0s autopkgtest [02:31:32]: starting date and time: 2026-02-10 02:31:32+0000 0s autopkgtest [02:31:32]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [02:31:32]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.lc6vwp38/out --timeout-copy=6000 --needs-internet=try --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:lattice --apt-upgrade r-cran-etm --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=lattice/0.22-9-1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-cpu2-ram4-disk20-amd64 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@sto01-14.secgroup --name adt-resolute-amd64-r-cran-etm-20260210-023132-juju-7f2275-prod-proposed-migration-environment-15-13909d5e-2963-45f7-b3fc-a1f62f49e909 --image adt/ubuntu-resolute-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-autopkgtest-workers-amd64 -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 3s Creating nova instance adt-resolute-amd64-r-cran-etm-20260210-023132-juju-7f2275-prod-proposed-migration-environment-15-13909d5e-2963-45f7-b3fc-a1f62f49e909 from image adt/ubuntu-resolute-amd64-server-20260204.img (UUID fedf54b4-458b-493e-8072-6425c19717b4)... 71s autopkgtest [02:32:43]: testbed dpkg architecture: amd64 71s autopkgtest [02:32:43]: testbed apt version: 3.1.14 72s autopkgtest [02:32:44]: @@@@@@@@@@@@@@@@@@@@ test bed setup 72s autopkgtest [02:32:44]: testbed release detected to be: None 72s autopkgtest [02:32:44]: updating testbed package index (apt update) 73s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 73s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 73s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 73s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 73s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [173 kB] 73s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [1637 kB] 73s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [29.4 kB] 73s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 Packages [253 kB] 73s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main i386 Packages [201 kB] 73s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 c-n-f Metadata [5996 B] 73s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/restricted amd64 c-n-f Metadata [316 B] 73s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 Packages [1584 kB] 74s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/universe i386 Packages [639 kB] 74s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 c-n-f Metadata [33.3 kB] 74s Get:15 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 Packages [25.2 kB] 74s Get:16 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse i386 Packages [4320 B] 74s Get:17 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 c-n-f Metadata [996 B] 74s Fetched 4710 kB in 1s (4131 kB/s) 75s Reading package lists... 75s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 76s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 76s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 76s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 76s Reading package lists... 76s Reading package lists... 76s Building dependency tree... 76s Reading state information... 77s Calculating upgrade... 77s The following package was automatically installed and is no longer required: 77s libpython3.13 77s Use 'sudo apt autoremove' to remove it. 77s The following NEW packages will be installed: 77s gcc-16-base libpython3.14 libpython3.14-minimal libpython3.14-stdlib 77s linux-headers-6.19.0-3 linux-headers-6.19.0-3-generic 77s linux-image-6.19.0-3-generic linux-modules-6.19.0-3-generic 77s linux-tools-6.19.0-3 linux-tools-6.19.0-3-generic 77s The following packages will be upgraded: 77s 3cpio amd64-microcode apt bpftool busybox-initramfs busybox-static 77s cryptsetup-bin dash dbus dbus-bin dbus-daemon dbus-session-bus-common 77s dbus-system-bus-common dbus-user-session debianutils dmsetup dracut-install 77s ethtool findutils gir1.2-girepository-3.0 gir1.2-glib-2.0 hwdata iproute2 77s iptables less libapt-pkg7.0 libatomic1 libattr1 libbpf1 libbsd0 77s libcryptsetup12 libdbus-1-3 libdevmapper1.02.1 libdrm-amdgpu1 libdrm-common 77s libdrm2 libevent-core-2.1-7t64 libgcc-s1 libgdbm-compat4t64 libgdbm6t64 77s libgirepository-2.0-0 libglib2.0-0t64 libglib2.0-data libgpm2 libgudev-1.0-0 77s libidn2-0 libip4tc2 libip6tc2 libjansson4 libkeyutils1 liblsof0 77s libmaxminddb0 libnetfilter-conntrack3 libnpth0t64 libonig5 libpcap0.8t64 77s libpci3 libsensors-config libsensors5 libstdc++6 libusb-1.0-0 libwrap0 77s libxau6 libxkbcommon0 libxtables12 linux-generic linux-headers-generic 77s linux-headers-virtual linux-image-generic linux-image-virtual linux-perf 77s linux-tools-common linux-virtual lsof man-db mawk patch pciutils pnp.ids 77s pollinate python3-linkify-it python3-markdown-it python3-referencing sed 77s shared-mime-info tar tcpdump ubuntu-kernel-accessories ubuntu-standard wget 77s 90 upgraded, 10 newly installed, 0 to remove and 0 not upgraded. 77s Need to get 237 MB of archives. 77s After this operation, 339 MB of additional disk space will be used. 77s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 debianutils amd64 5.23.2build1 [93.3 kB] 77s Get:2 http://ftpmaster.internal/ubuntu resolute/main amd64 dash amd64 0.5.12-12ubuntu3 [96.0 kB] 77s Get:3 http://ftpmaster.internal/ubuntu resolute/main amd64 findutils amd64 4.10.0-3build2 [307 kB] 77s Get:4 http://ftpmaster.internal/ubuntu resolute/main amd64 sed amd64 4.9-2build3 [195 kB] 77s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 tar amd64 1.35+dfsg-3.1build2 [257 kB] 77s Get:6 http://ftpmaster.internal/ubuntu resolute/main amd64 libattr1 amd64 1:2.5.2-3build2 [11.4 kB] 77s Get:7 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc-16-base amd64 16-20260208-1ubuntu1 [59.7 kB] 77s Get:8 http://ftpmaster.internal/ubuntu resolute/main amd64 libgcc-s1 amd64 16-20260208-1ubuntu1 [80.3 kB] 77s Get:9 http://ftpmaster.internal/ubuntu resolute/main amd64 libbsd0 amd64 0.12.2-2build2 [42.3 kB] 77s Get:10 http://ftpmaster.internal/ubuntu resolute/main amd64 mawk amd64 1.3.4.20260129-1 [133 kB] 77s Get:11 http://ftpmaster.internal/ubuntu resolute/main amd64 libstdc++6 amd64 16-20260208-1ubuntu1 [844 kB] 77s Get:12 http://ftpmaster.internal/ubuntu resolute/main amd64 libapt-pkg7.0 amd64 3.1.15 [1151 kB] 77s Get:13 http://ftpmaster.internal/ubuntu resolute/main amd64 apt amd64 3.1.15 [1479 kB] 77s Get:14 http://ftpmaster.internal/ubuntu resolute/main amd64 dbus-system-bus-common all 1.16.2-2ubuntu3 [55.8 kB] 77s Get:15 http://ftpmaster.internal/ubuntu resolute/main amd64 dbus-session-bus-common all 1.16.2-2ubuntu3 [54.4 kB] 77s Get:16 http://ftpmaster.internal/ubuntu resolute/main amd64 dbus-user-session amd64 1.16.2-2ubuntu3 [9696 B] 77s Get:17 http://ftpmaster.internal/ubuntu resolute/main amd64 dbus-daemon amd64 1.16.2-2ubuntu3 [119 kB] 77s Get:18 http://ftpmaster.internal/ubuntu resolute/main amd64 dbus-bin amd64 1.16.2-2ubuntu3 [40.1 kB] 77s Get:19 http://ftpmaster.internal/ubuntu resolute/main amd64 dbus amd64 1.16.2-2ubuntu3 [24.2 kB] 77s Get:20 http://ftpmaster.internal/ubuntu resolute/main amd64 libdbus-1-3 amd64 1.16.2-2ubuntu3 [185 kB] 77s Get:21 http://ftpmaster.internal/ubuntu resolute/main amd64 libdevmapper1.02.1 amd64 2:1.02.205-2ubuntu3 [142 kB] 77s Get:22 http://ftpmaster.internal/ubuntu resolute/main amd64 dmsetup amd64 2:1.02.205-2ubuntu3 [79.4 kB] 77s Get:23 http://ftpmaster.internal/ubuntu resolute/main amd64 ethtool amd64 1:6.15-3build1 [318 kB] 77s Get:24 http://ftpmaster.internal/ubuntu resolute/main amd64 gir1.2-girepository-3.0 amd64 2.87.2-2 [25.2 kB] 77s Get:25 http://ftpmaster.internal/ubuntu resolute/main amd64 libgirepository-2.0-0 amd64 2.87.2-2 [76.1 kB] 77s Get:26 http://ftpmaster.internal/ubuntu resolute/main amd64 libatomic1 amd64 16-20260208-1ubuntu1 [11.4 kB] 77s Get:27 http://ftpmaster.internal/ubuntu resolute/main amd64 gir1.2-glib-2.0 amd64 2.87.2-2 [182 kB] 77s Get:28 http://ftpmaster.internal/ubuntu resolute/main amd64 libglib2.0-0t64 amd64 2.87.2-2 [1613 kB] 77s Get:29 http://ftpmaster.internal/ubuntu resolute/main amd64 libbpf1 amd64 1:1.6.2-1build1 [184 kB] 77s Get:30 http://ftpmaster.internal/ubuntu resolute/main amd64 iptables amd64 1.8.11-2ubuntu3 [381 kB] 77s Get:31 http://ftpmaster.internal/ubuntu resolute/main amd64 libip4tc2 amd64 1.8.11-2ubuntu3 [24.2 kB] 77s Get:32 http://ftpmaster.internal/ubuntu resolute/main amd64 libip6tc2 amd64 1.8.11-2ubuntu3 [24.4 kB] 77s Get:33 http://ftpmaster.internal/ubuntu resolute/main amd64 libnetfilter-conntrack3 amd64 1.1.1-1 [47.5 kB] 77s Get:34 http://ftpmaster.internal/ubuntu resolute/main amd64 libxtables12 amd64 1.8.11-2ubuntu3 [36.6 kB] 77s Get:35 http://ftpmaster.internal/ubuntu resolute/main amd64 iproute2 amd64 6.18.0-1ubuntu1 [1178 kB] 77s Get:36 http://ftpmaster.internal/ubuntu resolute/main amd64 less amd64 668-1build1 [172 kB] 77s Get:37 http://ftpmaster.internal/ubuntu resolute/main amd64 libcryptsetup12 amd64 2:2.8.0-1ubuntu3 [283 kB] 77s Get:38 http://ftpmaster.internal/ubuntu resolute/main amd64 libglib2.0-data all 2.87.2-2 [58.2 kB] 77s Get:39 http://ftpmaster.internal/ubuntu resolute/main amd64 libidn2-0 amd64 2.3.8-4build1 [67.6 kB] 77s Get:40 http://ftpmaster.internal/ubuntu resolute/main amd64 libkeyutils1 amd64 1.6.3-6ubuntu3 [10.6 kB] 77s Get:41 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-linkify-it all 2.0.3-1ubuntu3 [19.4 kB] 77s Get:42 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-markdown-it all 3.0.0-3build1 [54.4 kB] 77s Get:43 http://ftpmaster.internal/ubuntu resolute/main amd64 shared-mime-info amd64 2.4-5build3 [476 kB] 77s Get:44 http://ftpmaster.internal/ubuntu resolute/main amd64 busybox-static amd64 1:1.37.0-7ubuntu1 [1034 kB] 77s Get:45 http://ftpmaster.internal/ubuntu resolute/main amd64 libdrm-common all 2.4.131-1 [9774 B] 77s Get:46 http://ftpmaster.internal/ubuntu resolute/main amd64 libdrm2 amd64 2.4.131-1 [42.3 kB] 77s Get:47 http://ftpmaster.internal/ubuntu resolute/main amd64 libgdbm6t64 amd64 1.26-1build1 [36.5 kB] 77s Get:48 http://ftpmaster.internal/ubuntu resolute/main amd64 libgpm2 amd64 1.20.7-12build1 [14.4 kB] 77s Get:49 http://ftpmaster.internal/ubuntu resolute/main amd64 libjansson4 amd64 2.14-2build4 [33.2 kB] 77s Get:50 http://ftpmaster.internal/ubuntu resolute/main amd64 lsof amd64 4.99.4+dfsg-2build2 [239 kB] 77s Get:51 http://ftpmaster.internal/ubuntu resolute/main amd64 liblsof0 amd64 4.99.4+dfsg-2build2 [56.5 kB] 77s Get:52 http://ftpmaster.internal/ubuntu resolute/main amd64 libmaxminddb0 amd64 1.12.2-1build2 [18.9 kB] 77s Get:53 http://ftpmaster.internal/ubuntu resolute/main amd64 libpcap0.8t64 amd64 1.10.5-2ubuntu3 [154 kB] 77s Get:54 http://ftpmaster.internal/ubuntu resolute/main amd64 pciutils amd64 1:3.14.0-1build2 [95.5 kB] 77s Get:55 http://ftpmaster.internal/ubuntu resolute/main amd64 libpci3 amd64 1:3.14.0-1build2 [38.1 kB] 77s Get:56 http://ftpmaster.internal/ubuntu resolute/main amd64 libsensors-config all 1:3.6.2-2build1 [6862 B] 77s Get:57 http://ftpmaster.internal/ubuntu resolute/main amd64 libsensors5 amd64 1:3.6.2-2build1 [28.9 kB] 77s Get:58 http://ftpmaster.internal/ubuntu resolute/main amd64 libusb-1.0-0 amd64 2:1.0.29-2build1 [56.9 kB] 77s Get:59 http://ftpmaster.internal/ubuntu resolute/main amd64 libxau6 amd64 1:1.0.11-1build2 [7502 B] 77s Get:60 http://ftpmaster.internal/ubuntu resolute/main amd64 libxkbcommon0 amd64 1.13.1-1 [159 kB] 77s Get:61 http://ftpmaster.internal/ubuntu resolute/main amd64 man-db amd64 2.13.1-1build1 [1392 kB] 77s Get:62 http://ftpmaster.internal/ubuntu resolute/main amd64 tcpdump amd64 4.99.5-2ubuntu3 [477 kB] 77s Get:63 http://ftpmaster.internal/ubuntu resolute/main amd64 wget amd64 1.25.0-2ubuntu4 [353 kB] 77s Get:64 http://ftpmaster.internal/ubuntu resolute/main amd64 ubuntu-standard amd64 1.564 [13.3 kB] 77s Get:65 http://ftpmaster.internal/ubuntu resolute/main amd64 3cpio amd64 0.14.0-1ubuntu1 [285 kB] 77s Get:66 http://ftpmaster.internal/ubuntu resolute/main amd64 bpftool amd64 7.7.0+6.19.0-3.3 [1229 kB] 77s Get:67 http://ftpmaster.internal/ubuntu resolute/main amd64 busybox-initramfs amd64 1:1.37.0-7ubuntu1 [191 kB] 77s Get:68 http://ftpmaster.internal/ubuntu resolute/main amd64 cryptsetup-bin amd64 2:2.8.0-1ubuntu3 [228 kB] 77s Get:69 http://ftpmaster.internal/ubuntu resolute/main amd64 dracut-install amd64 109-11ubuntu1 [45.8 kB] 77s Get:70 http://ftpmaster.internal/ubuntu resolute/main amd64 hwdata all 0.394-1build1 [1566 B] 77s Get:71 http://ftpmaster.internal/ubuntu resolute/main amd64 pnp.ids all 0.394-1build1 [29.6 kB] 77s Get:72 http://ftpmaster.internal/ubuntu resolute/main amd64 libdrm-amdgpu1 amd64 2.4.131-1 [23.2 kB] 77s Get:73 http://ftpmaster.internal/ubuntu resolute/main amd64 libevent-core-2.1-7t64 amd64 2.1.12-stable-10build2 [93.1 kB] 77s Get:74 http://ftpmaster.internal/ubuntu resolute/main amd64 libgdbm-compat4t64 amd64 1.26-1build1 [6796 B] 77s Get:75 http://ftpmaster.internal/ubuntu resolute/main amd64 libgudev-1.0-0 amd64 1:238-7build1 [15.9 kB] 77s Get:76 http://ftpmaster.internal/ubuntu resolute/main amd64 libnpth0t64 amd64 1.8-3build1 [9302 B] 77s Get:77 http://ftpmaster.internal/ubuntu resolute/main amd64 libonig5 amd64 6.9.10-1build1 [174 kB] 77s Get:78 http://ftpmaster.internal/ubuntu resolute/main amd64 libpython3.14-minimal amd64 3.14.2-1 [920 kB] 77s Get:79 http://ftpmaster.internal/ubuntu resolute/main amd64 libpython3.14-stdlib amd64 3.14.2-1 [2398 kB] 77s Get:80 http://ftpmaster.internal/ubuntu resolute/main amd64 libpython3.14 amd64 3.14.2-1 [2568 kB] 77s Get:81 http://ftpmaster.internal/ubuntu resolute/main amd64 libwrap0 amd64 7.6.q-36build2 [48.5 kB] 78s Get:82 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-modules-6.19.0-3-generic amd64 6.19.0-3.3 [171 MB] 81s 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] 81s Get:84 http://ftpmaster.internal/ubuntu resolute/main amd64 amd64-microcode amd64 3.20251202.1ubuntu1 [459 kB] 81s Get:85 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-generic amd64 6.19.0-3.3 [1698 B] 81s Get:86 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-image-generic amd64 6.19.0-3.3 [12.2 kB] 81s Get:87 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-virtual amd64 6.19.0-3.3 [1700 B] 81s Get:88 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-image-virtual amd64 6.19.0-3.3 [12.1 kB] 81s Get:89 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-headers-virtual amd64 6.19.0-3.3 [1646 B] 81s Get:90 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-headers-6.19.0-3 all 6.19.0-3.3 [14.9 MB] 81s Get:91 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-headers-6.19.0-3-generic amd64 6.19.0-3.3 [4330 kB] 81s Get:92 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-headers-generic amd64 6.19.0-3.3 [12.0 kB] 81s Get:93 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-perf amd64 6.19.0-3.3 [4480 kB] 82s Get:94 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-tools-common all 6.19.0-3.3 [345 kB] 82s Get:95 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-tools-6.19.0-3 amd64 6.19.0-3.3 [1455 kB] 82s Get:96 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-tools-6.19.0-3-generic amd64 6.19.0-3.3 [1612 B] 82s Get:97 http://ftpmaster.internal/ubuntu resolute/main amd64 patch amd64 2.8-2build1 [95.7 kB] 82s Get:98 http://ftpmaster.internal/ubuntu resolute/main amd64 pollinate all 4.33-4ubuntu5 [14.0 kB] 82s Get:99 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-referencing all 0.36.2-1ubuntu2 [22.2 kB] 82s Get:100 http://ftpmaster.internal/ubuntu resolute/main amd64 ubuntu-kernel-accessories amd64 1.564 [13.1 kB] 82s dpkg-preconfigure: unable to re-open stdin: No such file or directory 82s Fetched 237 MB in 5s (48.9 MB/s) 82s (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.) 82s Preparing to unpack .../debianutils_5.23.2build1_amd64.deb ... 82s Unpacking debianutils (5.23.2build1) over (5.23.2) ... 82s Setting up debianutils (5.23.2build1) ... 82s (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.) 82s Preparing to unpack .../dash_0.5.12-12ubuntu3_amd64.deb ... 82s Unpacking dash (0.5.12-12ubuntu3) over (0.5.12-12ubuntu2) ... 82s Setting up dash (0.5.12-12ubuntu3) ... 82s (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.) 82s Preparing to unpack .../findutils_4.10.0-3build2_amd64.deb ... 82s Unpacking findutils (4.10.0-3build2) over (4.10.0-3build1) ... 82s Setting up findutils (4.10.0-3build2) ... 82s (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.) 82s Preparing to unpack .../sed_4.9-2build3_amd64.deb ... 82s Unpacking sed (4.9-2build3) over (4.9-2build2) ... 82s Setting up sed (4.9-2build3) ... 83s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 83957 files and directories currently installed.) 83s Preparing to unpack .../tar_1.35+dfsg-3.1build2_amd64.deb ... 83s Unpacking tar (1.35+dfsg-3.1build2) over (1.35+dfsg-3.1build1) ... 83s Setting up tar (1.35+dfsg-3.1build2) ... 83s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 83957 files and directories currently installed.) 83s Preparing to unpack .../libattr1_1%3a2.5.2-3build2_amd64.deb ... 83s Unpacking libattr1:amd64 (1:2.5.2-3build2) over (1:2.5.2-3build1) ... 83s Setting up libattr1:amd64 (1:2.5.2-3build2) ... 83s Selecting previously unselected package gcc-16-base:amd64. 83s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 83957 files and directories currently installed.) 83s Preparing to unpack .../gcc-16-base_16-20260208-1ubuntu1_amd64.deb ... 83s Unpacking gcc-16-base:amd64 (16-20260208-1ubuntu1) ... 83s Setting up gcc-16-base:amd64 (16-20260208-1ubuntu1) ... 83s (Reading database ... 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(7.7.0+6.19.0-3.3) ... 90s Setting up libip6tc2:amd64 (1.8.11-2ubuntu3) ... 90s Setting up liblsof0 (4.99.4+dfsg-2build2) ... 90s Setting up libmaxminddb0:amd64 (1.12.2-1build2) ... 90s Setting up libpython3.14-minimal:amd64 (3.14.2-1) ... 90s Setting up libsensors-config (1:3.6.2-2build1) ... 90s Setting up less (668-1build1) ... 90s Setting up linux-headers-6.19.0-3 (6.19.0-3.3) ... 90s Setting up libidn2-0:amd64 (2.3.8-4build1) ... 90s Setting up amd64-microcode (3.20251202.1ubuntu1) ... 90s amd64-microcode: microcode will be updated at next boot 90s Setting up man-db (2.13.1-1build1) ... 90s Updating database of manual pages ... 92s man-db.service is a disabled or a static unit not running, not starting it. 92s Setting up libjansson4:amd64 (2.14-2build4) ... 92s Setting up libglib2.0-data (2.87.2-2) ... 92s Setting up pollinate (4.33-4ubuntu5) ... 102s Setting up busybox-static (1:1.37.0-7ubuntu1) ... 102s Setting up libwrap0:amd64 (7.6.q-36build2) ... 102s Setting up linux-image-6.19.0-3-generic (6.19.0-3.3+1) ... 103s I: /boot/vmlinuz is now a symlink to vmlinuz-6.19.0-3-generic 103s I: /boot/initrd.img is now a symlink to initrd.img-6.19.0-3-generic 104s Setting up libdbus-1-3:amd64 (1.16.2-2ubuntu3) ... 104s Setting up libatomic1:amd64 (16-20260208-1ubuntu1) ... 104s Setting up patch (2.8-2build1) ... 104s Setting up libsensors5:amd64 (1:3.6.2-2build1) ... 104s Setting up busybox-initramfs (1:1.37.0-7ubuntu1) ... 104s Setting up libxtables12:amd64 (1.8.11-2ubuntu3) ... 104s Setting up lsof (4.99.4+dfsg-2build2) ... 104s Setting up libpci3:amd64 (1:3.14.0-1build2) ... 104s Setting up libdevmapper1.02.1:amd64 (2:1.02.205-2ubuntu3) ... 104s Setting up dracut-install (109-11ubuntu1) ... 104s Setting up dmsetup (2:1.02.205-2ubuntu3) ... 104s Setting up libnetfilter-conntrack3:amd64 (1.1.1-1) ... 104s Setting up pnp.ids (0.394-1build1) ... 104s Setting up dbus-session-bus-common (1.16.2-2ubuntu3) ... 104s Setting up python3-linkify-it (2.0.3-1ubuntu3) ... 104s Setting up libpcap0.8t64:amd64 (1.10.5-2ubuntu3) ... 104s Setting up libcryptsetup12:amd64 (2:2.8.0-1ubuntu3) ... 104s Setting up mawk (1.3.4.20260129-1) ... 104s Setting up libevent-core-2.1-7t64:amd64 (2.1.12-stable-10build2) ... 104s Setting up libusb-1.0-0:amd64 (2:1.0.29-2build1) ... 104s Setting up linux-image-virtual (6.19.0-3.3) ... 104s Setting up dbus-system-bus-common (1.16.2-2ubuntu3) ... 104s Setting up libbsd0:amd64 (0.12.2-2build2) ... 104s Setting up libdrm-common (2.4.131-1) ... 104s Setting up libstdc++6:amd64 (16-20260208-1ubuntu1) ... 104s Setting up dbus-bin (1.16.2-2ubuntu3) ... 104s Setting up libonig5:amd64 (6.9.10-1build1) ... 104s Setting up libbpf1:amd64 (1:1.6.2-1build1) ... 104s Setting up ethtool (1:6.15-3build1) ... 104s Setting up python3-referencing (0.36.2-1ubuntu2) ... 104s Setting up libxkbcommon0:amd64 (1.13.1-1) ... 104s Setting up cryptsetup-bin (2:2.8.0-1ubuntu3) ... 104s Setting up linux-headers-6.19.0-3-generic (6.19.0-3.3) ... 104s Setting up tcpdump (4.99.5-2ubuntu3) ... 104s Setting up linux-image-generic (6.19.0-3.3) ... 104s Setting up wget (1.25.0-2ubuntu4) ... 104s Setting up libpython3.14-stdlib:amd64 (3.14.2-1) ... 104s Setting up iptables (1.8.11-2ubuntu3) ... 104s Setting up iproute2 (6.18.0-1ubuntu1) ... 104s Setting up linux-headers-generic (6.19.0-3.3) ... 104s Setting up dbus-daemon (1.16.2-2ubuntu3) ... 104s Setting up hwdata (0.394-1build1) ... 104s Setting up dbus-user-session (1.16.2-2ubuntu3) ... 104s Setting up libglib2.0-0t64:amd64 (2.87.2-2) ... 104s No schema files found: doing nothing. 104s Setting up dbus (1.16.2-2ubuntu3) ... 104s A reboot is required to replace the running dbus-daemon. 104s Please reboot the system when convenient. 104s Setting up shared-mime-info (2.4-5build3) ... 105s Setting up gir1.2-glib-2.0:amd64 (2.87.2-2) ... 105s Setting up pciutils (1:3.14.0-1build2) ... 105s Setting up python3-markdown-it (3.0.0-3build1) ... 105s Setting up libdrm2:amd64 (2.4.131-1) ... 105s Setting up libpython3.14:amd64 (3.14.2-1) ... 105s Setting up libapt-pkg7.0:amd64 (3.1.15) ... 105s Setting up linux-tools-common (6.19.0-3.3) ... 105s Setting up libgudev-1.0-0:amd64 (1:238-7build1) ... 105s Setting up libdrm-amdgpu1:amd64 (2.4.131-1) ... 105s Setting up apt (3.1.15) ... 106s Setting up linux-headers-virtual (6.19.0-3.3) ... 106s Setting up linux-generic (6.19.0-3.3) ... 106s Setting up libgirepository-2.0-0:amd64 (2.87.2-2) ... 106s Setting up linux-tools-6.19.0-3 (6.19.0-3.3) ... 106s Setting up ubuntu-standard (1.564) ... 106s Setting up gir1.2-girepository-3.0:amd64 (2.87.2-2) ... 106s Setting up linux-virtual (6.19.0-3.3) ... 106s Setting up linux-perf (6.19.0-3.3) ... 106s Setting up linux-tools-6.19.0-3-generic (6.19.0-3.3) ... 106s Processing triggers for debianutils (5.23.2build1) ... 106s Processing triggers for install-info (7.2-5) ... 106s Processing triggers for initramfs-tools (0.150ubuntu7) ... 106s update-initramfs: Generating /boot/initrd.img-6.18.0-9-generic 110s Processing triggers for libc-bin (2.42-2ubuntu4) ... 110s Processing triggers for linux-image-6.19.0-3-generic (6.19.0-3.3+1) ... 110s /etc/kernel/postinst.d/initramfs-tools: 110s update-initramfs: Generating /boot/initrd.img-6.19.0-3-generic 114s /etc/kernel/postinst.d/zz-update-grub: 114s Sourcing file `/etc/default/grub' 114s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 114s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg' 114s Generating grub configuration file ... 114s Found linux image: /boot/vmlinuz-6.19.0-3-generic 114s Found initrd image: /boot/initrd.img-6.19.0-3-generic 114s Found linux image: /boot/vmlinuz-6.18.0-9-generic 114s Found initrd image: /boot/initrd.img-6.18.0-9-generic 114s Warning: os-prober will not be executed to detect other bootable partitions. 114s Systems on them will not be added to the GRUB boot configuration. 114s Check GRUB_DISABLE_OS_PROBER documentation entry. 114s Adding boot menu entry for UEFI Firmware Settings ... 114s done 114s autopkgtest [02:33:26]: upgrading testbed (apt dist-upgrade and autopurge) 115s Reading package lists... 115s Building dependency tree... 115s Reading state information... 115s Calculating upgrade... 115s The following package was automatically installed and is no longer required: 115s libpython3.13 115s Use 'sudo apt autoremove' to remove it. 115s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 116s Reading package lists... 116s Building dependency tree... 116s Reading state information... 116s Solving dependencies... 116s The following packages will be REMOVED: 116s libpython3.13* 116s 0 upgraded, 0 newly installed, 1 to remove and 0 not upgraded. 116s After this operation, 7599 kB disk space will be freed. 116s (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.) 116s Removing libpython3.13:amd64 (3.13.11-1) ... 116s Processing triggers for libc-bin (2.42-2ubuntu4) ... 116s autopkgtest [02:33:28]: rebooting testbed after setup commands that affected boot 145s autopkgtest [02:33:57]: testbed running kernel: Linux 6.19.0-3-generic #3-Ubuntu SMP PREEMPT_DYNAMIC Fri Jan 23 20:01:24 UTC 2026 147s autopkgtest [02:33:59]: @@@@@@@@@@@@@@@@@@@@ apt-source r-cran-etm 149s Get:1 http://ftpmaster.internal/ubuntu resolute/universe r-cran-etm 1.1.1-1build1 (dsc) [2147 B] 149s Get:2 http://ftpmaster.internal/ubuntu resolute/universe r-cran-etm 1.1.1-1build1 (tar) [242 kB] 149s Get:3 http://ftpmaster.internal/ubuntu resolute/universe r-cran-etm 1.1.1-1build1 (diff) [3672 B] 149s gpgv: Signature made Fri Nov 28 21:46:53 2025 UTC 149s gpgv: using RSA key 92FE4F8B40CADC4ECCD60C1F5961FDBE9C619809 149s gpgv: Can't check signature: No public key 149s dpkg-source: warning: cannot verify inline signature for ./r-cran-etm_1.1.1-1build1.dsc: no acceptable signature found 149s autopkgtest [02:34:01]: testing package r-cran-etm version 1.1.1-1build1 149s autopkgtest [02:34:01]: build not needed 153s autopkgtest [02:34:05]: test run-unit-test: preparing testbed 153s Reading package lists... 153s Building dependency tree... 153s Reading state information... 153s Solving dependencies... 153s The following NEW packages will be installed: 153s fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono libblas3 153s libcairo2 libdatrie1 libdeflate0 libfontconfig1 libgfortran5 libgomp1 153s libgraphite2-3 libharfbuzz0b libice6 libjbig0 libjpeg-turbo8 libjpeg8 153s liblapack3 liblerc4 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 153s libpaper-utils libpaper2 libpixman-1-0 libsharpyuv0 libsm6 libtcl8.6 153s libthai-data libthai0 libtiff6 libtk8.6 libwebp7 libxcb-render0 libxcb-shm0 153s libxft2 libxrender1 libxss1 libxt6t64 r-base-core r-cran-data.table 153s r-cran-dbi r-cran-etm r-cran-kmi r-cran-lattice r-cran-littler r-cran-matrix 153s r-cran-mitools r-cran-pkgkitten r-cran-rcpp r-cran-rcpparmadillo 153s r-cran-survival unzip x11-common xdg-utils zip 153s 0 upgraded, 56 newly installed, 0 to remove and 0 not upgraded. 153s Need to get 61.0 MB of archives. 153s After this operation, 128 MB of additional disk space will be used. 153s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-dejavu-mono all 2.37-8build1 [502 kB] 153s Get:2 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-dejavu-core all 2.37-8build1 [834 kB] 153s Get:3 http://ftpmaster.internal/ubuntu resolute/main amd64 fontconfig-config amd64 2.17.1-3ubuntu1 [38.5 kB] 153s Get:4 http://ftpmaster.internal/ubuntu resolute/main amd64 libfontconfig1 amd64 2.17.1-3ubuntu1 [144 kB] 153s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 fontconfig amd64 2.17.1-3ubuntu1 [180 kB] 153s Get:6 http://ftpmaster.internal/ubuntu resolute/main amd64 libblas3 amd64 3.12.1-7ubuntu1 [260 kB] 153s Get:7 http://ftpmaster.internal/ubuntu resolute/main amd64 libpixman-1-0 amd64 0.46.4-1 [287 kB] 153s Get:8 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-render0 amd64 1.17.0-2ubuntu1 [16.2 kB] 153s Get:9 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-shm0 amd64 1.17.0-2ubuntu1 [5808 B] 153s Get:10 http://ftpmaster.internal/ubuntu resolute/main amd64 libxrender1 amd64 1:0.9.12-1 [19.8 kB] 153s Get:11 http://ftpmaster.internal/ubuntu resolute/main amd64 libcairo2 amd64 1.18.4-3 [579 kB] 153s Get:12 http://ftpmaster.internal/ubuntu resolute/main amd64 libdatrie1 amd64 0.2.14-1 [19.8 kB] 153s Get:13 http://ftpmaster.internal/ubuntu resolute/main amd64 libdeflate0 amd64 1.23-2build1 [51.6 kB] 154s Get:14 http://ftpmaster.internal/ubuntu resolute/main amd64 libgfortran5 amd64 16-20260208-1ubuntu1 [957 kB] 154s Get:15 http://ftpmaster.internal/ubuntu resolute/main amd64 libgomp1 amd64 16-20260208-1ubuntu1 [162 kB] 154s Get:16 http://ftpmaster.internal/ubuntu resolute/main amd64 libgraphite2-3 amd64 1.3.14-11ubuntu1 [73.7 kB] 154s Get:17 http://ftpmaster.internal/ubuntu resolute/main amd64 libharfbuzz0b amd64 12.3.2-1 [519 kB] 154s Get:18 http://ftpmaster.internal/ubuntu resolute/main amd64 x11-common all 1:7.7+24ubuntu1 [22.4 kB] 154s Get:19 http://ftpmaster.internal/ubuntu resolute/main amd64 libice6 amd64 2:1.1.1-1build1 [44.0 kB] 154s Get:20 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg-turbo8 amd64 2.1.5-4ubuntu3 [156 kB] 154s Get:21 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg8 amd64 8c-2ubuntu12 [2142 B] 154s Get:22 http://ftpmaster.internal/ubuntu resolute/main amd64 liblapack3 amd64 3.12.1-7ubuntu1 [2739 kB] 154s Get:23 http://ftpmaster.internal/ubuntu resolute/main amd64 liblerc4 amd64 4.0.0+ds-5ubuntu2 [207 kB] 154s Get:24 http://ftpmaster.internal/ubuntu resolute/main amd64 libthai-data all 0.1.30-1 [155 kB] 154s Get:25 http://ftpmaster.internal/ubuntu resolute/main amd64 libthai0 amd64 0.1.30-1 [19.2 kB] 154s Get:26 http://ftpmaster.internal/ubuntu resolute/main amd64 libpango-1.0-0 amd64 1.57.0-1 [241 kB] 154s Get:27 http://ftpmaster.internal/ubuntu resolute/main amd64 libpangoft2-1.0-0 amd64 1.57.0-1 [53.3 kB] 154s Get:28 http://ftpmaster.internal/ubuntu resolute/main amd64 libpangocairo-1.0-0 amd64 1.57.0-1 [29.0 kB] 154s Get:29 http://ftpmaster.internal/ubuntu resolute/main amd64 libpaper2 amd64 2.2.5-0.3build1 [17.3 kB] 154s Get:30 http://ftpmaster.internal/ubuntu resolute/main amd64 libpaper-utils amd64 2.2.5-0.3build1 [15.6 kB] 154s Get:31 http://ftpmaster.internal/ubuntu resolute/main amd64 libsharpyuv0 amd64 1.5.0-0.1build1 [17.6 kB] 154s Get:32 http://ftpmaster.internal/ubuntu resolute/main amd64 libsm6 amd64 2:1.2.6-1build1 [16.9 kB] 154s Get:33 http://ftpmaster.internal/ubuntu resolute/main amd64 libtcl8.6 amd64 8.6.17+dfsg-1build1 [1003 kB] 154s Get:34 http://ftpmaster.internal/ubuntu resolute/main amd64 libjbig0 amd64 2.1-6.1ubuntu3 [30.0 kB] 154s Get:35 http://ftpmaster.internal/ubuntu resolute/main amd64 libwebp7 amd64 1.5.0-0.1build1 [264 kB] 154s Get:36 http://ftpmaster.internal/ubuntu resolute/main amd64 libtiff6 amd64 4.7.0-3ubuntu3 [209 kB] 154s Get:37 http://ftpmaster.internal/ubuntu resolute/main amd64 libxft2 amd64 2.3.6-1build2 [45.1 kB] 154s Get:38 http://ftpmaster.internal/ubuntu resolute/main amd64 libxss1 amd64 1:1.2.3-1build4 [7084 B] 154s Get:39 http://ftpmaster.internal/ubuntu resolute/main amd64 libtk8.6 amd64 8.6.17-1 [823 kB] 154s Get:40 http://ftpmaster.internal/ubuntu resolute/main amd64 libxt6t64 amd64 1:1.2.1-1.3 [173 kB] 154s Get:41 http://ftpmaster.internal/ubuntu resolute/main amd64 zip amd64 3.0-15ubuntu3 [175 kB] 154s Get:42 http://ftpmaster.internal/ubuntu resolute/main amd64 unzip amd64 6.0-29ubuntu1 [180 kB] 154s Get:43 http://ftpmaster.internal/ubuntu resolute/main amd64 xdg-utils all 1.2.1-2ubuntu2 [66.1 kB] 154s Get:44 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-base-core amd64 4.5.2-1ubuntu2 [28.8 MB] 155s Get:45 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-data.table amd64 1.17.0+dfsg-1 [2168 kB] 155s Get:46 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-dbi all 1.2.3-1build1 [855 kB] 155s Get:47 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 r-cran-lattice amd64 0.22-9-1 [1399 kB] 155s Get:48 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-matrix amd64 1.7-4-1 [4220 kB] 156s Get:49 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-survival amd64 3.8-6-1 [8274 kB] 156s Get:50 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-littler amd64 0.3.22-1 [85.5 kB] 156s Get:51 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-pkgkitten all 0.2.4-1 [27.2 kB] 156s Get:52 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rcpp amd64 1.1.0-1 [2021 kB] 156s Get:53 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rcpparmadillo amd64 15.2.3-1-1 [919 kB] 156s Get:54 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-etm amd64 1.1.1-1build1 [485 kB] 156s Get:55 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-mitools all 2.4-2build2 [266 kB] 156s Get:56 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-kmi all 0.5.5-2build2 [78.9 kB] 156s Preconfiguring packages ... 156s Fetched 61.0 MB in 3s (21.6 MB/s) 156s Selecting previously unselected package fonts-dejavu-mono. 157s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 125269 files and directories currently installed.) 157s Preparing to unpack .../00-fonts-dejavu-mono_2.37-8build1_all.deb ... 157s Unpacking fonts-dejavu-mono (2.37-8build1) ... 157s Selecting previously unselected package fonts-dejavu-core. 157s Preparing to unpack .../01-fonts-dejavu-core_2.37-8build1_all.deb ... 157s Unpacking fonts-dejavu-core (2.37-8build1) ... 157s Selecting previously unselected package fontconfig-config. 157s Preparing to unpack .../02-fontconfig-config_2.17.1-3ubuntu1_amd64.deb ... 157s Unpacking fontconfig-config (2.17.1-3ubuntu1) ... 157s Selecting previously unselected package libfontconfig1:amd64. 157s Preparing to unpack .../03-libfontconfig1_2.17.1-3ubuntu1_amd64.deb ... 157s Unpacking libfontconfig1:amd64 (2.17.1-3ubuntu1) ... 157s Selecting previously unselected package fontconfig. 157s Preparing to unpack .../04-fontconfig_2.17.1-3ubuntu1_amd64.deb ... 157s Unpacking fontconfig (2.17.1-3ubuntu1) ... 157s Selecting previously unselected package libblas3:amd64. 157s Preparing to unpack .../05-libblas3_3.12.1-7ubuntu1_amd64.deb ... 157s Unpacking libblas3:amd64 (3.12.1-7ubuntu1) ... 157s Selecting previously unselected package libpixman-1-0:amd64. 157s Preparing to unpack .../06-libpixman-1-0_0.46.4-1_amd64.deb ... 157s Unpacking libpixman-1-0:amd64 (0.46.4-1) ... 157s Selecting previously unselected package libxcb-render0:amd64. 157s Preparing to unpack .../07-libxcb-render0_1.17.0-2ubuntu1_amd64.deb ... 157s Unpacking libxcb-render0:amd64 (1.17.0-2ubuntu1) ... 157s Selecting previously unselected package libxcb-shm0:amd64. 157s Preparing to unpack .../08-libxcb-shm0_1.17.0-2ubuntu1_amd64.deb ... 157s Unpacking libxcb-shm0:amd64 (1.17.0-2ubuntu1) ... 157s Selecting previously unselected package libxrender1:amd64. 157s Preparing to unpack .../09-libxrender1_1%3a0.9.12-1_amd64.deb ... 157s Unpacking libxrender1:amd64 (1:0.9.12-1) ... 157s Selecting previously unselected package libcairo2:amd64. 157s Preparing to unpack .../10-libcairo2_1.18.4-3_amd64.deb ... 157s Unpacking libcairo2:amd64 (1.18.4-3) ... 157s Selecting previously unselected package libdatrie1:amd64. 157s Preparing to unpack .../11-libdatrie1_0.2.14-1_amd64.deb ... 157s Unpacking libdatrie1:amd64 (0.2.14-1) ... 157s Selecting previously unselected package libdeflate0:amd64. 157s Preparing to unpack .../12-libdeflate0_1.23-2build1_amd64.deb ... 157s Unpacking libdeflate0:amd64 (1.23-2build1) ... 157s Selecting previously unselected package libgfortran5:amd64. 157s Preparing to unpack .../13-libgfortran5_16-20260208-1ubuntu1_amd64.deb ... 157s Unpacking libgfortran5:amd64 (16-20260208-1ubuntu1) ... 157s Selecting previously unselected package libgomp1:amd64. 157s Preparing to unpack .../14-libgomp1_16-20260208-1ubuntu1_amd64.deb ... 157s Unpacking libgomp1:amd64 (16-20260208-1ubuntu1) ... 157s Selecting previously unselected package libgraphite2-3:amd64. 157s Preparing to unpack .../15-libgraphite2-3_1.3.14-11ubuntu1_amd64.deb ... 157s Unpacking libgraphite2-3:amd64 (1.3.14-11ubuntu1) ... 157s Selecting previously unselected package libharfbuzz0b:amd64. 157s Preparing to unpack .../16-libharfbuzz0b_12.3.2-1_amd64.deb ... 157s Unpacking libharfbuzz0b:amd64 (12.3.2-1) ... 157s Selecting previously unselected package x11-common. 157s Preparing to unpack .../17-x11-common_1%3a7.7+24ubuntu1_all.deb ... 157s Unpacking x11-common (1:7.7+24ubuntu1) ... 157s Selecting previously unselected package libice6:amd64. 157s Preparing to unpack .../18-libice6_2%3a1.1.1-1build1_amd64.deb ... 157s Unpacking libice6:amd64 (2:1.1.1-1build1) ... 157s Selecting previously unselected package libjpeg-turbo8:amd64. 157s Preparing to unpack .../19-libjpeg-turbo8_2.1.5-4ubuntu3_amd64.deb ... 157s Unpacking libjpeg-turbo8:amd64 (2.1.5-4ubuntu3) ... 157s Selecting previously unselected package libjpeg8:amd64. 157s Preparing to unpack .../20-libjpeg8_8c-2ubuntu12_amd64.deb ... 157s Unpacking libjpeg8:amd64 (8c-2ubuntu12) ... 157s Selecting previously unselected package liblapack3:amd64. 157s Preparing to unpack .../21-liblapack3_3.12.1-7ubuntu1_amd64.deb ... 157s Unpacking liblapack3:amd64 (3.12.1-7ubuntu1) ... 157s Selecting previously unselected package liblerc4:amd64. 157s Preparing to unpack .../22-liblerc4_4.0.0+ds-5ubuntu2_amd64.deb ... 157s Unpacking liblerc4:amd64 (4.0.0+ds-5ubuntu2) ... 157s Selecting previously unselected package libthai-data. 157s Preparing to unpack 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project with many contributors. 162s Type 'contributors()' for more information and 162s 'citation()' on how to cite R or R packages in publications. 162s 162s Type 'demo()' for some demos, 'help()' for on-line help, or 162s 'help.start()' for an HTML browser interface to help. 162s Type 'q()' to quit R. 162s 162s > ### test file for etmCIF. 162s > ### Really simple tests and comparison with etm 162s > 162s > old <- options(digits = 5) 162s > 162s > require(etm) 162s Loading required package: etm 163s > 163s > if (!require(survival, quietly = TRUE)) { 163s + print("The following tests require the 'survival' package") 163s + } else { 163s + 163s + data(abortion) 163s + 163s + from <- rep(0, nrow(abortion)) 163s + to <- abortion$cause 163s + entry <- abortion$entry 163s + exit <- abortion$exit 163s + id <- 1:nrow(abortion) 163s + data <- data.frame(id, from, to, entry, exit, group = abortion$group) 163s + 163s + ## Computation of the CIFs with etm 163s + tra <- matrix(FALSE, 4, 4) 163s + tra[1, 2:4] <- TRUE 163s + 163s + cif.control <- etm(data[data$group == 0, ], c("0", "1", "2", "3"), 163s + tra, NULL, 0) 163s + cif.exposed <- etm(data[data$group == 1, ], c("0", "1", "2", "3"), 163s + tra, NULL, 0) 163s + 163s + 163s + ## Computation of the CIFs with etmCIF 163s + netm <- etmCIF(Surv(entry, exit, cause != 0) ~ group, abortion, 163s + etype = cause, failcode = 3) 163s + 163s + ### let's do some comparisons :-) 163s + 163s + all.equal(trprob(cif.control, "0 3"), netm[[1]]$est["0", "3", ]) 163s + all.equal(trprob(cif.control, "0 2"), netm[[1]]$est["0", "2", ]) 163s + all.equal(trprob(cif.control, "0 1"), netm[[1]]$est["0", "1", ]) 163s + 163s + all.equal(trprob(cif.exposed, "0 3"), netm[[2]]$est["0", "3", ]) 163s + all.equal(trprob(cif.exposed, "0 2"), netm[[2]]$est["0", "2", ]) 163s + all.equal(trprob(cif.exposed, "0 1"), netm[[2]]$est["0", "1", ]) 163s + 163s + 163s + all.equal(trcov(cif.control, "0 3"), netm[[1]]$cov["0 3", "0 3", ]) 163s + all.equal(trcov(cif.control, "0 2"), netm[[1]]$cov["0 2", "0 2", ]) 163s + all.equal(trcov(cif.control, "0 1"), netm[[1]]$cov["0 1", "0 1", ]) 163s + 163s + all.equal(trcov(cif.exposed, "0 3"), netm[[2]]$cov["0 3", "0 3", ]) 163s + all.equal(trcov(cif.exposed, "0 2"), netm[[2]]$cov["0 2", "0 2", ]) 163s + all.equal(trcov(cif.exposed, "0 1"), netm[[2]]$cov["0 1", "0 1", ]) 163s + 163s + 163s + netm 163s + 163s + ## test on the summary 163s + snetm <- summary(netm) 163s + 163s + snetm 163s + 163s + all.equal(unname(trprob(cif.control, "0 3")), snetm[[1]][[3]]$P) 163s + all.equal(unname(trprob(cif.control, "0 2")), snetm[[1]][[2]]$P) 163s + all.equal(unname(trprob(cif.control, "0 1")), snetm[[1]][[1]]$P) 163s + 163s + all.equal(unname(trprob(cif.exposed, "0 3")), snetm[[2]][[3]]$P) 163s + all.equal(unname(trprob(cif.exposed, "0 2")), snetm[[2]][[2]]$P) 163s + all.equal(unname(trprob(cif.exposed, "0 1")), snetm[[2]][[1]]$P) 163s + 163s + scif.control <- summary(cif.control, ci.fun = "cloglog") 163s + scif.exposed <- summary(cif.exposed, ci.fun = "cloglog") 163s + 163s + all.equal(scif.control[[4]]$lower, snetm[[1]][[3]]$lower) 163s + all.equal(scif.control[[4]]$upper, snetm[[1]][[3]]$upper) 163s + 163s + all.equal(scif.exposed[[4]]$lower, snetm[[2]][[3]]$lower) 163s + all.equal(scif.exposed[[4]]$upper, snetm[[2]][[3]]$upper) 163s + } 163s [1] TRUE 163s > 163s > ### test with factors in the input 163s > abortion$status <- with(abortion, ifelse(cause == 2, "life birth", 163s + ifelse(cause == 1, "ETOP", "spontaneous abortion"))) 163s > 163s > abortion$status <- factor(abortion$status) 163s > 163s > netm.factor <- etmCIF(Surv(entry, exit, status != "cens") ~ group, abortion, 163s + etype = status, failcode = "spontaneous abortion") 163s > 163s > 163s > all.equal(trprob(cif.control, "0 3"), netm.factor[[1]]$est["0", "spontaneous abortion", ]) 163s [1] TRUE 163s > all.equal(trprob(cif.control, "0 2"), netm.factor[[1]]$est["0", "life birth", ]) 163s [1] TRUE 163s > 163s > netm.factor 163s Call: etmCIF(formula = Surv(entry, exit, status != "cens") ~ group, 163s data = abortion, etype = status, failcode = "spontaneous abortion") 163s 163s Covariate: group 163s levels: 0 1 163s 163s 163s group = 0 163s time P se(P) n.event 163s CIF ETOP 43 0.040159 0.0092578 20 163s CIF life birth 43 0.799059 0.0221865 924 163s CIF spontaneous abortion 43 0.160781 0.0213261 69 163s 163s group = 1 163s time P se(P) n.event 163s CIF ETOP 42 0.28511 0.042493 38 163s CIF life birth 42 0.35257 0.042139 92 163s CIF spontaneous abortion 42 0.36232 0.049473 43 163s > 163s > summary(netm.factor) 163s 163s group=0 163s 163s CIF ETOP 163s P time var lower upper n.risk n.event 163s 0.000000 6 0.0000e+00 0.000000 0.000000 117 0 163s 0.038955 13 8.4440e-05 0.024488 0.061694 645 1 163s 0.040159 26 8.5707e-05 0.025513 0.062939 846 0 163s 0.040159 36 8.5707e-05 0.025513 0.062939 876 0 163s 0.040159 40 8.5707e-05 0.025513 0.062939 554 0 163s 0.040159 43 8.5707e-05 0.025513 0.062939 6 0 163s 163s CIF life birth 163s P time var lower upper n.risk n.event 163s 0.000000 6 0.0000e+00 0.000000 0.000000 117 0 163s 0.000000 13 0.0000e+00 0.000000 0.000000 645 0 163s 0.000000 26 0.0000e+00 0.000000 0.000000 846 0 163s 0.053197 36 4.6195e-05 0.041379 0.068268 876 25 163s 0.563121 40 3.8801e-04 0.524924 0.602021 554 280 163s 0.799059 43 4.9224e-04 0.753969 0.840613 6 6 163s 163s CIF spontaneous abortion 163s P time var lower upper n.risk n.event 163s 0.034188 6 0.00028222 0.01297 0.088523 117 4 163s 0.150468 13 0.00045513 0.11360 0.197901 645 1 163s 0.159904 26 0.00045498 0.12274 0.206925 846 1 163s 0.160781 36 0.00045480 0.12360 0.207757 876 1 163s 0.160781 40 0.00045480 0.12360 0.207757 554 0 163s 0.160781 43 0.00045480 0.12360 0.207757 6 0 163s 163s 163s group=1 163s 163s CIF ETOP 163s P time var lower upper n.risk n.event 163s 0.00000 6 0.0000000 0.00000 0.00000 35 0 163s 0.26048 13 0.0017854 0.18795 0.35425 90 0 163s 0.28115 21 0.0018028 0.20742 0.37423 93 1 163s 0.28511 34 0.0018057 0.21116 0.37806 89 0 163s 0.28511 39 0.0018057 0.21116 0.37806 59 0 163s 0.28511 42 0.0018057 0.21116 0.37806 6 0 163s 163s CIF life birth 163s P time var lower upper n.risk n.event 163s 0.000000 6 0.0000e+00 0.000000 0.000000 35 0 163s 0.000000 13 0.0000e+00 0.000000 0.000000 90 0 163s 0.000000 21 0.0000e+00 0.000000 0.000000 93 0 163s 0.023073 34 9.0514e-05 0.010252 0.051504 89 2 163s 0.180156 39 8.0126e-04 0.131765 0.243663 59 13 163s 0.352565 42 1.7757e-03 0.276882 0.441775 6 6 163s 163s CIF spontaneous abortion 163s P time var lower upper n.risk n.event 163s 0.057143 6 0.0015394 0.014605 0.20968 35 2 163s 0.333246 13 0.0025280 0.245337 0.44216 90 4 163s 0.350702 21 0.0024827 0.262769 0.45762 93 0 163s 0.358492 34 0.0024593 0.270627 0.46448 89 0 163s 0.358492 39 0.0024593 0.270627 0.46448 59 0 163s 0.362323 42 0.0024476 0.274499 0.46785 6 0 163s 163s > 163s > ### test with group as a character vector 163s > abortion$ttt <- with(abortion, ifelse(group == 0, "control", "exposed")) 163s > abortion$ttt <- factor(abortion$ttt) 163s > 163s > netm.ttt <- etmCIF(Surv(entry, exit, status != "cens") ~ ttt, abortion, 163s + etype = status, failcode = "spontaneous abortion") 163s > 163s > all.equal(trprob(cif.control, "0 3"), netm.ttt[[1]]$est["0", "spontaneous abortion", ]) 163s [1] TRUE 163s > all.equal(trprob(cif.control, "0 2"), netm.ttt[[1]]$est["0", "life birth", ]) 163s [1] TRUE 163s > 163s > netm.ttt 163s Call: etmCIF(formula = Surv(entry, exit, status != "cens") ~ ttt, data = abortion, 163s etype = status, failcode = "spontaneous abortion") 163s 163s Covariate: ttt 163s levels: control exposed 163s 163s 163s ttt = control 163s time P se(P) n.event 163s CIF ETOP 43 0.040159 0.0092578 20 163s CIF life birth 43 0.799059 0.0221865 924 163s CIF spontaneous abortion 43 0.160781 0.0213261 69 163s 163s ttt = exposed 163s time P se(P) n.event 163s CIF ETOP 42 0.28511 0.042493 38 163s CIF life birth 42 0.35257 0.042139 92 163s CIF spontaneous abortion 42 0.36232 0.049473 43 163s > 163s > summary(netm.ttt) 163s 163s ttt=control 163s 163s CIF ETOP 163s P time var lower upper n.risk n.event 163s 0.000000 6 0.0000e+00 0.000000 0.000000 117 0 163s 0.038955 13 8.4440e-05 0.024488 0.061694 645 1 163s 0.040159 26 8.5707e-05 0.025513 0.062939 846 0 163s 0.040159 36 8.5707e-05 0.025513 0.062939 876 0 163s 0.040159 40 8.5707e-05 0.025513 0.062939 554 0 163s 0.040159 43 8.5707e-05 0.025513 0.062939 6 0 163s 163s CIF life birth 163s P time var lower upper n.risk n.event 163s 0.000000 6 0.0000e+00 0.000000 0.000000 117 0 163s 0.000000 13 0.0000e+00 0.000000 0.000000 645 0 163s 0.000000 26 0.0000e+00 0.000000 0.000000 846 0 163s 0.053197 36 4.6195e-05 0.041379 0.068268 876 25 163s 0.563121 40 3.8801e-04 0.524924 0.602021 554 280 163s 0.799059 43 4.9224e-04 0.753969 0.840613 6 6 163s 163s CIF spontaneous abortion 163s P time var lower upper n.risk n.event 163s 0.034188 6 0.00028222 0.01297 0.088523 117 4 163s 0.150468 13 0.00045513 0.11360 0.197901 645 1 163s 0.159904 26 0.00045498 0.12274 0.206925 846 1 163s 0.160781 36 0.00045480 0.12360 0.207757 876 1 163s 0.160781 40 0.00045480 0.12360 0.207757 554 0 163s 0.160781 43 0.00045480 0.12360 0.207757 6 0 163s 163s 163s ttt=exposed 163s 163s CIF ETOP 163s P time var lower upper n.risk n.event 163s 0.00000 6 0.0000000 0.00000 0.00000 35 0 163s 0.26048 13 0.0017854 0.18795 0.35425 90 0 163s 0.28115 21 0.0018028 0.20742 0.37423 93 1 163s 0.28511 34 0.0018057 0.21116 0.37806 89 0 163s 0.28511 39 0.0018057 0.21116 0.37806 59 0 163s 0.28511 42 0.0018057 0.21116 0.37806 6 0 163s 163s CIF life birth 163s P time var lower upper n.risk n.event 163s 0.000000 6 0.0000e+00 0.000000 0.000000 35 0 163s 0.000000 13 0.0000e+00 0.000000 0.000000 90 0 163s 0.000000 21 0.0000e+00 0.000000 0.000000 93 0 163s 0.023073 34 9.0514e-05 0.010252 0.051504 89 2 163s 0.180156 39 8.0126e-04 0.131765 0.243663 59 13 163s 0.352565 42 1.7757e-03 0.276882 0.441775 6 6 163s 163s CIF spontaneous abortion 163s P time var lower upper n.risk n.event 163s 0.057143 6 0.0015394 0.014605 0.20968 35 2 163s 0.333246 13 0.0025280 0.245337 0.44216 90 4 163s 0.350702 21 0.0024827 0.262769 0.45762 93 0 163s 0.358492 34 0.0024593 0.270627 0.46448 89 0 163s 0.358492 39 0.0024593 0.270627 0.46448 59 0 163s 0.362323 42 0.0024476 0.274499 0.46785 6 0 163s 163s > 163s > 163s > ### A couple of comparisons with simulated data 163s > set.seed(1313) 163s > time <- rexp(100) 163s > to <- rbinom(100, 2, prob = c(1/3, 1/3, 1/3)) 163s > from <- rep(11, 100) 163s > id <- 1:100 163s > cov <- rbinom(100, 1, 0.5) 163s > 163s > dat.s <- data.frame(id, time, from, to, cov) 163s > 163s > traa <- matrix(FALSE, 3, 3) 163s > traa[1, 2:3] <- TRUE 163s > 163s > aa0 <- etm(dat.s[dat.s$cov == 0, ], c("11", "1", "2"), traa, "0", 0) 163s > aa1 <- etm(dat.s[dat.s$cov == 1, ], c("11", "1", "2"), traa, "0", 0) 163s > aa <- etm(dat.s, c("11", "1", "2"), traa, "0", 0) 163s > 163s > test <- etmCIF(Surv(time, to != 0) ~ 1, dat.s, etype = to) 163s > 163s > test.c <- etmCIF(Surv(time, to != 0) ~ cov, dat.s, etype = to) 163s > 163s > all.equal(trprob(aa, "11 1"), test[[1]]$est["0", "1", ]) 163s [1] TRUE 163s > all.equal(trprob(aa, "11 2"), test[[1]]$est["0", "2", ]) 163s [1] TRUE 163s > 163s > all.equal(trprob(aa0, "11 1"), test.c[[1]]$est["0", "1", ]) 163s [1] TRUE 163s > all.equal(trprob(aa0, "11 2"), test.c[[1]]$est["0", "2", ]) 163s [1] TRUE 163s > 163s > all.equal(trprob(aa1, "11 1"), test.c[[2]]$est["0", "1", ]) 163s [1] TRUE 163s > all.equal(trprob(aa1, "11 2"), test.c[[2]]$est["0", "2", ]) 163s [1] TRUE 163s > 163s > test 163s Call: etmCIF(formula = Surv(time, to != 0) ~ 1, data = dat.s, etype = to) 163s 163s time P se(P) n.event 163s CIF 1 4.9088 0.809108 0.079680 45 163s CIF 2 4.9088 0.096618 0.032905 8 163s > 163s > test.c 163s Call: etmCIF(formula = Surv(time, to != 0) ~ cov, data = dat.s, etype = to) 163s 163s Covariate: cov 163s levels: 0 1 163s 163s 163s cov = 0 163s time P se(P) n.event 163s CIF 1 2.1708 0.70246 0.105797 19 163s CIF 2 2.1708 0.11144 0.053384 4 163s 163s cov = 1 163s time P se(P) n.event 163s CIF 1 4.9088 0.80787 0.094051 26 163s CIF 2 4.9088 0.08436 0.040769 4 163s > 163s > summary(test) 163s 163s 163s 163s CIF 1 163s P time var lower upper n.risk n.event 163s 0.01000 0.0092099 0.0000990 0.0014147 0.068863 100 1 163s 0.11430 0.2663096 0.0010542 0.0649454 0.196993 81 1 163s 0.23451 0.7303091 0.0020436 0.1591107 0.337736 54 1 163s 0.40425 1.4299939 0.0032996 0.3020445 0.525741 29 1 163s 0.54593 2.0647206 0.0040836 0.4269008 0.673605 16 1 163s 0.80911 4.9087561 0.0063489 0.6359544 0.933733 2 1 163s 163s CIF 2 163s P time var lower upper n.risk n.event 163s 0.000000 0.0092099 0.00000000 0.000000 0.000000 100 0 163s 0.031657 0.2663096 0.00032353 0.010320 0.094942 81 0 163s 0.067029 0.7303091 0.00070366 0.030598 0.143503 54 0 163s 0.096618 1.4299939 0.00108275 0.049082 0.185474 29 0 163s 0.096618 2.0647206 0.00108275 0.049082 0.185474 16 0 163s 0.096618 4.9087561 0.00108275 0.049082 0.185474 2 0 163s 163s > summary(test.c) 163s 163s cov=0 163s 163s CIF 1 163s P time var lower upper n.risk n.event 163s 0.022222 0.0092099 0.00048285 0.0031605 0.14747 45 1 163s 0.092222 0.2982439 0.00193603 0.0355971 0.22762 36 0 163s 0.226684 0.7021938 0.00450954 0.1241760 0.39250 24 1 163s 0.378128 1.4299939 0.00760870 0.2337884 0.57145 13 1 163s 0.505736 1.6148774 0.00895330 0.3388425 0.69885 10 1 163s 0.702465 2.1708375 0.01119294 0.4944890 0.88399 3 1 163s 163s CIF 2 163s P time var lower upper n.risk n.event 163s 0.000000 0.0092099 0.0000000 0.000000 0.00000 45 0 163s 0.048441 0.2982439 0.0011168 0.012337 0.18013 36 1 163s 0.076411 0.7021938 0.0018104 0.025202 0.21928 24 0 163s 0.111440 1.4299939 0.0028499 0.042676 0.27392 13 0 163s 0.111440 1.6148774 0.0028499 0.042676 0.27392 10 0 163s 0.111440 2.1708375 0.0028499 0.042676 0.27392 3 0 163s 163s 163s cov=1 163s 163s CIF 1 163s P time var lower upper n.risk n.event 163s 0.018182 0.066692 0.00032457 0.0025813 0.12214 55 1 163s 0.112392 0.263808 0.00187215 0.0520925 0.23333 45 1 163s 0.241023 0.730309 0.00374499 0.1440057 0.38685 31 1 163s 0.401201 1.066913 0.00570788 0.2714008 0.56421 19 1 163s 0.592334 2.366275 0.00775985 0.4286230 0.76273 8 1 163s 0.807871 4.908756 0.00884554 0.6023185 0.94771 2 1 163s 163s CIF 2 163s P time var lower upper n.risk n.event 163s 0.000000 0.066692 0.00000000 0.000000 0.00000 55 0 163s 0.037434 0.263808 0.00067458 0.009494 0.14152 45 0 163s 0.059341 0.730309 0.00111295 0.019447 0.17351 31 0 163s 0.084360 1.066913 0.00166213 0.032211 0.21119 19 0 163s 0.084360 2.366275 0.00166213 0.032211 0.21119 8 0 163s 0.084360 4.908756 0.00166213 0.032211 0.21119 2 0 163s 163s > 163s > options(old) 163s > 163s BEGIN TEST tests.etm.R 163s 163s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 163s Copyright (C) 2025 The R Foundation for Statistical Computing 163s Platform: x86_64-pc-linux-gnu 163s 163s R is free software and comes with ABSOLUTELY NO WARRANTY. 163s You are welcome to redistribute it under certain conditions. 163s Type 'license()' or 'licence()' for distribution details. 163s 163s R is a collaborative project with many contributors. 163s Type 'contributors()' for more information and 163s 'citation()' on how to cite R or R packages in publications. 163s 163s Type 'demo()' for some demos, 'help()' for on-line help, or 163s 'help.start()' for an HTML browser interface to help. 163s Type 'q()' to quit R. 163s 163s Loading required package: etm 163s > require(etm) 164s > 164s > ## Print with a bit less precision to avoid lots of notes in the comparison 164s > old <- options(digits = 4) 164s > 164s > ### Simple test 164s > 164s > time <- id <- 1:10 164s > from <- rep(0, 10) 164s > to <- rep(1, 10) 164s > 164s > data1 <- data.frame(id, from, to, time) 164s > tra1 <- matrix(FALSE, 2, 2) 164s > tra1[1, 2] <- TRUE 164s > 164s > etm1 <- etm(data1, c("0", "1"), tra1, NULL, 0) 164s > 164s > all.equal(as.vector(trprob(etm1, "0 0")), cumprod((10:1 - 1) / (10:1))) 164s [1] TRUE 164s > 164s > etm1$cov["0 0", "0 0", ] 164s 1 2 3 4 5 6 7 8 9 10 164s 0.009 0.016 0.021 0.024 0.025 0.024 0.021 0.016 0.009 0.000 164s > 164s > all.equal(etm1$cov["0 0", "0 0",], trcov(etm1, "0 0")) 164s [1] TRUE 164s > 164s > ### A simple test from AHR's author, where the first time is censored 164s > if (!require(survival)) { 164s + stop("This test requires the survival package") 164s + } 164s Loading required package: survival 164s > 164s > data <- data.frame(id=1:10, time=1:10, from=0, to=1, status=TRUE) 164s > 164s > tra <- matrix(FALSE, nrow=2, ncol=2) 164s > tra[1, 2] <- TRUE 164s > 164s > data$to[1] <- "cens" 164s > data$status[1] <- FALSE 164s > 164s > fit.km <- survfit(Surv(time, status) ~ 1, data=data) 164s > fit.etm <- etm(data, c("0","1"), tra, "cens", s=0, t="last", covariance=FALSE) 164s > 164s > all.equal(fit.km$surv[data$status], fit.etm$est[1,1,], check.attributes = FALSE) 164s [1] TRUE 164s > 164s > data$to[2] <- "cens" 164s > data$status[2] <- FALSE 164s > 164s > fit.km <- survfit(Surv(time, status) ~ 1, data=data) 164s > fit.etm <- etm(data, c("0","1"), tra, "cens", s=0, t="last", covariance=FALSE) 164s > 164s > all.equal(fit.km$surv[data$status], fit.etm$est[1,1,], check.attributes = FALSE) 164s [1] TRUE 164s > 164s > ### a bit more complicated 164s > 164s > time <- id <- 1:10 164s > from <- rep(0, 10) 164s > to <- rep(c(1, 2), 5) 164s > data2 <- data.frame(id, from, to, time) 164s > 164s > tra2 <- matrix(FALSE, 3, 3) 164s > tra2[1, 2:3] <- TRUE 164s > 164s > etm2 <- etm(data2, c("0", "1", "2"), tra2, NULL, 0) 164s > 164s > aa <- table(time, to) 164s > 164s > cif1 <- cumsum(aa[, 1] / 10) 164s > cif2 <- cumsum(aa[, 2] / 10) 164s > surv <- cumprod((10:1 - 1) / (10:1)) 164s > 164s > all.equal(trprob(etm2, "0 1"), cif1) 164s [1] TRUE 164s > all.equal(trprob(etm2, "0 2"), cif2) 164s [1] TRUE 164s > all.equal(as.vector(trprob(etm2, "0 0")), surv) 164s [1] TRUE 164s > 164s > ## a test on id 164s > data2$id <- letters[1:10] 164s > 164s > etm3 <- etm(data2, c("0", "1", "2"), tra2, NULL, 0) 164s > 164s > all.equal(trprob(etm2, "0 1"), trprob(etm3, "0 1")) 164s [1] TRUE 164s > all.equal(trprob(etm2, "0 2"), trprob(etm3, "0 2")) 164s [1] TRUE 164s > all.equal(trprob(etm2, "0 0"), trprob(etm3, "0 0")) 164s [1] TRUE 164s > 164s > 164s > ### Test on sir.cont 164s > 164s > data(sir.cont) 164s > 164s > ## Modification for patients entering and leaving a state 164s > ## at the same date 164s > ## Change on ventilation status is considered 164s > ## to happen before end of hospital stay 164s > sir.cont <- sir.cont[order(sir.cont$id, sir.cont$time), ] 164s > for (i in 2:nrow(sir.cont)) { 164s + if (sir.cont$id[i]==sir.cont$id[i-1]) { 164s + if (sir.cont$time[i]==sir.cont$time[i-1]) { 164s + sir.cont$time[i-1] <- sir.cont$time[i-1] - 0.5 164s + } 164s + } 164s + } 164s > 164s > ### Computation of the transition probabilities 164s > ## Possible transitions. 164s > tra <- matrix(ncol=3,nrow=3,FALSE) 164s > tra[1, 2:3] <- TRUE 164s > tra[2, c(1, 3)] <- TRUE 164s > 164s > ## etm 164s > prob.sir <- etm(sir.cont, c("0", "1", "2"), tra, "cens", 1) 164s > 164s > prob.sir 164s Multistate model with 2 transient state(s) 164s and 1 absorbing state(s) 164s 164s Possible transitions: 164s from to 164s 0 1 164s 0 2 164s 1 0 164s 1 2 164s 164s Estimate of P(1, 183) 164s 0 1 2 164s 0 0 0 1 164s 1 0 0 1 164s 2 0 0 1 164s 164s > 164s > summ.sir <- summary(prob.sir) 164s > all.equal(summ.sir[['0 1']]$P, as.vector(trprob(prob.sir, "0 1"))) 164s [1] TRUE 164s > subset(summ.sir[[3]],time<183) # issue with precision on different architectures 164s P time var lower upper n.risk n.event 164s 1.5 0.0000 1.5 0.000e+00 0.00000 0.0000 394 0 164s 2 0.1187 2.0 2.641e-04 0.08683 0.1505 396 47 164s 2.5 0.1187 2.5 2.641e-04 0.08683 0.1505 364 0 164s 3 0.2454 3.0 4.465e-04 0.20398 0.2868 365 54 164s 3.5 0.2454 3.5 4.465e-04 0.20398 0.2868 328 0 164s 4 0.3806 4.0 5.416e-04 0.33501 0.4262 331 62 164s 4.5 0.3806 4.5 5.416e-04 0.33501 0.4262 280 0 164s 5 0.4792 5.0 5.480e-04 0.43333 0.5251 283 48 164s 5.5 0.4792 5.5 5.480e-04 0.43333 0.5251 248 0 164s 6 0.5693 6.0 5.141e-04 0.52482 0.6137 249 47 164s 7 0.6350 7.0 4.665e-04 0.59266 0.6773 212 36 164s 8 0.6795 8.0 4.202e-04 0.63931 0.7197 195 27 164s 8.5 0.6795 8.5 4.202e-04 0.63931 0.7197 172 0 164s 9 0.7325 9.0 3.580e-04 0.69541 0.7696 173 34 164s 10 0.7647 10.0 3.141e-04 0.72992 0.7994 148 21 164s 10.5 0.7647 10.5 3.141e-04 0.72992 0.7994 135 0 164s 11 0.7895 11.0 2.790e-04 0.75674 0.8222 136 18 164s 12 0.8138 12.0 2.420e-04 0.78330 0.8443 129 18 164s 12.5 0.8138 12.5 2.420e-04 0.78330 0.8443 117 0 164s 13 0.8294 13.0 2.182e-04 0.80045 0.8584 118 13 164s 14 0.8452 14.0 1.938e-04 0.81789 0.8725 115 14 164s 15 0.8625 15.0 1.670e-04 0.83714 0.8878 106 15 164s 16 0.8723 16.0 1.522e-04 0.84807 0.8964 93 9 164s 17 0.8852 17.0 1.330e-04 0.86256 0.9078 86 12 164s 17.5 0.8852 17.5 1.330e-04 0.86256 0.9078 77 0 164s 18 0.8960 18.0 1.168e-04 0.87484 0.9172 76 9 164s 19 0.9029 19.0 1.070e-04 0.88261 0.9232 71 7 164s 20 0.9125 20.0 9.367e-05 0.89356 0.9315 64 10 164s 21 0.9161 21.0 8.878e-05 0.89768 0.9346 57 4 164s 22 0.9226 22.0 7.996e-05 0.90504 0.9401 55 6 164s 23 0.9261 23.0 7.537e-05 0.90904 0.9431 51 4 164s 23.5 0.9261 23.5 7.537e-05 0.90904 0.9431 49 0 164s 24 0.9354 24.0 6.292e-05 0.91982 0.9509 50 9 164s 25 0.9385 25.0 5.878e-05 0.92352 0.9536 42 3 164s 26 0.9429 26.0 5.326e-05 0.92863 0.9572 39 5 164s 27 0.9477 27.0 4.749e-05 0.93417 0.9612 35 6 164s 27.5 0.9477 27.5 4.749e-05 0.93417 0.9612 29 0 164s 28 0.9531 28.0 4.093e-05 0.94059 0.9657 30 5 164s 29 0.9567 29.0 3.668e-05 0.94485 0.9686 31 4 164s 30 0.9592 30.0 3.384e-05 0.94779 0.9706 28 3 164s 30.5 0.9592 30.5 3.384e-05 0.94779 0.9706 29 0 164s 31 0.9642 31.0 2.821e-05 0.95383 0.9746 30 6 164s 32 0.9649 32.0 2.752e-05 0.95458 0.9751 25 1 164s 33 0.9669 33.0 2.533e-05 0.95708 0.9768 24 2 164s 34 0.9685 34.0 2.368e-05 0.95900 0.9781 26 2 164s 35 0.9697 35.0 2.252e-05 0.96036 0.9790 28 2 164s 36 0.9702 36.0 2.194e-05 0.96104 0.9794 26 1 164s 37 0.9718 37.0 2.043e-05 0.96290 0.9806 26 2 164s 38 0.9739 38.0 1.831e-05 0.96555 0.9823 25 4 164s 38.5 0.9739 38.5 1.831e-05 0.96555 0.9823 21 0 164s 39 0.9760 39.0 1.643e-05 0.96802 0.9839 23 3 164s 40 0.9769 40.0 1.558e-05 0.96918 0.9847 19 1 164s 41 0.9774 41.0 1.512e-05 0.96981 0.9851 22 1 164s 42 0.9779 42.0 1.476e-05 0.97032 0.9854 22 0 164s 43 0.9798 43.0 1.308e-05 0.97271 0.9869 22 3 164s 44 0.9803 44.0 1.265e-05 0.97333 0.9873 21 1 164s 45 0.9817 45.0 1.157e-05 0.97499 0.9883 19 1 164s 46 0.9822 46.0 1.116e-05 0.97561 0.9887 17 1 164s 47 0.9831 47.0 1.037e-05 0.97683 0.9895 18 2 164s 48 0.9836 48.0 9.987e-06 0.97743 0.9898 17 1 164s 49 0.9841 49.0 9.669e-06 0.97796 0.9901 17 0 164s 50 0.9845 50.0 9.297e-06 0.97856 0.9905 17 1 164s 50.5 0.9845 50.5 9.297e-06 0.97856 0.9905 16 0 164s 51 0.9860 51.0 8.214e-06 0.98037 0.9916 17 3 164s 52 0.9870 52.0 7.513e-06 0.98159 0.9923 14 2 164s 53 0.9879 53.0 6.875e-06 0.98276 0.9930 12 1 164s 54 0.9889 54.0 6.214e-06 0.98397 0.9937 12 2 164s 55 0.9903 55.0 5.254e-06 0.98581 0.9948 10 3 164s 56 0.9913 56.0 4.667e-06 0.98703 0.9955 6 1 164s 57 0.9917 57.0 4.364e-06 0.98765 0.9958 5 1 164s 58 0.9922 58.0 4.064e-06 0.98828 0.9962 4 1 164s 59 0.9927 59.0 3.769e-06 0.98891 0.9965 3 1 164s 60 0.9932 60.0 3.488e-06 0.98953 0.9969 3 1 164s 62 0.9937 62.0 3.230e-06 0.99016 0.9972 2 0 164s 63 0.9942 63.0 2.956e-06 0.99079 0.9975 2 1 164s 68 0.9942 68.0 2.956e-06 0.99079 0.9975 1 0 164s 70 0.9946 70.0 2.694e-06 0.99143 0.9979 2 1 164s 78 0.9951 78.0 2.442e-06 0.99207 0.9982 1 0 164s 80 0.9951 80.0 2.442e-06 0.99207 0.9982 1 0 164s 85 0.9966 85.0 1.695e-06 0.99404 0.9991 2 0 164s 89 0.9966 89.0 1.695e-06 0.99404 0.9991 2 0 164s 90 0.9966 90.0 1.695e-06 0.99404 0.9991 1 0 164s 95 0.9971 95.0 1.448e-06 0.99472 0.9994 2 0 164s 100 0.9976 100.0 1.203e-06 0.99542 0.9997 3 0 164s 101 0.9981 101.0 9.592e-07 0.99613 1.0000 3 1 164s 108 0.9985 108.0 7.169e-07 0.99688 1.0000 2 1 164s 113 0.9990 113.0 4.764e-07 0.99767 1.0000 1 0 164s 116 0.9990 116.0 4.764e-07 0.99767 1.0000 1 0 164s 124 0.9990 124.0 4.764e-07 0.99767 1.0000 2 0 164s 164 0.9990 164.0 4.764e-07 0.99767 1.0000 0 0 164s > 164s > ## gonna play a bit with the state names 164s > dd <- sir.cont 164s > dd$from <- ifelse(dd$from == 0, "initial state", "ventilation") 164s > dd$to <- as.character(dd$to) 164s > for (i in seq_len(nrow(dd))) { 164s + dd$to[i] <- switch(dd$to[i], 164s + "0" = "initial state", 164s + "1" = "ventilation", 164s + "2" = "end of story", 164s + "cens" = "cens" 164s + ) 164s + } 164s > 164s > test <- etm(dd, c("initial state", "ventilation", "end of story"), tra, "cens", 1) 164s > 164s > all.equal(test$est["initial state", "initial state", ], 164s + prob.sir$est["0", "0", ]) 164s [1] TRUE 164s > all.equal(trprob(test, "initial state initial state"), trprob(prob.sir, "0 0")) 164s [1] TRUE 164s > all.equal(trprob(test, "initial state ventilation"), trprob(prob.sir, "0 1")) 164s [1] TRUE 164s > all.equal(trprob(test, "initial state end of story"), trprob(prob.sir, "0 2")) 164s [1] TRUE 164s > 164s > all.equal(trcov(test, "initial state end of story"), trcov(prob.sir, "0 2")) 164s [1] TRUE 164s > 164s > aa <- summary(test) 164s > all.equal(summ.sir[[6]], aa[[6]]) 164s [1] TRUE 164s > all.equal(summ.sir[[4]], aa[[4]]) 164s [1] TRUE 164s > 164s > ### Test on abortion data 164s > 164s > data(abortion) 164s > 164s > from <- rep(0, nrow(abortion)) 164s > to <- abortion$cause 164s > entry <- abortion$entry 164s > exit <- abortion$exit 164s > id <- 1:nrow(abortion) 164s > data <- data.frame(id, from, to, entry, exit, group = abortion$group) 164s > 164s > ## Computation of the CIFs 164s > tra <- matrix(FALSE, 4, 4) 164s > tra[1, 2:4] <- TRUE 164s > 164s > cif.control <- etm(data[data$group == 0, ], c("0", "1", "2", "3"), 164s + tra, NULL, 0) 164s > cif.exposed <- etm(data[data$group == 1, ], c("0", "1", "2", "3"), 164s + tra, NULL, 0) 164s > 164s > all.equal(trprob(cif.control, "0 1"), cif.control$est["0", "1", ]) 164s [1] TRUE 164s > all.equal(trcov(cif.control, c("0 1", "0 2")), cif.control$cov["0 1", "0 2", ]) 164s [1] TRUE 164s > 164s > trprob(cif.control, "0 1") 164s 6 7 8 9 10 11 12 13 164s 0.000000 0.007401 0.014881 0.026509 0.033208 0.037694 0.037694 0.038955 164s 14 17 19 21 24 25 26 30 164s 0.040159 0.040159 0.040159 0.040159 0.040159 0.040159 0.040159 0.040159 164s 31 32 33 34 35 36 37 38 164s 0.040159 0.040159 0.040159 0.040159 0.040159 0.040159 0.040159 0.040159 164s 39 40 41 42 43 164s 0.040159 0.040159 0.040159 0.040159 0.040159 164s > trprob(cif.control, "0 2") 164s 6 7 8 9 10 11 12 13 164s 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 164s 14 17 19 21 24 25 26 30 164s 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.003657 164s 31 32 33 34 35 36 37 38 164s 0.006371 0.008175 0.013543 0.023317 0.031260 0.053197 0.084529 0.179163 164s 39 40 41 42 43 164s 0.322016 0.563121 0.742227 0.793893 0.799059 164s > trprob(cif.control, "0 0") 164s 6 7 8 9 10 11 12 13 164s 0.965812 0.932508 0.887628 0.862433 0.838989 0.822538 0.813099 0.810578 164s 14 17 19 21 24 25 26 30 164s 0.806964 0.805874 0.803810 0.802804 0.801837 0.800883 0.799937 0.796280 164s 31 32 33 34 35 36 37 38 164s 0.793565 0.791762 0.786394 0.776620 0.768677 0.745862 0.714531 0.619897 164s 39 40 41 42 43 164s 0.477043 0.235938 0.056832 0.005167 0.000000 164s > 164s > trcov(cif.control, "0 1") 164s 6 7 8 9 10 11 12 13 164s 0.000e+00 2.719e-05 4.533e-05 6.665e-05 7.698e-05 8.304e-05 8.304e-05 8.444e-05 164s 14 17 19 21 24 25 26 30 164s 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 164s 31 32 33 34 35 36 37 38 164s 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 164s 39 40 41 42 43 164s 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 164s > trcov(cif.control, "0 2") 164s 6 7 8 9 10 11 12 13 164s 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 164s 14 17 19 21 24 25 26 30 164s 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 3.338e-06 164s 31 32 33 34 35 36 37 38 164s 5.784e-06 7.401e-06 1.216e-05 2.072e-05 2.758e-05 4.619e-05 7.202e-05 1.461e-04 164s 39 40 41 42 43 164s 2.470e-04 3.880e-04 4.702e-04 4.903e-04 4.922e-04 164s > trcov(cif.control, "0 0") 164s 6 7 8 9 10 11 12 13 164s 2.822e-04 3.821e-04 4.527e-04 4.748e-04 4.875e-04 4.927e-04 4.941e-04 4.942e-04 164s 14 17 19 21 24 25 26 30 164s 4.941e-04 4.940e-04 4.936e-04 4.933e-04 4.931e-04 4.928e-04 4.926e-04 4.914e-04 164s 31 32 33 34 35 36 37 38 164s 4.905e-04 4.899e-04 4.880e-04 4.846e-04 4.816e-04 4.729e-04 4.601e-04 4.176e-04 164s 39 40 41 42 43 164s 3.425e-04 1.865e-04 4.797e-05 4.441e-06 0.000e+00 164s > 164s > aa <- summary(cif.control) 164s > aa$"0 1" 164s P time var lower upper n.risk n.event 164s 6 0.000000 6 0.000e+00 0.000000 0.00000 117 0 164s 7 0.007401 7 2.719e-05 0.000000 0.01762 261 2 164s 8 0.014881 8 4.533e-05 0.001685 0.02808 374 3 164s 9 0.026509 9 6.665e-05 0.010508 0.04251 458 6 164s 10 0.033208 10 7.698e-05 0.016011 0.05040 515 4 164s 11 0.037694 11 8.304e-05 0.019834 0.05555 561 3 164s 12 0.037694 12 8.304e-05 0.019834 0.05555 610 0 164s 13 0.038955 13 8.444e-05 0.020944 0.05697 645 1 164s 14 0.040159 14 8.571e-05 0.022014 0.05830 673 1 164s 17 0.040159 17 8.571e-05 0.022014 0.05830 740 0 164s 19 0.040159 19 8.571e-05 0.022014 0.05830 781 0 164s 21 0.040159 21 8.571e-05 0.022014 0.05830 799 0 164s 24 0.040159 24 8.571e-05 0.022014 0.05830 830 0 164s 25 0.040159 25 8.571e-05 0.022014 0.05830 841 0 164s 26 0.040159 26 8.571e-05 0.022014 0.05830 846 0 164s 30 0.040159 30 8.571e-05 0.022014 0.05830 875 0 164s 31 0.040159 31 8.571e-05 0.022014 0.05830 880 0 164s 32 0.040159 32 8.571e-05 0.022014 0.05830 880 0 164s 33 0.040159 33 8.571e-05 0.022014 0.05830 885 0 164s 34 0.040159 34 8.571e-05 0.022014 0.05830 885 0 164s 35 0.040159 35 8.571e-05 0.022014 0.05830 880 0 164s 36 0.040159 36 8.571e-05 0.022014 0.05830 876 0 164s 37 0.040159 37 8.571e-05 0.022014 0.05830 857 0 164s 38 0.040159 38 8.571e-05 0.022014 0.05830 823 0 164s 39 0.040159 39 8.571e-05 0.022014 0.05830 716 0 164s 40 0.040159 40 8.571e-05 0.022014 0.05830 554 0 164s 41 0.040159 41 8.571e-05 0.022014 0.05830 274 0 164s 42 0.040159 42 8.571e-05 0.022014 0.05830 66 0 164s 43 0.040159 43 8.571e-05 0.022014 0.05830 6 0 164s > all.equal(aa$"0 1"$P, as.vector(trprob(cif.control, "0 1"))) 164s [1] TRUE 164s > 164s > ### test on los data 164s > 164s > data(los.data) # in package changeLOS 164s > 164s > ## putting los.data in the long format (see changeLOS) 164s > my.observ <- prepare.los.data(x=los.data) 164s > 164s > tra <- matrix(FALSE, 4, 4) 164s > tra[1, 2:4] <- TRUE 164s > tra[2, 3:4] <- TRUE 164s > 164s > tr.prob <- etm(my.observ, c("0","1","2","3"), tra, NULL, 0) 164s > 164s > tr.prob 164s Multistate model with 2 transient state(s) 164s and 2 absorbing state(s) 164s 164s Possible transitions: 164s from to 164s 0 1 164s 0 2 164s 0 3 164s 1 2 164s 1 3 164s 164s Estimate of P(0, 82) 164s 0 1 2 3 164s 0 0 0 0.7474 0.2526 164s 1 0 0 0.7073 0.2927 164s 2 0 0 1.0000 0.0000 164s 3 0 0 0.0000 1.0000 164s 164s > summary(tr.prob) 164s Transition 0 0 164s P time var lower upper n.risk n.event 164s 0.882275 3 1.374e-04 0.8593018 0.905248 756 0 164s 0.112434 15 1.320e-04 0.0899155 0.134952 90 0 164s 0.031746 27 4.066e-05 0.0192484 0.044244 26 0 164s 0.006614 41 8.690e-06 0.0008359 0.012392 5 0 164s 0.002646 61 3.490e-06 0.0000000 0.006307 3 0 164s 0.000000 82 0.000e+00 0.0000000 0.000000 1 0 164s 164s Transition 0 1 164s P time var lower upper n.risk n.event 164s 0.017196 3 2.235e-05 0.0079289 0.02646 756 13 164s 0.063492 15 7.865e-05 0.0461099 0.08087 90 0 164s 0.030423 27 3.902e-05 0.0181805 0.04267 26 1 164s 0.015873 41 2.066e-05 0.0069637 0.02478 5 0 164s 0.005291 61 6.962e-06 0.0001197 0.01046 3 0 164s 0.000000 82 0.000e+00 0.0000000 0.00000 1 0 164s 164s Transition 0 2 164s P time var lower upper n.risk n.event 164s 0.08466 3 0.0001025 0.06481 0.1045 756 64 164s 0.62302 15 0.0003107 0.58847 0.6576 90 4 164s 0.69841 27 0.0002786 0.66570 0.7311 26 1 164s 0.72751 41 0.0002622 0.69578 0.7593 5 0 164s 0.74074 61 0.0002540 0.70950 0.7720 3 1 164s 0.74735 82 0.0002498 0.71638 0.7783 1 1 164s 164s Transition 0 3 164s P time var lower upper n.risk n.event 164s 0.01587 3 2.066e-05 0.006964 0.02478 756 12 164s 0.20106 15 2.125e-04 0.172489 0.22963 90 1 164s 0.23942 27 2.409e-04 0.208999 0.26984 26 0 164s 0.25000 41 2.480e-04 0.219133 0.28087 5 0 164s 0.25132 61 2.489e-04 0.220402 0.28224 3 0 164s 0.25265 82 2.498e-04 0.221671 0.28362 1 0 164s 164s Transition 1 1 164s P time var lower upper n.risk n.event 164s 1.00000 3 0.000e+00 1.00000 1.00000 0 0 164s 0.38661 15 2.358e-03 0.29143 0.48179 51 0 164s 0.12119 27 7.842e-04 0.06630 0.17607 23 0 164s 0.04593 41 2.405e-04 0.01554 0.07633 14 0 164s 0.01531 61 6.579e-05 0.00000 0.03121 4 0 164s 0.00000 82 0.000e+00 0.00000 0.00000 0 0 164s 164s Transition 1 2 164s P time var lower upper n.risk n.event 164s 0.0000 3 0.000000 0.0000 0.0000 0 0 164s 0.4107 15 0.002590 0.3110 0.5104 51 2 164s 0.6082 27 0.002254 0.5151 0.7012 23 1 164s 0.6652 41 0.002064 0.5761 0.7542 14 2 164s 0.6920 61 0.002000 0.6043 0.7796 4 0 164s 0.7073 82 0.001984 0.6200 0.7946 0 0 164s 164s Transition 1 3 164s P time var lower upper n.risk n.event 164s 0.0000 3 0.000000 0.0000 0.0000 0 0 164s 0.2027 15 0.001784 0.1199 0.2855 51 1 164s 0.2706 27 0.001968 0.1837 0.3576 23 0 164s 0.2889 41 0.001982 0.2016 0.3761 14 0 164s 0.2927 61 0.001984 0.2054 0.3800 4 0 164s 0.2927 82 0.001984 0.2054 0.3800 0 0 164s 164s > 164s > cLOS <- etm::clos(tr.prob, aw = TRUE) 164s > 164s > cLOS 164s The expected change in length of stay is: 164s 1.975 164s 164s Alternative weighting: 164s 164s Expected change in LOS with weight.1: 2.097 164s Expected change in LOS with weight.other: 1.951 164s > 164s > 164s > ### Tests on pseudo values 164s > t_pseudo <- closPseudo(my.observ, c("0","1","2","3"), tra, NULL, 164s + formula = ~ 1, aw = TRUE) 172s > 172s > cLOS$e.phi == t_pseudo$theta[, "e.phi"] 172s [,1] 172s [1,] TRUE 172s > cLOS$e.phi.weights.1 == t_pseudo$theta[, "e.phi.weights.1"] 172s [,1] 172s [1,] TRUE 172s > cLOS$e.phi.weights.other == t_pseudo$theta[, "e.phi.weights.other"] 172s [,1] 172s [1,] TRUE 172s > 172s > mean(t_pseudo$pseudoData$ps.e.phi) 172s [1] 1.968 172s > 172s > ### tests on etmprep 172s > 172s > ### creation of fake data in the wild format, following an illness-death model 172s > ## transition times 172s > tdisease <- c(3, 4, 3, 6, 8, 9) 172s > tdeath <- c(6, 9, 8, 6, 8, 9) 172s > 172s > ## transition status 172s > stat.disease <- c(1, 1, 1, 0, 0, 0) 172s > stat.death <- c(1, 1, 1, 1, 1, 0) 172s > 172s > ## a covariate that we want to keep in the new data 172s > set.seed(1313) 172s > cova <- rbinom(6, 1, 0.5) 172s > 172s > dat <- data.frame(tdisease, tdeath, 172s + stat.disease, stat.death, 172s + cova) 172s > 172s > ## Possible transitions 172s > tra <- matrix(FALSE, 3, 3) 172s > tra[1, 2:3] <- TRUE 172s > tra[2, 3] <- TRUE 172s > 172s > ## data preparation 172s > newdat <- etmprep(c(NA, "tdisease", "tdeath"), 172s + c(NA, "stat.disease", "stat.death"), 172s + data = dat, tra = tra, 172s + cens.name = "cens", keep = "cova") 172s > 172s > newdat 172s id entry exit from to cova 172s 1 1 0 3 0 1 1 172s 2 1 3 6 1 2 1 172s 3 2 0 4 0 1 0 172s 4 2 4 9 1 2 0 172s 5 3 0 3 0 1 1 172s 6 3 3 8 1 2 1 172s 7 4 0 6 0 2 0 172s 8 5 0 8 0 2 1 172s 9 6 0 9 0 cens 1 172s > 172s > ref <- data.frame(id = c(1, 1, 2, 2, 3, 3, 4, 5, 6), 172s + entry = c(0, 3, 0, 4, 0, 3, 0, 0, 0), 172s + exit = c(3, 6, 4, 9, 3, 8, 6, 8, 9), 172s + from = c(0, 1, 0, 1, 0, 1, 0, 0, 0), 172s + to = c(rep(c(1, 2), 3), 2, 2, "cens"), 172s + cova = c(1, 1, 0, 0, 1, 1, 0, 1, 1)) 172s > ref$from <- factor(as.character(ref$from), levels = c("0", "1", "2", "cens")) 172s > ref$to <- factor(as.character(ref$to), levels = c("0", "1", "2", "cens")) 172s > 172s > all.equal(ref, newdat) 172s [1] TRUE 172s > 172s > 172s > ###################################### 172s > ### Test the stratified calls 172s > ###################################### 172s > 172s > if (require("kmi", quietly = TRUE)) { 172s + library(etm) 172s + 172s + data(icu.pneu) 172s + my.icu.pneu <- icu.pneu 172s + 172s + my.icu.pneu <- my.icu.pneu[order(my.icu.pneu$id, my.icu.pneu$start), ] 172s + masque <- diff(my.icu.pneu$id) 172s + 172s + my.icu.pneu$from <- 0 172s + my.icu.pneu$from[c(1, masque) == 0] <- 1 172s + 172s + my.icu.pneu$to2 <- my.icu.pneu$event 172s + my.icu.pneu$to2[my.icu.pneu$status == 0] <- "cens" 172s + my.icu.pneu$to2[c(masque, 1) == 0] <- 1 172s + 172s + 172s + my.icu.pneu$to <- ifelse(my.icu.pneu$to2 %in% c(2, 3), 2, 172s + my.icu.pneu$to2) 172s + 172s + my.icu.pneu <- my.icu.pneu[, c("id", "start", "stop", "from", "to", 172s + "to2", "age", "sex")] 172s + names(my.icu.pneu)[c(2, 3)] <- c("entry", "exit") 172s + 172s + bouh_strat <- etm(my.icu.pneu, c("0", "1", "2"), tra_ill(), "cens", 0, strata = "sex") 172s + 172s + bouh_female <- etm(my.icu.pneu[my.icu.pneu$sex == "F", ], 172s + c("0", "1", "2"), tra_ill(), "cens", 0) 172s + 172s + all(bouh_strat[[1]]$est == bouh_female$est) 172s + 172s + ## Test the summary 172s + the_summary <- summary(bouh_strat) 172s + the_summary 172s + 172s + ## Test trprob 172s + all(trprob(bouh_strat, "0 1")[[1]] == trprob(bouh_female, "0 1")) 172s + all(trprob(bouh_strat, "0 1", c(0, 5, 10, 15))[[1]] == trprob(bouh_female, "0 1", c(0, 5, 10, 15))) 172s + 172s + ## Test trcov 172s + all(trcov(bouh_strat, "0 1")[[1]] == trcov(bouh_female, "0 1")) 172s + all(trcov(bouh_strat, c("0 1", "0 2"))[[1]] == trcov(bouh_female, c("0 1", "0 2"))) 172s + all(trcov(bouh_strat, "0 1", c(0, 5, 10, 15))[[1]] == trcov(bouh_female, "0 1", c(0, 5, 10, 15))) 172s + } else { 172s + print("These tests require the kmi package") 172s + } 172s [1] TRUE 172s > 172s > options(old) 172s > 172s autopkgtest [02:34:24]: test run-unit-test: -----------------------] 173s autopkgtest [02:34:25]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 173s run-unit-test PASS 173s autopkgtest [02:34:25]: test pkg-r-autopkgtest: preparing testbed 173s Reading package lists... 173s Building dependency tree... 173s Reading state information... 173s Solving dependencies... 173s The following NEW packages will be installed: 173s build-essential cpp cpp-15 cpp-15-x86-64-linux-gnu cpp-x86-64-linux-gnu 173s dctrl-tools g++ g++-15 g++-15-x86-64-linux-gnu g++-x86-64-linux-gnu gcc 173s gcc-15 gcc-15-x86-64-linux-gnu gcc-x86-64-linux-gnu gfortran gfortran-15 173s gfortran-15-x86-64-linux-gnu gfortran-x86-64-linux-gnu icu-devtools libasan8 173s libblas-dev libbz2-dev libc-dev-bin libc6-dev libcc1-0 libcrypt-dev 173s libdeflate-dev libgcc-15-dev libgfortran-15-dev libhwasan0 libicu-dev 173s libisl23 libitm1 libjpeg-dev libjpeg-turbo8-dev libjpeg8-dev liblapack-dev 173s liblsan0 liblzma-dev libmpc3 libncurses-dev libpcre2-16-0 libpcre2-32-0 173s libpcre2-dev libpcre2-posix3 libpkgconf3 libpng-dev libquadmath0 173s libreadline-dev libstdc++-15-dev libtirpc-dev libtsan2 libubsan1 libzstd-dev 173s linux-libc-dev pkg-r-autopkgtest pkgconf pkgconf-bin r-base-dev 173s r-cran-backports r-cran-broom r-cran-cli r-cran-cpp11 r-cran-dplyr 173s r-cran-fansi r-cran-farver r-cran-geepack r-cran-generics r-cran-ggplot2 173s r-cran-glue r-cran-gtable r-cran-isoband r-cran-labeling r-cran-lifecycle 173s r-cran-magrittr r-cran-mass r-cran-mgcv r-cran-nlme r-cran-pillar 173s r-cran-pkgconfig r-cran-purrr r-cran-r6 r-cran-rcolorbrewer r-cran-rlang 173s r-cran-scales r-cran-stringi r-cran-stringr r-cran-tibble r-cran-tidyr 173s r-cran-tidyselect r-cran-utf8 r-cran-vctrs r-cran-viridislite r-cran-withr 173s rpcsvc-proto zlib1g-dev 174s 0 upgraded, 96 newly installed, 0 to remove and 0 not upgraded. 174s Need to get 142 MB of archives. 174s After this operation, 450 MB of additional disk space will be used. 174s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 libc-dev-bin amd64 2.42-2ubuntu4 [23.3 kB] 174s Get:2 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-libc-dev amd64 6.19.0-3.3 [1846 kB] 174s Get:3 http://ftpmaster.internal/ubuntu resolute/main amd64 libcrypt-dev amd64 1:4.5.1-1 [122 kB] 174s Get:4 http://ftpmaster.internal/ubuntu resolute/main amd64 rpcsvc-proto amd64 1.4.3-1build1 [68.3 kB] 174s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 libc6-dev amd64 2.42-2ubuntu4 [2207 kB] 174s Get:6 http://ftpmaster.internal/ubuntu resolute/main amd64 libisl23 amd64 0.27-1build1 [691 kB] 174s Get:7 http://ftpmaster.internal/ubuntu resolute/main amd64 libmpc3 amd64 1.3.1-2 [54.8 kB] 174s Get:8 http://ftpmaster.internal/ubuntu resolute/main amd64 cpp-15-x86-64-linux-gnu amd64 15.2.0-12ubuntu1 [12.9 MB] 174s Get:9 http://ftpmaster.internal/ubuntu resolute/main amd64 cpp-15 amd64 15.2.0-12ubuntu1 [1034 B] 174s Get:10 http://ftpmaster.internal/ubuntu resolute/main amd64 cpp-x86-64-linux-gnu amd64 4:15.2.0-4ubuntu1 [5746 B] 174s Get:11 http://ftpmaster.internal/ubuntu resolute/main amd64 cpp amd64 4:15.2.0-4ubuntu1 [22.4 kB] 174s Get:12 http://ftpmaster.internal/ubuntu resolute/main amd64 libcc1-0 amd64 16-20260208-1ubuntu1 [51.2 kB] 174s Get:13 http://ftpmaster.internal/ubuntu resolute/main amd64 libitm1 amd64 16-20260208-1ubuntu1 [30.2 kB] 174s Get:14 http://ftpmaster.internal/ubuntu resolute/main amd64 libasan8 amd64 16-20260208-1ubuntu1 [3182 kB] 174s Get:15 http://ftpmaster.internal/ubuntu resolute/main amd64 liblsan0 amd64 16-20260208-1ubuntu1 [1392 kB] 174s Get:16 http://ftpmaster.internal/ubuntu resolute/main amd64 libtsan2 amd64 16-20260208-1ubuntu1 [2838 kB] 174s Get:17 http://ftpmaster.internal/ubuntu resolute/main amd64 libubsan1 amd64 16-20260208-1ubuntu1 [1238 kB] 175s Get:18 http://ftpmaster.internal/ubuntu resolute/main amd64 libhwasan0 amd64 16-20260208-1ubuntu1 [1729 kB] 175s Get:19 http://ftpmaster.internal/ubuntu resolute/main amd64 libquadmath0 amd64 16-20260208-1ubuntu1 [155 kB] 175s Get:20 http://ftpmaster.internal/ubuntu resolute/main amd64 libgcc-15-dev amd64 15.2.0-12ubuntu1 [2866 kB] 175s Get:21 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc-15-x86-64-linux-gnu amd64 15.2.0-12ubuntu1 [25.4 MB] 175s Get:22 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc-15 amd64 15.2.0-12ubuntu1 [530 kB] 175s Get:23 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc-x86-64-linux-gnu amd64 4:15.2.0-4ubuntu1 [1208 B] 175s Get:24 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc amd64 4:15.2.0-4ubuntu1 [5024 B] 175s Get:25 http://ftpmaster.internal/ubuntu resolute/main amd64 libstdc++-15-dev amd64 15.2.0-12ubuntu1 [2553 kB] 175s Get:26 http://ftpmaster.internal/ubuntu resolute/main amd64 g++-15-x86-64-linux-gnu amd64 15.2.0-12ubuntu1 [14.4 MB] 175s Get:27 http://ftpmaster.internal/ubuntu resolute/main amd64 g++-15 amd64 15.2.0-12ubuntu1 [25.3 kB] 175s Get:28 http://ftpmaster.internal/ubuntu resolute/main amd64 g++-x86-64-linux-gnu amd64 4:15.2.0-4ubuntu1 [966 B] 175s Get:29 http://ftpmaster.internal/ubuntu resolute/main amd64 g++ amd64 4:15.2.0-4ubuntu1 [1100 B] 175s Get:30 http://ftpmaster.internal/ubuntu resolute/main amd64 build-essential amd64 12.12ubuntu2 [5256 B] 175s Get:31 http://ftpmaster.internal/ubuntu resolute/main amd64 dctrl-tools amd64 2.24-3build4 [104 kB] 176s Get:32 http://ftpmaster.internal/ubuntu resolute/main amd64 libgfortran-15-dev amd64 15.2.0-12ubuntu1 [973 kB] 176s Get:33 http://ftpmaster.internal/ubuntu resolute/main amd64 gfortran-15-x86-64-linux-gnu amd64 15.2.0-12ubuntu1 [13.6 MB] 176s Get:34 http://ftpmaster.internal/ubuntu resolute/main amd64 gfortran-15 amd64 15.2.0-12ubuntu1 [18.1 kB] 176s Get:35 http://ftpmaster.internal/ubuntu resolute/main amd64 gfortran-x86-64-linux-gnu amd64 4:15.2.0-4ubuntu1 [1014 B] 176s Get:36 http://ftpmaster.internal/ubuntu resolute/main amd64 gfortran amd64 4:15.2.0-4ubuntu1 [1172 B] 176s Get:37 http://ftpmaster.internal/ubuntu resolute/main amd64 icu-devtools amd64 78.2-1ubuntu1 [214 kB] 176s Get:38 http://ftpmaster.internal/ubuntu resolute/main amd64 libblas-dev amd64 3.12.1-7ubuntu1 [235 kB] 176s Get:39 http://ftpmaster.internal/ubuntu resolute/main amd64 libbz2-dev amd64 1.0.8-6build2 [36.2 kB] 176s Get:40 http://ftpmaster.internal/ubuntu resolute/main amd64 libdeflate-dev amd64 1.23-2build1 [58.8 kB] 176s Get:41 http://ftpmaster.internal/ubuntu resolute/main amd64 libicu-dev amd64 78.2-1ubuntu1 [12.5 MB] 176s Get:42 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg-turbo8-dev amd64 2.1.5-4ubuntu3 [300 kB] 176s Get:43 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg8-dev amd64 8c-2ubuntu12 [1480 B] 176s Get:44 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg-dev amd64 8c-2ubuntu12 [1480 B] 176s Get:45 http://ftpmaster.internal/ubuntu resolute/main amd64 liblapack-dev amd64 3.12.1-7ubuntu1 [5433 kB] 176s Get:46 http://ftpmaster.internal/ubuntu resolute/main amd64 libncurses-dev amd64 6.6+20251231-1 [389 kB] 176s Get:47 http://ftpmaster.internal/ubuntu resolute/main amd64 libpcre2-16-0 amd64 10.46-1 [243 kB] 176s Get:48 http://ftpmaster.internal/ubuntu resolute/main amd64 libpcre2-32-0 amd64 10.46-1 [230 kB] 176s Get:49 http://ftpmaster.internal/ubuntu resolute/main amd64 libpcre2-posix3 amd64 10.46-1 [7354 B] 176s Get:50 http://ftpmaster.internal/ubuntu resolute/main amd64 libpcre2-dev amd64 10.46-1 [832 kB] 176s Get:51 http://ftpmaster.internal/ubuntu resolute/main amd64 libpkgconf3 amd64 1.8.1-4build1 [32.8 kB] 176s Get:52 http://ftpmaster.internal/ubuntu resolute/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1ubuntu2 [898 kB] 176s Get:53 http://ftpmaster.internal/ubuntu resolute/main amd64 libpng-dev amd64 1.6.54-1 [273 kB] 176s Get:54 http://ftpmaster.internal/ubuntu resolute/main amd64 libreadline-dev amd64 8.3-3 [189 kB] 176s Get:55 http://ftpmaster.internal/ubuntu resolute/main amd64 libzstd-dev amd64 1.5.7+dfsg-3 [376 kB] 176s Get:56 http://ftpmaster.internal/ubuntu resolute/main amd64 liblzma-dev amd64 5.8.2-2 [179 kB] 176s Get:57 http://ftpmaster.internal/ubuntu resolute/main amd64 pkgconf-bin amd64 1.8.1-4build1 [21.7 kB] 176s Get:58 http://ftpmaster.internal/ubuntu resolute/main amd64 pkgconf amd64 1.8.1-4build1 [16.8 kB] 176s Get:59 http://ftpmaster.internal/ubuntu resolute/main amd64 libtirpc-dev amd64 1.3.6+ds-1 [195 kB] 176s Get:60 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-base-dev all 4.5.2-1ubuntu2 [1880 B] 176s Get:61 http://ftpmaster.internal/ubuntu resolute/universe amd64 pkg-r-autopkgtest all 20250812 [6158 B] 176s Get:62 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-backports amd64 1.5.0-2 [121 kB] 176s Get:63 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-cli amd64 3.6.4-1 [1394 kB] 176s Get:64 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-generics all 0.1.4-1 [84.0 kB] 176s Get:65 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-glue amd64 1.8.0-1 [164 kB] 176s Get:66 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rlang amd64 1.1.5-3 [1721 kB] 176s Get:67 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-lifecycle all 1.0.5+dfsg-1 [120 kB] 176s Get:68 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-magrittr amd64 2.0.3-1 [154 kB] 176s Get:69 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-utf8 amd64 1.2.4-1 [140 kB] 176s Get:70 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-vctrs amd64 0.6.5-1 [1335 kB] 176s Get:71 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-pillar all 1.11.1+dfsg-1 [456 kB] 176s Get:72 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-r6 all 2.6.1-1 [101 kB] 177s Get:73 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-fansi amd64 1.0.6-2 [626 kB] 177s Get:74 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-pkgconfig all 2.0.3-2build2 [20.4 kB] 177s Get:75 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-tibble amd64 3.2.1+dfsg-3 [419 kB] 177s Get:76 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-withr all 3.0.2+dfsg-1 [214 kB] 177s Get:77 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-tidyselect amd64 1.2.1+dfsg-1 [222 kB] 177s Get:78 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-dplyr amd64 1.1.4-4 [1536 kB] 177s Get:79 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-purrr amd64 1.0.4-1 [552 kB] 177s Get:80 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-stringi amd64 1.8.4-1build2 [908 kB] 177s Get:81 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-stringr all 1.5.1-1 [290 kB] 177s Get:82 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-cpp11 all 0.5.3-1 [242 kB] 177s Get:83 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-tidyr amd64 1.3.1-1 [1156 kB] 177s Get:84 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-broom all 1.0.12+dfsg-1 [1708 kB] 177s Get:85 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-farver amd64 2.1.2-1 [1355 kB] 177s Get:86 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-mass amd64 7.3-65-1 [1116 kB] 177s Get:87 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-geepack amd64 1.3.12-1 [389 kB] 177s Get:88 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-gtable all 0.3.6+dfsg-1 [199 kB] 177s Get:89 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-isoband amd64 0.2.7-1 [1481 kB] 177s Get:90 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-nlme amd64 3.1.168-1 [2320 kB] 177s Get:91 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-mgcv amd64 1.9-4-1 [3556 kB] 177s Get:92 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-labeling all 0.4.3-1 [62.1 kB] 177s Get:93 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rcolorbrewer all 1.1-3-1build2 [54.0 kB] 177s Get:94 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-viridislite all 0.4.3-1 [1088 kB] 177s Get:95 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-scales all 1.4.0-1 [725 kB] 177s Get:96 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-ggplot2 all 3.5.1+dfsg-1 [3940 kB] 178s Fetched 142 MB in 4s (37.3 MB/s) 178s Selecting previously unselected package libc-dev-bin. 178s (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 ... 130505 files and directories currently installed.) 178s Preparing to unpack .../00-libc-dev-bin_2.42-2ubuntu4_amd64.deb ... 178s Unpacking libc-dev-bin (2.42-2ubuntu4) ... 178s Selecting previously unselected package linux-libc-dev:amd64. 178s Preparing to unpack .../01-linux-libc-dev_6.19.0-3.3_amd64.deb ... 178s Unpacking linux-libc-dev:amd64 (6.19.0-3.3) ... 178s Selecting previously unselected package libcrypt-dev:amd64. 178s Preparing to unpack .../02-libcrypt-dev_1%3a4.5.1-1_amd64.deb ... 178s Unpacking libcrypt-dev:amd64 (1:4.5.1-1) ... 178s Selecting previously unselected package rpcsvc-proto. 178s Preparing to unpack .../03-rpcsvc-proto_1.4.3-1build1_amd64.deb ... 178s Unpacking rpcsvc-proto (1.4.3-1build1) ... 178s Selecting previously unselected package libc6-dev:amd64. 178s Preparing to unpack .../04-libc6-dev_2.42-2ubuntu4_amd64.deb ... 178s Unpacking libc6-dev:amd64 (2.42-2ubuntu4) ... 178s Selecting previously unselected package libisl23:amd64. 178s Preparing to unpack .../05-libisl23_0.27-1build1_amd64.deb ... 178s Unpacking libisl23:amd64 (0.27-1build1) ... 178s Selecting previously unselected package libmpc3:amd64. 178s Preparing to unpack .../06-libmpc3_1.3.1-2_amd64.deb ... 178s Unpacking libmpc3:amd64 (1.3.1-2) ... 178s Selecting previously unselected package cpp-15-x86-64-linux-gnu. 178s Preparing to unpack .../07-cpp-15-x86-64-linux-gnu_15.2.0-12ubuntu1_amd64.deb ... 178s Unpacking cpp-15-x86-64-linux-gnu (15.2.0-12ubuntu1) ... 178s Selecting previously unselected package cpp-15. 178s Preparing to unpack .../08-cpp-15_15.2.0-12ubuntu1_amd64.deb ... 178s Unpacking cpp-15 (15.2.0-12ubuntu1) ... 178s Selecting previously unselected package cpp-x86-64-linux-gnu. 178s Preparing to unpack .../09-cpp-x86-64-linux-gnu_4%3a15.2.0-4ubuntu1_amd64.deb ... 178s Unpacking cpp-x86-64-linux-gnu (4:15.2.0-4ubuntu1) ... 178s Selecting previously unselected package cpp. 178s Preparing to unpack .../10-cpp_4%3a15.2.0-4ubuntu1_amd64.deb ... 178s Unpacking cpp (4:15.2.0-4ubuntu1) ... 178s Selecting previously unselected package libcc1-0:amd64. 178s Preparing to unpack .../11-libcc1-0_16-20260208-1ubuntu1_amd64.deb ... 178s Unpacking libcc1-0:amd64 (16-20260208-1ubuntu1) ... 178s Selecting previously unselected package libitm1:amd64. 178s Preparing to unpack .../12-libitm1_16-20260208-1ubuntu1_amd64.deb ... 178s Unpacking libitm1:amd64 (16-20260208-1ubuntu1) ... 178s Selecting previously unselected package libasan8:amd64. 178s Preparing to unpack .../13-libasan8_16-20260208-1ubuntu1_amd64.deb ... 178s Unpacking libasan8:amd64 (16-20260208-1ubuntu1) ... 178s Selecting previously unselected package liblsan0:amd64. 178s Preparing to unpack .../14-liblsan0_16-20260208-1ubuntu1_amd64.deb ... 178s Unpacking liblsan0:amd64 (16-20260208-1ubuntu1) ... 178s Selecting previously unselected package libtsan2:amd64. 178s Preparing to unpack .../15-libtsan2_16-20260208-1ubuntu1_amd64.deb ... 178s Unpacking libtsan2:amd64 (16-20260208-1ubuntu1) ... 178s Selecting previously unselected package libubsan1:amd64. 178s Preparing to unpack .../16-libubsan1_16-20260208-1ubuntu1_amd64.deb ... 178s Unpacking libubsan1:amd64 (16-20260208-1ubuntu1) ... 178s Selecting previously unselected package libhwasan0:amd64. 178s Preparing to unpack .../17-libhwasan0_16-20260208-1ubuntu1_amd64.deb ... 178s Unpacking libhwasan0:amd64 (16-20260208-1ubuntu1) ... 178s Selecting previously unselected package libquadmath0:amd64. 178s Preparing to unpack .../18-libquadmath0_16-20260208-1ubuntu1_amd64.deb ... 178s Unpacking libquadmath0:amd64 (16-20260208-1ubuntu1) ... 178s Selecting previously unselected package libgcc-15-dev:amd64. 178s Preparing to unpack .../19-libgcc-15-dev_15.2.0-12ubuntu1_amd64.deb ... 178s Unpacking libgcc-15-dev:amd64 (15.2.0-12ubuntu1) ... 178s Selecting previously unselected package gcc-15-x86-64-linux-gnu. 178s Preparing to unpack .../20-gcc-15-x86-64-linux-gnu_15.2.0-12ubuntu1_amd64.deb ... 178s Unpacking gcc-15-x86-64-linux-gnu (15.2.0-12ubuntu1) ... 178s Selecting previously unselected package gcc-15. 178s Preparing to unpack .../21-gcc-15_15.2.0-12ubuntu1_amd64.deb ... 178s Unpacking gcc-15 (15.2.0-12ubuntu1) ... 178s Selecting previously unselected package gcc-x86-64-linux-gnu. 178s Preparing to unpack .../22-gcc-x86-64-linux-gnu_4%3a15.2.0-4ubuntu1_amd64.deb ... 178s Unpacking gcc-x86-64-linux-gnu (4:15.2.0-4ubuntu1) ... 179s Selecting previously unselected package gcc. 179s Preparing to unpack .../23-gcc_4%3a15.2.0-4ubuntu1_amd64.deb ... 179s Unpacking gcc (4:15.2.0-4ubuntu1) ... 179s Selecting previously unselected package libstdc++-15-dev:amd64. 179s Preparing to unpack .../24-libstdc++-15-dev_15.2.0-12ubuntu1_amd64.deb ... 179s Unpacking libstdc++-15-dev:amd64 (15.2.0-12ubuntu1) ... 179s Selecting previously unselected package g++-15-x86-64-linux-gnu. 179s Preparing to unpack .../25-g++-15-x86-64-linux-gnu_15.2.0-12ubuntu1_amd64.deb ... 179s Unpacking g++-15-x86-64-linux-gnu (15.2.0-12ubuntu1) ... 179s Selecting previously unselected package g++-15. 179s Preparing to unpack .../26-g++-15_15.2.0-12ubuntu1_amd64.deb ... 179s Unpacking g++-15 (15.2.0-12ubuntu1) ... 179s Selecting previously unselected package g++-x86-64-linux-gnu. 179s Preparing to unpack .../27-g++-x86-64-linux-gnu_4%3a15.2.0-4ubuntu1_amd64.deb ... 179s Unpacking g++-x86-64-linux-gnu (4:15.2.0-4ubuntu1) ... 179s Selecting previously unselected package g++. 179s Preparing to unpack .../28-g++_4%3a15.2.0-4ubuntu1_amd64.deb ... 179s Unpacking g++ (4:15.2.0-4ubuntu1) ... 179s Selecting previously unselected package build-essential. 179s Preparing to unpack .../29-build-essential_12.12ubuntu2_amd64.deb ... 179s Unpacking build-essential (12.12ubuntu2) ... 179s Selecting previously unselected package dctrl-tools. 179s Preparing to unpack .../30-dctrl-tools_2.24-3build4_amd64.deb ... 179s Unpacking dctrl-tools (2.24-3build4) ... 179s Selecting previously unselected package libgfortran-15-dev:amd64. 179s Preparing to unpack .../31-libgfortran-15-dev_15.2.0-12ubuntu1_amd64.deb ... 179s Unpacking libgfortran-15-dev:amd64 (15.2.0-12ubuntu1) ... 179s Selecting previously unselected package gfortran-15-x86-64-linux-gnu. 179s Preparing to unpack .../32-gfortran-15-x86-64-linux-gnu_15.2.0-12ubuntu1_amd64.deb ... 179s Unpacking gfortran-15-x86-64-linux-gnu (15.2.0-12ubuntu1) ... 179s Selecting previously unselected package gfortran-15. 179s Preparing to unpack .../33-gfortran-15_15.2.0-12ubuntu1_amd64.deb ... 179s Unpacking gfortran-15 (15.2.0-12ubuntu1) ... 179s Selecting previously unselected package gfortran-x86-64-linux-gnu. 179s Preparing to unpack .../34-gfortran-x86-64-linux-gnu_4%3a15.2.0-4ubuntu1_amd64.deb ... 179s Unpacking gfortran-x86-64-linux-gnu (4:15.2.0-4ubuntu1) ... 179s Selecting previously unselected package gfortran. 179s Preparing to unpack .../35-gfortran_4%3a15.2.0-4ubuntu1_amd64.deb ... 179s Unpacking gfortran (4:15.2.0-4ubuntu1) ... 179s Selecting previously unselected package icu-devtools. 179s Preparing to unpack .../36-icu-devtools_78.2-1ubuntu1_amd64.deb ... 179s Unpacking icu-devtools (78.2-1ubuntu1) ... 179s Selecting previously unselected package libblas-dev:amd64. 179s Preparing to unpack .../37-libblas-dev_3.12.1-7ubuntu1_amd64.deb ... 179s Unpacking libblas-dev:amd64 (3.12.1-7ubuntu1) ... 179s Selecting previously unselected package libbz2-dev:amd64. 179s Preparing to unpack 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/usr/share/man/man1/gfortran.1.gz (of link group f77) doesn't exist 180s Setting up g++ (4:15.2.0-4ubuntu1) ... 180s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 180s Setting up build-essential (12.12ubuntu2) ... 180s Setting up r-base-dev (4.5.2-1ubuntu2) ... 180s Setting up pkg-r-autopkgtest (20250812) ... 180s Processing triggers for libc-bin (2.42-2ubuntu4) ... 180s Processing triggers for man-db (2.13.1-1build1) ... 181s Processing triggers for install-info (7.2-5) ... 182s autopkgtest [02:34:34]: test pkg-r-autopkgtest: /usr/share/dh-r/pkg-r-autopkgtest 182s autopkgtest [02:34:34]: test pkg-r-autopkgtest: [----------------------- 182s Test: Try to load the R library etm 182s 182s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 182s Copyright (C) 2025 The R Foundation for Statistical Computing 182s Platform: x86_64-pc-linux-gnu 182s 182s R is free software and comes with ABSOLUTELY NO WARRANTY. 182s You are welcome to redistribute it under certain conditions. 182s Type 'license()' or 'licence()' for distribution details. 182s 182s R is a collaborative project with many contributors. 182s Type 'contributors()' for more information and 182s 'citation()' on how to cite R or R packages in publications. 182s 182s Type 'demo()' for some demos, 'help()' for on-line help, or 182s 'help.start()' for an HTML browser interface to help. 182s Type 'q()' to quit R. 182s 182s > library('etm') 183s > 183s autopkgtest [02:34:35]: test pkg-r-autopkgtest: -----------------------] 184s pkg-r-autopkgtest PASS 184s autopkgtest [02:34:36]: test pkg-r-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 184s autopkgtest [02:34:36]: @@@@@@@@@@@@@@@@@@@@ summary 184s run-unit-test PASS 184s pkg-r-autopkgtest PASS