s > ## Print with a bit less precision to avoid lots of notes in the comparison 167s > old <- options(digits = 4) 167s > 167s > ### Simple test 167s > 167s > time <- id <- 1:10 167s > from <- rep(0, 10) 167s > to <- rep(1, 10) 167s > 167s > data1 <- data.frame(id, from, to, time) 167s > tra1 <- matrix(FALSE, 2, 2) 167s > tra1[1, 2] <- TRUE 167s > 167s > etm1 <- etm(data1, c("0", "1"), tra1, NULL, 0) 167s > 167s > all.equal(as.vector(trprob(etm1, "0 0")), cumprod((10:1 - 1) / (10:1))) 167s [1] TRUE 167s > 167s > etm1$cov["0 0", "0 0", ] 167s 1 2 3 4 5 6 7 8 Loading required package: survival 167s 9 10 167s 0.009 0.016 0.021 0.024 0.025 0.024 0.021 0.016 0.009 0.000 167s > 167s > all.equal(etm1$cov["0 0", "0 0",], trcov(etm1, "0 0")) 167s [1] TRUE 167s > 167s > ### A simple test from AHR's author, where the first time is censored 167s > if (!require(survival)) { 167s + stop("This test requires the survival package") 167s + } 167s > 167s > data <- data.frame(id=1:10, time=1:10, from=0, to=1, status=TRUE) 167s > 167s > tra <- matrix(FALSE, nrow=2, ncol=2) 167s > tra[1, 2] <- TRUE 167s > 167s > data$to[1] <- "cens" 167s > data$status[1] <- FALSE 167s > 167s > fit.km <- survfit(Surv(time, status) ~ 1, data=data) 167s > fit.etm <- etm(data, c("0","1"), tra, "cens", s=0, t="last", covariance=FALSE) 167s > 167s > all.equal(fit.km$surv[data$status], fit.etm$est[1,1,], check.attributes = FALSE) 167s [1] TRUE 167s > 167s > data$to[2] <- "cens" 167s > data$status[2] <- FALSE 167s > 167s > fit.km <- survfit(Surv(time, status) ~ 1, data=data) 167s > fit.etm <- etm(data, c("0","1"), tra, "cens", s=0, t="last", covariance=FALSE) 167s > 167s > all.equal(fit.km$surv[data$status], fit.etm$est[1,1,], check.attributes = FALSE) 167s [1] TRUE 167s > 167s > ### a bit more complicated 167s > 167s > time <- id <- 1:10 167s > from <- rep(0, 10) 167s > to <- rep(c(1, 2), 5) 167s > data2 <- data.frame(id, from, to, time) 167s > 167s > tra2 <- matrix(FALSE, 3, 3) 167s > tra2[1, 2:3] <- TRUE 167s > 167s > etm2 <- etm(data2, c("0", "1", "2"), tra2, NULL, 0) 167s > 167s > aa <- table(time, to) 167s > 167s > cif1 <- cumsum(aa[, 1] / 10) 167s > cif2 <- cumsum(aa[, 2] / 10) 167s > surv <- cumprod((10:1 - 1) / (10:1)) 167s > 167s > all.equal(trprob(etm2, "0 1"), cif1) 167s [1] TRUE 167s > all.equal(trprob(etm2, "0 2"), cif2) 167s [1] TRUE 167s > all.equal(as.vector(trprob(etm2, "0 0")), surv) 167s [1] TRUE 167s > 167s > ## a test on id 167s > data2$id <- letters[1:10] 167s > 167s > etm3 <- etm(data2, c("0", "1", "2"), tra2, NULL, 0) 167s > 167s > all.equal(trprob(etm2, "0 1"), trprob(etm3, "0 1")) 167s [1] TRUE 167s > all.equal(trprob(etm2, "0 2"), trprob(etm3, "0 2")) 167s [1] TRUE 167s > all.equal(trprob(etm2, "0 0"), trprob(etm3, "0 0")) 167s [1] TRUE 167s > 167s > 167s > ### Test on sir.cont 167s > 167s > data(sir.cont) 167s > 167s > ## Modification for patients entering and leaving a state 167s > ## at the same date 167s > ## Change on ventilation status is considered 167s > ## to happen before end of hospital stay 167s > sir.cont <- sir.cont[order(sir.cont$id, sir.cont$time), ] 167s > for (i in 2:nrow(sir.cont)) { 167s + if (sir.cont$id[i]==sir.cont$id[i-1]) { 167s + if (sir.cont$time[i]==sir.cont$time[i-1]) { 167s + sir.cont$time[i-1] <- sir.cont$time[i-1] - 0.5 167s + } 167s + } 167s + } 167s > 167s > ### Computation of the transition probabilities 167s > ## Possible transitions. 167s > tra <- matrix(ncol=3,nrow=3,FALSE) 167s > tra[1, 2:3] <- TRUE 167s > tra[2, c(1, 3)] <- TRUE 167s > 167s > ## etm 167s > prob.sir <- etm(sir.cont, c("0", "1", "2"), tra, "cens", 1) 167s > 167s > prob.sir 167s Multistate model with 2 transient state(s) 167s and 1 absorbing state(s) 167s 167s Possible transitions: 167s from to 167s 0 1 167s 0 2 167s 1 0 167s 1 2 167s 167s Estimate of P(1, 183) 167s 0 1 2 167s 0 0 0 1 167s 1 0 0 1 167s 2 0 0 1 167s 167s > 167s > summ.sir <- summary(prob.sir) 167s > all.equal(summ.sir[['0 1']]$P, as.vector(trprob(prob.sir, "0 1"))) 167s [1] TRUE 167s > subset(summ.sir[[3]],time<183) # issue with precision on different architectures 167s P time var lower upper n.risk n.event 167s 1.5 0.0000 1.5 0.000e+00 0.00000 0.0000 394 0 167s 2 0.1187 2.0 2.641e-04 0.08683 0.1505 396 47 167s 2.5 0.1187 2.5 2.641e-04 0.08683 0.1505 364 0 167s 3 0.2454 3.0 4.465e-04 0.20398 0.2868 365 54 167s 3.5 0.2454 3.5 4.465e-04 0.20398 0.2868 328 0 167s 4 0.3806 4.0 5.416e-04 0.33501 0.4262 331 62 167s 4.5 0.3806 4.5 5.416e-04 0.33501 0.4262 280 0 167s 5 0.4792 5.0 5.480e-04 0.43333 0.5251 283 48 167s 5.5 0.4792 5.5 5.480e-04 0.43333 0.5251 248 0 167s 6 0.5693 6.0 5.141e-04 0.52482 0.6137 249 47 167s 7 0.6350 7.0 4.665e-04 0.59266 0.6773 212 36 167s 8 0.6795 8.0 4.202e-04 0.63931 0.7197 195 27 167s 8.5 0.6795 8.5 4.202e-04 0.63931 0.7197 172 0 167s 9 0.7325 9.0 3.580e-04 0.69541 0.7696 173 34 167s 10 0.7647 10.0 3.141e-04 0.72992 0.7994 148 21 167s 10.5 0.7647 10.5 3.141e-04 0.72992 0.7994 135 0 167s 11 0.7895 11.0 2.790e-04 0.75674 0.8222 136 18 167s 12 0.8138 12.0 2.420e-04 0.78330 0.8443 129 18 167s 12.5 0.8138 12.5 2.420e-04 0.78330 0.8443 117 0 167s 13 0.8294 13.0 2.182e-04 0.80045 0.8584 118 13 167s 14 0.8452 14.0 1.938e-04 0.81789 0.8725 115 14 167s 15 0.8625 15.0 1.670e-04 0.83714 0.8878 106 15 167s 16 0.8723 16.0 1.522e-04 0.84807 0.8964 93 9 167s 17 0.8852 17.0 1.330e-04 0.86256 0.9078 86 12 167s 17.5 0.8852 17.5 1.330e-04 0.86256 0.9078 77 0 167s 18 0.8960 18.0 1.168e-04 0.87484 0.9172 76 9 167s 19 0.9029 19.0 1.070e-04 0.88261 0.9232 71 7 167s 20 0.9125 20.0 9.367e-05 0.89356 0.9315 64 10 167s 21 0.9161 21.0 8.878e-05 0.89768 0.9346 57 4 167s 22 0.9226 22.0 7.996e-05 0.90504 0.9401 55 6 167s 23 0.9261 23.0 7.537e-05 0.90904 0.9431 51 4 167s 23.5 0.9261 23.5 7.537e-05 0.90904 0.9431 49 0 167s 24 0.9354 24.0 6.292e-05 0.91982 0.9509 50 9 167s 25 0.9385 25.0 5.878e-05 0.92352 0.9536 42 3 167s 26 0.9429 26.0 5.326e-05 0.92863 0.9572 39 5 167s 27 0.9477 27.0 4.749e-05 0.93417 0.9612 35 6 167s 27.5 0.9477 27.5 4.749e-05 0.93417 0.9612 29 0 167s 28 0.9531 28.0 4.093e-05 0.94059 0.9657 30 5 167s 29 0.9567 29.0 3.668e-05 0.94485 0.9686 31 4 167s 30 0.9592 30.0 3.384e-05 0.94779 0.9706 28 3 167s 30.5 0.9592 30.5 3.384e-05 0.94779 0.9706 29 0 167s 31 0.9642 31.0 2.821e-05 0.95383 0.9746 30 6 167s 32 0.9649 32.0 2.752e-05 0.95458 0.9751 25 1 167s 33 0.9669 33.0 2.533e-05 0.95708 0.9768 24 2 167s 34 0.9685 34.0 2.368e-05 0.95900 0.9781 26 2 167s 35 0.9697 35.0 2.252e-05 0.96036 0.9790 28 2 167s 36 0.9702 36.0 2.194e-05 0.96104 0.9794 26 1 167s 37 0.9718 37.0 2.043e-05 0.96290 0.9806 26 2 167s 38 0.9739 38.0 1.831e-05 0.96555 0.9823 25 4 167s 38.5 0.9739 38.5 1.831e-05 0.96555 0.9823 21 0 167s 39 0.9760 39.0 1.643e-05 0.96802 0.9839 23 3 167s 40 0.9769 40.0 1.558e-05 0.96918 0.9847 19 1 167s 41 0.9774 41.0 1.512e-05 0.96981 0.9851 22 1 167s 42 0.9779 42.0 1.476e-05 0.97032 0.9854 22 0 167s 43 0.9798 43.0 1.308e-05 0.97271 0.9869 22 3 167s 44 0.9803 44.0 1.265e-05 0.97333 0.9873 21 1 167s 45 0.9817 45.0 1.157e-05 0.97499 0.9883 19 1 167s 46 0.9822 46.0 1.116e-05 0.97561 0.9887 17 1 167s 47 0.9831 47.0 1.037e-05 0.97683 0.9895 18 2 167s 48 0.9836 48.0 9.987e-06 0.97743 0.9898 17 1 167s 49 0.9841 49.0 9.669e-06 0.97796 0.9901 17 0 167s 50 0.9845 50.0 9.297e-06 0.97856 0.9905 17 1 167s 50.5 0.9845 50.5 9.297e-06 0.97856 0.9905 16 0 167s 51 0.9860 51.0 8.214e-06 0.98037 0.9916 17 3 167s 52 0.9870 52.0 7.513e-06 0.98159 0.9923 14 2 167s 53 0.9879 53.0 6.875e-06 0.98276 0.9930 12 1 167s 54 0.9889 54.0 6.214e-06 0.98397 0.9937 12 2 167s 55 0.9903 55.0 5.254e-06 0.98581 0.9948 10 3 167s 56 0.9913 56.0 4.667e-06 0.98703 0.9955 6 1 167s 57 0.9917 57.0 4.364e-06 0.98765 0.9958 5 1 167s 58 0.9922 58.0 4.064e-06 0.98828 0.9962 4 1 167s 59 0.9927 59.0 3.769e-06 0.98891 0.9965 3 1 167s 60 0.9932 60.0 3.488e-06 0.98953 0.9969 3 1 167s 62 0.9937 62.0 3.230e-06 0.99016 0.9972 2 0 167s 63 0.9942 63.0 2.956e-06 0.99079 0.9975 2 1 167s 68 0.9942 68.0 2.956e-06 0.99079 0.9975 1 0 167s 70 0.9946 70.0 2.694e-06 0.99143 0.9979 2 1 167s 78 0.9951 78.0 2.442e-06 0.99207 0.9982 1 0 167s 80 0.9951 80.0 2.442e-06 0.99207 0.9982 1 0 167s 85 0.9966 85.0 1.695e-06 0.99404 0.9991 2 0 167s 89 0.9966 89.0 1.695e-06 0.99404 0.9991 2 0 167s 90 0.9966 90.0 1.695e-06 0.99404 0.9991 1 0 167s 95 0.9971 95.0 1.448e-06 0.99472 0.9994 2 0 167s 100 0.9976 100.0 1.203e-06 0.99542 0.9997 3 0 167s 101 0.9981 101.0 9.592e-07 0.99613 1.0000 3 1 167s 108 0.9985 108.0 7.169e-07 0.99688 1.0000 2 1 167s 113 0.9990 113.0 4.764e-07 0.99767 1.0000 1 0 167s 116 0.9990 116.0 4.764e-07 0.99767 1.0000 1 0 167s 124 0.9990 124.0 4.764e-07 0.99767 1.0000 2 0 167s 164 0.9990 164.0 4.764e-07 0.99767 1.0000 0 0 167s > 167s > ## gonna play a bit with the state names 167s > dd <- sir.cont 167s > dd$from <- ifelse(dd$from == 0, "initial state", "ventilation") 167s > dd$to <- as.character(dd$to) 167s > for (i in seq_len(nrow(dd))) { 167s + dd$to[i] <- switch(dd$to[i], 167s + "0" = "initial state", 167s + "1" = "ventilation", 167s + "2" = "end of story", 167s + "cens" = "cens" 167s + ) 167s + } 167s > 167s > test <- etm(dd, c("initial state", "ventilation", "end of story"), tra, "cens", 1) 167s > 167s > all.equal(test$est["initial state", "initial state", ], 167s + prob.sir$est["0", "0", ]) 167s [1] TRUE 167s > all.equal(trprob(test, "initial state initial state"), trprob(prob.sir, "0 0")) 167s [1] TRUE 167s > all.equal(trprob(test, "initial state ventilation"), trprob(prob.sir, "0 1")) 167s [1] TRUE 167s > all.equal(trprob(test, "initial state end of story"), trprob(prob.sir, "0 2")) 167s [1] TRUE 167s > 167s > all.equal(trcov(test, "initial state end of story"), trcov(prob.sir, "0 2")) 167s [1] TRUE 167s > 167s > aa <- summary(test) 167s > all.equal(summ.sir[[6]], aa[[6]]) 167s [1] TRUE 167s > all.equal(summ.sir[[4]], aa[[4]]) 167s [1] TRUE 167s > 167s > ### Test on abortion data 167s > 167s > data(abortion) 167s > 167s > from <- rep(0, nrow(abortion)) 167s > to <- abortion$cause 167s > entry <- abortion$entry 167s > exit <- abortion$exit 167s > id <- 1:nrow(abortion) 167s > data <- data.frame(id, from, to, entry, exit, group = abortion$group) 167s > 167s > ## Computation of the CIFs 167s > tra <- matrix(FALSE, 4, 4) 167s > tra[1, 2:4] <- TRUE 167s > 167s > cif.control <- etm(data[data$group == 0, ], c("0", "1", "2", "3"), 167s + tra, NULL, 0) 167s > cif.exposed <- etm(data[data$group == 1, ], c("0", "1", "2", "3"), 167s + tra, NULL, 0) 167s > 167s > all.equal(trprob(cif.control, "0 1"), cif.control$est["0", "1", ]) 167s [1] TRUE 167s > all.equal(trcov(cif.control, c("0 1", "0 2")), cif.control$cov["0 1", "0 2", ]) 167s [1] TRUE 167s > 167s > trprob(cif.control, "0 1") 167s 6 7 8 9 10 11 12 13 167s 0.000000 0.007401 0.014881 0.026509 0.033208 0.037694 0.037694 0.038955 167s 14 17 19 21 24 25 26 30 167s 0.040159 0.040159 0.040159 0.040159 0.040159 0.040159 0.040159 0.040159 167s 31 32 33 34 35 36 37 38 167s 0.040159 0.040159 0.040159 0.040159 0.040159 0.040159 0.040159 0.040159 167s 39 40 41 42 43 167s 0.040159 0.040159 0.040159 0.040159 0.040159 167s > trprob(cif.control, "0 2") 167s 6 7 8 9 10 11 12 13 167s 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 167s 14 17 19 21 24 25 26 30 167s 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.003657 167s 31 32 33 34 35 36 37 38 167s 0.006371 0.008175 0.013543 0.023317 0.031260 0.053197 0.084529 0.179163 167s 39 40 41 42 43 167s 0.322016 0.563121 0.742227 0.793893 0.799059 167s > trprob(cif.control, "0 0") 167s 6 7 8 9 10 11 12 13 167s 0.965812 0.932508 0.887628 0.862433 0.838989 0.822538 0.813099 0.810578 167s 14 17 19 21 24 25 26 30 167s 0.806964 0.805874 0.803810 0.802804 0.801837 0.800883 0.799937 0.796280 167s 31 32 33 34 35 36 37 38 167s 0.793565 0.791762 0.786394 0.776620 0.768677 0.745862 0.714531 0.619897 167s 39 40 41 42 43 167s 0.477043 0.235938 0.056832 0.005167 0.000000 167s > 167s > trcov(cif.control, "0 1") 167s 6 7 8 9 10 11 12 13 167s 0.000e+00 2.719e-05 4.533e-05 6.665e-05 7.698e-05 8.304e-05 8.304e-05 8.444e-05 167s 14 17 19 21 24 25 26 30 167s 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 167s 31 32 33 34 35 36 37 38 167s 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 167s 39 40 41 42 43 167s 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 167s > trcov(cif.control, "0 2") 167s 6 7 8 9 10 11 12 13 167s 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 167s 14 17 19 21 24 25 26 30 167s 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 3.338e-06 167s 31 32 33 34 35 36 37 38 167s 5.784e-06 7.401e-06 1.216e-05 2.072e-05 2.758e-05 4.619e-05 7.202e-05 1.461e-04 167s 39 40 41 42 43 167s 2.470e-04 3.880e-04 4.702e-04 4.903e-04 4.922e-04 167s > trcov(cif.control, "0 0") 167s 6 7 8 9 10 11 12 13 167s 2.822e-04 3.821e-04 4.527e-04 4.748e-04 4.875e-04 4.927e-04 4.941e-04 4.942e-04 167s 14 17 19 21 24 25 26 30 167s 4.941e-04 4.940e-04 4.936e-04 4.933e-04 4.931e-04 4.928e-04 4.926e-04 4.914e-04 167s 31 32 33 34 35 36 37 38 167s 4.905e-04 4.899e-04 4.880e-04 4.846e-04 4.816e-04 4.729e-04 4.601e-04 4.176e-04 167s 39 40 41 42 43 167s 3.425e-04 1.865e-04 4.797e-05 4.441e-06 0.000e+00 167s > 167s > aa <- summary(cif.control) 167s > aa$"0 1" 167s P time var lower upper n.risk n.event 167s 6 0.000000 6 0.000e+00 0.000000 0.00000 117 0 167s 7 0.007401 7 2.719e-05 0.000000 0.01762 261 2 167s 8 0.014881 8 4.533e-05 0.001685 0.02808 374 3 167s 9 0.026509 9 6.665e-05 0.010508 0.04251 458 6 167s 10 0.033208 10 7.698e-05 0.016011 0.05040 515 4 167s 11 0.037694 11 8.304e-05 0.019834 0.05555 561 3 167s 12 0.037694 12 8.304e-05 0.019834 0.05555 610 0 167s 13 0.038955 13 8.444e-05 0.020944 0.05697 645 1 167s 14 0.040159 14 8.571e-05 0.022014 0.05830 673 1 167s 17 0.040159 17 8.571e-05 0.022014 0.05830 740 0 167s 19 0.040159 19 8.571e-05 0.022014 0.05830 781 0 167s 21 0.040159 21 8.571e-05 0.022014 0.05830 799 0 167s 24 0.040159 24 8.571e-05 0.022014 0.05830 830 0 167s 25 0.040159 25 8.571e-05 0.022014 0.05830 841 0 167s 26 0.040159 26 8.571e-05 0.022014 0.05830 846 0 167s 30 0.040159 30 8.571e-05 0.022014 0.05830 875 0 167s 31 0.040159 31 8.571e-05 0.022014 0.05830 880 0 167s 32 0.040159 32 8.571e-05 0.022014 0.05830 880 0 167s 33 0.040159 33 8.571e-05 0.022014 0.05830 885 0 167s 34 0.040159 34 8.571e-05 0.022014 0.05830 885 0 167s 35 0.040159 35 8.571e-05 0.022014 0.05830 880 0 167s 36 0.040159 36 8.571e-05 0.022014 0.05830 876 0 167s 37 0.040159 37 8.571e-05 0.022014 0.05830 857 0 167s 38 0.040159 38 8.571e-05 0.022014 0.05830 823 0 167s 39 0.040159 39 8.571e-05 0.022014 0.05830 716 0 167s 40 0.040159 40 8.571e-05 0.022014 0.05830 554 0 167s 41 0.040159 41 8.571e-05 0.022014 0.05830 274 0 167s 42 0.040159 42 8.571e-05 0.022014 0.05830 66 0 167s 43 0.040159 43 8.571e-05 0.022014 0.05830 6 0 167s > all.equal(aa$"0 1"$P, as.vector(trprob(cif.control, "0 1"))) 167s [1] TRUE 167s > 167s > ### test on los data 167s > 167s > data(los.data) # in package changeLOS 167s > 167s > ## putting los.data in the long format (see changeLOS) 167s > my.observ <- prepare.los.data(x=los.data) 167s > 167s > tra <- matrix(FALSE, 4, 4) 167s > tra[1, 2:4] <- TRUE 167s > tra[2, 3:4] <- TRUE 167s > 167s > tr.prob <- etm(my.observ, c("0","1","2","3"), tra, NULL, 0) 167s > 167s > tr.prob 167s Multistate model with 2 transient state(s) 167s and 2 absorbing state(s) 167s 167s Possible transitions: 167s from to 167s 0 1 167s 0 2 167s 0 3 167s 1 2 167s 1 3 167s 167s Estimate of P(0, 82) 167s 0 1 2 3 167s 0 0 0 0.7474 0.2526 167s 1 0 0 0.7073 0.2927 167s 2 0 0 1.0000 0.0000 167s 3 0 0 0.0000 1.0000 167s 167s > summary(tr.prob) 167s Transition 0 0 167s P time var lower upper n.risk n.event 167s 0.882275 3 1.374e-04 0.8593018 0.905248 756 0 167s 0.112434 15 1.320e-04 0.0899155 0.134952 90 0 167s 0.031746 27 4.066e-05 0.0192484 0.044244 26 0 167s 0.006614 41 8.690e-06 0.0008359 0.012392 5 0 167s 0.002646 61 3.490e-06 0.0000000 0.006307 3 0 167s 0.000000 82 0.000e+00 0.0000000 0.000000 1 0 167s 167s Transition 0 1 167s P time var lower upper n.risk n.event 167s 0.017196 3 2.235e-05 0.0079289 0.02646 756 13 167s 0.063492 15 7.865e-05 0.0461099 0.08087 90 0 167s 0.030423 27 3.902e-05 0.0181805 0.04267 26 1 167s 0.015873 41 2.066e-05 0.0069637 0.02478 5 0 167s 0.005291 61 6.962e-06 0.0001197 0.01046 3 0 167s 0.000000 82 0.000e+00 0.0000000 0.00000 1 0 167s 167s Transition 0 2 167s P time var lower upper n.risk n.event 167s 0.08466 3 0.0001025 0.06481 0.1045 756 64 167s 0.62302 15 0.0003107 0.58847 0.6576 90 4 167s 0.69841 27 0.0002786 0.66570 0.7311 26 1 167s 0.72751 41 0.0002622 0.69578 0.7593 5 0 167s 0.74074 61 0.0002540 0.70950 0.7720 3 1 167s 0.74735 82 0.0002498 0.71638 0.7783 1 1 167s 167s Transition 0 3 167s P time var lower upper n.risk n.event 167s 0.01587 3 2.066e-05 0.006964 0.02478 756 12 167s 0.20106 15 2.125e-04 0.172489 0.22963 90 1 167s 0.23942 27 2.409e-04 0.208999 0.26984 26 0 167s 0.25000 41 2.480e-04 0.219133 0.28087 5 0 167s 0.25132 61 2.489e-04 0.220402 0.28224 3 0 167s 0.25265 82 2.498e-04 0.221671 0.28362 1 0 167s 167s Transition 1 1 167s P time var lower upper n.risk n.event 167s 1.00000 3 0.000e+00 1.00000 1.00000 0 0 167s 0.38661 15 2.358e-03 0.29143 0.48179 51 0 167s 0.12119 27 7.842e-04 0.06630 0.17607 23 0 167s 0.04593 41 2.405e-04 0.01554 0.07633 14 0 167s 0.01531 61 6.579e-05 0.00000 0.03121 4 0 167s 0.00000 82 0.000e+00 0.00000 0.00000 0 0 167s 167s Transition 1 2 167s P time var lower upper n.risk n.event 167s 0.0000 3 0.000000 0.0000 0.0000 0 0 167s 0.4107 15 0.002590 0.3110 0.5104 51 2 167s 0.6082 27 0.002254 0.5151 0.7012 23 1 167s 0.6652 41 0.002064 0.5761 0.7542 14 2 167s 0.6920 61 0.002000 0.6043 0.7796 4 0 167s 0.7073 82 0.001984 0.6200 0.7946 0 0 167s 167s Transition 1 3 167s P time var lower upper n.risk n.event 167s 0.0000 3 0.000000 0.0000 0.0000 0 0 167s 0.2027 15 0.001784 0.1199 0.2855 51 1 167s 0.2706 27 0.001968 0.1837 0.3576 23 0 167s 0.2889 41 0.001982 0.2016 0.3761 14 0 167s 0.2927 61 0.001984 0.2054 0.3800 4 0 167s 0.2927 82 0.001984 0.2054 0.3800 0 0 167s 167s > 167s > cLOS <- etm::clos(tr.prob, aw = TRUE) 167s > 167s > cLOS 167s The expected change in length of stay is: 167s 1.975 167s 167s Alternative weighting: 167s 167s Expected change in LOS with weight.1: 2.097 167s Expected change in LOS with weight.other: 1.951 167s > 167s > 167s > ### Tests on pseudo values 167s > t_pseudo <- closPseudo(my.observ, c("0","1","2","3"), tra, NULL, 167s + formula = ~ 1, aw = TRUE) 174s > 174s > cLOS$e.phi == t_pseudo$theta[, "e.phi"] 174s [,1] 174s [1,] TRUE 174s > cLOS$e.phi.weights.1 == t_pseudo$theta[, "e.phi.weights.1"] 174s [,1] 174s [1,] TRUE 174s > cLOS$e.phi.weights.other == t_pseudo$theta[, "e.phi.weights.other"] 174s [,1] 174s [1,] TRUE 174s > 174s > mean(t_pseudo$pseudoData$ps.e.phi) 174s [1] 1.968 174s > 174s > ### tests on etmprep 174s > 174s > ### creation of fake data in the wild format, following an illness-death model 174s > ## transition times 174s > tdisease <- c(3, 4, 3, 6, 8, 9) 174s > tdeath <- c(6, 9, 8, 6, 8, 9) 174s > 174s > ## transition status 174s > stat.disease <- c(1, 1, 1, 0, 0, 0) 174s > stat.death <- c(1, 1, 1, 1, 1, 0) 174s > 174s > ## a covariate that we want to keep in the new data 174s > set.seed(1313) 174s > cova <- rbinom(6, 1, 0.5) 174s > 174s > dat <- data.frame(tdisease, tdeath, 174s + stat.disease, stat.death, 174s + cova) 174s > 174s > ## Possible transitions 174s > tra <- matrix(FALSE, 3, 3) 174s > tra[1, 2:3] <- TRUE 174s > tra[2, 3] <- TRUE 174s > 174s > ## data preparation 174s > newdat <- etmprep(c(NA, "tdisease", "tdeath"), 174s + c(NA, "stat.disease", "stat.death"), 174s + data = dat, tra = tra, 174s + cens.name = "cens", keep = "cova") 174s > 174s > newdat 174s id entry exit from to cova 174s 1 1 0 3 0 1 1 174s 2 1 3 6 1 2 1 174s 3 2 0 4 0 1 0 174s 4 2 4 9 1 2 0 174s 5 3 0 3 0 1 1 174s 6 3 3 8 1 2 1 174s 7 4 0 6 0 2 0 174s 8 5 0 8 0 2 1 174s 9 6 0 9 0 cens 1 174s > 174s > ref <- data.frame(id = c(1, 1, 2, 2, 3, 3, 4, 5, 6), 174s + entry = c(0, 3, 0, 4, 0, 3, 0, 0, 0), 174s + exit = c(3, 6, 4, 9, 3, 8, 6, 8, 9), 174s + from = c(0, 1, 0, 1, 0, 1, 0, 0, 0), 174s + to = c(rep(c(1, 2), 3), 2, 2, "cens"), 174s + cova = c(1, 1, 0, 0, 1, 1, 0, 1, 1)) 174s > ref$from <- factor(as.character(ref$from), levels = c("0", "1", "2", "cens")) 174s > ref$to <- factor(as.character(ref$to), levels = c("0", "1", "2", "cens")) 174s > 174s > all.equal(ref, newdat) 174s [1] TRUE 174s > 174s > 174s > ###################################### 174s > ### Test the stratified calls 174s > ###################################### 174s > 174s > if (require("kmi", quietly = TRUE)) { 174s + library(etm) 174s + 174s + data(icu.pneu) 174s + my.icu.pneu <- icu.pneu 174s + 174s + my.icu.pneu <- my.icu.pneu[order(my.icu.pneu$id, my.icu.pneu$start), ] 174s + masque <- diff(my.icu.pneu$id) 174s + 174s + my.icu.pneu$from <- 0 174s + my.icu.pneu$from[c(1, masque) == 0] <- 1 174s + 174s + my.icu.pneu$to2 <- my.icu.pneu$event 174s + my.icu.pneu$to2[my.icu.pneu$status == 0] <- "cens" 174s + my.icu.pneu$to2[c(masque, 1) == 0] <- 1 174s + 174s + 174s + my.icu.pneu$to <- ifelse(my.icu.pneu$to2 %in% c(2, 3), 2, 174s + my.icu.pneu$to2) 174s + 174s + my.icu.pneu <- my.icu.pneu[, c("id", "start", "stop", "from", "to", 174s + "to2", "age", "sex")] 174s + names(my.icu.pneu)[c(2, 3)] <- c("entry", "exit") 174s + 174s + bouh_strat <- etm(my.icu.pneu, c("0", "1", "2"), tra_ill(), "cens", 0, strata = "sex") 174s + 174s + bouh_female <- etm(my.icu.pneu[my.icu.pneu$sex == "F", ], 174s + c("0", "1", "2"), tra_ill(), "cens", 0) 174s + 174s + all(bouh_strat[[1]]$est == bouh_female$est) 174s + 174s + ## Test the summary 174s + the_summary <- summary(bouh_strat) 174s + the_summary 174s + 174s + ## Test trprob 174s + all(trprob(bouh_strat, "0 1")[[1]] == trprob(bouh_female, "0 1")) 174s + all(trprob(bouh_strat, "0 1", c(0, 5, 10, 15))[[1]] == trprob(bouh_female, "0 1", c(0, 5, 10, 15))) 174s + 174s + ## Test trcov 174s + all(trcov(bouh_strat, "0 1")[[1]] == trcov(bouh_female, "0 1")) 174s + all(trcov(bouh_strat, c("0 1", "0 2"))[[1]] == trcov(bouh_female, c("0 1", "0 2"))) 174s + all(trcov(bouh_strat, "0 1", c(0, 5, 10, 15))[[1]] == trcov(bouh_female, "0 1", c(0, 5, 10, 15))) 174s + } else { 174s + print("These tests require the kmi package") 174s + } 174s [1] TRUE 174s > 174s > options(old) 174s > 175s autopkgtest [04:58:16]: test run-unit-test: -----------------------] 175s run-unit-test PASS 175s autopkgtest [04:58:16]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 175s autopkgtest [04:58:16]: test pkg-r-autopkgtest: preparing testbed 175s Reading package lists... 176s Building dependency tree... 176s Reading state information... 176s Solving dependencies... 176s The following NEW packages will be installed: 176s build-essential cpp cpp-15 cpp-15-x86-64-linux-gnu cpp-x86-64-linux-gnu 176s dctrl-tools g++ g++-15 g++-15-x86-64-linux-gnu g++-x86-64-linux-gnu gcc 176s gcc-15 gcc-15-x86-64-linux-gnu gcc-x86-64-linux-gnu gfortran gfortran-15 176s gfortran-15-x86-64-linux-gnu gfortran-x86-64-linux-gnu icu-devtools libasan8 176s libblas-dev libbz2-dev libc-dev-bin libc6-dev libcc1-0 libcrypt-dev 176s libdeflate-dev libgcc-15-dev libgfortran-15-dev libhwasan0 libicu-dev 176s libisl23 libitm1 libjpeg-dev libjpeg-turbo8-dev libjpeg8-dev liblapack-dev 176s liblsan0 liblzma-dev libmpc3 libncurses-dev libpcre2-16-0 libpcre2-32-0 176s libpcre2-dev libpcre2-posix3 libpkgconf3 libpng-dev libquadmath0 176s libreadline-dev libstdc++-15-dev libtirpc-dev libtsan2 libubsan1 libzstd-dev 176s linux-libc-dev pkg-r-autopkgtest pkgconf pkgconf-bin r-base-dev 176s r-cran-backports r-cran-broom r-cran-cli r-cran-cpp11 r-cran-dplyr 176s r-cran-fansi r-cran-farver r-cran-geepack r-cran-generics r-cran-ggplot2 176s r-cran-glue r-cran-gtable r-cran-isoband r-cran-labeling r-cran-lifecycle 176s r-cran-magrittr r-cran-mass r-cran-pillar r-cran-pkgconfig r-cran-purrr 176s r-cran-r6 r-cran-rcolorbrewer r-cran-rlang r-cran-s7 r-cran-scales 176s r-cran-stringi r-cran-stringr r-cran-tibble r-cran-tidyr r-cran-tidyselect 176s r-cran-utf8 r-cran-vctrs r-cran-viridislite r-cran-withr rpcsvc-proto 176s zlib1g-dev 176s 0 upgraded, 95 newly installed, 0 to remove and 0 not upgraded. 176s Need to get 137 MB of archives. 176s After this operation, 445 MB of additional disk space will be used. 176s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 libc-dev-bin amd64 2.42-2ubuntu4 [23.3 kB] 176s Get:2 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-libc-dev amd64 6.19.0-3.3 [1846 kB] 176s Get:3 http://ftpmaster.internal/ubuntu resolute/main amd64 libcrypt-dev amd64 1:4.5.1-1 [122 kB] 176s Get:4 http://ftpmaster.internal/ubuntu resolute/main amd64 rpcsvc-proto amd64 1.4.3-1build1 [68.3 kB] 176s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 libc6-dev amd64 2.42-2ubuntu4 [2207 kB] 176s Get:6 http://ftpmaster.internal/ubuntu resolute/main amd64 libisl23 amd64 0.27-1build1 [691 kB] 176s Get:7 http://ftpmaster.internal/ubuntu resolute/main amd64 libmpc3 amd64 1.3.1-2 [54.8 kB] 176s Get:8 http://ftpmaster.internal/ubuntu resolute/main amd64 cpp-15-x86-64-linux-gnu amd64 15.2.0-12ubuntu1 [12.9 MB] 177s Get:9 http://ftpmaster.internal/ubuntu resolute/main amd64 cpp-15 amd64 15.2.0-12ubuntu1 [1034 B] 177s Get:10 http://ftpmaster.internal/ubuntu resolute/main amd64 cpp-x86-64-linux-gnu amd64 4:15.2.0-4ubuntu1 [5746 B] 177s Get:11 http://ftpmaster.internal/ubuntu resolute/main amd64 cpp amd64 4:15.2.0-4ubuntu1 [22.4 kB] 177s Get:12 http://ftpmaster.internal/ubuntu resolute/main amd64 libcc1-0 amd64 16-20260208-1ubuntu1 [51.2 kB] 177s Get:13 http://ftpmaster.internal/ubuntu resolute/main amd64 libitm1 amd64 16-20260208-1ubuntu1 [30.2 kB] 177s Get:14 http://ftpmaster.internal/ubuntu resolute/main amd64 libasan8 amd64 16-20260208-1ubuntu1 [3182 kB] 177s Get:15 http://ftpmaster.internal/ubuntu resolute/main amd64 liblsan0 amd64 16-20260208-1ubuntu1 [1392 kB] 177s Get:16 http://ftpmaster.internal/ubuntu resolute/main amd64 libtsan2 amd64 16-20260208-1ubuntu1 [2838 kB] 177s Get:17 http://ftpmaster.internal/ubuntu resolute/main amd64 libubsan1 amd64 16-20260208-1ubuntu1 [1238 kB] 177s Get:18 http://ftpmaster.internal/ubuntu resolute/main amd64 libhwasan0 amd64 16-20260208-1ubuntu1 [1729 kB] 177s Get:19 http://ftpmaster.internal/ubuntu resolute/main amd64 libquadmath0 amd64 16-20260208-1ubuntu1 [155 kB] 177s Get:20 http://ftpmaster.internal/ubuntu resolute/main amd64 libgcc-15-dev amd64 15.2.0-12ubuntu1 [2866 kB] 177s Get:21 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc-15-x86-64-linux-gnu amd64 15.2.0-12ubuntu1 [25.4 MB] 177s Get:22 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc-15 amd64 15.2.0-12ubuntu1 [530 kB] 177s Get:23 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc-x86-64-linux-gnu amd64 4:15.2.0-4ubuntu1 [1208 B] 177s Get:24 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc amd64 4:15.2.0-4ubuntu1 [5024 B] 177s Get:25 http://ftpmaster.internal/ubuntu resolute/main amd64 libstdc++-15-dev amd64 15.2.0-12ubuntu1 [2553 kB] 177s Get:26 http://ftpmaster.internal/ubuntu resolute/main amd64 g++-15-x86-64-linux-gnu amd64 15.2.0-12ubuntu1 [14.4 MB] 178s Get:27 http://ftpmaster.internal/ubuntu resolute/main amd64 g++-15 amd64 15.2.0-12ubuntu1 [25.3 kB] 178s Get:28 http://ftpmaster.internal/ubuntu resolute/main amd64 g++-x86-64-linux-gnu amd64 4:15.2.0-4ubuntu1 [966 B] 178s Get:29 http://ftpmaster.internal/ubuntu resolute/main amd64 g++ amd64 4:15.2.0-4ubuntu1 [1100 B] 178s Get:30 http://ftpmaster.internal/ubuntu resolute/main amd64 build-essential amd64 12.12ubuntu2 [5256 B] 178s Get:31 http://ftpmaster.internal/ubuntu resolute/main amd64 dctrl-tools amd64 2.24-3build4 [104 kB] 178s Get:32 http://ftpmaster.internal/ubuntu resolute/main amd64 libgfortran-15-dev amd64 15.2.0-12ubuntu1 [973 kB] 178s Get:33 http://ftpmaster.internal/ubuntu resolute/main amd64 gfortran-15-x86-64-linux-gnu amd64 15.2.0-12ubuntu1 [13.6 MB] 178s Get:34 http://ftpmaster.internal/ubuntu resolute/main amd64 gfortran-15 amd64 15.2.0-12ubuntu1 [18.1 kB] 178s Get:35 http://ftpmaster.internal/ubuntu resolute/main amd64 gfortran-x86-64-linux-gnu amd64 4:15.2.0-4ubuntu1 [1014 B] 178s Get:36 http://ftpmaster.internal/ubuntu resolute/main amd64 gfortran amd64 4:15.2.0-4ubuntu1 [1172 B] 178s Get:37 http://ftpmaster.internal/ubuntu resolute/main amd64 icu-devtools amd64 78.2-1ubuntu1 [214 kB] 178s Get:38 http://ftpmaster.internal/ubuntu resolute/main amd64 libblas-dev amd64 3.12.1-7ubuntu1 [235 kB] 178s Get:39 http://ftpmaster.internal/ubuntu resolute/main amd64 libbz2-dev amd64 1.0.8-6build2 [36.2 kB] 178s Get:40 http://ftpmaster.internal/ubuntu resolute/main amd64 libdeflate-dev amd64 1.23-2build1 [58.8 kB] 178s Get:41 http://ftpmaster.internal/ubuntu resolute/main amd64 libicu-dev amd64 78.2-1ubuntu1 [12.5 MB] 178s Get:42 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg-turbo8-dev amd64 2.1.5-4ubuntu3 [300 kB] 178s Get:43 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg8-dev amd64 8c-2ubuntu12 [1480 B] 178s Get:44 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg-dev amd64 8c-2ubuntu12 [1480 B] 178s Get:45 http://ftpmaster.internal/ubuntu resolute/main amd64 liblapack-dev amd64 3.12.1-7ubuntu1 [5433 kB] 178s Get:46 http://ftpmaster.internal/ubuntu resolute/main amd64 libncurses-dev amd64 6.6+20251231-1 [389 kB] 178s Get:47 http://ftpmaster.internal/ubuntu resolute/main amd64 libpcre2-16-0 amd64 10.46-1 [243 kB] 178s Get:48 http://ftpmaster.internal/ubuntu resolute/main amd64 libpcre2-32-0 amd64 10.46-1 [230 kB] 178s Get:49 http://ftpmaster.internal/ubuntu resolute/main amd64 libpcre2-posix3 amd64 10.46-1 [7354 B] 178s Get:50 http://ftpmaster.internal/ubuntu resolute/main amd64 libpcre2-dev amd64 10.46-1 [832 kB] 178s Get:51 http://ftpmaster.internal/ubuntu resolute/main amd64 libpkgconf3 amd64 1.8.1-4build1 [32.8 kB] 178s Get:52 http://ftpmaster.internal/ubuntu resolute/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1ubuntu2 [898 kB] 178s Get:53 http://ftpmaster.internal/ubuntu resolute/main amd64 libpng-dev amd64 1.6.54-1 [273 kB] 178s Get:54 http://ftpmaster.internal/ubuntu resolute/main amd64 libreadline-dev amd64 8.3-3 [189 kB] 178s Get:55 http://ftpmaster.internal/ubuntu resolute/main amd64 libzstd-dev amd64 1.5.7+dfsg-3 [376 kB] 178s Get:56 http://ftpmaster.internal/ubuntu resolute/main amd64 liblzma-dev amd64 5.8.2-2 [179 kB] 178s Get:57 http://ftpmaster.internal/ubuntu resolute/main amd64 pkgconf-bin amd64 1.8.1-4build1 [21.7 kB] 178s Get:58 http://ftpmaster.internal/ubuntu resolute/main amd64 pkgconf amd64 1.8.1-4build1 [16.8 kB] 178s Get:59 http://ftpmaster.internal/ubuntu resolute/main amd64 libtirpc-dev amd64 1.3.6+ds-1 [195 kB] 178s Get:60 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-base-dev all 4.5.2-1ubuntu2 [1880 B] 178s Get:61 http://ftpmaster.internal/ubuntu resolute/universe amd64 pkg-r-autopkgtest all 20250812 [6158 B] 178s Get:62 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-backports amd64 1.5.0-2 [121 kB] 178s Get:63 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-cli amd64 3.6.4-1 [1394 kB] 178s Get:64 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-generics all 0.1.4-1 [84.0 kB] 178s Get:65 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-glue amd64 1.8.0-1 [164 kB] 178s Get:66 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rlang amd64 1.1.5-3 [1721 kB] 178s Get:67 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-lifecycle all 1.0.5+dfsg-1 [120 kB] 178s Get:68 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-magrittr amd64 2.0.3-1 [154 kB] 178s Get:69 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-utf8 amd64 1.2.4-1 [140 kB] 179s Get:70 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-vctrs amd64 0.6.5-1 [1335 kB] 179s Get:71 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-pillar all 1.11.1+dfsg-1 [456 kB] 179s Get:72 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-r6 all 2.6.1-1 [101 kB] 179s Get:73 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-fansi amd64 1.0.6-2 [626 kB] 179s Get:74 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-pkgconfig all 2.0.3-2build2 [20.4 kB] 179s Get:75 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-tibble amd64 3.2.1+dfsg-3 [419 kB] 179s Get:76 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-withr all 3.0.2+dfsg-1 [214 kB] 179s Get:77 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-tidyselect amd64 1.2.1+dfsg-1 [222 kB] 179s Get:78 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-dplyr amd64 1.1.4-4 [1536 kB] 179s Get:79 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-purrr amd64 1.0.4-1 [552 kB] 179s Get:80 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-stringi amd64 1.8.4-1build2 [908 kB] 179s Get:81 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-stringr all 1.5.1-1 [290 kB] 179s Get:82 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-cpp11 all 0.5.3-1 [242 kB] 179s Get:83 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-tidyr amd64 1.3.1-1 [1156 kB] 179s Get:84 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-broom all 1.0.12+dfsg-1 [1708 kB] 179s Get:85 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-farver amd64 2.1.2-1 [1355 kB] 179s Get:86 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-mass amd64 7.3-65-1 [1116 kB] 179s Get:87 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-geepack amd64 1.3.12-1 [389 kB] 179s Get:88 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-gtable all 0.3.6+dfsg-1 [199 kB] 179s Get:89 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-isoband amd64 0.2.7-1 [1481 kB] 179s Get:90 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-s7 amd64 0.2.0-1 [328 kB] 179s Get:91 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-labeling all 0.4.3-1 [62.1 kB] 179s Get:92 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rcolorbrewer all 1.1-3-1build2 [54.0 kB] 179s Get:93 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-viridislite all 0.4.3-1 [1088 kB] 179s Get:94 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-scales all 1.4.0-1 [725 kB] 179s Get:95 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 r-cran-ggplot2 all 4.0.2+dfsg-1 [4941 kB] 180s Fetched 137 MB in 4s (36.7 MB/s) 180s Selecting previously unselected package libc-dev-bin. 180s (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 ... 130503 files and directories currently installed.) 180s Preparing to unpack .../00-libc-dev-bin_2.42-2ubuntu4_amd64.deb ... 180s Unpacking libc-dev-bin (2.42-2ubuntu4) ... 180s Selecting previously unselected package linux-libc-dev:amd64. 180s Preparing to unpack .../01-linux-libc-dev_6.19.0-3.3_amd64.deb ... 180s Unpacking linux-libc-dev:amd64 (6.19.0-3.3) ... 180s Selecting previously unselected package libcrypt-dev:amd64. 180s Preparing to unpack .../02-libcrypt-dev_1%3a4.5.1-1_amd64.deb ... 180s Unpacking libcrypt-dev:amd64 (1:4.5.1-1) ... 180s Selecting previously unselected package rpcsvc-proto. 180s Preparing to unpack .../03-rpcsvc-proto_1.4.3-1build1_amd64.deb ... 180s Unpacking rpcsvc-proto (1.4.3-1build1) ... 180s Selecting previously unselected package libc6-dev:amd64. 180s Preparing to unpack .../04-libc6-dev_2.42-2ubuntu4_amd64.deb ... 180s Unpacking libc6-dev:amd64 (2.42-2ubuntu4) ... 180s Selecting previously unselected package libisl23:amd64. 180s Preparing to unpack .../05-libisl23_0.27-1build1_amd64.deb ... 180s Unpacking libisl23:amd64 (0.27-1build1) ... 180s Selecting previously unselected package libmpc3:amd64. 180s Preparing to unpack .../06-libmpc3_1.3.1-2_amd64.deb ... 180s Unpacking libmpc3:amd64 (1.3.1-2) ... 180s Selecting previously unselected package cpp-15-x86-64-linux-gnu. 180s Preparing to unpack .../07-cpp-15-x86-64-linux-gnu_15.2.0-12ubuntu1_amd64.deb ... 180s Unpacking cpp-15-x86-64-linux-gnu (15.2.0-12ubuntu1) ... 180s Selecting previously unselected package cpp-15. 180s Preparing to unpack .../08-cpp-15_15.2.0-12ubuntu1_amd64.deb ... 180s Unpacking cpp-15 (15.2.0-12ubuntu1) ... 180s Selecting previously unselected package cpp-x86-64-linux-gnu. 180s Preparing to unpack .../09-cpp-x86-64-linux-gnu_4%3a15.2.0-4ubuntu1_amd64.deb ... 180s Unpacking cpp-x86-64-linux-gnu (4:15.2.0-4ubuntu1) ... 180s Selecting previously unselected package cpp. 180s Preparing to unpack .../10-cpp_4%3a15.2.0-4ubuntu1_amd64.deb ... 180s Unpacking cpp (4:15.2.0-4ubuntu1) ... 180s Selecting previously unselected package libcc1-0:amd64. 180s Preparing to unpack .../11-libcc1-0_16-20260208-1ubuntu1_amd64.deb ... 180s Unpacking libcc1-0:amd64 (16-20260208-1ubuntu1) ... 180s Selecting previously unselected package libitm1:amd64. 180s Preparing to unpack .../12-libitm1_16-20260208-1ubuntu1_amd64.deb ... 180s Unpacking libitm1:amd64 (16-20260208-1ubuntu1) ... 180s Selecting previously unselected package libasan8:amd64. 180s Preparing to unpack .../13-libasan8_16-20260208-1ubuntu1_amd64.deb ... 180s Unpacking libasan8:amd64 (16-20260208-1ubuntu1) ... 180s Selecting previously unselected package liblsan0:amd64. 180s Preparing to unpack .../14-liblsan0_16-20260208-1ubuntu1_amd64.deb ... 180s Unpacking liblsan0:amd64 (16-20260208-1ubuntu1) ... 180s Selecting previously unselected package libtsan2:amd64. 180s Preparing to unpack .../15-libtsan2_16-20260208-1ubuntu1_amd64.deb ... 180s Unpacking libtsan2:amd64 (16-20260208-1ubuntu1) ... 180s Selecting previously unselected package libubsan1:amd64. 180s Preparing to unpack .../16-libubsan1_16-20260208-1ubuntu1_amd64.deb ... 180s Unpacking libubsan1:amd64 (16-20260208-1ubuntu1) ... 180s Selecting previously unselected package libhwasan0:amd64. 180s Preparing to unpack .../17-libhwasan0_16-20260208-1ubuntu1_amd64.deb ... 180s Unpacking libhwasan0:amd64 (16-20260208-1ubuntu1) ... 180s Selecting previously unselected package libquadmath0:amd64. 180s Preparing to unpack .../18-libquadmath0_16-20260208-1ubuntu1_amd64.deb ... 180s Unpacking libquadmath0:amd64 (16-20260208-1ubuntu1) ... 180s Selecting previously unselected package libgcc-15-dev:amd64. 180s Preparing to unpack .../19-libgcc-15-dev_15.2.0-12ubuntu1_amd64.deb ... 180s Unpacking libgcc-15-dev:amd64 (15.2.0-12ubuntu1) ... 181s Selecting previously unselected package gcc-15-x86-64-linux-gnu. 181s Preparing to unpack .../20-gcc-15-x86-64-linux-gnu_15.2.0-12ubuntu1_amd64.deb ... 181s Unpacking gcc-15-x86-64-linux-gnu (15.2.0-12ubuntu1) ... 181s Selecting previously unselected package gcc-15. 181s Preparing to unpack .../21-gcc-15_15.2.0-12ubuntu1_amd64.deb ... 181s Unpacking gcc-15 (15.2.0-12ubuntu1) ... 181s Selecting previously unselected package gcc-x86-64-linux-gnu. 181s Preparing to unpack .../22-gcc-x86-64-linux-gnu_4%3a15.2.0-4ubuntu1_amd64.deb ... 181s Unpacking gcc-x86-64-linux-gnu (4:15.2.0-4ubuntu1) ... 181s Selecting previously unselected package gcc. 181s Preparing to unpack .../23-gcc_4%3a15.2.0-4ubuntu1_amd64.deb ... 181s Unpacking gcc (4:15.2.0-4ubuntu1) ... 181s Selecting previously unselected package libstdc++-15-dev:amd64. 181s Preparing to unpack .../24-libstdc++-15-dev_15.2.0-12ubuntu1_amd64.deb ... 181s Unpacking libstdc++-15-dev:amd64 (15.2.0-12ubuntu1) ... 181s Selecting previously unselected package g++-15-x86-64-linux-gnu. 181s Preparing to unpack .../25-g++-15-x86-64-linux-gnu_15.2.0-12ubuntu1_amd64.deb ... 181s Unpacking g++-15-x86-64-linux-gnu (15.2.0-12ubuntu1) ... 181s Selecting previously unselected package g++-15. 181s Preparing to unpack .../26-g++-15_15.2.0-12ubuntu1_amd64.deb ... 181s Unpacking g++-15 (15.2.0-12ubuntu1) ... 181s Selecting previously unselected package g++-x86-64-linux-gnu. 181s Preparing to unpack .../27-g++-x86-64-linux-gnu_4%3a15.2.0-4ubuntu1_amd64.deb ... 181s Unpacking g++-x86-64-linux-gnu (4:15.2.0-4ubuntu1) ... 181s Selecting previously unselected package g++. 181s Preparing to unpack .../28-g++_4%3a15.2.0-4ubuntu1_amd64.deb ... 181s Unpacking g++ (4:15.2.0-4ubuntu1) ... 181s Selecting previously unselected package build-essential. 181s Preparing to unpack .../29-build-essential_12.12ubuntu2_amd64.deb ... 181s Unpacking build-essential (12.12ubuntu2) ... 181s Selecting previously unselected package dctrl-tools. 181s Preparing to unpack .../30-dctrl-tools_2.24-3build4_amd64.deb ... 181s Unpacking dctrl-tools (2.24-3build4) ... 181s Selecting previously unselected package libgfortran-15-dev:amd64. 181s Preparing to unpack .../31-libgfortran-15-dev_15.2.0-12ubuntu1_amd64.deb ... 181s Unpacking libgfortran-15-dev:amd64 (15.2.0-12ubuntu1) ... 181s Selecting previously unselected package gfortran-15-x86-64-linux-gnu. 181s Preparing to unpack .../32-gfortran-15-x86-64-linux-gnu_15.2.0-12ubuntu1_amd64.deb ... 181s Unpacking gfortran-15-x86-64-linux-gnu (15.2.0-12ubuntu1) ... 181s Selecting previously unselected package gfortran-15. 181s Preparing to unpack .../33-gfortran-15_15.2.0-12ubuntu1_amd64.deb ... 181s Unpacking gfortran-15 (15.2.0-12ubuntu1) ... 181s Selecting previously unselected package gfortran-x86-64-linux-gnu. 181s Preparing to unpack .../34-gfortran-x86-64-linux-gnu_4%3a15.2.0-4ubuntu1_amd64.deb ... 181s Unpacking gfortran-x86-64-linux-gnu (4:15.2.0-4ubuntu1) ... 181s Selecting previously unselected package gfortran. 181s Preparing to unpack .../35-gfortran_4%3a15.2.0-4ubuntu1_amd64.deb ... 181s Unpacking gfortran (4:15.2.0-4ubuntu1) ... 181s Selecting previously unselected package icu-devtools. 181s Preparing to unpack .../36-icu-devtools_78.2-1ubuntu1_amd64.deb ... 181s Unpacking icu-devtools (78.2-1ubuntu1) ... 181s Selecting previously unselected package libblas-dev:amd64. 181s Preparing to unpack .../37-libblas-dev_3.12.1-7ubuntu1_amd64.deb ... 181s Unpacking libblas-dev:amd64 (3.12.1-7ubuntu1) ... 181s Selecting previously unselected package libbz2-dev:amd64. 181s Preparing to unpack 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.../43-libjpeg-dev_8c-2ubuntu12_amd64.deb ... 182s Unpacking libjpeg-dev:amd64 (8c-2ubuntu12) ... 182s Selecting previously unselected package liblapack-dev:amd64. 182s Preparing to unpack .../44-liblapack-dev_3.12.1-7ubuntu1_amd64.deb ... 182s Unpacking liblapack-dev:amd64 (3.12.1-7ubuntu1) ... 182s Selecting previously unselected package libncurses-dev:amd64. 182s Preparing to unpack .../45-libncurses-dev_6.6+20251231-1_amd64.deb ... 182s Unpacking libncurses-dev:amd64 (6.6+20251231-1) ... 182s Selecting previously unselected package libpcre2-16-0:amd64. 182s Preparing to unpack .../46-libpcre2-16-0_10.46-1_amd64.deb ... 182s Unpacking libpcre2-16-0:amd64 (10.46-1) ... 182s Selecting previously unselected package libpcre2-32-0:amd64. 182s Preparing to unpack .../47-libpcre2-32-0_10.46-1_amd64.deb ... 182s Unpacking libpcre2-32-0:amd64 (10.46-1) ... 182s Selecting previously unselected package libpcre2-posix3:amd64. 182s Preparing to unpack .../48-libpcre2-posix3_10.46-1_amd64.deb ... 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package r-cran-rlang. 182s Preparing to unpack .../65-r-cran-rlang_1.1.5-3_amd64.deb ... 182s Unpacking r-cran-rlang (1.1.5-3) ... 182s Selecting previously unselected package r-cran-lifecycle. 182s Preparing to unpack .../66-r-cran-lifecycle_1.0.5+dfsg-1_all.deb ... 182s Unpacking r-cran-lifecycle (1.0.5+dfsg-1) ... 182s Selecting previously unselected package r-cran-magrittr. 182s Preparing to unpack .../67-r-cran-magrittr_2.0.3-1_amd64.deb ... 182s Unpacking r-cran-magrittr (2.0.3-1) ... 182s Selecting previously unselected package r-cran-utf8. 182s Preparing to unpack .../68-r-cran-utf8_1.2.4-1_amd64.deb ... 182s Unpacking r-cran-utf8 (1.2.4-1) ... 182s Selecting previously unselected package r-cran-vctrs. 182s Preparing to unpack .../69-r-cran-vctrs_0.6.5-1_amd64.deb ... 182s Unpacking r-cran-vctrs (0.6.5-1) ... 182s Selecting previously unselected package r-cran-pillar. 182s Preparing to unpack .../70-r-cran-pillar_1.11.1+dfsg-1_all.deb ... 182s Unpacking r-cran-pillar 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libtirpc-dev:amd64 (1.3.6+ds-1) ... 183s Setting up libpkgconf3:amd64 (1.8.1-4build1) ... 183s Setting up rpcsvc-proto (1.4.3-1build1) ... 183s Setting up r-cran-stringi (1.8.4-1build2) ... 183s Setting up r-cran-s7 (0.2.0-1) ... 183s Setting up r-cran-cpp11 (0.5.3-1) ... 183s Setting up r-cran-rcolorbrewer (1.1-3-1build2) ... 183s Setting up r-cran-isoband (0.2.7-1) ... 183s Setting up libquadmath0:amd64 (16-20260208-1ubuntu1) ... 183s Setting up libmpc3:amd64 (1.3.1-2) ... 183s Setting up r-cran-gtable (0.3.6+dfsg-1) ... 183s Setting up r-cran-labeling (0.4.3-1) ... 183s Setting up icu-devtools (78.2-1ubuntu1) ... 183s Setting up pkgconf-bin (1.8.1-4build1) ... 183s Setting up r-cran-farver (2.1.2-1) ... 183s Setting up liblzma-dev:amd64 (5.8.2-2) ... 183s Setting up libubsan1:amd64 (16-20260208-1ubuntu1) ... 183s Setting up libpcre2-posix3:amd64 (10.46-1) ... 183s Setting up r-cran-viridislite (0.4.3-1) ... 183s Setting up libhwasan0:amd64 (16-20260208-1ubuntu1) ... 183s Setting up libcrypt-dev:amd64 (1:4.5.1-1) ... 183s Setting up libasan8:amd64 (16-20260208-1ubuntu1) ... 183s Setting up libtsan2:amd64 (16-20260208-1ubuntu1) ... 183s Setting up r-cran-r6 (2.6.1-1) ... 183s Setting up libisl23:amd64 (0.27-1build1) ... 183s Setting up libc-dev-bin (2.42-2ubuntu4) ... 183s Setting up libdeflate-dev:amd64 (1.23-2build1) ... 183s Setting up r-cran-magrittr (2.0.3-1) ... 183s Setting up libcc1-0:amd64 (16-20260208-1ubuntu1) ... 183s Setting up r-cran-vctrs (0.6.5-1) ... 183s Setting up liblsan0:amd64 (16-20260208-1ubuntu1) ... 183s Setting up libblas-dev:amd64 (3.12.1-7ubuntu1) ... 183s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so to provide /usr/lib/x86_64-linux-gnu/libblas.so (libblas.so-x86_64-linux-gnu) in auto mode 183s Setting up dctrl-tools (2.24-3build4) ... 183s Setting up libitm1:amd64 (16-20260208-1ubuntu1) ... 183s Setting up r-cran-pillar (1.11.1+dfsg-1) ... 183s Setting up libgcc-15-dev:amd64 (15.2.0-12ubuntu1) ... 183s Setting up r-cran-stringr (1.5.1-1) ... 183s Setting up r-cran-tibble (3.2.1+dfsg-3) ... 183s Setting up cpp-15-x86-64-linux-gnu (15.2.0-12ubuntu1) ... 183s Setting up libgfortran-15-dev:amd64 (15.2.0-12ubuntu1) ... 183s Setting up pkgconf:amd64 (1.8.1-4build1) ... 183s Setting up r-cran-tidyselect (1.2.1+dfsg-1) ... 183s Setting up gcc-15-x86-64-linux-gnu (15.2.0-12ubuntu1) ... 183s Setting up r-cran-scales (1.4.0-1) ... 183s Setting up liblapack-dev:amd64 (3.12.1-7ubuntu1) ... 183s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so to provide /usr/lib/x86_64-linux-gnu/liblapack.so (liblapack.so-x86_64-linux-gnu) in auto mode 183s Setting up r-cran-purrr (1.0.4-1) ... 183s Setting up cpp-15 (15.2.0-12ubuntu1) ... 183s Setting up libc6-dev:amd64 (2.42-2ubuntu4) ... 183s Setting up r-cran-dplyr (1.1.4-4) ... 183s Setting up libicu-dev:amd64 (78.2-1ubuntu1) ... 183s Setting up libbz2-dev:amd64 (1.0.8-6build2) ... 183s Setting up cpp-x86-64-linux-gnu (4:15.2.0-4ubuntu1) ... 183s Setting up gfortran-15-x86-64-linux-gnu (15.2.0-12ubuntu1) ... 183s Setting up libjpeg-turbo8-dev:amd64 (2.1.5-4ubuntu3) ... 183s Setting up libncurses-dev:amd64 (6.6+20251231-1) ... 183s Setting up libpcre2-dev:amd64 (10.46-1) ... 183s Setting up gcc-x86-64-linux-gnu (4:15.2.0-4ubuntu1) ... 183s Setting up r-cran-ggplot2 (4.0.2+dfsg-1) ... 183s Setting up libreadline-dev:amd64 (8.3-3) ... 183s Setting up gfortran-x86-64-linux-gnu (4:15.2.0-4ubuntu1) ... 183s Setting up gcc-15 (15.2.0-12ubuntu1) ... 183s Setting up libstdc++-15-dev:amd64 (15.2.0-12ubuntu1) ... 183s Setting up r-cran-tidyr (1.3.1-1) ... 183s Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1ubuntu2) ... 183s Setting up cpp (4:15.2.0-4ubuntu1) ... 183s Setting up libjpeg8-dev:amd64 (8c-2ubuntu12) ... 183s Setting up gfortran-15 (15.2.0-12ubuntu1) ... 183s Setting up g++-15-x86-64-linux-gnu (15.2.0-12ubuntu1) ... 183s Setting up libpng-dev:amd64 (1.6.54-1) ... 183s Setting up libjpeg-dev:amd64 (8c-2ubuntu12) ... 183s Setting up gcc (4:15.2.0-4ubuntu1) ... 183s Setting up r-cran-broom (1.0.12+dfsg-1) ... 183s Setting up g++-x86-64-linux-gnu (4:15.2.0-4ubuntu1) ... 183s Setting up g++-15 (15.2.0-12ubuntu1) ... 183s Setting up r-cran-geepack (1.3.12-1) ... 183s Setting up gfortran (4:15.2.0-4ubuntu1) ... 183s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode 183s 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 183s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode 183s 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 183s Setting up g++ (4:15.2.0-4ubuntu1) ... 183s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 183s Setting up build-essential (12.12ubuntu2) ... 183s Setting up r-base-dev (4.5.2-1ubuntu2) ... 183s Setting up pkg-r-autopkgtest (20250812) ... 183s Processing triggers for libc-bin (2.42-2ubuntu4) ... 183s Processing triggers for man-db (2.13.1-1build1) ... 183s Processing triggers for install-info (7.2-5) ... 184s autopkgtest [04:58:25]: test pkg-r-autopkgtest: /usr/share/dh-r/pkg-r-autopkgtest 184s autopkgtest [04:58:25]: test pkg-r-autopkgtest: [----------------------- 184s Test: Try to load the R library etm 184s 184s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 184s Copyright (C) 2025 The R Foundation for Statistical Computing 184s Platform: x86_64-pc-linux-gnu 184s 184s R is free software and comes with ABSOLUTELY NO WARRANTY. 184s You are welcome to redistribute it under certain conditions. 184s Type 'license()' or 'licence()' for distribution details. 184s 184s R is a collaborative project with many contributors. 184s Type 'contributors()' for more information and 184s 'citation()' on how to cite R or R packages in publications. 184s 184s Type 'demo()' for some demos, 'help()' for on-line help, or 184s 'help.start()' for an HTML browser interface to help. 184s Type 'q()' to quit R. 184s 184s > library('etm') 185s > 185s autopkgtest [04:58:26]: test pkg-r-autopkgtest: -----------------------] 186s pkg-r-autopkgtest PASS 186s autopkgtest [04:58:27]: test pkg-r-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 186s autopkgtest [04:58:27]: @@@@@@@@@@@@@@@@@@@@ summary 186s run-unit-test PASS 186s pkg-r-autopkgtest PASS