0s autopkgtest [23:32:33]: starting date and time: 2026-02-09 23:32:33+0000 0s autopkgtest [23:32:33]: git checkout: 508d4a25 a-v-ssh wait_for_ssh: demote "ssh connection failed" to a debug message 0s autopkgtest [23:32:33]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.d0m_3cnl/out --timeout-copy=6000 --setup-commands 'ln -s /dev/null /etc/systemd/system/bluetooth.service; printf "http_proxy=http://squid.internal:3128\nhttps_proxy=http://squid.internal:3128\nno_proxy=127.0.0.1,127.0.1.1,localhost,localdomain,internal,login.ubuntu.com,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com\n" >> /etc/environment' --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 -- lxd -r lxd-armhf-10.145.243.85 lxd-armhf-10.145.243.85:autopkgtest/ubuntu/resolute/armhf 26s autopkgtest [23:32:59]: testbed dpkg architecture: armhf 28s autopkgtest [23:33:01]: testbed apt version: 3.1.15 32s autopkgtest [23:33:05]: @@@@@@@@@@@@@@@@@@@@ test bed setup 35s autopkgtest [23:33:08]: testbed release detected to be: None 44s autopkgtest [23:33:17]: updating testbed package index (apt update) 45s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 46s Get:2 http://ftpmaster.internal/ubuntu resolute InRelease [124 kB] 46s Get:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease [124 kB] 46s Get:4 http://ftpmaster.internal/ubuntu resolute-security InRelease [124 kB] 47s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [1645 kB] 50s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [29.4 kB] 50s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [176 kB] 50s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf Packages [246 kB] 51s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/universe armhf Packages [1405 kB] 53s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse armhf Packages [7452 B] 53s Get:11 http://ftpmaster.internal/ubuntu resolute/main Sources [1398 kB] 56s Get:12 http://ftpmaster.internal/ubuntu resolute/restricted Sources [15.1 kB] 56s Get:13 http://ftpmaster.internal/ubuntu resolute/universe Sources [21.4 MB] 95s Get:14 http://ftpmaster.internal/ubuntu resolute/main armhf Packages [1374 kB] 97s Get:15 http://ftpmaster.internal/ubuntu resolute/universe armhf Packages [15.3 MB] 126s Fetched 43.5 MB in 1min 21s (537 kB/s) 127s Reading package lists... 133s autopkgtest [23:34:46]: upgrading testbed (apt dist-upgrade and autopurge) 135s Reading package lists... 136s Building dependency tree... 136s Reading state information... 136s Calculating upgrade... 137s The following packages will be upgraded: 137s cryptsetup-bin dracut-install iproute2 iptables libcryptsetup12 libip4tc2 137s libip6tc2 libxtables12 wget 137s 9 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 137s Need to get 2407 kB of archives. 137s After this operation, 152 kB of additional disk space will be used. 137s Get:1 http://ftpmaster.internal/ubuntu resolute/main armhf iptables armhf 1.8.11-2ubuntu3 [345 kB] 138s Get:2 http://ftpmaster.internal/ubuntu resolute/main armhf libip4tc2 armhf 1.8.11-2ubuntu3 [22.0 kB] 138s Get:3 http://ftpmaster.internal/ubuntu resolute/main armhf libip6tc2 armhf 1.8.11-2ubuntu3 [22.3 kB] 138s Get:4 http://ftpmaster.internal/ubuntu resolute/main armhf libxtables12 armhf 1.8.11-2ubuntu3 [33.5 kB] 138s Get:5 http://ftpmaster.internal/ubuntu resolute/main armhf iproute2 armhf 6.18.0-1ubuntu1 [1123 kB] 140s Get:6 http://ftpmaster.internal/ubuntu resolute/main armhf libcryptsetup12 armhf 2:2.8.0-1ubuntu3 [254 kB] 140s Get:7 http://ftpmaster.internal/ubuntu resolute/main armhf wget armhf 1.25.0-2ubuntu4 [327 kB] 141s Get:8 http://ftpmaster.internal/ubuntu resolute/main armhf cryptsetup-bin armhf 2:2.8.0-1ubuntu3 [232 kB] 141s Get:9 http://ftpmaster.internal/ubuntu resolute/main armhf dracut-install armhf 109-11ubuntu1 [47.9 kB] 142s Preconfiguring packages ... 142s Fetched 2407 kB in 5s (525 kB/s) 142s (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 ... 68683 files and directories currently installed.) 142s Preparing to unpack .../0-iptables_1.8.11-2ubuntu3_armhf.deb ... 142s Unpacking iptables (1.8.11-2ubuntu3) over (1.8.11-2ubuntu2) ... 142s Preparing to unpack .../1-libip4tc2_1.8.11-2ubuntu3_armhf.deb ... 142s Unpacking libip4tc2:armhf (1.8.11-2ubuntu3) over (1.8.11-2ubuntu2) ... 142s Preparing to unpack .../2-libip6tc2_1.8.11-2ubuntu3_armhf.deb ... 142s Unpacking libip6tc2:armhf (1.8.11-2ubuntu3) over (1.8.11-2ubuntu2) ... 142s Preparing to unpack .../3-libxtables12_1.8.11-2ubuntu3_armhf.deb ... 142s Unpacking libxtables12:armhf (1.8.11-2ubuntu3) over (1.8.11-2ubuntu2) ... 142s Preparing to unpack .../4-iproute2_6.18.0-1ubuntu1_armhf.deb ... 142s Unpacking iproute2 (6.18.0-1ubuntu1) over (6.16.0-1ubuntu3) ... 143s Preparing to unpack .../5-libcryptsetup12_2%3a2.8.0-1ubuntu3_armhf.deb ... 143s Unpacking libcryptsetup12:armhf (2:2.8.0-1ubuntu3) over (2:2.8.0-1ubuntu2) ... 143s Preparing to unpack .../6-wget_1.25.0-2ubuntu4_armhf.deb ... 143s Unpacking wget (1.25.0-2ubuntu4) over (1.25.0-2ubuntu3) ... 143s Preparing to unpack .../7-cryptsetup-bin_2%3a2.8.0-1ubuntu3_armhf.deb ... 143s Unpacking cryptsetup-bin (2:2.8.0-1ubuntu3) over (2:2.8.0-1ubuntu2) ... 143s Preparing to unpack .../8-dracut-install_109-11ubuntu1_armhf.deb ... 143s Unpacking dracut-install (109-11ubuntu1) over (109-9ubuntu1) ... 143s Setting up libip4tc2:armhf (1.8.11-2ubuntu3) ... 143s Setting up wget (1.25.0-2ubuntu4) ... 143s Setting up libip6tc2:armhf (1.8.11-2ubuntu3) ... 143s Setting up libxtables12:armhf (1.8.11-2ubuntu3) ... 143s Setting up dracut-install (109-11ubuntu1) ... 143s Setting up libcryptsetup12:armhf (2:2.8.0-1ubuntu3) ... 143s Setting up cryptsetup-bin (2:2.8.0-1ubuntu3) ... 143s Setting up iptables (1.8.11-2ubuntu3) ... 143s Setting up iproute2 (6.18.0-1ubuntu1) ... 143s Processing triggers for man-db (2.13.1-1build1) ... 144s Processing triggers for install-info (7.2-5) ... 144s Processing triggers for libc-bin (2.42-2ubuntu4) ... 147s Reading package lists... 147s Building dependency tree... 147s Reading state information... 147s Solving dependencies... 148s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 150s autopkgtest [23:35:03]: rebooting testbed after setup commands that affected boot 192s autopkgtest [23:35:45]: testbed running kernel: Linux 6.8.0-87-generic #88~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Tue Oct 14 14:00:09 UTC 2 218s autopkgtest [23:36:11]: @@@@@@@@@@@@@@@@@@@@ apt-source r-cran-lmertest 229s Get:1 http://ftpmaster.internal/ubuntu resolute/universe r-cran-lmertest 3.2-0-1 (dsc) [2247 B] 229s Get:2 http://ftpmaster.internal/ubuntu resolute/universe r-cran-lmertest 3.2-0-1 (tar) [198 kB] 229s Get:3 http://ftpmaster.internal/ubuntu resolute/universe r-cran-lmertest 3.2-0-1 (diff) [3788 B] 229s gpgv: Signature made Thu Jan 22 00:11:29 2026 UTC 229s gpgv: using RSA key 73471499CC60ED9EEE805946C5BD6C8F2295D502 229s gpgv: issuer "plessy@debian.org" 229s gpgv: Can't check signature: No public key 229s dpkg-source: warning: cannot verify inline signature for ./r-cran-lmertest_3.2-0-1.dsc: no acceptable signature found 229s autopkgtest [23:36:22]: testing package r-cran-lmertest version 3.2-0-1 232s autopkgtest [23:36:25]: build not needed 235s autopkgtest [23:36:28]: test run-unit-test: preparing testbed 237s Reading package lists... 237s Building dependency tree... 237s Reading state information... 238s Solving dependencies... 238s The following NEW packages will be installed: 238s fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono 238s fonts-glyphicons-halflings fonts-mathjax libblas3 libcairo2 libdatrie1 238s libdeflate0 libfontconfig1 libfreetype6 libgfortran5 libgomp1 libgraphite2-3 238s libharfbuzz0b libice6 libjbig0 libjpeg-turbo8 libjpeg8 libjs-bootstrap 238s libjs-highlight.js libjs-jquery libjs-jquery-datatables libjs-mathjax 238s liblapack3 liblerc4 libnlopt0 libpango-1.0-0 libpangocairo-1.0-0 238s libpangoft2-1.0-0 libpaper-utils libpaper2 libpixman-1-0 libsharpyuv0 libsm6 238s libtcl8.6 libthai-data libthai0 libtiff6 libtk8.6 libwebp7 libxcb-render0 238s libxcb-shm0 libxft2 libxrender1 libxss1 libxt6t64 node-normalize.css 238s r-base-core r-cran-backports r-cran-boot r-cran-broom r-cran-cli 238s r-cran-colorspace r-cran-cowplot r-cran-cpp11 r-cran-curl r-cran-deriv 238s r-cran-doby r-cran-dplyr r-cran-evaluate r-cran-fansi r-cran-farver 238s r-cran-forecast r-cran-fracdiff r-cran-generics r-cran-ggplot2 r-cran-glue 238s r-cran-gtable r-cran-highr r-cran-isoband r-cran-jsonlite r-cran-knitr 238s r-cran-labeling r-cran-lattice r-cran-lifecycle r-cran-littler r-cran-lme4 238s r-cran-lmertest r-cran-lmtest r-cran-magrittr r-cran-mass r-cran-matrix 238s r-cran-microbenchmark r-cran-minqa r-cran-modelr r-cran-nlme r-cran-nloptr 238s r-cran-nnet r-cran-numderiv r-cran-pbkrtest r-cran-pillar r-cran-pkgconfig 238s r-cran-pkgkitten r-cran-purrr r-cran-quadprog r-cran-quantmod r-cran-r6 238s r-cran-rbibutils r-cran-rcolorbrewer r-cran-rcpp r-cran-rcpparmadillo 238s r-cran-rcppeigen r-cran-rdpack r-cran-reformulas r-cran-rlang r-cran-s7 238s r-cran-scales r-cran-statmod r-cran-stringi r-cran-stringr r-cran-tibble 238s r-cran-tidyr r-cran-tidyselect r-cran-timedate r-cran-tseries r-cran-ttr 238s r-cran-urca r-cran-utf8 r-cran-vctrs r-cran-viridislite r-cran-withr 238s r-cran-xfun r-cran-xts r-cran-yaml r-cran-zoo unzip x11-common xdg-utils zip 239s 0 upgraded, 131 newly installed, 0 to remove and 0 not upgraded. 239s Need to get 111 MB of archives. 239s After this operation, 242 MB of additional disk space will be used. 239s Get:1 http://ftpmaster.internal/ubuntu resolute/main armhf libfreetype6 armhf 2.14.1+dfsg-2 [345 kB] 240s Get:2 http://ftpmaster.internal/ubuntu resolute/main armhf fonts-dejavu-mono all 2.37-8build1 [502 kB] 241s Get:3 http://ftpmaster.internal/ubuntu resolute/main armhf fonts-dejavu-core all 2.37-8build1 [834 kB] 243s Get:4 http://ftpmaster.internal/ubuntu resolute/main armhf fontconfig-config armhf 2.17.1-3ubuntu1 [38.5 kB] 243s Get:5 http://ftpmaster.internal/ubuntu resolute/main armhf libfontconfig1 armhf 2.17.1-3ubuntu1 [117 kB] 243s Get:6 http://ftpmaster.internal/ubuntu resolute/main armhf fontconfig armhf 2.17.1-3ubuntu1 [180 kB] 243s Get:7 http://ftpmaster.internal/ubuntu resolute/universe armhf fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-6 [119 kB] 244s Get:8 http://ftpmaster.internal/ubuntu resolute/main armhf fonts-mathjax all 2.7.9+dfsg-1build1 [2283 kB] 248s Get:9 http://ftpmaster.internal/ubuntu resolute/main armhf libblas3 armhf 3.12.1-7ubuntu1 [133 kB] 248s Get:10 http://ftpmaster.internal/ubuntu resolute/main armhf libpixman-1-0 armhf 0.46.4-1 [196 kB] 249s Get:11 http://ftpmaster.internal/ubuntu resolute/main armhf libxcb-render0 armhf 1.17.0-2ubuntu1 [15.5 kB] 249s Get:12 http://ftpmaster.internal/ubuntu resolute/main armhf libxcb-shm0 armhf 1.17.0-2ubuntu1 [5956 B] 249s Get:13 http://ftpmaster.internal/ubuntu resolute/main armhf libxrender1 armhf 1:0.9.12-1 [16.6 kB] 249s Get:14 http://ftpmaster.internal/ubuntu resolute/main armhf libcairo2 armhf 1.18.4-3 [489 kB] 250s Get:15 http://ftpmaster.internal/ubuntu resolute/main armhf libdatrie1 armhf 0.2.14-1 [16.4 kB] 250s Get:16 http://ftpmaster.internal/ubuntu resolute/main armhf libdeflate0 armhf 1.23-2build1 [38.8 kB] 250s Get:17 http://ftpmaster.internal/ubuntu resolute/main armhf libgfortran5 armhf 15.2.0-12ubuntu1 [334 kB] 251s Get:18 http://ftpmaster.internal/ubuntu resolute/main armhf libgomp1 armhf 15.2.0-12ubuntu1 [129 kB] 251s Get:19 http://ftpmaster.internal/ubuntu resolute/main armhf libgraphite2-3 armhf 1.3.14-11ubuntu1 [65.2 kB] 251s Get:20 http://ftpmaster.internal/ubuntu resolute/main armhf libharfbuzz0b armhf 12.3.2-1 [501 kB] 252s Get:21 http://ftpmaster.internal/ubuntu resolute/main armhf x11-common all 1:7.7+24ubuntu1 [22.4 kB] 252s Get:22 http://ftpmaster.internal/ubuntu resolute/main armhf libice6 armhf 2:1.1.1-1build1 [37.5 kB] 252s Get:23 http://ftpmaster.internal/ubuntu resolute/main armhf libjpeg-turbo8 armhf 2.1.5-4ubuntu3 [129 kB] 252s Get:24 http://ftpmaster.internal/ubuntu resolute/main armhf libjpeg8 armhf 8c-2ubuntu11 [2148 B] 252s Get:25 http://ftpmaster.internal/ubuntu resolute/universe armhf libjs-bootstrap all 3.4.1+dfsg-6 [129 kB] 252s Get:26 http://ftpmaster.internal/ubuntu resolute/universe armhf libjs-highlight.js all 10.7.3+dfsg-2 [144 kB] 253s Get:27 http://ftpmaster.internal/ubuntu resolute/main armhf libjs-jquery all 3.7.1+dfsg+~3.5.33-1build1 [321 kB] 253s Get:28 http://ftpmaster.internal/ubuntu resolute/universe armhf libjs-jquery-datatables all 1.11.5+dfsg-2build1 [145 kB] 253s Get:29 http://ftpmaster.internal/ubuntu resolute/main armhf liblapack3 armhf 3.12.1-7ubuntu1 [2090 kB] 257s Get:30 http://ftpmaster.internal/ubuntu resolute/main armhf liblerc4 armhf 4.0.0+ds-5ubuntu2 [162 kB] 258s Get:31 http://ftpmaster.internal/ubuntu resolute/main armhf libthai-data all 0.1.30-1 [155 kB] 258s Get:32 http://ftpmaster.internal/ubuntu resolute/main armhf libthai0 armhf 0.1.30-1 [15.4 kB] 258s Get:33 http://ftpmaster.internal/ubuntu resolute/main armhf libpango-1.0-0 armhf 1.57.0-1 [218 kB] 259s Get:34 http://ftpmaster.internal/ubuntu resolute/main armhf libpangoft2-1.0-0 armhf 1.57.0-1 [45.2 kB] 259s Get:35 http://ftpmaster.internal/ubuntu resolute/main armhf libpangocairo-1.0-0 armhf 1.57.0-1 [25.3 kB] 259s Get:36 http://ftpmaster.internal/ubuntu resolute/main armhf libpaper2 armhf 2.2.5-0.3build1 [16.3 kB] 259s Get:37 http://ftpmaster.internal/ubuntu resolute/main armhf libpaper-utils armhf 2.2.5-0.3build1 [14.2 kB] 259s Get:38 http://ftpmaster.internal/ubuntu resolute/main armhf libsharpyuv0 armhf 1.5.0-0.1build1 [16.3 kB] 259s Get:39 http://ftpmaster.internal/ubuntu resolute/main armhf libsm6 armhf 2:1.2.6-1build1 [15.3 kB] 259s Get:40 http://ftpmaster.internal/ubuntu resolute/main armhf libtcl8.6 armhf 8.6.17+dfsg-1build1 [918 kB] 262s Get:41 http://ftpmaster.internal/ubuntu resolute/main armhf libjbig0 armhf 2.1-6.1ubuntu3 [25.3 kB] 262s Get:42 http://ftpmaster.internal/ubuntu resolute/main armhf libwebp7 armhf 1.5.0-0.1build1 [189 kB] 262s Get:43 http://ftpmaster.internal/ubuntu resolute/main armhf libtiff6 armhf 4.7.0-3ubuntu3 [188 kB] 262s Get:44 http://ftpmaster.internal/ubuntu resolute/main armhf libxft2 armhf 2.3.6-1build2 [37.2 kB] 263s Get:45 http://ftpmaster.internal/ubuntu resolute/main armhf libxss1 armhf 1:1.2.3-1build4 [6328 B] 263s Get:46 http://ftpmaster.internal/ubuntu resolute/main armhf libtk8.6 armhf 8.6.17-1 [694 kB] 265s Get:47 http://ftpmaster.internal/ubuntu resolute/main armhf libxt6t64 armhf 1:1.2.1-1.3 [145 kB] 265s Get:48 http://ftpmaster.internal/ubuntu resolute/universe armhf node-normalize.css all 8.0.1-5.1 [10.4 kB] 265s Get:49 http://ftpmaster.internal/ubuntu resolute/main armhf zip armhf 3.0-15ubuntu3 [164 kB] 265s Get:50 http://ftpmaster.internal/ubuntu resolute/main armhf unzip armhf 6.0-29ubuntu1 [167 kB] 266s Get:51 http://ftpmaster.internal/ubuntu resolute/main armhf xdg-utils all 1.2.1-2ubuntu2 [66.1 kB] 266s Get:52 http://ftpmaster.internal/ubuntu resolute/universe armhf r-base-core armhf 4.5.2-1ubuntu2 [28.5 MB] 320s Get:53 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-backports armhf 1.5.0-2 [121 kB] 321s Get:54 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-boot all 1.3-32-1 [636 kB] 322s Get:55 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-cli armhf 3.6.4-1 [1377 kB] 324s Get:56 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-generics all 0.1.4-1 [84.0 kB] 324s Get:57 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-glue armhf 1.8.0-1 [162 kB] 324s Get:58 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-rlang armhf 1.1.5-3 [1700 kB] 327s Get:59 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-lifecycle all 1.0.5+dfsg-1 [120 kB] 327s Get:60 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-magrittr armhf 2.0.3-1 [154 kB] 327s Get:61 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-utf8 armhf 1.2.4-1 [136 kB] 328s Get:62 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-vctrs armhf 0.6.5-1 [1310 kB] 330s Get:63 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-pillar all 1.11.1+dfsg-1 [456 kB] 331s Get:64 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-r6 all 2.6.1-1 [101 kB] 331s Get:65 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-fansi armhf 1.0.6-2 [620 kB] 332s Get:66 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-pkgconfig all 2.0.3-2build2 [20.4 kB] 332s Get:67 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-tibble armhf 3.2.1+dfsg-3 [420 kB] 333s Get:68 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-withr all 3.0.2+dfsg-1 [214 kB] 333s Get:69 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-tidyselect armhf 1.2.1+dfsg-1 [222 kB] 334s Get:70 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-dplyr armhf 1.1.4-4 [1533 kB] 336s Get:71 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-purrr armhf 1.0.4-1 [550 kB] 337s Get:72 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-stringi armhf 1.8.4-1build2 [884 kB] 338s Get:73 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-stringr all 1.5.1-1 [290 kB] 339s Get:74 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-cpp11 all 0.5.3-1 [242 kB] 339s Get:75 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-tidyr armhf 1.3.1-1 [1152 kB] 341s Get:76 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-broom all 1.0.12+dfsg-1 [1708 kB] 344s Get:77 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-colorspace armhf 2.1-1+dfsg-1 [1561 kB] 346s Get:78 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-gtable all 0.3.6+dfsg-1 [199 kB] 346s Get:79 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-isoband armhf 0.2.7-1 [1477 kB] 349s Get:80 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-s7 armhf 0.2.0-1 [328 kB] 349s Get:81 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-farver armhf 2.1.2-1 [1355 kB] 352s Get:82 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-labeling all 0.4.3-1 [62.1 kB] 352s Get:83 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-rcolorbrewer all 1.1-3-1build2 [54.0 kB] 353s Get:84 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-viridislite all 0.4.3-1 [1088 kB] 355s Get:85 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-scales all 1.4.0-1 [725 kB] 356s Get:86 http://ftpmaster.internal/ubuntu resolute-proposed/universe armhf r-cran-ggplot2 all 4.0.2+dfsg-1 [4941 kB] 364s Get:87 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-cowplot all 1.1.3+dfsg-1 [614 kB] 365s Get:88 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-curl armhf 7.0.0+dfsg-1 [200 kB] 366s Get:89 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-deriv all 4.2.0-1 [154 kB] 366s Get:90 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-fracdiff armhf 1.5-3-1 [105 kB] 366s Get:91 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-lattice armhf 0.22-7-1 [1365 kB] 368s Get:92 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-zoo armhf 1.8-15-1 [1025 kB] 370s Get:93 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-lmtest armhf 0.9.40-1build1 [400 kB] 371s Get:94 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-nnet armhf 7.3-20-1 [111 kB] 371s Get:95 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-littler armhf 0.3.22-1 [81.0 kB] 371s Get:96 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-pkgkitten all 0.2.4-1 [27.2 kB] 371s Get:97 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-rcpp armhf 1.1.0-1 [2009 kB] 375s Get:98 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-timedate armhf 4052.112-1 [1299 kB] 377s Get:99 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-quadprog armhf 1.5-8-1build2 [29.8 kB] 377s Get:100 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-xts armhf 0.14.1-1 [1181 kB] 379s Get:101 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-ttr armhf 0.24.4-1 [509 kB] 380s Get:102 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-jsonlite armhf 1.9.1+dfsg-1 [440 kB] 381s Get:103 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-quantmod all 0.4.28-1 [1037 kB] 384s Get:104 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-tseries armhf 0.10-59-3 [379 kB] 384s Get:105 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-nlme armhf 3.1.168-1 [2304 kB] 393s Get:106 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-urca armhf 1.3-4-1build1 [1050 kB] 396s Get:107 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-rcpparmadillo armhf 15.2.3-1-1 [915 kB] 398s Get:108 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-forecast armhf 8.23.0-1 [1563 kB] 401s Get:109 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-mass armhf 7.3-65-1 [1108 kB] 402s Get:110 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-matrix armhf 1.7-4-1 [4139 kB] 409s Get:111 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-modelr all 0.1.11-1 [195 kB] 410s Get:112 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-microbenchmark armhf 1.5.0-1 [67.8 kB] 410s Get:113 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-doby all 4.7.1-3 [4741 kB] 418s Get:114 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-evaluate all 1.0.5-1 [117 kB] 418s Get:115 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-xfun armhf 0.55+dfsg-1 [589 kB] 420s Get:116 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-highr all 0.11+dfsg-1 [38.5 kB] 420s Get:117 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-yaml armhf 2.3.10-1 [101 kB] 420s Get:118 http://ftpmaster.internal/ubuntu resolute/main armhf libjs-mathjax all 2.7.9+dfsg-1build1 [6017 kB] 432s Get:119 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-knitr all 1.51+dfsg-1 [847 kB] 433s Get:120 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-minqa armhf 1.2.8-1 [108 kB] 433s Get:121 http://ftpmaster.internal/ubuntu resolute/universe armhf libnlopt0 armhf 2.7.1-7ubuntu1 [155 kB] 434s Get:122 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-nloptr armhf 2.2.1-2 [250 kB] 434s Get:123 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-rbibutils armhf 2.3-1 [943 kB] 444s Get:124 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-rdpack all 2.6.3-1 [636 kB] 446s Get:125 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-reformulas all 0.4.4-1 [151 kB] 446s Get:126 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-rcppeigen armhf 0.3.4.0.2-1 [1402 kB] 449s Get:127 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-statmod armhf 1.5.0-1 [294 kB] 449s Get:128 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-lme4 armhf 1.1-38-1 [4178 kB] 457s Get:129 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-numderiv all 2016.8-1.1-3build1 [116 kB] 457s Get:130 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-lmertest all 3.2-0-1 [535 kB] 458s Get:131 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-pbkrtest all 0.5.5-1 [217 kB] 459s Preconfiguring packages ... 459s Fetched 111 MB in 3min 40s (504 kB/s) 459s Selecting previously unselected package libfreetype6:armhf. 459s (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 ... 68686 files and directories currently installed.) 459s Preparing to unpack .../000-libfreetype6_2.14.1+dfsg-2_armhf.deb ... 459s Unpacking libfreetype6:armhf (2.14.1+dfsg-2) ... 459s Selecting previously unselected package fonts-dejavu-mono. 459s Preparing to unpack .../001-fonts-dejavu-mono_2.37-8build1_all.deb ... 459s Unpacking fonts-dejavu-mono (2.37-8build1) ... 459s Selecting previously unselected package fonts-dejavu-core. 459s Preparing to unpack .../002-fonts-dejavu-core_2.37-8build1_all.deb ... 459s Unpacking fonts-dejavu-core (2.37-8build1) ... 459s Selecting previously unselected package fontconfig-config. 459s Preparing to unpack .../003-fontconfig-config_2.17.1-3ubuntu1_armhf.deb ... 459s Unpacking fontconfig-config (2.17.1-3ubuntu1) ... 459s Selecting previously unselected package libfontconfig1:armhf. 459s Preparing to unpack .../004-libfontconfig1_2.17.1-3ubuntu1_armhf.deb ... 459s Unpacking libfontconfig1:armhf (2.17.1-3ubuntu1) ... 459s Selecting previously unselected package fontconfig. 459s Preparing to unpack .../005-fontconfig_2.17.1-3ubuntu1_armhf.deb ... 459s Unpacking fontconfig (2.17.1-3ubuntu1) ... 460s Selecting previously unselected package fonts-glyphicons-halflings. 460s Preparing to unpack .../006-fonts-glyphicons-halflings_1.009~3.4.1+dfsg-6_all.deb ... 460s Unpacking fonts-glyphicons-halflings (1.009~3.4.1+dfsg-6) ... 460s Selecting previously unselected package fonts-mathjax. 460s Preparing to unpack .../007-fonts-mathjax_2.7.9+dfsg-1build1_all.deb ... 460s Unpacking fonts-mathjax (2.7.9+dfsg-1build1) ... 460s Selecting previously unselected package libblas3:armhf. 460s Preparing to unpack .../008-libblas3_3.12.1-7ubuntu1_armhf.deb ... 460s Unpacking libblas3:armhf (3.12.1-7ubuntu1) ... 460s Selecting previously unselected package libpixman-1-0:armhf. 460s Preparing to unpack .../009-libpixman-1-0_0.46.4-1_armhf.deb ... 460s Unpacking libpixman-1-0:armhf (0.46.4-1) ... 460s Selecting previously unselected package libxcb-render0:armhf. 460s Preparing to unpack .../010-libxcb-render0_1.17.0-2ubuntu1_armhf.deb ... 460s Unpacking libxcb-render0:armhf (1.17.0-2ubuntu1) ... 460s Selecting previously unselected package libxcb-shm0:armhf. 460s Preparing to unpack .../011-libxcb-shm0_1.17.0-2ubuntu1_armhf.deb ... 460s Unpacking libxcb-shm0:armhf (1.17.0-2ubuntu1) ... 460s Selecting previously unselected package libxrender1:armhf. 460s Preparing to unpack .../012-libxrender1_1%3a0.9.12-1_armhf.deb ... 460s Unpacking libxrender1:armhf (1:0.9.12-1) ... 460s Selecting previously unselected package libcairo2:armhf. 460s Preparing to unpack .../013-libcairo2_1.18.4-3_armhf.deb ... 460s Unpacking libcairo2:armhf (1.18.4-3) ... 460s Selecting previously unselected package libdatrie1:armhf. 460s Preparing to unpack .../014-libdatrie1_0.2.14-1_armhf.deb ... 460s Unpacking libdatrie1:armhf (0.2.14-1) ... 460s Selecting previously unselected package libdeflate0:armhf. 460s Preparing to unpack .../015-libdeflate0_1.23-2build1_armhf.deb ... 460s Unpacking libdeflate0:armhf (1.23-2build1) ... 460s Selecting previously unselected package libgfortran5:armhf. 460s Preparing to unpack .../016-libgfortran5_15.2.0-12ubuntu1_armhf.deb ... 460s Unpacking libgfortran5:armhf (15.2.0-12ubuntu1) ... 460s Selecting previously unselected package libgomp1:armhf. 460s Preparing to unpack .../017-libgomp1_15.2.0-12ubuntu1_armhf.deb ... 460s Unpacking libgomp1:armhf (15.2.0-12ubuntu1) ... 460s Selecting previously unselected package libgraphite2-3:armhf. 460s Preparing to unpack .../018-libgraphite2-3_1.3.14-11ubuntu1_armhf.deb ... 460s Unpacking libgraphite2-3:armhf (1.3.14-11ubuntu1) ... 460s Selecting previously unselected package libharfbuzz0b:armhf. 460s Preparing to unpack .../019-libharfbuzz0b_12.3.2-1_armhf.deb ... 460s Unpacking libharfbuzz0b:armhf (12.3.2-1) ... 460s Selecting previously unselected package x11-common. 460s Preparing to unpack .../020-x11-common_1%3a7.7+24ubuntu1_all.deb ... 460s Unpacking x11-common (1:7.7+24ubuntu1) ... 460s Selecting previously unselected package libice6:armhf. 460s Preparing to unpack .../021-libice6_2%3a1.1.1-1build1_armhf.deb ... 460s Unpacking libice6:armhf (2:1.1.1-1build1) ... 460s Selecting previously unselected package libjpeg-turbo8:armhf. 460s Preparing to unpack .../022-libjpeg-turbo8_2.1.5-4ubuntu3_armhf.deb ... 460s Unpacking libjpeg-turbo8:armhf (2.1.5-4ubuntu3) ... 460s Selecting previously unselected package libjpeg8:armhf. 460s Preparing to unpack .../023-libjpeg8_8c-2ubuntu11_armhf.deb ... 460s Unpacking libjpeg8:armhf (8c-2ubuntu11) ... 460s Selecting previously unselected package libjs-bootstrap. 460s Preparing to unpack .../024-libjs-bootstrap_3.4.1+dfsg-6_all.deb ... 460s Unpacking libjs-bootstrap (3.4.1+dfsg-6) ... 460s Selecting previously unselected package libjs-highlight.js. 460s Preparing to unpack .../025-libjs-highlight.js_10.7.3+dfsg-2_all.deb ... 460s Unpacking libjs-highlight.js (10.7.3+dfsg-2) ... 460s Selecting previously unselected package libjs-jquery. 460s Preparing to unpack .../026-libjs-jquery_3.7.1+dfsg+~3.5.33-1build1_all.deb ... 460s Unpacking libjs-jquery (3.7.1+dfsg+~3.5.33-1build1) ... 460s Selecting previously unselected package libjs-jquery-datatables. 460s Preparing to unpack .../027-libjs-jquery-datatables_1.11.5+dfsg-2build1_all.deb ... 460s Unpacking libjs-jquery-datatables (1.11.5+dfsg-2build1) ... 461s Selecting previously unselected package liblapack3:armhf. 461s Preparing to unpack .../028-liblapack3_3.12.1-7ubuntu1_armhf.deb ... 461s Unpacking liblapack3:armhf (3.12.1-7ubuntu1) ... 461s Selecting previously unselected package liblerc4:armhf. 461s Preparing to unpack .../029-liblerc4_4.0.0+ds-5ubuntu2_armhf.deb ... 461s Unpacking liblerc4:armhf (4.0.0+ds-5ubuntu2) ... 461s Selecting previously unselected package libthai-data. 461s Preparing to unpack .../030-libthai-data_0.1.30-1_all.deb ... 461s Unpacking libthai-data (0.1.30-1) ... 461s Selecting previously unselected package libthai0:armhf. 461s Preparing to unpack .../031-libthai0_0.1.30-1_armhf.deb ... 461s Unpacking libthai0:armhf (0.1.30-1) ... 461s Selecting previously unselected package libpango-1.0-0:armhf. 461s Preparing to unpack .../032-libpango-1.0-0_1.57.0-1_armhf.deb ... 461s Unpacking libpango-1.0-0:armhf (1.57.0-1) ... 461s Selecting previously unselected package libpangoft2-1.0-0:armhf. 461s Preparing to unpack .../033-libpangoft2-1.0-0_1.57.0-1_armhf.deb ... 461s Unpacking libpangoft2-1.0-0:armhf (1.57.0-1) ... 461s Selecting previously unselected package libpangocairo-1.0-0:armhf. 461s Preparing to unpack .../034-libpangocairo-1.0-0_1.57.0-1_armhf.deb ... 461s Unpacking libpangocairo-1.0-0:armhf (1.57.0-1) ... 461s Selecting previously unselected package libpaper2:armhf. 461s Preparing to unpack .../035-libpaper2_2.2.5-0.3build1_armhf.deb ... 461s Unpacking libpaper2:armhf (2.2.5-0.3build1) ... 461s Selecting previously unselected package libpaper-utils. 461s Preparing to unpack .../036-libpaper-utils_2.2.5-0.3build1_armhf.deb ... 461s Unpacking libpaper-utils (2.2.5-0.3build1) ... 461s Selecting previously unselected package libsharpyuv0:armhf. 461s Preparing to unpack .../037-libsharpyuv0_1.5.0-0.1build1_armhf.deb ... 461s Unpacking libsharpyuv0:armhf (1.5.0-0.1build1) ... 461s Selecting previously unselected package libsm6:armhf. 461s Preparing to unpack .../038-libsm6_2%3a1.2.6-1build1_armhf.deb ... 461s Unpacking libsm6:armhf (2:1.2.6-1build1) ... 461s Selecting previously unselected package libtcl8.6:armhf. 461s Preparing to unpack .../039-libtcl8.6_8.6.17+dfsg-1build1_armhf.deb ... 461s Unpacking libtcl8.6:armhf (8.6.17+dfsg-1build1) ... 461s Selecting previously unselected package libjbig0:armhf. 461s Preparing to unpack .../040-libjbig0_2.1-6.1ubuntu3_armhf.deb ... 461s Unpacking libjbig0:armhf (2.1-6.1ubuntu3) ... 461s Selecting previously unselected package libwebp7:armhf. 461s Preparing to unpack .../041-libwebp7_1.5.0-0.1build1_armhf.deb ... 461s Unpacking libwebp7:armhf (1.5.0-0.1build1) ... 461s Selecting previously unselected package libtiff6:armhf. 461s Preparing to unpack .../042-libtiff6_4.7.0-3ubuntu3_armhf.deb ... 461s Unpacking libtiff6:armhf (4.7.0-3ubuntu3) ... 461s Selecting previously unselected package libxft2:armhf. 461s Preparing to unpack .../043-libxft2_2.3.6-1build2_armhf.deb ... 461s Unpacking libxft2:armhf (2.3.6-1build2) ... 461s Selecting previously unselected package libxss1:armhf. 461s Preparing to unpack .../044-libxss1_1%3a1.2.3-1build4_armhf.deb ... 461s Unpacking libxss1:armhf (1:1.2.3-1build4) ... 461s Selecting previously unselected package libtk8.6:armhf. 461s Preparing to unpack .../045-libtk8.6_8.6.17-1_armhf.deb ... 461s Unpacking libtk8.6:armhf (8.6.17-1) ... 461s Selecting previously unselected package libxt6t64:armhf. 461s Preparing to unpack .../046-libxt6t64_1%3a1.2.1-1.3_armhf.deb ... 461s Unpacking libxt6t64:armhf (1:1.2.1-1.3) ... 461s Selecting previously unselected package node-normalize.css. 461s Preparing to unpack .../047-node-normalize.css_8.0.1-5.1_all.deb ... 461s Unpacking node-normalize.css (8.0.1-5.1) ... 461s Selecting previously unselected package zip. 461s Preparing to unpack .../048-zip_3.0-15ubuntu3_armhf.deb ... 461s Unpacking zip (3.0-15ubuntu3) ... 461s Selecting previously unselected package unzip. 461s Preparing to unpack .../049-unzip_6.0-29ubuntu1_armhf.deb ... 461s Unpacking unzip (6.0-29ubuntu1) ... 461s Selecting previously unselected package xdg-utils. 461s Preparing to unpack .../050-xdg-utils_1.2.1-2ubuntu2_all.deb ... 461s Unpacking xdg-utils (1.2.1-2ubuntu2) ... 461s Selecting previously unselected package r-base-core. 461s Preparing to unpack .../051-r-base-core_4.5.2-1ubuntu2_armhf.deb ... 461s Unpacking r-base-core (4.5.2-1ubuntu2) ... 462s Selecting previously unselected package r-cran-backports. 462s Preparing to unpack .../052-r-cran-backports_1.5.0-2_armhf.deb ... 462s Unpacking r-cran-backports (1.5.0-2) ... 462s Selecting previously unselected package r-cran-boot. 462s Preparing to unpack .../053-r-cran-boot_1.3-32-1_all.deb ... 462s Unpacking r-cran-boot (1.3-32-1) ... 462s Selecting previously unselected package r-cran-cli. 462s Preparing to unpack .../054-r-cran-cli_3.6.4-1_armhf.deb ... 462s Unpacking r-cran-cli (3.6.4-1) ... 462s Selecting previously unselected package r-cran-generics. 462s Preparing to unpack .../055-r-cran-generics_0.1.4-1_all.deb ... 462s Unpacking r-cran-generics (0.1.4-1) ... 462s Selecting previously unselected package r-cran-glue. 462s Preparing to unpack .../056-r-cran-glue_1.8.0-1_armhf.deb ... 462s Unpacking r-cran-glue (1.8.0-1) ... 462s Selecting previously unselected package r-cran-rlang. 462s Preparing to unpack .../057-r-cran-rlang_1.1.5-3_armhf.deb ... 462s Unpacking r-cran-rlang (1.1.5-3) ... 462s Selecting previously unselected package r-cran-lifecycle. 462s Preparing to unpack .../058-r-cran-lifecycle_1.0.5+dfsg-1_all.deb ... 462s Unpacking r-cran-lifecycle (1.0.5+dfsg-1) ... 462s Selecting previously unselected package r-cran-magrittr. 462s Preparing to unpack .../059-r-cran-magrittr_2.0.3-1_armhf.deb ... 462s Unpacking r-cran-magrittr (2.0.3-1) ... 462s Selecting previously unselected package r-cran-utf8. 462s Preparing to unpack .../060-r-cran-utf8_1.2.4-1_armhf.deb ... 462s Unpacking r-cran-utf8 (1.2.4-1) ... 462s Selecting previously unselected package r-cran-vctrs. 462s Preparing to unpack .../061-r-cran-vctrs_0.6.5-1_armhf.deb ... 462s Unpacking r-cran-vctrs (0.6.5-1) ... 462s Selecting previously unselected package r-cran-pillar. 462s Preparing to unpack .../062-r-cran-pillar_1.11.1+dfsg-1_all.deb ... 462s Unpacking r-cran-pillar (1.11.1+dfsg-1) ... 462s Selecting previously unselected package r-cran-r6. 462s Preparing to unpack .../063-r-cran-r6_2.6.1-1_all.deb ... 462s Unpacking r-cran-r6 (2.6.1-1) ... 462s Selecting previously unselected package r-cran-fansi. 462s Preparing to unpack .../064-r-cran-fansi_1.0.6-2_armhf.deb ... 462s Unpacking r-cran-fansi (1.0.6-2) ... 462s Selecting previously unselected package r-cran-pkgconfig. 462s Preparing to unpack .../065-r-cran-pkgconfig_2.0.3-2build2_all.deb ... 462s Unpacking r-cran-pkgconfig (2.0.3-2build2) ... 462s Selecting previously unselected package r-cran-tibble. 463s Preparing to unpack .../066-r-cran-tibble_3.2.1+dfsg-3_armhf.deb ... 463s Unpacking r-cran-tibble (3.2.1+dfsg-3) ... 463s Selecting previously unselected package r-cran-withr. 463s Preparing to unpack .../067-r-cran-withr_3.0.2+dfsg-1_all.deb ... 463s Unpacking r-cran-withr (3.0.2+dfsg-1) ... 463s Selecting previously unselected package r-cran-tidyselect. 463s Preparing to unpack .../068-r-cran-tidyselect_1.2.1+dfsg-1_armhf.deb ... 463s Unpacking r-cran-tidyselect (1.2.1+dfsg-1) ... 463s Selecting previously unselected package r-cran-dplyr. 463s Preparing to unpack .../069-r-cran-dplyr_1.1.4-4_armhf.deb ... 463s Unpacking r-cran-dplyr (1.1.4-4) ... 463s Selecting previously unselected package r-cran-purrr. 463s Preparing to unpack .../070-r-cran-purrr_1.0.4-1_armhf.deb ... 463s Unpacking r-cran-purrr (1.0.4-1) ... 463s Selecting previously unselected package r-cran-stringi. 463s Preparing to unpack .../071-r-cran-stringi_1.8.4-1build2_armhf.deb ... 463s Unpacking r-cran-stringi (1.8.4-1build2) ... 463s Selecting previously unselected package r-cran-stringr. 463s Preparing to unpack .../072-r-cran-stringr_1.5.1-1_all.deb ... 463s Unpacking r-cran-stringr (1.5.1-1) ... 463s Selecting previously unselected package r-cran-cpp11. 463s Preparing to unpack .../073-r-cran-cpp11_0.5.3-1_all.deb ... 463s Unpacking r-cran-cpp11 (0.5.3-1) ... 463s Selecting previously unselected package r-cran-tidyr. 463s Preparing to unpack .../074-r-cran-tidyr_1.3.1-1_armhf.deb ... 463s Unpacking r-cran-tidyr (1.3.1-1) ... 463s Selecting previously unselected package r-cran-broom. 463s Preparing to unpack .../075-r-cran-broom_1.0.12+dfsg-1_all.deb ... 463s Unpacking r-cran-broom (1.0.12+dfsg-1) ... 463s Selecting previously unselected package r-cran-colorspace. 463s Preparing to unpack .../076-r-cran-colorspace_2.1-1+dfsg-1_armhf.deb ... 463s Unpacking r-cran-colorspace (2.1-1+dfsg-1) ... 463s Selecting previously unselected package r-cran-gtable. 463s Preparing to unpack .../077-r-cran-gtable_0.3.6+dfsg-1_all.deb ... 463s Unpacking r-cran-gtable (0.3.6+dfsg-1) ... 463s Selecting previously unselected package r-cran-isoband. 463s Preparing to unpack .../078-r-cran-isoband_0.2.7-1_armhf.deb ... 463s Unpacking r-cran-isoband (0.2.7-1) ... 463s Selecting previously unselected package r-cran-s7. 463s Preparing to unpack .../079-r-cran-s7_0.2.0-1_armhf.deb ... 463s Unpacking r-cran-s7 (0.2.0-1) ... 463s Selecting previously unselected package r-cran-farver. 463s Preparing to unpack .../080-r-cran-farver_2.1.2-1_armhf.deb ... 463s Unpacking r-cran-farver (2.1.2-1) ... 463s Selecting previously unselected package r-cran-labeling. 463s Preparing to unpack .../081-r-cran-labeling_0.4.3-1_all.deb ... 463s Unpacking r-cran-labeling (0.4.3-1) ... 463s Selecting previously unselected package r-cran-rcolorbrewer. 463s Preparing to unpack .../082-r-cran-rcolorbrewer_1.1-3-1build2_all.deb ... 463s Unpacking r-cran-rcolorbrewer (1.1-3-1build2) ... 463s Selecting previously unselected package r-cran-viridislite. 463s Preparing to unpack .../083-r-cran-viridislite_0.4.3-1_all.deb ... 463s Unpacking r-cran-viridislite (0.4.3-1) ... 463s Selecting previously unselected package r-cran-scales. 463s Preparing to unpack .../084-r-cran-scales_1.4.0-1_all.deb ... 463s Unpacking r-cran-scales (1.4.0-1) ... 463s Selecting previously unselected package r-cran-ggplot2. 463s Preparing to unpack .../085-r-cran-ggplot2_4.0.2+dfsg-1_all.deb ... 463s Unpacking r-cran-ggplot2 (4.0.2+dfsg-1) ... 464s Selecting previously unselected package r-cran-cowplot. 464s Preparing to unpack .../086-r-cran-cowplot_1.1.3+dfsg-1_all.deb ... 464s Unpacking r-cran-cowplot (1.1.3+dfsg-1) ... 464s Selecting previously unselected package r-cran-curl. 464s Preparing to unpack .../087-r-cran-curl_7.0.0+dfsg-1_armhf.deb ... 464s Unpacking r-cran-curl (7.0.0+dfsg-1) ... 464s Selecting previously unselected package r-cran-deriv. 464s Preparing to unpack .../088-r-cran-deriv_4.2.0-1_all.deb ... 464s Unpacking r-cran-deriv (4.2.0-1) ... 464s Selecting previously unselected package r-cran-fracdiff. 464s Preparing to unpack .../089-r-cran-fracdiff_1.5-3-1_armhf.deb ... 464s Unpacking r-cran-fracdiff (1.5-3-1) ... 464s Selecting previously unselected package r-cran-lattice. 464s Preparing to unpack .../090-r-cran-lattice_0.22-7-1_armhf.deb ... 464s Unpacking r-cran-lattice (0.22-7-1) ... 464s Selecting previously unselected package r-cran-zoo. 464s Preparing to unpack .../091-r-cran-zoo_1.8-15-1_armhf.deb ... 464s Unpacking r-cran-zoo (1.8-15-1) ... 464s Selecting previously unselected package r-cran-lmtest. 464s Preparing to unpack .../092-r-cran-lmtest_0.9.40-1build1_armhf.deb ... 464s Unpacking r-cran-lmtest (0.9.40-1build1) ... 464s Selecting previously unselected package r-cran-nnet. 464s Preparing to unpack .../093-r-cran-nnet_7.3-20-1_armhf.deb ... 464s Unpacking r-cran-nnet (7.3-20-1) ... 464s Selecting previously unselected package r-cran-littler. 464s Preparing to unpack .../094-r-cran-littler_0.3.22-1_armhf.deb ... 464s Unpacking r-cran-littler (0.3.22-1) ... 464s Selecting previously unselected package r-cran-pkgkitten. 464s Preparing to unpack .../095-r-cran-pkgkitten_0.2.4-1_all.deb ... 464s Unpacking r-cran-pkgkitten (0.2.4-1) ... 464s Selecting previously unselected package r-cran-rcpp. 464s Preparing to unpack .../096-r-cran-rcpp_1.1.0-1_armhf.deb ... 464s Unpacking r-cran-rcpp (1.1.0-1) ... 464s Selecting previously unselected package r-cran-timedate. 464s Preparing to unpack .../097-r-cran-timedate_4052.112-1_armhf.deb ... 464s Unpacking r-cran-timedate (4052.112-1) ... 464s Selecting previously unselected package r-cran-quadprog. 464s Preparing to unpack .../098-r-cran-quadprog_1.5-8-1build2_armhf.deb ... 464s Unpacking r-cran-quadprog (1.5-8-1build2) ... 464s Selecting previously unselected package r-cran-xts. 464s Preparing to unpack .../099-r-cran-xts_0.14.1-1_armhf.deb ... 464s Unpacking r-cran-xts (0.14.1-1) ... 465s Selecting previously unselected package r-cran-ttr. 465s Preparing to unpack .../100-r-cran-ttr_0.24.4-1_armhf.deb ... 465s Unpacking r-cran-ttr (0.24.4-1) ... 465s Selecting previously unselected package r-cran-jsonlite. 465s Preparing to unpack .../101-r-cran-jsonlite_1.9.1+dfsg-1_armhf.deb ... 465s Unpacking r-cran-jsonlite (1.9.1+dfsg-1) ... 465s Selecting previously unselected package r-cran-quantmod. 465s Preparing to unpack .../102-r-cran-quantmod_0.4.28-1_all.deb ... 465s Unpacking r-cran-quantmod (0.4.28-1) ... 465s Selecting previously unselected package r-cran-tseries. 465s Preparing to unpack .../103-r-cran-tseries_0.10-59-3_armhf.deb ... 465s Unpacking r-cran-tseries (0.10-59-3) ... 465s Selecting previously unselected package r-cran-nlme. 465s Preparing to unpack .../104-r-cran-nlme_3.1.168-1_armhf.deb ... 465s Unpacking r-cran-nlme (3.1.168-1) ... 465s Selecting previously unselected package r-cran-urca. 465s Preparing to unpack .../105-r-cran-urca_1.3-4-1build1_armhf.deb ... 465s Unpacking r-cran-urca (1.3-4-1build1) ... 465s Selecting previously unselected package r-cran-rcpparmadillo. 465s Preparing to unpack .../106-r-cran-rcpparmadillo_15.2.3-1-1_armhf.deb ... 465s Unpacking r-cran-rcpparmadillo (15.2.3-1-1) ... 465s Selecting previously unselected package r-cran-forecast. 465s Preparing to unpack .../107-r-cran-forecast_8.23.0-1_armhf.deb ... 465s Unpacking r-cran-forecast (8.23.0-1) ... 465s Selecting previously unselected package r-cran-mass. 465s Preparing to unpack .../108-r-cran-mass_7.3-65-1_armhf.deb ... 465s Unpacking r-cran-mass (7.3-65-1) ... 465s Selecting previously unselected package r-cran-matrix. 465s Preparing to unpack .../109-r-cran-matrix_1.7-4-1_armhf.deb ... 465s Unpacking r-cran-matrix (1.7-4-1) ... 465s Selecting previously unselected package r-cran-modelr. 465s Preparing to unpack .../110-r-cran-modelr_0.1.11-1_all.deb ... 465s Unpacking r-cran-modelr (0.1.11-1) ... 465s Selecting previously unselected package r-cran-microbenchmark. 465s Preparing to unpack .../111-r-cran-microbenchmark_1.5.0-1_armhf.deb ... 465s Unpacking r-cran-microbenchmark (1.5.0-1) ... 465s Selecting previously unselected package r-cran-doby. 465s Preparing to unpack .../112-r-cran-doby_4.7.1-3_all.deb ... 465s Unpacking r-cran-doby (4.7.1-3) ... 465s Selecting previously unselected package r-cran-evaluate. 465s Preparing to unpack .../113-r-cran-evaluate_1.0.5-1_all.deb ... 465s Unpacking r-cran-evaluate (1.0.5-1) ... 465s Selecting previously unselected package r-cran-xfun. 465s Preparing to unpack .../114-r-cran-xfun_0.55+dfsg-1_armhf.deb ... 465s Unpacking r-cran-xfun (0.55+dfsg-1) ... 465s Selecting previously unselected package r-cran-highr. 465s Preparing to unpack .../115-r-cran-highr_0.11+dfsg-1_all.deb ... 465s Unpacking r-cran-highr (0.11+dfsg-1) ... 465s Selecting previously unselected package r-cran-yaml. 465s Preparing to unpack .../116-r-cran-yaml_2.3.10-1_armhf.deb ... 465s Unpacking r-cran-yaml (2.3.10-1) ... 465s Selecting previously unselected package libjs-mathjax. 465s Preparing to unpack .../117-libjs-mathjax_2.7.9+dfsg-1build1_all.deb ... 465s Unpacking libjs-mathjax (2.7.9+dfsg-1build1) ... 466s Selecting previously unselected package r-cran-knitr. 466s Preparing to unpack .../118-r-cran-knitr_1.51+dfsg-1_all.deb ... 466s Unpacking r-cran-knitr (1.51+dfsg-1) ... 466s Selecting previously unselected package r-cran-minqa. 466s Preparing to unpack .../119-r-cran-minqa_1.2.8-1_armhf.deb ... 466s Unpacking r-cran-minqa (1.2.8-1) ... 466s Selecting previously unselected package libnlopt0:armhf. 466s Preparing to unpack .../120-libnlopt0_2.7.1-7ubuntu1_armhf.deb ... 466s Unpacking libnlopt0:armhf (2.7.1-7ubuntu1) ... 466s Selecting previously unselected package r-cran-nloptr. 466s Preparing to unpack .../121-r-cran-nloptr_2.2.1-2_armhf.deb ... 466s Unpacking r-cran-nloptr (2.2.1-2) ... 466s Selecting previously unselected package r-cran-rbibutils. 466s Preparing to unpack .../122-r-cran-rbibutils_2.3-1_armhf.deb ... 466s Unpacking r-cran-rbibutils (2.3-1) ... 466s Selecting previously unselected package r-cran-rdpack. 466s Preparing to unpack .../123-r-cran-rdpack_2.6.3-1_all.deb ... 466s Unpacking r-cran-rdpack (2.6.3-1) ... 466s Selecting previously unselected package r-cran-reformulas. 466s Preparing to unpack .../124-r-cran-reformulas_0.4.4-1_all.deb ... 467s Unpacking r-cran-reformulas (0.4.4-1) ... 467s Selecting previously unselected package r-cran-rcppeigen. 467s Preparing to unpack .../125-r-cran-rcppeigen_0.3.4.0.2-1_armhf.deb ... 467s Unpacking r-cran-rcppeigen (0.3.4.0.2-1) ... 467s Selecting previously unselected package r-cran-statmod. 467s Preparing to unpack .../126-r-cran-statmod_1.5.0-1_armhf.deb ... 467s Unpacking r-cran-statmod (1.5.0-1) ... 467s Selecting previously unselected package r-cran-lme4. 467s Preparing to unpack .../127-r-cran-lme4_1.1-38-1_armhf.deb ... 467s Unpacking r-cran-lme4 (1.1-38-1) ... 467s Selecting previously unselected package r-cran-numderiv. 467s Preparing to unpack .../128-r-cran-numderiv_2016.8-1.1-3build1_all.deb ... 467s Unpacking r-cran-numderiv (2016.8-1.1-3build1) ... 467s Selecting previously unselected package r-cran-lmertest. 467s Preparing to unpack .../129-r-cran-lmertest_3.2-0-1_all.deb ... 467s Unpacking r-cran-lmertest (3.2-0-1) ... 467s Selecting previously unselected package r-cran-pbkrtest. 467s Preparing to unpack .../130-r-cran-pbkrtest_0.5.5-1_all.deb ... 467s Unpacking r-cran-pbkrtest (0.5.5-1) ... 467s Setting up libgraphite2-3:armhf (1.3.14-11ubuntu1) ... 467s Setting up libpixman-1-0:armhf (0.46.4-1) ... 467s Setting up libsharpyuv0:armhf (1.5.0-0.1build1) ... 467s Setting up fonts-mathjax (2.7.9+dfsg-1build1) ... 467s Setting up liblerc4:armhf (4.0.0+ds-5ubuntu2) ... 467s Setting up libjs-mathjax (2.7.9+dfsg-1build1) ... 467s Setting up libxrender1:armhf (1:0.9.12-1) ... 467s Setting up libdatrie1:armhf (0.2.14-1) ... 467s Setting up libxcb-render0:armhf (1.17.0-2ubuntu1) ... 467s Setting up fonts-glyphicons-halflings (1.009~3.4.1+dfsg-6) ... 467s Setting up unzip (6.0-29ubuntu1) ... 467s Setting up x11-common (1:7.7+24ubuntu1) ... 467s Setting up libdeflate0:armhf (1.23-2build1) ... 467s Setting up libnlopt0:armhf (2.7.1-7ubuntu1) ... 467s Setting up libxcb-shm0:armhf (1.17.0-2ubuntu1) ... 467s Setting up libgomp1:armhf (15.2.0-12ubuntu1) ... 467s Setting up libjbig0:armhf (2.1-6.1ubuntu3) ... 467s Setting up zip (3.0-15ubuntu3) ... 467s Setting up libblas3:armhf (3.12.1-7ubuntu1) ... 467s update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode 467s Setting up libfreetype6:armhf (2.14.1+dfsg-2) ... 467s Setting up fonts-dejavu-mono (2.37-8build1) ... 467s Setting up libtcl8.6:armhf (8.6.17+dfsg-1build1) ... 467s Setting up fonts-dejavu-core (2.37-8build1) ... 467s Setting up libjpeg-turbo8:armhf (2.1.5-4ubuntu3) ... 467s Setting up libgfortran5:armhf (15.2.0-12ubuntu1) ... 467s Setting up libwebp7:armhf (1.5.0-0.1build1) ... 467s Setting up libjs-highlight.js (10.7.3+dfsg-2) ... 467s Setting up libharfbuzz0b:armhf (12.3.2-1) ... 467s Setting up libthai-data (0.1.30-1) ... 467s Setting up libxss1:armhf (1:1.2.3-1build4) ... 467s Setting up libpaper2:armhf (2.2.5-0.3build1) ... 468s Setting up libjs-jquery (3.7.1+dfsg+~3.5.33-1build1) ... 468s Setting up node-normalize.css (8.0.1-5.1) ... 468s Setting up xdg-utils (1.2.1-2ubuntu2) ... 468s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode 468s Setting up libjs-bootstrap (3.4.1+dfsg-6) ... 468s Setting up libjpeg8:armhf (8c-2ubuntu11) ... 468s Setting up libice6:armhf (2:1.1.1-1build1) ... 468s Setting up liblapack3:armhf (3.12.1-7ubuntu1) ... 468s update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode 468s Setting up fontconfig-config (2.17.1-3ubuntu1) ... 468s Setting up libpaper-utils (2.2.5-0.3build1) ... 468s Setting up libjs-jquery-datatables (1.11.5+dfsg-2build1) ... 468s Setting up libthai0:armhf (0.1.30-1) ... 468s Setting up libtiff6:armhf (4.7.0-3ubuntu3) ... 468s Setting up libfontconfig1:armhf (2.17.1-3ubuntu1) ... 468s Setting up libsm6:armhf (2:1.2.6-1build1) ... 468s Setting up fontconfig (2.17.1-3ubuntu1) ... 470s Regenerating fonts cache... done. 470s Setting up libxft2:armhf (2.3.6-1build2) ... 470s Setting up libtk8.6:armhf (8.6.17-1) ... 470s Setting up libpango-1.0-0:armhf (1.57.0-1) ... 470s Setting up libcairo2:armhf (1.18.4-3) ... 470s Setting up libxt6t64:armhf (1:1.2.1-1.3) ... 470s Setting up libpangoft2-1.0-0:armhf (1.57.0-1) ... 470s Setting up libpangocairo-1.0-0:armhf (1.57.0-1) ... 470s Setting up r-base-core (4.5.2-1ubuntu2) ... 470s Creating config file /etc/R/Renviron with new version 470s Setting up r-cran-labeling (0.4.3-1) ... 470s Setting up r-cran-lattice (0.22-7-1) ... 470s Setting up r-cran-nlme (3.1.168-1) ... 470s Setting up r-cran-farver (2.1.2-1) ... 470s Setting up r-cran-viridislite (0.4.3-1) ... 470s Setting up r-cran-statmod (1.5.0-1) ... 470s Setting up r-cran-nnet (7.3-20-1) ... 470s Setting up r-cran-r6 (2.6.1-1) ... 470s Setting up r-cran-pkgkitten (0.2.4-1) ... 470s Setting up r-cran-numderiv (2016.8-1.1-3build1) ... 470s Setting up r-cran-magrittr (2.0.3-1) ... 470s Setting up r-cran-microbenchmark (1.5.0-1) ... 470s Setting up r-cran-quadprog (1.5-8-1build2) ... 470s Setting up r-cran-littler (0.3.22-1) ... 470s Setting up r-cran-rcpp (1.1.0-1) ... 470s Setting up r-cran-curl (7.0.0+dfsg-1) ... 470s Setting up r-cran-nloptr (2.2.1-2) ... 470s Setting up r-cran-boot (1.3-32-1) ... 470s Setting up r-cran-rlang (1.1.5-3) ... 470s Setting up r-cran-xfun (0.55+dfsg-1) ... 470s Setting up r-cran-urca (1.3-4-1build1) ... 470s Setting up r-cran-withr (3.0.2+dfsg-1) ... 470s Setting up r-cran-backports (1.5.0-2) ... 470s Setting up r-cran-deriv (4.2.0-1) ... 470s Setting up r-cran-generics (0.1.4-1) ... 470s Setting up r-cran-yaml (2.3.10-1) ... 470s Setting up r-cran-evaluate (1.0.5-1) ... 470s Setting up r-cran-timedate (4052.112-1) ... 470s Setting up r-cran-highr (0.11+dfsg-1) ... 470s Setting up r-cran-fansi (1.0.6-2) ... 470s Setting up r-cran-mass (7.3-65-1) ... 470s Setting up r-cran-glue (1.8.0-1) ... 470s Setting up r-cran-fracdiff (1.5-3-1) ... 470s Setting up r-cran-cli (3.6.4-1) ... 470s Setting up r-cran-rbibutils (2.3-1) ... 470s Setting up r-cran-lifecycle (1.0.5+dfsg-1) ... 470s Setting up r-cran-jsonlite (1.9.1+dfsg-1) ... 470s Setting up r-cran-pkgconfig (2.0.3-2build2) ... 470s Setting up r-cran-utf8 (1.2.4-1) ... 470s Setting up r-cran-colorspace (2.1-1+dfsg-1) ... 470s Setting up r-cran-stringi (1.8.4-1build2) ... 470s Setting up r-cran-s7 (0.2.0-1) ... 470s Setting up r-cran-cpp11 (0.5.3-1) ... 470s Setting up r-cran-rcolorbrewer (1.1-3-1build2) ... 470s Setting up r-cran-isoband (0.2.7-1) ... 470s Setting up r-cran-scales (1.4.0-1) ... 470s Setting up r-cran-gtable (0.3.6+dfsg-1) ... 470s Setting up r-cran-zoo (1.8-15-1) ... 470s Setting up r-cran-matrix (1.7-4-1) ... 470s Setting up r-cran-knitr (1.51+dfsg-1) ... 470s Setting up r-cran-lmtest (0.9.40-1build1) ... 470s Setting up r-cran-rcpparmadillo (15.2.3-1-1) ... 470s Setting up r-cran-vctrs (0.6.5-1) ... 470s Setting up r-cran-rcppeigen (0.3.4.0.2-1) ... 470s Setting up r-cran-pillar (1.11.1+dfsg-1) ... 470s Setting up r-cran-minqa (1.2.8-1) ... 470s Setting up r-cran-stringr (1.5.1-1) ... 470s Setting up r-cran-ggplot2 (4.0.2+dfsg-1) ... 470s Setting up r-cran-tibble (3.2.1+dfsg-3) ... 470s Setting up r-cran-xts (0.14.1-1) ... 470s Setting up r-cran-rdpack (2.6.3-1) ... 470s Setting up r-cran-tidyselect (1.2.1+dfsg-1) ... 470s Setting up r-cran-purrr (1.0.4-1) ... 470s Setting up r-cran-dplyr (1.1.4-4) ... 470s Setting up r-cran-reformulas (0.4.4-1) ... 470s Setting up r-cran-ttr (0.24.4-1) ... 470s Setting up r-cran-cowplot (1.1.3+dfsg-1) ... 470s Setting up r-cran-lme4 (1.1-38-1) ... 470s Setting up r-cran-lmertest (3.2-0-1) ... 470s Setting up r-cran-tidyr (1.3.1-1) ... 470s Setting up r-cran-quantmod (0.4.28-1) ... 470s Setting up r-cran-tseries (0.10-59-3) ... 470s Setting up r-cran-broom (1.0.12+dfsg-1) ... 470s Setting up r-cran-forecast (8.23.0-1) ... 470s Setting up r-cran-modelr (0.1.11-1) ... 470s Setting up r-cran-doby (4.7.1-3) ... 470s Setting up r-cran-pbkrtest (0.5.5-1) ... 470s Processing triggers for libc-bin (2.42-2ubuntu4) ... 470s Processing triggers for man-db (2.13.1-1build1) ... 471s Processing triggers for install-info (7.2-5) ... 480s autopkgtest [23:40:33]: test run-unit-test: [----------------------- 486s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 486s BEGIN TEST test_a_utils.R 486s 486s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 486s Copyright (C) 2025 The R Foundation for Statistical Computing 486s Platform: arm-unknown-linux-gnueabihf (32-bit) 486s 486s R is free software and comes with ABSOLUTELY NO WARRANTY. 486s You are welcome to redistribute it under certain conditions. 486s Type 'license()' or 'licence()' for distribution details. 486s 486s R is a collaborative project with many contributors. 486s Type 'contributors()' for more information and 486s 'citation()' on how to cite R or R packages in publications. 486s 486s Type 'demo()' for some demos, 'help()' for on-line help, or 486s 'help.start()' for an HTML browser interface to help. 486s Type 'q()' to quit R. 486s 486s > # test_a_utils.R 486s > 486s > library(lmerTest) 486s Loading required package: lme4 486s Loading required package: Matrix 488s 488s Attaching package: 'lmerTest' 488s 488s The following object is masked from 'package:lme4': 488s 488s lmer 488s 488s The following object is masked from 'package:stats': 488s 488s step 488s 488s > 488s > # test safeDeparse() - equivalence and differences to deparse(): 488s > deparse_args <- formals(deparse) 488s > safeDeparse_args <- formals(lmerTest:::safeDeparse) 488s > stopifnot( 488s + all.equal(names(deparse_args), names(safeDeparse_args)), 488s + all.equal(deparse_args[!names(deparse_args) %in% c("control", "width.cutoff")], 488s + safeDeparse_args[!names(safeDeparse_args) %in% c("control", "width.cutoff")]), 488s + all.equal(deparse_args[["width.cutoff"]], 60L), 488s + all(eval(safeDeparse_args[["control"]]) %in% eval(deparse_args[["control"]])), 488s + all.equal(safeDeparse_args[["width.cutoff"]], 500L) 488s + ) 488s > 488s > 488s BEGIN TEST test_anova.R 488s 488s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 488s Copyright (C) 2025 The R Foundation for Statistical Computing 488s Platform: arm-unknown-linux-gnueabihf (32-bit) 488s 488s R is free software and comes with ABSOLUTELY NO WARRANTY. 488s You are welcome to redistribute it under certain conditions. 488s Type 'license()' or 'licence()' for distribution details. 488s 488s R is a collaborative project with many contributors. 488s Type 'contributors()' for more information and 488s 'citation()' on how to cite R or R packages in publications. 488s 488s Type 'demo()' for some demos, 'help()' for on-line help, or 488s 'help.start()' for an HTML browser interface to help. 488s Type 'q()' to quit R. 488s 489s > # test_anova.R 489s > library(lmerTest) 489s Loading required package: lme4 489s Loading required package: Matrix 491s 491s Attaching package: 'lmerTest' 491s 491s The following object is masked from 'package:lme4': 491s 491s lmer 491s 491s The following object is masked from 'package:stats': 491s 491s step 491s 491s > 491s > # WRE says "using if(requireNamespace("pkgname")) is preferred, if possible." 491s > # even in tests: 491s > assertError <- function(expr, ...) 491s + if(requireNamespace("tools")) tools::assertError(expr, ...) else invisible() 491s > assertWarning <- function(expr, ...) 491s + if(requireNamespace("tools")) tools::assertWarning(expr, ...) else invisible() 491s > 491s > # Kenward-Roger only available with pbkrtest and only then validated in R >= 3.3.3 491s > # (faulty results for R < 3.3.3 may be due to unstated dependencies in pbkrtest) 491s > has_pbkrtest <- requireNamespace("pbkrtest", quietly = TRUE) && getRversion() >= "3.3.3" 491s > 491s > data("sleepstudy", package="lme4") 491s > TOL <- 1e-4 491s > 491s > #################################### 491s > ## Basic anova tests 491s > #################################### 491s > 491s > m <- lmer(Reaction ~ Days + (Days | Subject), sleepstudy) 491s > 491s > ####### ddf argument: 491s > (an1 <- anova(m)) # Also testing print method. 491s Type III Analysis of Variance Table with Satterthwaite's method 491s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 491s Days 30031 30031 1 17 45.853 3.264e-06 *** 491s --- 491s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 491s > (an2 <- anova(m, ddf="Satterthwaite")) 491s Type III Analysis of Variance Table with Satterthwaite's method 491s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 491s Days 30031 30031 1 17 45.853 3.264e-06 *** 491s --- 491s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 491s > (an2b <- anova(m, ddf="Satterthwaite", type=3)) 491s Type III Analysis of Variance Table with Satterthwaite's method 491s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 491s Days 30031 30031 1 17 45.853 3.264e-06 *** 491s --- 491s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 491s > (an2c <- anova(m, ddf="Satterthwaite", type=2)) 491s Type II Analysis of Variance Table with Satterthwaite's method 491s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 491s Days 30031 30031 1 17 45.853 3.264e-06 *** 491s --- 491s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 491s > stopifnot(isTRUE( 491s + all.equal(an1, an2, tolerance=TOL) 491s + )) 491s > (an3 <- anova(m, ddf="Sat")) ## Abbreviated argument 491s Type III Analysis of Variance Table with Satterthwaite's method 491s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 491s Days 30031 30031 1 17 45.853 3.264e-06 *** 491s --- 491s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 491s > stopifnot(isTRUE( 491s + all.equal(an1, an3, tolerance=TOL) 491s + )) 491s > if(has_pbkrtest) { 491s + (anova(m, ddf="Kenward-Roger")) 491s + (anova(m, ddf="Kenward-Roger", type=3)) 491s + } 492s Type III Analysis of Variance Table with Kenward-Roger's method 492s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 492s Days 30031 30031 1 17 45.853 3.264e-06 *** 492s --- 492s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 492s > (an1 <- anova(m, ddf="lme4")) 492s Analysis of Variance Table 492s npar Sum Sq Mean Sq F value 492s Days 1 30031 30031 45.853 492s > (an2 <- anova(m, ddf="lme4", type=3)) # 'type' is ignored with ddf="lme4" 492s Analysis of Variance Table 492s npar Sum Sq Mean Sq F value 492s Days 1 30031 30031 45.853 492s > stopifnot(isTRUE( 492s + all.equal(an1, an2, tolerance=TOL) 492s + )) 492s > res <- assertError(anova(m, ddf="KR")) ## Error on incorrect arg. 492s > stopifnot( 492s + grepl("'arg' should be one of ", unlist(res[[1]])$message) 492s + ) 492s > 492s > ## lme4 method: 492s > an1 <- anova(m, ddf="lme4") 492s > an2 <- anova(as(m, "lmerMod")) 492s refitting model(s) with ML (instead of REML) 492s > stopifnot(isTRUE( 492s + all.equal(an1, an2, tolerance=TOL) 492s + )) 492s > 492s > ###### type argument: 492s > (an1 <- anova(m, type="1")) # valid type arg. 492s Type I Analysis of Variance Table with Satterthwaite's method 492s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 492s Days 30031 30031 1 17 45.853 3.264e-06 *** 492s --- 492s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 492s > (an2 <- anova(m, type="I")) # same 492s Type I Analysis of Variance Table with Satterthwaite's method 492s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 492s Days 30031 30031 1 17 45.853 3.264e-06 *** 492s --- 492s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 492s > stopifnot(isTRUE( 492s + all.equal(an1, an2, tolerance=TOL) 492s + )) 492s > (an3 <- anova(m, type=1)) # Not strictly valid, but accepted 492s Type I Analysis of Variance Table with Satterthwaite's method 492s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 492s Days 30031 30031 1 17 45.853 3.264e-06 *** 492s --- 492s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 492s > stopifnot(isTRUE( 492s + all.equal(an1, an3, tolerance=TOL) 492s + )) 492s > 492s > (an1 <- anova(m, type="2")) # valid type arg. 492s Type II Analysis of Variance Table with Satterthwaite's method 492s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 492s Days 30031 30031 1 17 45.853 3.264e-06 *** 492s --- 492s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 492s > (an2 <- anova(m, type="II")) # same 492s Type II Analysis of Variance Table with Satterthwaite's method 492s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 492s Days 30031 30031 1 17 45.853 3.264e-06 *** 492s --- 492s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 492s > stopifnot(isTRUE( 492s + all.equal(an1, an2, tolerance=TOL) 492s + )) 492s > (an3 <- anova(m, type=3)) # Not strictly valid, but accepted 492s Type III Analysis of Variance Table with Satterthwaite's method 492s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 492s Days 30031 30031 1 17 45.853 3.264e-06 *** 492s --- 492s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 492s > stopifnot(isTRUE( 492s + all.equal(an1, an3, check.attributes=FALSE, tolerance=TOL) 492s + )) 492s > 492s > (an1 <- anova(m, type="3")) # valid type arg. 492s Type III Analysis of Variance Table with Satterthwaite's method 492s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 492s Days 30031 30031 1 17 45.853 3.264e-06 *** 492s --- 492s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 492s > (an2 <- anova(m, type="III")) # same 492s Type III Analysis of Variance Table with Satterthwaite's method 492s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 492s Days 30031 30031 1 17 45.853 3.264e-06 *** 492s --- 492s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 492s > stopifnot(isTRUE( 492s + all.equal(an1, an2, tolerance=TOL) 492s + )) 492s > (an3 <- anova(m, type=3)) # Not strictly valid, but accepted 492s Type III Analysis of Variance Table with Satterthwaite's method 492s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 492s Days 30031 30031 1 17 45.853 3.264e-06 *** 492s --- 492s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 492s > stopifnot(isTRUE( 492s + all.equal(an1, an3, tolerance=TOL) 492s + )) 492s > assertError(anova(m, type=0)) # Not valid arg. 492s > assertError(anova(m, type="i")) # Not valid arg. 492s > 492s > ####### Model comparison: 492s > fm <- lm(Reaction ~ Days, sleepstudy) 492s > (an <- anova(m, fm)) 492s Data: sleepstudy 492s Models: 492s fm: Reaction ~ Days 492s m: Reaction ~ Days + (Days | Subject) 492s npar AIC BIC logLik -2*log(L) Chisq Df Pr(>Chisq) 492s fm 3 1906.3 1915.9 -950.15 1900.3 492s m 6 1763.9 1783.1 -875.97 1751.9 148.35 3 < 2.2e-16 *** 492s --- 492s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 492s > stopifnot( 492s + nrow(an) == 2L, 492s + rownames(an)[2] == "m" 492s + ) 492s > 492s > m2 <- lmer(Reaction ~ Days + I(Days^2) + (Days | Subject), sleepstudy) 492s > (an <- anova(m, m2, refit=FALSE)) 492s Data: sleepstudy 492s Models: 492s m: Reaction ~ Days + (Days | Subject) 492s m2: Reaction ~ Days + I(Days^2) + (Days | Subject) 492s npar AIC BIC logLik -2*log(L) Chisq Df Pr(>Chisq) 492s m 6 1755.6 1774.8 -871.81 1743.6 492s m2 7 1756.8 1779.2 -871.41 1742.8 0.8127 1 0.3673 492s > stopifnot( 492s + nrow(an) == 2L, 492s + rownames(an)[1] == "m" 492s + ) 492s > 492s > 492s > #################################### 492s > ## Example with factor fixef: 492s > #################################### 492s > 492s > ## 'temp' is continuous, 'temperature' an ordered factor with 6 levels 492s > data("cake", package="lme4") 492s > m <- lmer(angle ~ recipe * temp + (1|recipe:replicate), cake) 492s > (an <- anova(m)) 492s Type III Analysis of Variance Table with Satterthwaite's method 492s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 492s recipe 4.00 2.00 2 254.02 0.0957 0.9088 492s temp 1966.71 1966.71 1 222.00 94.1632 <2e-16 *** 492s recipe:temp 1.74 0.87 2 222.00 0.0417 0.9592 492s --- 492s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 492s > (an_lme4 <- anova(m, ddf="lme4")) 492s Analysis of Variance Table 492s npar Sum Sq Mean Sq F value 492s recipe 2 10.39 5.20 0.2488 492s temp 1 1966.71 1966.71 94.1632 492s recipe:temp 2 1.74 0.87 0.0417 492s > 492s > if(has_pbkrtest) { 492s + (an_KR <- anova(m, ddf="Kenward-Roger")) 492s + # res <- all.equal(an[, c("Sum Sq", "Mean Sq", "F value")], 492s + # an_lme4[, c("Sum Sq", "Mean Sq", "F value")]) 492s + # stopifnot(isTRUE(res)) 492s + res <- all.equal(an[, c("Sum Sq", "Mean Sq", "F value")], 492s + an_KR[, c("Sum Sq", "Mean Sq", "F value")], tolerance=TOL) 492s + stopifnot(isTRUE(res)) 492s + } 492s > stopifnot(all.equal(c(2, 1, 2), an$NumDF, tol=1e-6), 492s + all.equal(c(254.0157612, 222, 222), an$DenDF, tol=TOL)) 492s > 492s > an3 <- anova(m, type=3) 492s > an2 <- anova(m, type=2) 492s > an1 <- anova(m, type=1) 492s > 492s > ## Data is balanced, so Type II and III should be identical: 492s > ## One variable is continuous, so Type I and II/III are different: 492s > stopifnot( 492s + isTRUE(all.equal(an3, an2, check.attributes=FALSE, tolerance=TOL)), 492s + !isTRUE(all.equal(an1, an2, check.attributes=FALSE, tolerance=1e-8)) 492s + ) 492s > 492s > # Using an ordered factor: 492s > m <- lmer(angle ~ recipe * temperature + (1|recipe:replicate), cake) 492s > (an1 <- anova(m, type=1)) 492s Type I Analysis of Variance Table with Satterthwaite's method 492s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 492s recipe 10.19 5.09 2 42 0.2488 0.7809 492s temperature 2100.30 420.06 5 210 20.5199 <2e-16 *** 492s recipe:temperature 205.98 20.60 10 210 1.0062 0.4393 492s --- 492s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 492s > (an2 <- anova(m, type=2)) 492s Type II Analysis of Variance Table with Satterthwaite's method 492s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 492s recipe 10.19 5.09 2 42 0.2488 0.7809 492s temperature 2100.30 420.06 5 210 20.5199 <2e-16 *** 492s recipe:temperature 205.98 20.60 10 210 1.0062 0.4393 492s --- 492s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 492s > # Type 3 is also available with ordered factors: 492s > (an3 <- anova(m, type=3)) 492s Type III Analysis of Variance Table with Satterthwaite's method 492s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 492s recipe 10.19 5.09 2 42 0.2488 0.7809 492s temperature 2100.30 420.06 5 210 20.5199 <2e-16 *** 492s recipe:temperature 205.98 20.60 10 210 1.0062 0.4393 492s --- 492s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 492s > ## Balanced data and only factors: Type I, II and III should be the same: 492s > stopifnot( 492s + isTRUE(all.equal(an1, an2, check.attributes=FALSE, tolerance=TOL)), 492s + isTRUE(all.equal(an1, an3, check.attributes=FALSE, tolerance=TOL)) 492s + ) 492s > 492s > (an <- anova(m, type=1)) 492s Type I Analysis of Variance Table with Satterthwaite's method 492s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 492s recipe 10.19 5.09 2 42 0.2488 0.7809 492s temperature 2100.30 420.06 5 210 20.5199 <2e-16 *** 492s recipe:temperature 205.98 20.60 10 210 1.0062 0.4393 492s --- 492s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 492s > (an_lme4 <- anova(m, type=1, ddf="lme4")) 492s Analysis of Variance Table 492s npar Sum Sq Mean Sq F value 492s recipe 2 10.19 5.09 0.2488 492s temperature 5 2100.30 420.06 20.5199 492s recipe:temperature 10 205.98 20.60 1.0062 492s > res <- all.equal(an[, c("Sum Sq", "Mean Sq", "F value")], 492s + an_lme4[, c("Sum Sq", "Mean Sq", "F value")], tolerance=TOL) 492s > stopifnot(isTRUE(res)) 492s > if(has_pbkrtest) { 492s + (an_KR <- anova(m, type=1, ddf="Kenward-Roger")) 492s + res <- all.equal(an[, c("Sum Sq", "Mean Sq", "F value")], 492s + an_KR[, c("Sum Sq", "Mean Sq", "F value")], tolerance=TOL) 492s + stopifnot(isTRUE(res)) 492s + } 493s > stopifnot(all.equal(c(2, 5, 10), an$NumDF, tolerance=TOL), 493s + all.equal(c(42, 210, 210), an$DenDF, tolerance=TOL)) 493s > 493s > ######## 493s > ## Make case with balanced unordered factors: 493s > cake2 <- cake 493s > cake2$temperature <- factor(cake2$temperature, ordered = FALSE) 493s > # str(cake2) 493s > stopifnot( 493s + !is.ordered(cake2$temperature) 493s + ) 493s > m <- lmer(angle ~ recipe * temperature + (1|recipe:replicate), cake2) 493s > (an1 <- anova(m, type=1)) 493s Type I Analysis of Variance Table with Satterthwaite's method 493s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 493s recipe 10.19 5.09 2 42 0.2488 0.7809 493s temperature 2100.30 420.06 5 210 20.5199 <2e-16 *** 493s recipe:temperature 205.98 20.60 10 210 1.0062 0.4393 493s --- 493s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 493s > (an2 <- anova(m, type=2)) 493s Type II Analysis of Variance Table with Satterthwaite's method 493s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 493s recipe 10.19 5.09 2 42 0.2488 0.7809 493s temperature 2100.30 420.06 5 210 20.5199 <2e-16 *** 493s recipe:temperature 205.98 20.60 10 210 1.0062 0.4393 493s --- 493s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 493s > (an3 <- anova(m, type=3)) 493s Type III Analysis of Variance Table with Satterthwaite's method 493s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 493s recipe 10.19 5.09 2 42 0.2488 0.7809 493s temperature 2100.30 420.06 5 210 20.5199 <2e-16 *** 493s recipe:temperature 205.98 20.60 10 210 1.0062 0.4393 493s --- 493s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 493s > ## Balanced data and only factors: Type I, II, and III should be the same: 493s > stopifnot( 493s + isTRUE(all.equal(an1, an2, check.attributes=FALSE, tolerance=TOL)), 493s + isTRUE(all.equal(an3, an2, check.attributes=FALSE, tolerance=TOL)) 493s + ) 493s > ######## 493s > 493s > # No intercept: 493s > m <- lmer(angle ~ 0 + recipe * temp + (1|recipe:replicate), cake) 493s > (an <- anova(m, type=1)) 493s Type I Analysis of Variance Table with Satterthwaite's method 493s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 493s recipe 21442.9 7147.6 3 42 342.2200 <2e-16 *** 493s temp 1966.7 1966.7 1 222 94.1632 <2e-16 *** 493s recipe:temp 1.7 0.9 2 222 0.0417 0.9592 493s --- 493s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 493s > (an2 <- anova(m, type=2)) 493s Type II Analysis of Variance Table with Satterthwaite's method 493s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 493s recipe 4.48 1.49 3 254.02 0.0714 0.9752 493s temp 1966.71 1966.71 1 222.00 94.1632 <2e-16 *** 493s recipe:temp 1.74 0.87 2 222.00 0.0417 0.9592 493s --- 493s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 493s > (an2 <- anova(m, type=3)) 493s Type III Analysis of Variance Table with Satterthwaite's method 493s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 493s recipe 4.48 1.49 3 254.02 0.0714 0.9752 493s temp 1966.71 1966.71 1 222.00 94.1632 <2e-16 *** 493s recipe:temp 1.74 0.87 2 222.00 0.0417 0.9592 493s --- 493s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 493s > if(has_pbkrtest) 493s + (an_KR <- anova(m, ddf="Kenward-Roger")) 493s Type III Analysis of Variance Table with Kenward-Roger's method 493s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 493s recipe 4.48 1.49 3 254.02 0.0714 0.9752 493s temp 1966.71 1966.71 1 222.00 94.1632 <2e-16 *** 493s recipe:temp 1.74 0.87 2 222.00 0.0417 0.9592 493s --- 493s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 493s > (an_lme4 <- anova(m, ddf="lme4")) 493s Analysis of Variance Table 493s npar Sum Sq Mean Sq F value 493s recipe 3 21442.9 7147.6 342.2200 493s temp 1 1966.7 1966.7 94.1632 493s recipe:temp 2 1.7 0.9 0.0417 493s > res <- all.equal(an[, c("Sum Sq", "Mean Sq", "F value")], 493s + an_lme4[, c("Sum Sq", "Mean Sq", "F value")], tolerance=TOL) 493s > stopifnot(isTRUE(res)) 493s > 493s > # ML-fit: 493s > m <- lmer(angle ~ recipe * temp + (1|recipe:replicate), cake, REML=FALSE) 493s > (an <- anova(m, type=1)) 493s Type I Analysis of Variance Table with Satterthwaite's method 493s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 493s recipe 10.99 5.49 2 45 0.2666 0.7672 493s temp 1966.71 1966.71 1 225 95.4357 <2e-16 *** 493s recipe:temp 1.74 0.87 2 225 0.0423 0.9586 493s --- 493s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 493s > if(has_pbkrtest) 493s + assertError(an <- anova(m, ddf="Kenward-Roger")) # KR fits should be REML 493s > (an_lme4 <- anova(m, ddf="lme4")) 493s Analysis of Variance Table 493s npar Sum Sq Mean Sq F value 493s recipe 2 10.99 5.49 0.2666 493s temp 1 1966.71 1966.71 95.4357 493s recipe:temp 2 1.74 0.87 0.0423 493s > res <- all.equal(an[, c("Sum Sq", "Mean Sq", "F value")], 493s + an_lme4[, c("Sum Sq", "Mean Sq", "F value")], tolerance=TOL) 493s > stopifnot(isTRUE(res)) 493s > 493s > #################################### 493s > ## Using contr.sum: 493s > #################################### 493s > 493s > m <- lmer(angle ~ recipe * temp + (1|recipe:replicate), cake, 493s + contrasts = list('recipe' = "contr.sum")) 493s > (an <- anova(m, type=1)) 493s Type I Analysis of Variance Table with Satterthwaite's method 493s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 493s recipe 10.39 5.20 2 42 0.2488 0.7809 493s temp 1966.71 1966.71 1 222 94.1632 <2e-16 *** 493s recipe:temp 1.74 0.87 2 222 0.0417 0.9592 493s --- 493s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 493s > (an2 <- anova(m, type=2)) 493s Type II Analysis of Variance Table with Satterthwaite's method 493s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 493s recipe 4.00 2.00 2 254.02 0.0957 0.9088 493s temp 1966.71 1966.71 1 222.00 94.1632 <2e-16 *** 493s recipe:temp 1.74 0.87 2 222.00 0.0417 0.9592 493s --- 493s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 493s > (an3 <- anova(m, type=3)) 493s Type III Analysis of Variance Table with Satterthwaite's method 493s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 493s recipe 4.00 2.00 2 254.02 0.0957 0.9088 493s temp 1966.71 1966.71 1 222.00 94.1632 <2e-16 *** 493s recipe:temp 1.74 0.87 2 222.00 0.0417 0.9592 493s --- 493s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 493s > stopifnot( 493s + isTRUE(all.equal(an2, an3, check.attributes=FALSE, tolerance=TOL)) 493s + ) 493s > if(has_pbkrtest) 493s + (an_KR <- anova(m, type=1, ddf="Kenward-Roger")) 493s Type I Analysis of Variance Table with Kenward-Roger's method 493s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 493s recipe 10.39 5.20 2 42 0.2488 0.7809 493s temp 1966.71 1966.71 1 222 94.1632 <2e-16 *** 493s recipe:temp 1.74 0.87 2 222 0.0417 0.9592 493s --- 493s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 493s > (an_lme4 <- anova(m, ddf="lme4")) 493s Analysis of Variance Table 493s npar Sum Sq Mean Sq F value 493s recipe 2 10.39 5.20 0.2488 493s temp 1 1966.71 1966.71 94.1632 493s recipe:temp 2 1.74 0.87 0.0417 493s > res <- all.equal(an[, c("Sum Sq", "Mean Sq", "F value")], 493s + an_lme4[, c("Sum Sq", "Mean Sq", "F value")], tolerance=TOL) 493s > stopifnot(isTRUE(res)) 493s > 493s > 493s > #################################### 493s > ## Example with continuous fixef: 493s > #################################### 493s > 493s > # Example with no fixef: 493s > m <- lmer(Reaction ~ -1 + (Days | Subject), sleepstudy) 493s > # m <- lmer(Reaction ~ 0 + (Days | Subject), sleepstudy) # alternative 493s > stopifnot(length(fixef(m)) == 0L) 493s > (an <- anova(m, type=1)) 493s Type I Analysis of Variance Table with Satterthwaite's method 493s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 493s > (an_2 <- anova(m, type=2)) 493s Type II Analysis of Variance Table with Satterthwaite's method 493s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 493s > (an_3 <- anova(m, type=3)) 493s Type III Analysis of Variance Table with Satterthwaite's method 493s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 493s > stopifnot(nrow(an) == 0L, 493s + nrow(an_2) == 0L, 493s + nrow(an_3) == 0L) 493s > # anova(m, ddf="lme4") # Bug in lme4 it seems 493s > if(has_pbkrtest) { 493s + (an_KR <- anova(m, ddf="Kenward-Roger")) 493s + stopifnot( 493s + nrow(an_KR) == 0L 493s + ) 493s + } 493s > 493s > # Example with intercept only: 493s > m <- lmer(Reaction ~ (Days | Subject), sleepstudy) 493s > # m <- lmer(Reaction ~ 1 + (Days | Subject), sleepstudy) # alternative 493s > stopifnot(length(fixef(m)) == 1L, 493s + names(fixef(m)) == "(Intercept)") 493s > (an <- anova(m)) 493s Type III Analysis of Variance Table with Satterthwaite's method 493s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 493s > (an_2 <- anova(m, type=2)) 493s Type II Analysis of Variance Table with Satterthwaite's method 493s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 493s > (an_3 <- anova(m, type=3)) 493s Type III Analysis of Variance Table with Satterthwaite's method 493s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 493s > (an_lme4 <- anova(m, ddf="lme4")) 493s Analysis of Variance Table 493s npar Sum Sq Mean Sq F value 493s > stopifnot(nrow(an) == 0L, 493s + nrow(an_2) == 0L, 493s + nrow(an_3) == 0L, 493s + nrow(an_lme4) == 0L) 493s > if(has_pbkrtest) { 493s + (an_KR <- anova(m, ddf="Kenward-Roger")) 493s + stopifnot( 493s + nrow(an_KR) == 0L 493s + ) 493s + } 493s > 493s > # Example with 1 fixef without intercept: 493s > # for packageVersion("lme4") < 1.1.20 493s > # mOld <- lmer(Reaction ~ Days - 1 + (Days | Subject), sleepstudy) 493s > # for packageVersion("lme4") >= 1.1.20 we need to specify the old default 493s > # optimizer to get the model to converge well enough. 493s > m <- lmer(Reaction ~ Days - 1 + (Days | Subject), sleepstudy, 493s + control=lmerControl(optimizer="bobyqa")) 493s > # m <- lmer(Reaction ~ 0 + Days + (Days | Subject), sleepstudy) # alternative 493s > stopifnot(length(fixef(m)) == 1L, 493s + names(fixef(m)) == "Days") 493s > (an <- anova(m)) 493s Type III Analysis of Variance Table with Satterthwaite's method 493s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 493s Days 93564 93564 1 17 142.86 1.069e-09 *** 493s --- 493s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 493s > (an_2 <- anova(m, type=2)) 493s Type II Analysis of Variance Table with Satterthwaite's method 493s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 493s Days 93564 93564 1 17 142.86 1.069e-09 *** 493s --- 493s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 493s > (an_3 <- anova(m, type=3)) 493s Type III Analysis of Variance Table with Satterthwaite's method 493s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 493s Days 93564 93564 1 17 142.86 1.069e-09 *** 493s --- 493s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 493s > (an_lme4 <- anova(m, ddf="lme4")) 493s Analysis of Variance Table 493s npar Sum Sq Mean Sq F value 493s Days 1 93564 93564 142.86 493s > stopifnot(nrow(an) == 1L, 493s + nrow(an_2) == 1L, 493s + nrow(an_3) == 1L, 493s + nrow(an_lme4) == 1L) 493s > if(has_pbkrtest) { 493s + (an_KR <- anova(m, ddf="Kenward-Roger")) 493s + stopifnot( 493s + nrow(an_KR) == 1L 493s + ) 493s + } 494s > 494s > res <- all.equal(an[, c("Sum Sq", "Mean Sq", "F value")], 494s + an_lme4[, c("Sum Sq", "Mean Sq", "F value")], tolerance=TOL) 494s > stopifnot(isTRUE(res)) 494s > stopifnot(isTRUE(all.equal( 494s + c(1, 17), unname(unlist(an[, c("NumDF", "DenDF")])), tolerance=TOL 494s + ))) 494s > 494s > # Example with >1 fixef without intercept: 494s > m <- lmer(Reaction ~ Days - 1 + I(Days^2) + (Days | Subject), sleepstudy) 494s > stopifnot(length(fixef(m)) == 2L, 494s + names(fixef(m)) == c("Days", "I(Days^2)")) 494s > (an <- anova(m)) 494s Type III Analysis of Variance Table with Satterthwaite's method 494s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 494s Days 22127.2 22127.2 1 69.048 33.9280 1.65e-07 *** 494s I(Days^2) 744.7 744.7 1 143.679 1.1419 0.287 494s --- 494s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 494s > (an_2 <- anova(m, type=2)) 494s Type II Analysis of Variance Table with Satterthwaite's method 494s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 494s Days 22127.2 22127.2 1 69.048 33.9280 1.65e-07 *** 494s I(Days^2) 744.7 744.7 1 143.679 1.1419 0.287 494s --- 494s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 494s > (an_3 <- anova(m, type=3)) 494s Type III Analysis of Variance Table with Satterthwaite's method 494s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 494s Days 22127.2 22127.2 1 69.048 33.9280 1.65e-07 *** 494s I(Days^2) 744.7 744.7 1 143.679 1.1419 0.287 494s --- 494s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 494s > (an_lme4 <- anova(m, ddf="lme4")) 494s Analysis of Variance Table 494s npar Sum Sq Mean Sq F value 494s Days 1 93129 93129 142.7959 494s I(Days^2) 1 745 745 1.1419 494s > stopifnot(nrow(an) == 2L, 494s + nrow(an_3) == 2L, 494s + nrow(an_lme4) == 2L) 494s > if(has_pbkrtest) { 494s + (an_KR <- anova(m, ddf="Kenward-Roger")) 494s + stopifnot( 494s + nrow(an_KR) == 2L 494s + ) 494s + } 494s > # Here is a diff in SSQ which doesn't seem well-defined anyway... 494s > # SSQ for I(Days^2) agree though. 494s > # t-statistics also agree: 494s > coef(summary(m)) 494s Estimate Std. Error df t value Pr(>|t|) 494s Days 15.884431 2.7270460 69.04781 5.824776 1.649534e-07 494s I(Days^2) 0.279552 0.2616034 143.67926 1.068610 2.870375e-01 494s > Lmat <- diag(length(fixef(m))) 494s > lmerTest:::rbindall(lapply(1:nrow(Lmat), function(i) contest1D(m, Lmat[i, ]))) 494s Estimate Std. Error df t value Pr(>|t|) 494s 1 15.884431 2.7270460 69.04781 5.824776 1.649534e-07 494s 2 0.279552 0.2616034 143.67926 1.068610 2.870375e-01 494s > 494s > # Example with >1 fixef and intercept: 494s > m <- lmer(Reaction ~ Days + I(Days^2) + (Days | Subject), sleepstudy) 494s > stopifnot(length(fixef(m)) == 3L) 494s > (an <- anova(m, type=1)) 494s Type I Analysis of Variance Table with Satterthwaite's method 494s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 494s Days 29894.8 29894.8 1 17 45.8530 3.264e-06 *** 494s I(Days^2) 1079.5 1079.5 1 143 1.6558 0.2003 494s --- 494s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 494s > (an_2 <- anova(m, type=2)) 494s Type II Analysis of Variance Table with Satterthwaite's method 494s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 494s Days 4534.5 4534.5 1 114.43 6.9551 0.00952 ** 494s I(Days^2) 1079.5 1079.5 1 143.00 1.6558 0.20026 494s --- 494s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 494s > (an_3 <- anova(m, type=3)) 494s Type III Analysis of Variance Table with Satterthwaite's method 494s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 494s Days 4534.5 4534.5 1 114.43 6.9551 0.00952 ** 494s I(Days^2) 1079.5 1079.5 1 143.00 1.6558 0.20026 494s --- 494s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 494s > (an_lme4 <- anova(m, ddf="lme4")) 494s Analysis of Variance Table 494s npar Sum Sq Mean Sq F value 494s Days 1 29894.8 29894.8 45.8530 494s I(Days^2) 1 1079.5 1079.5 1.6558 494s > res <- all.equal(an[, c("Sum Sq", "Mean Sq", "F value")], 494s + an_lme4[, c("Sum Sq", "Mean Sq", "F value")], tolerance=TOL) 494s > stopifnot(isTRUE(res)) 494s > 494s > if(has_pbkrtest) { 494s + (an_KR <- anova(m, ddf="Kenward-Roger")) 494s + res <- all.equal(an_3[, c("Sum Sq", "Mean Sq", "DenDF", "F value")], 494s + an_KR[, c("Sum Sq", "Mean Sq", "DenDF", "F value")], tolerance=TOL) 494s + stopifnot(isTRUE(res)) 494s + } 494s > 494s > ## FIXME: Test the use of refit arg to lme4:::anova.merMod 494s > 494s > ############################## 494s > # Test that type III anova is the same regardless of contrast coding: 494s > # 3 x 3 factorial with missing diagonal 494s > data("cake", package="lme4") 494s > cake4 <- cake 494s > cake4$temperature <- factor(cake4$temperature, ordered=FALSE) 494s > cake4 <- droplevels(subset(cake4, temperature %in% levels(cake4$temperature)[1:3])) 494s > cake4 <- droplevels(subset(cake4, !((recipe == "A" & temperature == "175") | 494s + (recipe == "B" & temperature == "185") | 494s + (recipe == "C" & temperature == "195") ))) 494s > str(cake4) 494s 'data.frame': 90 obs. of 5 variables: 494s $ replicate : Factor w/ 15 levels "1","2","3","4",..: 1 1 1 1 1 1 2 2 2 2 ... 494s $ recipe : Factor w/ 3 levels "A","B","C": 1 1 2 2 3 3 1 1 2 2 ... 494s $ temperature: Factor w/ 3 levels "175","185","195": 2 3 1 3 1 2 2 3 1 3 ... 494s $ angle : int 46 47 39 51 46 44 29 35 35 47 ... 494s $ temp : num 185 195 175 195 175 185 185 195 175 195 ... 494s > with(cake4, table(recipe, temperature)) 494s temperature 494s recipe 175 185 195 494s A 0 15 15 494s B 15 0 15 494s C 15 15 0 494s > # load_all(r2path) 494s > 494s > fm1 <- lmer(angle ~ recipe * temperature + (1|recipe:replicate), cake4) 494s fixed-effect model matrix is rank deficient so dropping 3 columns / coefficients 494s > fm2 <- lmer(angle ~ recipe * temperature + (1|recipe:replicate), cake4, 494s + contrasts=list(recipe="contr.sum", temperature="contr.SAS")) 494s fixed-effect model matrix is rank deficient so dropping 3 columns / coefficients 494s > fm3 <- lmer(angle ~ recipe * temperature + (1|recipe:replicate), cake4, 494s + contrasts=list(recipe="contr.sum", temperature="contr.poly")) 494s fixed-effect model matrix is rank deficient so dropping 3 columns / coefficients 494s > fm4 <- lmer(angle ~ recipe * temperature + (1|recipe:replicate), cake4, 494s + contrasts=list(recipe=contr.helmert, temperature="contr.poly")) 494s fixed-effect model matrix is rank deficient so dropping 3 columns / coefficients 494s > (an1 <- anova(fm1)) 494s Missing cells for: recipeA:temperature175, recipeB:temperature185, recipeC:temperature195. 494s Interpret type III hypotheses with care. 494s Type III Analysis of Variance Table with Satterthwaite's method 494s Missing cells for: recipeA:temperature175, recipeB:temperature185, recipeC:temperature195. 494s Interpret type III hypotheses with care. 494s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 494s recipe 2.282 1.141 2 45.888 0.0871 0.916766 494s temperature 136.267 68.133 2 42.000 5.1998 0.009602 ** 494s recipe:temperature 52.900 52.900 1 42.000 4.0372 0.050963 . 494s --- 494s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 494s > (an2 <- anova(fm2)) 494s Type III Analysis of Variance Table with Satterthwaite's method 494s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 494s recipe 2.282 1.141 2 45.888 0.0871 0.916766 494s temperature 136.267 68.133 2 42.000 5.1998 0.009602 ** 494s recipe:temperature 52.900 52.900 1 42.000 4.0372 0.050963 . 494s --- 494s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 494s > (an3 <- anova(fm3)) 494s Missing cells for: recipeA:temperature175, recipeB:temperature185, recipeC:temperature195. 494s Interpret type III hypotheses with care. 494s Type III Analysis of Variance Table with Satterthwaite's method 494s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 494s recipe 2.282 1.141 2 45.888 0.0871 0.916766 494s temperature 136.267 68.133 2 42.000 5.1998 0.009602 ** 494s recipe:temperature 52.900 52.900 1 42.000 4.0372 0.050963 . 494s --- 494s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 494s > (an4 <- anova(fm4)) 494s Missing cells for: recipeA:temperature175, recipeB:temperature185, recipeC:temperature195. 494s Interpret type III hypotheses with care. 494s Type III Analysis of Variance Table with Satterthwaite's method 494s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 494s recipe 2.282 1.141 2 45.888 0.0871 0.916766 494s temperature 136.267 68.133 2 42.000 5.1998 0.009602 ** 494s recipe:temperature 52.900 52.900 1 42.000 4.0372 0.050963 . 494s --- 494s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 494s > options("contrasts") 494s $contrasts 494s unordered ordered 494s "contr.treatment" "contr.poly" 494s 494s > options(contrasts = c("contr.sum", "contr.poly")) 494s > fm5 <- lmer(angle ~ recipe * temperature + (1|recipe:replicate), cake4) 495s fixed-effect model matrix is rank deficient so dropping 3 columns / coefficients 495s > (an5 <- anova(fm5)) 495s Missing cells for: recipeA:temperature175, recipeB:temperature185, recipeC:temperature195. 495s Interpret type III hypotheses with care. 495s Type III Analysis of Variance Table with Satterthwaite's method 495s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 495s recipe 2.282 1.141 2 45.888 0.0871 0.916766 495s temperature 136.267 68.133 2 42.000 5.1998 0.009602 ** 495s recipe:temperature 52.900 52.900 1 42.000 4.0372 0.050963 . 495s --- 495s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 495s > options(contrasts = c("contr.treatment", "contr.poly")) 495s > options("contrasts") 495s $contrasts 495s [1] "contr.treatment" "contr.poly" 495s 495s > stopifnot( 495s + isTRUE(all.equal(an1, an2, check.attributes=FALSE, tolerance=TOL)), 495s + isTRUE(all.equal(an1, an3, check.attributes=FALSE, tolerance=TOL)), 495s + isTRUE(all.equal(an1, an4, check.attributes=FALSE, tolerance=TOL)), 495s + isTRUE(all.equal(an1, an5, check.attributes=FALSE, tolerance=TOL)) 495s + ) 495s > 495s > 495s BEGIN TEST test_compare_sas.R 495s 495s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 495s Copyright (C) 2025 The R Foundation for Statistical Computing 495s Platform: arm-unknown-linux-gnueabihf (32-bit) 495s 495s R is free software and comes with ABSOLUTELY NO WARRANTY. 495s You are welcome to redistribute it under certain conditions. 495s Type 'license()' or 'licence()' for distribution details. 495s 495s R is a collaborative project with many contributors. 495s Type 'contributors()' for more information and 495s 'citation()' on how to cite R or R packages in publications. 495s 495s Type 'demo()' for some demos, 'help()' for on-line help, or 495s 'help.start()' for an HTML browser interface to help. 495s Type 'q()' to quit R. 495s 495s > # test_compare_sas.R 495s > library(lmerTest) 495s Loading required package: lme4 495s Loading required package: Matrix 497s 497s Attaching package: 'lmerTest' 497s 497s > 497s > # WRE says "using if(requireNamespace("pkgname")) is preferred, if possible." 497s > # even in tests: 497s > assertError <- function(expr, ...) 497s + if(requireNamespace("tools")) tools::assertError(expr, ...) else invisible() 497s > assertWarning <- function(expr, ...) 497s + if(requireNamespace("tools")) tools::assertWarning(expr, ...) else invisible() 497s > 497s > ##################################################################### 497s > 497s > 497s > # Use contrasts to get particular estimates for the summary table: 497s > l <- list(Frequency="contr.SAS", Income="contr.SAS") 497s > m.carrots <- lmer(Preference ~ sens2*Frequency*Income 497s + +(1+sens2|Consumer), data=carrots, contrasts=l) 497s The following object is masked from 'package:lme4': 497s 497s lmer 497s 497s The following object is masked from 'package:stats': 497s 497s step 497s 497s fixed-effect model matrix is rank deficient so dropping 12 columns / coefficients 498s > an.m <- anova(m.carrots) 498s 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. 498s Interpret type III hypotheses with care. 498s > 498s > TOL <- 1e-4 498s > TOL2 <- 1e-5 498s > # with 4 decimals should agree with SAS output 498s > # numbers before decimals should agree with SAS output 498s > stopifnot( 498s + all.equal(an.m[,"Pr(>F)"], 498s + c(2e-5, 0.15512, 0.06939, 0.08223, 0.52459, 0.03119, 0.48344), 498s + tolerance = TOL), 498s + all.equal(round(an.m$DenDF), c(83, 83, 83, 83, 83, 83, 83)) 498s + ) 498s > 498s > sm <- summary(m.carrots) 498s > stopifnot( 498s + isTRUE(all.equal(sm$coefficients[,"Pr(>|t|)"], 498s + c(1e-10, 0.005061, 0.6865554, 0.342613, 0.129157, 498s + 0.088231, 0.846000, 0.354472, 0.526318, 0.020646, 0.010188, 498s + 0.031242, 0.055356, 0.694689, 0.099382, 0.28547, 498s + 0.977774, 0.855653, 0.427737, 0.321086, 0.417465 , 0.204385, 0.784437, 498s + 0.681434, 0.106180, 0.149122, 0.390870, 0.273686), tolerance=TOL, 498s + check.attributes = FALSE)) 498s + ) 498s > 498s > # Takes too long to run: 498s > # if(requireNamespace("pbkrtest", quietly = TRUE)) { 498s > # sm.kr <- summary(m.carrots, ddf = "Kenward-Roger") 498s > # 498s > # ## coefficients for Sat and KR agree in this example 498s > # # cbind(sm$coefficients[,"Pr(>|t|)"], sm.kr$coefficients[,"Pr(>|t|)"]) 498s > # all.equal(sm$coefficients[,"Pr(>|t|)"], sm.kr$coefficients[,"Pr(>|t|)"], 498s > # tol=TOL) 498s > # } 498s > 498s > ################################################################################ 498s > ## checking lsmeans and difflsmeans 498s > ## compare with SAS output 498s > m <- lmer(Informed.liking ~ Product*Information*Gender 498s + + (1|Product:Consumer) + (1|Consumer) , data=ham) 498s > 498s > 498s > lsm <- lsmeansLT(m, which = "Product") 498s > # head(lsm) 498s > 498s > stopifnot( 498s + isTRUE(all.equal(lsm[, "Estimate"], c(5.8084, 5.1012, 6.0909, 5.9256), 498s + tol=TOL, check.attributes = FALSE)), 498s + isTRUE(all.equal(round(lsm[, "t value"], 2), c(24.93, 21.89, 26.14, 25.43), tolerance=TOL, 498s + check.attributes = FALSE)), 498s + isTRUE(all.equal(lsm[, "lower"], c(5.3499, 4.6428, 5.6324, 5.4672), tolerance=TOL, 498s + check.attributes = FALSE)), 498s + isTRUE(all.equal(lsm[, "upper"], c(6.2668, 5.5597, 6.5493, 6.3840), tolerance=TOL, 498s + check.attributes = FALSE)) 498s + ) 498s > 498s > ################################################################################ 498s > # Not actually 'hard-coded' tests versus SAS results... 498s > 498s > m.carrots <- lmer(Preference ~ 0 + sens2 + Homesize + 498s + (1+sens2 | Consumer), data=carrots, 498s + control=lmerControl(optimizer="bobyqa")) 498s > summary(m.carrots) 498s Linear mixed model fit by REML. t-tests use Satterthwaite's method [ 498s lmerModLmerTest] 498s Formula: Preference ~ 0 + sens2 + Homesize + (1 + sens2 | Consumer) 498s Data: carrots 498s Control: lmerControl(optimizer = "bobyqa") 498s 498s REML criterion at convergence: 3748.9 498s 498s Scaled residuals: 498s Min 1Q Median 3Q Max 498s -3.5322 -0.5571 0.0308 0.6297 2.8552 498s 498s Random effects: 498s Groups Name Variance Std.Dev. Corr 498s Consumer (Intercept) 0.195168 0.44178 498s sens2 0.002779 0.05271 0.18 498s Residual 1.070441 1.03462 498s Number of obs: 1233, groups: Consumer, 103 498s 498s Fixed effects: 498s Estimate Std. Error df t value Pr(>|t|) 498s sens2 7.068e-02 9.545e-03 1.020e+02 7.404 3.89e-11 *** 498s Homesize1 4.910e+00 7.056e-02 1.013e+02 69.586 < 2e-16 *** 498s Homesize3 4.661e+00 7.850e-02 1.013e+02 59.374 < 2e-16 *** 498s --- 498s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 498s 498s Correlation of Fixed Effects: 498s sens2 Homsz1 498s Homesize1 0.061 498s Homesize3 0.055 0.003 498s > 498s > (an.1 <- anova(m.carrots, type=1)) 498s Type I Analysis of Variance Table with Satterthwaite's method 498s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 498s sens2 60.5 60.5 1 102.01 56.539 2.211e-11 *** 498s Homesize 8927.2 4463.6 2 101.31 4169.863 < 2.2e-16 *** 498s --- 498s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 498s > (an.3 <- anova(m.carrots)) 498s Type III Analysis of Variance Table with Satterthwaite's method 498s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 498s sens2 58.7 58.7 1 102.01 54.821 3.892e-11 *** 498s Homesize 8927.2 4463.6 2 101.31 4169.863 < 2.2e-16 *** 498s --- 498s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 498s > (an.lme4 <- anova(m.carrots, ddf = "lme4")) # difference in SSQ MS and F-values 498s Analysis of Variance Table 498s npar Sum Sq Mean Sq F value 498s sens2 1 0.0 0.0 0.0122 498s Homesize 2 8927.2 4463.6 4169.8634 498s > # Is this a problem with lme4? 498s > # fm <- lm(Preference ~ 0 + sens2 + Homesize, data=carrots) 498s > # anova(fm) 498s > # coef(summary(fm)) 498s > # Here the F value is a little greater than the squared t-value (as expected) 498s > 498s > stopifnot(all.equal(an.1[, "F value"], c(56.5394, 4169.87), tolerance = TOL2), 498s + all.equal(an.3[, "F value"], c(54.8206, 4169.87), tolerance = TOL2)) 498s > 498s > 498s > ################################################################################ 498s > # Check exmaple from GLM SAS report 498s > 498s > ### example from the paper GLM SAS 101 report 498s > a <- factor(c(1,1,1,2,2,2,2,2,1,2)) 498s > b <- factor(c(1,1,2,1,2,2,2,2,2,1)) 498s > f=factor(c(1,2,1,2,1,2,1,2,1,2)) 498s > y <- c(12,14,11,20,17,23,35,46,15,16) 498s > dd <- data.frame(a=a, b=b, y=y, f=f) 498s > 498s > ## check type 2 is order independent 498s > model <- lmer(y ~ a*b + (1|f), data=dd) 498s boundary (singular) fit: see help('isSingular') 498s > model2 <- lmer(y ~ b*a + (1|f), data=dd) 498s boundary (singular) fit: see help('isSingular') 498s > (an <- anova(model, type=2)) 498s Type II Analysis of Variance Table with Satterthwaite's method 498s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 498s a 336.00 336.00 1 6 3.9013 0.09566 . 498s b 114.33 114.33 1 6 1.3275 0.29308 498s a:b 85.75 85.75 1 6 0.9956 0.35689 498s --- 498s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 498s > (an2 <- anova(model2, type=2)) 498s Type II Analysis of Variance Table with Satterthwaite's method 498s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 498s b 114.33 114.33 1 6 1.3275 0.29308 498s a 336.00 336.00 1 6 3.9013 0.09566 . 498s b:a 85.75 85.75 1 6 0.9956 0.35689 498s --- 498s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 498s > stopifnot( 498s + isTRUE(all.equal(an,an2[c(2,1,3),], check.attributes = FALSE, tolerance=TOL2)) 498s + ) 498s > 498s > ## check the results are the same as from SAS proc mixed 498s > stopifnot( 498s + isTRUE(all.equal(an[,"F value"], c(3.90131, 1.32753, 0.99565), tolerance=TOL2)) 498s + ) 498s > ################################################################################ 498s > ## Check type II and III anova tables versus SAS 498s > 498s > m.carrots <- lmer(Preference ~ sens2*Homesize 498s + +(1+sens2|Consumer), data=carrots) 498s > (ancar <- anova(m.carrots, type=2)) 498s Type II Analysis of Variance Table with Satterthwaite's method 498s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 498s sens2 58.697 58.697 1 101.02 54.8339 4.042e-11 *** 498s Homesize 5.526 5.526 1 100.99 5.1621 0.02521 * 498s sens2:Homesize 1.103 1.103 1 101.02 1.0303 0.31251 498s --- 498s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 498s > 498s > stopifnot( 498s + isTRUE(all.equal(ancar[,"F value"], c(54.8361, 5.16138, 1.03035), tolerance = TOL)) 498s + ) 498s > 498s > m <- lmer(Informed.liking ~ Product*Age 498s + + (1|Consumer) , data=ham) 499s > (an <- anova(m, type=2)) 499s Type II Analysis of Variance Table with Satterthwaite's method 499s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 499s Product 32.498 10.8327 3 561 2.4814 0.06014 . 499s Age 0.024 0.0235 1 79 0.0054 0.94168 499s Product:Age 19.442 6.4808 3 561 1.4845 0.21772 499s --- 499s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 499s > 499s > stopifnot( 499s + isTRUE(all.equal(an[,"F value"], c(2.48135, .005387, 1.48451), tolerance = TOL2)) 499s + ) 499s > 499s > 499s > fm <- lmer(Preference ~ sens2*Homesize*sens1 + (1|Product), 499s + data=carrots) 499s > (ant2 <- anova(fm, type=2)) 499s Type II Analysis of Variance Table with Satterthwaite's method 499s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 499s sens2 21.0228 21.0228 1 7.97 16.4832 0.0036583 ** 499s Homesize 17.8570 17.8570 1 1217.01 14.0010 0.0001912 *** 499s sens1 0.6709 0.6709 1 7.98 0.5260 0.4889911 499s sens2:Homesize 1.5068 1.5068 1 1216.99 1.1814 0.2772780 499s sens2:sens1 0.1372 0.1372 1 7.98 0.1076 0.7513796 499s Homesize:sens1 0.4275 0.4275 1 1217.00 0.3352 0.5627339 499s sens2:Homesize:sens1 1.3512 1.3512 1 1216.99 1.0595 0.3035426 499s --- 499s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 499s > (ant3 <- anova(fm, type=3)) 499s Type III Analysis of Variance Table with Satterthwaite's method 499s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 499s sens2 21.5710 21.5710 1 8.02 16.9130 0.0033602 ** 499s Homesize 17.8570 17.8570 1 1217.01 14.0010 0.0001912 *** 499s sens1 0.6136 0.6136 1 8.03 0.4811 0.5074890 499s sens2:Homesize 1.5068 1.5068 1 1216.99 1.1814 0.2772780 499s sens2:sens1 0.0946 0.0946 1 8.02 0.0742 0.7922017 499s Homesize:sens1 0.4275 0.4275 1 1217.00 0.3352 0.5627339 499s sens2:Homesize:sens1 1.3512 1.3512 1 1216.99 1.0595 0.3035426 499s --- 499s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 499s > 499s > stopifnot( 499s + isTRUE(all.equal(ant2[,"F value"], 499s + c(16.4842, 14.0010, .526076, 1.18144, 499s + .107570, .335177, 1.05946), tolerance = TOL)), 499s + isTRUE(all.equal(ant3[,"F value"], 499s + c(16.9140, 14.0010,.481148, 1.18144, 499s + .074201, .335177, 1.05946), tolerance = TOL)) 499s + ) 499s > 499s > ################################################################################ 499s > 499s > 499s > 499s BEGIN TEST test_contest1D.R 499s 499s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 499s Copyright (C) 2025 The R Foundation for Statistical Computing 499s Platform: arm-unknown-linux-gnueabihf (32-bit) 499s 499s R is free software and comes with ABSOLUTELY NO WARRANTY. 499s You are welcome to redistribute it under certain conditions. 499s Type 'license()' or 'licence()' for distribution details. 499s 499s R is a collaborative project with many contributors. 499s Type 'contributors()' for more information and 499s 'citation()' on how to cite R or R packages in publications. 499s 499s Type 'demo()' for some demos, 'help()' for on-line help, or 499s 'help.start()' for an HTML browser interface to help. 499s Type 'q()' to quit R. 499s 499s > # test_contest1D.R 499s > library(lmerTest) 499s Loading required package: lme4 499s Loading required package: Matrix 501s 501s Attaching package: 'lmerTest' 501s 501s The following object is masked from 'package:lme4': 501s 501s lmer 501s 501s > 501s > # WRE says "using if(requireNamespace("pkgname")) is preferred, if possible." 501s > # even in tests: 501s > assertError <- function(expr, ...) 501s + if(requireNamespace("tools")) tools::assertError(expr, ...) else invisible() 501s > assertWarning <- function(expr, ...) 501s + if(requireNamespace("tools")) tools::assertWarning(expr, ...) else invisible() 501s > 501s > TOL <- 1e-4 501s > # Kenward-Roger only available with pbkrtest and only then validated in R >= 3.3.3 501s > # (faulty results for R < 3.3.3 may be due to unstated dependencies in pbkrtest) 501s > has_pbkrtest <- requireNamespace("pbkrtest", quietly = TRUE) && getRversion() >= "3.3.3" 501s The following object is masked from 'package:stats': 501s 501s step 501s 501s > 501s > data("sleepstudy", package="lme4") 501s > 501s > #################################### 501s > ## Tests of contest1D 501s > #################################### 501s > 501s > fm <- lmer(Reaction ~ Days + I(Days^2) + (1|Subject) + (0+Days|Subject), 501s + sleepstudy) 502s > # Basic tests: 502s > L <- c(0, 1, 0) 502s > contest1D(fm, L) 502s Estimate Std. Error df t value Pr(>|t|) 502s 1 7.434085 2.824283 114.9943 2.632203 0.00964808 502s > contest1D(fm, L, confint = TRUE) 502s Estimate Std. Error df t value lower upper Pr(>|t|) 502s 1 7.434085 2.824283 114.9943 2.632203 1.839722 13.02845 0.00964808 502s > contest1D(fm, L, confint = TRUE, level=0.99) 502s Estimate Std. Error df t value lower upper Pr(>|t|) 502s 1 7.434085 2.824283 114.9943 2.632203 0.03655396 14.83162 0.00964808 502s > if(has_pbkrtest) 502s + contest1D(fm, L, ddf="Kenward-Roger") 502s Estimate Std. Error df t value Pr(>|t|) 502s 1 7.434085 2.824283 115.5148 2.632203 0.009642692 502s > 502s > # Test too long L 502s > assertError(contest1D(fm, c(0, 1, 1, 1))) 502s > 502s > # Test too short L 502s > assertError(contest1D(fm, c(0, 1))) 502s > 502s > # Test matrix L 502s > contest1D(fm, matrix(L, nrow=1)) 502s Estimate Std. Error df t value Pr(>|t|) 502s 1 7.434085 2.824283 114.9943 2.632203 0.00964808 502s > contest1D(fm, matrix(L, ncol=1)) 502s Estimate Std. Error df t value Pr(>|t|) 502s 1 7.434085 2.824283 114.9943 2.632203 0.00964808 502s > assertError(contest1D(fm, matrix(c(0, 1), ncol=1))) 502s > assertError(contest1D(fm, matrix(c(0, 1, 0, 0), nrow=1))) 502s > L <- matrix(numeric(0L), ncol=3) 502s > assertError(contest1D(fm, L)) # "empty" matrix 502s > assertError(contest1D(fm, matrix(1, ncol=3, nrow=2))) 502s > 502s > # Test list L 502s > assertError(contest1D(fm, list(c(0, 1, 0)))) 502s > 502s > # Test equivalence to coef(summary(fm)): 502s > Lmat <- diag(length(fixef(fm))) 502s > (coef_mat <- lmerTest:::rbindall(lapply(1:ncol(Lmat), function(i) 502s + contest1D(fm, Lmat[i, ])))) 502s Estimate Std. Error df t value Pr(>|t|) 502s 1 255.4493728 7.5663677 26.22939 33.761163 3.810057e-23 502s 2 7.4340850 2.8242827 114.99433 2.632203 9.648080e-03 502s 3 0.3370223 0.2616475 144.63110 1.288078 1.997759e-01 502s > (coef_mat_lme4 <- coef(summary(fm, ddf="lme4"))) 502s Estimate Std. Error t value 502s (Intercept) 255.4493728 7.5663677 33.761163 502s Days 7.4340850 2.8242827 2.632203 502s I(Days^2) 0.3370223 0.2616475 1.288078 502s > rownames(coef_mat) <- rownames(coef_mat_lme4) 502s > stopifnot(isTRUE( 502s + all.equal(as.data.frame(coef_mat_lme4), 502s + coef_mat[, c("Estimate", "Std. Error", "t value")], tolerance=TOL) 502s + )) 502s > 502s > if(has_pbkrtest) { 502s + (coef_mat_KR <- lmerTest:::rbindall(lapply(1:ncol(Lmat), function(i) 502s + contest1D(fm, Lmat[i, ], ddf="Kenward-Roger")))) 502s + rownames(coef_mat_KR) <- rownames(coef_mat_lme4) 502s + stopifnot(isTRUE( 502s + all.equal(as.data.frame(coef_mat_lme4), 502s + coef_mat_KR[, c("Estimate", "Std. Error", "t value")], tolerance=TOL) 502s + )) 502s + } 502s > # Test of 0-length beta 502s > fm1 <- lmer(Reaction ~ 0 + (1|Subject) + (0+Days|Subject), 502s + sleepstudy) 502s > stopifnot(length(fixef(fm1)) == 0L) 502s > if(has_pbkrtest) { 502s + (ans <- contest1D(fm1, numeric(0L), ddf="Kenward-Roger")) 502s + stopifnot(nrow(ans) == 0L) 502s + } 502s > 502s > ## Test rhs argument: 502s > fm <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy) 502s > contest1D(fm, L=cbind(0, 1)) 502s Estimate Std. Error df t value Pr(>|t|) 502s 1 10.46729 1.54579 16.99998 6.771481 3.263824e-06 502s > contest1D(fm, L=cbind(0, 1), rhs=10) 502s Estimate Std. Error df t value Pr(>|t|) 502s 1 10.46729 1.54579 16.99998 0.302296 0.7660937 502s > if(has_pbkrtest) { 502s + contest1D(fm, L=cbind(0, 1), ddf="Kenward-Roger") 502s + contest1D(fm, L=cbind(0, 1), ddf="Kenward-Roger", rhs=10) 502s + } 503s Estimate Std. Error df t value Pr(>|t|) 503s 1 10.46729 1.54579 17 0.302296 0.7660937 503s > 503s > contest1D(fm, L=c(0, 1), rhs = 10.467) 503s Estimate Std. Error df t value Pr(>|t|) 503s 1 10.46729 1.54579 16.99998 0.0001849926 0.9998546 503s > 503s > (ct1 <- contest1D(fm, L=cbind(c(0, 1)), rhs = 10)) 503s Estimate Std. Error df t value Pr(>|t|) 503s 1 10.46729 1.54579 16.99998 0.302296 0.7660937 503s > (ct2 <- contestMD(fm, L=rbind(c(0, 1)), rhs = 10)) 503s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 503s 1 59.85028 59.85028 1 16.99998 0.09138285 0.7660937 503s > stopifnot( 503s + isTRUE(all.equal(ct1[, "t value"]^2, ct2[, "F value"], tolerance=1e-6)) 503s + ) 503s > 503s > ## Test 'lmerMod' method: 503s > fm <- lme4::lmer(Reaction ~ Days + I(Days^2) + (1|Subject) + (0+Days|Subject), 503s + sleepstudy) 503s > # Basic tests: 503s > L <- c(0, 1, 0) 503s > contest1D(fm, L) 503s Estimate Std. Error df t value Pr(>|t|) 503s 1 7.434085 2.824283 114.9943 2.632203 0.00964808 503s > contest1D(fm, L, confint = TRUE) 503s Estimate Std. Error df t value lower upper Pr(>|t|) 503s 1 7.434085 2.824283 114.9943 2.632203 1.839722 13.02845 0.00964808 503s > contest1D(fm, L, confint = TRUE, level=0.99) 503s Estimate Std. Error df t value lower upper Pr(>|t|) 503s 1 7.434085 2.824283 114.9943 2.632203 0.03655396 14.83162 0.00964808 503s > if(has_pbkrtest) 503s + contest1D(fm, L, ddf="Kenward-Roger") 503s Estimate Std. Error df t value Pr(>|t|) 503s 1 7.434085 2.824283 115.5148 2.632203 0.009642692 503s > 503s > 503s BEGIN TEST test_contestMD.R 503s 503s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 503s Copyright (C) 2025 The R Foundation for Statistical Computing 503s Platform: arm-unknown-linux-gnueabihf (32-bit) 503s 503s R is free software and comes with ABSOLUTELY NO WARRANTY. 503s You are welcome to redistribute it under certain conditions. 503s Type 'license()' or 'licence()' for distribution details. 503s 503s R is a collaborative project with many contributors. 503s Type 'contributors()' for more information and 503s 'citation()' on how to cite R or R packages in publications. 503s 503s Type 'demo()' for some demos, 'help()' for on-line help, or 503s 'help.start()' for an HTML browser interface to help. 503s Type 'q()' to quit R. 503s 503s Loading required package: lme4 503s > # test_contestMD.R 503s > library(lmerTest) 503s Loading required package: Matrix 505s 505s Attaching package: 'lmerTest' 505s 505s The following object is masked from 'package:lme4': 505s 505s lmer 505s 505s The following object is masked from 'package:stats': 505s 505s step 505s 505s > 505s > # WRE says "using if(requireNamespace("pkgname")) is preferred, if possible." 505s > # even in tests: 505s > assertError <- function(expr, ...) 505s + if(requireNamespace("tools")) tools::assertError(expr, ...) else invisible() 505s > assertWarning <- function(expr, ...) 505s + if(requireNamespace("tools")) tools::assertWarning(expr, ...) else invisible() 505s > 505s > # Kenward-Roger only available with pbkrtest and only then validated in R >= 3.3.3 505s > # (faulty results for R < 3.3.3 may be due to unstated dependencies in pbkrtest) 505s > has_pbkrtest <- requireNamespace("pbkrtest", quietly = TRUE) && getRversion() >= "3.3.3" 506s > 506s > data("sleepstudy", package="lme4") 506s > 506s > #################################### 506s > ## Tests of contestMD 506s > #################################### 506s > 506s > fm <- lmer(Reaction ~ Days + I(Days^2) + (1|Subject) + (0+Days|Subject), 506s + sleepstudy) 506s > # Basic tests: 506s > L <- diag(3L) 506s > contestMD(fm, L) 506s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 506s 1 990089.3 330029.8 3 42.15441 507.24 4.351211e-33 506s > 506s > # Tests of ddf arg: 506s > contestMD(fm, L, ddf="Sat") 506s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 506s 1 990089.3 330029.8 3 42.15441 507.24 4.351211e-33 506s > if(has_pbkrtest) 506s + contestMD(fm, L, ddf="Kenward-Roger") 506s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 506s 1 990089.3 330029.8 3 38.84733 490.1937 6.706733e-31 506s > assertError(contestMD(fm, L, ddf="sat")) # Invalid ddf arg. 506s > 506s > # Tests of simple 2-df test: 506s > (ans <- contestMD(fm, L[2:3, ], ddf="Sat")) 506s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 506s 1 30399.15 15199.57 2 54.40752 23.36102 4.744897e-08 506s > stopifnot(nrow(ans) == 1L, 506s + ans$NumDF == 2L) 506s > if(has_pbkrtest) { 506s + (ans <- contestMD(fm, L[2:3, ], ddf="Kenward-Roger")) 506s + stopifnot(nrow(ans) == 1L, 506s + ans$NumDF == 2L) 506s + } 506s > 506s > # Tests of simple 1-df test: 506s > (ans <- contestMD(fm, L[3, , drop=FALSE], ddf="Sat")) 506s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 506s 1 1079.503 1079.503 1 144.6311 1.659144 0.1997759 506s > stopifnot(nrow(ans) == 1L, 506s + ans$NumDF == 1L) 506s > if(has_pbkrtest) { 506s + (ans <- contestMD(fm, L[3, , drop=FALSE], ddf="Kenward-Roger")) 506s + stopifnot(nrow(ans) == 1L, 506s + ans$NumDF == 1L) 506s + } 506s > 506s > # Test of vector input: 506s > (ans <- contestMD(fm, L[3, ], ddf="Sat")) # OK since length(L[3, ]) == length(fixef(fm)) 506s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 506s 1 1079.503 1079.503 1 144.6311 1.659144 0.1997759 506s > stopifnot(nrow(ans) == 1L, 506s + ans$NumDF == 1L) 506s > assertError(contestMD(fm, c(1, 0))) # L is too short 506s > assertError(contestMD(fm, c(1, 0, 1, 1))) # L is too long 506s > 506s > # Test of list input: 506s > assertError(contestMD(fm, list(L[3, , drop=FALSE]), ddf="Sat")) # Need L to be a matrix 506s > 506s > # zero-row L's are allowed (if ncol(L) is correct): 506s > ans1 <- contestMD(fm, L[0, , drop=FALSE], ddf="Sat") 506s > stopifnot(nrow(ans1) == 0L) 506s > if(has_pbkrtest) { 506s + ans2 <- contestMD(fm, L[0, , drop=FALSE], ddf="Kenward-Roger") 506s + stopifnot(nrow(ans2) == 0L) 506s + } 506s > 506s > # Test wrong ncol(L): 506s > assertError(contestMD(fm, L[2:3, 2:3])) # need ncol(L) == length(fixef(fm)) 506s > 506s > # row-rank deficient L are allowed: 506s > L <- rbind(c(1, 0, 1), 506s + c(0, 1, 0), 506s + c(1, -1, 1)) 506s > ans <- contestMD(fm, L) 506s > stopifnot(nrow(L) == 3L, 506s + qr(L)$rank == 2, 506s + ans$NumDF == 2) 506s > if(has_pbkrtest) { 506s + ans_KR <- contestMD(fm, L, ddf="Kenward-Roger") 506s + stopifnot(ans_KR$NumDF == 2) 506s + } 506s > 506s > # Test of 0-length beta 506s > fm1 <- lmer(Reaction ~ 0 + (1|Subject) + (0+Days|Subject), 506s + sleepstudy) 506s > stopifnot(length(fixef(fm1)) == 0L) 506s > L <- numeric(0L) 506s > (ans <- contestMD(fm1, L)) 506s [1] Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 506s <0 rows> (or 0-length row.names) 506s > stopifnot(nrow(ans) == 0L) 506s > L <- matrix(numeric(0L), ncol=0L) 506s > (ans <- contestMD(fm1, L)) 506s [1] Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 506s <0 rows> (or 0-length row.names) 506s > stopifnot(nrow(ans) == 0L) 506s > 506s > 506s > ## rhs argument: 506s > data("cake", package="lme4") 506s > model <- lmer(angle ~ recipe * temp + (1|recipe:replicate), cake) 507s > (L <- diag(length(fixef(model)))[2:3, ]) 507s [,1] [,2] [,3] [,4] [,5] [,6] 507s [1,] 0 1 0 0 0 0 507s [2,] 0 0 1 0 0 0 507s > (an <- anova(model, type="marginal")) 507s Marginal Analysis of Variance Table with Satterthwaite's method 507s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 507s recipe 4.00 2.00 2 254.02 0.0957 0.9088 507s temp 620.24 620.24 1 222.00 29.6961 1.339e-07 *** 507s recipe:temp 1.74 0.87 2 222.00 0.0417 0.9592 507s --- 507s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 507s > 507s > ct <- contestMD(model, L, rhs = 0) 507s > ct2 <- contestMD(model, L, rhs = c(2, 2)) 507s > stopifnot( 507s + isTRUE(all.equal(ct[1, ], an[1, ], check.attributes=FALSE, tolerance=1e-6)), 507s + ct[, "F value"] < ct2[, "F value"] 507s + ) 507s > 507s > L2 <- rbind(L, L[1, ] + L[2, ]) # rank deficient! 507s > contestMD(model, L2, rhs = c(0, 0, 0)) # no warning 507s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 507s 1 3.996684 1.998342 2 254.0158 0.09567796 0.9087894 507s > assertWarning(contestMD(model, L2, rhs = c(2, 2, 2))) # warning since L2 is rank def. 507s > if(has_pbkrtest) 507s + assertWarning(contestMD(model, L2, rhs = c(2, 2, 2), ddf="Kenward-Roger")) 507s > 507s > fm <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy) 507s > contestMD(fm, L=cbind(0, 1)) 507s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 507s 1 30030.94 30030.94 1 16.99998 45.85296 3.263824e-06 507s > contestMD(fm, L=cbind(0, 1), rhs=10) 507s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 507s 1 59.85028 59.85028 1 16.99998 0.09138285 0.7660937 507s > if(has_pbkrtest) { 507s + contestMD(fm, L=cbind(0, 1), ddf="Kenward-Roger") 507s + contestMD(fm, L=cbind(0, 1), ddf="Kenward-Roger", rhs=10) 507s + } 507s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 507s 1 59.85028 59.85028 1 17 0.09138285 0.7660937 507s > 507s > 507s > ## Test 'lmerMod' method: 507s > fm <- lme4::lmer(Reaction ~ Days + (Days|Subject), sleepstudy) 507s > contestMD(fm, L=cbind(0, 1)) 507s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 507s 1 30030.94 30030.94 1 16.99998 45.85296 3.263824e-06 507s > contestMD(fm, L=cbind(0, 1), rhs=10) 507s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 507s 1 59.85028 59.85028 1 16.99998 0.09138285 0.7660937 507s > if(has_pbkrtest) { 507s + contestMD(fm, L=cbind(0, 1), ddf="Kenward-Roger") 507s + contestMD(fm, L=cbind(0, 1), ddf="Kenward-Roger", rhs=10) 507s + } 507s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 507s 1 59.85028 59.85028 1 17 0.09138285 0.7660937 507s > 507s BEGIN TEST test_contrast_utils.R 507s 507s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 507s Copyright (C) 2025 The R Foundation for Statistical Computing 507s Platform: arm-unknown-linux-gnueabihf (32-bit) 507s 507s R is free software and comes with ABSOLUTELY NO WARRANTY. 507s You are welcome to redistribute it under certain conditions. 507s Type 'license()' or 'licence()' for distribution details. 507s 507s R is a collaborative project with many contributors. 507s Type 'contributors()' for more information and 507s 'citation()' on how to cite R or R packages in publications. 507s 507s Type 'demo()' for some demos, 'help()' for on-line help, or 507s 'help.start()' for an HTML browser interface to help. 507s Type 'q()' to quit R. 507s 507s > # test_contrast_utils.R 507s > 507s > library(lmerTest) 507s Loading required package: lme4 508s Loading required package: Matrix 510s 510s Attaching package: 'lmerTest' 510s 510s The following object is masked from 'package:lme4': 510s 510s lmer 510s 510s The following object is masked from 'package:stats': 510s 510s step 510s 510s > 510s > ########## 510s > # Test that a message is printed if some cells have zero data: 510s > # Missing a single cell: 510s > data("cake", package="lme4") 510s > cake4 <- cake 510s > cake4$temperature <- factor(cake4$temperature, ordered=FALSE) 510s > cake4 <- droplevels(subset(cake4, !(recipe == "A" & temperature == "175") )) 510s > with(cake4, table(recipe, temperature)) 510s temperature 510s recipe 175 185 195 205 215 225 510s A 0 15 15 15 15 15 510s B 15 15 15 15 15 15 510s C 15 15 15 15 15 15 510s > 510s > fm1 <- lmer(angle ~ recipe * temperature + (1|recipe:replicate), cake4) 510s fixed-effect model matrix is rank deficient so dropping 1 column / coefficient 510s > an <- anova(fm1) 510s Missing cells for: recipeA:temperature175. 510s Interpret type III hypotheses with care. 510s > txt <- capture.output(an <- anova(fm1), type = "message") 510s > stopifnot(length(grep("Missing cells for:", txt)) > 0, 510s + length(grep("Interpret type III hypotheses with care.", txt)) > 0) 510s > 510s > ########## 510s > # Test that a message is printed if some cells have zero data: 510s > # Missing diagonal: 510s > cake4 <- cake 510s > cake4$temperature <- factor(cake4$temperature, ordered=FALSE) 510s > cake4 <- droplevels(subset(cake4, temperature %in% levels(cake4$temperature)[1:3])) 510s > cake4 <- droplevels(subset(cake4, !((recipe == "A" & temperature == "175") | 510s + (recipe == "B" & temperature == "185") | 510s + (recipe == "C" & temperature == "195") ))) 510s > cake4$temp0 <- cake4$temp - mean(cake4$temp) 510s > with(cake4, table(recipe, temperature)) 510s temperature 510s recipe 175 185 195 510s A 0 15 15 510s B 15 0 15 510s C 15 15 0 510s > 510s > fm1 <- lmer(angle ~ recipe * temperature + (1|recipe:replicate), cake4) 510s fixed-effect model matrix is rank deficient so dropping 3 columns / coefficients 510s > an <- anova(fm1) 510s Missing cells for: recipeA:temperature175, recipeB:temperature185, recipeC:temperature195. 510s Interpret type III hypotheses with care. 510s > txt <- capture.output(an <- anova(fm1), type = "message") 510s > stopifnot(length(grep("Missing cells for:", txt)) > 0, 510s + length(grep("Interpret type III hypotheses with care.", txt)) > 0) 510s > 510s > ########## 510s > # Test that a message is NOT printed with centered covariates: 510s > fm1 <- lmer(angle ~ recipe * temp0 + (1|recipe:replicate), cake4) 510s > an <- anova(fm1) 510s > txt <- capture.output(an <- anova(fm1), type = "message") 510s > stopifnot(length(grep("Missing cells for:", txt)) == 0, 510s + length(grep("Interpret type III hypotheses with care.", txt)) == 0) 510s > # Note: in many cases a message would not be printed anyway because the 510s > # columns sums in the rdX design matrix would not be exactly zero but just a 510s > # small number very close to zero. 510s > 510s > 510s > 510s > 510s BEGIN TEST test_devfun_vp.R 510s 510s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 510s Copyright (C) 2025 The R Foundation for Statistical Computing 510s Platform: arm-unknown-linux-gnueabihf (32-bit) 510s 510s R is free software and comes with ABSOLUTELY NO WARRANTY. 510s You are welcome to redistribute it under certain conditions. 510s Type 'license()' or 'licence()' for distribution details. 510s 510s R is a collaborative project with many contributors. 510s Type 'contributors()' for more information and 510s 'citation()' on how to cite R or R packages in publications. 510s 510s Type 'demo()' for some demos, 'help()' for on-line help, or 510s 'help.start()' for an HTML browser interface to help. 510s Type 'q()' to quit R. 510s 510s > # test_devfun_vp.R 510s > 510s > # library(devtools) 510s > # # has_devel() 510s > # r2path <- "~/GitHub/lmerTestR/lmerTest" 510s > # # document(pkg=r2path) 510s > # load_all(r2path) 510s > # 510s > # # ?`Covariance-class` 510s > 510s > library(lmerTest) 510s Loading required package: lme4 510s Loading required package: Matrix 513s 513s Attaching package: 'lmerTest' 513s 513s The following object is masked from 'package:lme4': 513s 513s lmer 513s 513s The following object is masked from 'package:stats': 513s 513s step 513s 513s > 513s > has_pkgs <- requireNamespace("utils", quietly = TRUE) && 513s + requireNamespace("numDeriv", quietly = TRUE) && 513s + requireNamespace("lme4", quietly = TRUE) 513s > is_lme4_2_0_0 <- utils::packageVersion("lme4") >= "2.0.0" 513s > 513s > if(has_pkgs && is_lme4_2_0_0) { 513s + ## Functions: 513s + devfun_vp <- lmerTest:::devfun_vp 513s + getOptPar <- lmerTest:::getOptPar 513s + getVarPar <- lmerTest:::getVarPar 513s + 513s + ## Unstructured 513s + fm1.us <- lme4::lmer(Reaction ~ Days + us(Days | Subject), sleepstudy) 513s + ## Diagional 513s + fm1.diag <- lme4::lmer(Reaction ~ Days + diag(Days | Subject), sleepstudy) 513s + fm1.diag.hom <- lme4::lmer(Reaction ~ Days + diag(Days | Subject, hom = TRUE), 513s + sleepstudy) 513s + ## Compound symmetry 513s + fm1.cs <- lme4::lmer(Reaction ~ Days + cs(Days | Subject), sleepstudy) 513s + fm1.cs.hom <- lme4::lmer(Reaction ~ Days + cs(Days | Subject, hom = TRUE), 513s + sleepstudy) 513s + ## Auto-regressive order 1 513s + sleepstudy$Daysf <- factor(sleepstudy$Days, ordered = TRUE) 513s + fm1.ar1 <- lme4::lmer(Reaction ~ Daysf + ar1(0 + Daysf | Subject, hom = TRUE), 513s + sleepstudy, REML = TRUE) 513s + 513s + lme4models <- namedList(fm1.us, 513s + fm1.diag, 513s + fm1.diag.hom, 513s + fm1.cs, 513s + fm1.cs.hom, 513s + fm1.ar1) 513s + 513s + for(model in lme4models) { # model <- lme4models[[1]] 513s + ## Native devfun: 513s + devfun <- update(model, devFunOnly=TRUE) 513s + ## Evaluate native devfun at optimum: 513s + devfun(getOptPar(model)) 513s + ## Check that devfun returns the same value as that saved in the model object: 513s + stopifnot( 513s + all.equal(unname(getME(model, "devcomp")$cmp["REML"]), 513s + devfun(getOptPar(model)), tolerance=1e-6) # TRUE 513s + ) 513s + ## Get varpar (including residual SD): 513s + (varpar <- getVarPar(model)) 513s + ## Evaluate devfun_vp at the optimum: 513s + devfun_vp(varpar, devfun, reml=TRUE) 513s + ## Check that devfun_vp returns the same value as native devfun: 513s + stopifnot( 513s + all.equal(unname(getME(model, "devcomp")$cmp["REML"]), 513s + devfun(getOptPar(model))) # TRUE 513s + ) 513s + } 513s + 513s + ## Here we also want to check that devfun and and devfun_vp returns the same 513s + ## value at non-optimum values of varpar. 513s + ## Because sigma is profiled out of devfun this cannot be done right away. 513s + ## We need to optimize over all parameters to get equivalence. 513s + ## We should be able to set one of the parameters in common to a 513s + ## particular value and optimize the rest. This will build confidence that 513s + ## the likelihood in devfun_vp is the same as that returned by 513s + ## lme4::lmer(., devFunOnly=TRUE). 513s + 513s + do_trace <- 0 513s + for(i in seq_along(lme4models)) { # i <- 4 513s + if(do_trace) print(i) 513s + model <- lme4models[[i]] 513s + devfun <- update(model, devFunOnly=TRUE) 513s + (optpar <- getOptPar(model)) 513s + (varpar <- getVarPar(model)) 513s + (optpar2 <- optpar * 1.1) 513s + (varpar2 <- c(optpar2, varpar[length(varpar)])) 513s + 513s + ## Evaluate gradients to ensure that devfun and devfun_vp are both 513s + ## functions with optima at optpar and varpar respectively: 513s + (g_devfun <- numDeriv::grad(devfun, optpar)) 513s + (g_devfun_vp <- numDeriv::grad(devfun_vp, varpar, devfun=devfun, reml=TRUE)) 513s + stopifnot( 513s + if(i != 4) all(abs(g_devfun) < 1e-3) else all(abs(g_devfun) < 1e-2), 513s + if(i != 4) all(abs(g_devfun_vp) < 1e-3) else all(abs(g_devfun_vp) < 1e-2) 513s + ) 513s + ## These are not zero as expected: 513s + (g_devfun <- numDeriv::grad(devfun, optpar2)) 513s + (g_devfun_vp <- numDeriv::grad(devfun_vp, varpar2, devfun=devfun, reml=TRUE)) 513s + ## Try optimizing devfun_vp: 513s + x <- nlminb(start=varpar2, objective = devfun_vp, devfun=devfun, reml=TRUE, 513s + control=list(trace=do_trace)) 513s + ## Check that the optimum is re-achieved: 513s + stopifnot( 513s + all(abs(varpar - x$par) < 1e-4), 513s + abs(devfun_vp(varpar, devfun=devfun, reml=TRUE) - 513s + devfun_vp(x$par, devfun=devfun, reml=TRUE)) < 1e-6 513s + ) 513s + 513s + ## Optimize devfun and devfun_vp over all but one of the parameters in turn to 513s + ## check that devfun and devfun_vp gives the same deviance and parameter values 513s + ## for settings away from the REML optimum. This is to build confidence that 513s + ## devfun_vp is a valid implementation of the deviance function from LLMs. 513s + if(length(optpar) > 1) for(j in seq_along(optpar)) { # j <- 1 513s + ## Check that all parameters are within bounds: 513s + stopifnot( 513s + model@lower < optpar, 513s + optpar < attr(model, "upper"), 513s + model@lower < optpar2, 513s + optpar2 < attr(model, "upper") 513s + ) 513s + ## Evaluate deviance function at optimum (for safety): 513s + devfun(optpar) 513s + ## Optimize devfun over all but the j'th parameter: 513s + (startpar <- optpar[-j]) 513s + res <- nlminb(start=startpar, objective = function(p) { 513s + (Par <- optpar2) 513s + (Par[-j] <- p) 513s + devfun(Par) 513s + }, control = list(trace=do_trace), 513s + lower = model@lower[-j], 513s + upper = attr(model, "upper")[-j]) 513s + ## Evaluate devfun_vp: 513s + devfun_vp(varpar, devfun=devfun, reml=TRUE) 513s + ## Optimize devfun_vp over all but the j'th parameter: 513s + (startpar_vp <- varpar[-j]) 513s + (np <- length(startpar_vp)) 513s + res_vp <- nlminb(start=startpar_vp, objective = function(p) { 513s + (Par <- optpar2) 513s + (Par[-j] <- p[-np]) 513s + Par <- c(Par, p[np]) 513s + devfun_vp(Par, devfun=devfun, reml=TRUE) 513s + }, control = list(trace=do_trace), 513s + lower = c(model@lower[-j], 0), 513s + upper = c(attr(model, "upper")[-j], Inf)) 513s + ## Compare parameter estimates (except for sigma): 513s + res$objective - res_vp$objective 513s + res$par - res_vp$par[seq_along(res$par)] 513s + ## Check that parameter estimates and deviance values agree: 513s + stopifnot( 513s + abs(res$objective - res_vp$objective) < 1e-8, 513s + all(abs(res$par - res_vp$par[seq_along(res$par)]) < 1e-4) 513s + ) 513s + } 513s + } 513s + 513s + } 513s > 513s > 513s > 513s BEGIN TEST test_drop1.R 513s 513s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 513s Copyright (C) 2025 The R Foundation for Statistical Computing 513s Platform: arm-unknown-linux-gnueabihf (32-bit) 513s 513s R is free software and comes with ABSOLUTELY NO WARRANTY. 513s You are welcome to redistribute it under certain conditions. 513s Type 'license()' or 'licence()' for distribution details. 513s 513s R is a collaborative project with many contributors. 513s Type 'contributors()' for more information and 513s 'citation()' on how to cite R or R packages in publications. 513s 513s Type 'demo()' for some demos, 'help()' for on-line help, or 513s 'help.start()' for an HTML browser interface to help. 513s Type 'q()' to quit R. 513s 513s > # test_drop1.R 513s > 513s > library(lmerTest) 513s Loading required package: lme4 513s Loading required package: Matrix 516s 516s Attaching package: 'lmerTest' 516s 516s The following object is masked from 'package:lme4': 516s 516s lmer 516s 516s > 516s > # WRE says "using if(requireNamespace("pkgname")) is preferred, if possible." 516s > # even in tests: 516s > assertError <- function(expr, ...) 516s + if(requireNamespace("tools")) tools::assertError(expr, ...) else invisible() 516s > assertWarning <- function(expr, ...) 516s + if(requireNamespace("tools")) tools::assertWarning(expr, ...) else invisible() 516s > 516s > TOL <- 1e-4 516s > # Kenward-Roger only available with pbkrtest and only then validated in R >= 3.3.3 516s > # (faulty results for R < 3.3.3 may be due to unstated dependencies in pbkrtest) 516s > has_pbkrtest <- requireNamespace("pbkrtest", quietly = TRUE) && getRversion() >= "3.3.3" 516s The following object is masked from 'package:stats': 516s 516s step 516s 516s > 516s > data("sleepstudy", package="lme4") 516s > 516s > ######### Basic usage 516s > 516s > data("cake", package="lme4") 516s > cake2 <- cake 516s > cake2$temperature <- factor(cake2$temperature, ordered = FALSE) 516s > fm <- lmer(angle ~ recipe + temperature + (1|recipe:replicate), cake2) 516s > (an1 <- drop1(fm)) 516s Single term deletions using Satterthwaite's method: 516s 516s Model: 516s angle ~ recipe + temperature + (1 | recipe:replicate) 516s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 516s recipe 10.19 5.09 2 42 0.2488 0.7809 516s temperature 2100.30 420.06 5 220 20.5141 <2e-16 *** 516s --- 516s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 516s > (an2 <- drop1(fm, force_get_contrasts = TRUE)) 516s Single term deletions using Satterthwaite's method: 516s 516s Model: 516s angle ~ recipe + temperature + (1 | recipe:replicate) 516s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 516s recipe 10.19 5.09 2 42 0.2488 0.7809 516s temperature 2100.30 420.06 5 220 20.5141 <2e-16 *** 516s --- 516s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 516s > drop1(fm, ddf="lme4", test="Chi") 516s Single term deletions 516s 516s Model: 516s angle ~ recipe + temperature + (1 | recipe:replicate) 516s npar AIC LRT Pr(Chi) 516s 1709.6 516s recipe 2 1706.1 0.530 0.7672 516s temperature 5 1785.7 86.106 <2e-16 *** 516s --- 516s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 516s > if(has_pbkrtest) 516s + drop1(fm, ddf="Kenward-Roger") 516s Single term deletions using Kenward-Roger's method: 516s 516s Model: 516s angle ~ recipe + temperature + (1 | recipe:replicate) 516s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 516s recipe 10.19 5.09 2 42 0.2488 0.7809 516s temperature 2100.30 420.06 5 220 20.5141 <2e-16 *** 516s --- 516s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 516s > 516s > tests1 <- show_tests(an1) 516s > tests2 <- show_tests(an2) 516s > 516s > stopifnot( 516s + # Tests are the same: 516s + isTRUE(all.equal(an1, an2, check.attributes = FALSE, tolerance=TOL)), 516s + # But contrast matrices are not: 516s + all(!mapply(function(x, y) isTRUE(all.equal(x, y)), tests1, tests2)) 516s + ) 516s > 516s > fm <- lmer(angle ~ recipe * temperature + (1|recipe:replicate), cake2) 517s > drop1(fm) 517s Single term deletions using Satterthwaite's method: 517s 517s Model: 517s angle ~ recipe * temperature + (1 | recipe:replicate) 517s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 517s recipe:temperature 205.98 20.598 10 210 1.0062 0.4393 517s > drop1(fm, ddf="lme4") 517s Single term deletions 517s 517s Model: 517s angle ~ recipe * temperature + (1 | recipe:replicate) 517s npar AIC 517s 1719.0 517s recipe:temperature 10 1709.6 517s > if(has_pbkrtest) 517s + drop1(fm, ddf="Kenward-Roger") 517s Single term deletions using Kenward-Roger's method: 517s 517s Model: 517s angle ~ recipe * temperature + (1 | recipe:replicate) 517s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 517s recipe:temperature 205.98 20.598 10 210 1.0062 0.4393 517s > 517s > # Incorrect arguments: 517s > assertError(drop1(fm, scope="recipe")) # Correct Error 517s > assertError(drop1(fm, scope=3)) # Correct Error 517s > assertError(drop1(fm, scope=list("recipe"))) # Correct Error 517s > 517s > # Polynomial terms: 517s > 517s > fm <- lmer(Reaction ~ 0 + (Days|Subject), sleepstudy) 517s > (an0 <- drop1(fm)) # No fixef! 517s Single term deletions using Satterthwaite's method: 517s 517s Model: 517s Reaction ~ 0 + (Days | Subject) 517s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 517s > fm <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy) 517s > (an1 <- drop1(fm)) 517s Single term deletions using Satterthwaite's method: 517s 517s Model: 517s Reaction ~ Days + (Days | Subject) 517s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 517s Days 30031 30031 1 17 45.853 3.264e-06 *** 517s --- 517s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 517s > fm <- lmer(Reaction ~ Days + I(Days^2) + (Days|Subject), sleepstudy) 517s > (an2 <- (drop1(fm))) 517s Single term deletions using Satterthwaite's method: 517s 517s Model: 517s Reaction ~ Days + I(Days^2) + (Days | Subject) 517s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 517s Days 4534.5 4534.5 1 114.43 6.9551 0.00952 ** 517s I(Days^2) 1079.5 1079.5 1 143.00 1.6558 0.20026 517s --- 517s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 517s > fm <- lmer(Reaction ~ poly(Days, 2) + (Days|Subject), sleepstudy) 517s > (an3 <- drop1(fm)) 517s Single term deletions using Satterthwaite's method: 517s 517s Model: 517s Reaction ~ poly(Days, 2) + (Days | Subject) 517s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 517s poly(Days, 2) 30974 15487 2 29.115 23.754 7.625e-07 *** 517s --- 517s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 517s > stopifnot( 517s + nrow(an0) == 0L, 517s + nrow(an1) == 1L, 517s + nrow(an2) == 2L, 517s + nrow(an3) == 1L 517s + ) 517s > 517s > # Consider a rank-deficient design matrix: 517s > fm <- lmer(angle ~ recipe + temp + temperature + (1|recipe:replicate), cake) 517s fixed-effect model matrix is rank deficient so dropping 1 column / coefficient 517s > # Here temp accounts for the linear effect of temperature, and 517s > # temperature is an (ordered) factor that accounts for the remaining 517s > # variation between temperatures (4 df). 517s > (an4 <- drop1(fm)) 517s Single term deletions using Satterthwaite's method: 517s 517s Model: 517s angle ~ recipe + temp + temperature + (1 | recipe:replicate) 517s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 517s recipe 10.189 5.094 2 42 0.2488 0.7809 517s temp 517s temperature 133.595 33.399 4 220 1.6311 0.1674 517s > # While temperature is in the model, we cannot test the effect of dropping 517s > # temp. After removing temperature we can test the effect of dropping temp: 517s > (an5 <- drop1(update(fm, ~.-temperature))) 517s Single term deletions using Satterthwaite's method: 517s 517s Model: 517s angle ~ recipe + temp + (1 | recipe:replicate) 517s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 517s recipe 10.3 5.15 2 42 0.2488 0.7809 517s temp 1966.7 1966.71 1 224 94.9759 <2e-16 *** 517s --- 517s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 517s > 517s > stopifnot( 517s + nrow(an4) == 3, 517s + rownames(an4)[2] == "temp", 517s + all(is.na(an4[2, ])), 517s + all(!is.na(an4[-2, ])), 517s + all(rownames(an5) == c("recipe", "temp")) 517s + ) 517s > 517s > 517s > 517s > 517s BEGIN TEST test_legacy.R 517s 517s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 517s Copyright (C) 2025 The R Foundation for Statistical Computing 517s Platform: arm-unknown-linux-gnueabihf (32-bit) 517s 517s R is free software and comes with ABSOLUTELY NO WARRANTY. 517s You are welcome to redistribute it under certain conditions. 517s Type 'license()' or 'licence()' for distribution details. 517s 517s R is a collaborative project with many contributors. 517s Type 'contributors()' for more information and 517s 'citation()' on how to cite R or R packages in publications. 517s 517s Type 'demo()' for some demos, 'help()' for on-line help, or 517s 'help.start()' for an HTML browser interface to help. 517s Type 'q()' to quit R. 517s 517s > # test_legacy.R 517s > library(lmerTest) 517s Loading required package: lme4 517s Loading required package: Matrix 520s 520s Attaching package: 'lmerTest' 520s 520s The following object is masked from 'package:lme4': 520s 520s lmer 520s 520s > TOL <- 1e-4 520s > ##################################################################### 520s > 520s > # Read in data set 520s > load(system.file("testdata", "legacy_fits.RData", package="lmerTest")) 520s The following object is masked from 'package:stats': 520s 520s step 520s 520s > # Generated with the following code using lmerTest version 2.0-37.9002 520s > # 520s > # library("lmerTest") 520s > # packageVersion("lmerTest") 520s > # fm1 <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy) 520s > # (an1 <- anova(fm1)) 520s > # (sfm1 <- summary(fm1)) 520s > # 520s > # fm2 <- lmer(Informed.liking ~ Product + Information + Gender + 520s > # (1|Product:Consumer) , data=ham) 520s > # (an2 <- anova(fm2)) 520s > # (sfm2 <- summary(fm2)) 520s > # 520s > # save(fm1, an1, sfm1, fm2, an2, sfm2, 520s > # file="~/GitHub/lmerTestR/package/inst/testdata/legacy_fits.RData") 520s > 520s > 520s > ####################################### 520s > ### Check that arguments for merModLmerTest and lmerModLmerTest methods match up: 520s > 520s > stopifnot( 520s + isTRUE(all.equal(formals(lmerTest:::anova.merModLmerTest), 520s + formals(lmerTest:::anova.lmerModLmerTest))), 520s + isTRUE(all.equal(formals(lmerTest:::summary.merModLmerTest), 520s + formals(lmerTest:::summary.lmerModLmerTest))), 520s + isTRUE(all.equal(formals(lmerTest:::drop1.merModLmerTest), 520s + formals(lmerTest:::drop1.lmerModLmerTest))), 520s + isTRUE(all.equal(formals(lmerTest:::step.merModLmerTest), 520s + formals(lmerTest:::step.lmerModLmerTest))), 520s + isTRUE(all.equal(formals(lmerTest:::ls_means.merModLmerTest), 520s + formals(lmerTest:::ls_means.lmerModLmerTest))), 520s + isTRUE(all.equal(formals(lmerTest:::difflsmeans.merModLmerTest), 520s + formals(lmerTest:::difflsmeans.lmerModLmerTest)))) 520s > 520s > 520s > ####################################### 520s > ## Tests for fm1: 520s > 520s > (an1new <- anova(fm1)) 520s Type III Analysis of Variance Table with Satterthwaite's method 520s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 520s Days 30031 30031 1 17 45.853 3.264e-06 *** 520s --- 520s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 520s > (sfm1new <- summary(fm1)) 520s Linear mixed model fit by REML. t-tests use Satterthwaite's method [ 520s lmerModLmerTest] 520s Formula: Reaction ~ Days + (Days | Subject) 520s Data: sleepstudy 520s 520s REML criterion at convergence: 1743.6 520s 520s Scaled residuals: 520s Min 1Q Median 3Q Max 520s -3.9536 -0.4634 0.0231 0.4634 5.1793 520s 520s Random effects: 520s Groups Name Variance Std.Dev. Corr 520s Subject (Intercept) 612.09 24.740 520s Days 35.07 5.922 0.07 520s Residual 654.94 25.592 520s Number of obs: 180, groups: Subject, 18 520s 520s Fixed effects: 520s Estimate Std. Error df t value Pr(>|t|) 520s (Intercept) 251.405 6.825 17.000 36.838 < 2e-16 *** 520s Days 10.467 1.546 17.000 6.771 3.26e-06 *** 520s --- 520s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 520s 520s Correlation of Fixed Effects: 520s (Intr) 520s Days -0.138 520s > 520s > stopifnot( 520s + isTRUE(all.equal(an1new, an1, check.attributes=FALSE, tol=TOL)), 520s + isTRUE(all.equal(coef(sfm1new), coef(sfm1), tol=TOL)) 520s + ) 520s > 520s > contest(fm1, c(0, 1)) 520s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 520s 1 30031.01 30031.01 1 17 45.853 3.26379e-06 520s > contest(fm1, c(0, 1), joint=FALSE) 520s Estimate Std. Error df t value lower upper Pr(>|t|) 520s 1 10.46729 1.545789 17 6.771485 7.205956 13.72862 3.26379e-06 520s > drop1(fm1) 520s Single term deletions using Satterthwaite's method: 520s 520s Model: 520s Reaction ~ Days + (Days | Subject) 520s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 520s Days 30031 30031 1 17 45.853 3.264e-06 *** 520s --- 520s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 520s > ranova(fm1) 520s ANOVA-like table for random-effects: Single term deletions 520s 520s Model: 520s Reaction ~ Days + (Days | Subject) 520s npar logLik AIC LRT Df Pr(>Chisq) 520s 6 -871.81 1755.6 520s Days in (Days | Subject) 4 -893.23 1794.5 42.837 2 4.99e-10 *** 520s --- 520s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 520s > step(fm1) 520s Backward reduced random-effect table: 520s 520s Eliminated npar logLik AIC LRT Df Pr(>Chisq) 520s 6 -871.81 1755.6 520s Days in (Days | Subject) 0 4 -893.23 1794.5 42.837 2 4.99e-10 520s 520s 520s Days in (Days | Subject) *** 520s --- 520s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 520s 520s Backward reduced fixed-effect table: 520s Degrees of freedom method: Satterthwaite 520s 520s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 520s Days 0 30031 30031 1 17 45.853 3.264e-06 *** 520s --- 520s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 520s 520s Model found: 520s Reaction ~ Days + (Days | Subject) 520s > 520s > fm1new <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy, 520s + control=lmerControl(optimizer="bobyqa")) 521s > stopifnot( 521s + isTRUE(all.equal(drop1(fm1), drop1(fm1new), tol=TOL)), 521s + isTRUE(all.equal(ranova(fm1), ranova(fm1new), tol=TOL)), 521s + isTRUE(all.equal(contest(fm1, c(0, 1)), contest(fm1new, c(0, 1)), tol=TOL)), 521s + isTRUE(all.equal(contest(fm1, c(0, 1), joint=FALSE), 521s + contest(fm1new, c(0, 1), joint=FALSE), tol=TOL)) 521s + ) 521s > 521s > # Test that lme4 methods work: 521s > coef(fm1) 521s $Subject 521s (Intercept) Days 521s 308 253.6637 19.6662579 521s 309 211.0065 1.8475828 521s 310 212.4449 5.0184061 521s 330 275.0956 5.6529547 521s 331 273.6653 7.3973914 521s 332 260.4446 10.1951153 521s 333 268.2455 10.2436615 521s 334 244.1725 11.5418620 521s 335 251.0714 -0.2848731 521s 337 286.2955 19.0955699 521s 349 226.1950 11.6407002 521s 350 238.3351 17.0814910 521s 351 255.9829 7.4520288 521s 352 272.2687 14.0032993 521s 369 254.6806 11.3395026 521s 370 225.7922 15.2897506 521s 371 252.2121 9.4791309 521s 372 263.7196 11.7513157 521s 521s attr(,"class") 521s [1] "coef.mer" 521s > fixef(fm1) 521s (Intercept) Days 521s 251.40510 10.46729 521s > resid(fm1) 521s 1 2 3 4 5 6 521s -4.1036703 -14.6252282 -42.1955860 8.7773561 24.5231982 62.6951403 521s 7 8 9 10 11 12 521s 10.5425825 -101.1788754 19.5915667 35.6935088 11.7273721 -7.5883107 521s 13 14 15 16 17 18 521s -11.7238935 -11.8422762 -10.6807590 -4.2826418 -8.4617246 -6.2124074 521s 19 20 21 22 23 24 521s -1.4914902 9.6794271 -13.3909590 -23.1310650 11.8383289 5.3415228 521s 25 26 27 28 29 30 521s -3.2110832 -17.0789893 -7.1344953 8.1773986 8.4203926 -10.0952135 521s 31 32 33 34 35 36 521s 46.4469967 19.6516420 -2.5450126 -6.9214673 -11.9101220 -5.7748766 521s 37 38 39 40 41 42 521s -28.7737313 3.5950141 -14.9697406 28.0765048 13.9425924 3.9373010 521s 43 44 45 46 47 48 521s 13.3605097 24.2578183 13.0224270 -17.3335644 -27.9746558 9.3706529 521s 49 50 51 52 53 54 521s -39.0975385 31.3392701 -25.5840308 -27.8279461 -7.8735614 18.7388233 521s 55 56 57 58 59 60 521s 16.2378080 -1.4226073 132.5465774 15.0206621 -11.7052532 -98.3362685 521s 61 62 63 64 65 66 521s 15.5968640 11.0658025 -11.9635591 0.8331794 -12.0491821 18.7026564 521s 67 68 69 70 71 72 521s 2.3189949 8.8887334 -16.8348282 1.6043103 21.3005744 20.4868123 521s 73 74 75 76 77 78 521s -23.8915497 -24.1258118 -11.3155738 -17.6906358 -7.8988979 6.5573401 521s 79 80 81 82 83 84 521s -0.7605219 29.2497160 -9.4631090 23.1606642 3.9890373 20.5853104 521s 85 86 87 88 89 90 521s 1.5199836 4.9891567 -3.9098701 -13.7662970 -13.0383239 -11.2609507 521s 91 92 93 94 95 96 521s 26.0711443 8.4147744 -32.8753955 2.5400346 3.0546647 10.0651947 521s 97 98 99 100 101 102 521s 3.3912248 -3.2721451 16.8042850 0.7611151 9.9082056 -7.5189947 521s 103 104 105 106 107 108 521s -10.5507949 -6.1950951 -22.0474953 -14.6240955 -14.4743957 0.4221041 521s 109 110 111 112 113 114 521s 16.9600039 20.6838037 17.9616518 -11.9623391 -16.2935301 -34.0525210 521s 115 116 117 118 119 120 521s -37.7446120 5.9820971 38.6204061 5.0128151 19.5001242 -3.0158668 521s 121 122 123 124 125 126 521s -5.4564400 36.6226312 -0.9930976 2.2500737 -13.9636551 11.3905161 521s 127 128 129 130 131 132 521s -12.9485127 -41.5516414 5.9426298 24.5143010 -50.5915973 11.9219034 521s 133 134 135 136 137 138 521s 26.6032041 32.5769048 20.4583056 10.5435063 -1.8618930 -9.8591922 521s 139 140 141 142 143 144 521s -8.6544915 -9.7566908 17.2429421 2.4168396 -20.1171630 -11.0424656 521s 145 146 147 148 149 150 521s 14.7836319 5.8354293 -24.5822732 14.0658242 -5.1165783 9.7770191 521s 151 152 153 154 155 156 521s -0.5282354 -6.5584860 -17.4709366 -31.1884871 -19.4139377 41.9527117 521s 157 158 159 160 161 162 521s -36.3826389 14.7650105 17.0527600 8.8288094 17.6682554 10.7515245 521s 163 164 165 166 167 168 521s 6.7284937 1.1399628 -10.9581681 -15.0957989 -49.8211298 -13.9354607 521s 169 170 171 172 173 174 521s 22.7355085 31.9448776 5.6920558 -1.9969599 10.3745244 11.6580087 521s 175 176 177 178 179 180 521s -23.5523070 7.1313773 0.2542616 -2.7589541 11.4115302 -5.3578855 521s > 521s > ####################################### 521s > ## Tests for fm2: 521s > (an2new <- anova(fm2)) 521s Type III Analysis of Variance Table with Satterthwaite's method 521s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 521s Product 17.6984 5.8995 3 319 3.5029 0.01577 * 521s Information 6.5201 6.5201 1 323 3.8714 0.04997 * 521s Gender 1.8634 1.8634 1 319 1.1064 0.29366 521s --- 521s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 521s > (sfm2new <- summary(fm2)) 521s Linear mixed model fit by REML. t-tests use Satterthwaite's method [ 521s lmerModLmerTest] 521s Formula: 521s Informed.liking ~ Product + Information + Gender + (1 | Product:Consumer) 521s Data: ham 521s 521s REML criterion at convergence: 2712.2 521s 521s Scaled residuals: 521s Min 1Q Median 3Q Max 521s -3.1568 -0.5087 0.0338 0.4913 3.1623 521s 521s Random effects: 521s Groups Name Variance Std.Dev. 521s Product:Consumer (Intercept) 3.526 1.878 521s Residual 1.684 1.298 521s Number of obs: 648, groups: Product:Consumer, 324 521s 521s Fixed effects: 521s Estimate Std. Error df t value Pr(>|t|) 521s (Intercept) 5.8290 0.2640 343.6885 22.082 <2e-16 *** 521s Product2 -0.7037 0.3284 319.0000 -2.143 0.0329 * 521s Product3 0.2840 0.3284 319.0000 0.865 0.3879 521s Product4 0.1173 0.3284 319.0000 0.357 0.7212 521s Information2 0.2006 0.1020 323.0000 1.968 0.0500 * 521s Gender2 -0.2443 0.2322 319.0000 -1.052 0.2937 521s --- 521s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 521s 521s Correlation of Fixed Effects: 521s (Intr) Prdct2 Prdct3 Prdct4 Infrm2 521s Product2 -0.622 521s Product3 -0.622 0.500 521s Product4 -0.622 0.500 0.500 521s Informatin2 -0.193 0.000 0.000 0.000 521s Gender2 -0.434 0.000 0.000 0.000 0.000 521s > 521s > stopifnot( 521s + isTRUE(all.equal(an2new, an2, check.attributes=FALSE, tol=TOL)), 521s + isTRUE(all.equal(coef(sfm2new), coef(sfm2), tol=TOL)) 521s + ) 521s > 521s > drop1(fm2) 521s Single term deletions using Satterthwaite's method: 521s 521s Model: 521s Informed.liking ~ Product + Information + Gender + (1 | Product:Consumer) 521s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 521s Product 17.6984 5.8995 3 319 3.5029 0.01577 * 521s Information 6.5201 6.5201 1 323 3.8714 0.04997 * 521s Gender 1.8634 1.8634 1 319 1.1064 0.29366 521s --- 521s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 521s > ranova(fm2) 521s ANOVA-like table for random-effects: Single term deletions 521s 521s Model: 521s Informed.liking ~ Product + Information + Gender + (1 | Product:Consumer) 521s npar logLik AIC LRT Df Pr(>Chisq) 521s 8 -1356.1 2728.2 521s (1 | Product:Consumer) 7 -1454.7 2923.4 197.19 1 < 2.2e-16 *** 521s --- 521s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 521s > ls_means(fm2) 521s Least Squares Means table: 521s 521s Estimate Std. Error df t value lower upper Pr(>|t|) 521s Product1 5.80713 0.23223 319.0 25.006 5.35025 6.26402 < 2.2e-16 *** 521s Product2 5.10343 0.23223 319.0 21.976 4.64654 5.56032 < 2.2e-16 *** 521s Product3 6.09108 0.23223 319.0 26.229 5.63420 6.54797 < 2.2e-16 *** 521s Product4 5.92442 0.23223 319.0 25.511 5.46753 6.38131 < 2.2e-16 *** 521s Information1 5.63121 0.12682 437.8 44.404 5.38196 5.88046 < 2.2e-16 *** 521s Information2 5.83183 0.12682 437.8 45.986 5.58258 6.08107 < 2.2e-16 *** 521s Gender1 5.85366 0.16320 319.0 35.868 5.53257 6.17475 < 2.2e-16 *** 521s Gender2 5.60937 0.16523 319.0 33.949 5.28430 5.93445 < 2.2e-16 *** 521s --- 521s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 521s 521s Confidence level: 95% 521s Degrees of freedom method: Satterthwaite 521s > difflsmeans(fm2) 521s Least Squares Means table: 521s 521s Estimate Std. Error df t value lower 521s Product1 - Product2 7.0370e-01 3.2841e-01 319 2.1428 5.7578e-02 521s Product1 - Product3 -2.8395e-01 3.2841e-01 319 -0.8646 -9.3008e-01 521s Product1 - Product4 -1.1728e-01 3.2841e-01 319 -0.3571 -7.6341e-01 521s Product2 - Product3 -9.8765e-01 3.2841e-01 319 -3.0074 -1.6338e+00 521s Product2 - Product4 -8.2099e-01 3.2841e-01 319 -2.4999 -1.4671e+00 521s Product3 - Product4 1.6667e-01 3.2841e-01 319 0.5075 -4.7946e-01 521s Information1 - Information2 -2.0062e-01 1.0196e-01 323 -1.9676 -4.0121e-01 521s Gender1 - Gender2 2.4428e-01 2.3224e-01 319 1.0519 -2.1263e-01 521s upper Pr(>|t|) 521s Product1 - Product2 1.3498e+00 0.032890 * 521s Product1 - Product3 3.6218e-01 0.387898 521s Product1 - Product4 5.2884e-01 0.721234 521s Product2 - Product3 -3.4153e-01 0.002845 ** 521s Product2 - Product4 -1.7486e-01 0.012926 * 521s Product3 - Product4 8.1279e-01 0.612159 521s Information1 - Information2 -2.6433e-05 0.049970 * 521s Gender1 - Gender2 7.0120e-01 0.293660 521s --- 521s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 521s 521s Confidence level: 95% 521s Degrees of freedom method: Satterthwaite 521s > nbeta <- length(fixef(fm2)) 521s > L <- diag(nbeta) 521s > L[1:4, ] <- 0 521s > contest(fm2, L) 521s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 521s 1 8.383419 4.19171 2 320.9875 2.488919 0.08460028 521s > contest(fm2, diag(nbeta), joint=FALSE) 521s Estimate Std. Error df t value lower upper 521s 1 5.8289672 0.2639677 343.6885 22.0821233 5.309772e+00 6.34816269 521s 2 -0.7037037 0.3284114 319.0000 -2.1427506 -1.349830e+00 -0.05757783 521s 3 0.2839506 0.3284114 319.0000 0.8646187 -3.621753e-01 0.93007650 521s 4 0.1172840 0.3284114 319.0000 0.3571251 -5.288419e-01 0.76340983 521s 5 0.2006173 0.1019607 323.0000 1.9675949 2.643318e-05 0.40120813 521s 6 -0.2442835 0.2322396 319.0000 -1.0518599 -7.011983e-01 0.21263128 521s Pr(>|t|) 521s 1 6.753241e-68 521s 2 3.288952e-02 521s 3 3.878978e-01 521s 4 7.212343e-01 521s 5 4.997000e-02 521s 6 2.936600e-01 521s > step(fm2) 521s Backward reduced random-effect table: 521s 521s Eliminated npar logLik AIC LRT Df Pr(>Chisq) 521s 8 -1356.1 2728.2 521s (1 | Product:Consumer) 0 7 -1454.7 2923.4 197.19 1 < 2.2e-16 *** 521s --- 521s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 521s 521s Backward reduced fixed-effect table: 521s Degrees of freedom method: Satterthwaite 521s 521s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 521s Gender 1 1.8634 1.8634 1 319 1.1064 0.29366 521s Product 0 17.6926 5.8975 3 320 3.5018 0.01579 * 521s Information 0 6.5201 6.5201 1 323 3.8714 0.04997 * 521s --- 521s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 521s 521s Model found: 521s Informed.liking ~ Product + Information + (1 | Product:Consumer) 521s > 521s > fm2new <- lmer(Informed.liking ~ Product + Information + Gender + 521s + (1|Product:Consumer), data=ham) 521s > stopifnot( 521s + isTRUE(all.equal(drop1(fm2), drop1(fm2new), tol=TOL)), 521s + isTRUE(all.equal(ranova(fm2), ranova(fm2new), tol=TOL)), 521s + isTRUE(all.equal(ls_means(fm2), ls_means(fm2new), tol=TOL)), 521s + isTRUE(all.equal(difflsmeans(fm2), difflsmeans(fm2new), tol=TOL)) 521s + ) 522s > 522s > # Test that lme4 methods work: 522s > coef(fm2) 522s $`Product:Consumer` 522s (Intercept) Product2 Product3 Product4 Information2 Gender2 522s 1:1 5.078836 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 1:2 5.276027 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 1:3 6.693279 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 1:4 6.693279 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 1:5 4.468805 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 1:6 5.078836 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 1:7 8.101302 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 1:8 6.289668 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 1:9 6.289668 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 1:10 5.482447 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 1:11 8.504912 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 1:12 3.661584 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 1:13 7.697691 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 1:14 8.101302 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 1:15 4.675225 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 1:16 4.872416 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 1:17 7.096889 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 1:18 7.500500 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 1:19 8.307721 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 1:20 6.693279 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 1:21 6.693279 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 1:22 6.083248 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 1:23 6.486859 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 1:24 7.500500 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 1:25 5.078836 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 1:26 7.294080 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 1:29 4.872416 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 1:30 6.083248 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 1:31 6.289668 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 1:32 7.697691 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 1:33 4.271615 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 1:34 4.675225 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 1:35 6.486859 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 1:36 6.083248 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 1:37 3.464393 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 1:38 6.289668 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 1:39 6.693279 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 1:40 3.661584 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 1:41 5.886057 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 1:42 5.482447 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 1:43 7.096889 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 1:44 6.083248 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 1:45 8.504912 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 1:46 5.078836 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 1:47 2.047141 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 1:48 6.890469 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 1:49 3.464393 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 1:50 3.257973 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 1:51 6.083248 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 1:52 8.504912 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 1:53 5.078836 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 1:54 3.661584 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 1:55 4.675225 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 1:56 6.486859 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 1:57 5.078836 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 1:58 5.482447 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 1:59 5.482447 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 1:60 5.482447 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 1:61 7.096889 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 1:62 5.276027 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 1:63 5.679637 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 1:64 4.872416 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 1:65 7.500500 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 1:66 6.083248 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 1:67 5.886057 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 1:68 7.294080 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 1:69 4.872416 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 1:70 6.486859 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 1:71 5.078836 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 1:73 2.854363 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 1:74 6.486859 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 1:75 4.675225 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 1:76 4.872416 -0.7037037 0.2839506 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2.821606 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 2:22 2.615186 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 2:23 2.615186 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 2:24 7.261323 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 2:25 6.857713 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 2:26 2.615186 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 2:29 2.615186 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 2:30 7.862125 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 2:31 7.664934 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 2:32 5.440461 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 2:33 2.417995 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 2:34 6.857713 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 2:35 5.036850 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 2:36 8.669346 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 2:37 6.857713 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 2:38 4.839659 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 2:39 7.261323 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 2:40 3.826018 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 2:41 5.243270 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 2:42 6.857713 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 2:43 4.436049 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 2:44 5.036850 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 2:45 5.440461 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 2:46 8.472155 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 2:47 5.844071 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 2:48 2.615186 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 2:49 7.261323 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 2:50 7.862125 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 2:51 8.265735 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 2:52 5.844071 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 2:53 8.068545 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 2:54 7.862125 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 2:55 5.243270 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 2:56 7.054903 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 2:57 6.857713 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 2:58 8.472155 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 2:59 8.068545 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 2:60 5.243270 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 2:61 4.839659 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 2:62 8.669346 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 2:63 7.862125 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 2:64 7.862125 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 2:65 4.436049 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 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6.795795 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 4:3 5.791383 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 4:4 5.387772 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 4:5 6.392185 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 4:6 4.984162 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 4:7 3.970521 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 4:8 7.405826 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 4:9 6.194994 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 4:10 6.598604 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 4:11 6.392185 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 4:12 7.603017 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 4:13 7.603017 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 4:14 5.988574 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 4:15 7.002215 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 4:16 6.392185 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 4:17 3.773330 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 4:18 7.002215 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 4:19 4.984162 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 4:20 4.984162 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 4:21 4.580551 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 4:22 3.970521 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 4:23 3.970521 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 4:24 7.002215 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 4:25 7.002215 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 4:26 4.777742 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 4:29 2.356078 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 4:30 6.392185 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 4:31 7.405826 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 4:32 5.988574 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 4:33 4.176940 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 4:34 7.002215 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 4:35 6.795795 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 4:36 6.795795 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 4:37 5.387772 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 4:38 4.580551 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 4:39 4.176940 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 4:40 7.603017 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 4:41 4.580551 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 4:42 7.809437 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 4:43 5.387772 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 4:44 2.759689 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 4:45 5.181353 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 4:46 1.755276 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 4:47 1.952467 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 4:48 5.988574 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 4:49 7.002215 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 4:50 6.392185 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 4:51 8.410238 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 4:52 3.970521 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 4:53 7.002215 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 4:54 7.603017 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 4:55 5.387772 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 4:56 2.759689 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 4:57 7.002215 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 4:58 7.405826 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 4:59 6.194994 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 4:60 4.580551 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 4:61 6.194994 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 4:62 8.006627 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 4:63 5.584963 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 4:64 5.584963 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 4:65 3.369719 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 4:66 5.988574 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 4:67 6.194994 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 4:68 5.584963 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 4:69 6.795795 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 4:70 6.795795 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 4:71 4.984162 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 4:73 5.988574 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 4:74 8.410238 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 4:75 7.405826 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 4:76 8.410238 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 4:77 8.410238 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 4:78 7.405826 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 4:79 5.988574 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 4:80 3.970521 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 4:81 4.580551 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 4:82 5.988574 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 4:83 5.791383 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 4:84 4.580551 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 522s 522s attr(,"class") 522s [1] "coef.mer" 522s > fixef(fm2) 522s (Intercept) Product2 Product3 Product4 Information2 Gender2 522s 5.8289672 -0.7037037 0.2839506 0.1172840 0.2006173 -0.2442835 522s > resid(fm2) 522s 1 2 3 4 5 6 522s -0.07883589 -0.27945318 -0.13595549 -0.33657278 -1.13357551 0.66580721 522s 7 8 9 10 11 12 522s 0.09133291 -0.10928437 -0.03174324 -0.23236053 0.27864107 1.07802378 522s 13 14 15 16 17 18 522s 0.49185308 0.29123580 0.33120421 0.13058692 0.30672140 0.10610412 522s 19 20 21 22 23 24 522s -1.94317685 1.85620587 -0.15162889 0.64775382 2.09133291 -2.10928437 522s 25 26 27 28 29 30 522s 0.30672140 0.10610412 0.07487654 -1.12574075 -0.13357551 -0.33419279 522s 31 32 33 34 35 36 522s -0.50505641 0.29432631 -1.22452189 0.57486083 -0.28164149 -0.48225877 522s 37 38 39 40 41 42 522s -0.89370421 0.90567850 0.73481489 -0.46580240 -0.07883589 -0.27945318 522s 43 44 45 46 47 48 522s 0.46043383 -0.74018345 0.44476043 0.24414315 -2.10144573 1.69793698 522s 49 50 51 52 53 54 522s 1.14298202 -0.05763526 -1.07080946 -0.27142674 -0.10453624 0.69484647 522s 55 56 57 58 59 60 522s 0.15647895 -1.04413834 -0.28966792 0.50971479 -0.34678752 0.45259519 522s 61 62 63 64 65 66 522s -1.15162889 1.64775382 0.47689021 0.27627292 -0.28966792 0.50971479 522s 67 68 69 70 71 72 522s -0.34678752 0.45259519 0.44476043 0.24414315 -1.31227776 1.48710495 522s 73 74 75 76 77 78 522s 0.51755343 -0.68306385 0.23154842 1.03093113 -0.55523957 1.24414315 522s 79 80 81 82 83 84 522s 0.28411156 0.08349428 0.73937134 0.53875406 -0.66719878 -0.86781607 522s 85 86 87 88 89 90 522s 3.10629579 -3.09432150 0.73481489 -0.46580240 -0.41730054 -0.61791782 522s 91 92 93 94 95 96 522s -0.66719878 -0.86781607 -0.29731489 0.50206783 0.52398286 0.32336557 522s 97 98 99 100 101 102 522s 0.54659270 0.34597541 -0.66719878 -0.86781607 0.50990646 -0.69071082 522s 103 104 105 106 107 108 522s 0.52398286 0.32336557 1.14298202 -0.05763526 -0.66719878 -0.86781607 522s 109 110 111 112 113 114 522s -0.87565083 -0.07626811 1.13842556 -1.06219172 -0.67522522 0.12415750 522s 115 116 117 118 119 120 522s -0.15400888 0.64537384 0.25198178 0.05136450 -0.11949912 0.67988360 522s 121 122 123 124 125 126 522s 2.37186743 -2.82874985 -0.66719878 -0.86781607 -0.89370421 0.90567850 522s 127 128 129 130 131 132 522s -1.26518511 1.53419760 -0.09688928 0.70249344 0.05682315 -0.14379413 522s 133 134 135 136 137 138 522s -0.15162889 0.64775382 0.10938630 -1.09123099 1.49950005 -0.70111724 522s 139 140 141 142 143 144 522s 0.07487654 -1.12574075 0.05920314 -0.14141415 -0.11949912 0.67988360 522s 145 146 147 148 149 150 522s 0.69227869 0.49166141 -0.71429143 -0.91490872 -0.90469010 -1.10530738 522s 151 152 153 154 155 156 522s -0.10144573 -0.30206302 0.30672140 0.10610412 -0.52151279 -0.72213007 522s 157 158 159 160 161 162 522s -0.15162889 0.64775382 0.89855427 -1.30206302 0.30672140 0.10610412 522s 163 164 165 166 167 168 522s -1.11790211 -0.31851939 0.07725652 -1.12336076 -0.69783506 0.10154766 522s 169 170 171 172 173 174 522s 2.16103540 -2.03958188 -0.66719878 -0.86781607 1.12434917 -2.07626811 522s 175 176 177 178 179 180 522s 0.15647895 -1.04413834 0.75742473 -0.44319256 -0.66719878 -0.86781607 522s 181 182 183 184 185 186 522s -0.66481880 -0.86543608 1.15647895 -2.04413834 0.49950005 0.29888276 522s 187 188 189 190 191 192 522s 0.44238045 0.24176316 1.04114975 -0.15946753 -0.11949912 0.67988360 522s 193 194 195 196 197 198 522s -0.07883589 -0.27945318 -0.15400888 0.64537384 -0.34440754 0.45497518 522s 199 200 201 202 203 204 522s -0.11949912 0.67988360 0.95020337 -0.25041391 -0.66719878 -0.86781607 522s 205 206 207 208 209 210 522s -0.70092557 1.09845715 1.34925759 -1.85135969 -3.62813257 3.17125015 522s 211 212 213 214 215 216 522s -0.66719878 -0.86781607 0.29907443 0.09845715 -1.22907835 -0.42969563 522s 217 218 219 220 221 222 522s 0.16103540 -0.03958188 1.08586242 -0.11475486 -0.29731489 0.50206783 522s 223 224 225 226 227 228 522s 0.73481489 -0.46580240 -0.28966792 0.50971479 1.03876977 -0.16184751 522s 229 230 231 232 233 234 522s 0.84837111 -0.35224618 0.47689021 0.27627292 0.54659270 0.34597541 522s 235 236 237 238 239 240 522s -0.49247352 0.30690920 0.49185308 0.29123580 -0.86157444 0.93780828 522s 241 242 243 244 245 246 522s -1.27161454 0.52776818 -0.71429143 -0.91490872 -1.71191145 0.08747127 522s 247 248 249 250 251 252 522s 1.70577562 -2.49484166 -0.67522522 0.12415750 -0.15400888 0.64537384 522s 253 254 255 256 257 258 522s 0.65559246 -0.54502482 -0.11949912 0.67988360 -1.24257527 1.55680744 522s 259 260 261 262 263 264 522s -1.08886284 0.71051987 -1.29731489 1.50206783 0.33120421 0.13058692 522s 265 266 267 268 269 270 522s 0.16103540 -0.03958188 0.27864107 1.07802378 0.29907443 0.09845715 522s 271 272 273 274 275 276 522s 1.33120421 -0.86941308 -1.46439319 0.33498953 -0.15400888 0.64537384 522s 277 278 279 280 281 282 522s 0.84837111 -0.35224618 -0.50505641 0.29432631 0.71033208 -0.49028521 522s 283 284 285 286 287 288 522s -0.13595549 -0.33657278 0.67364584 -1.52697144 0.30216494 -0.89845234 522s 289 290 291 292 293 294 522s -0.69327860 1.10610412 -0.55761955 1.24176316 -0.94079686 0.85858585 522s 295 296 297 298 299 300 522s -0.29422438 -0.49484166 -2.41730054 1.38208218 -0.87803081 -0.07864810 522s 301 302 303 304 305 306 522s 0.49185308 0.29123580 1.52398286 -0.67663443 0.11394275 -0.08667453 522s 307 308 309 310 311 312 522s -0.53956617 0.25981655 0.46281381 -0.73780347 0.30216494 -0.89845234 522s 313 314 315 316 317 318 522s -0.48244657 0.31693615 -0.15400888 0.64537384 -0.15162889 0.64775382 522s 319 320 321 322 323 324 522s 0.07327953 0.87266225 0.90311072 -0.29750656 1.26765518 -1.93296210 522s 325 326 327 328 329 330 522s -0.15162889 0.64775382 0.49494359 -0.70567369 -1.83896460 1.96041812 522s 331 332 333 334 335 336 522s -1.08886284 0.71051987 -0.27926151 -0.47987879 -0.63268902 -0.83330631 522s 337 338 339 340 341 342 522s 0.73937134 0.53875406 -1.49247352 1.30690920 -0.66481880 -0.86543608 522s 343 344 345 346 347 348 522s 0.94564692 -1.25497037 1.92116411 -2.27945318 1.23154842 0.03093113 522s 349 350 351 352 353 354 522s -2.53718619 2.26219653 -0.87256032 -1.07317760 -0.80285783 -1.00347511 522s 355 356 357 358 359 360 522s 4.10391580 -4.09670148 1.10629579 -1.09432150 -0.82546767 -1.02608496 522s 361 362 363 364 365 366 522s 0.35381405 0.15319677 -0.66719878 -0.86781607 -0.49009354 0.30928918 522s 367 368 369 370 371 372 522s 0.13842556 -0.06219172 -0.46439319 -0.66501047 -0.55761955 1.24176316 522s 373 374 375 376 377 378 522s -0.74801822 1.05136450 -0.11949912 0.67988360 -0.01368986 -1.21430714 522s 379 380 381 382 383 384 522s 0.08586242 0.88524514 0.68463173 0.48401444 -0.26518511 0.53419760 522s 385 386 387 388 389 390 522s -0.83896460 0.96041812 -0.31774826 1.48163446 0.68463173 0.48401444 522s 391 392 393 394 395 396 522s 0.71676150 0.51614422 0.73937134 0.53875406 0.10391580 -0.09670148 522s 397 398 399 400 401 402 522s -0.29731489 0.50206783 -0.84352105 -0.04413834 -0.07883589 -0.27945318 522s 403 404 405 406 407 408 522s 1.63515909 -0.56545819 -0.13357551 -0.33419279 0.88050088 -0.32011640 522s 409 410 411 412 413 414 522s -0.41730054 -0.61791782 0.08586242 0.88524514 -0.10453624 0.69484647 522s 415 416 417 418 419 420 522s 0.52398286 0.32336557 1.32477478 -1.87584250 -2.53956617 2.25981655 522s 421 422 423 424 425 426 522s 1.25198178 -0.94863550 -2.50505641 2.29432631 -0.24257527 0.55680744 522s 427 428 429 430 431 432 522s -0.10691623 0.69246649 -0.87565083 -0.07626811 -0.63268902 -0.83330631 522s 433 434 435 436 437 438 522s -0.07883589 -0.27945318 -0.15400888 0.64537384 -1.15162889 1.64775382 522s 439 440 441 442 443 444 522s -0.11949912 0.67988360 0.51755343 -0.68306385 0.23154842 1.03093113 522s 445 446 447 448 449 450 522s -0.55523957 1.24414315 0.47689021 0.27627292 -0.48244657 0.31693615 522s 451 452 453 454 455 456 522s -0.36484091 1.43454181 1.04114975 -0.15946753 0.68772224 -0.51289505 522s 457 458 459 460 461 462 522s 0.51755343 -0.68306385 0.46043383 -0.74018345 0.86642449 -1.33419279 522s 463 464 465 466 467 468 522s 1.30216494 -1.89845234 0.90311072 -0.29750656 -0.13595549 -0.33657278 522s 469 470 471 472 473 474 522s -0.13357551 -0.33419279 0.68772224 -0.51289505 -0.03174324 -0.23236053 522s 475 476 477 478 479 480 522s 0.27864107 1.07802378 1.08824240 -0.11237488 1.12037218 -0.08024511 522s 481 482 483 484 485 486 522s 0.56464608 -0.63597120 1.08586242 -0.11475486 -0.89370421 0.90567850 522s 487 488 489 490 491 492 522s 0.54203624 -0.65858105 1.37186743 -1.82874985 1.08586242 -0.11475486 522s 493 494 495 496 497 498 522s -0.29731489 0.50206783 0.54203624 -0.65858105 0.49950005 0.29888276 522s 499 500 501 502 503 504 522s -0.73234482 0.06703790 0.07725652 -1.12336076 -0.48700303 -0.68762031 522s 505 506 507 508 509 510 522s -0.83896460 0.96041812 2.10391580 -2.09670148 -2.87565083 1.92373189 522s 511 512 513 514 515 516 522s 2.13842556 -2.06219172 0.11394275 -0.08667453 1.03876977 -0.16184751 522s 517 518 519 520 521 522 522s 0.84837111 -0.35224618 -0.31227776 0.48710495 1.95020337 -1.25041391 522s 523 524 525 526 527 528 522s -0.87803081 -0.07864810 -0.85759745 -1.05821473 2.54203624 -2.65858105 522s 529 530 531 532 533 534 522s -0.62813257 0.17125015 0.48947310 0.28885581 -0.70092557 1.09845715 522s 535 536 537 538 539 540 522s 0.33120421 0.13058692 -0.24257527 0.55680744 -1.28164149 0.51774123 522s 541 542 543 544 545 546 522s -0.06842948 -1.26904676 -0.66879579 1.13058692 1.92116411 -2.27945318 522s 547 548 549 550 551 552 522s 0.03876977 0.83815249 0.63753908 0.43692179 -0.10144573 -0.30206302 522s 553 554 555 556 557 558 522s -1.61007918 0.18930353 0.87503039 0.67441311 0.68463173 0.48401444 522s 559 560 561 562 563 564 522s 0.13842556 -0.06219172 -0.24257527 0.55680744 -0.70330555 1.09607717 522s 565 566 567 568 569 570 522s 0.68463173 0.48401444 0.71676150 0.51614422 -0.67522522 0.12415750 522s 571 572 573 574 575 576 522s 0.82793774 0.62732046 -0.51913280 -0.71975009 0.47689021 0.27627292 522s 577 578 579 580 581 582 522s -2.62813257 2.17125015 -0.31774826 1.48163446 -2.89370421 2.90567850 522s 583 584 585 586 587 588 522s 0.71676150 0.51614422 -2.01368986 0.78569286 -0.31774826 1.48163446 522s 589 590 591 592 593 594 522s 0.29907443 0.09845715 0.71676150 0.51614422 0.92116411 -1.27945318 522s 595 596 597 598 599 600 522s -1.34678752 1.45259519 0.63753908 0.43692179 0.47689021 0.27627292 522s 601 602 603 604 605 606 522s -0.04979663 0.74958609 0.48947310 0.28885581 -0.27926151 -0.47987879 522s 607 608 609 610 611 612 522s 0.13842556 -0.06219172 -0.04979663 0.74958609 1.89308377 -1.30753351 522s 613 614 615 616 617 618 522s 0.93157052 -2.26904676 -0.84352105 -0.04413834 0.11394275 -0.08667453 522s 619 620 621 622 623 624 522s -0.32873414 -0.52935142 -0.92274348 -0.12336076 -1.69783506 1.10154766 522s 625 626 627 628 629 630 522s 2.35381405 -1.84680323 1.27864107 0.07802378 1.49185308 -0.70876420 522s 631 632 633 634 635 636 522s 0.13842556 -0.06219172 -2.86800386 1.93137885 -2.34678752 2.45259519 522s 637 638 639 640 641 642 522s -1.13357551 0.66580721 1.09133291 -1.10928437 0.51755343 -0.68306385 522s 643 644 645 646 647 648 522s 0.24960180 0.04898452 -1.94079686 1.85858585 0.30216494 -0.89845234 522s > 522s > 522s BEGIN TEST test_lmer.R 522s 522s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 522s Copyright (C) 2025 The R Foundation for Statistical Computing 522s Platform: arm-unknown-linux-gnueabihf (32-bit) 522s 522s R is free software and comes with ABSOLUTELY NO WARRANTY. 522s You are welcome to redistribute it under certain conditions. 522s Type 'license()' or 'licence()' for distribution details. 522s 522s R is a collaborative project with many contributors. 522s Type 'contributors()' for more information and 522s 'citation()' on how to cite R or R packages in publications. 522s 522s Type 'demo()' for some demos, 'help()' for on-line help, or 522s 'help.start()' for an HTML browser interface to help. 522s Type 'q()' to quit R. 522s 522s > # test_lmer.R 522s > 522s > stopifnot(!"lmerTest" %in% .packages()) # ensure that lmerTest is NOT attached 522s > data("sleepstudy", package="lme4") 522s > f <- function(form, data) lmerTest::lmer(form, data=data) 522s > form <- "Reaction ~ Days + (Days|Subject)" 522s > fm <- f(form, data=sleepstudy) 524s > anova(fm) 524s Type III Analysis of Variance Table with Satterthwaite's method 524s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 524s Days 30031 30031 1 17 45.853 3.264e-06 *** 524s --- 524s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 524s > summary(fm) 524s Linear mixed model fit by REML. t-tests use Satterthwaite's method [ 524s lmerModLmerTest] 524s Formula: form 524s Data: data 524s 524s REML criterion at convergence: 1743.6 524s 524s Scaled residuals: 524s Min 1Q Median 3Q Max 524s -3.9536 -0.4634 0.0231 0.4634 5.1793 524s 524s Random effects: 524s Groups Name Variance Std.Dev. Corr 524s Subject (Intercept) 612.10 24.741 524s Days 35.07 5.922 0.07 524s Residual 654.94 25.592 524s Number of obs: 180, groups: Subject, 18 524s 524s Fixed effects: 525s Estimate Std. Error df t value Pr(>|t|) 525s (Intercept) 251.405 6.825 17.000 36.838 < 2e-16 *** 525s Days 10.467 1.546 17.000 6.771 3.26e-06 *** 525s --- 525s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 525s 525s Correlation of Fixed Effects: 525s (Intr) 525s Days -0.138 525s > 525s > # cf. GitHub issue #2: 525s > test <- function() { 525s + tmp <- sleepstudy 525s + m <- lmerTest::lmer(Reaction ~ Days + (Days | Subject), data = tmp) 525s + summary(m) 525s + } 525s > test() 525s Linear mixed model fit by REML. t-tests use Satterthwaite's method [ 525s lmerModLmerTest] 525s Formula: Reaction ~ Days + (Days | Subject) 525s Data: tmp 525s 525s REML criterion at convergence: 1743.6 525s 525s Scaled residuals: 525s Min 1Q Median 3Q Max 525s -3.9536 -0.4634 0.0231 0.4634 5.1793 525s 525s Random effects: 525s Groups Name Variance Std.Dev. Corr 525s Subject (Intercept) 612.10 24.741 525s Days 35.07 5.922 0.07 525s Residual 654.94 25.592 525s Number of obs: 180, groups: Subject, 18 525s 525s Fixed effects: 525s Estimate Std. Error df t value Pr(>|t|) 525s (Intercept) 251.405 6.825 17.000 36.838 < 2e-16 *** 525s Days 10.467 1.546 17.000 6.771 3.26e-06 *** 525s --- 525s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 525s 525s Correlation of Fixed Effects: 525s (Intr) 525s Days -0.138 525s > test <- function() { 525s + tmp <- sleepstudy 525s + m <- lme4::lmer(Reaction ~ Days + (Days | Subject), data = tmp) 525s + if(requireNamespace("lmerTest", quietly = TRUE)) { 525s + summary(lmerTest::as_lmerModLmerTest(m)) 525s + } 525s + } 525s > test() 525s Linear mixed model fit by REML. t-tests use Satterthwaite's method [ 525s lmerModLmerTest] 525s Formula: Reaction ~ Days + (Days | Subject) 525s Data: tmp 525s 525s REML criterion at convergence: 1743.6 525s 525s Scaled residuals: 525s Min 1Q Median 3Q Max 525s -3.9536 -0.4634 0.0231 0.4634 5.1793 525s 525s Random effects: 525s Groups Name Variance Std.Dev. Corr 525s Subject (Intercept) 612.10 24.741 525s Days 35.07 5.922 0.07 525s Residual 654.94 25.592 525s Number of obs: 180, groups: Subject, 18 525s 525s Fixed effects: 525s Estimate Std. Error df t value Pr(>|t|) 525s (Intercept) 251.405 6.825 17.000 36.838 < 2e-16 *** 525s Days 10.467 1.546 17.000 6.771 3.26e-06 *** 525s --- 525s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 525s 525s Correlation of Fixed Effects: 525s (Intr) 525s Days -0.138 525s > 525s > library(lmerTest) 525s Loading required package: lme4 525s Loading required package: Matrix 525s 525s Attaching package: 'lmerTest' 525s 525s The following object is masked from 'package:lme4': 525s 525s lmer 525s 525s The following object is masked from 'package:stats': 525s 525s step 525s 525s > 525s > # WRE says "using if(requireNamespace("pkgname")) is preferred, if possible." 525s > # even in tests: 525s > assertError <- function(expr, ...) 525s + if(requireNamespace("tools")) tools::assertError(expr, ...) else invisible() 525s > assertWarning <- function(expr, ...) 525s + if(requireNamespace("tools")) tools::assertWarning(expr, ...) else invisible() 525s > 525s > TOL <- 1e-4 525s > 525s > ##################################################################### 525s > # Check that lme4::lmer and lmerTest::lmer have the same arguments 525s > 525s > lmer_args <- formals(lme4::lmer) 525s > names(lmer_args) 525s [1] "formula" "data" "REML" "control" "start" 525s [6] "verbose" "subset" "weights" "na.action" "offset" 525s [11] "contrasts" "devFunOnly" 525s > lmerTest_args <- formals(lmerTest::lmer) 525s > seq_args <- seq_along(lmerTest_args) 525s > if(packageVersion("lme4") > '1.1.21') { 525s + stopifnot( 525s + all.equal(names(lmer_args), names(lmerTest_args)), 525s + all.equal(lmer_args, lmerTest_args) 525s + ) 525s + } else { # Older versions of 'lme4' has a "..." argument: 525s + stopifnot( 525s + all.equal(names(lmer_args)[seq_args], names(lmerTest_args[seq_args])), 525s + all.equal(lmer_args[seq_args], lmerTest_args[seq_args]) 525s + ) 525s + } 525s > 525s > ##################################################################### 525s > # Test evaluation of update inside a function: 525s > myupdate <- function(m, ...) { 525s + update(m, ...) 525s + } 525s > 525s > data("sleepstudy", package="lme4") 525s > fm1 <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy) 525s > tmp <- sleepstudy 525s > rm(sleepstudy) 525s > fmA <- update(fm1, data = tmp) # works 525s > fmB <- myupdate(fm1, data = tmp) # also works 525s > # Same except for 'call': 525s > fmB@call <- fmA@call 525s > stopifnot(isTRUE(all.equal(fmA, fmB, tolerance=TOL))) 525s > # Based on bug-report by Henrik Singmann, github issue #3 525s > 525s > ##################################################################### 525s > # Test update when formula is a character vector: 525s > 525s > form <- "Informed.liking ~ Product+Information+ 525s + (1|Consumer) + (1|Product:Consumer) + (1|Information:Consumer)" 525s > m <- lmer(form, data=ham) 525s > class(m) 525s [1] "lmerModLmerTest" 525s attr(,"package") 525s [1] "lmerTest" 525s > class(update(m, ~.- Product)) 525s [1] "lmerModLmerTest" 525s attr(,"package") 525s [1] "lmerTest" 525s > stopifnot(inherits(update(m, ~.- Product), "lmerModLmerTest")) 526s > 526s > # In version < 3.0-1.9002 class(update(m, ~.- Product)) was "lmerMod" 526s > ##################################################################### 526s > # Test error message from as_lmerModLmerTest: 526s > data("sleepstudy", package="lme4") 526s > myfit <- function(formula, data) { 526s + lme4::lmer(formula = formula, data = data) 526s + } 526s > fm2 <- myfit(Reaction ~ Days + (Days|Subject), sleepstudy) 526s > m <- assertError(as_lmerModLmerTest(fm2)) 526s > stopifnot( 526s + grepl("Unable to extract deviance function from model fit", m[[1]], fixed=TRUE) 526s + ) 526s > 526s > ##################################################################### 526s > # Check that devFunOnly argument works: 526s > data("sleepstudy", package="lme4") 526s > fun <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy, devFunOnly = TRUE) 526s > stopifnot(is.function(fun)) # && names(formals(fun)[1]) == "theta") 526s > fm1 <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy) 526s > fun <- update(fm1, devFunOnly=TRUE) 526s > stopifnot(is.function(fun)) # && names(formals(fun)[1]) == "theta") 526s > # devFunOnly = FALSE: 526s > notfun <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy, devFunOnly = FALSE) 526s > stopifnot(inherits(notfun, "lmerModLmerTest")) 526s > # Partial matching: 526s > notfun <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy, devFun = FALSE) 526s > stopifnot(inherits(notfun, "lmerModLmerTest")) 526s > 526s > ##################################################################### 526s > # Use of as_lmerModLmerTest 526s > data("sleepstudy", package="lme4") 526s > m <- lme4::lmer(Reaction ~ Days + (Days | Subject), sleepstudy) 526s > bm <- lmerTest:::as_lmerModLmerTest(m) 526s > stopifnot( 526s + inherits(bm, "lmerModLmerTest"), 526s + !inherits(m, "lmerModLmerTest"), 526s + inherits(bm, "lmerMod"), 526s + all(c("vcov_varpar", "Jac_list", "vcov_beta", "sigma") %in% slotNames(bm)) 526s + ) 526s > 526s > ##################################################################### 526s > # Update method 526s > 526s > m <- lmer(Reaction ~ Days + (Days | Subject), sleepstudy) 526s > m1 <- update(m, ~.-Days) 526s > m2 <- lmer(Reaction ~ (Days | Subject), sleepstudy) 526s > 526s > stopifnot( 526s + inherits(m, "lmerModLmerTest"), 526s + inherits(m1, "lmerModLmerTest"), 526s + inherits(m2, "lmerModLmerTest"), 526s + all.equal(m1, m2, tolerance=1e-6) 526s + ) 526s > 526s > 526s BEGIN TEST test_lmerTest_paper.R 526s 526s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 526s Copyright (C) 2025 The R Foundation for Statistical Computing 526s Platform: arm-unknown-linux-gnueabihf (32-bit) 526s 526s R is free software and comes with ABSOLUTELY NO WARRANTY. 526s You are welcome to redistribute it under certain conditions. 526s Type 'license()' or 'licence()' for distribution details. 526s 526s R is a collaborative project with many contributors. 526s Type 'contributors()' for more information and 526s 'citation()' on how to cite R or R packages in publications. 526s 526s Type 'demo()' for some demos, 'help()' for on-line help, or 526s 'help.start()' for an HTML browser interface to help. 526s Type 'q()' to quit R. 526s 526s > # test_lmerTest_paper.R 526s > 526s > library(lmerTest) 526s Loading required package: lme4 526s Loading required package: Matrix 529s > 529s > # Kenward-Roger only available with pbkrtest and only then validated in R >= 3.3.3 529s > # (faulty results for R < 3.3.3 may be due to unstated dependencies in pbkrtest) 529s > has_pbkrtest <- requireNamespace("pbkrtest", quietly = TRUE) && getRversion() >= "3.3.3" 529s 529s Attaching package: 'lmerTest' 529s 529s The following object is masked from 'package:lme4': 529s 529s lmer 529s 529s The following object is masked from 'package:stats': 529s 529s step 529s 529s > 529s > # Read in data set 529s > load(system.file("testdata","test_paper_objects.RData", package="lmerTest")) 529s > 529s > # Evaluate code from paper: 529s > ## Section 8.2: 529s > tv <- lmer(Sharpnessofmovement ~ TVset * Picture + (1 | Assessor) + 529s + (1 | Assessor:TVset) + (1 | Assessor:Picture), data = TVbo, 529s + control=lmerControl(optimizer="bobyqa")) 529s > 529s > (an8.2 <- anova(tv)) 529s Type III Analysis of Variance Table with Satterthwaite's method 529s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 529s TVset 1.765 0.8825 2 14 0.2437 0.7869818 529s Picture 51.857 17.2857 3 21 4.7735 0.0108785 * 529s TVset:Picture 90.767 15.1279 6 138 4.1777 0.0006845 *** 529s --- 529s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 529s > 529s > if(has_pbkrtest) 529s + (ankr8.2 <- anova(tv, type=2, ddf="Kenward-Roger")) 530s Type II Analysis of Variance Table with Kenward-Roger's method 530s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 530s TVset 1.765 0.8825 2 14 0.2437 0.7869818 530s Picture 51.857 17.2857 3 21 4.7735 0.0108785 * 530s TVset:Picture 90.767 15.1279 6 138 4.1777 0.0006845 *** 530s --- 530s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 530s > 530s > ## Section 8.3: 530s > m.carrots <- lmer(Preference ~ sens1 + sens2 + (1 + sens1 + sens2 | Consumer) + 530s + (1 | Product), data=carrots, 530s + control=lmerControl(optimizer="bobyqa")) 531s boundary (singular) fit: see help('isSingular') 531s > (sum8.3 <- coef(summary(m.carrots))) 531s Estimate Std. Error df t value Pr(>|t|) 531s (Intercept) 4.79911155 0.07529225 20.721695 63.7397834 2.920391e-25 531s sens1 0.01082919 0.01502843 9.167967 0.7205799 4.891327e-01 531s sens2 0.07064553 0.01727803 10.944383 4.0887503 1.812078e-03 531s > 531s > ## Section 8.4: 531s > tv <- lmer(Sharpnessofmovement ~ TVset * Picture + 531s + (1 | Assessor:TVset) + (1 | Assessor:Picture) + 531s + (1 | Assessor:Picture:TVset) + (1 | Repeat) + (1 | Repeat:Picture) + 531s + (1 | Repeat:TVset) + (1 | Repeat:TVset:Picture) + (1 | Assessor), 531s + data = TVbo, 531s + control=lmerControl(optimizer="bobyqa")) 531s boundary (singular) fit: see help('isSingular') 531s > st <- step(tv) 532s boundary (singular) fit: see help('isSingular') 532s boundary (singular) fit: see help('isSingular') 532s boundary (singular) fit: see help('isSingular') 533s boundary (singular) fit: see help('isSingular') 533s boundary (singular) fit: see help('isSingular') 534s boundary (singular) fit: see help('isSingular') 534s boundary (singular) fit: see help('isSingular') 534s boundary (singular) fit: see help('isSingular') 535s boundary (singular) fit: see help('isSingular') 535s boundary (singular) fit: see help('isSingular') 535s boundary (singular) fit: see help('isSingular') 536s boundary (singular) fit: see help('isSingular') 536s boundary (singular) fit: see help('isSingular') 536s boundary (singular) fit: see help('isSingular') 537s boundary (singular) fit: see help('isSingular') 537s boundary (singular) fit: see help('isSingular') 537s boundary (singular) fit: see help('isSingular') 538s boundary (singular) fit: see help('isSingular') 538s boundary (singular) fit: see help('isSingular') 538s boundary (singular) fit: see help('isSingular') 538s boundary (singular) fit: see help('isSingular') 538s boundary (singular) fit: see help('isSingular') 539s boundary (singular) fit: see help('isSingular') 539s boundary (singular) fit: see help('isSingular') 539s boundary (singular) fit: see help('isSingular') 539s boundary (singular) fit: see help('isSingular') 539s boundary (singular) fit: see help('isSingular') 540s boundary (singular) fit: see help('isSingular') 540s boundary (singular) fit: see help('isSingular') 540s boundary (singular) fit: see help('isSingular') 540s boundary (singular) fit: see help('isSingular') 540s boundary (singular) fit: see help('isSingular') 540s boundary (singular) fit: see help('isSingular') 541s > (elim_tab_random8.4 <- st$random) 541s Backward reduced random-effect table: 541s 541s Eliminated npar logLik AIC LRT Df 541s 21 -412.70 867.41 541s (1 | Assessor:Picture:TVset) 1 20 -412.70 865.41 0.0000 1 541s (1 | Repeat) 2 19 -412.70 863.41 0.0000 1 541s (1 | Repeat:Picture) 3 18 -412.70 861.41 0.0000 1 541s (1 | Repeat:TVset) 4 17 -412.70 859.41 0.0000 1 541s (1 | Repeat:TVset:Picture) 5 16 -412.70 857.41 0.0000 1 541s (1 | Assessor:TVset) 0 15 -414.10 858.20 2.7891 1 541s (1 | Assessor:Picture) 0 15 -418.88 867.76 12.3473 1 541s (1 | Assessor) 0 15 -416.44 862.88 7.4698 1 541s Pr(>Chisq) 541s 541s (1 | Assessor:Picture:TVset) 1.0000000 541s (1 | Repeat) 1.0000000 541s (1 | Repeat:Picture) 0.9999996 541s (1 | Repeat:TVset) 1.0000000 541s (1 | Repeat:TVset:Picture) 1.0000000 541s (1 | Assessor:TVset) 0.0949061 . 541s (1 | Assessor:Picture) 0.0004416 *** 541s (1 | Assessor) 0.0062742 ** 541s --- 541s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 541s > (elim_tab_fixed8.4 <- st$fixed) 541s Backward reduced fixed-effect table: 541s Degrees of freedom method: Satterthwaite 541s 541s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 541s TVset:Picture 0 90.767 15.128 6 138 4.1777 0.0006845 *** 541s --- 541s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 541s > (an8.4 <- anova(get_model(st))) 541s Type III Analysis of Variance Table with Satterthwaite's method 541s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 541s TVset 1.765 0.8825 2 14 0.2437 0.7869818 541s Picture 51.857 17.2857 3 21 4.7735 0.0108785 * 541s TVset:Picture 90.767 15.1279 6 138 4.1777 0.0006845 *** 541s --- 541s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 541s > 541s > ## Section 8.5: 541s > # L <- matrix(0, ncol = 12, nrow = 6) 541s > # L[1, 7] <- L[2, 8] <- L[3, 9] <- L[4, 10] <- L[5, 11] <- L[6, 12] <- 1 541s > L <- cbind(array(0, dim=c(6, 6)), diag(6)) 541s > (con1_8.5 <- calcSatterth(tv, L)) 541s $denom 541s [1] 138 541s 541s $Fstat 541s [,1] 541s [1,] 4.177656 541s 541s $pvalue 541s [,1] 541s [1,] 0.0006844787 541s 541s $ndf 541s [1] 6 541s 541s > (con2_8.5 <- contest(tv, L)) 541s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 541s 1 90.76719 15.12786 6 138 4.177656 0.0006844787 541s > 541s > ## Section C: 541s > # m.carrots <- lmer(Preference ~ sens1 + sens2 + (1 + sens1 + sens2 | Consumer) + 541s > # (1 | product), data = carrots) 541s > # step(m.carrots, reduce.fixed = FALSE) 541s > (ran_C <- ranova(m.carrots)) 541s boundary (singular) fit: see help('isSingular') 542s boundary (singular) fit: see help('isSingular') 542s ANOVA-like table for random-effects: Single term deletions 542s 542s Model: 542s Preference ~ sens1 + sens2 + (1 + sens1 + sens2 | Consumer) + (1 | Product) 542s Warning message: 542s Model failed to converge with 1 negative eigenvalue: -1.5e+03 542s npar logLik AIC LRT Df 542s 11 -1869.7 3761.5 542s sens1 in (1 + sens1 + sens2 | Consumer) 8 -1870.7 3757.3 1.8274 3 542s sens2 in (1 + sens1 + sens2 | Consumer) 8 -1874.5 3765.0 9.5464 3 542s (1 | Product) 10 -1878.7 3777.4 17.9080 1 542s Pr(>Chisq) 542s 542s sens1 in (1 + sens1 + sens2 | Consumer) 0.60899 542s sens2 in (1 + sens1 + sens2 | Consumer) 0.02284 * 542s (1 | Product) 2.318e-05 *** 542s --- 542s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 542s > 542s > # Compare to validated outputs: 542s > TOL <- 1e-4 542s > stopifnot( 542s + isTRUE(all.equal(an8.2_save, an8.2, check.attributes = FALSE, tolerance=TOL)), 542s + isTRUE(all.equal(sum8.3_save, sum8.3, check.attributes = FALSE, tolerance=TOL)), 542s + isTRUE(all.equal(elim_tab_random8.4_save, elim_tab_random8.4, 542s + check.attributes = FALSE, tolerance=TOL)), 542s + isTRUE(all.equal(elim_tab_fixed8.4_save, elim_tab_fixed8.4, 542s + check.attributes = FALSE, tolerance=TOL)), 542s + isTRUE(all.equal(an8.4_save, an8.4, check.attributes = FALSE, tolerance=TOL)), 542s + isTRUE(all.equal(con1_8.5_save, con1_8.5, check.attributes = FALSE, tolerance=TOL)), 542s + isTRUE(all.equal(con2_8.5_save, con2_8.5, check.attributes = FALSE, tolerance=TOL)) 542s + ) 542s > if(has_pbkrtest) { 542s + stopifnot( 542s + isTRUE(all.equal(ankr8.2_save, ankr8.2, check.attributes = FALSE, tolerance=TOL)) 542s + ) 542s + } 542s > 542s > 542s BEGIN TEST test_ls_means.R 542s 542s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 542s Copyright (C) 2025 The R Foundation for Statistical Computing 542s Platform: arm-unknown-linux-gnueabihf (32-bit) 542s 542s R is free software and comes with ABSOLUTELY NO WARRANTY. 542s You are welcome to redistribute it under certain conditions. 542s Type 'license()' or 'licence()' for distribution details. 542s 542s R is a collaborative project with many contributors. 542s Type 'contributors()' for more information and 542s 'citation()' on how to cite R or R packages in publications. 542s 542s Type 'demo()' for some demos, 'help()' for on-line help, or 542s 'help.start()' for an HTML browser interface to help. 542s Type 'q()' to quit R. 542s 542s Loading required package: lme4 542s > # test_lsmeans.R 542s > 542s > library(lmerTest) 542s Loading required package: Matrix 544s 544s Attaching package: 'lmerTest' 544s 544s The following object is masked from 'package:lme4': 544s 544s lmer 544s 544s The following object is masked from 'package:stats': 544s 544s step 544s 544s > 544s > TOL <- 1e-4 544s > # Kenward-Roger only available with pbkrtest and only then validated in R >= 3.3.3 544s > # (faulty results for R < 3.3.3 may be due to unstated dependencies in pbkrtest) 544s > has_pbkrtest <- requireNamespace("pbkrtest", quietly = TRUE) && getRversion() >= "3.3.3" 545s > 545s > ########### Basic model structures: 545s > 545s > # Factor * covariate: 545s > data("cake", package="lme4") 545s > model <- lmer(angle ~ recipe * temp + (1|recipe:replicate), cake) 545s > (lsm <- ls_means(model)) 545s Least Squares Means table: 545s 545s Estimate Std. Error df t value lower upper Pr(>|t|) 545s recipeA 33.1222 1.7368 42 19.070 29.6172 36.6273 < 2.2e-16 *** 545s recipeB 31.6444 1.7368 42 18.220 28.1394 35.1495 < 2.2e-16 *** 545s recipeC 31.6000 1.7368 42 18.194 28.0949 35.1051 < 2.2e-16 *** 545s --- 545s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 545s 545s Confidence level: 95% 545s Degrees of freedom method: Satterthwaite 545s > stopifnot( 545s + nrow(lsm) == 3L, 545s + ncol(lsm) == 7L, 545s + # Balanced, so LS-means equal raw means: 545s + isTRUE(all.equal(c(with(cake, tapply(angle, recipe, mean))), lsm[, "Estimate"], 545s + check.attributes=FALSE, tolerance=TOL)) 545s + ) 545s > 545s > # Pairwise differences of LS-means: 545s > plsm <- ls_means(model, pairwise = TRUE) 545s > plsm2 <- difflsmeans(model) 545s > C <- as.matrix(lmerTest:::get_pairs(rownames(lsm))) 545s > stopifnot( 545s + isTRUE(all.equal(plsm, plsm2, tolerance=TOL)), 545s + isTRUE(all.equal(plsm[, "Estimate"], c(lsm[, "Estimate"] %*% C), 545s + check.attributes=FALSE, tolerance=TOL)) 545s + ) 545s > 545s > # Contrasts vectors: 545s > show_tests(lsm) 545s $recipe 545s (Intercept) recipeB recipeC temp recipeB:temp recipeC:temp 545s recipeA 1 0 0 200 0 0 545s recipeB 1 1 0 200 200 0 545s recipeC 1 0 1 200 0 200 545s 545s > show_tests(plsm) 545s $recipe 545s (Intercept) recipeB recipeC temp recipeB:temp recipeC:temp 545s recipeA - recipeB 0 -1 0 0 -200 0 545s recipeA - recipeC 0 0 -1 0 0 -200 545s recipeB - recipeC 0 1 -1 0 200 -200 545s 545s > 545s > # Factor * Ordered: 545s > model <- lmer(angle ~ recipe * temperature + (1|recipe:replicate), cake) 545s > (lsm2 <- ls_means(model)) 545s Least Squares Means table: 545s 545s Estimate Std. Error df t value lower upper 545s recipeA 33.1222 1.7368 42.0 19.070 29.6172 36.6273 545s recipeB 31.6444 1.7368 42.0 18.220 28.1394 35.1495 545s recipeC 31.6000 1.7368 42.0 18.194 28.0949 35.1051 545s temperature175 27.9778 1.1767 77.4 23.776 25.6349 30.3207 545s temperature185 29.9556 1.1767 77.4 25.457 27.6127 32.2985 545s temperature195 31.4222 1.1767 77.4 26.704 29.0793 33.7651 545s temperature205 32.1778 1.1767 77.4 27.346 29.8349 34.5207 545s temperature215 35.8444 1.1767 77.4 30.462 33.5015 38.1873 545s temperature225 35.3556 1.1767 77.4 30.046 33.0127 37.6985 545s recipeA:temperature175 29.1333 2.0381 77.4 14.294 25.0753 33.1913 545s recipeB:temperature175 26.8667 2.0381 77.4 13.182 22.8087 30.9247 545s recipeC:temperature175 27.9333 2.0381 77.4 13.706 23.8753 31.9913 545s recipeA:temperature185 31.5333 2.0381 77.4 15.472 27.4753 35.5913 545s recipeB:temperature185 29.4000 2.0381 77.4 14.425 25.3420 33.4580 545s recipeC:temperature185 28.9333 2.0381 77.4 14.196 24.8753 32.9913 545s recipeA:temperature195 30.8000 2.0381 77.4 15.112 26.7420 34.8580 545s recipeB:temperature195 31.7333 2.0381 77.4 15.570 27.6753 35.7913 545s recipeC:temperature195 31.7333 2.0381 77.4 15.570 27.6753 35.7913 545s recipeA:temperature205 33.5333 2.0381 77.4 16.453 29.4753 37.5913 545s recipeB:temperature205 32.1333 2.0381 77.4 15.766 28.0753 36.1913 545s recipeC:temperature205 30.8667 2.0381 77.4 15.145 26.8087 34.9247 545s recipeA:temperature215 38.6667 2.0381 77.4 18.972 34.6087 42.7247 545s recipeB:temperature215 34.4667 2.0381 77.4 16.911 30.4087 38.5247 545s recipeC:temperature215 34.4000 2.0381 77.4 16.878 30.3420 38.4580 545s recipeA:temperature225 35.0667 2.0381 77.4 17.206 31.0087 39.1247 545s recipeB:temperature225 35.2667 2.0381 77.4 17.304 31.2087 39.3247 545s recipeC:temperature225 35.7333 2.0381 77.4 17.533 31.6753 39.7913 545s Pr(>|t|) 545s recipeA < 2.2e-16 *** 545s recipeB < 2.2e-16 *** 545s recipeC < 2.2e-16 *** 545s temperature175 < 2.2e-16 *** 545s temperature185 < 2.2e-16 *** 545s temperature195 < 2.2e-16 *** 545s temperature205 < 2.2e-16 *** 545s temperature215 < 2.2e-16 *** 545s temperature225 < 2.2e-16 *** 545s recipeA:temperature175 < 2.2e-16 *** 545s recipeB:temperature175 < 2.2e-16 *** 545s recipeC:temperature175 < 2.2e-16 *** 545s recipeA:temperature185 < 2.2e-16 *** 545s recipeB:temperature185 < 2.2e-16 *** 545s recipeC:temperature185 < 2.2e-16 *** 545s recipeA:temperature195 < 2.2e-16 *** 545s recipeB:temperature195 < 2.2e-16 *** 545s recipeC:temperature195 < 2.2e-16 *** 545s recipeA:temperature205 < 2.2e-16 *** 545s recipeB:temperature205 < 2.2e-16 *** 545s recipeC:temperature205 < 2.2e-16 *** 545s recipeA:temperature215 < 2.2e-16 *** 545s recipeB:temperature215 < 2.2e-16 *** 545s recipeC:temperature215 < 2.2e-16 *** 545s recipeA:temperature225 < 2.2e-16 *** 545s recipeB:temperature225 < 2.2e-16 *** 545s recipeC:temperature225 < 2.2e-16 *** 545s --- 545s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 545s 545s Confidence level: 95% 545s Degrees of freedom method: Satterthwaite 545s > stopifnot( 545s + nrow(lsm2) == 3 + 6 + 3*6, 545s + ncol(lsm) == 7L, 545s + # Balanced, so LS-means equal raw means: 545s + isTRUE(all.equal(lsm[1:3, ], lsm2[1:3, ], 545s + check.attributes=FALSE, tolerance=TOL)) 545s + ) 545s > 545s > 545s > # Factor * Factor: 545s > cake2 <- cake 545s > cake2$temperature <- factor(cake2$temperature, ordered = FALSE) 545s > model <- lmer(angle ~ recipe * temperature + (1|recipe:replicate), cake2) 545s > (lsm3 <- ls_means(model)) 545s Least Squares Means table: 545s 545s Estimate Std. Error df t value lower upper 545s recipeA 33.1222 1.7368 42.0 19.070 29.6172 36.6273 545s recipeB 31.6444 1.7368 42.0 18.220 28.1394 35.1495 545s recipeC 31.6000 1.7368 42.0 18.194 28.0949 35.1051 545s temperature175 27.9778 1.1767 77.4 23.776 25.6349 30.3207 545s temperature185 29.9556 1.1767 77.4 25.457 27.6127 32.2985 545s temperature195 31.4222 1.1767 77.4 26.704 29.0793 33.7651 545s temperature205 32.1778 1.1767 77.4 27.346 29.8349 34.5207 545s temperature215 35.8444 1.1767 77.4 30.462 33.5015 38.1873 545s temperature225 35.3556 1.1767 77.4 30.046 33.0127 37.6985 545s recipeA:temperature175 29.1333 2.0381 77.4 14.294 25.0753 33.1913 545s recipeB:temperature175 26.8667 2.0381 77.4 13.182 22.8087 30.9247 545s recipeC:temperature175 27.9333 2.0381 77.4 13.706 23.8753 31.9913 545s recipeA:temperature185 31.5333 2.0381 77.4 15.472 27.4753 35.5913 545s recipeB:temperature185 29.4000 2.0381 77.4 14.425 25.3420 33.4580 545s recipeC:temperature185 28.9333 2.0381 77.4 14.196 24.8753 32.9913 545s recipeA:temperature195 30.8000 2.0381 77.4 15.112 26.7420 34.8580 545s recipeB:temperature195 31.7333 2.0381 77.4 15.570 27.6753 35.7913 545s recipeC:temperature195 31.7333 2.0381 77.4 15.570 27.6753 35.7913 545s recipeA:temperature205 33.5333 2.0381 77.4 16.453 29.4753 37.5913 545s recipeB:temperature205 32.1333 2.0381 77.4 15.766 28.0753 36.1913 545s recipeC:temperature205 30.8667 2.0381 77.4 15.145 26.8087 34.9247 545s recipeA:temperature215 38.6667 2.0381 77.4 18.972 34.6087 42.7247 545s recipeB:temperature215 34.4667 2.0381 77.4 16.911 30.4087 38.5247 545s recipeC:temperature215 34.4000 2.0381 77.4 16.878 30.3420 38.4580 545s recipeA:temperature225 35.0667 2.0381 77.4 17.206 31.0087 39.1247 545s recipeB:temperature225 35.2667 2.0381 77.4 17.304 31.2087 39.3247 545s recipeC:temperature225 35.7333 2.0381 77.4 17.533 31.6753 39.7913 545s Pr(>|t|) 545s recipeA < 2.2e-16 *** 545s recipeB < 2.2e-16 *** 545s recipeC < 2.2e-16 *** 545s temperature175 < 2.2e-16 *** 545s temperature185 < 2.2e-16 *** 545s temperature195 < 2.2e-16 *** 545s temperature205 < 2.2e-16 *** 545s temperature215 < 2.2e-16 *** 545s temperature225 < 2.2e-16 *** 545s recipeA:temperature175 < 2.2e-16 *** 545s recipeB:temperature175 < 2.2e-16 *** 545s recipeC:temperature175 < 2.2e-16 *** 545s recipeA:temperature185 < 2.2e-16 *** 545s recipeB:temperature185 < 2.2e-16 *** 545s recipeC:temperature185 < 2.2e-16 *** 545s recipeA:temperature195 < 2.2e-16 *** 545s recipeB:temperature195 < 2.2e-16 *** 545s recipeC:temperature195 < 2.2e-16 *** 545s recipeA:temperature205 < 2.2e-16 *** 545s recipeB:temperature205 < 2.2e-16 *** 545s recipeC:temperature205 < 2.2e-16 *** 545s recipeA:temperature215 < 2.2e-16 *** 545s recipeB:temperature215 < 2.2e-16 *** 545s recipeC:temperature215 < 2.2e-16 *** 545s recipeA:temperature225 < 2.2e-16 *** 545s recipeB:temperature225 < 2.2e-16 *** 545s recipeC:temperature225 < 2.2e-16 *** 545s --- 545s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 545s 545s Confidence level: 95% 545s Degrees of freedom method: Satterthwaite 545s > stopifnot( 545s + isTRUE(all.equal(lsm2, lsm3, check.attributes=FALSE, tolerance=TOL)) 545s + ) 545s > 545s > # Covariate (only): 545s > data("sleepstudy", package="lme4") 545s > m <- lmer(Reaction ~ Days + (Days | Subject), sleepstudy) 545s > (lsm <- ls_means(m)) 545s Least Squares Means table: 545s 545s Estimate Std. Error df t value lower upper Pr(>|t|) 545s 545s Confidence level: 95% 545s Degrees of freedom method: Satterthwaite 545s > stopifnot( 545s + nrow(lsm) == 0L, 545s + ncol(lsm) == 7L 545s + ) 545s > 545s > # No fixef: 545s > m <- lmer(Reaction ~ 0 + (Days | Subject), sleepstudy) 545s > (lsm <- ls_means(m)) 545s Least Squares Means table: 545s 545s Estimate Std. Error df t value lower upper Pr(>|t|) 545s 545s Confidence level: 95% 545s Degrees of freedom method: Satterthwaite 545s > stopifnot( 545s + nrow(lsm) == 0L, 545s + ncol(lsm) == 7L 545s + ) 545s > 545s > ########### Arguments and options: 545s > 545s > # which 545s > model <- lmer(angle ~ recipe * temperature + (1|recipe:replicate), cake2) 545s > (lsm4 <- ls_means(model, which = "recipe")) 545s Least Squares Means table: 545s 545s Estimate Std. Error df t value lower upper Pr(>|t|) 545s recipeA 33.1222 1.7368 42 19.070 29.6172 36.6273 < 2.2e-16 *** 545s recipeB 31.6444 1.7368 42 18.220 28.1394 35.1495 < 2.2e-16 *** 545s recipeC 31.6000 1.7368 42 18.194 28.0949 35.1051 < 2.2e-16 *** 545s --- 545s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 545s 545s Confidence level: 95% 545s Degrees of freedom method: Satterthwaite 545s > stopifnot( 545s + nrow(lsm4) == 3L, 545s + ncol(lsm4) == 7L, 545s + isTRUE(all.equal(lsm3[1:3, ], lsm4, check.attributes=FALSE, tolerance=TOL)) 545s + ) 545s > 545s > # KR: 545s > if(has_pbkrtest) 545s + (lsm5 <- ls_means(model, which = "recipe", ddf = "Kenward-Roger")) 546s Least Squares Means table: 546s 546s Estimate Std. Error df t value lower upper Pr(>|t|) 546s recipeA 33.1222 1.7368 42 19.070 29.6172 36.6273 < 2.2e-16 *** 546s recipeB 31.6444 1.7368 42 18.220 28.1394 35.1495 < 2.2e-16 *** 546s recipeC 31.6000 1.7368 42 18.194 28.0949 35.1051 < 2.2e-16 *** 546s --- 546s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 546s 546s Confidence level: 95% 546s Degrees of freedom method: Kenward-Roger 546s > 546s > # level: 546s > (lsm6 <- ls_means(model, which = "recipe", level=0.99)) 546s Least Squares Means table: 546s 546s Estimate Std. Error df t value lower upper Pr(>|t|) 546s recipeA 33.1222 1.7368 42 19.070 28.4361 37.8083 < 2.2e-16 *** 546s recipeB 31.6444 1.7368 42 18.220 26.9584 36.3305 < 2.2e-16 *** 546s recipeC 31.6000 1.7368 42 18.194 26.9139 36.2861 < 2.2e-16 *** 546s --- 546s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 546s 546s Confidence level: 99% 546s Degrees of freedom method: Satterthwaite 546s > 546s > stopifnot( 546s + all(lsm6[, "lower"] < lsm4[, "lower"]), 546s + all(lsm6[, "upper"] > lsm4[, "upper"]) 546s + ) 546s > 546s > 546s > 546s > ########### Missing cels -> unestimable contrasts: 546s > 546s > # Missing cell: 546s > cake3 <- cake 546s > cake3$temperature <- factor(cake3$temperature, ordered=FALSE) 546s > cake3 <- droplevels(subset(cake3, temperature %in% levels(cake3$temperature)[1:3])) 546s > cake3 <- droplevels(subset(cake3, !(recipe == "C" & temperature == "195") )) 546s > str(cake3) 546s 'data.frame': 120 obs. of 5 variables: 546s $ replicate : Factor w/ 15 levels "1","2","3","4",..: 1 1 1 1 1 1 1 1 2 2 ... 546s $ recipe : Factor w/ 3 levels "A","B","C": 1 1 1 2 2 2 3 3 1 1 ... 546s $ temperature: Factor w/ 3 levels "175","185","195": 1 2 3 1 2 3 1 2 1 2 ... 546s $ angle : int 42 46 47 39 46 51 46 44 47 29 ... 546s $ temp :fixed-effect model matrix is rank deficient so dropping 1 column / coefficient 546s num 175 185 195 175 185 195 175 185 175 185 ... 546s > with(cake3, table(recipe, temperature)) 546s temperature 546s recipe 175 185 195 546s A 15 15 15 546s B 15 15 15 546s C 15 15 0 546s > model <- lmer(angle ~ recipe * temperature + (1|recipe:replicate), cake3) 546s > (lsm7 <- ls_means(model)) 546s Least Squares Means table: 546s 546s Estimate Std. Error df t value lower upper 546s recipeA 30.4889 1.7407 40.3 17.515 26.9716 34.0062 546s recipeB 29.3333 1.7407 40.3 16.851 25.8160 32.8506 546s recipeC NA NA NA NA NA NA 546s temperature175 27.9778 1.1016 57.2 25.398 25.7720 30.1835 546s temperature185 29.9556 1.1016 57.2 27.193 27.7498 32.1613 546s temperature195 NA NA NA NA NA NA 546s recipeA:temperature175 29.1333 1.9080 57.2 15.269 25.3129 32.9538 546s recipeB:temperature175 26.8667 1.9080 57.2 14.081 23.0462 30.6871 546s recipeC:temperature175 27.9333 1.9080 57.2 14.640 24.1129 31.7538 546s recipeA:temperature185 31.5333 1.9080 57.2 16.527 27.7129 35.3538 546s recipeB:temperature185 29.4000 1.9080 57.2 15.409 25.5795 33.2205 546s recipeC:temperature185 28.9333 1.9080 57.2 15.164 25.1129 32.7538 546s recipeA:temperature195 30.8000 1.9080 57.2 16.143 26.9795 34.6205 546s recipeB:temperature195 31.7333 1.9080 57.2 16.632 27.9129 35.5538 546s recipeC:temperature195 NA NA NA NA NA NA 546s Pr(>|t|) 546s recipeA < 2.2e-16 *** 546s recipeB < 2.2e-16 *** 546s recipeC NA 546s temperature175 < 2.2e-16 *** 546s temperature185 < 2.2e-16 *** 546s temperature195 NA 546s recipeA:temperature175 < 2.2e-16 *** 546s recipeB:temperature175 < 2.2e-16 *** 546s recipeC:temperature175 < 2.2e-16 *** 546s recipeA:temperature185 < 2.2e-16 *** 546s recipeB:temperature185 < 2.2e-16 *** 546s recipeC:temperature185 < 2.2e-16 *** 546s recipeA:temperature195 < 2.2e-16 *** 546s recipeB:temperature195 < 2.2e-16 *** 546s recipeC:temperature195 NA 546s --- 546s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 546s 546s Confidence level: 95% 546s Degrees of freedom method: Satterthwaite 546s > 546s > # Using show_tests with options: 546s > show_tests(lsm7, fractions = TRUE) 546s $recipe 546s (Intercept) recipeB recipeC temperature185 temperature195 546s recipeA 1 0 0 1/3 1/3 546s recipeB 1 1 0 1/3 1/3 546s recipeC 1 0 1 1/3 1/3 546s recipeB:temperature185 recipeC:temperature185 recipeB:temperature195 546s recipeA 0 0 0 546s recipeB 1/3 0 1/3 546s recipeC 0 1/3 0 546s recipeC:temperature195 546s recipeA 0 546s recipeB 0 546s recipeC 1/3 546s 546s $temperature 546s (Intercept) recipeB recipeC temperature185 temperature195 546s temperature175 1 1/3 1/3 0 0 546s temperature185 1 1/3 1/3 1 0 546s temperature195 1 1/3 1/3 0 1 546s recipeB:temperature185 recipeC:temperature185 546s temperature175 0 0 546s temperature185 1/3 1/3 546s temperature195 0 0 546s recipeB:temperature195 recipeC:temperature195 546s temperature175 0 0 546s temperature185 0 0 546s temperature195 1/3 1/3 546s 546s $`recipe:temperature` 546s (Intercept) recipeB recipeC temperature185 546s recipeA:temperature175 1 0 0 0 546s recipeB:temperature175 1 1 0 0 546s recipeC:temperature175 1 0 1 0 546s recipeA:temperature185 1 0 0 1 546s recipeB:temperature185 1 1 0 1 546s recipeC:temperature185 1 0 1 1 546s recipeA:temperature195 1 0 0 0 546s recipeB:temperature195 1 1 0 0 546s recipeC:temperature195 1 0 1 0 546s temperature195 recipeB:temperature185 546s recipeA:temperature175 0 0 546s recipeB:temperature175 0 0 546s recipeC:temperature175 0 0 546s recipeA:temperature185 0 0 546s recipeB:temperature185 0 1 546s recipeC:temperature185 0 0 546s recipeA:temperature195 1 0 546s recipeB:temperature195 1 0 546s recipeC:temperature195 1 0 546s recipeC:temperature185 recipeB:temperature195 546s recipeA:temperature175 0 0 546s recipeB:temperature175 0 0 546s recipeC:temperature175 0 0 546s recipeA:temperature185 0 0 546s recipeB:temperature185 0 0 546s recipeC:temperature185 1 0 546s recipeA:temperature195 0 0 546s recipeB:temperature195 0 1 546s recipeC:temperature195 0 0 546s recipeC:temperature195 546s recipeA:temperature175 0 546s recipeB:temperature175 0 546s recipeC:temperature175 0 546s recipeA:temperature185 0 546s recipeB:temperature185 0 546s recipeC:temperature185 0 546s recipeA:temperature195 0 546s recipeB:temperature195 0 546s recipeC:temperature195 1 546s 546s > show_tests(lsm7, fractions = TRUE, names = FALSE) 546s $recipe 546s [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] 546s [1,] 1 0 0 1/3 1/3 0 0 0 0 546s [2,] 1 1 0 1/3 1/3 1/3 0 1/3 0 546s [3,] 1 0 1 1/3 1/3 0 1/3 0 1/3 546s 546s $temperature 546s [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] 546s [1,] 1 1/3 1/3 0 0 0 0 0 0 546s [2,] 1 1/3 1/3 1 0 1/3 1/3 0 0 546s [3,] 1 1/3 1/3 0 1 0 0 1/3 1/3 546s 546s $`recipe:temperature` 546s [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] 546s [1,] 1 0 0 0 0 0 0 0 0 546s [2,] 1 1 0 0 0 0 0 0 0 546s [3,] 1 0 1 0 0 0 0 0 0 546s [4,] 1 0 0 1 0 0 0 0 0 546s [5,] 1 1 0 1 0 1 0 0 0 546s [6,] 1 0 1 1 0 0 1 0 0 546s [7,] 1 0 0 0 1 0 0 0 0 546s [8,] 1 1 0 0 1 0 0 1 0 546s [9,] 1 0 1 0 1 0 0 0 1 546s 546s > 546s > # Missing diagonal: 546s > cake4 <- cake 546s > cake4$temperature <- factor(cake4$temperature, ordered=FALSE) 546s > cake4 <- droplevels(subset(cake4, temperature %in% levels(cake4$temperature)[1:3])) 546s > cake4 <- droplevels(subset(cake4, !((recipe == "A" & temperature == "175") | 546s + (recipe == "B" & temperature == "185") | 546s + (recipe == "C" & temperature == "195") ))) 546s > # str(cake4) 546s > with(cake4, table(recipe, temperature)) 546s temperature 546s recipe 175 185 195 546s A 0 15 15 546s B 15 0 15 546s C 15 15 0 546s > model <- lmer(angle ~ recipe * temperature + (1|recipe:replicate), cake4) 546s fixed-effect model matrix is rank deficient so dropping 3 columns / coefficients 546s > ls_means(model) 546s Least Squares Means table: 546s 546s Estimate Std. Error df t value lower upper 546s recipeA NA NA NA NA NA NA 546s recipeB NA NA NA NA NA NA 546s recipeC NA NA NA NA NA NA 546s temperature175 NA NA NA NA NA NA 546s temperature185 NA NA NA NA NA NA 546s temperature195 NA NA NA NA NA NA 546s recipeA:temperature175 NA NA NA NA NA NA 546s recipeB:temperature175 26.8667 1.8908 53.5 14.209 23.0750 30.6584 546s recipeC:temperature175 27.9333 1.8908 53.5 14.773 24.1416 31.7250 546s recipeA:temperature185 31.5333 1.8908 53.5 16.677 27.7416 35.3250 546s recipeB:temperature185 NA NA NA NA NA NA 546s recipeC:temperature185 28.9333 1.8908 53.5 15.302 25.1416 32.7250 546s recipeA:temperature195 30.8000 1.8908 53.5 16.289 27.0083 34.5917 546s recipeB:temperature195 31.7333 1.8908 53.5 16.783 27.9416 35.5250 546s recipeC:temperature195 NA NA NA NA NA NA 546s Pr(>|t|) 546s recipeA NA 546s recipeB NA 546s recipeC NA 546s temperature175 NA 546s temperature185 NA 546s temperature195 NA 546s recipeA:temperature175 NA 546s recipeB:temperature175 < 2.2e-16 *** 546s recipeC:temperature175 < 2.2e-16 *** 546s recipeA:temperature185 < 2.2e-16 *** 546s recipeB:temperature185 NA 546s recipeC:temperature185 < 2.2e-16 *** 546s recipeA:temperature195 < 2.2e-16 *** 546s recipeB:temperature195 < 2.2e-16 *** 546s recipeC:temperature195 NA 546s --- 546s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 546s 546s Confidence level: 95% 546s Degrees of freedom method: Satterthwaite 546s > 546s > 546s > ########### Various contrasts codings: 546s > 546s > model <- lmer(angle ~ recipe * temperature + (1|recipe:replicate), cake3, 546s + contrasts = list(recipe="contr.sum", temperature="contr.helmert")) 546s fixed-effect model matrix is rank deficient so dropping 1 column / coefficient 546s > (lsm8 <- ls_means(model)) 546s Least Squares Means table: 546s 546s Estimate Std. Error df t value lower upper 546s recipeA 30.4889 1.7407 40.3 17.515 26.9716 34.0062 546s recipeB 29.3333 1.7407 40.3 16.851 25.8160 32.8506 546s recipeC NA NA NA NA NA NA 546s temperature175 27.9778 1.1016 57.2 25.398 25.7720 30.1835 546s temperature185 29.9556 1.1016 57.2 27.193 27.7498 32.1613 546s temperature195 NA NA NA NA NA NA 546s recipeA:temperature175 29.1333 1.9080 57.2 15.269 25.3129 32.9538 546s recipeB:temperature175 26.8667 1.9080 57.2 14.081 23.0462 30.6871 546s recipeC:temperature175 27.9333 1.9080 57.2 14.640 24.1129 31.7538 546s recipeA:temperature185 31.5333 1.9080 57.2 16.527 27.7129 35.3538 546s recipeB:temperature185 29.4000 1.9080 57.2 15.409 25.5795 33.2205 546s recipeC:temperature185 28.9333 1.9080 57.2 15.164 25.1129 32.7538 546s recipeA:temperature195 30.8000 1.9080 57.2 16.143 26.9795 34.6205 546s recipeB:temperature195 31.7333 1.9080 57.2 16.632 27.9129 35.5538 546s recipeC:temperature195 NA NA NA NA NA NA 546s Pr(>|t|) 546s recipeA < 2.2e-16 *** 546s recipeB < 2.2e-16 *** 546s recipeC NA 546s temperature175 < 2.2e-16 *** 546s temperature185 < 2.2e-16 *** 546s temperature195 NA 546s recipeA:temperature175 < 2.2e-16 *** 546s recipeB:temperature175 < 2.2e-16 *** 546s recipeC:temperature175 < 2.2e-16 *** 546s recipeA:temperature185 < 2.2e-16 *** 546s recipeB:temperature185 < 2.2e-16 *** 546s recipeC:temperature185 < 2.2e-16 *** 546s recipeA:temperature195 < 2.2e-16 *** 546s recipeB:temperature195 < 2.2e-16 *** 546s recipeC:temperature195 NA 546s --- 546s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 546s 546s Confidence level: 95% 546s Degrees of freedom method: Satterthwaite 546s > # show_tests(lsm7) 546s > # show_tests(lsm8) 546s > stopifnot( 546s + isTRUE(all.equal(lsm7, lsm8, check.attributes=FALSE, tolerance=TOL)) 546s + ) 546s > 546s > # ambient contrasts not contr.treatment: 546s > options("contrasts") 546s $contrasts 546s unordered ordered 546s "contr.treatment" "contr.poly" 546s 546s > options(contrasts = c("contr.sum", "contr.poly")) 546s > model <- lmer(angle ~ recipe * temperature + (1|recipe:replicate), cake3) 546s fixed-effect model matrix is rank deficient so dropping 1 column / coefficient 546s > (lsm9 <- ls_means(model)) 546s Least Squares Means table: 546s 546s Estimate Std. Error df t value lower upper 546s recipeA 30.4889 1.7407 40.3 17.515 26.9716 34.0062 546s recipeB 29.3333 1.7407 40.3 16.851 25.8160 32.8506 546s recipeC NA NA NA NA NA NA 546s temperature175 27.9778 1.1016 57.2 25.398 25.7720 30.1835 546s temperature185 29.9556 1.1016 57.2 27.193 27.7498 32.1613 546s temperature195 NA NA NA NA NA NA 546s recipeA:temperature175 29.1333 1.9080 57.2 15.269 25.3129 32.9538 546s recipeB:temperature175 26.8667 1.9080 57.2 14.081 23.0462 30.6871 546s recipeC:temperature175 27.9333 1.9080 57.2 14.640 24.1129 31.7538 546s recipeA:temperature185 31.5333 1.9080 57.2 16.527 27.7129 35.3538 546s recipeB:temperature185 29.4000 1.9080 57.2 15.409 25.5795 33.2205 546s recipeC:temperature185 28.9333 1.9080 57.2 15.164 25.1129 32.7538 546s recipeA:temperature195 30.8000 1.9080 57.2 16.143 26.9795 34.6205 546s recipeB:temperature195 31.7333 1.9080 57.2 16.632 27.9129 35.5538 546s recipeC:temperature195 NA NA NA NA NA NA 546s Pr(>|t|) 546s recipeA < 2.2e-16 *** 546s recipeB < 2.2e-16 *** 546s recipeC NA 546s temperature175 < 2.2e-16 *** 546s temperature185 < 2.2e-16 *** 546s temperature195 NA 546s recipeA:temperature175 < 2.2e-16 *** 546s recipeB:temperature175 < 2.2e-16 *** 546s recipeC:temperature175 < 2.2e-16 *** 546s recipeA:temperature185 < 2.2e-16 *** 546s recipeB:temperature185 < 2.2e-16 *** 546s recipeC:temperature185 < 2.2e-16 *** 546s recipeA:temperature195 < 2.2e-16 *** 546s recipeB:temperature195 < 2.2e-16 *** 546s recipeC:temperature195 NA 546s --- 546s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 546s 546s Confidence level: 95% 546s Degrees of freedom method: Satterthwaite 546s > options(contrasts = c("contr.treatment", "contr.poly")) 546s > options("contrasts") 546s $contrasts 546s [1] "contr.treatment" "contr.poly" 546s 546s > stopifnot( 546s + isTRUE(all.equal(lsm7, lsm9, check.attributes=FALSE, tolerance=TOL)) 546s + ) 546s > 546s > 546s > 546s BEGIN TEST test_ranova_step.R 546s 546s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 546s Copyright (C) 2025 The R Foundation for Statistical Computing 546s Platform: arm-unknown-linux-gnueabihf (32-bit) 546s 546s R is free software and comes with ABSOLUTELY NO WARRANTY. 546s You are welcome to redistribute it under certain conditions. 546s Type 'license()' or 'licence()' for distribution details. 546s 546s R is a collaborative project with many contributors. 546s Type 'contributors()' for more information and 546s 'citation()' on how to cite R or R packages in publications. 546s 546s Type 'demo()' for some demos, 'help()' for on-line help, or 546s 'help.start()' for an HTML browser interface to help. 546s Type 'q()' to quit R. 546s 546s > # test_ranova.R 546s > 546s > # Test functionality _before_ attaching lmerTest 546s > stopifnot(!"lmerTest" %in% .packages()) # ensure that lmerTest is NOT attached 546s > data("sleepstudy", package="lme4") 546s > f <- function(form, data) lmerTest::lmer(form, data=data) 546s > form <- "Reaction ~ Days + (Days|Subject)" 546s > fm <- f(form, data=sleepstudy) 549s > lmerTest::ranova(fm) 549s ANOVA-like table for random-effects: Single term deletions 549s 549s Model: 549s Reaction ~ Days + (Days | Subject) 549s npar logLik AIC LRT Df Pr(>Chisq) 549s 6 -871.81 1755.6 549s Days in (Days | Subject) 4 -893.23 1794.5 42.837 2 4.99e-10 *** 549s --- 549s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 549s > lmerTest::rand(fm) 549s ANOVA-like table for random-effects: Single term deletions 549s 549s Model: 549s Reaction ~ Days + (Days | Subject) 549s npar logLik AIC LRT Df Pr(>Chisq) 549s 6 -871.81 1755.6 549s Days in (Days | Subject) 4 -893.23 1794.5 42.837 2 4.99e-10 *** 549s --- 549s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 549s > lmerTest::step(fm) 549s Backward reduced random-effect table: 549s 549s Eliminated npar logLik AIC LRT Df Pr(>Chisq) 549s 6 -871.81 1755.6 549s Days in (Days | Subject) 0 4 -893.23 1794.5 42.837 2 4.99e-10 549s 549s 549s Days in (Days | Subject) *** 549s --- 549s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 549s 549s Backward reduced fixed-effect table: 549s Degrees of freedom method: Satterthwaite 549s 549s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 549s Days 0 30031 30031 1 17 45.853 3.264e-06 *** 549s --- 549s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 549s 549s Model found: 549s Reaction ~ Days + (Days | Subject) 549s > 549s > library(lmerTest) 549s Loading required package: lme4 549s Loading required package: Matrix 549s 549s Attaching package: 'lmerTest' 549s 549s The following object is masked from 'package:lme4': 549s 549s lmer 549s 549s The following object is masked from 'package:stats': 549s 549s step 549s 549s > 549s > # WRE says "using if(requireNamespace("pkgname")) is preferred, if possible." 549s > # even in tests: 549s > assertError <- function(expr, ...) 549s + if(requireNamespace("tools")) tools::assertError(expr, ...) else invisible() 549s > assertWarning <- function(expr, ...) 549s + if(requireNamespace("tools")) tools::assertWarning(expr, ...) else invisible() 549s > 549s > TOL <- 1e-4 549s > ##################################################################### 549s > data("sleepstudy", package="lme4") 549s > 549s > # Test reduction of (Days | Subject) to (1 | Subject): 549s > fm1 <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy) 549s > (an <- rand(fm1)) # 2 df test 549s ANOVA-like table for random-effects: Single term deletions 549s 549s Model: 549s Reaction ~ Days + (Days | Subject) 549s npar logLik AIC LRT Df Pr(>Chisq) 549s 6 -871.81 1755.6 549s Days in (Days | Subject) 4 -893.23 1794.5 42.837 2 4.99e-10 *** 549s --- 549s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 549s > (an <- ranova(fm1)) # 2 df test 549s ANOVA-like table for random-effects: Single term deletions 549s 549s Model: 549s Reaction ~ Days + (Days | Subject) 549s npar logLik AIC LRT Df Pr(>Chisq) 549s 6 -871.81 1755.6 549s Days in (Days | Subject) 4 -893.23 1794.5 42.837 2 4.99e-10 *** 549s --- 549s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 549s > step(fm1) 549s Backward reduced random-effect table: 549s 549s Eliminated npar logLik AIC LRT Df Pr(>Chisq) 549s 6 -871.81 1755.6 549s Days in (Days | Subject) 0 4 -893.23 1794.5 42.837 2 4.99e-10 549s 549s 549s Days in (Days | Subject) *** 549s --- 549s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 549s 549s Backward reduced fixed-effect table: 549s Degrees of freedom method: Satterthwaite 549s 549s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 549s Days 0 30031 30031 1 17 45.853 3.264e-06 *** 549s --- 549s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 549s 549s Model found: 549s Reaction ~ Days + (Days | Subject) 549s > stopifnot( 549s + nrow(an) == 2L, 549s + an[2L, "Df"] == 2L 549s + ) 549s > 549s > # This test can also be achieved with anova(): 549s > fm2 <- lmer(Reaction ~ Days + (1|Subject), sleepstudy) 549s > (stp <- step(fm2)) 549s Backward reduced random-effect table: 549s 549s Eliminated npar logLik AIC LRT Df Pr(>Chisq) 549s 4 -893.23 1794.5 549s (1 | Subject) 0 3 -946.83 1899.7 107.2 1 < 2.2e-16 *** 549s --- 549s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 549s 549s Backward reduced fixed-effect table: 549s Degrees of freedom method: Satterthwaite 549s 549s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 549s Days 0 162703 162703 1 161 169.4 < 2.2e-16 *** 549s --- 549s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 549s 549s Model found: 549s Reaction ~ Days + (1 | Subject) 549s > get_model(stp) 549s Linear mixed model fit by REML ['lmerModLmerTest'] 549s Formula: Reaction ~ Days + (1 | Subject) 549s Data: sleepstudy 549s REML criterion at convergence: 1786.465 549s Random effects: 549s Groups Name Std.Dev. 549s Subject (Intercept) 37.12 549s Residual 30.99 549s Number of obs: 180, groups: Subject, 18 549s Fixed Effects: 549s (Intercept) Days 549s 251.41 10.47 549s > (ana <- anova(fm1, fm2, refit=FALSE)) 549s Data: sleepstudy 549s Models: 549s fm2: Reaction ~ Days + (1 | Subject) 549s fm1: Reaction ~ Days + (Days | Subject) 549s npar AIC BIC logLik -2*log(L) Chisq Df Pr(>Chisq) 549s fm2 4 1794.5 1807.2 -893.23 1786.5 549s fm1 6 1755.6 1774.8 -871.81 1743.6 42.837 2 4.99e-10 *** 549s --- 549s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 549s > 549s > stopifnot( 549s + all.equal(an[2L, "LRT"], ana[2L, "Chisq"], tolerance=TOL) 549s + ) 549s > 549s > # Illustrate complete.test argument: 549s > # Test removal of (Days | Subject): 549s > (an <- ranova(fm1, reduce.terms = FALSE)) # 3 df test 549s ANOVA-like table for random-effects: Single term deletions 549s 549s Model: 549s Reaction ~ Days + (Days | Subject) 549s npar logLik AIC LRT Df Pr(>Chisq) 549s 6 -871.81 1755.6 549s (Days | Subject) 3 -946.83 1899.7 150.03 3 < 2.2e-16 *** 549s --- 549s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 549s > 549s > # The likelihood ratio test statistic is in this case: 549s > fm3 <- lm(Reaction ~ Days, sleepstudy) 549s > LRT <- 2*c(logLik(fm1, REML=TRUE) - logLik(fm3, REML=TRUE)) # LRT 549s > stopifnot( 549s + nrow(an) == 2L, 549s + an[2L, "Df"] == 3L, 549s + all.equal(an[2L, "LRT"], LRT, tolerance=TOL) 549s + ) 549s > 549s > ## _NULL_ model: 549s > fm <- lmer(Reaction ~ -1 + (1|Subject), sleepstudy) 550s > step(fm) 550s Backward reduced random-effect table: 550s 550s Eliminated npar logLik AIC LRT Df Pr(>Chisq) 550s 2 -992.84 1989.7 550s (1 | Subject) 0 1 -1284.32 2570.7 582.97 1 < 2.2e-16 *** 550s --- 550s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 550s 550s Backward reduced fixed-effect table: 550s Degrees of freedom method: Satterthwaite 550s 550s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 550s 550s Model found: 550s Reaction ~ -1 + (1 | Subject) 550s > ranova(fm) 550s ANOVA-like table for random-effects: Single term deletions 550s 550s Model: 550s Reaction ~ -1 + (1 | Subject) 550s npar logLik AIC LRT Df Pr(>Chisq) 550s 2 -992.84 1989.7 550s (1 | Subject) 1 -1284.32 2570.7 582.97 1 < 2.2e-16 *** 550s --- 550s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 550s > lm1 <- lm(Reaction ~ 0, data=sleepstudy) 550s > LRT <- 2*c(logLik(fm, REML=FALSE) - logLik(lm1, REML=FALSE)) 550s > 550s > ## Tests of ML-fits agree with anova(): 550s > fm1 <- lmer(Reaction ~ Days + (1|Subject), sleepstudy, REML=FALSE) 550s > step(fm1) 550s Backward reduced random-effect table: 550s 550s Eliminated npar logLik AIC LRT Df Pr(>Chisq) 550s 4 -897.04 1802.1 550s (1 | Subject) 0 3 -950.15 1906.3 106.21 1 < 2.2e-16 *** 550s --- 550s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 550s 550s Backward reduced fixed-effect table: 550s Degrees of freedom method: Satterthwaite 550s 550s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 550s Days 0 162703 162703 1 162 170.45 < 2.2e-16 *** 550s --- 550s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 550s 550s Model found: 550s Reaction ~ Days + (1 | Subject) 550s > lm2 <- lm(Reaction ~ Days, sleepstudy) 550s > (an1 <- ranova(fm1)) 550s ANOVA-like table for random-effects: Single term deletions 550s 550s Model: 550s Reaction ~ Days + (1 | Subject) 550s npar logLik AIC LRT Df Pr(>Chisq) 550s 4 -897.04 1802.1 550s (1 | Subject) 3 -950.15 1906.3 106.21 1 < 2.2e-16 *** 550s --- 550s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 550s > (an2 <- anova(fm1, lm2)) 550s Data: sleepstudy 550s Models: 550s lm2: Reaction ~ Days 550s fm1: Reaction ~ Days + (1 | Subject) 550s npar AIC BIC logLik -2*log(L) Chisq Df Pr(>Chisq) 550s lm2 3 1906.3 1915.9 -950.15 1900.3 550s fm1 4 1802.1 1814.8 -897.04 1794.1 106.21 1 < 2.2e-16 *** 550s --- 550s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 550s > j <- grep("Chi Df|Df", colnames(an2)) 550s > stopifnot( 550s + all.equal(an1[2, "LRT"], an2[2, "Chisq"], tolerance=TOL), 550s + all.equal(an1[2, "Df"], an2[2, j[length(j)]], tolerance=TOL), 550s + all.equal(an1[1:2, "logLik"], an2[2:1, "logLik"], tolerance=TOL) 550s + ) 550s > ## Note that lme4 version <1.1-22 use "Chi Df" while >=1.1-22 use "Df" 550s > 550s > # Expect warnings when old (version < 3.0-0) arguments are used: 550s > assertWarning(step(fm, reduce.fixed = FALSE, reduce.random = FALSE, 550s + type=3, fixed.calc = FALSE, lsmeans.calc = FALSE, 550s + difflsmeans.calc = TRUE, test.effs = 42, keep.e="save")) 550s > assertWarning(step(fm, reduce.fixed = FALSE, reduce.random = FALSE, 550s + lsmeans=3)) 550s > 550s > 550s > check_nrow <- function(obj, expect_nrow) { 550s + stopifnot( 550s + is.numeric(expect_nrow), 550s + nrow(obj) == expect_nrow 550s + ) 550s + } 550s > 550s > # Statistical nonsense, but it works: 550s > fm1 <- lmer(Reaction ~ Days + (1 | Subject) + (0 + Days|Subject), sleepstudy) 550s > step(fm1) 550s Backward reduced random-effect table: 550s 550s Eliminated npar logLik AIC LRT Df 550s 5 -871.83 1753.7 550s (1 | Subject) 0 4 -883.26 1774.5 22.856 1 550s Days in (0 + Days | Subject) 0 4 -893.23 1794.5 42.796 1 550s Pr(>Chisq) 550s 550s (1 | Subject) 1.746e-06 *** 550s Days in (0 + Days | Subject) 6.076e-11 *** 550s --- 550s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 550s 550s Backward reduced fixed-effect table: 550s Degrees of freedom method: Satterthwaite 550s 550s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 550s Days 0 29442 29442 1 18.156 45.046 2.594e-06 *** 550s --- 550s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 550s 550s Model found: 550s Reaction ~ Days + (1 | Subject) + (0 + Days | Subject) 550s > (an <- ranova(fm1)) 550s ANOVA-like table for random-effects: Single term deletions 550s 550s Model: 550s Reaction ~ Days + (1 | Subject) + (0 + Days | Subject) 550s npar logLik AIC LRT Df Pr(>Chisq) 550s 5 -871.83 1753.7 550s (1 | Subject) 4 -883.26 1774.5 22.856 1 1.746e-06 *** 550s Days in (0 + Days | Subject) 4 -893.23 1794.5 42.796 1 6.076e-11 *** 550s --- 550s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 550s > check_nrow(an, 3) 550s > ranova(fm1, reduce.terms = FALSE) 550s ANOVA-like table for random-effects: Single term deletions 550s 550s Model: 550s Reaction ~ Days + (1 | Subject) + (0 + Days | Subject) 550s npar logLik AIC LRT Df Pr(>Chisq) 550s 5 -871.83 1753.7 550s (1 | Subject) 4 -883.26 1774.5 22.856 1 1.746e-06 *** 550s (0 + Days | Subject) 4 -893.23 1794.5 42.796 1 6.076e-11 *** 550s --- 550s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 550s > 550s > # Statistical nonsense, but it works: 550s > fm1 <- lmer(Reaction ~ Days + (0 + Days|Subject), sleepstudy) 550s > step(fm1) 550s Backward reduced random-effect table: 550s 550s Eliminated npar logLik AIC LRT Df Pr(>Chisq) 550s 4 -883.26 1774.5 550s Days in (0 + Days | Subject) 0 4 -893.23 1794.5 19.94 0 550s 550s Backward reduced fixed-effect table: 550s Degrees of freedom method: Satterthwaite 550s 550s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 550s Days 0 26395 26395 1 21.679 31.347 1.32e-05 *** 550s --- 550s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 550s 550s Model found: 550s Reaction ~ Days + (0 + Days | Subject) 550s > (an <- ranova(fm1)) # no test of non-nested models 550s ANOVA-like table for random-effects: Single term deletions 550s 550s Model: 550s Reaction ~ Days + (0 + Days | Subject) 550s npar logLik AIC LRT Df Pr(>Chisq) 550s 4 -883.26 1774.5 550s Days in (0 + Days | Subject) 4 -893.23 1794.5 19.94 0 550s > stopifnot( 550s + nrow(an) == 2L, 550s + an[2L, "Df"] == 0, 550s + all(is.na(an[2L, "Pr(>Chisq)"])) 550s + ) 550s > fm0 <- lmer(Reaction ~ Days + (1|Subject), sleepstudy) 550s > step(fm0) 550s Backward reduced random-effect table: 550s 550s Eliminated npar logLik AIC LRT Df Pr(>Chisq) 550s 4 -893.23 1794.5 550s (1 | Subject) 0 3 -946.83 1899.7 107.2 1 < 2.2e-16 *** 550s --- 550s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 550s 550s Backward reduced fixed-effect table: 550s Degrees of freedom method: Satterthwaite 550s 550s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 550s Days 0 162703 162703 1 161 169.4 < 2.2e-16 *** 550s --- 550s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 550s 550s Model found: 550s Reaction ~ Days + (1 | Subject) 550s > (an2 <- anova(fm1, fm0, refit=FALSE)) 550s Data: sleepstudy 550s Models: 550s fm1: Reaction ~ Days + (0 + Days | Subject) 550s fm0: Reaction ~ Days + (1 | Subject) 550s npar AIC BIC logLik -2*log(L) Chisq Df Pr(>Chisq) 550s fm1 4 1774.5 1787.3 -883.26 1766.5 550s fm0 4 1794.5 1807.2 -893.23 1786.5 0 0 550s > stopifnot( 550s + (packageVersion("lme4")<="1.1.23" && an2[2L, "Pr(>Chisq)"] == 1) || 550s + is.na(an2[2L, "Pr(>Chisq)"]) 550s + ) 550s > ranova(fm1, reduce.terms = FALSE) 550s ANOVA-like table for random-effects: Single term deletions 550s 550s Model: 550s Reaction ~ Days + (0 + Days | Subject) 550s npar logLik AIC LRT Df Pr(>Chisq) 550s 4 -883.26 1774.5 550s (0 + Days | Subject) 3 -946.83 1899.7 127.14 1 < 2.2e-16 *** 550s --- 550s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 550s > 550s > fm1 <- lmer(Reaction ~ Days + (-1 + Days|Subject), sleepstudy) 550s > step(fm1) 551s Backward reduced random-effect table: 551s 551s Eliminated npar logLik AIC LRT Df 551s 4 -883.26 1774.5 551s Days in (-1 + Days | Subject) 0 4 -893.23 1794.5 19.94 0 551s Pr(>Chisq) 551s 551s Days in (-1 + Days | Subject) 551s 551s Backward reduced fixed-effect table: 551s Degrees of freedom method: Satterthwaite 551s 551s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 551s Days 0 26395 26395 1 21.679 31.347 1.32e-05 *** 551s --- 551s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 551s 551s Model found: 551s Reaction ~ Days + (-1 + Days | Subject) 551s > (an3 <- ranova(fm1)) # no test of non-nested models 551s ANOVA-like table for random-effects: Single term deletions 551s 551s Model: 551s Reaction ~ Days + (-1 + Days | Subject) 551s npar logLik AIC LRT Df Pr(>Chisq) 551s 4 -883.26 1774.5 551s Days in (-1 + Days | Subject) 4 -893.23 1794.5 19.94 0 551s > stopifnot( 551s + all.equal(an, an3, check.attributes=FALSE, tolerance=TOL) 551s + ) 551s > 551s > # Example where comparison of non-nested models is generated 551s > fm <- lmer(Reaction ~ poly(Days, 2) + (0 + poly(Days, 2) | Subject), sleepstudy) 551s boundary (singular) fit: see help('isSingular') 551s > step(fm) 551s Backward reduced random-effect table: 551s 551s Eliminated npar logLik AIC 551s 7 -937.05 1888.1 551s poly(Days, 2) in (0 + poly(Days, 2) | Subject) 1 5 -884.67 1779.3 551s (1 | Subject) 0 4 -938.16 1884.3 551s LRT Df Pr(>Chisq) 551s 551s poly(Days, 2) in (0 + poly(Days, 2) | Subject) -104.77 2 1 551s (1 | Subject) 106.98 1 <2e-16 *** 551s --- 551s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 551s 551s Backward reduced fixed-effect table: 551s Degrees of freedom method: Satterthwaite 551s 551s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 551s poly(Days, 2) 0 163782 81891 2 160 85.329 < 2.2e-16 *** 551s --- 551s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 551s 551s Model found: 551s Reaction ~ poly(Days, 2) + (1 | Subject) 551s > an <- ranova(fm) 551s > stopifnot( 551s + nrow(an) == 2L, 551s + an[2, "Pr(>Chisq)"] == 1 551s + ) 551s > ranova(fm, reduce.terms = FALSE) # test of nested models 551s ANOVA-like table for random-effects: Single term deletions 551s 551s Model: 551s Reaction ~ poly(Days, 2) + (0 + poly(Days, 2) | Subject) 551s npar logLik AIC LRT Df Pr(>Chisq) 551s 7 -937.05 1888.1 551s (0 + poly(Days, 2) | Subject) 4 -938.16 1884.3 2.2153 3 0.5289 551s > 551s > # These models are nested, though: 551s > fm <- lmer(Reaction ~ poly(Days, 2) + (1 + poly(Days, 2) | Subject), sleepstudy) 551s > step(fm) 551s Backward reduced random-effect table: 551s 551s Eliminated npar logLik AIC 551s 10 -856.40 1732.8 551s poly(Days, 2) in (1 + poly(Days, 2) | Subject) 0 5 -884.67 1779.3 551s LRT Df Pr(>Chisq) 551s 551s poly(Days, 2) in (1 + poly(Days, 2) | Subject) 56.524 5 6.338e-11 *** 551s --- 551s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 551s 551s Backward reduced fixed-effect table: 551s Degrees of freedom method: Satterthwaite 551s 551s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 551s poly(Days, 2) 0 24216 12108 2 17 23.367 1.323e-05 *** 551s --- 551s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 551s 551s Model found: 551s Reaction ~ poly(Days, 2) + (1 + poly(Days, 2) | Subject) 551s > ranova(fm) 551s ANOVA-like table for random-effects: Single term deletions 551s 551s Model: 551s Reaction ~ poly(Days, 2) + (1 + poly(Days, 2) | Subject) 551s npar logLik AIC LRT Df 551s 10 -856.40 1732.8 551s poly(Days, 2) in (1 + poly(Days, 2) | Subject) 5 -884.67 1779.3 56.524 5 551s Pr(>Chisq) 551s 551s poly(Days, 2) in (1 + poly(Days, 2) | Subject) 6.338e-11 *** 551s --- 551s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 551s > fm0 <- lmer(Reaction ~ poly(Days, 2) + (1 | Subject), sleepstudy) 551s > step(fm0) 551s Backward reduced random-effect table: 551s 551s Eliminated npar logLik AIC LRT Df Pr(>Chisq) 551s 5 -884.67 1779.3 551s (1 | Subject) 0 4 -938.16 1884.3 106.98 1 < 2.2e-16 *** 551s --- 551s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 551s 551s Backward reduced fixed-effect table: 551s Degrees of freedom method: Satterthwaite 551s 551s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 551s poly(Days, 2) 0 163782 81891 2 160 85.329 < 2.2e-16 *** 551s --- 551s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 551s 551s Model found: 551s Reaction ~ poly(Days, 2) + (1 | Subject) 551s > anova(fm0, fm, refit=FALSE) 551s Data: sleepstudy 551s Models: 551s fm0: Reaction ~ poly(Days, 2) + (1 | Subject) 551s fm: Reaction ~ poly(Days, 2) + (1 + poly(Days, 2) | Subject) 551s npar AIC BIC logLik -2*log(L) Chisq Df Pr(>Chisq) 551s fm0 5 1779.3 1795.3 -884.67 1769.3 551s fm 10 1732.8 1764.7 -856.40 1712.8 56.524 5 6.338e-11 *** 551s --- 551s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 551s > ranova(fm, reduce.terms = FALSE) 551s ANOVA-like table for random-effects: Single term deletions 551s 551s Model: 551s Reaction ~ poly(Days, 2) + (1 + poly(Days, 2) | Subject) 551s npar logLik AIC LRT Df Pr(>Chisq) 551s 10 -856.40 1732.8 551s (1 + poly(Days, 2) | Subject) 4 -938.16 1884.3 163.51 6 < 2.2e-16 *** 551s --- 551s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 551s > 551s > # A model with ||-notation: 551s > fm1 <- lmer(Reaction ~ Days + (Days||Subject), sleepstudy) 551s > step(fm1) 552s Backward reduced random-effect table: 552s 552s Eliminated npar logLik AIC LRT Df 552s 5 -871.83 1753.7 552s (1 | Subject) 0 4 -883.26 1774.5 22.856 1 552s Days in (0 + Days | Subject) 0 4 -893.23 1794.5 42.796 1 552s Pr(>Chisq) 552s 552s (1 | Subject) 1.746e-06 *** 552s Days in (0 + Days | Subject) 6.076e-11 *** 552s --- 552s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 552s 552s Backward reduced fixed-effect table: 552s Degrees of freedom method: Satterthwaite 552s 552s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 552s Days 0 29442 29442 1 18.156 45.046 2.594e-06 *** 552s --- 552s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 552s 552s Model found: 552s Reaction ~ Days + ((1 | Subject) + (0 + Days | Subject)) 552s > ranova(fm1) 552s ANOVA-like table for random-effects: Single term deletions 552s 552s Model: 552s Reaction ~ Days + (1 | Subject) + (0 + Days | Subject) 552s npar logLik AIC LRT Df Pr(>Chisq) 552s 5 -871.83 1753.7 552s (1 | Subject) 4 -883.26 1774.5 22.856 1 1.746e-06 *** 552s Days in (0 + Days | Subject) 4 -893.23 1794.5 42.796 1 6.076e-11 *** 552s --- 552s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 552s > 552s > # What about models with nested factors? 552s > fm <- lmer(Coloursaturation ~ TVset*Picture + (1|Assessor:TVset) + (1|Assessor), 552s + data=TVbo) 552s > step(fm) 552s Backward reduced random-effect table: 552s 552s Eliminated npar logLik AIC LRT Df Pr(>Chisq) 552s 15 -280.22 590.44 552s (1 | Assessor) 1 14 -280.27 588.53 0.090 1 0.7643 552s (1 | Assessor:TVset) 0 13 -312.24 650.47 63.941 1 1.282e-15 *** 552s --- 552s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 552s 552s Backward reduced fixed-effect table: 552s Degrees of freedom method: Satterthwaite 552s 552s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 552s TVset:Picture 0 13.8 2.2999 6 159 2.6761 0.01679 * 552s --- 552s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 552s 552s Model found: 552s Coloursaturation ~ TVset + Picture + (1 | Assessor:TVset) + TVset:Picture 552s > (an1 <- ranova(fm)) 552s ANOVA-like table for random-effects: Single term deletions 552s 552s Model: 552s Coloursaturation ~ TVset * Picture + (1 | Assessor:TVset) + (1 | Assessor) 552s npar logLik AIC LRT Df Pr(>Chisq) 552s 15 -280.22 590.44 552s (1 | Assessor:TVset) 14 -302.61 633.22 44.777 1 2.208e-11 *** 552s (1 | Assessor) 14 -280.27 588.53 0.090 1 0.7643 552s --- 552s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 552s > 552s > fm <- lmer(Coloursaturation ~ TVset * Picture + 552s + (1|Assessor/TVset), data=TVbo) 552s > step(fm) 552s Backward reduced random-effect table: 552s 552s Eliminated npar logLik AIC LRT Df Pr(>Chisq) 552s 15 -280.22 590.44 552s (1 | Assessor) 1 14 -280.27 588.53 0.090 1 0.7643 552s (1 | TVset:Assessor) 0 13 -312.24 650.47 63.941 1 1.282e-15 *** 552s --- 552s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 552s 552s Backward reduced fixed-effect table: 552s Degrees of freedom method: Satterthwaite 552s 552s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 552s TVset:Picture 0 13.8 2.2999 6 159 2.6761 0.01679 * 552s --- 552s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 552s 552s Model found: 552s Coloursaturation ~ TVset + Picture + (1 | TVset:Assessor) + TVset:Picture 552s > (an2 <- ranova(fm)) 553s ANOVA-like table for random-effects: Single term deletions 553s 553s Model: 553s Coloursaturation ~ TVset * Picture + (1 | TVset:Assessor) + (1 | Assessor) 553s npar logLik AIC LRT Df Pr(>Chisq) 553s 15 -280.22 590.44 553s (1 | TVset:Assessor) 14 -302.61 633.22 44.777 1 2.208e-11 *** 553s (1 | Assessor) 14 -280.27 588.53 0.090 1 0.7643 553s --- 553s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 553s > stopifnot( 553s + all.equal(an1, an2, check.attributes=FALSE, tolerance=TOL) 553s + ) 553s > 553s > ##################################################################### 553s > # Test evaluation within functions, i.e. in other environments etc. 553s > attach(sleepstudy) 553s > fm <- lmer(Reaction ~ Days + (Days|Subject)) 553s > step(fm) 553s Backward reduced random-effect table: 553s 553s Eliminated npar logLik AIC LRT Df Pr(>Chisq) 553s 6 -871.81 1755.6 553s Days in (Days | Subject) 0 4 -893.23 1794.5 42.837 2 4.99e-10 553s 553s 553s Days in (Days | Subject) *** 553s --- 553s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 553s 553s Backward reduced fixed-effect table: 553s Degrees of freedom method: Satterthwaite 553s 553s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 553s Days 0 30031 30031 1 17 45.853 3.264e-06 *** 553s --- 553s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 553s 553s Model found: 553s Reaction ~ Days + (Days | Subject) 553s > ranova(fm) # OK 553s ANOVA-like table for random-effects: Single term deletions 553s 553s Model: 553s Reaction ~ Days + (Days | Subject) 553s npar logLik AIC LRT Df Pr(>Chisq) 553s 6 -871.81 1755.6 553s Days in (Days | Subject) 4 -893.23 1794.5 42.837 2 4.99e-10 *** 553s --- 553s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 553s > detach(sleepstudy) 553s > 553s > # Evaluating in a function works: 553s > f <- function(form, data) lmer(form, data=data) 553s > form <- "Informed.liking ~ Product+Information+ 553s + (1|Consumer) + (1|Product:Consumer) + (1|Information:Consumer)" 553s > fm <- f(form, data=ham) 553s > ranova(fm) 553s boundary (singular) fit: see help('isSingular') 553s ANOVA-like table for random-effects: Single term deletions 553s 553s Model: 553s Informed.liking ~ Product + Information + (1 | Consumer) + (1 | Product:Consumer) + (1 | Information:Consumer) 553s npar logLik AIC LRT Df Pr(>Chisq) 553s 9 -1353.9 2725.8 553s (1 | Consumer) 8 -1355.1 2726.1 2.295 1 0.1298 553s (1 | Product:Consumer) 8 -1436.3 2888.6 164.753 1 <2e-16 *** 553s (1 | Information:Consumer) 8 -1354.5 2725.1 1.255 1 0.2626 553s --- 553s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 553s > step_res <- step(fm) 553s boundary (singular) fit: see help('isSingular') 554s > stopifnot( 554s + all(c("Sum Sq", "Mean Sq", "NumDF", "DenDF", "F value", "Pr(>F)") %in% 554s + colnames(step_res$fixed)) 554s + ) 554s > 554s > ########################### 554s > # Evaluation in function without the formula: 554s > # Reported by Uwe Ligges 2025-01-16. 554s > f <- function(data) { 554s + lmer(Petal.Length ~ Sepal.Length + (1|Species), data=data) 554s + } 554s > 554s > res <- f(iris) 554s > ranova(res) # used to fail - now it works 554s ANOVA-like table for random-effects: Single term deletions 554s 554s Model: 554s Petal.Length ~ Sepal.Length + (1 | Species) 554s npar logLik AIC LRT Df Pr(>Chisq) 554s 4 -34.66 77.32 554s (1 | Species) 3 -193.84 393.68 318.36 1 < 2.2e-16 *** 554s --- 554s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 554s > 554s > data <- iris 554s > ranova(res) # now it works 554s ANOVA-like table for random-effects: Single term deletions 554s 554s Model: 554s Petal.Length ~ Sepal.Length + (1 | Species) 554s npar logLik AIC LRT Df Pr(>Chisq) 554s 4 -34.66 77.32 554s (1 | Species) 3 -193.84 393.68 318.36 1 < 2.2e-16 *** 554s --- 554s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 554s > ########################### 554s > # Evaluation in function without the formula(2): 554s > # A model with ||-notation: 554s > f2 <- function(data) { 554s + lmer(Reaction ~ Days + (Days||Subject), data) 554s + } 554s > res <- f2(sleepstudy) 554s > ranova(res) 554s ANOVA-like table for random-effects: Single term deletions 554s 554s Model: 554s Reaction ~ Days + (1 | Subject) + (0 + Days | Subject) 554s npar logLik AIC LRT Df Pr(>Chisq) 554s 5 -871.83 1753.7 554s (1 | Subject) 4 -883.26 1774.5 22.856 1 1.746e-06 *** 554s Days in (0 + Days | Subject) 4 -893.23 1794.5 42.796 1 6.076e-11 *** 554s --- 554s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 554s > 554s > # A model with multiple RE terms: 554s > f3 <- function(data) { 554s + lmer(Coloursaturation ~ TVset*Picture + (1|Assessor:TVset) + (1|Assessor), data) 554s + } 554s > res <- f3(TVbo) 554s > ranova(res) 554s ANOVA-like table for random-effects: Single term deletions 554s 554s Model: 554s Coloursaturation ~ TVset * Picture + (1 | Assessor:TVset) + (1 | Assessor) 554s npar logLik AIC LRT Df Pr(>Chisq) 554s 15 -280.22 590.44 554s (1 | Assessor:TVset) 14 -302.61 633.22 44.777 1 2.208e-11 *** 554s (1 | Assessor) 14 -280.27 588.53 0.090 1 0.7643 554s --- 554s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 554s > ########################### 554s > 554s > # Check that step works when form is a character vector 554s > m <- lmer(form, data=ham) 554s > step_res <- step(m) 555s boundary (singular) fit: see help('isSingular') 555s > (drop1_table <- attr(step_res, "drop1")) 555s Single term deletions using Satterthwaite's method: 555s 555s Model: 555s Informed.liking ~ Product + Information + (1 | Consumer) + (1 | Product:Consumer) 555s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 555s Product 19.3466 6.4489 3 240 3.8291 0.01048 * 555s Information 6.5201 6.5201 1 323 3.8714 0.04997 * 555s --- 555s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 555s > stopifnot( 555s + all(c("Sum Sq", "Mean Sq", "NumDF", "DenDF", "F value", "Pr(>F)") %in% 555s + colnames(drop1_table)) 555s + ) 555s > # In version < 3.0-1.9002 attr(step_res, "drop1") picked up lme4::drop1.merMod 555s > # and returned an AIC table after the model had been update'd. 555s > 555s > ##################################################################### 555s > # Model with 2 ranef covarites: 555s > 555s > # Model of the form (x1 + x2 | gr): 555s > model <- lmer(Preference ~ sens2 + Homesize + (sens1 + sens2 | Consumer) 555s + , data=carrots) 555s boundary (singular) fit: see help('isSingular') 555s > step(model) 555s Warning message: 555s Model failed to converge with 1 negative eigenvalue: -3.0e+02 555s boundary (singular) fit: see help('isSingular') 556s Backward reduced random-effect table: 556s 556s Eliminated npar logLik AIC LRT Df 556s 10 -1874.4 3768.8 556s sens1 in (sens1 + sens2 | Consumer) 1 7 -1874.5 3762.9 0.1333 3 556s sens2 in (sens2 | Consumer) 0 5 -1878.0 3765.9 6.9944 2 556s Pr(>Chisq) 556s 556s sens1 in (sens1 + sens2 | Consumer) 0.98757 556s sens2 in (sens2 | Consumer) 0.03028 * 556s --- 556s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 556s 556s Backward reduced fixed-effect table: 556s Degrees of freedom method: Satterthwaite 556s 556s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 556s sens2 0 58.685 58.685 1 102.02 54.8236 3.888e-11 *** 556s Homesize 0 5.979 5.979 1 100.95 5.5852 0.02003 * 556s --- 556s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 556s 556s Model found: 556s Preference ~ sens2 + Homesize + (sens2 | Consumer) 556s > stopifnot( 556s + nrow(ranova(model)) == 3L, 556s + nrow(ranova(model, reduce.terms = FALSE)) == 2L 556s + ) 556s boundary (singular) fit: see help('isSingular') 556s > 556s > # Model of the form (f1 + f2 | gr): 556s > model <- lmer(Preference ~ sens2 + Homesize + Gender + 556s + (Gender+Homesize|Consumer), data=carrots) 556s boundary (singular) fit: see help('isSingular') 556s > step(model) 557s Backward reduced random-effect table: 557s 557s Eliminated npar logLik AIC LRT 557s 11 -1872.3 3766.5 557s Gender in (Gender + Homesize | Consumer) 1 8 -1875.1 3766.3 5.7408 557s Homesize in (Homesize | Consumer) 0 6 -1878.4 3768.7 6.4705 557s Df Pr(>Chisq) 557s 557s Gender in (Gender + Homesize | Consumer) 3 0.12493 557s Homesize in (Homesize | Consumer) 2 0.03935 * 557s --- 557s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 557s 557s Backward reduced fixed-effect table: 557s Degrees of freedom method: Satterthwaite 557s 557s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 557s Gender 1 0.632 0.632 1 91.80 0.5686 0.45275 557s sens2 0 83.385 83.385 1 1129.09 75.0490 < 2e-16 *** 557s Homesize 0 6.212 6.212 1 97.82 5.5910 0.02003 * 557s --- 557s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 557s 557s Model found: 557s Preference ~ sens2 + Homesize + (Homesize | Consumer) 557s Warning messages: 557s 1: In checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, : 557s unable to evaluate scaled gradient 557s 2: In checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, : 557s Model failed to converge: degenerate Hessian with 1 negative eigenvalues 557s See ?lme4::convergence and ?lme4::troubleshooting. 557s 3: In checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, : 557s Model is nearly unidentifiable: large eigenvalue ratio 557s - Rescale variables? 557s 4: Model failed to converge with 1 negative eigenvalue: -2.7e-04 557s > stopifnot( 557s + nrow(ranova(model)) == 3L, 557s + nrow(ranova(model, reduce.terms = FALSE)) == 2L 557s + ) 557s Warning messages: 557s 1: In checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, : 557s unable to evaluate scaled gradient 557s 2: In checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, : 557s Model failed to converge: degenerate Hessian with 1 negative eigenvalues 557s See ?lme4::convergence and ?lme4::troubleshooting. 557s > 557s > # Model of the form (-1 + f2 | gr): 557s > model <- lmer(Preference ~ sens2 + Homesize + Gender + 557s + (Gender -1 |Consumer), data=carrots) 557s > step(model) 558s Backward reduced random-effect table: 558s 558s Eliminated npar logLik AIC LRT Df 558s 8 -1876.4 3768.9 558s Gender in (Gender - 1 | Consumer) 1 6 -1878.4 3768.7 3.863 2 558s (1 | Consumer) 0 5 -1917.2 3844.5 77.714 1 558s Pr(>Chisq) 558s 558s Gender in (Gender - 1 | Consumer) 0.145 558s (1 | Consumer) <2e-16 *** 558s --- 558s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 558s 558s Backward reduced fixed-effect table: 558s Degrees of freedom method: Satterthwaite 558s 558s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 558s Gender 1 1.879 1.879 1 99.98 1.6909 0.19647 558s sens2 0 83.363 83.363 1 1129.00 75.0256 < 2e-16 *** 558s Homesize 0 5.729 5.729 1 100.97 5.1557 0.02529 * 558s --- 558s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 558s 558s Model found: 558s Preference ~ sens2 + Homesize + (1 | Consumer) 558s > an1 <- ranova(model) 558s > an1b <- ranova(model, reduce.terms = FALSE) 558s > 558s > model <- lmer(Preference ~ sens2 + Homesize + Gender + 558s + (0 + Gender|Consumer), data=carrots) 558s > step(model) 558s Backward reduced random-effect table: 558s 558s Eliminated npar logLik AIC LRT Df 558s 8 -1876.4 3768.9 558s Gender in (0 + Gender | Consumer) 1 6 -1878.4 3768.7 3.863 2 558s (1 | Consumer) 0 5 -1917.2 3844.5 77.714 1 558s Pr(>Chisq) 558s 558s Gender in (0 + Gender | Consumer) 0.145 558s (1 | Consumer) <2e-16 *** 558s --- 558s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 558s 558s Backward reduced fixed-effect table: 558s Degrees of freedom method: Satterthwaite 558s 558s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 558s Gender 1 1.879 1.879 1 99.98 1.6909 0.19647 558s sens2 0 83.363 83.363 1 1129.00 75.0256 < 2e-16 *** 558s Homesize 0 5.729 5.729 1 100.97 5.1557 0.02529 * 558s --- 558s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 558s 558s Model found: 558s Preference ~ sens2 + Homesize + (1 | Consumer) 558s > an2 <- ranova(model) 558s > an2b <- ranova(model, reduce.terms = FALSE) 558s > 558s > stopifnot( 558s + all.equal(an1, an2, check.attributes=FALSE, tolerance=TOL), 558s + all.equal(an1b, an2b, check.attributes=FALSE, tolerance=TOL) 558s + ) 558s > 558s > ####### Polynomial terms: 558s > model <- lmer(Preference ~ sens2 + Gender + (poly(sens2, 2) | Consumer), 558s + data=carrots) 559s > (an <- ranova(model)) 559s ANOVA-like table for random-effects: Single term deletions 559s 559s Model: 559s Preference ~ sens2 + Gender + (poly(sens2, 2) | Consumer) 559s npar logLik AIC LRT Df 559s 10 -1874.1 3768.2 559s poly(sens2, 2) in (poly(sens2, 2) | Consumer) 5 -1879.9 3769.7 11.552 5 559s Pr(>Chisq) 559s 559s poly(sens2, 2) in (poly(sens2, 2) | Consumer) 0.04147 * 559s --- 559s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 559s > step(model) 559s Backward reduced random-effect table: 559s 559s Eliminated npar logLik AIC 559s 10 -1874.1 3768.2 559s poly(sens2, 2) in (poly(sens2, 2) | Consumer) 0 5 -1879.9 3769.7 559s LRT Df Pr(>Chisq) 559s 559s poly(sens2, 2) in (poly(sens2, 2) | Consumer) 11.552 5 0.04147 * 559s --- 559s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 559s 559s Backward reduced fixed-effect table: 559s Degrees of freedom method: Satterthwaite 559s 559s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 559s Gender 1 1.188 1.188 1 101.03 1.1263 0.2911 559s sens2 0 53.470 53.470 1 114.55 50.6962 1.013e-10 *** 559s --- 559s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 559s 559s Model found: 559s Preference ~ sens2 + (poly(sens2, 2) | Consumer) 559s > 559s > model <- lmer(Preference ~ sens2 + Gender + (sens2 + I(sens2^2) | Consumer), 559s + data=carrots) 559s Warning message: 559s In checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, : 559s Model failed to converge with max|grad| = 0.00339848 (tol = 0.002, component 1) 559s See ?lme4::convergence and ?lme4::troubleshooting. 560s Warning message: 560s In checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, : 560s Model failed to converge with max|grad| = 0.0818989 (tol = 0.002, component 1) 560s See ?lme4::convergence and ?lme4::troubleshooting. 560s > (an2 <- ranova(model)) 560s boundary (singular) fit: see help('isSingular') 560s ANOVA-like table for random-effects: Single term deletions 560s 560s Model: 560s Preference ~ sens2 + Gender + (sens2 + I(sens2^2) | Consumer) 560s npar logLik AIC LRT Df 560s 10 -1874.1 3768.2 560s sens2 in (sens2 + I(sens2^2) | Consumer) 7 -1879.8 3773.5 11.3658 3 560s I(sens2^2) in (sens2 + I(sens2^2) | Consumer) 7 -1876.5 3767.0 4.8775 3 560s Pr(>Chisq) 560s 560s sens2 in (sens2 + I(sens2^2) | Consumer) 0.009904 ** 560s I(sens2^2) in (sens2 + I(sens2^2) | Consumer) 0.180987 560s --- 560s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 560s > step(model) 560s boundary (singular) fit: see help('isSingular') 561s Backward reduced random-effect table: 561s 561s Eliminated npar logLik AIC 561s 10 -1874.1 3768.2 561s I(sens2^2) in (sens2 + I(sens2^2) | Consumer) 1 7 -1876.5 3767.0 561s sens2 in (sens2 | Consumer) 0 5 -1879.9 3769.7 561s LRT Df Pr(>Chisq) 561s 561s I(sens2^2) in (sens2 + I(sens2^2) | Consumer) 4.8775 3 0.18099 561s sens2 in (sens2 | Consumer) 6.6735 2 0.03555 * 561s --- 561s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 561s 561s Backward reduced fixed-effect table: 561s Degrees of freedom method: Satterthwaite 561s 561s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 561s Gender 1 1.211 1.211 1 101.02 1.1309 0.2901 561s sens2 0 58.688 58.688 1 102.01 54.8276 3.883e-11 *** 561s --- 561s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 561s 561s Model found: 561s Preference ~ sens2 + (sens2 | Consumer) 561s > stopifnot( 561s + nrow(an) == 2L, 561s + an[2L, "Df"] == 5L, 561s + nrow(an2) == 3L, 561s + all(an2[2:3, "Df"] == 3L) 561s + ) 561s > 561s > ######## Functions of terms in random effects: 561s > model <- lmer(Preference ~ sens2 + Gender + (log(10+sens2) | Consumer), 561s + data=carrots) 561s > ranova(model) # Works 561s ANOVA-like table for random-effects: Single term deletions 561s 561s Model: 561s Preference ~ sens2 + Gender + (log(10 + sens2) | Consumer) 561s npar logLik AIC LRT Df 561s 7 -1875.3 3764.6 561s log(10 + sens2) in (log(10 + sens2) | Consumer) 5 -1879.9 3769.7 9.0854 2 561s Pr(>Chisq) 561s 561s log(10 + sens2) in (log(10 + sens2) | Consumer) 0.01064 * 561s --- 561s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 561s > step(model) 561s Backward reduced random-effect table: 561s 561s Eliminated npar logLik AIC 561s 7 -1875.3 3764.6 561s log(10 + sens2) in (log(10 + sens2) | Consumer) 0 5 -1879.9 3769.7 561s LRT Df Pr(>Chisq) 561s 561s log(10 + sens2) in (log(10 + sens2) | Consumer) 9.0854 2 0.01064 * 561s --- 561s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 561s 561s Backward reduced fixed-effect table: 561s Degrees of freedom method: Satterthwaite 561s 561s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 561s Gender 1 1.200 1.200 1 101.03 1.1296 0.2904 561s sens2 0 54.184 54.184 1 109.20 51.0007 1.083e-10 *** 561s --- 561s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 561s 561s Model found: 561s Preference ~ sens2 + (log(10 + sens2) | Consumer) 561s > 561s > ##################################################################### 561s > 561s > # Missing values changes the number of observations in use: 561s > m <- lmer(Preference ~ sens2 + Homesize + 561s + (1 |Consumer:Income), data=carrots) 561s > assertError(step(m)) 561s > ans <- try(ranova(m), silent = TRUE) 561s > stopifnot( 561s + inherits(ans, "try-error"), 561s + grepl("number of rows in use has changed", ans) 561s + ) 561s > 561s > ## Removing missing values solves the problem: 561s > m2 <- lmer(Preference ~ sens2 + Homesize + 561s + (1 |Consumer:Income), data=carrots[complete.cases(carrots), ]) 561s > ranova(m2) # Works 561s ANOVA-like table for random-effects: Single term deletions 561s 561s Model: 561s Preference ~ sens2 + Homesize + (1 | Consumer:Income) 561s npar logLik AIC LRT Df Pr(>Chisq) 561s 5 -1752.0 3513.9 561s (1 | Consumer:Income) 4 -1778.6 3565.2 53.272 1 2.904e-13 *** 561s --- 561s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 561s > step(m2) 561s Backward reduced random-effect table: 561s 561s Eliminated npar logLik AIC LRT Df Pr(>Chisq) 561s 5 -1752.0 3513.9 561s (1 | Consumer:Income) 0 4 -1778.6 3565.2 53.272 1 2.904e-13 *** 561s --- 561s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 561s 561s Backward reduced fixed-effect table: 561s Degrees of freedom method: Satterthwaite 561s 561s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 561s sens2 0 77.308 77.308 1 1058.49 69.7915 < 2.2e-16 *** 561s Homesize 0 8.569 8.569 1 95.23 7.7355 0.006527 ** 561s --- 561s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 561s 561s Model found: 561s Preference ~ sens2 + Homesize + (1 | Consumer:Income) 561s > 561s > ## Including the variable with missing values (Income) among the fixed effects 561s > ## also solves the problem: 561s > m <- lmer(Preference ~ sens2 + Homesize + Income + #(1 + sens2 | Consumer) + 561s + (1 |Consumer:Income), data=carrots) 561s > ranova(m) 561s ANOVA-like table for random-effects: Single term deletions 561s 561s Model: 561s Preference ~ sens2 + Homesize + Income + (1 | Consumer:Income) 561s npar logLik AIC LRT Df Pr(>Chisq) 561s 8 -1766.0 3547.9 561s (1 | Consumer:Income) 7 -1791.1 3596.3 50.395 1 1.257e-12 *** 561s --- 561s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 561s > step(m) 562s Backward reduced random-effect table: 562s 562s Eliminated npar logLik AIC LRT Df Pr(>Chisq) 562s 8 -1766.0 3547.9 562s (1 | Consumer:Income) 0 7 -1791.1 3596.3 50.395 1 1.257e-12 *** 562s --- 562s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 562s 562s Backward reduced fixed-effect table: 562s Degrees of freedom method: Satterthwaite 562s 562s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 562s Income 1 3.567 1.189 3 91.92 1.0627 0.368918 562s sens2 0 78.191 78.191 1 1062.96 69.8919 < 2.2e-16 *** 562s Homesize 0 7.983 7.983 1 94.93 7.1355 0.008894 ** 562s --- 562s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 562s 562s Model found: 562s Preference ~ sens2 + Homesize + (1 | Consumer:Income) 562s > 562s > # Missing values in a an insignificant fixed effect causes the an error in step: 562s > m0 <- lmer(Preference ~ sens2 + Homesize + Income + #(1 + sens2 | Consumer) + 562s + (1 |Consumer), data=carrots) 562s > ranova(m0) 562s ANOVA-like table for random-effects: Single term deletions 562s 562s Model: 562s Preference ~ sens2 + Homesize + Income + (1 | Consumer) 562s npar logLik AIC LRT Df Pr(>Chisq) 562s 8 -1766.0 3547.9 562s (1 | Consumer) 7 -1791.1 3596.3 50.395 1 1.257e-12 *** 562s --- 562s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 562s > ans <- try(step(m0), silent = TRUE) 562s > stopifnot( 562s + inherits(ans, "try-error"), 562s + grepl("number of rows in use has changed", ans) 562s + ) 562s > 562s > # Check that step still works for linear models (etc.) 562s > flm <- lm(Coloursaturation ~ TVset * Picture, data=TVbo) 562s > res <- step(flm, trace=0) 562s > stopifnot( 562s + inherits(res, "lm") 562s + ) 562s > 562s > ##################### Using reduce and keep args: 562s > # Fit a model to the ham dataset: 562s > m <- lmer(Informed.liking ~ Product*Information+ 562s + (1|Consumer) + (1|Product:Consumer) 562s + + (1|Information:Consumer), data=ham) 562s > 562s > # Backward elimination using terms with default alpha-levels: 562s > (step_res <- step(m)) 562s boundary (singular) fit: see help('isSingular') 563s Backward reduced random-effect table: 563s 563s Eliminated npar logLik AIC LRT Df Pr(>Chisq) 563s 12 -1352.0 2728.1 563s (1 | Information:Consumer) 1 11 -1352.8 2727.5 1.444 1 0.22952 563s (1 | Consumer) 0 10 -1354.4 2728.7 3.184 1 0.07437 563s (1 | Product:Consumer) 0 10 -1435.0 2890.0 164.443 1 < 2e-16 563s 563s 563s (1 | Information:Consumer) 563s (1 | Consumer) . 563s (1 | Product:Consumer) *** 563s --- 563s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 563s 563s Backward reduced fixed-effect table: 563s Degrees of freedom method: Satterthwaite 563s 563s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 563s Product:Information 1 10.3873 3.4624 3 320 2.0765 0.10321 563s Product 0 19.3466 6.4489 3 240 3.8291 0.01048 * 563s Information 0 6.5201 6.5201 1 323 3.8714 0.04997 * 563s --- 563s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 563s 563s Model found: 563s Informed.liking ~ Product + Information + (1 | Consumer) + (1 | Product:Consumer) 563s > 563s > (step_res <- step(m, reduce.random = FALSE)) 563s boundary (singular) fit: see help('isSingular') 563s Backward reduced random-effect table: 563s 563s Eliminated npar logLik AIC LRT Df Pr(>Chisq) 563s 12 -1352.0 2728.1 563s (1 | Consumer) 0 11 -1353.2 2728.3 2.252 1 0.1335 563s (1 | Product:Consumer) 0 11 -1435.0 2892.0 165.887 1 <2e-16 563s (1 | Information:Consumer) 0 11 -1352.8 2727.5 1.444 1 0.2295 563s 563s 563s (1 | Consumer) 563s (1 | Product:Consumer) *** 563s (1 | Information:Consumer) 563s --- 563s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 563s 563s Backward reduced fixed-effect table: 563s Degrees of freedom method: Satterthwaite 563s 563s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 563s Product:Information 1 10.3873 3.4624 3 240 2.2014 0.08855 . 563s Information 2 5.3335 5.3335 1 80 3.3414 0.07129 . 563s Product 0 18.3361 6.1120 3 240 3.8291 0.01048 * 563s --- 563s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 563s 563s Model found: 563s Informed.liking ~ Product + (1 | Consumer) + (1 | Product:Consumer) + (1 | Information:Consumer) 563s > (step_res <- step(m, reduce.fixed = FALSE)) 564s boundary (singular) fit: see help('isSingular') 564s Backward reduced random-effect table: 564s 564s Eliminated npar logLik AIC LRT Df Pr(>Chisq) 564s 12 -1352.0 2728.1 564s (1 | Information:Consumer) 1 11 -1352.8 2727.5 1.444 1 0.22952 564s (1 | Consumer) 0 10 -1354.4 2728.7 3.184 1 0.07437 564s (1 | Product:Consumer) 0 10 -1435.0 2890.0 164.443 1 < 2e-16 564s 564s 564s (1 | Information:Consumer) 564s (1 | Consumer) . 564s (1 | Product:Consumer) *** 564s --- 564s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 564s 564s Backward reduced fixed-effect table: 564s Degrees of freedom method: Satterthwaite 564s 564s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 564s Product:Information 0 10.387 3.4624 3 320 2.0765 0.1032 564s 564s Model found: 564s Informed.liking ~ Product + Information + (1 | Consumer) + (1 | Product:Consumer) + Product:Information 564s > (step_res <- step(m, reduce.fixed = FALSE, reduce.random = FALSE)) 564s boundary (singular) fit: see help('isSingular') 564s Backward reduced random-effect table: 564s 564s Eliminated npar logLik AIC LRT Df Pr(>Chisq) 564s 12 -1352.0 2728.1 564s (1 | Consumer) 0 11 -1353.2 2728.3 2.252 1 0.1335 564s (1 | Product:Consumer) 0 11 -1435.0 2892.0 165.887 1 <2e-16 564s (1 | Information:Consumer) 0 11 -1352.8 2727.5 1.444 1 0.2295 564s 564s 564s (1 | Consumer) 564s (1 | Product:Consumer) *** 564s (1 | Information:Consumer) 564s --- 564s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 564s 564s Backward reduced fixed-effect table: 564s Degrees of freedom method: Satterthwaite 564s 564s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 564s Product:Information 0 10.387 3.4624 3 240 2.2014 0.08855 . 564s --- 564s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 564s 564s Model found: 564s Informed.liking ~ Product * Information + (1 | Consumer) + (1 | Product:Consumer) + (1 | Information:Consumer) 564s > 564s > (step_res <- step(m, reduce.random = FALSE, keep="Information")) 565s boundary (singular) fit: see help('isSingular') 565s Backward reduced random-effect table: 565s 565s Eliminated npar logLik AIC LRT Df Pr(>Chisq) 565s 12 -1352.0 2728.1 565s (1 | Consumer) 0 11 -1353.2 2728.3 2.252 1 0.1335 565s (1 | Product:Consumer) 0 11 -1435.0 2892.0 165.887 1 <2e-16 565s (1 | Information:Consumer) 0 11 -1352.8 2727.5 1.444 1 0.2295 565s 565s 565s (1 | Consumer) 565s (1 | Product:Consumer) *** 565s (1 | Information:Consumer) 565s --- 565s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 565s 565s Backward reduced fixed-effect table: 565s Degrees of freedom method: Satterthwaite 565s 565s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 565s Product:Information 1 10.3873 3.4624 3 240 2.2014 0.08855 . 565s Product 0 18.3363 6.1121 3 240 3.8292 0.01048 * 565s Information 0 5.3335 5.3335 1 80 3.3414 0.07129 . 565s --- 565s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 565s 565s Model found: 565s Informed.liking ~ Product + Information + (1 | Consumer) + (1 | Product:Consumer) + (1 | Information:Consumer) 565s > (step_res <- step(m, reduce.random = FALSE, keep="Product:Information")) 565s boundary (singular) fit: see help('isSingular') 565s Backward reduced random-effect table: 565s 565s Eliminated npar logLik AIC LRT Df Pr(>Chisq) 565s 12 -1352.0 2728.1 565s (1 | Consumer) 0 11 -1353.2 2728.3 2.252 1 0.1335 565s (1 | Product:Consumer) 0 11 -1435.0 2892.0 165.887 1 <2e-16 565s (1 | Information:Consumer) 0 11 -1352.8 2727.5 1.444 1 0.2295 565s 565s 565s (1 | Consumer) 565s (1 | Product:Consumer) *** 565s (1 | Information:Consumer) 565s --- 565s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 565s 565s Backward reduced fixed-effect table: 565s Degrees of freedom method: Satterthwaite 565s 565s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 565s Product:Information 0 10.387 3.4624 3 240 2.2014 0.08855 . 565s --- 565s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 565s 565s Model found: 565s Informed.liking ~ Product * Information + (1 | Consumer) + (1 | Product:Consumer) + (1 | Information:Consumer) 565s > 565s > 565s > ########################### 565s > ## Test that `step` works even if all random terms are reduced away: 565s > set.seed(101) 565s > test <- data.frame(TM = factor(rep(rep(c("org","min"),each=3),3)), 565s + dep = runif(18,0,20), 565s + ind = runif(18,0,7), 565s + dorp = factor(rep(1:3,each=6))) 565s > full.model <- lmer(dep ~ TM + ind + (1 | dorp), data=test) 565s > res <- step(full.model) 565s > # res$random 565s > # res$fixed 565s > # attr(res, "model") 565s > # attr(res, "drop1") 565s > 565s > 565s > 565s BEGIN TEST test_re_covar_structures.R 565s 565s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 565s Copyright (C) 2025 The R Foundation for Statistical Computing 565s Platform: arm-unknown-linux-gnueabihf (32-bit) 565s 565s R is free software and comes with ABSOLUTELY NO WARRANTY. 565s You are welcome to redistribute it under certain conditions. 565s Type 'license()' or 'licence()' for distribution details. 565s 565s R is a collaborative project with many contributors. 565s Type 'contributors()' for more information and 565s 'citation()' on how to cite R or R packages in publications. 565s 565s Type 'demo()' for some demos, 'help()' for on-line help, or 565s 'help.start()' for an HTML browser interface to help. 565s Type 'q()' to quit R. 565s 566s > # test_re_covar_structure.R 566s > library(lmerTest) 566s Loading required package: lme4 566s Loading required package: Matrix 568s 568s Attaching package: 'lmerTest' 568s 568s The following object is masked from 'package:lme4': 568s 568s lmer 568s 568s The following object is masked from 'package:stats': 568s 568s step 568s 568s > 568s > # WRE says "using if(requireNamespace("pkgname")) is preferred, if possible." 568s > # even in tests: 568s > assertError <- function(expr, ...) 568s + if(requireNamespace("tools")) tools::assertError(expr, ...) else invisible() 568s > assertWarning <- function(expr, ...) 568s + if(requireNamespace("tools")) tools::assertWarning(expr, ...) else invisible() 568s > 568s > # Kenward-Roger only available with pbkrtest and only then validated in R >= 3.3.3 568s > # (faulty results for R < 3.3.3 may be due to unstated dependencies in pbkrtest) 568s > has_pbkrtest <- requireNamespace("pbkrtest", quietly = TRUE) && getRversion() >= "3.3.3" 568s > 568s > data("sleepstudy", package="lme4") 568s > TOL <- 1e-4 568s > 568s > #################################### 568s > ## Test that lmerMod objects can be coerced to lmerModLmerTest and 568s > ## that the deviance function can be evaluated with expected results 568s > #################################### 568s > 568s > 568s > #################################### 568s > ## Basic tests of new (lme4 >= 2.0.0) covariance structure 568s > ## - simple sleepstudy data (random coefficient) 568s > #################################### 568s > 568s > has_pkgs <- requireNamespace("utils", quietly = TRUE) && 568s + requireNamespace("lme4", quietly = TRUE) && 568s + requireNamespace("pbkrtest", quietly = TRUE) && 568s + getRversion() >= "3.3.3" 568s > is_lme4_2_0_0 <- utils::packageVersion("lme4") >= "2.0.0" 568s > 568s > if(has_pkgs && is_lme4_2_0_0) { 568s + 568s + ## From the examples of ?`Covariance-class`: 568s + ## Unstructured 568s + fm1.us <- lmer(Reaction ~ Days + us(Days | Subject), sleepstudy) 568s + ## Diagional 568s + fm1.diag <- lmer(Reaction ~ Days + diag(Days | Subject), sleepstudy) 568s + fm1.diag.hom <- lmer(Reaction ~ Days + diag(Days | Subject, hom = TRUE), 568s + sleepstudy) 568s + ## Compound symmetry 568s + fm1.cs <- lmer(Reaction ~ Days + cs(1 + Days | Subject), sleepstudy) 568s + fm1.cs.hom <- lmer(Reaction ~ Days + cs(1 + Days | Subject, hom = TRUE), 568s + sleepstudy) 568s + ## Auto-regressive order 1 568s + sleepstudy$Daysf <- factor(sleepstudy$Days, ordered = TRUE) 568s + fm1.ar1 <- lmer(Reaction ~ Daysf + ar1(0 + Daysf | Subject, hom = TRUE), 568s + sleepstudy, REML = TRUE) 568s + 568s + ## Also adding a double-vertical-bar model (though not from 568s + ## 'Covariance-class' examples): 568s + fm1.bv <- lmer(Reaction ~ Days + (Days || Subject), sleepstudy) 568s + 568s + 568s + ltmodels <- namedList(fm1.us, 568s + fm1.diag, 568s + fm1.diag.hom, 568s + fm1.cs, 568s + fm1.cs.hom, 568s + fm1.ar1, 568s + fm1.bv) 568s + ## Run various methods on all models: 568s + for(model in ltmodels) { 568s + # model <- ltmodels[[5]] 568s + print(model) 568s + print(summary(model)) 568s + # model 568s + # summary(model) 568s + L <- diag(c(0, rep(1, length(fixef(model)) -1))) 568s + contest(model, L, joint = TRUE) 568s + contest(model, L[2, ], joint = FALSE) 568s + (an <- anova(model)) ## ddf is Satterthwaite 568s + anova(model, ddf = "Ken") 568s + anova(model, ddf="lme4") 568s + anova(model, type="I") 568s + anova(model, type="II") 568s + anova(model, type="III") 568s + show_tests(an) 568s + drop1(model) 568s + ranova(model) 568s + ranova(model, reduce.terms = FALSE) 568s + step(model) 568s + (lsm <- ls_means(model)) 568s + show_tests(lsm) 568s + (dlsm <- difflsmeans(model)) 568s + show_tests(dlsm) 568s + } 568s + } 568s > 568s > #################################### 568s > ## Basic tests of new (lme4 >= 2.0.0) covariance structure 568s > ## - Unbalanced categorical dataset with multiple RE terms 568s > #################################### 568s > 568s > 568s > 568s > 568s > 568s BEGIN TEST test_summary.R 568s 568s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 568s Copyright (C) 2025 The R Foundation for Statistical Computing 568s Platform: arm-unknown-linux-gnueabihf (32-bit) 568s 568s R is free software and comes with ABSOLUTELY NO WARRANTY. 568s You are welcome to redistribute it under certain conditions. 568s Type 'license()' or 'licence()' for distribution details. 568s 568s R is a collaborative project with many contributors. 568s Type 'contributors()' for more information and 568s 'citation()' on how to cite R or R packages in publications. 568s 568s Type 'demo()' for some demos, 'help()' for on-line help, or 568s 'help.start()' for an HTML browser interface to help. 568s Type 'q()' to quit R. 568s 568s > # test_summary.R 568s > 568s > # WRE says "using if(requireNamespace("pkgname")) is preferred, if possible." 568s > # even in tests: 568s > assertError <- function(expr, ...) 568s + if(requireNamespace("tools")) tools::assertError(expr, ...) else invisible() 568s > assertWarning <- function(expr, ...) 568s + if(requireNamespace("tools")) tools::assertWarning(expr, ...) else invisible() 568s > 568s > # Kenward-Roger only available with pbkrtest and only then validated in R >= 3.3.3 568s > # (faulty results for R < 3.3.3 may be due to unstated dependencies in pbkrtest) 568s > has_pbkrtest <- requireNamespace("pbkrtest", quietly = TRUE) && getRversion() >= "3.3.3" 570s > 570s > library(lmerTest) 570s Loading required package: lme4 570s Loading required package: Matrix 571s 571s Attaching package: 'lmerTest' 571s 571s The following object is masked from 'package:lme4': 571s 571s lmer 571s 571s The following object is masked from 'package:stats': 571s 571s step 571s 571s > 571s > data("sleepstudy", package="lme4") 571s > data("cake", package="lme4") 571s > 571s > # Fit basic model and compute summary: 571s > fm <- lmer(Reaction ~ Days + (1|Subject) + (0+Days|Subject), sleepstudy) 571s > (sfm <- summary(fm)) 571s Linear mixed model fit by REML. t-tests use Satterthwaite's method [ 571s lmerModLmerTest] 571s Formula: Reaction ~ Days + (1 | Subject) + (0 + Days | Subject) 571s Data: sleepstudy 571s 571s REML criterion at convergence: 1743.7 571s 571s Scaled residuals: 571s Min 1Q Median 3Q Max 571s -3.9626 -0.4625 0.0204 0.4653 5.1860 571s 571s Random effects: 571s Groups Name Variance Std.Dev. 571s Subject (Intercept) 627.57 25.051 571s Subject.1 Days 35.86 5.988 571s Residual 653.58 25.565 571s Number of obs: 180, groups: Subject, 18 571s 571s Fixed effects: 571s Estimate Std. Error df t value Pr(>|t|) 571s (Intercept) 251.405 6.885 18.156 36.513 < 2e-16 *** 571s Days 10.467 1.560 18.156 6.712 2.59e-06 *** 571s --- 571s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 571s 571s Correlation of Fixed Effects: 571s (Intr) 571s Days -0.184 571s > 571s > ## Test class: 571s > stopifnot(all( 571s + class(sfm) == c("summary.lmerModLmerTest", "summary.merMod"), 571s + all(c("df", "Pr(>|t|)") %in% colnames(coef(sfm))) 571s + )) 571s > stopifnot(class(summary(fm, ddf="lme4")) == "summary.merMod") 571s > 571s > ## Test coefficient table names: 571s > mat <- coef(summary(fm)) 571s > stopifnot(all( # colnames 571s + colnames(mat) == c("Estimate", "Std. Error", "df", "t value", "Pr(>|t|)") 571s + )) 571s > stopifnot(all( # rownames 571s + names(fixef(fm)) == rownames(mat) 571s + )) 571s > 571s > ## Test pass of 'correlation' argument to lme4:::summary.merMod: 571s > x <- capture.output(summary(fm)) 571s > x_nocor <- capture.output(summary(fm, correlation=FALSE)) 571s > txt <- "Correlation of Fixed Effects:" 571s > stopifnot( 571s + any(grep(txt, x)), 571s + !any(grepl(txt, x_nocor)) 571s + ) 571s > 571s > # Test warning with unrecognized arguments (caught by lme4:::summary.merMod): 571s > assertWarning(summary(fm, false_arg=FALSE)) 571s > 571s > ## Test pass of extra arguments to lme4:::print.summary.merMod: 571s > x <- capture.output(print(summary(fm), signif.stars=TRUE)) 571s > x_nocor <- capture.output(print(summary(fm), signif.stars=FALSE)) 571s > txt <- "Signif. codes:" 571s > stopifnot( 571s + any(grep(txt, x)), 571s + !any(grepl(txt, x_nocor)) 571s + ) 571s > 571s > ####### ddf argument: 571s > (an1 <- summary(fm)) # Also testing print method. 571s Linear mixed model fit by REML. t-tests use Satterthwaite's method [ 571s lmerModLmerTest] 571s Formula: Reaction ~ Days + (1 | Subject) + (0 + Days | Subject) 571s Data: sleepstudy 571s 571s REML criterion at convergence: 1743.7 571s 571s Scaled residuals: 571s Min 1Q Median 3Q Max 571s -3.9626 -0.4625 0.0204 0.4653 5.1860 571s 571s Random effects: 571s Groups Name Variance Std.Dev. 571s Subject (Intercept) 627.57 25.051 571s Subject.1 Days 35.86 5.988 571s Residual 653.58 25.565 571s Number of obs: 180, groups: Subject, 18 571s 571s Fixed effects: 571s Estimate Std. Error df t value Pr(>|t|) 571s (Intercept) 251.405 6.885 18.156 36.513 < 2e-16 *** 571s Days 10.467 1.560 18.156 6.712 2.59e-06 *** 571s --- 571s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 571s 571s Correlation of Fixed Effects: 571s (Intr) 571s Days -0.184 571s > (an2 <- summary(fm, ddf="Satterthwaite")) 571s Linear mixed model fit by REML. t-tests use Satterthwaite's method [ 571s lmerModLmerTest] 571s Formula: Reaction ~ Days + (1 | Subject) + (0 + Days | Subject) 571s Data: sleepstudy 571s 571s REML criterion at convergence: 1743.7 571s 571s Scaled residuals: 571s Min 1Q Median 3Q Max 571s -3.9626 -0.4625 0.0204 0.4653 5.1860 571s 571s Random effects: 571s Groups Name Variance Std.Dev. 571s Subject (Intercept) 627.57 25.051 571s Subject.1 Days 35.86 5.988 571s Residual 653.58 25.565 571s Number of obs: 180, groups: Subject, 18 571s 571s Fixed effects: 571s Estimate Std. Error df t value Pr(>|t|) 571s (Intercept) 251.405 6.885 18.156 36.513 < 2e-16 *** 571s Days 10.467 1.560 18.156 6.712 2.59e-06 *** 571s --- 571s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 571s 571s Correlation of Fixed Effects: 571s (Intr) 571s Days -0.184 571s > stopifnot(isTRUE( 571s + all.equal(an1, an2) 571s + )) 571s > (an3 <- summary(fm, ddf="Sat")) ## Abbreviated argument 571s Linear mixed model fit by REML. t-tests use Satterthwaite's method [ 571s lmerModLmerTest] 571s Formula: Reaction ~ Days + (1 | Subject) + (0 + Days | Subject) 571s Data: sleepstudy 571s 571s REML criterion at convergence: 1743.7 571s 571s Scaled residuals: 571s Min 1Q Median 3Q Max 571s -3.9626 -0.4625 0.0204 0.4653 5.1860 571s 571s Random effects: 571s Groups Name Variance Std.Dev. 571s Subject (Intercept) 627.57 25.051 571s Subject.1 Days 35.86 5.988 571s Residual 653.58 25.565 571s Number of obs: 180, groups: Subject, 18 571s 571s Fixed effects: 571s Estimate Std. Error df t value Pr(>|t|) 571s (Intercept) 251.405 6.885 18.156 36.513 < 2e-16 *** 571s Days 10.467 1.560 18.156 6.712 2.59e-06 *** 571s --- 571s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 571s 571s Correlation of Fixed Effects: 571s (Intr) 571s Days -0.184 571s > stopifnot(isTRUE( 571s + all.equal(an1, an3) 571s + )) 571s > (summary(fm, ddf="lme4")) 571s Linear mixed model fit by REML ['lmerMod'] 571s Formula: Reaction ~ Days + (1 | Subject) + (0 + Days | Subject) 571s Data: sleepstudy 571s 571s REML criterion at convergence: 1743.7 571s 571s Scaled residuals: 571s Min 1Q Median 3Q Max 571s -3.9626 -0.4625 0.0204 0.4653 5.1860 571s 571s Random effects: 571s Groups Name Variance Std.Dev. 571s Subject (Intercept) 627.57 25.051 571s Subject.1 Days 35.86 5.988 571s Residual 653.58 25.565 571s Number of obs: 180, groups: Subject, 18 571s 571s Fixed effects: 571s Estimate Std. Error t value 571s (Intercept) 251.405 6.885 36.513 571s Days 10.467 1.560 6.712 571s 571s Correlation of Fixed Effects: 571s (Intr) 571s Days -0.184 571s > if(has_pbkrtest) { 571s + (summary(fm, ddf="Kenward-Roger")) 571s + assertError(summary(fm, ddf="KR")) ## Error on incorrect arg. 571s + } 571s > 571s > ## lme4 method: 571s > an1 <- summary(fm, ddf="lme4") 571s > an2 <- summary(as(fm, "lmerMod")) 571s > stopifnot(isTRUE( 571s + all.equal(an1, an2) 571s + )) 571s > 571s > 571s > # Test printed output 571s > # - Satterthwaite 571s > x <- capture.output(sfm) # equal to output of 'print(sfm)' 571s > txt <- c("lmerModLmerTest", "t-tests use Satterthwaite's method", 571s + "df", "t value", "Pr(>|t|)") 571s > stopifnot(all( 571s + sapply(txt, function(text) any(grepl(text, x))) 571s + )) 571s > 571s > # Test printed output 571s > # - KR 571s > if(has_pbkrtest) { 571s + (sfm <- summary(fm, ddf="Kenward-Roger")) 571s + x <- capture.output(sfm) 571s + txt <- c("lmerModLmerTest", "t-tests use Kenward-Roger's method", 571s + "df", "t value", "Pr(>|t|)") 571s + stopifnot(all( 571s + sapply(txt, function(text) any(grepl(text, x))) 571s + )) 571s + } 571s > 571s > #################################### 571s > ## Test 'boundary' fixef structures: 571s > #################################### 571s > 571s > # Example with no fixef: 571s > m <- lmer(Reaction ~ -1 + (Days | Subject), sleepstudy) 571s > # m <- lmer(Reaction ~ 0 + (Days | Subject), sleepstudy) # alternative 571s > stopifnot(length(fixef(m)) == 0L) 571s > stopifnot( 571s + nrow(coef(summary(m))) == 0L, 571s + nrow(coef(summary(m, ddf="lme4"))) == 0L 571s + ) 571s > if(has_pbkrtest){ 571s + stopifnot(nrow(coef(summary(m, ddf="Kenward-Roger"))) == 0L) 571s + } 571s > 571s > # Example with intercept only: 571s > m <- lmer(Reaction ~ (Days | Subject), sleepstudy) 572s > # m <- lmer(Reaction ~ 1 + (Days | Subject), sleepstudy) # alternative 572s > stopifnot(length(fixef(m)) == 1L, 572s + names(fixef(m)) == "(Intercept)") 572s > stopifnot( 572s + nrow(coef(summary(m))) == 1L, 572s + nrow(coef(summary(m, ddf="lme4"))) == 1L 572s + ) 572s > if(has_pbkrtest){ 572s + stopifnot(nrow(coef(summary(m, ddf="Kenward-Roger"))) == 1L) 572s + } 572s > 572s > # Example with >1 fixef without intercept: 572s > m <- lmer(Reaction ~ Days - 1 + I(Days^2) + (Days | Subject), sleepstudy) 572s > stopifnot(length(fixef(m)) == 2L, 572s + names(fixef(m)) == c("Days", "I(Days^2)")) 572s > stopifnot( 572s + nrow(coef(summary(m))) == 2L, 572s + nrow(coef(summary(m, ddf="lme4"))) == 2L 572s + ) 572s > if(has_pbkrtest){ 572s + stopifnot(nrow(coef(summary(m, ddf="Kenward-Roger"))) == 2L) 572s + } 572s > 572s > 572s BEGIN TEST test_zerovar.R 572s 572s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 572s Copyright (C) 2025 The R Foundation for Statistical Computing 572s Platform: arm-unknown-linux-gnueabihf (32-bit) 572s 572s R is free software and comes with ABSOLUTELY NO WARRANTY. 572s You are welcome to redistribute it under certain conditions. 572s Type 'license()' or 'licence()' for distribution details. 572s 572s R is a collaborative project with many contributors. 572s Type 'contributors()' for more information and 572s 'citation()' on how to cite R or R packages in publications. 572s 572s Type 'demo()' for some demos, 'help()' for on-line help, or 572s 'help.start()' for an HTML browser interface to help. 572s Type 'q()' to quit R. 572s 572s > # test_zerovar.R 572s > 572s > library(lmerTest) 572s Loading required package: lme4 572s Loading required package: Matrix 574s 574s Attaching package: 'lmerTest' 574s 574s > data("sleepstudy", package="lme4") 574s The following object is masked from 'package:lme4': 574s 574s lmer 574s 574s The following object is masked from 'package:stats': 574s 574s step 574s 574s > 574s > # Baseline fit: 574s > m0 <- lmer(Reaction ~ Days + (Days | Subject), sleepstudy, 574s + control=lmerControl(optimizer="bobyqa")) 575s > ## default optimizer does not converge proporly 575s > m0 575s Linear mixed model fit by REML ['lmerModLmerTest'] 575s Formula: Reaction ~ Days + (Days | Subject) 575s Data: sleepstudy 575s REML criterion at convergence: 1743.628 575s Random effects: 575s Groups Name Std.Dev. Corr 575s Subject (Intercept) 24.740 575s Days 5.922 0.07 575s Residual 25.592 575s Number of obs: 180, groups: Subject, 18 575s Fixed Effects: 575s (Intercept) Days 575s 251.41 10.47 575s > (an0 <- anova(m0)) 575s boundary (singular) fit: see help('isSingular') 575s Type III Analysis of Variance Table with Satterthwaite's method 575s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 575s Days 30031 30031 1 17 45.853 3.264e-06 *** 575s --- 575s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 575s > 575s > # Make a fit with a zero variance estimate: 575s > n <- nrow(sleepstudy) 575s > g <- factor(rep(1:2, c(n - 10, 10))) 575s > m <- lmer(Reaction ~ Days + (Days | Subject) + (1|g), sleepstudy, 575s + control=lmerControl(optimizer="bobyqa")) 575s > m 575s Linear mixed model fit by REML ['lmerModLmerTest'] 575s Formula: Reaction ~ Days + (Days | Subject) + (1 | g) 575s Data: sleepstudy 575s REML criterion at convergence: 1743.628 575s Random effects: 575s Groups Name Std.Dev. Corr 575s Subject (Intercept) 24.740 575s Days 5.922 0.07 575s g (Intercept) 0.000 575s Residual 25.592 575s Number of obs: 180, groups: Subject, 18; g, 2 575s Fixed Effects: 575s (Intercept) Days 575s 251.41 10.47 575s optimizer (bobyqa) convergence code: 0 (OK) ; 0 optimizer warnings; 1 lme4 warnings 575s > (an <- anova(m)) 575s Type III Analysis of Variance Table with Satterthwaite's method 575s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 575s Days 30031 30031 1 17 45.853 3.264e-06 *** 575s --- 575s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 575s > 575s > # check that fit has a zero variance 575s > vc <- as.data.frame(VarCorr(m)) 575s > stopifnot(isTRUE( 575s + all.equal(0, vc[vc$grp == "g", "sdcor"], tolerance=1e-4) 575s + )) 575s > # The hessian/vcov is actually positive definite: 575s > stopifnot(isTRUE( 575s + all(eigen(m@vcov_varpar, only.values = TRUE)$values > 0) 575s + )) 575s > 575s > # Check that ANOVA tables are the same: 575s > stopifnot(isTRUE( 575s + all.equal(an0[, 1:5], an[, 1:5], tolerance=1e-4) 575s + )) 575s > 575s > stopifnot(isTRUE( # Equality of summary tables 575s + all.equal(coef(summary(m0)), coef(summary(m)), tolerance=1e-4) 575s + )) 575s > stopifnot(isTRUE( # Equality of lme4-anova tables 575s + all.equal(anova(m0, ddf="lme4"), anova(m, ddf="lme4"), tolerance=1e-4) 575s + )) 575s > 575s > 575s BEGIN TEST zlmerTest_zeroDenom.R 575s 575s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 575s Copyright (C) 2025 The R Foundation for Statistical Computing 575s Platform: arm-unknown-linux-gnueabihf (32-bit) 575s 575s R is free software and comes with ABSOLUTELY NO WARRANTY. 575s You are welcome to redistribute it under certain conditions. 575s Type 'license()' or 'licence()' for distribution details. 575s 575s R is a collaborative project with many contributors. 575s Type 'contributors()' for more information and 575s 'citation()' on how to cite R or R packages in publications. 575s 575s Type 'demo()' for some demos, 'help()' for on-line help, or 575s 'help.start()' for an HTML browser interface to help. 575s Type 'q()' to quit R. 575s 575s > library(lmerTest) 575s Loading required package: lme4 575s Loading required package: Matrix 577s 577s Attaching package: 'lmerTest' 577s 577s The following object is masked from 'package:lme4': 577s 577s lmer 577s 577s The following object is masked from 'package:stats': 577s 577s step 577s 577s > 577s > # Read in data set 577s > load(system.file("testdata","potdata.RData", package="lmerTest")) 577s > 577s > # Mixed model 577s > lmerout <- lmer(biomass ~ CO2*nutrients + (1|chamber),data=potdata) 577s > summary(lmerout) 577s Linear mixed model fit by REML. t-tests use Satterthwaite's method [ 577s lmerModLmerTest] 577s Formula: biomass ~ CO2 * nutrients + (1 | chamber) 577s Data: potdata 577s 577s REML criterion at convergence: 49.2 577s 577s Scaled residuals: 577s Min 1Q Median 3Q Max 577s -1.4159 -0.5588 0.0000 0.5588 1.4159 577s 577s Random effects: 577s Groups Name Variance Std.Dev. 577s chamber (Intercept) 0.2437 0.4936 577s Residual 1.5797 1.2568 577s Number of obs: 24, groups: chamber, 4 577s 577s Fixed effects: 577s Estimate Std. Error df t value Pr(>|t|) 577s (Intercept) 12.8500 0.9548 11.0163 13.458 3.49e-08 *** 577s CO2675 2.0000 1.3503 11.0163 1.481 0.166595 577s nutrients2 7.3500 1.2568 10.0000 5.848 0.000162 *** 577s nutrients3 10.4500 1.2568 10.0000 8.314 8.39e-06 *** 577s nutrients4 18.6500 1.2568 10.0000 14.839 3.88e-08 *** 577s nutrients5 25.0500 1.2568 10.0000 19.931 2.22e-09 *** 577s nutrients6 29.0000 1.2568 10.0000 23.074 5.28e-10 *** 577s CO2675:nutrients2 -0.5000 1.7775 10.0000 -0.281 0.784214 577s CO2675:nutrients3 1.9000 1.7775 10.0000 1.069 0.310218 577s CO2675:nutrients4 3.4500 1.7775 10.0000 1.941 0.080949 . 577s CO2675:nutrients5 5.9000 1.7775 10.0000 3.319 0.007756 ** 577s CO2675:nutrients6 5.2500 1.7775 10.0000 2.954 0.014444 * 577s --- 577s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 577s 577s Correlation of Fixed Effects: 577s (Intr) CO2675 ntrnt2 ntrnt3 ntrnt4 ntrnt5 ntrnt6 CO2675:2 CO2675:3 577s CO2675 -0.707 577s nutrients2 -0.658 0.465 577s nutrients3 -0.658 0.465 0.500 577s nutrients4 -0.658 0.465 0.500 0.500 577s nutrients5 -0.658 0.465 0.500 0.500 0.500 577s nutrients6 -0.658 0.465 0.500 0.500 0.500 0.500 577s CO2675:ntr2 0.465 -0.658 -0.707 -0.354 -0.354 -0.354 -0.354 577s CO2675:ntr3 0.465 -0.658 -0.354 -0.707 -0.354 -0.354 -0.354 0.500 577s CO2675:ntr4 0.465 -0.658 -0.354 -0.354 -0.707 -0.354 -0.354 0.500 0.500 577s CO2675:ntr5 0.465 -0.658 -0.354 -0.354 -0.354 -0.707 -0.354 0.500 0.500 577s CO2675:ntr6 0.465 -0.658 -0.354 -0.354 -0.354 -0.354 -0.707 0.500 0.500 577s CO2675:4 CO2675:5 577s CO2675 577s nutrients2 577s nutrients3 577s nutrients4 577s nutrients5 577s nutrients6 577s CO2675:ntr2 577s CO2675:ntr3 577s CO2675:ntr4 577s CO2675:ntr5 0.500 577s CO2675:ntr6 0.500 0.500 577s > 577s > an.sat <- anova(lmerout) 577s > anova(lmerout, ddf="lme4") 577s Analysis of Variance Table 577s npar Sum Sq Mean Sq F value 577s CO2 1 67.86 67.86 42.9589 577s nutrients 5 3050.44 610.09 386.2129 577s CO2:nutrients 5 35.47 7.09 4.4906 577s > TOL <- 1e-5 577s > stopifnot(isTRUE(all.equal( 577s + an.sat[,"DenDF"], c(2, 10, 10), tolerance=TOL 577s + ))) 577s > 577s > stopifnot(isTRUE( 577s + all.equal(an.sat[,"Pr(>F)"], c(0.0224955602, 1e-11, 0.020905569), tolerance=TOL) 577s + )) 577s > 577s > # if(require(pbkrtest)) 577s > # an.kr <- anova(lmerout, ddf="Kenward-Roger") 577s > # 577s > # TOL <- 1e-7 577s > # stopifnot(all.equal(an.kr[,"Pr(>F)"], c(0.0224955602, 1e-11, 0.020905569) , 577s > # tol=TOL), 577s > # all.equal(an.kr[,"DenDF"], 577s > # c(2, 10, 10) , tol=TOL), 577s > # TRUE) 577s > 578s autopkgtest [23:42:11]: test run-unit-test: -----------------------] 583s run-unit-test PASS 583s autopkgtest [23:42:16]: test run-unit-test: - 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will be installed: 824s build-essential cpp cpp-15 cpp-15-arm-linux-gnueabihf 824s cpp-arm-linux-gnueabihf dctrl-tools fontconfig fontconfig-config 824s fonts-dejavu-core fonts-dejavu-mono fonts-glyphicons-halflings fonts-mathjax 824s g++ g++-15 g++-15-arm-linux-gnueabihf g++-arm-linux-gnueabihf gcc gcc-15 824s gcc-15-arm-linux-gnueabihf gcc-arm-linux-gnueabihf gfortran gfortran-15 824s gfortran-15-arm-linux-gnueabihf gfortran-arm-linux-gnueabihf icu-devtools 824s libasan8 libblas-dev libblas3 libbz2-dev libc-dev-bin libc6-dev libcairo2 824s libcc1-0 libcrypt-dev libdatrie1 libdeflate-dev libdeflate0 libfontconfig1 824s libfreetype6 libgcc-15-dev libgfortran-15-dev libgfortran5 libgomp1 824s libgraphite2-3 libharfbuzz0b libice6 libicu-dev libisl23 libjbig0 824s libjpeg-dev libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8 libjpeg8-dev 824s libjs-bootstrap libjs-highlight.js libjs-jquery libjs-jquery-datatables 824s libjs-mathjax liblapack-dev liblapack3 liblerc4 liblzma-dev libmpc3 824s libncurses-dev libnlopt0 libpango-1.0-0 libpangocairo-1.0-0 824s libpangoft2-1.0-0 libpaper-utils libpaper2 libpcre2-16-0 libpcre2-32-0 824s libpcre2-dev libpcre2-posix3 libpixman-1-0 libpkgconf3 libpng-dev 824s libreadline-dev libsharpyuv0 libsm6 libstdc++-15-dev libtcl8.6 libthai-data 824s libthai0 libtiff6 libtirpc-dev libtk8.6 libubsan1 libwebp7 libxcb-render0 824s libxcb-shm0 libxft2 libxrender1 libxss1 libxt6t64 libzstd-dev linux-libc-dev 824s node-normalize.css pkg-r-autopkgtest pkgconf pkgconf-bin r-base-core 824s r-base-dev r-cran-backports r-cran-boot r-cran-broom r-cran-cli 824s r-cran-colorspace r-cran-cowplot r-cran-cpp11 r-cran-curl r-cran-deriv 824s r-cran-doby r-cran-dplyr r-cran-evaluate r-cran-fansi r-cran-farver 824s r-cran-forecast r-cran-fracdiff r-cran-generics r-cran-ggplot2 r-cran-glue 824s r-cran-gtable r-cran-highr r-cran-isoband r-cran-jsonlite r-cran-knitr 824s r-cran-labeling r-cran-lattice r-cran-lifecycle r-cran-littler r-cran-lme4 824s r-cran-lmertest r-cran-lmtest r-cran-magrittr r-cran-mass r-cran-matrix 824s r-cran-microbenchmark r-cran-minqa r-cran-modelr r-cran-nlme r-cran-nloptr 824s r-cran-nnet r-cran-numderiv r-cran-pbkrtest r-cran-pillar r-cran-pkgconfig 824s r-cran-pkgkitten r-cran-purrr r-cran-quadprog r-cran-quantmod r-cran-r6 824s r-cran-rbibutils r-cran-rcolorbrewer r-cran-rcpp r-cran-rcpparmadillo 824s r-cran-rcppeigen r-cran-rdpack r-cran-reformulas r-cran-rlang r-cran-s7 824s r-cran-scales r-cran-statmod r-cran-stringi r-cran-stringr r-cran-tibble 824s r-cran-tidyr r-cran-tidyselect r-cran-timedate r-cran-tseries r-cran-ttr 824s r-cran-urca r-cran-utf8 r-cran-vctrs r-cran-viridislite r-cran-withr 824s r-cran-xfun r-cran-xts r-cran-yaml r-cran-zoo rpcsvc-proto unzip x11-common 824s xdg-utils zip zlib1g-dev 825s 0 upgraded, 187 newly installed, 0 to remove and 0 not upgraded. 825s Need to get 194 MB of archives. 825s After this operation, 495 MB of additional disk space will be used. 825s Get:1 http://ftpmaster.internal/ubuntu resolute/main armhf libc-dev-bin armhf 2.42-2ubuntu4 [21.8 kB] 825s Get:2 http://ftpmaster.internal/ubuntu resolute/main armhf linux-libc-dev armhf 6.19.0-3.3 [1804 kB] 833s Get:3 http://ftpmaster.internal/ubuntu resolute/main armhf libcrypt-dev armhf 1:4.5.1-1 [128 kB] 834s Get:4 http://ftpmaster.internal/ubuntu resolute/main armhf rpcsvc-proto armhf 1.4.3-1build1 [62.6 kB] 834s Get:5 http://ftpmaster.internal/ubuntu resolute/main armhf libc6-dev armhf 2.42-2ubuntu4 [1416 kB] 841s Get:6 http://ftpmaster.internal/ubuntu resolute/main armhf libisl23 armhf 0.27-1build1 [553 kB] 844s Get:7 http://ftpmaster.internal/ubuntu resolute/main armhf libmpc3 armhf 1.3.1-2 [47.0 kB] 844s Get:8 http://ftpmaster.internal/ubuntu resolute/main armhf cpp-15-arm-linux-gnueabihf armhf 15.2.0-12ubuntu1 [10.1 MB] 874s Get:9 http://ftpmaster.internal/ubuntu resolute/main armhf cpp-15 armhf 15.2.0-12ubuntu1 [1032 B] 874s Get:10 http://ftpmaster.internal/ubuntu resolute/main armhf cpp-arm-linux-gnueabihf armhf 4:15.2.0-4ubuntu1 [5756 B] 874s Get:11 http://ftpmaster.internal/ubuntu resolute/main armhf cpp armhf 4:15.2.0-4ubuntu1 [22.4 kB] 875s Get:12 http://ftpmaster.internal/ubuntu resolute/main armhf libcc1-0 armhf 15.2.0-12ubuntu1 [43.5 kB] 875s Get:13 http://ftpmaster.internal/ubuntu resolute/main armhf libgomp1 armhf 15.2.0-12ubuntu1 [129 kB] 875s Get:14 http://ftpmaster.internal/ubuntu resolute/main armhf libasan8 armhf 15.2.0-12ubuntu1 [2949 kB] 882s Get:15 http://ftpmaster.internal/ubuntu resolute/main armhf libubsan1 armhf 15.2.0-12ubuntu1 [1187 kB] 884s Get:16 http://ftpmaster.internal/ubuntu resolute/main armhf libgcc-15-dev armhf 15.2.0-12ubuntu1 [898 kB] 886s Get:17 http://ftpmaster.internal/ubuntu resolute/main armhf gcc-15-arm-linux-gnueabihf armhf 15.2.0-12ubuntu1 [19.5 MB] 927s Get:18 http://ftpmaster.internal/ubuntu resolute/main armhf gcc-15 armhf 15.2.0-12ubuntu1 [499 kB] 928s Get:19 http://ftpmaster.internal/ubuntu resolute/main armhf gcc-arm-linux-gnueabihf armhf 4:15.2.0-4ubuntu1 [1220 B] 928s Get:20 http://ftpmaster.internal/ubuntu resolute/main armhf gcc armhf 4:15.2.0-4ubuntu1 [5022 B] 928s Get:21 http://ftpmaster.internal/ubuntu resolute/main armhf libstdc++-15-dev armhf 15.2.0-12ubuntu1 [2638 kB] 933s Get:22 http://ftpmaster.internal/ubuntu resolute/main armhf g++-15-arm-linux-gnueabihf armhf 15.2.0-12ubuntu1 [11.4 MB] 957s Get:23 http://ftpmaster.internal/ubuntu resolute/main armhf g++-15 armhf 15.2.0-12ubuntu1 [25.3 kB] 957s Get:24 http://ftpmaster.internal/ubuntu resolute/main armhf g++-arm-linux-gnueabihf armhf 4:15.2.0-4ubuntu1 [968 B] 957s Get:25 http://ftpmaster.internal/ubuntu resolute/main armhf g++ armhf 4:15.2.0-4ubuntu1 [1086 B] 957s Get:26 http://ftpmaster.internal/ubuntu resolute/main armhf build-essential armhf 12.12ubuntu2 [5256 B] 957s Get:27 http://ftpmaster.internal/ubuntu resolute/main armhf dctrl-tools armhf 2.24-3build4 [95.0 kB] 958s Get:28 http://ftpmaster.internal/ubuntu resolute/main armhf libfreetype6 armhf 2.14.1+dfsg-2 [345 kB] 959s Get:29 http://ftpmaster.internal/ubuntu resolute/main armhf fonts-dejavu-mono all 2.37-8build1 [502 kB] 961s Get:30 http://ftpmaster.internal/ubuntu resolute/main armhf fonts-dejavu-core all 2.37-8build1 [834 kB] 966s Get:31 http://ftpmaster.internal/ubuntu resolute/main armhf fontconfig-config armhf 2.17.1-3ubuntu1 [38.5 kB] 966s Get:32 http://ftpmaster.internal/ubuntu resolute/main armhf libfontconfig1 armhf 2.17.1-3ubuntu1 [117 kB] 967s Get:33 http://ftpmaster.internal/ubuntu resolute/main armhf fontconfig armhf 2.17.1-3ubuntu1 [180 kB] 968s Get:34 http://ftpmaster.internal/ubuntu resolute/universe armhf fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-6 [119 kB] 969s Get:35 http://ftpmaster.internal/ubuntu resolute/main armhf fonts-mathjax all 2.7.9+dfsg-1build1 [2283 kB] 980s Get:36 http://ftpmaster.internal/ubuntu resolute/main armhf libgfortran5 armhf 15.2.0-12ubuntu1 [334 kB] 982s Get:37 http://ftpmaster.internal/ubuntu resolute/main armhf libgfortran-15-dev armhf 15.2.0-12ubuntu1 [380 kB] 984s Get:38 http://ftpmaster.internal/ubuntu resolute/main armhf gfortran-15-arm-linux-gnueabihf armhf 15.2.0-12ubuntu1 [10.7 MB] 1030s Get:39 http://ftpmaster.internal/ubuntu resolute/main armhf gfortran-15 armhf 15.2.0-12ubuntu1 [18.1 kB] 1030s Get:40 http://ftpmaster.internal/ubuntu resolute/main armhf gfortran-arm-linux-gnueabihf armhf 4:15.2.0-4ubuntu1 [1020 B] 1030s Get:41 http://ftpmaster.internal/ubuntu resolute/main armhf gfortran armhf 4:15.2.0-4ubuntu1 [1162 B] 1030s Get:42 http://ftpmaster.internal/ubuntu resolute/main armhf icu-devtools armhf 78.2-1ubuntu1 [203 kB] 1031s Get:43 http://ftpmaster.internal/ubuntu resolute/main armhf libblas3 armhf 3.12.1-7ubuntu1 [133 kB] 1031s Get:44 http://ftpmaster.internal/ubuntu resolute/main armhf libblas-dev armhf 3.12.1-7ubuntu1 [141 kB] 1031s Get:45 http://ftpmaster.internal/ubuntu resolute/main armhf libbz2-dev armhf 1.0.8-6build2 [31.2 kB] 1031s Get:46 http://ftpmaster.internal/ubuntu resolute/main armhf libpixman-1-0 armhf 0.46.4-1 [196 kB] 1032s Get:47 http://ftpmaster.internal/ubuntu resolute/main armhf libxcb-render0 armhf 1.17.0-2ubuntu1 [15.5 kB] 1032s Get:48 http://ftpmaster.internal/ubuntu resolute/main armhf libxcb-shm0 armhf 1.17.0-2ubuntu1 [5956 B] 1032s Get:49 http://ftpmaster.internal/ubuntu resolute/main armhf libxrender1 armhf 1:0.9.12-1 [16.6 kB] 1032s Get:50 http://ftpmaster.internal/ubuntu resolute/main armhf libcairo2 armhf 1.18.4-3 [489 kB] 1033s Get:51 http://ftpmaster.internal/ubuntu resolute/main armhf libdatrie1 armhf 0.2.14-1 [16.4 kB] 1033s Get:52 http://ftpmaster.internal/ubuntu resolute/main armhf libdeflate0 armhf 1.23-2build1 [38.8 kB] 1033s Get:53 http://ftpmaster.internal/ubuntu resolute/main armhf libdeflate-dev armhf 1.23-2build1 [45.1 kB] 1033s Get:54 http://ftpmaster.internal/ubuntu resolute/main armhf libgraphite2-3 armhf 1.3.14-11ubuntu1 [65.2 kB] 1033s Get:55 http://ftpmaster.internal/ubuntu resolute/main armhf libharfbuzz0b armhf 12.3.2-1 [501 kB] 1034s Get:56 http://ftpmaster.internal/ubuntu resolute/main armhf x11-common all 1:7.7+24ubuntu1 [22.4 kB] 1034s Get:57 http://ftpmaster.internal/ubuntu resolute/main armhf libice6 armhf 2:1.1.1-1build1 [37.5 kB] 1034s Get:58 http://ftpmaster.internal/ubuntu resolute/main armhf libicu-dev armhf 78.2-1ubuntu1 [12.2 MB] 1068s Get:59 http://ftpmaster.internal/ubuntu resolute/main armhf libjpeg-turbo8 armhf 2.1.5-4ubuntu3 [129 kB] 1069s Get:60 http://ftpmaster.internal/ubuntu resolute/main armhf libjpeg-turbo8-dev armhf 2.1.5-4ubuntu3 [265 kB] 1069s Get:61 http://ftpmaster.internal/ubuntu resolute/main armhf libjpeg8 armhf 8c-2ubuntu11 [2148 B] 1069s Get:62 http://ftpmaster.internal/ubuntu resolute/main armhf libjpeg8-dev armhf 8c-2ubuntu11 [1484 B] 1069s Get:63 http://ftpmaster.internal/ubuntu resolute/main armhf libjpeg-dev armhf 8c-2ubuntu11 [1482 B] 1069s Get:64 http://ftpmaster.internal/ubuntu resolute/universe armhf libjs-bootstrap all 3.4.1+dfsg-6 [129 kB] 1069s Get:65 http://ftpmaster.internal/ubuntu resolute/universe armhf libjs-highlight.js all 10.7.3+dfsg-2 [144 kB] 1070s Get:66 http://ftpmaster.internal/ubuntu resolute/main armhf libjs-jquery all 3.7.1+dfsg+~3.5.33-1build1 [321 kB] 1070s Get:67 http://ftpmaster.internal/ubuntu resolute/universe armhf libjs-jquery-datatables all 1.11.5+dfsg-2build1 [145 kB] 1071s Get:68 http://ftpmaster.internal/ubuntu resolute/main armhf liblapack3 armhf 3.12.1-7ubuntu1 [2090 kB] 1075s Get:69 http://ftpmaster.internal/ubuntu resolute/main armhf liblapack-dev armhf 3.12.1-7ubuntu1 [2207 kB] 1080s Get:70 http://ftpmaster.internal/ubuntu resolute/main armhf liblerc4 armhf 4.0.0+ds-5ubuntu2 [162 kB] 1080s Get:71 http://ftpmaster.internal/ubuntu resolute/main armhf libncurses-dev armhf 6.6+20251231-1 [348 kB] 1081s Get:72 http://ftpmaster.internal/ubuntu resolute/main armhf libthai-data all 0.1.30-1 [155 kB] 1081s Get:73 http://ftpmaster.internal/ubuntu resolute/main armhf libthai0 armhf 0.1.30-1 [15.4 kB] 1081s Get:74 http://ftpmaster.internal/ubuntu resolute/main armhf libpango-1.0-0 armhf 1.57.0-1 [218 kB] 1082s Get:75 http://ftpmaster.internal/ubuntu resolute/main armhf libpangoft2-1.0-0 armhf 1.57.0-1 [45.2 kB] 1082s Get:76 http://ftpmaster.internal/ubuntu resolute/main armhf libpangocairo-1.0-0 armhf 1.57.0-1 [25.3 kB] 1082s Get:77 http://ftpmaster.internal/ubuntu resolute/main armhf libpaper2 armhf 2.2.5-0.3build1 [16.3 kB] 1082s Get:78 http://ftpmaster.internal/ubuntu resolute/main armhf libpaper-utils armhf 2.2.5-0.3build1 [14.2 kB] 1082s Get:79 http://ftpmaster.internal/ubuntu resolute/main armhf libpcre2-16-0 armhf 10.46-1 [206 kB] 1082s Get:80 http://ftpmaster.internal/ubuntu resolute/main armhf libpcre2-32-0 armhf 10.46-1 [197 kB] 1083s Get:81 http://ftpmaster.internal/ubuntu resolute/main armhf libpcre2-posix3 armhf 10.46-1 [6286 B] 1083s Get:82 http://ftpmaster.internal/ubuntu resolute/main armhf libpcre2-dev armhf 10.46-1 [744 kB] 1084s Get:83 http://ftpmaster.internal/ubuntu resolute/main armhf libpkgconf3 armhf 1.8.1-4build1 [26.6 kB] 1085s Get:84 http://ftpmaster.internal/ubuntu resolute/main armhf zlib1g-dev armhf 1:1.3.dfsg+really1.3.1-1ubuntu2 [881 kB] 1086s Get:85 http://ftpmaster.internal/ubuntu resolute/main armhf libpng-dev armhf 1.6.54-1 [252 kB] 1087s Get:86 http://ftpmaster.internal/ubuntu resolute/main armhf libreadline-dev armhf 8.3-3 [165 kB] 1087s Get:87 http://ftpmaster.internal/ubuntu resolute/main armhf libsharpyuv0 armhf 1.5.0-0.1build1 [16.3 kB] 1087s Get:88 http://ftpmaster.internal/ubuntu resolute/main armhf libsm6 armhf 2:1.2.6-1build1 [15.3 kB] 1087s Get:89 http://ftpmaster.internal/ubuntu resolute/main armhf libtcl8.6 armhf 8.6.17+dfsg-1build1 [918 kB] 1090s Get:90 http://ftpmaster.internal/ubuntu resolute/main armhf libjbig0 armhf 2.1-6.1ubuntu3 [25.3 kB] 1090s Get:91 http://ftpmaster.internal/ubuntu resolute/main armhf libwebp7 armhf 1.5.0-0.1build1 [189 kB] 1090s Get:92 http://ftpmaster.internal/ubuntu resolute/main armhf libtiff6 armhf 4.7.0-3ubuntu3 [188 kB] 1091s Get:93 http://ftpmaster.internal/ubuntu resolute/main armhf libxft2 armhf 2.3.6-1build2 [37.2 kB] 1091s Get:94 http://ftpmaster.internal/ubuntu resolute/main armhf libxss1 armhf 1:1.2.3-1build4 [6328 B] 1091s Get:95 http://ftpmaster.internal/ubuntu resolute/main armhf libtk8.6 armhf 8.6.17-1 [694 kB] 1093s Get:96 http://ftpmaster.internal/ubuntu resolute/main armhf libxt6t64 armhf 1:1.2.1-1.3 [145 kB] 1093s Get:97 http://ftpmaster.internal/ubuntu resolute/main armhf libzstd-dev armhf 1.5.7+dfsg-3 [342 kB] 1094s Get:98 http://ftpmaster.internal/ubuntu resolute/universe armhf node-normalize.css all 8.0.1-5.1 [10.4 kB] 1094s Get:99 http://ftpmaster.internal/ubuntu resolute/main armhf zip armhf 3.0-15ubuntu3 [164 kB] 1094s Get:100 http://ftpmaster.internal/ubuntu resolute/main armhf unzip armhf 6.0-29ubuntu1 [167 kB] 1095s Get:101 http://ftpmaster.internal/ubuntu resolute/main armhf xdg-utils all 1.2.1-2ubuntu2 [66.1 kB] 1095s Get:102 http://ftpmaster.internal/ubuntu resolute/universe armhf r-base-core armhf 4.5.2-1ubuntu2 [28.5 MB] 1165s Get:103 http://ftpmaster.internal/ubuntu resolute/main armhf liblzma-dev armhf 5.8.2-2 [167 kB] 1166s Get:104 http://ftpmaster.internal/ubuntu resolute/main armhf pkgconf-bin armhf 1.8.1-4build1 [21.4 kB] 1166s Get:105 http://ftpmaster.internal/ubuntu resolute/main armhf pkgconf armhf 1.8.1-4build1 [16.8 kB] 1166s Get:106 http://ftpmaster.internal/ubuntu resolute/main armhf libtirpc-dev armhf 1.3.6+ds-1 [184 kB] 1166s Get:107 http://ftpmaster.internal/ubuntu resolute/universe armhf r-base-dev all 4.5.2-1ubuntu2 [1880 B] 1166s Get:108 http://ftpmaster.internal/ubuntu resolute/universe armhf pkg-r-autopkgtest all 20250812 [6158 B] 1166s Get:109 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-backports armhf 1.5.0-2 [121 kB] 1166s Get:110 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-boot all 1.3-32-1 [636 kB] 1167s Get:111 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-cli armhf 3.6.4-1 [1377 kB] 1170s Get:112 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-generics all 0.1.4-1 [84.0 kB] 1170s Get:113 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-glue armhf 1.8.0-1 [162 kB] 1171s Get:114 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-rlang armhf 1.1.5-3 [1700 kB] 1174s Get:115 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-lifecycle all 1.0.5+dfsg-1 [120 kB] 1174s Get:116 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-magrittr armhf 2.0.3-1 [154 kB] 1175s Get:117 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-utf8 armhf 1.2.4-1 [136 kB] 1175s Get:118 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-vctrs armhf 0.6.5-1 [1310 kB] 1177s Get:119 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-pillar all 1.11.1+dfsg-1 [456 kB] 1178s Get:120 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-r6 all 2.6.1-1 [101 kB] 1179s Get:121 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-fansi armhf 1.0.6-2 [620 kB] 1180s Get:122 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-pkgconfig all 2.0.3-2build2 [20.4 kB] 1180s Get:123 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-tibble armhf 3.2.1+dfsg-3 [420 kB] 1181s Get:124 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-withr all 3.0.2+dfsg-1 [214 kB] 1182s Get:125 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-tidyselect armhf 1.2.1+dfsg-1 [222 kB] 1182s Get:126 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-dplyr armhf 1.1.4-4 [1533 kB] 1186s Get:127 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-purrr armhf 1.0.4-1 [550 kB] 1187s Get:128 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-stringi armhf 1.8.4-1build2 [884 kB] 1189s Get:129 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-stringr all 1.5.1-1 [290 kB] 1190s Get:130 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-cpp11 all 0.5.3-1 [242 kB] 1190s Get:131 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-tidyr armhf 1.3.1-1 [1152 kB] 1192s Get:132 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-broom all 1.0.12+dfsg-1 [1708 kB] 1196s Get:133 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-colorspace armhf 2.1-1+dfsg-1 [1561 kB] 1199s Get:134 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-gtable all 0.3.6+dfsg-1 [199 kB] 1199s Get:135 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-isoband armhf 0.2.7-1 [1477 kB] 1202s Get:136 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-s7 armhf 0.2.0-1 [328 kB] 1202s Get:137 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-farver armhf 2.1.2-1 [1355 kB] 1205s Get:138 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-labeling all 0.4.3-1 [62.1 kB] 1205s Get:139 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-rcolorbrewer all 1.1-3-1build2 [54.0 kB] 1205s Get:140 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-viridislite all 0.4.3-1 [1088 kB] 1207s Get:141 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-scales all 1.4.0-1 [725 kB] 1209s Get:142 http://ftpmaster.internal/ubuntu resolute-proposed/universe armhf r-cran-ggplot2 all 4.0.2+dfsg-1 [4941 kB] 1218s Get:143 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-cowplot all 1.1.3+dfsg-1 [614 kB] 1219s Get:144 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-curl armhf 7.0.0+dfsg-1 [200 kB] 1219s Get:145 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-deriv all 4.2.0-1 [154 kB] 1220s Get:146 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-fracdiff armhf 1.5-3-1 [105 kB] 1220s Get:147 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-lattice armhf 0.22-7-1 [1365 kB] 1223s Get:148 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-zoo armhf 1.8-15-1 [1025 kB] 1224s Get:149 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-lmtest armhf 0.9.40-1build1 [400 kB] 1225s Get:150 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-nnet armhf 7.3-20-1 [111 kB] 1225s Get:151 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-littler armhf 0.3.22-1 [81.0 kB] 1225s Get:152 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-pkgkitten all 0.2.4-1 [27.2 kB] 1225s Get:153 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-rcpp armhf 1.1.0-1 [2009 kB] 1229s Get:154 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-timedate armhf 4052.112-1 [1299 kB] 1232s Get:155 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-quadprog armhf 1.5-8-1build2 [29.8 kB] 1232s Get:156 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-xts armhf 0.14.1-1 [1181 kB] 1235s Get:157 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-ttr armhf 0.24.4-1 [509 kB] 1236s Get:158 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-jsonlite armhf 1.9.1+dfsg-1 [440 kB] 1237s Get:159 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-quantmod all 0.4.28-1 [1037 kB] 1240s Get:160 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-tseries armhf 0.10-59-3 [379 kB] 1241s Get:161 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-nlme armhf 3.1.168-1 [2304 kB] 1245s Get:162 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-urca armhf 1.3-4-1build1 [1050 kB] 1247s Get:163 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-rcpparmadillo armhf 15.2.3-1-1 [915 kB] 1249s Get:164 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-forecast armhf 8.23.0-1 [1563 kB] 1252s Get:165 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-mass armhf 7.3-65-1 [1108 kB] 1254s Get:166 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-matrix armhf 1.7-4-1 [4139 kB] 1261s Get:167 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-modelr all 0.1.11-1 [195 kB] 1262s Get:168 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-microbenchmark armhf 1.5.0-1 [67.8 kB] 1262s Get:169 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-doby all 4.7.1-3 [4741 kB] 1270s Get:170 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-evaluate all 1.0.5-1 [117 kB] 1270s Get:171 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-xfun armhf 0.55+dfsg-1 [589 kB] 1272s Get:172 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-highr all 0.11+dfsg-1 [38.5 kB] 1272s Get:173 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-yaml armhf 2.3.10-1 [101 kB] 1272s Get:174 http://ftpmaster.internal/ubuntu resolute/main armhf libjs-mathjax all 2.7.9+dfsg-1build1 [6017 kB] 1284s Get:175 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-knitr all 1.51+dfsg-1 [847 kB] 1286s Get:176 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-minqa armhf 1.2.8-1 [108 kB] 1286s Get:177 http://ftpmaster.internal/ubuntu resolute/universe armhf libnlopt0 armhf 2.7.1-7ubuntu1 [155 kB] 1286s Get:178 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-nloptr armhf 2.2.1-2 [250 kB] 1287s Get:179 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-rbibutils armhf 2.3-1 [943 kB] 1288s Get:180 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-rdpack all 2.6.3-1 [636 kB] 1290s Get:181 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-reformulas all 0.4.4-1 [151 kB] 1290s Get:182 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-rcppeigen armhf 0.3.4.0.2-1 [1402 kB] 1292s Get:183 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-statmod armhf 1.5.0-1 [294 kB] 1293s Get:184 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-lme4 armhf 1.1-38-1 [4178 kB] 1300s Get:185 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-numderiv all 2016.8-1.1-3build1 [116 kB] 1301s Get:186 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-lmertest all 3.2-0-1 [535 kB] 1302s Get:187 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-pbkrtest all 0.5.5-1 [217 kB] 1303s Preconfiguring packages ... 1303s Fetched 194 MB in 7min 58s (406 kB/s) 1303s Selecting previously unselected package libc-dev-bin. 1303s (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 ... 68686 files and directories currently installed.) 1303s Preparing to unpack .../000-libc-dev-bin_2.42-2ubuntu4_armhf.deb ... 1303s Unpacking libc-dev-bin (2.42-2ubuntu4) ... 1303s Selecting previously unselected package linux-libc-dev:armhf. 1303s Preparing to unpack .../001-linux-libc-dev_6.19.0-3.3_armhf.deb ... 1303s Unpacking linux-libc-dev:armhf (6.19.0-3.3) ... 1304s Selecting previously unselected package libcrypt-dev:armhf. 1304s Preparing to unpack .../002-libcrypt-dev_1%3a4.5.1-1_armhf.deb ... 1304s Unpacking libcrypt-dev:armhf (1:4.5.1-1) ... 1304s Selecting previously unselected package rpcsvc-proto. 1304s Preparing to unpack .../003-rpcsvc-proto_1.4.3-1build1_armhf.deb ... 1304s Unpacking rpcsvc-proto (1.4.3-1build1) ... 1304s Selecting previously unselected package libc6-dev:armhf. 1304s Preparing to unpack .../004-libc6-dev_2.42-2ubuntu4_armhf.deb ... 1304s Unpacking libc6-dev:armhf (2.42-2ubuntu4) ... 1304s Selecting previously unselected package libisl23:armhf. 1304s Preparing to unpack .../005-libisl23_0.27-1build1_armhf.deb ... 1304s Unpacking libisl23:armhf (0.27-1build1) ... 1304s Selecting previously unselected package libmpc3:armhf. 1304s Preparing to unpack .../006-libmpc3_1.3.1-2_armhf.deb ... 1304s Unpacking libmpc3:armhf (1.3.1-2) ... 1304s Selecting previously unselected package cpp-15-arm-linux-gnueabihf. 1304s Preparing to unpack .../007-cpp-15-arm-linux-gnueabihf_15.2.0-12ubuntu1_armhf.deb ... 1304s Unpacking cpp-15-arm-linux-gnueabihf (15.2.0-12ubuntu1) ... 1304s Selecting previously unselected package cpp-15. 1304s Preparing to unpack .../008-cpp-15_15.2.0-12ubuntu1_armhf.deb ... 1304s Unpacking cpp-15 (15.2.0-12ubuntu1) ... 1304s Selecting previously unselected package cpp-arm-linux-gnueabihf. 1304s Preparing to unpack .../009-cpp-arm-linux-gnueabihf_4%3a15.2.0-4ubuntu1_armhf.deb ... 1304s Unpacking cpp-arm-linux-gnueabihf (4:15.2.0-4ubuntu1) ... 1304s Selecting previously unselected package cpp. 1304s Preparing to unpack .../010-cpp_4%3a15.2.0-4ubuntu1_armhf.deb ... 1304s Unpacking cpp (4:15.2.0-4ubuntu1) ... 1304s Selecting previously unselected package libcc1-0:armhf. 1304s Preparing to unpack .../011-libcc1-0_15.2.0-12ubuntu1_armhf.deb ... 1304s Unpacking libcc1-0:armhf (15.2.0-12ubuntu1) ... 1304s Selecting previously unselected package libgomp1:armhf. 1304s Preparing to unpack .../012-libgomp1_15.2.0-12ubuntu1_armhf.deb ... 1304s Unpacking libgomp1:armhf (15.2.0-12ubuntu1) ... 1304s Selecting previously unselected package libasan8:armhf. 1304s Preparing to unpack .../013-libasan8_15.2.0-12ubuntu1_armhf.deb ... 1304s Unpacking libasan8:armhf (15.2.0-12ubuntu1) ... 1304s Selecting previously unselected package libubsan1:armhf. 1304s Preparing to unpack .../014-libubsan1_15.2.0-12ubuntu1_armhf.deb ... 1304s Unpacking libubsan1:armhf (15.2.0-12ubuntu1) ... 1304s Selecting previously unselected package libgcc-15-dev:armhf. 1304s Preparing to unpack .../015-libgcc-15-dev_15.2.0-12ubuntu1_armhf.deb ... 1304s Unpacking libgcc-15-dev:armhf (15.2.0-12ubuntu1) ... 1304s Selecting previously unselected package gcc-15-arm-linux-gnueabihf. 1305s Preparing to unpack .../016-gcc-15-arm-linux-gnueabihf_15.2.0-12ubuntu1_armhf.deb ... 1305s Unpacking gcc-15-arm-linux-gnueabihf (15.2.0-12ubuntu1) ... 1305s Selecting previously unselected package gcc-15. 1305s Preparing to unpack .../017-gcc-15_15.2.0-12ubuntu1_armhf.deb ... 1305s Unpacking gcc-15 (15.2.0-12ubuntu1) ... 1305s Selecting previously unselected package gcc-arm-linux-gnueabihf. 1305s Preparing to unpack .../018-gcc-arm-linux-gnueabihf_4%3a15.2.0-4ubuntu1_armhf.deb ... 1305s Unpacking gcc-arm-linux-gnueabihf (4:15.2.0-4ubuntu1) ... 1305s Selecting previously unselected package gcc. 1305s Preparing to unpack .../019-gcc_4%3a15.2.0-4ubuntu1_armhf.deb ... 1305s Unpacking gcc (4:15.2.0-4ubuntu1) ... 1305s Selecting previously unselected package libstdc++-15-dev:armhf. 1305s Preparing to unpack .../020-libstdc++-15-dev_15.2.0-12ubuntu1_armhf.deb ... 1305s Unpacking libstdc++-15-dev:armhf (15.2.0-12ubuntu1) ... 1305s Selecting previously unselected package g++-15-arm-linux-gnueabihf. 1305s Preparing to unpack .../021-g++-15-arm-linux-gnueabihf_15.2.0-12ubuntu1_armhf.deb ... 1305s Unpacking g++-15-arm-linux-gnueabihf (15.2.0-12ubuntu1) ... 1306s Selecting previously unselected package g++-15. 1306s Preparing to unpack .../022-g++-15_15.2.0-12ubuntu1_armhf.deb ... 1306s Unpacking g++-15 (15.2.0-12ubuntu1) ... 1306s Selecting previously unselected package g++-arm-linux-gnueabihf. 1306s Preparing to unpack .../023-g++-arm-linux-gnueabihf_4%3a15.2.0-4ubuntu1_armhf.deb ... 1306s Unpacking g++-arm-linux-gnueabihf (4:15.2.0-4ubuntu1) ... 1306s Selecting previously unselected package g++. 1306s Preparing to unpack .../024-g++_4%3a15.2.0-4ubuntu1_armhf.deb ... 1306s Unpacking g++ (4:15.2.0-4ubuntu1) ... 1306s Selecting previously unselected package build-essential. 1306s Preparing to unpack .../025-build-essential_12.12ubuntu2_armhf.deb ... 1306s Unpacking build-essential (12.12ubuntu2) ... 1306s Selecting previously unselected package dctrl-tools. 1306s Preparing to unpack .../026-dctrl-tools_2.24-3build4_armhf.deb ... 1306s Unpacking dctrl-tools (2.24-3build4) ... 1306s Selecting previously unselected package libfreetype6:armhf. 1306s Preparing to unpack .../027-libfreetype6_2.14.1+dfsg-2_armhf.deb ... 1306s Unpacking libfreetype6:armhf (2.14.1+dfsg-2) ... 1306s Selecting previously unselected package fonts-dejavu-mono. 1306s Preparing to unpack .../028-fonts-dejavu-mono_2.37-8build1_all.deb ... 1306s Unpacking fonts-dejavu-mono (2.37-8build1) ... 1306s Selecting previously unselected package fonts-dejavu-core. 1306s Preparing to unpack .../029-fonts-dejavu-core_2.37-8build1_all.deb ... 1306s Unpacking fonts-dejavu-core (2.37-8build1) ... 1306s Selecting previously unselected package fontconfig-config. 1306s Preparing to unpack .../030-fontconfig-config_2.17.1-3ubuntu1_armhf.deb ... 1306s Unpacking fontconfig-config (2.17.1-3ubuntu1) ... 1306s Selecting previously unselected package libfontconfig1:armhf. 1306s Preparing to unpack .../031-libfontconfig1_2.17.1-3ubuntu1_armhf.deb ... 1306s Unpacking libfontconfig1:armhf (2.17.1-3ubuntu1) ... 1306s Selecting previously unselected package fontconfig. 1306s Preparing to unpack .../032-fontconfig_2.17.1-3ubuntu1_armhf.deb ... 1306s Unpacking fontconfig (2.17.1-3ubuntu1) ... 1306s Selecting previously unselected package fonts-glyphicons-halflings. 1306s Preparing to unpack .../033-fonts-glyphicons-halflings_1.009~3.4.1+dfsg-6_all.deb ... 1306s Unpacking fonts-glyphicons-halflings (1.009~3.4.1+dfsg-6) ... 1306s Selecting previously unselected package fonts-mathjax. 1306s Preparing to unpack .../034-fonts-mathjax_2.7.9+dfsg-1build1_all.deb ... 1306s Unpacking fonts-mathjax (2.7.9+dfsg-1build1) ... 1306s Selecting previously unselected package libgfortran5:armhf. 1307s Preparing to unpack .../035-libgfortran5_15.2.0-12ubuntu1_armhf.deb ... 1307s Unpacking libgfortran5:armhf (15.2.0-12ubuntu1) ... 1307s Selecting previously unselected package libgfortran-15-dev:armhf. 1307s Preparing to unpack .../036-libgfortran-15-dev_15.2.0-12ubuntu1_armhf.deb ... 1307s Unpacking libgfortran-15-dev:armhf (15.2.0-12ubuntu1) ... 1307s Selecting previously unselected package gfortran-15-arm-linux-gnueabihf. 1307s Preparing to unpack .../037-gfortran-15-arm-linux-gnueabihf_15.2.0-12ubuntu1_armhf.deb ... 1307s Unpacking gfortran-15-arm-linux-gnueabihf (15.2.0-12ubuntu1) ... 1307s Selecting previously unselected package gfortran-15. 1307s Preparing to unpack .../038-gfortran-15_15.2.0-12ubuntu1_armhf.deb ... 1307s Unpacking gfortran-15 (15.2.0-12ubuntu1) ... 1307s Selecting previously unselected package gfortran-arm-linux-gnueabihf. 1307s Preparing to unpack .../039-gfortran-arm-linux-gnueabihf_4%3a15.2.0-4ubuntu1_armhf.deb ... 1307s Unpacking gfortran-arm-linux-gnueabihf (4:15.2.0-4ubuntu1) ... 1307s Selecting previously unselected package gfortran. 1307s Preparing to unpack .../040-gfortran_4%3a15.2.0-4ubuntu1_armhf.deb ... 1307s Unpacking gfortran (4:15.2.0-4ubuntu1) ... 1307s Selecting previously unselected package icu-devtools. 1307s Preparing to unpack .../041-icu-devtools_78.2-1ubuntu1_armhf.deb ... 1307s Unpacking icu-devtools (78.2-1ubuntu1) ... 1307s Selecting previously unselected package libblas3:armhf. 1307s Preparing to unpack .../042-libblas3_3.12.1-7ubuntu1_armhf.deb ... 1307s Unpacking libblas3:armhf (3.12.1-7ubuntu1) ... 1307s Selecting previously unselected package libblas-dev:armhf. 1307s Preparing to unpack .../043-libblas-dev_3.12.1-7ubuntu1_armhf.deb ... 1307s Unpacking libblas-dev:armhf (3.12.1-7ubuntu1) ... 1307s Selecting previously unselected package libbz2-dev:armhf. 1307s Preparing to unpack .../044-libbz2-dev_1.0.8-6build2_armhf.deb ... 1307s Unpacking libbz2-dev:armhf (1.0.8-6build2) ... 1307s Selecting previously unselected package libpixman-1-0:armhf. 1307s Preparing to unpack .../045-libpixman-1-0_0.46.4-1_armhf.deb ... 1307s Unpacking libpixman-1-0:armhf (0.46.4-1) ... 1307s Selecting previously unselected package libxcb-render0:armhf. 1307s Preparing to unpack .../046-libxcb-render0_1.17.0-2ubuntu1_armhf.deb ... 1307s Unpacking libxcb-render0:armhf (1.17.0-2ubuntu1) ... 1307s Selecting previously unselected package libxcb-shm0:armhf. 1307s Preparing to unpack .../047-libxcb-shm0_1.17.0-2ubuntu1_armhf.deb ... 1307s Unpacking libxcb-shm0:armhf (1.17.0-2ubuntu1) ... 1307s Selecting previously unselected package libxrender1:armhf. 1307s Preparing to unpack .../048-libxrender1_1%3a0.9.12-1_armhf.deb ... 1307s Unpacking libxrender1:armhf (1:0.9.12-1) ... 1307s Selecting previously unselected package libcairo2:armhf. 1307s Preparing to unpack .../049-libcairo2_1.18.4-3_armhf.deb ... 1307s Unpacking libcairo2:armhf (1.18.4-3) ... 1307s Selecting previously unselected package libdatrie1:armhf. 1307s Preparing to unpack .../050-libdatrie1_0.2.14-1_armhf.deb ... 1307s Unpacking libdatrie1:armhf (0.2.14-1) ... 1307s Selecting previously unselected package libdeflate0:armhf. 1307s Preparing to unpack .../051-libdeflate0_1.23-2build1_armhf.deb ... 1307s Unpacking libdeflate0:armhf (1.23-2build1) ... 1307s Selecting previously unselected package libdeflate-dev:armhf. 1307s Preparing to unpack .../052-libdeflate-dev_1.23-2build1_armhf.deb ... 1307s Unpacking libdeflate-dev:armhf (1.23-2build1) ... 1307s Selecting previously unselected package libgraphite2-3:armhf. 1307s Preparing to unpack .../053-libgraphite2-3_1.3.14-11ubuntu1_armhf.deb ... 1307s Unpacking libgraphite2-3:armhf (1.3.14-11ubuntu1) ... 1307s Selecting previously unselected package libharfbuzz0b:armhf. 1307s Preparing to unpack .../054-libharfbuzz0b_12.3.2-1_armhf.deb ... 1307s Unpacking libharfbuzz0b:armhf (12.3.2-1) ... 1307s Selecting previously unselected package x11-common. 1307s Preparing to unpack .../055-x11-common_1%3a7.7+24ubuntu1_all.deb ... 1307s Unpacking x11-common (1:7.7+24ubuntu1) ... 1307s Selecting previously unselected package libice6:armhf. 1308s Preparing to unpack .../056-libice6_2%3a1.1.1-1build1_armhf.deb ... 1308s Unpacking libice6:armhf (2:1.1.1-1build1) ... 1308s Selecting previously unselected package libicu-dev:armhf. 1308s Preparing to unpack .../057-libicu-dev_78.2-1ubuntu1_armhf.deb ... 1308s Unpacking libicu-dev:armhf (78.2-1ubuntu1) ... 1308s Selecting previously unselected package libjpeg-turbo8:armhf. 1308s Preparing to unpack .../058-libjpeg-turbo8_2.1.5-4ubuntu3_armhf.deb ... 1308s Unpacking libjpeg-turbo8:armhf (2.1.5-4ubuntu3) ... 1308s Selecting previously unselected package libjpeg-turbo8-dev:armhf. 1308s Preparing to unpack .../059-libjpeg-turbo8-dev_2.1.5-4ubuntu3_armhf.deb ... 1308s Unpacking libjpeg-turbo8-dev:armhf (2.1.5-4ubuntu3) ... 1308s Selecting previously unselected package libjpeg8:armhf. 1308s Preparing to unpack .../060-libjpeg8_8c-2ubuntu11_armhf.deb ... 1308s Unpacking libjpeg8:armhf (8c-2ubuntu11) ... 1308s Selecting previously unselected package libjpeg8-dev:armhf. 1308s Preparing to unpack .../061-libjpeg8-dev_8c-2ubuntu11_armhf.deb ... 1308s Unpacking libjpeg8-dev:armhf (8c-2ubuntu11) ... 1308s Selecting previously unselected package libjpeg-dev:armhf. 1308s Preparing to unpack .../062-libjpeg-dev_8c-2ubuntu11_armhf.deb ... 1308s Unpacking libjpeg-dev:armhf (8c-2ubuntu11) ... 1308s Selecting previously unselected package libjs-bootstrap. 1308s Preparing to unpack .../063-libjs-bootstrap_3.4.1+dfsg-6_all.deb ... 1308s Unpacking libjs-bootstrap (3.4.1+dfsg-6) ... 1308s Selecting previously unselected package libjs-highlight.js. 1308s Preparing to unpack .../064-libjs-highlight.js_10.7.3+dfsg-2_all.deb ... 1308s Unpacking libjs-highlight.js (10.7.3+dfsg-2) ... 1308s Selecting previously unselected package libjs-jquery. 1308s Preparing to unpack .../065-libjs-jquery_3.7.1+dfsg+~3.5.33-1build1_all.deb ... 1308s Unpacking libjs-jquery (3.7.1+dfsg+~3.5.33-1build1) ... 1308s Selecting previously unselected package libjs-jquery-datatables. 1308s Preparing to unpack .../066-libjs-jquery-datatables_1.11.5+dfsg-2build1_all.deb ... 1308s Unpacking libjs-jquery-datatables (1.11.5+dfsg-2build1) ... 1308s Selecting previously unselected package liblapack3:armhf. 1308s Preparing to unpack .../067-liblapack3_3.12.1-7ubuntu1_armhf.deb ... 1308s Unpacking liblapack3:armhf (3.12.1-7ubuntu1) ... 1308s Selecting previously unselected package liblapack-dev:armhf. 1309s Preparing to unpack .../068-liblapack-dev_3.12.1-7ubuntu1_armhf.deb ... 1309s Unpacking liblapack-dev:armhf (3.12.1-7ubuntu1) ... 1309s Selecting previously unselected package liblerc4:armhf. 1309s Preparing to unpack .../069-liblerc4_4.0.0+ds-5ubuntu2_armhf.deb ... 1309s Unpacking liblerc4:armhf (4.0.0+ds-5ubuntu2) ... 1309s Selecting previously unselected package libncurses-dev:armhf. 1309s Preparing to unpack .../070-libncurses-dev_6.6+20251231-1_armhf.deb ... 1309s Unpacking libncurses-dev:armhf (6.6+20251231-1) ... 1309s Selecting previously unselected package libthai-data. 1309s Preparing to unpack .../071-libthai-data_0.1.30-1_all.deb ... 1309s Unpacking libthai-data (0.1.30-1) ... 1309s Selecting previously unselected package libthai0:armhf. 1309s Preparing to unpack .../072-libthai0_0.1.30-1_armhf.deb ... 1309s Unpacking libthai0:armhf (0.1.30-1) ... 1309s Selecting previously unselected package libpango-1.0-0:armhf. 1309s Preparing to unpack .../073-libpango-1.0-0_1.57.0-1_armhf.deb ... 1309s Unpacking libpango-1.0-0:armhf (1.57.0-1) ... 1309s Selecting previously unselected package libpangoft2-1.0-0:armhf. 1309s Preparing to unpack .../074-libpangoft2-1.0-0_1.57.0-1_armhf.deb ... 1309s Unpacking libpangoft2-1.0-0:armhf (1.57.0-1) ... 1309s Selecting previously unselected package libpangocairo-1.0-0:armhf. 1309s Preparing to unpack .../075-libpangocairo-1.0-0_1.57.0-1_armhf.deb ... 1309s Unpacking libpangocairo-1.0-0:armhf (1.57.0-1) ... 1309s Selecting previously unselected package libpaper2:armhf. 1309s Preparing to unpack .../076-libpaper2_2.2.5-0.3build1_armhf.deb ... 1309s Unpacking libpaper2:armhf (2.2.5-0.3build1) ... 1309s Selecting previously unselected package libpaper-utils. 1309s Preparing to unpack .../077-libpaper-utils_2.2.5-0.3build1_armhf.deb ... 1309s Unpacking libpaper-utils (2.2.5-0.3build1) ... 1309s Selecting previously unselected package libpcre2-16-0:armhf. 1309s Preparing to unpack .../078-libpcre2-16-0_10.46-1_armhf.deb ... 1309s Unpacking libpcre2-16-0:armhf (10.46-1) ... 1309s Selecting previously unselected package libpcre2-32-0:armhf. 1309s Preparing to unpack .../079-libpcre2-32-0_10.46-1_armhf.deb ... 1309s Unpacking libpcre2-32-0:armhf (10.46-1) ... 1309s Selecting previously unselected package libpcre2-posix3:armhf. 1309s Preparing to unpack .../080-libpcre2-posix3_10.46-1_armhf.deb ... 1309s Unpacking libpcre2-posix3:armhf (10.46-1) ... 1309s Selecting previously unselected package libpcre2-dev:armhf. 1309s Preparing to unpack .../081-libpcre2-dev_10.46-1_armhf.deb ... 1309s Unpacking libpcre2-dev:armhf (10.46-1) ... 1309s Selecting previously unselected package libpkgconf3:armhf. 1309s Preparing to unpack .../082-libpkgconf3_1.8.1-4build1_armhf.deb ... 1309s Unpacking libpkgconf3:armhf (1.8.1-4build1) ... 1309s Selecting previously unselected package zlib1g-dev:armhf. 1309s Preparing to unpack .../083-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1ubuntu2_armhf.deb ... 1309s Unpacking zlib1g-dev:armhf (1:1.3.dfsg+really1.3.1-1ubuntu2) ... 1309s Selecting previously unselected package libpng-dev:armhf. 1309s Preparing to unpack .../084-libpng-dev_1.6.54-1_armhf.deb ... 1309s Unpacking libpng-dev:armhf (1.6.54-1) ... 1309s Selecting previously unselected package libreadline-dev:armhf. 1309s Preparing to unpack .../085-libreadline-dev_8.3-3_armhf.deb ... 1309s Unpacking libreadline-dev:armhf (8.3-3) ... 1309s Selecting previously unselected package libsharpyuv0:armhf. 1309s Preparing to unpack .../086-libsharpyuv0_1.5.0-0.1build1_armhf.deb ... 1309s Unpacking libsharpyuv0:armhf (1.5.0-0.1build1) ... 1309s Selecting previously unselected package libsm6:armhf. 1309s Preparing to unpack .../087-libsm6_2%3a1.2.6-1build1_armhf.deb ... 1309s Unpacking libsm6:armhf (2:1.2.6-1build1) ... 1309s Selecting previously unselected package libtcl8.6:armhf. 1309s Preparing to unpack .../088-libtcl8.6_8.6.17+dfsg-1build1_armhf.deb ... 1309s Unpacking libtcl8.6:armhf (8.6.17+dfsg-1build1) ... 1310s Selecting previously unselected package libjbig0:armhf. 1310s Preparing to unpack .../089-libjbig0_2.1-6.1ubuntu3_armhf.deb ... 1310s Unpacking libjbig0:armhf (2.1-6.1ubuntu3) ... 1310s Selecting previously unselected package libwebp7:armhf. 1310s Preparing to unpack .../090-libwebp7_1.5.0-0.1build1_armhf.deb ... 1310s Unpacking libwebp7:armhf (1.5.0-0.1build1) ... 1310s Selecting previously unselected package libtiff6:armhf. 1310s Preparing to unpack .../091-libtiff6_4.7.0-3ubuntu3_armhf.deb ... 1310s Unpacking libtiff6:armhf (4.7.0-3ubuntu3) ... 1310s Selecting previously unselected package libxft2:armhf. 1310s Preparing to unpack .../092-libxft2_2.3.6-1build2_armhf.deb ... 1310s Unpacking libxft2:armhf (2.3.6-1build2) ... 1310s Selecting previously unselected package libxss1:armhf. 1310s Preparing to unpack .../093-libxss1_1%3a1.2.3-1build4_armhf.deb ... 1310s Unpacking libxss1:armhf (1:1.2.3-1build4) ... 1310s Selecting previously unselected package libtk8.6:armhf. 1310s Preparing to unpack .../094-libtk8.6_8.6.17-1_armhf.deb ... 1310s Unpacking libtk8.6:armhf (8.6.17-1) ... 1310s Selecting previously unselected package libxt6t64:armhf. 1310s Preparing to unpack .../095-libxt6t64_1%3a1.2.1-1.3_armhf.deb ... 1310s Unpacking libxt6t64:armhf (1:1.2.1-1.3) ... 1310s Selecting previously unselected package libzstd-dev:armhf. 1310s Preparing to unpack .../096-libzstd-dev_1.5.7+dfsg-3_armhf.deb ... 1310s Unpacking libzstd-dev:armhf (1.5.7+dfsg-3) ... 1310s Selecting previously unselected package node-normalize.css. 1310s Preparing to unpack .../097-node-normalize.css_8.0.1-5.1_all.deb ... 1310s Unpacking node-normalize.css (8.0.1-5.1) ... 1310s Selecting previously unselected package zip. 1310s Preparing to unpack .../098-zip_3.0-15ubuntu3_armhf.deb ... 1310s Unpacking zip (3.0-15ubuntu3) ... 1310s Selecting previously unselected package unzip. 1310s Preparing to unpack .../099-unzip_6.0-29ubuntu1_armhf.deb ... 1310s Unpacking unzip (6.0-29ubuntu1) ... 1310s Selecting previously unselected package xdg-utils. 1310s Preparing to unpack .../100-xdg-utils_1.2.1-2ubuntu2_all.deb ... 1310s Unpacking xdg-utils (1.2.1-2ubuntu2) ... 1310s Selecting previously unselected package r-base-core. 1310s Preparing to unpack .../101-r-base-core_4.5.2-1ubuntu2_armhf.deb ... 1310s Unpacking r-base-core (4.5.2-1ubuntu2) ... 1310s Selecting previously unselected package liblzma-dev:armhf. 1310s Preparing to unpack .../102-liblzma-dev_5.8.2-2_armhf.deb ... 1310s Unpacking liblzma-dev:armhf (5.8.2-2) ... 1310s Selecting previously unselected package pkgconf-bin. 1310s Preparing to unpack .../103-pkgconf-bin_1.8.1-4build1_armhf.deb ... 1310s Unpacking pkgconf-bin (1.8.1-4build1) ... 1310s Selecting previously unselected package pkgconf:armhf. 1310s Preparing to unpack .../104-pkgconf_1.8.1-4build1_armhf.deb ... 1310s Unpacking pkgconf:armhf (1.8.1-4build1) ... 1310s Selecting previously unselected package libtirpc-dev:armhf. 1311s Preparing to unpack .../105-libtirpc-dev_1.3.6+ds-1_armhf.deb ... 1311s Unpacking libtirpc-dev:armhf (1.3.6+ds-1) ... 1311s Selecting previously unselected package r-base-dev. 1311s Preparing to unpack .../106-r-base-dev_4.5.2-1ubuntu2_all.deb ... 1311s Unpacking r-base-dev (4.5.2-1ubuntu2) ... 1311s Selecting previously unselected package pkg-r-autopkgtest. 1311s Preparing to unpack .../107-pkg-r-autopkgtest_20250812_all.deb ... 1311s Unpacking pkg-r-autopkgtest (20250812) ... 1311s Selecting previously unselected package r-cran-backports. 1311s Preparing to unpack .../108-r-cran-backports_1.5.0-2_armhf.deb ... 1311s Unpacking r-cran-backports (1.5.0-2) ... 1311s Selecting previously unselected package r-cran-boot. 1311s Preparing to unpack .../109-r-cran-boot_1.3-32-1_all.deb ... 1311s Unpacking r-cran-boot (1.3-32-1) ... 1311s Selecting previously unselected package r-cran-cli. 1311s Preparing to unpack .../110-r-cran-cli_3.6.4-1_armhf.deb ... 1311s Unpacking r-cran-cli (3.6.4-1) ... 1311s Selecting previously unselected package r-cran-generics. 1311s Preparing to unpack .../111-r-cran-generics_0.1.4-1_all.deb ... 1311s Unpacking r-cran-generics (0.1.4-1) ... 1311s Selecting previously unselected package r-cran-glue. 1311s Preparing to unpack .../112-r-cran-glue_1.8.0-1_armhf.deb ... 1311s Unpacking r-cran-glue (1.8.0-1) ... 1311s Selecting previously unselected package r-cran-rlang. 1311s Preparing to unpack .../113-r-cran-rlang_1.1.5-3_armhf.deb ... 1311s Unpacking r-cran-rlang (1.1.5-3) ... 1311s Selecting previously unselected package r-cran-lifecycle. 1311s Preparing to unpack .../114-r-cran-lifecycle_1.0.5+dfsg-1_all.deb ... 1311s Unpacking r-cran-lifecycle (1.0.5+dfsg-1) ... 1311s Selecting previously unselected package r-cran-magrittr. 1311s Preparing to unpack .../115-r-cran-magrittr_2.0.3-1_armhf.deb ... 1311s Unpacking r-cran-magrittr (2.0.3-1) ... 1311s Selecting previously unselected package r-cran-utf8. 1311s Preparing to unpack .../116-r-cran-utf8_1.2.4-1_armhf.deb ... 1311s Unpacking r-cran-utf8 (1.2.4-1) ... 1311s Selecting previously unselected package r-cran-vctrs. 1311s Preparing to unpack .../117-r-cran-vctrs_0.6.5-1_armhf.deb ... 1311s Unpacking r-cran-vctrs (0.6.5-1) ... 1311s Selecting previously unselected package r-cran-pillar. 1311s Preparing to unpack .../118-r-cran-pillar_1.11.1+dfsg-1_all.deb ... 1311s Unpacking r-cran-pillar (1.11.1+dfsg-1) ... 1311s Selecting previously unselected package r-cran-r6. 1311s Preparing to unpack .../119-r-cran-r6_2.6.1-1_all.deb ... 1311s Unpacking r-cran-r6 (2.6.1-1) ... 1311s Selecting previously unselected package r-cran-fansi. 1311s Preparing to unpack .../120-r-cran-fansi_1.0.6-2_armhf.deb ... 1311s Unpacking r-cran-fansi (1.0.6-2) ... 1311s Selecting previously unselected package r-cran-pkgconfig. 1311s Preparing to unpack .../121-r-cran-pkgconfig_2.0.3-2build2_all.deb ... 1311s Unpacking r-cran-pkgconfig (2.0.3-2build2) ... 1311s Selecting previously unselected package r-cran-tibble. 1311s Preparing to unpack .../122-r-cran-tibble_3.2.1+dfsg-3_armhf.deb ... 1311s Unpacking r-cran-tibble (3.2.1+dfsg-3) ... 1311s Selecting previously unselected package r-cran-withr. 1311s Preparing to unpack .../123-r-cran-withr_3.0.2+dfsg-1_all.deb ... 1311s Unpacking r-cran-withr (3.0.2+dfsg-1) ... 1311s Selecting previously unselected package r-cran-tidyselect. 1311s Preparing to unpack .../124-r-cran-tidyselect_1.2.1+dfsg-1_armhf.deb ... 1311s Unpacking r-cran-tidyselect (1.2.1+dfsg-1) ... 1311s Selecting previously unselected package r-cran-dplyr. 1312s Preparing to unpack .../125-r-cran-dplyr_1.1.4-4_armhf.deb ... 1312s Unpacking r-cran-dplyr (1.1.4-4) ... 1312s Selecting previously unselected package r-cran-purrr. 1312s Preparing to unpack .../126-r-cran-purrr_1.0.4-1_armhf.deb ... 1312s Unpacking r-cran-purrr (1.0.4-1) ... 1312s Selecting previously unselected package r-cran-stringi. 1312s Preparing to unpack .../127-r-cran-stringi_1.8.4-1build2_armhf.deb ... 1312s Unpacking r-cran-stringi (1.8.4-1build2) ... 1312s Selecting previously unselected package r-cran-stringr. 1312s Preparing to unpack .../128-r-cran-stringr_1.5.1-1_all.deb ... 1312s Unpacking r-cran-stringr (1.5.1-1) ... 1312s Selecting previously unselected package r-cran-cpp11. 1312s Preparing to unpack .../129-r-cran-cpp11_0.5.3-1_all.deb ... 1312s Unpacking r-cran-cpp11 (0.5.3-1) ... 1312s Selecting previously unselected package r-cran-tidyr. 1312s Preparing to unpack .../130-r-cran-tidyr_1.3.1-1_armhf.deb ... 1312s Unpacking r-cran-tidyr (1.3.1-1) ... 1312s Selecting previously unselected package r-cran-broom. 1312s Preparing to unpack .../131-r-cran-broom_1.0.12+dfsg-1_all.deb ... 1312s Unpacking r-cran-broom (1.0.12+dfsg-1) ... 1312s Selecting previously unselected package r-cran-colorspace. 1312s Preparing to unpack .../132-r-cran-colorspace_2.1-1+dfsg-1_armhf.deb ... 1312s Unpacking r-cran-colorspace (2.1-1+dfsg-1) ... 1312s Selecting previously unselected package r-cran-gtable. 1312s Preparing to unpack .../133-r-cran-gtable_0.3.6+dfsg-1_all.deb ... 1312s Unpacking r-cran-gtable (0.3.6+dfsg-1) ... 1312s Selecting previously unselected package r-cran-isoband. 1312s Preparing to unpack .../134-r-cran-isoband_0.2.7-1_armhf.deb ... 1312s Unpacking r-cran-isoband (0.2.7-1) ... 1312s Selecting previously unselected package r-cran-s7. 1312s Preparing to unpack .../135-r-cran-s7_0.2.0-1_armhf.deb ... 1312s Unpacking r-cran-s7 (0.2.0-1) ... 1312s Selecting previously unselected package r-cran-farver. 1312s Preparing to unpack .../136-r-cran-farver_2.1.2-1_armhf.deb ... 1312s Unpacking r-cran-farver (2.1.2-1) ... 1312s Selecting previously unselected package r-cran-labeling. 1312s Preparing to unpack .../137-r-cran-labeling_0.4.3-1_all.deb ... 1312s Unpacking r-cran-labeling (0.4.3-1) ... 1312s Selecting previously unselected package r-cran-rcolorbrewer. 1312s Preparing to unpack .../138-r-cran-rcolorbrewer_1.1-3-1build2_all.deb ... 1312s Unpacking r-cran-rcolorbrewer (1.1-3-1build2) ... 1312s Selecting previously unselected package r-cran-viridislite. 1312s Preparing to unpack .../139-r-cran-viridislite_0.4.3-1_all.deb ... 1312s Unpacking r-cran-viridislite (0.4.3-1) ... 1312s Selecting previously unselected package r-cran-scales. 1312s Preparing to unpack .../140-r-cran-scales_1.4.0-1_all.deb ... 1312s Unpacking r-cran-scales (1.4.0-1) ... 1312s Selecting previously unselected package r-cran-ggplot2. 1312s Preparing to unpack .../141-r-cran-ggplot2_4.0.2+dfsg-1_all.deb ... 1312s Unpacking r-cran-ggplot2 (4.0.2+dfsg-1) ... 1313s Selecting previously unselected package r-cran-cowplot. 1313s Preparing to unpack .../142-r-cran-cowplot_1.1.3+dfsg-1_all.deb ... 1313s Unpacking r-cran-cowplot (1.1.3+dfsg-1) ... 1313s Selecting previously unselected package r-cran-curl. 1313s Preparing to unpack .../143-r-cran-curl_7.0.0+dfsg-1_armhf.deb ... 1313s Unpacking r-cran-curl (7.0.0+dfsg-1) ... 1313s Selecting previously unselected package r-cran-deriv. 1313s Preparing to unpack .../144-r-cran-deriv_4.2.0-1_all.deb ... 1313s Unpacking r-cran-deriv (4.2.0-1) ... 1313s Selecting previously unselected package r-cran-fracdiff. 1313s Preparing to unpack .../145-r-cran-fracdiff_1.5-3-1_armhf.deb ... 1313s Unpacking r-cran-fracdiff (1.5-3-1) ... 1313s Selecting previously unselected package r-cran-lattice. 1313s Preparing to unpack .../146-r-cran-lattice_0.22-7-1_armhf.deb ... 1313s Unpacking r-cran-lattice (0.22-7-1) ... 1313s Selecting previously unselected package r-cran-zoo. 1313s Preparing to unpack .../147-r-cran-zoo_1.8-15-1_armhf.deb ... 1313s Unpacking r-cran-zoo (1.8-15-1) ... 1313s Selecting previously unselected package r-cran-lmtest. 1313s Preparing to unpack .../148-r-cran-lmtest_0.9.40-1build1_armhf.deb ... 1313s Unpacking r-cran-lmtest (0.9.40-1build1) ... 1313s Selecting previously unselected package r-cran-nnet. 1313s Preparing to unpack .../149-r-cran-nnet_7.3-20-1_armhf.deb ... 1313s Unpacking r-cran-nnet (7.3-20-1) ... 1313s Selecting previously unselected package r-cran-littler. 1313s Preparing to unpack .../150-r-cran-littler_0.3.22-1_armhf.deb ... 1313s Unpacking r-cran-littler (0.3.22-1) ... 1313s Selecting previously unselected package r-cran-pkgkitten. 1313s Preparing to unpack .../151-r-cran-pkgkitten_0.2.4-1_all.deb ... 1313s Unpacking r-cran-pkgkitten (0.2.4-1) ... 1313s Selecting previously unselected package r-cran-rcpp. 1313s Preparing to unpack .../152-r-cran-rcpp_1.1.0-1_armhf.deb ... 1313s Unpacking r-cran-rcpp (1.1.0-1) ... 1313s Selecting previously unselected package r-cran-timedate. 1313s Preparing to unpack .../153-r-cran-timedate_4052.112-1_armhf.deb ... 1313s Unpacking r-cran-timedate (4052.112-1) ... 1313s Selecting previously unselected package r-cran-quadprog. 1313s Preparing to unpack .../154-r-cran-quadprog_1.5-8-1build2_armhf.deb ... 1313s Unpacking r-cran-quadprog (1.5-8-1build2) ... 1313s Selecting previously unselected package r-cran-xts. 1313s Preparing to unpack .../155-r-cran-xts_0.14.1-1_armhf.deb ... 1313s Unpacking r-cran-xts (0.14.1-1) ... 1313s Selecting previously unselected package r-cran-ttr. 1313s Preparing to unpack .../156-r-cran-ttr_0.24.4-1_armhf.deb ... 1313s Unpacking r-cran-ttr (0.24.4-1) ... 1313s Selecting previously unselected package r-cran-jsonlite. 1313s Preparing to unpack .../157-r-cran-jsonlite_1.9.1+dfsg-1_armhf.deb ... 1313s Unpacking r-cran-jsonlite (1.9.1+dfsg-1) ... 1313s Selecting previously unselected package r-cran-quantmod. 1313s Preparing to unpack .../158-r-cran-quantmod_0.4.28-1_all.deb ... 1313s Unpacking r-cran-quantmod (0.4.28-1) ... 1313s Selecting previously unselected package r-cran-tseries. 1313s Preparing to unpack .../159-r-cran-tseries_0.10-59-3_armhf.deb ... 1313s Unpacking r-cran-tseries (0.10-59-3) ... 1313s Selecting previously unselected package r-cran-nlme. 1313s Preparing to unpack .../160-r-cran-nlme_3.1.168-1_armhf.deb ... 1313s Unpacking r-cran-nlme (3.1.168-1) ... 1314s Selecting previously unselected package r-cran-urca. 1314s Preparing to unpack .../161-r-cran-urca_1.3-4-1build1_armhf.deb ... 1314s Unpacking r-cran-urca (1.3-4-1build1) ... 1314s Selecting previously unselected package r-cran-rcpparmadillo. 1314s Preparing to unpack .../162-r-cran-rcpparmadillo_15.2.3-1-1_armhf.deb ... 1314s Unpacking r-cran-rcpparmadillo (15.2.3-1-1) ... 1314s Selecting previously unselected package r-cran-forecast. 1314s Preparing to unpack .../163-r-cran-forecast_8.23.0-1_armhf.deb ... 1314s Unpacking r-cran-forecast (8.23.0-1) ... 1314s Selecting previously unselected package r-cran-mass. 1314s Preparing to unpack .../164-r-cran-mass_7.3-65-1_armhf.deb ... 1314s Unpacking r-cran-mass (7.3-65-1) ... 1314s Selecting previously unselected package r-cran-matrix. 1314s Preparing to unpack .../165-r-cran-matrix_1.7-4-1_armhf.deb ... 1314s Unpacking r-cran-matrix (1.7-4-1) ... 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r-cran-doby (4.7.1-3) ... 1319s Setting up r-cran-pbkrtest (0.5.5-1) ... 1319s Processing triggers for libc-bin (2.42-2ubuntu4) ... 1319s Processing triggers for man-db (2.13.1-1build1) ... 1320s Processing triggers for install-info (7.2-5) ... 1335s autopkgtest [23:54:48]: test pkg-r-autopkgtest: /usr/share/dh-r/pkg-r-autopkgtest 1335s autopkgtest [23:54:48]: test pkg-r-autopkgtest: [----------------------- 1337s Test: Try to load the R library lmerTest 1337s 1337s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 1337s Copyright (C) 2025 The R Foundation for Statistical Computing 1337s Platform: arm-unknown-linux-gnueabihf (32-bit) 1337s 1337s R is free software and comes with ABSOLUTELY NO WARRANTY. 1337s You are welcome to redistribute it under certain conditions. 1337s Type 'license()' or 'licence()' for distribution details. 1337s 1337s R is a collaborative project with many contributors. 1337s Type 'contributors()' for more information and 1337s 'citation()' on how to cite R or R packages in publications. 1337s 1337s Type 'demo()' for some demos, 'help()' for on-line help, or 1337s 'help.start()' for an HTML browser interface to help. 1337s Type 'q()' to quit R. 1337s 1337s Loading required package: lme4 1337s Loading required package: Matrix 1337s > library('lmerTest') 1339s 1339s Attaching package: ‘lmerTest’ 1339s 1339s The following object is masked from ‘package:lme4’: 1339s 1339s lmer 1339s 1339s The following object is masked from ‘package:stats’: 1339s 1339s step 1339s 1339s > 1340s autopkgtest [23:54:53]: test pkg-r-autopkgtest: -----------------------] 1344s pkg-r-autopkgtest PASS 1344s autopkgtest [23:54:57]: test pkg-r-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 1348s autopkgtest [23:55:01]: @@@@@@@@@@@@@@@@@@@@ summary 1348s run-unit-test PASS 1348s pkg-r-autopkgtest PASS