0s autopkgtest [05:24:06]: starting date and time: 2026-02-10 05:24:06+0000 0s autopkgtest [05:24:06]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [05:24:06]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.0al3zdn5/out --timeout-copy=6000 --needs-internet=try --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:r-cran-ggplot2 --apt-upgrade r-cran-lmertest --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=r-cran-ggplot2/4.0.2+dfsg-1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-cpu2-ram4-disk20-amd64 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@sto01-13.secgroup --name adt-resolute-amd64-r-cran-lmertest-20260210-052406-juju-7f2275-prod-proposed-migration-environment-20-a41f0f74-8854-4e6b-a45c-7c7a43f23a2c --image adt/ubuntu-resolute-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-autopkgtest-workers-amd64 -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 3s Creating nova instance adt-resolute-amd64-r-cran-lmertest-20260210-052406-juju-7f2275-prod-proposed-migration-environment-20-a41f0f74-8854-4e6b-a45c-7c7a43f23a2c from image adt/ubuntu-resolute-amd64-server-20260204.img (UUID fedf54b4-458b-493e-8072-6425c19717b4)... 75s autopkgtest [05:25:21]: testbed dpkg architecture: amd64 75s autopkgtest [05:25:21]: testbed apt version: 3.1.14 75s autopkgtest [05:25:21]: @@@@@@@@@@@@@@@@@@@@ test bed setup 76s autopkgtest [05:25:22]: testbed release detected to be: None 76s autopkgtest [05:25:22]: updating testbed package index (apt update) 76s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 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 Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [178 kB] 77s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [1727 kB] 77s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [31.1 kB] 77s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 Packages [266 kB] 77s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main i386 Packages [219 kB] 77s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 c-n-f Metadata [6184 B] 77s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/restricted amd64 c-n-f Metadata [120 B] 77s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/universe i386 Packages [792 kB] 77s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 Packages [1787 kB] 77s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 c-n-f Metadata [32.5 kB] 77s Get:15 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 Packages [26.4 kB] 77s Get:16 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse i386 Packages [5020 B] 77s Get:17 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 c-n-f Metadata [996 B] 78s Fetched 5197 kB in 1s (7418 kB/s) 78s Reading package lists... 79s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 79s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 79s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 79s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 79s Reading package lists... 79s Reading package lists... 80s Building dependency tree... 80s Reading state information... 80s Calculating upgrade... 80s The following package was automatically installed and is no longer required: 80s libpython3.13 80s Use 'sudo apt autoremove' to remove it. 80s The following NEW packages will be installed: 80s gcc-16-base libpython3.14 libpython3.14-minimal libpython3.14-stdlib 80s linux-headers-6.19.0-3 linux-headers-6.19.0-3-generic 80s linux-image-6.19.0-3-generic linux-modules-6.19.0-3-generic 80s linux-tools-6.19.0-3 linux-tools-6.19.0-3-generic 80s The following packages will be upgraded: 80s 3cpio amd64-microcode apt bpftool busybox-initramfs busybox-static 80s cryptsetup-bin dash dbus dbus-bin dbus-daemon dbus-session-bus-common 80s dbus-system-bus-common dbus-user-session debianutils dmsetup dracut-install 80s ethtool findutils gir1.2-girepository-3.0 gir1.2-glib-2.0 hwdata iproute2 80s iptables less libapt-pkg7.0 libatomic1 libattr1 libbpf1 libbrotli1 libbsd0 80s libcryptsetup12 libdbus-1-3 libdevmapper1.02.1 libdrm-amdgpu1 libdrm-common 80s libdrm2 libevent-core-2.1-7t64 libgcc-s1 libgdbm-compat4t64 libgdbm6t64 80s libgirepository-2.0-0 libglib2.0-0t64 libglib2.0-data libgpm2 libgudev-1.0-0 80s libidn2-0 libip4tc2 libip6tc2 libjansson4 libkeyutils1 liblsof0 80s libmaxminddb0 libnetfilter-conntrack3 libnpth0t64 libonig5 libpcap0.8t64 80s libpci3 libsensors-config libsensors5 libstdc++6 libusb-1.0-0 libwrap0 80s libxau6 libxkbcommon0 libxtables12 linux-generic linux-headers-generic 80s linux-headers-virtual linux-image-generic linux-image-virtual linux-perf 80s linux-tools-common linux-virtual lsof man-db mawk patch pciutils pnp.ids 80s pollinate python3-linkify-it python3-markdown-it python3-referencing sed 80s shared-mime-info tar tcpdump ubuntu-kernel-accessories ubuntu-standard wget 80s 91 upgraded, 10 newly installed, 0 to remove and 0 not upgraded. 80s Need to get 237 MB of archives. 80s After this operation, 339 MB of additional disk space will be used. 80s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 debianutils amd64 5.23.2build1 [93.3 kB] 80s Get:2 http://ftpmaster.internal/ubuntu resolute/main amd64 dash amd64 0.5.12-12ubuntu3 [96.0 kB] 80s Get:3 http://ftpmaster.internal/ubuntu resolute/main amd64 findutils amd64 4.10.0-3build2 [307 kB] 80s Get:4 http://ftpmaster.internal/ubuntu resolute/main amd64 sed amd64 4.9-2build3 [195 kB] 80s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 tar amd64 1.35+dfsg-3.1build2 [257 kB] 80s Get:6 http://ftpmaster.internal/ubuntu resolute/main amd64 libattr1 amd64 1:2.5.2-3build2 [11.4 kB] 80s Get:7 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc-16-base amd64 16-20260208-1ubuntu1 [59.7 kB] 80s Get:8 http://ftpmaster.internal/ubuntu resolute/main amd64 libgcc-s1 amd64 16-20260208-1ubuntu1 [80.3 kB] 80s Get:9 http://ftpmaster.internal/ubuntu resolute/main amd64 libbsd0 amd64 0.12.2-2build2 [42.3 kB] 80s Get:10 http://ftpmaster.internal/ubuntu resolute/main amd64 mawk amd64 1.3.4.20260129-1 [133 kB] 80s Get:11 http://ftpmaster.internal/ubuntu resolute/main amd64 libstdc++6 amd64 16-20260208-1ubuntu1 [844 kB] 80s Get:12 http://ftpmaster.internal/ubuntu resolute/main amd64 libapt-pkg7.0 amd64 3.1.15 [1151 kB] 80s Get:13 http://ftpmaster.internal/ubuntu resolute/main amd64 apt amd64 3.1.15 [1479 kB] 80s Get:14 http://ftpmaster.internal/ubuntu resolute/main amd64 dbus-system-bus-common all 1.16.2-2ubuntu3 [55.8 kB] 80s Get:15 http://ftpmaster.internal/ubuntu resolute/main amd64 dbus-session-bus-common all 1.16.2-2ubuntu3 [54.4 kB] 80s Get:16 http://ftpmaster.internal/ubuntu resolute/main amd64 dbus-user-session amd64 1.16.2-2ubuntu3 [9696 B] 80s Get:17 http://ftpmaster.internal/ubuntu resolute/main amd64 dbus-daemon amd64 1.16.2-2ubuntu3 [119 kB] 80s Get:18 http://ftpmaster.internal/ubuntu resolute/main amd64 dbus-bin amd64 1.16.2-2ubuntu3 [40.1 kB] 80s Get:19 http://ftpmaster.internal/ubuntu resolute/main amd64 dbus amd64 1.16.2-2ubuntu3 [24.2 kB] 80s Get:20 http://ftpmaster.internal/ubuntu resolute/main amd64 libdbus-1-3 amd64 1.16.2-2ubuntu3 [185 kB] 80s Get:21 http://ftpmaster.internal/ubuntu resolute/main amd64 libdevmapper1.02.1 amd64 2:1.02.205-2ubuntu3 [142 kB] 80s Get:22 http://ftpmaster.internal/ubuntu resolute/main amd64 dmsetup amd64 2:1.02.205-2ubuntu3 [79.4 kB] 80s Get:23 http://ftpmaster.internal/ubuntu resolute/main amd64 ethtool amd64 1:6.15-3build1 [318 kB] 80s Get:24 http://ftpmaster.internal/ubuntu resolute/main amd64 gir1.2-girepository-3.0 amd64 2.87.2-2 [25.2 kB] 80s Get:25 http://ftpmaster.internal/ubuntu resolute/main amd64 libgirepository-2.0-0 amd64 2.87.2-2 [76.1 kB] 80s Get:26 http://ftpmaster.internal/ubuntu resolute/main amd64 libatomic1 amd64 16-20260208-1ubuntu1 [11.4 kB] 80s Get:27 http://ftpmaster.internal/ubuntu resolute/main amd64 gir1.2-glib-2.0 amd64 2.87.2-2 [182 kB] 80s Get:28 http://ftpmaster.internal/ubuntu resolute/main amd64 libglib2.0-0t64 amd64 2.87.2-2 [1613 kB] 80s Get:29 http://ftpmaster.internal/ubuntu resolute/main amd64 libbpf1 amd64 1:1.6.2-1build1 [184 kB] 80s Get:30 http://ftpmaster.internal/ubuntu resolute/main amd64 iptables amd64 1.8.11-2ubuntu3 [381 kB] 80s Get:31 http://ftpmaster.internal/ubuntu resolute/main amd64 libip4tc2 amd64 1.8.11-2ubuntu3 [24.2 kB] 80s Get:32 http://ftpmaster.internal/ubuntu resolute/main amd64 libip6tc2 amd64 1.8.11-2ubuntu3 [24.4 kB] 80s Get:33 http://ftpmaster.internal/ubuntu resolute/main amd64 libnetfilter-conntrack3 amd64 1.1.1-1 [47.5 kB] 80s Get:34 http://ftpmaster.internal/ubuntu resolute/main amd64 libxtables12 amd64 1.8.11-2ubuntu3 [36.6 kB] 80s Get:35 http://ftpmaster.internal/ubuntu resolute/main amd64 iproute2 amd64 6.18.0-1ubuntu1 [1178 kB] 80s Get:36 http://ftpmaster.internal/ubuntu resolute/main amd64 less amd64 668-1build1 [172 kB] 80s Get:37 http://ftpmaster.internal/ubuntu resolute/main amd64 libcryptsetup12 amd64 2:2.8.0-1ubuntu3 [283 kB] 80s Get:38 http://ftpmaster.internal/ubuntu resolute/main amd64 libglib2.0-data all 2.87.2-2 [58.2 kB] 80s Get:39 http://ftpmaster.internal/ubuntu resolute/main amd64 libidn2-0 amd64 2.3.8-4build1 [67.6 kB] 80s Get:40 http://ftpmaster.internal/ubuntu resolute/main amd64 libkeyutils1 amd64 1.6.3-6ubuntu3 [10.6 kB] 80s Get:41 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-linkify-it all 2.0.3-1ubuntu3 [19.4 kB] 80s Get:42 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-markdown-it all 3.0.0-3build1 [54.4 kB] 80s Get:43 http://ftpmaster.internal/ubuntu resolute/main amd64 shared-mime-info amd64 2.4-5build3 [476 kB] 80s Get:44 http://ftpmaster.internal/ubuntu resolute/main amd64 busybox-static amd64 1:1.37.0-7ubuntu1 [1034 kB] 80s Get:45 http://ftpmaster.internal/ubuntu resolute/main amd64 libdrm-common all 2.4.131-1 [9774 B] 80s Get:46 http://ftpmaster.internal/ubuntu resolute/main amd64 libdrm2 amd64 2.4.131-1 [42.3 kB] 80s Get:47 http://ftpmaster.internal/ubuntu resolute/main amd64 libgdbm6t64 amd64 1.26-1build1 [36.5 kB] 80s Get:48 http://ftpmaster.internal/ubuntu resolute/main amd64 libgpm2 amd64 1.20.7-12build1 [14.4 kB] 80s Get:49 http://ftpmaster.internal/ubuntu resolute/main amd64 libjansson4 amd64 2.14-2build4 [33.2 kB] 80s Get:50 http://ftpmaster.internal/ubuntu resolute/main amd64 lsof amd64 4.99.4+dfsg-2build2 [239 kB] 80s Get:51 http://ftpmaster.internal/ubuntu resolute/main amd64 liblsof0 amd64 4.99.4+dfsg-2build2 [56.5 kB] 80s Get:52 http://ftpmaster.internal/ubuntu resolute/main amd64 libmaxminddb0 amd64 1.12.2-1build2 [18.9 kB] 80s Get:53 http://ftpmaster.internal/ubuntu resolute/main amd64 libpcap0.8t64 amd64 1.10.5-2ubuntu3 [154 kB] 80s Get:54 http://ftpmaster.internal/ubuntu resolute/main amd64 pciutils amd64 1:3.14.0-1build2 [95.5 kB] 80s Get:55 http://ftpmaster.internal/ubuntu resolute/main amd64 libpci3 amd64 1:3.14.0-1build2 [38.1 kB] 80s Get:56 http://ftpmaster.internal/ubuntu resolute/main amd64 libsensors-config all 1:3.6.2-2build1 [6862 B] 80s Get:57 http://ftpmaster.internal/ubuntu resolute/main amd64 libsensors5 amd64 1:3.6.2-2build1 [28.9 kB] 80s Get:58 http://ftpmaster.internal/ubuntu resolute/main amd64 libusb-1.0-0 amd64 2:1.0.29-2build1 [56.9 kB] 80s Get:59 http://ftpmaster.internal/ubuntu resolute/main amd64 libxau6 amd64 1:1.0.11-1build2 [7502 B] 80s Get:60 http://ftpmaster.internal/ubuntu resolute/main amd64 libxkbcommon0 amd64 1.13.1-1 [159 kB] 80s Get:61 http://ftpmaster.internal/ubuntu resolute/main amd64 man-db amd64 2.13.1-1build1 [1392 kB] 80s Get:62 http://ftpmaster.internal/ubuntu resolute/main amd64 tcpdump amd64 4.99.5-2ubuntu3 [477 kB] 81s Get:63 http://ftpmaster.internal/ubuntu resolute/main amd64 wget amd64 1.25.0-2ubuntu4 [353 kB] 81s Get:64 http://ftpmaster.internal/ubuntu resolute/main amd64 ubuntu-standard amd64 1.564 [13.3 kB] 81s Get:65 http://ftpmaster.internal/ubuntu resolute/main amd64 3cpio amd64 0.14.0-1ubuntu1 [285 kB] 81s Get:66 http://ftpmaster.internal/ubuntu resolute/main amd64 bpftool amd64 7.7.0+6.19.0-3.3 [1229 kB] 81s Get:67 http://ftpmaster.internal/ubuntu resolute/main amd64 busybox-initramfs amd64 1:1.37.0-7ubuntu1 [191 kB] 81s Get:68 http://ftpmaster.internal/ubuntu resolute/main amd64 cryptsetup-bin amd64 2:2.8.0-1ubuntu3 [228 kB] 81s Get:69 http://ftpmaster.internal/ubuntu resolute/main amd64 dracut-install amd64 109-11ubuntu1 [45.8 kB] 81s Get:70 http://ftpmaster.internal/ubuntu resolute/main amd64 hwdata all 0.394-1build1 [1566 B] 81s Get:71 http://ftpmaster.internal/ubuntu resolute/main amd64 pnp.ids all 0.394-1build1 [29.6 kB] 81s Get:72 http://ftpmaster.internal/ubuntu resolute/main amd64 libbrotli1 amd64 1.2.0-3 [343 kB] 81s Get:73 http://ftpmaster.internal/ubuntu resolute/main amd64 libdrm-amdgpu1 amd64 2.4.131-1 [23.2 kB] 81s Get:74 http://ftpmaster.internal/ubuntu resolute/main amd64 libevent-core-2.1-7t64 amd64 2.1.12-stable-10build2 [93.1 kB] 81s Get:75 http://ftpmaster.internal/ubuntu resolute/main amd64 libgdbm-compat4t64 amd64 1.26-1build1 [6796 B] 81s Get:76 http://ftpmaster.internal/ubuntu resolute/main amd64 libgudev-1.0-0 amd64 1:238-7build1 [15.9 kB] 81s Get:77 http://ftpmaster.internal/ubuntu resolute/main amd64 libnpth0t64 amd64 1.8-3build1 [9302 B] 81s Get:78 http://ftpmaster.internal/ubuntu resolute/main amd64 libonig5 amd64 6.9.10-1build1 [174 kB] 81s Get:79 http://ftpmaster.internal/ubuntu resolute/main amd64 libpython3.14-minimal amd64 3.14.2-1 [920 kB] 81s Get:80 http://ftpmaster.internal/ubuntu resolute/main amd64 libpython3.14-stdlib amd64 3.14.2-1 [2398 kB] 81s Get:81 http://ftpmaster.internal/ubuntu resolute/main amd64 libpython3.14 amd64 3.14.2-1 [2568 kB] 81s Get:82 http://ftpmaster.internal/ubuntu resolute/main amd64 libwrap0 amd64 7.6.q-36build2 [48.5 kB] 81s Get:83 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-modules-6.19.0-3-generic amd64 6.19.0-3.3 [171 MB] 85s Get:84 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-image-6.19.0-3-generic amd64 6.19.0-3.3+1 [16.8 MB] 85s Get:85 http://ftpmaster.internal/ubuntu resolute/main amd64 amd64-microcode amd64 3.20251202.1ubuntu1 [459 kB] 85s Get:86 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-generic amd64 6.19.0-3.3 [1698 B] 85s Get:87 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-image-generic amd64 6.19.0-3.3 [12.2 kB] 85s Get:88 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-virtual amd64 6.19.0-3.3 [1700 B] 85s Get:89 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-image-virtual amd64 6.19.0-3.3 [12.1 kB] 85s Get:90 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-headers-virtual amd64 6.19.0-3.3 [1646 B] 85s Get:91 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-headers-6.19.0-3 all 6.19.0-3.3 [14.9 MB] 85s Get:92 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-headers-6.19.0-3-generic amd64 6.19.0-3.3 [4330 kB] 85s Get:93 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-headers-generic amd64 6.19.0-3.3 [12.0 kB] 86s Get:94 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-perf amd64 6.19.0-3.3 [4480 kB] 86s Get:95 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-tools-common all 6.19.0-3.3 [345 kB] 86s Get:96 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-tools-6.19.0-3 amd64 6.19.0-3.3 [1455 kB] 86s Get:97 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-tools-6.19.0-3-generic amd64 6.19.0-3.3 [1612 B] 86s Get:98 http://ftpmaster.internal/ubuntu resolute/main amd64 patch amd64 2.8-2build1 [95.7 kB] 86s Get:99 http://ftpmaster.internal/ubuntu resolute/main amd64 pollinate all 4.33-4ubuntu5 [14.0 kB] 86s Get:100 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-referencing all 0.36.2-1ubuntu2 [22.2 kB] 86s Get:101 http://ftpmaster.internal/ubuntu resolute/main amd64 ubuntu-kernel-accessories amd64 1.564 [13.1 kB] 86s dpkg-preconfigure: unable to re-open stdin: No such file or directory 86s Fetched 237 MB in 6s (40.2 MB/s) 86s (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.) 86s Preparing to unpack .../debianutils_5.23.2build1_amd64.deb ... 86s Unpacking debianutils (5.23.2build1) over (5.23.2) ... 86s Setting up debianutils (5.23.2build1) ... 86s (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.) 86s Preparing to unpack .../dash_0.5.12-12ubuntu3_amd64.deb ... 86s Unpacking dash (0.5.12-12ubuntu3) over (0.5.12-12ubuntu2) ... 86s Setting up dash (0.5.12-12ubuntu3) ... 86s (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.) 86s Preparing to unpack .../findutils_4.10.0-3build2_amd64.deb ... 86s Unpacking findutils (4.10.0-3build2) over (4.10.0-3build1) ... 86s Setting up findutils (4.10.0-3build2) ... 86s (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.) 86s Preparing to unpack .../sed_4.9-2build3_amd64.deb ... 86s Unpacking sed (4.9-2build3) over (4.9-2build2) ... 86s Setting up sed (4.9-2build3) ... 86s (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.) 86s Preparing to unpack .../tar_1.35+dfsg-3.1build2_amd64.deb ... 87s Unpacking tar (1.35+dfsg-3.1build2) over (1.35+dfsg-3.1build1) ... 87s Setting up tar (1.35+dfsg-3.1build2) ... 87s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 83957 files and directories currently installed.) 87s Preparing to unpack .../libattr1_1%3a2.5.2-3build2_amd64.deb ... 87s Unpacking libattr1:amd64 (1:2.5.2-3build2) over (1:2.5.2-3build1) ... 87s Setting up libattr1:amd64 (1:2.5.2-3build2) ... 87s Selecting previously unselected package gcc-16-base:amd64. 87s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 83957 files and directories currently installed.) 87s Preparing to unpack .../gcc-16-base_16-20260208-1ubuntu1_amd64.deb ... 87s Unpacking gcc-16-base:amd64 (16-20260208-1ubuntu1) ... 87s Setting up gcc-16-base:amd64 (16-20260208-1ubuntu1) ... 87s (Reading database ... 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Setting up libgdbm-compat4t64:amd64 (1.26-1build1) ... 94s Setting up bpftool (7.7.0+6.19.0-3.3) ... 94s Setting up libip6tc2:amd64 (1.8.11-2ubuntu3) ... 94s Setting up liblsof0 (4.99.4+dfsg-2build2) ... 94s Setting up libmaxminddb0:amd64 (1.12.2-1build2) ... 94s Setting up libbrotli1:amd64 (1.2.0-3) ... 94s Setting up libpython3.14-minimal:amd64 (3.14.2-1) ... 94s Setting up libsensors-config (1:3.6.2-2build1) ... 94s Setting up less (668-1build1) ... 94s Setting up linux-headers-6.19.0-3 (6.19.0-3.3) ... 94s Setting up libidn2-0:amd64 (2.3.8-4build1) ... 94s Setting up amd64-microcode (3.20251202.1ubuntu1) ... 94s amd64-microcode: microcode will be updated at next boot 94s Setting up man-db (2.13.1-1build1) ... 94s Updating database of manual pages ... 96s man-db.service is a disabled or a static unit not running, not starting it. 96s Setting up libjansson4:amd64 (2.14-2build4) ... 96s Setting up libglib2.0-data (2.87.2-2) ... 96s Setting up pollinate (4.33-4ubuntu5) ... 106s Setting up busybox-static (1:1.37.0-7ubuntu1) ... 106s Setting up libwrap0:amd64 (7.6.q-36build2) ... 106s Setting up linux-image-6.19.0-3-generic (6.19.0-3.3+1) ... 107s I: /boot/vmlinuz is now a symlink to vmlinuz-6.19.0-3-generic 107s I: /boot/initrd.img is now a symlink to initrd.img-6.19.0-3-generic 107s Setting up libdbus-1-3:amd64 (1.16.2-2ubuntu3) ... 107s Setting up libatomic1:amd64 (16-20260208-1ubuntu1) ... 107s Setting up patch (2.8-2build1) ... 107s Setting up libsensors5:amd64 (1:3.6.2-2build1) ... 107s Setting up busybox-initramfs (1:1.37.0-7ubuntu1) ... 107s Setting up libxtables12:amd64 (1.8.11-2ubuntu3) ... 107s Setting up lsof (4.99.4+dfsg-2build2) ... 107s Setting up libpci3:amd64 (1:3.14.0-1build2) ... 107s Setting up libdevmapper1.02.1:amd64 (2:1.02.205-2ubuntu3) ... 107s Setting up dracut-install (109-11ubuntu1) ... 107s Setting up dmsetup (2:1.02.205-2ubuntu3) ... 107s Setting up libnetfilter-conntrack3:amd64 (1.1.1-1) ... 107s Setting up pnp.ids (0.394-1build1) ... 107s Setting up dbus-session-bus-common (1.16.2-2ubuntu3) ... 107s Setting up python3-linkify-it (2.0.3-1ubuntu3) ... 107s Setting up libpcap0.8t64:amd64 (1.10.5-2ubuntu3) ... 107s Setting up libcryptsetup12:amd64 (2:2.8.0-1ubuntu3) ... 107s Setting up mawk (1.3.4.20260129-1) ... 107s Setting up libevent-core-2.1-7t64:amd64 (2.1.12-stable-10build2) ... 107s Setting up libusb-1.0-0:amd64 (2:1.0.29-2build1) ... 107s Setting up linux-image-virtual (6.19.0-3.3) ... 107s Setting up dbus-system-bus-common (1.16.2-2ubuntu3) ... 107s Setting up libbsd0:amd64 (0.12.2-2build2) ... 107s Setting up libdrm-common (2.4.131-1) ... 107s Setting up libstdc++6:amd64 (16-20260208-1ubuntu1) ... 107s Setting up dbus-bin (1.16.2-2ubuntu3) ... 107s Setting up libonig5:amd64 (6.9.10-1build1) ... 107s Setting up libbpf1:amd64 (1:1.6.2-1build1) ... 107s Setting up ethtool (1:6.15-3build1) ... 107s Setting up python3-referencing (0.36.2-1ubuntu2) ... 108s Setting up libxkbcommon0:amd64 (1.13.1-1) ... 108s Setting up cryptsetup-bin (2:2.8.0-1ubuntu3) ... 108s Setting up linux-headers-6.19.0-3-generic (6.19.0-3.3) ... 108s Setting up tcpdump (4.99.5-2ubuntu3) ... 108s Setting up linux-image-generic (6.19.0-3.3) ... 108s Setting up wget (1.25.0-2ubuntu4) ... 108s Setting up libpython3.14-stdlib:amd64 (3.14.2-1) ... 108s Setting up iptables (1.8.11-2ubuntu3) ... 108s Setting up iproute2 (6.18.0-1ubuntu1) ... 108s Setting up linux-headers-generic (6.19.0-3.3) ... 108s Setting up dbus-daemon (1.16.2-2ubuntu3) ... 108s Setting up hwdata (0.394-1build1) ... 108s Setting up dbus-user-session (1.16.2-2ubuntu3) ... 108s Setting up libglib2.0-0t64:amd64 (2.87.2-2) ... 108s No schema files found: doing nothing. 108s Setting up dbus (1.16.2-2ubuntu3) ... 108s A reboot is required to replace the running dbus-daemon. 108s Please reboot the system when convenient. 108s Setting up shared-mime-info (2.4-5build3) ... 109s Setting up gir1.2-glib-2.0:amd64 (2.87.2-2) ... 109s Setting up pciutils (1:3.14.0-1build2) ... 109s Setting up python3-markdown-it (3.0.0-3build1) ... 109s Setting up libdrm2:amd64 (2.4.131-1) ... 109s Setting up libpython3.14:amd64 (3.14.2-1) ... 109s Setting up libapt-pkg7.0:amd64 (3.1.15) ... 109s Setting up linux-tools-common (6.19.0-3.3) ... 109s Setting up libgudev-1.0-0:amd64 (1:238-7build1) ... 109s Setting up libdrm-amdgpu1:amd64 (2.4.131-1) ... 109s Setting up apt (3.1.15) ... 109s Setting up linux-headers-virtual (6.19.0-3.3) ... 109s Setting up linux-generic (6.19.0-3.3) ... 109s Setting up libgirepository-2.0-0:amd64 (2.87.2-2) ... 109s Setting up linux-tools-6.19.0-3 (6.19.0-3.3) ... 109s Setting up ubuntu-standard (1.564) ... 109s Setting up gir1.2-girepository-3.0:amd64 (2.87.2-2) ... 109s Setting up linux-virtual (6.19.0-3.3) ... 109s Setting up linux-perf (6.19.0-3.3) ... 109s Setting up linux-tools-6.19.0-3-generic (6.19.0-3.3) ... 109s Processing triggers for debianutils (5.23.2build1) ... 109s Processing triggers for install-info (7.2-5) ... 109s Processing triggers for initramfs-tools (0.150ubuntu7) ... 109s update-initramfs: Generating /boot/initrd.img-6.18.0-9-generic 114s Processing triggers for libc-bin (2.42-2ubuntu4) ... 114s Processing triggers for linux-image-6.19.0-3-generic (6.19.0-3.3+1) ... 114s /etc/kernel/postinst.d/initramfs-tools: 114s update-initramfs: Generating /boot/initrd.img-6.19.0-3-generic 117s /etc/kernel/postinst.d/zz-update-grub: 117s Sourcing file `/etc/default/grub' 117s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 117s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg' 117s Generating grub configuration file ... 118s Found linux image: /boot/vmlinuz-6.19.0-3-generic 118s Found initrd image: /boot/initrd.img-6.19.0-3-generic 118s Found linux image: /boot/vmlinuz-6.18.0-9-generic 118s Found initrd image: /boot/initrd.img-6.18.0-9-generic 118s Warning: os-prober will not be executed to detect other bootable partitions. 118s Systems on them will not be added to the GRUB boot configuration. 118s Check GRUB_DISABLE_OS_PROBER documentation entry. 118s Adding boot menu entry for UEFI Firmware Settings ... 118s done 118s autopkgtest [05:26:04]: upgrading testbed (apt dist-upgrade and autopurge) 119s Reading package lists... 119s Building dependency tree... 119s Reading state information... 119s Calculating upgrade... 119s The following package was automatically installed and is no longer required: 119s libpython3.13 119s Use 'sudo apt autoremove' to remove it. 119s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 119s Reading package lists... 119s Building dependency tree... 119s Reading state information... 119s Solving dependencies... 119s The following packages will be REMOVED: 119s libpython3.13* 120s 0 upgraded, 0 newly installed, 1 to remove and 0 not upgraded. 120s After this operation, 7599 kB disk space will be freed. 120s (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.) 120s Removing libpython3.13:amd64 (3.13.11-1) ... 120s Processing triggers for libc-bin (2.42-2ubuntu4) ... 120s autopkgtest [05:26:06]: rebooting testbed after setup commands that affected boot 148s autopkgtest [05:26:34]: testbed running kernel: Linux 6.19.0-3-generic #3-Ubuntu SMP PREEMPT_DYNAMIC Fri Jan 23 20:01:24 UTC 2026 150s autopkgtest [05:26:36]: @@@@@@@@@@@@@@@@@@@@ apt-source r-cran-lmertest 151s Get:1 http://ftpmaster.internal/ubuntu resolute/universe r-cran-lmertest 3.2-0-1 (dsc) [2247 B] 151s Get:2 http://ftpmaster.internal/ubuntu resolute/universe r-cran-lmertest 3.2-0-1 (tar) [198 kB] 151s Get:3 http://ftpmaster.internal/ubuntu resolute/universe r-cran-lmertest 3.2-0-1 (diff) [3788 B] 152s gpgv: Signature made Thu Jan 22 00:11:29 2026 UTC 152s gpgv: using RSA key 73471499CC60ED9EEE805946C5BD6C8F2295D502 152s gpgv: issuer "plessy@debian.org" 152s gpgv: Can't check signature: No public key 152s dpkg-source: warning: cannot verify inline signature for ./r-cran-lmertest_3.2-0-1.dsc: no acceptable signature found 152s autopkgtest [05:26:38]: testing package r-cran-lmertest version 3.2-0-1 152s autopkgtest [05:26:38]: build not needed 153s autopkgtest [05:26:39]: test run-unit-test: preparing testbed 153s Reading package lists... 154s Building dependency tree... 154s Reading state information... 154s Solving dependencies... 154s The following NEW packages will be installed: 154s fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono 154s fonts-glyphicons-halflings fonts-mathjax libblas3 libcairo2 libdatrie1 154s libdeflate0 libfontconfig1 libgfortran5 libgomp1 libgraphite2-3 154s libharfbuzz0b libice6 libjbig0 libjpeg-turbo8 libjpeg8 libjs-bootstrap 154s libjs-highlight.js libjs-jquery libjs-jquery-datatables libjs-mathjax 154s liblapack3 liblerc4 libnlopt0 libpango-1.0-0 libpangocairo-1.0-0 154s libpangoft2-1.0-0 libpaper-utils libpaper2 libpixman-1-0 libsharpyuv0 libsm6 154s libtcl8.6 libthai-data libthai0 libtiff6 libtk8.6 libwebp7 libxcb-render0 154s libxcb-shm0 libxft2 libxrender1 libxss1 libxt6t64 node-normalize.css 154s r-base-core r-cran-backports r-cran-boot r-cran-broom r-cran-cli 154s r-cran-colorspace r-cran-cowplot r-cran-cpp11 r-cran-curl r-cran-deriv 154s r-cran-doby r-cran-dplyr r-cran-evaluate r-cran-fansi r-cran-farver 154s r-cran-forecast r-cran-fracdiff r-cran-generics r-cran-ggplot2 r-cran-glue 154s r-cran-gtable r-cran-highr r-cran-isoband r-cran-jsonlite r-cran-knitr 154s r-cran-labeling r-cran-lattice r-cran-lifecycle r-cran-littler r-cran-lme4 154s r-cran-lmertest r-cran-lmtest r-cran-magrittr r-cran-mass r-cran-matrix 154s r-cran-microbenchmark r-cran-minqa r-cran-modelr r-cran-nlme r-cran-nloptr 154s r-cran-nnet r-cran-numderiv r-cran-pbkrtest r-cran-pillar r-cran-pkgconfig 154s r-cran-pkgkitten r-cran-purrr r-cran-quadprog r-cran-quantmod r-cran-r6 154s r-cran-rbibutils r-cran-rcolorbrewer r-cran-rcpp r-cran-rcpparmadillo 154s r-cran-rcppeigen r-cran-rdpack r-cran-reformulas r-cran-rlang r-cran-s7 154s r-cran-scales r-cran-statmod r-cran-stringi r-cran-stringr r-cran-tibble 154s r-cran-tidyr r-cran-tidyselect r-cran-timedate r-cran-tseries r-cran-ttr 154s r-cran-urca r-cran-utf8 r-cran-vctrs r-cran-viridislite r-cran-withr 154s r-cran-xfun r-cran-xts r-cran-yaml r-cran-zoo unzip x11-common xdg-utils zip 154s 0 upgraded, 130 newly installed, 0 to remove and 0 not upgraded. 154s Need to get 114 MB of archives. 154s After this operation, 256 MB of additional disk space will be used. 154s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-dejavu-mono all 2.37-8build1 [502 kB] 154s Get:2 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-dejavu-core all 2.37-8build1 [834 kB] 154s Get:3 http://ftpmaster.internal/ubuntu resolute/main amd64 fontconfig-config amd64 2.17.1-3ubuntu1 [38.5 kB] 154s Get:4 http://ftpmaster.internal/ubuntu resolute/main amd64 libfontconfig1 amd64 2.17.1-3ubuntu1 [144 kB] 154s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 fontconfig amd64 2.17.1-3ubuntu1 [180 kB] 154s Get:6 http://ftpmaster.internal/ubuntu resolute/universe amd64 fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-6 [119 kB] 154s Get:7 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-mathjax all 2.7.9+dfsg-1build1 [2283 kB] 154s Get:8 http://ftpmaster.internal/ubuntu resolute/main amd64 libblas3 amd64 3.12.1-7ubuntu1 [260 kB] 154s Get:9 http://ftpmaster.internal/ubuntu resolute/main amd64 libpixman-1-0 amd64 0.46.4-1 [287 kB] 154s Get:10 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-render0 amd64 1.17.0-2ubuntu1 [16.2 kB] 154s Get:11 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-shm0 amd64 1.17.0-2ubuntu1 [5808 B] 154s Get:12 http://ftpmaster.internal/ubuntu resolute/main amd64 libxrender1 amd64 1:0.9.12-1 [19.8 kB] 154s Get:13 http://ftpmaster.internal/ubuntu resolute/main amd64 libcairo2 amd64 1.18.4-3 [579 kB] 154s Get:14 http://ftpmaster.internal/ubuntu resolute/main amd64 libdatrie1 amd64 0.2.14-1 [19.8 kB] 154s Get:15 http://ftpmaster.internal/ubuntu resolute/main amd64 libdeflate0 amd64 1.23-2build1 [51.6 kB] 154s Get:16 http://ftpmaster.internal/ubuntu resolute/main amd64 libgfortran5 amd64 16-20260208-1ubuntu1 [957 kB] 154s Get:17 http://ftpmaster.internal/ubuntu resolute/main amd64 libgomp1 amd64 16-20260208-1ubuntu1 [162 kB] 154s Get:18 http://ftpmaster.internal/ubuntu resolute/main amd64 libgraphite2-3 amd64 1.3.14-11ubuntu1 [73.7 kB] 154s Get:19 http://ftpmaster.internal/ubuntu resolute/main amd64 libharfbuzz0b amd64 12.3.2-1 [519 kB] 154s Get:20 http://ftpmaster.internal/ubuntu resolute/main amd64 x11-common all 1:7.7+24ubuntu1 [22.4 kB] 154s Get:21 http://ftpmaster.internal/ubuntu resolute/main amd64 libice6 amd64 2:1.1.1-1build1 [44.0 kB] 154s Get:22 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg-turbo8 amd64 2.1.5-4ubuntu3 [156 kB] 154s Get:23 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg8 amd64 8c-2ubuntu12 [2142 B] 154s Get:24 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-bootstrap all 3.4.1+dfsg-6 [129 kB] 154s Get:25 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-highlight.js all 10.7.3+dfsg-2 [144 kB] 154s Get:26 http://ftpmaster.internal/ubuntu resolute/main amd64 libjs-jquery all 3.7.1+dfsg+~3.5.33-1build1 [321 kB] 154s Get:27 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-jquery-datatables all 1.11.5+dfsg-2build1 [145 kB] 154s Get:28 http://ftpmaster.internal/ubuntu resolute/main amd64 liblapack3 amd64 3.12.1-7ubuntu1 [2739 kB] 154s Get:29 http://ftpmaster.internal/ubuntu resolute/main amd64 liblerc4 amd64 4.0.0+ds-5ubuntu2 [207 kB] 154s Get:30 http://ftpmaster.internal/ubuntu resolute/main amd64 libthai-data all 0.1.30-1 [155 kB] 154s Get:31 http://ftpmaster.internal/ubuntu resolute/main amd64 libthai0 amd64 0.1.30-1 [19.2 kB] 154s Get:32 http://ftpmaster.internal/ubuntu resolute/main amd64 libpango-1.0-0 amd64 1.57.0-1 [241 kB] 154s Get:33 http://ftpmaster.internal/ubuntu resolute/main amd64 libpangoft2-1.0-0 amd64 1.57.0-1 [53.3 kB] 154s Get:34 http://ftpmaster.internal/ubuntu resolute/main amd64 libpangocairo-1.0-0 amd64 1.57.0-1 [29.0 kB] 154s Get:35 http://ftpmaster.internal/ubuntu resolute/main amd64 libpaper2 amd64 2.2.5-0.3build1 [17.3 kB] 154s Get:36 http://ftpmaster.internal/ubuntu resolute/main amd64 libpaper-utils amd64 2.2.5-0.3build1 [15.6 kB] 154s Get:37 http://ftpmaster.internal/ubuntu resolute/main amd64 libsharpyuv0 amd64 1.5.0-0.1build1 [17.6 kB] 154s Get:38 http://ftpmaster.internal/ubuntu resolute/main amd64 libsm6 amd64 2:1.2.6-1build1 [16.9 kB] 154s Get:39 http://ftpmaster.internal/ubuntu resolute/main amd64 libtcl8.6 amd64 8.6.17+dfsg-1build1 [1003 kB] 154s Get:40 http://ftpmaster.internal/ubuntu resolute/main amd64 libjbig0 amd64 2.1-6.1ubuntu3 [30.0 kB] 154s Get:41 http://ftpmaster.internal/ubuntu resolute/main amd64 libwebp7 amd64 1.5.0-0.1build1 [264 kB] 154s Get:42 http://ftpmaster.internal/ubuntu resolute/main amd64 libtiff6 amd64 4.7.0-3ubuntu3 [209 kB] 154s Get:43 http://ftpmaster.internal/ubuntu resolute/main amd64 libxft2 amd64 2.3.6-1build2 [45.1 kB] 154s Get:44 http://ftpmaster.internal/ubuntu resolute/main amd64 libxss1 amd64 1:1.2.3-1build4 [7084 B] 154s Get:45 http://ftpmaster.internal/ubuntu resolute/main amd64 libtk8.6 amd64 8.6.17-1 [823 kB] 154s Get:46 http://ftpmaster.internal/ubuntu resolute/main amd64 libxt6t64 amd64 1:1.2.1-1.3 [173 kB] 154s Get:47 http://ftpmaster.internal/ubuntu resolute/universe amd64 node-normalize.css all 8.0.1-5.1 [10.4 kB] 154s Get:48 http://ftpmaster.internal/ubuntu resolute/main amd64 zip amd64 3.0-15ubuntu3 [175 kB] 154s Get:49 http://ftpmaster.internal/ubuntu resolute/main amd64 unzip amd64 6.0-29ubuntu1 [180 kB] 154s Get:50 http://ftpmaster.internal/ubuntu resolute/main amd64 xdg-utils all 1.2.1-2ubuntu2 [66.1 kB] 154s Get:51 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-base-core amd64 4.5.2-1ubuntu2 [28.8 MB] 155s Get:52 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-backports amd64 1.5.0-2 [121 kB] 155s Get:53 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-boot all 1.3-32-1 [636 kB] 155s Get:54 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-cli amd64 3.6.4-1 [1394 kB] 155s Get:55 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-generics all 0.1.4-1 [84.0 kB] 155s Get:56 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-glue amd64 1.8.0-1 [164 kB] 155s Get:57 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rlang amd64 1.1.5-3 [1721 kB] 155s Get:58 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-lifecycle all 1.0.5+dfsg-1 [120 kB] 155s Get:59 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-magrittr amd64 2.0.3-1 [154 kB] 155s Get:60 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-utf8 amd64 1.2.4-1 [140 kB] 155s Get:61 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-vctrs amd64 0.6.5-1 [1335 kB] 155s Get:62 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-pillar all 1.11.1+dfsg-1 [456 kB] 155s Get:63 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-r6 all 2.6.1-1 [101 kB] 155s Get:64 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-fansi amd64 1.0.6-2 [626 kB] 155s Get:65 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-pkgconfig all 2.0.3-2build2 [20.4 kB] 155s Get:66 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-tibble amd64 3.2.1+dfsg-3 [419 kB] 155s Get:67 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-withr all 3.0.2+dfsg-1 [214 kB] 155s Get:68 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-tidyselect amd64 1.2.1+dfsg-1 [222 kB] 155s Get:69 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-dplyr amd64 1.1.4-4 [1536 kB] 156s Get:70 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-purrr amd64 1.0.4-1 [552 kB] 156s Get:71 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-stringi amd64 1.8.4-1build2 [908 kB] 156s Get:72 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-stringr all 1.5.1-1 [290 kB] 156s Get:73 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-cpp11 all 0.5.3-1 [242 kB] 156s Get:74 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-tidyr amd64 1.3.1-1 [1156 kB] 156s Get:75 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-broom all 1.0.12+dfsg-1 [1708 kB] 156s Get:76 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-colorspace amd64 2.1-1+dfsg-1 [1563 kB] 156s Get:77 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-gtable all 0.3.6+dfsg-1 [199 kB] 156s Get:78 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-isoband amd64 0.2.7-1 [1481 kB] 156s Get:79 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-s7 amd64 0.2.0-1 [328 kB] 156s Get:80 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-farver amd64 2.1.2-1 [1355 kB] 156s Get:81 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-labeling all 0.4.3-1 [62.1 kB] 156s Get:82 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rcolorbrewer all 1.1-3-1build2 [54.0 kB] 156s Get:83 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-viridislite all 0.4.3-1 [1088 kB] 156s Get:84 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-scales all 1.4.0-1 [725 kB] 156s Get:85 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 r-cran-ggplot2 all 4.0.2+dfsg-1 [4941 kB] 156s Get:86 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-cowplot all 1.1.3+dfsg-1 [614 kB] 156s Get:87 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-curl amd64 7.0.0+dfsg-1 [202 kB] 156s Get:88 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-deriv all 4.2.0-1 [154 kB] 156s Get:89 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-fracdiff amd64 1.5-3-1 [108 kB] 157s Get:90 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-lattice amd64 0.22-7-1 [1367 kB] 157s Get:91 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-zoo amd64 1.8-15-1 [1025 kB] 157s Get:92 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-lmtest amd64 0.9.40-1build1 [400 kB] 157s Get:93 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-nnet amd64 7.3-20-1 [116 kB] 157s Get:94 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-littler amd64 0.3.22-1 [85.5 kB] 157s Get:95 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-pkgkitten all 0.2.4-1 [27.2 kB] 157s Get:96 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rcpp amd64 1.1.0-1 [2021 kB] 157s Get:97 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-timedate amd64 4052.112-1 [1298 kB] 157s Get:98 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-quadprog amd64 1.5-8-1build2 [32.6 kB] 157s Get:99 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-xts amd64 0.14.1-1 [1198 kB] 157s Get:100 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-ttr amd64 0.24.4-1 [511 kB] 157s Get:101 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-jsonlite amd64 1.9.1+dfsg-1 [447 kB] 157s Get:102 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-quantmod all 0.4.28-1 [1037 kB] 157s Get:103 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-tseries amd64 0.10-59-3 [382 kB] 157s Get:104 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-nlme amd64 3.1.168-1 [2320 kB] 157s Get:105 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-urca amd64 1.3-4-1build1 [1052 kB] 157s Get:106 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rcpparmadillo amd64 15.2.3-1-1 [919 kB] 157s Get:107 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-forecast amd64 8.23.0-1 [1569 kB] 157s Get:108 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-mass amd64 7.3-65-1 [1116 kB] 157s Get:109 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-matrix amd64 1.7-4-1 [4220 kB] 157s Get:110 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-modelr all 0.1.11-1 [195 kB] 157s Get:111 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-microbenchmark amd64 1.5.0-1 [67.4 kB] 157s Get:112 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-doby all 4.7.1-3 [4741 kB] 157s Get:113 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-evaluate all 1.0.5-1 [117 kB] 157s Get:114 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-xfun amd64 0.55+dfsg-1 [587 kB] 157s Get:115 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-highr all 0.11+dfsg-1 [38.5 kB] 157s Get:116 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-yaml amd64 2.3.10-1 [109 kB] 157s Get:117 http://ftpmaster.internal/ubuntu resolute/main amd64 libjs-mathjax all 2.7.9+dfsg-1build1 [6017 kB] 158s Get:118 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-knitr all 1.51+dfsg-1 [847 kB] 158s Get:119 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-minqa amd64 1.2.8-1 [119 kB] 158s Get:120 http://ftpmaster.internal/ubuntu resolute/universe amd64 libnlopt0 amd64 2.7.1-7ubuntu1 [189 kB] 158s Get:121 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-nloptr amd64 2.2.1-2 [251 kB] 158s Get:122 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rbibutils amd64 2.3-1 [1023 kB] 158s Get:123 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rdpack all 2.6.3-1 [636 kB] 158s Get:124 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-reformulas all 0.4.4-1 [151 kB] 158s Get:125 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rcppeigen amd64 0.3.4.0.2-1 [1428 kB] 158s Get:126 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-statmod amd64 1.5.0-1 [295 kB] 158s Get:127 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-lme4 amd64 1.1-38-1 [4197 kB] 158s Get:128 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-numderiv all 2016.8-1.1-3build1 [116 kB] 158s Get:129 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-lmertest all 3.2-0-1 [535 kB] 158s Get:130 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-pbkrtest all 0.5.5-1 [217 kB] 158s Preconfiguring packages ... 158s Fetched 114 MB in 4s (27.9 MB/s) 158s Selecting previously unselected package fonts-dejavu-mono. 158s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 125269 files and directories currently installed.) 158s Preparing to unpack .../000-fonts-dejavu-mono_2.37-8build1_all.deb ... 158s Unpacking fonts-dejavu-mono (2.37-8build1) ... 158s Selecting previously unselected package fonts-dejavu-core. 158s Preparing to unpack .../001-fonts-dejavu-core_2.37-8build1_all.deb ... 158s Unpacking fonts-dejavu-core (2.37-8build1) ... 158s Selecting previously unselected package fontconfig-config. 158s Preparing to unpack .../002-fontconfig-config_2.17.1-3ubuntu1_amd64.deb ... 159s Unpacking fontconfig-config (2.17.1-3ubuntu1) ... 159s Selecting previously unselected package libfontconfig1:amd64. 159s Preparing to unpack .../003-libfontconfig1_2.17.1-3ubuntu1_amd64.deb ... 159s Unpacking libfontconfig1:amd64 (2.17.1-3ubuntu1) ... 159s Selecting previously unselected package fontconfig. 159s Preparing to unpack .../004-fontconfig_2.17.1-3ubuntu1_amd64.deb ... 159s Unpacking fontconfig (2.17.1-3ubuntu1) ... 159s Selecting previously unselected package fonts-glyphicons-halflings. 159s Preparing to unpack .../005-fonts-glyphicons-halflings_1.009~3.4.1+dfsg-6_all.deb ... 159s Unpacking fonts-glyphicons-halflings (1.009~3.4.1+dfsg-6) ... 159s Selecting previously unselected package fonts-mathjax. 159s Preparing to unpack .../006-fonts-mathjax_2.7.9+dfsg-1build1_all.deb ... 159s Unpacking fonts-mathjax (2.7.9+dfsg-1build1) ... 159s Selecting previously unselected package libblas3:amd64. 159s Preparing to unpack .../007-libblas3_3.12.1-7ubuntu1_amd64.deb ... 159s Unpacking libblas3:amd64 (3.12.1-7ubuntu1) ... 159s Selecting previously unselected package libpixman-1-0:amd64. 159s Preparing to unpack .../008-libpixman-1-0_0.46.4-1_amd64.deb ... 159s Unpacking libpixman-1-0:amd64 (0.46.4-1) ... 159s Selecting previously unselected package libxcb-render0:amd64. 159s Preparing to unpack .../009-libxcb-render0_1.17.0-2ubuntu1_amd64.deb ... 159s Unpacking libxcb-render0:amd64 (1.17.0-2ubuntu1) ... 159s Selecting previously unselected package libxcb-shm0:amd64. 159s Preparing to unpack .../010-libxcb-shm0_1.17.0-2ubuntu1_amd64.deb ... 159s Unpacking libxcb-shm0:amd64 (1.17.0-2ubuntu1) ... 159s Selecting previously unselected package libxrender1:amd64. 159s Preparing to unpack .../011-libxrender1_1%3a0.9.12-1_amd64.deb ... 159s Unpacking libxrender1:amd64 (1:0.9.12-1) ... 159s Selecting previously unselected package libcairo2:amd64. 159s Preparing to unpack .../012-libcairo2_1.18.4-3_amd64.deb ... 159s Unpacking libcairo2:amd64 (1.18.4-3) ... 159s Selecting previously unselected package libdatrie1:amd64. 159s Preparing to unpack .../013-libdatrie1_0.2.14-1_amd64.deb ... 159s Unpacking libdatrie1:amd64 (0.2.14-1) ... 159s Selecting previously unselected package libdeflate0:amd64. 159s Preparing to unpack .../014-libdeflate0_1.23-2build1_amd64.deb ... 159s Unpacking libdeflate0:amd64 (1.23-2build1) ... 159s Selecting previously unselected package libgfortran5:amd64. 159s Preparing to unpack .../015-libgfortran5_16-20260208-1ubuntu1_amd64.deb ... 159s Unpacking libgfortran5:amd64 (16-20260208-1ubuntu1) ... 159s Selecting previously unselected package libgomp1:amd64. 159s Preparing to unpack .../016-libgomp1_16-20260208-1ubuntu1_amd64.deb ... 159s Unpacking libgomp1:amd64 (16-20260208-1ubuntu1) ... 159s Selecting previously unselected package libgraphite2-3:amd64. 159s Preparing to unpack .../017-libgraphite2-3_1.3.14-11ubuntu1_amd64.deb ... 159s Unpacking libgraphite2-3:amd64 (1.3.14-11ubuntu1) ... 159s Selecting previously unselected package libharfbuzz0b:amd64. 159s Preparing to unpack .../018-libharfbuzz0b_12.3.2-1_amd64.deb ... 159s Unpacking libharfbuzz0b:amd64 (12.3.2-1) ... 159s Selecting previously unselected package x11-common. 159s Preparing to unpack .../019-x11-common_1%3a7.7+24ubuntu1_all.deb ... 159s Unpacking x11-common (1:7.7+24ubuntu1) ... 159s Selecting previously unselected package libice6:amd64. 159s Preparing to unpack .../020-libice6_2%3a1.1.1-1build1_amd64.deb ... 159s Unpacking libice6:amd64 (2:1.1.1-1build1) ... 159s Selecting previously unselected package libjpeg-turbo8:amd64. 159s Preparing to unpack .../021-libjpeg-turbo8_2.1.5-4ubuntu3_amd64.deb ... 159s Unpacking libjpeg-turbo8:amd64 (2.1.5-4ubuntu3) ... 159s Selecting previously unselected package libjpeg8:amd64. 159s Preparing to unpack .../022-libjpeg8_8c-2ubuntu12_amd64.deb ... 159s Unpacking libjpeg8:amd64 (8c-2ubuntu12) ... 159s Selecting previously unselected package libjs-bootstrap. 159s Preparing to unpack .../023-libjs-bootstrap_3.4.1+dfsg-6_all.deb ... 159s Unpacking libjs-bootstrap (3.4.1+dfsg-6) ... 159s Selecting previously unselected package libjs-highlight.js. 159s Preparing to unpack .../024-libjs-highlight.js_10.7.3+dfsg-2_all.deb ... 159s Unpacking libjs-highlight.js (10.7.3+dfsg-2) ... 159s Selecting previously unselected package libjs-jquery. 159s Preparing to unpack .../025-libjs-jquery_3.7.1+dfsg+~3.5.33-1build1_all.deb ... 159s Unpacking libjs-jquery (3.7.1+dfsg+~3.5.33-1build1) ... 159s Selecting previously unselected package libjs-jquery-datatables. 159s Preparing to unpack .../026-libjs-jquery-datatables_1.11.5+dfsg-2build1_all.deb ... 159s Unpacking libjs-jquery-datatables (1.11.5+dfsg-2build1) ... 159s Selecting previously unselected package liblapack3:amd64. 159s Preparing to unpack .../027-liblapack3_3.12.1-7ubuntu1_amd64.deb ... 159s Unpacking liblapack3:amd64 (3.12.1-7ubuntu1) ... 159s Selecting previously unselected package liblerc4:amd64. 159s Preparing to unpack .../028-liblerc4_4.0.0+ds-5ubuntu2_amd64.deb ... 159s Unpacking liblerc4:amd64 (4.0.0+ds-5ubuntu2) ... 159s Selecting previously unselected package libthai-data. 159s Preparing to unpack .../029-libthai-data_0.1.30-1_all.deb ... 159s Unpacking libthai-data (0.1.30-1) ... 159s Selecting previously unselected package libthai0:amd64. 159s Preparing to unpack .../030-libthai0_0.1.30-1_amd64.deb ... 159s Unpacking libthai0:amd64 (0.1.30-1) ... 159s Selecting previously unselected package libpango-1.0-0:amd64. 159s Preparing to unpack .../031-libpango-1.0-0_1.57.0-1_amd64.deb ... 159s Unpacking libpango-1.0-0:amd64 (1.57.0-1) ... 159s Selecting previously unselected package libpangoft2-1.0-0:amd64. 159s Preparing to unpack .../032-libpangoft2-1.0-0_1.57.0-1_amd64.deb ... 159s Unpacking libpangoft2-1.0-0:amd64 (1.57.0-1) ... 159s Selecting previously unselected package libpangocairo-1.0-0:amd64. 159s Preparing to unpack .../033-libpangocairo-1.0-0_1.57.0-1_amd64.deb ... 159s Unpacking libpangocairo-1.0-0:amd64 (1.57.0-1) ... 159s Selecting previously unselected package libpaper2:amd64. 159s Preparing to unpack .../034-libpaper2_2.2.5-0.3build1_amd64.deb ... 159s Unpacking libpaper2:amd64 (2.2.5-0.3build1) ... 159s Selecting previously unselected package libpaper-utils. 159s Preparing to unpack .../035-libpaper-utils_2.2.5-0.3build1_amd64.deb ... 159s Unpacking libpaper-utils (2.2.5-0.3build1) ... 159s Selecting previously unselected package libsharpyuv0:amd64. 159s Preparing to unpack .../036-libsharpyuv0_1.5.0-0.1build1_amd64.deb ... 159s Unpacking libsharpyuv0:amd64 (1.5.0-0.1build1) ... 159s Selecting previously unselected package libsm6:amd64. 159s Preparing to unpack .../037-libsm6_2%3a1.2.6-1build1_amd64.deb ... 159s Unpacking libsm6:amd64 (2:1.2.6-1build1) ... 159s Selecting previously unselected package libtcl8.6:amd64. 159s Preparing to unpack .../038-libtcl8.6_8.6.17+dfsg-1build1_amd64.deb ... 159s Unpacking libtcl8.6:amd64 (8.6.17+dfsg-1build1) ... 159s Selecting previously unselected package libjbig0:amd64. 159s Preparing to unpack .../039-libjbig0_2.1-6.1ubuntu3_amd64.deb ... 159s Unpacking libjbig0:amd64 (2.1-6.1ubuntu3) ... 159s Selecting previously unselected package libwebp7:amd64. 159s Preparing to unpack .../040-libwebp7_1.5.0-0.1build1_amd64.deb ... 159s Unpacking libwebp7:amd64 (1.5.0-0.1build1) ... 159s Selecting previously unselected package libtiff6:amd64. 159s Preparing to unpack .../041-libtiff6_4.7.0-3ubuntu3_amd64.deb ... 159s Unpacking libtiff6:amd64 (4.7.0-3ubuntu3) ... 159s Selecting previously unselected package libxft2:amd64. 159s Preparing to unpack .../042-libxft2_2.3.6-1build2_amd64.deb ... 159s Unpacking libxft2:amd64 (2.3.6-1build2) ... 159s Selecting previously unselected package libxss1:amd64. 159s Preparing to unpack .../043-libxss1_1%3a1.2.3-1build4_amd64.deb ... 159s Unpacking libxss1:amd64 (1:1.2.3-1build4) ... 159s Selecting previously unselected package libtk8.6:amd64. 159s Preparing to unpack .../044-libtk8.6_8.6.17-1_amd64.deb ... 159s Unpacking libtk8.6:amd64 (8.6.17-1) ... 159s Selecting previously unselected package libxt6t64:amd64. 159s Preparing to unpack .../045-libxt6t64_1%3a1.2.1-1.3_amd64.deb ... 159s Unpacking libxt6t64:amd64 (1:1.2.1-1.3) ... 159s Selecting previously unselected package node-normalize.css. 159s Preparing to unpack .../046-node-normalize.css_8.0.1-5.1_all.deb ... 159s Unpacking node-normalize.css (8.0.1-5.1) ... 159s Selecting previously unselected package zip. 159s Preparing to unpack .../047-zip_3.0-15ubuntu3_amd64.deb ... 159s Unpacking zip (3.0-15ubuntu3) ... 159s Selecting previously unselected package unzip. 159s Preparing to unpack .../048-unzip_6.0-29ubuntu1_amd64.deb ... 159s Unpacking unzip (6.0-29ubuntu1) ... 159s Selecting previously unselected package xdg-utils. 159s Preparing to unpack .../049-xdg-utils_1.2.1-2ubuntu2_all.deb ... 159s Unpacking xdg-utils (1.2.1-2ubuntu2) ... 159s Selecting previously unselected package r-base-core. 159s Preparing to unpack .../050-r-base-core_4.5.2-1ubuntu2_amd64.deb ... 159s Unpacking r-base-core (4.5.2-1ubuntu2) ... 159s Selecting previously unselected package r-cran-backports. 159s Preparing to unpack .../051-r-cran-backports_1.5.0-2_amd64.deb ... 159s Unpacking r-cran-backports (1.5.0-2) ... 159s Selecting previously unselected package r-cran-boot. 159s Preparing to unpack .../052-r-cran-boot_1.3-32-1_all.deb ... 159s Unpacking r-cran-boot (1.3-32-1) ... 159s Selecting previously unselected package r-cran-cli. 159s Preparing to unpack .../053-r-cran-cli_3.6.4-1_amd64.deb ... 159s Unpacking r-cran-cli (3.6.4-1) ... 159s Selecting previously unselected package r-cran-generics. 159s Preparing to unpack .../054-r-cran-generics_0.1.4-1_all.deb ... 159s Unpacking r-cran-generics (0.1.4-1) ... 159s Selecting previously unselected package r-cran-glue. 159s Preparing to unpack .../055-r-cran-glue_1.8.0-1_amd64.deb ... 159s Unpacking r-cran-glue (1.8.0-1) ... 159s Selecting previously unselected package r-cran-rlang. 159s Preparing to unpack .../056-r-cran-rlang_1.1.5-3_amd64.deb ... 159s Unpacking r-cran-rlang (1.1.5-3) ... 160s Selecting previously unselected package r-cran-lifecycle. 160s Preparing to unpack .../057-r-cran-lifecycle_1.0.5+dfsg-1_all.deb ... 160s Unpacking r-cran-lifecycle (1.0.5+dfsg-1) ... 160s Selecting previously unselected package r-cran-magrittr. 160s Preparing to unpack .../058-r-cran-magrittr_2.0.3-1_amd64.deb ... 160s Unpacking r-cran-magrittr (2.0.3-1) ... 160s Selecting previously unselected package r-cran-utf8. 160s Preparing to unpack .../059-r-cran-utf8_1.2.4-1_amd64.deb ... 160s Unpacking r-cran-utf8 (1.2.4-1) ... 160s Selecting previously unselected package r-cran-vctrs. 160s Preparing to unpack .../060-r-cran-vctrs_0.6.5-1_amd64.deb ... 160s Unpacking r-cran-vctrs (0.6.5-1) ... 160s Selecting previously unselected package r-cran-pillar. 160s Preparing to unpack .../061-r-cran-pillar_1.11.1+dfsg-1_all.deb ... 160s Unpacking r-cran-pillar (1.11.1+dfsg-1) ... 160s Selecting previously unselected package r-cran-r6. 160s Preparing to unpack .../062-r-cran-r6_2.6.1-1_all.deb ... 160s Unpacking r-cran-r6 (2.6.1-1) ... 160s Selecting previously unselected package r-cran-fansi. 160s Preparing to unpack .../063-r-cran-fansi_1.0.6-2_amd64.deb ... 160s Unpacking r-cran-fansi (1.0.6-2) ... 160s Selecting previously unselected package r-cran-pkgconfig. 160s Preparing to unpack .../064-r-cran-pkgconfig_2.0.3-2build2_all.deb ... 160s Unpacking r-cran-pkgconfig (2.0.3-2build2) ... 160s Selecting previously unselected package r-cran-tibble. 160s Preparing to unpack .../065-r-cran-tibble_3.2.1+dfsg-3_amd64.deb ... 160s Unpacking r-cran-tibble (3.2.1+dfsg-3) ... 160s Selecting previously unselected package r-cran-withr. 160s Preparing to unpack .../066-r-cran-withr_3.0.2+dfsg-1_all.deb ... 160s Unpacking r-cran-withr (3.0.2+dfsg-1) ... 160s Selecting previously unselected package r-cran-tidyselect. 160s Preparing to unpack .../067-r-cran-tidyselect_1.2.1+dfsg-1_amd64.deb ... 160s Unpacking r-cran-tidyselect (1.2.1+dfsg-1) ... 160s Selecting previously unselected package r-cran-dplyr. 160s Preparing to unpack .../068-r-cran-dplyr_1.1.4-4_amd64.deb ... 160s Unpacking r-cran-dplyr (1.1.4-4) ... 160s Selecting previously unselected package r-cran-purrr. 160s Preparing to unpack .../069-r-cran-purrr_1.0.4-1_amd64.deb ... 160s Unpacking r-cran-purrr (1.0.4-1) ... 160s Selecting previously unselected package r-cran-stringi. 160s Preparing to unpack .../070-r-cran-stringi_1.8.4-1build2_amd64.deb ... 160s Unpacking r-cran-stringi (1.8.4-1build2) ... 160s Selecting previously unselected package r-cran-stringr. 160s Preparing to unpack .../071-r-cran-stringr_1.5.1-1_all.deb ... 160s Unpacking r-cran-stringr (1.5.1-1) ... 160s Selecting previously unselected package r-cran-cpp11. 160s Preparing to unpack .../072-r-cran-cpp11_0.5.3-1_all.deb ... 160s Unpacking r-cran-cpp11 (0.5.3-1) ... 160s Selecting previously unselected package r-cran-tidyr. 160s Preparing to unpack .../073-r-cran-tidyr_1.3.1-1_amd64.deb ... 160s Unpacking r-cran-tidyr (1.3.1-1) ... 160s Selecting previously unselected package r-cran-broom. 160s Preparing to unpack .../074-r-cran-broom_1.0.12+dfsg-1_all.deb ... 160s Unpacking r-cran-broom (1.0.12+dfsg-1) ... 160s Selecting previously unselected package r-cran-colorspace. 160s Preparing to unpack .../075-r-cran-colorspace_2.1-1+dfsg-1_amd64.deb ... 160s Unpacking r-cran-colorspace (2.1-1+dfsg-1) ... 160s Selecting previously unselected package r-cran-gtable. 160s Preparing to unpack .../076-r-cran-gtable_0.3.6+dfsg-1_all.deb ... 160s Unpacking r-cran-gtable (0.3.6+dfsg-1) ... 160s Selecting previously unselected package r-cran-isoband. 160s Preparing to unpack .../077-r-cran-isoband_0.2.7-1_amd64.deb ... 160s Unpacking r-cran-isoband (0.2.7-1) ... 160s Selecting previously unselected package r-cran-s7. 160s Preparing to unpack .../078-r-cran-s7_0.2.0-1_amd64.deb ... 160s Unpacking r-cran-s7 (0.2.0-1) ... 160s Selecting previously unselected package r-cran-farver. 160s Preparing to unpack .../079-r-cran-farver_2.1.2-1_amd64.deb ... 160s Unpacking r-cran-farver (2.1.2-1) ... 160s Selecting previously unselected package r-cran-labeling. 160s Preparing to unpack .../080-r-cran-labeling_0.4.3-1_all.deb ... 160s Unpacking r-cran-labeling (0.4.3-1) ... 160s Selecting previously unselected package r-cran-rcolorbrewer. 160s Preparing to unpack .../081-r-cran-rcolorbrewer_1.1-3-1build2_all.deb ... 160s Unpacking r-cran-rcolorbrewer (1.1-3-1build2) ... 160s Selecting previously unselected package r-cran-viridislite. 160s Preparing to unpack .../082-r-cran-viridislite_0.4.3-1_all.deb ... 160s Unpacking r-cran-viridislite (0.4.3-1) ... 160s Selecting previously unselected package r-cran-scales. 160s Preparing to unpack .../083-r-cran-scales_1.4.0-1_all.deb ... 160s Unpacking r-cran-scales (1.4.0-1) ... 160s Selecting previously unselected package r-cran-ggplot2. 160s Preparing to unpack .../084-r-cran-ggplot2_4.0.2+dfsg-1_all.deb ... 160s Unpacking r-cran-ggplot2 (4.0.2+dfsg-1) ... 160s Selecting previously unselected package r-cran-cowplot. 160s Preparing to unpack .../085-r-cran-cowplot_1.1.3+dfsg-1_all.deb ... 160s Unpacking r-cran-cowplot (1.1.3+dfsg-1) ... 160s Selecting previously unselected package r-cran-curl. 160s Preparing to unpack .../086-r-cran-curl_7.0.0+dfsg-1_amd64.deb ... 160s Unpacking r-cran-curl (7.0.0+dfsg-1) ... 160s Selecting previously unselected package r-cran-deriv. 160s Preparing to unpack .../087-r-cran-deriv_4.2.0-1_all.deb ... 160s Unpacking r-cran-deriv (4.2.0-1) ... 160s Selecting previously unselected package r-cran-fracdiff. 160s Preparing to unpack .../088-r-cran-fracdiff_1.5-3-1_amd64.deb ... 160s Unpacking r-cran-fracdiff (1.5-3-1) ... 160s Selecting previously unselected package r-cran-lattice. 160s Preparing to unpack .../089-r-cran-lattice_0.22-7-1_amd64.deb ... 160s Unpacking r-cran-lattice (0.22-7-1) ... 160s Selecting previously unselected package r-cran-zoo. 160s Preparing to unpack .../090-r-cran-zoo_1.8-15-1_amd64.deb ... 160s Unpacking r-cran-zoo (1.8-15-1) ... 160s Selecting previously unselected package r-cran-lmtest. 160s Preparing to unpack .../091-r-cran-lmtest_0.9.40-1build1_amd64.deb ... 160s Unpacking r-cran-lmtest (0.9.40-1build1) ... 160s Selecting previously unselected package r-cran-nnet. 160s Preparing to unpack .../092-r-cran-nnet_7.3-20-1_amd64.deb ... 160s Unpacking r-cran-nnet (7.3-20-1) ... 160s Selecting previously unselected package r-cran-littler. 160s Preparing to unpack .../093-r-cran-littler_0.3.22-1_amd64.deb ... 160s Unpacking r-cran-littler (0.3.22-1) ... 160s Selecting previously unselected package r-cran-pkgkitten. 160s Preparing to unpack .../094-r-cran-pkgkitten_0.2.4-1_all.deb ... 160s Unpacking r-cran-pkgkitten (0.2.4-1) ... 160s Selecting previously unselected package r-cran-rcpp. 160s Preparing to unpack .../095-r-cran-rcpp_1.1.0-1_amd64.deb ... 160s Unpacking r-cran-rcpp (1.1.0-1) ... 160s Selecting previously unselected package r-cran-timedate. 160s Preparing to unpack .../096-r-cran-timedate_4052.112-1_amd64.deb ... 160s Unpacking r-cran-timedate (4052.112-1) ... 160s Selecting previously unselected package r-cran-quadprog. 160s Preparing to unpack .../097-r-cran-quadprog_1.5-8-1build2_amd64.deb ... 160s Unpacking r-cran-quadprog (1.5-8-1build2) ... 160s Selecting previously unselected package r-cran-xts. 160s Preparing to unpack .../098-r-cran-xts_0.14.1-1_amd64.deb ... 160s Unpacking r-cran-xts (0.14.1-1) ... 160s Selecting previously unselected package r-cran-ttr. 160s Preparing to unpack .../099-r-cran-ttr_0.24.4-1_amd64.deb ... 160s Unpacking r-cran-ttr (0.24.4-1) ... 160s Selecting previously unselected package r-cran-jsonlite. 160s Preparing to unpack .../100-r-cran-jsonlite_1.9.1+dfsg-1_amd64.deb ... 160s Unpacking r-cran-jsonlite (1.9.1+dfsg-1) ... 160s Selecting previously unselected package r-cran-quantmod. 160s Preparing to unpack .../101-r-cran-quantmod_0.4.28-1_all.deb ... 160s Unpacking r-cran-quantmod (0.4.28-1) ... 160s Selecting previously unselected package r-cran-tseries. 160s Preparing to unpack .../102-r-cran-tseries_0.10-59-3_amd64.deb ... 160s Unpacking r-cran-tseries (0.10-59-3) ... 160s Selecting previously unselected package r-cran-nlme. 160s Preparing to unpack .../103-r-cran-nlme_3.1.168-1_amd64.deb ... 160s Unpacking r-cran-nlme (3.1.168-1) ... 160s Selecting previously unselected package r-cran-urca. 160s Preparing to unpack .../104-r-cran-urca_1.3-4-1build1_amd64.deb ... 160s Unpacking r-cran-urca (1.3-4-1build1) ... 160s Selecting previously unselected package r-cran-rcpparmadillo. 160s Preparing to unpack .../105-r-cran-rcpparmadillo_15.2.3-1-1_amd64.deb ... 160s Unpacking r-cran-rcpparmadillo (15.2.3-1-1) ... 160s Selecting previously unselected package r-cran-forecast. 160s Preparing to unpack .../106-r-cran-forecast_8.23.0-1_amd64.deb ... 160s Unpacking r-cran-forecast (8.23.0-1) ... 160s Selecting previously unselected package r-cran-mass. 160s Preparing to unpack .../107-r-cran-mass_7.3-65-1_amd64.deb ... 160s Unpacking r-cran-mass (7.3-65-1) ... 160s Selecting previously unselected package r-cran-matrix. 160s Preparing to unpack .../108-r-cran-matrix_1.7-4-1_amd64.deb ... 160s Unpacking r-cran-matrix (1.7-4-1) ... 160s Selecting previously unselected package r-cran-modelr. 160s Preparing to unpack .../109-r-cran-modelr_0.1.11-1_all.deb ... 160s Unpacking r-cran-modelr (0.1.11-1) ... 160s Selecting previously unselected package r-cran-microbenchmark. 161s Preparing to unpack .../110-r-cran-microbenchmark_1.5.0-1_amd64.deb ... 161s Unpacking r-cran-microbenchmark (1.5.0-1) ... 161s Selecting previously unselected package r-cran-doby. 161s Preparing to unpack .../111-r-cran-doby_4.7.1-3_all.deb ... 161s Unpacking r-cran-doby 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Setting up libpaper2:amd64 (2.2.5-0.3build1) ... 161s Setting up libjs-jquery (3.7.1+dfsg+~3.5.33-1build1) ... 161s Setting up node-normalize.css (8.0.1-5.1) ... 161s Setting up xdg-utils (1.2.1-2ubuntu2) ... 161s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode 161s Setting up libjs-bootstrap (3.4.1+dfsg-6) ... 161s Setting up libjpeg8:amd64 (8c-2ubuntu12) ... 161s Setting up libice6:amd64 (2:1.1.1-1build1) ... 161s Setting up liblapack3:amd64 (3.12.1-7ubuntu1) ... 161s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode 161s Setting up fontconfig-config (2.17.1-3ubuntu1) ... 162s Setting up libpaper-utils (2.2.5-0.3build1) ... 162s Setting up libjs-jquery-datatables (1.11.5+dfsg-2build1) ... 162s Setting up libthai0:amd64 (0.1.30-1) ... 162s Setting up libtiff6:amd64 (4.7.0-3ubuntu3) ... 162s Setting up libfontconfig1:amd64 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(1.0.12+dfsg-1) ... 164s Setting up r-cran-forecast (8.23.0-1) ... 164s Setting up r-cran-modelr (0.1.11-1) ... 164s Setting up r-cran-doby (4.7.1-3) ... 164s Setting up r-cran-pbkrtest (0.5.5-1) ... 164s Processing triggers for libc-bin (2.42-2ubuntu4) ... 164s Processing triggers for man-db (2.13.1-1build1) ... 164s Processing triggers for install-info (7.2-5) ... 165s autopkgtest [05:26:51]: test run-unit-test: [----------------------- 166s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 166s BEGIN TEST test_a_utils.R 166s 166s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 166s Copyright (C) 2025 The R Foundation for Statistical Computing 166s Platform: x86_64-pc-linux-gnu 166s 166s R is free software and comes with ABSOLUTELY NO WARRANTY. 166s You are welcome to redistribute it under certain conditions. 166s Type 'license()' or 'licence()' for distribution details. 166s 166s R is a collaborative project with many contributors. 166s Type 'contributors()' for more information and 166s 'citation()' on how to cite R or R packages in publications. 166s 166s Type 'demo()' for some demos, 'help()' for on-line help, or 166s 'help.start()' for an HTML browser interface to help. 166s Type 'q()' to quit R. 166s 166s > # test_a_utils.R 166s > 166s > library(lmerTest) 166s Loading required package: lme4 166s Loading required package: Matrix 167s 167s Attaching package: 'lmerTest' 167s 167s > 167s > # test safeDeparse() - equivalence and differences to deparse(): 167s > deparse_args <- formals(deparse) 167s > safeDeparse_args <- formals(lmerTest:::safeDeparse) 167s The following object is masked from 'package:lme4': 167s 167s lmer 167s 167s The following object is masked from 'package:stats': 167s 167s step 167s 167s > stopifnot( 167s + all.equal(names(deparse_args), names(safeDeparse_args)), 167s + all.equal(deparse_args[!names(deparse_args) %in% c("control", "width.cutoff")], 167s + safeDeparse_args[!names(safeDeparse_args) %in% c("control", "width.cutoff")]), 167s + all.equal(deparse_args[["width.cutoff"]], 60L), 167s + all(eval(safeDeparse_args[["control"]]) %in% eval(deparse_args[["control"]])), 167s + all.equal(safeDeparse_args[["width.cutoff"]], 500L) 167s + ) 167s > 167s > 167s BEGIN TEST test_anova.R 167s 167s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 167s Copyright (C) 2025 The R Foundation for Statistical Computing 167s Platform: x86_64-pc-linux-gnu 167s 167s R is free software and comes with ABSOLUTELY NO WARRANTY. 167s You are welcome to redistribute it under certain conditions. 167s Type 'license()' or 'licence()' for distribution details. 167s 167s R is a collaborative project with many contributors. 167s Type 'contributors()' for more information and 167s 'citation()' on how to cite R or R packages in publications. 167s 167s Type 'demo()' for some demos, 'help()' for on-line help, or 167s 'help.start()' for an HTML browser interface to help. 167s Type 'q()' to quit R. 167s 167s > # test_anova.R 167s > library(lmerTest) 167s Loading required package: lme4 167s Loading required package: Matrix 168s 168s Attaching package: 'lmerTest' 168s 168s > 168s > # WRE says "using if(requireNamespace("pkgname")) is preferred, if possible." 168s > # even in tests: 168s > assertError <- function(expr, ...) 168s + if(requireNamespace("tools")) tools::assertError(expr, ...) else invisible() 168s > assertWarning <- function(expr, ...) 168s + if(requireNamespace("tools")) tools::assertWarning(expr, ...) else invisible() 168s > 168s > # Kenward-Roger only available with pbkrtest and only then validated in R >= 3.3.3 168s > # (faulty results for R < 3.3.3 may be due to unstated dependencies in pbkrtest) 168s > has_pbkrtest <- requireNamespace("pbkrtest", quietly = TRUE) && getRversion() >= "3.3.3" 168s The following object is masked from 'package:lme4': 168s 168s lmer 168s 168s The following object is masked from 'package:stats': 168s 168s step 168s 168s > 168s > data("sleepstudy", package="lme4") 168s > TOL <- 1e-4 168s > 168s > #################################### 168s > ## Basic anova tests 168s > #################################### 168s > 168s > m <- lmer(Reaction ~ Days + (Days | Subject), sleepstudy) 168s > 168s > ####### ddf argument: 168s > (an1 <- anova(m)) # Also testing print method. 168s Type III Analysis of Variance Table with Satterthwaite's method 168s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 168s Days 30031 30031 1 17 45.853 3.264e-06 *** 168s --- 168s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 168s > (an2 <- anova(m, ddf="Satterthwaite")) 168s Type III Analysis of Variance Table with Satterthwaite's method 168s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 168s Days 30031 30031 1 17 45.853 3.264e-06 *** 168s --- 168s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 168s > (an2b <- anova(m, ddf="Satterthwaite", type=3)) 168s Type III Analysis of Variance Table with Satterthwaite's method 168s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 168s Days 30031 30031 1 17 45.853 3.264e-06 *** 168s --- 168s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 168s > (an2c <- anova(m, ddf="Satterthwaite", type=2)) 168s Type II Analysis of Variance Table with Satterthwaite's method 168s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 168s Days 30031 30031 1 17 45.853 3.264e-06 *** 168s --- 168s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 168s > stopifnot(isTRUE( 168s + all.equal(an1, an2, tolerance=TOL) 168s + )) 168s > (an3 <- anova(m, ddf="Sat")) ## Abbreviated argument 168s Type III Analysis of Variance Table with Satterthwaite's method 168s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 168s Days 30031 30031 1 17 45.853 3.264e-06 *** 168s --- 168s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 168s > stopifnot(isTRUE( 168s + all.equal(an1, an3, tolerance=TOL) 168s + )) 168s > if(has_pbkrtest) { 168s + (anova(m, ddf="Kenward-Roger")) 168s + (anova(m, ddf="Kenward-Roger", type=3)) 168s + } 168s Type III Analysis of Variance Table with Kenward-Roger's method 168s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 168s Days 30031 30031 1 17 45.853 3.264e-06 *** 168s --- 168s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 168s > (an1 <- anova(m, ddf="lme4")) 168s Analysis of Variance Table 168s npar Sum Sq Mean Sq F value 168s Days 1 30031 30031 45.853 168s > (an2 <- anova(m, ddf="lme4", type=3)) # 'type' is ignored with ddf="lme4" 168s Analysis of Variance Table 168s npar Sum Sq Mean Sq F value 168s Days 1 30031 30031 45.853 168s > stopifnot(isTRUE( 168s + all.equal(an1, an2, tolerance=TOL) 168s + )) 168s > res <- assertError(anova(m, ddf="KR")) ## Error on incorrect arg. 168s > stopifnot( 168s + grepl("'arg' should be one of ", unlist(res[[1]])$message) 168s + ) 168s > 168s > ## lme4 method: 168s > an1 <- anova(m, ddf="lme4") 168s > an2 <- anova(as(m, "lmerMod")) 168s > stopifnot(isTRUE( 168s + all.equal(an1, an2, tolerance=TOL) 168s + )) 168s > 168s > ###### type argument: 168s > (an1 <- anova(m, type="1")) # valid type arg. 168s Type I Analysis of Variance Table with Satterthwaite's method 168s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 168s Days 30031 30031 1 17 45.853 3.264e-06 *** 168s --- 168s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 168s > (an2 <- anova(m, type="I")) # same 168s Type I Analysis of Variance Table with Satterthwaite's method 168s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 168s Days 30031 30031 1 17 45.853 3.264e-06 *** 168s --- 168s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 168s > stopifnot(isTRUE( 168s + all.equal(an1, an2, tolerance=TOL) 168s + )) 168s > (an3 <- anova(m, type=1)) # Not strictly valid, but accepted 168s Type I Analysis of Variance Table with Satterthwaite's method 168s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 168s Days 30031 30031 1 17 45.853 3.264e-06 *** 168s --- 168s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 168s > stopifnot(isTRUE( 168s + all.equal(an1, an3, tolerance=TOL) 168s + )) 168s > 168s > (an1 <- anova(m, type="2")) # valid type arg. 168s Type II Analysis of Variance Table with Satterthwaite's method 168s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 168s Days 30031 30031 1 17 45.853 3.264e-06 *** 168s --- 168s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 168s > (an2 <- anova(m, type="II")) # same 168s Type II Analysis of Variance Table with Satterthwaite's method 168s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 168s Days 30031 30031 1 17 45.853 3.264e-06 *** 168s --- 168s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 168s > stopifnot(isTRUE( 168s + all.equal(an1, an2, tolerance=TOL) 168s + )) 168s > (an3 <- anova(m, type=3)) # Not strictly valid, but accepted 168s Type III Analysis of Variance Table with Satterthwaite's method 168s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 168s Days 30031 30031 1 17 45.853 3.264e-06 *** 168s --- 168s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 168s > stopifnot(isTRUE( 168s + all.equal(an1, an3, check.attributes=FALSE, tolerance=TOL) 168s + )) 168s > 168s > (an1 <- anova(m, type="3")) # valid type arg. 168s Type III Analysis of Variance Table with Satterthwaite's method 168s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 168s Days 30031 30031 1 17 45.853 3.264e-06 *** 168s --- 168s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 168s > (an2 <- anova(m, type="III")) # same 168s Type III Analysis of Variance Table with Satterthwaite's method 168s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 168s Days 30031 30031 1 17 45.853 3.264e-06 *** 168s --- 168s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 168s > stopifnot(isTRUE( 168s + all.equal(an1, an2, tolerance=TOL) 168s + )) 168s > (an3 <- anova(m, type=3)) # Not strictly valid, but accepted 168s Type III Analysis of Variance Table with Satterthwaite's method 168s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 168s Days 30031 30031 1 17 45.853 3.264e-06 *** 168s --- 168s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 168s > stopifnot(isTRUE( 168s + all.equal(an1, an3, tolerance=TOL) 168s + )) 168s > assertError(anova(m, type=0)) # Not valid arg. 168s > assertError(anova(m, type="i")) # Not valid arg. 168s > 168s > ####### Model comparison: 168s > fm <- lm(Reaction ~ Days, sleepstudy) 168s > (an <- anova(m, fm)) 168s Data: sleepstudy 168s Models: 168s fm: Reaction ~ Days 168s m: Reaction ~ Days + (Days | Subject) 168s npar AIC BIC logLik -2*log(L) Chisq Df Pr(>Chisq) 168s fm 3 1906.3 1915.9 -950.15 1900.3 168s m 6 1763.9 1783.1 -875.97 1751.9 148.35 3 < 2.2e-16 *** 168s --- 168s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 168s > stopifnot( 168s + nrow(an) == 2L, 168s + rownames(an)[2] == "m" 168s + ) 168s > 168s > m2 <- lmer(Reaction ~ Days + I(Days^2) + (Days | Subject), sleepstudy) 168s refitting model(s) with ML (instead of REML) 169s > (an <- anova(m, m2, refit=FALSE)) 169s Data: sleepstudy 169s Models: 169s m: Reaction ~ Days + (Days | Subject) 169s m2: Reaction ~ Days + I(Days^2) + (Days | Subject) 169s npar AIC BIC logLik -2*log(L) Chisq Df Pr(>Chisq) 169s m 6 1755.6 1774.8 -871.81 1743.6 169s m2 7 1756.8 1779.2 -871.41 1742.8 0.8127 1 0.3673 169s > stopifnot( 169s + nrow(an) == 2L, 169s + rownames(an)[1] == "m" 169s + ) 169s > 169s > 169s > #################################### 169s > ## Example with factor fixef: 169s > #################################### 169s > 169s > ## 'temp' is continuous, 'temperature' an ordered factor with 6 levels 169s > data("cake", package="lme4") 169s > m <- lmer(angle ~ recipe * temp + (1|recipe:replicate), cake) 169s > (an <- anova(m)) 169s Type III Analysis of Variance Table with Satterthwaite's method 169s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 169s recipe 4.00 2.00 2 254.02 0.0957 0.9088 169s temp 1966.71 1966.71 1 222.00 94.1632 <2e-16 *** 169s recipe:temp 1.74 0.87 2 222.00 0.0417 0.9592 169s --- 169s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 169s > (an_lme4 <- anova(m, ddf="lme4")) 169s Analysis of Variance Table 169s npar Sum Sq Mean Sq F value 169s recipe 2 10.39 5.20 0.2488 169s temp 1 1966.71 1966.71 94.1632 169s recipe:temp 2 1.74 0.87 0.0417 169s > 169s > if(has_pbkrtest) { 169s + (an_KR <- anova(m, ddf="Kenward-Roger")) 169s + # res <- all.equal(an[, c("Sum Sq", "Mean Sq", "F value")], 169s + # an_lme4[, c("Sum Sq", "Mean Sq", "F value")]) 169s + # stopifnot(isTRUE(res)) 169s + res <- all.equal(an[, c("Sum Sq", "Mean Sq", "F value")], 169s + an_KR[, c("Sum Sq", "Mean Sq", "F value")], tolerance=TOL) 169s + stopifnot(isTRUE(res)) 169s + } 169s > stopifnot(all.equal(c(2, 1, 2), an$NumDF, tol=1e-6), 169s + all.equal(c(254.0157612, 222, 222), an$DenDF, tol=TOL)) 169s > 169s > an3 <- anova(m, type=3) 169s > an2 <- anova(m, type=2) 169s > an1 <- anova(m, type=1) 169s > 169s > ## Data is balanced, so Type II and III should be identical: 169s > ## One variable is continuous, so Type I and II/III are different: 169s > stopifnot( 169s + isTRUE(all.equal(an3, an2, check.attributes=FALSE, tolerance=TOL)), 169s + !isTRUE(all.equal(an1, an2, check.attributes=FALSE, tolerance=1e-8)) 169s + ) 169s > 169s > # Using an ordered factor: 169s > m <- lmer(angle ~ recipe * temperature + (1|recipe:replicate), cake) 169s > (an1 <- anova(m, type=1)) 169s Type I Analysis of Variance Table with Satterthwaite's method 169s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 169s recipe 10.19 5.09 2 42 0.2488 0.7809 169s temperature 2100.30 420.06 5 210 20.5199 <2e-16 *** 169s recipe:temperature 205.98 20.60 10 210 1.0062 0.4393 169s --- 169s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 169s > (an2 <- anova(m, type=2)) 169s Type II Analysis of Variance Table with Satterthwaite's method 169s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 169s recipe 10.19 5.09 2 42 0.2488 0.7809 169s temperature 2100.30 420.06 5 210 20.5199 <2e-16 *** 169s recipe:temperature 205.98 20.60 10 210 1.0062 0.4393 169s --- 169s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 169s > # Type 3 is also available with ordered factors: 169s > (an3 <- anova(m, type=3)) 169s Type III Analysis of Variance Table with Satterthwaite's method 169s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 169s recipe 10.19 5.09 2 42 0.2488 0.7809 169s temperature 2100.30 420.06 5 210 20.5199 <2e-16 *** 169s recipe:temperature 205.98 20.60 10 210 1.0062 0.4393 169s --- 169s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 169s > ## Balanced data and only factors: Type I, II and III should be the same: 169s > stopifnot( 169s + isTRUE(all.equal(an1, an2, check.attributes=FALSE, tolerance=TOL)), 169s + isTRUE(all.equal(an1, an3, check.attributes=FALSE, tolerance=TOL)) 169s + ) 169s > 169s > (an <- anova(m, type=1)) 169s Type I Analysis of Variance Table with Satterthwaite's method 169s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 169s recipe 10.19 5.09 2 42 0.2488 0.7809 169s temperature 2100.30 420.06 5 210 20.5199 <2e-16 *** 169s recipe:temperature 205.98 20.60 10 210 1.0062 0.4393 169s --- 169s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 169s > (an_lme4 <- anova(m, type=1, ddf="lme4")) 169s Analysis of Variance Table 169s npar Sum Sq Mean Sq F value 169s recipe 2 10.19 5.09 0.2488 169s temperature 5 2100.30 420.06 20.5199 169s recipe:temperature 10 205.98 20.60 1.0062 169s > res <- all.equal(an[, c("Sum Sq", "Mean Sq", "F value")], 169s + an_lme4[, c("Sum Sq", "Mean Sq", "F value")], tolerance=TOL) 169s > stopifnot(isTRUE(res)) 169s > if(has_pbkrtest) { 169s + (an_KR <- anova(m, type=1, ddf="Kenward-Roger")) 169s + res <- all.equal(an[, c("Sum Sq", "Mean Sq", "F value")], 169s + an_KR[, c("Sum Sq", "Mean Sq", "F value")], tolerance=TOL) 169s + stopifnot(isTRUE(res)) 169s + } 169s > stopifnot(all.equal(c(2, 5, 10), an$NumDF, tolerance=TOL), 169s + all.equal(c(42, 210, 210), an$DenDF, tolerance=TOL)) 169s > 169s > ######## 169s > ## Make case with balanced unordered factors: 169s > cake2 <- cake 169s > cake2$temperature <- factor(cake2$temperature, ordered = FALSE) 169s > # str(cake2) 169s > stopifnot( 169s + !is.ordered(cake2$temperature) 169s + ) 169s > m <- lmer(angle ~ recipe * temperature + (1|recipe:replicate), cake2) 169s > (an1 <- anova(m, type=1)) 169s Type I Analysis of Variance Table with Satterthwaite's method 169s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 169s recipe 10.19 5.09 2 42 0.2488 0.7809 169s temperature 2100.30 420.06 5 210 20.5199 <2e-16 *** 169s recipe:temperature 205.98 20.60 10 210 1.0062 0.4393 169s --- 169s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 169s > (an2 <- anova(m, type=2)) 169s Type II Analysis of Variance Table with Satterthwaite's method 169s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 169s recipe 10.19 5.09 2 42 0.2488 0.7809 169s temperature 2100.30 420.06 5 210 20.5199 <2e-16 *** 169s recipe:temperature 205.98 20.60 10 210 1.0062 0.4393 169s --- 169s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 169s > (an3 <- anova(m, type=3)) 169s Type III Analysis of Variance Table with Satterthwaite's method 169s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 169s recipe 10.19 5.09 2 42 0.2488 0.7809 169s temperature 2100.30 420.06 5 210 20.5199 <2e-16 *** 169s recipe:temperature 205.98 20.60 10 210 1.0062 0.4393 169s --- 169s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 169s > ## Balanced data and only factors: Type I, II, and III should be the same: 169s > stopifnot( 169s + isTRUE(all.equal(an1, an2, check.attributes=FALSE, tolerance=TOL)), 169s + isTRUE(all.equal(an3, an2, check.attributes=FALSE, tolerance=TOL)) 169s + ) 169s > ######## 169s > 169s > # No intercept: 169s > m <- lmer(angle ~ 0 + recipe * temp + (1|recipe:replicate), cake) 169s > (an <- anova(m, type=1)) 169s Type I Analysis of Variance Table with Satterthwaite's method 169s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 169s recipe 21442.9 7147.6 3 42 342.2200 <2e-16 *** 169s temp 1966.7 1966.7 1 222 94.1632 <2e-16 *** 169s recipe:temp 1.7 0.9 2 222 0.0417 0.9592 169s --- 169s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 169s > (an2 <- anova(m, type=2)) 169s Type II Analysis of Variance Table with Satterthwaite's method 169s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 169s recipe 4.48 1.49 3 254.02 0.0714 0.9752 169s temp 1966.71 1966.71 1 222.00 94.1632 <2e-16 *** 169s recipe:temp 1.74 0.87 2 222.00 0.0417 0.9592 169s --- 169s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 169s > (an2 <- anova(m, type=3)) 169s Type III Analysis of Variance Table with Satterthwaite's method 169s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 169s recipe 4.48 1.49 3 254.02 0.0714 0.9752 169s temp 1966.71 1966.71 1 222.00 94.1632 <2e-16 *** 169s recipe:temp 1.74 0.87 2 222.00 0.0417 0.9592 169s --- 169s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 169s > if(has_pbkrtest) 169s + (an_KR <- anova(m, ddf="Kenward-Roger")) 169s Type III Analysis of Variance Table with Kenward-Roger's method 169s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 169s recipe 4.48 1.49 3 254.02 0.0714 0.9752 169s temp 1966.71 1966.71 1 222.00 94.1632 <2e-16 *** 169s recipe:temp 1.74 0.87 2 222.00 0.0417 0.9592 169s --- 169s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 169s > (an_lme4 <- anova(m, ddf="lme4")) 169s Analysis of Variance Table 169s npar Sum Sq Mean Sq F value 169s recipe 3 21442.9 7147.6 342.2200 169s temp 1 1966.7 1966.7 94.1632 169s recipe:temp 2 1.7 0.9 0.0417 169s > res <- all.equal(an[, c("Sum Sq", "Mean Sq", "F value")], 169s + an_lme4[, c("Sum Sq", "Mean Sq", "F value")], tolerance=TOL) 169s > stopifnot(isTRUE(res)) 169s > 169s > # ML-fit: 169s > m <- lmer(angle ~ recipe * temp + (1|recipe:replicate), cake, REML=FALSE) 169s > (an <- anova(m, type=1)) 169s Type I Analysis of Variance Table with Satterthwaite's method 169s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 169s recipe 10.99 5.49 2 45 0.2666 0.7672 169s temp 1966.71 1966.71 1 225 95.4357 <2e-16 *** 169s recipe:temp 1.74 0.87 2 225 0.0423 0.9586 169s --- 169s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 169s > if(has_pbkrtest) 169s + assertError(an <- anova(m, ddf="Kenward-Roger")) # KR fits should be REML 169s > (an_lme4 <- anova(m, ddf="lme4")) 169s Analysis of Variance Table 169s npar Sum Sq Mean Sq F value 169s recipe 2 10.99 5.49 0.2666 169s temp 1 1966.71 1966.71 95.4357 169s recipe:temp 2 1.74 0.87 0.0423 169s > res <- all.equal(an[, c("Sum Sq", "Mean Sq", "F value")], 169s + an_lme4[, c("Sum Sq", "Mean Sq", "F value")], tolerance=TOL) 169s > stopifnot(isTRUE(res)) 169s > 169s > #################################### 169s > ## Using contr.sum: 169s > #################################### 169s > 169s > m <- lmer(angle ~ recipe * temp + (1|recipe:replicate), cake, 169s + contrasts = list('recipe' = "contr.sum")) 169s > (an <- anova(m, type=1)) 169s Type I Analysis of Variance Table with Satterthwaite's method 169s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 169s recipe 10.39 5.20 2 42 0.2488 0.7809 169s temp 1966.71 1966.71 1 222 94.1632 <2e-16 *** 169s recipe:temp 1.74 0.87 2 222 0.0417 0.9592 169s --- 169s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 169s > (an2 <- anova(m, type=2)) 169s Type II Analysis of Variance Table with Satterthwaite's method 169s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 169s recipe 4.00 2.00 2 254.02 0.0957 0.9088 169s temp 1966.71 1966.71 1 222.00 94.1632 <2e-16 *** 169s recipe:temp 1.74 0.87 2 222.00 0.0417 0.9592 169s --- 169s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 169s > (an3 <- anova(m, type=3)) 169s Type III Analysis of Variance Table with Satterthwaite's method 169s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 169s recipe 4.00 2.00 2 254.02 0.0957 0.9088 169s temp 1966.71 1966.71 1 222.00 94.1632 <2e-16 *** 169s recipe:temp 1.74 0.87 2 222.00 0.0417 0.9592 169s --- 169s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 169s > stopifnot( 169s + isTRUE(all.equal(an2, an3, check.attributes=FALSE, tolerance=TOL)) 169s + ) 169s > if(has_pbkrtest) 169s + (an_KR <- anova(m, type=1, ddf="Kenward-Roger")) 169s Type I Analysis of Variance Table with Kenward-Roger's method 169s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 169s recipe 10.39 5.20 2 42 0.2488 0.7809 169s temp 1966.71 1966.71 1 222 94.1632 <2e-16 *** 169s recipe:temp 1.74 0.87 2 222 0.0417 0.9592 169s --- 169s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 169s > (an_lme4 <- anova(m, ddf="lme4")) 169s Analysis of Variance Table 169s npar Sum Sq Mean Sq F value 169s recipe 2 10.39 5.20 0.2488 169s temp 1 1966.71 1966.71 94.1632 169s recipe:temp 2 1.74 0.87 0.0417 169s > res <- all.equal(an[, c("Sum Sq", "Mean Sq", "F value")], 169s + an_lme4[, c("Sum Sq", "Mean Sq", "F value")], tolerance=TOL) 169s > stopifnot(isTRUE(res)) 169s > 169s > 169s > #################################### 169s > ## Example with continuous fixef: 169s > #################################### 169s > 169s > # Example with no fixef: 169s > m <- lmer(Reaction ~ -1 + (Days | Subject), sleepstudy) 169s > # m <- lmer(Reaction ~ 0 + (Days | Subject), sleepstudy) # alternative 169s > stopifnot(length(fixef(m)) == 0L) 169s > (an <- anova(m, type=1)) 169s Type I Analysis of Variance Table with Satterthwaite's method 169s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 169s > (an_2 <- anova(m, type=2)) 169s Type II Analysis of Variance Table with Satterthwaite's method 169s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 169s > (an_3 <- anova(m, type=3)) 169s Type III Analysis of Variance Table with Satterthwaite's method 169s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 169s > stopifnot(nrow(an) == 0L, 169s + nrow(an_2) == 0L, 169s + nrow(an_3) == 0L) 169s > # anova(m, ddf="lme4") # Bug in lme4 it seems 169s > if(has_pbkrtest) { 169s + (an_KR <- anova(m, ddf="Kenward-Roger")) 169s + stopifnot( 169s + nrow(an_KR) == 0L 169s + ) 169s + } 169s > 169s > # Example with intercept only: 169s > m <- lmer(Reaction ~ (Days | Subject), sleepstudy) 169s > # m <- lmer(Reaction ~ 1 + (Days | Subject), sleepstudy) # alternative 169s > stopifnot(length(fixef(m)) == 1L, 169s + names(fixef(m)) == "(Intercept)") 169s > (an <- anova(m)) 169s Type III Analysis of Variance Table with Satterthwaite's method 169s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 169s > (an_2 <- anova(m, type=2)) 169s Type II Analysis of Variance Table with Satterthwaite's method 169s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 169s > (an_3 <- anova(m, type=3)) 169s Type III Analysis of Variance Table with Satterthwaite's method 169s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 169s > (an_lme4 <- anova(m, ddf="lme4")) 169s Analysis of Variance Table 169s npar Sum Sq Mean Sq F value 169s > stopifnot(nrow(an) == 0L, 169s + nrow(an_2) == 0L, 169s + nrow(an_3) == 0L, 169s + nrow(an_lme4) == 0L) 169s > if(has_pbkrtest) { 169s + (an_KR <- anova(m, ddf="Kenward-Roger")) 169s + stopifnot( 169s + nrow(an_KR) == 0L 169s + ) 169s + } 169s > 169s > # Example with 1 fixef without intercept: 169s > # for packageVersion("lme4") < 1.1.20 169s > # mOld <- lmer(Reaction ~ Days - 1 + (Days | Subject), sleepstudy) 169s > # for packageVersion("lme4") >= 1.1.20 we need to specify the old default 169s > # optimizer to get the model to converge well enough. 169s > m <- lmer(Reaction ~ Days - 1 + (Days | Subject), sleepstudy, 169s + control=lmerControl(optimizer="bobyqa")) 169s > # m <- lmer(Reaction ~ 0 + Days + (Days | Subject), sleepstudy) # alternative 169s > stopifnot(length(fixef(m)) == 1L, 169s + names(fixef(m)) == "Days") 169s > (an <- anova(m)) 169s Type III Analysis of Variance Table with Satterthwaite's method 169s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 169s Days 93564 93564 1 17 142.86 1.069e-09 *** 169s --- 169s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 169s > (an_2 <- anova(m, type=2)) 169s Type II Analysis of Variance Table with Satterthwaite's method 169s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 169s Days 93564 93564 1 17 142.86 1.069e-09 *** 169s --- 169s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 169s > (an_3 <- anova(m, type=3)) 169s Type III Analysis of Variance Table with Satterthwaite's method 169s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 169s Days 93564 93564 1 17 142.86 1.069e-09 *** 169s --- 169s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 169s > (an_lme4 <- anova(m, ddf="lme4")) 169s Analysis of Variance Table 169s npar Sum Sq Mean Sq F value 169s Days 1 93564 93564 142.86 169s > stopifnot(nrow(an) == 1L, 169s + nrow(an_2) == 1L, 169s + nrow(an_3) == 1L, 169s + nrow(an_lme4) == 1L) 169s > if(has_pbkrtest) { 169s + (an_KR <- anova(m, ddf="Kenward-Roger")) 169s + stopifnot( 169s + nrow(an_KR) == 1L 169s + ) 169s + } 169s > 169s > res <- all.equal(an[, c("Sum Sq", "Mean Sq", "F value")], 169s + an_lme4[, c("Sum Sq", "Mean Sq", "F value")], tolerance=TOL) 169s > stopifnot(isTRUE(res)) 169s > stopifnot(isTRUE(all.equal( 169s + c(1, 17), unname(unlist(an[, c("NumDF", "DenDF")])), tolerance=TOL 169s + ))) 169s > 169s > # Example with >1 fixef without intercept: 169s > m <- lmer(Reaction ~ Days - 1 + I(Days^2) + (Days | Subject), sleepstudy) 169s > stopifnot(length(fixef(m)) == 2L, 169s + names(fixef(m)) == c("Days", "I(Days^2)")) 169s > (an <- anova(m)) 169s Type III Analysis of Variance Table with Satterthwaite's method 169s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 169s Days 22127.2 22127.2 1 69.048 33.9280 1.65e-07 *** 169s I(Days^2) 744.7 744.7 1 143.679 1.1419 0.287 169s --- 169s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 169s > (an_2 <- anova(m, type=2)) 169s Type II Analysis of Variance Table with Satterthwaite's method 169s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 169s Days 22127.2 22127.2 1 69.048 33.9280 1.65e-07 *** 169s I(Days^2) 744.7 744.7 1 143.679 1.1419 0.287 169s --- 169s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 169s > (an_3 <- anova(m, type=3)) 169s Type III Analysis of Variance Table with Satterthwaite's method 169s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 169s Days 22127.2 22127.2 1 69.048 33.9280 1.65e-07 *** 169s I(Days^2) 744.7 744.7 1 143.679 1.1419 0.287 169s --- 169s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 169s > (an_lme4 <- anova(m, ddf="lme4")) 169s Analysis of Variance Table 169s npar Sum Sq Mean Sq F value 169s Days 1 93129 93129 142.7959 169s I(Days^2) 1 745 745 1.1419 169s > stopifnot(nrow(an) == 2L, 169s + nrow(an_3) == 2L, 169s + nrow(an_lme4) == 2L) 169s > if(has_pbkrtest) { 169s + (an_KR <- anova(m, ddf="Kenward-Roger")) 169s + stopifnot( 169s + nrow(an_KR) == 2L 169s + ) 169s + } 169s > # Here is a diff in SSQ which doesn't seem well-defined anyway... 169s > # SSQ for I(Days^2) agree though. 169s > # t-statistics also agree: 169s > coef(summary(m)) 169s Estimate Std. Error df t value Pr(>|t|) 169s Days 15.884431 2.7270460 69.04781 5.824776 1.649534e-07 169s I(Days^2) 0.279552 0.2616034 143.67926 1.068610 2.870375e-01 169s > Lmat <- diag(length(fixef(m))) 169s > lmerTest:::rbindall(lapply(1:nrow(Lmat), function(i) contest1D(m, Lmat[i, ]))) 169s Estimate Std. Error df t value Pr(>|t|) 169s 1 15.884431 2.7270460 69.04781 5.824776 1.649534e-07 169s 2 0.279552 0.2616034 143.67926 1.068610 2.870375e-01 169s > 169s > # Example with >1 fixef and intercept: 169s > m <- lmer(Reaction ~ Days + I(Days^2) + (Days | Subject), sleepstudy) 169s > stopifnot(length(fixef(m)) == 3L) 169s > (an <- anova(m, type=1)) 169s Type I Analysis of Variance Table with Satterthwaite's method 169s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 169s Days 29894.8 29894.8 1 17 45.8530 3.264e-06 *** 169s I(Days^2) 1079.5 1079.5 1 143 1.6558 0.2003 169s --- 169s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 169s > (an_2 <- anova(m, type=2)) 169s Type II Analysis of Variance Table with Satterthwaite's method 169s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 169s Days 4534.5 4534.5 1 114.43 6.9551 0.00952 ** 169s I(Days^2) 1079.5 1079.5 1 143.00 1.6558 0.20026 169s --- 169s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 169s > (an_3 <- anova(m, type=3)) 169s Type III Analysis of Variance Table with Satterthwaite's method 169s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 169s Days 4534.5 4534.5 1 114.43 6.9551 0.00952 ** 169s I(Days^2) 1079.5 1079.5 1 143.00 1.6558 0.20026 169s --- 169s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 169s > (an_lme4 <- anova(m, ddf="lme4")) 169s Analysis of Variance Table 169s npar Sum Sq Mean Sq F value 169s Days 1 29894.8 29894.8 45.8530 169s I(Days^2) 1 1079.5 1079.5 1.6558 169s > res <- all.equal(an[, c("Sum Sq", "Mean Sq", "F value")], 169s + an_lme4[, c("Sum Sq", "Mean Sq", "F value")], tolerance=TOL) 169s > stopifnot(isTRUE(res)) 169s > 169s > if(has_pbkrtest) { 169s + (an_KR <- anova(m, ddf="Kenward-Roger")) 169s + res <- all.equal(an_3[, c("Sum Sq", "Mean Sq", "DenDF", "F value")], 169s + an_KR[, c("Sum Sq", "Mean Sq", "DenDF", "F value")], tolerance=TOL) 169s + stopifnot(isTRUE(res)) 169s + } 169s > 169s > ## FIXME: Test the use of refit arg to lme4:::anova.merMod 169s > 169s > ############################## 169s > # Test that type III anova is the same regardless of contrast coding: 169s > # 3 x 3 factorial with missing diagonal 169s > data("cake", package="lme4") 169s > cake4 <- cake 169s > cake4$temperature <- factor(cake4$temperature, ordered=FALSE) 169s > cake4 <- droplevels(subset(cake4, temperature %in% levels(cake4$temperature)[1:3])) 169s > cake4 <- droplevels(subset(cake4, !((recipe == "A" & temperature == "175") | 169s + (recipe == "B" & temperature == "185") | 169s + (recipe == "C" & temperature == "195") ))) 169s > str(cake4) 169s 'data.frame': 90 obs. of 5 variables: 169s $ replicate : Factor w/ 15 levels "1","2","3","4",..: 1 1 1 1 1 1 2 2 2 2 ... 169s $ recipe : Factor w/ 3 levels "A","B","C": 1 1 2 2 3 3 1 1 2 2 ... 169s $ temperature: Factor w/ 3 levels "175","185","195": 2 3 1 3 1 2 2 3 1 3 ... 169s $ angle : int 46 47 39 51 46 44 29 35 35 47 ... 169s $ temp : num 185 195 175 195 175 185 185 195 175 195 ... 169s > with(cake4, table(recipe, temperature)) 169s temperature 169s recipe 175 185 195 169s A 0 15 15 169s B 15 0 15 169s C 15 15 0 169s > # load_all(r2path) 169s > 169s > fm1 <- lmer(angle ~ recipe * temperature + (1|recipe:replicate), cake4) 169s fixed-effect model matrix is rank deficient so dropping 3 columns / coefficients 169s > fm2 <- lmer(angle ~ recipe * temperature + (1|recipe:replicate), cake4, 169s + contrasts=list(recipe="contr.sum", temperature="contr.SAS")) 169s fixed-effect model matrix is rank deficient so dropping 3 columns / coefficients 169s > fm3 <- lmer(angle ~ recipe * temperature + (1|recipe:replicate), cake4, 169s + contrasts=list(recipe="contr.sum", temperature="contr.poly")) 169s fixed-effect model matrix is rank deficient so dropping 3 columns / coefficients 169s > fm4 <- lmer(angle ~ recipe * temperature + (1|recipe:replicate), cake4, 169s + contrasts=list(recipe=contr.helmert, temperature="contr.poly")) 169s fixed-effect model matrix is rank deficient so dropping 3 columns / coefficients 170s > (an1 <- anova(fm1)) 170s Missing cells for: recipeA:temperature175, recipeB:temperature185, recipeC:temperature195. 170s Interpret type III hypotheses with care. 170s Type III Analysis of Variance Table with Satterthwaite's method 170s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 170s recipe 2.282 1.141 2 45.888 0.0871 0.916766 170s temperature 136.267 68.133 2 42.000 5.1998 0.009602 ** 170s recipe:temperature 52.900 52.900 1 42.000 4.0372 0.050963 . 170s --- 170s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 170s > (an2 <- anova(fm2)) 170s Missing cells for: recipeA:temperature175, recipeB:temperature185, recipeC:temperature195. 170s Interpret type III hypotheses with care. 170s Type III Analysis of Variance Table with Satterthwaite's method 170s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 170s recipe 2.282 1.141 2 45.888 0.0871 0.916766 170s temperature 136.267 68.133 2 42.000 5.1998 0.009602 ** 170s recipe:temperature 52.900 52.900 1 42.000 4.0372 0.050963 . 170s --- 170s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 170s > (an3 <- anova(fm3)) 170s Missing cells for: recipeA:temperature175, recipeB:temperature185, recipeC:temperature195. 170s Interpret type III hypotheses with care. 170s Type III Analysis of Variance Table with Satterthwaite's method 170s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 170s recipe 2.282 1.141 2 45.888 0.0871 0.916766 170s temperature 136.267 68.133 2 42.000 5.1998 0.009602 ** 170s recipe:temperature 52.900 52.900 1 42.000 4.0372 0.050963 . 170s --- 170s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 170s > (an4 <- anova(fm4)) 170s Missing cells for: recipeA:temperature175, recipeB:temperature185, recipeC:temperature195. 170s Interpret type III hypotheses with care. 170s Type III Analysis of Variance Table with Satterthwaite's method 170s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 170s recipe 2.282 1.141 2 45.888 0.0871 0.916766 170s temperature 136.267 68.133 2 42.000 5.1998 0.009602 ** 170s recipe:temperature 52.900 52.900 1 42.000 4.0372 0.050963 . 170s --- 170s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 170s > options("contrasts") 170s $contrasts 170s unordered ordered 170s "contr.treatment" "contr.poly" 170s 170s > options(contrasts = c("contr.sum", "contr.poly")) 170s > fm5 <- lmer(angle ~ recipe * temperature + (1|recipe:replicate), cake4) 170s fixed-effect model matrix is rank deficient so dropping 3 columns / coefficients 170s > (an5 <- anova(fm5)) 170s Missing cells for: recipeA:temperature175, recipeB:temperature185, recipeC:temperature195. 170s Interpret type III hypotheses with care. 170s Type III Analysis of Variance Table with Satterthwaite's method 170s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 170s recipe 2.282 1.141 2 45.888 0.0871 0.916766 170s temperature 136.267 68.133 2 42.000 5.1998 0.009602 ** 170s recipe:temperature 52.900 52.900 1 42.000 4.0372 0.050963 . 170s --- 170s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 170s > options(contrasts = c("contr.treatment", "contr.poly")) 170s > options("contrasts") 170s $contrasts 170s [1] "contr.treatment" "contr.poly" 170s 170s > stopifnot( 170s + isTRUE(all.equal(an1, an2, check.attributes=FALSE, tolerance=TOL)), 170s + isTRUE(all.equal(an1, an3, check.attributes=FALSE, tolerance=TOL)), 170s + isTRUE(all.equal(an1, an4, check.attributes=FALSE, tolerance=TOL)), 170s + isTRUE(all.equal(an1, an5, check.attributes=FALSE, tolerance=TOL)) 170s + ) 170s > 170s > 170s BEGIN TEST test_compare_sas.R 170s 170s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 170s Copyright (C) 2025 The R Foundation for Statistical Computing 170s Platform: x86_64-pc-linux-gnu 170s 170s R is free software and comes with ABSOLUTELY NO WARRANTY. 170s You are welcome to redistribute it under certain conditions. 170s Type 'license()' or 'licence()' for distribution details. 170s 170s R is a collaborative project with many contributors. 170s Type 'contributors()' for more information and 170s 'citation()' on how to cite R or R packages in publications. 170s 170s Type 'demo()' for some demos, 'help()' for on-line help, or 170s 'help.start()' for an HTML browser interface to help. 170s Type 'q()' to quit R. 170s 170s > # test_compare_sas.R 170s > library(lmerTest) 170s Loading required package: lme4 170s Loading required package: Matrix 171s > 171s > # WRE says "using if(requireNamespace("pkgname")) is preferred, if possible." 171s > # even in tests: 171s > assertError <- function(expr, ...) 171s + if(requireNamespace("tools")) tools::assertError(expr, ...) else invisible() 171s > assertWarning <- function(expr, ...) 171s + if(requireNamespace("tools")) tools::assertWarning(expr, ...) else invisible() 171s > 171s > ##################################################################### 171s > 171s > 171s > # Use contrasts to get particular estimates for the summary table: 171s > l <- list(Frequency="contr.SAS", Income="contr.SAS") 171s > m.carrots <- lmer(Preference ~ sens2*Frequency*Income 171s + +(1+sens2|Consumer), data=carrots, contrasts=l) 171s 171s Attaching package: 'lmerTest' 171s 171s The following object is masked from 'package:lme4': 171s 171s lmer 171s 171s The following object is masked from 'package:stats': 171s 171s step 171s 171s fixed-effect model matrix is rank deficient so dropping 12 columns / coefficients 171s > an.m <- anova(m.carrots) 171s Missing cells for: Frequency3:Income1, Frequency5:Income1, Frequency4:Income2, Frequency3:Income4, Frequency4:Income4, Frequency5:Income4, sens2:Frequency3:Income1, sens2:Frequency5:Income1, sens2:Frequency4:Income2, sens2:Frequency3:Income4, sens2:Frequency4:Income4, sens2:Frequency5:Income4. 171s Interpret type III hypotheses with care. 171s > 171s > TOL <- 1e-4 171s > TOL2 <- 1e-5 171s > # with 4 decimals should agree with SAS output 171s > # numbers before decimals should agree with SAS output 171s > stopifnot( 171s + all.equal(an.m[,"Pr(>F)"], 171s + c(2e-5, 0.15512, 0.06939, 0.08223, 0.52459, 0.03119, 0.48344), 171s + tolerance = TOL), 171s + all.equal(round(an.m$DenDF), c(83, 83, 83, 83, 83, 83, 83)) 171s + ) 171s > 171s > sm <- summary(m.carrots) 171s > stopifnot( 171s + isTRUE(all.equal(sm$coefficients[,"Pr(>|t|)"], 171s + c(1e-10, 0.005061, 0.6865554, 0.342613, 0.129157, 171s + 0.088231, 0.846000, 0.354472, 0.526318, 0.020646, 0.010188, 171s + 0.031242, 0.055356, 0.694689, 0.099382, 0.28547, 171s + 0.977774, 0.855653, 0.427737, 0.321086, 0.417465 , 0.204385, 0.784437, 171s + 0.681434, 0.106180, 0.149122, 0.390870, 0.273686), tolerance=TOL, 171s + check.attributes = FALSE)) 171s + ) 171s > 171s > # Takes too long to run: 171s > # if(requireNamespace("pbkrtest", quietly = TRUE)) { 171s > # sm.kr <- summary(m.carrots, ddf = "Kenward-Roger") 171s > # 171s > # ## coefficients for Sat and KR agree in this example 171s > # # cbind(sm$coefficients[,"Pr(>|t|)"], sm.kr$coefficients[,"Pr(>|t|)"]) 171s > # all.equal(sm$coefficients[,"Pr(>|t|)"], sm.kr$coefficients[,"Pr(>|t|)"], 171s > # tol=TOL) 171s > # } 171s > 171s > ################################################################################ 171s > ## checking lsmeans and difflsmeans 171s > ## compare with SAS output 171s > m <- lmer(Informed.liking ~ Product*Information*Gender 171s + + (1|Product:Consumer) + (1|Consumer) , data=ham) 171s > 171s > 171s > lsm <- lsmeansLT(m, which = "Product") 171s > # head(lsm) 171s > 171s > stopifnot( 171s + isTRUE(all.equal(lsm[, "Estimate"], c(5.8084, 5.1012, 6.0909, 5.9256), 171s + tol=TOL, check.attributes = FALSE)), 171s + isTRUE(all.equal(round(lsm[, "t value"], 2), c(24.93, 21.89, 26.14, 25.43), tolerance=TOL, 171s + check.attributes = FALSE)), 171s + isTRUE(all.equal(lsm[, "lower"], c(5.3499, 4.6428, 5.6324, 5.4672), tolerance=TOL, 171s + check.attributes = FALSE)), 171s + isTRUE(all.equal(lsm[, "upper"], c(6.2668, 5.5597, 6.5493, 6.3840), tolerance=TOL, 171s + check.attributes = FALSE)) 171s + ) 171s > 171s > ################################################################################ 171s > # Not actually 'hard-coded' tests versus SAS results... 171s > 171s > m.carrots <- lmer(Preference ~ 0 + sens2 + Homesize + 171s + (1+sens2 | Consumer), data=carrots, 171s + control=lmerControl(optimizer="bobyqa")) 171s > summary(m.carrots) 171s Linear mixed model fit by REML. t-tests use Satterthwaite's method [ 171s lmerModLmerTest] 171s Formula: Preference ~ 0 + sens2 + Homesize + (1 + sens2 | Consumer) 171s Data: carrots 171s Control: lmerControl(optimizer = "bobyqa") 171s 171s REML criterion at convergence: 3748.9 171s 171s Scaled residuals: 171s Min 1Q Median 3Q Max 171s -3.5322 -0.5571 0.0308 0.6297 2.8552 171s 171s Random effects: 171s Groups Name Variance Std.Dev. Corr 171s Consumer (Intercept) 0.195168 0.44178 171s sens2 0.002779 0.05271 0.18 171s Residual 1.070441 1.03462 171s Number of obs: 1233, groups: Consumer, 103 171s 171s Fixed effects: 171s Estimate Std. Error df t value Pr(>|t|) 171s sens2 7.068e-02 9.545e-03 1.020e+02 7.404 3.89e-11 *** 171s Homesize1 4.910e+00 7.056e-02 1.013e+02 69.586 < 2e-16 *** 171s Homesize3 4.661e+00 7.850e-02 1.013e+02 59.374 < 2e-16 *** 171s --- 171s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 171s 171s Correlation of Fixed Effects: 171s sens2 Homsz1 171s Homesize1 0.061 171s Homesize3 0.055 0.003 171s > 171s > (an.1 <- anova(m.carrots, type=1)) 171s Type I Analysis of Variance Table with Satterthwaite's method 171s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 171s sens2 60.5 60.5 1 102.01 56.539 2.211e-11 *** 171s Homesize 8927.2 4463.6 2 101.31 4169.863 < 2.2e-16 *** 171s --- 171s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 171s > (an.3 <- anova(m.carrots)) 171s Type III Analysis of Variance Table with Satterthwaite's method 171s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 171s sens2 58.7 58.7 1 102.01 54.821 3.892e-11 *** 171s Homesize 8927.2 4463.6 2 101.31 4169.863 < 2.2e-16 *** 171s --- 171s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 171s > (an.lme4 <- anova(m.carrots, ddf = "lme4")) # difference in SSQ MS and F-values 171s Analysis of Variance Table 171s npar Sum Sq Mean Sq F value 171s sens2 1 0.0 0.0 0.0122 171s Homesize 2 8927.2 4463.6 4169.8633 171s > # Is this a problem with lme4? 171s > # fm <- lm(Preference ~ 0 + sens2 + Homesize, data=carrots) 171s > # anova(fm) 171s > # coef(summary(fm)) 171s > # Here the F value is a little greater than the squared t-value (as expected) 171s > 171s > stopifnot(all.equal(an.1[, "F value"], c(56.5394, 4169.87), tolerance = TOL2), 171s + all.equal(an.3[, "F value"], c(54.8206, 4169.87), tolerance = TOL2)) 171s > 171s > 171s > ################################################################################ 171s > # Check exmaple from GLM SAS report 171s > 171s > ### example from the paper GLM SAS 101 report 171s > a <- factor(c(1,1,1,2,2,2,2,2,1,2)) 171s > b <- factor(c(1,1,2,1,2,2,2,2,2,1)) 171s > f=factor(c(1,2,1,2,1,2,1,2,1,2)) 171s > y <- c(12,14,11,20,17,23,35,46,15,16) 171s > dd <- data.frame(a=a, b=b, y=y, f=f) 171s > 171s > ## check type 2 is order independent 171s > model <- lmer(y ~ a*b + (1|f), data=dd) 171s boundary (singular) fit: see help('isSingular') 171s > model2 <- lmer(y ~ b*a + (1|f), data=dd) 171s boundary (singular) fit: see help('isSingular') 171s > (an <- anova(model, type=2)) 171s Type II Analysis of Variance Table with Satterthwaite's method 171s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 171s a 336.00 336.00 1 6 3.9013 0.09566 . 171s b 114.33 114.33 1 6 1.3275 0.29308 171s a:b 85.75 85.75 1 6 0.9956 0.35689 171s --- 171s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 171s > (an2 <- anova(model2, type=2)) 171s Type II Analysis of Variance Table with Satterthwaite's method 171s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 171s b 114.33 114.33 1 6 1.3275 0.29308 171s a 336.00 336.00 1 6 3.9013 0.09566 . 171s b:a 85.75 85.75 1 6 0.9956 0.35689 171s --- 171s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 171s > stopifnot( 171s + isTRUE(all.equal(an,an2[c(2,1,3),], check.attributes = FALSE, tolerance=TOL2)) 171s + ) 171s > 171s > ## check the results are the same as from SAS proc mixed 171s > stopifnot( 171s + isTRUE(all.equal(an[,"F value"], c(3.90131, 1.32753, 0.99565), tolerance=TOL2)) 171s + ) 171s > ################################################################################ 171s > ## Check type II and III anova tables versus SAS 171s > 171s > m.carrots <- lmer(Preference ~ sens2*Homesize 171s + +(1+sens2|Consumer), data=carrots) 171s > (ancar <- anova(m.carrots, type=2)) 171s Type II Analysis of Variance Table with Satterthwaite's method 171s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 171s sens2 58.697 58.697 1 101.02 54.8339 4.042e-11 *** 171s Homesize 5.526 5.526 1 100.99 5.1621 0.02521 * 171s sens2:Homesize 1.103 1.103 1 101.02 1.0303 0.31251 171s --- 171s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 171s > 171s > stopifnot( 171s + isTRUE(all.equal(ancar[,"F value"], c(54.8361, 5.16138, 1.03035), tolerance = TOL)) 171s + ) 171s > 171s > m <- lmer(Informed.liking ~ Product*Age 171s + + (1|Consumer) , data=ham) 172s > (an <- anova(m, type=2)) 172s Type II Analysis of Variance Table with Satterthwaite's method 172s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 172s Product 32.498 10.8327 3 561 2.4814 0.06014 . 172s Age 0.024 0.0235 1 79 0.0054 0.94168 172s Product:Age 19.442 6.4808 3 561 1.4845 0.21772 172s --- 172s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 172s > 172s > stopifnot( 172s + isTRUE(all.equal(an[,"F value"], c(2.48135, .005387, 1.48451), tolerance = TOL2)) 172s + ) 172s > 172s > 172s > fm <- lmer(Preference ~ sens2*Homesize*sens1 + (1|Product), 172s + data=carrots) 172s > (ant2 <- anova(fm, type=2)) 172s Type II Analysis of Variance Table with Satterthwaite's method 172s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 172s sens2 21.0228 21.0228 1 7.97 16.4832 0.0036583 ** 172s Homesize 17.8570 17.8570 1 1217.01 14.0010 0.0001912 *** 172s sens1 0.6709 0.6709 1 7.98 0.5260 0.4889911 172s sens2:Homesize 1.5068 1.5068 1 1216.99 1.1814 0.2772780 172s sens2:sens1 0.1372 0.1372 1 7.98 0.1076 0.7513796 172s Homesize:sens1 0.4275 0.4275 1 1217.00 0.3352 0.5627339 172s sens2:Homesize:sens1 1.3512 1.3512 1 1216.99 1.0595 0.3035426 172s --- 172s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 172s > (ant3 <- anova(fm, type=3)) 172s Type III Analysis of Variance Table with Satterthwaite's method 172s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 172s sens2 21.5710 21.5710 1 8.02 16.9130 0.0033602 ** 172s Homesize 17.8570 17.8570 1 1217.01 14.0010 0.0001912 *** 172s sens1 0.6136 0.6136 1 8.03 0.4811 0.5074890 172s sens2:Homesize 1.5068 1.5068 1 1216.99 1.1814 0.2772780 172s sens2:sens1 0.0946 0.0946 1 8.02 0.0742 0.7922017 172s Homesize:sens1 0.4275 0.4275 1 1217.00 0.3352 0.5627339 172s sens2:Homesize:sens1 1.3512 1.3512 1 1216.99 1.0595 0.3035426 172s --- 172s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 172s > 172s > stopifnot( 172s + isTRUE(all.equal(ant2[,"F value"], 172s + c(16.4842, 14.0010, .526076, 1.18144, 172s + .107570, .335177, 1.05946), tolerance = TOL)), 172s + isTRUE(all.equal(ant3[,"F value"], 172s + c(16.9140, 14.0010,.481148, 1.18144, 172s + .074201, .335177, 1.05946), tolerance = TOL)) 172s + ) 172s > 172s > ################################################################################ 172s > 172s > 172s > 172s BEGIN TEST test_contest1D.R 172s 172s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 172s Copyright (C) 2025 The R Foundation for Statistical Computing 172s Platform: x86_64-pc-linux-gnu 172s 172s R is free software and comes with ABSOLUTELY NO WARRANTY. 172s You are welcome to redistribute it under certain conditions. 172s Type 'license()' or 'licence()' for distribution details. 172s 172s R is a collaborative project with many contributors. 172s Type 'contributors()' for more information and 172s 'citation()' on how to cite R or R packages in publications. 172s 172s Type 'demo()' for some demos, 'help()' for on-line help, or 172s 'help.start()' for an HTML browser interface to help. 172s Type 'q()' to quit R. 172s 172s > # test_contest1D.R 172s > library(lmerTest) 172s Loading required package: lme4 172s Loading required package: Matrix 173s 173s Attaching package: 'lmerTest' 173s 173s The following object is masked from 'package:lme4': 173s 173s lmer 173s 173s > 173s > # WRE says "using if(requireNamespace("pkgname")) is preferred, if possible." 173s > # even in tests: 173s > assertError <- function(expr, ...) 173s + if(requireNamespace("tools")) tools::assertError(expr, ...) else invisible() 173s > assertWarning <- function(expr, ...) 173s + if(requireNamespace("tools")) tools::assertWarning(expr, ...) else invisible() 173s > 173s > TOL <- 1e-4 173s The following object is masked from 'package:stats': 173s 173s step 173s 173s > # Kenward-Roger only available with pbkrtest and only then validated in R >= 3.3.3 173s > # (faulty results for R < 3.3.3 may be due to unstated dependencies in pbkrtest) 173s > has_pbkrtest <- requireNamespace("pbkrtest", quietly = TRUE) && getRversion() >= "3.3.3" 173s > 173s > data("sleepstudy", package="lme4") 173s > 173s > #################################### 173s > ## Tests of contest1D 173s > #################################### 173s > 173s > fm <- lmer(Reaction ~ Days + I(Days^2) + (1|Subject) + (0+Days|Subject), 173s + sleepstudy) 173s > # Basic tests: 173s > L <- c(0, 1, 0) 173s > contest1D(fm, L) 173s Estimate Std. Error df t value Pr(>|t|) 173s 1 7.434085 2.824283 114.9943 2.632203 0.00964808 173s > contest1D(fm, L, confint = TRUE) 173s Estimate Std. Error df t value lower upper Pr(>|t|) 173s 1 7.434085 2.824283 114.9943 2.632203 1.839722 13.02845 0.00964808 173s > contest1D(fm, L, confint = TRUE, level=0.99) 173s Estimate Std. Error df t value lower upper Pr(>|t|) 173s 1 7.434085 2.824283 114.9943 2.632203 0.03655396 14.83162 0.00964808 173s > if(has_pbkrtest) 173s + contest1D(fm, L, ddf="Kenward-Roger") 173s Estimate Std. Error df t value Pr(>|t|) 173s 1 7.434085 2.824283 115.5148 2.632203 0.009642692 173s > 173s > # Test too long L 173s > assertError(contest1D(fm, c(0, 1, 1, 1))) 173s > 173s > # Test too short L 173s > assertError(contest1D(fm, c(0, 1))) 173s > 173s > # Test matrix L 173s > contest1D(fm, matrix(L, nrow=1)) 173s Estimate Std. Error df t value Pr(>|t|) 173s 1 7.434085 2.824283 114.9943 2.632203 0.00964808 173s > contest1D(fm, matrix(L, ncol=1)) 173s Estimate Std. Error df t value Pr(>|t|) 173s 1 7.434085 2.824283 114.9943 2.632203 0.00964808 173s > assertError(contest1D(fm, matrix(c(0, 1), ncol=1))) 173s > assertError(contest1D(fm, matrix(c(0, 1, 0, 0), nrow=1))) 173s > L <- matrix(numeric(0L), ncol=3) 173s > assertError(contest1D(fm, L)) # "empty" matrix 173s > assertError(contest1D(fm, matrix(1, ncol=3, nrow=2))) 173s > 173s > # Test list L 173s > assertError(contest1D(fm, list(c(0, 1, 0)))) 173s > 173s > # Test equivalence to coef(summary(fm)): 173s > Lmat <- diag(length(fixef(fm))) 173s > (coef_mat <- lmerTest:::rbindall(lapply(1:ncol(Lmat), function(i) 173s + contest1D(fm, Lmat[i, ])))) 173s Estimate Std. Error df t value Pr(>|t|) 173s 1 255.4493728 7.5663677 26.22939 33.761163 3.810057e-23 173s 2 7.4340850 2.8242827 114.99433 2.632203 9.648080e-03 173s 3 0.3370223 0.2616475 144.63110 1.288078 1.997759e-01 173s > (coef_mat_lme4 <- coef(summary(fm, ddf="lme4"))) 173s Estimate Std. Error t value 173s (Intercept) 255.4493728 7.5663677 33.761163 173s Days 7.4340850 2.8242827 2.632203 173s I(Days^2) 0.3370223 0.2616475 1.288078 173s > rownames(coef_mat) <- rownames(coef_mat_lme4) 173s > stopifnot(isTRUE( 173s + all.equal(as.data.frame(coef_mat_lme4), 173s + coef_mat[, c("Estimate", "Std. Error", "t value")], tolerance=TOL) 173s + )) 173s > 173s > if(has_pbkrtest) { 173s + (coef_mat_KR <- lmerTest:::rbindall(lapply(1:ncol(Lmat), function(i) 173s + contest1D(fm, Lmat[i, ], ddf="Kenward-Roger")))) 173s + rownames(coef_mat_KR) <- rownames(coef_mat_lme4) 173s + stopifnot(isTRUE( 173s + all.equal(as.data.frame(coef_mat_lme4), 173s + coef_mat_KR[, c("Estimate", "Std. Error", "t value")], tolerance=TOL) 173s + )) 173s + } 173s > # Test of 0-length beta 173s > fm1 <- lmer(Reaction ~ 0 + (1|Subject) + (0+Days|Subject), 173s + sleepstudy) 173s > stopifnot(length(fixef(fm1)) == 0L) 173s > if(has_pbkrtest) { 173s + (ans <- contest1D(fm1, numeric(0L), ddf="Kenward-Roger")) 173s + stopifnot(nrow(ans) == 0L) 173s + } 173s > 173s > ## Test rhs argument: 173s > fm <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy) 173s > contest1D(fm, L=cbind(0, 1)) 173s Estimate Std. Error df t value Pr(>|t|) 173s 1 10.46729 1.54579 16.99998 6.771481 3.263824e-06 173s > contest1D(fm, L=cbind(0, 1), rhs=10) 173s Estimate Std. Error df t value Pr(>|t|) 173s 1 10.46729 1.54579 16.99998 0.302296 0.7660937 173s > if(has_pbkrtest) { 173s + contest1D(fm, L=cbind(0, 1), ddf="Kenward-Roger") 173s + contest1D(fm, L=cbind(0, 1), ddf="Kenward-Roger", rhs=10) 173s + } 173s Estimate Std. Error df t value Pr(>|t|) 173s 1 10.46729 1.54579 17 0.302296 0.7660937 173s > 173s > contest1D(fm, L=c(0, 1), rhs = 10.467) 173s Estimate Std. Error df t value Pr(>|t|) 173s 1 10.46729 1.54579 16.99998 0.0001849926 0.9998546 173s > 173s > (ct1 <- contest1D(fm, L=cbind(c(0, 1)), rhs = 10)) 173s Estimate Std. Error df t value Pr(>|t|) 173s 1 10.46729 1.54579 16.99998 0.302296 0.7660937 173s > (ct2 <- contestMD(fm, L=rbind(c(0, 1)), rhs = 10)) 173s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 173s 1 59.85028 59.85028 1 16.99998 0.09138285 0.7660937 173s > stopifnot( 173s + isTRUE(all.equal(ct1[, "t value"]^2, ct2[, "F value"], tolerance=1e-6)) 173s + ) 173s > 173s > ## Test 'lmerMod' method: 173s > fm <- lme4::lmer(Reaction ~ Days + I(Days^2) + (1|Subject) + (0+Days|Subject), 173s + sleepstudy) 174s > # Basic tests: 174s > L <- c(0, 1, 0) 174s > contest1D(fm, L) 174s Estimate Std. Error df t value Pr(>|t|) 174s 1 7.434085 2.824283 114.9943 2.632203 0.00964808 174s > contest1D(fm, L, confint = TRUE) 174s Estimate Std. Error df t value lower upper Pr(>|t|) 174s 1 7.434085 2.824283 114.9943 2.632203 1.839722 13.02845 0.00964808 174s > contest1D(fm, L, confint = TRUE, level=0.99) 174s Estimate Std. Error df t value lower upper Pr(>|t|) 174s 1 7.434085 2.824283 114.9943 2.632203 0.03655396 14.83162 0.00964808 174s > if(has_pbkrtest) 174s + contest1D(fm, L, ddf="Kenward-Roger") 174s Estimate Std. Error df t value Pr(>|t|) 174s 1 7.434085 2.824283 115.5148 2.632203 0.009642692 174s > 174s > 174s BEGIN TEST test_contestMD.R 174s 174s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 174s Copyright (C) 2025 The R Foundation for Statistical Computing 174s Platform: x86_64-pc-linux-gnu 174s 174s R is free software and comes with ABSOLUTELY NO WARRANTY. 174s You are welcome to redistribute it under certain conditions. 174s Type 'license()' or 'licence()' for distribution details. 174s 174s R is a collaborative project with many contributors. 174s Type 'contributors()' for more information and 174s 'citation()' on how to cite R or R packages in publications. 174s 174s Type 'demo()' for some demos, 'help()' for on-line help, or 174s 'help.start()' for an HTML browser interface to help. 174s Type 'q()' to quit R. 174s 174s > # test_contestMD.R 174s > library(lmerTest) 174s Loading required package: lme4 174s Loading required package: Matrix 175s 175s Attaching package: 'lmerTest' 175s 175s The following object is masked from 'package:lme4': 175s 175s lmer 175s 175s The following object is masked from 'package:stats': 175s 175s step 175s 175s > 175s > # WRE says "using if(requireNamespace("pkgname")) is preferred, if possible." 175s > # even in tests: 175s > assertError <- function(expr, ...) 175s + if(requireNamespace("tools")) tools::assertError(expr, ...) else invisible() 175s > assertWarning <- function(expr, ...) 175s + if(requireNamespace("tools")) tools::assertWarning(expr, ...) else invisible() 175s > 175s > # Kenward-Roger only available with pbkrtest and only then validated in R >= 3.3.3 175s > # (faulty results for R < 3.3.3 may be due to unstated dependencies in pbkrtest) 175s > has_pbkrtest <- requireNamespace("pbkrtest", quietly = TRUE) && getRversion() >= "3.3.3" 175s > 175s > data("sleepstudy", package="lme4") 175s > 175s > #################################### 175s > ## Tests of contestMD 175s > #################################### 175s > 175s > fm <- lmer(Reaction ~ Days + I(Days^2) + (1|Subject) + (0+Days|Subject), 175s + sleepstudy) 175s > # Basic tests: 175s > L <- diag(3L) 175s > contestMD(fm, L) 175s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 175s 1 990089.3 330029.8 3 42.15441 507.24 4.351211e-33 175s > 175s > # Tests of ddf arg: 175s > contestMD(fm, L, ddf="Sat") 175s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 175s 1 990089.3 330029.8 3 42.15441 507.24 4.351211e-33 175s > if(has_pbkrtest) 175s + contestMD(fm, L, ddf="Kenward-Roger") 175s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 175s 1 990089.3 330029.8 3 38.84733 490.1937 6.706733e-31 175s > assertError(contestMD(fm, L, ddf="sat")) # Invalid ddf arg. 175s > 175s > # Tests of simple 2-df test: 175s > (ans <- contestMD(fm, L[2:3, ], ddf="Sat")) 175s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 175s 1 30399.15 15199.57 2 54.40752 23.36102 4.744897e-08 175s > stopifnot(nrow(ans) == 1L, 175s + ans$NumDF == 2L) 175s > if(has_pbkrtest) { 175s + (ans <- contestMD(fm, L[2:3, ], ddf="Kenward-Roger")) 175s + stopifnot(nrow(ans) == 1L, 175s + ans$NumDF == 2L) 175s + } 175s > 175s > # Tests of simple 1-df test: 175s > (ans <- contestMD(fm, L[3, , drop=FALSE], ddf="Sat")) 175s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 175s 1 1079.503 1079.503 1 144.6311 1.659144 0.1997759 175s > stopifnot(nrow(ans) == 1L, 175s + ans$NumDF == 1L) 175s > if(has_pbkrtest) { 175s + (ans <- contestMD(fm, L[3, , drop=FALSE], ddf="Kenward-Roger")) 175s + stopifnot(nrow(ans) == 1L, 175s + ans$NumDF == 1L) 175s + } 175s > 175s > # Test of vector input: 175s > (ans <- contestMD(fm, L[3, ], ddf="Sat")) # OK since length(L[3, ]) == length(fixef(fm)) 175s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 175s 1 1079.503 1079.503 1 144.6311 1.659144 0.1997759 175s > stopifnot(nrow(ans) == 1L, 175s + ans$NumDF == 1L) 175s > assertError(contestMD(fm, c(1, 0))) # L is too short 175s > assertError(contestMD(fm, c(1, 0, 1, 1))) # L is too long 175s > 175s > # Test of list input: 175s > assertError(contestMD(fm, list(L[3, , drop=FALSE]), ddf="Sat")) # Need L to be a matrix 175s > 175s > # zero-row L's are allowed (if ncol(L) is correct): 175s > ans1 <- contestMD(fm, L[0, , drop=FALSE], ddf="Sat") 175s > stopifnot(nrow(ans1) == 0L) 175s > if(has_pbkrtest) { 175s + ans2 <- contestMD(fm, L[0, , drop=FALSE], ddf="Kenward-Roger") 175s + stopifnot(nrow(ans2) == 0L) 175s + } 175s > 175s > # Test wrong ncol(L): 175s > assertError(contestMD(fm, L[2:3, 2:3])) # need ncol(L) == length(fixef(fm)) 175s > 175s > # row-rank deficient L are allowed: 175s > L <- rbind(c(1, 0, 1), 175s + c(0, 1, 0), 175s + c(1, -1, 1)) 175s > ans <- contestMD(fm, L) 175s > stopifnot(nrow(L) == 3L, 175s + qr(L)$rank == 2, 175s + ans$NumDF == 2) 175s > if(has_pbkrtest) { 175s + ans_KR <- contestMD(fm, L, ddf="Kenward-Roger") 175s + stopifnot(ans_KR$NumDF == 2) 175s + } 175s > 175s > # Test of 0-length beta 175s > fm1 <- lmer(Reaction ~ 0 + (1|Subject) + (0+Days|Subject), 175s + sleepstudy) 175s > stopifnot(length(fixef(fm1)) == 0L) 175s > L <- numeric(0L) 175s > (ans <- contestMD(fm1, L)) 175s [1] Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 175s <0 rows> (or 0-length row.names) 175s > stopifnot(nrow(ans) == 0L) 175s > L <- matrix(numeric(0L), ncol=0L) 175s > (ans <- contestMD(fm1, L)) 175s [1] Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 175s <0 rows> (or 0-length row.names) 175s > stopifnot(nrow(ans) == 0L) 175s > 175s > 175s > ## rhs argument: 175s > data("cake", package="lme4") 175s > model <- lmer(angle ~ recipe * temp + (1|recipe:replicate), cake) 175s > (L <- diag(length(fixef(model)))[2:3, ]) 175s [,1] [,2] [,3] [,4] [,5] [,6] 175s [1,] 0 1 0 0 0 0 175s [2,] 0 0 1 0 0 0 175s > (an <- anova(model, type="marginal")) 175s Marginal Analysis of Variance Table with Satterthwaite's method 175s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 175s recipe 4.00 2.00 2 254.02 0.0957 0.9088 175s temp 620.24 620.24 1 222.00 29.6961 1.339e-07 *** 175s recipe:temp 1.74 0.87 2 222.00 0.0417 0.9592 175s --- 175s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 175s > 175s > ct <- contestMD(model, L, rhs = 0) 175s > ct2 <- contestMD(model, L, rhs = c(2, 2)) 175s > stopifnot( 175s + isTRUE(all.equal(ct[1, ], an[1, ], check.attributes=FALSE, tolerance=1e-6)), 175s + ct[, "F value"] < ct2[, "F value"] 175s + ) 175s > 175s > L2 <- rbind(L, L[1, ] + L[2, ]) # rank deficient! 175s > contestMD(model, L2, rhs = c(0, 0, 0)) # no warning 175s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 175s 1 3.996684 1.998342 2 254.0158 0.09567796 0.9087894 175s > assertWarning(contestMD(model, L2, rhs = c(2, 2, 2))) # warning since L2 is rank def. 175s > if(has_pbkrtest) 175s + assertWarning(contestMD(model, L2, rhs = c(2, 2, 2), ddf="Kenward-Roger")) 175s > 175s > fm <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy) 175s > contestMD(fm, L=cbind(0, 1)) 175s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 175s 1 30030.94 30030.94 1 16.99998 45.85296 3.263824e-06 175s > contestMD(fm, L=cbind(0, 1), rhs=10) 175s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 175s 1 59.85028 59.85028 1 16.99998 0.09138285 0.7660937 175s > if(has_pbkrtest) { 175s + contestMD(fm, L=cbind(0, 1), ddf="Kenward-Roger") 175s + contestMD(fm, L=cbind(0, 1), ddf="Kenward-Roger", rhs=10) 175s + } 176s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 176s 1 59.85028 59.85028 1 17 0.09138285 0.7660937 176s > 176s > 176s > ## Test 'lmerMod' method: 176s > fm <- lme4::lmer(Reaction ~ Days + (Days|Subject), sleepstudy) 176s > contestMD(fm, L=cbind(0, 1)) 176s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 176s 1 30030.94 30030.94 1 16.99998 45.85296 3.263824e-06 176s > contestMD(fm, L=cbind(0, 1), rhs=10) 176s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 176s 1 59.85028 59.85028 1 16.99998 0.09138285 0.7660937 176s > if(has_pbkrtest) { 176s + contestMD(fm, L=cbind(0, 1), ddf="Kenward-Roger") 176s + contestMD(fm, L=cbind(0, 1), ddf="Kenward-Roger", rhs=10) 176s + } 176s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 176s 1 59.85028 59.85028 1 17 0.09138285 0.7660937 176s > 176s BEGIN TEST test_contrast_utils.R 176s 176s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 176s Copyright (C) 2025 The R Foundation for Statistical Computing 176s Platform: x86_64-pc-linux-gnu 176s 176s R is free software and comes with ABSOLUTELY NO WARRANTY. 176s You are welcome to redistribute it under certain conditions. 176s Type 'license()' or 'licence()' for distribution details. 176s 176s R is a collaborative project with many contributors. 176s Type 'contributors()' for more information and 176s 'citation()' on how to cite R or R packages in publications. 176s 176s Type 'demo()' for some demos, 'help()' for on-line help, or 176s 'help.start()' for an HTML browser interface to help. 176s Type 'q()' to quit R. 176s 176s > # test_contrast_utils.R 176s > 176s > library(lmerTest) 176s Loading required package: lme4 176s Loading required package: Matrix 177s > 177s > ########## 177s > # Test that a message is printed if some cells have zero data: 177s > # Missing a single cell: 177s > data("cake", package="lme4") 177s > cake4 <- cake 177s > cake4$temperature <- factor(cake4$temperature, ordered=FALSE) 177s > cake4 <- droplevels(subset(cake4, !(recipe == "A" & temperature == "175") )) 177s > with(cake4, table(recipe, temperature)) 177s temperature 177s recipe 175 185 195 205 215 225 177s A 0 15 15 15 15 15 177s B 15 15 15 15 15 15 177s C 15 15 15 15 15 15 177s > 177s > fm1 <- lmer(angle ~ recipe * temperature + (1|recipe:replicate), cake4) 177s 177s Attaching package: 'lmerTest' 177s 177s The following object is masked from 'package:lme4': 177s 177s lmer 177s 177s The following object is masked from 'package:stats': 177s 177s step 177s 177s fixed-effect model matrix is rank deficient so dropping 1 column / coefficient 177s > an <- anova(fm1) 177s Missing cells for: recipeA:temperature175. 177s Interpret type III hypotheses with care. 177s > txt <- capture.output(an <- anova(fm1), type = "message") 177s > stopifnot(length(grep("Missing cells for:", txt)) > 0, 177s + length(grep("Interpret type III hypotheses with care.", txt)) > 0) 177s > 177s > ########## 177s > # Test that a message is printed if some cells have zero data: 177s > # Missing diagonal: 177s > cake4 <- cake 177s > cake4$temperature <- factor(cake4$temperature, ordered=FALSE) 177s > cake4 <- droplevels(subset(cake4, temperature %in% levels(cake4$temperature)[1:3])) 177s > cake4 <- droplevels(subset(cake4, !((recipe == "A" & temperature == "175") | 177s + (recipe == "B" & temperature == "185") | 177s + (recipe == "C" & temperature == "195") ))) 177s > cake4$temp0 <- cake4$temp - mean(cake4$temp) 177s > with(cake4, table(recipe, temperature)) 177s temperature 177s recipe 175 185 195 177s A 0 15 15 177s B 15 0 15 177s C 15 15 0 177s > 177s > fm1 <- lmer(angle ~ recipe * temperature + (1|recipe:replicate), cake4) 177s fixed-effect model matrix is rank deficient so dropping 3 columns / coefficients 177s > an <- anova(fm1) 177s Missing cells for: recipeA:temperature175, recipeB:temperature185, recipeC:temperature195. 177s Interpret type III hypotheses with care. 177s > txt <- capture.output(an <- anova(fm1), type = "message") 177s > stopifnot(length(grep("Missing cells for:", txt)) > 0, 177s + length(grep("Interpret type III hypotheses with care.", txt)) > 0) 177s > 177s > ########## 177s > # Test that a message is NOT printed with centered covariates: 177s > fm1 <- lmer(angle ~ recipe * temp0 + (1|recipe:replicate), cake4) 177s > an <- anova(fm1) 177s > txt <- capture.output(an <- anova(fm1), type = "message") 177s > stopifnot(length(grep("Missing cells for:", txt)) == 0, 177s + length(grep("Interpret type III hypotheses with care.", txt)) == 0) 177s > # Note: in many cases a message would not be printed anyway because the 177s > # columns sums in the rdX design matrix would not be exactly zero but just a 177s > # small number very close to zero. 177s > 177s > 177s > 177s > 177s BEGIN TEST test_devfun_vp.R 177s 177s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 177s Copyright (C) 2025 The R Foundation for Statistical Computing 177s Platform: x86_64-pc-linux-gnu 177s 177s R is free software and comes with ABSOLUTELY NO WARRANTY. 177s You are welcome to redistribute it under certain conditions. 177s Type 'license()' or 'licence()' for distribution details. 177s 177s R is a collaborative project with many contributors. 177s Type 'contributors()' for more information and 177s 'citation()' on how to cite R or R packages in publications. 177s 177s Type 'demo()' for some demos, 'help()' for on-line help, or 177s 'help.start()' for an HTML browser interface to help. 177s Type 'q()' to quit R. 177s 177s Loading required package: lme4 177s Loading required package: Matrix 177s > # test_devfun_vp.R 177s > 177s > # library(devtools) 177s > # # has_devel() 177s > # r2path <- "~/GitHub/lmerTestR/lmerTest" 177s > # # document(pkg=r2path) 177s > # load_all(r2path) 177s > # 177s > # # ?`Covariance-class` 177s > 177s > library(lmerTest) 178s 178s Attaching package: 'lmerTest' 178s 178s The following object is masked from 'package:lme4': 178s 178s lmer 178s 178s The following object is masked from 'package:stats': 178s 178s step 178s 178s > 178s > has_pkgs <- requireNamespace("utils", quietly = TRUE) && 178s + requireNamespace("numDeriv", quietly = TRUE) && 178s + requireNamespace("lme4", quietly = TRUE) 178s > is_lme4_2_0_0 <- utils::packageVersion("lme4") >= "2.0.0" 178s > 178s > if(has_pkgs && is_lme4_2_0_0) { 178s + ## Functions: 178s + devfun_vp <- lmerTest:::devfun_vp 178s + getOptPar <- lmerTest:::getOptPar 178s + getVarPar <- lmerTest:::getVarPar 178s + 178s + ## Unstructured 178s + fm1.us <- lme4::lmer(Reaction ~ Days + us(Days | Subject), sleepstudy) 178s + ## Diagional 178s + fm1.diag <- lme4::lmer(Reaction ~ Days + diag(Days | Subject), sleepstudy) 178s + fm1.diag.hom <- lme4::lmer(Reaction ~ Days + diag(Days | Subject, hom = TRUE), 178s + sleepstudy) 178s + ## Compound symmetry 178s + fm1.cs <- lme4::lmer(Reaction ~ Days + cs(Days | Subject), sleepstudy) 178s + fm1.cs.hom <- lme4::lmer(Reaction ~ Days + cs(Days | Subject, hom = TRUE), 178s + sleepstudy) 178s + ## Auto-regressive order 1 178s + sleepstudy$Daysf <- factor(sleepstudy$Days, ordered = TRUE) 178s + fm1.ar1 <- lme4::lmer(Reaction ~ Daysf + ar1(0 + Daysf | Subject, hom = TRUE), 178s + sleepstudy, REML = TRUE) 178s + 178s + lme4models <- namedList(fm1.us, 178s + fm1.diag, 178s + fm1.diag.hom, 178s + fm1.cs, 178s + fm1.cs.hom, 178s + fm1.ar1) 178s + 178s + for(model in lme4models) { # model <- lme4models[[1]] 178s + ## Native devfun: 178s + devfun <- update(model, devFunOnly=TRUE) 178s + ## Evaluate native devfun at optimum: 178s + devfun(getOptPar(model)) 178s + ## Check that devfun returns the same value as that saved in the model object: 178s + stopifnot( 178s + all.equal(unname(getME(model, "devcomp")$cmp["REML"]), 178s + devfun(getOptPar(model)), tolerance=1e-6) # TRUE 178s + ) 178s + ## Get varpar (including residual SD): 178s + (varpar <- getVarPar(model)) 178s + ## Evaluate devfun_vp at the optimum: 178s + devfun_vp(varpar, devfun, reml=TRUE) 178s + ## Check that devfun_vp returns the same value as native devfun: 178s + stopifnot( 178s + all.equal(unname(getME(model, "devcomp")$cmp["REML"]), 178s + devfun(getOptPar(model))) # TRUE 178s + ) 178s + } 178s + 178s + ## Here we also want to check that devfun and and devfun_vp returns the same 178s + ## value at non-optimum values of varpar. 178s + ## Because sigma is profiled out of devfun this cannot be done right away. 178s + ## We need to optimize over all parameters to get equivalence. 178s + ## We should be able to set one of the parameters in common to a 178s + ## particular value and optimize the rest. This will build confidence that 178s + ## the likelihood in devfun_vp is the same as that returned by 178s + ## lme4::lmer(., devFunOnly=TRUE). 178s + 178s + do_trace <- 0 178s + for(i in seq_along(lme4models)) { # i <- 4 178s + if(do_trace) print(i) 178s + model <- lme4models[[i]] 178s + devfun <- update(model, devFunOnly=TRUE) 178s + (optpar <- getOptPar(model)) 178s + (varpar <- getVarPar(model)) 178s + (optpar2 <- optpar * 1.1) 178s + (varpar2 <- c(optpar2, varpar[length(varpar)])) 178s + 178s + ## Evaluate gradients to ensure that devfun and devfun_vp are both 178s + ## functions with optima at optpar and varpar respectively: 178s + (g_devfun <- numDeriv::grad(devfun, optpar)) 178s + (g_devfun_vp <- numDeriv::grad(devfun_vp, varpar, devfun=devfun, reml=TRUE)) 178s + stopifnot( 178s + if(i != 4) all(abs(g_devfun) < 1e-3) else all(abs(g_devfun) < 1e-2), 178s + if(i != 4) all(abs(g_devfun_vp) < 1e-3) else all(abs(g_devfun_vp) < 1e-2) 178s + ) 178s + ## These are not zero as expected: 178s + (g_devfun <- numDeriv::grad(devfun, optpar2)) 178s + (g_devfun_vp <- numDeriv::grad(devfun_vp, varpar2, devfun=devfun, reml=TRUE)) 178s + ## Try optimizing devfun_vp: 178s + x <- nlminb(start=varpar2, objective = devfun_vp, devfun=devfun, reml=TRUE, 178s + control=list(trace=do_trace)) 178s + ## Check that the optimum is re-achieved: 178s + stopifnot( 178s + all(abs(varpar - x$par) < 1e-4), 178s + abs(devfun_vp(varpar, devfun=devfun, reml=TRUE) - 178s + devfun_vp(x$par, devfun=devfun, reml=TRUE)) < 1e-6 178s + ) 178s + 178s + ## Optimize devfun and devfun_vp over all but one of the parameters in turn to 178s + ## check that devfun and devfun_vp gives the same deviance and parameter values 178s + ## for settings away from the REML optimum. This is to build confidence that 178s + ## devfun_vp is a valid implementation of the deviance function from LLMs. 178s + if(length(optpar) > 1) for(j in seq_along(optpar)) { # j <- 1 178s + ## Check that all parameters are within bounds: 178s + stopifnot( 178s + model@lower < optpar, 178s + optpar < attr(model, "upper"), 178s + model@lower < optpar2, 178s + optpar2 < attr(model, "upper") 178s + ) 178s + ## Evaluate deviance function at optimum (for safety): 178s + devfun(optpar) 178s + ## Optimize devfun over all but the j'th parameter: 178s + (startpar <- optpar[-j]) 178s + res <- nlminb(start=startpar, objective = function(p) { 178s + (Par <- optpar2) 178s + (Par[-j] <- p) 178s + devfun(Par) 178s + }, control = list(trace=do_trace), 178s + lower = model@lower[-j], 178s + upper = attr(model, "upper")[-j]) 178s + ## Evaluate devfun_vp: 178s + devfun_vp(varpar, devfun=devfun, reml=TRUE) 178s + ## Optimize devfun_vp over all but the j'th parameter: 178s + (startpar_vp <- varpar[-j]) 178s + (np <- length(startpar_vp)) 178s + res_vp <- nlminb(start=startpar_vp, objective = function(p) { 178s + (Par <- optpar2) 178s + (Par[-j] <- p[-np]) 178s + Par <- c(Par, p[np]) 178s + devfun_vp(Par, devfun=devfun, reml=TRUE) 178s + }, control = list(trace=do_trace), 178s + lower = c(model@lower[-j], 0), 178s + upper = c(attr(model, "upper")[-j], Inf)) 178s + ## Compare parameter estimates (except for sigma): 178s + res$objective - res_vp$objective 178s + res$par - res_vp$par[seq_along(res$par)] 178s + ## Check that parameter estimates and deviance values agree: 178s + stopifnot( 178s + abs(res$objective - res_vp$objective) < 1e-8, 178s + all(abs(res$par - res_vp$par[seq_along(res$par)]) < 1e-4) 178s + ) 178s + } 178s + } 178s + 178s + } 178s > 178s > 178s > 178s BEGIN TEST test_drop1.R 178s 178s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 178s Copyright (C) 2025 The R Foundation for Statistical Computing 178s Platform: x86_64-pc-linux-gnu 178s 178s R is free software and comes with ABSOLUTELY NO WARRANTY. 178s You are welcome to redistribute it under certain conditions. 178s Type 'license()' or 'licence()' for distribution details. 178s 178s R is a collaborative project with many contributors. 178s Type 'contributors()' for more information and 178s 'citation()' on how to cite R or R packages in publications. 178s 178s Type 'demo()' for some demos, 'help()' for on-line help, or 178s 'help.start()' for an HTML browser interface to help. 178s Type 'q()' to quit R. 178s 178s > # test_drop1.R 178s > 178s > library(lmerTest) 178s Loading required package: lme4 178s Loading required package: Matrix 180s 180s Attaching package: 'lmerTest' 180s 180s The following object is masked from 'package:lme4': 180s 180s lmer 180s 180s The following object is masked from 'package:stats': 180s 180s step 180s 180s > 180s > # WRE says "using if(requireNamespace("pkgname")) is preferred, if possible." 180s > # even in tests: 180s > assertError <- function(expr, ...) 180s + if(requireNamespace("tools")) tools::assertError(expr, ...) else invisible() 180s > assertWarning <- function(expr, ...) 180s + if(requireNamespace("tools")) tools::assertWarning(expr, ...) else invisible() 180s > 180s > TOL <- 1e-4 180s > # Kenward-Roger only available with pbkrtest and only then validated in R >= 3.3.3 180s > # (faulty results for R < 3.3.3 may be due to unstated dependencies in pbkrtest) 180s > has_pbkrtest <- requireNamespace("pbkrtest", quietly = TRUE) && getRversion() >= "3.3.3" 180s > 180s > data("sleepstudy", package="lme4") 180s > 180s > ######### Basic usage 180s > 180s > data("cake", package="lme4") 180s > cake2 <- cake 180s > cake2$temperature <- factor(cake2$temperature, ordered = FALSE) 180s > fm <- lmer(angle ~ recipe + temperature + (1|recipe:replicate), cake2) 180s > (an1 <- drop1(fm)) 180s Single term deletions using Satterthwaite's method: 180s 180s Model: 180s angle ~ recipe + temperature + (1 | recipe:replicate) 180s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 180s recipe 10.19 5.09 2 42 0.2488 0.7809 180s temperature 2100.30 420.06 5 220 20.5141 <2e-16 *** 180s --- 180s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 180s > (an2 <- drop1(fm, force_get_contrasts = TRUE)) 180s Single term deletions using Satterthwaite's method: 180s 180s Model: 180s angle ~ recipe + temperature + (1 | recipe:replicate) 180s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 180s recipe 10.19 5.09 2 42 0.2488 0.7809 180s temperature 2100.30 420.06 5 220 20.5141 <2e-16 *** 180s --- 180s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 180s > drop1(fm, ddf="lme4", test="Chi") 180s Single term deletions 180s 180s Model: 180s angle ~ recipe + temperature + (1 | recipe:replicate) 180s npar AIC LRT Pr(Chi) 180s 1709.6 180s recipe 2 1706.1 0.530 0.7672 180s temperature 5 1785.7 86.106 <2e-16 *** 180s --- 180s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 180s > if(has_pbkrtest) 180s + drop1(fm, ddf="Kenward-Roger") 180s Single term deletions using Kenward-Roger's method: 180s 180s Model: 180s angle ~ recipe + temperature + (1 | recipe:replicate) 180s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 180s recipe 10.19 5.09 2 42 0.2488 0.7809 180s temperature 2100.30 420.06 5 220 20.5141 <2e-16 *** 180s --- 180s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 180s > 180s > tests1 <- show_tests(an1) 180s > tests2 <- show_tests(an2) 180s > 180s > stopifnot( 180s + # Tests are the same: 180s + isTRUE(all.equal(an1, an2, check.attributes = FALSE, tolerance=TOL)), 180s + # But contrast matrices are not: 180s + all(!mapply(function(x, y) isTRUE(all.equal(x, y)), tests1, tests2)) 180s + ) 180s > 180s > fm <- lmer(angle ~ recipe * temperature + (1|recipe:replicate), cake2) 180s > drop1(fm) 180s Single term deletions using Satterthwaite's method: 180s 180s Model: 180s angle ~ recipe * temperature + (1 | recipe:replicate) 180s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 180s recipe:temperature 205.98 20.598 10 210 1.0062 0.4393 180s > drop1(fm, ddf="lme4") 180s Single term deletions 180s 180s Model: 180s angle ~ recipe * temperature + (1 | recipe:replicate) 180s npar AIC 180s 1719.0 180s recipe:temperature 10 1709.6 180s > if(has_pbkrtest) 180s + drop1(fm, ddf="Kenward-Roger") 180s Single term deletions using Kenward-Roger's method: 180s 180s Model: 180s angle ~ recipe * temperature + (1 | recipe:replicate) 180s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 180s recipe:temperature 205.98 20.598 10 210 1.0062 0.4393 180s > 180s > # Incorrect arguments: 180s > assertError(drop1(fm, scope="recipe")) # Correct Error 180s > assertError(drop1(fm, scope=3)) # Correct Error 180s > assertError(drop1(fm, scope=list("recipe"))) # Correct Error 180s > 180s > # Polynomial terms: 180s > 180s > fm <- lmer(Reaction ~ 0 + (Days|Subject), sleepstudy) 180s > (an0 <- drop1(fm)) # No fixef! 180s Single term deletions using Satterthwaite's method: 180s 180s Model: 180s Reaction ~ 0 + (Days | Subject) 180s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 180s > fm <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy) 180s > (an1 <- drop1(fm)) 180s Single term deletions using Satterthwaite's method: 180s 180s Model: 180s Reaction ~ Days + (Days | Subject) 180s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 180s Days 30031 30031 1 17 45.853 3.264e-06 *** 180s --- 180s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 180s > fm <- lmer(Reaction ~ Days + I(Days^2) + (Days|Subject), sleepstudy) 180s > (an2 <- (drop1(fm))) 180s Single term deletions using Satterthwaite's method: 180s 180s Model: 180s Reaction ~ Days + I(Days^2) + (Days | Subject) 180s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 180s Days 4534.5 4534.5 1 114.43 6.9551 0.00952 ** 180s I(Days^2) 1079.5 1079.5 1 143.00 1.6558 0.20026 180s --- 180s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 180s > fm <- lmer(Reaction ~ poly(Days, 2) + (Days|Subject), sleepstudy) 180s > (an3 <- drop1(fm)) 180s Single term deletions using Satterthwaite's method: 180s 180s Model: 180s Reaction ~ poly(Days, 2) + (Days | Subject) 180s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 180s poly(Days, 2) 30974 15487 2 29.115 23.754 7.625e-07 *** 180s --- 180s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 180s > stopifnot( 180s + nrow(an0) == 0L, 180s + nrow(an1) == 1L, 180s + nrow(an2) == 2L, 180s + nrow(an3) == 1L 180s + ) 180s > 180s > # Consider a rank-deficient design matrix: 180s > fm <- lmer(angle ~ recipe + temp + temperature + (1|recipe:replicate), cake) 180s fixed-effect model matrix is rank deficient so dropping 1 column / coefficient 180s > # Here temp accounts for the linear effect of temperature, and 180s > # temperature is an (ordered) factor that accounts for the remaining 180s > # variation between temperatures (4 df). 180s > (an4 <- drop1(fm)) 180s Single term deletions using Satterthwaite's method: 180s 180s Model: 180s angle ~ recipe + temp + temperature + (1 | recipe:replicate) 180s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 180s recipe 10.189 5.094 2 42 0.2488 0.7809 180s temp 180s temperature 133.595 33.399 4 220 1.6311 0.1674 180s > # While temperature is in the model, we cannot test the effect of dropping 180s > # temp. After removing temperature we can test the effect of dropping temp: 180s > (an5 <- drop1(update(fm, ~.-temperature))) 180s Single term deletions using Satterthwaite's method: 180s 180s Model: 180s angle ~ recipe + temp + (1 | recipe:replicate) 180s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 180s recipe 10.3 5.15 2 42 0.2488 0.7809 180s temp 1966.7 1966.71 1 224 94.9759 <2e-16 *** 180s --- 180s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 180s > 180s > stopifnot( 180s + nrow(an4) == 3, 180s + rownames(an4)[2] == "temp", 180s + all(is.na(an4[2, ])), 180s + all(!is.na(an4[-2, ])), 180s + all(rownames(an5) == c("recipe", "temp")) 180s + ) 180s > 180s > 180s > 180s > 180s BEGIN TEST test_legacy.R 180s 180s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 180s Copyright (C) 2025 The R Foundation for Statistical Computing 180s Platform: x86_64-pc-linux-gnu 180s 180s R is free software and comes with ABSOLUTELY NO WARRANTY. 180s You are welcome to redistribute it under certain conditions. 180s Type 'license()' or 'licence()' for distribution details. 180s 180s R is a collaborative project with many contributors. 180s Type 'contributors()' for more information and 180s 'citation()' on how to cite R or R packages in publications. 180s 180s Type 'demo()' for some demos, 'help()' for on-line help, or 180s 'help.start()' for an HTML browser interface to help. 180s Type 'q()' to quit R. 180s 180s > # test_legacy.R 180s > library(lmerTest) 180s Loading required package: lme4 180s Loading required package: Matrix 182s 182s Attaching package: 'lmerTest' 182s 182s > TOL <- 1e-4 182s The following object is masked from 'package:lme4': 182s 182s lmer 182s 182s The following object is masked from 'package:stats': 182s 182s step 182s 182s > ##################################################################### 182s > 182s > # Read in data set 182s > load(system.file("testdata", "legacy_fits.RData", package="lmerTest")) 182s > # Generated with the following code using lmerTest version 2.0-37.9002 182s > # 182s > # library("lmerTest") 182s > # packageVersion("lmerTest") 182s > # fm1 <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy) 182s > # (an1 <- anova(fm1)) 182s > # (sfm1 <- summary(fm1)) 182s > # 182s > # fm2 <- lmer(Informed.liking ~ Product + Information + Gender + 182s > # (1|Product:Consumer) , data=ham) 182s > # (an2 <- anova(fm2)) 182s > # (sfm2 <- summary(fm2)) 182s > # 182s > # save(fm1, an1, sfm1, fm2, an2, sfm2, 182s > # file="~/GitHub/lmerTestR/package/inst/testdata/legacy_fits.RData") 182s > 182s > 182s > ####################################### 182s > ### Check that arguments for merModLmerTest and lmerModLmerTest methods match up: 182s > 182s > stopifnot( 182s + isTRUE(all.equal(formals(lmerTest:::anova.merModLmerTest), 182s + formals(lmerTest:::anova.lmerModLmerTest))), 182s + isTRUE(all.equal(formals(lmerTest:::summary.merModLmerTest), 182s + formals(lmerTest:::summary.lmerModLmerTest))), 182s + isTRUE(all.equal(formals(lmerTest:::drop1.merModLmerTest), 182s + formals(lmerTest:::drop1.lmerModLmerTest))), 182s + isTRUE(all.equal(formals(lmerTest:::step.merModLmerTest), 182s + formals(lmerTest:::step.lmerModLmerTest))), 182s + isTRUE(all.equal(formals(lmerTest:::ls_means.merModLmerTest), 182s + formals(lmerTest:::ls_means.lmerModLmerTest))), 182s + isTRUE(all.equal(formals(lmerTest:::difflsmeans.merModLmerTest), 182s + formals(lmerTest:::difflsmeans.lmerModLmerTest)))) 182s > 182s > 182s > ####################################### 182s > ## Tests for fm1: 182s > 182s > (an1new <- anova(fm1)) 182s Type III Analysis of Variance Table with Satterthwaite's method 182s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 182s Days 30031 30031 1 17 45.853 3.264e-06 *** 182s --- 182s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 182s > (sfm1new <- summary(fm1)) 182s Linear mixed model fit by REML. t-tests use Satterthwaite's method [ 182s lmerModLmerTest] 182s Formula: Reaction ~ Days + (Days | Subject) 182s Data: sleepstudy 182s 182s REML criterion at convergence: 1743.6 182s 182s Scaled residuals: 182s Min 1Q Median 3Q Max 182s -3.9536 -0.4634 0.0231 0.4634 5.1793 182s 182s Random effects: 182s Groups Name Variance Std.Dev. Corr 182s Subject (Intercept) 612.09 24.740 182s Days 35.07 5.922 0.07 182s Residual 654.94 25.592 182s Number of obs: 180, groups: Subject, 18 182s 182s Fixed effects: 182s Estimate Std. Error df t value Pr(>|t|) 182s (Intercept) 251.405 6.825 17.000 36.838 < 2e-16 *** 182s Days 10.467 1.546 17.000 6.771 3.26e-06 *** 182s --- 182s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 182s 182s Correlation of Fixed Effects: 182s (Intr) 182s Days -0.138 182s > 182s > stopifnot( 182s + isTRUE(all.equal(an1new, an1, check.attributes=FALSE, tol=TOL)), 182s + isTRUE(all.equal(coef(sfm1new), coef(sfm1), tol=TOL)) 182s + ) 182s > 182s > contest(fm1, c(0, 1)) 182s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 182s 1 30031.01 30031.01 1 17 45.853 3.26379e-06 182s > contest(fm1, c(0, 1), joint=FALSE) 182s Estimate Std. Error df t value lower upper Pr(>|t|) 182s 1 10.46729 1.545789 17 6.771485 7.205956 13.72862 3.26379e-06 182s > drop1(fm1) 182s Single term deletions using Satterthwaite's method: 182s 182s Model: 182s Reaction ~ Days + (Days | Subject) 182s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 182s Days 30031 30031 1 17 45.853 3.264e-06 *** 182s --- 182s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 182s > ranova(fm1) 182s ANOVA-like table for random-effects: Single term deletions 182s 182s Model: 182s Reaction ~ Days + (Days | Subject) 182s npar logLik AIC LRT Df Pr(>Chisq) 182s 6 -871.81 1755.6 182s Days in (Days | Subject) 4 -893.23 1794.5 42.837 2 4.99e-10 *** 182s --- 182s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 182s > step(fm1) 182s Backward reduced random-effect table: 182s 182s Eliminated npar logLik AIC LRT Df Pr(>Chisq) 182s 6 -871.81 1755.6 182s Days in (Days | Subject) 0 4 -893.23 1794.5 42.837 2 4.99e-10 182s 182s 182s Days in (Days | Subject) *** 182s --- 182s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 182s 182s Backward reduced fixed-effect table: 182s Degrees of freedom method: Satterthwaite 182s 182s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 182s Days 0 30031 30031 1 17 45.853 3.264e-06 *** 182s --- 182s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 182s 182s Model found: 182s Reaction ~ Days + (Days | Subject) 182s > 182s > fm1new <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy, 182s + control=lmerControl(optimizer="bobyqa")) 182s > stopifnot( 182s + isTRUE(all.equal(drop1(fm1), drop1(fm1new), tol=TOL)), 182s + isTRUE(all.equal(ranova(fm1), ranova(fm1new), tol=TOL)), 182s + isTRUE(all.equal(contest(fm1, c(0, 1)), contest(fm1new, c(0, 1)), tol=TOL)), 182s + isTRUE(all.equal(contest(fm1, c(0, 1), joint=FALSE), 182s + contest(fm1new, c(0, 1), joint=FALSE), tol=TOL)) 182s + ) 182s > 182s > # Test that lme4 methods work: 182s > coef(fm1) 182s $Subject 182s (Intercept) Days 182s 308 253.6637 19.6662579 182s 309 211.0065 1.8475828 182s 310 212.4449 5.0184061 182s 330 275.0956 5.6529547 182s 331 273.6653 7.3973914 182s 332 260.4446 10.1951153 182s 333 268.2455 10.2436615 182s 334 244.1725 11.5418620 182s 335 251.0714 -0.2848731 182s 337 286.2955 19.0955699 182s 349 226.1950 11.6407002 182s 350 238.3351 17.0814910 182s 351 255.9829 7.4520288 182s 352 272.2687 14.0032993 182s 369 254.6806 11.3395026 182s 370 225.7922 15.2897506 182s 371 252.2121 9.4791309 182s 372 263.7196 11.7513157 182s 182s attr(,"class") 182s [1] "coef.mer" 182s > fixef(fm1) 182s (Intercept) Days 182s 251.40510 10.46729 182s > resid(fm1) 182s 1 2 3 4 5 6 182s -4.1036703 -14.6252282 -42.1955860 8.7773561 24.5231982 62.6951403 182s 7 8 9 10 11 12 182s 10.5425825 -101.1788754 19.5915667 35.6935088 11.7273721 -7.5883107 182s 13 14 15 16 17 18 182s -11.7238935 -11.8422762 -10.6807590 -4.2826418 -8.4617246 -6.2124074 182s 19 20 21 22 23 24 182s -1.4914902 9.6794271 -13.3909590 -23.1310650 11.8383289 5.3415228 182s 25 26 27 28 29 30 182s -3.2110832 -17.0789893 -7.1344953 8.1773986 8.4203926 -10.0952135 182s 31 32 33 34 35 36 182s 46.4469967 19.6516420 -2.5450126 -6.9214673 -11.9101220 -5.7748766 182s 37 38 39 40 41 42 182s -28.7737313 3.5950141 -14.9697406 28.0765048 13.9425924 3.9373010 182s 43 44 45 46 47 48 182s 13.3605097 24.2578183 13.0224270 -17.3335644 -27.9746558 9.3706529 182s 49 50 51 52 53 54 182s -39.0975385 31.3392701 -25.5840308 -27.8279461 -7.8735614 18.7388233 182s 55 56 57 58 59 60 182s 16.2378080 -1.4226073 132.5465774 15.0206621 -11.7052532 -98.3362685 182s 61 62 63 64 65 66 182s 15.5968640 11.0658025 -11.9635591 0.8331794 -12.0491821 18.7026564 182s 67 68 69 70 71 72 182s 2.3189949 8.8887334 -16.8348282 1.6043103 21.3005744 20.4868123 182s 73 74 75 76 77 78 182s -23.8915497 -24.1258118 -11.3155738 -17.6906358 -7.8988979 6.5573401 182s 79 80 81 82 83 84 182s -0.7605219 29.2497160 -9.4631090 23.1606642 3.9890373 20.5853104 182s 85 86 87 88 89 90 182s 1.5199836 4.9891567 -3.9098701 -13.7662970 -13.0383239 -11.2609507 182s 91 92 93 94 95 96 182s 26.0711443 8.4147744 -32.8753955 2.5400346 3.0546647 10.0651947 182s 97 98 99 100 101 102 182s 3.3912248 -3.2721451 16.8042850 0.7611151 9.9082056 -7.5189947 182s 103 104 105 106 107 108 182s -10.5507949 -6.1950951 -22.0474953 -14.6240955 -14.4743957 0.4221041 182s 109 110 111 112 113 114 182s 16.9600039 20.6838037 17.9616518 -11.9623391 -16.2935301 -34.0525210 182s 115 116 117 118 119 120 182s -37.7446120 5.9820971 38.6204061 5.0128151 19.5001242 -3.0158668 182s 121 122 123 124 125 126 182s -5.4564400 36.6226312 -0.9930976 2.2500737 -13.9636551 11.3905161 182s 127 128 129 130 131 132 182s -12.9485127 -41.5516414 5.9426298 24.5143010 -50.5915973 11.9219034 182s 133 134 135 136 137 138 182s 26.6032041 32.5769048 20.4583056 10.5435063 -1.8618930 -9.8591922 182s 139 140 141 142 143 144 182s -8.6544915 -9.7566908 17.2429421 2.4168396 -20.1171630 -11.0424656 182s 145 146 147 148 149 150 182s 14.7836319 5.8354293 -24.5822732 14.0658242 -5.1165783 9.7770191 182s 151 152 153 154 155 156 182s -0.5282354 -6.5584860 -17.4709366 -31.1884871 -19.4139377 41.9527117 182s 157 158 159 160 161 162 182s -36.3826389 14.7650105 17.0527600 8.8288094 17.6682554 10.7515245 182s 163 164 165 166 167 168 182s 6.7284937 1.1399628 -10.9581681 -15.0957989 -49.8211298 -13.9354607 182s 169 170 171 172 173 174 182s 22.7355085 31.9448776 5.6920558 -1.9969599 10.3745244 11.6580087 182s 175 176 177 178 179 180 182s -23.5523070 7.1313773 0.2542616 -2.7589541 11.4115302 -5.3578855 182s > 182s > ####################################### 182s > ## Tests for fm2: 182s > (an2new <- anova(fm2)) 182s Type III Analysis of Variance Table with Satterthwaite's method 182s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 182s Product 17.6984 5.8995 3 319 3.5029 0.01577 * 182s Information 6.5201 6.5201 1 323 3.8714 0.04997 * 182s Gender 1.8634 1.8634 1 319 1.1064 0.29366 182s --- 182s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 182s > (sfm2new <- summary(fm2)) 182s Linear mixed model fit by REML. t-tests use Satterthwaite's method [ 182s lmerModLmerTest] 182s Formula: 182s Informed.liking ~ Product + Information + Gender + (1 | Product:Consumer) 182s Data: ham 182s 182s REML criterion at convergence: 2712.2 182s 182s Scaled residuals: 182s Min 1Q Median 3Q Max 182s -3.1568 -0.5087 0.0338 0.4913 3.1623 182s 182s Random effects: 182s Groups Name Variance Std.Dev. 182s Product:Consumer (Intercept) 3.526 1.878 182s Residual 1.684 1.298 182s Number of obs: 648, groups: Product:Consumer, 324 182s 182s Fixed effects: 182s Estimate Std. Error df t value Pr(>|t|) 182s (Intercept) 5.8290 0.2640 343.6885 22.082 <2e-16 *** 182s Product2 -0.7037 0.3284 319.0000 -2.143 0.0329 * 182s Product3 0.2840 0.3284 319.0000 0.865 0.3879 182s Product4 0.1173 0.3284 319.0000 0.357 0.7212 182s Information2 0.2006 0.1020 323.0000 1.968 0.0500 * 182s Gender2 -0.2443 0.2322 319.0000 -1.052 0.2937 182s --- 182s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 182s 182s Correlation of Fixed Effects: 182s (Intr) Prdct2 Prdct3 Prdct4 Infrm2 182s Product2 -0.622 182s Product3 -0.622 0.500 182s Product4 -0.622 0.500 0.500 182s Informatin2 -0.193 0.000 0.000 0.000 182s Gender2 -0.434 0.000 0.000 0.000 0.000 182s > 182s > stopifnot( 182s + isTRUE(all.equal(an2new, an2, check.attributes=FALSE, tol=TOL)), 182s + isTRUE(all.equal(coef(sfm2new), coef(sfm2), tol=TOL)) 182s + ) 182s > 182s > drop1(fm2) 182s Single term deletions using Satterthwaite's method: 182s 182s Model: 182s Informed.liking ~ Product + Information + Gender + (1 | Product:Consumer) 182s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 182s Product 17.6984 5.8995 3 319 3.5029 0.01577 * 182s Information 6.5201 6.5201 1 323 3.8714 0.04997 * 182s Gender 1.8634 1.8634 1 319 1.1064 0.29366 182s --- 182s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 182s > ranova(fm2) 182s ANOVA-like table for random-effects: Single term deletions 182s 182s Model: 182s Informed.liking ~ Product + Information + Gender + (1 | Product:Consumer) 182s npar logLik AIC LRT Df Pr(>Chisq) 182s 8 -1356.1 2728.2 182s (1 | Product:Consumer) 7 -1454.7 2923.4 197.19 1 < 2.2e-16 *** 182s --- 182s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 182s > ls_means(fm2) 182s Least Squares Means table: 182s 182s Estimate Std. Error df t value lower upper Pr(>|t|) 182s Product1 5.80713 0.23223 319.0 25.006 5.35025 6.26402 < 2.2e-16 *** 182s Product2 5.10343 0.23223 319.0 21.976 4.64654 5.56032 < 2.2e-16 *** 182s Product3 6.09108 0.23223 319.0 26.229 5.63420 6.54797 < 2.2e-16 *** 182s Product4 5.92442 0.23223 319.0 25.511 5.46753 6.38131 < 2.2e-16 *** 182s Information1 5.63121 0.12682 437.8 44.404 5.38196 5.88046 < 2.2e-16 *** 182s Information2 5.83183 0.12682 437.8 45.986 5.58258 6.08107 < 2.2e-16 *** 182s Gender1 5.85366 0.16320 319.0 35.868 5.53257 6.17475 < 2.2e-16 *** 182s Gender2 5.60937 0.16523 319.0 33.949 5.28430 5.93445 < 2.2e-16 *** 182s --- 182s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 182s 182s Confidence level: 95% 182s Degrees of freedom method: Satterthwaite 182s > difflsmeans(fm2) 182s Least Squares Means table: 182s 182s Estimate Std. Error df t value lower 182s Product1 - Product2 7.0370e-01 3.2841e-01 319 2.1428 5.7578e-02 182s Product1 - Product3 -2.8395e-01 3.2841e-01 319 -0.8646 -9.3008e-01 182s Product1 - Product4 -1.1728e-01 3.2841e-01 319 -0.3571 -7.6341e-01 182s Product2 - Product3 -9.8765e-01 3.2841e-01 319 -3.0074 -1.6338e+00 182s Product2 - Product4 -8.2099e-01 3.2841e-01 319 -2.4999 -1.4671e+00 182s Product3 - Product4 1.6667e-01 3.2841e-01 319 0.5075 -4.7946e-01 182s Information1 - Information2 -2.0062e-01 1.0196e-01 323 -1.9676 -4.0121e-01 182s Gender1 - Gender2 2.4428e-01 2.3224e-01 319 1.0519 -2.1263e-01 182s upper Pr(>|t|) 182s Product1 - Product2 1.3498e+00 0.032890 * 182s Product1 - Product3 3.6218e-01 0.387898 182s Product1 - Product4 5.2884e-01 0.721234 182s Product2 - Product3 -3.4153e-01 0.002845 ** 182s Product2 - Product4 -1.7486e-01 0.012926 * 182s Product3 - Product4 8.1279e-01 0.612159 182s Information1 - Information2 -2.6433e-05 0.049970 * 182s Gender1 - Gender2 7.0120e-01 0.293660 182s --- 182s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 182s 182s Confidence level: 95% 182s Degrees of freedom method: Satterthwaite 182s > nbeta <- length(fixef(fm2)) 182s > L <- diag(nbeta) 182s > L[1:4, ] <- 0 182s > contest(fm2, L) 182s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 182s 1 8.383419 4.19171 2 320.9875 2.488919 0.08460028 182s > contest(fm2, diag(nbeta), joint=FALSE) 182s Estimate Std. Error df t value lower upper 182s 1 5.8289672 0.2639677 343.6885 22.0821233 5.309772e+00 6.34816269 182s 2 -0.7037037 0.3284114 319.0000 -2.1427506 -1.349830e+00 -0.05757783 182s 3 0.2839506 0.3284114 319.0000 0.8646187 -3.621753e-01 0.93007650 182s 4 0.1172840 0.3284114 319.0000 0.3571251 -5.288419e-01 0.76340983 182s 5 0.2006173 0.1019607 323.0000 1.9675949 2.643318e-05 0.40120813 182s 6 -0.2442835 0.2322396 319.0000 -1.0518599 -7.011983e-01 0.21263128 182s Pr(>|t|) 182s 1 6.753241e-68 182s 2 3.288952e-02 182s 3 3.878978e-01 182s 4 7.212343e-01 182s 5 4.997000e-02 182s 6 2.936600e-01 182s > step(fm2) 182s Backward reduced random-effect table: 182s 182s Eliminated npar logLik AIC LRT Df Pr(>Chisq) 182s 8 -1356.1 2728.2 182s (1 | Product:Consumer) 0 7 -1454.7 2923.4 197.19 1 < 2.2e-16 *** 182s --- 182s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 182s 182s Backward reduced fixed-effect table: 182s Degrees of freedom method: Satterthwaite 182s 182s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 182s Gender 1 1.8634 1.8634 1 319 1.1064 0.29366 182s Product 0 17.6926 5.8975 3 320 3.5018 0.01579 * 182s Information 0 6.5201 6.5201 1 323 3.8714 0.04997 * 182s --- 182s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 182s 182s Model found: 182s Informed.liking ~ Product + Information + (1 | Product:Consumer) 182s > 182s > fm2new <- lmer(Informed.liking ~ Product + Information + Gender + 182s + (1|Product:Consumer), data=ham) 182s > stopifnot( 182s + isTRUE(all.equal(drop1(fm2), drop1(fm2new), tol=TOL)), 182s + isTRUE(all.equal(ranova(fm2), ranova(fm2new), tol=TOL)), 182s + isTRUE(all.equal(ls_means(fm2), ls_means(fm2new), tol=TOL)), 182s + isTRUE(all.equal(difflsmeans(fm2), difflsmeans(fm2new), tol=TOL)) 182s + ) 183s > 183s > # Test that lme4 methods work: 183s > coef(fm2) 183s $`Product:Consumer` 183s (Intercept) Product2 Product3 Product4 Information2 Gender2 183s 1:1 5.078836 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 1:2 5.276027 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 1:3 6.693279 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 1:4 6.693279 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 1:5 4.468805 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 1:6 5.078836 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 1:7 8.101302 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 1:8 6.289668 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 1:9 6.289668 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 1:10 5.482447 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 1:11 8.504912 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 1:12 3.661584 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 1:13 7.697691 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 1:14 8.101302 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 1:15 4.675225 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 1:16 4.872416 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 1:17 7.096889 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 1:18 7.500500 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 1:19 8.307721 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 1:20 6.693279 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 1:21 6.693279 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 1:22 6.083248 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 1:23 6.486859 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 1:24 7.500500 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 1:25 5.078836 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 1:26 7.294080 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 1:29 4.872416 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 1:30 6.083248 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 1:31 6.289668 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 1:32 7.697691 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 1:33 4.271615 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 1:34 4.675225 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 1:35 6.486859 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 1:36 6.083248 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 1:37 3.464393 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 1:38 6.289668 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 1:39 6.693279 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 1:40 3.661584 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 1:41 5.886057 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 1:42 5.482447 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 1:43 7.096889 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 1:44 6.083248 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 1:45 8.504912 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 1:46 5.078836 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 1:47 2.047141 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 1:48 6.890469 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 1:49 3.464393 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 1:50 3.257973 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 1:51 6.083248 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 1:52 8.504912 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 1:53 5.078836 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 1:54 3.661584 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 1:55 4.675225 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 1:56 6.486859 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 1:57 5.078836 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 1:58 5.482447 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 1:59 5.482447 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 1:60 5.482447 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 1:61 7.096889 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 1:62 5.276027 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 1:63 5.679637 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 1:64 4.872416 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 1:65 7.500500 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 1:66 6.083248 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 1:67 5.886057 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 1:68 7.294080 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 1:69 4.872416 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 1:70 6.486859 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 1:71 5.078836 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 1:73 2.854363 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 1:74 6.486859 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 1:75 4.675225 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 1:76 4.872416 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 1:77 3.257973 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 1:78 5.078836 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 1:79 7.294080 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 1:80 7.294080 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 1:81 5.886057 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 1:82 6.890469 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 1:83 3.868004 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 1:84 5.482447 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 2:1 4.839659 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 2:2 8.669346 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 2:3 5.646881 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 2:4 3.628827 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 2:5 4.229629 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 2:6 5.243270 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 2:7 3.018797 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 2:8 6.050491 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 2:9 6.050491 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 2:10 8.472155 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 2:11 2.615186 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 2:12 2.615186 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 2:13 2.615186 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 2:14 2.615186 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 2:15 6.857713 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 2:16 2.615186 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 2:17 5.646881 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 2:18 3.628827 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 2:19 2.417995 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 2:20 3.225216 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 2:21 2.821606 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 2:22 2.615186 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 2:23 2.615186 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 2:24 7.261323 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 2:25 6.857713 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 2:26 2.615186 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 2:29 2.615186 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 2:30 7.862125 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 2:31 7.664934 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 2:32 5.440461 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 2:33 2.417995 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 2:34 6.857713 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 2:35 5.036850 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 2:36 8.669346 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 2:37 6.857713 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 2:38 4.839659 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 2:39 7.261323 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 2:40 3.826018 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 2:41 5.243270 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 2:42 6.857713 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 2:43 4.436049 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 2:44 5.036850 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 2:45 5.440461 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 2:46 8.472155 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 2:47 5.844071 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 2:48 2.615186 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 2:49 7.261323 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 2:50 7.862125 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 2:51 8.265735 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 2:52 5.844071 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 2:53 8.068545 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 2:54 7.862125 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 2:55 5.243270 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 2:56 7.054903 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 2:57 6.857713 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 2:58 8.472155 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 2:59 8.068545 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 2:60 5.243270 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 2:61 4.839659 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 2:62 8.669346 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 2:63 7.862125 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 2:64 7.862125 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 2:65 4.436049 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 2:66 5.844071 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 2:67 7.664934 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 2:68 3.826018 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 2:69 7.458514 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 2:70 4.229629 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 2:71 7.664934 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 2:73 9.072957 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 2:74 6.651293 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 2:75 8.875766 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 2:76 8.265735 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 2:77 8.265735 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 2:78 6.050491 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 2:79 7.458514 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 2:80 7.054903 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 2:81 4.032438 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 2:82 8.669346 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 2:83 6.050491 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 2:84 6.454102 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 3:1 4.849625 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 3:2 7.468480 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 3:3 6.867678 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 3:4 4.849625 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 3:5 5.854037 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 3:6 7.271289 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 3:7 7.064869 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 3:8 6.867678 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 3:9 7.271289 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 3:10 7.271289 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 3:11 5.854037 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 3:12 6.257648 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 3:13 5.450426 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 3:14 3.835984 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 3:15 6.464068 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 3:16 5.854037 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 3:17 6.867678 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 3:18 5.656846 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 3:19 1.620739 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 3:20 6.867678 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 3:21 3.638793 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 3:22 3.835984 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 3:23 2.625152 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 3:24 7.674900 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 3:25 6.060457 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 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-0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 3:43 6.867678 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 3:44 4.239594 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 3:45 2.625152 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 3:46 5.253236 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 3:47 5.854037 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 3:48 5.450426 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 3:49 6.464068 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 3:50 8.275701 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 3:51 8.275701 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 3:52 6.257648 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 3:53 4.849625 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 3:54 7.064869 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 3:55 6.464068 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 3:56 3.835984 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 3:57 6.867678 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 3:58 7.271289 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 3:59 7.674900 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 3:60 4.849625 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 3:61 4.849625 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 3:62 7.872091 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 3:63 5.854037 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 3:64 6.257648 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 3:65 3.638793 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 3:66 3.835984 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 3:67 6.867678 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 3:68 1.817930 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 3:69 6.661258 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 3:70 3.028762 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 3:71 8.078510 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 3:73 8.275701 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 3:74 8.275701 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 3:75 3.235182 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 3:76 5.854037 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 3:77 6.661258 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 3:78 8.078510 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 3:79 4.239594 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 3:80 3.028762 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 3:81 3.638793 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 3:82 7.468480 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 3:83 4.849625 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 3:84 5.656846 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 4:1 5.791383 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 4:2 6.795795 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 4:3 5.791383 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 4:4 5.387772 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 4:5 6.392185 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 4:6 4.984162 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 4:7 3.970521 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 4:8 7.405826 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 4:9 6.194994 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 4:10 6.598604 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 4:11 6.392185 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 4:12 7.603017 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 4:13 7.603017 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 4:14 5.988574 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 4:15 7.002215 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 4:16 6.392185 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 4:17 3.773330 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 4:18 7.002215 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 4:19 4.984162 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 4:20 4.984162 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 4:21 4.580551 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 4:22 3.970521 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 4:23 3.970521 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 4:24 7.002215 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 4:25 7.002215 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 4:26 4.777742 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 4:29 2.356078 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 4:30 6.392185 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 4:31 7.405826 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 4:32 5.988574 -0.7037037 0.2839506 0.117284 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0.117284 0.2006173 -0.2442835 183s 4:77 8.410238 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 4:78 7.405826 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 4:79 5.988574 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 4:80 3.970521 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 4:81 4.580551 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 4:82 5.988574 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 4:83 5.791383 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 4:84 4.580551 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 183s 183s attr(,"class") 183s [1] "coef.mer" 183s > fixef(fm2) 183s (Intercept) Product2 Product3 Product4 Information2 Gender2 183s 5.8289672 -0.7037037 0.2839506 0.1172840 0.2006173 -0.2442835 183s > resid(fm2) 183s 1 2 3 4 5 6 183s -0.07883589 -0.27945318 -0.13595549 -0.33657278 -1.13357551 0.66580721 183s 7 8 9 10 11 12 183s 0.09133291 -0.10928437 -0.03174324 -0.23236053 0.27864107 1.07802378 183s 13 14 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-0.53956617 0.25981655 0.46281381 -0.73780347 0.30216494 -0.89845234 183s 313 314 315 316 317 318 183s -0.48244657 0.31693615 -0.15400888 0.64537384 -0.15162889 0.64775382 183s 319 320 321 322 323 324 183s 0.07327953 0.87266225 0.90311072 -0.29750656 1.26765518 -1.93296210 183s 325 326 327 328 329 330 183s -0.15162889 0.64775382 0.49494359 -0.70567369 -1.83896460 1.96041812 183s 331 332 333 334 335 336 183s -1.08886284 0.71051987 -0.27926151 -0.47987879 -0.63268902 -0.83330631 183s 337 338 339 340 341 342 183s 0.73937134 0.53875406 -1.49247352 1.30690920 -0.66481880 -0.86543608 183s 343 344 345 346 347 348 183s 0.94564692 -1.25497037 1.92116411 -2.27945318 1.23154842 0.03093113 183s 349 350 351 352 353 354 183s -2.53718619 2.26219653 -0.87256032 -1.07317760 -0.80285783 -1.00347511 183s 355 356 357 358 359 360 183s 4.10391580 -4.09670148 1.10629579 -1.09432150 -0.82546767 -1.02608496 183s 361 362 363 364 365 366 183s 0.35381405 0.15319677 -0.66719878 -0.86781607 -0.49009354 0.30928918 183s 367 368 369 370 371 372 183s 0.13842556 -0.06219172 -0.46439319 -0.66501047 -0.55761955 1.24176316 183s 373 374 375 376 377 378 183s -0.74801822 1.05136450 -0.11949912 0.67988360 -0.01368986 -1.21430714 183s 379 380 381 382 383 384 183s 0.08586242 0.88524514 0.68463173 0.48401444 -0.26518511 0.53419760 183s 385 386 387 388 389 390 183s -0.83896460 0.96041812 -0.31774826 1.48163446 0.68463173 0.48401444 183s 391 392 393 394 395 396 183s 0.71676150 0.51614422 0.73937134 0.53875406 0.10391580 -0.09670148 183s 397 398 399 400 401 402 183s -0.29731489 0.50206783 -0.84352105 -0.04413834 -0.07883589 -0.27945318 183s 403 404 405 406 407 408 183s 1.63515909 -0.56545819 -0.13357551 -0.33419279 0.88050088 -0.32011640 183s 409 410 411 412 413 414 183s -0.41730054 -0.61791782 0.08586242 0.88524514 -0.10453624 0.69484647 183s 415 416 417 418 419 420 183s 0.52398286 0.32336557 1.32477478 -1.87584250 -2.53956617 2.25981655 183s 421 422 423 424 425 426 183s 1.25198178 -0.94863550 -2.50505641 2.29432631 -0.24257527 0.55680744 183s 427 428 429 430 431 432 183s -0.10691623 0.69246649 -0.87565083 -0.07626811 -0.63268902 -0.83330631 183s 433 434 435 436 437 438 183s -0.07883589 -0.27945318 -0.15400888 0.64537384 -1.15162889 1.64775382 183s 439 440 441 442 443 444 183s -0.11949912 0.67988360 0.51755343 -0.68306385 0.23154842 1.03093113 183s 445 446 447 448 449 450 183s -0.55523957 1.24414315 0.47689021 0.27627292 -0.48244657 0.31693615 183s 451 452 453 454 455 456 183s -0.36484091 1.43454181 1.04114975 -0.15946753 0.68772224 -0.51289505 183s 457 458 459 460 461 462 183s 0.51755343 -0.68306385 0.46043383 -0.74018345 0.86642449 -1.33419279 183s 463 464 465 466 467 468 183s 1.30216494 -1.89845234 0.90311072 -0.29750656 -0.13595549 -0.33657278 183s 469 470 471 472 473 474 183s -0.13357551 -0.33419279 0.68772224 -0.51289505 -0.03174324 -0.23236053 183s 475 476 477 478 479 480 183s 0.27864107 1.07802378 1.08824240 -0.11237488 1.12037218 -0.08024511 183s 481 482 483 484 485 486 183s 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541 542 543 544 545 546 183s -0.06842948 -1.26904676 -0.66879579 1.13058692 1.92116411 -2.27945318 183s 547 548 549 550 551 552 183s 0.03876977 0.83815249 0.63753908 0.43692179 -0.10144573 -0.30206302 183s 553 554 555 556 557 558 183s -1.61007918 0.18930353 0.87503039 0.67441311 0.68463173 0.48401444 183s 559 560 561 562 563 564 183s 0.13842556 -0.06219172 -0.24257527 0.55680744 -0.70330555 1.09607717 183s 565 566 567 568 569 570 183s 0.68463173 0.48401444 0.71676150 0.51614422 -0.67522522 0.12415750 183s 571 572 573 574 575 576 183s 0.82793774 0.62732046 -0.51913280 -0.71975009 0.47689021 0.27627292 183s 577 578 579 580 581 582 183s -2.62813257 2.17125015 -0.31774826 1.48163446 -2.89370421 2.90567850 183s 583 584 585 586 587 588 183s 0.71676150 0.51614422 -2.01368986 0.78569286 -0.31774826 1.48163446 183s 589 590 591 592 593 594 183s 0.29907443 0.09845715 0.71676150 0.51614422 0.92116411 -1.27945318 183s 595 596 597 598 599 600 183s -1.34678752 1.45259519 0.63753908 0.43692179 0.47689021 0.27627292 183s 601 602 603 604 605 606 183s -0.04979663 0.74958609 0.48947310 0.28885581 -0.27926151 -0.47987879 183s 607 608 609 610 611 612 183s 0.13842556 -0.06219172 -0.04979663 0.74958609 1.89308377 -1.30753351 183s 613 614 615 616 617 618 183s 0.93157052 -2.26904676 -0.84352105 -0.04413834 0.11394275 -0.08667453 183s 619 620 621 622 623 624 183s -0.32873414 -0.52935142 -0.92274348 -0.12336076 -1.69783506 1.10154766 183s 625 626 627 628 629 630 183s 2.35381405 -1.84680323 1.27864107 0.07802378 1.49185308 -0.70876420 183s 631 632 633 634 635 636 183s 0.13842556 -0.06219172 -2.86800386 1.93137885 -2.34678752 2.45259519 183s 637 638 639 640 641 642 183s -1.13357551 0.66580721 1.09133291 -1.10928437 0.51755343 -0.68306385 183s 643 644 645 646 647 648 183s 0.24960180 0.04898452 -1.94079686 1.85858585 0.30216494 -0.89845234 183s > 183s > 183s BEGIN TEST test_lmer.R 183s 183s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 183s Copyright (C) 2025 The R Foundation for Statistical Computing 183s Platform: x86_64-pc-linux-gnu 183s 183s R is free software and comes with ABSOLUTELY NO WARRANTY. 183s You are welcome to redistribute it under certain conditions. 183s Type 'license()' or 'licence()' for distribution details. 183s 183s R is a collaborative project with many contributors. 183s Type 'contributors()' for more information and 183s 'citation()' on how to cite R or R packages in publications. 183s 183s Type 'demo()' for some demos, 'help()' for on-line help, or 183s 'help.start()' for an HTML browser interface to help. 183s Type 'q()' to quit R. 183s 183s > # test_lmer.R 183s > 183s > stopifnot(!"lmerTest" %in% .packages()) # ensure that lmerTest is NOT attached 183s > data("sleepstudy", package="lme4") 183s > f <- function(form, data) lmerTest::lmer(form, data=data) 183s > form <- "Reaction ~ Days + (Days|Subject)" 183s > fm <- f(form, data=sleepstudy) 184s > anova(fm) 184s Type III Analysis of Variance Table with Satterthwaite's method 184s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 184s Days 30031 30031 1 17 45.853 3.264e-06 *** 184s --- 184s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 184s > summary(fm) 184s Linear mixed model fit by REML. t-tests use Satterthwaite's method [ 184s lmerModLmerTest] 184s Formula: form 184s Data: data 184s 184s REML criterion at convergence: 1743.6 184s 184s Scaled residuals: 184s Min 1Q Median 3Q Max 184s -3.9536 -0.4634 0.0231 0.4634 5.1793 184s 184s Random effects: 184s Groups Name Variance Std.Dev. Corr 184s Subject (Intercept) 612.10 24.741 184s Days 35.07 5.922 0.07 184s Residual 654.94 25.592 184s Number of obs: 180, groups: Subject, 18 184s 184s Fixed effects: 184s Estimate Std. Error df t value Pr(>|t|) 184s (Intercept) 251.405 6.825 17.000 36.838 < 2e-16 *** 184s Days 10.467 1.546 17.000 6.771 3.26e-06 *** 184s --- 184s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 184s 184s Correlation of Fixed Effects: 184s (Intr) 184s Days -0.138 184s > 184s > # cf. GitHub issue #2: 184s > test <- function() { 184s + tmp <- sleepstudy 184s + m <- lmerTest::lmer(Reaction ~ Days + (Days | Subject), data = tmp) 184s + summary(m) 184s + } 184s > test() 184s Linear mixed model fit by REML. t-tests use Satterthwaite's method [ 184s lmerModLmerTest] 184s Formula: Reaction ~ Days + (Days | Subject) 184s Data: tmp 184s 184s REML criterion at convergence: 1743.6 184s 184s Scaled residuals: 184s Min 1Q Median 3Q Max 184s -3.9536 -0.4634 0.0231 0.4634 5.1793 184s 184s Random effects: 184s Groups Name Variance Std.Dev. Corr 184s Subject (Intercept) 612.10 24.741 184s Days 35.07 5.922 0.07 184s Residual 654.94 25.592 184s Number of obs: 180, groups: Subject, 18 184s 184s Fixed effects: 184s Estimate Std. Error df t value Pr(>|t|) 184s (Intercept) 251.405 6.825 17.000 36.838 < 2e-16 *** 184s Days 10.467 1.546 17.000 6.771 3.26e-06 *** 184s --- 184s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 184s 184s Correlation of Fixed Effects: 184s (Intr) 184s Days -0.138 184s > test <- function() { 184s + tmp <- sleepstudy 184s + m <- lme4::lmer(Reaction ~ Days + (Days | Subject), data = tmp) 184s + if(requireNamespace("lmerTest", quietly = TRUE)) { 184s + summary(lmerTest::as_lmerModLmerTest(m)) 184s + } 184s + } 184s > test() 184s Linear mixed model fit by REML. t-tests use Satterthwaite's method [ 184s lmerModLmerTest] 184s Formula: Reaction ~ Days + (Days | Subject) 184s Data: tmp 184s 184s REML criterion at convergence: 1743.6 184s 184s Scaled residuals: 184s Min 1Q Median 3Q Max 184s -3.9536 -0.4634 0.0231 0.4634 5.1793 184s 184s Random effects: 184s Groups Name Variance Std.Dev. Corr 184s Subject (Intercept) 612.10 24.741 184s Days 35.07 5.922 0.07 184s Residual 654.94 25.592 184s Number of obs: 180, groups: Subject, 18 184s 184s Fixed effects: 184s Estimate Std. Error df t value Pr(>|t|) 184s (Intercept) 251.405 6.825 17.000 36.838 < 2e-16 *** 184s Days 10.467 1.546 17.000 6.771 3.26e-06 *** 184s --- 184s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 184s 184s Correlation of Fixed Effects: 184s (Intr) 184s Days -0.138 184s > 184s > library(lmerTest) 184s Loading required package: lme4 184s Loading required package: Matrix 184s 184s Attaching package: 'lmerTest' 184s 184s The following object is masked from 'package:lme4': 184s 184s lmer 184s 184s The following object is masked from 'package:stats': 184s 184s step 184s 184s > 184s > # WRE says "using if(requireNamespace("pkgname")) is preferred, if possible." 184s > # even in tests: 184s > assertError <- function(expr, ...) 184s + if(requireNamespace("tools")) tools::assertError(expr, ...) else invisible() 184s > assertWarning <- function(expr, ...) 184s + if(requireNamespace("tools")) tools::assertWarning(expr, ...) else invisible() 184s > 184s > TOL <- 1e-4 184s > 184s > ##################################################################### 184s > # Check that lme4::lmer and lmerTest::lmer have the same arguments 184s > 184s > lmer_args <- formals(lme4::lmer) 184s > names(lmer_args) 184s [1] "formula" "data" "REML" "control" "start" 184s [6] "verbose" "subset" "weights" "na.action" "offset" 184s [11] "contrasts" "devFunOnly" 184s > lmerTest_args <- formals(lmerTest::lmer) 184s > seq_args <- seq_along(lmerTest_args) 184s > if(packageVersion("lme4") > '1.1.21') { 184s + stopifnot( 184s + all.equal(names(lmer_args), names(lmerTest_args)), 184s + all.equal(lmer_args, lmerTest_args) 184s + ) 184s + } else { # Older versions of 'lme4' has a "..." argument: 184s + stopifnot( 184s + all.equal(names(lmer_args)[seq_args], names(lmerTest_args[seq_args])), 184s + all.equal(lmer_args[seq_args], lmerTest_args[seq_args]) 184s + ) 184s + } 184s > 184s > ##################################################################### 184s > # Test evaluation of update inside a function: 184s > myupdate <- function(m, ...) { 184s + update(m, ...) 184s + } 184s > 184s > data("sleepstudy", package="lme4") 184s > fm1 <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy) 184s > tmp <- sleepstudy 184s > rm(sleepstudy) 184s > fmA <- update(fm1, data = tmp) # works 184s > fmB <- myupdate(fm1, data = tmp) # also works 184s > # Same except for 'call': 184s > fmB@call <- fmA@call 184s > stopifnot(isTRUE(all.equal(fmA, fmB, tolerance=TOL))) 184s > # Based on bug-report by Henrik Singmann, github issue #3 184s > 184s > ##################################################################### 184s > # Test update when formula is a character vector: 184s > 184s > form <- "Informed.liking ~ Product+Information+ 184s + (1|Consumer) + (1|Product:Consumer) + (1|Information:Consumer)" 184s > m <- lmer(form, data=ham) 184s > class(m) 184s [1] "lmerModLmerTest" 184s attr(,"package") 184s [1] "lmerTest" 184s > class(update(m, ~.- Product)) 184s [1] "lmerModLmerTest" 184s attr(,"package") 184s [1] "lmerTest" 184s > stopifnot(inherits(update(m, ~.- Product), "lmerModLmerTest")) 184s > 184s > # In version < 3.0-1.9002 class(update(m, ~.- Product)) was "lmerMod" 184s > ##################################################################### 184s > # Test error message from as_lmerModLmerTest: 184s > data("sleepstudy", package="lme4") 184s > myfit <- function(formula, data) { 184s + lme4::lmer(formula = formula, data = data) 184s + } 184s > fm2 <- myfit(Reaction ~ Days + (Days|Subject), sleepstudy) 184s > m <- assertError(as_lmerModLmerTest(fm2)) 184s > stopifnot( 184s + grepl("Unable to extract deviance function from model fit", m[[1]], fixed=TRUE) 184s + ) 184s > 184s > ##################################################################### 184s > # Check that devFunOnly argument works: 184s > data("sleepstudy", package="lme4") 184s > fun <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy, devFunOnly = TRUE) 184s > stopifnot(is.function(fun)) # && names(formals(fun)[1]) == "theta") 184s > fm1 <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy) 184s > fun <- update(fm1, devFunOnly=TRUE) 184s > stopifnot(is.function(fun)) # && names(formals(fun)[1]) == "theta") 184s > # devFunOnly = FALSE: 184s > notfun <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy, devFunOnly = FALSE) 184s > stopifnot(inherits(notfun, "lmerModLmerTest")) 184s > # Partial matching: 184s > notfun <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy, devFun = FALSE) 184s > stopifnot(inherits(notfun, "lmerModLmerTest")) 184s > 184s > ##################################################################### 184s > # Use of as_lmerModLmerTest 184s > data("sleepstudy", package="lme4") 184s > m <- lme4::lmer(Reaction ~ Days + (Days | Subject), sleepstudy) 184s > bm <- lmerTest:::as_lmerModLmerTest(m) 184s > stopifnot( 184s + inherits(bm, "lmerModLmerTest"), 184s + !inherits(m, "lmerModLmerTest"), 184s + inherits(bm, "lmerMod"), 184s + all(c("vcov_varpar", "Jac_list", "vcov_beta", "sigma") %in% slotNames(bm)) 184s + ) 184s > 184s > ##################################################################### 184s > # Update method 184s > 184s > m <- lmer(Reaction ~ Days + (Days | Subject), sleepstudy) 185s > m1 <- update(m, ~.-Days) 185s > m2 <- lmer(Reaction ~ (Days | Subject), sleepstudy) 185s > 185s > stopifnot( 185s + inherits(m, "lmerModLmerTest"), 185s + inherits(m1, "lmerModLmerTest"), 185s + inherits(m2, "lmerModLmerTest"), 185s + all.equal(m1, m2, tolerance=1e-6) 185s + ) 185s > 185s > 185s BEGIN TEST test_lmerTest_paper.R 185s 185s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 185s Copyright (C) 2025 The R Foundation for Statistical Computing 185s Platform: x86_64-pc-linux-gnu 185s 185s R is free software and comes with ABSOLUTELY NO WARRANTY. 185s You are welcome to redistribute it under certain conditions. 185s Type 'license()' or 'licence()' for distribution details. 185s 185s R is a collaborative project with many contributors. 185s Type 'contributors()' for more information and 185s 'citation()' on how to cite R or R packages in publications. 185s 185s Type 'demo()' for some demos, 'help()' for on-line help, or 185s 'help.start()' for an HTML browser interface to help. 185s Type 'q()' to quit R. 185s 185s > # test_lmerTest_paper.R 185s > 185s > library(lmerTest) 185s Loading required package: lme4 185s Loading required package: Matrix 186s 186s Attaching package: 'lmerTest' 186s 186s The following object is masked from 'package:lme4': 186s 186s lmer 186s 186s The following object is masked from 'package:stats': 186s 186s step 186s 186s > 186s > # Kenward-Roger only available with pbkrtest and only then validated in R >= 3.3.3 186s > # (faulty results for R < 3.3.3 may be due to unstated dependencies in pbkrtest) 186s > has_pbkrtest <- requireNamespace("pbkrtest", quietly = TRUE) && getRversion() >= "3.3.3" 186s > 186s > # Read in data set 186s > load(system.file("testdata","test_paper_objects.RData", package="lmerTest")) 186s > 186s > # Evaluate code from paper: 186s > ## Section 8.2: 186s > tv <- lmer(Sharpnessofmovement ~ TVset * Picture + (1 | Assessor) + 186s + (1 | Assessor:TVset) + (1 | Assessor:Picture), data = TVbo, 186s + control=lmerControl(optimizer="bobyqa")) 186s > 186s > (an8.2 <- anova(tv)) 186s Type III Analysis of Variance Table with Satterthwaite's method 186s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 186s TVset 1.765 0.8825 2 14 0.2437 0.7869818 186s Picture 51.857 17.2857 3 21 4.7735 0.0108785 * 186s TVset:Picture 90.767 15.1279 6 138 4.1777 0.0006845 *** 186s --- 186s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 186s > 186s > if(has_pbkrtest) 186s + (ankr8.2 <- anova(tv, type=2, ddf="Kenward-Roger")) 186s Type II Analysis of Variance Table with Kenward-Roger's method 186s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 186s TVset 1.765 0.8825 2 14 0.2437 0.7869818 186s Picture 51.857 17.2857 3 21 4.7735 0.0108785 * 186s TVset:Picture 90.767 15.1279 6 138 4.1777 0.0006845 *** 186s --- 186s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 186s > 186s > ## Section 8.3: 186s > m.carrots <- lmer(Preference ~ sens1 + sens2 + (1 + sens1 + sens2 | Consumer) + 186s + (1 | Product), data=carrots, 186s + control=lmerControl(optimizer="bobyqa")) 187s boundary (singular) fit: see help('isSingular') 187s > (sum8.3 <- coef(summary(m.carrots))) 187s Estimate Std. Error df t value Pr(>|t|) 187s (Intercept) 4.79911155 0.07529236 20.721527 63.7396848 2.921549e-25 187s sens1 0.01082919 0.01502847 9.167909 0.7205783 4.891337e-01 187s sens2 0.07064553 0.01727806 10.944315 4.0887415 1.812128e-03 187s > 187s > ## Section 8.4: 187s > tv <- lmer(Sharpnessofmovement ~ TVset * Picture + 187s + (1 | Assessor:TVset) + (1 | Assessor:Picture) + 187s + (1 | Assessor:Picture:TVset) + (1 | Repeat) + (1 | Repeat:Picture) + 187s + (1 | Repeat:TVset) + (1 | Repeat:TVset:Picture) + (1 | Assessor), 187s + data = TVbo, 187s + control=lmerControl(optimizer="bobyqa")) 187s boundary (singular) fit: see help('isSingular') 187s > st <- step(tv) 187s boundary (singular) fit: see help('isSingular') 187s boundary (singular) fit: see help('isSingular') 187s boundary (singular) fit: see help('isSingular') 188s boundary (singular) fit: see help('isSingular') 188s boundary (singular) fit: see help('isSingular') 188s boundary (singular) fit: see help('isSingular') 188s boundary (singular) fit: see help('isSingular') 188s boundary (singular) fit: see help('isSingular') 188s boundary (singular) fit: see help('isSingular') 189s boundary (singular) fit: see help('isSingular') 189s boundary (singular) fit: see help('isSingular') 189s boundary (singular) fit: see help('isSingular') 189s boundary (singular) fit: see help('isSingular') 189s boundary (singular) fit: see help('isSingular') 189s boundary (singular) fit: see help('isSingular') 189s boundary (singular) fit: see help('isSingular') 189s boundary (singular) fit: see help('isSingular') 190s boundary (singular) fit: see help('isSingular') 190s boundary (singular) fit: see help('isSingular') 190s boundary (singular) fit: see help('isSingular') 190s boundary (singular) fit: see help('isSingular') 190s boundary (singular) fit: see help('isSingular') 190s boundary (singular) fit: see help('isSingular') 190s boundary (singular) fit: see help('isSingular') 190s boundary (singular) fit: see help('isSingular') 190s boundary (singular) fit: see help('isSingular') 190s boundary (singular) fit: see help('isSingular') 190s boundary (singular) fit: see help('isSingular') 190s boundary (singular) fit: see help('isSingular') 191s boundary (singular) fit: see help('isSingular') 191s boundary (singular) fit: see help('isSingular') 191s boundary (singular) fit: see help('isSingular') 191s boundary (singular) fit: see help('isSingular') 191s > (elim_tab_random8.4 <- st$random) 191s Backward reduced random-effect table: 191s 191s Eliminated npar logLik AIC LRT Df 191s 21 -412.70 867.41 191s (1 | Assessor:Picture:TVset) 1 20 -412.70 865.41 0.0000 1 191s (1 | Repeat) 2 19 -412.70 863.41 0.0000 1 191s (1 | Repeat:Picture) 3 18 -412.70 861.41 0.0000 1 191s (1 | Repeat:TVset) 4 17 -412.70 859.41 0.0000 1 191s (1 | Repeat:TVset:Picture) 5 16 -412.70 857.41 0.0000 1 191s (1 | Assessor:TVset) 0 15 -414.10 858.20 2.7891 1 191s (1 | Assessor:Picture) 0 15 -418.88 867.76 12.3473 1 191s (1 | Assessor) 0 15 -416.44 862.88 7.4698 1 191s Pr(>Chisq) 191s 191s (1 | Assessor:Picture:TVset) 1.0000000 191s (1 | Repeat) 1.0000000 191s (1 | Repeat:Picture) 0.9999996 191s (1 | Repeat:TVset) 1.0000000 191s (1 | Repeat:TVset:Picture) 0.9999997 191s (1 | Assessor:TVset) 0.0949061 . 191s (1 | Assessor:Picture) 0.0004416 *** 191s (1 | Assessor) 0.0062742 ** 191s --- 191s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 191s > (elim_tab_fixed8.4 <- st$fixed) 191s Backward reduced fixed-effect table: 191s Degrees of freedom method: Satterthwaite 191s 191s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 191s TVset:Picture 0 90.767 15.128 6 138 4.1777 0.0006845 *** 191s --- 191s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 191s > (an8.4 <- anova(get_model(st))) 191s Type III Analysis of Variance Table with Satterthwaite's method 191s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 191s TVset 1.765 0.8825 2 14 0.2437 0.7869818 191s Picture 51.857 17.2857 3 21 4.7735 0.0108785 * 191s TVset:Picture 90.767 15.1279 6 138 4.1777 0.0006845 *** 191s --- 191s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 191s > 191s > ## Section 8.5: 191s > # L <- matrix(0, ncol = 12, nrow = 6) 191s > # L[1, 7] <- L[2, 8] <- L[3, 9] <- L[4, 10] <- L[5, 11] <- L[6, 12] <- 1 191s > L <- cbind(array(0, dim=c(6, 6)), diag(6)) 191s > (con1_8.5 <- calcSatterth(tv, L)) 191s $denom 191s [1] 138 191s 191s $Fstat 191s [,1] 191s [1,] 4.177656 191s 191s $pvalue 191s [,1] 191s [1,] 0.0006844787 191s 191s $ndf 191s [1] 6 191s 191s > (con2_8.5 <- contest(tv, L)) 191s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 191s 1 90.76719 15.12786 6 138 4.177656 0.0006844787 191s > 191s > ## Section C: 191s > # m.carrots <- lmer(Preference ~ sens1 + sens2 + (1 + sens1 + sens2 | Consumer) + 191s > # (1 | product), data = carrots) 191s > # step(m.carrots, reduce.fixed = FALSE) 191s > (ran_C <- ranova(m.carrots)) 191s boundary (singular) fit: see help('isSingular') 191s boundary (singular) fit: see help('isSingular') 191s ANOVA-like table for random-effects: Single term deletions 191s 191s Model: 191s Preference ~ sens1 + sens2 + (1 + sens1 + sens2 | Consumer) + (1 | Product) 191s npar logLik AIC LRT Df 191s Warning message: 191s Model failed to converge with 1 negative eigenvalue: -1.5e+03 191s 11 -1869.7 3761.5 191s sens1 in (1 + sens1 + sens2 | Consumer) 8 -1870.7 3757.3 1.8274 3 191s sens2 in (1 + sens1 + sens2 | Consumer) 8 -1874.5 3765.0 9.5464 3 191s (1 | Product) 10 -1878.7 3777.4 17.9080 1 191s Pr(>Chisq) 191s 191s sens1 in (1 + sens1 + sens2 | Consumer) 0.60899 191s sens2 in (1 + sens1 + sens2 | Consumer) 0.02284 * 191s (1 | Product) 2.318e-05 *** 191s --- 191s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 191s > 191s > # Compare to validated outputs: 191s > TOL <- 1e-4 191s > stopifnot( 191s + isTRUE(all.equal(an8.2_save, an8.2, check.attributes = FALSE, tolerance=TOL)), 191s + isTRUE(all.equal(sum8.3_save, sum8.3, check.attributes = FALSE, tolerance=TOL)), 191s + isTRUE(all.equal(elim_tab_random8.4_save, elim_tab_random8.4, 191s + check.attributes = FALSE, tolerance=TOL)), 191s + isTRUE(all.equal(elim_tab_fixed8.4_save, elim_tab_fixed8.4, 191s + check.attributes = FALSE, tolerance=TOL)), 191s + isTRUE(all.equal(an8.4_save, an8.4, check.attributes = FALSE, tolerance=TOL)), 191s + isTRUE(all.equal(con1_8.5_save, con1_8.5, check.attributes = FALSE, tolerance=TOL)), 191s + isTRUE(all.equal(con2_8.5_save, con2_8.5, check.attributes = FALSE, tolerance=TOL)) 191s + ) 191s > if(has_pbkrtest) { 191s + stopifnot( 191s + isTRUE(all.equal(ankr8.2_save, ankr8.2, check.attributes = FALSE, tolerance=TOL)) 191s + ) 191s + } 191s > 191s > 191s BEGIN TEST test_ls_means.R 191s 191s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 191s Copyright (C) 2025 The R Foundation for Statistical Computing 191s Platform: x86_64-pc-linux-gnu 191s 191s R is free software and comes with ABSOLUTELY NO WARRANTY. 191s You are welcome to redistribute it under certain conditions. 191s Type 'license()' or 'licence()' for distribution details. 191s 191s R is a collaborative project with many contributors. 191s Type 'contributors()' for more information and 191s 'citation()' on how to cite R or R packages in publications. 191s 191s Type 'demo()' for some demos, 'help()' for on-line help, or 191s 'help.start()' for an HTML browser interface to help. 191s Type 'q()' to quit R. 191s 191s > # test_lsmeans.R 191s > 191s > library(lmerTest) 191s Loading required package: lme4 191s Loading required package: Matrix 193s 193s Attaching package: 'lmerTest' 193s 193s The following object is masked from 'package:lme4': 193s 193s lmer 193s 193s The following object is masked from 'package:stats': 193s 193s step 193s 193s > 193s > TOL <- 1e-4 193s > # Kenward-Roger only available with pbkrtest and only then validated in R >= 3.3.3 193s > # (faulty results for R < 3.3.3 may be due to unstated dependencies in pbkrtest) 193s > has_pbkrtest <- requireNamespace("pbkrtest", quietly = TRUE) && getRversion() >= "3.3.3" 193s > 193s > ########### Basic model structures: 193s > 193s > # Factor * covariate: 193s > data("cake", package="lme4") 193s > model <- lmer(angle ~ recipe * temp + (1|recipe:replicate), cake) 193s > (lsm <- ls_means(model)) 193s Least Squares Means table: 193s 193s Estimate Std. Error df t value lower upper Pr(>|t|) 193s recipeA 33.1222 1.7368 42 19.070 29.6172 36.6273 < 2.2e-16 *** 193s recipeB 31.6444 1.7368 42 18.220 28.1394 35.1495 < 2.2e-16 *** 193s recipeC 31.6000 1.7368 42 18.194 28.0949 35.1051 < 2.2e-16 *** 193s --- 193s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 193s 193s Confidence level: 95% 193s Degrees of freedom method: Satterthwaite 193s > stopifnot( 193s + nrow(lsm) == 3L, 193s + ncol(lsm) == 7L, 193s + # Balanced, so LS-means equal raw means: 193s + isTRUE(all.equal(c(with(cake, tapply(angle, recipe, mean))), lsm[, "Estimate"], 193s + check.attributes=FALSE, tolerance=TOL)) 193s + ) 193s > 193s > # Pairwise differences of LS-means: 193s > plsm <- ls_means(model, pairwise = TRUE) 193s > plsm2 <- difflsmeans(model) 193s > C <- as.matrix(lmerTest:::get_pairs(rownames(lsm))) 193s > stopifnot( 193s + isTRUE(all.equal(plsm, plsm2, tolerance=TOL)), 193s + isTRUE(all.equal(plsm[, "Estimate"], c(lsm[, "Estimate"] %*% C), 193s + check.attributes=FALSE, tolerance=TOL)) 193s + ) 193s > 193s > # Contrasts vectors: 193s > show_tests(lsm) 193s $recipe 193s (Intercept) recipeB recipeC temp recipeB:temp recipeC:temp 193s recipeA 1 0 0 200 0 0 193s recipeB 1 1 0 200 200 0 193s recipeC 1 0 1 200 0 200 193s 193s > show_tests(plsm) 193s $recipe 193s (Intercept) recipeB recipeC temp recipeB:temp recipeC:temp 193s recipeA - recipeB 0 -1 0 0 -200 0 193s recipeA - recipeC 0 0 -1 0 0 -200 193s recipeB - recipeC 0 1 -1 0 200 -200 193s 193s > 193s > # Factor * Ordered: 193s > model <- lmer(angle ~ recipe * temperature + (1|recipe:replicate), cake) 193s > (lsm2 <- ls_means(model)) 193s Least Squares Means table: 193s 193s Estimate Std. Error df t value lower upper 193s recipeA 33.1222 1.7368 42.0 19.070 29.6172 36.6273 193s recipeB 31.6444 1.7368 42.0 18.220 28.1394 35.1495 193s recipeC 31.6000 1.7368 42.0 18.194 28.0949 35.1051 193s temperature175 27.9778 1.1767 77.4 23.776 25.6349 30.3207 193s temperature185 29.9556 1.1767 77.4 25.457 27.6127 32.2985 193s temperature195 31.4222 1.1767 77.4 26.704 29.0793 33.7651 193s temperature205 32.1778 1.1767 77.4 27.346 29.8349 34.5207 193s temperature215 35.8444 1.1767 77.4 30.462 33.5015 38.1873 193s temperature225 35.3556 1.1767 77.4 30.046 33.0127 37.6985 193s recipeA:temperature175 29.1333 2.0381 77.4 14.294 25.0753 33.1913 193s recipeB:temperature175 26.8667 2.0381 77.4 13.182 22.8087 30.9247 193s recipeC:temperature175 27.9333 2.0381 77.4 13.706 23.8753 31.9913 193s recipeA:temperature185 31.5333 2.0381 77.4 15.472 27.4753 35.5913 193s recipeB:temperature185 29.4000 2.0381 77.4 14.425 25.3420 33.4580 193s recipeC:temperature185 28.9333 2.0381 77.4 14.196 24.8753 32.9913 193s recipeA:temperature195 30.8000 2.0381 77.4 15.112 26.7420 34.8580 193s recipeB:temperature195 31.7333 2.0381 77.4 15.570 27.6753 35.7913 193s recipeC:temperature195 31.7333 2.0381 77.4 15.570 27.6753 35.7913 193s recipeA:temperature205 33.5333 2.0381 77.4 16.453 29.4753 37.5913 193s recipeB:temperature205 32.1333 2.0381 77.4 15.766 28.0753 36.1913 193s recipeC:temperature205 30.8667 2.0381 77.4 15.145 26.8087 34.9247 193s recipeA:temperature215 38.6667 2.0381 77.4 18.972 34.6087 42.7247 193s recipeB:temperature215 34.4667 2.0381 77.4 16.911 30.4087 38.5247 193s recipeC:temperature215 34.4000 2.0381 77.4 16.878 30.3420 38.4580 193s recipeA:temperature225 35.0667 2.0381 77.4 17.206 31.0087 39.1247 193s recipeB:temperature225 35.2667 2.0381 77.4 17.304 31.2087 39.3247 193s recipeC:temperature225 35.7333 2.0381 77.4 17.533 31.6753 39.7913 193s Pr(>|t|) 193s recipeA < 2.2e-16 *** 193s recipeB < 2.2e-16 *** 193s recipeC < 2.2e-16 *** 193s temperature175 < 2.2e-16 *** 193s temperature185 < 2.2e-16 *** 193s temperature195 < 2.2e-16 *** 193s temperature205 < 2.2e-16 *** 193s temperature215 < 2.2e-16 *** 193s temperature225 < 2.2e-16 *** 193s recipeA:temperature175 < 2.2e-16 *** 193s recipeB:temperature175 < 2.2e-16 *** 193s recipeC:temperature175 < 2.2e-16 *** 193s recipeA:temperature185 < 2.2e-16 *** 193s recipeB:temperature185 < 2.2e-16 *** 193s recipeC:temperature185 < 2.2e-16 *** 193s recipeA:temperature195 < 2.2e-16 *** 193s recipeB:temperature195 < 2.2e-16 *** 193s recipeC:temperature195 < 2.2e-16 *** 193s recipeA:temperature205 < 2.2e-16 *** 193s recipeB:temperature205 < 2.2e-16 *** 193s recipeC:temperature205 < 2.2e-16 *** 193s recipeA:temperature215 < 2.2e-16 *** 193s recipeB:temperature215 < 2.2e-16 *** 193s recipeC:temperature215 < 2.2e-16 *** 193s recipeA:temperature225 < 2.2e-16 *** 193s recipeB:temperature225 < 2.2e-16 *** 193s recipeC:temperature225 < 2.2e-16 *** 193s --- 193s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 193s 193s Confidence level: 95% 193s Degrees of freedom method: Satterthwaite 193s > stopifnot( 193s + nrow(lsm2) == 3 + 6 + 3*6, 193s + ncol(lsm) == 7L, 193s + # Balanced, so LS-means equal raw means: 193s + isTRUE(all.equal(lsm[1:3, ], lsm2[1:3, ], 193s + check.attributes=FALSE, tolerance=TOL)) 193s + ) 193s > 193s > 193s > # Factor * Factor: 193s > cake2 <- cake 193s > cake2$temperature <- factor(cake2$temperature, ordered = FALSE) 193s > model <- lmer(angle ~ recipe * temperature + (1|recipe:replicate), cake2) 193s > (lsm3 <- ls_means(model)) 193s Least Squares Means table: 193s 193s Estimate Std. Error df t value lower upper 193s recipeA 33.1222 1.7368 42.0 19.070 29.6172 36.6273 193s recipeB 31.6444 1.7368 42.0 18.220 28.1394 35.1495 193s recipeC 31.6000 1.7368 42.0 18.194 28.0949 35.1051 193s temperature175 27.9778 1.1767 77.4 23.776 25.6349 30.3207 193s temperature185 29.9556 1.1767 77.4 25.457 27.6127 32.2985 193s temperature195 31.4222 1.1767 77.4 26.704 29.0793 33.7651 193s temperature205 32.1778 1.1767 77.4 27.346 29.8349 34.5207 193s temperature215 35.8444 1.1767 77.4 30.462 33.5015 38.1873 193s temperature225 35.3556 1.1767 77.4 30.046 33.0127 37.6985 193s recipeA:temperature175 29.1333 2.0381 77.4 14.294 25.0753 33.1913 193s recipeB:temperature175 26.8667 2.0381 77.4 13.182 22.8087 30.9247 193s recipeC:temperature175 27.9333 2.0381 77.4 13.706 23.8753 31.9913 193s recipeA:temperature185 31.5333 2.0381 77.4 15.472 27.4753 35.5913 193s recipeB:temperature185 29.4000 2.0381 77.4 14.425 25.3420 33.4580 193s recipeC:temperature185 28.9333 2.0381 77.4 14.196 24.8753 32.9913 193s recipeA:temperature195 30.8000 2.0381 77.4 15.112 26.7420 34.8580 193s recipeB:temperature195 31.7333 2.0381 77.4 15.570 27.6753 35.7913 193s recipeC:temperature195 31.7333 2.0381 77.4 15.570 27.6753 35.7913 193s recipeA:temperature205 33.5333 2.0381 77.4 16.453 29.4753 37.5913 193s recipeB:temperature205 32.1333 2.0381 77.4 15.766 28.0753 36.1913 193s recipeC:temperature205 30.8667 2.0381 77.4 15.145 26.8087 34.9247 193s recipeA:temperature215 38.6667 2.0381 77.4 18.972 34.6087 42.7247 193s recipeB:temperature215 34.4667 2.0381 77.4 16.911 30.4087 38.5247 193s recipeC:temperature215 34.4000 2.0381 77.4 16.878 30.3420 38.4580 193s recipeA:temperature225 35.0667 2.0381 77.4 17.206 31.0087 39.1247 193s recipeB:temperature225 35.2667 2.0381 77.4 17.304 31.2087 39.3247 193s recipeC:temperature225 35.7333 2.0381 77.4 17.533 31.6753 39.7913 193s Pr(>|t|) 193s recipeA < 2.2e-16 *** 193s recipeB < 2.2e-16 *** 193s recipeC < 2.2e-16 *** 193s temperature175 < 2.2e-16 *** 193s temperature185 < 2.2e-16 *** 193s temperature195 < 2.2e-16 *** 193s temperature205 < 2.2e-16 *** 193s temperature215 < 2.2e-16 *** 193s temperature225 < 2.2e-16 *** 193s recipeA:temperature175 < 2.2e-16 *** 193s recipeB:temperature175 < 2.2e-16 *** 193s recipeC:temperature175 < 2.2e-16 *** 193s recipeA:temperature185 < 2.2e-16 *** 193s recipeB:temperature185 < 2.2e-16 *** 193s recipeC:temperature185 < 2.2e-16 *** 193s recipeA:temperature195 < 2.2e-16 *** 193s recipeB:temperature195 < 2.2e-16 *** 193s recipeC:temperature195 < 2.2e-16 *** 193s recipeA:temperature205 < 2.2e-16 *** 193s recipeB:temperature205 < 2.2e-16 *** 193s recipeC:temperature205 < 2.2e-16 *** 193s recipeA:temperature215 < 2.2e-16 *** 193s recipeB:temperature215 < 2.2e-16 *** 193s recipeC:temperature215 < 2.2e-16 *** 193s recipeA:temperature225 < 2.2e-16 *** 193s recipeB:temperature225 < 2.2e-16 *** 193s recipeC:temperature225 < 2.2e-16 *** 193s --- 193s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 193s 193s Confidence level: 95% 193s Degrees of freedom method: Satterthwaite 193s > stopifnot( 193s + isTRUE(all.equal(lsm2, lsm3, check.attributes=FALSE, tolerance=TOL)) 193s + ) 193s > 193s > # Covariate (only): 193s > data("sleepstudy", package="lme4") 193s > m <- lmer(Reaction ~ Days + (Days | Subject), sleepstudy) 193s > (lsm <- ls_means(m)) 193s Least Squares Means table: 193s 193s Estimate Std. Error df t value lower upper Pr(>|t|) 193s 193s Confidence level: 95% 193s Degrees of freedom method: Satterthwaite 193s > stopifnot( 193s + nrow(lsm) == 0L, 193s + ncol(lsm) == 7L 193s + ) 193s > 193s > # No fixef: 193s > m <- lmer(Reaction ~ 0 + (Days | Subject), sleepstudy) 193s > (lsm <- ls_means(m)) 193s Least Squares Means table: 193s 193s Estimate Std. Error df t value lower upper Pr(>|t|) 193s 193s Confidence level: 95% 193s Degrees of freedom method: Satterthwaite 193s > stopifnot( 193s + nrow(lsm) == 0L, 193s + ncol(lsm) == 7L 193s + ) 193s > 193s > ########### Arguments and options: 193s > 193s > # which 193s > model <- lmer(angle ~ recipe * temperature + (1|recipe:replicate), cake2) 193s > (lsm4 <- ls_means(model, which = "recipe")) 193s Least Squares Means table: 193s 193s Estimate Std. Error df t value lower upper Pr(>|t|) 193s recipeA 33.1222 1.7368 42 19.070 29.6172 36.6273 < 2.2e-16 *** 193s recipeB 31.6444 1.7368 42 18.220 28.1394 35.1495 < 2.2e-16 *** 193s recipeC 31.6000 1.7368 42 18.194 28.0949 35.1051 < 2.2e-16 *** 193s --- 193s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 193s 193s Confidence level: 95% 193s Degrees of freedom method: Satterthwaite 193s > stopifnot( 193s + nrow(lsm4) == 3L, 193s + ncol(lsm4) == 7L, 193s + isTRUE(all.equal(lsm3[1:3, ], lsm4, check.attributes=FALSE, tolerance=TOL)) 193s + ) 193s > 193s > # KR: 193s > if(has_pbkrtest) 193s + (lsm5 <- ls_means(model, which = "recipe", ddf = "Kenward-Roger")) 193s Least Squares Means table: 193s 193s Estimate Std. Error df t value lower upper Pr(>|t|) 193s recipeA 33.1222 1.7368 42 19.070 29.6172 36.6273 < 2.2e-16 *** 193s recipeB 31.6444 1.7368 42 18.220 28.1394 35.1495 < 2.2e-16 *** 193s recipeC 31.6000 1.7368 42 18.194 28.0949 35.1051 < 2.2e-16 *** 193s --- 193s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 193s 193s Confidence level: 95% 193s Degrees of freedom method: Kenward-Roger 193s > 193s > # level: 193s > (lsm6 <- ls_means(model, which = "recipe", level=0.99)) 193s Least Squares Means table: 193s 193s Estimate Std. Error df t value lower upper Pr(>|t|) 193s recipeA 33.1222 1.7368 42 19.070 28.4361 37.8083 < 2.2e-16 *** 193s recipeB 31.6444 1.7368 42 18.220 26.9584 36.3305 < 2.2e-16 *** 193s recipeC 31.6000 1.7368 42 18.194 26.9139 36.2861 < 2.2e-16 *** 193s --- 193s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 193s 193s Confidence level: 99% 193s Degrees of freedom method: Satterthwaite 193s > 193s > stopifnot( 193s + all(lsm6[, "lower"] < lsm4[, "lower"]), 193s + all(lsm6[, "upper"] > lsm4[, "upper"]) 193s + ) 193s > 193s > 193s > 193s > ########### Missing cels -> unestimable contrasts: 193s > 193s > # Missing cell: 193s > cake3 <- cake 193s > cake3$temperature <- factor(cake3$temperature, ordered=FALSE) 193s > cake3 <- droplevels(subset(cake3, temperature %in% levels(cake3$temperature)[1:3])) 193s > cake3 <- droplevels(subset(cake3, !(recipe == "C" & temperature == "195") )) 193s > str(cake3) 193s 'data.frame': 120 obs. of 5 variables: 193s $ replicate : Factor w/ 15 levels "1","2","3","4",..: 1 1 1 1 1 1 1 1 2 2 ... 193s $ recipe : Factor w/ 3 levels "A","B","C": 1 1 1 2 2 2 3 3 1 1 ... 193s $ temperature: Factor w/ 3 levels "175","185","195": 1 2 3 1 2 3 1 2 1 2 ... 193s $ angle : int 42 46 47 39 46 51 46 44 47 29 ... 193s $ temp : num 175 185 195 175 185 195 175 185 175 185 ... 193s > with(cake3, table(recipe, temperature)) 193s temperature 193s recipe 175 185 195 193s A 15 15 15 193s B 15 15 15 193s C 15 15 0 193s > model <- lmer(angle ~ recipe * temperature + (1|recipe:replicate), cake3) 193s fixed-effect model matrix is rank deficient so dropping 1 column / coefficient 193s > (lsm7 <- ls_means(model)) 193s Least Squares Means table: 193s 193s Estimate Std. Error df t value lower upper 193s recipeA 30.4889 1.7407 40.3 17.515 26.9716 34.0062 193s recipeB 29.3333 1.7407 40.3 16.851 25.8160 32.8506 193s recipeC NA NA NA NA NA NA 193s temperature175 27.9778 1.1016 57.2 25.398 25.7720 30.1835 193s temperature185 29.9556 1.1016 57.2 27.193 27.7498 32.1613 193s temperature195 NA NA NA NA NA NA 193s recipeA:temperature175 29.1333 1.9080 57.2 15.269 25.3129 32.9538 193s recipeB:temperature175 26.8667 1.9080 57.2 14.081 23.0462 30.6871 193s recipeC:temperature175 27.9333 1.9080 57.2 14.640 24.1129 31.7538 193s recipeA:temperature185 31.5333 1.9080 57.2 16.527 27.7129 35.3538 193s recipeB:temperature185 29.4000 1.9080 57.2 15.409 25.5795 33.2205 193s recipeC:temperature185 28.9333 1.9080 57.2 15.164 25.1129 32.7538 193s recipeA:temperature195 30.8000 1.9080 57.2 16.143 26.9795 34.6205 193s recipeB:temperature195 31.7333 1.9080 57.2 16.632 27.9129 35.5538 193s recipeC:temperature195 NA NA NA NA NA NA 193s Pr(>|t|) 193s recipeA < 2.2e-16 *** 193s recipeB < 2.2e-16 *** 193s recipeC NA 193s temperature175 < 2.2e-16 *** 193s temperature185 < 2.2e-16 *** 193s temperature195 NA 193s recipeA:temperature175 < 2.2e-16 *** 193s recipeB:temperature175 < 2.2e-16 *** 193s recipeC:temperature175 < 2.2e-16 *** 193s recipeA:temperature185 < 2.2e-16 *** 193s recipeB:temperature185 < 2.2e-16 *** 193s recipeC:temperature185 < 2.2e-16 *** 193s recipeA:temperature195 < 2.2e-16 *** 193s recipeB:temperature195 < 2.2e-16 *** 193s recipeC:temperature195 NA 193s --- 193s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 193s 193s Confidence level: 95% 193s Degrees of freedom method: Satterthwaite 193s > 193s > # Using show_tests with options: 193s > show_tests(lsm7, fractions = TRUE) 193s $recipe 193s (Intercept) recipeB recipeC temperature185 temperature195 193s recipeA 1 0 0 1/3 1/3 193s recipeB 1 1 0 1/3 1/3 193s recipeC 1 0 1 1/3 1/3 193s recipeB:temperature185 recipeC:temperature185 recipeB:temperature195 193s recipeA 0 0 0 193s recipeB 1/3 0 1/3 193s recipeC 0 1/3 0 193s recipeC:temperature195 193s recipeA 0 193s recipeB 0 193s recipeC 1/3 193s 193s $temperature 193s (Intercept) recipeB recipeC temperature185 temperature195 193s temperature175 1 1/3 1/3 0 0 193s temperature185 1 1/3 1/3 1 0 193s temperature195 1 1/3 1/3 0 1 193s recipeB:temperature185 recipeC:temperature185 193s temperature175 0 0 193s temperature185 1/3 1/3 193s temperature195 0 0 193s recipeB:temperature195 recipeC:temperature195 193s temperature175 0 0 193s temperature185 0 0 193s temperature195 1/3 1/3 193s 193s $`recipe:temperature` 193s (Intercept) recipeB recipeC temperature185 193s recipeA:temperature175 1 0 0 0 193s recipeB:temperature175 1 1 0 0 193s recipeC:temperature175 1 0 1 0 193s recipeA:temperature185 1 0 0 1 193s recipeB:temperature185 1 1 0 1 193s recipeC:temperature185 1 0 1 1 193s recipeA:temperature195 1 0 0 0 193s recipeB:temperature195 1 1 0 0 193s recipeC:temperature195 1 0 1 0 193s temperature195 recipeB:temperature185 193s recipeA:temperature175 0 0 193s recipeB:temperature175 0 0 193s recipeC:temperature175 0 0 193s recipeA:temperature185 0 0 193s recipeB:temperature185 0 1 193s recipeC:temperature185 0 0 193s recipeA:temperature195 1 0 193s recipeB:temperature195 1 0 193s recipeC:temperature195 1 0 193s recipeC:temperature185 recipeB:temperature195 193s recipeA:temperature175 0 0 193s recipeB:temperature175 0 0 193s recipeC:temperature175 0 0 193s recipeA:temperature185 0 0 193s recipeB:temperature185 0 0 193s recipeC:temperature185 1 0 193s recipeA:temperature195 0 0 193s recipeB:temperature195 0 1 193s recipeC:temperature195 0 0 193s recipeC:temperature195 193s recipeA:temperature175 0 193s recipeB:temperature175 0 193s recipeC:temperature175 0 193s recipeA:temperature185 0 193s recipeB:temperature185 0 193s recipeC:temperature185 0 193s recipeA:temperature195 0 193s recipeB:temperature195 0 193s recipeC:temperature195 1 193s 193s > show_tests(lsm7, fractions = TRUE, names = FALSE) 193s $recipe 193s [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] 193s [1,] 1 0 0 1/3 1/3 0 0 0 0 193s [2,] 1 1 0 1/3 1/3 1/3 0 1/3 0 193s [3,] 1 0 1 1/3 1/3 0 1/3 0 1/3 193s 193s $temperature 193s [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] 193s [1,] 1 1/3 1/3 0 0 0 0 0 0 193s [2,] 1 1/3 1/3 1 0 1/3 1/3 0 0 193s [3,] 1 1/3 1/3 0 1 0 0 1/3 1/3 193s 193s $`recipe:temperature` 193s [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] 193s [1,] 1 0 0 0 0 0 0 0 0 193s [2,] 1 1 0 0 0 0 0 0 0 193s [3,] 1 0 1 0 0 0 0 0 0 193s [4,] 1 0 0 1 0 0 0 0 0 193s [5,] 1 1 0 1 0 1 0 0 0 193s [6,] 1 0 1 1 0 0 1 0 0 193s [7,] 1 0 0 0 1 0 0 0 0 193s [8,] 1 1 0 0 1 0 0 1 0 193s [9,] 1 0 1 0 1 0 0 0 1 193s 193s > 193s > # Missing diagonal: 193s > cake4 <- cake 193s > cake4$temperature <- factor(cake4$temperature, ordered=FALSE) 193s > cake4 <- droplevels(subset(cake4, temperature %in% levels(cake4$temperature)[1:3])) 193s > cake4 <- droplevels(subset(cake4, !((recipe == "A" & temperature == "175") | 193s + (recipe == "B" & temperature == "185") | 193s + (recipe == "C" & temperature == "195") ))) 193s > # str(cake4) 193s > with(cake4, table(recipe, temperature)) 193s temperature 193s recipe 175 185 195 193s A 0 15 15 193s B 15 0 15 193s C 15 15 0 193s > model <- lmer(angle ~ recipe * temperature + (1|recipe:replicate), cake4) 193s fixed-effect model matrix is rank deficient so dropping 3 columns / coefficients 193s > ls_means(model) 193s Least Squares Means table: 193s 193s Estimate Std. Error df t value lower upper 193s recipeA NA NA NA NA NA NA 193s recipeB NA NA NA NA NA NA 193s recipeC NA NA NA NA NA NA 193s temperature175 NA NA NA NA NA NA 193s temperature185 NA NA NA NA NA NA 193s temperature195 NA NA NA NA NA NA 193s recipeA:temperature175 NA NA NA NA NA NA 193s recipeB:temperature175 26.8667 1.8908 53.5 14.209 23.0750 30.6584 193s recipeC:temperature175 27.9333 1.8908 53.5 14.773 24.1416 31.7250 193s recipeA:temperature185 31.5333 1.8908 53.5 16.677 27.7416 35.3250 193s recipeB:temperature185 NA NA NA NA NA NA 193s recipeC:temperature185 28.9333 1.8908 53.5 15.302 25.1416 32.7250 193s recipeA:temperature195 30.8000 1.8908 53.5 16.289 27.0083 34.5917 193s recipeB:temperature195 31.7333 1.8908 53.5 16.783 27.9416 35.5250 193s recipeC:temperature195 NA NA NA NA NA NA 193s Pr(>|t|) 193s recipeA NA 193s recipeB NA 193s recipeC NA 193s temperature175 NA 193s temperature185 NA 193s temperature195 NA 193s recipeA:temperature175 NA 193s recipeB:temperature175 < 2.2e-16 *** 193s recipeC:temperature175 < 2.2e-16 *** 193s recipeA:temperature185 < 2.2e-16 *** 193s recipeB:temperature185 NA 193s recipeC:temperature185 < 2.2e-16 *** 193s recipeA:temperature195 < 2.2e-16 *** 193s recipeB:temperature195 < 2.2e-16 *** 193s recipeC:temperature195 NA 193s --- 193s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 193s 193s Confidence level: 95% 193s Degrees of freedom method: Satterthwaite 193s > 193s > 193s > ########### Various contrasts codings: 193s > 193s > model <- lmer(angle ~ recipe * temperature + (1|recipe:replicate), cake3, 193s + contrasts = list(recipe="contr.sum", temperature="contr.helmert")) 193s fixed-effect model matrix is rank deficient so dropping 1 column / coefficient 193s > (lsm8 <- ls_means(model)) 193s Least Squares Means table: 193s 193s Estimate Std. Error df t value lower upper 193s recipeA 30.4889 1.7407 40.3 17.515 26.9716 34.0062 193s recipeB 29.3333 1.7407 40.3 16.851 25.8160 32.8506 193s recipeC NA NA NA NA NA NA 193s temperature175 27.9778 1.1016 57.2 25.398 25.7720 30.1835 193s temperature185 29.9556 1.1016 57.2 27.193 27.7498 32.1613 193s temperature195 NA NA NA NA NA NA 193s recipeA:temperature175 29.1333 1.9080 57.2 15.269 25.3129 32.9538 193s recipeB:temperature175 26.8667 1.9080 57.2 14.081 23.0462 30.6871 193s recipeC:temperature175 27.9333 1.9080 57.2 14.640 24.1129 31.7538 193s recipeA:temperature185 31.5333 1.9080 57.2 16.527 27.7129 35.3538 193s recipeB:temperature185 29.4000 1.9080 57.2 15.409 25.5795 33.2205 193s recipeC:temperature185 28.9333 1.9080 57.2 15.164 25.1129 32.7538 193s recipeA:temperature195 30.8000 1.9080 57.2 16.143 26.9795 34.6205 193s recipeB:temperature195 31.7333 1.9080 57.2 16.632 27.9129 35.5538 193s recipeC:temperature195 NA NA NA NA NA NA 193s Pr(>|t|) 193s recipeA < 2.2e-16 *** 193s recipeB < 2.2e-16 *** 193s recipeC NA 193s temperature175 < 2.2e-16 *** 193s temperature185 < 2.2e-16 *** 193s temperature195 NA 193s recipeA:temperature175 < 2.2e-16 *** 193s recipeB:temperature175 < 2.2e-16 *** 193s recipeC:temperature175 < 2.2e-16 *** 193s recipeA:temperature185 < 2.2e-16 *** 193s recipeB:temperature185 < 2.2e-16 *** 193s recipeC:temperature185 < 2.2e-16 *** 193s recipeA:temperature195 < 2.2e-16 *** 193s recipeB:temperature195 < 2.2e-16 *** 193s recipeC:temperature195 NA 193s --- 193s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 193s 193s Confidence level: 95% 193s Degrees of freedom method: Satterthwaite 193s > # show_tests(lsm7) 193s > # show_tests(lsm8) 193s > stopifnot( 193s + isTRUE(all.equal(lsm7, lsm8, check.attributes=FALSE, tolerance=TOL)) 193s + ) 193s > 193s > # ambient contrasts not contr.treatment: 193s > options("contrasts") 193s $contrasts 193s unordered ordered 193s "contr.treatment" "contr.poly" 193s 193s > options(contrasts = c("contr.sum", "contr.poly")) 193s > model <- lmer(angle ~ recipe * temperature + (1|recipe:replicate), cake3) 193s fixed-effect model matrix is rank deficient so dropping 1 column / coefficient 193s > (lsm9 <- ls_means(model)) 193s Least Squares Means table: 193s 193s Estimate Std. Error df t value lower upper 193s recipeA 30.4889 1.7407 40.3 17.515 26.9716 34.0062 193s recipeB 29.3333 1.7407 40.3 16.851 25.8160 32.8506 193s recipeC NA NA NA NA NA NA 193s temperature175 27.9778 1.1016 57.2 25.398 25.7720 30.1835 193s temperature185 29.9556 1.1016 57.2 27.193 27.7498 32.1613 193s temperature195 NA NA NA NA NA NA 193s recipeA:temperature175 29.1333 1.9080 57.2 15.269 25.3129 32.9538 193s recipeB:temperature175 26.8667 1.9080 57.2 14.081 23.0462 30.6871 193s recipeC:temperature175 27.9333 1.9080 57.2 14.640 24.1129 31.7538 193s recipeA:temperature185 31.5333 1.9080 57.2 16.527 27.7129 35.3538 193s recipeB:temperature185 29.4000 1.9080 57.2 15.409 25.5795 33.2205 193s recipeC:temperature185 28.9333 1.9080 57.2 15.164 25.1129 32.7538 193s recipeA:temperature195 30.8000 1.9080 57.2 16.143 26.9795 34.6205 193s recipeB:temperature195 31.7333 1.9080 57.2 16.632 27.9129 35.5538 193s recipeC:temperature195 NA NA NA NA NA NA 193s Pr(>|t|) 193s recipeA < 2.2e-16 *** 193s recipeB < 2.2e-16 *** 193s recipeC NA 193s temperature175 < 2.2e-16 *** 193s temperature185 < 2.2e-16 *** 193s temperature195 NA 193s recipeA:temperature175 < 2.2e-16 *** 193s recipeB:temperature175 < 2.2e-16 *** 193s recipeC:temperature175 < 2.2e-16 *** 193s recipeA:temperature185 < 2.2e-16 *** 193s recipeB:temperature185 < 2.2e-16 *** 193s recipeC:temperature185 < 2.2e-16 *** 193s recipeA:temperature195 < 2.2e-16 *** 193s recipeB:temperature195 < 2.2e-16 *** 193s recipeC:temperature195 NA 193s --- 193s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 193s 193s Confidence level: 95% 193s Degrees of freedom method: Satterthwaite 193s > options(contrasts = c("contr.treatment", "contr.poly")) 193s > options("contrasts") 193s $contrasts 193s [1] "contr.treatment" "contr.poly" 193s 193s > stopifnot( 193s + isTRUE(all.equal(lsm7, lsm9, check.attributes=FALSE, tolerance=TOL)) 193s + ) 193s > 193s > 193s > 193s BEGIN TEST test_ranova_step.R 193s 193s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 193s Copyright (C) 2025 The R Foundation for Statistical Computing 193s Platform: x86_64-pc-linux-gnu 193s 193s R is free software and comes with ABSOLUTELY NO WARRANTY. 193s You are welcome to redistribute it under certain conditions. 193s Type 'license()' or 'licence()' for distribution details. 193s 193s R is a collaborative project with many contributors. 193s Type 'contributors()' for more information and 193s 'citation()' on how to cite R or R packages in publications. 193s 193s Type 'demo()' for some demos, 'help()' for on-line help, or 193s 'help.start()' for an HTML browser interface to help. 193s Type 'q()' to quit R. 193s 193s > # test_ranova.R 193s > 193s > # Test functionality _before_ attaching lmerTest 193s > stopifnot(!"lmerTest" %in% .packages()) # ensure that lmerTest is NOT attached 193s > data("sleepstudy", package="lme4") 193s > f <- function(form, data) lmerTest::lmer(form, data=data) 193s > form <- "Reaction ~ Days + (Days|Subject)" 193s > fm <- f(form, data=sleepstudy) 195s > lmerTest::ranova(fm) 195s ANOVA-like table for random-effects: Single term deletions 195s 195s Model: 195s Reaction ~ Days + (Days | Subject) 195s npar logLik AIC LRT Df Pr(>Chisq) 195s 6 -871.81 1755.6 195s Days in (Days | Subject) 4 -893.23 1794.5 42.837 2 4.99e-10 *** 195s --- 195s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 195s > lmerTest::rand(fm) 195s ANOVA-like table for random-effects: Single term deletions 195s 195s Model: 195s Reaction ~ Days + (Days | Subject) 195s npar logLik AIC LRT Df Pr(>Chisq) 195s 6 -871.81 1755.6 195s Days in (Days | Subject) 4 -893.23 1794.5 42.837 2 4.99e-10 *** 195s --- 195s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 195s > lmerTest::step(fm) 195s Backward reduced random-effect table: 195s 195s Eliminated npar logLik AIC LRT Df Pr(>Chisq) 195s Loading required package: lme4 195s Loading required package: Matrix 195s 6 -871.81 1755.6 195s Days in (Days | Subject) 0 4 -893.23 1794.5 42.837 2 4.99e-10 195s 195s 195s Days in (Days | Subject) *** 195s --- 195s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 195s 195s Backward reduced fixed-effect table: 195s Degrees of freedom method: Satterthwaite 195s 195s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 195s Days 0 30031 30031 1 17 45.853 3.264e-06 *** 195s --- 195s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 195s 195s Model found: 195s Reaction ~ Days + (Days | Subject) 195s > 195s > library(lmerTest) 195s 195s Attaching package: 'lmerTest' 195s 195s The following object is masked from 'package:lme4': 195s 195s lmer 195s 195s The following object is masked from 'package:stats': 195s 195s step 195s 195s > 195s > # WRE says "using if(requireNamespace("pkgname")) is preferred, if possible." 195s > # even in tests: 195s > assertError <- function(expr, ...) 195s + if(requireNamespace("tools")) tools::assertError(expr, ...) else invisible() 195s > assertWarning <- function(expr, ...) 195s + if(requireNamespace("tools")) tools::assertWarning(expr, ...) else invisible() 195s > 195s > TOL <- 1e-4 195s > ##################################################################### 195s > data("sleepstudy", package="lme4") 195s > 195s > # Test reduction of (Days | Subject) to (1 | Subject): 195s > fm1 <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy) 195s > (an <- rand(fm1)) # 2 df test 195s ANOVA-like table for random-effects: Single term deletions 195s 195s Model: 195s Reaction ~ Days + (Days | Subject) 195s npar logLik AIC LRT Df Pr(>Chisq) 195s 6 -871.81 1755.6 195s Days in (Days | Subject) 4 -893.23 1794.5 42.837 2 4.99e-10 *** 195s --- 195s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 195s > (an <- ranova(fm1)) # 2 df test 195s ANOVA-like table for random-effects: Single term deletions 195s 195s Model: 195s Reaction ~ Days + (Days | Subject) 195s npar logLik AIC LRT Df Pr(>Chisq) 195s 6 -871.81 1755.6 195s Days in (Days | Subject) 4 -893.23 1794.5 42.837 2 4.99e-10 *** 195s --- 195s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 195s > step(fm1) 195s Backward reduced random-effect table: 195s 195s Eliminated npar logLik AIC LRT Df Pr(>Chisq) 195s 6 -871.81 1755.6 195s Days in (Days | Subject) 0 4 -893.23 1794.5 42.837 2 4.99e-10 195s 195s 195s Days in (Days | Subject) *** 195s --- 195s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 195s 195s Backward reduced fixed-effect table: 195s Degrees of freedom method: Satterthwaite 195s 195s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 195s Days 0 30031 30031 1 17 45.853 3.264e-06 *** 195s --- 195s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 195s 195s Model found: 195s Reaction ~ Days + (Days | Subject) 195s > stopifnot( 195s + nrow(an) == 2L, 195s + an[2L, "Df"] == 2L 195s + ) 195s > 195s > # This test can also be achieved with anova(): 195s > fm2 <- lmer(Reaction ~ Days + (1|Subject), sleepstudy) 195s > (stp <- step(fm2)) 195s Backward reduced random-effect table: 195s 195s Eliminated npar logLik AIC LRT Df Pr(>Chisq) 195s 4 -893.23 1794.5 195s (1 | Subject) 0 3 -946.83 1899.7 107.2 1 < 2.2e-16 *** 195s --- 195s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 195s 195s Backward reduced fixed-effect table: 195s Degrees of freedom method: Satterthwaite 195s 195s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 195s Days 0 162703 162703 1 161 169.4 < 2.2e-16 *** 195s --- 195s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 195s 195s Model found: 195s Reaction ~ Days + (1 | Subject) 195s > get_model(stp) 195s Linear mixed model fit by REML ['lmerModLmerTest'] 195s Formula: Reaction ~ Days + (1 | Subject) 195s Data: sleepstudy 195s REML criterion at convergence: 1786.465 195s Random effects: 195s Groups Name Std.Dev. 195s Subject (Intercept) 37.12 195s Residual 30.99 195s Number of obs: 180, groups: Subject, 18 195s Fixed Effects: 195s (Intercept) Days 195s 251.41 10.47 195s > (ana <- anova(fm1, fm2, refit=FALSE)) 195s Data: sleepstudy 195s Models: 195s fm2: Reaction ~ Days + (1 | Subject) 195s fm1: Reaction ~ Days + (Days | Subject) 195s npar AIC BIC logLik -2*log(L) Chisq Df Pr(>Chisq) 195s fm2 4 1794.5 1807.2 -893.23 1786.5 195s fm1 6 1755.6 1774.8 -871.81 1743.6 42.837 2 4.99e-10 *** 195s --- 195s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 195s > 195s > stopifnot( 195s + all.equal(an[2L, "LRT"], ana[2L, "Chisq"], tolerance=TOL) 195s + ) 195s > 195s > # Illustrate complete.test argument: 195s > # Test removal of (Days | Subject): 195s > (an <- ranova(fm1, reduce.terms = FALSE)) # 3 df test 195s ANOVA-like table for random-effects: Single term deletions 195s 195s Model: 195s Reaction ~ Days + (Days | Subject) 195s npar logLik AIC LRT Df Pr(>Chisq) 195s 6 -871.81 1755.6 195s (Days | Subject) 3 -946.83 1899.7 150.03 3 < 2.2e-16 *** 195s --- 195s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 195s > 195s > # The likelihood ratio test statistic is in this case: 195s > fm3 <- lm(Reaction ~ Days, sleepstudy) 195s > LRT <- 2*c(logLik(fm1, REML=TRUE) - logLik(fm3, REML=TRUE)) # LRT 195s > stopifnot( 195s + nrow(an) == 2L, 195s + an[2L, "Df"] == 3L, 195s + all.equal(an[2L, "LRT"], LRT, tolerance=TOL) 195s + ) 195s > 195s > ## _NULL_ model: 195s > fm <- lmer(Reaction ~ -1 + (1|Subject), sleepstudy) 195s > step(fm) 195s Backward reduced random-effect table: 195s 195s Eliminated npar logLik AIC LRT Df Pr(>Chisq) 195s 2 -992.84 1989.7 195s (1 | Subject) 0 1 -1284.32 2570.7 582.97 1 < 2.2e-16 *** 195s --- 195s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 195s 195s Backward reduced fixed-effect table: 195s Degrees of freedom method: Satterthwaite 195s 195s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 195s 195s Model found: 195s Reaction ~ -1 + (1 | Subject) 195s > ranova(fm) 195s ANOVA-like table for random-effects: Single term deletions 195s 195s Model: 195s Reaction ~ -1 + (1 | Subject) 195s npar logLik AIC LRT Df Pr(>Chisq) 195s 2 -992.84 1989.7 195s (1 | Subject) 1 -1284.32 2570.7 582.97 1 < 2.2e-16 *** 195s --- 195s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 195s > lm1 <- lm(Reaction ~ 0, data=sleepstudy) 195s > LRT <- 2*c(logLik(fm, REML=FALSE) - logLik(lm1, REML=FALSE)) 195s > 195s > ## Tests of ML-fits agree with anova(): 195s > fm1 <- lmer(Reaction ~ Days + (1|Subject), sleepstudy, REML=FALSE) 195s > step(fm1) 195s Backward reduced random-effect table: 195s 195s Eliminated npar logLik AIC LRT Df Pr(>Chisq) 195s 4 -897.04 1802.1 195s (1 | Subject) 0 3 -950.15 1906.3 106.21 1 < 2.2e-16 *** 195s --- 195s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 195s 195s Backward reduced fixed-effect table: 195s Degrees of freedom method: Satterthwaite 195s 195s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 195s Days 0 162703 162703 1 162 170.45 < 2.2e-16 *** 195s --- 195s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 195s 195s Model found: 195s Reaction ~ Days + (1 | Subject) 195s > lm2 <- lm(Reaction ~ Days, sleepstudy) 195s > (an1 <- ranova(fm1)) 195s ANOVA-like table for random-effects: Single term deletions 195s 195s Model: 195s Reaction ~ Days + (1 | Subject) 195s npar logLik AIC LRT Df Pr(>Chisq) 195s 4 -897.04 1802.1 195s (1 | Subject) 3 -950.15 1906.3 106.21 1 < 2.2e-16 *** 195s --- 195s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 195s > (an2 <- anova(fm1, lm2)) 195s Data: sleepstudy 195s Models: 195s lm2: Reaction ~ Days 195s fm1: Reaction ~ Days + (1 | Subject) 195s npar AIC BIC logLik -2*log(L) Chisq Df Pr(>Chisq) 195s lm2 3 1906.3 1915.9 -950.15 1900.3 195s fm1 4 1802.1 1814.8 -897.04 1794.1 106.21 1 < 2.2e-16 *** 195s --- 195s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 195s > j <- grep("Chi Df|Df", colnames(an2)) 195s > stopifnot( 195s + all.equal(an1[2, "LRT"], an2[2, "Chisq"], tolerance=TOL), 195s + all.equal(an1[2, "Df"], an2[2, j[length(j)]], tolerance=TOL), 195s + all.equal(an1[1:2, "logLik"], an2[2:1, "logLik"], tolerance=TOL) 195s + ) 195s > ## Note that lme4 version <1.1-22 use "Chi Df" while >=1.1-22 use "Df" 195s > 195s > # Expect warnings when old (version < 3.0-0) arguments are used: 195s > assertWarning(step(fm, reduce.fixed = FALSE, reduce.random = FALSE, 195s + type=3, fixed.calc = FALSE, lsmeans.calc = FALSE, 195s + difflsmeans.calc = TRUE, test.effs = 42, keep.e="save")) 195s > assertWarning(step(fm, reduce.fixed = FALSE, reduce.random = FALSE, 195s + lsmeans=3)) 195s > 195s > 195s > check_nrow <- function(obj, expect_nrow) { 195s + stopifnot( 195s + is.numeric(expect_nrow), 195s + nrow(obj) == expect_nrow 195s + ) 195s + } 195s > 195s > # Statistical nonsense, but it works: 195s > fm1 <- lmer(Reaction ~ Days + (1 | Subject) + (0 + Days|Subject), sleepstudy) 195s > step(fm1) 195s Backward reduced random-effect table: 195s 195s Eliminated npar logLik AIC LRT Df 195s 5 -871.83 1753.7 195s (1 | Subject) 0 4 -883.26 1774.5 22.856 1 195s Days in (0 + Days | Subject) 0 4 -893.23 1794.5 42.796 1 195s Pr(>Chisq) 195s 195s (1 | Subject) 1.746e-06 *** 195s Days in (0 + Days | Subject) 6.076e-11 *** 195s --- 195s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 195s 195s Backward reduced fixed-effect table: 195s Degrees of freedom method: Satterthwaite 195s 195s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 195s Days 0 29442 29442 1 18.156 45.046 2.594e-06 *** 195s --- 195s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 195s 195s Model found: 195s Reaction ~ Days + (1 | Subject) + (0 + Days | Subject) 195s > (an <- ranova(fm1)) 195s ANOVA-like table for random-effects: Single term deletions 195s 195s Model: 195s Reaction ~ Days + (1 | Subject) + (0 + Days | Subject) 195s npar logLik AIC LRT Df Pr(>Chisq) 195s 5 -871.83 1753.7 195s (1 | Subject) 4 -883.26 1774.5 22.856 1 1.746e-06 *** 195s Days in (0 + Days | Subject) 4 -893.23 1794.5 42.796 1 6.076e-11 *** 195s --- 195s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 195s > check_nrow(an, 3) 195s > ranova(fm1, reduce.terms = FALSE) 195s ANOVA-like table for random-effects: Single term deletions 195s 195s Model: 195s Reaction ~ Days + (1 | Subject) + (0 + Days | Subject) 195s npar logLik AIC LRT Df Pr(>Chisq) 195s 5 -871.83 1753.7 195s (1 | Subject) 4 -883.26 1774.5 22.856 1 1.746e-06 *** 195s (0 + Days | Subject) 4 -893.23 1794.5 42.796 1 6.076e-11 *** 195s --- 195s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 195s > 195s > # Statistical nonsense, but it works: 195s > fm1 <- lmer(Reaction ~ Days + (0 + Days|Subject), sleepstudy) 195s > step(fm1) 195s Backward reduced random-effect table: 195s 195s Eliminated npar logLik AIC LRT Df Pr(>Chisq) 195s 4 -883.26 1774.5 195s Days in (0 + Days | Subject) 0 4 -893.23 1794.5 19.94 0 195s 195s Backward reduced fixed-effect table: 195s Degrees of freedom method: Satterthwaite 195s 195s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 195s Days 0 26395 26395 1 21.679 31.347 1.32e-05 *** 195s --- 195s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 195s 195s Model found: 195s Reaction ~ Days + (0 + Days | Subject) 195s > (an <- ranova(fm1)) # no test of non-nested models 195s ANOVA-like table for random-effects: Single term deletions 195s 195s Model: 195s Reaction ~ Days + (0 + Days | Subject) 195s npar logLik AIC LRT Df Pr(>Chisq) 195s 4 -883.26 1774.5 195s Days in (0 + Days | Subject) 4 -893.23 1794.5 19.94 0 195s > stopifnot( 195s + nrow(an) == 2L, 195s + an[2L, "Df"] == 0, 195s + all(is.na(an[2L, "Pr(>Chisq)"])) 195s + ) 195s > fm0 <- lmer(Reaction ~ Days + (1|Subject), sleepstudy) 195s > step(fm0) 195s Backward reduced random-effect table: 195s 195s Eliminated npar logLik AIC LRT Df Pr(>Chisq) 195s 4 -893.23 1794.5 195s (1 | Subject) 0 3 -946.83 1899.7 107.2 1 < 2.2e-16 *** 195s --- 195s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 195s 195s Backward reduced fixed-effect table: 195s Degrees of freedom method: Satterthwaite 195s 195s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 195s Days 0 162703 162703 1 161 169.4 < 2.2e-16 *** 195s --- 195s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 195s 195s Model found: 195s Reaction ~ Days + (1 | Subject) 195s > (an2 <- anova(fm1, fm0, refit=FALSE)) 195s Data: sleepstudy 195s Models: 195s fm1: Reaction ~ Days + (0 + Days | Subject) 195s fm0: Reaction ~ Days + (1 | Subject) 195s npar AIC BIC logLik -2*log(L) Chisq Df Pr(>Chisq) 195s fm1 4 1774.5 1787.3 -883.26 1766.5 195s fm0 4 1794.5 1807.2 -893.23 1786.5 0 0 195s > stopifnot( 195s + (packageVersion("lme4")<="1.1.23" && an2[2L, "Pr(>Chisq)"] == 1) || 195s + is.na(an2[2L, "Pr(>Chisq)"]) 195s + ) 195s > ranova(fm1, reduce.terms = FALSE) 195s ANOVA-like table for random-effects: Single term deletions 195s 195s Model: 195s Reaction ~ Days + (0 + Days | Subject) 195s npar logLik AIC LRT Df Pr(>Chisq) 195s 4 -883.26 1774.5 195s (0 + Days | Subject) 3 -946.83 1899.7 127.14 1 < 2.2e-16 *** 195s --- 195s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 195s > 195s > fm1 <- lmer(Reaction ~ Days + (-1 + Days|Subject), sleepstudy) 195s > step(fm1) 195s Backward reduced random-effect table: 195s 195s Eliminated npar logLik AIC LRT Df 195s 4 -883.26 1774.5 195s Days in (-1 + Days | Subject) 0 4 -893.23 1794.5 19.94 0 195s Pr(>Chisq) 195s 195s Days in (-1 + Days | Subject) 195s 195s Backward reduced fixed-effect table: 195s Degrees of freedom method: Satterthwaite 195s 195s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 195s Days 0 26395 26395 1 21.679 31.347 1.32e-05 *** 195s --- 195s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 195s 195s Model found: 195s Reaction ~ Days + (-1 + Days | Subject) 195s > (an3 <- ranova(fm1)) # no test of non-nested models 195s ANOVA-like table for random-effects: Single term deletions 195s 195s Model: 195s Reaction ~ Days + (-1 + Days | Subject) 195s npar logLik AIC LRT Df Pr(>Chisq) 195s 4 -883.26 1774.5 195s Days in (-1 + Days | Subject) 4 -893.23 1794.5 19.94 0 195s > stopifnot( 195s + all.equal(an, an3, check.attributes=FALSE, tolerance=TOL) 195s + ) 195s > 195s > # Example where comparison of non-nested models is generated 195s > fm <- lmer(Reaction ~ poly(Days, 2) + (0 + poly(Days, 2) | Subject), sleepstudy) 196s boundary (singular) fit: see help('isSingular') 196s > step(fm) 196s Backward reduced random-effect table: 196s 196s Eliminated npar logLik AIC 196s 7 -937.05 1888.1 196s poly(Days, 2) in (0 + poly(Days, 2) | Subject) 1 5 -884.67 1779.3 196s (1 | Subject) 0 4 -938.16 1884.3 196s LRT Df Pr(>Chisq) 196s 196s poly(Days, 2) in (0 + poly(Days, 2) | Subject) -104.77 2 1 196s (1 | Subject) 106.98 1 <2e-16 *** 196s --- 196s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 196s 196s Backward reduced fixed-effect table: 196s Degrees of freedom method: Satterthwaite 196s 196s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 196s poly(Days, 2) 0 163782 81891 2 160 85.329 < 2.2e-16 *** 196s --- 196s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 196s 196s Model found: 196s Reaction ~ poly(Days, 2) + (1 | Subject) 196s > an <- ranova(fm) 196s > stopifnot( 196s + nrow(an) == 2L, 196s + an[2, "Pr(>Chisq)"] == 1 196s + ) 196s > ranova(fm, reduce.terms = FALSE) # test of nested models 196s ANOVA-like table for random-effects: Single term deletions 196s 196s Model: 196s Reaction ~ poly(Days, 2) + (0 + poly(Days, 2) | Subject) 196s npar logLik AIC LRT Df Pr(>Chisq) 196s 7 -937.05 1888.1 196s (0 + poly(Days, 2) | Subject) 4 -938.16 1884.3 2.2153 3 0.5289 196s > 196s > # These models are nested, though: 196s > fm <- lmer(Reaction ~ poly(Days, 2) + (1 + poly(Days, 2) | Subject), sleepstudy) 196s > step(fm) 196s Backward reduced random-effect table: 196s 196s Eliminated npar logLik AIC 196s 10 -856.40 1732.8 196s poly(Days, 2) in (1 + poly(Days, 2) | Subject) 0 5 -884.67 1779.3 196s LRT Df Pr(>Chisq) 196s 196s poly(Days, 2) in (1 + poly(Days, 2) | Subject) 56.524 5 6.338e-11 *** 196s --- 196s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 196s 196s Backward reduced fixed-effect table: 196s Degrees of freedom method: Satterthwaite 196s 196s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 196s poly(Days, 2) 0 24216 12108 2 17 23.367 1.323e-05 *** 196s --- 196s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 196s 196s Model found: 196s Reaction ~ poly(Days, 2) + (1 + poly(Days, 2) | Subject) 196s > ranova(fm) 196s ANOVA-like table for random-effects: Single term deletions 196s 196s Model: 196s Reaction ~ poly(Days, 2) + (1 + poly(Days, 2) | Subject) 196s npar logLik AIC LRT Df 196s 10 -856.40 1732.8 196s poly(Days, 2) in (1 + poly(Days, 2) | Subject) 5 -884.67 1779.3 56.524 5 196s Pr(>Chisq) 196s 196s poly(Days, 2) in (1 + poly(Days, 2) | Subject) 6.338e-11 *** 196s --- 196s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 196s > fm0 <- lmer(Reaction ~ poly(Days, 2) + (1 | Subject), sleepstudy) 196s > step(fm0) 196s Backward reduced random-effect table: 196s 196s Eliminated npar logLik AIC LRT Df Pr(>Chisq) 196s 5 -884.67 1779.3 196s (1 | Subject) 0 4 -938.16 1884.3 106.98 1 < 2.2e-16 *** 196s --- 196s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 196s 196s Backward reduced fixed-effect table: 196s Degrees of freedom method: Satterthwaite 196s 196s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 196s poly(Days, 2) 0 163782 81891 2 160 85.329 < 2.2e-16 *** 196s --- 196s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 196s 196s Model found: 196s Reaction ~ poly(Days, 2) + (1 | Subject) 196s > anova(fm0, fm, refit=FALSE) 196s Data: sleepstudy 196s Models: 196s fm0: Reaction ~ poly(Days, 2) + (1 | Subject) 196s fm: Reaction ~ poly(Days, 2) + (1 + poly(Days, 2) | Subject) 196s npar AIC BIC logLik -2*log(L) Chisq Df Pr(>Chisq) 196s fm0 5 1779.3 1795.3 -884.67 1769.3 196s fm 10 1732.8 1764.7 -856.40 1712.8 56.524 5 6.338e-11 *** 196s --- 196s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 196s > ranova(fm, reduce.terms = FALSE) 196s ANOVA-like table for random-effects: Single term deletions 196s 196s Model: 196s Reaction ~ poly(Days, 2) + (1 + poly(Days, 2) | Subject) 196s npar logLik AIC LRT Df Pr(>Chisq) 196s 10 -856.40 1732.8 196s (1 + poly(Days, 2) | Subject) 4 -938.16 1884.3 163.51 6 < 2.2e-16 *** 196s --- 196s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 196s > 196s > # A model with ||-notation: 196s > fm1 <- lmer(Reaction ~ Days + (Days||Subject), sleepstudy) 196s > step(fm1) 196s Backward reduced random-effect table: 196s 196s Eliminated npar logLik AIC LRT Df 196s 5 -871.83 1753.7 196s (1 | Subject) 0 4 -883.26 1774.5 22.856 1 196s Days in (0 + Days | Subject) 0 4 -893.23 1794.5 42.796 1 196s Pr(>Chisq) 196s 196s (1 | Subject) 1.746e-06 *** 196s Days in (0 + Days | Subject) 6.076e-11 *** 196s --- 196s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 196s 196s Backward reduced fixed-effect table: 196s Degrees of freedom method: Satterthwaite 196s 196s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 196s Days 0 29442 29442 1 18.156 45.046 2.594e-06 *** 196s --- 196s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 196s 196s Model found: 196s Reaction ~ Days + ((1 | Subject) + (0 + Days | Subject)) 196s > ranova(fm1) 196s ANOVA-like table for random-effects: Single term deletions 196s 196s Model: 196s Reaction ~ Days + (1 | Subject) + (0 + Days | Subject) 196s npar logLik AIC LRT Df Pr(>Chisq) 196s 5 -871.83 1753.7 196s (1 | Subject) 4 -883.26 1774.5 22.856 1 1.746e-06 *** 196s Days in (0 + Days | Subject) 4 -893.23 1794.5 42.796 1 6.076e-11 *** 196s --- 196s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 196s > 196s > # What about models with nested factors? 196s > fm <- lmer(Coloursaturation ~ TVset*Picture + (1|Assessor:TVset) + (1|Assessor), 196s + data=TVbo) 196s > step(fm) 196s Backward reduced random-effect table: 196s 196s Eliminated npar logLik AIC LRT Df Pr(>Chisq) 196s 15 -280.22 590.44 196s (1 | Assessor) 1 14 -280.27 588.53 0.090 1 0.7643 196s (1 | Assessor:TVset) 0 13 -312.24 650.47 63.941 1 1.282e-15 *** 196s --- 196s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 196s 196s Backward reduced fixed-effect table: 196s Degrees of freedom method: Satterthwaite 196s 196s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 196s TVset:Picture 0 13.8 2.2999 6 159 2.6761 0.01679 * 196s --- 196s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 196s 196s Model found: 196s Coloursaturation ~ TVset + Picture + (1 | Assessor:TVset) + TVset:Picture 196s > (an1 <- ranova(fm)) 196s ANOVA-like table for random-effects: Single term deletions 196s 196s Model: 196s Coloursaturation ~ TVset * Picture + (1 | Assessor:TVset) + (1 | Assessor) 196s npar logLik AIC LRT Df Pr(>Chisq) 196s 15 -280.22 590.44 196s (1 | Assessor:TVset) 14 -302.61 633.22 44.777 1 2.208e-11 *** 196s (1 | Assessor) 14 -280.27 588.53 0.090 1 0.7643 196s --- 196s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 196s > 196s > fm <- lmer(Coloursaturation ~ TVset * Picture + 196s + (1|Assessor/TVset), data=TVbo) 196s > step(fm) 196s Backward reduced random-effect table: 196s 196s Eliminated npar logLik AIC LRT Df Pr(>Chisq) 196s 15 -280.22 590.44 196s (1 | Assessor) 1 14 -280.27 588.53 0.090 1 0.7643 196s (1 | TVset:Assessor) 0 13 -312.24 650.47 63.941 1 1.282e-15 *** 196s --- 196s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 196s 196s Backward reduced fixed-effect table: 196s Degrees of freedom method: Satterthwaite 196s 196s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 196s TVset:Picture 0 13.8 2.2999 6 159 2.6761 0.01679 * 196s --- 196s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 196s 196s Model found: 196s Coloursaturation ~ TVset + Picture + (1 | TVset:Assessor) + TVset:Picture 196s > (an2 <- ranova(fm)) 196s ANOVA-like table for random-effects: Single term deletions 196s 196s Model: 196s Coloursaturation ~ TVset * Picture + (1 | TVset:Assessor) + (1 | Assessor) 196s npar logLik AIC LRT Df Pr(>Chisq) 196s 15 -280.22 590.44 196s (1 | TVset:Assessor) 14 -302.61 633.22 44.777 1 2.208e-11 *** 196s (1 | Assessor) 14 -280.27 588.53 0.090 1 0.7643 196s --- 196s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 196s > stopifnot( 196s + all.equal(an1, an2, check.attributes=FALSE, tolerance=TOL) 196s + ) 196s > 196s > ##################################################################### 196s > # Test evaluation within functions, i.e. in other environments etc. 196s > attach(sleepstudy) 196s > fm <- lmer(Reaction ~ Days + (Days|Subject)) 196s > step(fm) 196s Backward reduced random-effect table: 196s 196s Eliminated npar logLik AIC LRT Df Pr(>Chisq) 196s 6 -871.81 1755.6 196s Days in (Days | Subject) 0 4 -893.23 1794.5 42.837 2 4.99e-10 196s 196s 196s Days in (Days | Subject) *** 196s --- 196s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 196s 196s Backward reduced fixed-effect table: 196s Degrees of freedom method: Satterthwaite 196s 196s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 196s Days 0 30031 30031 1 17 45.853 3.264e-06 *** 196s --- 196s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 196s 196s Model found: 196s Reaction ~ Days + (Days | Subject) 196s > ranova(fm) # OK 196s ANOVA-like table for random-effects: Single term deletions 196s 196s Model: 196s Reaction ~ Days + (Days | Subject) 196s npar logLik AIC LRT Df Pr(>Chisq) 196s 6 -871.81 1755.6 196s Days in (Days | Subject) 4 -893.23 1794.5 42.837 2 4.99e-10 *** 196s --- 196s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 196s > detach(sleepstudy) 196s > 196s > # Evaluating in a function works: 196s > f <- function(form, data) lmer(form, data=data) 196s > form <- "Informed.liking ~ Product+Information+ 196s + (1|Consumer) + (1|Product:Consumer) + (1|Information:Consumer)" 196s > fm <- f(form, data=ham) 197s > ranova(fm) 197s boundary (singular) fit: see help('isSingular') 197s ANOVA-like table for random-effects: Single term deletions 197s 197s Model: 197s Informed.liking ~ Product + Information + (1 | Consumer) + (1 | Product:Consumer) + (1 | Information:Consumer) 197s npar logLik AIC LRT Df Pr(>Chisq) 197s 9 -1353.9 2725.8 197s (1 | Consumer) 8 -1355.1 2726.1 2.295 1 0.1298 197s (1 | Product:Consumer) 8 -1436.3 2888.6 164.753 1 <2e-16 *** 197s (1 | Information:Consumer) 8 -1354.5 2725.1 1.255 1 0.2626 197s --- 197s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 197s > step_res <- step(fm) 197s boundary (singular) fit: see help('isSingular') 197s > stopifnot( 197s + all(c("Sum Sq", "Mean Sq", "NumDF", "DenDF", "F value", "Pr(>F)") %in% 197s + colnames(step_res$fixed)) 197s + ) 197s > 197s > ########################### 197s > # Evaluation in function without the formula: 197s > # Reported by Uwe Ligges 2025-01-16. 197s > f <- function(data) { 197s + lmer(Petal.Length ~ Sepal.Length + (1|Species), data=data) 197s + } 197s > 197s > res <- f(iris) 197s > ranova(res) # used to fail - now it works 197s ANOVA-like table for random-effects: Single term deletions 197s 197s Model: 197s Petal.Length ~ Sepal.Length + (1 | Species) 197s npar logLik AIC LRT Df Pr(>Chisq) 197s 4 -34.66 77.32 197s (1 | Species) 3 -193.84 393.68 318.36 1 < 2.2e-16 *** 197s --- 197s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 197s > 197s > data <- iris 197s > ranova(res) # now it works 197s ANOVA-like table for random-effects: Single term deletions 197s 197s Model: 197s Petal.Length ~ Sepal.Length + (1 | Species) 197s npar logLik AIC LRT Df Pr(>Chisq) 197s 4 -34.66 77.32 197s (1 | Species) 3 -193.84 393.68 318.36 1 < 2.2e-16 *** 197s --- 197s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 197s > ########################### 197s > # Evaluation in function without the formula(2): 197s > # A model with ||-notation: 197s > f2 <- function(data) { 197s + lmer(Reaction ~ Days + (Days||Subject), data) 197s + } 197s > res <- f2(sleepstudy) 197s > ranova(res) 197s ANOVA-like table for random-effects: Single term deletions 197s 197s Model: 197s Reaction ~ Days + (1 | Subject) + (0 + Days | Subject) 197s npar logLik AIC LRT Df Pr(>Chisq) 197s 5 -871.83 1753.7 197s (1 | Subject) 4 -883.26 1774.5 22.856 1 1.746e-06 *** 197s Days in (0 + Days | Subject) 4 -893.23 1794.5 42.796 1 6.076e-11 *** 197s --- 197s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 197s > 197s > # A model with multiple RE terms: 197s > f3 <- function(data) { 197s + lmer(Coloursaturation ~ TVset*Picture + (1|Assessor:TVset) + (1|Assessor), data) 197s + } 197s > res <- f3(TVbo) 197s > ranova(res) 197s ANOVA-like table for random-effects: Single term deletions 197s 197s Model: 197s Coloursaturation ~ TVset * Picture + (1 | Assessor:TVset) + (1 | Assessor) 197s npar logLik AIC LRT Df Pr(>Chisq) 197s 15 -280.22 590.44 197s (1 | Assessor:TVset) 14 -302.61 633.22 44.777 1 2.208e-11 *** 197s (1 | Assessor) 14 -280.27 588.53 0.090 1 0.7643 197s --- 197s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 197s > ########################### 197s > 197s > # Check that step works when form is a character vector 197s > m <- lmer(form, data=ham) 197s > step_res <- step(m) 197s boundary (singular) fit: see help('isSingular') 197s > (drop1_table <- attr(step_res, "drop1")) 197s Single term deletions using Satterthwaite's method: 197s 197s Model: 197s Informed.liking ~ Product + Information + (1 | Consumer) + (1 | Product:Consumer) 197s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 197s Product 19.3466 6.4489 3 240 3.8291 0.01048 * 197s Information 6.5201 6.5201 1 323 3.8714 0.04997 * 197s --- 197s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 197s > stopifnot( 197s + all(c("Sum Sq", "Mean Sq", "NumDF", "DenDF", "F value", "Pr(>F)") %in% 197s + colnames(drop1_table)) 197s + ) 197s > # In version < 3.0-1.9002 attr(step_res, "drop1") picked up lme4::drop1.merMod 197s > # and returned an AIC table after the model had been update'd. 197s > 197s > ##################################################################### 197s > # Model with 2 ranef covarites: 197s > 197s > # Model of the form (x1 + x2 | gr): 197s > model <- lmer(Preference ~ sens2 + Homesize + (sens1 + sens2 | Consumer) 197s + , data=carrots) 198s boundary (singular) fit: see help('isSingular') 198s Warning message: 198s Model failed to converge with 1 negative eigenvalue: -3.1e+02 198s > step(model) 198s boundary (singular) fit: see help('isSingular') 198s Backward reduced random-effect table: 198s 198s Eliminated npar logLik AIC LRT Df 198s 10 -1874.4 3768.8 198s sens1 in (sens1 + sens2 | Consumer) 1 7 -1874.5 3762.9 0.1333 3 198s sens2 in (sens2 | Consumer) 0 5 -1878.0 3765.9 6.9944 2 198s Pr(>Chisq) 198s 198s sens1 in (sens1 + sens2 | Consumer) 0.98757 198s sens2 in (sens2 | Consumer) 0.03028 * 198s --- 198s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 198s 198s Backward reduced fixed-effect table: 198s Degrees of freedom method: Satterthwaite 198s 198s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 198s sens2 0 58.685 58.685 1 102.02 54.8236 3.888e-11 *** 198s Homesize 0 5.979 5.979 1 100.95 5.5852 0.02003 * 198s --- 198s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 198s 198s Model found: 198s Preference ~ sens2 + Homesize + (sens2 | Consumer) 198s > stopifnot( 198s + nrow(ranova(model)) == 3L, 198s + nrow(ranova(model, reduce.terms = FALSE)) == 2L 198s + ) 198s boundary (singular) fit: see help('isSingular') 198s > 198s > # Model of the form (f1 + f2 | gr): 198s > model <- lmer(Preference ~ sens2 + Homesize + Gender + 198s + (Gender+Homesize|Consumer), data=carrots) 198s boundary (singular) fit: see help('isSingular') 198s > step(model) 198s Backward reduced random-effect table: 198s 198s Eliminated npar logLik AIC LRT 198s 11 -1872.3 3766.5 198s Gender in (Gender + Homesize | Consumer) 1 8 -1875.1 3766.3 5.7408 198s Homesize in (Homesize | Consumer) 0 6 -1878.4 3768.7 6.4705 198s Df Pr(>Chisq) 198s 198s Gender in (Gender + Homesize | Consumer) 3 0.12493 198s Homesize in (Homesize | Consumer) 2 0.03935 * 198s --- 198s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 198s 198s Backward reduced fixed-effect table: 198s Degrees of freedom method: Satterthwaite 198s 198s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 198s Gender 1 0.632 0.632 1 91.80 0.5686 0.45275 198s sens2 0 83.385 83.385 1 1129.09 75.0490 < 2e-16 *** 198s Homesize 0 6.212 6.212 1 97.82 5.5910 0.02003 * 198s Warning messages: 198s 1: In checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, : 198s unable to evaluate scaled gradient 198s 2: In checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, :--- 198s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 198s 198s Model found: 198s Preference ~ sens2 + Homesize + (Homesize | Consumer) 198s > stopifnot( 198s + nrow(ranova(model)) == 3L, 198s + 198s Model failed to converge: degenerate Hessian with 1 negative eigenvalues 198s See ?lme4::convergence and ?lme4::troubleshooting. 198s 3: In checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, : 198s unable to evaluate scaled gradient 198s 4: In checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, : 198s Model failed to converge: degenerate Hessian with 1 negative eigenvalues 198s See ?lme4::convergence and ?lme4::troubleshooting. 198s 5: Model failed to converge with 1 negative eigenvalue: -2.7e-04 198s nrow(ranova(model, reduce.terms = FALSE)) == 2L 198s + ) 198s > 198s > # Model of the form (-1 + f2 | gr): 198s > model <- lmer(Preference ~ sens2 + Homesize + Gender + 198s + (Gender -1 |Consumer), data=carrots) 198s Warning messages: 198s 1: In checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, : 198s unable to evaluate scaled gradient 198s 2: In checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, : 198s Model failed to converge: degenerate Hessian with 1 negative eigenvalues 198s See ?lme4::convergence and ?lme4::troubleshooting. 198s > step(model) 198s Warning message: 198s In checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, : 198s Model is nearly unidentifiable: large eigenvalue ratio 198s - Rescale variables? 199s Backward reduced random-effect table: 199s 199s Eliminated npar logLik AIC LRT Df 199s 8 -1876.4 3768.9 199s Gender in (Gender - 1 | Consumer) 1 6 -1878.4 3768.7 3.863 2 199s (1 | Consumer) 0 5 -1917.2 3844.5 77.714 1 199s Pr(>Chisq) 199s 199s Gender in (Gender - 1 | Consumer) 0.145 199s (1 | Consumer) <2e-16 *** 199s --- 199s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 199s 199s Backward reduced fixed-effect table: 199s Degrees of freedom method: Satterthwaite 199s 199s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 199s Gender 1 1.879 1.879 1 99.98 1.6909 0.19647 199s sens2 0 83.363 83.363 1 1129.00 75.0256 < 2e-16 *** 199s Homesize 0 5.729 5.729 1 100.97 5.1557 0.02529 * 199s --- 199s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 199s 199s Model found: 199s Preference ~ sens2 + Homesize + (1 | Consumer) 199s > an1 <- ranova(model) 199s > an1b <- ranova(model, reduce.terms = FALSE) 199s > 199s > model <- lmer(Preference ~ sens2 + Homesize + Gender + 199s + (0 + Gender|Consumer), data=carrots) 199s Warning message: 199s In checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, : 199s Model is nearly unidentifiable: large eigenvalue ratio 199s - Rescale variables? 199s > step(model) 199s Backward reduced random-effect table: 199s 199s Eliminated npar logLik AIC LRT Df 199s 8 -1876.4 3768.9 199s Gender in (0 + Gender | Consumer) 1 6 -1878.4 3768.7 3.863 2 199s (1 | Consumer) 0 5 -1917.2 3844.5 77.714 1 199s Pr(>Chisq) 199s 199s Gender in (0 + Gender | Consumer) 0.145 199s (1 | Consumer) <2e-16 *** 199s --- 199s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 199s 199s Backward reduced fixed-effect table: 199s Degrees of freedom method: Satterthwaite 199s 199s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 199s Gender 1 1.879 1.879 1 99.98 1.6909 0.19647 199s sens2 0 83.363 83.363 1 1129.00 75.0256 < 2e-16 *** 199s Homesize 0 5.729 5.729 1 100.97 5.1557 0.02529 * 199s --- 199s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 199s 199s Model found: 199s Preference ~ sens2 + Homesize + (1 | Consumer) 199s > an2 <- ranova(model) 199s > an2b <- ranova(model, reduce.terms = FALSE) 199s > 199s > stopifnot( 199s + all.equal(an1, an2, check.attributes=FALSE, tolerance=TOL), 199s + all.equal(an1b, an2b, check.attributes=FALSE, tolerance=TOL) 199s + ) 199s > 199s > ####### Polynomial terms: 199s > model <- lmer(Preference ~ sens2 + Gender + (poly(sens2, 2) | Consumer), 199s + data=carrots) 199s > (an <- ranova(model)) 199s ANOVA-like table for random-effects: Single term deletions 199s 199s Model: 199s Preference ~ sens2 + Gender + (poly(sens2, 2) | Consumer) 199s npar logLik AIC LRT Df 199s 10 -1874.1 3768.2 199s poly(sens2, 2) in (poly(sens2, 2) | Consumer) 5 -1879.9 3769.7 11.552 5 199s Pr(>Chisq) 199s 199s poly(sens2, 2) in (poly(sens2, 2) | Consumer) 0.04147 * 199s --- 199s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 199s > step(model) 199s Backward reduced random-effect table: 199s 199s Eliminated npar logLik AIC 199s 10 -1874.1 3768.2 199s poly(sens2, 2) in (poly(sens2, 2) | Consumer) 0 5 -1879.9 3769.7 199s LRT Df Pr(>Chisq) 199s 199s poly(sens2, 2) in (poly(sens2, 2) | Consumer) 11.552 5 0.04147 * 199s --- 199s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 199s 199s Backward reduced fixed-effect table: 199s Degrees of freedom method: Satterthwaite 199s 199s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 199s Gender 1 1.188 1.188 1 101.03 1.1262 0.2911 199s sens2 0 53.447 53.447 1 114.59 50.6761 1.019e-10 *** 199s --- 199s Signif. codes: Warning message: 199s Model failed to converge with 1 negative eigenvalue: -2.7e-02 199s 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 199s 199s Model found: 199s Preference ~ sens2 + (poly(sens2, 2) | Consumer) 199s > 199s > model <- lmer(Preference ~ sens2 + Gender + (sens2 + I(sens2^2) | Consumer), 199s + data=carrots) 200s > (an2 <- ranova(model)) 200s Warning message: 200s In checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, : 200s Model failed to converge with max|grad| = 0.099278 (tol = 0.002, component 1) 200s See ?lme4::convergence and ?lme4::troubleshooting. 200s boundary (singular) fit: see help('isSingular') 200s ANOVA-like table for random-effects: Single term deletions 200s 200s Model: 200s Preference ~ sens2 + Gender + (sens2 + I(sens2^2) | Consumer) 200s npar logLik AIC LRT Df 200s 10 -1874.1 3768.2 200s sens2 in (sens2 + I(sens2^2) | Consumer) 7 -1879.8 3773.5 11.3637 3 200s I(sens2^2) in (sens2 + I(sens2^2) | Consumer) 7 -1876.5 3767.0 4.8755 3 200s Pr(>Chisq) 200s 200s sens2 in (sens2 + I(sens2^2) | Consumer) 0.009913 ** 200s I(sens2^2) in (sens2 + I(sens2^2) | Consumer) 0.181146 200s --- 200s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 200s > step(model) 200s boundary (singular) fit: see help('isSingular') 200s Backward reduced random-effect table: 200s 200s Eliminated npar logLik AIC 200s 10 -1874.1 3768.2 200s I(sens2^2) in (sens2 + I(sens2^2) | Consumer) 1 7 -1876.5 3767.0 200s sens2 in (sens2 | Consumer) 0 5 -1879.9 3769.7 200s LRT Df Pr(>Chisq) 200s 200s I(sens2^2) in (sens2 + I(sens2^2) | Consumer) 4.8755 3 0.18115 200s sens2 in (sens2 | Consumer) 6.6735 2 0.03555 * 200s --- 200s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 200s 200s Backward reduced fixed-effect table: 200s Degrees of freedom method: Satterthwaite 200s 200s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 200s Gender 1 1.211 1.211 1 101.02 1.1309 0.2901 200s sens2 0 58.688 58.688 1 102.01 54.8276 3.883e-11 *** 200s --- 200s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 200s 200s Model found: 200s Preference ~ sens2 + (sens2 | Consumer) 200s > stopifnot( 200s + nrow(an) == 2L, 200s + an[2L, "Df"] == 5L, 200s + nrow(an2) == 3L, 200s + all(an2[2:3, "Df"] == 3L) 200s + ) 200s > 200s > ######## Functions of terms in random effects: 200s > model <- lmer(Preference ~ sens2 + Gender + (log(10+sens2) | Consumer), 200s + data=carrots) 200s > ranova(model) # Works 200s ANOVA-like table for random-effects: Single term deletions 200s 200s Model: 200s Preference ~ sens2 + Gender + (log(10 + sens2) | Consumer) 200s npar logLik AIC LRT Df 200s 7 -1875.3 3764.6 200s log(10 + sens2) in (log(10 + sens2) | Consumer) 5 -1879.9 3769.7 9.0854 2 200s Pr(>Chisq) 200s 200s log(10 + sens2) in (log(10 + sens2) | Consumer) 0.01064 * 200s --- 200s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 200s > step(model) 200s Backward reduced random-effect table: 200s 200s Eliminated npar logLik AIC 200s 7 -1875.3 3764.6 200s log(10 + sens2) in (log(10 + sens2) | Consumer) 0 5 -1879.9 3769.7 200s LRT Df Pr(>Chisq) 200s 200s log(10 + sens2) in (log(10 + sens2) | Consumer) 9.0854 2 0.01064 * 200s --- 200s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 200s 200s Backward reduced fixed-effect table: 200s Degrees of freedom method: Satterthwaite 200s 200s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 200s Gender 1 1.200 1.200 1 101.03 1.1296 0.2904 200s sens2 0 54.185 54.185 1 109.20 51.0020 1.083e-10 *** 200s --- 200s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 200s 200s Model found: 200s Preference ~ sens2 + (log(10 + sens2) | Consumer) 200s > 200s > ##################################################################### 200s > 200s > # Missing values changes the number of observations in use: 200s > m <- lmer(Preference ~ sens2 + Homesize + 200s + (1 |Consumer:Income), data=carrots) 200s > assertError(step(m)) 200s > ans <- try(ranova(m), silent = TRUE) 200s > stopifnot( 200s + inherits(ans, "try-error"), 200s + grepl("number of rows in use has changed", ans) 200s + ) 200s > 200s > ## Removing missing values solves the problem: 200s > m2 <- lmer(Preference ~ sens2 + Homesize + 200s + (1 |Consumer:Income), data=carrots[complete.cases(carrots), ]) 200s > ranova(m2) # Works 200s ANOVA-like table for random-effects: Single term deletions 200s 200s Model: 200s Preference ~ sens2 + Homesize + (1 | Consumer:Income) 200s npar logLik AIC LRT Df Pr(>Chisq) 200s 5 -1752.0 3513.9 200s (1 | Consumer:Income) 4 -1778.6 3565.2 53.272 1 2.904e-13 *** 200s --- 200s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 200s > step(m2) 200s Backward reduced random-effect table: 200s 200s Eliminated npar logLik AIC LRT Df Pr(>Chisq) 200s 5 -1752.0 3513.9 200s (1 | Consumer:Income) 0 4 -1778.6 3565.2 53.272 1 2.904e-13 *** 200s --- 200s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 200s 200s Backward reduced fixed-effect table: 200s Degrees of freedom method: Satterthwaite 200s 200s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 200s sens2 0 77.308 77.308 1 1058.49 69.7915 < 2.2e-16 *** 200s Homesize 0 8.569 8.569 1 95.23 7.7355 0.006527 ** 200s --- 200s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 200s 200s Model found: 200s Preference ~ sens2 + Homesize + (1 | Consumer:Income) 200s > 200s > ## Including the variable with missing values (Income) among the fixed effects 200s > ## also solves the problem: 200s > m <- lmer(Preference ~ sens2 + Homesize + Income + #(1 + sens2 | Consumer) + 200s + (1 |Consumer:Income), data=carrots) 200s > ranova(m) 200s ANOVA-like table for random-effects: Single term deletions 200s 200s Model: 200s Preference ~ sens2 + Homesize + Income + (1 | Consumer:Income) 200s npar logLik AIC LRT Df Pr(>Chisq) 200s 8 -1766.0 3547.9 200s (1 | Consumer:Income) 7 -1791.1 3596.3 50.395 1 1.257e-12 *** 200s --- 200s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 200s > step(m) 200s Backward reduced random-effect table: 200s 200s Eliminated npar logLik AIC LRT Df Pr(>Chisq) 200s 8 -1766.0 3547.9 200s (1 | Consumer:Income) 0 7 -1791.1 3596.3 50.395 1 1.257e-12 *** 200s --- 200s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 200s 200s Backward reduced fixed-effect table: 200s Degrees of freedom method: Satterthwaite 200s 200s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 200s Income 1 3.567 1.189 3 91.92 1.0627 0.368918 200s sens2 0 78.191 78.191 1 1062.96 69.8919 < 2.2e-16 *** 200s Homesize 0 7.983 7.983 1 94.93 7.1355 0.008894 ** 200s --- 200s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 200s 200s Model found: 200s Preference ~ sens2 + Homesize + (1 | Consumer:Income) 200s > 200s > # Missing values in a an insignificant fixed effect causes the an error in step: 200s > m0 <- lmer(Preference ~ sens2 + Homesize + Income + #(1 + sens2 | Consumer) + 200s + (1 |Consumer), data=carrots) 200s > ranova(m0) 200s ANOVA-like table for random-effects: Single term deletions 200s 200s Model: 200s Preference ~ sens2 + Homesize + Income + (1 | Consumer) 200s npar logLik AIC LRT Df Pr(>Chisq) 200s 8 -1766.0 3547.9 200s (1 | Consumer) 7 -1791.1 3596.3 50.395 1 1.257e-12 *** 200s --- 200s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 200s > ans <- try(step(m0), silent = TRUE) 200s > stopifnot( 200s + inherits(ans, "try-error"), 200s + grepl("number of rows in use has changed", ans) 200s + ) 200s > 200s > # Check that step still works for linear models (etc.) 200s > flm <- lm(Coloursaturation ~ TVset * Picture, data=TVbo) 200s > res <- step(flm, trace=0) 200s > stopifnot( 200s + inherits(res, "lm") 200s + ) 200s > 200s > ##################### Using reduce and keep args: 200s > # Fit a model to the ham dataset: 200s > m <- lmer(Informed.liking ~ Product*Information+ 200s + (1|Consumer) + (1|Product:Consumer) 200s + + (1|Information:Consumer), data=ham) 200s > 200s > # Backward elimination using terms with default alpha-levels: 200s > (step_res <- step(m)) 200s boundary (singular) fit: see help('isSingular') 201s Backward reduced random-effect table: 201s 201s Eliminated npar logLik AIC LRT Df Pr(>Chisq) 201s 12 -1352.0 2728.1 201s (1 | Information:Consumer) 1 11 -1352.8 2727.5 1.444 1 0.22952 201s (1 | Consumer) 0 10 -1354.4 2728.7 3.184 1 0.07437 201s (1 | Product:Consumer) 0 10 -1435.0 2890.0 164.443 1 < 2e-16 201s 201s 201s (1 | Information:Consumer) 201s (1 | Consumer) . 201s (1 | Product:Consumer) *** 201s --- 201s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 201s 201s Backward reduced fixed-effect table: 201s Degrees of freedom method: Satterthwaite 201s 201s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 201s Product:Information 1 10.3873 3.4624 3 320 2.0765 0.10321 201s Product 0 19.3466 6.4489 3 240 3.8291 0.01048 * 201s Information 0 6.5201 6.5201 1 323 3.8714 0.04997 * 201s --- 201s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 201s 201s Model found: 201s Informed.liking ~ Product + Information + (1 | Consumer) + (1 | Product:Consumer) 201s > 201s > (step_res <- step(m, reduce.random = FALSE)) 201s boundary (singular) fit: see help('isSingular') 201s Backward reduced random-effect table: 201s 201s Eliminated npar logLik AIC LRT Df Pr(>Chisq) 201s 12 -1352.0 2728.1 201s (1 | Consumer) 0 11 -1353.2 2728.3 2.252 1 0.1335 201s (1 | Product:Consumer) 0 11 -1435.0 2892.0 165.887 1 <2e-16 201s (1 | Information:Consumer) 0 11 -1352.8 2727.5 1.444 1 0.2295 201s 201s 201s (1 | Consumer) 201s (1 | Product:Consumer) *** 201s (1 | Information:Consumer) 201s --- 201s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 201s 201s Backward reduced fixed-effect table: 201s Degrees of freedom method: Satterthwaite 201s 201s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 201s Product:Information 1 10.3873 3.4624 3 240 2.2014 0.08855 . 201s Information 2 5.3335 5.3335 1 80 3.3414 0.07129 . 201s Product 0 18.3361 6.1120 3 240 3.8291 0.01048 * 201s --- 201s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 201s 201s Model found: 201s Informed.liking ~ Product + (1 | Consumer) + (1 | Product:Consumer) + (1 | Information:Consumer) 201s > (step_res <- step(m, reduce.fixed = FALSE)) 201s boundary (singular) fit: see help('isSingular') 201s Backward reduced random-effect table: 201s 201s Eliminated npar logLik AIC LRT Df Pr(>Chisq) 201s 12 -1352.0 2728.1 201s (1 | Information:Consumer) 1 11 -1352.8 2727.5 1.444 1 0.22952 201s (1 | Consumer) 0 10 -1354.4 2728.7 3.184 1 0.07437 201s (1 | Product:Consumer) 0 10 -1435.0 2890.0 164.443 1 < 2e-16 201s 201s 201s (1 | Information:Consumer) 201s (1 | Consumer) . 201s (1 | Product:Consumer) *** 201s --- 201s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 201s 201s Backward reduced fixed-effect table: 201s Degrees of freedom method: Satterthwaite 201s 201s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 201s Product:Information 0 10.387 3.4624 3 320 2.0765 0.1032 201s 201s Model found: 201s Informed.liking ~ Product + Information + (1 | Consumer) + (1 | Product:Consumer) + Product:Information 201s > (step_res <- step(m, reduce.fixed = FALSE, reduce.random = FALSE)) 201s boundary (singular) fit: see help('isSingular') 202s Backward reduced random-effect table: 202s 202s Eliminated npar logLik AIC LRT Df Pr(>Chisq) 202s 12 -1352.0 2728.1 202s (1 | Consumer) 0 11 -1353.2 2728.3 2.252 1 0.1335 202s (1 | Product:Consumer) 0 11 -1435.0 2892.0 165.887 1 <2e-16 202s (1 | Information:Consumer) 0 11 -1352.8 2727.5 1.444 1 0.2295 202s 202s 202s (1 | Consumer) 202s (1 | Product:Consumer) *** 202s (1 | Information:Consumer) 202s --- 202s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 202s 202s Backward reduced fixed-effect table: 202s Degrees of freedom method: Satterthwaite 202s 202s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 202s Product:Information 0 10.387 3.4624 3 240 2.2014 0.08855 . 202s --- 202s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 202s 202s Model found: 202s Informed.liking ~ Product * Information + (1 | Consumer) + (1 | Product:Consumer) + (1 | Information:Consumer) 202s > 202s > (step_res <- step(m, reduce.random = FALSE, keep="Information")) 202s boundary (singular) fit: see help('isSingular') 202s Backward reduced random-effect table: 202s 202s Eliminated npar logLik AIC LRT Df Pr(>Chisq) 202s 12 -1352.0 2728.1 202s (1 | Consumer) 0 11 -1353.2 2728.3 2.252 1 0.1335 202s (1 | Product:Consumer) 0 11 -1435.0 2892.0 165.887 1 <2e-16 202s (1 | Information:Consumer) 0 11 -1352.8 2727.5 1.444 1 0.2295 202s 202s 202s (1 | Consumer) 202s (1 | Product:Consumer) *** 202s (1 | Information:Consumer) 202s --- 202s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 202s 202s Backward reduced fixed-effect table: 202s Degrees of freedom method: Satterthwaite 202s 202s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 202s Product:Information 1 10.3873 3.4624 3 240 2.2014 0.08855 . 202s Product 0 18.3363 6.1121 3 240 3.8292 0.01048 * 202s Information 0 5.3335 5.3335 1 80 3.3414 0.07129 . 202s --- 202s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 202s 202s Model found: 202s Informed.liking ~ Product + Information + (1 | Consumer) + (1 | Product:Consumer) + (1 | Information:Consumer) 202s > (step_res <- step(m, reduce.random = FALSE, keep="Product:Information")) 202s boundary (singular) fit: see help('isSingular') 202s Backward reduced random-effect table: 202s 202s Eliminated npar logLik AIC LRT Df Pr(>Chisq) 202s 12 -1352.0 2728.1 202s (1 | Consumer) 0 11 -1353.2 2728.3 2.252 1 0.1335 202s (1 | Product:Consumer) 0 11 -1435.0 2892.0 165.887 1 <2e-16 202s (1 | Information:Consumer) 0 11 -1352.8 2727.5 1.444 1 0.2295 202s 202s 202s (1 | Consumer) 202s (1 | Product:Consumer) *** 202s (1 | Information:Consumer) 202s --- 202s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 202s 202s Backward reduced fixed-effect table: 202s Degrees of freedom method: Satterthwaite 202s 202s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 202s Product:Information 0 10.387 3.4624 3 240 2.2014 0.08855 . 202s --- 202s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 202s 202s Model found: 202s Informed.liking ~ Product * Information + (1 | Consumer) + (1 | Product:Consumer) + (1 | Information:Consumer) 202s > 202s > 202s > ########################### 202s > ## Test that `step` works even if all random terms are reduced away: 202s > set.seed(101) 202s > test <- data.frame(TM = factor(rep(rep(c("org","min"),each=3),3)), 202s + dep = runif(18,0,20), 202s + ind = runif(18,0,7), 202s + dorp = factor(rep(1:3,each=6))) 202s > full.model <- lmer(dep ~ TM + ind + (1 | dorp), data=test) 202s > res <- step(full.model) 202s > # res$random 202s > # res$fixed 202s > # attr(res, "model") 202s > # attr(res, "drop1") 202s > 202s > 202s > 202s BEGIN TEST test_re_covar_structures.R 202s 202s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 202s Copyright (C) 2025 The R Foundation for Statistical Computing 202s Platform: x86_64-pc-linux-gnu 202s 202s R is free software and comes with ABSOLUTELY NO WARRANTY. 202s You are welcome to redistribute it under certain conditions. 202s Type 'license()' or 'licence()' for distribution details. 202s 202s R is a collaborative project with many contributors. 202s Type 'contributors()' for more information and 202s 'citation()' on how to cite R or R packages in publications. 202s 202s Type 'demo()' for some demos, 'help()' for on-line help, or 202s 'help.start()' for an HTML browser interface to help. 202s Type 'q()' to quit R. 202s 202s > # test_re_covar_structure.R 202s > library(lmerTest) 202s Loading required package: lme4 202s Loading required package: Matrix 203s 203s Attaching package: 'lmerTest' 203s 203s > 203s > # WRE says "using if(requireNamespace("pkgname")) is preferred, if possible." 203s > # even in tests: 203s > assertError <- function(expr, ...) 203s + if(requireNamespace("tools")) tools::assertError(expr, ...) else invisible() 203s > assertWarning <- function(expr, ...) 203s + if(requireNamespace("tools")) tools::assertWarning(expr, ...) else invisible() 203s > 203s > # Kenward-Roger only available with pbkrtest and only then validated in R >= 3.3.3 203s > # (faulty results for R < 3.3.3 may be due to unstated dependencies in pbkrtest) 203s > has_pbkrtest <- requireNamespace("pbkrtest", quietly = TRUE) && getRversion() >= "3.3.3" 203s The following object is masked from 'package:lme4': 203s 203s lmer 203s 203s The following object is masked from 'package:stats': 203s 203s step 203s 203s > 203s > data("sleepstudy", package="lme4") 203s > TOL <- 1e-4 203s > 203s > #################################### 203s > ## Test that lmerMod objects can be coerced to lmerModLmerTest and 203s > ## that the deviance function can be evaluated with expected results 203s > #################################### 203s > 203s > 203s > #################################### 203s > ## Basic tests of new (lme4 >= 2.0.0) covariance structure 203s > ## - simple sleepstudy data (random coefficient) 203s > #################################### 203s > 203s > has_pkgs <- requireNamespace("utils", quietly = TRUE) && 203s + requireNamespace("lme4", quietly = TRUE) && 203s + requireNamespace("pbkrtest", quietly = TRUE) && 203s + getRversion() >= "3.3.3" 203s > is_lme4_2_0_0 <- utils::packageVersion("lme4") >= "2.0.0" 203s > 203s > if(has_pkgs && is_lme4_2_0_0) { 203s + 203s + ## From the examples of ?`Covariance-class`: 203s + ## Unstructured 203s + fm1.us <- lmer(Reaction ~ Days + us(Days | Subject), sleepstudy) 203s + ## Diagional 203s + fm1.diag <- lmer(Reaction ~ Days + diag(Days | Subject), sleepstudy) 203s + fm1.diag.hom <- lmer(Reaction ~ Days + diag(Days | Subject, hom = TRUE), 203s + sleepstudy) 203s + ## Compound symmetry 203s + fm1.cs <- lmer(Reaction ~ Days + cs(1 + Days | Subject), sleepstudy) 203s + fm1.cs.hom <- lmer(Reaction ~ Days + cs(1 + Days | Subject, hom = TRUE), 203s + sleepstudy) 203s + ## Auto-regressive order 1 203s + sleepstudy$Daysf <- factor(sleepstudy$Days, ordered = TRUE) 203s + fm1.ar1 <- lmer(Reaction ~ Daysf + ar1(0 + Daysf | Subject, hom = TRUE), 203s + sleepstudy, REML = TRUE) 203s + 203s + ## Also adding a double-vertical-bar model (though not from 203s + ## 'Covariance-class' examples): 203s + fm1.bv <- lmer(Reaction ~ Days + (Days || Subject), sleepstudy) 203s + 203s + 203s + ltmodels <- namedList(fm1.us, 203s + fm1.diag, 203s + fm1.diag.hom, 203s + fm1.cs, 203s + fm1.cs.hom, 203s + fm1.ar1, 203s + fm1.bv) 203s + ## Run various methods on all models: 203s + for(model in ltmodels) { 203s + # model <- ltmodels[[5]] 203s + print(model) 203s + print(summary(model)) 203s + # model 203s + # summary(model) 203s + L <- diag(c(0, rep(1, length(fixef(model)) -1))) 203s + contest(model, L, joint = TRUE) 203s + contest(model, L[2, ], joint = FALSE) 203s + (an <- anova(model)) ## ddf is Satterthwaite 203s + anova(model, ddf = "Ken") 203s + anova(model, ddf="lme4") 203s + anova(model, type="I") 203s + anova(model, type="II") 203s + anova(model, type="III") 203s + show_tests(an) 203s + drop1(model) 203s + ranova(model) 203s + ranova(model, reduce.terms = FALSE) 203s + step(model) 203s + (lsm <- ls_means(model)) 203s + show_tests(lsm) 203s + (dlsm <- difflsmeans(model)) 203s + show_tests(dlsm) 203s + } 203s + } 203s > 203s > #################################### 203s > ## Basic tests of new (lme4 >= 2.0.0) covariance structure 203s > ## - Unbalanced categorical dataset with multiple RE terms 203s > #################################### 203s > 203s > 203s > 203s > 203s > 203s BEGIN TEST test_summary.R 203s 203s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 203s Copyright (C) 2025 The R Foundation for Statistical Computing 203s Platform: x86_64-pc-linux-gnu 203s 203s R is free software and comes with ABSOLUTELY NO WARRANTY. 203s You are welcome to redistribute it under certain conditions. 203s Type 'license()' or 'licence()' for distribution details. 203s 203s R is a collaborative project with many contributors. 203s Type 'contributors()' for more information and 203s 'citation()' on how to cite R or R packages in publications. 203s 203s Type 'demo()' for some demos, 'help()' for on-line help, or 203s 'help.start()' for an HTML browser interface to help. 203s Type 'q()' to quit R. 203s 203s > # test_summary.R 203s > 203s > # WRE says "using if(requireNamespace("pkgname")) is preferred, if possible." 203s > # even in tests: 203s > assertError <- function(expr, ...) 203s + if(requireNamespace("tools")) tools::assertError(expr, ...) else invisible() 203s > assertWarning <- function(expr, ...) 203s + if(requireNamespace("tools")) tools::assertWarning(expr, ...) else invisible() 203s > 203s > # Kenward-Roger only available with pbkrtest and only then validated in R >= 3.3.3 203s > # (faulty results for R < 3.3.3 may be due to unstated dependencies in pbkrtest) 203s > has_pbkrtest <- requireNamespace("pbkrtest", quietly = TRUE) && getRversion() >= "3.3.3" 204s > 204s > library(lmerTest) 204s Loading required package: lme4 204s Loading required package: Matrix 205s 205s Attaching package: 'lmerTest' 205s 205s The following object is masked from 'package:lme4': 205s 205s lmer 205s 205s The following object is masked from 'package:stats': 205s 205s step 205s 205s > 205s > data("sleepstudy", package="lme4") 205s > data("cake", package="lme4") 205s > 205s > # Fit basic model and compute summary: 205s > fm <- lmer(Reaction ~ Days + (1|Subject) + (0+Days|Subject), sleepstudy) 205s > (sfm <- summary(fm)) 205s Linear mixed model fit by REML. t-tests use Satterthwaite's method [ 205s lmerModLmerTest] 205s Formula: Reaction ~ Days + (1 | Subject) + (0 + Days | Subject) 205s Data: sleepstudy 205s 205s REML criterion at convergence: 1743.7 205s 205s Scaled residuals: 205s Min 1Q Median 3Q Max 205s -3.9626 -0.4625 0.0204 0.4653 5.1860 205s 205s Random effects: 205s Groups Name Variance Std.Dev. 205s Subject (Intercept) 627.57 25.051 205s Subject.1 Days 35.86 5.988 205s Residual 653.58 25.565 205s Number of obs: 180, groups: Subject, 18 205s 205s Fixed effects: 205s Estimate Std. Error df t value Pr(>|t|) 205s (Intercept) 251.405 6.885 18.156 36.513 < 2e-16 *** 205s Days 10.467 1.560 18.156 6.712 2.59e-06 *** 205s --- 205s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 205s 205s Correlation of Fixed Effects: 205s (Intr) 205s Days -0.184 205s > 205s > ## Test class: 205s > stopifnot(all( 205s + class(sfm) == c("summary.lmerModLmerTest", "summary.merMod"), 205s + all(c("df", "Pr(>|t|)") %in% colnames(coef(sfm))) 205s + )) 205s > stopifnot(class(summary(fm, ddf="lme4")) == "summary.merMod") 205s > 205s > ## Test coefficient table names: 205s > mat <- coef(summary(fm)) 205s > stopifnot(all( # colnames 205s + colnames(mat) == c("Estimate", "Std. Error", "df", "t value", "Pr(>|t|)") 205s + )) 205s > stopifnot(all( # rownames 205s + names(fixef(fm)) == rownames(mat) 205s + )) 205s > 205s > ## Test pass of 'correlation' argument to lme4:::summary.merMod: 205s > x <- capture.output(summary(fm)) 205s > x_nocor <- capture.output(summary(fm, correlation=FALSE)) 205s > txt <- "Correlation of Fixed Effects:" 205s > stopifnot( 205s + any(grep(txt, x)), 205s + !any(grepl(txt, x_nocor)) 205s + ) 205s > 205s > # Test warning with unrecognized arguments (caught by lme4:::summary.merMod): 205s > assertWarning(summary(fm, false_arg=FALSE)) 205s > 205s > ## Test pass of extra arguments to lme4:::print.summary.merMod: 205s > x <- capture.output(print(summary(fm), signif.stars=TRUE)) 205s > x_nocor <- capture.output(print(summary(fm), signif.stars=FALSE)) 205s > txt <- "Signif. codes:" 205s > stopifnot( 205s + any(grep(txt, x)), 205s + !any(grepl(txt, x_nocor)) 205s + ) 205s > 205s > ####### ddf argument: 205s > (an1 <- summary(fm)) # Also testing print method. 205s Linear mixed model fit by REML. t-tests use Satterthwaite's method [ 205s lmerModLmerTest] 205s Formula: Reaction ~ Days + (1 | Subject) + (0 + Days | Subject) 205s Data: sleepstudy 205s 205s REML criterion at convergence: 1743.7 205s 205s Scaled residuals: 205s Min 1Q Median 3Q Max 205s -3.9626 -0.4625 0.0204 0.4653 5.1860 205s 205s Random effects: 205s Groups Name Variance Std.Dev. 205s Subject (Intercept) 627.57 25.051 205s Subject.1 Days 35.86 5.988 205s Residual 653.58 25.565 205s Number of obs: 180, groups: Subject, 18 205s 205s Fixed effects: 205s Estimate Std. Error df t value Pr(>|t|) 205s (Intercept) 251.405 6.885 18.156 36.513 < 2e-16 *** 205s Days 10.467 1.560 18.156 6.712 2.59e-06 *** 205s --- 205s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 205s 205s Correlation of Fixed Effects: 205s (Intr) 205s Days -0.184 205s > (an2 <- summary(fm, ddf="Satterthwaite")) 205s Linear mixed model fit by REML. t-tests use Satterthwaite's method [ 205s lmerModLmerTest] 205s Formula: Reaction ~ Days + (1 | Subject) + (0 + Days | Subject) 205s Data: sleepstudy 205s 205s REML criterion at convergence: 1743.7 205s 205s Scaled residuals: 205s Min 1Q Median 3Q Max 205s -3.9626 -0.4625 0.0204 0.4653 5.1860 205s 205s Random effects: 205s Groups Name Variance Std.Dev. 205s Subject (Intercept) 627.57 25.051 205s Subject.1 Days 35.86 5.988 205s Residual 653.58 25.565 205s Number of obs: 180, groups: Subject, 18 205s 205s Fixed effects: 205s Estimate Std. Error df t value Pr(>|t|) 205s (Intercept) 251.405 6.885 18.156 36.513 < 2e-16 *** 205s Days 10.467 1.560 18.156 6.712 2.59e-06 *** 205s --- 205s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 205s 205s Correlation of Fixed Effects: 205s (Intr) 205s Days -0.184 205s > stopifnot(isTRUE( 205s + all.equal(an1, an2) 205s + )) 205s > (an3 <- summary(fm, ddf="Sat")) ## Abbreviated argument 205s Linear mixed model fit by REML. t-tests use Satterthwaite's method [ 205s lmerModLmerTest] 205s Formula: Reaction ~ Days + (1 | Subject) + (0 + Days | Subject) 205s Data: sleepstudy 205s 205s REML criterion at convergence: 1743.7 205s 205s Scaled residuals: 205s Min 1Q Median 3Q Max 205s -3.9626 -0.4625 0.0204 0.4653 5.1860 205s 205s Random effects: 205s Groups Name Variance Std.Dev. 205s Subject (Intercept) 627.57 25.051 205s Subject.1 Days 35.86 5.988 205s Residual 653.58 25.565 205s Number of obs: 180, groups: Subject, 18 205s 205s Fixed effects: 205s Estimate Std. Error df t value Pr(>|t|) 205s (Intercept) 251.405 6.885 18.156 36.513 < 2e-16 *** 205s Days 10.467 1.560 18.156 6.712 2.59e-06 *** 205s --- 205s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 205s 205s Correlation of Fixed Effects: 205s (Intr) 205s Days -0.184 205s > stopifnot(isTRUE( 205s + all.equal(an1, an3) 205s + )) 205s > (summary(fm, ddf="lme4")) 205s Linear mixed model fit by REML ['lmerMod'] 205s Formula: Reaction ~ Days + (1 | Subject) + (0 + Days | Subject) 205s Data: sleepstudy 205s 205s REML criterion at convergence: 1743.7 205s 205s Scaled residuals: 205s Min 1Q Median 3Q Max 205s -3.9626 -0.4625 0.0204 0.4653 5.1860 205s 205s Random effects: 205s Groups Name Variance Std.Dev. 205s Subject (Intercept) 627.57 25.051 205s Subject.1 Days 35.86 5.988 205s Residual 653.58 25.565 205s Number of obs: 180, groups: Subject, 18 205s 205s Fixed effects: 205s Estimate Std. Error t value 205s (Intercept) 251.405 6.885 36.513 205s Days 10.467 1.560 6.712 205s 205s Correlation of Fixed Effects: 205s (Intr) 205s Days -0.184 205s > if(has_pbkrtest) { 205s + (summary(fm, ddf="Kenward-Roger")) 205s + assertError(summary(fm, ddf="KR")) ## Error on incorrect arg. 205s + } 205s > 205s > ## lme4 method: 205s > an1 <- summary(fm, ddf="lme4") 205s > an2 <- summary(as(fm, "lmerMod")) 205s > stopifnot(isTRUE( 205s + all.equal(an1, an2) 205s + )) 205s > 205s > 205s > # Test printed output 205s > # - Satterthwaite 205s > x <- capture.output(sfm) # equal to output of 'print(sfm)' 205s > txt <- c("lmerModLmerTest", "t-tests use Satterthwaite's method", 205s + "df", "t value", "Pr(>|t|)") 205s > stopifnot(all( 205s + sapply(txt, function(text) any(grepl(text, x))) 205s + )) 205s > 205s > # Test printed output 205s > # - KR 205s > if(has_pbkrtest) { 205s + (sfm <- summary(fm, ddf="Kenward-Roger")) 205s + x <- capture.output(sfm) 205s + txt <- c("lmerModLmerTest", "t-tests use Kenward-Roger's method", 205s + "df", "t value", "Pr(>|t|)") 205s + stopifnot(all( 205s + sapply(txt, function(text) any(grepl(text, x))) 205s + )) 205s + } 205s > 205s > #################################### 205s > ## Test 'boundary' fixef structures: 205s > #################################### 205s > 205s > # Example with no fixef: 205s > m <- lmer(Reaction ~ -1 + (Days | Subject), sleepstudy) 205s > # m <- lmer(Reaction ~ 0 + (Days | Subject), sleepstudy) # alternative 205s > stopifnot(length(fixef(m)) == 0L) 205s > stopifnot( 205s + nrow(coef(summary(m))) == 0L, 205s + nrow(coef(summary(m, ddf="lme4"))) == 0L 205s + ) 205s > if(has_pbkrtest){ 205s + stopifnot(nrow(coef(summary(m, ddf="Kenward-Roger"))) == 0L) 205s + } 205s > 205s > # Example with intercept only: 205s > m <- lmer(Reaction ~ (Days | Subject), sleepstudy) 205s > # m <- lmer(Reaction ~ 1 + (Days | Subject), sleepstudy) # alternative 205s > stopifnot(length(fixef(m)) == 1L, 205s + names(fixef(m)) == "(Intercept)") 205s > stopifnot( 205s + nrow(coef(summary(m))) == 1L, 205s + nrow(coef(summary(m, ddf="lme4"))) == 1L 205s + ) 205s > if(has_pbkrtest){ 205s + stopifnot(nrow(coef(summary(m, ddf="Kenward-Roger"))) == 1L) 205s + } 205s > 205s > # Example with >1 fixef without intercept: 205s > m <- lmer(Reaction ~ Days - 1 + I(Days^2) + (Days | Subject), sleepstudy) 205s > stopifnot(length(fixef(m)) == 2L, 205s + names(fixef(m)) == c("Days", "I(Days^2)")) 205s > stopifnot( 205s + nrow(coef(summary(m))) == 2L, 205s + nrow(coef(summary(m, ddf="lme4"))) == 2L 205s + ) 205s > if(has_pbkrtest){ 205s + stopifnot(nrow(coef(summary(m, ddf="Kenward-Roger"))) == 2L) 205s + } 205s > 205s > 205s BEGIN TEST test_zerovar.R 205s 205s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 205s Copyright (C) 2025 The R Foundation for Statistical Computing 205s Platform: x86_64-pc-linux-gnu 205s 205s R is free software and comes with ABSOLUTELY NO WARRANTY. 205s You are welcome to redistribute it under certain conditions. 205s Type 'license()' or 'licence()' for distribution details. 205s 205s R is a collaborative project with many contributors. 205s Type 'contributors()' for more information and 205s 'citation()' on how to cite R or R packages in publications. 205s 205s Type 'demo()' for some demos, 'help()' for on-line help, or 205s 'help.start()' for an HTML browser interface to help. 205s Type 'q()' to quit R. 205s 205s > # test_zerovar.R 205s > 205s > library(lmerTest) 205s Loading required package: lme4 205s Loading required package: Matrix 206s 206s Attaching package: 'lmerTest' 206s 206s > data("sleepstudy", package="lme4") 206s The following object is masked from 'package:lme4': 206s 206s lmer 206s 206s The following object is masked from 'package:stats': 206s 206s step 206s 206s > 206s > # Baseline fit: 206s > m0 <- lmer(Reaction ~ Days + (Days | Subject), sleepstudy, 206s + control=lmerControl(optimizer="bobyqa")) 206s > ## default optimizer does not converge proporly 206s > m0 206s Linear mixed model fit by REML ['lmerModLmerTest'] 206s Formula: Reaction ~ Days + (Days | Subject) 206s Data: sleepstudy 206s REML criterion at convergence: 1743.628 206s Random effects: 206s Groups Name Std.Dev. Corr 206s Subject (Intercept) 24.740 206s Days 5.922 0.07 206s Residual 25.592 206s Number of obs: 180, groups: Subject, 18 206s Fixed Effects: 206s (Intercept) Days 206s 251.41 10.47 206s > (an0 <- anova(m0)) 206s Type III Analysis of Variance Table with Satterthwaite's method 206s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 206s Days 30031 30031 1 17 45.853 3.264e-06 *** 206s --- 206s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 206s > 206s > # Make a fit with a zero variance estimate: 206s > n <- nrow(sleepstudy) 206s > g <- factor(rep(1:2, c(n - 10, 10))) 206s > m <- lmer(Reaction ~ Days + (Days | Subject) + (1|g), sleepstudy, 206s + control=lmerControl(optimizer="bobyqa")) 206s boundary (singular) fit: see help('isSingular') 206s > m 206s Linear mixed model fit by REML ['lmerModLmerTest'] 206s Formula: Reaction ~ Days + (Days | Subject) + (1 | g) 206s Data: sleepstudy 206s REML criterion at convergence: 1743.628 206s Random effects: 206s Groups Name Std.Dev. Corr 206s Subject (Intercept) 24.740 206s Days 5.922 0.07 206s g (Intercept) 0.000 206s Residual 25.592 206s Number of obs: 180, groups: Subject, 18; g, 2 206s Fixed Effects: 206s (Intercept) Days 206s 251.41 10.47 206s optimizer (bobyqa) convergence code: 0 (OK) ; 0 optimizer warnings; 1 lme4 warnings 206s > (an <- anova(m)) 206s Type III Analysis of Variance Table with Satterthwaite's method 206s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 206s Days 30031 30031 1 17 45.853 3.264e-06 *** 206s --- 206s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 206s > 206s > # check that fit has a zero variance 206s > vc <- as.data.frame(VarCorr(m)) 206s > stopifnot(isTRUE( 206s + all.equal(0, vc[vc$grp == "g", "sdcor"], tolerance=1e-4) 206s + )) 206s > # The hessian/vcov is actually positive definite: 206s > stopifnot(isTRUE( 206s + all(eigen(m@vcov_varpar, only.values = TRUE)$values > 0) 206s + )) 206s > 206s > # Check that ANOVA tables are the same: 206s > stopifnot(isTRUE( 206s + all.equal(an0[, 1:5], an[, 1:5], tolerance=1e-4) 206s + )) 206s > 206s > stopifnot(isTRUE( # Equality of summary tables 206s + all.equal(coef(summary(m0)), coef(summary(m)), tolerance=1e-4) 206s + )) 206s > stopifnot(isTRUE( # Equality of lme4-anova tables 206s + all.equal(anova(m0, ddf="lme4"), anova(m, ddf="lme4"), tolerance=1e-4) 206s + )) 206s > 206s > 206s BEGIN TEST zlmerTest_zeroDenom.R 206s 206s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 206s Copyright (C) 2025 The R Foundation for Statistical Computing 206s Platform: x86_64-pc-linux-gnu 206s 206s R is free software and comes with ABSOLUTELY NO WARRANTY. 206s You are welcome to redistribute it under certain conditions. 206s Type 'license()' or 'licence()' for distribution details. 206s 206s R is a collaborative project with many contributors. 206s Type 'contributors()' for more information and 206s 'citation()' on how to cite R or R packages in publications. 206s 206s Type 'demo()' for some demos, 'help()' for on-line help, or 206s 'help.start()' for an HTML browser interface to help. 206s Type 'q()' to quit R. 206s 207s > library(lmerTest) 207s Loading required package: lme4 207s Loading required package: Matrix 208s 208s Attaching package: 'lmerTest' 208s 208s The following object is masked from 'package:lme4': 208s 208s lmer 208s 208s > 208s > # Read in data set 208s > load(system.file("testdata","potdata.RData", package="lmerTest")) 208s The following object is masked from 'package:stats': 208s 208s step 208s 208s > 208s > # Mixed model 208s > lmerout <- lmer(biomass ~ CO2*nutrients + (1|chamber),data=potdata) 208s > summary(lmerout) 208s Linear mixed model fit by REML. t-tests use Satterthwaite's method [ 208s lmerModLmerTest] 208s Formula: biomass ~ CO2 * nutrients + (1 | chamber) 208s Data: potdata 208s 208s REML criterion at convergence: 49.2 208s 208s Scaled residuals: 208s Min 1Q Median 3Q Max 208s -1.4159 -0.5588 0.0000 0.5588 1.4159 208s 208s Random effects: 208s Groups Name Variance Std.Dev. 208s chamber (Intercept) 0.2437 0.4936 208s Residual 1.5797 1.2568 208s Number of obs: 24, groups: chamber, 4 208s 208s Fixed effects: 208s Estimate Std. Error df t value Pr(>|t|) 208s (Intercept) 12.8500 0.9548 11.0163 13.458 3.49e-08 *** 208s CO2675 2.0000 1.3503 11.0163 1.481 0.166595 208s nutrients2 7.3500 1.2568 10.0000 5.848 0.000162 *** 208s nutrients3 10.4500 1.2568 10.0000 8.314 8.39e-06 *** 208s nutrients4 18.6500 1.2568 10.0000 14.839 3.88e-08 *** 208s nutrients5 25.0500 1.2568 10.0000 19.931 2.22e-09 *** 208s nutrients6 29.0000 1.2568 10.0000 23.074 5.28e-10 *** 208s CO2675:nutrients2 -0.5000 1.7775 10.0000 -0.281 0.784214 208s CO2675:nutrients3 1.9000 1.7775 10.0000 1.069 0.310218 208s CO2675:nutrients4 3.4500 1.7775 10.0000 1.941 0.080949 . 208s CO2675:nutrients5 5.9000 1.7775 10.0000 3.319 0.007756 ** 208s CO2675:nutrients6 5.2500 1.7775 10.0000 2.954 0.014444 * 208s --- 208s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 208s 208s Correlation of Fixed Effects: 208s (Intr) CO2675 ntrnt2 ntrnt3 ntrnt4 ntrnt5 ntrnt6 CO2675:2 CO2675:3 208s CO2675 -0.707 208s nutrients2 -0.658 0.465 208s nutrients3 -0.658 0.465 0.500 208s nutrients4 -0.658 0.465 0.500 0.500 208s nutrients5 -0.658 0.465 0.500 0.500 0.500 208s nutrients6 -0.658 0.465 0.500 0.500 0.500 0.500 208s CO2675:ntr2 0.465 -0.658 -0.707 -0.354 -0.354 -0.354 -0.354 208s CO2675:ntr3 0.465 -0.658 -0.354 -0.707 -0.354 -0.354 -0.354 0.500 208s CO2675:ntr4 0.465 -0.658 -0.354 -0.354 -0.707 -0.354 -0.354 0.500 0.500 208s CO2675:ntr5 0.465 -0.658 -0.354 -0.354 -0.354 -0.707 -0.354 0.500 0.500 208s CO2675:ntr6 0.465 -0.658 -0.354 -0.354 -0.354 -0.354 -0.707 0.500 0.500 208s CO2675:4 CO2675:5 208s CO2675 208s nutrients2 208s nutrients3 208s nutrients4 208s nutrients5 208s nutrients6 208s CO2675:ntr2 208s CO2675:ntr3 208s CO2675:ntr4 208s CO2675:ntr5 0.500 208s CO2675:ntr6 0.500 0.500 208s > 208s > an.sat <- anova(lmerout) 208s > anova(lmerout, ddf="lme4") 208s Analysis of Variance Table 208s npar Sum Sq Mean Sq F value 208s CO2 1 67.86 67.86 42.9589 208s nutrients 5 3050.44 610.09 386.2129 208s CO2:nutrients 5 35.47 7.09 4.4906 208s > TOL <- 1e-5 208s > stopifnot(isTRUE(all.equal( 208s + an.sat[,"DenDF"], c(2, 10, 10), tolerance=TOL 208s + ))) 208s > 208s > stopifnot(isTRUE( 208s + all.equal(an.sat[,"Pr(>F)"], c(0.0224955602, 1e-11, 0.020905569), tolerance=TOL) 208s + )) 208s > 208s > # if(require(pbkrtest)) 208s > # an.kr <- anova(lmerout, ddf="Kenward-Roger") 208s > # 208s > # TOL <- 1e-7 208s > # stopifnot(all.equal(an.kr[,"Pr(>F)"], c(0.0224955602, 1e-11, 0.020905569) , 208s > # tol=TOL), 208s > # all.equal(an.kr[,"DenDF"], 208s > # c(2, 10, 10) , tol=TOL), 208s > # TRUE) 208s > 208s autopkgtest [05:27:34]: test run-unit-test: -----------------------] 209s autopkgtest [05:27:35]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 209s run-unit-test PASS 209s autopkgtest [05:27:35]: test pkg-r-autopkgtest: preparing testbed 228s Creating nova instance adt-resolute-amd64-r-cran-lmertest-20260210-052406-juju-7f2275-prod-proposed-migration-environment-20-a41f0f74-8854-4e6b-a45c-7c7a43f23a2c from image adt/ubuntu-resolute-amd64-server-20260204.img (UUID fedf54b4-458b-493e-8072-6425c19717b4)... 301s autopkgtest [05:29:07]: testbed dpkg architecture: amd64 301s autopkgtest [05:29:07]: testbed apt version: 3.1.14 302s autopkgtest [05:29:08]: @@@@@@@@@@@@@@@@@@@@ test bed setup 302s autopkgtest [05:29:08]: testbed release detected to be: resolute 302s autopkgtest [05:29:08]: updating testbed package index (apt update) 302s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 302s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 303s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 303s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 303s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [1727 kB] 303s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [178 kB] 303s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [31.1 kB] 303s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main i386 Packages [219 kB] 303s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 Packages [266 kB] 303s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 c-n-f Metadata [6184 B] 303s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/restricted amd64 c-n-f Metadata [120 B] 303s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/universe i386 Packages [792 kB] 303s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 Packages [1787 kB] 303s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 c-n-f Metadata [32.5 kB] 303s Get:15 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse i386 Packages [5020 B] 303s Get:16 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 Packages [26.4 kB] 304s Get:17 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 c-n-f Metadata [996 B] 304s Fetched 5197 kB in 1s (4524 kB/s) 305s Reading package lists... 305s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 305s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 305s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 305s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 306s Reading package lists... 306s Reading package lists... 306s Building dependency tree... 306s Reading state information... 306s Calculating upgrade... 306s The following package was automatically installed and is no longer required: 306s libpython3.13 306s Use 'sudo apt autoremove' to remove it. 306s The following NEW packages will be installed: 306s gcc-16-base libpython3.14 libpython3.14-minimal libpython3.14-stdlib 306s linux-headers-6.19.0-3 linux-headers-6.19.0-3-generic 306s linux-image-6.19.0-3-generic linux-modules-6.19.0-3-generic 306s linux-tools-6.19.0-3 linux-tools-6.19.0-3-generic 306s The following packages will be upgraded: 306s 3cpio amd64-microcode apt bpftool busybox-initramfs busybox-static 306s cryptsetup-bin dash dbus dbus-bin dbus-daemon dbus-session-bus-common 306s dbus-system-bus-common dbus-user-session debianutils dmsetup dracut-install 306s ethtool findutils gir1.2-girepository-3.0 gir1.2-glib-2.0 hwdata iproute2 306s iptables less libapt-pkg7.0 libatomic1 libattr1 libbpf1 libbrotli1 libbsd0 306s libcryptsetup12 libdbus-1-3 libdevmapper1.02.1 libdrm-amdgpu1 libdrm-common 306s libdrm2 libevent-core-2.1-7t64 libgcc-s1 libgdbm-compat4t64 libgdbm6t64 306s libgirepository-2.0-0 libglib2.0-0t64 libglib2.0-data libgpm2 libgudev-1.0-0 306s libidn2-0 libip4tc2 libip6tc2 libjansson4 libkeyutils1 liblsof0 306s libmaxminddb0 libnetfilter-conntrack3 libnpth0t64 libonig5 libpcap0.8t64 306s libpci3 libsensors-config libsensors5 libstdc++6 libusb-1.0-0 libwrap0 306s libxau6 libxkbcommon0 libxtables12 linux-generic linux-headers-generic 306s linux-headers-virtual linux-image-generic linux-image-virtual linux-perf 306s linux-tools-common linux-virtual lsof man-db mawk patch pciutils pnp.ids 306s pollinate python3-linkify-it python3-markdown-it python3-referencing sed 306s shared-mime-info tar tcpdump ubuntu-kernel-accessories ubuntu-standard wget 306s 91 upgraded, 10 newly installed, 0 to remove and 0 not upgraded. 306s Need to get 237 MB of archives. 306s After this operation, 339 MB of additional disk space will be used. 306s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 debianutils amd64 5.23.2build1 [93.3 kB] 306s Get:2 http://ftpmaster.internal/ubuntu resolute/main amd64 dash amd64 0.5.12-12ubuntu3 [96.0 kB] 306s Get:3 http://ftpmaster.internal/ubuntu resolute/main amd64 findutils amd64 4.10.0-3build2 [307 kB] 306s Get:4 http://ftpmaster.internal/ubuntu resolute/main amd64 sed amd64 4.9-2build3 [195 kB] 306s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 tar amd64 1.35+dfsg-3.1build2 [257 kB] 306s Get:6 http://ftpmaster.internal/ubuntu resolute/main amd64 libattr1 amd64 1:2.5.2-3build2 [11.4 kB] 306s Get:7 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc-16-base amd64 16-20260208-1ubuntu1 [59.7 kB] 306s Get:8 http://ftpmaster.internal/ubuntu resolute/main amd64 libgcc-s1 amd64 16-20260208-1ubuntu1 [80.3 kB] 306s Get:9 http://ftpmaster.internal/ubuntu resolute/main amd64 libbsd0 amd64 0.12.2-2build2 [42.3 kB] 306s Get:10 http://ftpmaster.internal/ubuntu resolute/main amd64 mawk amd64 1.3.4.20260129-1 [133 kB] 306s Get:11 http://ftpmaster.internal/ubuntu resolute/main amd64 libstdc++6 amd64 16-20260208-1ubuntu1 [844 kB] 306s Get:12 http://ftpmaster.internal/ubuntu resolute/main amd64 libapt-pkg7.0 amd64 3.1.15 [1151 kB] 307s Get:13 http://ftpmaster.internal/ubuntu resolute/main amd64 apt amd64 3.1.15 [1479 kB] 307s Get:14 http://ftpmaster.internal/ubuntu resolute/main amd64 dbus-system-bus-common all 1.16.2-2ubuntu3 [55.8 kB] 307s Get:15 http://ftpmaster.internal/ubuntu resolute/main amd64 dbus-session-bus-common all 1.16.2-2ubuntu3 [54.4 kB] 307s Get:16 http://ftpmaster.internal/ubuntu resolute/main amd64 dbus-user-session amd64 1.16.2-2ubuntu3 [9696 B] 307s Get:17 http://ftpmaster.internal/ubuntu resolute/main amd64 dbus-daemon amd64 1.16.2-2ubuntu3 [119 kB] 307s Get:18 http://ftpmaster.internal/ubuntu resolute/main amd64 dbus-bin amd64 1.16.2-2ubuntu3 [40.1 kB] 307s Get:19 http://ftpmaster.internal/ubuntu resolute/main amd64 dbus amd64 1.16.2-2ubuntu3 [24.2 kB] 307s Get:20 http://ftpmaster.internal/ubuntu resolute/main amd64 libdbus-1-3 amd64 1.16.2-2ubuntu3 [185 kB] 307s Get:21 http://ftpmaster.internal/ubuntu resolute/main amd64 libdevmapper1.02.1 amd64 2:1.02.205-2ubuntu3 [142 kB] 307s Get:22 http://ftpmaster.internal/ubuntu resolute/main amd64 dmsetup amd64 2:1.02.205-2ubuntu3 [79.4 kB] 307s Get:23 http://ftpmaster.internal/ubuntu resolute/main amd64 ethtool amd64 1:6.15-3build1 [318 kB] 307s Get:24 http://ftpmaster.internal/ubuntu resolute/main amd64 gir1.2-girepository-3.0 amd64 2.87.2-2 [25.2 kB] 307s Get:25 http://ftpmaster.internal/ubuntu resolute/main amd64 libgirepository-2.0-0 amd64 2.87.2-2 [76.1 kB] 307s Get:26 http://ftpmaster.internal/ubuntu resolute/main amd64 libatomic1 amd64 16-20260208-1ubuntu1 [11.4 kB] 307s Get:27 http://ftpmaster.internal/ubuntu resolute/main amd64 gir1.2-glib-2.0 amd64 2.87.2-2 [182 kB] 307s Get:28 http://ftpmaster.internal/ubuntu resolute/main amd64 libglib2.0-0t64 amd64 2.87.2-2 [1613 kB] 307s Get:29 http://ftpmaster.internal/ubuntu resolute/main amd64 libbpf1 amd64 1:1.6.2-1build1 [184 kB] 307s Get:30 http://ftpmaster.internal/ubuntu resolute/main amd64 iptables amd64 1.8.11-2ubuntu3 [381 kB] 307s Get:31 http://ftpmaster.internal/ubuntu resolute/main amd64 libip4tc2 amd64 1.8.11-2ubuntu3 [24.2 kB] 307s Get:32 http://ftpmaster.internal/ubuntu resolute/main amd64 libip6tc2 amd64 1.8.11-2ubuntu3 [24.4 kB] 307s Get:33 http://ftpmaster.internal/ubuntu resolute/main amd64 libnetfilter-conntrack3 amd64 1.1.1-1 [47.5 kB] 307s Get:34 http://ftpmaster.internal/ubuntu resolute/main amd64 libxtables12 amd64 1.8.11-2ubuntu3 [36.6 kB] 307s Get:35 http://ftpmaster.internal/ubuntu resolute/main amd64 iproute2 amd64 6.18.0-1ubuntu1 [1178 kB] 307s Get:36 http://ftpmaster.internal/ubuntu resolute/main amd64 less amd64 668-1build1 [172 kB] 307s Get:37 http://ftpmaster.internal/ubuntu resolute/main amd64 libcryptsetup12 amd64 2:2.8.0-1ubuntu3 [283 kB] 307s Get:38 http://ftpmaster.internal/ubuntu resolute/main amd64 libglib2.0-data all 2.87.2-2 [58.2 kB] 307s Get:39 http://ftpmaster.internal/ubuntu resolute/main amd64 libidn2-0 amd64 2.3.8-4build1 [67.6 kB] 307s Get:40 http://ftpmaster.internal/ubuntu resolute/main amd64 libkeyutils1 amd64 1.6.3-6ubuntu3 [10.6 kB] 307s Get:41 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-linkify-it all 2.0.3-1ubuntu3 [19.4 kB] 307s Get:42 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-markdown-it all 3.0.0-3build1 [54.4 kB] 307s Get:43 http://ftpmaster.internal/ubuntu resolute/main amd64 shared-mime-info amd64 2.4-5build3 [476 kB] 307s Get:44 http://ftpmaster.internal/ubuntu resolute/main amd64 busybox-static amd64 1:1.37.0-7ubuntu1 [1034 kB] 307s Get:45 http://ftpmaster.internal/ubuntu resolute/main amd64 libdrm-common all 2.4.131-1 [9774 B] 307s Get:46 http://ftpmaster.internal/ubuntu resolute/main amd64 libdrm2 amd64 2.4.131-1 [42.3 kB] 307s Get:47 http://ftpmaster.internal/ubuntu resolute/main amd64 libgdbm6t64 amd64 1.26-1build1 [36.5 kB] 307s Get:48 http://ftpmaster.internal/ubuntu resolute/main amd64 libgpm2 amd64 1.20.7-12build1 [14.4 kB] 307s Get:49 http://ftpmaster.internal/ubuntu resolute/main amd64 libjansson4 amd64 2.14-2build4 [33.2 kB] 307s Get:50 http://ftpmaster.internal/ubuntu resolute/main amd64 lsof amd64 4.99.4+dfsg-2build2 [239 kB] 307s Get:51 http://ftpmaster.internal/ubuntu resolute/main amd64 liblsof0 amd64 4.99.4+dfsg-2build2 [56.5 kB] 307s Get:52 http://ftpmaster.internal/ubuntu resolute/main amd64 libmaxminddb0 amd64 1.12.2-1build2 [18.9 kB] 307s Get:53 http://ftpmaster.internal/ubuntu resolute/main amd64 libpcap0.8t64 amd64 1.10.5-2ubuntu3 [154 kB] 307s Get:54 http://ftpmaster.internal/ubuntu resolute/main amd64 pciutils amd64 1:3.14.0-1build2 [95.5 kB] 307s Get:55 http://ftpmaster.internal/ubuntu resolute/main amd64 libpci3 amd64 1:3.14.0-1build2 [38.1 kB] 307s Get:56 http://ftpmaster.internal/ubuntu resolute/main amd64 libsensors-config all 1:3.6.2-2build1 [6862 B] 307s Get:57 http://ftpmaster.internal/ubuntu resolute/main amd64 libsensors5 amd64 1:3.6.2-2build1 [28.9 kB] 307s Get:58 http://ftpmaster.internal/ubuntu resolute/main amd64 libusb-1.0-0 amd64 2:1.0.29-2build1 [56.9 kB] 307s Get:59 http://ftpmaster.internal/ubuntu resolute/main amd64 libxau6 amd64 1:1.0.11-1build2 [7502 B] 307s Get:60 http://ftpmaster.internal/ubuntu resolute/main amd64 libxkbcommon0 amd64 1.13.1-1 [159 kB] 307s Get:61 http://ftpmaster.internal/ubuntu resolute/main amd64 man-db amd64 2.13.1-1build1 [1392 kB] 307s Get:62 http://ftpmaster.internal/ubuntu resolute/main amd64 tcpdump amd64 4.99.5-2ubuntu3 [477 kB] 307s Get:63 http://ftpmaster.internal/ubuntu resolute/main amd64 wget amd64 1.25.0-2ubuntu4 [353 kB] 307s Get:64 http://ftpmaster.internal/ubuntu resolute/main amd64 ubuntu-standard amd64 1.564 [13.3 kB] 307s Get:65 http://ftpmaster.internal/ubuntu resolute/main amd64 3cpio amd64 0.14.0-1ubuntu1 [285 kB] 307s Get:66 http://ftpmaster.internal/ubuntu resolute/main amd64 bpftool amd64 7.7.0+6.19.0-3.3 [1229 kB] 307s Get:67 http://ftpmaster.internal/ubuntu resolute/main amd64 busybox-initramfs amd64 1:1.37.0-7ubuntu1 [191 kB] 307s Get:68 http://ftpmaster.internal/ubuntu resolute/main amd64 cryptsetup-bin amd64 2:2.8.0-1ubuntu3 [228 kB] 307s Get:69 http://ftpmaster.internal/ubuntu resolute/main amd64 dracut-install amd64 109-11ubuntu1 [45.8 kB] 307s Get:70 http://ftpmaster.internal/ubuntu resolute/main amd64 hwdata all 0.394-1build1 [1566 B] 307s Get:71 http://ftpmaster.internal/ubuntu resolute/main amd64 pnp.ids all 0.394-1build1 [29.6 kB] 307s Get:72 http://ftpmaster.internal/ubuntu resolute/main amd64 libbrotli1 amd64 1.2.0-3 [343 kB] 307s Get:73 http://ftpmaster.internal/ubuntu resolute/main amd64 libdrm-amdgpu1 amd64 2.4.131-1 [23.2 kB] 307s Get:74 http://ftpmaster.internal/ubuntu resolute/main amd64 libevent-core-2.1-7t64 amd64 2.1.12-stable-10build2 [93.1 kB] 307s Get:75 http://ftpmaster.internal/ubuntu resolute/main amd64 libgdbm-compat4t64 amd64 1.26-1build1 [6796 B] 307s Get:76 http://ftpmaster.internal/ubuntu resolute/main amd64 libgudev-1.0-0 amd64 1:238-7build1 [15.9 kB] 307s Get:77 http://ftpmaster.internal/ubuntu resolute/main amd64 libnpth0t64 amd64 1.8-3build1 [9302 B] 307s Get:78 http://ftpmaster.internal/ubuntu resolute/main amd64 libonig5 amd64 6.9.10-1build1 [174 kB] 307s Get:79 http://ftpmaster.internal/ubuntu resolute/main amd64 libpython3.14-minimal amd64 3.14.2-1 [920 kB] 307s Get:80 http://ftpmaster.internal/ubuntu resolute/main amd64 libpython3.14-stdlib amd64 3.14.2-1 [2398 kB] 307s Get:81 http://ftpmaster.internal/ubuntu resolute/main amd64 libpython3.14 amd64 3.14.2-1 [2568 kB] 308s Get:82 http://ftpmaster.internal/ubuntu resolute/main amd64 libwrap0 amd64 7.6.q-36build2 [48.5 kB] 308s Get:83 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-modules-6.19.0-3-generic amd64 6.19.0-3.3 [171 MB] 313s Get:84 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-image-6.19.0-3-generic amd64 6.19.0-3.3+1 [16.8 MB] 313s Get:85 http://ftpmaster.internal/ubuntu resolute/main amd64 amd64-microcode amd64 3.20251202.1ubuntu1 [459 kB] 313s Get:86 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-generic amd64 6.19.0-3.3 [1698 B] 313s Get:87 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-image-generic amd64 6.19.0-3.3 [12.2 kB] 313s Get:88 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-virtual amd64 6.19.0-3.3 [1700 B] 313s Get:89 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-image-virtual amd64 6.19.0-3.3 [12.1 kB] 313s Get:90 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-headers-virtual amd64 6.19.0-3.3 [1646 B] 313s Get:91 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-headers-6.19.0-3 all 6.19.0-3.3 [14.9 MB] 313s Get:92 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-headers-6.19.0-3-generic amd64 6.19.0-3.3 [4330 kB] 313s Get:93 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-headers-generic amd64 6.19.0-3.3 [12.0 kB] 314s Get:94 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-perf amd64 6.19.0-3.3 [4480 kB] 314s Get:95 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-tools-common all 6.19.0-3.3 [345 kB] 314s Get:96 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-tools-6.19.0-3 amd64 6.19.0-3.3 [1455 kB] 314s Get:97 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-tools-6.19.0-3-generic amd64 6.19.0-3.3 [1612 B] 314s Get:98 http://ftpmaster.internal/ubuntu resolute/main amd64 patch amd64 2.8-2build1 [95.7 kB] 314s Get:99 http://ftpmaster.internal/ubuntu resolute/main amd64 pollinate all 4.33-4ubuntu5 [14.0 kB] 314s Get:100 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-referencing all 0.36.2-1ubuntu2 [22.2 kB] 314s Get:101 http://ftpmaster.internal/ubuntu resolute/main amd64 ubuntu-kernel-accessories amd64 1.564 [13.1 kB] 314s dpkg-preconfigure: unable to re-open stdin: No such file or directory 314s Fetched 237 MB in 8s (31.5 MB/s) 314s (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.) 314s Preparing to unpack .../debianutils_5.23.2build1_amd64.deb ... 314s Unpacking debianutils (5.23.2build1) over (5.23.2) ... 314s Setting up debianutils (5.23.2build1) ... 314s (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.) 314s Preparing to unpack .../dash_0.5.12-12ubuntu3_amd64.deb ... 314s Unpacking dash (0.5.12-12ubuntu3) over (0.5.12-12ubuntu2) ... 314s Setting up dash (0.5.12-12ubuntu3) ... 315s (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.) 315s Preparing to unpack .../findutils_4.10.0-3build2_amd64.deb ... 315s Unpacking findutils (4.10.0-3build2) over (4.10.0-3build1) ... 315s Setting up findutils (4.10.0-3build2) ... 315s (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.) 315s Preparing to unpack .../sed_4.9-2build3_amd64.deb ... 315s Unpacking sed (4.9-2build3) over (4.9-2build2) ... 315s Setting up sed (4.9-2build3) ... 315s (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.) 315s Preparing to unpack .../tar_1.35+dfsg-3.1build2_amd64.deb ... 315s Unpacking tar (1.35+dfsg-3.1build2) over (1.35+dfsg-3.1build1) ... 315s Setting up tar (1.35+dfsg-3.1build2) ... 315s (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.) 315s Preparing to unpack .../libattr1_1%3a2.5.2-3build2_amd64.deb ... 315s Unpacking libattr1:amd64 (1:2.5.2-3build2) over (1:2.5.2-3build1) ... 315s Setting up libattr1:amd64 (1:2.5.2-3build2) ... 315s Selecting previously unselected package gcc-16-base:amd64. 315s (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.) 315s Preparing to unpack .../gcc-16-base_16-20260208-1ubuntu1_amd64.deb ... 315s Unpacking gcc-16-base:amd64 (16-20260208-1ubuntu1) ... 315s Setting up gcc-16-base:amd64 (16-20260208-1ubuntu1) ... 315s (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 ... 83962 files and directories currently installed.) 315s Preparing to unpack .../libgcc-s1_16-20260208-1ubuntu1_amd64.deb ... 315s Unpacking libgcc-s1:amd64 (16-20260208-1ubuntu1) over (15.2.0-12ubuntu1) ... 315s Setting up libgcc-s1:amd64 (16-20260208-1ubuntu1) ... 315s (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 ... 83962 files and directories currently installed.) 315s Preparing to unpack .../00-libbsd0_0.12.2-2build2_amd64.deb ... 315s Unpacking libbsd0:amd64 (0.12.2-2build2) over (0.12.2-2build1) ... 315s Preparing to unpack .../01-mawk_1.3.4.20260129-1_amd64.deb ... 315s Unpacking mawk (1.3.4.20260129-1) over (1.3.4.20250131-2) ... 315s Preparing to unpack .../02-libstdc++6_16-20260208-1ubuntu1_amd64.deb ... 315s Unpacking libstdc++6:amd64 (16-20260208-1ubuntu1) over (15.2.0-12ubuntu1) ... 315s Preparing to unpack .../03-libapt-pkg7.0_3.1.15_amd64.deb ... 315s Unpacking libapt-pkg7.0:amd64 (3.1.15) over (3.1.14) ... 315s Preparing to unpack .../04-apt_3.1.15_amd64.deb ... 315s Unpacking apt (3.1.15) over (3.1.14) ... 315s Preparing to unpack .../05-dbus-system-bus-common_1.16.2-2ubuntu3_all.deb ... 315s Unpacking dbus-system-bus-common (1.16.2-2ubuntu3) over (1.16.2-2ubuntu2) ... 315s Preparing to unpack .../06-dbus-session-bus-common_1.16.2-2ubuntu3_all.deb ... 315s Unpacking dbus-session-bus-common (1.16.2-2ubuntu3) over (1.16.2-2ubuntu2) ... 315s Preparing to unpack .../07-dbus-user-session_1.16.2-2ubuntu3_amd64.deb ... 315s Unpacking dbus-user-session (1.16.2-2ubuntu3) over (1.16.2-2ubuntu2) ... 315s Preparing to unpack .../08-dbus-daemon_1.16.2-2ubuntu3_amd64.deb ... 315s Unpacking dbus-daemon (1.16.2-2ubuntu3) over (1.16.2-2ubuntu2) ... 315s Preparing to unpack .../09-dbus-bin_1.16.2-2ubuntu3_amd64.deb ... 315s Unpacking dbus-bin (1.16.2-2ubuntu3) over (1.16.2-2ubuntu2) ... 315s Preparing to unpack .../10-dbus_1.16.2-2ubuntu3_amd64.deb ... 315s Unpacking dbus (1.16.2-2ubuntu3) over (1.16.2-2ubuntu2) ... 315s Preparing to unpack .../11-libdbus-1-3_1.16.2-2ubuntu3_amd64.deb ... 315s Unpacking libdbus-1-3:amd64 (1.16.2-2ubuntu3) over (1.16.2-2ubuntu2) ... 315s Preparing to unpack .../12-libdevmapper1.02.1_2%3a1.02.205-2ubuntu3_amd64.deb ... 315s Unpacking libdevmapper1.02.1:amd64 (2:1.02.205-2ubuntu3) over (2:1.02.205-2ubuntu2) ... 316s Preparing to unpack .../13-dmsetup_2%3a1.02.205-2ubuntu3_amd64.deb ... 316s Unpacking dmsetup (2:1.02.205-2ubuntu3) over (2:1.02.205-2ubuntu2) ... 316s Preparing to unpack .../14-ethtool_1%3a6.15-3build1_amd64.deb ... 316s Unpacking ethtool (1:6.15-3build1) over (1:6.15-3) ... 316s Preparing to unpack .../15-gir1.2-girepository-3.0_2.87.2-2_amd64.deb ... 316s Unpacking gir1.2-girepository-3.0:amd64 (2.87.2-2) over (2.86.3-4) ... 316s Preparing to unpack .../16-libgirepository-2.0-0_2.87.2-2_amd64.deb ... 316s Unpacking libgirepository-2.0-0:amd64 (2.87.2-2) over (2.86.3-4) ... 316s Preparing to unpack .../17-libatomic1_16-20260208-1ubuntu1_amd64.deb ... 316s Unpacking libatomic1:amd64 (16-20260208-1ubuntu1) over (15.2.0-12ubuntu1) ... 316s Preparing to unpack .../18-gir1.2-glib-2.0_2.87.2-2_amd64.deb ... 316s Unpacking gir1.2-glib-2.0:amd64 (2.87.2-2) over (2.86.3-4) ... 316s Preparing to unpack .../19-libglib2.0-0t64_2.87.2-2_amd64.deb ... 316s Unpacking libglib2.0-0t64:amd64 (2.87.2-2) over (2.86.3-4) ... 316s Preparing to unpack .../20-libbpf1_1%3a1.6.2-1build1_amd64.deb ... 316s Unpacking libbpf1:amd64 (1:1.6.2-1build1) over (1:1.6.2-1) ... 316s Preparing to unpack .../21-iptables_1.8.11-2ubuntu3_amd64.deb ... 316s Unpacking iptables (1.8.11-2ubuntu3) over (1.8.11-2ubuntu2) ... 316s Preparing to unpack .../22-libip4tc2_1.8.11-2ubuntu3_amd64.deb ... 316s Unpacking libip4tc2:amd64 (1.8.11-2ubuntu3) over (1.8.11-2ubuntu2) ... 316s Preparing to unpack .../23-libip6tc2_1.8.11-2ubuntu3_amd64.deb ... 316s Unpacking libip6tc2:amd64 (1.8.11-2ubuntu3) over (1.8.11-2ubuntu2) ... 316s Preparing to unpack .../24-libnetfilter-conntrack3_1.1.1-1_amd64.deb ... 316s Unpacking libnetfilter-conntrack3:amd64 (1.1.1-1) over (1.1.0-1build1) ... 316s Preparing to unpack .../25-libxtables12_1.8.11-2ubuntu3_amd64.deb ... 316s Unpacking libxtables12:amd64 (1.8.11-2ubuntu3) over (1.8.11-2ubuntu2) ... 316s Preparing to unpack .../26-iproute2_6.18.0-1ubuntu1_amd64.deb ... 316s Unpacking iproute2 (6.18.0-1ubuntu1) over (6.16.0-1ubuntu3) ... 316s Preparing to unpack .../27-less_668-1build1_amd64.deb ... 316s Unpacking less (668-1build1) over (668-1) ... 316s Preparing to unpack .../28-libcryptsetup12_2%3a2.8.0-1ubuntu3_amd64.deb ... 316s Unpacking libcryptsetup12:amd64 (2:2.8.0-1ubuntu3) over (2:2.8.0-1ubuntu2) ... 316s Preparing to unpack .../29-libglib2.0-data_2.87.2-2_all.deb ... 316s Unpacking libglib2.0-data (2.87.2-2) over (2.86.3-4) 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321s Setting up ubuntu-kernel-accessories (1.564) ... 321s Setting up libgpm2:amd64 (1.20.7-12build1) ... 321s Setting up libgdbm6t64:amd64 (1.26-1build1) ... 321s Setting up linux-modules-6.19.0-3-generic (6.19.0-3.3) ... 322s Setting up libgdbm-compat4t64:amd64 (1.26-1build1) ... 322s Setting up bpftool (7.7.0+6.19.0-3.3) ... 322s Setting up libip6tc2:amd64 (1.8.11-2ubuntu3) ... 322s Setting up liblsof0 (4.99.4+dfsg-2build2) ... 322s Setting up libmaxminddb0:amd64 (1.12.2-1build2) ... 322s Setting up libbrotli1:amd64 (1.2.0-3) ... 322s Setting up libpython3.14-minimal:amd64 (3.14.2-1) ... 322s Setting up libsensors-config (1:3.6.2-2build1) ... 322s Setting up less (668-1build1) ... 322s Setting up linux-headers-6.19.0-3 (6.19.0-3.3) ... 322s Setting up libidn2-0:amd64 (2.3.8-4build1) ... 322s Setting up amd64-microcode (3.20251202.1ubuntu1) ... 322s amd64-microcode: microcode will be updated at next boot 322s Setting up man-db (2.13.1-1build1) ... 322s Updating database of manual pages ... 324s man-db.service is a disabled or a static unit not running, not starting it. 324s Setting up libjansson4:amd64 (2.14-2build4) ... 324s Setting up libglib2.0-data (2.87.2-2) ... 324s Setting up pollinate (4.33-4ubuntu5) ... 334s Setting up busybox-static (1:1.37.0-7ubuntu1) ... 334s Setting up libwrap0:amd64 (7.6.q-36build2) ... 334s Setting up linux-image-6.19.0-3-generic (6.19.0-3.3+1) ... 335s I: /boot/vmlinuz is now a symlink to vmlinuz-6.19.0-3-generic 335s I: /boot/initrd.img is now a symlink to initrd.img-6.19.0-3-generic 335s Setting up libdbus-1-3:amd64 (1.16.2-2ubuntu3) ... 335s Setting up libatomic1:amd64 (16-20260208-1ubuntu1) ... 335s Setting up patch (2.8-2build1) ... 335s Setting up libsensors5:amd64 (1:3.6.2-2build1) ... 335s Setting up busybox-initramfs (1:1.37.0-7ubuntu1) ... 335s Setting up libxtables12:amd64 (1.8.11-2ubuntu3) ... 335s Setting up lsof (4.99.4+dfsg-2build2) ... 335s Setting up libpci3:amd64 (1:3.14.0-1build2) ... 335s Setting up libdevmapper1.02.1:amd64 (2:1.02.205-2ubuntu3) ... 335s Setting up dracut-install (109-11ubuntu1) ... 335s Setting up dmsetup (2:1.02.205-2ubuntu3) ... 335s Setting up libnetfilter-conntrack3:amd64 (1.1.1-1) ... 335s Setting up pnp.ids (0.394-1build1) ... 335s Setting up dbus-session-bus-common (1.16.2-2ubuntu3) ... 335s Setting up python3-linkify-it (2.0.3-1ubuntu3) ... 336s Setting up libpcap0.8t64:amd64 (1.10.5-2ubuntu3) ... 336s Setting up libcryptsetup12:amd64 (2:2.8.0-1ubuntu3) ... 336s Setting up mawk (1.3.4.20260129-1) ... 336s Setting up libevent-core-2.1-7t64:amd64 (2.1.12-stable-10build2) ... 336s Setting up libusb-1.0-0:amd64 (2:1.0.29-2build1) ... 336s Setting up linux-image-virtual (6.19.0-3.3) ... 336s Setting up dbus-system-bus-common (1.16.2-2ubuntu3) ... 336s Setting up libbsd0:amd64 (0.12.2-2build2) ... 336s Setting up libdrm-common (2.4.131-1) ... 336s Setting up libstdc++6:amd64 (16-20260208-1ubuntu1) ... 336s Setting up dbus-bin (1.16.2-2ubuntu3) ... 336s Setting up libonig5:amd64 (6.9.10-1build1) ... 336s Setting up libbpf1:amd64 (1:1.6.2-1build1) ... 336s Setting up ethtool (1:6.15-3build1) ... 336s Setting up python3-referencing (0.36.2-1ubuntu2) ... 336s Setting up libxkbcommon0:amd64 (1.13.1-1) ... 336s Setting up cryptsetup-bin (2:2.8.0-1ubuntu3) ... 336s Setting up linux-headers-6.19.0-3-generic (6.19.0-3.3) ... 336s Setting up tcpdump (4.99.5-2ubuntu3) ... 336s Setting up linux-image-generic (6.19.0-3.3) ... 336s Setting up wget (1.25.0-2ubuntu4) ... 336s Setting up libpython3.14-stdlib:amd64 (3.14.2-1) ... 336s Setting up iptables (1.8.11-2ubuntu3) ... 336s Setting up iproute2 (6.18.0-1ubuntu1) ... 336s Setting up linux-headers-generic (6.19.0-3.3) ... 336s Setting up dbus-daemon (1.16.2-2ubuntu3) ... 336s Setting up hwdata (0.394-1build1) ... 336s Setting up dbus-user-session (1.16.2-2ubuntu3) ... 336s Setting up libglib2.0-0t64:amd64 (2.87.2-2) ... 336s No schema files found: doing nothing. 336s Setting up dbus (1.16.2-2ubuntu3) ... 336s A reboot is required to replace the running dbus-daemon. 336s Please reboot the system when convenient. 336s Setting up shared-mime-info (2.4-5build3) ... 337s Setting up gir1.2-glib-2.0:amd64 (2.87.2-2) ... 337s Setting up pciutils (1:3.14.0-1build2) ... 337s Setting up python3-markdown-it (3.0.0-3build1) ... 337s Setting up libdrm2:amd64 (2.4.131-1) ... 337s Setting up libpython3.14:amd64 (3.14.2-1) ... 337s Setting up libapt-pkg7.0:amd64 (3.1.15) ... 337s Setting up linux-tools-common (6.19.0-3.3) ... 337s Setting up libgudev-1.0-0:amd64 (1:238-7build1) ... 337s Setting up libdrm-amdgpu1:amd64 (2.4.131-1) ... 337s Setting up apt (3.1.15) ... 337s Setting up linux-headers-virtual (6.19.0-3.3) ... 337s Setting up linux-generic (6.19.0-3.3) ... 337s Setting up libgirepository-2.0-0:amd64 (2.87.2-2) ... 337s Setting up linux-tools-6.19.0-3 (6.19.0-3.3) ... 337s Setting up ubuntu-standard (1.564) ... 337s Setting up gir1.2-girepository-3.0:amd64 (2.87.2-2) ... 337s Setting up linux-virtual (6.19.0-3.3) ... 337s Setting up linux-perf (6.19.0-3.3) ... 337s Setting up linux-tools-6.19.0-3-generic (6.19.0-3.3) ... 337s Processing triggers for debianutils (5.23.2build1) ... 338s Processing triggers for install-info (7.2-5) ... 338s Processing triggers for initramfs-tools (0.150ubuntu7) ... 338s update-initramfs: Generating /boot/initrd.img-6.18.0-9-generic 342s Processing triggers for libc-bin (2.42-2ubuntu4) ... 342s Processing triggers for linux-image-6.19.0-3-generic (6.19.0-3.3+1) ... 342s /etc/kernel/postinst.d/initramfs-tools: 342s update-initramfs: Generating /boot/initrd.img-6.19.0-3-generic 346s /etc/kernel/postinst.d/zz-update-grub: 346s Sourcing file `/etc/default/grub' 346s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 346s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg' 346s Generating grub configuration file ... 346s Found linux image: /boot/vmlinuz-6.19.0-3-generic 346s Found initrd image: /boot/initrd.img-6.19.0-3-generic 346s Found linux image: /boot/vmlinuz-6.18.0-9-generic 346s Found initrd image: /boot/initrd.img-6.18.0-9-generic 346s Warning: os-prober will not be executed to detect other bootable partitions. 346s Systems on them will not be added to the GRUB boot configuration. 346s Check GRUB_DISABLE_OS_PROBER documentation entry. 346s Adding boot menu entry for UEFI Firmware Settings ... 346s done 346s autopkgtest [05:29:52]: upgrading testbed (apt dist-upgrade and autopurge) 347s Reading package lists... 347s Building dependency tree... 347s Reading state information... 347s Calculating upgrade... 347s The following package was automatically installed and is no longer required: 347s libpython3.13 347s Use 'sudo apt autoremove' to remove it. 347s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 347s Reading package lists... 347s Building dependency tree... 347s Reading state information... 347s Solving dependencies... 347s The following packages will be REMOVED: 347s libpython3.13* 348s 0 upgraded, 0 newly installed, 1 to remove and 0 not upgraded. 348s After this operation, 7599 kB disk space will be freed. 348s (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.) 348s Removing libpython3.13:amd64 (3.13.11-1) ... 348s Processing triggers for libc-bin (2.42-2ubuntu4) ... 348s autopkgtest [05:29:54]: rebooting testbed after setup commands that affected boot 380s Reading package lists... 380s Building dependency tree... 380s Reading state information... 380s Solving dependencies... 380s The following NEW packages will be installed: 380s build-essential cpp cpp-15 cpp-15-x86-64-linux-gnu cpp-x86-64-linux-gnu 380s dctrl-tools fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono 380s fonts-glyphicons-halflings fonts-mathjax g++ g++-15 g++-15-x86-64-linux-gnu 380s g++-x86-64-linux-gnu gcc gcc-15 gcc-15-x86-64-linux-gnu gcc-x86-64-linux-gnu 380s gfortran gfortran-15 gfortran-15-x86-64-linux-gnu gfortran-x86-64-linux-gnu 380s icu-devtools libasan8 libblas-dev libblas3 libbz2-dev libc-dev-bin libc6-dev 380s libcairo2 libcc1-0 libcrypt-dev libdatrie1 libdeflate-dev libdeflate0 380s libfontconfig1 libgcc-15-dev libgfortran-15-dev libgfortran5 libgomp1 380s libgraphite2-3 libharfbuzz0b libhwasan0 libice6 libicu-dev libisl23 libitm1 380s libjbig0 libjpeg-dev libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8 libjpeg8-dev 380s libjs-bootstrap libjs-highlight.js libjs-jquery libjs-jquery-datatables 380s libjs-mathjax liblapack-dev liblapack3 liblerc4 liblsan0 liblzma-dev libmpc3 380s libncurses-dev libnlopt0 libpango-1.0-0 libpangocairo-1.0-0 380s libpangoft2-1.0-0 libpaper-utils libpaper2 libpcre2-16-0 libpcre2-32-0 380s libpcre2-dev libpcre2-posix3 libpixman-1-0 libpkgconf3 libpng-dev 380s libquadmath0 libreadline-dev libsharpyuv0 libsm6 libstdc++-15-dev libtcl8.6 380s libthai-data libthai0 libtiff6 libtirpc-dev libtk8.6 libtsan2 libubsan1 380s libwebp7 libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxss1 libxt6t64 380s libzstd-dev linux-libc-dev node-normalize.css pkg-r-autopkgtest pkgconf 380s pkgconf-bin r-base-core r-base-dev r-cran-backports r-cran-boot r-cran-broom 380s r-cran-cli r-cran-colorspace r-cran-cowplot r-cran-cpp11 r-cran-curl 380s r-cran-deriv r-cran-doby r-cran-dplyr r-cran-evaluate r-cran-fansi 380s r-cran-farver r-cran-forecast r-cran-fracdiff r-cran-generics r-cran-ggplot2 380s r-cran-glue r-cran-gtable r-cran-highr r-cran-isoband r-cran-jsonlite 380s r-cran-knitr r-cran-labeling r-cran-lattice r-cran-lifecycle r-cran-littler 380s r-cran-lme4 r-cran-lmertest r-cran-lmtest r-cran-magrittr r-cran-mass 380s r-cran-matrix r-cran-microbenchmark r-cran-minqa r-cran-modelr r-cran-nlme 380s r-cran-nloptr r-cran-nnet r-cran-numderiv r-cran-pbkrtest r-cran-pillar 380s r-cran-pkgconfig r-cran-pkgkitten r-cran-purrr r-cran-quadprog 380s r-cran-quantmod r-cran-r6 r-cran-rbibutils r-cran-rcolorbrewer r-cran-rcpp 380s r-cran-rcpparmadillo r-cran-rcppeigen r-cran-rdpack r-cran-reformulas 380s r-cran-rlang r-cran-s7 r-cran-scales r-cran-statmod r-cran-stringi 380s r-cran-stringr r-cran-tibble r-cran-tidyr r-cran-tidyselect r-cran-timedate 380s r-cran-tseries r-cran-ttr r-cran-urca r-cran-utf8 r-cran-vctrs 380s r-cran-viridislite r-cran-withr r-cran-xfun r-cran-xts r-cran-yaml 380s r-cran-zoo rpcsvc-proto unzip x11-common xdg-utils zip zlib1g-dev 380s 0 upgraded, 191 newly installed, 0 to remove and 0 not upgraded. 380s Need to get 225 MB of archives. 380s After this operation, 658 MB of additional disk space will be used. 380s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 libc-dev-bin amd64 2.42-2ubuntu4 [23.3 kB] 380s Get:2 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-libc-dev amd64 6.19.0-3.3 [1846 kB] 381s Get:3 http://ftpmaster.internal/ubuntu resolute/main amd64 libcrypt-dev amd64 1:4.5.1-1 [122 kB] 381s Get:4 http://ftpmaster.internal/ubuntu resolute/main amd64 rpcsvc-proto amd64 1.4.3-1build1 [68.3 kB] 381s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 libc6-dev amd64 2.42-2ubuntu4 [2207 kB] 381s Get:6 http://ftpmaster.internal/ubuntu resolute/main amd64 libisl23 amd64 0.27-1build1 [691 kB] 381s Get:7 http://ftpmaster.internal/ubuntu resolute/main amd64 libmpc3 amd64 1.3.1-2 [54.8 kB] 381s Get:8 http://ftpmaster.internal/ubuntu resolute/main amd64 cpp-15-x86-64-linux-gnu amd64 15.2.0-12ubuntu1 [12.9 MB] 381s Get:9 http://ftpmaster.internal/ubuntu resolute/main amd64 cpp-15 amd64 15.2.0-12ubuntu1 [1034 B] 381s Get:10 http://ftpmaster.internal/ubuntu resolute/main amd64 cpp-x86-64-linux-gnu amd64 4:15.2.0-4ubuntu1 [5746 B] 381s Get:11 http://ftpmaster.internal/ubuntu resolute/main amd64 cpp amd64 4:15.2.0-4ubuntu1 [22.4 kB] 381s Get:12 http://ftpmaster.internal/ubuntu resolute/main amd64 libcc1-0 amd64 16-20260208-1ubuntu1 [51.2 kB] 381s Get:13 http://ftpmaster.internal/ubuntu resolute/main amd64 libgomp1 amd64 16-20260208-1ubuntu1 [162 kB] 381s Get:14 http://ftpmaster.internal/ubuntu resolute/main amd64 libitm1 amd64 16-20260208-1ubuntu1 [30.2 kB] 381s Get:15 http://ftpmaster.internal/ubuntu resolute/main amd64 libasan8 amd64 16-20260208-1ubuntu1 [3182 kB] 381s Get:16 http://ftpmaster.internal/ubuntu resolute/main amd64 liblsan0 amd64 16-20260208-1ubuntu1 [1392 kB] 381s Get:17 http://ftpmaster.internal/ubuntu resolute/main amd64 libtsan2 amd64 16-20260208-1ubuntu1 [2838 kB] 381s Get:18 http://ftpmaster.internal/ubuntu resolute/main amd64 libubsan1 amd64 16-20260208-1ubuntu1 [1238 kB] 381s Get:19 http://ftpmaster.internal/ubuntu resolute/main amd64 libhwasan0 amd64 16-20260208-1ubuntu1 [1729 kB] 381s Get:20 http://ftpmaster.internal/ubuntu resolute/main amd64 libquadmath0 amd64 16-20260208-1ubuntu1 [155 kB] 382s Get:21 http://ftpmaster.internal/ubuntu resolute/main amd64 libgcc-15-dev amd64 15.2.0-12ubuntu1 [2866 kB] 382s Get:22 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc-15-x86-64-linux-gnu amd64 15.2.0-12ubuntu1 [25.4 MB] 382s Get:23 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc-15 amd64 15.2.0-12ubuntu1 [530 kB] 382s Get:24 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc-x86-64-linux-gnu amd64 4:15.2.0-4ubuntu1 [1208 B] 382s Get:25 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc amd64 4:15.2.0-4ubuntu1 [5024 B] 382s Get:26 http://ftpmaster.internal/ubuntu resolute/main amd64 libstdc++-15-dev amd64 15.2.0-12ubuntu1 [2553 kB] 382s Get:27 http://ftpmaster.internal/ubuntu resolute/main amd64 g++-15-x86-64-linux-gnu amd64 15.2.0-12ubuntu1 [14.4 MB] 382s Get:28 http://ftpmaster.internal/ubuntu resolute/main amd64 g++-15 amd64 15.2.0-12ubuntu1 [25.3 kB] 382s Get:29 http://ftpmaster.internal/ubuntu resolute/main amd64 g++-x86-64-linux-gnu amd64 4:15.2.0-4ubuntu1 [966 B] 382s Get:30 http://ftpmaster.internal/ubuntu resolute/main amd64 g++ amd64 4:15.2.0-4ubuntu1 [1100 B] 382s Get:31 http://ftpmaster.internal/ubuntu resolute/main amd64 build-essential amd64 12.12ubuntu2 [5256 B] 382s Get:32 http://ftpmaster.internal/ubuntu resolute/main amd64 dctrl-tools amd64 2.24-3build4 [104 kB] 382s Get:33 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-dejavu-mono all 2.37-8build1 [502 kB] 382s Get:34 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-dejavu-core all 2.37-8build1 [834 kB] 382s Get:35 http://ftpmaster.internal/ubuntu resolute/main amd64 fontconfig-config amd64 2.17.1-3ubuntu1 [38.5 kB] 382s Get:36 http://ftpmaster.internal/ubuntu resolute/main amd64 libfontconfig1 amd64 2.17.1-3ubuntu1 [144 kB] 382s Get:37 http://ftpmaster.internal/ubuntu resolute/main amd64 fontconfig amd64 2.17.1-3ubuntu1 [180 kB] 383s Get:38 http://ftpmaster.internal/ubuntu resolute/universe amd64 fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-6 [119 kB] 383s Get:39 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-mathjax all 2.7.9+dfsg-1build1 [2283 kB] 383s Get:40 http://ftpmaster.internal/ubuntu resolute/main amd64 libgfortran5 amd64 16-20260208-1ubuntu1 [957 kB] 383s Get:41 http://ftpmaster.internal/ubuntu resolute/main amd64 libgfortran-15-dev amd64 15.2.0-12ubuntu1 [973 kB] 383s Get:42 http://ftpmaster.internal/ubuntu resolute/main amd64 gfortran-15-x86-64-linux-gnu amd64 15.2.0-12ubuntu1 [13.6 MB] 383s Get:43 http://ftpmaster.internal/ubuntu resolute/main amd64 gfortran-15 amd64 15.2.0-12ubuntu1 [18.1 kB] 383s Get:44 http://ftpmaster.internal/ubuntu resolute/main amd64 gfortran-x86-64-linux-gnu amd64 4:15.2.0-4ubuntu1 [1014 B] 383s Get:45 http://ftpmaster.internal/ubuntu resolute/main amd64 gfortran amd64 4:15.2.0-4ubuntu1 [1172 B] 383s Get:46 http://ftpmaster.internal/ubuntu resolute/main amd64 icu-devtools amd64 78.2-1ubuntu1 [214 kB] 383s Get:47 http://ftpmaster.internal/ubuntu resolute/main amd64 libblas3 amd64 3.12.1-7ubuntu1 [260 kB] 383s Get:48 http://ftpmaster.internal/ubuntu resolute/main amd64 libblas-dev amd64 3.12.1-7ubuntu1 [235 kB] 383s Get:49 http://ftpmaster.internal/ubuntu resolute/main amd64 libbz2-dev amd64 1.0.8-6build2 [36.2 kB] 383s Get:50 http://ftpmaster.internal/ubuntu resolute/main amd64 libpixman-1-0 amd64 0.46.4-1 [287 kB] 383s Get:51 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-render0 amd64 1.17.0-2ubuntu1 [16.2 kB] 383s Get:52 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-shm0 amd64 1.17.0-2ubuntu1 [5808 B] 383s Get:53 http://ftpmaster.internal/ubuntu resolute/main amd64 libxrender1 amd64 1:0.9.12-1 [19.8 kB] 383s Get:54 http://ftpmaster.internal/ubuntu resolute/main amd64 libcairo2 amd64 1.18.4-3 [579 kB] 383s Get:55 http://ftpmaster.internal/ubuntu resolute/main amd64 libdatrie1 amd64 0.2.14-1 [19.8 kB] 383s Get:56 http://ftpmaster.internal/ubuntu resolute/main amd64 libdeflate0 amd64 1.23-2build1 [51.6 kB] 383s Get:57 http://ftpmaster.internal/ubuntu resolute/main amd64 libdeflate-dev amd64 1.23-2build1 [58.8 kB] 383s Get:58 http://ftpmaster.internal/ubuntu resolute/main amd64 libgraphite2-3 amd64 1.3.14-11ubuntu1 [73.7 kB] 383s Get:59 http://ftpmaster.internal/ubuntu resolute/main amd64 libharfbuzz0b amd64 12.3.2-1 [519 kB] 383s Get:60 http://ftpmaster.internal/ubuntu resolute/main amd64 x11-common all 1:7.7+24ubuntu1 [22.4 kB] 383s Get:61 http://ftpmaster.internal/ubuntu resolute/main amd64 libice6 amd64 2:1.1.1-1build1 [44.0 kB] 383s Get:62 http://ftpmaster.internal/ubuntu resolute/main amd64 libicu-dev amd64 78.2-1ubuntu1 [12.5 MB] 383s Get:63 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg-turbo8 amd64 2.1.5-4ubuntu3 [156 kB] 383s Get:64 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg-turbo8-dev amd64 2.1.5-4ubuntu3 [300 kB] 383s Get:65 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg8 amd64 8c-2ubuntu12 [2142 B] 383s Get:66 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg8-dev amd64 8c-2ubuntu12 [1480 B] 383s Get:67 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg-dev amd64 8c-2ubuntu12 [1480 B] 383s Get:68 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-bootstrap all 3.4.1+dfsg-6 [129 kB] 383s Get:69 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-highlight.js all 10.7.3+dfsg-2 [144 kB] 383s Get:70 http://ftpmaster.internal/ubuntu resolute/main amd64 libjs-jquery all 3.7.1+dfsg+~3.5.33-1build1 [321 kB] 383s Get:71 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-jquery-datatables all 1.11.5+dfsg-2build1 [145 kB] 383s Get:72 http://ftpmaster.internal/ubuntu resolute/main amd64 liblapack3 amd64 3.12.1-7ubuntu1 [2739 kB] 383s Get:73 http://ftpmaster.internal/ubuntu resolute/main amd64 liblapack-dev amd64 3.12.1-7ubuntu1 [5433 kB] 383s Get:74 http://ftpmaster.internal/ubuntu resolute/main amd64 liblerc4 amd64 4.0.0+ds-5ubuntu2 [207 kB] 383s Get:75 http://ftpmaster.internal/ubuntu resolute/main amd64 libncurses-dev amd64 6.6+20251231-1 [389 kB] 383s Get:76 http://ftpmaster.internal/ubuntu resolute/main amd64 libthai-data all 0.1.30-1 [155 kB] 383s Get:77 http://ftpmaster.internal/ubuntu resolute/main amd64 libthai0 amd64 0.1.30-1 [19.2 kB] 383s Get:78 http://ftpmaster.internal/ubuntu resolute/main amd64 libpango-1.0-0 amd64 1.57.0-1 [241 kB] 383s Get:79 http://ftpmaster.internal/ubuntu resolute/main amd64 libpangoft2-1.0-0 amd64 1.57.0-1 [53.3 kB] 383s Get:80 http://ftpmaster.internal/ubuntu resolute/main amd64 libpangocairo-1.0-0 amd64 1.57.0-1 [29.0 kB] 383s Get:81 http://ftpmaster.internal/ubuntu resolute/main amd64 libpaper2 amd64 2.2.5-0.3build1 [17.3 kB] 383s Get:82 http://ftpmaster.internal/ubuntu resolute/main amd64 libpaper-utils amd64 2.2.5-0.3build1 [15.6 kB] 383s Get:83 http://ftpmaster.internal/ubuntu resolute/main amd64 libpcre2-16-0 amd64 10.46-1 [243 kB] 383s Get:84 http://ftpmaster.internal/ubuntu resolute/main amd64 libpcre2-32-0 amd64 10.46-1 [230 kB] 384s Get:85 http://ftpmaster.internal/ubuntu resolute/main amd64 libpcre2-posix3 amd64 10.46-1 [7354 B] 384s Get:86 http://ftpmaster.internal/ubuntu resolute/main amd64 libpcre2-dev amd64 10.46-1 [832 kB] 384s Get:87 http://ftpmaster.internal/ubuntu resolute/main amd64 libpkgconf3 amd64 1.8.1-4build1 [32.8 kB] 384s Get:88 http://ftpmaster.internal/ubuntu resolute/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1ubuntu2 [898 kB] 384s Get:89 http://ftpmaster.internal/ubuntu resolute/main amd64 libpng-dev amd64 1.6.54-1 [273 kB] 384s Get:90 http://ftpmaster.internal/ubuntu resolute/main amd64 libreadline-dev amd64 8.3-3 [189 kB] 384s Get:91 http://ftpmaster.internal/ubuntu resolute/main amd64 libsharpyuv0 amd64 1.5.0-0.1build1 [17.6 kB] 384s Get:92 http://ftpmaster.internal/ubuntu resolute/main amd64 libsm6 amd64 2:1.2.6-1build1 [16.9 kB] 384s Get:93 http://ftpmaster.internal/ubuntu resolute/main amd64 libtcl8.6 amd64 8.6.17+dfsg-1build1 [1003 kB] 384s Get:94 http://ftpmaster.internal/ubuntu resolute/main amd64 libjbig0 amd64 2.1-6.1ubuntu3 [30.0 kB] 384s Get:95 http://ftpmaster.internal/ubuntu resolute/main amd64 libwebp7 amd64 1.5.0-0.1build1 [264 kB] 384s Get:96 http://ftpmaster.internal/ubuntu resolute/main amd64 libtiff6 amd64 4.7.0-3ubuntu3 [209 kB] 384s Get:97 http://ftpmaster.internal/ubuntu resolute/main amd64 libxft2 amd64 2.3.6-1build2 [45.1 kB] 384s Get:98 http://ftpmaster.internal/ubuntu resolute/main amd64 libxss1 amd64 1:1.2.3-1build4 [7084 B] 384s Get:99 http://ftpmaster.internal/ubuntu resolute/main amd64 libtk8.6 amd64 8.6.17-1 [823 kB] 384s Get:100 http://ftpmaster.internal/ubuntu resolute/main amd64 libxt6t64 amd64 1:1.2.1-1.3 [173 kB] 384s Get:101 http://ftpmaster.internal/ubuntu resolute/main amd64 libzstd-dev amd64 1.5.7+dfsg-3 [376 kB] 384s Get:102 http://ftpmaster.internal/ubuntu resolute/universe amd64 node-normalize.css all 8.0.1-5.1 [10.4 kB] 384s Get:103 http://ftpmaster.internal/ubuntu resolute/main amd64 zip amd64 3.0-15ubuntu3 [175 kB] 384s Get:104 http://ftpmaster.internal/ubuntu resolute/main amd64 unzip amd64 6.0-29ubuntu1 [180 kB] 384s Get:105 http://ftpmaster.internal/ubuntu resolute/main amd64 xdg-utils all 1.2.1-2ubuntu2 [66.1 kB] 384s Get:106 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-base-core amd64 4.5.2-1ubuntu2 [28.8 MB] 384s Get:107 http://ftpmaster.internal/ubuntu resolute/main amd64 liblzma-dev amd64 5.8.2-2 [179 kB] 384s Get:108 http://ftpmaster.internal/ubuntu resolute/main amd64 pkgconf-bin amd64 1.8.1-4build1 [21.7 kB] 384s Get:109 http://ftpmaster.internal/ubuntu resolute/main amd64 pkgconf amd64 1.8.1-4build1 [16.8 kB] 384s Get:110 http://ftpmaster.internal/ubuntu resolute/main amd64 libtirpc-dev amd64 1.3.6+ds-1 [195 kB] 384s Get:111 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-base-dev all 4.5.2-1ubuntu2 [1880 B] 384s Get:112 http://ftpmaster.internal/ubuntu resolute/universe amd64 pkg-r-autopkgtest all 20250812 [6158 B] 384s Get:113 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-backports amd64 1.5.0-2 [121 kB] 384s Get:114 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-boot all 1.3-32-1 [636 kB] 385s Get:115 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-cli amd64 3.6.4-1 [1394 kB] 385s Get:116 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-generics all 0.1.4-1 [84.0 kB] 385s Get:117 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-glue amd64 1.8.0-1 [164 kB] 385s Get:118 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rlang amd64 1.1.5-3 [1721 kB] 385s Get:119 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-lifecycle all 1.0.5+dfsg-1 [120 kB] 385s Get:120 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-magrittr amd64 2.0.3-1 [154 kB] 385s Get:121 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-utf8 amd64 1.2.4-1 [140 kB] 385s Get:122 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-vctrs amd64 0.6.5-1 [1335 kB] 385s Get:123 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-pillar all 1.11.1+dfsg-1 [456 kB] 385s Get:124 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-r6 all 2.6.1-1 [101 kB] 385s Get:125 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-fansi amd64 1.0.6-2 [626 kB] 385s Get:126 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-pkgconfig all 2.0.3-2build2 [20.4 kB] 385s Get:127 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-tibble amd64 3.2.1+dfsg-3 [419 kB] 385s Get:128 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-withr all 3.0.2+dfsg-1 [214 kB] 385s Get:129 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-tidyselect amd64 1.2.1+dfsg-1 [222 kB] 385s Get:130 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-dplyr amd64 1.1.4-4 [1536 kB] 385s Get:131 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-purrr amd64 1.0.4-1 [552 kB] 385s Get:132 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-stringi amd64 1.8.4-1build2 [908 kB] 385s Get:133 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-stringr all 1.5.1-1 [290 kB] 385s Get:134 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-cpp11 all 0.5.3-1 [242 kB] 385s Get:135 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-tidyr amd64 1.3.1-1 [1156 kB] 385s Get:136 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-broom all 1.0.12+dfsg-1 [1708 kB] 385s Get:137 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-colorspace amd64 2.1-1+dfsg-1 [1563 kB] 385s Get:138 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-gtable all 0.3.6+dfsg-1 [199 kB] 385s Get:139 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-isoband amd64 0.2.7-1 [1481 kB] 385s Get:140 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-s7 amd64 0.2.0-1 [328 kB] 385s Get:141 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-farver amd64 2.1.2-1 [1355 kB] 385s Get:142 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-labeling all 0.4.3-1 [62.1 kB] 385s Get:143 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rcolorbrewer all 1.1-3-1build2 [54.0 kB] 385s Get:144 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-viridislite all 0.4.3-1 [1088 kB] 385s Get:145 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-scales all 1.4.0-1 [725 kB] 385s Get:146 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 r-cran-ggplot2 all 4.0.2+dfsg-1 [4941 kB] 386s Get:147 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-cowplot all 1.1.3+dfsg-1 [614 kB] 386s Get:148 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-curl amd64 7.0.0+dfsg-1 [202 kB] 386s Get:149 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-deriv all 4.2.0-1 [154 kB] 386s Get:150 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-fracdiff amd64 1.5-3-1 [108 kB] 386s Get:151 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-lattice amd64 0.22-7-1 [1367 kB] 386s Get:152 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-zoo amd64 1.8-15-1 [1025 kB] 386s Get:153 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-lmtest amd64 0.9.40-1build1 [400 kB] 386s Get:154 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-nnet amd64 7.3-20-1 [116 kB] 386s Get:155 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-littler amd64 0.3.22-1 [85.5 kB] 386s Get:156 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-pkgkitten all 0.2.4-1 [27.2 kB] 386s Get:157 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rcpp amd64 1.1.0-1 [2021 kB] 386s Get:158 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-timedate amd64 4052.112-1 [1298 kB] 386s Get:159 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-quadprog amd64 1.5-8-1build2 [32.6 kB] 386s Get:160 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-xts amd64 0.14.1-1 [1198 kB] 386s Get:161 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-ttr amd64 0.24.4-1 [511 kB] 386s Get:162 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-jsonlite amd64 1.9.1+dfsg-1 [447 kB] 386s Get:163 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-quantmod all 0.4.28-1 [1037 kB] 386s Get:164 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-tseries amd64 0.10-59-3 [382 kB] 386s Get:165 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-nlme amd64 3.1.168-1 [2320 kB] 386s Get:166 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-urca amd64 1.3-4-1build1 [1052 kB] 386s Get:167 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rcpparmadillo amd64 15.2.3-1-1 [919 kB] 386s Get:168 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-forecast amd64 8.23.0-1 [1569 kB] 386s Get:169 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-mass amd64 7.3-65-1 [1116 kB] 386s Get:170 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-matrix amd64 1.7-4-1 [4220 kB] 386s Get:171 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-modelr all 0.1.11-1 [195 kB] 386s Get:172 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-microbenchmark amd64 1.5.0-1 [67.4 kB] 386s Get:173 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-doby all 4.7.1-3 [4741 kB] 387s Get:174 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-evaluate all 1.0.5-1 [117 kB] 387s Get:175 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-xfun amd64 0.55+dfsg-1 [587 kB] 387s Get:176 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-highr all 0.11+dfsg-1 [38.5 kB] 387s Get:177 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-yaml amd64 2.3.10-1 [109 kB] 387s Get:178 http://ftpmaster.internal/ubuntu resolute/main amd64 libjs-mathjax all 2.7.9+dfsg-1build1 [6017 kB] 387s Get:179 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-knitr all 1.51+dfsg-1 [847 kB] 387s Get:180 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-minqa amd64 1.2.8-1 [119 kB] 387s Get:181 http://ftpmaster.internal/ubuntu resolute/universe amd64 libnlopt0 amd64 2.7.1-7ubuntu1 [189 kB] 387s Get:182 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-nloptr amd64 2.2.1-2 [251 kB] 387s Get:183 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rbibutils amd64 2.3-1 [1023 kB] 387s Get:184 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rdpack all 2.6.3-1 [636 kB] 387s Get:185 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-reformulas all 0.4.4-1 [151 kB] 387s Get:186 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rcppeigen amd64 0.3.4.0.2-1 [1428 kB] 387s Get:187 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-statmod amd64 1.5.0-1 [295 kB] 387s Get:188 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-lme4 amd64 1.1-38-1 [4197 kB] 387s Get:189 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-numderiv all 2016.8-1.1-3build1 [116 kB] 387s Get:190 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-lmertest all 3.2-0-1 [535 kB] 387s Get:191 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-pbkrtest all 0.5.5-1 [217 kB] 387s Preconfiguring packages ... 387s Fetched 225 MB in 7s (32.7 MB/s) 387s Selecting previously unselected package libc-dev-bin. 388s (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.) 388s Preparing to unpack .../000-libc-dev-bin_2.42-2ubuntu4_amd64.deb ... 388s Unpacking libc-dev-bin (2.42-2ubuntu4) ... 388s Selecting previously unselected package linux-libc-dev:amd64. 388s Preparing to unpack .../001-linux-libc-dev_6.19.0-3.3_amd64.deb ... 388s Unpacking linux-libc-dev:amd64 (6.19.0-3.3) ... 388s Selecting previously unselected package libcrypt-dev:amd64. 388s Preparing to unpack .../002-libcrypt-dev_1%3a4.5.1-1_amd64.deb ... 388s Unpacking libcrypt-dev:amd64 (1:4.5.1-1) ... 388s Selecting previously unselected package rpcsvc-proto. 388s Preparing to unpack .../003-rpcsvc-proto_1.4.3-1build1_amd64.deb ... 388s Unpacking rpcsvc-proto (1.4.3-1build1) ... 388s Selecting previously unselected package libc6-dev:amd64. 388s Preparing to unpack .../004-libc6-dev_2.42-2ubuntu4_amd64.deb ... 388s Unpacking libc6-dev:amd64 (2.42-2ubuntu4) ... 388s Selecting previously unselected package libisl23:amd64. 388s Preparing to unpack .../005-libisl23_0.27-1build1_amd64.deb ... 388s Unpacking libisl23:amd64 (0.27-1build1) ... 388s Selecting previously unselected package libmpc3:amd64. 388s Preparing to unpack .../006-libmpc3_1.3.1-2_amd64.deb ... 388s Unpacking libmpc3:amd64 (1.3.1-2) ... 388s Selecting previously unselected package cpp-15-x86-64-linux-gnu. 388s Preparing to unpack .../007-cpp-15-x86-64-linux-gnu_15.2.0-12ubuntu1_amd64.deb ... 388s Unpacking cpp-15-x86-64-linux-gnu (15.2.0-12ubuntu1) ... 388s Selecting previously unselected package cpp-15. 388s Preparing to unpack .../008-cpp-15_15.2.0-12ubuntu1_amd64.deb ... 388s Unpacking cpp-15 (15.2.0-12ubuntu1) ... 388s Selecting previously unselected package cpp-x86-64-linux-gnu. 388s Preparing to unpack .../009-cpp-x86-64-linux-gnu_4%3a15.2.0-4ubuntu1_amd64.deb ... 388s Unpacking cpp-x86-64-linux-gnu (4:15.2.0-4ubuntu1) ... 388s Selecting previously unselected package cpp. 388s Preparing to unpack .../010-cpp_4%3a15.2.0-4ubuntu1_amd64.deb ... 388s Unpacking cpp (4:15.2.0-4ubuntu1) ... 388s Selecting previously unselected package libcc1-0:amd64. 388s Preparing to unpack .../011-libcc1-0_16-20260208-1ubuntu1_amd64.deb ... 388s Unpacking libcc1-0:amd64 (16-20260208-1ubuntu1) ... 388s Selecting previously unselected package libgomp1:amd64. 388s Preparing to unpack .../012-libgomp1_16-20260208-1ubuntu1_amd64.deb ... 388s Unpacking libgomp1:amd64 (16-20260208-1ubuntu1) ... 388s Selecting previously unselected package libitm1:amd64. 388s Preparing to unpack .../013-libitm1_16-20260208-1ubuntu1_amd64.deb ... 388s Unpacking libitm1:amd64 (16-20260208-1ubuntu1) ... 388s Selecting previously unselected package libasan8:amd64. 388s Preparing to unpack .../014-libasan8_16-20260208-1ubuntu1_amd64.deb ... 388s Unpacking libasan8:amd64 (16-20260208-1ubuntu1) ... 388s Selecting previously unselected package liblsan0:amd64. 388s Preparing to unpack .../015-liblsan0_16-20260208-1ubuntu1_amd64.deb ... 388s Unpacking liblsan0:amd64 (16-20260208-1ubuntu1) ... 388s Selecting previously unselected package libtsan2:amd64. 388s Preparing to unpack .../016-libtsan2_16-20260208-1ubuntu1_amd64.deb ... 388s Unpacking libtsan2:amd64 (16-20260208-1ubuntu1) ... 388s Selecting previously unselected package libubsan1:amd64. 388s Preparing to unpack .../017-libubsan1_16-20260208-1ubuntu1_amd64.deb ... 388s Unpacking libubsan1:amd64 (16-20260208-1ubuntu1) ... 388s Selecting previously unselected package libhwasan0:amd64. 388s Preparing to unpack .../018-libhwasan0_16-20260208-1ubuntu1_amd64.deb ... 388s Unpacking libhwasan0:amd64 (16-20260208-1ubuntu1) ... 388s Selecting previously unselected package libquadmath0:amd64. 388s Preparing to unpack .../019-libquadmath0_16-20260208-1ubuntu1_amd64.deb ... 388s Unpacking libquadmath0:amd64 (16-20260208-1ubuntu1) ... 388s Selecting previously unselected package libgcc-15-dev:amd64. 388s Preparing to unpack .../020-libgcc-15-dev_15.2.0-12ubuntu1_amd64.deb ... 388s Unpacking libgcc-15-dev:amd64 (15.2.0-12ubuntu1) ... 388s Selecting previously unselected package gcc-15-x86-64-linux-gnu. 388s Preparing to unpack .../021-gcc-15-x86-64-linux-gnu_15.2.0-12ubuntu1_amd64.deb ... 388s Unpacking gcc-15-x86-64-linux-gnu (15.2.0-12ubuntu1) ... 389s Selecting previously unselected package gcc-15. 389s Preparing to unpack .../022-gcc-15_15.2.0-12ubuntu1_amd64.deb ... 389s Unpacking gcc-15 (15.2.0-12ubuntu1) ... 389s Selecting previously unselected package gcc-x86-64-linux-gnu. 389s Preparing to unpack .../023-gcc-x86-64-linux-gnu_4%3a15.2.0-4ubuntu1_amd64.deb ... 389s Unpacking gcc-x86-64-linux-gnu (4:15.2.0-4ubuntu1) ... 389s Selecting previously unselected package gcc. 389s Preparing to unpack .../024-gcc_4%3a15.2.0-4ubuntu1_amd64.deb ... 389s Unpacking gcc (4:15.2.0-4ubuntu1) ... 389s Selecting previously unselected package libstdc++-15-dev:amd64. 389s Preparing to unpack .../025-libstdc++-15-dev_15.2.0-12ubuntu1_amd64.deb ... 389s Unpacking libstdc++-15-dev:amd64 (15.2.0-12ubuntu1) ... 389s Selecting previously unselected package g++-15-x86-64-linux-gnu. 389s Preparing to unpack .../026-g++-15-x86-64-linux-gnu_15.2.0-12ubuntu1_amd64.deb ... 389s Unpacking g++-15-x86-64-linux-gnu (15.2.0-12ubuntu1) ... 389s Selecting previously unselected package g++-15. 389s Preparing to unpack .../027-g++-15_15.2.0-12ubuntu1_amd64.deb ... 389s Unpacking g++-15 (15.2.0-12ubuntu1) ... 389s Selecting previously unselected package g++-x86-64-linux-gnu. 389s Preparing to unpack .../028-g++-x86-64-linux-gnu_4%3a15.2.0-4ubuntu1_amd64.deb ... 389s Unpacking g++-x86-64-linux-gnu (4:15.2.0-4ubuntu1) ... 389s Selecting previously unselected package g++. 389s Preparing to unpack .../029-g++_4%3a15.2.0-4ubuntu1_amd64.deb ... 389s Unpacking g++ (4:15.2.0-4ubuntu1) ... 389s Selecting previously unselected package build-essential. 389s Preparing to unpack .../030-build-essential_12.12ubuntu2_amd64.deb ... 389s Unpacking build-essential (12.12ubuntu2) ... 389s Selecting previously unselected package dctrl-tools. 389s Preparing to unpack .../031-dctrl-tools_2.24-3build4_amd64.deb ... 389s Unpacking dctrl-tools (2.24-3build4) ... 389s Selecting previously unselected package fonts-dejavu-mono. 389s Preparing to unpack .../032-fonts-dejavu-mono_2.37-8build1_all.deb ... 389s Unpacking fonts-dejavu-mono (2.37-8build1) ... 389s Selecting previously unselected package fonts-dejavu-core. 389s Preparing to unpack .../033-fonts-dejavu-core_2.37-8build1_all.deb ... 389s Unpacking fonts-dejavu-core (2.37-8build1) ... 389s Selecting previously unselected package fontconfig-config. 389s Preparing to unpack .../034-fontconfig-config_2.17.1-3ubuntu1_amd64.deb ... 389s Unpacking fontconfig-config (2.17.1-3ubuntu1) ... 389s Selecting previously unselected package libfontconfig1:amd64. 389s Preparing to unpack .../035-libfontconfig1_2.17.1-3ubuntu1_amd64.deb ... 389s Unpacking libfontconfig1:amd64 (2.17.1-3ubuntu1) ... 389s Selecting previously unselected package fontconfig. 389s Preparing to unpack .../036-fontconfig_2.17.1-3ubuntu1_amd64.deb ... 389s Unpacking fontconfig (2.17.1-3ubuntu1) ... 389s Selecting previously unselected package fonts-glyphicons-halflings. 389s Preparing to unpack .../037-fonts-glyphicons-halflings_1.009~3.4.1+dfsg-6_all.deb ... 389s Unpacking fonts-glyphicons-halflings (1.009~3.4.1+dfsg-6) ... 389s Selecting previously unselected package fonts-mathjax. 389s Preparing to unpack .../038-fonts-mathjax_2.7.9+dfsg-1build1_all.deb ... 389s Unpacking fonts-mathjax (2.7.9+dfsg-1build1) ... 389s Selecting previously unselected package libgfortran5:amd64. 389s Preparing to unpack .../039-libgfortran5_16-20260208-1ubuntu1_amd64.deb ... 389s Unpacking libgfortran5:amd64 (16-20260208-1ubuntu1) ... 389s Selecting previously unselected package libgfortran-15-dev:amd64. 389s Preparing to unpack .../040-libgfortran-15-dev_15.2.0-12ubuntu1_amd64.deb ... 389s Unpacking libgfortran-15-dev:amd64 (15.2.0-12ubuntu1) ... 389s Selecting previously unselected package gfortran-15-x86-64-linux-gnu. 389s Preparing to unpack .../041-gfortran-15-x86-64-linux-gnu_15.2.0-12ubuntu1_amd64.deb ... 389s Unpacking gfortran-15-x86-64-linux-gnu (15.2.0-12ubuntu1) ... 389s Selecting previously unselected package gfortran-15. 389s Preparing to unpack .../042-gfortran-15_15.2.0-12ubuntu1_amd64.deb ... 389s Unpacking gfortran-15 (15.2.0-12ubuntu1) ... 389s Selecting previously unselected package gfortran-x86-64-linux-gnu. 389s Preparing to unpack .../043-gfortran-x86-64-linux-gnu_4%3a15.2.0-4ubuntu1_amd64.deb ... 389s Unpacking gfortran-x86-64-linux-gnu (4:15.2.0-4ubuntu1) ... 389s Selecting previously unselected package gfortran. 389s Preparing to unpack .../044-gfortran_4%3a15.2.0-4ubuntu1_amd64.deb ... 389s Unpacking gfortran (4:15.2.0-4ubuntu1) ... 389s Selecting previously unselected package icu-devtools. 389s Preparing to unpack .../045-icu-devtools_78.2-1ubuntu1_amd64.deb ... 389s Unpacking icu-devtools (78.2-1ubuntu1) ... 389s Selecting previously unselected package libblas3:amd64. 389s Preparing to unpack .../046-libblas3_3.12.1-7ubuntu1_amd64.deb ... 389s Unpacking libblas3:amd64 (3.12.1-7ubuntu1) ... 389s Selecting previously unselected package libblas-dev:amd64. 389s Preparing to unpack .../047-libblas-dev_3.12.1-7ubuntu1_amd64.deb ... 389s Unpacking libblas-dev:amd64 (3.12.1-7ubuntu1) ... 389s Selecting previously unselected package libbz2-dev:amd64. 389s Preparing to unpack .../048-libbz2-dev_1.0.8-6build2_amd64.deb ... 389s Unpacking libbz2-dev:amd64 (1.0.8-6build2) ... 389s Selecting previously unselected package libpixman-1-0:amd64. 389s Preparing to unpack .../049-libpixman-1-0_0.46.4-1_amd64.deb ... 389s Unpacking libpixman-1-0:amd64 (0.46.4-1) ... 389s Selecting previously unselected package libxcb-render0:amd64. 389s Preparing to unpack .../050-libxcb-render0_1.17.0-2ubuntu1_amd64.deb ... 389s Unpacking libxcb-render0:amd64 (1.17.0-2ubuntu1) ... 389s Selecting previously unselected package libxcb-shm0:amd64. 389s Preparing to unpack .../051-libxcb-shm0_1.17.0-2ubuntu1_amd64.deb ... 389s Unpacking libxcb-shm0:amd64 (1.17.0-2ubuntu1) ... 389s Selecting previously unselected package libxrender1:amd64. 389s Preparing to unpack .../052-libxrender1_1%3a0.9.12-1_amd64.deb ... 389s Unpacking libxrender1:amd64 (1:0.9.12-1) ... 389s Selecting previously unselected package libcairo2:amd64. 389s Preparing to unpack .../053-libcairo2_1.18.4-3_amd64.deb ... 389s Unpacking libcairo2:amd64 (1.18.4-3) ... 389s Selecting previously unselected package libdatrie1:amd64. 390s Preparing to unpack .../054-libdatrie1_0.2.14-1_amd64.deb ... 390s Unpacking libdatrie1:amd64 (0.2.14-1) ... 390s Selecting previously unselected package libdeflate0:amd64. 390s Preparing to unpack .../055-libdeflate0_1.23-2build1_amd64.deb ... 390s Unpacking libdeflate0:amd64 (1.23-2build1) ... 390s Selecting previously unselected package libdeflate-dev:amd64. 390s Preparing to unpack .../056-libdeflate-dev_1.23-2build1_amd64.deb ... 390s Unpacking libdeflate-dev:amd64 (1.23-2build1) ... 390s Selecting previously unselected package libgraphite2-3:amd64. 390s Preparing to unpack .../057-libgraphite2-3_1.3.14-11ubuntu1_amd64.deb ... 390s Unpacking libgraphite2-3:amd64 (1.3.14-11ubuntu1) ... 390s Selecting previously unselected package libharfbuzz0b:amd64. 390s Preparing to unpack .../058-libharfbuzz0b_12.3.2-1_amd64.deb ... 390s Unpacking libharfbuzz0b:amd64 (12.3.2-1) ... 390s Selecting previously unselected package x11-common. 390s Preparing to unpack .../059-x11-common_1%3a7.7+24ubuntu1_all.deb ... 390s Unpacking x11-common (1:7.7+24ubuntu1) ... 390s Selecting previously unselected package libice6:amd64. 390s Preparing to unpack .../060-libice6_2%3a1.1.1-1build1_amd64.deb ... 390s Unpacking libice6:amd64 (2:1.1.1-1build1) ... 390s Selecting previously unselected package libicu-dev:amd64. 390s Preparing to unpack .../061-libicu-dev_78.2-1ubuntu1_amd64.deb ... 390s Unpacking libicu-dev:amd64 (78.2-1ubuntu1) ... 390s Selecting previously unselected package libjpeg-turbo8:amd64. 390s Preparing to unpack .../062-libjpeg-turbo8_2.1.5-4ubuntu3_amd64.deb ... 390s Unpacking libjpeg-turbo8:amd64 (2.1.5-4ubuntu3) ... 390s Selecting previously unselected package libjpeg-turbo8-dev:amd64. 390s Preparing to unpack .../063-libjpeg-turbo8-dev_2.1.5-4ubuntu3_amd64.deb ... 390s Unpacking libjpeg-turbo8-dev:amd64 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package libjs-jquery. 390s Preparing to unpack .../069-libjs-jquery_3.7.1+dfsg+~3.5.33-1build1_all.deb ... 390s Unpacking libjs-jquery (3.7.1+dfsg+~3.5.33-1build1) ... 390s Selecting previously unselected package libjs-jquery-datatables. 390s Preparing to unpack .../070-libjs-jquery-datatables_1.11.5+dfsg-2build1_all.deb ... 390s Unpacking libjs-jquery-datatables (1.11.5+dfsg-2build1) ... 390s Selecting previously unselected package liblapack3:amd64. 390s Preparing to unpack .../071-liblapack3_3.12.1-7ubuntu1_amd64.deb ... 390s Unpacking liblapack3:amd64 (3.12.1-7ubuntu1) ... 390s Selecting previously unselected package liblapack-dev:amd64. 390s Preparing to unpack .../072-liblapack-dev_3.12.1-7ubuntu1_amd64.deb ... 390s Unpacking liblapack-dev:amd64 (3.12.1-7ubuntu1) ... 390s Selecting previously unselected package liblerc4:amd64. 390s Preparing to unpack .../073-liblerc4_4.0.0+ds-5ubuntu2_amd64.deb ... 390s Unpacking liblerc4:amd64 (4.0.0+ds-5ubuntu2) ... 390s Selecting previously unselected package libncurses-dev:amd64. 390s Preparing to unpack .../074-libncurses-dev_6.6+20251231-1_amd64.deb ... 390s Unpacking libncurses-dev:amd64 (6.6+20251231-1) ... 390s Selecting previously unselected package libthai-data. 390s Preparing to unpack .../075-libthai-data_0.1.30-1_all.deb ... 390s Unpacking libthai-data (0.1.30-1) ... 390s Selecting previously unselected package libthai0:amd64. 390s Preparing to unpack .../076-libthai0_0.1.30-1_amd64.deb ... 390s Unpacking libthai0:amd64 (0.1.30-1) ... 390s Selecting previously unselected package libpango-1.0-0:amd64. 390s Preparing to unpack .../077-libpango-1.0-0_1.57.0-1_amd64.deb ... 390s Unpacking libpango-1.0-0:amd64 (1.57.0-1) ... 390s Selecting previously unselected package libpangoft2-1.0-0:amd64. 390s Preparing to unpack .../078-libpangoft2-1.0-0_1.57.0-1_amd64.deb ... 390s Unpacking libpangoft2-1.0-0:amd64 (1.57.0-1) ... 390s Selecting previously unselected package libpangocairo-1.0-0:amd64. 390s Preparing to unpack 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libtiff6:amd64. 390s Preparing to unpack .../095-libtiff6_4.7.0-3ubuntu3_amd64.deb ... 390s Unpacking libtiff6:amd64 (4.7.0-3ubuntu3) ... 390s Selecting previously unselected package libxft2:amd64. 390s Preparing to unpack .../096-libxft2_2.3.6-1build2_amd64.deb ... 390s Unpacking libxft2:amd64 (2.3.6-1build2) ... 390s Selecting previously unselected package libxss1:amd64. 390s Preparing to unpack .../097-libxss1_1%3a1.2.3-1build4_amd64.deb ... 390s Unpacking libxss1:amd64 (1:1.2.3-1build4) ... 390s Selecting previously unselected package libtk8.6:amd64. 390s Preparing to unpack .../098-libtk8.6_8.6.17-1_amd64.deb ... 390s Unpacking libtk8.6:amd64 (8.6.17-1) ... 390s Selecting previously unselected package libxt6t64:amd64. 390s Preparing to unpack .../099-libxt6t64_1%3a1.2.1-1.3_amd64.deb ... 390s Unpacking libxt6t64:amd64 (1:1.2.1-1.3) ... 390s Selecting previously unselected package libzstd-dev:amd64. 390s Preparing to unpack .../100-libzstd-dev_1.5.7+dfsg-3_amd64.deb ... 390s Unpacking libzstd-dev:amd64 (1.5.7+dfsg-3) ... 390s Selecting previously unselected package node-normalize.css. 390s Preparing to unpack .../101-node-normalize.css_8.0.1-5.1_all.deb ... 390s Unpacking node-normalize.css (8.0.1-5.1) ... 390s Selecting previously unselected package zip. 390s Preparing to unpack .../102-zip_3.0-15ubuntu3_amd64.deb ... 390s Unpacking zip (3.0-15ubuntu3) ... 390s Selecting previously unselected package unzip. 390s Preparing to unpack .../103-unzip_6.0-29ubuntu1_amd64.deb ... 390s Unpacking unzip (6.0-29ubuntu1) ... 390s Selecting previously unselected package xdg-utils. 391s Preparing to unpack .../104-xdg-utils_1.2.1-2ubuntu2_all.deb ... 391s Unpacking xdg-utils (1.2.1-2ubuntu2) ... 391s Selecting previously unselected package r-base-core. 391s Preparing to unpack .../105-r-base-core_4.5.2-1ubuntu2_amd64.deb ... 391s Unpacking r-base-core (4.5.2-1ubuntu2) ... 391s Selecting previously unselected package liblzma-dev:amd64. 391s Preparing to unpack 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Selecting previously unselected package r-cran-backports. 391s Preparing to unpack .../112-r-cran-backports_1.5.0-2_amd64.deb ... 391s Unpacking r-cran-backports (1.5.0-2) ... 391s Selecting previously unselected package r-cran-boot. 391s Preparing to unpack .../113-r-cran-boot_1.3-32-1_all.deb ... 391s Unpacking r-cran-boot (1.3-32-1) ... 391s Selecting previously unselected package r-cran-cli. 391s Preparing to unpack .../114-r-cran-cli_3.6.4-1_amd64.deb ... 391s Unpacking r-cran-cli (3.6.4-1) ... 391s Selecting previously unselected package r-cran-generics. 391s Preparing to unpack .../115-r-cran-generics_0.1.4-1_all.deb ... 391s Unpacking r-cran-generics (0.1.4-1) ... 391s Selecting previously unselected package r-cran-glue. 391s Preparing to unpack .../116-r-cran-glue_1.8.0-1_amd64.deb ... 391s Unpacking r-cran-glue (1.8.0-1) ... 391s Selecting previously unselected package r-cran-rlang. 391s Preparing to unpack .../117-r-cran-rlang_1.1.5-3_amd64.deb ... 391s Unpacking 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Unpacking r-cran-tidyr (1.3.1-1) ... 391s Selecting previously unselected package r-cran-broom. 391s Preparing to unpack .../135-r-cran-broom_1.0.12+dfsg-1_all.deb ... 391s Unpacking r-cran-broom (1.0.12+dfsg-1) ... 391s Selecting previously unselected package r-cran-colorspace. 391s Preparing to unpack .../136-r-cran-colorspace_2.1-1+dfsg-1_amd64.deb ... 391s Unpacking r-cran-colorspace (2.1-1+dfsg-1) ... 391s Selecting previously unselected package r-cran-gtable. 391s Preparing to unpack .../137-r-cran-gtable_0.3.6+dfsg-1_all.deb ... 391s Unpacking r-cran-gtable (0.3.6+dfsg-1) ... 391s Selecting previously unselected package r-cran-isoband. 391s Preparing to unpack .../138-r-cran-isoband_0.2.7-1_amd64.deb ... 391s Unpacking r-cran-isoband (0.2.7-1) ... 391s Selecting previously unselected package r-cran-s7. 391s Preparing to unpack .../139-r-cran-s7_0.2.0-1_amd64.deb ... 391s Unpacking r-cran-s7 (0.2.0-1) ... 391s Selecting previously unselected package r-cran-farver. 391s Preparing to unpack .../140-r-cran-farver_2.1.2-1_amd64.deb ... 391s Unpacking r-cran-farver (2.1.2-1) ... 391s Selecting previously unselected package r-cran-labeling. 391s Preparing to unpack .../141-r-cran-labeling_0.4.3-1_all.deb ... 391s Unpacking r-cran-labeling (0.4.3-1) ... 391s Selecting previously unselected package r-cran-rcolorbrewer. 391s Preparing to unpack .../142-r-cran-rcolorbrewer_1.1-3-1build2_all.deb ... 391s Unpacking r-cran-rcolorbrewer (1.1-3-1build2) ... 391s Selecting previously unselected package r-cran-viridislite. 391s Preparing to unpack .../143-r-cran-viridislite_0.4.3-1_all.deb ... 391s Unpacking r-cran-viridislite (0.4.3-1) ... 391s Selecting previously unselected package r-cran-scales. 391s Preparing to unpack .../144-r-cran-scales_1.4.0-1_all.deb ... 391s Unpacking r-cran-scales (1.4.0-1) ... 391s Selecting previously unselected package r-cran-ggplot2. 391s Preparing to unpack .../145-r-cran-ggplot2_4.0.2+dfsg-1_all.deb ... 391s Unpacking r-cran-ggplot2 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package r-cran-timedate. 392s Preparing to unpack .../157-r-cran-timedate_4052.112-1_amd64.deb ... 392s Unpacking r-cran-timedate (4052.112-1) ... 392s Selecting previously unselected package r-cran-quadprog. 392s Preparing to unpack .../158-r-cran-quadprog_1.5-8-1build2_amd64.deb ... 392s Unpacking r-cran-quadprog (1.5-8-1build2) ... 392s Selecting previously unselected package r-cran-xts. 392s Preparing to unpack .../159-r-cran-xts_0.14.1-1_amd64.deb ... 392s Unpacking r-cran-xts (0.14.1-1) ... 392s Selecting previously unselected package r-cran-ttr. 392s Preparing to unpack .../160-r-cran-ttr_0.24.4-1_amd64.deb ... 392s Unpacking r-cran-ttr (0.24.4-1) ... 392s Selecting previously unselected package r-cran-jsonlite. 392s Preparing to unpack .../161-r-cran-jsonlite_1.9.1+dfsg-1_amd64.deb ... 392s Unpacking r-cran-jsonlite (1.9.1+dfsg-1) ... 392s Selecting previously unselected package r-cran-quantmod. 392s Preparing to unpack .../162-r-cran-quantmod_0.4.28-1_all.deb ... 392s 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build-essential (12.12ubuntu2) ... 396s Setting up r-cran-rcpparmadillo (15.2.3-1-1) ... 396s Setting up r-cran-vctrs (0.6.5-1) ... 396s Setting up r-cran-rcppeigen (0.3.4.0.2-1) ... 396s Setting up r-cran-pillar (1.11.1+dfsg-1) ... 396s Setting up r-cran-minqa (1.2.8-1) ... 396s Setting up r-base-dev (4.5.2-1ubuntu2) ... 396s Setting up r-cran-stringr (1.5.1-1) ... 396s Setting up r-cran-ggplot2 (4.0.2+dfsg-1) ... 396s Setting up r-cran-tibble (3.2.1+dfsg-3) ... 396s Setting up r-cran-xts (0.14.1-1) ... 396s Setting up r-cran-rdpack (2.6.3-1) ... 396s Setting up r-cran-tidyselect (1.2.1+dfsg-1) ... 396s Setting up r-cran-purrr (1.0.4-1) ... 396s Setting up pkg-r-autopkgtest (20250812) ... 396s Setting up r-cran-dplyr (1.1.4-4) ... 396s Setting up r-cran-reformulas (0.4.4-1) ... 396s Setting up r-cran-ttr (0.24.4-1) ... 396s Setting up r-cran-cowplot (1.1.3+dfsg-1) ... 396s Setting up r-cran-lme4 (1.1-38-1) ... 396s Setting up r-cran-lmertest (3.2-0-1) ... 396s Setting up r-cran-tidyr (1.3.1-1) ... 396s Setting up r-cran-quantmod (0.4.28-1) ... 396s Setting up r-cran-tseries (0.10-59-3) ... 396s Setting up r-cran-broom (1.0.12+dfsg-1) ... 396s Setting up r-cran-forecast (8.23.0-1) ... 396s Setting up r-cran-modelr (0.1.11-1) ... 396s Setting up r-cran-doby (4.7.1-3) ... 396s Setting up r-cran-pbkrtest (0.5.5-1) ... 396s Processing triggers for libc-bin (2.42-2ubuntu4) ... 396s Processing triggers for man-db (2.13.1-1build1) ... 397s Processing triggers for install-info (7.2-5) ... 399s autopkgtest [05:30:45]: test pkg-r-autopkgtest: /usr/share/dh-r/pkg-r-autopkgtest 399s autopkgtest [05:30:45]: test pkg-r-autopkgtest: [----------------------- 399s Test: Try to load the R library lmerTest 399s 399s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 399s Copyright (C) 2025 The R Foundation for Statistical Computing 399s Platform: x86_64-pc-linux-gnu 399s 399s R is free software and comes with ABSOLUTELY NO WARRANTY. 399s You are welcome to redistribute it under certain conditions. 399s Type 'license()' or 'licence()' for distribution details. 399s 399s R is a collaborative project with many contributors. 399s Type 'contributors()' for more information and 399s 'citation()' on how to cite R or R packages in publications. 399s 399s Type 'demo()' for some demos, 'help()' for on-line help, or 399s 'help.start()' for an HTML browser interface to help. 399s Type 'q()' to quit R. 399s 399s > library('lmerTest') 399s Loading required package: lme4 399s Loading required package: Matrix 400s 400s Attaching package: ‘lmerTest’ 400s 400s The following object is masked from ‘package:lme4’: 400s 400s lmer 400s 400s > 400s The following object is masked from ‘package:stats’: 400s 400s step 400s 400s autopkgtest [05:30:46]: test pkg-r-autopkgtest: -----------------------] 401s autopkgtest [05:30:47]: test pkg-r-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 401s pkg-r-autopkgtest PASS 401s autopkgtest [05:30:47]: @@@@@@@@@@@@@@@@@@@@ summary 401s run-unit-test PASS 401s pkg-r-autopkgtest PASS